Phaeobacter porticola strain P97 plasmid pP97_b, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Roseobacteraceae; Phaeobacter.
Adaptation of Surface-Associated Bacteria to the Open Ocean: A Genomically Distinct Subpopulation of Phaeobacter gallaeciensis Colonizes Pacific Mesozooplankton
Phaeobacter porticola sp. nov., an antibiotic-producing bacterium isolated from a sea harbour
Submitted (06-JUL-2016) Microbial Ecology and Diversity, Leibniz Institute DSMZ, Inhoffenstr. 7 B, Braunschweig 38124, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP016366.1.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Method :: HGAP SMRTPortal v. 2.3.0\nAssembly Name :: p97_hgap_1c_gs\nGenome Coverage :: 140x\nSequencing Technology :: PacBio; Illumina HiSeq 2500\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/13/2023 02:25:34\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) :: 4,020\nCDSs (total) :: 3,948\nGenes (coding) :: 3,898\nCDSs (with protein) :: 3,898\nGenes (RNA) :: 72\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 57\nncRNAs :: 3\nPseudo Genes (total) :: 50\nCDSs (without protein) :: 50\nPseudo Genes (ambiguous residues) :: 0 of 50\nPseudo Genes (frameshifted) :: 23 of 50\nPseudo Genes (incomplete) :: 31 of 50\nPseudo Genes (internal stop) :: 18 of 50\nPseudo Genes (multiple problems) :: 18 of 50\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_005854399.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007802646.1
COORDINATES: protein motif:HMM:NF040974.1
COORDINATES: similar to AA sequence:RefSeq:WP_009177164.1
COORDINATES: similar to AA sequence:RefSeq:WP_011539288.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010512685.1
COORDINATES: similar to AA sequence:RefSeq:WP_008958835.1
type II toxin-antitoxin system CcdA family antitoxin
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011911214.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611539.1
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_037302177.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
internal stop; 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_010656056.1
COORDINATES: protein motif:HMM:NF024242.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF012371.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612004.1
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_009807962.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120639.1
COORDINATES: similar to AA sequence:RefSeq:WP_013662923.1
COORDINATES: protein motif:HMM:NF037997.1
GO:0015114 - phosphate ion transmembrane transporter activity [Evidence IEA]; GO:0005436 - sodium:phosphate symporter activity [Evidence IEA]
GO:0035435 - phosphate ion transmembrane transport [Evidence IEA]; GO:0044341 - sodium-dependent phosphate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015495123.1
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014875622.1
COORDINATES: similar to AA sequence:RefSeq:WP_017181657.1
COORDINATES: similar to AA sequence:RefSeq:WP_011539228.1
serine hydrolase domain-containing protein
COORDINATES: protein motif:HMM:TIGR02913.1
COORDINATES: similar to AA sequence:RefSeq:WP_011588635.1
COORDINATES: similar to AA sequence:RefSeq:WP_005851840.1
COORDINATES: similar to AA sequence:RefSeq:WP_016962496.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_009703030.1
enoyl-CoA hydratase/isomerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014881795.1
COORDINATES: protein motif:HMM:NF033546.1
COORDINATES: protein motif:HMM:NF024109.2
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003052710.1
COORDINATES: protein motif:HMM:NF013088.2
COORDINATES: similar to AA sequence:RefSeq:WP_009178491.1
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011454575.1
GO:0033735 - aspartate dehydrogenase activity [Evidence IEA]
GO:0009435 - NAD biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009178401.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009724062.1
COORDINATES: similar to AA sequence:RefSeq:WP_016916444.1
COORDINATES: similar to AA sequence:RefSeq:WP_016916443.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018062663.1
tripartite tricarboxylate transporter permease
COORDINATES: protein motif:HMM:NF018979.2
tripartite tricarboxylate transporter TctB family protein
COORDINATES: protein motif:HMM:NF015366.2
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013531745.1
GO:0030429 - kynureninase activity [Evidence IEA]
GO:0019441 - tryptophan catabolic process to kynurenine [Evidence IEA]
COORDINATES: protein motif:HMM:NF019349.2
COORDINATES: similar to AA sequence:RefSeq:WP_007426134.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_005605943.1
GO:0000334 - 3-hydroxyanthranilate 3,4-dioxygenase activity [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF019310.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008203763.1
COORDINATES: protein motif:HMM:NF025606.2
DUF4344 domain-containing metallopeptidase
COORDINATES: similar to AA sequence:RefSeq:WP_076611355.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF017727.2
COORDINATES: protein motif:HMM:NF040453.1
COORDINATES: similar to AA sequence:RefSeq:WP_009816853.1
COORDINATES: similar to AA sequence:RefSeq:WP_014881749.1
COORDINATES: similar to AA sequence:RefSeq:WP_009570069.1
COORDINATES: similar to AA sequence:RefSeq:WP_015920882.1
COORDINATES: similar to AA sequence:RefSeq:WP_020043551.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
GO:0009060 - aerobic respiration [Evidence IEA]
cbb3-type cytochrome c oxidase subunit I
COORDINATES: similar to AA sequence:RefSeq:WP_002720490.1
COORDINATES: similar to AA sequence:RefSeq:WP_019298191.1
COORDINATES: similar to AA sequence:RefSeq:WP_009570073.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_002725071.1
COORDINATES: similar to AA sequence:RefSeq:WP_009564086.1
GO:0050304 - nitrous-oxide reductase activity [Evidence IEA]
GO:0019333 - denitrification pathway [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012179855.1
nitrous oxide reductase family maturation protein NosD
COORDINATES: similar to AA sequence:RefSeq:WP_010396556.1
COORDINATES: similar to AA sequence:RefSeq:WP_012643415.1
COORDINATES: similar to AA sequence:RefSeq:WP_009817862.1
nitrous oxide reductase accessory protein NosL
COORDINATES: similar to AA sequence:RefSeq:WP_013069297.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427422.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009815135.1
COORDINATES: protein motif:HMM:NF012573.2
COORDINATES: similar to AA sequence:RefSeq:WP_013637091.1
COORDINATES: similar to AA sequence:RefSeq:WP_005628222.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_005628224.1
COORDINATES: similar to AA sequence:RefSeq:WP_008029685.1
COORDINATES: protein motif:HMM:NF004767.0
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]; GO:0008483 - transaminase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012366413.1
COORDINATES: similar to AA sequence:RefSeq:WP_012114065.1
transketolase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005634485.1
COORDINATES: protein motif:HMM:NF012428.2
aspartate aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004885370.1
COORDINATES: similar to AA sequence:RefSeq:WP_005652678.1
COORDINATES: similar to AA sequence:RefSeq:WP_013637084.1
COORDINATES: similar to AA sequence:RefSeq:WP_009804208.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120602.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120603.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574105.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120605.1
COORDINATES: protein motif:HMM:NF016957.2
VirB3 family type IV secretion system protein
COORDINATES: protein motif:HMM:NF025073.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006937131.1
HpcH/HpaI aldolase/citrate lyase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014873203.1
GO:0018817 - 2-oxo-hept-3-ene-1,7-dioate hydratase activity [Evidence IEA]
2-oxo-hepta-3-ene-1,7-dioic acid hydratase
COORDINATES: similar to AA sequence:RefSeq:WP_010441602.1
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009158900.1
GO:0016831 - carboxy-lyase activity [Evidence IEA]; GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0019752 - carboxylic acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017968753.1
COORDINATES: similar to AA sequence:RefSeq:WP_014881314.1
GO:0008687 - 3,4-dihydroxyphenylacetate 2,3-dioxygenase activity [Evidence IEA]
3,4-dihydroxyphenylacetate 2,3-dioxygenase
COORDINATES: similar to AA sequence:RefSeq:WP_008205136.1
GO:0008687 - 3,4-dihydroxyphenylacetate 2,3-dioxygenase activity [Evidence IEA]; GO:0008198 - ferrous iron binding [Evidence IEA]
GO:0006725 - cellular aromatic compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014881315.1
GO:0018480 - 5-carboxymethyl-2-hydroxymuconic-semialdehyde dehydrogenase activity [Evidence IEA]
GO:1901023 - 4-hydroxyphenylacetate catabolic process [Evidence IEA]
5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_014873199.1
5-carboxymethyl-2-hydroxymuconate Delta-isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_009157305.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]
homoprotocatechuate degradation operon regulator HpaR
COORDINATES: similar to AA sequence:RefSeq:WP_009831476.1
Tm-1-like ATP-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014873197.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014873196.1
COORDINATES: similar to AA sequence:RefSeq:WP_014873195.1
COORDINATES: similar to AA sequence:RefSeq:WP_014873194.1
tripartite tricarboxylate transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011456630.1
COORDINATES: similar to AA sequence:RefSeq:WP_009831456.1
COORDINATES: similar to AA sequence:RefSeq:WP_007256784.1
COORDINATES: similar to AA sequence:RefSeq:WP_009831480.1
aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_009831461.1
COORDINATES: similar to AA sequence:RefSeq:WP_010322101.1
COORDINATES: similar to AA sequence:RefSeq:WP_013959844.1
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.
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016733082.1