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
Q5VUM1 UniProt NPD GO	CF057_HUMAN	Uncharacterized protein C6orf57 precursor	0.27	-	mit	0	Secreted protein (Potential)				108
P39563 UniProt NPD GO	YAN4_YEAST	Uncharacterized protein YAR064W	0.27	-	nuc	0					99
P25366 UniProt NPD GO	YCY5_YEAST	Uncharacterized protein YCR095C	0.27	-	nuc	0		cytoplasm [IDA]			362
Q8TGU4 UniProt NPD GO	YE175_YEAST	Uncharacterized protein YER175W-A	0.27	-	nuc	0					54
Q8TGU2 UniProt NPD GO	YF032_YEAST	Uncharacterized protein YFR032C-B	0.27	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				87
P43611 UniProt NPD GO	YFK9_YEAST	Uncharacterized protein YFR039C	0.27	-	mit	0					510
P36136 UniProt NPD GO	YK23_YEAST	Uncharacterized protein YKR043C	0.27	-	mit	0		cytoplasm [IDA] nucleus [IDA]			271
Q06538 UniProt NPD GO	YL241_YEAST	Uncharacterized protein YLR241W	0.27	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				782
Q8TGS4 UniProt NPD GO	YM315_YEAST	Uncharacterized protein YMR315W-A precursor	0.27	-	mit	0					35
P53898 UniProt NPD GO	YNP6_YEAST	Uncharacterized protein YNL156C	0.27	-	cyt	2	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			299
P42840 UniProt NPD GO	YN60_YEAST	Uncharacterized protein YNL320W	0.27	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				284
P15700 UniProt NPD GO	UMPK_YEAST	Uridylate kinase (EC 2.7.4.-) (UK) (Uridine monophosphate kinase) (UMP kinase)	0.27	-	cyt	0	Cytoplasm. 80%: Nucleus. 20%	cytoplasm [IDA] nucleus [IDA]		1UKZ	204
Q9GK80 UniProt NPD GO	UPAR_PANTR	Urokinase plasminogen activator surface receptor precursor (uPAR) (U-PAR)	0.27	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				335
Q03405 UniProt NPD GO	UPAR_HUMAN	Urokinase plasminogen activator surface receptor precursor (uPAR) (U-PAR) (Monocyte activation antig ...	0.27	-	exc	0	Isoform 1: Cell membrane; lipid-anchor; GPI-anchor. Isoform 2: Secreted protein (Probable)	cell surface [IEP] extrinsic to membrane [TAS] integral to membrane [NAS] plasma membrane [TAS]	173391	1YWH	335
P49616 UniProt NPD GO	UPAR_RAT	Urokinase plasminogen activator surface receptor, GPI-anchored form precursor (uPAR) (U-PAR) (CD87 a ...	0.27	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				328
P04185 UniProt NPD GO	UROK_PIG	Urokinase-type plasminogen activator precursor (EC 3.4.21.73) (uPA) (U-plasminogen activator) [Conta ...	0.27	-	exc	0					442
P31411 UniProt NPD GO	VATB_SCHPO	Vacuolar ATP synthase subunit B (EC 3.6.3.14) (V-ATPase B subunit) (Vacuolar proton pump B subunit) ...	0.27	-	cyt	0					503
Q01278 UniProt NPD GO	VATE_NEUCR	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit) ...	0.27	-	cyt	0					230
Q8R307 UniProt NPD GO	VPS18_MOUSE	Vacuolar protein sorting 18	0.27	-	cyt	0	Late endosome; late endosomal membrane; peripheral membrane protein (By similarity). Lysosome; lysos ...	actin filament [IDA] early endosome [IDA]			973
Q6TNP8 UniProt NPD GO	VP26A_BRARE	Vacuolar protein sorting 26A (Vesicle protein sorting 26A)	0.27	-	cyt	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein (By similarity)				327
Q5E9A6 UniProt NPD GO	VPS25_BOVIN	Vacuolar protein sorting protein 25	0.27	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Distributes diffusely throughout the cytoplasm a ...				176
Q91XD6 UniProt NPD GO	VPS36_MOUSE	Vacuolar protein sorting protein 36	0.27	-	cyt	0	Cytoplasm (By similarity). Endosome; late endosome (By similarity). Colocalizes with ubiquitinated p ...	late endosome [IDA] lysosome [IDA]			386
Q13488 UniProt NPD GO	VPP3_HUMAN	Vacuolar proton translocating ATPase 116 kDa subunit a isoform 3 (V-ATPase 116 kDa isoform a3) (Oste ...	0.27	+	end	8	Membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS] plasma membrane [TAS]	604592		830
P26331 UniProt NPD GO	VSM1_TRYBB	Variant surface glycoprotein MITAT 1.1 precursor (VSG)	0.27	-	nuc	1 *	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				492
P50412 UniProt NPD GO	VEGFA_SHEEP	Vascular endothelial growth factor A precursor (VEGF-A) (Vascular permeability factor) (VPF)	0.27	-	exc	0					146
P48974 UniProt NPD GO	V1BR_RAT	Vasopressin V1b receptor (V1bR) (AVPR V1b) (Vasopressin V3 receptor) (AVPR V3) (Antidiuretic hormone ...	0.27	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IDA]			425
P32307 UniProt NPD GO	V2R_PIG	Vasopressin V2 receptor (Renal-type arginine vasopressin receptor) (Antidiuretic hormone receptor) ( ...	0.27	-	end	7 *	Membrane; multi-pass membrane protein				370
P16041 UniProt NPD GO	NEU3_ONCKE	Vasotocin-neurophysin VT 1 precursor [Contains: Vasotocin (VT); Neurophysin VT 1]	0.27	-	exc	0	Secreted protein				153
O74332 UniProt NPD GO	YH0C_SCHPO	Very hypothetical protein C1685.12c precursor	0.27	-	nuc	0					117
Q9UT66 UniProt NPD GO	YQA5_SCHPO	Very hypothetical protein C4F11.05 in chromosome III	0.27	-	nuc	0					80
P63026 UniProt NPD GO	VAMP2_BOVIN	Vesicle-associated membrane protein 2 (VAMP-2) (Synaptobrevin-2)	0.27	-	nuc	1	Synaptic vesicle; synaptic vesicle membrane; single-pass type IV membrane protein. Neuronal synaptic ...				115
P63027 UniProt NPD GO	VAMP2_HUMAN	Vesicle-associated membrane protein 2 (VAMP-2) (Synaptobrevin-2)	0.27	-	nuc	1	Synaptic vesicle; synaptic vesicle membrane; single-pass type IV membrane protein. Neuronal synaptic ...		185881	1F83	115
P63044 UniProt NPD GO	VAMP2_MOUSE	Vesicle-associated membrane protein 2 (VAMP-2) (Synaptobrevin-2)	0.27	-	nuc	1	Synaptic vesicle; synaptic vesicle membrane; single-pass type IV membrane protein. Neuronal synaptic ...	secretory granule [IDA] synaptic vesicle membrane [IDA] zymogen granule membrane [IDA]			115
P63045 UniProt NPD GO	VAMP2_RAT	Vesicle-associated membrane protein 2 (VAMP-2) (Synaptobrevin-2)	0.27	-	nuc	1	Synaptic vesicle; synaptic vesicle membrane; single-pass type IV membrane protein. Neuronal synaptic ...	plasma membrane [IDA] secretory granule [IPI]		2BU0	115
O75379 UniProt NPD GO	VAMP4_HUMAN	Vesicle-associated membrane protein 4 (VAMP-4)	0.27	-	nuc	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type IV membrane pro ...	endosome [TAS] Golgi membrane [TAS] lysosome [TAS]	606909		141
P18708 UniProt NPD GO	NSF_CRIGR	Vesicle-fusing ATPase (EC 3.6.4.6) (Vesicular-fusion protein NSF) (N-ethylmaleimide sensitive fusion ...	0.27	-	cyt	0	Cytoplasm			1QDN	744
Q91498 UniProt NPD GO	VACHT_TORMA	Vesicular acetylcholine transporter (VAChT) (Vesamicol-binding protein)	0.27	-	end	10 *	Membrane; multi-pass membrane protein				511
P54351 UniProt NPD GO	NSF2_DROME	Vesicular-fusion protein Nsf2 (N-ethylmaleimide-sensitive fusion protein 2) (NEM-sensitive fusion pr ...	0.27	-	nuc	0	Cytoplasm	cytoplasm [NAS]			752
P22728 UniProt NPD GO	VISI_CHICK	Visinin	0.27	-	mit	0					191
P19518 UniProt NPD GO	CCG1_RABIT	Voltage-dependent calcium channel gamma-1 subunit (Dihydropyridine-sensitive L-type, skeletal muscle ...	0.27	-	end	4 *	Membrane; multi-pass membrane protein				222
Q9PTM5 UniProt NPD GO	KCAB2_XENLA	Voltage-gated potassium channel subunit beta-2 (K(+) channel subunit beta-2) (Kv-beta-2)	0.27	-	nuc	0	Cytoplasm (Potential)				367
Q8IUB2 UniProt NPD GO	WFDC3_HUMAN	WAP four-disulfide core domain protein 3 precursor (Putative protease inhibitor WAP14)	0.27	-	exc	0	Secreted protein (Potential)				231
Q8R3E3 UniProt NPD GO	WIPI1_MOUSE	WD repeat domain phosphoinositide-interacting protein 1 (WIPI-1) (WD40 repeat protein interacting wi ...	0.27	-	nuc	0	Trans elements of the Golgi and peripheral endosomes. Dynamically cycles through these compartments ...				446
Q6PFM9 UniProt NPD GO	WDR48_BRARE	WD repeat protein 48	0.27	-	nuc	0	Lysosome (By similarity)				677
Q5F3K4 UniProt NPD GO	WDR48_CHICK	WD repeat protein 48	0.27	-	nuc	0	Lysosome (By similarity)				678
O54775 UniProt NPD GO	WISP1_MOUSE	WNT1-inducible signaling pathway protein 1 precursor (WISP-1) (ELM-1)	0.27	-	mit	0	Secreted protein (By similarity)				367
O76076 UniProt NPD GO	WISP2_HUMAN	WNT1-inducible signaling pathway protein 2 precursor (WISP-2) (Connective tissue growth factor-like ...	0.27	-	nuc	0	Secreted protein (Probable)	soluble fraction [TAS]	603399		250
P22811 UniProt NPD GO	XDH_DROPS	Xanthine dehydrogenase (EC 1.17.1.4) (XD) (Protein rosy locus)	0.27	-	cyt	0	Peroxisome				1343
Q9FKK7 UniProt NPD GO	XYLA_ARATH	Xylose isomerase (EC 5.3.1.5)	0.27	-	exc	0					472
O95619 UniProt NPD GO	YETS4_HUMAN	YEATS domain-containing protein 4 (Glioma-amplified sequence-41) (Gas41) (NuMA-binding protein 1) (N ...	0.27	-	cyt	0	Nucleus	nucleus [TAS]	602116		227

You are viewing entries 43801 to 43850 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.