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
P24157 UniProt NPD GO	ACCO4_LYCES	1-aminocyclopropane-1-carboxylate oxidase 4 (EC 1.14.17.4) (ACC oxidase 4) (Ethylene-forming enzyme) ...	0.02	-	cyt	0					316
Q01912 UniProt NPD GO	1A1C_PHAAU	1-aminocyclopropane-1-carboxylate synthase (EC 4.4.1.14) (ACC synthase) (S-adenosyl-L-methionine met ...	0.02	-	cyt	0					368
Q06402 UniProt NPD GO	1A12_ARATH	1-aminocyclopropane-1-carboxylate synthase 2 (EC 4.4.1.14) (ACC synthase 2) (S-adenosyl-L-methionine ...	0.02	-	cyt	0					496
P21671 UniProt NPD GO	PIP7_BOVIN	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta 2 (EC 3.1.4.11) (Phosphoinositide ph ...	0.02	-	cyt	0					37
P82445 UniProt NPD GO	CWP37_TOBAC	10 kDa cell wall protein (Fragment)	0.02	-		0	Cell wall				7
Q96539 UniProt NPD GO	CH10_BRANA	10 kDa chaperonin (Protein CPN10) (Protein groES)	0.02	-	nuc	0	Cytoplasm (Potential)				98
Q37761 UniProt NPD GO	CH10_CYAPA	10 kDa chaperonin (Protein Cpn10) (groES protein)	0.02	-	cyt	0	Plastid; cyanelle				103
O59804 UniProt NPD GO	CH10_SCHPO	10 kDa heat shock protein, mitochondrial (HSP10) (10 kDa chaperonin)	0.02	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P18646 UniProt NPD GO	10KD_VIGUN	10 kDa protein precursor (Clone PSAS10)	0.02	-	exc	1 *					75
P22943 UniProt NPD GO	HSP12_YEAST	12 kDa heat shock protein (Glucose and lipid-regulated protein)	0.02	-	mit	0		cytoplasm [IDA] nucleus [IDA] plasma membrane [IDA]			109
P83468 UniProt NPD GO	PHP14_RABIT	14 kDa phosphohistidine phosphatase (EC 3.1.3.-) (Phosphohistidine phosphatase 1) (Protein histidine ...	0.02	-	cyt	0	Cytoplasm (By similarity)	cytosol [ISS]			125
P42856 UniProt NPD GO	ZB14_MAIZE	14 kDa zinc-binding protein (Protein kinase C inhibitor) (PKCI)	0.02	-	cyt	0					128
P42855 UniProt NPD GO	ZB14_BRAJU	14 kDa zinc-binding protein (Protein kinase C inhibitor) (PKCI) (Fragment)	0.02	-	cyt	0					113
Q6ZKC0 UniProt NPD GO	14333_ORYSA	14-3-3-like protein GF14-C (G-box factor 14-3-3 homolog C)	0.02	-	cyt	0	Cytoplasm. Nucleus				256
O18518 UniProt NPD GO	ES15_HAECO	15 kDa excretory/secretory protein precursor (15 kDa ES)	0.02	-	exc	0	Secreted protein				148
P15428 UniProt NPD GO	PGDH_HUMAN	15-hydroxyprostaglandin dehydrogenase [NAD+] (EC 1.1.1.141) (PGDH) (Prostaglandin dehydrogenase 1)	0.02	-	cyt	0	Cytoplasm	cytosol [TAS]	601688	2GDZ	266
Q8MJY8 UniProt NPD GO	PGDH_MACFA	15-hydroxyprostaglandin dehydrogenase [NAD+] (EC 1.1.1.141) (PGDH) (Prostaglandin dehydrogenase 1)	0.02	-	cyt	0	Cytoplasm (By similarity)	cytosol [ISS]			266
Q9ZT46 UniProt NPD GO	PP16B_CUCMA	16 kDa phloem protein 2	0.02	-	cyt	0					137
P68514 UniProt NPD GO	YMX1_RAPSA	16.0 kDa protein (ORF138)	0.02	-	nuc	1 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein				138
P19036 UniProt NPD GO	HSP11_ARATH	17.4 kDa class I heat shock protein (HSP 17.4)	0.02	-	cyt	0	Cytoplasm				156
P13853 UniProt NPD GO	HSP12_ARATH	17.6 kDa class I heat shock protein (HSP 17.6)	0.02	-	cyt	0	Cytoplasm				157
P19037 UniProt NPD GO	HSP13_ARATH	18.2 kDa class I heat shock protein (HSP 18.2)	0.02	-	cyt	0	Cytoplasm				161
Q42908 UniProt NPD GO	PMGI_MESCR	2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.1) (Phosphoglyceromutase) (BPG ...	0.02	-	nuc	0	Cytoplasm				559
P35493 UniProt NPD GO	PMGI_RICCO	2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.1) (Phosphoglyceromutase) (BPG ...	0.02	-	cyt	0	Cytoplasm				556
Q9CQ62 UniProt NPD GO	DECR_MOUSE	2,4-dienoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.34) (2,4-dienoyl-CoA reductase [NADPH]) ...	0.02	-	mit	0	Mitochondrion (By similarity)	mitochondrion [IDA]			335
Q64591 UniProt NPD GO	DECR_RAT	2,4-dienoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.34) (2,4-dienoyl-CoA reductase [NADPH]) ...	0.02	-	mit	0	Mitochondrion				335
Q01284 UniProt NPD GO	2NPD_NEUCR	2-nitropropane dioxygenase precursor (EC 1.13.11.32) (Nitroalkane oxidase) (2-NPD)	0.02	-	cyt	0					378
Q41364 UniProt NPD GO	SOT1_SPIOL	2-oxoglutarate/malate translocator, chloroplast precursor	0.02	-	end	13	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein				569
P19244 UniProt NPD GO	HSP41_PEA	22.7 kDa class IV heat shock protein precursor	0.02	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Probable). In the endomembrane, probably in the ...				197
P80819 UniProt NPD GO	CWP23_LYCES	23 kDa cell wall protein (Fragment)	0.02	-		0	Cell wall				14
P82430 UniProt NPD GO	CWP22_TOBAC	25 kDa cell wall protein (Fragment)	0.02	-		0	Cell wall				15
P91799 UniProt NPD GO	IM25_SCHJA	25 kDa integral membrane protein (Sj25) (Sj25/TM4)	0.02	-	end	4 *	Membrane; multi-pass membrane protein	integral to membrane of membrane fraction [NAS]			224
P80851 UniProt NPD GO	CWP31_ARATH	27 kDa cell wall protein (Fragment)	0.02	-		0	Cell wall				18
P83632 UniProt NPD GO	P27K_GALME	27 kDa hemolymph protein precursor (P27K) (27k)	0.02	-	mit	0	Secreted protein				236
P82919 UniProt NPD GO	RT18A_BOVIN	28S ribosomal protein S18a, mitochondrial (MRP-S18-a) (Mrps18a) (MRP-S18-3) (Fragments)	0.02	-	cyt	0	Mitochondrion				36
O35296 UniProt NPD GO	3BHS3_MESAU	3 beta-hydroxysteroid dehydrogenase type 3 (3 beta-hydroxysteroid dehydrogenase type III) (3Beta-HSD ...	0.02	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...				372
Q9EQC1 UniProt NPD GO	3BHS7_MOUSE	3 beta-hydroxysteroid dehydrogenase type 7 (3 beta-hydroxysteroid dehydrogenase type VII) (3Beta-HSD ...	0.02	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				369
P14893 UniProt NPD GO	3BHS_BOVIN	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase (3Beta-HSD) [Includes: 3-beta-hydroxy-delt ...	0.02	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...	smooth endoplasmic reticulum membrane [IDA]			372
Q9Z1N4 UniProt NPD GO	BPNT1_RAT	3'(2'),5'-bisphosphate nucleotidase 1 (EC 3.1.3.7) (Bisphosphate 3'-nucleotidase 1) (PAP-inositol-1, ...	0.02	-	mit	0				1JP4	308
O60181 UniProt NPD GO	RIB3_SCHPO	3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase)	0.02	-	cyt	0					204
O02691 UniProt NPD GO	HCD2_BOVIN	3-hydroxyacyl-CoA dehydrogenase type-2 (EC 1.1.1.35) (3-hydroxyacyl-CoA dehydrogenase type II) (Type ...	0.02	-	mit	0	Mitochondrion	mitochondrion [ISS]			260
O08756 UniProt NPD GO	HCD2_MOUSE	3-hydroxyacyl-CoA dehydrogenase type-2 (EC 1.1.1.35) (3-hydroxyacyl-CoA dehydrogenase type II) (Type ...	0.02	-	mit	0		endoplasmic reticulum [IDA] mitochondrial inner membrane [IDA] mitochondrion [IDA]			260
O70351 UniProt NPD GO	HCD2_RAT	3-hydroxyacyl-CoA dehydrogenase type-2 (EC 1.1.1.35) (3-hydroxyacyl-CoA dehydrogenase type II) (Type ...	0.02	-	mit	0	Mitochondrion (By similarity)	mitochondrion [ISS]		1E6W	260
Q9HDQ5 UniProt NPD GO	LEU3_CANRU	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.02	-	cyt	0	Cytoplasm				359
O94114 UniProt NPD GO	LEU3_PICST	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.02	-	cyt	0	Cytoplasm				373
Q6TWC4 UniProt NPD GO	LEU3_SORMA	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.02	-	cyt	0	Cytoplasm				368
P41926 UniProt NPD GO	LEU3_YAMOH	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.02	-	cyt	0	Cytoplasm				368
Q96WI0 UniProt NPD GO	LEU3_ZYGRO	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.02	-	cyt	0	Cytoplasm				362
Q74ZZ0 UniProt NPD GO	ERG27_ASHGO	3-keto-steroid reductase (EC 1.1.1.270)	0.02	-	cyt	1					348
Q758B6 UniProt NPD GO	TSC10_ASHGO	3-ketodihydrosphingosine reductase TSC10 (EC 1.1.1.102) (3-dehydrosphinganine reductase) (KDS reduct ...	0.02	-	cyt	1	Endoplasmic reticulum (By similarity)				307

You are viewing entries 82101 to 82150 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.