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
O13287 UniProt NPD GO	6PGD_CANAL	6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44)	0.01	-	nuc	0					517
P78812 UniProt NPD GO	6PGD_SCHPO	6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44)	0.01	-	cyt	0					492
P19407 UniProt NPD GO	OEC6_SPIOL	6.7 kDa chloroplast outer envelope membrane protein (E 6.7)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein				62
P80765 UniProt NPD GO	CWP06_PHAVU	60 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				9
P26317 UniProt NPD GO	CH60_HELVI	60 kDa chaperonin, mitochondrial (P60) (Fragment)	0.01	-	cyt	0	Mitochondrion				24
P39096 UniProt NPD GO	RLA0_LEICH	60S acidic ribosomal protein P0	0.01	-	nuc	0					322
Q95140 UniProt NPD GO	RLA0_BOVIN	60S acidic ribosomal protein P0 (L10E)	0.01	-	cyt	0					318
Q9PV90 UniProt NPD GO	RLA0_BRARE	60S acidic ribosomal protein P0 (L10E)	0.01	-	cyt	0					319
P05388 UniProt NPD GO	RLA0_HUMAN	60S acidic ribosomal protein P0 (L10E)	0.01	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]	180510		317
Q9DG68 UniProt NPD GO	RLA0_RANSY	60S acidic ribosomal protein P0 (L10E)	0.01	-	cyt	0					315
P05317 UniProt NPD GO	RLA0_YEAST	60S acidic ribosomal protein P0 (L10E)	0.01	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			312
P27464 UniProt NPD GO	RLA1_POLPE	60S acidic ribosomal protein P1 (A1)	0.01	-	cyt	0					103
P50344 UniProt NPD GO	RLA1_CLAHE	60S acidic ribosomal protein P1 (Allergen Cla h 12) (Cla h XII)	0.01	-	cyt	0					110
P02402 UniProt NPD GO	RLA1_ARTSA	60S acidic ribosomal protein P1 (EL12'/ EL12'-P)	0.01	-	cyt	0					109
P52855 UniProt NPD GO	RLA1_MAIZE	60S acidic ribosomal protein P1 (L12)	0.01	-	cyt	0					109
Q9HFQ7 UniProt NPD GO	RLA1_CANAL	60S acidic ribosomal protein P1-A (CaRP1A)	0.01	-	cyt	0					106
Q9HFQ6 UniProt NPD GO	RLA3_CANAL	60S acidic ribosomal protein P1-B (CaRP1B)	0.01	-	cyt	0					108
P10622 UniProt NPD GO	RLA3_YEAST	60S acidic ribosomal protein P1-beta (L44') (L12EIIB)	0.01	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			105
P42899 UniProt NPD GO	RLA2_BOVIN	60S acidic ribosomal protein P2	0.01	-	mit	0					115
O01725 UniProt NPD GO	RLA2_BRAFL	60S acidic ribosomal protein P2	0.01	-	vac	0					116
O01504 UniProt NPD GO	RLA2_CAEEL	60S acidic ribosomal protein P2	0.01	-	exc	0					107
Q967Y9 UniProt NPD GO	RLA2_EIMTE	60S acidic ribosomal protein P2	0.01	-	cyt	0					114
Q6X9Z5 UniProt NPD GO	RLA2_HORSE	60S acidic ribosomal protein P2	0.01	-	cyt	0					115
P99027 UniProt NPD GO	RLA2_MOUSE	60S acidic ribosomal protein P2	0.01	-	mit	0					115
O00806 UniProt NPD GO	RLA2_PLAFA	60S acidic ribosomal protein P2	0.01	-	cyt	0					112
Q9C3Z5 UniProt NPD GO	RLA2_PODAN	60S acidic ribosomal protein P2	0.01	-	exc	0					111
P02401 UniProt NPD GO	RLA2_RAT	60S acidic ribosomal protein P2	0.01	-	cyt	0					115
P50879 UniProt NPD GO	RLA2_TAESO	60S acidic ribosomal protein P2	0.01	-	nuc	0					121
P51408 UniProt NPD GO	RLA2_TRYBB	60S acidic ribosomal protein P2	0.01	-	cyt	0					107
P19943 UniProt NPD GO	RLA2_RABIT	60S acidic ribosomal protein P2 (Acidic phosphoprotein P3) (Fragment)	0.01	-	exc	0					44
O43940 UniProt NPD GO	RLA2_LEIDO	60S acidic ribosomal protein P2 (Acidic ribosomal protein 1)	0.01	-	cyt	0					105
Q96UQ7 UniProt NPD GO	RLA2_RHOGU	60S acidic ribosomal protein P2 (Acyl carrier protein)	0.01	-	exc	0	Cytoplasm	ribosome [NAS]			110
Q9UUZ6 UniProt NPD GO	RLA2_ASPFU	60S acidic ribosomal protein P2 (Allergen Asp f 8) (AfP2)	0.01	-	exc	0					111
P02399 UniProt NPD GO	RLA2_ARTSA	60S acidic ribosomal protein P2 (EL12)	0.01	-	cyt	0					111
P05387 UniProt NPD GO	RLA2_HUMAN	60S acidic ribosomal protein P2 (NY-REN-44 antigen)	0.01	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]	180530	1S4J	115
Q06383 UniProt NPD GO	RLA2_LEIIN	60S acidic ribosomal protein P2-1	0.01	-	cyt	0					106
P26795 UniProt NPD GO	RLA3_TRYCR	60S acidic ribosomal protein P2-B (P2B)	0.01	-	cyt	0					112
P02400 UniProt NPD GO	RLA4_YEAST	60S acidic ribosomal protein P2-beta (L45) (YL44C) (YPA1) (L12EIA)	0.01	-	exc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			110
Q8L9S1 UniProt NPD GO	R18A1_ARATH	60S ribosomal protein L18a-1	0.01	-	end	2					158
P52816 UniProt NPD GO	RL23_ONCVO	60S ribosomal protein L23 (Fragment)	0.01	-	cyt	0					48
P51419 UniProt NPD GO	RL273_ARATH	60S ribosomal protein L27-3	0.01	-	cyt	0					135
Q08962 UniProt NPD GO	NIP7_YEAST	60S ribosome subunit biogenesis protein NIP7	0.01	-	cyt	0	Cytoplasm. Nucleus; nucleolus	cytosolic large ribosomal subunit (sensu Eu... [TAS] nucleolus [TAS]			181
P80817 UniProt NPD GO	CWP21_LYCES	64 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				14
P80798 UniProt NPD GO	CWP01_LYCES	65 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				15
P80782 UniProt NPD GO	CWP05_TOBAC	66 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				13
P81421 UniProt NPD GO	ODP2_SOLTU	78 kDa dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (EC ...	0.01	-	nuc	0	Mitochondrion; mitochondrial matrix				21
P80814 UniProt NPD GO	CWP18_LYCES	80 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				10
P80833 UniProt NPD GO	CWP11_ARATH	96 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				10
O00909 UniProt NPD GO	ARF1_DICDI	ADP-ribosylation factor 1	0.01	-	nuc	0					181
Q9JKX6 UniProt NPD GO	NUDT5_MOUSE	ADP-sugar pyrophosphatase (EC 3.6.1.13) (EC 3.6.1.-) (Nucleoside diphosphate-linked moiety X motif 5 ...	0.01	-	cyt	0					218

You are viewing entries 86401 to 86450 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.