Roseibium alexandrii DFL-11 plasmid pLADFL_1, whole genome shotgun sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales; Stappiaceae; Roseibium.
Submitted (10-APR-2013) Microbiology, DSMZ German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7b, Braunschweig, Lower Saxony 38124, Germany
Submitted (23-JAN-2008) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCM011003.1.\nBacteria available from DSM 17067.\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 :: consed v. 20.0\nGenome Coverage :: 9.1x\nSequencing Technology :: Sanger dideoxy sequencing\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 11/22/2022 02:55:10\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 5,069\nCDSs (total) :: 5,004\nGenes (coding) :: 4,973\nCDSs (with protein) :: 4,973\nGenes (RNA) :: 65\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 52\nncRNAs :: 4\nPseudo Genes (total) :: 31\nCDSs (without protein) :: 31\nPseudo Genes (ambiguous residues) :: 0 of 31\nPseudo Genes (frameshifted) :: 9 of 31\nPseudo Genes (incomplete) :: 16 of 31\nPseudo Genes (internal stop) :: 9 of 31\nPseudo Genes (multiple problems) :: 3 of 31\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_002718991.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011505086.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012654880.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012655055.1
COORDINATES: similar to AA sequence:RefSeq:WP_007816901.1
COORDINATES: similar to AA sequence:RefSeq:WP_018431448.1
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_012564797.1
COORDINATES: similar to AA sequence:RefSeq:WP_003525125.1
COORDINATES: similar to AA sequence:RefSeq:WP_012655047.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011313597.1
COORDINATES: similar to AA sequence:RefSeq:WP_011313598.1
COORDINATES: similar to AA sequence:RefSeq:WP_011082894.1
COORDINATES: similar to AA sequence:RefSeq:WP_013913714.1
COORDINATES: similar to AA sequence:RefSeq:WP_014330240.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002718002.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007010057.1
COORDINATES: similar to AA sequence:RefSeq:WP_018431401.1
COORDINATES: similar to AA sequence:RefSeq:WP_006938639.1
COORDINATES: protein motif:HMM:TIGR03454.1
COORDINATES: similar to AA sequence:RefSeq:WP_018391648.1
COORDINATES: similar to AA sequence:RefSeq:WP_003527383.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009465873.1
GSU2403 family nucleotidyltransferase fold protein
COORDINATES: similar to AA sequence:RefSeq:WP_012655120.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505223.1
COORDINATES: similar to AA sequence:RefSeq:WP_013984785.1
COORDINATES: similar to AA sequence:RefSeq:WP_018325669.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505220.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_018329028.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_003523580.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654963.1
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_011505215.1
COORDINATES: similar to AA sequence:RefSeq:WP_020046771.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_015500693.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008892256.1
mercuric transporter MerT family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007253830.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819805.1
mercury resistance system transport protein MerF
COORDINATES: similar to AA sequence:RefSeq:WP_009805216.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011713390.1
COORDINATES: similar to AA sequence:RefSeq:WP_007090922.1
COORDINATES: similar to AA sequence:RefSeq:WP_011314727.1
COORDINATES: similar to AA sequence:RefSeq:WP_009467802.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00174
cobalamin riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_005981986.1
COORDINATES: similar to AA sequence:RefSeq:WP_005981979.1
COORDINATES: similar to AA sequence:RefSeq:WP_005981976.1
COORDINATES: protein motif:HMM:NF019460.2
COORDINATES: similar to AA sequence:RefSeq:WP_006932372.1
COORDINATES: similar to AA sequence:RefSeq:WP_008190788.1
COORDINATES: similar to AA sequence:RefSeq:WP_009605913.1
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]
manganese-binding transcriptional regulator MntR
COORDINATES: similar to AA sequence:RefSeq:WP_014131966.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820127.1
phosphate/phosphite/phosphonate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008282839.1
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_013652379.1
transglutaminase-like cysteine peptidase
COORDINATES: similar to AA sequence:RefSeq:WP_007197771.1
COORDINATES: similar to AA sequence:RefSeq:WP_018428811.1
COORDINATES: similar to AA sequence:RefSeq:WP_009452655.1
heparan-alpha-glucosaminide N-acetyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_006097163.1
COORDINATES: similar to AA sequence:RefSeq:WP_009452580.1
COORDINATES: similar to AA sequence:RefSeq:WP_009209139.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611540.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018303595.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_009807986.1
COORDINATES: similar to AA sequence:RefSeq:WP_018303599.1
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_009503840.1
COORDINATES: similar to AA sequence:RefSeq:WP_008889345.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803465.1
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: protein motif:HMM:NF015038.2
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: protein motif:HMM:NF025189.2
COORDINATES: protein motif:HMM:NF013540.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009469696.1
COORDINATES: similar to AA sequence:RefSeq:WP_012648975.1
COORDINATES: similar to AA sequence:RefSeq:WP_006470243.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129996.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0008233 - peptidase activity [Evidence IEA]
conjugative transfer signal peptidase TraF
COORDINATES: similar to AA sequence:RefSeq:WP_020048127.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: protein motif:HMM:NF019437.2
COORDINATES: similar to AA sequence:RefSeq:WP_013913801.1
COORDINATES: similar to AA sequence:RefSeq:WP_010892380.1
Ti-type conjugative transfer system protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_010915775.1
COORDINATES: similar to AA sequence:RefSeq:WP_012477327.1
COORDINATES: similar to AA sequence:RefSeq:WP_018516741.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011578758.1
COORDINATES: similar to AA sequence:RefSeq:WP_018116061.1
COORDINATES: similar to AA sequence:RefSeq:WP_018116060.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_007010038.1