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
P24626 UniProt NPD GO	CHI1_ORYSA	Basic endochitinase 1 precursor (EC 3.2.1.14)	0.05	-	exc	0					320
P18762 UniProt NPD GO	ADRB2_MOUSE	Beta-2 adrenergic receptor (Beta-2 adrenoceptor) (Beta-2 adrenoreceptor)	0.05	-	end	7 *	Membrane; multi-pass membrane protein	apical plasma membrane [IDA] membrane fraction [IDA] nucleus [IDA]			418
P10608 UniProt NPD GO	ADRB2_RAT	Beta-2 adrenergic receptor (Beta-2 adrenoceptor) (Beta-2 adrenoreceptor)	0.05	-	end	7 *	Membrane; multi-pass membrane protein	caveola [TAS]			418
P17690 UniProt NPD GO	APOH_BOVIN	Beta-2-glycoprotein 1 precursor (Beta-2-glycoprotein I) (Apolipoprotein H) (Apo-H) (B2GPI) (Beta(2)G ...	0.05	-	exc	0	Secreted protein				345
P01885 UniProt NPD GO	B2MG_RABIT	Beta-2-microglobulin	0.05	-	cyt	0	Secreted protein				99
P61771 UniProt NPD GO	B2MG_GORGO	Beta-2-microglobulin precursor	0.05	-	vac	0	Secreted protein				119
P61770 UniProt NPD GO	B2MG_PANTR	Beta-2-microglobulin precursor	0.05	-	vac	0	Secreted protein			2BVP	119
P16213 UniProt NPD GO	B2MG_PONPY	Beta-2-microglobulin precursor	0.05	-	vac	0	Secreted protein				119
P07151 UniProt NPD GO	B2MG_RAT	Beta-2-microglobulin precursor	0.05	-	exc	1 *	Secreted protein			3FRU	119
Q9IA97 UniProt NPD GO	B2MG_XENLA	Beta-2-microglobulin precursor	0.05	-	exc	0	Secreted protein				115
P61769 UniProt NPD GO	B2MG_HUMAN	Beta-2-microglobulin precursor [Contains: Beta-2-microglobulin variant pI 5.3]	0.05	-	vac	0	Secreted protein		109700	3HLA	119
P13945 UniProt NPD GO	ADRB3_HUMAN	Beta-3 adrenergic receptor (Beta-3 adrenoceptor) (Beta-3 adrenoreceptor)	0.05	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	109691		408
P43141 UniProt NPD GO	ADB4C_MELGA	Beta-4C adrenergic receptor (Beta-4C adrenoceptor) (Beta-4C adrenoreceptor)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				428
P42025 UniProt NPD GO	ACTY_HUMAN	Beta-centractin (Actin-related protein 1B) (ARP1B)	0.05	-	cyt	0		dynactin complex [TAS]	605144		376
Q5J600 UniProt NPD GO	DB121_MACMU	Beta-defensin 121 precursor (Defensin, beta 121)	0.05	-	mit	0	Secreted protein (Potential)				76
Q30KP9 UniProt NPD GO	DB135_HUMAN	Beta-defensin 135 precursor (Defensin, beta 135)	0.05	-	cyt	0	Secreted protein (Potential)				77
P82020 UniProt NPD GO	BD02_MOUSE	Beta-defensin 2 precursor (Defensin, beta 2) (BD-2) (mBD-2)	0.05	-	exc	0	Secreted protein (By similarity)				71
P48980 UniProt NPD GO	BGAL_LYCES	Beta-galactosidase precursor (EC 3.2.1.23) (Lactase) (Acid beta-galactosidase) (Exo-(1-->4)-beta-D-g ...	0.05	-	exc	0					835
P22506 UniProt NPD GO	BGL1_SACFI	Beta-glucosidase 1 precursor (EC 3.2.1.21) (Gentiobiase) (Cellobiase) (Beta-D-glucoside glucohydrola ...	0.05	-	vac	0					876
P02756 UniProt NPD GO	LACB_CAPHI	Beta-lactoglobulin precursor (Beta-LG)	0.05	-	nuc	0	Secreted protein				180
P67976 UniProt NPD GO	LACB_SHEEP	Beta-lactoglobulin-1/B precursor (Beta-LG)	0.05	-	nuc	0					180
P08118 UniProt NPD GO	MSMB_HUMAN	Beta-microseminoprotein precursor (Prostate secreted seminal plasma protein) (Prostate secretory pro ...	0.05	-	exc	1 *	Secreted protein. Sperm surface	extracellular space [TAS] nucleus [TAS]	157145		114
O02826 UniProt NPD GO	MSMB_PIG	Beta-microseminoprotein precursor (Prostate secreted seminal plasma protein) (Prostate secretory pro ...	0.05	-	exc	0	Secreted protein. Sperm surface (By similarity)			1XHH	111
O81395 UniProt NPD GO	DRTS_MAIZE	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolate reducta ...	0.05	-	cyt	0					521
Q5ZKA5 UniProt NPD GO	MTDC_CHICK	Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial precursor [Includ ...	0.05	-	mit	0	Mitochondrion (By similarity)				337
P13995 UniProt NPD GO	MTDC_HUMAN	Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial precursor [Includ ...	0.05	-	mit	0	Mitochondrion	mitochondrion [ISS]	604887		344
Q13867 UniProt NPD GO	BLMH_HUMAN	Bleomycin hydrolase (EC 3.4.22.40) (BLM hydrolase) (BMH) (BH)	0.05	-	cyt	0	Cytoplasm	cytoplasm [TAS] nucleus [TAS]	602403	2CB5	455
P84214 UniProt NPD GO	BOMB_BOMBO	Bombesin	0.05	-		0	Secreted protein	extracellular region [IDA]			14
P15410 UniProt NPD GO	BXC1_BOMMO	Bombyxin C-1 precursor (BBX-C1) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin C-1 B ...	0.05	-	exc	1 *	Secreted protein				91
O09210 UniProt NPD GO	BXRB_AGRCO	Bombyxin-related peptide B precursor (ABRP) [Contains: Bombyxin-related peptide B chain B; Bombyxin- ...	0.05	-	exc	0	Secreted protein (By similarity)	extracellular region [IC]			93
Q8VYR7 UniProt NPD GO	BOR1_ARATH	Boron transporter 1	0.05	-	end	10 *	Membrane; multi-pass membrane protein				704
Q93Z13 UniProt NPD GO	BORL1_ARATH	Boron transporter-like protein 1	0.05	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				732
P84824 UniProt NPD GO	BRK11_ASCTR	Bradykinin-like peptide RD-11	0.05	-		0	Secreted protein	extracellular region [IDA]			11
P53727 UniProt NPD GO	BUD17_YEAST	Bud site selection protein BUD17	0.05	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			317
P11586 UniProt NPD GO	C1TC_HUMAN	C-1-tetrahydrofolate synthase, cytoplasmic (C1-THF synthase) [Includes: Methylenetetrahydrofolate de ...	0.05	-	nuc	0	Cytoplasm	mitochondrion [TAS]	172460	1DIG	934
Q27772 UniProt NPD GO	C1TC_SPOFR	C-1-tetrahydrofolate synthase, cytoplasmic (C1-THF synthase) [Includes: Methylenetetrahydrofolate de ...	0.05	-	cyt	0	Cytoplasm (By similarity)				933
Q8NJ57 UniProt NPD GO	ERG3_CANDU	C-5 sterol desaturase (EC 1.3.3.-) (Sterol-C5-desaturase) (Ergosterol delta 5,6 desaturase)	0.05	-	end	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				386
P32360 UniProt NPD GO	ERG2_USTMA	C-8 sterol isomerase (Delta-8--delta-7 sterol isomerase)	0.05	-	mit	1 *	Endoplasmic reticulum				241
P49254 UniProt NPD GO	CRP_CAVPO	C-reactive protein precursor	0.05	-	vac	0	Secreted protein				225
P02741 UniProt NPD GO	CRP_HUMAN	C-reactive protein precursor [Contains: C-reactive protein(1-205)]	0.05	-	exc	0	Secreted protein	extracellular region [NAS]	123260	1LJ7	224
P08607 UniProt NPD GO	C4BP_MOUSE	C4b-binding protein precursor (C4bp)	0.05	-	mit	0					469
P30993 UniProt NPD GO	C5AR_MOUSE	C5a anaphylatoxin chemotactic receptor (C5a-R) (C5aR) (CD88 antigen)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				347
Q9Y256 UniProt NPD GO	FACE2_HUMAN	CAAX prenyl protease 2 (EC 3.4.22.-) (Prenyl protein-specific endoprotease 2) (Farnesylated proteins ...	0.05	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS]	605385		329
P32763 UniProt NPD GO	CD52_MACFA	CAMPATH-1 antigen precursor (Cambridge pathology 1 antigen) (CD52 antigen) (CDw52)	0.05	-	exc	2 *	Cell membrane; lipid-anchor; GPI-anchor				60
P31358 UniProt NPD GO	CD52_HUMAN	CAMPATH-1 antigen precursor (Cambridge pathology 1 antigen) (Epididymal secretory protein E5) (CD52 ...	0.05	-	end	2 *	Cell membrane; lipid-anchor; GPI-anchor	integral to plasma membrane [TAS] membrane fraction [TAS]	114280		61
Q28896 UniProt NPD GO	CD52_CANFA	CAMPATH-1 antigen precursor (Epididymal secretory protein E5) (CD52 antigen) (CDw52)	0.05	-	nuc	2 *	Cell membrane; lipid-anchor; GPI-anchor				67
Q64389 UniProt NPD GO	CD52_MOUSE	CAMPATH-1 antigen precursor (Lymphocyte differentiation antigen B7) (CD52 antigen) (CDw52)	0.05	-	mit	2 *	Cell membrane; lipid-anchor; GPI-anchor				74
P40240 UniProt NPD GO	CD9_MOUSE	CD9 antigen	0.05	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS] plasma membrane [TAS]			225
Q8LBA6 UniProt NPD GO	PIS1_ARATH	CDP-diacylglycerol--inositol 3-phosphatidyltransferase 1 (EC 2.7.8.11) (Phosphatidylinositol synthas ...	0.05	-	end	4 *	Membrane; multi-pass membrane protein				227
Q9XH44 UniProt NPD GO	CET1_TOBAC	CEN-like protein 1	0.05	-	cyt	0	Cytoplasm (By similarity)				174

You are viewing entries 73901 to 73950 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.