NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q5BDI8 UniProt NPD GO	SPC25_EMENI	Probable kinetochore protein spc25	0.57	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				257
Q9P241 UniProt NPD GO	AT10D_HUMAN	Probable phospholipid-transporting ATPase VD (EC 3.6.3.1) (ATPVD)	0.57	-	end	11	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			1426
Q6I588 UniProt NPD GO	ABIL4_ORYSA	Probable protein ABIL4 (Abl interactor-like protein 4)	0.57	-	nuc	0					302
P33181 UniProt NPD GO	SUC1_CANAL	Probable sucrose utilization protein SUC1	0.57	-	nuc	0	Nucleus (Probable)				501
P34547 UniProt NPD GO	UBPX_CAEEL	Probable ubiquitin carboxyl-terminal hydrolase R10E11.3 (EC 3.1.2.15) (Ubiquitin thioesterase) (Ubiq ...	0.57	-	nuc	0					410
P06401 UniProt NPD GO	PRGR_HUMAN	Progesterone receptor (PR)	0.57	+	nuc	0	Nucleus		607311	1ZUC	933
P32453 UniProt NPD GO	ATP11_YEAST	Protein ATP11, mitochondrial precursor	0.57	-	mit	0	Mitochondrion	mitochondrial matrix [TAS]			318
Q8LSN2 UniProt NPD GO	BBM2_BRANA	Protein BABY BOOM 2 (BnBBM2)	0.57	-	nuc	0	Nucleus (Probable)				579
Q9NWD9 UniProt NPD GO	BEX4_HUMAN	Protein BEX4 (Brain-expressed X-linked protein 4) (BEX1-like 1) (Nerve growth factor receptor-associ ...	0.57	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				120
Q86Y37 UniProt NPD GO	CJ046_HUMAN	Protein C10orf46	0.57	-	nuc	0					369
Q9UID3 UniProt NPD GO	CK002_HUMAN	Protein C11orf2 (Another new gene 2 protein)	0.57	-	cyt	0		integral to membrane [TAS]			782
Q9H714 UniProt NPD GO	CM018_HUMAN	Protein C13orf18	0.57	-	nuc	0					635
Q5H9T9 UniProt NPD GO	CN155_HUMAN	Protein C14orf155	0.57	-	nuc	0					837
Q68US5 UniProt NPD GO	CU063_PANTR	Protein C21orf63 homolog precursor	0.57	-	nuc	1					441
P59051 UniProt NPD GO	CU087_HUMAN	Protein C21orf87	0.57	+	nuc	0					145
Q5T5N4 UniProt NPD GO	CF118_HUMAN	Protein C6orf118	0.57	-	nuc	0					469
Q8BGA7 UniProt NPD GO	CG026_MOUSE	Protein C7orf26 homolog	0.57	-	mit	0					448
Q5T8R8 UniProt NPD GO	CI066_HUMAN	Protein C9orf66	0.57	-	mit	0					295
Q9NX05 UniProt NPD GO	CX017_HUMAN	Protein CXorf17 (Tumor antigen BJ-HCC-21)	0.57	-	nuc	0					1096
Q5RBE4 UniProt NPD GO	DEPP_PONPY	Protein DEPP	0.57	-	nuc	0					212
Q9NTK1 UniProt NPD GO	DEPP_HUMAN	Protein DEPP (Decidual protein induced by progesterone) (Fasting-induced gene protein) (FIG)	0.57	-	nuc	0					212
Q5RAG2 UniProt NPD GO	FA62A_PONPY	Protein FAM62A	0.57	-	nuc	2	Membrane; multi-pass membrane protein (Potential)				1104
Q9BSJ8 UniProt NPD GO	FA62A_HUMAN	Protein FAM62A (Membrane-bound C2 domain-containing protein)	0.57	+	nuc	2	Membrane; multi-pass membrane protein (Potential)				1104
Q96EK5 UniProt NPD GO	K1279_HUMAN	Protein KIAA1279	0.57	-	nuc	0			609460		621
P20484 UniProt NPD GO	MAK11_YEAST	Protein MAK11 (Maintenance of killer protein 11)	0.57	-	cyt	0	Nucleus; nucleolus. Membrane associated	membrane fraction [IDA]			468
O13364 UniProt NPD GO	PET54_SACBA	Protein PET54 (Petite colonies protein 54)	0.57	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				294
P10834 UniProt NPD GO	PET54_YEAST	Protein PET54 (Petite colonies protein 54)	0.57	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein	mitochondrial inner membrane [IDA] mitochondrial matrix [IDA]			293
P51534 UniProt NPD GO	SHE4_YEAST	Protein SHE4	0.57	-	cyt	0	Cytoplasm (Potential)	cytoplasm [IDA]			789
P36167 UniProt NPD GO	SLR3_YEAST	Protein SRL3 (RAD53 lethality suppressor protein 3)	0.57	-	nuc	0	Cytoplasm	cytoplasm [IDA]			246
Q7RTT3 UniProt NPD GO	SSX9_HUMAN	Protein SSX9	0.57	-	nuc	0			300544		188
P47002 UniProt NPD GO	SSY5_YEAST	Protein SSY5	0.57	-	nuc	0		extrinsic to plasma membrane [IDA]			687
P25344 UniProt NPD GO	STE50_YEAST	Protein STE50	0.57	-	nuc	0		cytoplasm [IDA]		1Z1V	346
P22812 UniProt NPD GO	TUBE_DROME	Protein Tube	0.57	-	nuc	0	Cytoplasm	cytoplasm [NAS]		1D2Z	462
P28119 UniProt NPD GO	WNT51_EPTST	Protein Wnt-5(I) (Fragment)	0.57	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				116
P32315 UniProt NPD GO	FKH2_XENLA	Protein XFKH2	0.57	+	nuc	0	Nucleus (Probable)				427
Q26974 UniProt NPD GO	DECA_TRICA	Protein decapentaplegic precursor	0.57	-	exc	0	Secreted protein (By similarity)				372
Q23973 UniProt NPD GO	MTRM_DROME	Protein matrimony (Cell cycle arrest protein D52)	0.57	-	nuc	0	Nucleus	nucleus [IMP]			217
Q96A00 UniProt NPD GO	PP14A_HUMAN	Protein phosphatase 1 regulatory subunit 14A (17 kDa PKC-potentiated inhibitory protein of PP1) (CPI ...	0.57	-	mit	0	Cytoplasm (By similarity)		608153		147
Q9NV79 UniProt NPD GO	PCMD2_HUMAN	Protein-L-isoaspartate O-methyltransferase domain-containing protein 2	0.57	+	cyt	0	Cytoplasm (By similarity)				361
Q5DRA5 UniProt NPD GO	PCDGJ_PANTR	Protocadherin gamma B7 precursor (PCDH-gamma-B7)	0.57	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				929
Q8TAB3 UniProt NPD GO	PCD19_HUMAN	Protocadherin-19 precursor	0.57	-	end	1	Membrane; single-pass type I membrane protein (By similarity)		300460		1148
Q9FNS4 UniProt NPD GO	MBB1_CHLRE	PsbB mRNA maturation factor Mbb1, chloroplast precursor	0.57	-	mit	0	Plastid; chloroplast; chloroplast stroma				662
P08770 UniProt NPD GO	TRA1_MAIZE	Putative AC transposase (ORFA)	0.57	-	mit	0					806
P40072 UniProt NPD GO	YEU6_YEAST	Putative RING finger protein YER116C	0.57	-	nuc	0					274
Q9FNI6 UniProt NPD GO	SM3L2_ARATH	Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member ...	0.57	-	nuc	0	Nucleus (By similarity)				1029
Q20257 UniProt NPD GO	TBX11_CAEEL	Putative T-box protein 11	0.57	-	nuc	0	Nucleus (Potential)				322
Q8S9J8 UniProt NPD GO	CAP1_ARATH	Putative clathrin assembly protein At4g32285	0.57	-	nuc	0					635
Q7XA39 UniProt NPD GO	RGA4_SOLBU	Putative disease resistance protein RGA4 (RGA4-blb)	0.57	-	cyt	0					988
Q6L440 UniProt NPD GO	R1A3_SOLDE	Putative late blight resistance protein homolog R1A-3	0.57	-	mit	0	Cytoplasm (By similarity)				760
P40890 UniProt NPD GO	YJW2_YEAST	Putative membrane glycoprotein YJL222W precursor	0.57	-	end	1					1549

You are viewing entries 20951 to 21000 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.