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
P21555 UniProt NPD GO	NPY1R_RAT	Neuropeptide Y receptor type 1 (NPY1-R) (FC5)	0.21	-	end	7 *	Membrane; multi-pass membrane protein				382
P83558 UniProt NPD GO	TXMG2_MACGS	Neurotoxin magi-2 precursor	0.21	-	exc	0	Secreted protein				121
Q8GUM5 UniProt NPD GO	NICA_ARATH	Nicastrin precursor	0.21	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				676
Q861Y6 UniProt NPD GO	NICN1_CANFA	Nicolin-1	0.21	-	mit	0	Nucleus (By similarity)				213
P83997 UniProt NPD GO	TX16_PHONI	Non-toxic venom protein PNTx16C1	0.21	-	nuc	0	Secreted protein				68
Q8TEM1 UniProt NPD GO	PO210_HUMAN	Nuclear pore membrane glycoprotein 210 precursor (POM210) (Nuclear pore protein gp210)	0.21	-	end	2 *	Nucleus; nuclear envelope; nuclear pore complex; single-pass type I membrane protein. Endoplasmic re ...		607703		1887
P12904 UniProt NPD GO	SNF4_YEAST	Nuclear protein SNF4 (Regulatory protein CAT3)	0.21	-	cyt	0	Nucleus	cytoplasm [IDA] nucleus [IDA] plasma membrane [IDA]			322
P11930 UniProt NPD GO	NUD19_MOUSE	Nucleoside diphosphate-linked moiety X motif 19 (EC 3.-.-.-) (Nudix motif 19) (Testosterone-regulate ...	0.21	-	mit	0		mitochondrion [IDA]			357
O01670 UniProt NPD GO	OAR2_LYMST	Octopamine receptor 2 (OA2)	0.21	-	end	7	Membrane; multi-pass membrane protein				578
P29110 UniProt NPD GO	OLEO3_BRANA	Oleosin Bn-III (BnIII)	0.21	-	end	2	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface				195
P29109 UniProt NPD GO	OLEO5_BRANA	Oleosin Bn-V (BnV) (Fragment)	0.21	-	mit	2	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface				183
Q6IF42 UniProt NPD GO	OR2A2_HUMAN	Olfactory receptor 2A2 (Olfactory receptor OR7-11)	0.21	-	end	5 *	Membrane; multi-pass membrane protein				318
Q8N146 UniProt NPD GO	OR8H3_HUMAN	Olfactory receptor 8H3	0.21	-	end	6 *	Membrane; multi-pass membrane protein				312
P51879 UniProt NPD GO	ONCO_MOUSE	Oncomodulin (OM) (Parvalbumin beta)	0.21	-	nuc	0					108
P18740 UniProt NPD GO	ZO14_XENLA	Oocyte zinc finger protein XLCOF14 (Fragment)	0.21	-	nuc	0	Nucleus (Potential)				139
O77668 UniProt NPD GO	OREX_PIG	Orexin precursor (Hypocretin) (Hcrt) [Contains: Orexin-A (Hypocretin-1) (Hcrt1); Orexin-B (Hypocreti ...	0.21	-	exc	1 *	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Associated with perikaryal rough ...				131
O55232 UniProt NPD GO	OREX_RAT	Orexin precursor (Hypocretin) (Hcrt) [Contains: Orexin-A (Hypocretin-1) (Hcrt1); Orexin-B (Hypocreti ...	0.21	-	exc	1 *	Endoplasmic reticulum; rough endoplasmic reticulum. Associated with perikaryal rough endoplasmic ret ...	secretory granule [IDA]			130
Q9WUV0 UniProt NPD GO	ORC5_MOUSE	Origin recognition complex subunit 5	0.21	-	cyt	0	Nucleus				435
P09463 UniProt NPD GO	PYRF_PENCH	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.21	-	mit	0					278
P54615 UniProt NPD GO	OSTR_MOUSE	Osteocalcin-related protein precursor (OC-X) (Nephrocalcin)	0.21	-	exc	0	Secreted protein				95
Q6FSN5 UniProt NPD GO	OXR1_CANGA	Oxidation resistance protein 1	0.21	-	mit	0	Mitochondrion (By similarity)				271
P27665 UniProt NPD GO	PSBO_WHEAT	Oxygen-evolving enhancer protein 1, chloroplast precursor (OEE1) (33 kDa subunit of oxygen evolving ...	0.21	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				325
Q41932 UniProt NPD GO	PSBQ2_ARATH	Oxygen-evolving enhancer protein 3-2, chloroplast precursor (OEE3) (16 kDa subunit of oxygen evolvin ...	0.21	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				230
P59902 UniProt NPD GO	P2RY1_CAVPO	P2Y purinoceptor 1 (ATP receptor) (P2Y1) (Purinergic receptor)	0.21	-	end	6 *	Membrane; multi-pass membrane protein				373
P49651 UniProt NPD GO	P2RY1_RAT	P2Y purinoceptor 1 (ATP receptor) (P2Y1) (Purinergic receptor)	0.21	-	end	7 *	Membrane; multi-pass membrane protein	apical plasma membrane [IDA] basolateral plasma membrane [IDA]			373
Q15391 UniProt NPD GO	P2Y14_HUMAN	P2Y purinoceptor 14 (P2Y14) (UDP-glucose receptor) (G-protein coupled receptor 105)	0.21	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			338
O35881 UniProt NPD GO	P2Y14_RAT	P2Y purinoceptor 14 (P2Y14) (UDP-glucose receptor) (G-protein coupled receptor 105) (VTR 15-20)	0.21	-	end	6 *	Membrane; multi-pass membrane protein	integral to membrane [ISS]			305
P58825 UniProt NPD GO	P2RY2_CRIGR	P2Y purinoceptor 2 (P2Y2) (Fragment)	0.21	-	mit	3 *	Membrane; multi-pass membrane protein				166
O93361 UniProt NPD GO	P2RY3_MELGA	P2Y purinoceptor 3 (P2Y3) (Nucleoside diphosphate receptor)	0.21	-	end	6 *	Membrane; multi-pass membrane protein				328
Q9JJS7 UniProt NPD GO	P2RY4_MOUSE	P2Y purinoceptor 4 (P2Y4)	0.21	-	end	6 *	Membrane; multi-pass membrane protein				361
O70209 UniProt NPD GO	PDLI3_MOUSE	PDZ and LIM domain protein 3 (Actinin-associated LIM protein) (Alpha-actinin-2-associated LIM protei ...	0.21	-	nuc	0	Localizes to myofiber Z-lines (By similarity)	actin cytoskeleton [IPI] Z disc [TAS]		1X64	316
Q6CPU8 UniProt NPD GO	PFA3_KLULA	Palmitoyltransferase PFA3 (EC 2.3.1.-) (Protein fatty acyltransferase 3)	0.21	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				325
P06884 UniProt NPD GO	PAHO_FELCA	Pancreatic prohormone precursor (Pancreatic polypeptide) (PP) [Contains: Pancreatic hormone; Pancrea ...	0.21	-	nuc	0	Secreted protein				66
Q9JIP4 UniProt NPD GO	PANX1_MOUSE	Pannexin-1	0.21	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				426
Q8BHK0 UniProt NPD GO	PNMA2_MOUSE	Paraneoplastic antigen Ma2 homolog	0.21	-	cyt	0	Nucleus; nucleolus (By similarity)				365
P01268 UniProt NPD GO	PTHY_BOVIN	Parathyroid hormone precursor (Parathyrin) (PTH)	0.21	-	cyt	0	Secreted protein			1ZWC	115
Q9R154 UniProt NPD GO	S26A4_RAT	Pendrin (Sodium-independent chloride/iodide transporter) (Solute carrier family 26 member 4)	0.21	-	end	11	Membrane; multi-pass membrane protein (Probable)				780
P32901 UniProt NPD GO	PTR2_YEAST	Peptide transporter PTR2 (Peptide permease PTR2)	0.21	-	end	11	Membrane; multi-pass membrane protein	plasma membrane [IMP]			601
Q95T64 UniProt NPD GO	PGPLA_DROME	Peptidoglycan-recognition protein-LA	0.21	-	nuc	1		integral to plasma membrane [NAS]			368
P91686 UniProt NPD GO	PER_DRONE	Period circadian protein (Fragment)	0.21	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				385
Q25206 UniProt NPD GO	PER_DROPI	Period circadian protein (Fragment)	0.21	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				143
Q25221 UniProt NPD GO	PER_LOXAL	Period circadian protein (Fragment)	0.21	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				109
P37835 UniProt NPD GO	PER2_ORYSA	Peroxidase 2 precursor (EC 1.11.1.7)	0.21	-	exc	0	Secreted protein (By similarity)				314
P24101 UniProt NPD GO	PER33_ARATH	Peroxidase 33 precursor (EC 1.11.1.7) (Atperox P33) (ATPCa) (Neutral peroxidase C) (PERC)	0.21	-	exc	1 *	Or: Secreted protein (Probable). Or: Vacuole (Probable). Carboxy-terminal extension appears to targe ...				354
Q42578 UniProt NPD GO	PER53_ARATH	Peroxidase 53 precursor (EC 1.11.1.7) (Atperox P53) (ATPA2)	0.21	-	nuc	1 *	Secreted protein (By similarity)			1QO4	335
P28314 UniProt NPD GO	PER_COPCI	Peroxidase precursor (EC 1.11.1.7)	0.21	-	vac	0	Secreted protein			1LYK	363
Q74Z13 UniProt NPD GO	PEX6_ASHGO	Peroxisomal biogenesis factor 6 (Peroxin-6)	0.21	-	nuc	0					1021
P53248 UniProt NPD GO	PEX8_YEAST	Peroxisomal biogenesis factor 8 (Peroxin-8) (Peroxisomal protein PAS6)	0.21	-	end	0	Peroxisome; peroxisomal matrix (Potential)	peroxisomal membrane [IDA]			589
Q9Y6I8 UniProt NPD GO	PXMP4_HUMAN	Peroxisomal membrane protein 4 (24 kDa peroxisomal intrinsic membrane protein)	0.21	-	nuc	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein (By similarity)	integral to membrane [TAS] membrane fraction [TAS] peroxisomal membrane [TAS]			211
O70579 UniProt NPD GO	PM34_MOUSE	Peroxisomal membrane protein PMP34 (34 kDa peroxisomal membrane protein) (Solute carrier family 25 m ...	0.21	-	end	5 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein	mitochondrion [IDA] peroxisomal membrane [IDA]			307

You are viewing entries 49801 to 49850 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.