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
Q9Y6B7 UniProt NPD GO	AP4B1_HUMAN	AP-4 complex subunit beta-1 (Adapter-related protein complex 4 beta 1 subunit) (Beta subunit of AP-4 ...	0.17	-	cyt	0	Golgi apparatus; trans-Golgi network. Associated with the trans-Golgi network. Found in soma and den ...	Golgi trans face [TAS] soluble fraction [TAS]	607245		739
Q5RFH9 UniProt NPD GO	AT5F1_PONPY	ATP synthase B chain, mitochondrial precursor (EC 3.6.3.14)	0.17	-	mit	0	Mitochondrion (By similarity)				256
Q9DB20 UniProt NPD GO	ATPO_MOUSE	ATP synthase O subunit, mitochondrial precursor (EC 3.6.3.14) (Oligomycin sensitivity conferral prot ...	0.17	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			213
Q06647 UniProt NPD GO	ATPO_RAT	ATP synthase O subunit, mitochondrial precursor (EC 3.6.3.14) (Oligomycin sensitivity conferral prot ...	0.17	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS] proton-transporting ATP synthase complex, c... [TAS]			213
O21402 UniProt NPD GO	ATP6_STRCA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.17	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q8S8W9 UniProt NPD GO	ATPE_ATRBE	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.17	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				133
Q9BBT9 UniProt NPD GO	ATPE_LOTJA	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.17	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				133
Q9TKI6 UniProt NPD GO	ATPE_MEDSA	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.17	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				137
Q9XMN9 UniProt NPD GO	ATP8_CERCA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.17	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				53
P92479 UniProt NPD GO	ATP8_EQUAS	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.17	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				67
Q9TBI5 UniProt NPD GO	ATP8_OPIHO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.17	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				55
Q35587 UniProt NPD GO	ATP8_PANPA	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.17	-	nuc	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				68
Q85FQ8 UniProt NPD GO	ATPA_CYAME	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.17	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				495
P06283 UniProt NPD GO	ATPA_MARPO	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.17	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
P08428 UniProt NPD GO	ATPA_XENLA	ATP synthase subunit alpha, mitochondrial precursor (EC 3.6.3.14)	0.17	-	mit	0	Mitochondrion; mitochondrial inner membrane				545
Q99766 UniProt NPD GO	ATP5S_HUMAN	ATP synthase subunit s, mitochondrial precursor (ATP synthase coupling factor B) (Mitochondrial ATP ...	0.17	-	cyt	0	Mitochondrion (By similarity)				215
Q7TMS5 UniProt NPD GO	ABCG2_MOUSE	ATP-binding cassette sub-family G member 2 (Breast cancer resistance protein 1 homolog)	0.17	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)				657
Q99PE8 UniProt NPD GO	ABCG5_MOUSE	ATP-binding cassette sub-family G member 5 (Sterolin-1)	0.17	-	end	6	Membrane; multi-pass membrane protein (Probable)				652
O78410 UniProt NPD GO	CLPC_GUITH	ATP-dependent Clp protease ATP-binding subunit clpA homolog	0.17	-	nuc	0	Plastid; chloroplast				819
Q9VNV3 UniProt NPD GO	DDX1_DROME	ATP-dependent RNA helicase Ddx1 (EC 3.6.1.-) (DEAD box protein 1)	0.17	-	cyt	0					727
P24782 UniProt NPD GO	DBP2_SCHPO	ATP-dependent RNA helicase dbp2 (EC 3.6.1.-) (p68-like protein)	0.17	+	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				550
Q8N2K0 UniProt NPD GO	ABD12_HUMAN	Abhydrolase domain-containing protein 12	0.17	-	mit	1					398
P27819 UniProt NPD GO	ILV3_BRANA	Acetolactate synthase 3, chloroplast precursor (EC 2.2.1.6) (Acetolactate synthase III) (Acetohydrox ...	0.17	-	mit	0	Plastid; chloroplast				652
Q6SSJ3 UniProt NPD GO	ILVB_CRYNV	Acetolactate synthase, mitochondrial precursor (EC 2.2.1.6) (Acetohydroxy-acid synthase) (ALS) (AHAS ...	0.17	-	mit	0	Mitochondrion (By similarity)				718
O19903 UniProt NPD GO	ACCA_CYACA	Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha (EC 6.4.1.2) (Acetyl-CoA carboxylas ...	0.17	-	nuc	0	Plastid; chloroplast				324
P25110 UniProt NPD GO	ACHD_RAT	Acetylcholine receptor protein subunit delta precursor	0.17	-	end	4	Membrane; multi-pass membrane protein	nicotinic acetylcholine-gated receptor-chan... [IMP]		1CEK	517
P49580 UniProt NPD GO	ACHE_XENLA	Acetylcholine receptor protein subunit epsilon precursor	0.17	-	end	4	Membrane; multi-pass membrane protein				504
Q92035 UniProt NPD GO	ACES_BUNFA	Acetylcholinesterase precursor (EC 3.1.1.7) (AChE)	0.17	-	vac	0	Secreted protein				606
P78617 UniProt NPD GO	TREA_EMENI	Acid trehalase precursor (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase ...	0.17	-	exc	0					1054
Q9JI19 UniProt NPD GO	FIBP_MOUSE	Acidic fibroblast growth factor intracellular-binding protein (aFGF intracellular-binding protein) ( ...	0.17	-	cyt	0	Nucleus (By similarity). Intracellular membrane; peripheral membrane protein (By similarity). Also a ...				357
P23343 UniProt NPD GO	ACT1_DAUCA	Actin-1	0.17	-	cyt	0	Cytoplasm				380
P52411 UniProt NPD GO	ACP1_CUPLA	Acyl carrier protein 1, chloroplast precursor (ACP)	0.17	-	mit	0	Plastid; chloroplast				140
P52412 UniProt NPD GO	ACP2_CUPLA	Acyl carrier protein 2, chloroplast precursor (ACP)	0.17	-	mit	0	Plastid; chloroplast				137
P52414 UniProt NPD GO	ACP4_CUPLA	Acyl carrier protein 4, chloroplast precursor (ACP)	0.17	-	mit	0	Plastid; chloroplast				139
Q95MI7 UniProt NPD GO	ACOD_CAPHI	Acyl-CoA desaturase (EC 1.14.19.1) (Stearoyl-CoA desaturase) (Fatty acid desaturase) (Delta(9)-desat ...	0.17	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				359
Q5KFA4 UniProt NPD GO	APTH1_CRYNE	Acyl-protein thioesterase 1 (EC 3.1.2.-)	0.17	-	mit	0	Cytoplasm (By similarity)				238
Q6GP70 UniProt NPD GO	ADA_XENLA	Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase)	0.17	-	cyt	0					358
Q63ZU0 UniProt NPD GO	ADA_XENTR	Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase)	0.17	-	cyt	0					358
Q15109 UniProt NPD GO	RAGE_HUMAN	Advanced glycosylation end product-specific receptor precursor (Receptor for advanced glycosylation ...	0.17	-	end	2 *	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein	integral to plasma membrane [TAS] plasma membrane [NAS]	600214	1PWI	404
Q8CG76 UniProt NPD GO	ARK72_MOUSE	Aflatoxin B1 aldehyde reductase member 2 (EC 1.-.-.-)	0.17	-	mit	0	Golgi apparatus (By similarity)	mitochondrion [IDA]		2C91	367
P29118 UniProt NPD GO	ALP_CEPAC	Alkaline proteinase precursor (EC 3.4.21.-) (ALP)	0.17	-	exc	0					402
Q93ZC5 UniProt NPD GO	AOC4_ARATH	Allene oxide cyclase 4, chloroplast precursor (EC 5.3.99.6)	0.17	-	mit	0	Plastid; chloroplast				254
P24622 UniProt NPD GO	CRYAA_MOUSE	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.17	-	cyt	0		cytoplasm [IDA]			196
P24623 UniProt NPD GO	CRYAA_RAT	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.17	-	cyt	0					196
P16234 UniProt NPD GO	PGFRA_HUMAN	Alpha platelet-derived growth factor receptor precursor (EC 2.7.10.1) (PDGF-R-alpha) (CD140a antigen ...	0.17	-	end	3 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	173490	1GQ5	1089
P22083 UniProt NPD GO	FUT4_HUMAN	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferase ...	0.17	-	gol	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...	Golgi apparatus [TAS] membrane fraction [TAS]	104230		405
P97718 UniProt NPD GO	ADA1A_MOUSE	Alpha-1A adrenergic receptor (Alpha 1A-adrenoceptor) (Alpha 1A-adrenoreceptor) (Alpha-1C adrenergic ...	0.17	-	end	7 *	Membrane; multi-pass membrane protein	membrane fraction [IDA]			466
P43140 UniProt NPD GO	ADA1A_RAT	Alpha-1A adrenergic receptor (Alpha 1A-adrenoceptor) (Alpha 1A-adrenoreceptor) (Alpha-1C adrenergic ...	0.17	-	end	7 *	Membrane; multi-pass membrane protein				466
Q9N2D0 UniProt NPD GO	FETUA_PANTR	Alpha-2-HS-glycoprotein precursor (Fetuin-A) [Contains: Alpha-2-HS-glycoprotein chain A; Alpha-2-HS- ...	0.17	-	end	0	Secreted protein	extracellular space [ISS]			367
P17050 UniProt NPD GO	NAGAB_HUMAN	Alpha-N-acetylgalactosaminidase precursor (EC 3.2.1.49) (Alpha-galactosidase B)	0.17	-	cyt	0	Lysosome		609242		411

You are viewing entries 54001 to 54050 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.