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
O88890 UniProt NPD GO	SH21A_MOUSE	SH2 domain protein 1A (Signaling lymphocyte activation molecule-associated protein) (SLAM-associated ...	0.06	-	nuc	0	Cytoplasm (Potential)				126
Q9FHW7 UniProt NPD GO	SKP1B_ARATH	SKP1-like protein 1B (SKP1-like 2) (UFO-binding protein 2)	0.06	-	nuc	0	Nucleus (By similarity)				171
P15844 UniProt NPD GO	SPE2D_STRPU	SPEC 2D protein	0.06	-	cyt	0					141
Q4FZT8 UniProt NPD GO	SPRY4_RAT	SPRY domain-containing protein 4	0.06	-	cyt	0					207
Q6CN23 UniProt NPD GO	HSV2_KLULA	SVP1-like protein 2	0.06	-	cyt	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Cytoplasmic vesicle; cytopl ...				339
Q7SG97 UniProt NPD GO	HSV2_NEUCR	SVP1-like protein 2	0.06	-	cyt	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Cytoplasmic vesicle; cytopl ...				310
Q6CEI9 UniProt NPD GO	HSV2_YARLI	SVP1-like protein 2	0.06	-	cyt	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Cytoplasmic vesicle; cytopl ...				359
P19972 UniProt NPD GO	TOXK_PICFA	Salt-mediated killer protoxin 1 precursor [Contains: Salt-mediated killer toxin 1 alpha chain (SMK t ...	0.06	-	mit	2 *				1KVE	222
O55143 UniProt NPD GO	AT2A2_MOUSE	Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (EC 3.6.3.8) (Calcium pump 2) (SERCA2) (SR Ca(2+ ...	0.06	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...	microsome [IDA] sarcoplasmic reticulum [TAS]			1044
P11607 UniProt NPD GO	AT2A2_PIG	Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (EC 3.6.3.8) (Calcium pump 2) (SERCA2) (SR Ca(2+ ...	0.06	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...				1042
P24489 UniProt NPD GO	SRX22_SARPE	Sarcotoxin II-2 precursor	0.06	-	nuc	0	Secreted protein				294
P18312 UniProt NPD GO	SRX1D_SARPE	Sarcotoxin-1D (Sarcotoxin ID)	0.06	-	cyt	0	Secreted protein				40
Q90WJ7 UniProt NPD GO	SXT1_TAKPA	Saxitoxin and tetrodotoxin-binding protein 1 precursor	0.06	-	end	0	Secreted protein				391
O18824 UniProt NPD GO	SCRB1_BOVIN	Scavenger receptor class B member 1 (SRB1) (SR-BI)	0.06	-	end	2 *	Cell membrane; multi-pass membrane protein (By similarity). Predominantly localized to cholesterol a ...				509
P08170 UniProt NPD GO	LOX1_SOYBN	Seed lipoxygenase-1 (EC 1.13.11.12) (L-1)	0.06	-	nuc	0	Cytoplasm			2SBL	839
Q41065 UniProt NPD GO	IBBA_PEA	Seed trypsin/chymotrypsin inhibitor IVA precursor (PSTI IVA) (TI12-36) [Contains: Seed trypsin/chymo ...	0.06	-	nuc	0					96
P56679 UniProt NPD GO	IBBB_PEA	Seed trypsin/chymotrypsin inhibitor IVB (PSTI-IVB) [Contains: Seed trypsin/chymotrypsin inhibitor II ...	0.06	-	nuc	0				1PBI	72
Q9VKY8 UniProt NPD GO	SPS2_DROME	Selenide, water dikinase 2 (EC 2.7.9.3) (Selenophosphate synthetase 2) (Selenium donor protein 2) (D ...	0.06	-	cyt	0					370
Q8WWX9 UniProt NPD GO	SELM_HUMAN	Selenoprotein M precursor (Protein SelM)	0.06	-	exc	1 *	Cytoplasm; perinuclear region. Localized to perinuclear structures corresponding to Golgi and endopl ...				145
P63302 UniProt NPD GO	SEPW1_HUMAN	Selenoprotein W	0.06	-	cyt	0	Cytoplasm	cytoplasm [NAS] plasma membrane [ISS]	603235		86
P63303 UniProt NPD GO	SEPW1_MACMU	Selenoprotein W	0.06	-	cyt	0	Cytoplasm	cytoplasm [ISS] mitochondrion [NAS] plasma membrane [ISS]			86
Q8TDE0 UniProt NPD GO	SNSR2_HUMAN	Sensory neuron-specific G-protein coupled receptor 2	0.06	-	end	7 *	Membrane; multi-pass membrane protein				322
Q8TDD9 UniProt NPD GO	SNSR3_HUMAN	Sensory neuron-specific G-protein coupled receptor 3	0.06	-	end	7 *	Membrane; multi-pass membrane protein				322
Q6FUP6 UniProt NPD GO	GLYC_CANGA	Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) (Serine methylase) (Glycine hydroxymethyltra ...	0.06	-	cyt	0	Cytoplasm (Potential)				469
P34896 UniProt NPD GO	GLYC_HUMAN	Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) (Serine methylase) (Glycine hydroxymethyltra ...	0.06	-	cyt	0	Cytoplasm	cytosol [TAS]	182144	1BJ4	483
O13426 UniProt NPD GO	GLYC_CANAL	Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) (Serine methylase) (Glycine hydroxymethyltra ...	0.06	-	nuc	0	Cytoplasm				469
P13582 UniProt NPD GO	EAST_DROME	Serine protease easter precursor (EC 3.4.21.-)	0.06	-	exc	0	Secreted protein	extracellular region [IDA]			392
P84188 UniProt NPD GO	SGAT_WHEAT	Serine--glyoxylate aminotransferase (EC 2.6.1.45) (SGAT) (Alanine--glyoxylate aminotransferase) (EC ...	0.06	-	cyt	0	Peroxisome				78
Q922R0 UniProt NPD GO	PRKX_MOUSE	Serine/threonine-protein kinase PRKX (EC 2.7.11.1) (PKA-related protein kinase)	0.06	-	cyt	0					355
Q4QQT4 UniProt NPD GO	2AAB_RAT	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform (PP2A, subunit A, P ...	0.06	-	cyt	0					601
P32345 UniProt NPD GO	PP4C_YEAST	Serine/threonine-protein phosphatase 4 catalytic subunit (EC 3.1.3.16) (PP4C) (Phosphatase PP2A-like ...	0.06	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			308
P12346 UniProt NPD GO	TRFE_RAT	Serotransferrin precursor (Transferrin) (Siderophilin) (Beta-1-metal-binding globulin)	0.06	-	end	0	Secreted protein				698
O61898 UniProt NPD GO	SRE12_CAEEL	Serpentine receptor class epsilon-12 (Protein sre-12)	0.06	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				341
O02275 UniProt NPD GO	SRE45_CAEEL	Serpentine receptor class epsilon-45 (Protein sre-45)	0.06	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				369
P91535 UniProt NPD GO	SRG20_CAEEL	Serpentine receptor class gamma-20 (Protein srg-20)	0.06	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				337
P18575 UniProt NPD GO	SAA1_MUSVI	Serum amyloid A-1 protein precursor	0.06	-	exc	0					129
P00975 UniProt NPD GO	IBPS_BOVIN	Serum basic protease inhibitor (Serum BPI)	0.06	-	nuc	0	Secreted protein				60
P20348 UniProt NPD GO	JANA_DROME	Sex-regulated protein janus-A	0.06	-	mit	0					135
Q9BM89 UniProt NPD GO	JANB_DROOR	Sex-regulated protein janus-B	0.06	-	mit	0					140
Q9BM92 UniProt NPD GO	JANB_DROYA	Sex-regulated protein janus-B	0.06	-	mit	0					140
P40900 UniProt NPD GO	ISP4_SCHPO	Sexual differentiation process protein isp4	0.06	-	end	14	Membrane; multi-pass membrane protein (Probable)				785
Q9YGI8 UniProt NPD GO	NXSH4_BUNMU	Short neurotoxin homolog NTL4 precursor	0.06	-	nuc	1 *	Secreted protein				86
Q96DR5 UniProt NPD GO	SPLC2_HUMAN	Short palate, lung and nasal epithelium carcinoma-associated protein 2 precursor (Parotid secretory ...	0.06	-	exc	0	Secreted protein (By similarity)				249
Q92341 UniProt NPD GO	STR3_SCHPO	Siderophore iron transporter 3	0.06	-	end	13	Membrane; multi-pass membrane protein (Probable)				630
Q8X1Z7 UniProt NPD GO	MIRA_EMENI	Siderophore iron transporter mirA (Major facilitator iron-regulated transporter A) (Enterobactin per ...	0.06	-	end	11	Membrane; multi-pass membrane protein (Potential)				609
Q3TD49 UniProt NPD GO	PSL1_MOUSE	Signal peptide peptidase-like 2B (EC 3.4.23.-) (Protein SPP-like 2B) (Protein SPPL2b)	0.06	-	end	8 *	Membrane; multi-pass membrane protein (Probable)				578
Q5PQL3 UniProt NPD GO	PSL1_RAT	Signal peptide peptidase-like 2B (EC 3.4.23.-) (Protein SPP-like 2B) (Protein SPPL2b)	0.06	-	end	9	Membrane; multi-pass membrane protein (Probable)				577
P97884 UniProt NPD GO	CCL20_RAT	Small inducible cytokine A20 precursor (CCL20) (Macrophage inflammatory protein 3 alpha) (MIP-3-alph ...	0.06	-	exc	0	Secreted protein				96
P50229 UniProt NPD GO	CCL3_RAT	Small inducible cytokine A3 precursor (CCL3) (Macrophage inflammatory protein 1-alpha) (MIP-1-alpha) ...	0.06	-	exc	0	Secreted protein				92
P30882 UniProt NPD GO	CCL5_MOUSE	Small inducible cytokine A5 precursor (CCL5) (T-cell-specific RANTES protein) (SIS-delta) (MuRantes) ...	0.06	-	exc	0	Secreted protein				91

You are viewing entries 73151 to 73200 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.