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
Q6DHR0 UniProt NPD GO	RSPO1_BRARE	R-spondin-1 precursor (Roof plate-specific spondin-1)	0.82	-	nuc	0	Secreted protein (By similarity)				261
Q2MKA7 UniProt NPD GO	RSPO1_HUMAN	R-spondin-1 precursor (Roof plate-specific spondin-1) (hRspo1)	0.82	+	mit	0	Secreted protein (By similarity)		609595		263
Q96B01 UniProt NPD GO	R51A1_HUMAN	RAD51-associated protein 1 (RAD51-interacting protein)	0.82	-	nuc	0	Nucleus (By similarity). Colocalizes with RAD51 to multiple nuclear foci (By similarity)	nucleus [IC]	603070		352
Q9UKL0 UniProt NPD GO	RCOR1_HUMAN	REST corepressor 1 (Protein CoREST)	0.82	+	nuc	0	Nucleus. Upon infection by HSV-1, it is partially translocated into the cytoplasm in an HSV-1-depend ...		607675		482
Q6NYV9 UniProt NPD GO	LEO1_BRARE	RNA polymerase-associated protein LEO1	0.82	+	nuc	0	Nucleus (By similarity)				696
Q9CQT2 UniProt NPD GO	RBM7_MOUSE	RNA-binding protein 7 (RNA-binding motif protein 7)	0.82	-	nuc	0					265
P58069 UniProt NPD GO	RASA2_MOUSE	Ras GTPase-activating protein 2 (GAP1m)	0.82	-	nuc	0	Cell membrane (Potential)				848
Q9JKF1 UniProt NPD GO	IQGA1_MOUSE	Ras GTPase-activating-like protein IQGAP1	0.82	+	nuc	0	Cell membrane (By similarity)	cytoplasm [IDA]			1657
P46940 UniProt NPD GO	IQGA1_HUMAN	Ras GTPase-activating-like protein IQGAP1 (p195)	0.82	+	nuc	0	Cell membrane	actin filament [TAS]	603379	1X0H	1657
Q13576 UniProt NPD GO	IQGA2_HUMAN	Ras GTPase-activating-like protein IQGAP2	0.82	-	nuc	0		actin cytoskeleton [TAS]	605401		1574
O76081 UniProt NPD GO	RGS20_HUMAN	Regulator of G-protein signaling 20 (RGS20) (Regulator of Gz-selective protein signaling 1) (Gz-sele ...	0.82	-	nuc	0	Membrane; lipid-anchor		607193		388
P11978 UniProt NPD GO	SIR4_YEAST	Regulatory protein SIR4 (Silent information regulator 4)	0.82	-	nuc	0	Nucleus	chromatin silencing complex [IDA] nuclear telomere cap complex [IDA] nuclear telomeric heterochromatin [IDA]		1PL5	1358
P10276 UniProt NPD GO	RARA_HUMAN	Retinoic acid receptor alpha (RAR-alpha)	0.82	+	nuc	0	Nucleus		180240	1DSZ	462
P10826 UniProt NPD GO	RARB_HUMAN	Retinoic acid receptor beta (RAR-beta) (RAR-epsilon) (HBV-activated protein)	0.82	+	nuc	0	Isoform beta-1, isoform beta-2: Nucleus. Isoform beta-4: Cytoplasm		180220	1XAP	455
P20825 UniProt NPD GO	POL2_DROME	Retrovirus-related Pol polyprotein from transposon 297 [Includes: Protease (EC 3.4.23.-); Reverse tr ...	0.82	-	nuc	0					1059
Q9N0A8 UniProt NPD GO	ARHG3_MACFA	Rho guanine nucleotide exchange factor 3	0.82	-	nuc	0	Cytoplasm (By similarity)				526
Q9NR81 UniProt NPD GO	ARHG3_HUMAN	Rho guanine nucleotide exchange factor 3 (Exchange factor found in platelets and leukemic and neuron ...	0.82	-	nuc	0	Cytoplasm (By similarity)				526
Q08965 UniProt NPD GO	BMS1_YEAST	Ribosome biogenesis protein BMS1	0.82	+	nuc	0	Cytoplasm. Nucleus; nucleolus	cytoplasm [IDA] mitochondrion [IDA] nucleolus [IDA] nucleus [IDA]			1183
Q99PL5 UniProt NPD GO	RRBP1_MOUSE	Ribosome-binding protein 1 (Ribosome receptor protein) (mRRp)	0.82	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...	integral to endoplasmic reticulum membrane [ISS]			1605
P32372 UniProt NPD GO	RAD4_SCHPO	S-M checkpoint control protein rad4 (Protein cut5) (P74)	0.82	-	nuc	0	Nucleus				648
Q5VZ18 UniProt NPD GO	SHE_HUMAN	SH2 domain-containing adapter protein E	0.82	-	nuc	0					495
Q9ESJ4 UniProt NPD GO	SPN90_MOUSE	SH3 adapter protein SPIN90 (NCK-interacting protein with SH3 domain) (SH3 protein interacting with N ...	0.82	-	nuc	0	Nucleus (By similarity). Colocalizes with DRF1 at membrane ruffles, and with Nck at Z-disks in matur ...				714
Q9UPX8 UniProt NPD GO	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains protein 2 (Shank2)	0.82	-	nuc	0	Cytoplasm; postsynaptic density of neuronal cells (By similarity)		603290		1253
O15370 UniProt NPD GO	SOX12_HUMAN	SOX-12 protein (SOX-22 protein)	0.82	-	nuc	0	Nucleus		601947		315
P40649 UniProt NPD GO	SOX12_XENLA	SOX-12 protein (xSOX-12)	0.82	-	nuc	0	Nucleus (Potential)				470
Q04891 UniProt NPD GO	SOX13_MOUSE	SOX-13 protein	0.82	-	end	0	Nucleus (Potential)				985
O64645 UniProt NPD GO	SOC1_ARATH	SUPPRESSOR OF CONSTANS OVEREXPRESSION 1 protein (Agamous-like MADS-box protein AGL20)	0.82	-	nuc	0	Nucleus (Probable)				214
Q92922 UniProt NPD GO	SMRC1_HUMAN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 1 (SWI/S ...	0.82	+	nuc	0	Nucleus	nucleoplasm [TAS] SWI/SNF complex [IDA]	601732		1105
P97496 UniProt NPD GO	SMRC1_MOUSE	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 1 (SWI/S ...	0.82	+	nuc	0	Nucleus	intracellular [IDA] SWI/SNF complex [TAS]			1104
Q9H4B6 UniProt NPD GO	SAV1_HUMAN	Salvador homolog 1 protein (45 kDa WW domain protein) (hWW45)	0.82	-	nuc	0			607203		383
Q5R5D2 UniProt NPD GO	SOSD1_PONPY	Sclerostin domain-containing protein 1 precursor	0.82	-	nuc	0	Secreted protein (By similarity)				206
Q6X4U4 UniProt NPD GO	SOSD1_HUMAN	Sclerostin domain-containing protein 1 precursor (Ectodermal BMP inhibitor) (Ectodin) (Uterine sensi ...	0.82	-	nuc	0	Secreted protein		609675		206
Q9GLG4 UniProt NPD GO	SCG1_PIG	Secretogranin-1 precursor (Secretogranin I) (SgI) (Chromogranin B) (CgB) [Contains: Peptide SR-17; P ...	0.82	-	exc	0	Neuroendocrine and endocrine secretory granules	secretory granule [IEP]			668
O14640 UniProt NPD GO	DVL1_HUMAN	Segment polarity protein dishevelled homolog DVL-1 (Dishevelled-1) (DSH homolog 1)	0.82	+	nuc	0		cytoplasm [TAS]	601365		670
Q5IS48 UniProt NPD GO	DVL1_PANTR	Segment polarity protein dishevelled homolog DVL-1 (Dishevelled-1) (DSH homolog 1)	0.82	+	nuc	0					670
O02491 UniProt NPD GO	HMEN_ANOGA	Segmentation polarity homeobox protein engrailed	0.82	+	nuc	0	Nucleus (Potential)				596
P02836 UniProt NPD GO	HMEN_DROME	Segmentation polarity homeobox protein engrailed	0.82	+	nuc	0	Nucleus	nucleus [IDA]		3HDD	552
P09145 UniProt NPD GO	HMEN_DROVI	Segmentation polarity homeobox protein engrailed	0.82	+	nuc	0	Nucleus				584
O95025 UniProt NPD GO	SEM3D_HUMAN	Semaphorin-3D precursor	0.82	+	nuc	1 *	Secreted protein (By similarity)		609907		777
Q5U7M7 UniProt NPD GO	SEMG2_ATEGE	Semenogelin-2 precursor (Semenogelin II) (SGII)	0.82	-	nuc	0	Secreted protein (By similarity)				514
Q10199 UniProt NPD GO	IMP2_SCHPO	Septation protein imp2	0.82	-	nuc	0	Cytoplasm. Associates with the medial ring during septation	contractile ring (sensu Fungi) [IDA]			670
Q5REG8 UniProt NPD GO	SEP10_PONPY	Septin-10	0.82	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				467
Q13188 UniProt NPD GO	STK3_HUMAN	Serine/threonine-protein kinase 3 (EC 2.7.11.1) (STE20-like kinase MST2) (MST-2) (Mammalian STE20-li ...	0.82	-	nuc	0	Cytoplasm; the caspase-cleaved form cycles between nucleus and cytoplasm (By similarity)		605030		491
Q6P3Q4 UniProt NPD GO	STK4_XENTR	Serine/threonine-protein kinase 4 (EC 2.7.11.1)	0.82	-	nuc	0	Cytoplasm. The caspase-cleaved form cycles between the nucleus and cytoplasm (By similarity)				485
Q9HFW2 UniProt NPD GO	CLA4_ASHGO	Serine/threonine-protein kinase CLA4 (EC 2.7.11.1)	0.82	-	nuc	0					793
Q9BZL6 UniProt NPD GO	KPCD2_HUMAN	Serine/threonine-protein kinase D2 (EC 2.7.11.13) (nPKC-D2)	0.82	-	nuc	0		intracellular [NAS]	607074	2COA	878
O08679 UniProt NPD GO	MARK2_RAT	Serine/threonine-protein kinase MARK2 (EC 2.7.11.1) (MAP/microtubule affinity-regulating kinase 2) ( ...	0.82	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity). Phosphorylated by PRKCZ in polarized epi ...	membrane [ISS]		1ZMW	722
Q9NYY3 UniProt NPD GO	PLK2_HUMAN	Serine/threonine-protein kinase PLK2 (EC 2.7.11.21) (Polo-like kinase 1) (PLK-2) (Serine/threonine-p ...	0.82	-	nuc	0			607023		685
Q9R012 UniProt NPD GO	PLK2_RAT	Serine/threonine-protein kinase PLK2 (EC 2.7.11.21) (Polo-like kinase 1) (PLK-2) (Serine/threonine-p ...	0.82	-	nuc	0					682
Q5REX1 UniProt NPD GO	SN1L2_PONPY	Serine/threonine-protein kinase SNF1-like kinase 2 (EC 2.7.11.1)	0.82	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			925

You are viewing entries 8051 to 8100 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.