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
Q13884 UniProt NPD GO	SNTB1_HUMAN	Beta-1-syntrophin (59 kDa dystrophin-associated protein A1 basic component 1) (DAPA1B) (Tax interact ...	0.46	-	cyt	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side (By similarity). In ...	dystrophin-associated glycoprotein complex [TAS]	600026		537
Q9H3R1 UniProt NPD GO	NDST4_HUMAN	Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 4 (EC 2.8.2.8) (Glucosaminyl N-deacety ...	0.46	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				872
Q08754 UniProt NPD GO	BUD7_YEAST	Bud site selection protein 7	0.46	-	cyt	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane				746
Q5E9N0 UniProt NPD GO	BYST_BOVIN	Bystin	0.46	-	nuc	0	Cytoplasm (By similarity)				435
Q694B3 UniProt NPD GO	ABEC1_PONPY	C->U-editing enzyme APOBEC-1 (EC 3.5.4.-) (Apolipoprotein B mRNA-editing enzyme 1)	0.46	-	nuc	0					236
Q8BYB9 UniProt NPD GO	CLP46_MOUSE	CAP10-like 46 kDa protein precursor	0.46	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				392
P14745 UniProt NPD GO	CD44_PAPHA	CD44 antigen precursor (Phagocytic glycoprotein I) (PGP-1) (HUTCH-I) (Extracellular matrix receptor- ...	0.46	-	end	1	Membrane; single-pass type I membrane protein				362
Q9JLH7 UniProt NPD GO	CK5P3_RAT	CDK5 regulatory subunit-associated protein 3 (CDK5 activator-binding protein C53)	0.46	-	cyt	0					504
Q8H0V1 UniProt NPD GO	CK5P1_ARATH	CDK5RAP1-like protein	0.46	-	mit	0					640
Q9U2Y2 UniProt NPD GO	CK5P3_CAEEL	CDK5RAP3-like protein	0.46	-	cyt	0					489
Q95SK3 UniProt NPD GO	CK5P3_DROME	CDK5RAP3-like protein	0.46	-	cyt	0					509
P16209 UniProt NPD GO	1A01_PANTR	CHLA class I histocompatibility antigen, A-2 alpha chain precursor	0.46	-	end	1	Membrane; single-pass type I membrane protein				365
Q6P0H6 UniProt NPD GO	CSN4_BRARE	COP9 signalosome complex subunit 4 (Signalosome subunit 4)	0.46	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				406
Q9DB40 UniProt NPD GO	CRSP8_MOUSE	CRSP complex subunit 8 (Cofactor required for Sp1 transcriptional activation subunit 8)	0.46	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			311
Q6P2C8 UniProt NPD GO	CRSP8_HUMAN	CRSP complex subunit 8 (Cofactor required for Sp1 transcriptional activation subunit 8) (Transcripti ...	0.46	-	nuc	0	Nucleus	nucleus [IDA]	605044		311
O35161 UniProt NPD GO	CELR1_MOUSE	Cadherin EGF LAG seven-pass G-type receptor 1 precursor	0.46	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			3034
P62344 UniProt NPD GO	CDPK1_PLAF7	Calcium-dependent protein kinase 1 (EC 2.7.11.1)	0.46	-	nuc	0	Membrane; lipid-anchor (By similarity). In the parasite and on erithrocytic membrane at a lower leve ...				523
P62343 UniProt NPD GO	CDPK1_PLAFK	Calcium-dependent protein kinase 1 (EC 2.7.11.1) (PfCPK) (PfCDPK1)	0.46	-	nuc	0	Membrane; lipid-anchor. In the parasite and on erithrocytic membrane at a lower level				523
Q01061 UniProt NPD GO	PDE1B_BOVIN	Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (EC 3.1.4.17) (Cam-PDE 1B) ...	0.46	-	mit	0	Cytoplasm				534
Q01065 UniProt NPD GO	PDE1B_MOUSE	Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (EC 3.1.4.17) (Cam-PDE 1B) ...	0.46	-	mit	0	Cytoplasm				535
Q00771 UniProt NPD GO	KCC1_EMENI	Calcium/calmodulin-dependent protein kinase (EC 2.7.11.17) (CMPK)	0.46	-	cyt	0					414
Q9CXW3 UniProt NPD GO	CYBP_MOUSE	Calcyclin-binding protein (CacyBP) (Siah-interacting protein)	0.46	-	nuc	0	Nucleus. Cytoplasm. Cytoplasmic in unstimulated cultured neurons. Upon increase of calcium, it local ...	cytoplasm [IDA] nuclear envelope lumen [IDA]		1YSM	229
P34308 UniProt NPD GO	CAN_CAEEL	Calpain clp-1 (EC 3.4.22.-)	0.46	+	cyt	0					780
Q6BH66 UniProt NPD GO	PALB_DEBHA	Calpain-like protease palB/RIM13 (EC 3.4.22.-) (Cysteine protease RIM13)	0.46	-	nuc	0					764
Q9NS84 UniProt NPD GO	CHST7_HUMAN	Carbohydrate sulfotransferase 7 (EC 2.8.2.17) (EC 2.8.2.-) (Chondroitin 6-sulfotransferase 2) (C6ST- ...	0.46	+	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to membrane [TAS] intrinsic to Golgi membrane [ISS]	300375		486
Q924X2 UniProt NPD GO	CPT1B_MOUSE	Carnitine O-palmitoyltransferase I, muscle isoform (EC 2.3.1.21) (CPT I) (CPTI-M) (Carnitine palmito ...	0.46	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)	mitochondrial outer membrane [TAS] mitochondrion [IDA]			772
O75339 UniProt NPD GO	CILP1_HUMAN	Cartilage intermediate layer protein 1 precursor (CILP-1) (Cartilage intermediate-layer protein) [Co ...	0.46	-	exc	0	Secreted protein; extracellular space; extracellular matrix		603489		1184
Q6QNL9 UniProt NPD GO	KC1_EIMTE	Casein kinase I (EC 2.7.11.1)	0.46	-	cyt	0					335
P21869 UniProt NPD GO	CSK22_CHICK	Casein kinase II subunit alpha' (EC 2.7.11.1) (CK II)	0.46	-	cyt	0					350
P40228 UniProt NPD GO	CSK2B_ARATH	Casein kinase II subunit beta (CK II beta)	0.46	-	nuc	0					287
P55211 UniProt NPD GO	CASP9_HUMAN	Caspase-9 precursor (EC 3.4.22.-) (CASP-9) (ICE-like apoptotic protease 6) (ICE-LAP6) (Apoptotic pro ...	0.46	-	cyt	0			602234	3YGS	416
Q18879 UniProt NPD GO	CAV2_CAEEL	Caveolin-2	0.46	-	mit	2	Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic side (By similarity). Memb ...				351
Q9UHD4 UniProt NPD GO	CIDEB_HUMAN	Cell death activator CIDE-B (Cell death-inducing DFFA-like effector B)	0.46	-	cyt	0		cytosol [IDA]	604441	1D4B	219
Q24570 UniProt NPD GO	GRIM_DROME	Cell death protein Grim	0.46	-	mit	0		cytoplasm [IDA] mitochondrion [IDA]		1JD5	138
P41208 UniProt NPD GO	CETN2_HUMAN	Centrin-2 (Caltractin isoform 1)	0.46	-	nuc	0	Centrosome. Centrosome of interphase and mitotic cells	centrosome [NAS]	300006	2GGM	172
Q3SX42 UniProt NPD GO	CHM2B_BOVIN	Charged multivesicular body protein 2b (Chromatin-modifying protein 2b) (CHMP2b)	0.46	-	nuc	0	Cytoplasm; cytosol (By similarity)				213
Q5F3A2 UniProt NPD GO	CHM2B_CHICK	Charged multivesicular body protein 2b (Chromatin-modifying protein 2b) (CHMP2b)	0.46	-	nuc	0	Cytoplasm; cytosol (By similarity)				214
Q8BHB9 UniProt NPD GO	CLIC6_MOUSE	Chloride intracellular channel 6	0.46	-	nuc	0	Cytoplasm (By similarity). Predominantly. Cell membrane (By similarity). Upon chloride ion efflux fr ...				596
Q6B8Y1 UniProt NPD GO	RR10_GRATL	Chloroplast 30S ribosomal protein S10	0.46	-	nuc	0	Plastid; chloroplast				105
Q6ENE1 UniProt NPD GO	RR11_ORYNI	Chloroplast 30S ribosomal protein S11	0.46	-	nuc	0	Plastid; chloroplast				143
P12096 UniProt NPD GO	RR11_ORYSA	Chloroplast 30S ribosomal protein S11	0.46	-	nuc	0	Plastid; chloroplast				143
Q8MCA0 UniProt NPD GO	RR11_PHAAN	Chloroplast 30S ribosomal protein S11	0.46	-	mit	0	Plastid; chloroplast				138
Q32RM9 UniProt NPD GO	RR11_ZYGCR	Chloroplast 30S ribosomal protein S11	0.46	-	nuc	0	Plastid; chloroplast				130
P49168 UniProt NPD GO	RR12_PINCO	Chloroplast 30S ribosomal protein S12 (Fragment)	0.46	-	nuc	0	Plastid; chloroplast				38
Q7YJS7 UniProt NPD GO	RR15_CALFE	Chloroplast 30S ribosomal protein S15	0.46	-	nuc	0	Plastid; chloroplast				88
O78488 UniProt NPD GO	RR18_GUITH	Chloroplast 30S ribosomal protein S18	0.46	-	nuc	0	Plastid; chloroplast				73
P56797 UniProt NPD GO	RR2_ARATH	Chloroplast 30S ribosomal protein S2	0.46	-	mit	0	Plastid; chloroplast				236
Q1XDN4 UniProt NPD GO	RR20_PORYE	Chloroplast 30S ribosomal protein S20	0.46	-	nuc	0	Plastid; chloroplast				95
P56365 UniProt NPD GO	RR3_CHLVU	Chloroplast 30S ribosomal protein S3	0.46	-	cyt	0	Plastid; chloroplast				231
P48270 UniProt NPD GO	RR4_CHLRE	Chloroplast 30S ribosomal protein S4	0.46	-	mit	0	Plastid; chloroplast				257

You are viewing entries 27451 to 27500 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.