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
Q96MF2 UniProt NPD GO	STAC3_HUMAN	SH3 and cysteine-rich domain-containing protein 3	0.30	-	nuc	0				2DB6	364
Q62421 UniProt NPD GO	SH3G3_MOUSE	SH3-containing GRB2-like protein 3 (SH3 domain protein 2C) (SH3p13)	0.30	-	cyt	0					347
Q91X78 UniProt NPD GO	SPFH1_MOUSE	SPFH domain-containing protein 1 precursor (KE04 protein homolog)	0.30	-	mit	1 *	Membrane; peripheral membrane protein (Probable)				346
P98121 UniProt NPD GO	URTB_DESRO	Salivary plasminogen activator beta precursor (EC 3.4.21.68) (DSPA beta)	0.30	-	exc	0					431
Q99P68 UniProt NPD GO	SOST_MOUSE	Sclerostin precursor	0.30	-	exc	0	Secreted protein (Potential)				211
Q5FVJ6 UniProt NPD GO	BSCL2_RAT	Seipin (Bernardinelli-Seip congenital lipodystrophy type 2 protein homolog)	0.30	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	integral to endoplasmic reticulum membrane [ISS]			377
Q8BZ10 UniProt NPD GO	DESC4_MOUSE	Serine protease DESC4 precursor (EC 3.4.21.-) [Contains: Serine protease DESC4 non-catalytic chain; ...	0.30	-	mit	1 *	Membrane; single-pass type II membrane protein (By similarity)				417
Q03734 UniProt NPD GO	SPA3M_MOUSE	Serine protease inhibitor A3M precursor (Serpin A3M)	0.30	-	end	0	Secreted protein (By similarity)				418
Q91WP6 UniProt NPD GO	SPA3N_MOUSE	Serine protease inhibitor A3N precursor (Serpin A3N)	0.30	-	end	0	Secreted protein (By similarity)				418
Q8L7U5 UniProt NPD GO	BSL1_ARATH	Serine/threonine-protein phosphatase BSL1 (EC 3.1.3.16) (BSU1-like protein 1)	0.30	-	cyt	0	Nucleus (By similarity)				881
P23777 UniProt NPD GO	PP1_BRANA	Serine/threonine-protein phosphatase PP1 (EC 3.1.3.16) (Fragment)	0.30	-	cyt	0					255
P23733 UniProt NPD GO	PP11_TRYBB	Serine/threonine-protein phosphatase PP1(4.8) (EC 3.1.3.16)	0.30	-	cyt	0					346
Q19549 UniProt NPD GO	SRA27_CAEEL	Serpentine receptor class alpha-27 (Protein sra-27)	0.30	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				344
P26636 UniProt NPD GO	SYS_CRIGR	Seryl-tRNA synthetase (EC 6.1.1.11) (Serine--tRNA ligase) (SerRS) (Fragment)	0.30	-	nuc	0					199
Q62588 UniProt NPD GO	SHBG_PHOSU	Sex hormone-binding globulin precursor (SHBG) (Sex steroid-binding protein) (SBP) (Testis-specific a ...	0.30	-	mit	0	Secreted protein (By similarity). In testis, it is synthesized by the Sertoli cells, secreted into t ...				399
P08689 UniProt NPD GO	SHBG_RAT	Sex hormone-binding globulin precursor (SHBG) (Sex steroid-binding protein) (SBP) (Testis-specific a ...	0.30	-	cyt	0	Secreted protein. In testis, it is synthesized by the Sertoli cells, secreted into the lumen of the ...				403
P40899 UniProt NPD GO	ISP3_SCHPO	Sexual differentiation process protein isp3 (Meiotic expression up-regulated protein 4)	0.30	-	nuc	0					182
P01425 UniProt NPD GO	NXS1_HEMHA	Short neurotoxin 1 (Toxin II)	0.30	-	nuc	0	Secreted protein				61
Q07417 UniProt NPD GO	ACADS_MOUSE	Short-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.2) (SCAD) (Butyryl-C ...	0.30	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			412
Q6P4A7 UniProt NPD GO	SFXN4_HUMAN	Sideroflexin-4 (Breast cancer resistance marker 1)	0.30	-	nuc	4	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				337
O94407 UniProt NPD GO	SEC65_SCHPO	Signal recognition particle sec65 subunit	0.30	-	nuc	0	Cytoplasm (By similarity)				199
Q8MKD0 UniProt NPD GO	CCL5_HORSE	Small inducible cytokine A5 precursor (CCL5) (T-cell-specific RANTES protein)	0.30	-	exc	0	Secreted protein				91
P17515 UniProt NPD GO	SCYBA_MOUSE	Small inducible cytokine B10 precursor (CXCL10) (Interferon-gamma-induced protein CRG-2) (Gamma-IP10 ...	0.30	-	exc	1 *	Secreted protein				98
Q5ZME8 UniProt NPD GO	SMU1_CHICK	Smu-1 suppressor of mec-8 and unc-52 protein homolog	0.30	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				513
Q12691 UniProt NPD GO	ATN5_YEAST	Sodium transport ATPase 5 (EC 3.6.3.7)	0.30	-	end	10	Cell membrane; multi-pass membrane protein				1091
P13607 UniProt NPD GO	ATNA_DROME	Sodium/potassium-transporting ATPase alpha chain (EC 3.6.3.9) (Sodium pump) (Na+/K+ ATPase)	0.30	-	end	8	Membrane; multi-pass membrane protein	plasma membrane [IDA] septate junction [IDA]			1041
O46383 UniProt NPD GO	NCKX1_BISBI	Sodium/potassium/calcium exchanger 1 (Na(+)/K(+)/Ca(2+)-exchange protein 1) (Retinal rod Na-Ca+K exc ...	0.30	-	cyt	0	Membrane; multi-pass membrane protein				300
P32745 UniProt NPD GO	SSR3_HUMAN	Somatostatin receptor type 3 (SS3R) (SSR-28)	0.30	-	end	7 *	Membrane; multi-pass membrane protein. Internalized into endoplasmic vesicles upon somatostatin-stim ...	integral to plasma membrane [TAS]	182453		418
P46404 UniProt NPD GO	SOMA_FELCA	Somatotropin precursor (Growth hormone)	0.30	-	exc	0	Secreted protein				216
P34745 UniProt NPD GO	SOMA_ICTPU	Somatotropin precursor (Growth hormone)	0.30	-	exc	0	Secreted protein				200
P22077 UniProt NPD GO	SOMA_MELGA	Somatotropin precursor (Growth hormone)	0.30	-	exc	0	Secreted protein				216
P19795 UniProt NPD GO	SOMA_MUSVI	Somatotropin precursor (Growth hormone)	0.30	-	exc	0	Secreted protein				216
P10814 UniProt NPD GO	SOMA_SALSA	Somatotropin precursor (Growth hormone)	0.30	-	exc	0	Secreted protein				210
P26773 UniProt NPD GO	SOMA1_ACIGU	Somatotropin-1 (Somatotropin I) (Growth hormone I)	0.30	-	nuc	0	Secreted protein				190
Q5MJ68 UniProt NPD GO	SPDYC_HUMAN	Speedy protein C (Rapid inducer of G2/M progression in oocytes C) (RINGO C) (hSpy/Ringo C)	0.30	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			293
P15265 UniProt NPD GO	MCSP_MOUSE	Sperm mitochondrial-associated cysteine-rich protein	0.30	-	nuc	0	Cytoplasm. Becomes associated with the spermatid mitochondrion capsule at step 16 of spermatogenesis ...	cytoplasm [IDA] mitochondrial outer membrane [TAS] mitochondrion [IDA]			143
Q62100 UniProt NPD GO	HSP3_MOUSE	Sperm protamine P3	0.30	-	nuc	0	Nucleus				102
P54218 UniProt NPD GO	SPE27_CAEEL	Spermatocyte protein spe-27 precursor	0.30	-	exc	0					131
Q9NRA0 UniProt NPD GO	SPHK2_HUMAN	Sphingosine kinase 2 (EC 2.7.1.-) (SK 2) (SPK 2)	0.30	-	nuc	0		cytosol [IEP] membrane fraction [IEP]	607092		654
Q18212 UniProt NPD GO	UAP56_CAEEL	Spliceosome RNA helicase BAT1 homolog (EC 3.6.1.-) (DEAD box protein UAP56)	0.30	-	cyt	0	Nucleus (Probable)				425
P15270 UniProt NPD GO	SP60_DICDI	Spore coat protein SP60 precursor	0.30	-	exc	0					424
O97561 UniProt NPD GO	STC2_MACNE	Stanniocalcin-2 precursor (STC-2)	0.30	-	exc	0	Secreted protein (Potential)				302
P28862 UniProt NPD GO	MMP3_MOUSE	Stromelysin-1 precursor (EC 3.4.24.17) (Matrix metalloproteinase-3) (MMP-3) (Transin-1) (SL-1) (EMS- ...	0.30	-	exc	0					477
P09238 UniProt NPD GO	MMP10_HUMAN	Stromelysin-2 precursor (EC 3.4.24.22) (Matrix metalloproteinase-10) (MMP-10) (Transin-2) (SL-2)	0.30	-	exc	0		extracellular matrix (sensu Metazoa) [TAS] extracellular space [TAS]	185260	1Q3A	476
P08536 UniProt NPD GO	MET3_YEAST	Sulfate adenylyltransferase (EC 2.7.7.4) (Sulfate adenylate transferase) (SAT) (ATP-sulfurylase) (Me ...	0.30	-	cyt	0	Cytoplasm	cytoplasm [IDA] mitochondrion [IDA]		1R6X	511
O00338 UniProt NPD GO	ST1C1_HUMAN	Sulfotransferase 1C1 (EC 2.8.2.-) (SULT1C#1) (ST1C2) (humSULTC2)	0.30	-	nuc	0	Cytoplasm	cytoplasm [TAS]	602385	2ETG	296
P47194 UniProt NPD GO	SYB_LOLPE	Synaptobrevin	0.30	-	nuc	1	Synaptic vesicle; synaptic vesicle membrane; single-pass type IV membrane protein. Neuronal synaptic ...			1L4A	125
P13701 UniProt NPD GO	SYB_TORCA	Synaptobrevin (Synaptic vesicle-associated integral membrane protein) (VAMP-1)	0.30	-	nuc	1	Synaptic vesicle; synaptic vesicle membrane; single-pass type IV membrane protein. Neuronal synaptic ...				120
P36977 UniProt NPD GO	SN25A_CARAU	Synaptosomal-associated protein 25A (SNAP-25A)	0.30	-	nuc	0	Complexed with macromolecular elements of the nerve terminal				204
Q60HC0 UniProt NPD GO	SYT1_MACFA	Synaptotagmin-1 (Synaptotagmin I) (SytI)	0.30	-	nuc	1	Synaptic vesicles and chromaffin granules (By similarity)				419

You are viewing entries 40751 to 40800 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.