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
P38081 UniProt NPD GO	YBQ6_YEAST	Uncharacterized glycosyl hydrolase YBR056W (EC 3.2.1.-)	0.14	-	cyt	0		cytoplasm [IDA]			501
Q4WLB9 UniProt NPD GO	YA090_ASPFU	Uncharacterized protein Afu6g14090 precursor	0.14	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				305
Q9CPY6 UniProt NPD GO	CQ039_MOUSE	Uncharacterized protein C17orf39 homolog	0.14	-	cyt	0					217
Q9NUB4 UniProt NPD GO	CT141_HUMAN	Uncharacterized protein C20orf141	0.14	-	end	0					165
P25587 UniProt NPD GO	YCA5_YEAST	Uncharacterized protein YCL005W	0.14	-	mit	2 *		lipid particle [IDA] mitochondrion [IDA]			256
P25566 UniProt NPD GO	YCD3_YEAST	Uncharacterized protein YCL033C	0.14	-	mit	0					168
P25607 UniProt NPD GO	YCZ1_YEAST	Uncharacterized protein YCR101C	0.14	-	end	0		membrane fraction [IDA]			182
P53209 UniProt NPD GO	YG1A_YEAST	Uncharacterized protein YGR016W	0.14	-	end	4	Membrane; multi-pass membrane protein (Potential)				190
P53314 UniProt NPD GO	YG59_YEAST	Uncharacterized protein YGR247W	0.14	-	cyt	0					239
Q12253 UniProt NPD GO	YL046_YEAST	Uncharacterized protein YLR046C	0.14	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				270
Q8TGJ4 UniProt NPD GO	YL466_YEAST	Uncharacterized protein YLR466C-B	0.14	-	nuc	0					38
Q08300 UniProt NPD GO	YO159_YEAST	Uncharacterized protein YOL159C	0.14	-	exc	0	Cytoplasm (Probable)	soluble fraction [IDA]			171
Q09504 UniProt NPD GO	YQI2_CAEEL	Uncharacterized tRNA-dihydrouridine synthase-like protein C45G9.2 (EC 1.-.-.-)	0.14	-	mit	0					284
Q6A3P9 UniProt NPD GO	UREA_ASPFU	Urease (EC 3.5.1.5) (Urea amidohydrolase)	0.14	-	cyt	0					838
P11645 UniProt NPD GO	URIC_RABIT	Uricase (EC 1.7.3.3) (Urate oxidase)	0.14	-	cyt	0	Peroxisome				300
P17559 UniProt NPD GO	UTER_RAT	Uteroglobin precursor (Secretoglobin family 1A member 1) (Clara cell phospholipid-binding protein) ( ...	0.14	-	exc	0	Secreted protein			1UTR	96
Q9Y279 UniProt NPD GO	VSIG4_HUMAN	V-set and immunoglobulin domain-containing protein 4 precursor (Protein Z39Ig)	0.14	-	end	1	Membrane; single-pass type I membrane protein (Probable)		300353		399
P04566 UniProt NPD GO	VIP_CAVPO	VIP peptides precursor [Contains: Intestinal peptide PHI-27 (Peptide histidine isoleucinamide 27); V ...	0.14	-	cyt	0	Secreted protein				72
Q26976 UniProt NPD GO	VATB_TRYCO	Vacuolar ATP synthase subunit B (EC 3.6.3.14) (V-ATPase B subunit) (Vacuolar proton pump B subunit)	0.14	-	cyt	0					485
P31409 UniProt NPD GO	VATB_DROME	Vacuolar ATP synthase subunit B (EC 3.6.3.14) (V-ATPase B subunit) (Vacuolar proton pump B subunit) ...	0.14	-	cyt	0					490
P62814 UniProt NPD GO	VATB2_MOUSE	Vacuolar ATP synthase subunit B, brain isoform (EC 3.6.3.14) (V-ATPase B2 subunit) (Vacuolar proton ...	0.14	-	cyt	0	Membrane; peripheral membrane protein. Endomembrane				511
P62815 UniProt NPD GO	VATB2_RAT	Vacuolar ATP synthase subunit B, brain isoform (EC 3.6.3.14) (V-ATPase B2 subunit) (Vacuolar proton ...	0.14	-	cyt	0	Membrane; peripheral membrane protein (By similarity). Endomembrane (By similarity)				511
P21281 UniProt NPD GO	VATB2_HUMAN	Vacuolar ATP synthase subunit B, brain isoform (EC 3.6.3.14) (V-ATPase B2 subunit) (Vacuolar proton ...	0.14	-	cyt	0	Membrane; peripheral membrane protein. Endomembrane		606939		511
O13687 UniProt NPD GO	VATE_SCHPO	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit) ...	0.14	-	cyt	0					227
P39981 UniProt NPD GO	AVT2_YEAST	Vacuolar amino acid transporter 2	0.14	-	end	11	Vacuole; vacuolar membrane; multi-pass membrane protein	endoplasmic reticulum [NAS]			480
Q9W552 UniProt NPD GO	VPS26_DROME	Vacuolar protein sorting 26 homolog (VPS26 protein homolog)	0.14	-	nuc	0					478
P49047 UniProt NPD GO	VPEA_ARATH	Vacuolar-processing enzyme alpha-isozyme precursor (EC 3.4.22.-) (Alpha-VPE)	0.14	-	end	1 *	Vacuole				478
Q39044 UniProt NPD GO	VPEB_ARATH	Vacuolar-processing enzyme beta-isozyme precursor (EC 3.4.22.-) (Beta-VPE)	0.14	-	exc	0	Vacuole				486
O24325 UniProt NPD GO	VPE1_PHAVU	Vacuolar-processing enzyme precursor (EC 3.4.22.-) (VPE) (Legumain-like proteinase) (LLP)	0.14	-	vac	1 *					484
P10736 UniProt NPD GO	VA52_DOLMA	Venom allergen 5.01 precursor (Antigen 5 form 2) (Ag5-2) (Allergen Dol m 5.01) (Dol m V-A)	0.14	-	nuc	1 *	Secreted protein. Venom reservoirs				227
P84032 UniProt NPD GO	PN16_PHONI	Venom protein PN16C3	0.14	-	nuc	0	Secreted protein				128
Q9PT40 UniProt NPD GO	VSP2_VIPLE	Venom serine proteinase-like protein 2 precursor	0.14	-	exc	0	Secreted protein (Potential)				260
O94341 UniProt NPD GO	YHM8_SCHPO	Very hypothetical protein C1271.08c in chromosome II	0.14	-	nuc	1	Membrane; multi-pass membrane protein (Potential)				140
P45953 UniProt NPD GO	ACADV_RAT	Very-long-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.-) (VLCAD)	0.14	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [TAS]			655
P50544 UniProt NPD GO	ACADV_MOUSE	Very-long-chain specific acyl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.-) (VLCAD) (MVLC ...	0.14	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA]			656
O23429 UniProt NPD GO	VA724_ARATH	Vesicle-associated membrane protein 724 (AtVAMP724) (SYBL1-like protein)	0.14	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				222
O48850 UniProt NPD GO	VA725_ARATH	Vesicle-associated membrane protein 725 (AtVAMP725)	0.14	-	end	2 *	Membrane; single-pass type IV membrane protein (By similarity)				285
O95292 UniProt NPD GO	VAPB_HUMAN	Vesicle-associated membrane protein-associated protein B/C (VAMP-associated protein B/C) (VAMP-B/VAM ...	0.14	-	nuc	1	Cell membrane; single-pass type IV membrane protein (By similarity). Intracellular membrane; single- ...	integral to plasma membrane [TAS]	608627		242
P46461 UniProt NPD GO	NSF1_DROME	Vesicular-fusion protein Nsf1 (N-ethylmaleimide-sensitive fusion protein 1) (NEM-sensitive fusion pr ...	0.14	-	cyt	0	Cytoplasm	cytoplasm [NAS]			745
Q9CQW3 UniProt NPD GO	PROZ_MOUSE	Vitamin K-dependent protein Z precursor	0.14	-	mit	0	Secreted protein	extracellular region [IDA]			399
P07447 UniProt NPD GO	VCLY_TEGPF	Vitelline coat lysin	0.14	-	nuc	0					118
Q7YRP1 UniProt NPD GO	VN1R5_GORGO	Vomeronasal type-1 receptor 5 (V1r-like receptor 5)	0.14	-	end	7 *	Membrane; multi-pass membrane protein				357
Q3SZD4 UniProt NPD GO	WDR18_BOVIN	WD repeat protein 18	0.14	-	nuc	0					432
Q3UDP0 UniProt NPD GO	WDR41_MOUSE	WD repeat protein 41	0.14	-	cyt	0					460
Q4R8E7 UniProt NPD GO	WDR69_MACFA	WD repeat protein 69	0.14	-	cyt	0					415
Q802B2 UniProt NPD GO	TW10_NAJSP	Weak neurotoxin 10 precursor (Wntx-10)	0.14	-	gol	1 *	Secreted protein				86
Q5GH77 UniProt NPD GO	XKR3_HUMAN	XK-related protein 3 (XTES)	0.14	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				459
Q9HCN4 UniProt NPD GO	XAB1_HUMAN	XPA-binding protein 1	0.14	-	cyt	0	Cytoplasm				374
Q96DZ1 UniProt NPD GO	XTP3B_HUMAN	XTP3-transactivated gene B protein precursor	0.14	-	mit	0	Secreted protein (Potential)				483
Q5R830 UniProt NPD GO	XYLB_PONPY	Xylulose kinase (EC 2.7.1.17) (Xylulokinase)	0.14	-	cyt	0					580

You are viewing entries 59201 to 59250 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.