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
Q8BGN6 UniProt NPD GO	TMG4_MOUSE	Transmembrane gamma-carboxyglutamic acid protein 4 precursor (Proline-rich Gla protein 4) (Proline-r ...	0.37	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				226
Q3T144 UniProt NPD GO	T106C_BOVIN	Transmembrane protein 106C	0.37	-	mit	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				249
Q9BVX2 UniProt NPD GO	T106C_HUMAN	Transmembrane protein 106C (Endoplasmic reticulum membrane protein overexpressed in cancer)	0.37	-	mit	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				250
Q9ERP3 UniProt NPD GO	TRI54_MOUSE	Tripartite motif-containing protein 54 (Muscle-specific RING finger protein 3) (MuRF3) (MURF-3) (Mus ...	0.37	-	nuc	0	Cytoplasm. Associates with microtubules. Localizes to the Z-lines in skeletal muscles	microtubule associated complex [IDA]			366
Q923T7 UniProt NPD GO	TRIM7_MOUSE	Tripartite motif-containing protein 7 (Glycogenin-interacting protein)	0.37	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			510
Q9NG56 UniProt NPD GO	TPM_BLAGE	Tropomyosin	0.37	-	nuc	0					284
Q9NDS0 UniProt NPD GO	TPM_BRABE	Tropomyosin	0.37	-	nuc	0					284
Q9GZ70 UniProt NPD GO	TPM_PERVI	Tropomyosin	0.37	-	nuc	0					284
P17536 UniProt NPD GO	TPM1_YEAST	Tropomyosin 1	0.37	-	nuc	0		actin cable [IDA] contractile ring (sensu Saccharomyces) [IDA]			199
P07951 UniProt NPD GO	TPM2_HUMAN	Tropomyosin beta chain (Tropomyosin 2) (Beta-tropomyosin)	0.37	-	nuc	0		muscle thin filament tropomyosin [TAS]	609285		284
P58774 UniProt NPD GO	TPM2_MOUSE	Tropomyosin beta chain (Tropomyosin 2) (Beta-tropomyosin)	0.37	-	nuc	0		muscle thin filament tropomyosin [TAS]			284
P58776 UniProt NPD GO	TPM2_RABIT	Tropomyosin beta chain (Tropomyosin 2) (Beta-tropomyosin)	0.37	-	nuc	0					284
P58775 UniProt NPD GO	TPM2_RAT	Tropomyosin beta chain (Tropomyosin 2) (Beta-tropomyosin)	0.37	-	nuc	0					284
Q12594 UniProt NPD GO	DMAW_CLAFS	Tryptophan dimethylallyltransferase (EC 2.5.1.34) (DMATS) (All-trans-hexaprenyl-diphosphate synthase ...	0.37	-	cyt	0					455
Q9C141 UniProt NPD GO	DMAW2_CLAPU	Tryptophan dimethylallyltransferase 2 (EC 2.5.1.34) (DMATS 2) (All-trans-hexaprenyl-diphosphate synt ...	0.37	-	nuc	0					448
P17248 UniProt NPD GO	SYW_BOVIN	Tryptophanyl-tRNA synthetase (EC 6.1.1.2) (Tryptophan--tRNA ligase) (TrpRS)	0.37	-	cyt	0					476
P23612 UniProt NPD GO	SYW_RABIT	Tryptophanyl-tRNA synthetase (EC 6.1.1.2) (Tryptophan--tRNA ligase) (TrpRS)	0.37	-	cyt	0					475
Q41807 UniProt NPD GO	TBG1_MAIZE	Tubulin gamma-1 chain (Gamma-1 tubulin)	0.37	-	cyt	0					469
Q8K1H1 UniProt NPD GO	TDRD7_MOUSE	Tudor domain-containing protein 7 (Tudor repeat associator with PCTAIRE 2) (Trap)	0.37	-	cyt	0	Cytoplasm. Mainly				1086
O95407 UniProt NPD GO	TNR6B_HUMAN	Tumor necrosis factor receptor superfamily member 6B precursor (Decoy receptor for Fas ligand) (Deco ...	0.37	-	exc	0	Secreted protein	soluble fraction [TAS]	603361		300
Q96A56 UniProt NPD GO	T53I1_HUMAN	Tumor protein p53-inducible nuclear protein 1 (p53-dependent damage-inducible nuclear protein 1) (p5 ...	0.37	-	nuc	0	Nucleus. Concentrated in PML/POD/ND10 nuclear bodies		606185		240
Q61187 UniProt NPD GO	TS101_MOUSE	Tumor susceptibility gene 101 protein	0.37	-	nuc	0	Cytoplasm. Mainly. Membrane; peripheral membrane protein. Membrane-associated when active and solubl ...	nucleus [IC]			391
O80365 UniProt NPD GO	ARR8_ARATH	Two-component response regulator ARR8 (Response reactor 3)	0.37	-	nuc	0	Nucleus (Probable)				225
Q08963 UniProt NPD GO	RU2A_YEAST	U2 small nuclear ribonucleoprotein A' (U2 snRNP-A') (Looks exceptionally like U2A protein 1)	0.37	-	nuc	0	Nucleus	cytoplasm [IDA] snRNP U2 [IDA]			238
Q5JCS9 UniProt NPD GO	B3GN3_MOUSE	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3 (EC 2.4.1.-) (Beta3Gn-T3) (BGnT-3) (Co ...	0.37	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				372
Q9Y2A9 UniProt NPD GO	B3GN3_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3 (EC 2.4.1.-) (Beta3Gn-T3) (BGnT-3) (Co ...	0.37	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)	integral to plasma membrane [TAS]	605863		372
Q10409 UniProt NPD GO	YD84_SCHPO	UPF0293 protein C1F3.04c	0.37	-	nuc	0					288
Q29RK4 UniProt NPD GO	RD23B_BOVIN	UV excision repair protein RAD23 homolog B	0.37	-	nuc	0	Nucleus (By similarity)				408
Q4WLA7 UniProt NPD GO	UBC2_ASPFU	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase ubc2) (Ubiquitin carrier p ...	0.37	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				151
P43613 UniProt NPD GO	YFL1_YEAST	Uncharacterized J domain-containing protein YFR041C precursor	0.37	-	exc	2 *		endoplasmic reticulum [IDA]			295
P68537 UniProt NPD GO	MI25_TRITI	Uncharacterized mitochondrial 22 kDa protein (ORF 25)	0.37	-	exc	0					192
P68538 UniProt NPD GO	MI25_WHEAT	Uncharacterized mitochondrial 22 kDa protein (ORF 25)	0.37	-	exc	0					192
Q8N787 UniProt NPD GO	CR030_HUMAN	Uncharacterized protein C18orf30	0.37	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				583
Q6ZRH7 UniProt NPD GO	CS015_HUMAN	Uncharacterized protein C19orf15 precursor	0.37	-	end	1	Membrane; single-pass type I membrane protein (Potential)				1159
Q09766 UniProt NPD GO	YA7D_SCHPO	Uncharacterized protein C24H6.13	0.37	+	end	11 *	Membrane; multi-pass membrane protein (Potential)				871
P39735 UniProt NPD GO	YAC7_YEAST	Uncharacterized protein YAL027W	0.37	-	nuc	0		nucleus [IDA]			261
P38758 UniProt NPD GO	YHG9_YEAST	Uncharacterized protein YHR009C	0.37	-	nuc	0	Cytoplasm	cytoplasm [IDA]			523
P47072 UniProt NPD GO	YJB6_YEAST	Uncharacterized protein YJL016W/YJL017W	0.37	-	nuc	0	Cytoplasm	cytoplasm [IDA]			561
Q3E7Z9 UniProt NPD GO	YO038_YEAST	Uncharacterized protein YOL038C-A	0.37	-	nuc	0					31
Q12496 UniProt NPD GO	YO098_YEAST	Uncharacterized protein YOL098C	0.37	-	nuc	0		cytoplasm [IDA]			1037
Q03083 UniProt NPD GO	YP034_YEAST	Uncharacterized protein YPL034W	0.37	-	nuc	0					165
P40474 UniProt NPD GO	YIM1_YEAST	Uncharacterized transporter YIL121W	0.37	-	end	12	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [IDA]			542
O74834 UniProt NPD GO	UNG_SCHPO	Uracil-DNA glycosylase (EC 3.2.2.-) (UDG)	0.37	-	nuc	0	Nucleus	mitochondrion [IDA] nucleus [IDA]			322
Q05589 UniProt NPD GO	UROK_BOVIN	Urokinase-type plasminogen activator precursor (EC 3.4.21.73) (uPA) (U-plasminogen activator) [Conta ...	0.37	-	exc	0					433
P15120 UniProt NPD GO	UROK_CHICK	Urokinase-type plasminogen activator precursor (EC 3.4.21.73) (uPA) (U-plasminogen activator) [Conta ...	0.37	-	nuc	0					434
P29598 UniProt NPD GO	UROK_RAT	Urokinase-type plasminogen activator precursor (EC 3.4.21.73) (uPA) (U-plasminogen activator) [Conta ...	0.37	-	exc	0					432
Q9MB46 UniProt NPD GO	VATE_CITUN	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit)	0.37	-	nuc	0					230
Q9SWE7 UniProt NPD GO	VATE_CITLI	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit) ...	0.37	-	nuc	0					230
O43046 UniProt NPD GO	VATF_SCHPO	Vacuolar ATP synthase subunit F (EC 3.6.3.14) (V-ATPase F subunit) (Vacuolar proton pump F subunit) ...	0.37	-	cyt	0					120
Q920Q4 UniProt NPD GO	VPS16_MOUSE	Vacuolar protein sorting 16 (mVPS16)	0.37	-	cyt	0	Late endosome; late endosomal membrane; peripheral membrane protein (By similarity). Lysosome; lysos ...	actin filament [IDA] early endosome [IDA]			839

You are viewing entries 34601 to 34650 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.