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
Q1XDQ6 UniProt NPD GO	IF3C_PORYE	Translation initiation factor IF-3, chloroplast	0.44	-	nuc	0	Plastid; chloroplast				182
Q5R461 UniProt NPD GO	TMM10_PONPY	Transmembrane protein 10	0.44	-	nuc	1 *	Membrane; single-pass membrane protein				141
Q9H8W5 UniProt NPD GO	TRI45_HUMAN	Tripartite motif-containing protein 45 (RING finger protein 99)	0.44	-	cyt	0	Cytoplasm. Nucleus		609318		580
Q7TNM2 UniProt NPD GO	TRI46_MOUSE	Tripartite motif-containing protein 46 (Tripartite, fibronectin type-III and C-terminal SPRY motif p ...	0.44	-	cyt	0					759
Q5IS74 UniProt NPD GO	TPP1_PANTR	Tripeptidyl-peptidase 1 precursor (EC 3.4.14.9) (Tripeptidyl-peptidase I) (TPP-I) (Tripeptidyl amino ...	0.44	-	mit	0	Lysosome (By similarity)				563
P53781 UniProt NPD GO	TTP_BOVIN	Tristetraproline (TTP) (Zinc finger protein 36 homolog) (Zfp-36) (TIS11A protein) (TIS11)	0.44	-	nuc	0	Nucleus				324
P70567 UniProt NPD GO	TMOD1_RAT	Tropomodulin-1 (Erythrocyte tropomodulin) (E-Tmod)	0.44	-	nuc	0					359
O97192 UniProt NPD GO	TPM_HELAS	Tropomyosin (Allergen Hel as 1)	0.44	-	nuc	0					284
P27673 UniProt NPD GO	TNNI3_CHICK	Troponin I, cardiac muscle (Cardiac troponin I) (Fragment)	0.44	-	nuc	0					168
Q9XFG3 UniProt NPD GO	TBG_PHYPA	Tubulin gamma chain (Gamma tubulin)	0.44	-	cyt	0					475
Q5U508 UniProt NPD GO	TBCE_XENLA	Tubulin-specific chaperone E (Tubulin-folding cofactor E)	0.44	-	nuc	0					522
Q80VL1 UniProt NPD GO	TDRKH_MOUSE	Tudor and KH domain-containing protein	0.44	-	nuc	1 *				1WE8	560
O60522 UniProt NPD GO	TDRD6_HUMAN	Tudor domain-containing protein 6 (Aantigen NY-CO-45) (Fragment)	0.44	-	nuc	0					753
P50592 UniProt NPD GO	TNF10_MOUSE	Tumor necrosis factor ligand superfamily member 10 (TNF-related apoptosis-inducing ligand) (Protein ...	0.44	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				291
Q8CFU8 UniProt NPD GO	T53I2_MOUSE	Tumor protein p53-inducible nuclear protein 2 (Diabetes and obesity-regulated protein)	0.44	-	nuc	0	Nucleus (By similarity)				221
Q5ZM35 UniProt NPD GO	TWF2_CHICK	Twinfilin-2	0.44	-	cyt	0	Cytoplasm (By similarity). Cytoplasm; perinuclear region (By similarity). Perinuclear and G-actin-ri ...				349
Q9BMN8 UniProt NPD GO	LAR_CAEEL	Tyrosine-protein phosphatase Lar-like precursor (EC 3.1.3.48) (Protein-tyrosine phosphate 3)	0.44	-	mit	1 *	Cell membrane; cell-cell junction; adherens junction; single-pass type I membrane protein	adherens junction [IMP]			2200
Q9D1H6 UniProt NPD GO	CF066_MOUSE	UPF0240 protein C6orf66 homolog	0.44	-	nuc	0					173
Q5DHJ5 UniProt NPD GO	U360_SCHJA	UPF0360 protein	0.44	-	nuc	0					330
Q9WUP7 UniProt NPD GO	UCHL5_MOUSE	Ubiquitin carboxyl-terminal hydrolase isozyme L5 (EC 3.4.19.12) (UCH-L5) (Ubiquitin thioesterase L5) ...	0.44	-	nuc	0					329
Q96DC9 UniProt NPD GO	OTUB2_HUMAN	Ubiquitin thioesterase protein OTUB2 (EC 3.4.-.-) (Otubain 2) (OTU domain-containing ubiquitin aldeh ...	0.44	-	cyt	0			608338	1TFF	234
Q58FS2 UniProt NPD GO	UBC2_TRIHA	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC2) (Ubiquitin carrier p ...	0.44	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				151
P78717 UniProt NPD GO	UBC2_NECHA	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC2) (Ubiquitin carrier p ...	0.44	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				151
Q93408 UniProt NPD GO	YRGK_CAEEL	Uncharacterized protein D2005.3	0.44	-	nuc	0					130
Q02831 UniProt NPD GO	YP077_YEAST	Uncharacterized protein YPL077C	0.44	-	nuc	0					240
Q9U1G5 UniProt NPD GO	VATE_HETSC	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit)	0.44	-	nuc	0					226
Q63615 UniProt NPD GO	VP33A_RAT	Vacuolar protein sorting 33A (r-vps33a)	0.44	-	cyt	0	Late endosome; late endosomal membrane; peripheral membrane protein (By similarity). Lysosome; lysos ...				597
P38932 UniProt NPD GO	VPS45_YEAST	Vacuolar protein sorting-associated protein 45	0.44	-	nuc	0	Cytoplasm. Vacuole; vacuolar membrane; peripheral membrane protein; cytoplasmic side. Cycles between ...	cytosol [IDA] extrinsic to membrane [IDA] Golgi membrane [IDA]			577
P07208 UniProt NPD GO	VSIB_TRYBB	Variant surface glycoprotein ILTAT 1.1BC precursor (VSG)	0.44	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				471
Q9XS49 UniProt NPD GO	VEGFB_BOVIN	Vascular endothelial growth factor B precursor (VEGF-B) (VEGF-related factor) (VRF)	0.44	-	exc	0	Secreted protein (By similarity). Secreted but remains associated to cells or to the extracellular m ...				207
Q28858 UniProt NPD GO	CSPG2_MACNE	Versican core protein (Large fibroblast proteoglycan) (Chondroitin sulfate proteoglycan core protein ...	0.44	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				862
Q9LVP9 UniProt NPD GO	VTI13_ARATH	Vesicle transport v-SNARE 13 (AtVTI13) (Vesicle transport v-SNARE protein VTI13) (Vesicle soluble NS ...	0.44	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				221
Q6BZQ6 UniProt NPD GO	BOS1_YARLI	Vesicular transport protein BOS1	0.44	-	nuc	1	Secretory vesicle; secretory vesicle membrane; peripheral membrane protein (By similarity). Secretor ...				226
O81643 UniProt NPD GO	VILI1_ARATH	Villin-1	0.44	-	nuc	0					910
P26234 UniProt NPD GO	VINC_PIG	Vinculin (Metavinculin)	0.44	-	nuc	0	Cytoskeleton. Cell membrane; cell-cell junction; adherens junction; cytoplasmic side. Cell membrane; ...	adherens junction [ISS] costamere [ISS] focal adhesion [ISS] intercellular junction [ISS]			1134
Q04615 UniProt NPD GO	VINC_XENLA	Vinculin (Metavinculin) (Fragment)	0.44	-	nuc	0	Cytoskeleton. Cell membrane; cell-cell junction; adherens junction; cytoplasmic side. Cell membrane; ...				235
P48819 UniProt NPD GO	VTNC_PIG	Vitronectin precursor (Serum-spreading factor) (S-protein)	0.44	-	exc	0	Secreted protein; extracellular space				459
Q02789 UniProt NPD GO	CAC1S_MOUSE	Voltage-dependent L-type calcium channel subunit alpha-1S (Voltage-gated calcium channel subunit alp ...	0.44	+	end	19	Membrane; multi-pass membrane protein				1880
Q9H1F0 UniProt NPD GO	WF10A_HUMAN	WAP four-disulfide core domain protein 10A precursor (Putative protease inhibitor WAP10A)	0.44	-	exc	1 *	Secreted protein (Potential)				79
Q7ZVL2 UniProt NPD GO	WDR24_BRARE	WD repeat protein 24	0.44	-	mit	0					779
Q9H6Y2 UniProt NPD GO	WDR55_HUMAN	WD repeat protein 55	0.44	-	cyt	0					383
Q96DI7 UniProt NPD GO	WDR57_HUMAN	WD repeat protein 57 (Prp8-binding protein) (hPRP8BP) (U5 snRNP-specific 40 kDa protein) (38 kDa-spl ...	0.44	-	mit	0	Nucleus				357
Q9C8K2 UniProt NPD GO	WBC12_ARATH	White-brown complex homolog protein 12 (Protein ECERIFERUM5)	0.44	+	end	7	Cell membrane; multi-pass membrane protein				687
Q9C8J8 UniProt NPD GO	WBC13_ARATH	White-brown complex homolog protein 13	0.44	-	end	5	Membrane; multi-pass membrane protein (By similarity)				678
Q06250 UniProt NPD GO	WIT1_HUMAN	Wilms' tumor-associated protein (WIT-1) (Wilms tumor upstream neighbor 1 gene protein)	0.44	-	mit	0			607899		92
O43516 UniProt NPD GO	WASIP_HUMAN	Wiskott-Aldrich syndrome protein-interacting protein (WASP-interacting protein) (PRPL-2 protein)	0.44	-	nuc	0	Vesicle surfaces and along actin tails. Co-localized with actin stress fibers. When co-expressed wit ...	actin cytoskeleton [TAS]	602357	2A41	503
P42826 UniProt NPD GO	XKS1_YEAST	Xylulose kinase (EC 2.7.1.17) (Xylulokinase)	0.44	-	nuc	0		cytoplasm [IDA]			600
Q4R8V9 UniProt NPD GO	YJDC_MACFA	YjeF domain-containing protein 1	0.44	-	nuc	0	Cytoplasm (By similarity). Processing bodies (PB) (By similarity)				508
O48772 UniProt NPD GO	ZFN2_ARATH	Zinc finger CCCH domain-containing protein ZFN2	0.44	-	nuc	0	Nucleus (By similarity)				453
Q13105 UniProt NPD GO	ZBT17_HUMAN	Zinc finger and BTB domain-containing protein 17 (Zinc finger protein 151) (Myc-interacting zinc fin ...	0.44	-	nuc	0	Nucleus		604084		803

You are viewing entries 29351 to 29400 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.