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
P47890 UniProt NPD GO	OR1G1_HUMAN	Olfactory receptor 1G1 (Olfactory receptor 17-209) (OR17-209)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				313
Q96R48 UniProt NPD GO	OR2A5_HUMAN	Olfactory receptor 2A5 (Olfactory receptor 7-138/7-141) (OR7-138) (OR7-141)	0.20	-	end	6 *	Membrane; multi-pass membrane protein				311
Q8NGZ0 UniProt NPD GO	O2AJ1_HUMAN	Olfactory receptor 2AJ1	0.20	-	end	6 *	Membrane; multi-pass membrane protein				328
Q15615 UniProt NPD GO	OR4D1_HUMAN	Olfactory receptor 4D1 (Olfactory receptor TPCR16)	0.20	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			310
Q8NGI6 UniProt NPD GO	OR4DA_HUMAN	Olfactory receptor 4D10 (Olfactory receptor OR11-251)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				311
Q8N162 UniProt NPD GO	OR8H2_HUMAN	Olfactory receptor 8H2	0.20	-	end	6 *	Membrane; multi-pass membrane protein				312
P91679 UniProt NPD GO	OPT1_DROME	Oligopeptide transporter 1 (Protein YIN)	0.20	-	end	10	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			743
P81598 UniProt NPD GO	TOT1E_HADVE	Omega-atracotoxin-Hv1e (Omega-AcTx-Hv1e)	0.20	+	nuc	0	Secreted protein				37
P05484 UniProt NPD GO	CXO7A_CONMA	Omega-conotoxin MVIIa precursor (SNX-111) (Ziconotide) (Prialt)	0.20	-	exc	1 *	Secreted protein			1TTK	71
O43913 UniProt NPD GO	ORC5_HUMAN	Origin recognition complex subunit 5	0.20	-	cyt	0	Nucleus	nucleus [TAS]	602331		435
O42767 UniProt NPD GO	PYRE_METAN	Orotate phosphoribosyltransferase (EC 2.4.2.10) (OPRT) (OPRTase)	0.20	-	mit	0					234
P12547 UniProt NPD GO	ORYZ_ASPOR	Oryzin precursor (EC 3.4.21.63) (Alkaline proteinase) (ALP) (Aspergillus proteinase B) (Aspergillope ...	0.20	-	exc	0	Secreted protein				403
P40478 UniProt NPD GO	VDAC2_YEAST	Outer mitochondrial membrane protein porin 2 (Voltage-dependent anion-selective channel protein 2) ( ...	0.20	-	nuc	0	Mitochondrion; mitochondrial outer membrane (Potential)	mitochondrial outer membrane [IDA] mitochondrion [IDA]			281
Q28542 UniProt NPD GO	OVGP1_SHEEP	Oviduct-specific glycoprotein precursor (Oviductal glycoprotein) (Oviductin) (Estrogen-dependent ovi ...	0.20	-	cyt	0	Secretory granules				539
Q41643 UniProt NPD GO	PSBQ_VOLCA	Oxygen-evolving enhancer protein 3, chloroplast precursor (OEE3)	0.20	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				202
P49650 UniProt NPD GO	P2RY1_MOUSE	P2Y purinoceptor 1 (ATP receptor) (P2Y1) (Purinergic receptor)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				373
O18951 UniProt NPD GO	P2RY2_BOVIN	P2Y purinoceptor 2 (P2Y2) (Fragment)	0.20	-	mit	2 *	Membrane; multi-pass membrane protein				133
Q5JVF3 UniProt NPD GO	PCID2_HUMAN	PCI domain-containing protein 2 (CSN12-like protein)	0.20	-	cyt	0					399
Q96S96 UniProt NPD GO	PEBPL_HUMAN	PEBP family protein precursor	0.20	-	exc	0	Secreted protein (Potential)				223
P59267 UniProt NPD GO	ZDHC2_MOUSE	Palmitoyltransferase ZDHHC2 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 2) (DHHC-2)	0.20	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				366
Q5R5J8 UniProt NPD GO	ZDHC9_PONPY	Palmitoyltransferase ZDHHC9 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 9) (DHHC-9) (DH ...	0.20	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				364
P18107 UniProt NPD GO	PAHO_DIDMA	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.20	-	nuc	0	Secreted protein				36
P81635 UniProt NPD GO	IPK1_MONDO	Pancreatic secretory trypsin inhibitor	0.20	-	nuc	0	Secreted protein				55
P25621 UniProt NPD GO	FEN2_YEAST	Pantothenate transporter FEN2 (Fenpropimorph resistance protein 2)	0.20	-	end	12 *	Cell membrane; multi-pass membrane protein	plasma membrane [IGI]			512
P08814 UniProt NPD GO	PTMS_BOVIN	Parathymosin	0.20	-	nuc	0					101
Q96M98 UniProt NPD GO	PACRG_HUMAN	Parkin coregulated gene protein (PARK2 coregulated) (Molecular chaperone/chaperonin-binding protein) ...	0.20	-	cyt	0			608427		296
Q03602 UniProt NPD GO	PTR9_CAEEL	Patched-related protein 9	0.20	-	end	11 *					844
Q9ASS6 UniProt NPD GO	CP20B_ARATH	Peptidyl-prolyl cis-trans isomerase CYP20-2, chloroplast precursor (EC 5.2.1.8) (PPIase CYP20-2) (Ro ...	0.20	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen. Plastid; chloroplast; chloroplast membrane; perip ...				259
Q94A16 UniProt NPD GO	CP21C_ARATH	Peptidyl-prolyl cis-trans isomerase CYP21-3, mitochondrial precursor (EC 5.2.1.8) (PPIase CYP21-3) ( ...	0.20	-	mit	1 *	Mitochondrion (Potential)				230
Q17285 UniProt NPD GO	PER_BERVA	Period circadian protein (Fragment)	0.20	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				107
Q25435 UniProt NPD GO	PER_MUSDO	Period circadian protein (Fragment)	0.20	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				109
Q12524 UniProt NPD GO	PCD1_YEAST	Peroxisomal coenzyme A diphosphatase 1, peroxisomal precursor (EC 3.6.1.-)	0.20	-	mit	0	Peroxisome	peroxisome [IDA]			340
Q00316 UniProt NPD GO	PX11A_CANBO	Peroxisomal membrane protein PMP30A (PMP31) (Peroxin-11A)	0.20	-	cyt	0	Peroxisome; peroxisomal membrane; peripheral membrane protein				256
Q92265 UniProt NPD GO	PEX10_PICPA	Peroxisome assembly protein 10 (Peroxin-10) (Peroxisome biogenesis factor 10) (Peroxisome assembly p ...	0.20	-	cyt	3	Peroxisome; peroxisomal membrane; peripheral membrane protein				419
Q95N78 UniProt NPD GO	PPARA_CANFA	Peroxisome proliferator-activated receptor alpha (PPAR-alpha)	0.20	+	cyt	0	Nucleus				468
P24481 UniProt NPD GO	PAL1_PETCR	Phenylalanine ammonia-lyase 1 (EC 4.3.1.5)	0.20	-	nuc	0	Cytoplasm (Probable)			1W27	716
O64963 UniProt NPD GO	PAL1_PRUAV	Phenylalanine ammonia-lyase 1 (EC 4.3.1.5)	0.20	-	nuc	0	Cytoplasm (Probable)				717
Q43052 UniProt NPD GO	PAL2_POPKI	Phenylalanine ammonia-lyase G2B (EC 4.3.1.5)	0.20	-	nuc	0	Cytoplasm (Probable)				710
Q19713 UniProt NPD GO	SYFB_CAEEL	Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) (Phenylalanine--tRNA ligase beta chain) (PheRS ...	0.20	-	nuc	0	Cytoplasm (By similarity)				591
Q13794 UniProt NPD GO	APR_HUMAN	Phorbol-12-myristate-13-acetate-induced protein 1 (PMA-induced protein 1) (Immediate-early-response ...	0.20	-	nuc	0			604959		54
Q12017 UniProt NPD GO	PLP2_YEAST	Phosducin-like protein 2 (Viral IAP-associated factor 1 homolog)	0.20	-	cyt	0	Cytoplasm	cytoplasm [IPI]			286
Q14442 UniProt NPD GO	PIGH_HUMAN	Phosphatidylinositol N-acetylglucosaminyltransferase subunit H (EC 2.4.1.198) (Phosphatidylinositol- ...	0.20	-	mit	2 *	Cytoplasm	endoplasmic reticulum [TAS]	600154		188
Q9UG56 UniProt NPD GO	PISD_HUMAN	Phosphatidylserine decarboxylase proenzyme (EC 4.1.1.65) [Contains: Phosphatidylserine decarboxylase ...	0.20	-	mit	0	Mitochondrion (By similarity)				408
Q5R8I8 UniProt NPD GO	PISD_PONPY	Phosphatidylserine decarboxylase proenzyme (EC 4.1.1.65) [Contains: Phosphatidylserine decarboxylase ...	0.20	-	mit	0	Mitochondrion (By similarity)				409
P39006 UniProt NPD GO	PSD1_YEAST	Phosphatidylserine decarboxylase proenzyme 1, mitochondrial precursor (EC 4.1.1.65) [Contains: Phosp ...	0.20	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [TAS] mitochondrion [IDA]			500
Q8TCT1 UniProt NPD GO	PHOP1_HUMAN	Phosphoethanolamine/phosphocholine phosphatase (EC 3.1.3.75)	0.20	-	cyt	0					267
Q8R2H9 UniProt NPD GO	PHOP1_MOUSE	Phosphoethanolamine/phosphocholine phosphatase (EC 3.1.3.75)	0.20	-	nuc	0					267
P51528 UniProt NPD GO	PA1_VESMC	Phospholipase A1 (EC 3.1.1.32) (EC 3.1.1.4) (Allergen Ves m 1) (Ves m I)	0.20	-	nuc	0					300
Q8UUH9 UniProt NPD GO	PA24_LATCO	Phospholipase A2 PC9 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.20	-	exc	0	Secreted protein (By similarity)				155
P20256 UniProt NPD GO	PA2C_PSEAU	Phospholipase A2 isozyme PA-12C (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.20	-	nuc	0	Secreted protein				118

You are viewing entries 50951 to 51000 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.