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
Q6PI62 UniProt NPD GO	GP173_MOUSE	Probable G-protein coupled receptor 173 (Super conserved receptor expressed in brain 3)	0.08	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				373
Q9JJH2 UniProt NPD GO	GP173_RAT	Probable G-protein coupled receptor 173 (Super conserved receptor expressed in brain 3)	0.08	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				373
O16452 UniProt NPD GO	NHX3_CAEEL	Probable Na(+)/H(+) antiporter nhx-3 (Na(+)-H(+) exchanger protein 3)	0.08	-	end	11 *	Intracytoplasmic membrane; multi-pass membrane protein. Intracellular organelles				670
Q13304 UniProt NPD GO	GPR17_HUMAN	Probable P2Y purinoceptor GPR17 (G protein-coupled receptor 17) (P2Y-like receptor) (R12)	0.08	-	end	6	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	603071		367
Q9C2L8 UniProt NPD GO	RAB7_NEUCR	Probable Ras-related protein Rab7	0.08	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				205
Q8GY63 UniProt NPD GO	DPNP3_ARATH	Probable SAL3 phosphatase (3'(2'),5'-bisphosphate nucleotidase 3) (EC 3.1.3.7) (3'(2'),5'-bisphospho ...	0.08	-	nuc	0					357
Q8LP10 UniProt NPD GO	SPY_EUSGR	Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY (EC 2.4.1.-) (EgSP ...	0.08	-	nuc	0	Nucleus (By similarity)				918
Q9FSC2 UniProt NPD GO	ACS3_RUTGR	Probable acridone synthase 3 (EC 2.3.1.159) (Acridone synthase III)	0.08	-	cyt	0					391
Q9ZUU1 UniProt NPD GO	KADC1_ARATH	Probable adenylate kinase 1, chloroplast precursor (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.08	-	mit	0	Plastid; chloroplast (By similarity)				284
Q8L9J9 UniProt NPD GO	CAES_ARATH	Probable carbohydrate esterase At4g34215 (EC 3.1.-.-)	0.08	-	cyt	0				2APJ	260
O01916 UniProt NPD GO	CRLS1_CAEEL	Probable cardiolipin synthetase (EC 2.7.8.-) (Cardiolipin synthase) (CLS)	0.08	-	nuc	4	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				246
O17901 UniProt NPD GO	COPZ_CAEEL	Probable coatomer subunit zeta (Zeta-coat protein) (Zeta-COP)	0.08	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				184
Q9LQI7 UniProt NPD GO	CIA30_ARATH	Probable complex I intermediate-associated protein 30	0.08	-	mit	0	Mitochondrion				208
Q9VE01 UniProt NPD GO	C12A5_DROME	Probable cytochrome P450 12a5, mitochondrial precursor (EC 1.14.-.-) (CYPXIIA5)	0.08	-	cyt	0	Mitochondrion (Potential)				536
O22912 UniProt NPD GO	CX5C1_ARATH	Probable cytochrome c oxidase polypeptide Vc-1 (EC 1.9.3.1) (Cytochrome c oxidase subunit 5c-1)	0.08	-	mit	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)	mitochondrion [IDA]			64
Q9VL18 UniProt NPD GO	EF1D_DROME	Probable elongation factor 1-delta (EF-1-delta)	0.08	-	cyt	0					256
Q9UKR5 UniProt NPD GO	ERG28_HUMAN	Probable ergosterol biosynthetic protein 28	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]	604576		140
Q5R589 UniProt NPD GO	ERG28_PONPY	Probable ergosterol biosynthetic protein 28	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				140
Q04951 UniProt NPD GO	SCW10_YEAST	Probable family 17 glucosidase SCW10 precursor (EC 3.2.1.-) (Soluble cell wall protein 10)	0.08	-	mit	0	Cell wall	cell wall (sensu Fungi) [IDA] cytoplasm [IDA] endoplasmic reticulum [IDA]			389
P53334 UniProt NPD GO	SCW4_YEAST	Probable family 17 glucosidase SCW4 precursor (EC 3.2.1.-) (Soluble cell wall protein 4)	0.08	-	exc	0	Cell wall	cell wall (sensu Fungi) [IDA]			386
Q21743 UniProt NPD GO	GST9_CAEEL	Probable glutathione S-transferase 9 (EC 2.5.1.18) (GST class-sigma)	0.08	-	cyt	0					206
P30635 UniProt NPD GO	GSHR_CAEEL	Probable glutathione reductase (EC 1.8.1.7) (GR) (GRase)	0.08	-	mit	0	Cytoplasm (By similarity)				503
Q6ZL43 UniProt NPD GO	H2A1_ORYSA	Probable histone H2A.1	0.08	-	cyt	0	Nucleus (By similarity)				135
Q9C681 UniProt NPD GO	H2A1_ARATH	Probable histone H2A.1 (HTA10)	0.08	-	nuc	0	Nucleus (By similarity)				132
Q84NJ4 UniProt NPD GO	H2A3_ORYSA	Probable histone H2A.3	0.08	-	nuc	0	Nucleus (By similarity)				134
Q24572 UniProt NPD GO	CAF1_DROME	Probable histone-binding protein Caf1 (Chromatin assembly factor 1 p55 subunit) (CAF-1 p55 subunit) ...	0.08	-	cyt	0	Nucleus	ESC/E(Z) complex [IDA] Myb complex [IDA] nucleus [IDA] NURF complex [IPI] polytene chromosome [IDA] transcription factor complex [IPI]			430
P78827 UniProt NPD GO	ILV5_SCHPO	Probable ketol-acid reductoisomerase, mitochondrial precursor (EC 1.1.1.86) (Acetohydroxy-acid reduc ...	0.08	-	mit	0	Mitochondrion (By similarity)				404
Q9LVZ3 UniProt NPD GO	ADS32_ARATH	Probable lipid-desaturase ADS3.2, chloroplast precursor (EC 1.14.19.-)	0.08	-	mit	3	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				354
Q17693 UniProt NPD GO	MTHR_CAEEL	Probable methylenetetrahydrofolate reductase (EC 1.5.1.20)	0.08	-	cyt	0					663
P62506 UniProt NPD GO	RM44_SCHPO	Probable mitochondrial 60S ribosomal protein L44	0.08	-	nuc	0	Mitochondrion (By similarity)				100
P39953 UniProt NPD GO	YEA6_YEAST	Probable mitochondrial carrier YEL006W	0.08	-	end	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			335
O43020 UniProt NPD GO	RT16_SCHPO	Probable mitochondrial ribosomal protein S16	0.08	-	nuc	0	Mitochondrion (Probable)				96
P43217 UniProt NPD GO	NLT11_PARJU	Probable nonspecific lipid-transfer protein (LTP) (Major pollen allergen Par j 1.0101) (Par j I) (P5 ...	0.08	-	nuc	0					139
Q8N2H3 UniProt NPD GO	CJ033_HUMAN	Probable oxidoreductase C10orf33 (EC 1.-.-.-)	0.08	-	mit	0					581
Q3MHH6 UniProt NPD GO	CJ033_BOVIN	Probable oxidoreductase C10orf33 homolog (EC 1.-.-.-)	0.08	-	mit	0					581
Q9H8X9 UniProt NPD GO	ZDH11_HUMAN	Probable palmitoyltransferase ZDHHC11 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 11) ( ...	0.08	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				412
Q96GR4 UniProt NPD GO	ZDH12_HUMAN	Probable palmitoyltransferase ZDHHC12 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 12) ( ...	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				267
Q5REH2 UniProt NPD GO	ZDHC6_PONPY	Probable palmitoyltransferase ZDHHC6 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 6) (DH ...	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				413
Q9CPV7 UniProt NPD GO	ZDHC6_MOUSE	Probable palmitoyltransferase ZDHHC6 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 6) (DH ...	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				413
Q9H6R6 UniProt NPD GO	ZDHC6_HUMAN	Probable palmitoyltransferase ZDHHC6 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 6) (DH ...	0.08	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				413
Q12040 UniProt NPD GO	YO283_YEAST	Probable phosphoglycerate mutase YOR283W (EC 5.4.2.1) (Phosphoglyceromutase YOR283W)	0.08	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			230
Q6YSA9 UniProt NPD GO	HAK4_ORYSA	Probable potassium transporter 4 (OsHAK4)	0.08	-	end	9 *	Membrane; multi-pass membrane protein (By similarity)				697
Q9UT97 UniProt NPD GO	PSA5_SCHPO	Probable proteasome subunit alpha type 5 (EC 3.4.25.1)	0.08	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [TAS]			247
Q9VPP5 UniProt NPD GO	RNHL_DROME	Probable ribonuclease HI large subunit (EC 3.1.26.4) (RNase HI large subunit) (RNase H(35))	0.08	-	cyt	0					347
P83105 UniProt NPD GO	HTRA4_HUMAN	Probable serine protease HTRA4 precursor (EC 3.4.21.-)	0.08	-	mit	1 *					476
Q9C1W3 UniProt NPD GO	ERG1_SCHPO	Probable squalene monooxygenase (EC 1.14.99.7) (Squalene epoxidase) (SE)	0.08	-	end	3 *	Microsome; microsomal membrane; multi-pass membrane protein (By similarity)				457
P51358 UniProt NPD GO	YCF27_PORPU	Probable transcriptional regulator ycf27 (OmpR-like protein)	0.08	-	cyt	0	Plastid; chloroplast				243
Q9URM2 UniProt NPD GO	TKT_SCHPO	Probable transketolase (EC 2.2.1.1) (TK)	0.08	-	cyt	0					685
Q752I1 UniProt NPD GO	MCH1_ASHGO	Probable transporter MCH1	0.08	-	end	11 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				450
Q6CPY8 UniProt NPD GO	MCH1_KLULA	Probable transporter MCH1	0.08	-	end	12 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				479

You are viewing entries 68751 to 68800 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.