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
Q9BTY2 UniProt NPD GO	FUCO2_HUMAN	Plasma alpha-L-fucosidase precursor (EC 3.2.1.51) (Alpha-L-fucosidase 2) (Alpha-L-fucoside fucohydro ...	0.08	-	exc	0	Secreted protein (Probable)		136820		467
P54210 UniProt NPD GO	PMA1_DUNAC	Plasma membrane ATPase (EC 3.6.3.6) (Proton pump)	0.08	-	end	9	Cell membrane; multi-pass membrane protein				1103
P40975 UniProt NPD GO	PMP2_YEAST	Plasma membrane ATPase proteolipid 2 precursor	0.08	-	mit	1 *	Cell membrane	membrane [IDA]			43
P83006 UniProt NPD GO	PAFA2_RAT	Platelet-activating factor acetylhydrolase 2, cytoplasmic (EC 3.1.1.47) (Serine-dependent phospholip ...	0.08	-	cyt	0	Cytoplasm (By similarity)				390
Q15102 UniProt NPD GO	PA1B3_HUMAN	Platelet-activating factor acetylhydrolase IB subunit gamma (EC 3.1.1.47) (PAF acetylhydrolase 29 kD ...	0.08	-	cyt	0	Cytoplasm		603074		231
O35263 UniProt NPD GO	PA1B3_RAT	Platelet-activating factor acetylhydrolase IB subunit gamma (EC 3.1.1.47) (PAF acetylhydrolase 29 kD ...	0.08	-	cyt	0	Cytoplasm (By similarity)				232
Q5RJP7 UniProt NPD GO	PGFRL_RAT	Platelet-derived growth factor receptor-like protein precursor	0.08	-	exc	0	Secreted protein (Probable)				375
Q15198 UniProt NPD GO	PGFRL_HUMAN	Platelet-derived growth factor receptor-like protein precursor (PDGF receptor beta-like tumor suppre ...	0.08	-	vac	0	Secreted protein (Probable)		604584		375
P36990 UniProt NPD GO	TXP10_PLETR	Plectoxin-10 (Plectoxin X) (PLT-X) (PLTX)	0.08	-	nuc	0	Secreted protein				49
P36983 UniProt NPD GO	TXP56_PLETR	Plectoxin-5/6 precursor (Plectoxin V/VI) (PLT-V/PLT-VI) (PLTVI)	0.08	-	exc	0	Secreted protein				82
P36984 UniProt NPD GO	TXP8_PLETR	Plectoxin-8 precursor (Plectoxin VIII) (PLT-VIII) (PLTVIII) (Fragment)	0.08	-	nuc	0	Secreted protein				61
P29162 UniProt NPD GO	NTP3_TOBAC	Pollen-specific protein NTP303 precursor	0.08	-	exc	0	Secreted protein; extracellular space (Probable)				554
O59925 UniProt NPD GO	PGLR_PENEN	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.08	-	exc	0					378
O42809 UniProt NPD GO	PGLR4_ASPNG	Polygalacturonase-4 precursor (EC 3.2.1.15) (Polygalacturonase IV) (PG-IV) (Pectinase-4)	0.08	-	vac	0					378
P17576 UniProt NPD GO	CARP_IRPLA	Polyporopepsin (EC 3.4.23.29) (Aspartic proteinase)	0.08	-	cyt	0				1WKR	340
P82423 UniProt NPD GO	PCW1_PACGO	Ponericin-W1	0.08	-	mit	0	Secreted protein				25
P82424 UniProt NPD GO	PCW2_PACGO	Ponericin-W2	0.08	-	mit	0	Secreted protein				25
P82425 UniProt NPD GO	PCW3_PACGO	Ponericin-W3	0.08	-	mit	0	Secreted protein				26
Q96T55 UniProt NPD GO	KCNKG_HUMAN	Potassium channel subfamily K member 16 (TWIK-related alkaline pH-activated K(+) channel 1) (2P doma ...	0.08	-	end	6 *	Membrane; multi-pass membrane protein		607369		309
Q96T54 UniProt NPD GO	KCNKH_HUMAN	Potassium channel subfamily K member 17 (TWIK-related alkaline pH-activated K(+) channel 2) (2P doma ...	0.08	-	end	6 *	Membrane; multi-pass membrane protein	membrane [NAS]	607370		332
P45629 UniProt NPD GO	KAX23_CENLL	Potassium channel toxin alpha-KTx 2.3 (Toxin-1) (Toxin I) (Toxin II.10.9.1) (CllTx1)	0.08	-	nuc	0	Secreted protein				38
Q86QU6 UniProt NPD GO	KGX14_CENSC	Potassium channel toxin gamma-KTx 1.4 (Ergtoxin-like protein 1) (ErgTx1) (CsErg1) (CsErgTx1)	0.08	-	nuc	0	Secreted protein				42
Q86QU1 UniProt NPD GO	KGX16_CENEX	Potassium channel toxin gamma-KTx 1.6 (Ergtoxin-like protein 1) (ErgTx1) (CexErg1) (CexErgTx1)	0.08	-	nuc	0	Secreted protein				42
Q86QU9 UniProt NPD GO	KGX41_CENLL	Potassium channel toxin gamma-KTx 4.1 (Ergtoxin-like protein 2) (ErgTx2) (CllErg2) (CllErgTx2)	0.08	-	nuc	0	Secreted protein				43
Q86QV8 UniProt NPD GO	KGX4B_CENNO	Potassium channel toxin gamma-KTx 4.11 (Ergtoxin-like protein 4) (ErgTx4) (CnErg4) (CnErgTx4)	0.08	-	nuc	0	Secreted protein				43
Q86QV1 UniProt NPD GO	KGX52_CENGR	Potassium channel toxin gamma-KTx 5.2 (Ergtoxin-like protein 3) (ErgTx3) (CgErg3) (CgErgTx3)	0.08	-	nuc	0	Secreted protein				47
Q8LPL8 UniProt NPD GO	POT13_ARATH	Potassium transporter 13 (AtPOT13) (AtKT5)	0.08	-	end	11	Cell membrane; multi-pass membrane protein (Potential)				855
P15382 UniProt NPD GO	KCNE1_HUMAN	Potassium voltage-gated channel subfamily E member 1 (IKs producing slow voltage-gated potassium cha ...	0.08	-	mit	1 *	Membrane; single-pass type I membrane protein	voltage-gated potassium channel complex [TAS]	220400		129
Q99LI9 UniProt NPD GO	CLP1_MOUSE	Pre-mRNA cleavage complex II protein Clp1	0.08	-	cyt	0	Nucleus (By similarity)				425
Q6FJZ9 UniProt NPD GO	PRP46_CANGA	Pre-mRNA-splicing factor PRP46 (Pre-mRNA-processing protein 46)	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				427
Q6CAH5 UniProt NPD GO	RSE1_YARLI	Pre-mRNA-splicing factor RSE1	0.08	-	cyt	0	Nucleus (By similarity)				1143
Q9UHV9 UniProt NPD GO	PFD2_HUMAN	Prefoldin subunit 2	0.08	-	nuc	0		prefoldin complex [NAS]			154
P83498 UniProt NPD GO	PA60F_SHEEP	Pregnancy-associated glycoprotein 60f (EC 3.4.23.-) (ovPAG 60f) (Fragment)	0.08	-		0					20
Q9UI14 UniProt NPD GO	PRAF1_HUMAN	Prenylated Rab acceptor protein 1 (PRA1 family protein 1)	0.08	-	end	2	Cell membrane; multi-pass membrane protein (By similarity). Cytoplasm (By similarity). Golgi apparat ...		604925		185
Q9CQF9 UniProt NPD GO	PCYOX_MOUSE	Prenylcysteine oxidase precursor (EC 1.8.3.5)	0.08	-	end	1 *	Lysosome (By similarity)				505
P05223 UniProt NPD GO	CAER2_XENLA	Preprocaerulein type I' precursor (Fragment)	0.08	-	exc	0	Secreted protein				136
Q8HXW5 UniProt NPD GO	PSN1_MACFA	Presenilin-1 (EC 3.4.23.-) (PS-1) [Contains: Presenilin-1 NTF subunit; Presenilin-1 CTF subunit; Pre ...	0.08	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum [ISS] Golgi apparatus [ISS] integral to nuclear inner membrane [ISS] integral to plasma membrane [ISS] kinetochore [ISS] membrane fraction [ISS] mitochondrion [ISS]			467
Q5R780 UniProt NPD GO	PSN1_PONPY	Presenilin-1 (EC 3.4.23.-) (PS-1) [Contains: Presenilin-1 NTF subunit; Presenilin-1 CTF subunit; Pre ...	0.08	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum [ISS] Golgi apparatus [ISS] integral to nuclear inner membrane [ISS] integral to plasma membrane [ISS] kinetochore [ISS] membrane fraction [ISS] mitochondrion [ISS]			467
Q9W6T7 UniProt NPD GO	PSN1_BRARE	Presenilin-1 (EC 3.4.23.-) (PS1) (Zf-PS1)	0.08	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...	endoplasmic reticulum [ISS] Golgi apparatus [ISS] integral to nuclear inner membrane [ISS] integral to plasma membrane [ISS] kinetochore [ISS] membrane fraction [ISS] mitochondrion [ISS]			456
O62690 UniProt NPD GO	MCH_HYLLA	Pro-MCH precursor (Fragment)	0.08	-	exc	1 *	Secreted protein (By similarity)				71
P26779 UniProt NPD GO	SAP_BOVIN	Proactivator polypeptide precursor [Contains: Saposin A (Protein A); Saposin B (Sphingolipid activat ...	0.08	-	end	0	Lysosome				525
Q9LHN4 UniProt NPD GO	LPAT5_ARATH	Probable 1-acyl-sn-glycerol-3-phosphate acyltransferase 5 (EC 2.3.1.51) (Lysophosphatidyl acyltransf ...	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				375
O74445 UniProt NPD GO	PRS10_SCHPO	Probable 26S protease subunit rpt4	0.08	-	cyt	0		nucleus [TAS]			388
Q9SUC0 UniProt NPD GO	3HIDH_ARATH	Probable 3-hydroxyisobutyrate dehydrogenase, mitochondrial precursor (EC 1.1.1.31) (HIBADH)	0.08	-	mit	0	Mitochondrion (By similarity)				347
Q9Y235 UniProt NPD GO	ABEC2_HUMAN	Probable C->U-editing enzyme APOBEC-2 (EC 3.5.4.-)	0.08	-	cyt	0			604797		224
Q94261 UniProt NPD GO	CSN7_CAEEL	Probable COP9 signalosome complex subunit 7 (Signalosome subunit 7)	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				390
Q91178 UniProt NPD GO	GPRX_ORYLA	Probable G-protein coupled receptor (Fragment)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				428
Q9Z282 UniProt NPD GO	GP132_MOUSE	Probable G-protein coupled receptor 132 (G2 accumulation protein)	0.08	-	end	7 *	Membrane; multi-pass membrane protein (Probable). Internalized and accumulated in endosomal compartm ...				382
Q7TSN5 UniProt NPD GO	GP151_RAT	Probable G-protein coupled receptor 151 (GPCR-2037)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				421
Q9NS66 UniProt NPD GO	GP173_HUMAN	Probable G-protein coupled receptor 173 (Super conserved receptor expressed in brain 3)	0.08	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)		300253		373

You are viewing entries 68701 to 68750 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.