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
P01066 UniProt NPD GO	IBB1_ARAHY	Bowman-Birk type proteinase inhibitor A-II [Contains: Bowman-Birk type proteinase inhibitor A-I; Bow ...	0.26	-	nuc	0					70
Q7YRB4 UniProt NPD GO	BDNF_CANFA	Brain-derived neurotrophic factor precursor (BDNF)	0.26	-	nuc	0	Secreted protein				247
Q5IS78 UniProt NPD GO	BDNF_PANTR	Brain-derived neurotrophic factor precursor (BDNF)	0.26	-	nuc	0	Secreted protein (By similarity)				247
P23560 UniProt NPD GO	BDNF_HUMAN	Brain-derived neurotrophic factor precursor (BDNF) (Abrineurin)	0.26	-	nuc	0	Secreted protein		113505	1BND	247
Q28062 UniProt NPD GO	PGCB_BOVIN	Brevican core protein precursor	0.26	-	vac	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				912
Q7KYR7 UniProt NPD GO	BT2A1_HUMAN	Butyrophilin subfamily 2 member A1 precursor	0.26	-	exc	1 *	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]			528
P78410 UniProt NPD GO	BT3A2_HUMAN	Butyrophilin subfamily 3 member A2 precursor	0.26	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				334
Q9XSD7 UniProt NPD GO	CCRL2_MACMU	C-C chemokine receptor-like 2	0.26	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				344
Q805D5 UniProt NPD GO	ANFC2_FUGRU	C-type natriuretic peptide 2 precursor	0.26	-	exc	0	Secreted protein				130
Q61839 UniProt NPD GO	ANFC_MOUSE	C-type natriuretic peptide precursor [Contains: CNP-22; CNP-29; CNP-53]	0.26	-	exc	0	Secreted protein	extracellular region [TAS]			126
Q91ZX1 UniProt NPD GO	C209A_MOUSE	CD209 antigen-like protein A (Dendritic cell-specific ICAM-3-grabbing nonintegrin) (DC-SIGN)	0.26	-	mit	1	Membrane; single-pass type II membrane protein (Potential)				238
P29620 UniProt NPD GO	KC47_ORYSA	CDC2+/CDC28-related protein kinase R2 (EC 2.7.11.22)	0.26	-	cyt	0	Nucleus (By similarity)				424
Q6VSV1 UniProt NPD GO	COBL5_ORYSA	COBRA-like 5 protein precursor (Protein BRITTLE CULM1)	0.26	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				468
Q8GZ17 UniProt NPD GO	COBL7_ARATH	COBRA-like protein 7 precursor	0.26	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				661
Q9LIB6 UniProt NPD GO	COBL8_ARATH	COBRA-like protein 8 precursor	0.26	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				653
Q9FJ13 UniProt NPD GO	COBL9_ARATH	COBRA-like protein 9 precursor	0.26	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor (Potential)	anchored to membrane [TAS]			663
Q8JZY2 UniProt NPD GO	COMDA_MOUSE	COMM domain-containing protein 10 (Down regulated in W/WV mouse stomach 2) (mDRWMS2)	0.26	-	nuc	0					202
Q5E9K1 UniProt NPD GO	COMD5_BOVIN	COMM domain-containing protein 5	0.26	-	mit	0	Nucleus (By similarity)				224
Q8BG94 UniProt NPD GO	COMD7_MOUSE	COMM domain-containing protein 7	0.26	-	cyt	0					200
Q6BGR7 UniProt NPD GO	CSN12_DEBHA	COP9 signalosome complex subunit 12	0.26	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				438
O13873 UniProt NPD GO	CSN12_SCHPO	COP9 signalosome complex subunit 12	0.26	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				423
Q5R762 UniProt NPD GO	CSN7A_PONPY	COP9 signalosome complex subunit 7a (Signalosome subunit 7a) (SGN7a) (JAB1-containing signalosome su ...	0.26	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				275
Q9UBW8 UniProt NPD GO	CSN7A_HUMAN	COP9 signalosome complex subunit 7a (Signalosome subunit 7a) (SGN7a) (JAB1-containing signalosome su ...	0.26	-	cyt	0	Cytoplasm. Nucleus				275
Q750S5 UniProt NPD GO	CSN9_ASHGO	COP9 signalosome complex subunit 9	0.26	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				163
Q6PEI7 UniProt NPD GO	PYRG1_BRARE	CTP synthase 1 (EC 6.3.4.2) (UTP--ammonia ligase 1) (CTP synthetase 1)	0.26	-	cyt	0					591
P17812 UniProt NPD GO	PYRG1_HUMAN	CTP synthase 1 (EC 6.3.4.2) (UTP--ammonia ligase 1) (CTP synthetase 1)	0.26	-	cyt	0			123860	2C5M	591
P35411 UniProt NPD GO	CX3C1_RAT	CX3C chemokine receptor 1 (C-X3-C CKR-1) (CX3CR1) (Fractalkine receptor) (RBS11)	0.26	-	end	7 *	Membrane; multi-pass membrane protein				354
P55284 UniProt NPD GO	CADH5_MOUSE	Cadherin-5 precursor (Vascular endothelial-cadherin) (VE-cadherin) (CD144 antigen)	0.26	-	end	2 *	Membrane; single-pass type I membrane protein	tight junction [IDA]			784
P07171 UniProt NPD GO	CALB1_RAT	Calbindin (Vitamin D-dependent calcium-binding protein, avian-type) (Calbindin D28) (D-28K) (Spot 35 ...	0.26	-	cyt	0					260
O81445 UniProt NPD GO	CNBL1_ARATH	Calcineurin B-like protein 1 (SOS3-like calcium-binding protein 5)	0.26	-	cyt	0	Cell membrane; lipid-anchor				212
P11924 UniProt NPD GO	ELHB_APLCA	Califin-B [Contains: Califin-B large subunit; Califin-B small subunit]	0.26	-	nuc	0	Secreted protein				54
Q9HC96 UniProt NPD GO	CAN10_HUMAN	Calpain-10 (EC 3.4.22.-) (Calcium-activated neutral proteinase 10) (CANP 10)	0.26	-	mit	0		cytoplasm [NAS]	605286		672
P26932 UniProt NPD GO	CNN1_CHICK	Calponin-1 (Calponin, smooth muscle)	0.26	-	nuc	0				1H67	292
Q3SYU6 UniProt NPD GO	CNN2_BOVIN	Calponin-2 (Calponin H2, smooth muscle) (Neutral calponin)	0.26	-	nuc	0					308
P22075 UniProt NPD GO	CALU_CAVPO	Caltrin-like protein 2 (Caltrin-like protein II)	0.26	-	mit	0					55
Q9QUP4 UniProt NPD GO	CHST5_MOUSE	Carbohydrate sulfotransferase 5 (EC 2.8.2.-) (N-acetylglucosamine 6-O-sulfotransferase 3) (GlcNAc6ST ...	0.26	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane (By similarity). Golgi membrane, early ...	intrinsic to Golgi membrane [ISS]			395
Q66HG6 UniProt NPD GO	CAH5B_RAT	Carbonic anhydrase 5B, mitochondrial precursor (EC 4.2.1.1) (Carbonic anhydrase VB) (Carbonate dehyd ...	0.26	-	mit	0	Mitochondrion (By similarity)				317
P15087 UniProt NPD GO	CBPE_RAT	Carboxypeptidase E precursor (EC 3.4.17.10) (CPE) (Carboxypeptidase H) (CPH) (Enkephalin convertase) ...	0.26	-	exc	0	Secretory granules of pancreatic islets, adrenal gland, pituitary and brain				476
P31997 UniProt NPD GO	CEAM8_HUMAN	Carcinoembryonic antigen-related cell adhesion molecule 8 precursor (Carcinoembryonic antigen CGM6) ...	0.26	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor	extracellular space [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	114890		349
Q868T3 UniProt NPD GO	CCAPR_DROME	Cardioacceleratory peptide receptor	0.26	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [NAS]			506
Q6R2R2 UniProt NPD GO	CTF2_PANTR	Cardiotrophin-2 precursor (CT-2) (Neuropoietin) (Np)	0.26	-	exc	0	Secreted protein (By similarity)				203
P15790 UniProt NPD GO	CSK21_YEAST	Casein kinase II subunit alpha (EC 2.7.11.1) (CK II alpha subunit)	0.26	-	cyt	0		protein kinase CK2 complex [IDA]			372
P28021 UniProt NPD GO	CSK2B_XENLA	Casein kinase II subunit beta (CK II beta) (Phosvitin)	0.26	-	cyt	0				1RQF	215
P42574 UniProt NPD GO	CASP3_HUMAN	Caspase-3 precursor (EC 3.4.22.-) (CASP-3) (Apopain) (Cysteine protease CPP32) (Yama protein) (CPP-3 ...	0.26	-	nuc	0	Cytoplasm		600636	1RHU	277
P55210 UniProt NPD GO	CASP7_HUMAN	Caspase-7 precursor (EC 3.4.22.-) (CASP-7) (ICE-like apoptotic protease 3) (ICE-LAP3) (Apoptotic pro ...	0.26	-	cyt	0	Cytoplasm	cytoplasm [TAS] endoplasmic reticulum membrane [TAS] mitochondrial membrane [TAS]	601761	1SHL	303
Q9BXQ6 UniProt NPD GO	CECR6_HUMAN	Cat eye syndrome critical region protein 6	0.26	+	end	4					578
O97492 UniProt NPD GO	CATA_CANFA	Catalase (EC 1.11.1.6)	0.26	-	cyt	0	Peroxisome (By similarity)				526
Q9PWF7 UniProt NPD GO	CATA_RANRU	Catalase (EC 1.11.1.6)	0.26	-	mit	0	Peroxisome (By similarity)				527
P30567 UniProt NPD GO	CATA2_GOSHI	Catalase isozyme 2 (EC 1.11.1.6)	0.26	-	cyt	0	Peroxisome				492
Q86VU5 UniProt NPD GO	CMTD1_HUMAN	Catechol-O-methyltransferase domain-containing protein 1 (EC 2.1.1.-)	0.26	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)			2AVD	262

You are viewing entries 44001 to 44050 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.