YRC Public Data Repository - Protein Structure Prediction

Protein:	MED4
Organism:	Saccharomyces cerevisiae
Length:	284 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

[What does the above image mean?]

[Show Ginzu Version Information]

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 MED4.

Description	E-value	Query Range	Subject Range
gi\|151945791 - gi\|151945791\|gb\|EDN64032.1\| mediator complex subunit [Saccharomyces cerevisiae YJM789] gi\|190407490 - gi\|190407490\|gb\|EDV10757.1\| RNA polymerase II mediator complex subunit 4 [Saccharomyces cerevisiae R... MED4_YEAST - Mediator of RNA polymerase II transcription subunit 4 OS=Saccharomyces cerevisiae (strain ATCC 20450... MED4 - Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form ...	6.0E-90	[1..268]	[1..268]
MED4_MOUSE - Mediator of RNA polymerase II transcription subunit 4 OS=Mus musculus GN=Med4 PE=2 SV=1	2.0E-63	[58..263]	[54..256]
MED4_YARLI - Mediator of RNA polymerase II transcription subunit 4 OS=Yarrowia lipolytica (strain CLIB 122 / E 15... MED4_YARLI - Mediator of RNA polymerase II transcription subunit 4 OS=Yarrowia lipolytica GN=MED4 PE=3 SV=1	2.0E-60	[16..279]	[79..326]
gi\|114649587 - gi\|114649587\|ref\|XP_509775.2\| PREDICTED: similar to VDRIP isoform 3 [Pan troglodytes] MED4 - mediator complex subunit 4	5.0E-60	[58..263]	[54..256]
pmc4 - RNA polymerase II holoenzyme component Pmc4 MED4_SCHPO - Mediator of RNA polymerase II transcription subunit 4 OS=Schizosaccharomyces pombe (strain 972 / ATC...	1.0E-58	[58..282]	[23..234]
MED4_ARATH - Mediator of RNA polymerase II transcription subunit 4 OS=Arabidopsis thaliana GN=MED4 PE=1 SV=1	4.0E-39	[78..240]	[153..334]
gi\|220944668, gi... - gi\|220954472\|gb\|ACL89779.1\| MED4-PA [synthetic construct], gi\|220944668\|gb\|ACL84877.1\| MED4-PA [synt... MED4-PA - The gene Mediator complex subunit 4 is referred to in FlyBase by the symbol Dmel\MED4 (CG8609, FBgn0...	8.0E-35	[68..204]	[40..174]

Back

Predicted Domain #1

Region A:
Residues: [1-64]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSVQDTKAVE FSMGHIRSSS VSLVAEATSN TNSEDKLSKV QLYEDLCRYE DTLSKLVESV  60
   61 DRFK

[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	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.648	0.978	transcription from RNA polymerase II promoter	a.4.1	Homeodomain-like
View	Download	0.611	0.978	transcription from RNA polymerase II promoter	a.60.5	Barrier-to-autointegration factor, BAF
View	Download	0.643	0.978	transcription from RNA polymerase II promoter	a.4.1	Homeodomain-like
View	Download	0.558	0.978	transcription from RNA polymerase II promoter	a.144.1	PABC (PABP) domain
View	Download	0.520	0.978	transcription from RNA polymerase II promoter	a.4.8	Ribosomal protein S18
View	Download	0.516	0.978	transcription from RNA polymerase II promoter	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.487	0.978	transcription from RNA polymerase II promoter	a.56.1	CO dehydrogenase ISP C-domain like
View	Download	0.480	0.978	transcription from RNA polymerase II promoter	a.60.11	Hypothetical protein YjbJ
View	Download	0.470	0.978	transcription from RNA polymerase II promoter	a.60.4	DNA repair protein Rad51, N-terminal domain
View	Download	0.448	0.978	transcription from RNA polymerase II promoter	a.159.2	FF domain
View	Download	0.416	0.978	transcription from RNA polymerase II promoter	a.4.11	RNA polymerase subunit RPB10
View	Download	0.410	0.978	transcription from RNA polymerase II promoter	a.74.1	Cyclin-like
View	Download	0.410	0.978	transcription from RNA polymerase II promoter	a.112.1	Description not found.
View	Download	0.409	0.978	transcription from RNA polymerase II promoter	a.36.1	Signal peptide-binding domain
View	Download	0.407	0.978	transcription from RNA polymerase II promoter	a.4.13	Sigma3 and sigma4 domains of RNA polymerase sigma factors
View	Download	0.404	0.978	transcription from RNA polymerase II promoter	a.46.2	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
View	Download	0.393	0.978	transcription from RNA polymerase II promoter	d.15.7	Immunoglobulin-binding domains
View	Download	0.391	0.978	transcription from RNA polymerase II promoter	a.74.1	Cyclin-like
View	Download	0.370	0.978	transcription from RNA polymerase II promoter	a.112.1	Description not found.
View	Download	0.361	0.978	transcription from RNA polymerase II promoter	a.56.1	CO dehydrogenase ISP C-domain like
View	Download	0.358	0.978	transcription from RNA polymerase II promoter	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.358	0.978	transcription from RNA polymerase II promoter	a.56.1	CO dehydrogenase ISP C-domain like
View	Download	0.349	0.978	transcription from RNA polymerase II promoter	b.84.2	Rudiment single hybrid motif
View	Download	0.345	0.978	transcription from RNA polymerase II promoter	a.144.2	Ribosomal protein L20
View	Download	0.318	0.978	transcription from RNA polymerase II promoter	a.4.13	Sigma3 and sigma4 domains of RNA polymerase sigma factors
View	Download	0.317	0.978	transcription from RNA polymerase II promoter	a.65.1	Annexin
View	Download	0.313	0.978	transcription from RNA polymerase II promoter	a.3.1	Cytochrome c
View	Download	0.301	0.978	transcription from RNA polymerase II promoter	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.300	0.978	transcription from RNA polymerase II promoter	a.153.1	Nuclear receptor coactivator interlocking domain
View	Download	0.296	0.978	transcription from RNA polymerase II promoter	d.74.2	C-terminal domain of arginine repressor
View	Download	0.272	0.978	transcription from RNA polymerase II promoter	a.159.1	Protein serine/threonine phosphatase 2C, C-terminal domain
View	Download	0.258	0.978	transcription from RNA polymerase II promoter	a.60.6	DNA polymerase beta, N-terminal domain-like
View	Download	0.255	0.978	transcription from RNA polymerase II promoter	a.60.2	RuvA domain 2-like
View	Download	0.251	0.978	transcription from RNA polymerase II promoter	a.5.6	Hypothetical protein MTH1615
View	Download	0.248	0.978	transcription from RNA polymerase II promoter	b.55.1	PH domain-like
View	Download	0.246	0.978	transcription from RNA polymerase II promoter	a.150.1	Anti-sigma factor AsiA
View	Download	0.245	0.978	transcription from RNA polymerase II promoter	g.34.1	HIV-1 VPU cytoplasmic domain
View	Download	0.242	0.978	transcription from RNA polymerase II promoter	d.214.1	Hypothetical protein MTH1880
View	Download	0.241	0.978	transcription from RNA polymerase II promoter	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.234	0.978	transcription from RNA polymerase II promoter	d.54.1	Enolase N-terminal domain-like
View	Download	0.221	0.978	transcription from RNA polymerase II promoter	a.4.1	Homeodomain-like
View	Download	0.219	0.978	transcription from RNA polymerase II promoter	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.218	0.978	transcription from RNA polymerase II promoter	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.217	0.978	transcription from RNA polymerase II promoter	a.105.1	FIS-like
View	Download	0.204	0.978	transcription from RNA polymerase II promoter	a.55.1	IHF-like DNA-binding proteins
View	Download	0.204	0.978	transcription from RNA polymerase II promoter	a.48.3	Conserved domain common to transcription factors TFIIS, elongin A, CRSP70

Predicted Domain #2

Region A:
Residues: [65-284]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PNLDIAKDLI RTDEALFENV KLLAEYDNIY RNLQKIDKDS EELDSKTRKI LEILNECHDE  60
   61 LKALPMLEQV EFEKNTILQQ RSKINSTELL DYATKLSKFT KIPPTFDKGA VGPNNFIWPA 120
  121 EDALRRGMLA MASLHSKELT RIPGEEVEET EVPTVPPSQS EEQKGQMAKK EGTPKTDSFI 180
  181 FDGTAKEVGD EADNTKDKEK EENNDDALDL DLDLFDPDDF

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

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.

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits