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
P23398 UniProt NPD GO	UBIQ_STRPU	Ubiquitin	0.22	-	nuc	0	Cytoplasm. Nucleus				76
Q17361 UniProt NPD GO	UBP14_CAEEL	Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.1.2.15) (Ubiquitin thioesterase 14) (Ubiquitin-specif ...	0.22	+	cyt	0					489
Q5ZIJ9 UniProt NPD GO	MIB2_CHICK	Ubiquitin ligase protein MIB2 (EC 6.3.2.-) (Mind bomb homolog 2)	0.22	-	nuc	0	Cytoplasm (By similarity)				954
O94609 UniProt NPD GO	UBA1_SCHPO	Ubiquitin-activating enzyme E1 1 (Poly(A)+ RNA transport protein 3)	0.22	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			1012
O42646 UniProt NPD GO	UBC6_SCHPO	Ubiquitin-conjugating enzyme E2 6 (EC 6.3.2.19) (Ubiquitin-protein ligase ubc6) (Ubiquitin carrier p ...	0.22	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane (By similarity)				227
Q05948 UniProt NPD GO	YL225_YEAST	Uncharacterized SVF1-like protein YLR225C	0.22	-	nuc	0	Cytoplasm	cytoplasm [IDA]			407
Q06139 UniProt NPD GO	YL346_YEAST	Uncharacterized mitochondrial protein YLR346C	0.22	-	nuc	0	Mitochondrion	mitochondrion [IDA]			101
Q12746 UniProt NPD GO	YMM5_YEAST	Uncharacterized oxidoreductase YML125C (EC 1.-.-.-)	0.22	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			312
Q96MM1 UniProt NPD GO	CN081_HUMAN	Uncharacterized protein C14orf81	0.22	+	cyt	0					181
Q9D742 UniProt NPD GO	CT029_MOUSE	Uncharacterized protein C20orf29 homolog	0.22	-	mit	0					170
Q96KT6 UniProt NPD GO	CH014_HUMAN	Uncharacterized protein C8orf14	0.22	-	nuc	0					92
Q12378 UniProt NPD GO	YD066_YEAST	Uncharacterized protein YDR066C	0.22	-	cyt	0	Cytoplasm	cytoplasm [IDA]			196
P40098 UniProt NPD GO	YE12_YEAST	Uncharacterized protein YER182W	0.22	-	mit	1 *	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			244
P38844 UniProt NPD GO	YHU3_YEAST	Uncharacterized protein YHR143W precursor	0.22	-	exc	0		cell wall (sensu Fungi) [IDA] extracellular region [IDA]			325
Q8TGT2 UniProt NPD GO	YK096_YEAST	Uncharacterized protein YKL096C-B	0.22	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				49
Q3E760 UniProt NPD GO	YM030_YEAST	Uncharacterized protein YMR030W-A	0.22	-	nuc	1	Membrane; single-pass membrane protein (Potential)				96
Q04773 UniProt NPD GO	YMW4_YEAST	Uncharacterized protein YMR074C	0.22	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			145
Q12351 UniProt NPD GO	YO012_YEAST	Uncharacterized protein YOR012W	0.22	-	nuc	0					137
Q12032 UniProt NPD GO	YO215_YEAST	Uncharacterized protein YOR215C, mitochondrial precursor	0.22	-	mit	0	Mitochondrion	mitochondrion [IDA]			185
Q01630 UniProt NPD GO	UNC33_CAEEL	Uncoordinated protein 33 (Protein unc-33)	0.22	-	nuc	0	Cytoplasm				854
P32528 UniProt NPD GO	DUR1_YEAST	Urea amidolyase [Includes: Urea carboxylase (EC 6.3.4.6); Allophanate hydrolase (EC 3.5.1.54)]	0.22	-	nuc	0		cytoplasm [IDA]			1835
Q9USJ5 UniProt NPD GO	DCUP_SCHPO	Uroporphyrinogen decarboxylase (EC 4.1.1.37) (URO-D) (UPD)	0.22	-	mit	0	Cytoplasm (By similarity)				370
Q95J46 UniProt NPD GO	UTS2_PIG	Urotensin-2 precursor (Urotensin-II) (U-II) (UII)	0.22	-	exc	0	Secreted protein				121
P11592 UniProt NPD GO	VATA_NEUCR	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.22	-	cyt	0					607
P32366 UniProt NPD GO	VA0D_YEAST	Vacuolar ATP synthase subunit d (EC 3.6.3.14) (V-ATPase d subunit) (Vacuolar proton pump subunit d) ...	0.22	-	cyt	0	Vacuole; vacuolar membrane; peripheral membrane protein	hydrogen-transporting ATPase V0 domain [TAS] vacuolar membrane [IDA]			345
Q5TKG3 UniProt NPD GO	CAX1B_ORYSA	Vacuolar cation/proton exchanger 1b (Ca(2+)/H(+) exchanger 1b) (OsCAX1b)	0.22	-	end	10	Vacuole; vacuolar membrane; multi-pass membrane protein (Probable). Tonoplast				453
P28350 UniProt NPD GO	SYV_NEUCR	Valyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.9) (Valine--tRNA ligase) (ValRS)	0.22	-	mit	0	Mitochondrion. Cytoplasm				1093
O13057 UniProt NPD GO	VSP2_TRIFL	Venom serine proteinase 2 precursor (EC 3.4.21.-)	0.22	-	mit	0	Secreted protein				260
P83962 UniProt NPD GO	ANFV_ACITR	Ventricular natriuretic peptide precursor	0.22	-	end	1 *	Secreted protein				145
P38252 UniProt NPD GO	YBT9_YEAST	Very hypothetical protein YBR089W	0.22	-	nuc	0					199
Q62442 UniProt NPD GO	VAMP1_MOUSE	Vesicle-associated membrane protein 1 (VAMP-1) (Synaptobrevin-1)	0.22	-	nuc	1	Synaptic vesicle; synaptic vesicle membrane; single-pass type IV membrane protein. Neuronal synaptic ...				118
Q9WV55 UniProt NPD GO	VAPA_MOUSE	Vesicle-associated membrane protein-associated protein A (VAMP-associated protein A) (VAMP-A) (VAP-A ...	0.22	-	nuc	1	Cell membrane; single-pass type IV membrane protein (By similarity). Intracellular membrane; single- ...	endoplasmic reticulum [IDA] microtubule [IDA]		2CRI	242
P08943 UniProt NPD GO	THNB_VISAL	Viscotoxin B precursor [Contains: Viscotoxin B; Acidic protein] (Fragment)	0.22	-	nuc	0	Secreted protein			1ORL	103
P83554 UniProt NPD GO	THNC_VISAL	Viscotoxin C1	0.22	-	mit	0				1ORL	46
Q14722 UniProt NPD GO	KCAB1_HUMAN	Voltage-gated potassium channel subunit beta-1 (K(+) channel subunit beta-1) (Kv-beta-1)	0.22	-	nuc	0	Cytoplasm (Potential)		601141		419
Q5J3L4 UniProt NPD GO	V1B14_RAT	Vomeronasal type-1 receptor B14	0.22	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				319
Q9DAU7 UniProt NPD GO	WFDC2_MOUSE	WAP four-disulfide core domain protein 2 precursor (WAP domain-containing protein HE4)	0.22	-	exc	1 *	Secreted protein (Potential)				174
Q9NYS7 UniProt NPD GO	WSB2_HUMAN	WD repeat and SOCS box-containing protein 2 (WSB-2) (CS box-containing WD protein)	0.22	-	cyt	0					404
Q8TBZ3 UniProt NPD GO	WDR20_HUMAN	WD repeat protein 20 (DMR protein)	0.22	-	nuc	0					569
Q8NA23 UniProt NPD GO	WDR31_HUMAN	WD repeat protein 31	0.22	-	mit	0					367
Q6P2Y2 UniProt NPD GO	WDR69_XENTR	WD repeat protein 69	0.22	-	mit	0					415
P09837 UniProt NPD GO	WAP_CAMDR	Whey acidic protein (WAP)	0.22	-	nuc	0	Secreted protein				117
Q9Y5W5 UniProt NPD GO	WIF1_HUMAN	Wnt inhibitory factor 1 precursor (WIF-1)	0.22	-	exc	0	Secreted protein		605186	2D3J	379
Q9SB61 UniProt NPD GO	Y4466_ARATH	ZF-HD homeobox protein At4g24660 (AtHB-22)	0.22	-	nuc	0	Nucleus (Probable)			1WH7	220
Q5NAV3 UniProt NPD GO	ZFNL3_ORYSA	Zinc finger CCCH domain-containing protein ZFN-like 3	0.22	-	nuc	0	Nucleus (By similarity)				466
O43345 UniProt NPD GO	ZN208_HUMAN	Zinc finger protein 208	0.22	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	606760		1167
Q8N7Q3 UniProt NPD GO	ZN676_HUMAN	Zinc finger protein 676	0.22	-	nuc	0	Nucleus (Probable)				404
P51503 UniProt NPD GO	ZNF80_GORGO	Zinc finger protein 80	0.22	-	nuc	0	Nucleus (Probable)				273
Q5RFP4 UniProt NPD GO	OZF_PONPY	Zinc finger protein OZF (Only zinc finger protein) (Zinc finger protein 146)	0.22	-	nuc	0	Nucleus (By similarity)				292
Q9VSL7 UniProt NPD GO	FOI_DROME	Zinc transporter foi precursor (Protein fear-of-intimacy) (Protein kastchen)	0.22	-	end	6	Cell membrane; multi-pass membrane protein	integral to plasma membrane [IDA] plasma membrane [IDA]			706

You are viewing entries 49051 to 49100 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.