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
Q4P6X6 UniProt NPD GO	PPIH_USTMA	Peptidyl-prolyl cis-trans isomerase H (EC 5.2.1.8) (PPIase H) (Rotamase H) (Fragment)	0.07	-	cyt	0	Nucleus (By similarity)				156
Q8R2Y8 UniProt NPD GO	PTH2_MOUSE	Peptidyl-tRNA hydrolase 2, mitochondrial precursor (EC 3.1.1.29) (PTH 2)	0.07	-	end	1 *	Mitochondrion (By similarity)				181
Q04535 UniProt NPD GO	PER_DROMS	Period circadian protein (Fragment)	0.07	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				63
Q04537 UniProt NPD GO	PER_DROSR	Period circadian protein (Fragment)	0.07	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				141
Q9ZV04 UniProt NPD GO	PER24_ARATH	Peroxidase 24 precursor (EC 1.11.1.7) (Atperox P24) (ATP47)	0.07	-	exc	0	Secreted protein (By similarity)				350
O80822 UniProt NPD GO	PER25_ARATH	Peroxidase 25 precursor (EC 1.11.1.7) (Atperox P25)	0.07	-	end	0	Secreted protein (By similarity)				328
Q90384 UniProt NPD GO	TDX_CYNPY	Peroxiredoxin (EC 1.11.1.15) (Thioredoxin peroxidase) (Thioredoxin-dependent peroxide reductase) (An ...	0.07	-	cyt	0	Cytoplasm (By similarity)				200
Q01373 UniProt NPD GO	FOX2_NEUCR	Peroxisomal hydratase-dehydrogenase-epimerase (HDE) (Multifunctional beta-oxidation protein) (MFP) [ ...	0.07	-	cyt	0	Catalase-free microbodies				894
P42925 UniProt NPD GO	PXMP2_MOUSE	Peroxisomal membrane protein 2 (22 kDa peroxisomal membrane protein)	0.07	-	nuc	3 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein				193
Q9ZS51 UniProt NPD GO	PMP22_ARATH	Peroxisomal membrane protein PMP22 (22 kDa peroxisomal membrane protein)	0.07	-	cyt	4	Peroxisome; peroxisomal membrane; multi-pass membrane protein				190
Q758W8 UniProt NPD GO	PEX22_ASHGO	Peroxisome assembly protein 22 (Peroxin-22)	0.07	-	mit	1 *	Peroxisome; peroxisomal membrane; single-pass membrane protein (By similarity)				144
O04058 UniProt NPD GO	PALY_HELAN	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.07	-	nuc	0	Cytoplasm (Probable)				667
Q8VEM8 UniProt NPD GO	MPCP_MOUSE	Phosphate carrier protein, mitochondrial precursor (PTP) (Solute carrier family 25 member 3)	0.07	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA] mitochondrion [IDA]			357
P16036 UniProt NPD GO	MPCP_RAT	Phosphate carrier protein, mitochondrial precursor (PTP) (Solute carrier family 25 member 3)	0.07	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrion [IDA]			356
P38361 UniProt NPD GO	PHO89_YEAST	Phosphate permease PHO89 (Na(+)/Pi cotransporter PHO89)	0.07	-	end	10 *	Membrane; multi-pass membrane protein	plasma membrane [IMP]			574
P98191 UniProt NPD GO	CDS1_MOUSE	Phosphatidate cytidylyltransferase 1 (EC 2.7.7.41) (CDP-diglyceride synthetase 1) (CDP-diglyceride p ...	0.07	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...	endoplasmic reticulum [IDA]			461
P04180 UniProt NPD GO	LCAT_HUMAN	Phosphatidylcholine-sterol acyltransferase precursor (EC 2.3.1.43) (Lecithin-cholesterol acyltransfe ...	0.07	-	mit	2 *		extracellular region [NAS]	606967		440
P53761 UniProt NPD GO	LCAT_RABIT	Phosphatidylcholine-sterol acyltransferase precursor (EC 2.3.1.43) (Lecithin-cholesterol acyltransfe ...	0.07	-	exc	2 *					440
P37287 UniProt NPD GO	PIGA_HUMAN	Phosphatidylinositol N-acetylglucosaminyltransferase subunit A (EC 2.4.1.198) (GlcNAc-PI synthesis p ...	0.07	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IDA] glycosylphosphatidylinositol-N-acetylglucos... [IDA]	311770		484
P57054 UniProt NPD GO	PIGP_HUMAN	Phosphatidylinositol N-acetylglucosaminyltransferase subunit P (EC 2.4.1.198) (Phosphatidylinositol- ...	0.07	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]	605938		158
P53810 UniProt NPD GO	PIPNA_MOUSE	Phosphatidylinositol transfer protein alpha isoform (PtdIns transfer protein alpha) (PtdInsTP) (PI-T ...	0.07	-	cyt	0	Cytoplasm			1KCM	270
Q60GF7 UniProt NPD GO	PIGX_RAT	Phosphatidylinositol-glycan biosynthesis class X protein precursor (PIG-X)	0.07	-	exc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein				252
Q15127 UniProt NPD GO	PHLD2_HUMAN	Phosphatidylinositol-glycan-specific phospholipase D 2 precursor (EC 3.1.4.50) (PI-G PLD) (Glycoprot ...	0.07	-	mit	0	Secreted protein		602515		841
P13735 UniProt NPD GO	PPCK_TRYBB	Phosphoenolpyruvate carboxykinase [ATP], glycosomal (EC 4.1.1.49) (Glycosomal protein P60)	0.07	-	cyt	0	Glycosome				472
P07379 UniProt NPD GO	PPCKC_RAT	Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) (Phosphoenolpyruvate carboxylase) ( ...	0.07	-	nuc	0	Cytoplasm				622
Q15124 UniProt NPD GO	PGM5_HUMAN	Phosphoglucomutase-like protein 5 (Phosphoglucomutase-related protein) (PGM-RP) (Aciculin)	0.07	-	cyt	0	Cell membrane; cell-cell junction; adherens junction. Adherens-type cellular junctions		600981		506
P00622 UniProt NPD GO	PA2_BITCA	Phospholipase A2 (EC 3.1.1.4) (Caudoxin) (Phosphatidylcholine 2-acylhydrolase)	0.07	-	nuc	0	Secreted protein				121
Q9BMK4 UniProt NPD GO	PA2_APICC	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.07	-	nuc	0	Secreted protein (By similarity)				134
P00620 UniProt NPD GO	PA2_BITGA	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.07	-	nuc	0	Secreted protein				118
P14419 UniProt NPD GO	PA21B_SHEEP	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Group IB phospholipase A2)	0.07	-	nuc	0	Secreted protein				123
Q8UW31 UniProt NPD GO	PA25_LAPHA	Phospholipase A2 57 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.07	-	exc	1 *	Secreted protein (By similarity)				152
Q805A2 UniProt NPD GO	PA2N_TRIFL	Phospholipase A2 PLA-N/PLA-N(O) precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.07	-	mit	1 *	Secreted protein (By similarity)				138
P81458 UniProt NPD GO	PA2_DABRR	Phospholipase A2 RVV-VD (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.07	-	nuc	0	Secreted protein			1VIP	121
Q9PVF1 UniProt NPD GO	PA2A_AGKRH	Phospholipase A2 S1E6-a precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.07	-	cyt	0	Secreted protein				126
Q9PVF0 UniProt NPD GO	PA2B_AGKRH	Phospholipase A2 S1E6-b precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.07	-	cyt	0	Secreted protein				126
Q9I844 UniProt NPD GO	PA2D_LATSE	Phospholipase A2 cPt10 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.07	-	exc	1 *	Secreted protein (By similarity)				145
P04084 UniProt NPD GO	PA2I_VIPAE	Phospholipase A2 inhibitor (Vipoxin toxic component) (Vipoxin A chain) (Inh)	0.07	-	cyt	0	Secreted protein			1VPI	122
P00599 UniProt NPD GO	PA21B_NAJME	Phospholipase A2 isozyme DE-I (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.07	-	nuc	0	Secreted protein			1OO1	118
P00601 UniProt NPD GO	PA23_NAJME	Phospholipase A2 isozyme DE-III (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.07	-	nuc	0	Secreted protein				119
Q02517 UniProt NPD GO	PA2W_TRIFL	Phospholipase A2 isozyme PL-X' precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.07	-	mit	1 *	Secreted protein				138
Q90Y77 UniProt NPD GO	PA2Y_TRIFL	Phospholipase A2 isozyme PL-Y precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.07	-	end	1 *	Secreted protein (By similarity)				138
P00629 UniProt NPD GO	PA2B_BUNFA	Phospholipase A2 isozyme VB-2 (EC 3.1.1.4) (Toxin V-3) (Phosphatidylcholine 2-acylhydrolase)	0.07	-	nuc	0	Secreted protein				118
Q8JIG0 UniProt NPD GO	PA2Q_TRIFL	Phospholipase A2 isozyme cPLA-B'(A) precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.07	-	mit	1 *	Secreted protein (Probable)				138
Q45Z25 UniProt NPD GO	PA26_TROCA	Phospholipase A2, acidic 6 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase 6) (PLA-6)	0.07	-	exc	1 *	Secreted protein				151
Q5KGS6 UniProt NPD GO	PUR6_CRYNE	Phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) (AIR carboxylase) (AIRC)	0.07	-	mit	0					582
P0C017 UniProt NPD GO	PUR6_CRYNV	Phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) (AIR carboxylase) (AIRC)	0.07	-	mit	0					582
P55195 UniProt NPD GO	PUR6_VIGAC	Phosphoribosylaminoimidazole carboxylase, chloroplast precursor (EC 4.1.1.21) (AIR carboxylase) (AIR ...	0.07	-	cyt	0	Plastid; chloroplast (Probable)				557
Q9MTL1 UniProt NPD GO	YCF4_OENHO	Photosystem I assembly protein ycf4	0.07	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				186
P69416 UniProt NPD GO	PSAC_HORVU	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.07	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q6ENA6 UniProt NPD GO	PSAC_ORYNI	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.07	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80

You are viewing entries 70651 to 70700 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.