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
P61815 UniProt NPD GO	CCR5_MACNE	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
Q95ND2 UniProt NPD GO	CCR5_MANLE	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
Q95NC3 UniProt NPD GO	CCR5_MIOTA	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
Q95NC7 UniProt NPD GO	CCR5_NASLA	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
P60574 UniProt NPD GO	CCR5_PANPA	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
P56440 UniProt NPD GO	CCR5_PANTR	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
P68269 UniProt NPD GO	CCR5_PAPAN	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
P68270 UniProt NPD GO	CCR5_PAPHA	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
P61756 UniProt NPD GO	CCR5_PONPA	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
O97881 UniProt NPD GO	CCR5_PONPY	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
O97880 UniProt NPD GO	CCR5_PYGBI	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
O97882 UniProt NPD GO	CCR5_PYGNE	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
Q95NC1 UniProt NPD GO	CCR5_THEGE	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
P51681 UniProt NPD GO	CCR5_HUMAN	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (HIV-1 fusion coreceptor) (CHEMR ...	0.16	-	end	6 *	Membrane; multi-pass membrane protein	cell surface [IDA] cytoplasm [TAS] endosome [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	601373	1OPW	352
P25930 UniProt NPD GO	CXCR4_BOVIN	C-X-C chemokine receptor type 4 (CXC-R4) (CXCR-4) (SDF-1 receptor) (Stromal cell-derived factor 1 re ...	0.16	-	end	7 *	Membrane; multi-pass membrane protein				353
Q66KU1 UniProt NPD GO	CLC3A_XENLA	C-type lectin domain family 3 member A homolog precursor (C-type lectin superfamily member 1 homolog ...	0.16	-	vac	0					193
Q28066 UniProt NPD GO	C4BB_BOVIN	C4b-binding protein beta chain precursor	0.16	-	nuc	0					198
P21730 UniProt NPD GO	C5AR_HUMAN	C5a anaphylatoxin chemotactic receptor (C5a-R) (C5aR) (CD88 antigen)	0.16	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	113995		350
Q91Y74 UniProt NPD GO	SIA4C_MOUSE	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase (EC 2.4.99.-) (Beta-galactosi ...	0.16	-	end	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				333
Q02745 UniProt NPD GO	SIA4A_PIG	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase (EC 2.4.99.4) (Beta-galactosi ...	0.16	-	end	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...				343
Q7XR91 UniProt NPD GO	COBL7_ORYSA	COBRA-like 7 protein precursor (BRITTLE CULM1-like 3 protein)	0.16	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				439
Q9WTP5 UniProt NPD GO	CAD22_MOUSE	Cadherin-22 precursor (Pituitary and brain cadherin) (PB-cadherin)	0.16	-	end	2 *	Membrane; single-pass type I membrane protein				813
O54800 UniProt NPD GO	CADH8_RAT	Cadherin-8 precursor	0.16	-	nuc	1 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]			799
Q874T7 UniProt NPD GO	CANB_KLULA	Calcineurin subunit B (Protein phosphatase 2B regulatory subunit) (Calcineurin regulatory subunit)	0.16	-	nuc	0					175
Q9UJS0 UniProt NPD GO	CMC2_HUMAN	Calcium-binding mitochondrial carrier protein Aralar2 (Mitochondrial aspartate glutamate carrier 2) ...	0.16	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	integral to plasma membrane [TAS] mitochondrion [TAS]	605814		675
Q8HXW2 UniProt NPD GO	CMC2_MACFA	Calcium-binding mitochondrial carrier protein Aralar2 (Mitochondrial aspartate glutamate carrier 2) ...	0.16	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				674
Q9QXX4 UniProt NPD GO	CMC2_MOUSE	Calcium-binding mitochondrial carrier protein Aralar2 (Mitochondrial aspartate glutamate carrier 2) ...	0.16	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			676
Q9NZU6 UniProt NPD GO	CABP3_HUMAN	Calcium-binding protein 3 (CaBP3)	0.16	-	mit	0			607315		192
Q8IU85 UniProt NPD GO	KCC1D_HUMAN	Calcium/calmodulin-dependent protein kinase type 1D (EC 2.7.11.17) (CaM kinase ID) (CaM kinase I del ...	0.16	-	mit	0	Cytoplasm (Probable). Predominantly. Nucleus (Probable). Also nuclear upon activation (Probable)	calcium- and calmodulin-dependent protein k... [TAS]	607957		385
Q8BW96 UniProt NPD GO	KCC1D_MOUSE	Calcium/calmodulin-dependent protein kinase type 1D (EC 2.7.11.17) (CaM kinase ID) (CaM kinase I del ...	0.16	-	mit	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Nuclear upon activation (By simil ...				385
Q9BXU9 UniProt NPD GO	CALN1_HUMAN	Calneuron-1 (Calcium-binding protein CaBP8)	0.16	-	nuc	1			607176		219
Q91053 UniProt NPD GO	VSP1_AGKCA	Calobin precursor (EC 3.4.21.-)	0.16	-	exc	0	Secreted protein				262
Q9ZPP1 UniProt NPD GO	CALR_BERST	Calreticulin precursor	0.16	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				416
P27798 UniProt NPD GO	CALR_CAEEL	Calreticulin precursor	0.16	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				395
P93508 UniProt NPD GO	CALR_RICCO	Calreticulin precursor	0.16	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				415
Q9EPL2 UniProt NPD GO	CSTN1_MOUSE	Calsyntenin-1 precursor	0.16	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)	extracellular region [IEP] integral to membrane [IDA] postsynaptic membrane [IEP]			979
Q9SEA0 UniProt NPD GO	CCS_CITSI	Capsanthin/capsorubin synthase, chloroplast precursor (EC 5.3.99.8)	0.16	-	cyt	0	Plastid; chloroplast (By similarity). Plastid; chromoplast (By similarity)				503
Q6GNS1 UniProt NPD GO	CHSTA_XENLA	Carbohydrate sulfotransferase 10 (EC 2.8.2.-) (HNK-1 sulfotransferase) (HNK1ST) (HNK-1ST)	0.16	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				355
P00732 UniProt NPD GO	CBPB1_BOVIN	Carboxypeptidase B (EC 3.4.17.2)	0.16	-	nuc	0	Secreted protein			1CPB	306
P22790 UniProt NPD GO	CEP1_ACHFU	Cardio-excitatory peptide 1 (ACEP-1)	0.16	-		0	Secreted protein				11
Q9UJA2 UniProt NPD GO	CRLS1_HUMAN	Cardiolipin synthetase (EC 2.7.8.-) (Cardiolipin synthase) (CLS) (Protein GCD10 homolog)	0.16	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein		608188		301
Q9R0G6 UniProt NPD GO	COMP_MOUSE	Cartilage oligomeric matrix protein precursor (COMP)	0.16	-	exc	0	Secreted protein			1MZ9	755
P89116 UniProt NPD GO	CASP1_SPOFR	Caspase-1 precursor (EC 3.4.22.-) [Contains: Caspase-1 subunit p19/18; Caspase-1 subunit p12]	0.16	-	cyt	0				1M72	299
P41735 UniProt NPD GO	CAT5_YEAST	Catabolite repression protein CAT5 (Ubiquinone biosynthesis protein COQ7) (Coenzyme Q biosynthesis p ...	0.16	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [TAS]			233
P55310 UniProt NPD GO	CATA_SECCE	Catalase (EC 1.11.1.6)	0.16	-	cyt	0	Peroxisome (By similarity). Glyoxysome (By similarity)				492
P55311 UniProt NPD GO	CATA_SOLME	Catalase (EC 1.11.1.6)	0.16	-	cyt	0	Peroxisome (By similarity). Glyoxysome (By similarity)				492
Q9M5L6 UniProt NPD GO	CATA_CAPAN	Catalase (EC 1.11.1.6) (CaCat1)	0.16	-	cyt	0	Peroxisome (By similarity)				492
P17598 UniProt NPD GO	CATA1_GOSHI	Catalase isozyme 1 (EC 1.11.1.6)	0.16	-	cyt	0	Peroxisome				492
P49319 UniProt NPD GO	CATA1_TOBAC	Catalase isozyme 1 (EC 1.11.1.6) (Salicylic acid-binding protein) (SABP)	0.16	-	cyt	0	Peroxisome (By similarity). Glyoxysome (By similarity)				492
P49316 UniProt NPD GO	CATA2_NICPL	Catalase isozyme 2 (EC 1.11.1.6)	0.16	-	cyt	0	Peroxisome (Potential)				492

You are viewing entries 55401 to 55450 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.