Croceicoccus naphthovorans strain PQ-2 plasmid p1, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Erythrobacteraceae; Croceicoccus.
Submitted (05-JUN-2015) Environmental Science, Zhejiang University, 688 Yu Hang Tang Road, Hangzhou, Zhejiang 310058, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP011771.1.\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 v. 2.2.0\nGenome Coverage :: 100\nSequencing Technology :: PacBio RS II\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/03/2023 03:27:14\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) :: 3,899\nCDSs (total) :: 3,848\nGenes (coding) :: 3,764\nCDSs (with protein) :: 3,764\nGenes (RNA) :: 51\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 45\nncRNAs :: 3\nPseudo Genes (total) :: 84\nCDSs (without protein) :: 84\nPseudo Genes (ambiguous residues) :: 0 of 84\nPseudo Genes (frameshifted) :: 29 of 84\nPseudo Genes (incomplete) :: 55 of 84\nPseudo Genes (internal stop) :: 13 of 84\nPseudo Genes (multiple problems) :: 12 of 84\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Croceicoccus naphthovorans
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF018381.2
internal stop; 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_006949398.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006949401.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054469.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006949406.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949408.1
COORDINATES: similar to AA sequence:RefSeq:WP_010335690.1
COORDINATES: similar to AA sequence:RefSeq:WP_018859495.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949410.1
COORDINATES: similar to AA sequence:RefSeq:WP_011579856.1
type II toxin-antitoxin system Y4mF family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_011579857.1
type II toxin-antitoxin system HipA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011443932.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890951.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890953.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949427.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054379.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007015866.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054377.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949446.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949450.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015861.1
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950641.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054087.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890973.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015857.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_007015856.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: similar to AA sequence:RefSeq:WP_015460511.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_010890976.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829960.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_011906604.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054095.1
type-F conjugative transfer system protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_019054096.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949478.1
COORDINATES: similar to AA sequence:RefSeq:WP_011906601.1
COORDINATES: similar to AA sequence:RefSeq:WP_010339784.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949487.1
COORDINATES: similar to AA sequence:RefSeq:WP_007016044.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_006949489.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_019054103.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_010890987.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053908.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019054819.1
COORDINATES: similar to AA sequence:RefSeq:WP_011906598.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012975307.1
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_010913709.1
COORDINATES: similar to AA sequence:RefSeq:WP_007678521.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_006379760.1
COORDINATES: similar to AA sequence:RefSeq:WP_011087945.1
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_011082855.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834080.1
GO:0006629 - lipid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010890882.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0009410 - response to xenobiotic stimulus [Evidence IEA]; GO:0006855 - xenobiotic transmembrane transport [Evidence IEA]
DHA2 family efflux MFS transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_010890883.1
EmrA/EmrK family multidrug efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013847673.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
efflux transporter outer membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_010890885.1
GO:0016790 - thiolester hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012110688.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011906632.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012521738.1
COORDINATES: similar to AA sequence:RefSeq:WP_018147836.1
COORDINATES: similar to AA sequence:RefSeq:WP_006834181.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012111125.1
COORDINATES: similar to AA sequence:RefSeq:WP_012110717.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007226716.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006834185.1
COORDINATES: similar to AA sequence:RefSeq:WP_012110714.1
COORDINATES: similar to AA sequence:RefSeq:WP_006834188.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016703 - oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of one atom of oxygen (internal monooxygenases or internal mixed function oxidases) [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006834189.1
COORDINATES: similar to AA sequence:RefSeq:WP_006438771.1
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_004617931.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007016019.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834075.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834074.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_013834073.1
GO:0009027 - tartrate dehydrogenase activity [Evidence IEA]
GO:0046395 - carboxylic acid catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013834072.1
GO:0008677 - 2-dehydropantoate 2-reductase activity [Evidence IEA]
GO:0015940 - pantothenate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013832849.1
GO:0009436 - glyoxylate catabolic process [Evidence IEA]; GO:0071704 - organic substance metabolic process [Evidence IEA]
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008827667.1
alcohol dehydrogenase catalytic domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013834068.1
GO:0019439 - aromatic compound catabolic process [Evidence IEA]; GO:0006725 - cellular aromatic compound metabolic process [Evidence IEA]
aromatic-ring-hydroxylating dioxygenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_013832845.1
aromatic ring-hydroxylating dioxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_013832844.1
GO:0005215 - transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013834065.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611345.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013634994.1
COORDINATES: similar to AA sequence:RefSeq:WP_011341074.1
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_007016000.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834082.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834083.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015997.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013832834.1
GO:0006725 - cellular aromatic compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007015995.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013832832.1
GO:0016829 - lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013832831.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_008829811.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834092.1
GO:0043565 - sequence-specific DNA binding [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007015990.1
COORDINATES: similar to AA sequence:RefSeq:WP_013834112.1
3-(cis-5,6-dihydroxycyclohexa-1, 3-dien-1-yl)propanoate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_013832820.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891012.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832819.1
GO:0016862 - intramolecular oxidoreductase activity, interconverting keto- and enol-groups [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013832818.1
GO:0003824 - catalytic activity [Evidence IEA]
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013832817.1
GO:0008701 - 4-hydroxy-2-oxovalerate aldolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013832816.1
GO:0008774 - acetaldehyde dehydrogenase (acetylating) activity [Evidence IEA]
acetaldehyde dehydrogenase (acetylating)
COORDINATES: similar to AA sequence:RefSeq:WP_013832815.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828138.1
GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [Evidence IEA]
2-hydroxymuconic semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_013832813.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015979.1
GO:0018577 - catechol 2,3-dioxygenase activity [Evidence IEA]
GO:0009712 - catechol-containing compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013832811.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832810.1
GO:0005515 - protein binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010891023.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832808.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832807.1
4-hydroxythreonine-4-phosphate dehydrogenase PdxA
COORDINATES: similar to AA sequence:RefSeq:WP_013832806.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832805.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]
GO:0044237 - cellular metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013832804.1
COORDINATES: similar to AA sequence:RefSeq:WP_008828127.1
non-heme iron oxygenase ferredoxin subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013832802.1
COORDINATES: similar to AA sequence:RefSeq:WP_013832801.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015007020.1
2-hydroxychromene-2-carboxylate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_007015966.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015965.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_076611527.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF019310.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013832783.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831440.1
COORDINATES: protein motif:HMM:NF014898.2
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00914.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_007015151.1
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_003046513.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007015769.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007015950.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_019054306.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015948.1
Mu transposase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF017243.2
COORDINATES: similar to AA sequence:RefSeq:WP_019054311.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_006949340.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949342.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949343.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949344.1
COORDINATES: similar to AA sequence:RefSeq:WP_019053429.1
COORDINATES: similar to AA sequence:RefSeq:WP_017503700.1
COORDINATES: similar to AA sequence:RefSeq:WP_010408889.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015936.1
COORDINATES: similar to AA sequence:RefSeq:WP_016510924.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054498.1
strawberry notch C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012760251.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054765.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006949349.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019054763.1
COORDINATES: protein motif:HMM:NF019997.2
COORDINATES: protein motif:HMM:NF037521.2
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006949361.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015910.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015909.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015908.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015907.1
COORDINATES: protein motif:HMM:NF019371.2
COORDINATES: similar to AA sequence:RefSeq:WP_008390679.1
COORDINATES: similar to AA sequence:RefSeq:WP_020817927.1
COORDINATES: similar to AA sequence:RefSeq:WP_011910433.1
COORDINATES: similar to AA sequence:RefSeq:WP_014072622.1
IS66 family transposase zinc-finger binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017183759.1
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_011950830.1
COORDINATES: similar to AA sequence:RefSeq:WP_016921086.1
COORDINATES: similar to AA sequence:RefSeq:WP_013040336.1
COORDINATES: similar to AA sequence:RefSeq:WP_008878444.1
COORDINATES: similar to AA sequence:RefSeq:WP_015235485.1
multiubiquitin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009797786.1
COORDINATES: similar to AA sequence:RefSeq:WP_007013873.1
COORDINATES: similar to AA sequence:RefSeq:WP_019054215.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949380.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949381.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015888.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
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: similar to AA sequence:RefSeq:WP_007015887.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015886.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015885.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015884.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949390.1
COORDINATES: similar to AA sequence:RefSeq:WP_006949392.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015881.1
COORDINATES: protein motif:HMM:NF041492.1
COORDINATES: protein motif:HMM:NF024991.2