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
P92980 UniProt NPD GO	APR3_ARATH	5'-adenylylsulfate reductase 3, chloroplast precursor (EC 1.8.4.9) (Adenosine 5'-phosphosulfate 5'-a ...	0.03	-	mit	0	Plastid; chloroplast (Potential)				458
P97267 UniProt NPD GO	5HT2B_CAVPO	5-hydroxytryptamine 2B receptor (5-HT-2B) (Serotonin receptor 2B) (5-HT2B) (Fragment)	0.03	-	nuc	1 *	Membrane; multi-pass membrane protein				96
P32304 UniProt NPD GO	5HT7R_MOUSE	5-hydroxytryptamine 7 receptor (5-HT-7) (Serotonin receptor 7) (5-HT-X) (5HT7)	0.03	-	end	7	Membrane; multi-pass membrane protein				448
O22386 UniProt NPD GO	RK12_ORYSA	50S ribosomal protein L12, chloroplast precursor (CL12)	0.03	-	mit	0	Plastid; chloroplast				185
Q02764 UniProt NPD GO	RK24_TOBAC	50S ribosomal protein L24, chloroplast precursor (CL24)	0.03	-	nuc	0	Plastid; chloroplast				187
P41573 UniProt NPD GO	6PGD_DROSI	6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44)	0.03	-	cyt	0					481
P00349 UniProt NPD GO	6PGD_SHEEP	6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44)	0.03	-	cyt	0				2PGD	482
Q9R1Z7 UniProt NPD GO	PTPS_MOUSE	6-pyruvoyl tetrahydrobiopterin synthase (EC 4.2.3.12) (PTPS) (PTP synthase)	0.03	-	mit	0					144
P80081 UniProt NPD GO	PTPS_SALSA	6-pyruvoyl tetrahydrobiopterin synthase (EC 4.2.3.12) (PTPS) (PTP synthase) (Fragments)	0.03	-	cyt	0					103
P27213 UniProt NPD GO	PTPS_RAT	6-pyruvoyl tetrahydrobiopterin synthase precursor (EC 4.2.3.12) (PTPS) (PTP synthase)	0.03	-	mit	0				1GTQ	144
P39097 UniProt NPD GO	RLA0_LEIIN	60S acidic ribosomal protein P0	0.03	-	nuc	0					323
O24573 UniProt NPD GO	RLA0_MAIZE	60S acidic ribosomal protein P0	0.03	-	cyt	0					318
Q9C3Z6 UniProt NPD GO	RLA0_PODAN	60S acidic ribosomal protein P0	0.03	-	mit	0					314
P50346 UniProt NPD GO	RLA0_SOYBN	60S acidic ribosomal protein P0	0.03	-	cyt	0					320
P26796 UniProt NPD GO	RLA0_TRYCR	60S acidic ribosomal protein P0	0.03	-	nuc	0					323
P19889 UniProt NPD GO	RLA0_DROME	60S acidic ribosomal protein P0 (DNA-(apurinic or apyrimidinic site) lyase) (EC 4.2.99.18) (Apurinic ...	0.03	-	cyt	0	Cytoplasm. Nucleus	cytosolic ribosome (sensu Eukaryota) [NAS]			317
Q42112 UniProt NPD GO	RLA02_ARATH	60S acidic ribosomal protein P0-2	0.03	-	cyt	0					320
P57691 UniProt NPD GO	RLA03_ARATH	60S acidic ribosomal protein P0-3	0.03	-	cyt	0					323
O46313 UniProt NPD GO	RLA1_LEIPE	60S acidic ribosomal protein P1	0.03	-	cyt	0					107
P17476 UniProt NPD GO	RLA1_SCHPO	60S acidic ribosomal protein P1-alpha 1 (A1)	0.03	-	cyt	0					109
P17477 UniProt NPD GO	RLA3_SCHPO	60S acidic ribosomal protein P1-alpha 3 (A3)	0.03	-	cyt	0					110
P90703 UniProt NPD GO	RLA2_BRUMA	60S acidic ribosomal protein P2	0.03	-	cyt	0					114
Q9SLF7 UniProt NPD GO	RLA22_ARATH	60S acidic ribosomal protein P2-2	0.03	-	cyt	0					115
P17478 UniProt NPD GO	RLA4_SCHPO	60S acidic ribosomal protein P2-beta (A4)	0.03	-	cyt	0					110
Q9SW75 UniProt NPD GO	RL10A_CHLRE	60S ribosomal protein L10a	0.03	+	cyt	0					213
O15613 UniProt NPD GO	RL10A_ENTHI	60S ribosomal protein L10a (Fragment)	0.03	-	nuc	0					165
P61865 UniProt NPD GO	RL12_CAEBR	60S ribosomal protein L12	0.03	-	cyt	0					165
P61866 UniProt NPD GO	RL12_CAEEL	60S ribosomal protein L12	0.03	-	cyt	0					165
P50884 UniProt NPD GO	RL12_CHLRE	60S ribosomal protein L12 (Fragment)	0.03	-	cyt	0					157
P49628 UniProt NPD GO	RL21_XENLA	60S ribosomal protein L21 (Fragment)	0.03	-	mit	0					33
Q6C4U7 UniProt NPD GO	RL30_YARLI	60S ribosomal protein L30	0.03	-	mit	0					109
Q9USG6 UniProt NPD GO	RL33B_SCHPO	60S ribosomal protein L33-B (L37B)	0.03	-	nuc	0					108
Q90YT3 UniProt NPD GO	RL35A_ICTPU	60S ribosomal protein L35a	0.03	-	mit	0					110
O15574 UniProt NPD GO	RL8_ENTHI	60S ribosomal protein L8 (60S ribosomal protein L2) (Fragment)	0.03	-	nuc	0					158
Q963B7 UniProt NPD GO	RL9_SPOFR	60S ribosomal protein L9	0.03	-	cyt	0					190
P05738 UniProt NPD GO	RL9A_YEAST	60S ribosomal protein L9-A (L8) (YL11) (RP25)	0.03	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	191
O74905 UniProt NPD GO	RL9B_SCHPO	60S ribosomal protein L9-B	0.03	-	cyt	0					189
P25420 UniProt NPD GO	CH63_HELVI	63 kDa chaperonin, mitochondrial precursor (p63)	0.03	-	mit	0	Mitochondrion				569
P82436 UniProt NPD GO	CWP28_TOBAC	65 kDa cell wall protein (Fragment)	0.03	-		0	Cell wall				11
P80751 UniProt NPD GO	CWP01_DAUCA	66 kDa cell wall protein (Fragment)	0.03	-		0	Cell wall				9
P82442 UniProt NPD GO	CWP34_TOBAC	68 kDa cell wall protein (Fragment)	0.03	-		0	Cell wall				15
O88455 UniProt NPD GO	DHCR7_MOUSE	7-dehydrocholesterol reductase (EC 1.3.1.21) (7-DHC reductase) (Sterol delta-7-reductase)	0.03	-	mit	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				471
Q9UBM7 UniProt NPD GO	DHCR7_HUMAN	7-dehydrocholesterol reductase (EC 1.3.1.21) (7-DHC reductase) (Sterol delta-7-reductase) (Putative ...	0.03	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA] nuclear outer membrane [IDA]	602858		475
P81424 UniProt NPD GO	FA71_TETPY	71 kDa F-actin-binding protein (Fragment)	0.03	-	cyt	0					21
P29241 UniProt NPD GO	NADA_APLCA	ADP-ribosyl cyclase precursor (EC 3.2.2.5) (NAD(+) nucleosidase) (NADase) (NAD glycohydrolase) (ADRC ...	0.03	-	vac	0	Localized to vesicles or granules within ova of all stages			1R16	282
P22274 UniProt NPD GO	ARF_CANAL	ADP-ribosylation factor	0.03	-	cyt	0					178
O48920 UniProt NPD GO	ARF_VIGUN	ADP-ribosylation factor	0.03	-	cyt	0					180
P36397 UniProt NPD GO	ARF1_ARATH	ADP-ribosylation factor 1	0.03	-	cyt	0					180
Q94650 UniProt NPD GO	ARF1_PLAFA	ADP-ribosylation factor 1	0.03	-	nuc	0					180
Q25761 UniProt NPD GO	ARF1_PLAFO	ADP-ribosylation factor 1	0.03	-	nuc	0					180

You are viewing entries 78901 to 78950 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.