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
P05981 UniProt NPD GO	HEPS_HUMAN	Serine protease hepsin (EC 3.4.21.-) (Transmembrane protease, serine 1) [Contains: Serine protease h ...	0.10	-	mit	1 *	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS]	142440	1Z8G	417
Q05511 UniProt NPD GO	HEPS_RAT	Serine protease hepsin (EC 3.4.21.-) [Contains: Serine protease hepsin non-catalytic chain; Serine p ...	0.10	-	mit	1 *	Membrane; single-pass type II membrane protein				416
P58517 UniProt NPD GO	SPI4_SOLTU	Serine protease inhibitor 4 (PI-4) (Fragment)	0.10	-	vac	0	Vacuole (By similarity)				103
Q5I2A0 UniProt NPD GO	SPA3G_MOUSE	Serine protease inhibitor A3G (Serine protease inhibitor 2A) (Serpin A3G) (Serpin 2A)	0.10	-	cyt	0	Cytoplasm. Nucleus				440
O14730 UniProt NPD GO	RIOK3_HUMAN	Serine/threonine-protein kinase RIO3 (EC 2.7.11.1) (RIO kinase 3) (sudD homolog)	0.10	-	cyt	0			603579		519
Q84TC6 UniProt NPD GO	SAPK2_ORYSA	Serine/threonine-protein kinase SAPK2 (EC 2.7.11.1) (Osmotic stress/abscisic acid-activated protein ...	0.10	-	cyt	0					339
P36615 UniProt NPD GO	CSK1_SCHPO	Serine/threonine-protein kinase csk1 (EC 2.7.11.22) (CAK-activating kinase) (CAKAK)	0.10	-	cyt	0					306
Q76MZ3 UniProt NPD GO	2AAA_MOUSE	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform (PP2A, subunit A, ...	0.10	-	cyt	0		cytosol [IDA]			588
P54612 UniProt NPD GO	2AAA_PIG	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform (PP2A, subunit A, ...	0.10	-	cyt	0					588
P30153 UniProt NPD GO	2AAA_HUMAN	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform (PP2A, subunit A, ...	0.10	-	cyt	0		cytosol [TAS] membrane [NAS] microtubule cytoskeleton [NAS] mitochondrion [NAS] nucleus [NAS] protein phosphatase type 2A complex [TAS] soluble fraction [NAS]	605983	1B3U	588
Q9SHS7 UniProt NPD GO	BSL3_ARATH	Serine/threonine-protein phosphatase BSL3 (EC 3.1.3.16) (BSU1-like protein 3)	0.10	-	cyt	0	Nucleus (By similarity)				715
Q9LR78 UniProt NPD GO	BSU1_ARATH	Serine/threonine-protein phosphatase BSU1 (EC 3.1.3.16) (Bri1 suppressor protein 1)	0.10	-	cyt	0	Nucleus				793
Q9SBW3 UniProt NPD GO	PP2A4_ORYSA	Serine/threonine-protein phosphatase PP2A-4 catalytic subunit (EC 3.1.3.16)	0.10	-	nuc	0	Cytoplasm (By similarity)				314
O17847 UniProt NPD GO	SRA25_CAEEL	Serpentine receptor class alpha-25 (Protein sra-25)	0.10	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				335
O16444 UniProt NPD GO	SRB18_CAEEL	Serpentine receptor class beta-18 (Protein srb-18)	0.10	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				352
P91209 UniProt NPD GO	SRD30_CAEEL	Serpentine receptor class delta-30 (Protein srd-30)	0.10	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				324
Q20249 UniProt NPD GO	SRE8_CAEEL	Serpentine receptor class epsilon-8 (Protein sre-8)	0.10	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				341
P54126 UniProt NPD GO	SRG4_CAEEL	Serpentine receptor class gamma-4 (Protein srg-4)	0.10	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				316
Q03156 UniProt NPD GO	ALBU2_SALSA	Serum albumin 2 precursor	0.10	-	exc	0	Secreted protein				608
P19708 UniProt NPD GO	SAA_CANFA	Serum amyloid A protein precursor (SAA) [Contains: Amyloid protein A (Amyloid fibril protein AA)]	0.10	-	exc	0					129
Q9BM90 UniProt NPD GO	JANB_DROER	Sex-regulated protein janus-B	0.10	-	mit	0					140
P17503 UniProt NPD GO	SSSP_PLAFO	Sexual stage-specific protein precursor	0.10	-	mit	2 *	Membrane; single-pass type I membrane protein (Potential)				157
P00348 UniProt NPD GO	HCDH_PIG	Short chain 3-hydroxyacyl-CoA dehydrogenase, mitochondrial precursor (EC 1.1.1.35) (HCDH) (Medium an ...	0.10	-	mit	0	Mitochondrion; mitochondrial matrix			3HDH	314
P60774 UniProt NPD GO	NXS1_NAJSA	Short neurotoxin 1 (NTX I)	0.10	-	nuc	0	Secreted protein				61
P19959 UniProt NPD GO	NXS2_AIPLA	Short neurotoxin B precursor	0.10	-	nuc	1 *	Secreted protein				81
Q9D365 UniProt NPD GO	SPCS3_MOUSE	Signal peptidase complex subunit 3 (EC 3.4.-.-) (Microsomal signal peptidase 23 kDa subunit) (SPase ...	0.10	-	mit	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (By similarity)				180
Q568Z4 UniProt NPD GO	SPCS3_RAT	Signal peptidase complex subunit 3 (EC 3.4.-.-) (Microsomal signal peptidase 23 kDa subunit) (SPase ...	0.10	-	mit	1 *	Microsome; microsomal membrane; single-pass type II membrane protein (Potential)				180
Q8TCT7 UniProt NPD GO	PSL1_HUMAN	Signal peptide peptidase-like 2B (EC 3.4.23.-) (Protein SPP-like 2B) (Protein SPPL2b) (Intramembrane ...	0.10	-	end	9 *	Membrane; multi-pass membrane protein (Probable)		608239		592
Q53HV7 UniProt NPD GO	SMUG1_HUMAN	Single-strand selective monofunctional uracil DNA glycosylase (EC 3.2.2.-)	0.10	-	cyt	0	Nucleus		607753		270
Q99616 UniProt NPD GO	CCL13_HUMAN	Small inducible cytokine A13 precursor (CCL13) (Monocyte chemotactic protein 4) (MCP-4) (Monocyte ch ...	0.10	-	exc	0	Secreted protein	extracellular space [TAS]	601391		98
Q9EQ25 UniProt NPD GO	S38A4_RAT	Sodium-coupled neutral amino acid transporter 4 (Na(+)-coupled neutral amino acid transporter 4) (Am ...	0.10	-	end	11	Cell membrane; multi-pass membrane protein (By similarity)				547
Q8N130 UniProt NPD GO	NPT2C_HUMAN	Sodium-dependent phosphate transport protein 2C (Sodium/phosphate cotransporter 2C) (Na(+)/Pi cotran ...	0.10	-	end	11	Membrane; multi-pass membrane protein	apical plasma membrane [ISS]	609826		599
P48768 UniProt NPD GO	NAC2_RAT	Sodium/calcium exchanger 2 precursor (Na(+)/Ca(2+)-exchange protein 2)	0.10	-	end	9	Membrane; multi-pass membrane protein				921
Q09573 UniProt NPD GO	KCC2_CAEEL	Sodium/chloride cotransporter type 2	0.10	-	end	11	Membrane; multi-pass membrane protein (Potential)				1020
Q84WG1 UniProt NPD GO	NHX3_ARATH	Sodium/hydrogen exchanger 3 (Na(+)/H(+) exchanger 3) (NHE-3)	0.10	-	end	10 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				503
P16225 UniProt NPD GO	SPAI_PIG	Sodium/potassium ATPase inhibitor SPAI-2 precursor (WAP-2 protein)	0.10	-	mit	0					187
P35317 UniProt NPD GO	AT1A_HYDAT	Sodium/potassium-transporting ATPase alpha chain (EC 3.6.3.9) (Sodium pump) (Na+/K+ ATPase)	0.10	-	end	8	Membrane; multi-pass membrane protein				1031
Q04680 UniProt NPD GO	ATNG_SHEEP	Sodium/potassium-transporting ATPase gamma chain (Sodium pump gamma chain) (Na+/K+ ATPase subunit ga ...	0.10	-	nuc	1 *	Membrane; single-pass type III membrane protein (Potential)				53
P05027 UniProt NPD GO	AT1B1_PIG	Sodium/potassium-transporting ATPase subunit beta-1 (Sodium/potassium-dependent ATPase beta-1 subuni ...	0.10	-	mit	1 *	Membrane; single-pass type II membrane protein				303
Q9EPQ0 UniProt NPD GO	NCKX3_RAT	Sodium/potassium/calcium exchanger 3 precursor (Na(+)/K(+)/Ca(2+)-exchange protein 3) (Fragment)	0.10	-	end	10 *	Membrane; multi-pass membrane protein				624
Q9H2X9 UniProt NPD GO	S12A5_HUMAN	Solute carrier family 12 member 5 (Electroneutral potassium-chloride cotransporter 2) (Erythroid K-C ...	0.10	-	end	12	Membrane; multi-pass membrane protein	integral to membrane [NAS]	606726		1116
Q9UHW9 UniProt NPD GO	S12A6_HUMAN	Solute carrier family 12 member 6 (Electroneutral potassium-chloride cotransporter 3) (K-Cl cotransp ...	0.10	-	end	12	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	604878		1150
Q9Z2J0 UniProt NPD GO	S23A1_MOUSE	Solute carrier family 23 member 1 (Sodium-dependent vitamin C transporter 1) (Na(+)/L-ascorbic acid ...	0.10	-	end	11	Membrane; multi-pass membrane protein				605
Q4P1V3 UniProt NPD GO	SNX3_USTMA	Sorting nexin-3	0.10	-	cyt	0	Cytoplasm (By similarity)				129
Q26627 UniProt NPD GO	SUREJ_STRPU	Sperm receptor for egg jelly precursor (suREJ)	0.10	-	end	1	Cell membrane; single-pass type I membrane protein. Present on the surface of the sperm flagellum an ...				1450
Q5ZML3 UniProt NPD GO	SFRS1_CHICK	Splicing factor, arginine/serine-rich 1	0.10	-	nuc	0	Nucleus (By similarity)				256
P81728 UniProt NPD GO	SPRT_RAT	Sproutin (TA20)	0.10	-	nuc	0					50
O75908 UniProt NPD GO	SOAT2_HUMAN	Sterol O-acyltransferase 2 (EC 2.3.1.26) (Cholesterol acyltransferase 2) (Acyl coenzyme A:cholestero ...	0.10	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein		601311		522
Q64077 UniProt NPD GO	NK2R_CAVPO	Substance-K receptor (SKR) (Neurokinin A receptor) (NK-2 receptor) (NK-2R) (Tachykinin receptor 2)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				402
Q5DUB3 UniProt NPD GO	NK1R_CANFA	Substance-P receptor (SPR) (NK-1 receptor) (NK-1R) (Tachykinin receptor 1)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				407

You are viewing entries 65251 to 65300 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.