Salipiger abyssi strain JLT2014 plasmid pPABY5, 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\nCP015089.1.\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: similar to AA sequence:RefSeq:WP_007803969.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
flagellar basal body P-ring protein FlgI
COORDINATES: similar to AA sequence:RefSeq:WP_007803967.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012874.2
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0071973 - bacterial-type flagellum-dependent cell motility [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR02492.1
GO:0009424 - bacterial-type flagellum hook [Evidence IEA]
GO:0001539 - cilium or flagellum-dependent cell motility [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803962.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007803959.1
COORDINATES: similar to AA sequence:RefSeq:WP_005849013.1
GO:0009426 - bacterial-type flagellum basal body, distal rod [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803956.1
GO:0009428 - bacterial-type flagellum basal body, distal rod, P ring [Evidence IEA]
flagellar basal body P-ring formation chaperone FlgA
COORDINATES: similar to AA sequence:RefSeq:WP_007117648.1
GO:0009427 - bacterial-type flagellum basal body, distal rod, L ring [Evidence IEA]
GO:0003774 - cytoskeletal motor activity [Evidence IEA]
flagellar basal body L-ring protein FlgH
COORDINATES: protein motif:HMM:NF025229.2
COORDINATES: protein motif:HMM:NF014207.2
flagellar hook-length control protein FliK
COORDINATES: similar to AA sequence:RefSeq:WP_007803946.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_007803942.1
COORDINATES: similar to AA sequence:RefSeq:WP_007254899.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF017277.2
COORDINATES: protein motif:HMM:NF012698.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF024824.2
COORDINATES: protein motif:HMM:NF016908.2
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009804002.1
COORDINATES: protein motif:HMM:NF014144.2
GO:0009288 - bacterial-type flagellum [Evidence IEA]
COORDINATES: protein motif:HMM:NF012738.2
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF012235.2
COORDINATES: protein motif:HMM:NF020650.2
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009573234.1
COORDINATES: similar to AA sequence:RefSeq:WP_019056333.1
COORDINATES: similar to AA sequence:RefSeq:WP_009450438.1
COORDINATES: similar to AA sequence:RefSeq:WP_015494256.1
COORDINATES: similar to AA sequence:RefSeq:WP_053111714.1
COORDINATES: protein motif:HMM:NF013756.2
COORDINATES: similar to AA sequence:RefSeq:WP_007767502.1
COORDINATES: similar to AA sequence:RefSeq:WP_006462171.1
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007767504.1
COORDINATES: similar to AA sequence:RefSeq:WP_009451302.1
COORDINATES: similar to AA sequence:RefSeq:WP_007002902.1
COORDINATES: similar to AA sequence:RefSeq:WP_006904563.1
ATP-binding cassette domain-containing protein
COORDINATES: protein motif:HMM:NF019310.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012241570.1
COORDINATES: similar to AA sequence:RefSeq:WP_009451301.1
COORDINATES: similar to AA sequence:RefSeq:WP_014132906.1
TetR/AcrR family transcriptional regulator
COORDINATES: nucleotide motif:Rfam:14.4:RF00059
TPP riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_011253730.1
GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
GO:0009228 - thiamine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007799990.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013196132.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009093096.1
COORDINATES: similar to AA sequence:RefSeq:WP_011253733.1
GO:0004789 - thiamine-phosphate diphosphorylase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009572570.1
COORDINATES: similar to AA sequence:RefSeq:WP_007792510.1
COORDINATES: similar to AA sequence:RefSeq:WP_020298638.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
GMC family oxidoreductase N-terminal domain-containing protein
COORDINATES: protein motif:HMM:TIGR01187.1
COORDINATES: similar to AA sequence:RefSeq:WP_011042860.1
COORDINATES: similar to AA sequence:RefSeq:WP_005861194.1
COORDINATES: similar to AA sequence:RefSeq:WP_011042858.1
COORDINATES: similar to AA sequence:RefSeq:WP_005861215.1
COORDINATES: similar to AA sequence:RefSeq:WP_009831017.1
COORDINATES: similar to AA sequence:RefSeq:WP_013949561.1
COORDINATES: similar to AA sequence:RefSeq:WP_018063363.1
COORDINATES: similar to AA sequence:RefSeq:WP_009502341.1
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006938114.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]; GO:0008483 - transaminase activity [Evidence IEA]
aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_013167428.1
GO:0008777 - acetylornithine deacetylase activity [Evidence IEA]
GO:0006592 - ornithine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006272105.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_007539776.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009804016.1
flagellar type III secretion system protein FlhB
COORDINATES: similar to AA sequence:RefSeq:WP_007803907.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803909.1
COORDINATES: protein motif:HMM:NF013618.2
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017929967.1
GO:0009306 - protein secretion [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007117617.1
GO:0003774 - cytoskeletal motor activity [Evidence IEA]; GO:0005198 - structural molecule activity [Evidence IEA]
flagellar hook-basal body complex protein FliE
COORDINATES: similar to AA sequence:RefSeq:WP_007803917.1
GO:0009425 - bacterial-type flagellum basal body [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803919.1
COORDINATES: similar to AA sequence:RefSeq:WP_017929963.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827317.1
COORDINATES: similar to AA sequence:RefSeq:WP_010443756.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574266.1
COORDINATES: similar to AA sequence:RefSeq:WP_020039397.1
COORDINATES: similar to AA sequence:RefSeq:WP_007088771.1
COORDINATES: similar to AA sequence:RefSeq:WP_019298067.1
COORDINATES: similar to AA sequence:RefSeq:WP_014528042.1
GO:0008660 - 1-aminocyclopropane-1-carboxylate deaminase activity [Evidence IEA]
GO:0042217 - 1-aminocyclopropane-1-carboxylate catabolic process [Evidence IEA]
1-aminocyclopropane-1-carboxylate deaminase
COORDINATES: similar to AA sequence:RefSeq:WP_005858682.1
Lrp/AsnC ligand binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020039046.1
COORDINATES: similar to AA sequence:RefSeq:WP_005862472.1
COORDINATES: similar to AA sequence:RefSeq:WP_012650244.1
COORDINATES: similar to AA sequence:RefSeq:WP_008168732.1
GO:0008721 - D-serine ammonia-lyase activity [Evidence IEA]; GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0046416 - D-amino acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008328109.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005858686.1
COORDINATES: similar to AA sequence:RefSeq:WP_005858687.1
COORDINATES: similar to AA sequence:RefSeq:WP_005858689.1
COORDINATES: similar to AA sequence:RefSeq:WP_005858691.1
COORDINATES: similar to AA sequence:RefSeq:WP_005858693.1
COORDINATES: similar to AA sequence:RefSeq:WP_005858695.1
COORDINATES: similar to AA sequence:RefSeq:WP_007691270.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819735.1
COORDINATES: similar to AA sequence:RefSeq:WP_011747391.1
COORDINATES: protein motif:HMM:NF024770.2
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009503866.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011331447.1
COORDINATES: protein motif:HMM:TIGR02123.1
COORDINATES: protein motif:HMM:TIGR02122.1
GO:0005215 - transporter activity [Evidence IEA]
TAXI family TRAP transporter solute-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013651868.1
class II aldolase/adducin family protein
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_008558507.1
COORDINATES: similar to AA sequence:RefSeq:WP_007254913.1
COORDINATES: similar to AA sequence:RefSeq:WP_008885253.1
COORDINATES: similar to AA sequence:RefSeq:WP_009506470.1
GO:0004450 - isocitrate dehydrogenase (NADP+) activity [Evidence IEA]
GO:0006099 - tricarboxylic acid cycle [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008887349.1
COORDINATES: similar to AA sequence:RefSeq:WP_008029866.1
COORDINATES: similar to AA sequence:RefSeq:WP_007802615.1
COORDINATES: similar to AA sequence:RefSeq:WP_007802616.1
COORDINATES: similar to AA sequence:RefSeq:WP_012177126.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_008887473.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887340.1
COORDINATES: protein motif:HMM:NF013884.2
COORDINATES: similar to AA sequence:RefSeq:WP_007804000.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803998.1
COORDINATES: protein motif:HMM:NF014235.2
FliM/FliN family flagellar motor switch protein
COORDINATES: protein motif:HMM:NF015693.2
GO:0071973 - bacterial-type flagellum-dependent cell motility [Evidence IEA]; GO:0006935 - chemotaxis [Evidence IEA]
flagellar basal body-associated FliL family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007803992.1
GO:0009431 - bacterial-type flagellum basal body, MS ring [Evidence IEA]
flagellar basal-body MS-ring/collar protein FliF
COORDINATES: protein motif:HMM:NF014196.2
COORDINATES: similar to AA sequence:RefSeq:WP_009824335.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803988.1
The bacterial flagellar biogenesis protein FliP forms a type III secretion system (T3SS)-type pore required for flagellar assembly; Derived by automated computational analysis using gene prediction method: Protein Homology.
flagellar type III secretion system pore protein FliP
COORDINATES: similar to AA sequence:RefSeq:WP_007803985.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803983.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803980.1
COORDINATES: similar to AA sequence:RefSeq:WP_017929983.1
GO:0044781 - bacterial-type flagellum organization [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009803976.1
COORDINATES: similar to AA sequence:RefSeq:WP_007117639.1