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
P78798 UniProt NPD GO	PEX7_SCHPO	Peroxisomal targeting signal 2 receptor (PTS2 receptor) (Peroxin-7)	0.08	-	cyt	0	Peroxisome (By similarity). Cytoplasm (By similarity)				308
P45735 UniProt NPD GO	PALY_VITVI	Phenylalanine ammonia-lyase (EC 4.3.1.5) (Fragment)	0.08	-	nuc	0	Cytoplasm (Probable)				416
P10938 UniProt NPD GO	PNMT_BOVIN	Phenylethanolamine N-methyltransferase (EC 2.1.1.28) (PNMTase) (Noradrenaline N-methyltransferase)	0.08	-	cyt	0					283
P53174 UniProt NPD GO	PRM8_YEAST	Pheromone-regulated membrane protein 8 (DUP240 protein PRM8) (Protein DUP1)	0.08	-	end	2 *	Membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum	endoplasmic reticulum [IDA] plasma membrane [IDA]			237
O35052 UniProt NPD GO	CDS1_RAT	Phosphatidate cytidylyltransferase 1 (EC 2.7.7.41) (CDP-diglyceride synthetase 1) (CDP-diglyceride p ...	0.08	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Cytoplasmic aspe ...	endoplasmic reticulum membrane [IDA]			461
Q8VCQ6 UniProt NPD GO	SMS1_MOUSE	Phosphatidylcholine:ceramide cholinephosphotransferase 1 (EC 2.7.-.-) (Transmembrane protein 23) (Sp ...	0.08	-	end	6	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)	integral to Golgi membrane [ISS]			419
P05374 UniProt NPD GO	PEM1_YEAST	Phosphatidylethanolamine N-methyltransferase (EC 2.1.1.17) (PEAMT)	0.08	-	end	8					869
Q04082 UniProt NPD GO	GPI19_YEAST	Phosphatidylinositol N-acetylglucosaminyltransferase subunit GPI19 (EC 2.4.1.198)	0.08	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA] glycosylphosphatidylinositol-N-acetylglucos... [IPI] integral to endoplasmic reticulum membrane [IDA] nuclear envelope [IDA]			140
P16446 UniProt NPD GO	PIPNA_RAT	Phosphatidylinositol transfer protein alpha isoform (PtdIns transfer protein alpha) (PtdInsTP) (PI-T ...	0.08	-	cyt	0	Cytoplasm			1T27	270
P57750 UniProt NPD GO	AGM1_ARATH	Phosphoacetylglucosamine mutase (EC 5.4.2.3) (PAGM) (Acetylglucosamine phosphomutase) (N-acetylgluco ...	0.08	-	nuc	0					556
Q753M0 UniProt NPD GO	PPCK_ASHGO	Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49)	0.08	-	nuc	0					541
P57749 UniProt NPD GO	PGM_ASPOR	Phosphoglucomutase (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.08	-	cyt	0	Cytoplasm (By similarity)				555
Q8CAA7 UniProt NPD GO	PGM2L_MOUSE	Phosphoglucomutase-2-like 1 (EC 5.4.2.2)	0.08	-	cyt	0					621
P84397 UniProt NPD GO	PA22_BOTIN	Phospholipase A2 2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.08	-	nuc	0	Secreted protein				122
Q8UUI3 UniProt NPD GO	PA23_LATLA	Phospholipase A2 PC14 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.08	-	exc	1 *	Secreted protein (By similarity)				145
Q8UUH8 UniProt NPD GO	PA25_LATCO	Phospholipase A2 PC17 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.08	-	exc	1 *	Secreted protein (By similarity)				145
Q7LZI2 UniProt NPD GO	PA2J_NAJKA	Phospholipase A2 inhibitor 25 kDa subunit	0.08	-	nuc	0	Secreted protein				185
Q9PWI3 UniProt NPD GO	PLIGB_ELAQU	Phospholipase A2 inhibitor subunit gamma B precursor (PLI-gamma B)	0.08	-	mit	0	Secreted protein				200
P21790 UniProt NPD GO	PA21B_MICNI	Phospholipase A2 isozyme 1 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.08	-	cyt	0	Secreted protein				27
P20257 UniProt NPD GO	PA2E_PSEAU	Phospholipase A2 isozyme PA-15 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.08	-	nuc	0	Secreted protein				118
Q9PUH4 UniProt NPD GO	PA210_AUSSU	Phospholipase A2 isozyme S5-32M precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA1 ...	0.08	-	exc	0	Secreted protein (By similarity)				146
Q9PUI1 UniProt NPD GO	PA22_AUSSU	Phospholipase A2 isozyme S6-45 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA2) ...	0.08	-	exc	0	Secreted protein (By similarity)				145
Q9PUH9 UniProt NPD GO	PA25_AUSSU	Phospholipase A2 isozyme S9-53F precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA5 ...	0.08	-	exc	0	Secreted protein (By similarity)				147
P00628 UniProt NPD GO	PA2A_BUNFA	Phospholipase A2 isozyme VA (EC 3.1.1.4) (Toxin V-2) (Phosphatidylcholine 2-acylhydrolase)	0.08	-	nuc	0	Secreted protein				118
Q9I900 UniProt NPD GO	PA2D_NAJSP	Phospholipase A2, acidic D precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (APLA)	0.08	-	exc	0	Secreted protein				146
P82893 UniProt NPD GO	PA2B2_TRIST	Phospholipase A2, basic 2 (EC 3.1.1.4) (PA2-II) (PLA2-II) (Phosphatidylcholine 2-acylhydrolase) (Fra ...	0.08	-	nuc	0	Secreted protein				70
Q9PTA5 UniProt NPD GO	PA2D_BUNMU	Phospholipase A2, beta bungarotoxin A-AL4 chain precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhy ...	0.08	-	nuc	0	Secreted protein (By similarity)				137
P00619 UniProt NPD GO	PA23_BUNMU	Phospholipase A2, beta bungarotoxin A3 chain precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydro ...	0.08	-	exc	0	Secreted protein				147
P00592 UniProt NPD GO	PA21B_PIG	Phospholipase A2, major isoenzyme precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Grou ...	0.08	-	exc	0	Secreted protein			5P2P	146
P00616 UniProt NPD GO	PA23_OXYSC	Phospholipase A2, taipoxin gamma chain (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.08	-	nuc	0	Secreted protein				133
P24521 UniProt NPD GO	ERG8_YEAST	Phosphomevalonate kinase (EC 2.7.4.2)	0.08	-	mit	0	Cytoplasm				451
Q9HAB8 UniProt NPD GO	PPCS_HUMAN	Phosphopantothenate--cysteine ligase (EC 6.3.2.5) (Phosphopantothenoylcysteine synthetase) (PPC synt ...	0.08	-	cyt	0			609853	1P9O	311
Q63530 UniProt NPD GO	PTER_RAT	Phosphotriesterase-related protein (Parathion hydrolase-related protein) (Resiniferotoxin-binding ph ...	0.08	-	cyt	0					349
Q8M9V9 UniProt NPD GO	PSAB_CHAGL	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.08	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q85FL1 UniProt NPD GO	YCF4_ADICA	Photosystem I assembly protein ycf4	0.08	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
O78467 UniProt NPD GO	YCF4_GUITH	Photosystem I assembly protein ycf4	0.08	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				181
Q5SCW2 UniProt NPD GO	YCF4_HUPLU	Photosystem I assembly protein ycf4	0.08	-	cyt	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
Q9TKZ3 UniProt NPD GO	YCF4_NEPOL	Photosystem I assembly protein ycf4 (RF4)	0.08	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				183
Q5SCZ7 UniProt NPD GO	PSAC_HUPLU	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.08	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				81
Q9S7N7 UniProt NPD GO	PSAG_ARATH	Photosystem I reaction center subunit V, chloroplast precursor (PSI-G)	0.08	-	mit	2	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				160
P20143 UniProt NPD GO	PSAH_HORVU	Photosystem I reaction center subunit VI, chloroplast precursor (PSI-H) (Light-harvesting complex I ...	0.08	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				143
Q39654 UniProt NPD GO	PSAL_CUCSA	Photosystem I reaction center subunit XI, chloroplast precursor (PSI-L) (PSI subunit V)	0.08	-	mit	2	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				217
P49508 UniProt NPD GO	PSBW_ODOSI	Photosystem II reaction center W protein	0.08	-	cyt	0	Plastid; chloroplast				115
P61231 UniProt NPD GO	TXP2_PARSR	Phrixotoxin-2 (PaTX2)	0.08	-	cyt	0	Secreted protein				31
P30942 UniProt NPD GO	PHE1_RHOS2	Phycoerythrin alpha-1 chain (Fragment)	0.08	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen				44
P48537 UniProt NPD GO	CRTI_CERNC	Phytoene dehydrogenase (EC 1.14.99.-) (Phytoene desaturase)	0.08	-	nuc	1					621
O42490 UniProt NPD GO	OPSP_PETMA	Pineal opsin (P-opsin) (Pineal gland-specific opsin)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				444
O00625 UniProt NPD GO	PIR_HUMAN	Pirin	0.08	-	cyt	0	Nucleus. Predominantly localized in dot-like subnuclear structures	nucleus [TAS]	603329	1J1L	290
P83204 UniProt NPD GO	PLAC_SHEEP	Placental protein (Fragment)	0.08	-		0	Secreted protein				15
O00059 UniProt NPD GO	PIG11_UROFA	Planta-induced rust protein 11	0.08	-	nuc	0					24

You are viewing entries 68651 to 68700 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.