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
Q3SAT7 UniProt NPD GO	BDNF_SELTH	Brain-derived neurotrophic factor precursor (BDNF)	0.27	-	nuc	0	Secreted protein				247
O18753 UniProt NPD GO	BDNF_URSML	Brain-derived neurotrophic factor precursor (BDNF)	0.27	-	nuc	0	Secreted protein				247
Q12140 UniProt NPD GO	BSC1_YEAST	Bypass of stop codon protein 1	0.27	-	nuc	0					328
P23582 UniProt NPD GO	ANFC_HUMAN	C-type natriuretic peptide precursor [Contains: CNP-22; CNP-29; CNP-53]	0.27	-	exc	0	Secreted protein	extracellular region [NAS]	600296	1JDP	126
Q5E9Q1 UniProt NPD GO	CLP46_BOVIN	CAP10-like 46 kDa protein precursor	0.27	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				392
O35112 UniProt NPD GO	CD166_RAT	CD166 antigen precursor (Activated leukocyte-cell adhesion molecule) (ALCAM) (MEMD protein) (HB2) (S ...	0.27	-	end	1 *	Membrane; single-pass type I membrane protein				583
Q9BDM7 UniProt NPD GO	CD40L_MACNE	CD40 ligand (CD40-L) (Tumor necrosis factor ligand superfamily member 5) (CD154 antigen) [Contains: ...	0.27	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	integral to membrane [ISS]			240
P29965 UniProt NPD GO	CD40L_HUMAN	CD40 ligand (CD40-L) (Tumor necrosis factor ligand superfamily member 5) (TNF-related activation pro ...	0.27	-	mit	1 *	Cell membrane; single-pass type II membrane protein. Processed form: Secreted protein. Also exists a ...	integral to plasma membrane [TAS] soluble fraction [TAS]	300386	1I9R	261
Q9XH43 UniProt NPD GO	CET2_TOBAC	CEN-like protein 2	0.27	-	cyt	0	Cytoplasm (By similarity)				175
Q8K4M5 UniProt NPD GO	COMD1_MOUSE	COMM domain-containing protein 1 (Protein Murr1)	0.27	-	cyt	0					188
Q6P9U3 UniProt NPD GO	COMD3_RAT	COMM domain-containing protein 3	0.27	-	nuc	0					195
Q75BU2 UniProt NPD GO	CSN12_ASHGO	COP9 signalosome complex subunit 12	0.27	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				412
Q9CZ04 UniProt NPD GO	CSN7A_MOUSE	COP9 signalosome complex subunit 7a (Signalosome subunit 7a) (SGN7a) (JAB1-containing signalosome su ...	0.27	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				275
Q8CGA0 UniProt NPD GO	PPM1F_MOUSE	Ca(2+)/calmodulin-dependent protein kinase phosphatase (EC 3.1.3.16) (CaM-kinase phosphatase) (CaMKP ...	0.27	-	cyt	0					452
P24503 UniProt NPD GO	CADH4_CHICK	Cadherin-4 precursor (Retinal-cadherin) (R-cadherin) (R-CAD)	0.27	-	end	1	Membrane; single-pass type I membrane protein				913
P12658 UniProt NPD GO	CALB1_MOUSE	Calbindin (Vitamin D-dependent calcium-binding protein, avian-type) (Calbindin D28) (D-28K) (Spot 35 ...	0.27	-	cyt	0		cytoplasm [IDA]			260
Q86W47 UniProt NPD GO	KCMB4_HUMAN	Calcium-activated potassium channel subunit beta 4 (Calcium-activated potassium channel, subfamily M ...	0.27	-	end	2 *	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [IDA]	605223		210
Q37145 UniProt NPD GO	ACA1_ARATH	Calcium-transporting ATPase 1, chloroplast precursor (EC 3.6.3.8) (Ca(2+)-ATPase isoform 1) (Plastid ...	0.27	-	end	8	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (Probable)				1020
P08413 UniProt NPD GO	KCC2B_RAT	Calcium/calmodulin-dependent protein kinase type II beta chain (EC 2.7.11.17) (CaM-kinase II beta ch ...	0.27	-	mit	0		calcium- and calmodulin-dependent protein k... [TAS]			542
P00789 UniProt NPD GO	CANX_CHICK	Calpain-1 catalytic subunit (EC 3.4.22.52) (Calpain-1 large subunit) (Calcium-activated neutral prot ...	0.27	-	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocates to the plasma membrane upon C ...				705
Q27177 UniProt NPD GO	CATR1_PARTE	Caltractin ICL1A (Centrin)	0.27	-	mit	0	ICL, innermost fibrous network of the cortical cytoskeleton				181
Q9Y4C5 UniProt NPD GO	CHST2_HUMAN	Carbohydrate sulfotransferase 2 (EC 2.8.2.-) (N-acetylglucosamine 6-O-sulfotransferase 1) (GlcNAc6ST ...	0.27	-	mit	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type II membrane pro ...	Golgi trans face [IDA] intrinsic to Golgi membrane [NAS]	603798		530
Q9R1I1 UniProt NPD GO	CHST4_MOUSE	Carbohydrate sulfotransferase 4 (EC 2.8.2.-) (N-acetylglucosamine 6-O-sulfotransferase 2) (GlcNAc6ST ...	0.27	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				388
P48283 UniProt NPD GO	CAH4_RABIT	Carbonic anhydrase 4 precursor (EC 4.2.1.1) (Carbonic anhydrase IV) (Carbonate dehydratase IV) (CA-I ...	0.27	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				308
P42787 UniProt NPD GO	CBPD_DROME	Carboxypeptidase D precursor (EC 3.4.17.22) (Metallocarboxypeptidase D) (Protein silver)	0.27	-	end	1	Membrane; single-pass type I membrane protein (Potential)				1406
Q9EQV8 UniProt NPD GO	CBPN_RAT	Carboxypeptidase N catalytic chain precursor (EC 3.4.17.3) (CPN) (Carboxypeptidase N polypeptide 1) ...	0.27	-	mit	0	Secreted protein; extracellular space (By similarity)				457
P83714 UniProt NPD GO	CTF2_MOUSE	Cardiotrophin-2 precursor (CT-2) (Neuropoietin) (Np)	0.27	-	end	0	Secreted protein (By similarity)				204
Q4U925 UniProt NPD GO	CSK2A_THEAN	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II) (TaCKIIalpha)	0.27	-	cyt	0	Cytoplasm				348
Q08467 UniProt NPD GO	CSK21_ARATH	Casein kinase II subunit alpha-1 (EC 2.7.11.1) (CK II)	0.27	-	cyt	0					333
O89094 UniProt NPD GO	CASPE_MOUSE	Caspase-14 precursor (EC 3.4.22.-) (CASP-14) (Mini-ICE) (MICE) [Contains: Caspase-14 subunit 1; Casp ...	0.27	-	cyt	0	Cytoplasm (By similarity)				257
Q5IS54 UniProt NPD GO	CASP3_PANTR	Caspase-3 precursor (EC 3.4.22.-) (CASP-3) [Contains: Caspase-3 p17 subunit; Caspase-3 p12 subunit]	0.27	-	nuc	0	Cytoplasm (By similarity)				277
P04040 UniProt NPD GO	CATA_HUMAN	Catalase (EC 1.11.1.6)	0.27	-	cyt	0	Peroxisome		115500	1QQW	526
P48350 UniProt NPD GO	CATA1_CUCPE	Catalase isozyme 1 (EC 1.11.1.6)	0.27	-	nuc	0	Glyoxysome				492
P48352 UniProt NPD GO	CATA3_CUCPE	Catalase isozyme 3 (EC 1.11.1.6)	0.27	-	cyt	0	Peroxisome (By similarity)				492
P51437 UniProt NPD GO	CRAMP_MOUSE	Cathelin-related antimicrobial peptide precursor (Cramp) (Cathelin-like protein) (CLP)	0.27	-	nuc	0	Secreted protein				173
Q9UKI2 UniProt NPD GO	BORG2_HUMAN	Cdc42 effector protein 3 (Binder of Rho GTPases 2) (MSE55-related Cdc42-binding protein)	0.27	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein		606133		254
O70303 UniProt NPD GO	CIDEB_MOUSE	Cell death activator CIDE-B (Cell death-inducing DFFA-like effector B)	0.27	-	cyt	0					219
Q24475 UniProt NPD GO	RPR_DROME	Cell death protein rpr (Protein reaper)	0.27	-	nuc	0		cytoplasm [TAS] mitochondrion [IDA]			65
P43290 UniProt NPD GO	CDC2_PETHY	Cell division control protein 2 homolog (EC 2.7.11.22) (EC 2.7.11.23) (p34cdc2) (Fragment)	0.27	-	cyt	0					90
Q941L0 UniProt NPD GO	CESA3_ARATH	Cellulose synthase A catalytic subunit 3 [UDP-forming] (EC 2.4.1.12) (AtCesA-3) (Constitutive expres ...	0.27	-	end	8	Cell membrane; multi-pass membrane protein (Probable)				1065
Q5RE16 UniProt NPD GO	CEP27_PONPY	Centrosomal protein of 27 kDa (Cep27 protein)	0.27	-	cyt	0	Centrosome (By similarity)				204
Q7SZB5 UniProt NPD GO	CHM1B_XENLA	Charged multivesicular body protein 1b (Chromatin-modifying protein 1b) (CHMP1b)	0.27	-	nuc	0	Cytoplasm (By similarity)				199
Q6NRM7 UniProt NPD GO	CHMP3_XENLA	Charged multivesicular body protein 3 (Chromatin-modifying protein 3) (Vacuolar protein sorting 24)	0.27	-	nuc	0	Intracytoplasmic membrane; lipid-anchor (By similarity)				219
Q9Y3E7 UniProt NPD GO	CHMP3_HUMAN	Charged multivesicular body protein 3 (Chromatin-modifying protein 3) (Vacuolar protein sorting 24) ...	0.27	-	nuc	0	Cytoplasm; cytosol. Membrane; lipid-anchor		610052		221
Q8K572 UniProt NPD GO	HUS1B_MOUSE	Checkpoint protein HUS1B (mHUS1B)	0.27	-	mit	0					276
P54267 UniProt NPD GO	CHSG_ASPFU	Chitin synthase G (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase G) (Class-III chitin syn ...	0.27	-	end	7	Cell membrane; multi-pass membrane protein				911
Q9D7P7 UniProt NPD GO	CLIC3_MOUSE	Chloride intracellular channel protein 3	0.27	-	cyt	0	Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			237
Q3BAK4 UniProt NPD GO	RR11_PHAAO	Chloroplast 30S ribosomal protein S11	0.27	-	mit	0	Plastid; chloroplast				138
P14149 UniProt NPD GO	RR12_CHLRE	Chloroplast 30S ribosomal protein S12	0.27	-	mit	0	Plastid; chloroplast				132
P12340 UniProt NPD GO	RR12_MAIZE	Chloroplast 30S ribosomal protein S12	0.27	-	mit	0	Plastid; chloroplast				124

You are viewing entries 43001 to 43050 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.