YRC Public Data Repository - Protein Structure Prediction

Protein:	RPN11
Organism:	Saccharomyces cerevisiae
Length:	306 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 RPN11.

Description	E-value	Query Range	Subject Range
gi\|2505940, gi\|1... - gi\|2505940\|emb\|CAA73514.1\| 26S proteasome, non-ATPase subunit [Mus musculus], gi\|10946952\|ref\|NP_067...	0.0	[1..306]	[1..309]
gi\|115435850, gi... - gi\|6630689\|dbj\|BAA88535.1\| putative Pad1 [Oryza sativa Japonica Group], gi\|34903124\|ref\|NP_912909.1\|... gi\|125525319 - gi\|125525319\|gb\|EAY73433.1\| hypothetical protein OsI_01313 [Oryza sativa Indica Group]	0.0	[1..305]	[1..307]
PSDE_ARATH - 26S proteasome non-ATPase regulatory subunit 14 homolog OS=Arabidopsis thaliana GN=RPN11 PE=1 SV=1	0.0	[1..305]	[1..308]
PSDE_MOUSE - 26S proteasome non-ATPase regulatory subunit 14 OS=Mus musculus GN=Psmd14 PE=1 SV=2 gi\|114581427 - gi\|114581427\|ref\|XP_515855.2\| PREDICTED: similar to 26S proteasome-associated pad1 homolog [Pan trog... gi\|90075820 - gi\|90075820\|dbj\|BAE87590.1\| unnamed protein product [Macaca fascicularis] tr\|M3X474\|M3X474... - Proteasome 26S subunit, non-ATPase 14 OS=Felis catus GN=PSMD14 PE=4 SV=1 gi\|71043862, gi\|... - gi\|71043862\|ref\|NP_001020860.1\| proteasome 26S subunit, non-ATPase 14 [Rattus norvegicus], gi\|669114... tr\|G3I179\|G3I179... - 26S proteasome non-ATPase regulatory subunit 14 OS=Cricetulus griseus GN=I79_017128 PE=4 SV=1 PSMD14 - proteasome (prosome, macropain) 26S subunit, non-ATPase, 14 gi\|149730649 - gi\|149730649\|ref\|XP_001493670.1\| PREDICTED: similar to proteasome (prosome, macropain) 26S subunit, ... gi\|109099850 - gi\|109099850\|ref\|XP_001096177.1\| PREDICTED: similar to proteasome (prosome, macropain) 26S subunit, ... gi\|109658277, gi... - gi\|115497090\|ref\|NP_001069535.1\| proteasome 26S subunit, non-ATPase 14 [Bos taurus], gi\|109658277\|gb...	0.0	[1..306]	[1..310]
gi\|2345100 - gi\|2345100\|gb\|AAC02298.1\| Pad1 homolog [Schistosoma mansoni]	0.0	[1..305]	[1..312]
gi\|14034117 - gi\|14034117\|emb\|CAC38736.1\| potential multidrug resistance protein [Aphrocallistes vastus]	0.0	[4..305]	[7..308]
gi\|14041178 - gi\|14041178\|emb\|CAC38755.1\| putative multidrug resistance protein [Geodia cydonium]	0.0	[1..305]	[1..309]
rpn11 - 19S proteasome regulatory subunit Rpn11 RPN11_SCHPO - 26S proteasome regulatory subunit rpn11 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rp...	0.0	[1..305]	[1..308]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[1..305]	[1..308]

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Predicted Domain #1

Region A:
Residues: [1-159]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MERLQRLMMN SKVGSADTGR DDTKETVYIS SIALLKMLKH GRAGVPMEVM GLMLGEFVDD  60
   61 YTVNVVDVFA MPQSGTGVSV EAVDDVFQAK MMDMLKQTGR DQMVVGWYHS HPGFGCWLSS 120
  121 VDVNTQKSFE QLNSRAVAVV VDPIQSVKGK VVIDAFRLI

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	44.958607
Match:	PF01398
Description:	Mov34/MPN/PAD-1 family

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 #2

Region A:
Residues: [160-211]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DTGALINNLE PRQTTSNTGL LNKANIQALI HGLNRHYYSL NIDYHKTAKE TK

[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	0.455	a.144.1	PABC (PABP) domain
View	Download	0.621	a.4.1	Homeodomain-like
View	Download	0.604	a.8.1	Bacterial immunoglobulin/albumin-binding domains
View	Download	0.929	a.2.6	Effector domain of the protein kinase pkn/prk1
View	Download	0.735	a.23.1	HSC20 (HSCB), C-terminal oligomerisation domain
View	Download	0.695	a.23.1	HSC20 (HSCB), C-terminal oligomerisation domain
View	Download	0.678	a.2.7	tRNA-binding arm
View	Download	0.676	a.7.2	Enzyme IIa from lactose specific PTS, IIa-lac
View	Download	0.459	g.63.1	Mollusk pheromone
View	Download	0.424	a.5.2	UBA-like
View	Download	0.305	a.4.1	Homeodomain-like
View	Download	0.304	a.144.2	Ribosomal protein L20
View	Download	0.301	a.5.2	UBA-like
View	Download	0.300	a.5.1	DNA helicase RuvA subunit, C-terminal domain
View	Download	0.299	d.47.1	Ribosomal protein L11, N-terminal domain
View	Download	0.282	a.36.1	Signal peptide-binding domain
View	Download	0.211	a.60.1	SAM/Pointed domain
View	Download	0.208	a.4.5	"Winged helix" DNA-binding domain

Predicted Domain #3

Region A:
Residues: [212-306]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLMNLHKEQW QSGLKMYDYE EKEESNLAAT KSMVKIAEQY SKRIEEEKEL TEEELKTRYV  60
   61 GRQDPKKHLS ETADETLENN IVSVLTAGVN SVAIK

[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.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.627	0.023	ubiquitin-dependent protein catabolic process	a.2.11	Fe,Mn superoxide dismutase (SOD), N-terminal domain
View	Download	0.678	0.006	ubiquitin-dependent protein catabolic process	a.2.7	tRNA-binding arm
View	Download	0.929	0.004	ubiquitin-dependent protein catabolic process	a.2.6	Effector domain of the protein kinase pkn/prk1
View	Download	0.671	0.001	ubiquitin-dependent protein catabolic process	a.7.2	Enzyme IIa from lactose specific PTS, IIa-lac
View	Download	0.735	N/A	N/A	a.23.1	HSC20 (HSCB), C-terminal oligomerisation domain
View	Download	0.548	N/A	N/A	a.7.1	Spectrin repeat
View	Download	0.529	N/A	N/A	a.47.2	t-snare proteins
View	Download	0.520	N/A	N/A	a.4.1	Homeodomain-like
View	Download	0.487	N/A	N/A	a.7.1	Spectrin repeat
View	Download	0.464	N/A	N/A	a.47.2	t-snare proteins
View	Download	0.409	N/A	N/A	a.7.1	Spectrin repeat
View	Download	0.409	N/A	N/A	a.2.1	GreA transcript cleavage protein, N-terminal domain
View	Download	0.394	N/A	N/A	a.7.1	Spectrin repeat
View	Download	0.345	N/A	N/A	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.325	N/A	N/A	a.133.1	Phospholipase A2, PLA2
View	Download	0.319	N/A	N/A	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.311	N/A	N/A	a.29.5	alpha-ketoacid dehydrogenase kinase, N-terminal domain
View	Download	0.301	N/A	N/A	a.24.3	Cytochromes
View	Download	0.300	N/A	N/A	a.24.10	Histidine-containing phosphotransfer domain, HPT domain
View	Download	0.297	N/A	N/A	i.11.1	Computational models partly based on NMR data
View	Download	0.289	N/A	N/A	f.36.1	Neurotransmitter-gated ion-channel pransmembrane pore
View	Download	0.273	N/A	N/A	a.2.2	Ribosomal protein L29 (L29p)
View	Download	0.254	N/A	N/A	f.14.1	Voltage-gated potassium channels
View	Download	0.241	N/A	N/A	a.7.1	Spectrin repeat
View	Download	0.241	N/A	N/A	a.4.9	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
View	Download	0.237	N/A	N/A	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.234	N/A	N/A	a.7.3	Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain
View	Download	0.233	N/A	N/A	a.2.3	Chaperone J-domain
View	Download	0.226	N/A	N/A	a.27.1	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
View	Download	0.217	N/A	N/A	a.181.1	Antibiotic binding domain of TipA-like multidrug resistance regulators
View	Download	0.216	N/A	N/A	a.18.1	T4 endonuclease V
View	Download	0.212	N/A	N/A	a.26.1	4-helical cytokines
View	Download	0.209	N/A	N/A	a.7.8	GAT domain
View	Download	0.206	N/A	N/A	a.24.3	Cytochromes
View	Download	0.206	N/A	N/A	a.2.7	tRNA-binding arm
View	Download	0.201	N/A	N/A	a.30.2	Homodimeric domain of signal transducing histidine kinase

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