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
P53247 UniProt NPD GO	YG2E_YEAST	Putative uncharacterized protein YGR073C	0.03	-	mit	0	Membrane; multi-pass membrane protein (Potential)				123
Q9FKL8 UniProt NPD GO	XTH13_ARATH	Putative xyloglucan endotransglucosylase/hydrolase protein 13 precursor (EC 2.4.1.207) (At-XTH13) (X ...	0.03	-	exc	0	Secreted protein; extracellular space; apoplast (Probable)				284
Q9SVV2 UniProt NPD GO	XTH26_ARATH	Putative xyloglucan endotransglucosylase/hydrolase protein 26 precursor (EC 2.4.1.207) (At-XTH26) (X ...	0.03	-	end	0	Secreted protein; extracellular space; apoplast (Probable)				292
O14295 UniProt NPD GO	PLR1_SCHPO	Pyridoxal reductase (EC 1.1.1.65) (PL reductase) (PL-red)	0.03	-	nuc	0		membrane [NAS]			333
Q9AT63 UniProt NPD GO	PDX1_GINBI	Pyridoxin biosynthesis protein PDX1 (Sor-like protein)	0.03	-	cyt	0					309
Q9NXJ5 UniProt NPD GO	PGPI_HUMAN	Pyroglutamyl-peptidase 1 (EC 3.4.19.3) (Pyroglutamyl-peptidase I) (Pyrrolidone-carboxylate peptidase ...	0.03	-	cyt	0	Cytoplasm (By similarity)				209
Q9ESW8 UniProt NPD GO	PGPI_MOUSE	Pyroglutamyl-peptidase 1 (EC 3.4.19.3) (Pyroglutamyl-peptidase I) (Pyrrolidone-carboxylate peptidase ...	0.03	-	cyt	0	Cytoplasm (By similarity)				209
P82691 UniProt NPD GO	PPK1_PERAM	Pyrokinin-1 (Pea-PK-1) (FXPRL-amide)	0.03	-		0	Secreted protein				9
P82619 UniProt NPD GO	PPK4_PERAM	Pyrokinin-4 (Pea-PK-4) (YXPRL-amide)	0.03	-		0	Secreted protein				12
P84410 UniProt NPD GO	PPK4_BLAOR	Pyrokinin-4 (YXPRL-amide)	0.03	-		0	Secreted protein				12
P84415 UniProt NPD GO	PPK4_DEREJ	Pyrokinin-4 (YXPRL-amide)	0.03	-		0	Secreted protein				12
P84414 UniProt NPD GO	PPK4_DERER	Pyrokinin-4 (YXPRL-amide)	0.03	-		0	Secreted protein				12
P84416 UniProt NPD GO	PPK4_DERKE	Pyrokinin-4 (YXPRL-amide)	0.03	-		0	Secreted protein				12
P84413 UniProt NPD GO	PPK4_EURFL	Pyrokinin-4 (YXPRL-amide)	0.03	-		0	Secreted protein				12
P84412 UniProt NPD GO	PPK4_NEORO	Pyrokinin-4 (YXPRL-amide)	0.03	-		0	Secreted protein				12
P84409 UniProt NPD GO	PPK4_PERAU	Pyrokinin-4 (YXPRL-amide)	0.03	-		0	Secreted protein				12
P84419 UniProt NPD GO	PPK4_PSEBJ	Pyrokinin-4 (YXPRL-amide)	0.03	-		0	Secreted protein				12
P84418 UniProt NPD GO	PPK4_PSEFO	Pyrokinin-4 (YXPRL-amide)	0.03	-		0	Secreted protein				12
P84417 UniProt NPD GO	PPK4_PSEFV	Pyrokinin-4 (YXPRL-amide)	0.03	-		0	Secreted protein				12
P84411 UniProt NPD GO	PPK4_SHELA	Pyrokinin-4 (YXPRL-amide)	0.03	-		0	Secreted protein				12
P84666 UniProt NPD GO	PPK5_APTFU	Pyrokinin-5 (Aptfu-PK-5) (FXPRL-amide)	0.03	-		0	Secreted protein				17
Q12641 UniProt NPD GO	P5CR_NEUCR	Pyrroline-5-carboxylate reductase (EC 1.5.1.2) (P5CR) (P5C reductase)	0.03	-	exc	0					311
Q5RAQ3 UniProt NPD GO	P5CR2_PONPY	Pyrroline-5-carboxylate reductase 2 (EC 1.5.1.2) (P5CR 2) (P5C reductase 2)	0.03	-	cyt	0					320
P87208 UniProt NPD GO	PDC_EMENI	Pyruvate decarboxylase (EC 4.1.1.1)	0.03	-	mit	0					566
P26267 UniProt NPD GO	ODPA_ASCSU	Pyruvate dehydrogenase E1 component alpha subunit type I, mitochondrial precursor (EC 1.2.4.1) (PDHE ...	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix				396
P11966 UniProt NPD GO	ODPB_BOVIN	Pyruvate dehydrogenase E1 component subunit beta (EC 1.2.4.1) (Fragment)	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix				24
P11177 UniProt NPD GO	ODPB_HUMAN	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial precursor (EC 1.2.4.1) (PDHE1-B)	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix		179060	1NI4	359
P32473 UniProt NPD GO	ODPB_YEAST	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial precursor (EC 1.2.4.1) (Pyruvate deh ...	0.03	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial nucleoid [IDA] mitochondrion [IDA] pyruvate dehydrogenase complex (sensu Eukar... [TAS]			366
P22439 UniProt NPD GO	ODPX_BOVIN	Pyruvate dehydrogenase protein X component (Dihydrolipoamide dehydrogenase-binding protein of pyruva ...	0.03	-	nuc	0	Mitochondrion; mitochondrial matrix				46
Q759A9 UniProt NPD GO	KPYK_ASHGO	Pyruvate kinase (EC 2.7.1.40) (PK)	0.03	-	cyt	0					501
Q12669 UniProt NPD GO	KPYK_ASPNG	Pyruvate kinase (EC 2.7.1.40) (PK)	0.03	-	cyt	0					526
Q27686 UniProt NPD GO	KPYK_LEIME	Pyruvate kinase (EC 2.7.1.40) (PK)	0.03	-	cyt	0				1PKL	499
P11979 UniProt NPD GO	KPYM_FELCA	Pyruvate kinase isozyme M1 (EC 2.7.1.40) (Pyruvate kinase muscle isozyme)	0.03	-	cyt	0				1PKM	530
Q7SIC2 UniProt NPD GO	QDOI_ASPJA	Quercetin 2,3-dioxygenase (EC 1.13.11.24) (2,3QD) (Quercetinase) (Flavonol 2,4-dioxygenase)	0.03	-	cyt	0				1JUH	350
P59859 UniProt NPD GO	PHCB_POLUR	R-phycocyanin beta chain	0.03	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen. Phycobilisome rod			1F99	172
P28559 UniProt NPD GO	PHEA_AGLNE	R-phycoerythrin alpha chain	0.03	-	cyt	0	Periphery of the rods of the phycobilisome				163
P68939 UniProt NPD GO	PHEB_PORTE	R-phycoerythrin beta chain	0.03	-	nuc	0	Periphery of the rods of the phycobilisome				177
P68940 UniProt NPD GO	PHEB_PORYE	R-phycoerythrin beta chain	0.03	-	nuc	0	Periphery of the rods of the phycobilisome				177
Q24814 UniProt NPD GO	RACA_ENTHI	RAS-related protein racA	0.03	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				196
O48670 UniProt NPD GO	RER1A_ARATH	RER1A protein (AtRER1A)	0.03	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				191
Q28446 UniProt NPD GO	RHL_HYLPI	RH-like protein (Rhesus-like protein)	0.03	-	end	8 *	Membrane; multi-pass membrane protein				353
Q8LBA0 UniProt NPD GO	ATL1Q_ARATH	RING-H2 finger protein ATL1Q	0.03	-	end	2 *					223
Q940X7 UniProt NPD GO	RBX1A_ARATH	RING-box protein 1a (RBX1a-At) (At-Rbx1;1) (RBX1-2)	0.03	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				118
P20755 UniProt NPD GO	HA2P_RABIT	RLA class II histocompatibility antigen, DP alpha-1 chain (D10 haplotype) (Fragment)	0.03	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)				226
Q6BVH4 UniProt NPD GO	TFB5_DEBHA	RNA polymerase II transcription factor B subunit 5 (General transcription and DNA repair factor IIH ...	0.03	-	cyt	0	Nucleus (By similarity)				69
Q8VIL2 UniProt NPD GO	RWDD3_MOUSE	RWD domain-containing protein 3	0.03	-	cyt	0					267
Q9LMK7 UniProt NPD GO	RBP1A_ARATH	Ran-binding protein 1 homolog a (Ran-binding protein siRanBP)	0.03	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity)				228
P29207 UniProt NPD GO	TKNA_RANRI	Ranakinin (Substance-P-related peptide)	0.03	-		0	Secreted protein				11
Q8QFQ4 UniProt NPD GO	RN2P_RANPI	Ranatuerin-2P precursor	0.03	-	exc	0	Secreted protein				71
P31582 UniProt NPD GO	RHA1_ARATH	Ras-related protein RHA1	0.03	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				200

You are viewing entries 81501 to 81550 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.