Nodes:
Network nodes represent proteins
splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus.
Node Color
colored nodes:
query proteins and first shell of interactors
white nodes:
second shell of interactors
Node Content
empty nodes:
proteins of unknown 3D structure
filled nodes:
a 3D structure is known or predicted
Edges:
Edges represent protein-protein associations
associations are meant to be specific and meaningful, i.e. proteins jointly contribute to a shared function; this does not necessarily mean they are physically binding to each other.
Knowledge-based Evidence
from curated databases
textmining
Assay-based Predictions
experimentally determined
co-expression
Genomic Predictions
gene neighborhood
gene co-occurrence
gene fusions
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[Homology]
Score
dctP4PFAM: TRAP dicarboxylate transporter- DctP subunit KEGG: rde:RD1_1478 C4-dicarboxylate transport system C4-dicarboxylate-binding protein, putative. BLAST hit, good RBS 6nt upstream. (327 aa)    
Predicted Functional Partners:
dctQ4
PFAM: Tripartite ATP-independent periplasmic transporter DctQ component. BLAST hit to Proteobacteria.
 
    0.916
dctM2
TIGRFAM: TRAP dicarboxylate transporter, DctM subunit PFAM: Citrate transporter; TRAP C4-dicarboxylate transport system permease DctM subunit KEGG: rde:RD1_1476 TrapT family, DctM subunit, putative. Good BLAST hit to Rhodobacterales, gene cluster.
 
    0.908
mcd
PFAM: Malonyl-CoA decarboxylase KEGG: rde:RD1_1475 malonyl-CoA decarboxylase. Good Pfam hit, good BLAST hit to several Roseobacter species, RBS 10nt upstream.
 
    0.842
Dshi_3004
PFAM: regulatory protein GntR HTH; GntR domain protein KEGG: rde:RD1_1479 GntR-family transcription regulator, putative; GntR family.
 
     0.810
fadD1
SWISSPROT P69451: Long-chain-fatty-acid--CoA ligase; COG: COG0318 - Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II; PFAM: PF00501; PRINTS: PR00154; PROSITE: PS00455.
 
     0.734
Dshi_1090
Tripartite ATP-independent periplasmic transporter DctQ component; TRAP gene cluster - dctPQM.
 
    0.628
Dshi_0461
Conserved hypothetical protein; Unsure GC frame plot, no conserved domains (except for one signalpep. and one transmembr. region); good Ref YP hit to hypothetical protein RD1_0877 from Roseobacter denitrificans OCh 114; bad swissprot hit to Transposon Ty2-GR1 Gag-Pol polyprotein from Saccharomyces cerevisiae; Dshi_0463 transposase family protein.
  
     0.441
Dshi_0462
Conserved hypothetical protein; No significant swissprot, unsure GC frame plot; high Ref YP hit to hypothetical protein RD1_0878 from Roseobacter denitrificans OCh 114.
  
     0.431
dctQ1
PFAM: Tripartite ATP-independent periplasmic transporter DctQ component.
 
    0.410
Your Current Organism:
Dinoroseobacter shibae
NCBI taxonomy Id: 398580
Other names: D. shibae DFL 12 = DSM 16493, Dinoroseobacter shibae DFL 12, Dinoroseobacter shibae DFL 12 = DSM 16493, Dinoroseobacter shibae DSM 16493, Dinoroseobacter shibae DSM 16493 = DFL 12, Jannaschia sp. DFL-12
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