From AureoWiki
Jump to navigation Jump to search
VisualWikitext
m (Text replacement - "* <aureodatabase>protein Genbank</aureodatabase> " to "")
m (Text replacement - "gene Genbank" to "gene RefSeq")
 
Line 1: Line 1:
__TOC__
<protect>
<protect>
<aureodatabase>NCBI date</aureodatabase>
<aureodatabase>annotation</aureodatabase>


=Summary=
=Summary=


* <aureodatabase>organism</aureodatabase>
*<aureodatabase>organism</aureodatabase>
* <aureodatabase>locus</aureodatabase>
*<aureodatabase>locus</aureodatabase>
* <aureodatabase>pan locus</aureodatabase>
*<aureodatabase>pan locus</aureodatabase>
* <aureodatabase>gene symbol</aureodatabase>
*<aureodatabase>gene symbol</aureodatabase>
* <aureodatabase>pan gene symbol</aureodatabase>
*<aureodatabase>pan gene symbol</aureodatabase>
* <aureodatabase>gene synonyms</aureodatabase>
*<aureodatabase>gene synonyms</aureodatabase>
* <aureodatabase>product</aureodatabase>
*<aureodatabase>product</aureodatabase>
</protect>
</protect>


Line 24: Line 25:
==General==
==General==


* <aureodatabase>gene type</aureodatabase>
*<aureodatabase>gene type</aureodatabase>
* <aureodatabase>locus</aureodatabase>
*<aureodatabase>locus</aureodatabase>
* <aureodatabase>gene symbol</aureodatabase>
*<aureodatabase>gene symbol</aureodatabase>
* <aureodatabase>product</aureodatabase>
*<aureodatabase>product</aureodatabase>
* <aureodatabase>gene replicon</aureodatabase>
*<aureodatabase>gene replicon</aureodatabase>
* <aureodatabase>strand</aureodatabase>
*<aureodatabase>strand</aureodatabase>
* <aureodatabase>gene coordinates</aureodatabase>
*<aureodatabase>gene coordinates</aureodatabase>
* <aureodatabase>gene length</aureodatabase>
*<aureodatabase>gene length</aureodatabase>
* <aureodatabase>essential</aureodatabase>
*<aureodatabase>essential</aureodatabase>
*<aureodatabase>gene comment</aureodatabase>
</protect>
</protect>


Line 38: Line 40:
==Accession numbers==
==Accession numbers==


* <aureodatabase>gene GI</aureodatabase>
*<aureodatabase>gene location</aureodatabase>
* <aureodatabase>gene Genbank</aureodatabase>
*<aureodatabase>gene BioCyc</aureodatabase>
*<aureodatabase>gene MicrobesOnline</aureodatabase>
</protect>
</protect>
   
   
<protect>  
<protect>
==Phenotype==
==Phenotype==
</protect>
</protect>
* Share your knowledge and add information here. [<span class="plainlinks">[http://www.protecs.uni-greifswald.de/aureowiki/index.php?title={{PAGENAMEE}}&action=edit&section=6 edit]</span>]
Share your knowledge and add information here. [<span class="plainlinks">[//aureowiki.med.uni-greifswald.de/index.php?title={{PAGENAMEE}}&veaction=edit&section=6 edit]</span>]


<protect>
<protect>
==DNA sequence==
==DNA sequence==


* <aureodatabase>gene sequence</aureodatabase>
*<aureodatabase>gene sequence</aureodatabase>
</protect>
</protect>


<protect>
<protect>
<aureodatabase>RNA regulated operons</aureodatabase>
</protect>


<protect>
=Protein=
=Protein=
<aureodatabase>protein 3D view</aureodatabase>
<aureodatabase>protein 3D view</aureodatabase>
==General==
==General==


* <aureodatabase>locus</aureodatabase>
*<aureodatabase>locus</aureodatabase>
* <aureodatabase>protein symbol</aureodatabase>
*<aureodatabase>protein symbol</aureodatabase>
* <aureodatabase>protein description</aureodatabase>
*<aureodatabase>protein description</aureodatabase>
* <aureodatabase>protein length</aureodatabase>
*<aureodatabase>protein length</aureodatabase>
* <aureodatabase>theoretical pI</aureodatabase>
*<aureodatabase>theoretical pI</aureodatabase>
* <aureodatabase>theoretical MW</aureodatabase>
*<aureodatabase>theoretical MW</aureodatabase>
* <aureodatabase>GRAVY</aureodatabase>
*<aureodatabase>GRAVY</aureodatabase>
</protect>
</protect>


Line 71: Line 77:
==Function==
==Function==


* <aureodatabase>protein reaction</aureodatabase>
*<aureodatabase>protein reaction</aureodatabase>
* <aureodatabase>protein TIGRFAM</aureodatabase>
*<aureodatabase>protein TIGRFAM</aureodatabase>
* <aureodatabase>protein TheSeed</aureodatabase>
*<aureodatabase>protein TheSeed</aureodatabase>
* <aureodatabase>protein PFAM</aureodatabase>
*<aureodatabase>protein PFAM</aureodatabase>
</protect>
</protect>


<protect>
<protect>
==Structure, modifications & interactions==
==Structure, modifications & cofactors==


* <aureodatabase>protein domains</aureodatabase>
*<aureodatabase>protein domains</aureodatabase>
* <aureodatabase>protein modifications</aureodatabase>
*<aureodatabase>protein modifications</aureodatabase>
* <aureodatabase>protein cofactors</aureodatabase>
*<aureodatabase>protein cofactors</aureodatabase>
* <aureodatabase>protein effectors</aureodatabase>
*<aureodatabase>protein effectors</aureodatabase>
* <aureodatabase>protein partners</aureodatabase>
*<aureodatabase>protein regulated operons</aureodatabase>
</protect>
</protect>


Line 90: Line 96:
==Localization==
==Localization==


* <aureodatabase>protein Psortb</aureodatabase>
*<aureodatabase>protein Psortb</aureodatabase>
* <aureodatabase>protein LocateP</aureodatabase>
*<aureodatabase>protein LocateP</aureodatabase>
* <aureodatabase>protein SignalP</aureodatabase>
*<aureodatabase>protein SignalP</aureodatabase>
* <aureodatabase>protein TMHMM</aureodatabase>
*<aureodatabase>protein TMHMM</aureodatabase>
</protect>
</protect>


Line 99: Line 105:
==Accession numbers==
==Accession numbers==


* <aureodatabase>protein GI</aureodatabase>
*<aureodatabase>protein GI</aureodatabase>
* <aureodatabase>protein UniProt</aureodatabase>
*<aureodatabase>protein RefSeq</aureodatabase>
* <aureodatabase>protein RefSeq</aureodatabase>
*<aureodatabase>protein UniProt</aureodatabase>
</protect>
</protect>


Line 107: Line 113:
==Protein sequence==
==Protein sequence==


* <aureodatabase>protein sequence</aureodatabase>
*<aureodatabase>protein sequence</aureodatabase>
</protect>
</protect>


<protect>
<protect>
==Peptides==
==Experimental data==


* <aureodatabase>protein validated peptides</aureodatabase>
*<aureodatabase>protein validated peptides</aureodatabase>
*<aureodatabase>protein validated localization</aureodatabase>
*<aureodatabase>protein validated quantitative data</aureodatabase>
*<aureodatabase>protein partners</aureodatabase>
</protect>
</protect>


Line 124: Line 133:
==Operon==
==Operon==


* <aureodatabase>operons</aureodatabase>
*<aureodatabase>operons</aureodatabase>
</protect>
</protect>


Line 130: Line 139:
==Regulation==
==Regulation==


* <aureodatabase>sigma factors</aureodatabase>
*<aureodatabase>regulators</aureodatabase>
* <aureodatabase>regulators</aureodatabase>
</protect>
</protect>


Line 137: Line 145:
==Transcription pattern==
==Transcription pattern==


* <aureodatabase>expression browser</aureodatabase>
*<aureodatabase>expression browser</aureodatabase>
</protect>
</protect>


Line 143: Line 151:
==Protein synthesis (provided by Aureolib)==
==Protein synthesis (provided by Aureolib)==


* <aureodatabase>protein synthesis Aureolib</aureodatabase>
*<aureodatabase>protein synthesis Aureolib</aureodatabase>
</protect>
</protect>


<protect>
<protect>
==Stability==
==Protein stability==


* <aureodatabase>protein half-life</aureodatabase>
*<aureodatabase>protein half-life</aureodatabase>
</protect>
</protect>


Latest revision as of 13:41, 11 March 2016

NCBI: 02-MAR-2017

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus USA300_FPR3757
  • locus tag: SAUSA300_RS07435 [old locus tag: SAUSA300_1363 ]
  • pan locus tag?: SAUPAN003935000
  • symbol: SAUSA300_RS07435
  • pan gene symbol?: gpsA
  • synonym:
  • product: glycerol-3-phosphate dehydrogenase (NAD(P)(+))

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SAUSA300_RS07435 [old locus tag: SAUSA300_1363 ]
  • symbol: SAUSA300_RS07435
  • product: glycerol-3-phosphate dehydrogenase (NAD(P)(+))
  • replicon: chromosome
  • strand: -
  • coordinates: 1529425..1530423
  • length: 999
  • essential: unknown other strains

⊟Accession numbers[edit | edit source]

⊟Phenotype[edit | edit source]

Share your knowledge and add information here. [edit]

⊟DNA sequence[edit | edit source]

  • 1
    61
    121
    181
    241
    301
    361
    421
    481
    541
    601
    661
    721
    781
    841
    901
    961
    ATGACTAAAATTACCGTTTTTGGTATGGGAAGTTTTGGGACAGCCCTTGCCAATGTTCTT
    GCAGAAAATGGACATGATGTTTTGATGTGGGGTAAAAATCAAGATGCTGTTGATGAATTA
    AATACATGTCATACAAATAAAAAGTATTTAAAATACGCGAAATTAGATGTTAACATCATC
    GCTACTTCAGATATGACCAAAGCAATTCAATTTGCAGATATTTACTTAATGGCTTTACCT
    ACTAAAGCAATGCGAGAAGTTGCTTCTCAAATTAATGATAAGCTGACCTCTAAAAAGACT
    TTTATACATGTTGCTAAAGGTATTGAAAATGGGACGTTTAAACGTGTGTCAGAAATGATT
    GAAGATTCTATTTCACCTGAATATAATGCAGGTATTGGCGTGTTGTCAGGGCCAAGTCAT
    GCGGAAGAAGTTGTAGTCAAGCAACCAACTACAGTTGCTGCTTCATCAAAAGATAAAAGT
    GTAAGTAAATTAACGCAAGATTTATTTATGAATGATTATTTGCGTGTGTACACGAATGAT
    GACTTGATTGGTGTTGAACTTGGTGGTGCATTGAAAAATATCATCGCAGTAGCAAGTGGT
    ATCGTAGCTGGAATTGGCTACGGTGATAATGCAAAAGCTGCATTAATGACTCGTGGCTTA
    GCGGAAATTAGTAGATTAGGTGAAAAGTTAGGTGCCGATCCTATGACATTTCTAGGTTTA
    GGTGGTATCGGTGACTTAATCGTTACTTGCACATCAACACATTCTCGGAATTTCACATTA
    GGATATAAACTTGGACAAGGTGAATCAATGGATCAAGCATTATCTGAAATGAATATGGTT
    GTTGAAGGTATTTATACAACTAAATCAGTTTATCATTTAGCTAAAGAAAAAAATGTGGAT
    ATGCCAATTACAAATGCATTATATAGAGTATTATTTGAAAATATCTCAGTAAAAGAATGC
    GTAAAAGATTTAATGGAGCGCGATAAAAAATCTGAATAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    999

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SAUSA300_RS07435 [old locus tag: SAUSA300_1363 ]
  • symbol: SAUSA300_RS07435
  • description: glycerol-3-phosphate dehydrogenase (NAD(P)(+))
  • length: 332
  • theoretical pI: 6.26285
  • theoretical MW: 36071.3
  • GRAVY: -0.0858434

⊟Function[edit | edit source]

  • reaction:
    EC 1.1.1.8?  ExPASy
    Glycerol-3-phosphate dehydrogenase (NAD+) sn-glycerol 3-phosphate + NAD+ = glycerone phosphate + NADH
    EC 1.1.1.94?  ExPASy
    Glycerol-3-phosphate dehydrogenase (NAD(P)+) sn-glycerol 3-phosphate + NAD(P)+ = glycerone phosphate + NAD(P)H
  • TIGRFAM:
    glycerol-3-phosphate dehydrogenase (NAD(+)) (TIGR03376; EC 1.1.1.8; HMM-score: 236.2)
    and 8 more
    nucleotide sugar dehydrogenase (TIGR03026; HMM-score: 40)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Pantothenate and coenzyme A 2-dehydropantoate 2-reductase (TIGR00745; EC 1.1.1.-; HMM-score: 31.2)
    Metabolism Energy metabolism Electron transport NADPH-dependent F420 reductase (TIGR01915; HMM-score: 24.5)
    Metabolism Amino acid biosynthesis Glutamate family pyrroline-5-carboxylate reductase (TIGR00112; EC 1.5.1.2; HMM-score: 22.4)
    Metabolism Energy metabolism Pentose phosphate pathway 6-phosphogluconate dehydrogenase (decarboxylating) (TIGR00872; EC 1.1.1.44; HMM-score: 22)
    3-hydroxyacyl-CoA dehydrogenase PaaC (TIGR02279; EC 1.1.1.-; HMM-score: 15.5)
    Metabolism Energy metabolism Pentose phosphate pathway 6-phosphogluconate dehydrogenase (decarboxylating) (TIGR00873; EC 1.1.1.44; HMM-score: 13.6)
    Metabolism Amino acid biosynthesis Pyruvate family ketol-acid reductoisomerase (TIGR00465; EC 1.1.1.86; HMM-score: 13.3)
  • TheSEED: see SAUSA300_1363
  • PFAM:
    6PGD_C (CL0106) NAD_Gly3P_dh_C; NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus (PF07479; HMM-score: 192.5)
    NADP_Rossmann (CL0063) NAD_Gly3P_dh_N; NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus (PF01210; HMM-score: 175)
    and 12 more
    F420_oxidored; NADP oxidoreductase coenzyme F420-dependent (PF03807; HMM-score: 42.9)
    UDPG_MGDP_dh_N; UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain (PF03721; HMM-score: 35.7)
    ApbA; Ketopantoate reductase PanE/ApbA (PF02558; HMM-score: 33.4)
    NAD_binding_2; NAD binding domain of 6-phosphogluconate dehydrogenase (PF03446; HMM-score: 29.1)
    IlvN; Acetohydroxy acid isomeroreductase, NADPH-binding domain (PF07991; HMM-score: 23.4)
    3HCDH_N; 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain (PF02737; HMM-score: 23.1)
    TrkA_N; TrkA-N domain (PF02254; HMM-score: 17.9)
    2-Hacid_dh_C; D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain (PF02826; HMM-score: 15.4)
    6PGD_C (CL0106) ApbA_C; Ketopantoate reductase PanE/ApbA C terminal (PF08546; HMM-score: 14.9)
    Nucleot_cyclase (CL0276) GCH_III; GTP cyclohydrolase III (PF05165; HMM-score: 14.5)
    NADP_Rossmann (CL0063) Shikimate_DH; Shikimate / quinate 5-dehydrogenase (PF01488; HMM-score: 13.8)
    PDH; Prephenate dehydrogenase (PF02153; HMM-score: 12.5)

⊟Structure, modifications & cofactors[edit | edit source]

  • domains:
  • modifications:
  • cofactors:
  • effectors:

⊟Localization[edit | edit source]

  • PSORTb: Cytoplasmic
    • Cytoplasmic Score: 7.5
    • Cytoplasmic Membrane Score: 1.15
    • Cellwall Score: 0.62
    • Extracellular Score: 0.73
    • Internal Helices: 0
  • LocateP:
  • SignalP: Signal peptide SP(Sec/SPI) length 21 aa
    • SP(Sec/SPI): 0.614414
    • TAT(Tat/SPI): 0.005277
    • LIPO(Sec/SPII): 0.014003
    • Cleavage Site: CS pos: 21-22. VLA-EN. Pr: 0.5386
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MTKITVFGMGSFGTALANVLAENGHDVLMWGKNQDAVDELNTCHTNKKYLKYAKLDVNIIATSDMTKAIQFADIYLMALPTKAMREVASQINDKLTSKKTFIHVAKGIENGTFKRVSEMIEDSISPEYNAGIGVLSGPSHAEEVVVKQPTTVAASSKDKSVSKLTQDLFMNDYLRVYTNDDLIGVELGGALKNIIAVASGIVAGIGYGDNAKAALMTRGLAEISRLGEKLGADPMTFLGLGGIGDLIVTCTSTHSRNFTLGYKLGQGESMDQALSEMNMVVEGIYTTKSVYHLAKEKNVDMPITNALYRVLFENISVKECVKDLMERDKKSE

⊟Experimental data[edit | edit source]

  • experimentally validated: data available for COL, NCTC8325
  • protein localization: data available for COL
  • quantitative data / protein copy number per cell:
  • interaction partners:

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

⊟Regulation[edit | edit source]

  • regulator:

⊟Transcription pattern[edit | edit source]

⊟Protein synthesis (provided by Aureolib)[edit | edit source]

⊟Protein stability[edit | edit source]

  • half-life: no data available

⊟Biological Material[edit | edit source]

⊟Mutants[edit | edit source]

⊟Expression vector[edit | edit source]

⊟lacZ fusion[edit | edit source]

⊟GFP fusion[edit | edit source]

⊟two-hybrid system[edit | edit source]

⊟FLAG-tag construct[edit | edit source]

⊟Antibody[edit | edit source]

⊟Other Information[edit | edit source]

You are kindly invited to share additional interesting facts.

⊟Literature[edit | edit source]

⊟References[edit | edit source]

⊟Relevant publications[edit | edit source]

Retrieved from "http://fungenwikiserver.biologie.uni-greifswald.de/aureowiki/index.php?title=SAUSA300_RS07435&oldid=101683"