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
Q64433 UniProt NPD GO	CH10_MOUSE	10 kDa heat shock protein, mitochondrial (Hsp10) (10 kDa chaperonin) (CPN10)	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [ISS]			101
Q9W6X3 UniProt NPD GO	CH10_ORYLA	10 kDa heat shock protein, mitochondrial (Hsp10) (10 kDa chaperonin) (CPN10)	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				99
P26772 UniProt NPD GO	CH10_RAT	10 kDa heat shock protein, mitochondrial (Hsp10) (10 kDa chaperonin) (CPN10)	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA] mitochondrion [ISS]			101
P61604 UniProt NPD GO	CH10_HUMAN	10 kDa heat shock protein, mitochondrial (Hsp10) (10 kDa chaperonin) (CPN10) (Early-pregnancy factor ...	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]	600141		101
P48375 UniProt NPD GO	FKB12_DROME	12 kDa FK506-binding protein (EC 5.2.1.8) (FKBP) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rot ...	0.01	-	cyt	0	Cytoplasm				108
P83010 UniProt NPD GO	13KDA_TRISC	13 kDa protein (Fragment)	0.01	-		0	Microsome				13
P29498 UniProt NPD GO	FABP_SCHMA	14 kDa fatty acid-binding protein (Sm14)	0.01	-	cyt	0	Cytoplasm (By similarity)			1VYG	133
P14009 UniProt NPD GO	14KD_DAUCA	14 kDa proline-rich protein DC2.15 precursor	0.01	-	nuc	1 *					137
P80840 UniProt NPD GO	CWP19_ARATH	17 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				10
P04795 UniProt NPD GO	HSP15_SOYBN	17.6 kDa class I heat shock protein (HSP 17.6-L)	0.01	-	cyt	0	Cytoplasm				154
O04499 UniProt NPD GO	PMG1_ARATH	2,3-bisphosphoglycerate-independent phosphoglycerate mutase 1 (EC 5.4.2.1) (Phosphoglyceromutase 1) ...	0.01	-	cyt	0	Cytoplasm (By similarity)				557
P80346 UniProt NPD GO	DHBD_ASPNG	2,3-dihydroxybenzoic acid decarboxylase (EC 4.1.1.46) (DHBD) (o-pyrocatechuate decarboxylase) (2,3-D ...	0.01	-	cyt	0					292
O50044 UniProt NPD GO	KDSA_PEA	2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) (Phospho-2-dehydro-3-deoxyoctonate aldolase) ...	0.01	-	cyt	0	Cytoplasm (By similarity)				290
P38773 UniProt NPD GO	DOG2_YEAST	2-deoxyglucose-6-phosphate phosphatase 2 (EC 3.1.3.68) (2-DOG-6-P 2) (2-deoxyglucose-6-phosphatase 2 ...	0.01	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			246
Q64676 UniProt NPD GO	CGT_MOUSE	2-hydroxyacylsphingosine 1-beta-galactosyltransferase precursor (EC 2.4.1.45) (UDP-galactose-ceramid ...	0.01	-	end	2 *					541
Q09426 UniProt NPD GO	CGT_RAT	2-hydroxyacylsphingosine 1-beta-galactosyltransferase precursor (EC 2.4.1.45) (UDP-galactose-ceramid ...	0.01	-	end	2 *					541
Q9TEM3 UniProt NPD GO	PRPC_EMENI	2-methylcitrate synthase, mitochondrial precursor (EC 2.3.3.5) (Methylcitrate synthase) (Citrate syn ...	0.01	-	mit	0	Mitochondrion; mitochondrial matrix (Probable)	mitochondrial matrix [NAS]			460
P31233 UniProt NPD GO	CH10C_PEA	20 kDa chaperonin, chloroplast (Protein Cpn21) (Chloroplast protein Cpn10) (Chloroplast chaperonin 1 ...	0.01	-	cyt	0	Plastid; chloroplast				21
P81096 UniProt NPD GO	PC20_BRANA	20 kDa pollen coat protein (Fragment)	0.01	-		0					15
P80803 UniProt NPD GO	CWP06_LYCES	21 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				13
P80813 UniProt NPD GO	CWP17_LYCES	22 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				7
Q04620 UniProt NPD GO	OS24_PLABA	24 kDa ookinete surface protein precursor (Pbs21)	0.01	-	nuc	1	Cell membrane; lipid-anchor; GPI-anchor (Potential)				213
O82427 UniProt NPD GO	SMT2_ORYSA	24-methylenesterol C-methyltransferase 2 (EC 2.1.1.143) (24-sterol C-methyltransferase 2) (Sterol-C- ...	0.01	-	cyt	1 *					363
P80773 UniProt NPD GO	CWP14_PHAVU	26 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				15
P82441 UniProt NPD GO	CWP33_TOBAC	26 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				12
P80793 UniProt NPD GO	CWP16_TOBAC	28 kDa cell wall protein (Fragment)	0.01	-		0	Cell wall				15
P28644 UniProt NPD GO	ROC1_SPIOL	28 kDa ribonucleoprotein, chloroplast (28RNP)	0.01	-	cyt	0	Plastid; chloroplast				233
Q9H2F3 UniProt NPD GO	3BHS7_HUMAN	3 beta-hydroxysteroid dehydrogenase type 7 (3 beta-hydroxysteroid dehydrogenase type VII) (3Beta-HSD ...	0.01	-	cyt	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein		607765		369
P27365 UniProt NPD GO	3BHS_MACMU	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase (3Beta-HSD) [Includes: 3-beta-hydroxy-delt ...	0.01	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...				372
P26439 UniProt NPD GO	3BHS2_HUMAN	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type II (3Beta-HSD II) [Includes: 3-beta-h ...	0.01	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...	endoplasmic reticulum [NAS] integral to membrane [NAS] microsome [ISS] mitochondrial inner membrane [ISS] mitochondrial intermembrane space [ISS] smooth endoplasmic reticulum membrane [ISS]	201810		371
P32179 UniProt NPD GO	HAL2_YEAST	3'(2'),5'-bisphosphate nucleotidase (EC 3.1.3.7) (3'(2'),5-bisphosphonucleoside 3'(2')-phosphohydrol ...	0.01	-	mit	0		cytoplasm [IDA]		1QGX	357
O95861 UniProt NPD GO	BPNT1_HUMAN	3'(2'),5'-bisphosphate nucleotidase 1 (EC 3.1.3.7) (Bisphosphate 3'-nucleotidase 1) (PAP-inositol-1, ...	0.01	-	mit	0			604053		308
Q9Z0S1 UniProt NPD GO	BPNT1_MOUSE	3'(2'),5'-bisphosphate nucleotidase 1 (EC 3.1.3.7) (Bisphosphate 3'-nucleotidase 1) (PAP-inositol-1, ...	0.01	-	mit	0					308
P42125 UniProt NPD GO	D3D2_MOUSE	3,2-trans-enoyl-CoA isomerase, mitochondrial precursor (EC 5.3.3.8) (Dodecenoyl-CoA isomerase) (Delt ...	0.01	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA] mitochondrion [IDA]			289
P50234 UniProt NPD GO	SUHA_CAVPO	3-alpha-hydroxysteroid sulfotransferase (EC 2.8.2.2) (Alcohol sulfotransferase) (HST1)	0.01	-	cyt	0	Cytoplasm (Potential)				286
Q15125 UniProt NPD GO	EBP_HUMAN	3-beta-hydroxysteroid-delta(8),delta(7)-isomerase (EC 5.3.3.5) (Cholestenol delta-isomerase) (Delta8 ...	0.01	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] integral to plasma membrane [TAS]	302960		229
P70245 UniProt NPD GO	EBP_MOUSE	3-beta-hydroxysteroid-delta(8),delta(7)-isomerase (EC 5.3.3.5) (Cholestenol delta-isomerase) (Delta8 ...	0.01	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [TAS]			229
Q9JJ46 UniProt NPD GO	EBP_RAT	3-beta-hydroxysteroid-delta(8),delta(7)-isomerase (EC 5.3.3.5) (Cholestenol delta-isomerase) (Delta8 ...	0.01	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				229
Q99714 UniProt NPD GO	HCD2_HUMAN	3-hydroxyacyl-CoA dehydrogenase type-2 (EC 1.1.1.35) (3-hydroxyacyl-CoA dehydrogenase type II) (Type ...	0.01	-	mit	0		cytoplasm [TAS] mitochondrion [ISS] plasma membrane [TAS]	300256	1U7T	260
O18404 UniProt NPD GO	HCD2_DROME	3-hydroxyacyl-CoA dehydrogenase type-2 (EC 1.1.1.35) (3-hydroxyacyl-CoA dehydrogenase type II) (Type ...	0.01	-	cyt	0	Mitochondrion (By similarity)	cytosol [NAS] mitochondrion [ISS]			255
P32185 UniProt NPD GO	3HIDH_RABIT	3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (HIBADH) (Fragment)	0.01	-	cyt	0	Mitochondrion				35
Q8NKB8 UniProt NPD GO	LEU3_ARXAD	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.01	-	cyt	0	Cytoplasm				362
O14429 UniProt NPD GO	LEU3_CANGA	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.01	-	cyt	0	Cytoplasm				365
P34738 UniProt NPD GO	LEU3_NEUCR	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.01	-	cyt	0	Cytoplasm				368
P34733 UniProt NPD GO	LEU3_PICAN	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.01	-	cyt	0	Cytoplasm				362
Q96WT9 UniProt NPD GO	LEU3_SACEX	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.01	-	cyt	0	Cytoplasm (By similarity)				365
P18869 UniProt NPD GO	LEU3_SCHPO	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.01	-	cyt	0	Cytoplasm				371
Q9P3Y0 UniProt NPD GO	LEU3_ZYGBA	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.01	-	cyt	0	Cytoplasm				362
Q8VCX1 UniProt NPD GO	AK1D1_MOUSE	3-oxo-5-beta-steroid 4-dehydrogenase (EC 1.3.99.6) (Delta(4)-3-ketosteroid 5-beta-reductase) (Aldo-k ...	0.01	-	cyt	0	Cytoplasm (By similarity)				325
P27583 UniProt NPD GO	FABG_PERAE	3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) (3-ketoacyl-acyl carrier protein reductase ...	0.01	-	cyt	0	Plastid; chloroplast. Plastid. And non-photosynthetic plastids				106

You are viewing entries 86301 to 86350 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.