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
Q61941 UniProt NPD GO	NNTM_MOUSE	NAD(P) transhydrogenase, mitochondrial precursor (EC 1.6.1.2) (Pyridine nucleotide transhydrogenase) ...	0.05	-	end	12	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (Potential)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			1086
Q9P8R5 UniProt NPD GO	XYL1_ASPNG	NAD(P)H-dependent D-xylose reductase (EC 1.1.1.-) (XR)	0.05	-	cyt	0					319
Q9TL07 UniProt NPD GO	NU2C_NEPOL	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.05	-	end	12 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				506
Q32RW1 UniProt NPD GO	NU2C_STAPU	NAD(P)H-quinone oxidoreductase chain 2, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 2) (N ...	0.05	-	end	14 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				513
Q9MTI0 UniProt NPD GO	NU4LC_OENHO	NAD(P)H-quinone oxidoreductase chain 4L, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4L) ...	0.05	-	end	3 *	Plastid; chloroplast				101
Q9TKV6 UniProt NPD GO	NUCC_NEPOL	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.05	-	cyt	0	Plastid; chloroplast				391
Q85BB2 UniProt NPD GO	NUGC_ANTFO	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.05	-	cyt	0	Plastid; chloroplast				169
P92309 UniProt NPD GO	NUGC_LUPLU	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.05	-	cyt	0	Plastid; chloroplast				158
Q9MTP3 UniProt NPD GO	NUGC_OENHO	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.05	-	cyt	0	Plastid; chloroplast				158
P12201 UniProt NPD GO	NUGC_TOBAC	NAD(P)H-quinone oxidoreductase chain J, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain J) (N ...	0.05	-	cyt	0	Plastid; chloroplast				158
Q9CPP6 UniProt NPD GO	NDUA5_MOUSE	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.05	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side	mitochondrion [IDA]			115
O43674 UniProt NPD GO	NDUB5_HUMAN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial precursor (EC 1.6.5.3) (E ...	0.05	-	mit	1	Mitochondrion; mitochondrial inner membrane; matrix side		603841		189
Q02372 UniProt NPD GO	NDUB8_BOVIN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial precursor (EC 1.6.5.3) (E ...	0.05	-	mit	1	Mitochondrion; mitochondrial inner membrane; matrix side				186
Q9D6J6 UniProt NPD GO	NUHM_MOUSE	NADH-ubiquinone oxidoreductase 24 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3)	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA]			248
P80264 UniProt NPD GO	NUCM_SOLTU	NADH-ubiquinone oxidoreductase 49 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (NADH dehydrogenase subunit ...	0.05	-	cyt	0	Mitochondrion; mitochondrial inner membrane; matrix side				46
P18936 UniProt NPD GO	NU1M_CHICK	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.05	-	vac	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				324
O63623 UniProt NPD GO	NU1M_DALCH	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.05	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				310
Q8M880 UniProt NPD GO	NU1M_EPTNI	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.05	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
P09045 UniProt NPD GO	NU1M_LOCMI	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.05	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				313
P24995 UniProt NPD GO	NU1M_PISOC	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.05	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				324
O78711 UniProt NPD GO	NU1M_SARHA	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.05	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
O78715 UniProt NPD GO	NU1M_SMICR	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.05	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
Q8M888 UniProt NPD GO	NU1M_TADIN	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1)	0.05	-	end	8 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				318
Q8HEC4 UniProt NPD GO	NU1M_CAEBR	NADH-ubiquinone oxidoreductase chain 1 (EC 1.6.5.3) (NADH dehydrogenase subunit 1) (Fragments)	0.05	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				291
P15957 UniProt NPD GO	NU3M_GADMO	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.05	-	end	3 *					116
P27062 UniProt NPD GO	NU3M_PANGI	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.05	-	mit	2 *					118
P92817 UniProt NPD GO	NU3M_PAROL	NADH-ubiquinone oxidoreductase chain 3 (EC 1.6.5.3) (NADH dehydrogenase subunit 3)	0.05	-	end	3 *					116
Q9MIY1 UniProt NPD GO	NU4M_BRARE	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.05	-	end	12 *					460
P18931 UniProt NPD GO	NU4M_DROME	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.05	-	end	12 *					446
Q36424 UniProt NPD GO	NU4M_LOCMI	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.05	-	end	12 *					444
O47497 UniProt NPD GO	NU4M_METSE	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.05	-	end	14 *					491
Q9ZZM4 UniProt NPD GO	NU4M_SALSA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4)	0.05	-	end	13 *					460
O03698 UniProt NPD GO	NU4M_BOTBI	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.05	-	end	6 *					231
O03733 UniProt NPD GO	NU4M_HYPHY	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.05	-	exc	6 *					231
O03807 UniProt NPD GO	NU4M_TRIWA	NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (NADH dehydrogenase subunit 4) (Fragment)	0.05	-	end	6 *					231
Q37403 UniProt NPD GO	NU4LM_ALLMA	NADH-ubiquinone oxidoreductase chain 4L (EC 1.6.5.3) (NADH dehydrogenase subunit 4L)	0.05	-	end	3 *					99
Q8HHD2 UniProt NPD GO	NU5M_CRYPA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3)	0.05	-	end	17 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				656
Q6V9D9 UniProt NPD GO	NU5M_PENMA	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3)	0.05	-	end	17 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				658
O78688 UniProt NPD GO	NU5M_CARAU	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.05	-	end	15 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				607
P48920 UniProt NPD GO	NU5M_CHOCR	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.05	-	end	19 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				666
Q36428 UniProt NPD GO	NU5M_LOCMI	NADH-ubiquinone oxidoreductase chain 5 (EC 1.6.5.3) (NADH dehydrogenase subunit 5)	0.05	-	end	17 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Probable)				572
Q2I3G3 UniProt NPD GO	NU6M_ELEMA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.05	-	end	6 *					175
P48927 UniProt NPD GO	NU6M_PICCA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.05	-	end	5 *					207
P28475 UniProt NPD GO	S6PD_MALDO	NADP-dependent D-sorbitol-6-phosphate dehydrogenase (EC 1.1.1.200) (Aldose-6-phosphate reductase [NA ...	0.05	-	cyt	0					310
P40927 UniProt NPD GO	MAOX_COLLI	NADP-dependent malic enzyme (EC 1.1.1.40) (NADP-ME)	0.05	-	cyt	0	Cytoplasm			1GQ2	557
O93934 UniProt NPD GO	DHE4_BOTCI	NADP-specific glutamate dehydrogenase (EC 1.4.1.4) (NADP-GDH) (NADP-dependent glutamate dehydrogenas ...	0.05	-	cyt	0					450
P40471 UniProt NPD GO	AYR1_YEAST	NADPH-dependent 1-acyldihydroxyacetone phosphate reductase (EC 1.1.1.101) (Acylglycerone-phosphate r ...	0.05	-	cyt	0	Lipid particle. Endoplasmic reticulum	cytoplasm [IDA] endoplasmic reticulum [IDA] lipid particle [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			297
Q12068 UniProt NPD GO	GRE2_YEAST	NADPH-dependent methylglyoxal reductase GRE2 (EC 1.1.1.283) (Genes de respuesta a estres protein 2)	0.05	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			342
P0C073 UniProt NPD GO	RUB1_DESAN	NEDD8-like protein RUB1 precursor (DaRUB1)	0.05	-	cyt	0					77
Q9SHE7 UniProt NPD GO	RUB1_ARATH	NEDD8-like protein RUB1 precursor (Ubiquitin-related protein 1) (AtRUB1)	0.05	-	cyt	0				1BT0	80

You are viewing entries 74951 to 75000 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.