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
Q2V2P4 UniProt NPD GO	YI156_YEAST	Uncharacterized protein YIL156W-B precursor	0.07	-	cyt	0					73
Q3E737 UniProt NPD GO	YJ047_YEAST	Uncharacterized protein YJL047C-A	0.07	-	nuc	0					44
Q8TGT3 UniProt NPD GO	YJ077_YEAST	Uncharacterized protein YJL077W-B	0.07	-	nuc	0					32
Q3E765 UniProt NPD GO	YK183_YEAST	Uncharacterized protein YKL183C-A	0.07	-	vac	1 *	Membrane; single-pass membrane protein (Potential)				70
Q3E814 UniProt NPD GO	YL006_YEAST	Uncharacterized protein YLL006W-A	0.07	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				58
Q3E767 UniProt NPD GO	YN067_YEAST	Uncharacterized protein YNL067W-B	0.07	-	cyt	0					46
Q08726 UniProt NPD GO	YO262_YEAST	Uncharacterized protein YOR262W	0.07	-	cyt	0	Cytoplasm	cytoplasm [IDA]			347
Q8TGJ0 UniProt NPD GO	YO394_YEAST	Uncharacterized protein YOR394C-A	0.07	-	mit	0					55
P38355 UniProt NPD GO	YB8B_YEAST	Uncharacterized transporter YBR287W	0.07	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			427
Q9SMN1 UniProt NPD GO	UMP8_ARATH	Unknown mitochondrial protein At3g48680	0.07	-	mit	0	Mitochondrion				256
P83899 UniProt NPD GO	NF19_NAEFO	Unknown protein NF019 from 2D-PAGE (Fragment)	0.07	-		0					20
P81106 UniProt NPD GO	UN01_PINPS	Unknown protein from 2D-PAGE of needles (S1247/S1248) (N150/N151) (Fragment)	0.07	-		0					15
P53766 UniProt NPD GO	UNG_DICDI	Uracil-DNA glycosylase (EC 3.2.2.-) (UDG) (Fragment)	0.07	-	nuc	0					257
P40751 UniProt NPD GO	TKU1_UREUN	Urechistachykinin-1 (Urechistachykinin I)	0.07	-		0	Secreted protein				10
Q93Z75 UniProt NPD GO	UPS5_ARATH	Ureide permease 5 (AtUPS5)	0.07	-	end	10 *	Membrane; multi-pass membrane protein (Probable)				413
Q8MKJ2 UniProt NPD GO	URIC_AOTTR	Uricase (EC 1.7.3.3) (Urate oxidase)	0.07	-	nuc	0	Peroxisome				303
P32347 UniProt NPD GO	DCUP_YEAST	Uroporphyrinogen decarboxylase (EC 4.1.1.37) (URO-D) (UPD)	0.07	-	nuc	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			362
O22886 UniProt NPD GO	DCUP_ARATH	Uroporphyrinogen decarboxylase, chloroplast precursor (EC 4.1.1.37) (URO-D) (UPD)	0.07	-	mit	0	Plastid; chloroplast				394
Q8VIH9 UniProt NPD GO	UR2R_MOUSE	Urotensin II receptor (UR-II-R) (G-protein coupled receptor 14)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				385
Q40002 UniProt NPD GO	VATA_HORVU	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.07	-	cyt	0					580
P49087 UniProt NPD GO	VATA_MAIZE	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.07	-	cyt	0					561
Q04238 UniProt NPD GO	VATA2_EQUAR	Vacuolar ATP synthase catalytic subunit A, isoform 2 (EC 3.6.3.14) (Fragment)	0.07	-	cyt	0					30
Q28029 UniProt NPD GO	VATF_BOVIN	Vacuolar ATP synthase subunit F (EC 3.6.3.14) (V-ATPase F subunit) (Vacuolar proton pump F subunit) ...	0.07	-	cyt	0					119
Q9D1K2 UniProt NPD GO	VATF_MOUSE	Vacuolar ATP synthase subunit F (EC 3.6.3.14) (V-ATPase F subunit) (Vacuolar proton pump F subunit) ...	0.07	-	cyt	0					119
Q9Y756 UniProt NPD GO	VATF_NEUCR	Vacuolar ATP synthase subunit F (EC 3.6.3.14) (V-ATPase F subunit) (Vacuolar proton pump F subunit) ...	0.07	-	cyt	0					124
P50408 UniProt NPD GO	VATF_RAT	Vacuolar ATP synthase subunit F (EC 3.6.3.14) (V-ATPase F subunit) (Vacuolar proton pump F subunit) ...	0.07	-	cyt	0					119
Q25531 UniProt NPD GO	VA0D_MANSE	Vacuolar ATP synthase subunit d (EC 3.6.3.14) (V-ATPase d subunit) (Vacuolar proton pump subunit d) ...	0.07	-	cyt	0					348
Q3E7B6 UniProt NPD GO	VA0E_YEAST	Vacuolar ATP synthase subunit e (EC 3.6.3.14) (V-ATPase e subunit) (Vacuolar proton pump e subunit) ...	0.07	-	end	2 *	Vacuole; vacuolar membrane; multi-pass membrane protein	hydrogen-transporting ATPase V0 domain [IMP] vacuolar membrane [IMP]			73
P40501 UniProt NPD GO	AVT7_YEAST	Vacuolar amino acid transporter 7	0.07	-	end	10 *	Vacuole; vacuolar membrane; multi-pass membrane protein				490
Q8I4T1 UniProt NPD GO	VPS26_PLAF7	Vacuolar protein sorting 26 homolog (VPS26 protein homolog)	0.07	-	cyt	0					297
Q5RJU0 UniProt NPD GO	SNF8_XENTR	Vacuolar sorting protein SNF8	0.07	-	cyt	0	Cytoplasm (By similarity)				257
Q12483 UniProt NPD GO	SNF8_YEAST	Vacuolar sorting protein SNF8 (Vacuolar protein sorting-associated protein VPS22)	0.07	-	cyt	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein	ESCRT II complex [IDA]		1W7P	233
O24326 UniProt NPD GO	VPE2_PHAVU	Vacuolar-processing enzyme precursor (EC 3.4.22.-) (Pv-VPE)	0.07	-	mit	0					493
Q9NH75 UniProt NPD GO	VA4_SOLGE	Venom allergen 4 precursor (Venom allergen IV) (Allergen Sol g 4)	0.07	-	mit	1 *	Secreted protein				137
P35780 UniProt NPD GO	VA5_POLFU	Venom allergen 5 (Antigen 5) (Ag5) (Allergen Pol f 5) (Pol f V)	0.07	-	nuc	0	Secreted protein. Venom reservoirs				205
P49266 UniProt NPD GO	TXP5_BRASM	Venom protein 5 (TXP5)	0.07	-	nuc	0	Secreted protein				34
Q9I8W9 UniProt NPD GO	VSP4_AGKAC	Venom serine proteinase Dav-X precursor (EC 3.4.21.-)	0.07	-	exc	0	Secreted protein				260
Q9P776 UniProt NPD GO	YNYF_SCHPO	Very hypothetical protein C1711.15c in chromosome II	0.07	-	cyt	0					32
O74973 UniProt NPD GO	YOKC_SCHPO	Very hypothetical protein C4B4.12c in chromosome II	0.07	-	cyt	0					110
O74506 UniProt NPD GO	YJD3_SCHPO	Very hypothetical protein C594.03 in chromosome III	0.07	-	mit	0					108
Q9QY76 UniProt NPD GO	VAPB_MOUSE	Vesicle-associated membrane protein-associated protein B (VAMP-associated protein B) (VAMP-associate ...	0.07	-	nuc	1	Cell membrane; single-pass type IV membrane protein (By similarity). Intracellular membrane; single- ...				242
Q16572 UniProt NPD GO	VACHT_HUMAN	Vesicular acetylcholine transporter (VAChT) (Solute carrier family 18 member 3)	0.07	-	end	10 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	600336		532
Q7M3T3 UniProt NPD GO	VESP_VESMA	Vespakinin-M	0.07	-		0	Secreted protein. Venom reservoirs				12
P02640 UniProt NPD GO	VILI_CHICK	Villin-1	0.07	-	cyt	0				2VIL	826
Q29261 UniProt NPD GO	VILI_PIG	Villin-1 (Fragment)	0.07	-	cyt	0					131
P01538 UniProt NPD GO	THN3_VISAL	Viscotoxin A3 precursor [Contains: Viscotoxin A3; Acidic protein]	0.07	-	exc	0	Secreted protein			1OKH	111
Q90578 UniProt NPD GO	VDHAP_CHICK	Vitamin D3 hydroxylase-associated protein (VDHAP)	0.07	-	nuc	0	Mitochondrion; mitochondrial inner membrane				463
P22891 UniProt NPD GO	PROZ_HUMAN	Vitamin K-dependent protein Z precursor	0.07	-	mit	0	Secreted protein		176895		400
P41366 UniProt NPD GO	VMO1_CHICK	Vitelline membrane outer layer protein 1 precursor (VMO-1) (VMO-I) (VMOI)	0.07	-	vac	0	Secreted protein			1VMO	183
Q9PS49 UniProt NPD GO	VMO2_CHICK	Vitelline membrane outer layer protein 2 (Vitelline membrane outer layer protein II) (VMO-II) (VMOII ...	0.07	-		0					20

You are viewing entries 71251 to 71300 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.