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
O09101 UniProt NPD GO	PIGF_MOUSE	Phosphatidylinositol-glycan biosynthesis class F protein (PIG-F)	0.09	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IDA]			219
Q07326 UniProt NPD GO	PIGF_HUMAN	Phosphatidylinositol-glycan biosynthesis class F protein (PIG-F) (GPI11 homolog)	0.09	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum membrane [ISS]	600153		219
Q9Z2V4 UniProt NPD GO	PPCKC_MOUSE	Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) (Phosphoenolpyruvate carboxylase) ( ...	0.09	-	nuc	0	Cytoplasm				622
O00940 UniProt NPD GO	PGK_CONMG	Phosphoglycerate kinase (EC 2.7.2.3) (Fragment)	0.09	-	cyt	0					378
P41762 UniProt NPD GO	PGKG_TRYCO	Phosphoglycerate kinase, glycosomal (EC 2.7.2.3)	0.09	-	cyt	0	Glycosome				509
P36623 UniProt NPD GO	PMGY_SCHPO	Phosphoglycerate mutase (EC 5.4.2.1) (Phosphoglyceromutase) (PGAM) (MPGM) (BPG-dependent PGAM)	0.09	-	cyt	0				1FZT	211
P82971 UniProt NPD GO	PA2_BOMTE	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Allergen Bom t 1)	0.09	-	nuc	0	Secreted protein				136
P14420 UniProt NPD GO	PA21B_VIPAE	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Vipoxin non-toxic component) (V ...	0.09	-	nuc	0	Secreted protein			1RGB	122
O42187 UniProt NPD GO	PA24_AGKHP	Phospholipase A2 B precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (BPLA(2))	0.09	-	end	1 *	Secreted protein (By similarity)			1JIA	138
P19000 UniProt NPD GO	PA21B_LATLA	Phospholipase A2 P'513 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.09	-	exc	1 *	Secreted protein				145
O42188 UniProt NPD GO	PA29_AGKHP	Phospholipase A2 homolog	0.09	-	nuc	0	Secreted protein (By similarity)				122
Q9PUH3 UniProt NPD GO	PA211_AUSSU	Phospholipase A2 isozyme S13-69J precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA ...	0.09	-	exc	0	Secreted protein (By similarity)				146
Q9PUH1 UniProt NPD GO	PA213_AUSSU	Phospholipase A2 isozyme S14-72F precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA ...	0.09	-	exc	0	Secreted protein (By similarity)				146
Q9PUH7 UniProt NPD GO	PA27_AUSSU	Phospholipase A2 isozyme S15-109 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA ...	0.09	-	exc	0	Secreted protein (By similarity)				144
P59359 UniProt NPD GO	PA21B_AUSSU	Phospholipase A2 isozyme S2-22 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.09	-	exc	0	Secreted protein (By similarity)				145
Q9PUH2 UniProt NPD GO	PA212_AUSSU	Phospholipase A2 isozyme S4-30 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA12 ...	0.09	-	exc	0	Secreted protein (By similarity)				146
Q9PUI0 UniProt NPD GO	PA24_AUSSU	Phospholipase A2 isozyme S7-48J precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA4 ...	0.09	-	exc	0	Secreted protein (By similarity)				147
P45881 UniProt NPD GO	PA21B_BOTJR	Phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (BJUPLA2)	0.09	-	end	0	Secreted protein				138
P04054 UniProt NPD GO	PA21B_HUMAN	Phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Group IB phospholipas ...	0.09	-	exc	0	Secreted protein		172410		148
Q90W39 UniProt NPD GO	PA2A_TRIMU	Phospholipase A2 trimucrotoxin precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.09	-	end	1 *	Secreted protein				138
Q45Z26 UniProt NPD GO	PA25_TROCA	Phospholipase A2, acidic 5 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase 5) (PLA-5)	0.09	-	exc	1 *	Secreted protein				151
P00617 UniProt NPD GO	PA21B_BUNMU	Phospholipase A2, beta bungarotoxin A1 chain precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydro ...	0.09	-	exc	0	Secreted protein			1BUN	147
P17934 UniProt NPD GO	PA24_BUNMU	Phospholipase A2, beta bungarotoxin A4 chain precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydro ...	0.09	-	exc	0	Secreted protein				147
Q9PU97 UniProt NPD GO	PA27_BUNMU	Phospholipase A2, beta bungarotoxin A7 chain precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydro ...	0.09	-	nuc	0	Secreted protein (By similarity)				137
P14422 UniProt NPD GO	PA2GA_RABIT	Phospholipase A2, membrane associated (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Group IIA ...	0.09	-	cyt	0	Membrane; peripheral membrane protein				68
P14421 UniProt NPD GO	PA23_AGKHP	Phospholipase A2, neutral (EC 3.1.1.4) (Agkistrotoxin) (ATX) (Phosphatidylcholine 2-acylhydrolase)	0.09	-	nuc	0	Secreted protein			1BJJ	122
Q9NRY6 UniProt NPD GO	PLS3_HUMAN	Phospholipid scramblase 3 (PL scramblase 3) (Ca(2+)-dependent phospholipid scramblase 3)	0.09	-	cyt	0	Membrane; single-pass type II membrane protein (By similarity)	plasma membrane [NAS]	607611		295
P52424 UniProt NPD GO	PUR5_VIGUN	Phosphoribosylformylglycinamidine cyclo-ligase, chloroplast/mitochondrial precursor (EC 6.3.3.1) (AI ...	0.09	-	mit	0	Plastid; chloroplast. Mitochondrion				388
P12205 UniProt NPD GO	YCF4_MARPO	Photosystem I assembly protein ycf4	0.09	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
Q9M3L5 UniProt NPD GO	YCF4_SPIOL	Photosystem I assembly protein ycf4	0.09	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
O96800 UniProt NPD GO	PSAD_SKECO	Photosystem I reaction center subunit II (Photosystem I 16 kDa polypeptide) (PSI-D)	0.09	-	nuc	0	Plastid; chloroplast				139
Q39615 UniProt NPD GO	PSAD_CHLRE	Photosystem I reaction center subunit II, chloroplast precursor (Photosystem I 20 kDa subunit) (PSI- ...	0.09	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Stromal side (By ...				196
P20119 UniProt NPD GO	PSAF_PEA	Photosystem I reaction center subunit III (Light-harvesting complex I 17 kDa protein) (PSI-F) (Fragm ...	0.09	-		0	Plastid; chloroplast; chloroplast thylakoid lumen				20
Q9S831 UniProt NPD GO	PSAE1_ARATH	Photosystem I reaction center subunit IV A, chloroplast precursor (PSI-E A)	0.09	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				143
O65101 UniProt NPD GO	PSAH_MAIZE	Photosystem I reaction center subunit VI, chloroplast precursor (PSI-H) (Light-harvesting complex I ...	0.09	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				142
P22179 UniProt NPD GO	PSAH_SPIOL	Photosystem I reaction center subunit VI, chloroplast precursor (PSI-H) (Light-harvesting complex I ...	0.09	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				144
O82660 UniProt NPD GO	P2SAF_ARATH	Photosystem II stability/assembly factor HCF136, chloroplast precursor	0.09	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; lumenal side. Res ...				403
P54982 UniProt NPD GO	CRTI_PHYBL	Phytoene dehydrogenase (EC 1.14.99.-) (Phytoene desaturase)	0.09	-	nuc	1					583
Q40406 UniProt NPD GO	CRTI_NARPS	Phytoene dehydrogenase, chloroplast precursor (EC 1.14.99.-) (Phytoene desaturase)	0.09	-	cyt	0	Plastid; chloroplast. Plastid; chromoplast. Exists as an inactive soluble form and an active membran ...				570
P09929 UniProt NPD GO	PDH_ROMMI	Pigment-dispersing factor precursor [Contains: PDF precursor-related peptide; Pigment-dispersing fac ...	0.09	-	exc	1 *	Secreted protein				89
Q12645 UniProt NPD GO	PID9_FUSSO	Pisatin demethylase (EC 1.14.-.-) (Cytochrome P450 57A1)	0.09	-	nuc	1 *					515
Q9JI48 UniProt NPD GO	PLAC8_MOUSE	Placenta-specific gene 8 protein (C15 protein) (Onzin)	0.09	-	exc	0					112
P19203 UniProt NPD GO	PLSC_PHYPO	Plasmin C precursor	0.09	-	exc	0					150
P68401 UniProt NPD GO	PA1B2_BOVIN	Platelet-activating factor acetylhydrolase IB subunit beta (EC 3.1.1.47) (PAF acetylhydrolase 30 kDa ...	0.09	-	cyt	0	Cytoplasm			1FXW	229
P68402 UniProt NPD GO	PA1B2_HUMAN	Platelet-activating factor acetylhydrolase IB subunit beta (EC 3.1.1.47) (PAF acetylhydrolase 30 kDa ...	0.09	-	cyt	0	Cytoplasm		602508	1VYH	229
O35264 UniProt NPD GO	PA1B2_RAT	Platelet-activating factor acetylhydrolase IB subunit beta (EC 3.1.1.47) (PAF acetylhydrolase 30 kDa ...	0.09	-	cyt	0	Cytoplasm (By similarity)				229
Q29460 UniProt NPD GO	PA1B3_BOVIN	Platelet-activating factor acetylhydrolase IB subunit gamma (EC 3.1.1.47) (PAF acetylhydrolase 29 kD ...	0.09	-	cyt	0	Cytoplasm			1WAB	232
Q22943 UniProt NPD GO	PAFA_CAEEL	Platelet-activating factor acetylhydrolase homolog 2 (EC 3.1.1.47)	0.09	-	mit	0					388
P27762 UniProt NPD GO	MPAA2_AMBAR	Pollen allergen Amb a 2 precursor (Antigen K) (Antigen Amb a II)	0.09	-	exc	0					397
P48978 UniProt NPD GO	PGLR_MALDO	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.09	-	exc	1 *	Secreted protein				460

You are viewing entries 66751 to 66800 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.