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
P30087 UniProt NPD GO	UPA1_HUMAN	Unknown protein from 2D-PAGE of plasma (Spot 2) (Fragment)	0.09	-		0					8
P18562 UniProt NPD GO	UPP_YEAST	Uracil phosphoribosyltransferase (EC 2.4.2.9) (UMP pyrophosphorylase) (UPRTase)	0.09	-	mit	0		intracellular [IC]			251
Q13336 UniProt NPD GO	UT1_HUMAN	Urea transporter, erythrocyte	0.09	-	end	8	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	111000		389
Q9ZPR7 UniProt NPD GO	UPS1_ARATH	Ureide permease 1 (AtUPS1)	0.09	-	end	10 *	Membrane; multi-pass membrane protein				390
Q3MHG7 UniProt NPD GO	URIC_BOVIN	Uricase (EC 1.7.3.3) (Urate oxidase)	0.09	-	cyt	0	Peroxisome (By similarity)				303
P27515 UniProt NPD GO	URK1_YEAST	Uridine kinase (EC 2.7.1.48) (Uridine monophosphokinase)	0.09	-	mit	0		cytoplasm [IDA] nucleus [IDA]			501
P38196 UniProt NPD GO	FUI1_YEAST	Uridine permease	0.09	-	end	10	Membrane; multi-pass membrane protein	plasma membrane [IGI]			639
O81220 UniProt NPD GO	DCUP_MAIZE	Uroporphyrinogen decarboxylase, chloroplast precursor (EC 4.1.1.37) (URO-D) (UPD)	0.09	-	mit	0	Plastid; chloroplast				393
P51163 UniProt NPD GO	HEM4_MOUSE	Uroporphyrinogen-III synthase (EC 4.2.1.75) (UROS) (Uroporphyrinogen-III cosynthetase) (Hydroxymethy ...	0.09	-	nuc	0					265
P49684 UniProt NPD GO	UR2R_RAT	Urotensin II receptor (UR-II-R) (G-protein coupled receptor 14) (G-protein coupled sensory epithelia ...	0.09	-	end	7	Membrane; multi-pass membrane protein				386
P21857 UniProt NPD GO	UTS2_PLAFE	Urotensin-2 precursor (Urotensin II) (U-II) (UII) (Fragments)	0.09	-	cyt	0	Secreted protein				83
Q765I0 UniProt NPD GO	UTS2B_HUMAN	Urotensin-2B precursor (Urotensin-IIB) (U-IIB) (UIIB) (Urotensin II-related peptide) (Urotensin 2 do ...	0.09	-	exc	1 *	Secreted protein (By similarity)				119
Q96IQ7 UniProt NPD GO	VSIG2_HUMAN	V-set and immunoglobulin domain-containing protein 2 precursor (CT-like protein) (Cortical thymocyte ...	0.09	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)		606011		327
Q26975 UniProt NPD GO	VATA_TRYCO	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.09	-	cyt	0					610
Q9XGM1 UniProt NPD GO	VATD_ARATH	Vacuolar ATP synthase subunit D (EC 3.6.3.14) (V-ATPase D subunit) (Vacuolar proton pump D subunit)	0.09	-	cyt	0					261
P51863 UniProt NPD GO	VA0D_MOUSE	Vacuolar ATP synthase subunit d (EC 3.6.3.14) (V-ATPase d subunit) (Vacuolar proton pump subunit d) ...	0.09	-	cyt	0					351
P38176 UniProt NPD GO	AVT5_YEAST	Vacuolar amino acid transporter 5	0.09	-	end	9 *	Vacuole; vacuolar membrane; multi-pass membrane protein				459
O01258 UniProt NPD GO	VPS26_CAEEL	Vacuolar protein sorting 26 homolog (VPS26 protein homolog)	0.09	-	cyt	0					356
P15920 UniProt NPD GO	VPP2_MOUSE	Vacuolar proton translocating ATPase 116 kDa subunit a isoform 2 (V-ATPase 116 kDa isoform a2) (Immu ...	0.09	-	end	6	Membrane; multi-pass membrane protein (By similarity)	acrosome [IDA]			856
Q9Y487 UniProt NPD GO	VPP2_HUMAN	Vacuolar proton translocating ATPase 116 kDa subunit a isoform 2 (V-ATPase 116 kDa isoform a2) (TJ6) ...	0.09	-	end	6	Membrane; multi-pass membrane protein (By similarity)				856
P09194 UniProt NPD GO	PHLC_TRYBB	Variant-surface-glycoprotein phospholipase C (EC 4.6.1.14) (VSG lipase) (Glycosylphosphatidylinosito ...	0.09	-	cyt	0	Membrane; peripheral membrane protein				358
Q28992 UniProt NPD GO	VIPR1_PIG	Vasoactive intestinal polypeptide receptor 1 precursor (VIP-R-1) (Pituitary adenylate cyclase-activa ...	0.09	-	end	8 *	Membrane; multi-pass membrane protein				458
P14327 UniProt NPD GO	VSH7_DICDI	Vegetative-specific protein H7	0.09	-	nuc	0					104
P35778 UniProt NPD GO	VA3_SOLIN	Venom allergen 3 precursor (Venom allergen III) (Allergen Sol i 3) (Sol i III)	0.09	-	nuc	0					234
P00991 UniProt NPD GO	IVBI1_VIPAA	Venom basic protease inhibitor 1 (Venom trypsin inhibitor I)	0.09	-	nuc	0	Secreted protein				61
O94299 UniProt NPD GO	YOOG_SCHPO	Very hypothetical protein C887.16 in chromosome II	0.09	-	nuc	1					109
Q14138 UniProt NPD GO	Y0125_HUMAN	Very hypothetical protein KIAA0125	0.09	-	exc	0					76
P38173 UniProt NPD GO	YBJ4_YEAST	Very hypothetical protein YBL094C	0.09	-	nuc	1	Membrane; multi-pass membrane protein (Potential)				110
O14975 UniProt NPD GO	S27A2_HUMAN	Very-long-chain acyl-CoA synthetase (EC 6.2.1.-) (VLCS) (Very-long-chain-fatty-acid-CoA ligase) (VLA ...	0.09	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Peroxisome; pero ...	endoplasmic reticulum [TAS] peroxisomal matrix [TAS]	603247		620
Q587I9 UniProt NPD GO	SFT2C_HUMAN	Vesicle transport protein SFT2C (SFT2 domain-containing protein 3)	0.09	-	end	4	Membrane; multi-pass membrane protein (Potential)				215
Q9FMR5 UniProt NPD GO	VA714_ARATH	Vesicle-associated membrane protein 714 (AtVAMP714)	0.09	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				221
Q9Z269 UniProt NPD GO	VAPB_RAT	Vesicle-associated membrane protein-associated protein B (VAMP-associated protein B) (VAMP-B) (VAP-B ...	0.09	-	nuc	1	Cell membrane; single-pass type IV membrane protein (By similarity). Intracellular membrane; single- ...				242
O65039 UniProt NPD GO	CYSEP_RICCO	Vignain precursor (EC 3.4.22.-) (Cysteine endopeptidase)	0.09	-	end	0	The pro-endopeptidase accumulates in the ricinosomes			1S4V	360
P83416 UniProt NPD GO	VIRE_HELVI	Virescein	0.09	-	cyt	0	Secreted protein				41
P97382 UniProt NPD GO	KCAB3_MOUSE	Voltage-gated potassium channel subunit beta-3 (K(+) channel subunit beta-3) (Kv-beta-3)	0.09	-	mit	0	Cytoplasm (Potential)				249
Q7YRP2 UniProt NPD GO	VN1R4_PONPY	Vomeronasal type-1 receptor 4 (V1r-like receptor 4)	0.09	-	end	3 *	Membrane; multi-pass membrane protein				301
Q9JHY3 UniProt NPD GO	WFD12_MOUSE	WAP four-disulfide core domain protein 12 precursor (Whey acidic protein 2) (Single WAP motif protei ...	0.09	-	exc	0	Secreted protein (Potential)				85
Q28894 UniProt NPD GO	WFDC2_CANFA	WAP four-disulfide core domain protein 2 precursor (Major epididymis-specific protein E4) (CE4) (Epi ...	0.09	-	exc	0	Secreted protein (Potential)				124
Q28631 UniProt NPD GO	WFDC2_RABIT	WAP four-disulfide core domain protein 2 precursor (Major epididymis-specific protein E4) (Epididyma ...	0.09	-	exc	0	Secreted protein				123
Q7ZUW6 UniProt NPD GO	WIPI3_BRARE	WD repeat domain phosphoinositide-interacting protein 3 (WIPI-3) (WD repeat protein 45-like) (WDR45- ...	0.09	-	cyt	0					344
Q9CR39 UniProt NPD GO	WIPI3_MOUSE	WD repeat domain phosphoinositide-interacting protein 3 (WIPI-3) (WD repeat protein 45-like) (WDR45- ...	0.09	-	cyt	0					344
Q5MNZ6 UniProt NPD GO	WIPI3_HUMAN	WD repeat domain phosphoinositide-interacting protein 3 (WIPI-3) (WD repeat protein 45-like) (WDR45- ...	0.09	-	cyt	0			609226		344
Q8NBT0 UniProt NPD GO	WD51A_HUMAN	WD repeat protein 51A	0.09	-	cyt	0					407
P61962 UniProt NPD GO	WDR68_HUMAN	WD repeat protein 68 (WD repeat protein An11 homolog)	0.09	-	nuc	0	Cytoplasm (Probable)	cytoplasm [TAS]	605973		342
P61963 UniProt NPD GO	WDR68_MOUSE	WD repeat protein 68 (WD repeat protein An11 homolog)	0.09	-	nuc	0	Cytoplasm (Probable)				342
P25676 UniProt NPD GO	TXW1C_HEMHA	Weak toxin CM-1c	0.09	-	nuc	0	Secreted protein				61
P01412 UniProt NPD GO	TXW1_OPHHA	Weak toxin DE-1	0.09	-	nuc	0	Secreted protein				60
O43895 UniProt NPD GO	XPP2_HUMAN	Xaa-Pro aminopeptidase 2 precursor (EC 3.4.11.9) (X-Pro aminopeptidase 2) (Membrane-bound aminopepti ...	0.09	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	membrane [TAS]	300145		674
P38951 UniProt NPD GO	XEN2_XENLA	Xenoxin-2	0.09	-	nuc	0	Secreted protein				66
Q39099 UniProt NPD GO	XTH4_ARATH	Xyloglucan endotransglucosylase/hydrolase protein 4 precursor (EC 2.4.1.207) (At-XTH4) (XTH-4)	0.09	-	exc	1 *	Secreted protein; extracellular space; apoplast (Probable)	cell wall (sensu Magnoliophyta) [IDA] cytoplasm [IDA]			296

You are viewing entries 67301 to 67350 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.