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View Structure Prediction Details

Protein: RGD2
Organism: Saccharomyces cerevisiae
Length: 714 amino acids
Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076



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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for RGD2.

Description E-value Query
Range
Subject
Range
RGD2_YEAST - Rho-GTPase-activating protein RGD2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RGD2 ...
RGD2 - GTPase-activating protein (RhoGAP) for Cdc42p and Rho5p
0.0 [1..714] [1..714]
gi|25535897, gi|... - gi|3413874|dbj|BAA32301.1| KIAA0456 protein [Homo sapiens], pir||C59437 KIAA0456 protein [imported] ...
0.0 [13..710] [52..709]
RGA8_SCHPO - Rho-GTPase-activating protein 8 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rga8 PE=1 ...
rga8 - GTPase activating protein Rga8
0.0 [1..712] [2..658]
gi|20137012, gi|... - gi|20137012|ref|NP_619536.1| Rho GTPase activating protein 4 [Mus musculus], gi|18034447|gb|AAL57498...
0.0 [13..707] [28..709]
RGA7_SCHPO - Probable Rho-GTPase-activating protein 7 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=r...
rga7 - GTPase activating protein Rga7
3.0E-97 [16..704] [44..692]

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Predicted Domain #1
Region A:
Residues: [1-225]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLSFCDYFWS EDLVSGLDVL FDRLYHGCEQ CDLFIQLFAS RMQFEVSHGR QLFGIEAGMD  60
   61 NLKAVQEDED EGVTVSRALR GILQEMSQEG THHLTIASNI ESLVLQPFSK WCIEHRERIQ 120
  121 YSEKTLLTNV NNFRKSKKYV GKLEKEYFNK CRQLEEFKRT HFNEDELANA MKSLKIQNKY 180
  181 EEDVAREKDH RFFNRIAGID FDYKTMKETL QLLLTKLPKT DYKLP

[Run NCBI BLAST on this sequence.]

Detection Method: ORFEUS
Confidence: 9.07
Match: 1av1A
Description: Apolipoprotein A-I
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
cytoskeletal protein binding 3.124619761789 bayes_pls_golite062009
binding 2.22529267810903 bayes_pls_golite062009
protein binding 1.87308005875135 bayes_pls_golite062009
identical protein binding 0.909409198394921 bayes_pls_golite062009
enzyme binding 0.58709209959999 bayes_pls_golite062009
GTPase binding 0.50066793947946 bayes_pls_golite062009
GTPase regulator activity 0.459881864914566 bayes_pls_golite062009
nucleoside-triphosphatase regulator activity 0.456472132383968 bayes_pls_golite062009
enzyme regulator activity 0.180886944097381 bayes_pls_golite062009
small GTPase binding 0.0531578648468707 bayes_pls_golite062009

Predicted Domain #2
Region A:
Residues: [226-299]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LISYSLSNTN NGGEITKFLL DHMSLKDIDQ AETFGQDLLN LGFLKYCNGV GNTFVNSKKF  60
   61 QYQWKNTAYM FANV

[Run NCBI BLAST on this sequence.]

Detection Method: Pfam
Confidence: 12.180456
Match: PF00610
Description: Domain found in Dishevelled, Egl-10, and Pleckstrin

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this domain.

Predicted Domain #3
Region A:
Residues: [300-366]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PMPGSEEPTT GESLISRFNN WDGSSAKEII QSKIGNDQGA AKIQAPHISD NERTLFRMMD  60
   61 ALAASDK

[Run NCBI BLAST on this sequence.]

Detection Method: deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

    MCM
Score
SCOP
Match
SCOP Description
View Download 0.513 a.35.1 lambda repressor-like DNA-binding domains
View Download 0.642 a.77.1 DEATH domain
View Download 0.534 a.159.1 Protein serine/threonine phosphatase 2C, C-terminal domain
View Download 0.494 a.46.1 Methionine synthase domain
View Download 0.454 a.64.2 Bacteriocin AS-48
View Download 0.437 a.156.1 S13-like H2TH domain
View Download 0.428 a.118.13 Arp2/3 complex 16 kDa subunit ARPC5
View Download 0.395 a.39.1 EF-hand
View Download 0.392 a.46.2 Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
View Download 0.391 a.156.1 S13-like H2TH domain
View Download 0.378 a.60.5 Barrier-to-autointegration factor, BAF
View Download 0.363 a.4.5 "Winged helix" DNA-binding domain
View Download 0.350 a.140.4 Recombination endonuclease VII, C-terminal and dimerization domains
View Download 0.329 a.4.1 Homeodomain-like
View Download 0.328 a.60.11 Hypothetical protein YjbJ
View Download 0.314 a.181.1 Antibiotic binding domain of TipA-like multidrug resistance regulators
View Download 0.304 a.4.1 Homeodomain-like
View Download 0.301 a.28.3 Retrovirus capsid protein C-terminal domain
View Download 0.285 a.64.1 Saposin
View Download 0.283 a.28.2 Colicin E immunity proteins
View Download 0.280 a.144.2 Ribosomal protein L20
View Download 0.271 a.8.1 Bacterial immunoglobulin/albumin-binding domains
View Download 0.268 a.7.7 BAG domain
View Download 0.263 a.65.1 Annexin
View Download 0.259 a.4.13 Sigma3 and sigma4 domains of RNA polymerase sigma factors
View Download 0.259 a.60.2 RuvA domain 2-like
View Download 0.258 a.4.5 "Winged helix" DNA-binding domain
View Download 0.252 a.40.1 Calponin-homology domain, CH-domain
View Download 0.251 a.118.11 Cytochrome c oxidase subunit E
View Download 0.246 a.28.1 ACP-like
View Download 0.237 a.4.1 Homeodomain-like
View Download 0.237 a.6.1 Putative DNA-binding domain
View Download 0.230 a.4.13 Sigma3 and sigma4 domains of RNA polymerase sigma factors
View Download 0.230 a.3.1 Cytochrome c
View Download 0.229 a.39.1 EF-hand
View Download 0.228 c.9.1 Barstar (barnase inhibitor)
View Download 0.228 a.35.1 lambda repressor-like DNA-binding domains
View Download 0.226 a.23.5 Hemolysin expression modulating protein HHA
View Download 0.225 a.140.1 LEM domain
View Download 0.220 a.112.1 Description not found.
View Download 0.217 b.85.2 Head decoration protein D (gpD, major capsid protein D)
View Download 0.214 a.35.1 lambda repressor-like DNA-binding domains
View Download 0.208 a.5.6 Hypothetical protein MTH1615
View Download 0.206 a.4.1 Homeodomain-like

Predicted functions:

Term Confidence Notes
GTPase regulator activity 5.23789256375467 bayes_pls_golite062009
nucleoside-triphosphatase regulator activity 5.21562004568462 bayes_pls_golite062009
small GTPase regulator activity 4.91645234075732 bayes_pls_golite062009
GTPase activator activity 4.81440293338491 bayes_pls_golite062009
Ras GTPase activator activity 4.76400460221691 bayes_pls_golite062009
Rho GTPase activator activity 4.58620967349979 bayes_pls_golite062009
enzyme regulator activity 4.5322075775333 bayes_pls_golite062009
Rac GTPase activator activity 4.48279904625182 bayes_pls_golite062009
enzyme activator activity 4.29367232260052 bayes_pls_golite062009
cytoskeletal protein binding 3.68681762274025 bayes_pls_golite062009
actin binding 3.68337819140185 bayes_pls_golite062009
actin filament binding 2.37781909937968 bayes_pls_golite062009
microfilament motor activity 2.15518436158221 bayes_pls_golite062009
binding 1.62780792681766 bayes_pls_golite062009
protein binding 1.21496582666968 bayes_pls_golite062009
Rho guanyl-nucleotide exchange factor activity 0.967362611034944 bayes_pls_golite062009
enzyme binding 0.56024350956935 bayes_pls_golite062009
GTPase binding 0.54882559587114 bayes_pls_golite062009
small GTPase binding 0.36738560339155 bayes_pls_golite062009

Predicted Domain #4
Region A:
Residues: [367-569]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KYYQECFKMD ALRCSVEELL IDHLSFMEKC ESDRLNAIKK ATLDFCSTLG NKISSLRLCI  60
   61 DKMLTLENDI DPTADLLQLL VKYKTGSFKP QAIVYNNYYN PGSFQNFGVD LETRCRLDKK 120
  121 VVPLIISSIF SYMDKIYPDL PNDKVRTSIW TDSVKLSLTH QLRNLLNKQQ FHNEGEIFDI 180
  181 LSTSKLEPST IASVVKIYLL ELP

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 38.0
Match: 1rgp__
Description: p50 RhoGAP domain
Matching Structure (courtesy of the PDB):

Predicted Domain #5
Region A:
Residues: [570-714]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DPLIPNDVSD ILRVLYLDYP PLVETALQNS TSSPENQQDD DNEEGFDTKR IRGLYTTLSS  60
   61 LSKPHIATLD AITTHFYRLI KILKMGENGN EVADEFTVSI SQEFANCIIQ SKITDDNEIG 120
  121 FKIFYDLLTH KKQIFHELKR QNSKN

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 38.0
Match: 1rgp__
Description: p50 RhoGAP domain
Matching Structure (courtesy of the PDB):

YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle