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
Q9FTZ2 UniProt NPD GO	EBP_ORYSA	Probable 3-beta-hydroxysteroid-delta(8),delta(7)-isomerase (EC 5.3.3.5) (Cholestenol delta-isomerase ...	0.02	-	mit	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				219
Q9XTI0 UniProt NPD GO	3HIDH_CAEEL	Probable 3-hydroxyisobutyrate dehydrogenase, mitochondrial (EC 1.1.1.31) (HIBADH)	0.02	-	cyt	0	Mitochondrion (By similarity)				299
Q9V8M5 UniProt NPD GO	3HIDH_DROME	Probable 3-hydroxyisobutyrate dehydrogenase, mitochondrial precursor (EC 1.1.1.31) (HIBADH)	0.02	-	mit	0	Mitochondrion (By similarity)				324
Q4WHU1 UniProt NPD GO	HPPD1_ASPFU	Probable 4-hydroxyphenylpyruvate dioxygenase 1 (EC 1.13.11.27) (4HPPD 1) (HPD 1) (HPPDase 1)	0.02	-	cyt	0					403
P53315 UniProt NPD GO	SOL4_YEAST	Probable 6-phosphogluconolactonase 4 (EC 3.1.1.31) (6PGL)	0.02	-	cyt	0		cytoplasm [IDA] cytosol [IDA] nucleus [IDA]			255
O94457 UniProt NPD GO	ERG31_SCHPO	Probable C-5 sterol desaturase 1 (EC 1.3.3.-) (Sterol-C5-desaturase 1) (Ergosterol delta 5,6 desatur ...	0.02	-	cyt	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				300
Q8IER7 UniProt NPD GO	RPO2J_PLAF7	Probable DNA-directed RNA polymerase II subunit J (EC 2.7.7.6)	0.02	-	nuc	0	Nucleus (By similarity)				126
Q7TQP3 UniProt NPD GO	GP119_MOUSE	Probable G-protein coupled receptor 119	0.02	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]			335
O14626 UniProt NPD GO	GP171_HUMAN	Probable G-protein coupled receptor 171 (G-protein coupled receptor H963)	0.02	-	end	6 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			319
O75388 UniProt NPD GO	GPR32_HUMAN	Probable G-protein coupled receptor 32	0.02	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	603195		356
Q9NQS5 UniProt NPD GO	GPR84_HUMAN	Probable G-protein coupled receptor 84 (Inflammation-related G-protein coupled receptor EX33)	0.02	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	606383		396
Q09554 UniProt NPD GO	YQV5_CAEEL	Probable G-protein coupled receptor F27E5.5	0.02	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				377
Q6AV34 UniProt NPD GO	ARGC_ORYSA	Probable N-acetyl-gamma-glutamyl-phosphate reductase, chloroplast precursor (EC 1.2.1.38) (AGPR) (N- ...	0.02	-	cyt	0	Plastid; chloroplast (Potential)			2CVO	415
Q39172 UniProt NPD GO	P1_ARATH	Probable NADP-dependent oxidoreductase P1 (EC 1.3.1.74)	0.02	-	cyt	0					345
Q39173 UniProt NPD GO	P2_ARATH	Probable NADP-dependent oxidoreductase P2 (EC 1.3.1.74)	0.02	-	cyt	0					343
Q9C578 UniProt NPD GO	RCL1_ARATH	Probable RNA 3'-terminal phosphate cyclase-like protein	0.02	-	mit	0	Nucleus; nucleolus (By similarity)				375
Q9GP33 UniProt NPD GO	RAB4A_ECHMU	Probable Ras-related protein Rab-4A	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				223
P50305 UniProt NPD GO	METK_CAEEL	Probable S-adenosylmethionine synthetase C06E7.1 (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoM ...	0.02	-	cyt	0					404
Q9W0P5 UniProt NPD GO	GALE_DROME	Probable UDP-glucose 4-epimerase (EC 5.1.3.2) (Galactowaldenase) (UDP-galactose 4-epimerase)	0.02	-	cyt	0					350
Q20140 UniProt NPD GO	KAD1_CAEEL	Probable adenylate kinase isoenzyme F38B2.4 (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.02	-	pox	0	Cytoplasm (By similarity)				210
P07631 UniProt NPD GO	SUH2_RAT	Probable alcohol sulfotransferase (EC 2.8.2.2) (Hydroxysteroid sulfotransferase) (ST) (Senescence ma ...	0.02	-	cyt	0	Cytoplasm				285
P47039 UniProt NPD GO	BNA3_YEAST	Probable aminotransferase BNA3 (EC 2.6.1.-) (Biosynthesis of nicotinic acid protein 3)	0.02	-	mit	0	Cytoplasm. Mitochondrion	cytoplasm [IDA] mitochondrion [IDA]			444
Q9SV84 UniProt NPD GO	NIP51_ARATH	Probable aquaporin NIP5.1 (NOD26-like intrinsic protein 5.1) (Nodulin-26-like major intrinsic protei ...	0.02	-	end	5	Membrane; multi-pass membrane protein (Probable)				304
Q08451 UniProt NPD GO	PIP1_LYCES	Probable aquaporin PIP-type pTOM75 (Ripening-associated membrane protein) (RAMP)	0.02	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)				286
Q9FK43 UniProt NPD GO	SIP12_ARATH	Probable aquaporin SIP1.2 (Small basic intrinsic protein 1.2)	0.02	-	end	5 *	Membrane; multi-pass membrane protein (Probable)				243
Q7XU31 UniProt NPD GO	TIP51_ORYSA	Probable aquaporin TIP5.1 (Tonoplast intrinsic protein 5.1) (OsTIP5.1)	0.02	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				269
Q9ZPF5 UniProt NPD GO	ARGI2_ARATH	Probable arginase (EC 3.5.3.1)	0.02	-	mit	0					344
O60163 UniProt NPD GO	AK_SCHPO	Probable aspartokinase (EC 2.7.2.4) (Aspartate kinase)	0.02	-	cyt	0					519
Q9SQH6 UniProt NPD GO	PIN6_ARATH	Probable auxin efflux carrier component 6 (AtPIN6)	0.02	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				570
Q9LE06 UniProt NPD GO	BCAT4_ARATH	Probable branched-chain-amino-acid aminotransferase 4 (Atbcat-4)	0.02	-	cyt	0	Cytoplasm (Probable)				354
O49499 UniProt NPD GO	CAMT4_ARATH	Probable caffeoyl-CoA O-methyltransferase At4g34050 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltra ...	0.02	-	cyt	0					259
Q4X1N0 UniProt NPD GO	CUTI1_ASPFU	Probable cutinase 1 precursor (EC 3.1.1.74) (Cutin hydrolase 1)	0.02	-	end	0	Secreted protein (By similarity)				211
Q9VHS2 UniProt NPD GO	COX7A_DROME	Probable cytochrome c oxidase polypeptide VIIa, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c o ...	0.02	-	mit	1	Mitochondrion; mitochondrial inner membrane (By similarity)				89
Q94748 UniProt NPD GO	DYL2_SCHMA	Probable dynein light chain (T-cell-stimulating antigen SM10)	0.02	-	cyt	0	Cytoplasm (By similarity)				89
Q8J0W1 UniProt NPD GO	ETFA_CRYNE	Probable electron transfer flavoprotein subunit alpha, mitochondrial precursor (Alpha-ETF)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				346
Q08822 UniProt NPD GO	ETFD_YEAST	Probable electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (EC 1.5.5 ...	0.02	-	cyt	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA]			631
Q9LNE3 UniProt NPD GO	SCRK2_ARATH	Probable fructokinase-2 (EC 2.7.1.4)	0.02	-	cyt	0					329
Q9UT44 UniProt NPD GO	PROA_SCHPO	Probable gamma-glutamyl phosphate reductase (GPR) (EC 1.2.1.41) (Glutamate-5-semialdehyde dehydrogen ...	0.02	-	cyt	0					451
Q9MAA7 UniProt NPD GO	GI1L1_ARATH	Probable gibberellin receptor GID1L1 (EC 3.-.-.-) (GID1-like protein 1)	0.02	-	cyt	0	Nucleus (By similarity)				345
Q940G6 UniProt NPD GO	GI1L3_ARATH	Probable gibberellin receptor GID1L3 (EC 3.-.-.-) (GID1-like protein 3)	0.02	-	cyt	0	Nucleus (By similarity)				344
Q9VAI0 UniProt NPD GO	GNA1_DROME	Probable glucosamine 6-phosphate N-acetyltransferase (EC 2.3.1.4) (Phosphoglucosamine transacetylase ...	0.02	-	cyt	0					219
Q03664 UniProt NPD GO	GSTX3_TOBAC	Probable glutathione S-transferase (EC 2.5.1.18) (Auxin-induced protein PCNT103)	0.02	-	cyt	0					223
Q03662 UniProt NPD GO	GSTX1_TOBAC	Probable glutathione S-transferase (EC 2.5.1.18) (Auxin-induced protein PGNT1/PCNT110)	0.02	-	cyt	0					223
Q8L910 UniProt NPD GO	GPX4_ARATH	Probable glutathione peroxidase 4 (EC 1.11.1.9)	0.02	-	cyt	0					170
Q26547 UniProt NPD GO	GLO2_SCHMA	Probable hydroxyacylglutathione hydrolase (EC 3.1.2.6) (Glyoxalase II) (Glx II)	0.02	-	cyt	0					240
Q8N8Q8 UniProt NPD GO	OXAL2_HUMAN	Probable inner membrane protein OXA1L2, mitochondrial precursor	0.02	-	end	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				333
Q5R7D0 UniProt NPD GO	OXAL2_PONPY	Probable inner membrane protein OXA1L2, mitochondrial precursor	0.02	-	end	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				334
P39567 UniProt NPD GO	IMDH1_YEAST	Probable inosine-5'-monophosphate dehydrogenase IMD1 (EC 1.1.1.205) (IMP dehydrogenase) (IMPDH) (IMP ...	0.02	-	mit	0					403
Q5Z8T3 UniProt NPD GO	MIOX_ORYSA	Probable inositol oxygenase (EC 1.13.99.1) (Myo-inositol oxygenase)	0.02	-	cyt	0	Cytoplasm (By similarity)				308
Q21506 UniProt NPD GO	ILA3_CAEEL	Probable insulin-like peptide alpha-type 3 precursor	0.02	-	exc	0	Secreted protein (Potential)				76

You are viewing entries 85151 to 85200 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.