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
Q9Y3E5 UniProt NPD GO	PTH2_HUMAN	Peptidyl-tRNA hydrolase 2, mitochondrial precursor (EC 3.1.1.29) (PTH 2) (Bcl-2 inhibitor of transcr ...	0.03	-	nuc	1 *	Mitochondrion		608625	1Q7S	179
P83931 UniProt NPD GO	PVK3_LEUMA	Periviscerokinin-3 (Lem-PVK-3)	0.03	-		0	Secreted protein				11
P83933 UniProt NPD GO	PVK3_BLACR	Periviscerokinin-3 (PVK-3)	0.03	-		0	Secreted protein				11
P83934 UniProt NPD GO	PVK3_BLADU	Periviscerokinin-3 (PVK-3)	0.03	-		0	Secreted protein				11
P84593 UniProt NPD GO	PVK3_BLAGI	Periviscerokinin-3 (PVK-3)	0.03	-		0	Secreted protein				11
P83935 UniProt NPD GO	PVK3_GROPO	Periviscerokinin-3 (PVK-3)	0.03	-		0	Secreted protein				11
P83932 UniProt NPD GO	PVK3_NAUCI	Periviscerokinin-3 (PVK-3)	0.03	-		0	Secreted protein	mitochondrial small ribosomal subunit [IDA]			11
P84662 UniProt NPD GO	PVK3_PANVI	Periviscerokinin-3 (Panvi-PVK-3)	0.03	-		0	Secreted protein				11
Q9FX85 UniProt NPD GO	PER10_ARATH	Peroxidase 10 precursor (EC 1.11.1.7) (Atperox P10) (ATP5a)	0.03	-	mit	1 *	Secreted protein (By similarity)				350
O49293 UniProt NPD GO	PER13_ARATH	Peroxidase 13 precursor (EC 1.11.1.7) (Atperox P13)	0.03	-	cyt	0	Secreted protein (By similarity)				319
P19136 UniProt NPD GO	PEM4_PHACH	Peroxidase manganese-dependent H4 precursor (EC 1.11.1.13) (MP-I)	0.03	-	vac	0	Secreted protein				382
Q9NL98 UniProt NPD GO	PRDX_ASCSU	Peroxiredoxin (EC 1.11.1.15) (AsPrx) (Thioredoxin peroxidase)	0.03	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [NAS]			195
O04005 UniProt NPD GO	REHY_ARATH	Peroxiredoxin (EC 1.11.1.15) (Thioredoxin peroxidase) (Rehydrin homolog)	0.03	-	cyt	0					216
Q02207 UniProt NPD GO	FOX2_YEAST	Peroxisomal hydratase-dehydrogenase-epimerase (HDE) (Multifunctional beta-oxidation protein) (MFP) [ ...	0.03	-	pox	0	Peroxisome				900
Q5MJP5 UniProt NPD GO	SCX1_ANUPH	Phaiodotoxin precursor	0.03	-	vac	0	Secreted protein	extracellular space [IDA]			90
Q5MJP4 UniProt NPD GO	SCX2_ANUPH	Phaiodotoxin-2 (Fragment)	0.03	-	nuc	0	Secreted protein (By similarity)	extracellular space [ISS]			72
Q5MJP3 UniProt NPD GO	SCX3_ANUPH	Phaiodotoxin-3 (Fragment)	0.03	-	nuc	0	Secreted protein (By similarity)	extracellular space [ISS]			72
Q99L43 UniProt NPD GO	CDS2_MOUSE	Phosphatidate cytidylyltransferase 2 (EC 2.7.7.41) (CDP-diglyceride synthetase 2) (CDP-diglyceride p ...	0.03	-	end	8	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (Potential)	endoplasmic reticulum [IDA]			444
O16264 UniProt NPD GO	PEBPH_CAEEL	Phosphatidylethanolamine-binding protein homolog F40A3.3	0.03	-	mit	0					221
O94183 UniProt NPD GO	NPC2_ASPOR	Phosphatidylglycerol/phosphatidylinositol transfer protein precursor (PG/PI-TP)	0.03	-	exc	0	Cytoplasm. Cytoplasmic vesicle. Also associated with Golgi-like vesicles				175
Q92535 UniProt NPD GO	PIGC_HUMAN	Phosphatidylinositol N-acetylglucosaminyltransferase subunit C (EC 2.4.1.198) (Phosphatidylinositol- ...	0.03	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum membrane [TAS]	601730		297
Q9CXR4 UniProt NPD GO	PIGC_MOUSE	Phosphatidylinositol N-acetylglucosaminyltransferase subunit C (EC 2.4.1.198) (Phosphatidylinositol- ...	0.03	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				297
Q5PQQ4 UniProt NPD GO	PIGC_RAT	Phosphatidylinositol N-acetylglucosaminyltransferase subunit C (EC 2.4.1.198) (Phosphatidylinositol- ...	0.03	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				297
Q9JHG1 UniProt NPD GO	PIGP_MOUSE	Phosphatidylinositol N-acetylglucosaminyltransferase subunit P (EC 2.4.1.198) (Phosphatidylinositol- ...	0.03	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				132
Q8TBF5 UniProt NPD GO	PIGX_HUMAN	Phosphatidylinositol-glycan biosynthesis class X protein precursor (PIG-X)	0.03	-	exc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				258
Q99LV7 UniProt NPD GO	PIGX_MOUSE	Phosphatidylinositol-glycan biosynthesis class X protein precursor (PIG-X)	0.03	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				254
Q9P4V2 UniProt NPD GO	AGM1_CANAL	Phosphoacetylglucosamine mutase (EC 5.4.2.3) (PAGM) (Acetylglucosamine phosphomutase) (N-acetylgluco ...	0.03	-	nuc	0				2DKD	544
Q96UL8 UniProt NPD GO	PPCK_EMENI	Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49)	0.03	-	cyt	0					556
Q9VUY9 UniProt NPD GO	PGM_DROME	Phosphoglucomutase (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.03	-	cyt	0		cytoplasm [ISS]			560
Q7KHA1 UniProt NPD GO	PGM_DROSI	Phosphoglucomutase (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.03	-	cyt	0		cytoplasm [ISS]			560
P93262 UniProt NPD GO	PGMC_MESCR	Phosphoglucomutase, cytoplasmic (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.03	-	cyt	0	Cytoplasm (By similarity)				583
Q9M4G4 UniProt NPD GO	PGMC_SOLTU	Phosphoglucomutase, cytoplasmic (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.03	-	cyt	0	Cytoplasm (By similarity)				583
P93805 UniProt NPD GO	PGMC2_MAIZE	Phosphoglucomutase, cytoplasmic 2 (EC 5.4.2.2) (Glucose phosphomutase 2) (PGM 2)	0.03	-	cyt	0	Cytoplasm				583
P11977 UniProt NPD GO	PGK_EMENI	Phosphoglycerate kinase (EC 2.7.2.3)	0.03	-	cyt	0	Cytoplasm (By similarity)				421
O02608 UniProt NPD GO	PGK_EUPCR	Phosphoglycerate kinase (EC 2.7.2.3)	0.03	-	cyt	0					418
O00852 UniProt NPD GO	PGK_GLACH	Phosphoglycerate kinase (EC 2.7.2.3) (Fragment)	0.03	-	cyt	0					376
P29408 UniProt NPD GO	PGK1_MACEU	Phosphoglycerate kinase 1 (EC 2.7.2.3)	0.03	-	nuc	0	Cytoplasm (By similarity)				416
P00950 UniProt NPD GO	PMG1_YEAST	Phosphoglycerate mutase 1 (EC 5.4.2.1) (Phosphoglyceromutase 1) (PGAM 1) (MPGM 1) (BPG-dependent PGA ...	0.03	-	cyt	0		cytosol [IDA]		5PGM	246
P20259 UniProt NPD GO	PA2B_PSEPO	Phospholipase A2 (EC 3.1.1.4) (Pseudexin B chain) (Phosphatidylcholine 2-acylhydrolase)	0.03	-	nuc	0	Secreted protein				117
P00598 UniProt NPD GO	PA21_NAJAT	Phospholipase A2 1 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.03	-	mit	0	Secreted protein			1POB	146
Q9W7J4 UniProt NPD GO	PA21B_PSETE	Phospholipase A2 1 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Pt-PLA1)	0.03	-	exc	0	Secreted protein (By similarity)				154
Q9W7J3 UniProt NPD GO	PA22_PSETE	Phospholipase A2 2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Pt-PLA2)	0.03	-	exc	0	Secreted protein (By similarity)				154
P59172 UniProt NPD GO	PA25_ECHPL	Phospholipase A2 5 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.03	-	nuc	0	Secreted protein (By similarity)				139
P62022 UniProt NPD GO	PA2B_CRODU	Phospholipase A2 CB1 precursor (EC 3.1.1.4) (Crotoxin basic chain 1) (Phosphatidylcholine 2-acylhydr ...	0.03	-	vac	0	Secreted protein				138
P24027 UniProt NPD GO	PA2C_CRODU	Phospholipase A2 CB2 precursor (EC 3.1.1.4) (Crotoxin basic chain 2) (Phosphatidylcholine 2-acylhydr ...	0.03	-	vac	1 *	Secreted protein				138
P62023 UniProt NPD GO	PA2B_CROSS	Phospholipase A2 Mtx-b precursor (EC 3.1.1.4) (Mojave toxin basic chain) (Phosphatidylcholine 2-acyl ...	0.03	-	vac	0	Secreted protein				138
Q9I842 UniProt NPD GO	PA2F_LATSE	Phospholipase A2 cPm08 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.03	-	exc	1 *	Secreted protein (By similarity)				145
P58399 UniProt NPD GO	PA21B_BOTPI	Phospholipase A2 homolog 1 (Piratoxin-I) (PrTX-I) (Myotoxin SIV-SP5)	0.03	-	nuc	0	Secreted protein				121
Q9PVE3 UniProt NPD GO	PA23_BOTAS	Phospholipase A2 homolog 3 precursor (Myotoxin III) (M1-3-3)	0.03	-	exc	0	Secreted protein (By similarity)				138
P80963 UniProt NPD GO	PA2H_BOTSC	Phospholipase A2 homolog Bsc-K49 precursor (Myotoxin II)	0.03	-	exc	0	Secreted protein				137

You are viewing entries 81001 to 81050 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.