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
Q8C4P0 UniProt NPD GO	K1958_MOUSE	Protein KIAA1958 homolog	0.67	-	nuc	0					716
Q9V4Z9 UniProt NPD GO	LINES_DROME	Protein Lines	0.67	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic in the half of the parasegment, posterior to the engrailed (en) doma ...	cytoplasm [IDA] nucleus [IDA]			858
Q5K8P4 UniProt NPD GO	SEY1_CRYNE	Protein SEY1	0.67	-	nuc	2	Membrane; multi-pass membrane protein (Potential)				829
Q9JHE7 UniProt NPD GO	TSSC4_MOUSE	Protein TSSC4	0.67	-	nuc	0					317
Q08438 UniProt NPD GO	VHS3_YEAST	Protein VHS3 (Viable in a HAL3 SIT4 background protein 3)	0.67	-	nuc	0					674
Q6YBV1 UniProt NPD GO	WUS_ANTMA	Protein WUSCHEL (Protein ROSULATA)	0.67	-	nuc	0	Nucleus (By similarity)				281
P28026 UniProt NPD GO	WNT8_XENLA	Protein Wnt-8 precursor (XWnt-8)	0.67	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix				358
P38274 UniProt NPD GO	HSL7_YEAST	Protein arginine N-methyltransferase HSL7 (EC 2.1.1.125)	0.67	-	nuc	0	Bud neck. Associates with the septin ring of the bud neck during cell division	bud neck [IDA]			827
Q9TUB3 UniProt NPD GO	FOSB_CANFA	Protein fosB	0.67	+	nuc	0	Nucleus				338
P09083 UniProt NPD GO	GSBN_DROME	Protein gooseberry-neuro (Protein gooseberry proximal) (BSH4)	0.67	+	nuc	0	Nucleus	nucleus [IDA]			449
P23938 UniProt NPD GO	NG1_DROME	Protein new-glue 1 precursor (NG-1) (Salivary glue protein homolog)	0.67	+	nuc	0	Secreted protein (Potential)				107
O61345 UniProt NPD GO	PEN_DROME	Protein penguin	0.67	+	nuc	0					737
Q6MFY6 UniProt NPD GO	PP1RB_RAT	Protein phosphatase 1 regulatory subunit 11	0.67	+	nuc	0					127
Q99K43 UniProt NPD GO	PRC1_MOUSE	Protein regulator of cytokinesis 1	0.67	-	nuc	0	Nucleus (By similarity). Predominantly localized to the nucleus of interphase cells. Cytoplasm (By s ...				603
P30052 UniProt NPD GO	SCAL_DROME	Protein scalloped	0.67	-	nuc	0	Nucleus	nucleus [IDA]			440
Q752V4 UniProt NPD GO	SEC9_ASHGO	Protein transport protein SEC9	0.67	-	nuc	0					533
Q9MUP8 UniProt NPD GO	YCF2_MESVI	Protein ycf2 (RF2)	0.67	-	mit	0	Plastid; chloroplast; chloroplast stroma (By similarity)				890
Q91496 UniProt NPD GO	FOS_TETFL	Proto-oncogene protein c-fos (Cellular oncogene fos)	0.67	+	nuc	0	Nucleus				374
O55134 UniProt NPD GO	PCD12_MOUSE	Protocadherin-12 precursor (Vascular cadherin-2) (Vascular endothelial cadherin-2) (VE-cadherin-2) ( ...	0.67	-	exc	1	Membrane; single-pass type I membrane protein	intercellular junction [IDA]			1180
Q80TF3 UniProt NPD GO	PCD19_MOUSE	Protocadherin-19 precursor	0.67	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1145
Q80U58 UniProt NPD GO	PUM2_MOUSE	Pumilio homolog 2	0.67	-	nuc	0	Cytoplasm (Probable)				1066
Q8MNV7 UniProt NPD GO	SMAL1_CAEEL	Putative SMARCAL1-like protein (EC 3.6.1.-)	0.67	-	cyt	0	Nucleus (By similarity)				690
Q9M0A4 UniProt NPD GO	CNGC9_ARATH	Putative cyclic nucleotide-gated ion channel 9 (Cyclic nucleotide- and calmodulin-regulated ion chan ...	0.67	-	end	5	Cell membrane; multi-pass membrane protein (Potential)				733
O13779 UniProt NPD GO	YF2E_SCHPO	Putative metal ion transporter C17A12.14	0.67	-	end	2	Membrane; multi-pass membrane protein (Potential)				617
P49391 UniProt NPD GO	RT14_CAEEL	Putative mitochondrial 40S ribosomal protein S14	0.67	-	nuc	0	Mitochondrion (By similarity)				199
Q09793 UniProt NPD GO	NG79_SCHPO	Putative nucleoporin C22G7.09c	0.67	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex (Potential)	nuclear pore [TAS]			425
O74769 UniProt NPD GO	YO38_SCHPO	Putative protein SPBC24C6.08c	0.67	-	nuc	0					367
Q09499 UniProt NPD GO	YQG4_CAEEL	Putative serine/threonine-protein kinase C41C4.4 precursor (EC 2.7.11.1)	0.67	-	end	1 *					983
Q08172 UniProt NPD GO	YO024_YEAST	Putative uncharacterized protein YOL024W	0.67	-	nuc	0					172
P98163 UniProt NPD GO	YL_DROME	Putative vitellogenin receptor precursor (Protein yolkless) (YL)	0.67	-	mit	1					1984
Q6PGA0 UniProt NPD GO	RCOR3_MOUSE	REST corepressor 3	0.67	-	nuc	0	Nucleus (By similarity)				451
Q8L9T5 UniProt NPD GO	ATL3F_ARATH	RING-H2 finger protein ATL3F (RING-H2 finger protein ATL2)	0.67	-	nuc	2 *					304
Q12321 UniProt NPD GO	MED1_YEAST	RNA polymerase II mediator complex subunit 1	0.67	-	nuc	0	Nucleus	mediator complex [IDA]			566
Q9Y821 UniProt NPD GO	MED4_SCHPO	RNA polymerase II mediator complex subunit 4 (RNA polymerase II mediator complex protein pmc4)	0.67	-	nuc	0	Nucleus (Probable)				239
Q15414 UniProt NPD GO	RBY1A_HUMAN	RNA-binding motif protein, Y chromosome, family 1 member A1 (RNA-binding motif protein 1)	0.67	-	nuc	0		nucleus [TAS]	400006		496
Q8BIJ7 UniProt NPD GO	RUFY1_MOUSE	RUN and FYVE domain-containing protein 1 (Rab4-interacting protein)	0.67	-	nuc	0	Cytoplasm. Early endosome; endosomal membrane; peripheral membrane protein	cytoplasm [IDA]			712
O18973 UniProt NPD GO	RABX5_BOVIN	Rab5 GDP/GTP exchange factor (Rabex-5)	0.67	-	nuc	0	Cytoplasm. Endosome; early endosome. Endosome; recycling endosome			2FIF	492
Q80UQ2 UniProt NPD GO	RASF6_MOUSE	Ras association domain-containing protein 6	0.67	-	nuc	0					353
Q9Z268 UniProt NPD GO	RASL1_MOUSE	RasGAP-activating-like protein 1	0.67	-	nuc	0					799
Q4VSN5 UniProt NPD GO	RIPK5_PANTR	Receptor-interacting serine/threonine-protein kinase 5 (EC 2.7.11.1) (Dusty protein kinase) (Dusty P ...	0.67	-	cyt	0	Cytoplasm (Probable)				930
O75916 UniProt NPD GO	RGS9_HUMAN	Regulator of G-protein signaling 9 (RGS9)	0.67	-	nuc	0			608415		674
O42358 UniProt NPD GO	RX3_BRARE	Retinal homeobox protein Rx3	0.67	+	nuc	0	Nucleus (By similarity)				292
P10394 UniProt NPD GO	POL4_DROME	Retrovirus-related Pol polyprotein from transposon 412 [Includes: Protease (EC 3.4.23.-); Reverse tr ...	0.67	-	nuc	0					1237
Q8I7P9 UniProt NPD GO	POL5_DROME	Retrovirus-related Pol polyprotein from transposon opus [Includes: Protease (EC 3.4.23.-); Reverse t ...	0.67	-	nuc	0		nucleus [NAS]			1003
P43556 UniProt NPD GO	RGD2_YEAST	Rho-GTPase-activating protein RGD2	0.67	-	nuc	0		bud neck [IDA] cytoplasm [IDA]			714
Q8MIT6 UniProt NPD GO	ROCK1_BOVIN	Rho-associated protein kinase 1 (EC 2.7.11.1) (Rho-associated, coiled-coil-containing protein kinase ...	0.67	+	nuc	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein (By similarity). A small pro ...				441
O44476 UniProt NPD GO	RNZ_CAEEL	Ribonuclease Z (EC 3.1.26.11) (RNase Z) (tRNase Z) (tRNA 3 endonuclease) (Homolog of ELAC2 protein 1 ...	0.67	-	nuc	0	Nucleus (Probable)				833
Q02997 UniProt NPD GO	PET56_SACKL	Ribose methyltransferase PET56 (EC 2.1.1.-) (Mitochondrial large ribosomal RNA ribose methylase) (21 ...	0.67	-	nuc	0	Mitochondrion				138
P25368 UniProt NPD GO	RRP7_YEAST	Ribosomal RNA-processing protein 7	0.67	-	nuc	0		nucleolus [IDA] nucleus [IDA]			297
Q6CK62 UniProt NPD GO	RSA3_KLULA	Ribosome assembly protein 3	0.67	+	nuc	0	Nucleus; nucleolus (By similarity)				203

You are viewing entries 15451 to 15500 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.