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
P43200 UniProt NPD GO	NU6M_FRAAR	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P43201 UniProt NPD GO	NU6M_FRACR	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P55783 UniProt NPD GO	NU6M_GADMO	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P41322 UniProt NPD GO	NU6M_LARCA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
O03175 UniProt NPD GO	NU6M_LATCH	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P43202 UniProt NPD GO	NU6M_LUNCI	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P03925 UniProt NPD GO	NU6M_MOUSE	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					172
Q9G2W7 UniProt NPD GO	NU6M_MYXGL	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	4 *					167
P48177 UniProt NPD GO	NU6M_ONCMY	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P12777 UniProt NPD GO	NU6M_PARLI	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					160
Q35544 UniProt NPD GO	NU6M_PETMA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					172
Q95919 UniProt NPD GO	NU6M_POLOR	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					167
P43203 UniProt NPD GO	NU6M_PTYAL	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P03926 UniProt NPD GO	NU6M_RAT	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					172
Q9ZZM2 UniProt NPD GO	NU6M_SALSA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
O79412 UniProt NPD GO	NU6M_SCYCA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
Q9ZZ43 UniProt NPD GO	NU6M_SQUAC	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
O21407 UniProt NPD GO	NU6M_STRCA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P15553 UniProt NPD GO	NU6M_STRPU	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	4 *					165
P43204 UniProt NPD GO	NU6M_SYNAN	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P43205 UniProt NPD GO	NU6M_SYNHY	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P43206 UniProt NPD GO	NU6M_SYNWU	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
Q8W9G2 UniProt NPD GO	NU6M_TACAC	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					166
Q4JQH6 UniProt NPD GO	NU6M_TETNG	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					173
P43207 UniProt NPD GO	NU6M_URIAL	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					172
P43208 UniProt NPD GO	NU6M_URILO	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					172
P03927 UniProt NPD GO	NU6M_XENLA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					170
Q9B6E9 UniProt NPD GO	NU6M_YARLI	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6)	0.00	-	end	5 *					185
Q08084 UniProt NPD GO	NU6M_ALBTU	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6) (Fragment)	0.00	-	end	2 *					96
Q06059 UniProt NPD GO	NU6M_ANAPL	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6) (Fragment)	0.00	-	end	3 *					81
P19048 UniProt NPD GO	NU6M_ARTSA	NADH-ubiquinone oxidoreductase chain 6 (EC 1.6.5.3) (NADH dehydrogenase subunit 6) (Fragment)	0.00	-	end	2 *					56
P30826 UniProt NPD GO	NUIM_TRYBB	NADH-ubiquinone oxidoreductase subunit 8 (EC 1.6.5.3) (Maxicircle iron-sulfur protein 1)	0.00	-	end	2 *	Mitochondrion				145
P55804 UniProt NPD GO	DHGP_ASPNG	NADP(+)-dependent glycerol dehydrogenase (EC 1.1.1.72) (Fragments)	0.00	-	cyt	0					99
P35630 UniProt NPD GO	ADH1_ENTHI	NADP-dependent alcohol dehydrogenase (EC 1.1.1.2)	0.00	-	nuc	0	Cytoplasm			1Y9A	360
P25377 UniProt NPD GO	ADH7_YEAST	NADP-dependent alcohol dehydrogenase 7 (EC 1.1.1.2) (NADP-dependent alcohol dehydrogenase VII) (ADHV ...	0.00	-	end	0		soluble fraction [IDA]			361
Q14914 UniProt NPD GO	LTB4D_HUMAN	NADP-dependent leukotriene B4 12-hydroxydehydrogenase (EC 1.3.1.74) (15-oxoprostaglandin 13-reductas ...	0.00	-	mit	0	Cytoplasm	cytoplasm [NAS]	601274	1ZSV	329
Q91YR9 UniProt NPD GO	LTB4D_MOUSE	NADP-dependent leukotriene B4 12-hydroxydehydrogenase (EC 1.3.1.74) (15-oxoprostaglandin 13-reductas ...	0.00	-	cyt	0	Cytoplasm (By similarity)				329
Q29073 UniProt NPD GO	LTB4D_PIG	NADP-dependent leukotriene B4 12-hydroxydehydrogenase (EC 1.3.1.74) (15-oxoprostaglandin 13-reductas ...	0.00	-	cyt	0	Cytoplasm				329
P97584 UniProt NPD GO	LTB4D_RAT	NADP-dependent leukotriene B4 12-hydroxydehydrogenase (EC 1.3.1.74) (15-oxoprostaglandin 13-reductas ...	0.00	-	cyt	0	Cytoplasm (By similarity)				329
Q28719 UniProt NPD GO	LTB4D_RABIT	NADP-dependent leukotriene B4 12-hydroxydehydrogenase (EC 1.3.1.74) (ADRAB-F) (15-oxoprostaglandin 1 ...	0.00	-	cyt	0	Cytoplasm (By similarity)				349
Q9EQZ5 UniProt NPD GO	LTB4D_CAVPO	NADP-dependent leukotriene B4 12-hydroxydehydrogenase (EC 1.3.1.74) (LTB4) (12-HD) (15-oxoprostaglan ...	0.00	-	mit	0	Cytoplasm (By similarity)			1V3V	329
P29507 UniProt NPD GO	DHE4_DEBOC	NADP-specific glutamate dehydrogenase (EC 1.4.1.4) (NADP-GDH) (NADP-dependent glutamate dehydrogenas ...	0.00	-	cyt	0					459
P28724 UniProt NPD GO	DHE4_GIALA	NADP-specific glutamate dehydrogenase (EC 1.4.1.4) (NADP-GDH) (NADP-dependent glutamate dehydrogenas ...	0.00	-	cyt	0					449
P39708 UniProt NPD GO	DHE5_YEAST	NADP-specific glutamate dehydrogenase 2 (EC 1.4.1.4) (NADP-GDH 2) (NADP-dependent glutamate dehydrog ...	0.00	-	cyt	0		mitochondrion [IDA] nucleus [IDA] soluble fraction [IDA]			457
P53081 UniProt NPD GO	NIF3_YEAST	NGG1-interacting factor 3	0.00	-	mit	0		cytoplasm [IDA] mitochondrion [IDA]			288
Q6NVV3 UniProt NPD GO	NPAL1_HUMAN	NIPA-like protein 1	0.00	-	end	9	Membrane; multi-pass membrane protein (Potential)				410
Q5RDB8 UniProt NPD GO	NPAL1_PONPY	NIPA-like protein 1	0.00	-	end	9	Membrane; multi-pass membrane protein (Potential)				410
P36606 UniProt NPD GO	NAH_SCHPO	Na(+)/H(+) antiporter	0.00	-	end	9 *	Membrane; multi-pass membrane protein	nuclear envelope-endoplasmic reticulum network [IDA] plasma membrane [IDA]			468
Q8CFD9 UniProt NPD GO	NCTR3_RAT	Natural cytotoxicity triggering receptor 3 precursor (Natural killer cell p30-related protein) (NKp3 ...	0.00	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				192
P51027 UniProt NPD GO	NRAM1_CHICK	Natural resistance-associated macrophage protein 1 (NRAMP 1)	0.00	-	end	11	Membrane; multi-pass membrane protein (Probable)				555

You are viewing entries 95951 to 96000 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.