Salipiger abyssi strain JLT2014 plasmid pPABY3, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Roseobacteraceae; Salipiger.
Deep-sea bacteria in the southern Pacific
Submitted (06-APR-2016) State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Zhoulongquan Building A2-319, Xianan, Xiamen 361005, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP015092.1.\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 :: 02/06/2023 04:28:10\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) :: 5,147\nCDSs (total) :: 5,091\nGenes (coding) :: 5,023\nCDSs (with protein) :: 5,023\nGenes (RNA) :: 56\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 46\nncRNAs :: 4\nPseudo Genes (total) :: 68\nCDSs (without protein) :: 68\nPseudo Genes (ambiguous residues) :: 0 of 68\nPseudo Genes (frameshifted) :: 32 of 68\nPseudo Genes (incomplete) :: 33 of 68\nPseudo Genes (internal stop) :: 6 of 68\nPseudo Genes (multiple problems) :: 2 of 68\nCRISPR Arrays :: 2\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_009505369.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009503875.1
COORDINATES: similar to AA sequence:RefSeq:WP_007817689.1
COORDINATES: similar to AA sequence:RefSeq:WP_019953310.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065899.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827215.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574206.1
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF015393.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03453.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503864.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803223.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803221.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803220.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065890.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803217.1
GO:0004803 - transposase activity [Evidence IEA]
IS5-like element ISRhba5 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_007803215.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573576.1
COORDINATES: similar to AA sequence:RefSeq:WP_015931502.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007803209.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612002.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007789120.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808024.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808025.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808026.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807937.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012222369.1
COORDINATES: protein motif:HMM:NF025819.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611905.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013094.2
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF037736.2
COORDINATES: similar to AA sequence:RefSeq:WP_009808070.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120671.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187154.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820228.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327387.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536592.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808064.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820232.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120678.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009503800.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807508.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008327373.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808058.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327370.1
COORDINATES: similar to AA sequence:RefSeq:WP_008282965.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503806.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612055.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120686.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009808043.1
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_018303594.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807491.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_008282972.1
transglutaminase-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005645239.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018303599.1
COORDINATES: similar to AA sequence:RefSeq:WP_013959866.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803474.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018001721.1
COORDINATES: similar to AA sequence:RefSeq:WP_005647556.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803468.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803467.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803465.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803463.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803461.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009815491.1
GO:0016410 - N-acyltransferase activity [Evidence IEA]
GO:0042158 - lipoprotein biosynthetic process [Evidence IEA]; GO:0006497 - protein lipidation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008282832.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820123.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0017000 - antibiotic biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009824428.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820125.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0046983 - protein dimerization activity [Evidence IEA]; GO:0046914 - transition metal ion binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
manganese-binding transcriptional regulator MntR
COORDINATES: similar to AA sequence:RefSeq:WP_009820126.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017927568.1
phosphate/phosphite/phosphonate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009824423.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009824422.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0015416 - ABC-type phosphonate transporter activity [Evidence IEA]
GO:0015716 - organic phosphonate transport [Evidence IEA]
phosphonate ABC transporter, permease protein PhnE
COORDINATES: similar to AA sequence:RefSeq:WP_008889351.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803450.1
COORDINATES: similar to AA sequence:RefSeq:WP_005613342.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503854.1
COORDINATES: similar to AA sequence:RefSeq:WP_005613345.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_009807500.1
COORDINATES: similar to AA sequence:RefSeq:WP_005613347.1
COORDINATES: similar to AA sequence:RefSeq:WP_005613348.1
COORDINATES: similar to AA sequence:RefSeq:WP_008282847.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824415.1
GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009824414.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]; GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005613352.1
COORDINATES: similar to AA sequence:RefSeq:WP_005613353.1
GO:0017004 - cytochrome complex assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005613354.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824511.1
COORDINATES: similar to AA sequence:RefSeq:WP_005613358.1
COORDINATES: similar to AA sequence:RefSeq:WP_005613360.1
COORDINATES: similar to AA sequence:RefSeq:WP_005613361.1
COORDINATES: similar to AA sequence:RefSeq:WP_005613363.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824505.1
COORDINATES: similar to AA sequence:RefSeq:WP_005613366.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824503.1
DsbE family thiol:disulfide interchange protein
COORDINATES: similar to AA sequence:RefSeq:WP_009824502.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824501.1
COORDINATES: similar to AA sequence:RefSeq:WP_017927551.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573583.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824498.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824496.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006878 - cellular copper ion homeostasis [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Cu(I)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009824495.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005619156.1
protein-disulfide reductase DsbD family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008330690.1
COORDINATES: protein motif:HMM:NF015658.2
COORDINATES: similar to AA sequence:RefSeq:WP_086558194.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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: similar to AA sequence:RefSeq:WP_018273520.1
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_007813144.1
COORDINATES: similar to AA sequence:RefSeq:WP_005619161.1
COORDINATES: similar to AA sequence:RefSeq:WP_005619163.1
COORDINATES: similar to AA sequence:RefSeq:WP_005619165.1
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009824487.1
COORDINATES: similar to AA sequence:RefSeq:WP_005619169.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824486.1
COORDINATES: similar to AA sequence:RefSeq:WP_005619174.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824484.1
COORDINATES: similar to AA sequence:RefSeq:WP_005619178.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807486.1
COORDINATES: similar to AA sequence:RefSeq:WP_011567396.1
COORDINATES: similar to AA sequence:RefSeq:WP_005619187.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824480.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005619190.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824478.1
COORDINATES: similar to AA sequence:RefSeq:WP_005619195.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824476.1
GO:0051082 - unfolded protein binding [Evidence IEA]
c-type cytochrome biogenesis protein CcmI
COORDINATES: similar to AA sequence:RefSeq:WP_005619199.1
cytochrome c-type biogenesis protein CcmH
COORDINATES: similar to AA sequence:RefSeq:WP_009824474.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803387.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824472.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824471.1
rhodanese-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005619214.1
GO:0005507 - copper ion binding [Evidence IEA]
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018065796.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824465.1
GO:0045275 - respiratory chain complex III [Evidence IEA]
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0008121 - ubiquinol-cytochrome-c reductase activity [Evidence IEA]
GO:0009060 - aerobic respiration [Evidence IEA]
ubiquinol-cytochrome c reductase iron-sulfur subunit
COORDINATES: similar to AA sequence:RefSeq:WP_009824464.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005619220.1
COORDINATES: similar to AA sequence:RefSeq:WP_005619223.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009824460.1
GO:0008961 - phosphatidylglycerol-prolipoprotein diacylglyceryl transferase activity [Evidence IEA]
GO:0009249 - protein lipoylation [Evidence IEA]
prolipoprotein diacylglyceryl transferase
COORDINATES: protein motif:HMM:NF022694.2
COORDINATES: protein motif:HMM:NF019352.2
COORDINATES: protein motif:HMM:NF019351.2
GO:0005507 - copper ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005619237.1
COORDINATES: similar to AA sequence:RefSeq:WP_011455675.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807474.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009824455.1
COORDINATES: similar to AA sequence:RefSeq:WP_005611038.1
mercury resistance system transport protein MerF
COORDINATES: similar to AA sequence:RefSeq:WP_009824453.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824452.1
mercuric transporter MerT family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005611030.1
COORDINATES: similar to AA sequence:RefSeq:WP_009824450.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008335981.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503412.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503879.1