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
Q9GM50 UniProt NPD GO	UCHL1_HORSE	Ubiquitin carboxyl-terminal hydrolase isozyme L1 (EC 3.4.19.12) (EC 6.-.-.-) (UCH-L1) (Ubiquitin thi ...	0.11	-	nuc	0	Cytoplasm (By similarity)				223
Q5R8X4 UniProt NPD GO	UE1D1_PONPY	Ubiquitin-activating enzyme E1 domain-containing protein 1 (UFM1-activating enzyme)	0.11	-	nuc	1					404
Q9GZZ9 UniProt NPD GO	UE1D1_HUMAN	Ubiquitin-activating enzyme E1 domain-containing protein 1 (UFM1-activating enzyme) (Ubiquitin-activ ...	0.11	-	nuc	1					404
P15731 UniProt NPD GO	UBC4_YEAST	Ubiquitin-conjugating enzyme E2 4 (EC 6.3.2.19) (Ubiquitin-protein ligase 4) (Ubiquitin carrier prot ...	0.11	-	nuc	0		proteasome complex (sensu Eukaryota) [IPI]		1QCQ	148
Q2TA10 UniProt NPD GO	UB2D1_BOVIN	Ubiquitin-conjugating enzyme E2 D1 (EC 6.3.2.19) (Ubiquitin-protein ligase D1) (Ubiquitin carrier pr ...	0.11	-	nuc	0					147
P51668 UniProt NPD GO	UB2D1_HUMAN	Ubiquitin-conjugating enzyme E2 D1 (EC 6.3.2.19) (Ubiquitin-protein ligase D1) (Ubiquitin carrier pr ...	0.11	-	nuc	0			602961		147
P61080 UniProt NPD GO	UB2D1_MOUSE	Ubiquitin-conjugating enzyme E2 D1 (EC 6.3.2.19) (Ubiquitin-protein ligase D1) (Ubiquitin carrier pr ...	0.11	-	nuc	0					147
Q32LN1 UniProt NPD GO	UBE2H_BOVIN	Ubiquitin-conjugating enzyme E2 H (EC 6.3.2.19) (Ubiquitin-protein ligase H) (Ubiquitin carrier prot ...	0.11	-	cyt	0					183
P62257 UniProt NPD GO	UBE2H_MOUSE	Ubiquitin-conjugating enzyme E2 H (EC 6.3.2.19) (Ubiquitin-protein ligase H) (Ubiquitin carrier prot ...	0.11	-	cyt	0					183
P62256 UniProt NPD GO	UBE2H_HUMAN	Ubiquitin-conjugating enzyme E2 H (EC 6.3.2.19) (Ubiquitin-protein ligase H) (Ubiquitin carrier prot ...	0.11	-	cyt	0			601082	1YH6	183
Q9UBE0 UniProt NPD GO	ULE1A_HUMAN	Ubiquitin-like 1-activating enzyme E1A (SUMO-1-activating enzyme subunit 1)	0.11	-	cyt	0		nucleus [NAS]		1Y8R	346
O35445 UniProt NPD GO	RNF5_MOUSE	Ubiquitin-protein ligase RMA1 (EC 6.3.2.-) (RING finger protein 5)	0.11	-	cyt	2	Membrane; multi-pass membrane protein (Potential). Predominantly located in the plasma membrane, wit ...				180
Q5M807 UniProt NPD GO	RNF5_RAT	Ubiquitin-protein ligase RMA1 (EC 6.3.2.-) (RING finger protein 5)	0.11	-	cyt	2	Membrane; multi-pass membrane protein (Potential). Predominantly located in the plasma membrane, wit ...				180
Q9ZVJ2 UniProt NPD GO	AMR1_ARATH	Uncharacterized protein At2g38710	0.11	-	cyt	0					214
Q9NQ32 UniProt NPD GO	CK016_HUMAN	Uncharacterized protein C11orf16	0.11	-	cyt	0					404
Q9NRQ5 UniProt NPD GO	CK075_HUMAN	Uncharacterized protein C11orf75 (Protein FN5)	0.11	-	mit	1 *			609477		59
Q5RAS8 UniProt NPD GO	CQ032_PONPY	Uncharacterized protein C17orf32 homolog	0.11	-	end	2	Membrane; multi-pass membrane protein (Potential)				208
O95568 UniProt NPD GO	CA156_HUMAN	Uncharacterized protein C1orf156 (Arsenic-transactivated protein 2) (AsTP2)	0.11	-	cyt	0					372
P38331 UniProt NPD GO	YB92_YEAST	Uncharacterized protein YBR242W	0.11	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			238
P38343 UniProt NPD GO	YB9L_YEAST	Uncharacterized protein YBR266C	0.11	-	mit	2	Membrane; multi-pass membrane protein (Potential)				150
P25353 UniProt NPD GO	YCR6_YEAST	Uncharacterized protein YCR026C	0.11	-	mit	1					742
P53095 UniProt NPD GO	YGU6_YEAST	Uncharacterized protein YGL196W	0.11	-	cyt	0					428
P53077 UniProt NPD GO	YGX6_YEAST	Uncharacterized protein YGL226W	0.11	-	mit	1		mitochondrion [IDA]			123
P53332 UniProt NPD GO	YG5T_YEAST	Uncharacterized protein YGR277C	0.11	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			305
P40540 UniProt NPD GO	YIC7_YEAST	Uncharacterized protein YIL027C	0.11	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			141
Q3E798 UniProt NPD GO	YL099_YEAST	Uncharacterized protein YLR099W-A	0.11	-	cyt	0					87
Q3E7Z2 UniProt NPD GO	YN042_YEAST	Uncharacterized protein YNL042W-B	0.11	-	nuc	0					85
P53729 UniProt NPD GO	YN8H_YEAST	Uncharacterized protein YNR029C	0.11	-	cyt	0		cytoplasm [IDA]			429
Q12274 UniProt NPD GO	YOR97_YEAST	Uncharacterized protein YOR097C	0.11	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				175
Q3E7Y7 UniProt NPD GO	YO293_YEAST	Uncharacterized protein YOR293C-A	0.11	-	mit	0					49
Q08912 UniProt NPD GO	YO389_YEAST	Uncharacterized protein YOR389W precursor	0.11	-	mit	1 *	Secreted protein (Potential)				624
P83890 UniProt NPD GO	NF15_NAEFO	Unknown protein NF015 from 2D-PAGE (Fragment)	0.11	-		0					20
Q9ZQ89 UniProt NPD GO	UPS2_ARATH	Ureide permease 2 (AtUPS2)	0.11	-	end	10 *	Membrane; multi-pass membrane protein (Probable)				398
P32362 UniProt NPD GO	DCUP_RAT	Uroporphyrinogen decarboxylase (EC 4.1.1.37) (URO-D) (UPD) (Fragment)	0.11	-	mit	0	Cytoplasm				364
Q9Z109 UniProt NPD GO	VSIG2_MOUSE	V-set and immunoglobulin domain-containing protein 2 precursor (CT-like protein) (Cortical thymocyte ...	0.11	-	nuc	1 *	Membrane; single-pass type I membrane protein (Potential)				328
P37296 UniProt NPD GO	STV1_YEAST	Vacuolar ATP synthase subunit a, Golgi isoform (EC 3.6.3.14) (V-ATPase 101 kDa subunit) (V-ATPase su ...	0.11	-	end	7	Endosome; endosomal membrane; multi-pass membrane protein. Golgi apparatus; Golgi membrane; multi-pa ...	Golgi apparatus [IDA] hydrogen-transporting ATPase V0 domain [IGI] late endosome [IDA]			890
P53659 UniProt NPD GO	VA0D_NEUCR	Vacuolar ATP synthase subunit d (EC 3.6.3.14) (V-ATPase d subunit) (Vacuolar proton pump subunit d) ...	0.11	-	nuc	0					364
P40336 UniProt NPD GO	VP26A_MOUSE	Vacuolar protein sorting 26A (Vesicle protein sorting 26A) (mVPS26) (H58 protein) (H beta 58)	0.11	-	cyt	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein	cytosol [ISS] endosome [IDA]			327
P53142 UniProt NPD GO	VPS73_YEAST	Vacuolar protein sorting protein 73	0.11	-	end	10 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Probable)	mitochondrion [IDA]			486
P49043 UniProt NPD GO	VPE_CITSI	Vacuolar-processing enzyme precursor (EC 3.4.22.-) (VPE)	0.11	-	exc	0					494
P46216 UniProt NPD GO	SYV_TRIVA	Valyl-tRNA synthetase (EC 6.1.1.9) (Valine--tRNA ligase) (ValRS) (Fragment)	0.11	-	cyt	0					489
P92127 UniProt NPD GO	VS41_GIALA	Variant-specific surface protein VSP4A1 precursor (CRISP-90)	0.11	-	exc	1	Cell membrane; single-pass type I membrane protein				687
P35777 UniProt NPD GO	VA4_SOLIN	Venom allergen 4 precursor (Venom allergen IV) (Allergen Sol i 4) (Sol i IV)	0.11	-	mit	0	Secreted protein				137
Q05110 UniProt NPD GO	VA5_VESVU	Venom allergen 5 precursor (Antigen 5) (Ag5) (Allergen Ves v 5) (Ves v V)	0.11	-	nuc	0	Secreted protein. Venom reservoirs			1QNX	227
P38209 UniProt NPD GO	YBB2_YEAST	Very hypothetical protein YBL012C	0.11	-	mit	1					133
P36074 UniProt NPD GO	YKL1_YEAST	Very hypothetical protein YKL111C	0.11	-	cyt	0					111
P53922 UniProt NPD GO	YNM0_YEAST	Very hypothetical protein YNL120C	0.11	-	nuc	1					161
O35488 UniProt NPD GO	S27A2_MOUSE	Very-long-chain acyl-CoA synthetase (EC 6.2.1.-) (VLCS) (Very-long-chain-fatty-acid-CoA ligase) (VLA ...	0.11	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...	endoplasmic reticulum [TAS] mitochondrion [IDA] peroxisome [TAS]			620
Q9Z2P8 UniProt NPD GO	VAMP5_MOUSE	Vesicle-associated membrane protein 5 (VAMP-5) (Myobrevin)	0.11	-	mit	1	Cell membrane; single-pass type IV membrane protein (Probable). Intracellular membrane; single-pass ...	integral to plasma membrane [IDA]			102
P32880 UniProt NPD GO	THN2_VISAL	Viscotoxin A2	0.11	-	nuc	0	Secreted protein			1JMN	46

You are viewing entries 63701 to 63750 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.