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
Q04373 UniProt NPD GO	PUF6_YEAST	Protein PUF6	0.66	-	nuc	0		nucleolus [IDA] nucleus [IDA]			656
P42223 UniProt NPD GO	SBE2_YEAST	Protein SBE2	0.66	-	nuc	0		Golgi apparatus [IDA]			864
Q02328 UniProt NPD GO	SLAP2_CAEEL	Protein SLA2 homolog	0.66	-	nuc	0					927
P50078 UniProt NPD GO	TOS2_YEAST	Protein TOS2 (Target of SBF 2)	0.66	-	nuc	1 *		bud neck [IDA] bud tip [IDA]			622
Q6CY29 UniProt NPD GO	VTS1_KLULA	Protein VTS1	0.66	-	nuc	0	Cytoplasm (By similarity)				459
Q9GZT5 UniProt NPD GO	WN10A_HUMAN	Protein Wnt-10a precursor	0.66	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix		606268		417
O76924 UniProt NPD GO	ARI2_DROME	Protein ariadne-2 (Ari-2)	0.66	-	nuc	0	Nucleus (By similarity)				509
Q640S2 UniProt NPD GO	CRBN_XENTR	Protein cereblon	0.66	-	nuc	0					447
Q9Y7B3 UniProt NPD GO	DOP1_EMENI	Protein dopey	0.66	-	mit	0	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; single-pass membrane protein (By sim ...				1858
P51558 UniProt NPD GO	DPY20_CAEBR	Protein dpy-20	0.66	-	nuc	0					439
Q9UNF0 UniProt NPD GO	PACN2_HUMAN	Protein kinase C and casein kinase substrate in neurons protein 2	0.66	-	nuc	0	Cytoplasmic vesicle (By similarity). Vesicle-like cytoplasmic distribution (By similarity)	cytoplasm [TAS]	604960		486
Q9DDA9 UniProt NPD GO	PACN2_XENLA	Protein kinase C and casein kinase substrate in neurons protein 2 (x-PACSIN2)	0.66	-	nuc	0	Cell membrane. Cytoplasmic vesicle. Membrane ruffles and cytoplasmic vesicles				477
P15792 UniProt NPD GO	KPK1_PHAVU	Protein kinase PVPK-1 (EC 2.7.11.1)	0.66	-	nuc	0					609
O61967 UniProt NPD GO	LAP1_CAEEL	Protein lap1 (Protein lethal-413)	0.66	-	nuc	0	Cell membrane; basolateral cell membrane; peripheral membrane protein. Basolateral membrane of epith ...	adherens junction [IDA] basolateral plasma membrane [IDA]			699
Q10574 UniProt NPD GO	LIN32_CAEEL	Protein lin-32 (Abnormal cell lineage protein 32)	0.66	-	nuc	0	Nucleus				142
Q568K2 UniProt NPD GO	PP1RB_BRARE	Protein phosphatase 1 regulatory subunit 11	0.66	-	nuc	0					122
Q9NXH3 UniProt NPD GO	PP14D_HUMAN	Protein phosphatase 1 regulatory subunit 14D (Gastrointestinal and brain-specific PP1-inhibitory pro ...	0.66	-	nuc	0	Cytoplasm (Probable)				145
P54631 UniProt NPD GO	SCW_DROME	Protein screw precursor	0.66	-	nuc	0	Secreted protein				400
Q9M291 UniProt NPD GO	SC24C_ARATH	Protein transport protein Sec24-like CEF	0.66	-	nuc	0					1097
Q24648 UniProt NPD GO	ZEN_DROSU	Protein zerknuellt	0.66	+	nuc	0	Nucleus (By similarity)				373
P28301 UniProt NPD GO	LYOX_MOUSE	Protein-lysine 6-oxidase precursor (EC 1.4.3.13) (Lysyl oxidase) (RAS excision protein)	0.66	-	exc	0	Secreted protein; extracellular space				411
O77628 UniProt NPD GO	FOS_BOVIN	Proto-oncogene protein c-fos (Cellular oncogene fos)	0.66	+	nuc	0	Nucleus				380
P15498 UniProt NPD GO	VAV_HUMAN	Proto-oncogene vav	0.66	-	mit	0			164875	2CRH	845
Q4WP81 UniProt NPD GO	COX10_ASPFU	Protoheme IX farnesyltransferase, mitochondrial precursor (EC 2.5.1.-) (Heme O synthase)	0.66	-	mit	7	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				512
Q8TB72 UniProt NPD GO	PUM2_HUMAN	Pumilio homolog 2 (Pumilio-2)	0.66	-	nuc	0	Cytoplasm (Probable)		607205		1066
P34534 UniProt NPD GO	TOP2M_CAEEL	Putative DNA topoisomerase II, mitochondrial precursor (EC 5.99.1.3)	0.66	-	nuc	0	Mitochondrion (By similarity)				1053
Q9ZVN6 UniProt NPD GO	CAP5_ARATH	Putative clathrin assembly protein At1g05020	0.66	-	nuc	0					653
Q9SKD6 UniProt NPD GO	CNG11_ARATH	Putative cyclic nucleotide-gated ion channel 11 (Cyclic nucleotide-and calmodulin-regulated ion chan ...	0.66	-	end	5 *	Cell membrane; multi-pass membrane protein (Potential)				621
Q9FXH6 UniProt NPD GO	CNGC8_ARATH	Putative cyclic nucleotide-gated ion channel 8 (Cyclic nucleotide- and calmodulin-regulated ion chan ...	0.66	-	end	5	Cell membrane; multi-pass membrane protein (Potential)				753
Q25197 UniProt NPD GO	HTK7_HYDAT	Putative insulin-like peptide receptor precursor (EC 2.7.10.1)	0.66	+	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				1477
Q8MYY6 UniProt NPD GO	GLT13_DROME	Putative polypeptide N-acetylgalactosaminyltransferase 13 (EC 2.4.1.41) (Protein-UDP acetylgalactosa ...	0.66	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi stack [ISS]			558
Q9LZJ8 UniProt NPD GO	ARR20_ARATH	Putative two-component response regulator ARR20	0.66	-	nuc	0	Nucleus				426
Q2I0M5 UniProt NPD GO	RSPO4_HUMAN	R-spondin-4 precursor (Roof plate-specific spondin-4) (hRspo4)	0.66	+	nuc	0	Secreted protein (By similarity)				234
Q5EAE9 UniProt NPD GO	ATL5C_ARATH	RING-H2 finger protein ATL5C precursor	0.66	+	exc	2 *					407
Q02983 UniProt NPD GO	RRN5_YEAST	RNA polymerase I-specific transcription initiation factor RRN5	0.66	-	nuc	0	Nucleus; nucleolus	RNA polymerase I upstream activating factor... [TAS]			363
P87306 UniProt NPD GO	MED17_SCHPO	RNA polymerase II mediator complex subunit 17 (Suppressor of RNA polymerase B 4 homolog)	0.66	-	nuc	0	Nucleus (Probable)				545
Q91W59 UniProt NPD GO	RBMS1_MOUSE	RNA-binding motif, single-stranded-interacting protein 1 (Single-stranded DNA-binding protein MSSP-1 ...	0.66	-	nuc	0	Nucleus (By similarity)				403
Q8BQP8 UniProt NPD GO	RFIP4_MOUSE	Rab11 family-interacting protein 4 (Rab11-FIP4)	0.66	-	nuc	0	Endosome; recycling endosome; recycling endosomal membrane; peripheral membrane protein (By similari ...				635
Q6XUX3 UniProt NPD GO	RIPK5_HUMAN	Receptor-interacting serine/threonine-protein kinase 5 (EC 2.7.11.1) (Dusty protein kinase) (Dusty P ...	0.66	-	cyt	0	Cytoplasm (Probable)				929
Q16827 UniProt NPD GO	PTPRO_HUMAN	Receptor-type tyrosine-protein phosphatase O precursor (EC 3.1.3.48) (Glomerular epithelial protein ...	0.66	-	end	2	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	600579	2GJT	1216
P23468 UniProt NPD GO	PTPRD_HUMAN	Receptor-type tyrosine-protein phosphatase delta precursor (EC 3.1.3.48) (Protein-tyrosine phosphata ...	0.66	+	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	601598	1X5Z	1912
Q9UJD0 UniProt NPD GO	RIMS3_HUMAN	Regulating synaptic membrane exocytosis protein 3 (Nim3) (Rab-3-interacting molecule 3) (RIM 3) (RIM ...	0.66	-	nuc	0					308
P10069 UniProt NPD GO	BRLA_EMENI	Regulatory protein brlA (Bristle A protein)	0.66	-	nuc	0	Nucleus				432
Q8IWW6 UniProt NPD GO	RHG12_HUMAN	Rho-GTPase-activating protein 12	0.66	-	nuc	0					846
Q8N392 UniProt NPD GO	RHG18_HUMAN	Rho-GTPase-activating protein 18 (MacGAP)	0.66	+	nuc	0					663
Q94913 UniProt NPD GO	REG5_DROME	Rhythmically expressed gene 5 protein (dReg-5)	0.66	-	nuc	1 *					288
Q02773 UniProt NPD GO	RPM2_YEAST	Ribonuclease P protein component, mitochondrial precursor (EC 3.1.26.5) (RNase P)	0.66	-	nuc	0	Mitochondrion	mitochondrion [IDA]			1202
Q9CR08 UniProt NPD GO	RPP29_MOUSE	Ribonuclease P protein subunit p29 (EC 3.1.26.5)	0.66	-	nuc	0	Nucleus; nucleolus (By similarity)				221
Q84TX2 UniProt NPD GO	SCRL1_ORYSA	SCAR-like protein 1	0.66	-	nuc	0					2097
Q62419 UniProt NPD GO	SH3G1_MOUSE	SH3-containing GRB2-like protein 1 (SH3 domain protein 2B) (SH3p8)	0.66	+	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Associated with internal membranes. Concentrated i ...				368

You are viewing entries 16001 to 16050 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.