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
Q9VLM5 UniProt NPD GO	DAD1_DROME	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 (EC 2.4.1.119) (Oligosac ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				112
P61803 UniProt NPD GO	DAD1_HUMAN	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 (EC 2.4.1.119) (Oligosac ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	oligosaccharyl transferase complex [TAS]	600243		112
P61806 UniProt NPD GO	DAD1_MESAU	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 (EC 2.4.1.119) (Oligosac ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				112
P61804 UniProt NPD GO	DAD1_MOUSE	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 (EC 2.4.1.119) (Oligosac ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	oligosaccharyl transferase complex [ISS]			112
P61805 UniProt NPD GO	DAD1_RAT	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 (EC 2.4.1.119) (Oligosac ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	oligosaccharyl transferase complex [ISS]			112
Q99380 UniProt NPD GO	OST4_YEAST	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4 (EC 2.4.1.119) (Oligosac ...	0.00	-	nuc	1 *	Membrane; single-pass membrane protein	oligosaccharyl transferase complex [IPI]		1RKL	36
Q92316 UniProt NPD GO	OST5_YEAST	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 (EC 2.4.1.119) (Oligosac ...	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	oligosaccharyl transferase complex [IPI]			86
Q02795 UniProt NPD GO	OSTD_YEAST	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1 precursor (EC 2.4.1.119) ...	0.00	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)	oligosaccharyl transferase complex [IPI]			286
P46967 UniProt NPD GO	DAD1_XENLA	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit dad1 (EC 2.4.1.119) (Oligosac ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				113
P41596 UniProt NPD GO	DOPR1_DROME	Dopamine receptor 1 precursor (D-DOP1) (dDA1)	0.00	-	end	8 *	Membrane; multi-pass membrane protein				511
P0C1B7 UniProt NPD GO	DORT_PARTR	Dortoxin	0.00	-	cyt	0	Secreted protein				58
P41964 UniProt NPD GO	DMYC_DROME	Drosomycin precursor (Cysteine-rich peptide)	0.00	-	vac	1 *	Secreted protein	extracellular region [IDA]		1MYN	70
P39746 UniProt NPD GO	MP2K3_XENLA	Dual specificity mitogen-activated protein kinase kinase 3 (EC 2.7.12.2) (MAP kinase kinase 3) (MAPK ...	0.00	-	nuc	0					62
Q8R4V2 UniProt NPD GO	DUS15_MOUSE	Dual specificity protein phosphatase 15 (EC 3.1.3.48) (EC 3.1.3.16) (Dual specificity protein phosph ...	0.00	-	cyt	0					125
P82082 UniProt NPD GO	DYS4_LIMSA	Dynastin-4	0.00	-		0	Secreted protein				8
P82083 UniProt NPD GO	DYS5_LIMSA	Dynastin-5	0.00	-		0	Secreted protein				8
Q39580 UniProt NPD GO	DYL1_CHLRE	Dynein 8 kDa light chain, flagellar outer arm	0.00	-	cyt	0					91
Q759T0 UniProt NPD GO	DYL1_ASHGO	Dynein light chain 1, cytoplasmic	0.00	-	cyt	0	Cytoplasm (By similarity)				88
Q22799 UniProt NPD GO	DYL1_CAEEL	Dynein light chain 1, cytoplasmic	0.00	-	cyt	0	Cytoplasm (By similarity)				89
Q6CWX4 UniProt NPD GO	DYL1_KLULA	Dynein light chain 1, cytoplasmic	0.00	-	cyt	0	Cytoplasm (By similarity)				87
Q9UR05 UniProt NPD GO	DYL1_SCHPO	Dynein light chain 1, cytoplasmic	0.00	-	cyt	0	Cytoplasm				85
Q02647 UniProt NPD GO	DYL1_YEAST	Dynein light chain 1, cytoplasmic	0.00	-	cyt	0	Cytoplasm	cytoplasmic microtubule [TAS]			92
Q24117 UniProt NPD GO	DYL1_DROME	Dynein light chain 1, cytoplasmic (8 kDa dynein light chain) (Cut up protein)	0.00	-	cyt	0	Cytoplasm			1RHW	89
P61285 UniProt NPD GO	DYL1_BOVIN	Dynein light chain 1, cytoplasmic (Dynein light chain LC8-type 1)	0.00	-	cyt	0	Cytoplasm (By similarity)				89
P61273 UniProt NPD GO	DYL1_MACFA	Dynein light chain 1, cytoplasmic (Dynein light chain LC8-type 1)	0.00	-	cyt	0	Cytoplasm (By similarity)				89
P63167 UniProt NPD GO	DYL1_HUMAN	Dynein light chain 1, cytoplasmic (Dynein light chain LC8-type 1) (8 kDa dynein light chain) (DLC8) ...	0.00	-	cyt	0	Cytoplasm		601562	1CMI	89
P63169 UniProt NPD GO	DYL1_RABIT	Dynein light chain 1, cytoplasmic (Dynein light chain LC8-type 1) (8 kDa dynein light chain) (DLC8) ...	0.00	-	cyt	0	Cytoplasm (By similarity)				89
P63170 UniProt NPD GO	DYL1_RAT	Dynein light chain 1, cytoplasmic (Dynein light chain LC8-type 1) (8 kDa dynein light chain) (DLC8) ...	0.00	-	cyt	0	Cytoplasm (By similarity)			1F96	89
P63168 UniProt NPD GO	DYL1_MOUSE	Dynein light chain 1, cytoplasmic (Dynein light chain LC8-type 1) (8 kDa dynein light chain) (DLC8) ...	0.00	-	cyt	0	Cytoplasm (By similarity)				89
Q3MHR3 UniProt NPD GO	DYL2_BOVIN	Dynein light chain 2, cytoplasmic	0.00	-	cyt	0	Cytoplasm (By similarity)				89
O96860 UniProt NPD GO	DYL2_DROME	Dynein light chain 2, cytoplasmic (8 kDa dynein light chain)	0.00	-	cyt	0	Cytoplasm				89
Q96FJ2 UniProt NPD GO	DYL2_HUMAN	Dynein light chain 2, cytoplasmic (Dynein light chain LC8-type 2)	0.00	-	cyt	0	Cytoplasm (By similarity)	dynein complex [ISS] myosin [ISS]	608942		89
Q78P75 UniProt NPD GO	DYL2_RAT	Dynein light chain 2, cytoplasmic (Dynein light chain LC8-type 2)	0.00	-	cyt	0	Cytoplasm			1PWK	89
Q9D0M5 UniProt NPD GO	DYL2_MOUSE	Dynein light chain 2, cytoplasmic (Dynein light chain LC8-type 2) (8 kDa dynein light chain) (DLC8) ...	0.00	-	cyt	0	Cytoplasm	dynein complex [NAS] myosin [IDA]		1PWK	89
O02414 UniProt NPD GO	DYL1_ANTCR	Dynein light chain LC6, flagellar outer arm	0.00	-	cyt	0					89
Q5NVF5 UniProt NPD GO	DYLT3_PONPY	Dynein light chain Tctex-type 3	0.00	-	cyt	0					116
Q8SPS9 UniProt NPD GO	DYLT3_CANFA	Dynein light chain Tctex-type 3 (T-complex-associated testis-expressed 1-like)	0.00	-	cyt	0					116
Q6XXL8 UniProt NPD GO	DYLT3_SHEEP	Dynein light chain Tctex-type 3 (T-complex-associated testis-expressed 1-like)	0.00	-	cyt	0					116
P51808 UniProt NPD GO	DYLT3_HUMAN	Dynein light chain Tctex-type 3 (T-complex-associated testis-expressed 1-like) (Protein 91/23)	0.00	-	cyt	0			300302		116
P56387 UniProt NPD GO	DYLT3_MOUSE	Dynein light chain Tctex-type 3 (T-complex-associated testis-expressed 1-like) (Protein 91/23)	0.00	-	cyt	0					116
Q5G8Z3 UniProt NPD GO	EA1_MAIZE	EGG APPARATUS-1 protein (ZmEA1)	0.00	-	nuc	1 *	Membrane; single-pass type II membrane protein (Probable)				94
O42580 UniProt NPD GO	ERD2_XENLA	ER lumen protein retaining receptor (KDEL receptor) (KDEL endoplasmic reticulum protein retention re ...	0.00	-	end	4 *	Membrane; multi-pass membrane protein				214
P33946 UniProt NPD GO	ERD21_BOVIN	ER lumen protein retaining receptor 1 (KDEL receptor 1) (KDEL endoplasmic reticulum protein retentio ...	0.00	-	end	5 *	Membrane; multi-pass membrane protein				212
P24390 UniProt NPD GO	ERD21_HUMAN	ER lumen protein retaining receptor 1 (KDEL receptor 1) (KDEL endoplasmic reticulum protein retentio ...	0.00	-	end	4 *	Membrane; multi-pass membrane protein	ER-Golgi intermediate compartment [IDA] integral to membrane [TAS] membrane fraction [TAS]	131235		212
Q99JH8 UniProt NPD GO	ERD21_MOUSE	ER lumen protein retaining receptor 1 (KDEL receptor 1) (KDEL endoplasmic reticulum protein retentio ...	0.00	-	end	4 *	Membrane; multi-pass membrane protein				212
P53173 UniProt NPD GO	ERV14_YEAST	ER-derived vesicles protein ERV14	0.00	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum membrane [IDA] ER to Golgi transport vesicle [IDA]			137
Q9D172 UniProt NPD GO	ES1_MOUSE	ES1 protein homolog, mitochondrial precursor	0.00	-	mit	0	Mitochondrion (Potential)	mitochondrion [IDA]			266
P56571 UniProt NPD GO	ES1_RAT	ES1 protein homolog, mitochondrial precursor	0.00	-	mit	0	Mitochondrion (Potential)				266
P55962 UniProt NPD GO	NO40_TOBAC	Early nodulin 40 homolog	0.00	-		0					10
Q25481 UniProt NPD GO	ES16_MANSE	Ecdysteroid-regulated 16 kDa protein precursor	0.00	-	vac	0	Secreted protein (Potential)				145

You are viewing entries 94351 to 94400 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.