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
P81164 UniProt NPD GO	NODX_STRHE	Nodulin (Fragments)	0.19	-	nuc	0					95
P53615 UniProt NPD GO	NCE3_YEAST	Non-classical export protein 3	0.19	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			221
P47783 UniProt NPD GO	RNAS2_MACFA	Nonsecretory ribonuclease precursor (EC 3.1.27.5) (Ribonuclease US) (Eosinophil-derived neurotoxin) ...	0.19	-	exc	0	Lysosome (Probable). Matrix of eosinophil's large specific granule				160
Q7S7L4 UniProt NPD GO	NUDFB_NEUCR	Nuclear distribution protein pac-1b (nudF homolog B)	0.19	-	cyt	0	Cytoplasm. Localizes to the plus ends of microtubules and the mitotic spindle poles (By similarity)				471
P17624 UniProt NPD GO	NUDC_EMENI	Nuclear movement protein nudC	0.19	-	nuc	0	Cytoplasm				198
Q01085 UniProt NPD GO	TIAR_HUMAN	Nucleolysin TIAR (TIA-1-related protein)	0.19	-	cyt	0	Cytoplasmic granule. Cytoplasmic granules of cytolytic T-lymphocytes	lysosome [TAS]	603413	2CQI	375
Q9GZU5 UniProt NPD GO	NYX_HUMAN	Nyctalopin precursor	0.19	-	end	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)	intracellular [IEP]	310500		481
O75147 UniProt NPD GO	OBSL1_HUMAN	Obscurin-like protein 1 precursor	0.19	-	cyt	0				2CPC	1401
Q9NPH6 UniProt NPD GO	OBP2B_HUMAN	Odorant-binding protein 2b precursor (OBPIIb)	0.19	-	cyt	0	Secreted protein (Probable)		604606		170
Q39165 UniProt NPD GO	OLEO2_ARATH	Oleosin 21.2 kDa (Oleosin type 2)	0.19	-	end	3	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface (By similarity)				199
P70526 UniProt NPD GO	OLF1_RAT	Olfactory receptor 1 (Olfactory receptor 1469) (Olfactory receptor OR5) (Olfactory receptor HGL-SP1) ...	0.19	-	end	6 *	Membrane; multi-pass membrane protein				314
Q60881 UniProt NPD GO	OL142_MOUSE	Olfactory receptor 142 (Olfactory receptor 4C) (Olfactory receptor 227-2)	0.19	-	end	7 *	Membrane; multi-pass membrane protein				305
O95013 UniProt NPD GO	OR4F3_HUMAN	Olfactory receptor 4F3	0.19	-	end	7 *	Membrane; multi-pass membrane protein				312
P81595 UniProt NPD GO	TOT1B_HADVE	Omega-atracotoxin-Hv1b (Omega-AcTx-Hv1b)	0.19	+	nuc	0	Secreted protein				37
P30841 UniProt NPD GO	CROM_OCTDO	Omega-crystallin	0.19	-	cyt	0				1P3S	495
P78605 UniProt NPD GO	OTC_TRAHI	Ornithine carbamoyltransferase, mitochondrial precursor (EC 2.1.3.3) (OTCase) (Ornithine transcarbam ...	0.19	-	mit	0	Mitochondrion; mitochondrial matrix				375
Q755A3 UniProt NPD GO	OXR1_ASHGO	Oxidation resistance protein 1	0.19	-	cyt	0	Mitochondrion (By similarity)				237
Q6CMK8 UniProt NPD GO	OXR1_KLULA	Oxidation resistance protein 1	0.19	-	cyt	0	Mitochondrion (By similarity)				250
Q874Z5 UniProt NPD GO	OXR1_PODAN	Oxidation resistance protein 1	0.19	-	nuc	0	Mitochondrion (By similarity)				346
P48042 UniProt NPD GO	P2RY1_BOVIN	P2Y purinoceptor 1 (ATP receptor) (P2Y1) (Purinergic receptor)	0.19	-	end	6	Membrane; multi-pass membrane protein				373
Q9BPV8 UniProt NPD GO	P2Y13_HUMAN	P2Y purinoceptor 13 (P2Y13) (G-protein coupled receptor 86) (G-protein coupled receptor 94)	0.19	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	606380		333
Q98907 UniProt NPD GO	P2RY3_CHICK	P2Y purinoceptor 3 (P2Y3) (Nucleoside diphosphate receptor)	0.19	-	end	6 *	Membrane; multi-pass membrane protein				328
P32250 UniProt NPD GO	P2RY5_CHICK	P2Y purinoceptor 5 (P2Y5) (Purinergic receptor 5) (6H1)	0.19	-	end	7 *	Membrane; multi-pass membrane protein				308
P81139 UniProt NPD GO	LIPR2_CAVPO	Pancreatic lipase-related protein 2 (EC 3.1.1.3) (GPL)	0.19	-	nuc	0	Secreted protein				434
P13083 UniProt NPD GO	PAHO_CAVPO	Pancreatic prohormone precursor (Pancreatic polypeptide) (PP) [Contains: Pancreatic hormone; Pancrea ...	0.19	-	exc	1 *	Secreted protein				126
P43305 UniProt NPD GO	PRVU_CHICK	Parvalbumin, thymic CPV3 (Parvalbumin 3)	0.19	-	nuc	0					109
P54153 UniProt NPD GO	MSRA_LYCES	Peptide methionine sulfoxide reductase (EC 1.8.4.6) (Protein-methionine-S-oxide reductase) (Peptide ...	0.19	-	nuc	0					196
Q6CBP4 UniProt NPD GO	PPID_YARLI	Peptidyl-prolyl cis-trans isomerase D (EC 5.2.1.8) (PPIase D) (Rotamase D)	0.19	-	cyt	0	Cytoplasm (By similarity)				367
Q2TZ33 UniProt NPD GO	PPIH_ASPOR	Peptidyl-prolyl cis-trans isomerase H (EC 5.2.1.8) (PPIase H) (Rotamase H)	0.19	-	cyt	0	Nucleus (By similarity)				181
P23942 UniProt NPD GO	RDS_HUMAN	Peripherin (Retinal degeneration slow protein) (Tetraspanin-22) (Tspan-22)	0.19	-	end	3 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]	608161		346
Q43735 UniProt NPD GO	PER27_ARATH	Peroxidase 27 precursor (EC 1.11.1.7) (Atperox P27) (PRXR7) (ATP12a)	0.19	-	exc	0	Secreted protein (By similarity)				321
P17180 UniProt NPD GO	PER3_ARMRU	Peroxidase C3 precursor (EC 1.11.1.7)	0.19	-	exc	0	Or: Secreted protein (Probable). Or: Vacuole (Probable). Carboxy-terminal extension appears to targe ...				349
Q96VB8 UniProt NPD GO	CATA_CANBO	Peroxisomal catalase (EC 1.11.1.6)	0.19	-	mit	0	Peroxisome. Bimodally distributed between the cytosol and peroxisomes in methanol-grown cells but is ...				504
Q96HA9 UniProt NPD GO	PX11C_HUMAN	Peroxisomal membrane protein 11C (Peroxin-11C) (Peroxisomal biogenesis factor 11C) (PEX11gamma) (Pex ...	0.19	-	cyt	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein		607583		241
O35507 UniProt NPD GO	PPARA_CAVPO	Peroxisome proliferator-activated receptor alpha (PPAR-alpha)	0.19	+	cyt	0	Nucleus				467
P45730 UniProt NPD GO	PALY_POPTR	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.19	-	nuc	0	Cytoplasm (Probable)				715
Q99M01 UniProt NPD GO	SYFM_MOUSE	Phenylalanyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.20) (Phenylalanine--tRNA ligase) (Ph ...	0.19	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				451
O04940 UniProt NPD GO	CDS1_SOLTU	Phosphatidate cytidylyltransferase (EC 2.7.7.41) (CDP-diglyceride synthetase) (CDP-diglyceride pyrop ...	0.19	+	end	7	Membrane; multi-pass membrane protein (Potential)				424
Q7Z7B1 UniProt NPD GO	PIGW_HUMAN	Phosphatidylinositol-glycan biosynthesis class W protein (EC 2.3.-.-) (PIG-W)	0.19	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				504
P48651 UniProt NPD GO	PTSS1_HUMAN	Phosphatidylserine synthase 1 (EC 2.7.8.-) (PtdSer synthase 1) (PSS-1) (Serine-exchange enzyme I)	0.19	-	end	9 *	Membrane; multi-pass membrane protein				473
P49292 UniProt NPD GO	PEPC1_UROPA	Phosphoenolpyruvate carboxykinase [ATP] 1 (EC 4.1.1.49)	0.19	-	cyt	0	Cytoplasm				624
Q9XFA2 UniProt NPD GO	PEPC2_UROPA	Phosphoenolpyruvate carboxykinase [ATP] 2 (EC 4.1.1.49)	0.19	-	cyt	0	Cytoplasm				626
Q9Y263 UniProt NPD GO	PLAP_HUMAN	Phospholipase A-2-activating protein (PLAP) (PLA2P)	0.19	-	mit	0			603873		795
O04883 UniProt NPD GO	PLDA1_PIMBR	Phospholipase D alpha 1 (EC 3.1.4.4) (PLD alpha 1) (Choline phosphatase 1) (Phosphatidylcholine-hydr ...	0.19	-	mit	0					808
Q9DCW2 UniProt NPD GO	PLS2_MOUSE	Phospholipid scramblase 2 (PL scramblase 2) (Ca(2+)-dependent phospholipid scramblase 2)	0.19	-	cyt	0	Membrane; single-pass type II membrane protein (By similarity)				307
Q9Z2M7 UniProt NPD GO	PMM2_MOUSE	Phosphomannomutase 2 (EC 5.4.2.8) (PMM 2)	0.19	-	cyt	0	Cytoplasm (By similarity)				242
P38972 UniProt NPD GO	PUR4_YEAST	Phosphoribosylformylglycinamidine synthase (EC 6.3.5.3) (FGAM synthase) (FGAMS) (Formylglycinamide r ...	0.19	-	nuc	0	Cytoplasm	cytoplasm [IDA]			1358
P51487 UniProt NPD GO	ARRB_CALVI	Phosrestin-1 (Phosrestin I) (Arrestin B) (Arrestin-2)	0.19	-	cyt	0					400
Q85FT1 UniProt NPD GO	YCF3_CYAME	Photosystem I assembly protein ycf3	0.19	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				158
Q9MUT7 UniProt NPD GO	YCF3_MESVI	Photosystem I assembly protein ycf3	0.19	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				173

You are viewing entries 52201 to 52250 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.