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
Q751U4 UniProt NPD GO	UCR7_ASHGO	Ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2) (Complex III subunit VII)	0.15	-	cyt	0	Mitochondrion; mitochondrial inner membrane (Potential)				126
P08565 UniProt NPD GO	UBIQ_TRYCR	Ubiquitin	0.15	-	cyt	0	Cytoplasm. Nucleus				76
Q921A3 UniProt NPD GO	UBD_RAT	Ubiquitin D (Ubiquitin-like protein FAT10) (Diubiquitin)	0.15	-	nuc	0					161
Q68LP1 UniProt NPD GO	MIB2_RAT	Ubiquitin ligase protein MIB2 (EC 6.3.2.-) (Mind bomb homolog 2) (RBSC-skeletrophin/dystrophin-like ...	0.15	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity). Colocalizes with endosomal compartments (By sim ...				971
Q8N2K1 UniProt NPD GO	UB2J2_HUMAN	Ubiquitin-conjugating enzyme E2 J2 (EC 6.3.2.19) (Non-canonical ubiquitin-conjugating enzyme 2) (NCU ...	0.15	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein (By simi ...			2F4W	259
Q9Z2R6 UniProt NPD GO	UN119_MOUSE	Unc-119 protein homolog (Retinal protein 4) (MRG4)	0.15	-	nuc	0					240
Q6QA74 UniProt NPD GO	CN109_PIG	Uncharacterized protein C14orf109 homolog	0.15	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				163
Q6AXS8 UniProt NPD GO	CR010_RAT	Uncharacterized protein C18orf10 homolog	0.15	-	nuc	0					249
Q9CZ09 UniProt NPD GO	CA156_MOUSE	Uncharacterized protein C1orf156 homolog	0.15	-	cyt	0					362
Q5JX69 UniProt NPD GO	CT107_HUMAN	Uncharacterized protein C20orf107 precursor	0.15	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)				171
Q8TCU8 UniProt NPD GO	CH015_HUMAN	Uncharacterized protein C8orf15	0.15	-	nuc	0					101
P25576 UniProt NPD GO	YCE7_YEAST	Uncharacterized protein YCL047C	0.15	-	cyt	0					258
P25659 UniProt NPD GO	YCW6_YEAST	Uncharacterized protein YCR076C	0.15	-	nuc	0					250
P40045 UniProt NPD GO	YEQ1_YEAST	Uncharacterized protein YER071C	0.15	-	nuc	0		cytoplasm [IDA]			126
P43591 UniProt NPD GO	YFH7_YEAST	Uncharacterized protein YFR007W	0.15	-	nuc	0					353
P43622 UniProt NPD GO	YFM4_YEAST	Uncharacterized protein YFR054C	0.15	-	nuc	0					192
Q3E744 UniProt NPD GO	YG161_YEAST	Uncharacterized protein YGR161W-C	0.15	-	nuc	0					92
P38837 UniProt NPD GO	YHT3_YEAST	Uncharacterized protein YHR133C	0.15	-	end	5	Membrane; multi-pass membrane protein (Potential)				291
Q05809 UniProt NPD GO	YL218_YEAST	Uncharacterized protein YLR218C	0.15	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			150
Q3E825 UniProt NPD GO	YL307_YEAST	Uncharacterized protein YLR307C-A	0.15	-	mit	0					87
Q3E823 UniProt NPD GO	YP189_YEAST	Uncharacterized protein YPL189C-A	0.15	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				68
Q12428 UniProt NPD GO	YP002_YEAST	Uncharacterized protein YPR002W	0.15	-	nuc	0		cytoplasm [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			516
P40445 UniProt NPD GO	YIQ6_YEAST	Uncharacterized transporter YIL166C	0.15	-	end	12	Membrane; multi-pass membrane protein (Potential)				542
Q12235 UniProt NPD GO	YL055_YEAST	Uncharacterized transporter YLL055W	0.15	-	end	10	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			531
P80612 UniProt NPD GO	UC06_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 1131) (Fragment)	0.15	-		0					15
P82333 UniProt NPD GO	UT118_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 118) (Fragment)	0.15	-		0	Plastid; chloroplast; chloroplast thylakoid				14
P38572 UniProt NPD GO	UPK1A_BOVIN	Uroplakin-1a (Uroplakin Ia) (UPIa)	0.15	-	end	4 *	Membrane; multi-pass membrane protein	endoplasmic reticulum [IDA] integral to membrane [IDA] plasma membrane [IDA]			258
O00322 UniProt NPD GO	UPK1A_HUMAN	Uroplakin-1a (Uroplakin Ia) (UPIa) (UPKa) (Tetraspanin-21) (Tspan-21)	0.15	-	end	4 *	Membrane; multi-pass membrane protein	endoplasmic reticulum [ISS] integral to membrane [ISS] plasma membrane [TAS]			258
Q06318 UniProt NPD GO	UTER_MOUSE	Uteroglobin precursor (Secretoglobin family 1A member 1) (Clara cell phospholipid-binding protein) ( ...	0.15	-	exc	0	Secreted protein				96
P54647 UniProt NPD GO	VATA_DICDI	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.15	-	cyt	0					618
Q40079 UniProt NPD GO	VATB2_HORVU	Vacuolar ATP synthase subunit B isoform 2 (EC 3.6.3.14) (V-ATPase B subunit 2) (Vacuolar proton pump ...	0.15	-	cyt	0					483
P15313 UniProt NPD GO	VATB1_HUMAN	Vacuolar ATP synthase subunit B, kidney isoform (EC 3.6.3.14) (V-ATPase B1 subunit) (Vacuolar proton ...	0.15	-	cyt	0	Membrane; peripheral membrane protein. Endomembrane		267300		513
P21283 UniProt NPD GO	VATC_HUMAN	Vacuolar ATP synthase subunit C (EC 3.6.3.14) (V-ATPase C subunit) (Vacuolar proton pump C subunit)	0.15	-	cyt	0		proton-transporting two-sector ATPase complex [TAS]	603097		381
Q9U5N1 UniProt NPD GO	VATC_MANSE	Vacuolar ATP synthase subunit C (EC 3.6.3.14) (V-ATPase C subunit) (Vacuolar proton pump C subunit)	0.15	-	cyt	0					385
O74920 UniProt NPD GO	VPH2_SCHPO	Vacuolar ATPase assembly integral membrane protein vph2	0.15	-	mit	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				186
Q6IRD0 UniProt NPD GO	V26AA_XENLA	Vacuolar protein sorting 26A-A (Vesicle protein sorting 26A-A)	0.15	-	cyt	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein (By similarity)				326
P38085 UniProt NPD GO	VAL1_YEAST	Valine/tyrosine/tryptophan amino-acid permease	0.15	-	end	12	Membrane; multi-pass membrane protein				619
P06013 UniProt NPD GO	VSI0_TRYBB	Variant surface glycoprotein ILTAT 1.2 (VSG) (Fragment)	0.15	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				320
P26333 UniProt NPD GO	VSM5_TRYBB	Variant surface glycoprotein MITAT 1.5 precursor (VSG 118)	0.15	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				474
Q90308 UniProt NPD GO	VIPR_CARAU	Vasoactive intestinal polypeptide receptor (VIP-R) (VIP receptor)	0.15	-	end	7	Membrane; multi-pass membrane protein				447
P01181 UniProt NPD GO	NEU2_SHEEP	Vasopressin-neurophysin 2-copeptin precursor (AVP-NPII) [Contains: Arg-vasopressin; Neurophysin 2 (N ...	0.15	-	nuc	0	Secreted protein				147
Q86RQ7 UniProt NPD GO	VPI_MESMA	Venom peptide BmKAPi precursor (Putative anticoagulant peptide BmAP1)	0.15	-	exc	1 *	Secreted protein				89
O94293 UniProt NPD GO	YOO8_SCHPO	Very hypothetical protein C887.08 in chromosome II	0.15	-	nuc	0					124
O49377 UniProt NPD GO	VA711_ARATH	Vesicle-associated membrane protein 711 (AtVAMP711) (v-SNARE synaptobrevin 7C) (AtVAMP7C)	0.15	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				219
Q9ZTW3 UniProt NPD GO	VA721_ARATH	Vesicle-associated membrane protein 721 (AtVAMP721) (v-SNARE synaptobrevin 7B) (AtVAMP7B)	0.15	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				219
P47192 UniProt NPD GO	VA722_ARATH	Vesicle-associated membrane protein 722 (AtVAMP722) (Synaptobrevin-related protein 1)	0.15	-	nuc	1	Membrane; single-pass type IV membrane protein (Probable)				221
Q28487 UniProt NPD GO	VACHT_MACFU	Vesicular acetylcholine transporter (VAChT) (Solute carrier family 18 member 3) (Fragment)	0.15	-	nuc	0	Membrane; multi-pass membrane protein	integral to membrane [ISS]			66
P09327 UniProt NPD GO	VILI_HUMAN	Villin-1	0.15	-	cyt	0			193040	1UNC	826
Q5ZHN3 UniProt NPD GO	WIPI2_CHICK	WD repeat domain phosphoinositide-interacting protein 2 (WIPI-2)	0.15	-	cyt	0					436
Q9JHB4 UniProt NPD GO	WDR31_MOUSE	WD repeat protein 31 (Spermatid WD repeat protein) (spWD)	0.15	-	cyt	0					367

You are viewing entries 57801 to 57850 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.