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
P33745 UniProt NPD GO	MCH1_ONCMY	Pro-MCH 1 precursor [Contains: Neuropeptide-glutamic acid-valine (NEV) (Neuropeptide E-V); Melanin-c ...	0.13	-	exc	0					132
O48962 UniProt NPD GO	EBP_ARATH	Probable 3-beta-hydroxysteroid-delta(8),delta(7)-isomerase (EC 5.3.3.5) (Cholestenol delta-isomerase ...	0.13	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				223
P46769 UniProt NPD GO	RSSA_CAEEL	Probable 40S ribosomal protein SA (p40)	0.13	-	nuc	0	Cytoplasm				275
P50278 UniProt NPD GO	SOL1_YEAST	Probable 6-phosphogluconolactonase 1 (EC 3.1.1.31) (6PGL)	0.13	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			321
P48255 UniProt NPD GO	ABCX_CYAPA	Probable ATP-dependent transporter ycf16	0.13	-	cyt	0	Plastid; cyanelle				259
P35020 UniProt NPD GO	ABCX_GALSU	Probable ATP-dependent transporter ycf16	0.13	-	cyt	0	Plastid; chloroplast				257
Q95LH1 UniProt NPD GO	GPR1_MACFA	Probable G-protein coupled receptor 1	0.13	-	end	7 *	Membrane; multi-pass membrane protein				355
Q9D2L6 UniProt NPD GO	GP115_MOUSE	Probable G-protein coupled receptor 115 precursor	0.13	-	end	7	Membrane; multi-pass membrane protein				698
Q8IZ08 UniProt NPD GO	GP135_HUMAN	Probable G-protein coupled receptor 135	0.13	-	end	7	Membrane; multi-pass membrane protein		607970		494
O54897 UniProt NPD GO	GPR27_MOUSE	Probable G-protein coupled receptor 27 (Super conserved receptor expressed in brain 1)	0.13	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				379
Q9JJH3 UniProt NPD GO	GPR27_RAT	Probable G-protein coupled receptor 27 (Super conserved receptor expressed in brain 1)	0.13	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				377
O13691 UniProt NPD GO	NUHM_SCHPO	Probable NADH-ubiquinone oxidoreductase 24 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6 ...	0.13	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity). Matrix and cytoplasmic side of the mito ...				162
Q43582 UniProt NPD GO	LSM4_TOBAC	Probable U6 snRNA-associated Sm-like protein LSm4 (Glycine-rich protein 10) (GRP 10)	0.13	-	nuc	0	Nucleus (Potential)				146
Q8RVB2 UniProt NPD GO	SPY_LYCES	Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY (EC 2.4.1.-) (LeSP ...	0.13	-	cyt	0	Nucleus (By similarity)				931
P78811 UniProt NPD GO	UGPA1_SCHPO	Probable UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (UDP-glucose pyrophosphorylase) ( ...	0.13	-	nuc	0					506
Q9HE76 UniProt NPD GO	KAD_NEUCR	Probable adenylate kinase (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.13	-	nuc	0					236
P46985 UniProt NPD GO	MNN11_YEAST	Probable alpha-1,6-mannosyltransferase MNN11 (EC 2.4.1.-) (Mannan polymerase II complex MNN11 subuni ...	0.13	-	mit	1 *	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; single-pass type II membrane protein ...	alpha-1,6-mannosyltransferase complex [IDA]			422
Q628Z2 UniProt NPD GO	CMC3_CAEBR	Probable calcium-binding mitochondrial carrier CBG00135	0.13	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				532
Q7XPF7 UniProt NPD GO	HKT7_ORYSA	Probable cation transporter HKT7 (OsHKT7)	0.13	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				500
Q9H7F0 UniProt NPD GO	AT133_HUMAN	Probable cation-transporting ATPase 13A3 (EC 3.6.3.-) (ATPase family homolog up-regulated in senesce ...	0.13	-	end	9 *	Membrane; multi-pass membrane protein (By similarity)				1130
Q9W5U2 UniProt NPD GO	CHIT3_DROME	Probable chitinase 3 (EC 3.2.1.14)	0.13	-	cyt	0					458
O13739 UniProt NPD GO	CHMU_SCHPO	Probable chorismate mutase (EC 5.4.99.5) (CM)	0.13	-	nuc	0					251
Q9VG17 UniProt NPD GO	CP304_DROME	Probable cytochrome P450 304a1 (EC 1.14.-.-) (CYPCCCIVA1)	0.13	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				510
Q09522 UniProt NPD GO	DIMI_CAEEL	Probable dimethyladenosine transferase (EC 2.1.1.-) (S-adenosylmethionine-6-N',N'-adenosyl(rRNA) dim ...	0.13	-	cyt	0	Nucleus; nucleolus (By similarity)				308
Q84WD3 UniProt NPD GO	DRL26_ARATH	Probable disease resistance protein At4g19060	0.13	-	nuc	0					383
O43053 UniProt NPD GO	ALG6_SCHPO	Probable dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase (EC 2.4.1.-) (Dolichyl-P-G ...	0.13	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				506
Q27536 UniProt NPD GO	GALT_CAEEL	Probable galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (Gal-1-P uridylyltransferase) (UDP- ...	0.13	-	cyt	0					352
Q10242 UniProt NPD GO	GNTK_SCHPO	Probable gluconokinase (EC 2.7.1.12) (Gluconate kinase)	0.13	-	nuc	0					193
Q8H7Y8 UniProt NPD GO	H2AV1_ORYSA	Probable histone H2A variant 1	0.13	-	nuc	0	Nucleus (By similarity)				138
Q7XIN9 UniProt NPD GO	GH38_ORYSA	Probable indole-3-acetic acid-amido synthetase GH3.8 (EC 6.3.2.-) (Auxin-responsive GH3-like protein ...	0.13	-	cyt	0					605
O63264 UniProt NPD GO	ZBI1_ZYGBI	Probable intron-encoded endonuclease I-ZbiI (EC 3.1.-.-)	0.13	-	nuc	0	Mitochondrion				239
Q22347 UniProt NPD GO	ACADM_CAEEL	Probable medium-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.3) (MCAD)	0.13	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				417
Q6FL44 UniProt NPD GO	ARX1_CANGA	Probable metalloprotease ARX1 (EC 3.-.-.-) (Associated with ribosomal export complex protein 1)	0.13	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				588
Q12251 UniProt NPD GO	YP011_YEAST	Probable mitochondrial carrier YPR011C	0.13	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				326
Q6DGF5 UniProt NPD GO	ZDH12_RAT	Probable palmitoyltransferase ZDHHC12 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 12) ( ...	0.13	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				267
Q9SCP2 UniProt NPD GO	PEL12_ARATH	Probable pectate lyase 12 precursor (EC 4.2.2.2)	0.13	-	end	2 *					483
Q5N9J9 UniProt NPD GO	PHYK2_ORYSA	Probable phytol kinase 2, chloroplast precursor (EC 2.7.-.-) (Fragment)	0.13	-	vac	6	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				296
Q9ZQA8 UniProt NPD GO	PABPX_ARATH	Probable polyadenylate-binding protein At2g36660 (Poly(A)-binding protein At2g36660) (PABP)	0.13	-	nuc	0					609
P25332 UniProt NPD GO	RBSK_YEAST	Probable ribokinase (EC 2.7.1.15)	0.13	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			333
Q9SEZ6 UniProt NPD GO	RNHL_ARATH	Probable ribonuclease HI large subunit (EC 3.1.26.4) (RNase HI large subunit) (RNase H(35))	0.13	-	cyt	0					296
P38063 UniProt NPD GO	KPR4_YEAST	Probable ribose-phosphate pyrophosphokinase 4 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase ...	0.13	-	cyt	0		cytoplasm [IDA]			355
O65693 UniProt NPD GO	RBFA_ARATH	Probable ribosome-binding factor A, chloroplast precursor	0.13	-	mit	0	Plastid; chloroplast (Potential)				215
Q8R127 UniProt NPD GO	SCPDH_MOUSE	Probable saccharopine dehydrogenase (EC 1.5.1.9)	0.13	-	nuc	1					429
O14036 UniProt NPD GO	SMD2_SCHPO	Probable small nuclear ribonucleoprotein Sm D2 (snRNP core protein D2) (Sm-D2)	0.13	-	cyt	0	Nucleus (By similarity)				115
Q10269 UniProt NPD GO	AREH_SCHPO	Probable sterol O-acyltransferase (EC 2.3.1.26) (Sterol-ester synthase)	0.13	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				537
Q9P567 UniProt NPD GO	SUCB_NEUCR	Probable succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial precursor (EC 6.2.1.4) (Succiny ...	0.13	-	mit	0	Mitochondrion (By similarity)				447
Q9Y7Z9 UniProt NPD GO	COQ6_SCHPO	Probable ubiquinone biosynthesis monooxygenase coq6 (EC 1.14.13.-)	0.13	-	gol	0					466
Q19626 UniProt NPD GO	VATB_CAEEL	Probable vacuolar ATP synthase subunit B (EC 3.6.3.14) (V-ATPase B subunit) (Vacuolar proton pump B ...	0.13	-	cyt	0					491
Q8LG58 UniProt NPD GO	XTH16_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 16 precursor (EC 2.4.1.207) (At-XTH16) (X ...	0.13	-	end	0	Secreted protein; extracellular space; apoplast (Probable)				291
Q8LC45 UniProt NPD GO	XTH33_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 33 precursor (EC 2.4.1.207) (At-XTH33) (X ...	0.13	-	mit	0	Secreted protein; extracellular space; apoplast (Probable)				310

You are viewing entries 60201 to 60250 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.