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
P21126 UniProt NPD GO	UBL4A_MOUSE	Ubiquitin-like protein 4A (Ubiquitin-like protein GDX)	0.24	-	cyt	0					157
Q5JW98 UniProt NPD GO	CF078_HUMAN	Uncharacterized protein C6orf78	0.24	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				314
Q6Q5X2 UniProt NPD GO	YD034_YEAST	Uncharacterized protein YDR034W-B	0.24	-	nuc	0	Cytoplasm; cell cortex				51
P53230 UniProt NPD GO	YG1W_YEAST	Uncharacterized protein YGR046W	0.24	-	mit	0		mitochondrion [IDA]			385
Q04489 UniProt NPD GO	YMJ6_YEAST	Uncharacterized protein YML096W	0.24	-	nuc	0		cytoplasm [IDA]			525
Q03516 UniProt NPD GO	YM8G_YEAST	Uncharacterized protein YMR266W	0.24	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				953
Q3E7A8 UniProt NPD GO	YN162_YEAST	Uncharacterized protein YNL162W-A	0.24	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			72
Q9SDS7 UniProt NPD GO	VATC_ARATH	Vacuolar ATP synthase subunit C (EC 3.6.3.14) (V-ATPase C subunit) (Vacuolar proton pump C subunit)	0.24	-	cyt	0					375
Q28HT6 UniProt NPD GO	VP26A_XENTR	Vacuolar protein sorting 26A (Vesicle protein sorting 26A)	0.24	-	cyt	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein (By similarity)				326
Q02767 UniProt NPD GO	VPS28_YEAST	Vacuolar protein sorting-associated protein VPS28	0.24	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity)	endosome [IDA] ESCRT I complex [IDA]		2G3K	242
P29533 UniProt NPD GO	VCAM1_MOUSE	Vascular cell adhesion protein 1 precursor (V-CAM 1)	0.24	+	end	1 *	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Cell membrane; lipid-ancho ...				739
P30560 UniProt NPD GO	V1AR_RAT	Vasopressin V1a receptor (V1aR) (Vascular/hepatic-type arginine vasopressin receptor) (Antidiuretic ...	0.24	-	end	7	Cell membrane; multi-pass membrane protein. Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi ...	cytoplasmic vesicle [IDA] integral to membrane [NAS]			424
P35455 UniProt NPD GO	NEU2_MOUSE	Vasopressin-neurophysin 2-copeptin precursor (AVP-NPII) [Contains: Arg-vasopressin; Neurophysin 2 (N ...	0.24	-	exc	0	Secreted protein				168
P24787 UniProt NPD GO	NEUV_CHICK	Vasotocin-neurophysin VT precursor [Contains: Vasotocin (VT); Neurophysin VT]	0.24	-	nuc	0	Secreted protein				161
Q9Y7P7 UniProt NPD GO	YQ63_SCHPO	Very hypothetical protein C191.03c in chromosome III	0.24	-	nuc	1					117
P53910 UniProt NPD GO	YNO0_YEAST	Very hypothetical protein YNL140C	0.24	-	cyt	0					189
Q9UI56 UniProt NPD GO	YYY4_HUMAN	Very very hypothetical protein from MEG3 locus	0.24	-	nuc	0			605636		68
Q9Z2J5 UniProt NPD GO	VAMP5_RAT	Vesicle-associated membrane protein 5 (VAMP-5) (Myobrevin)	0.24	-	mit	1	Cell membrane; single-pass type IV membrane protein (Probable). Intracellular membrane; single-pass ...	Golgi trans face [IDA] plasma membrane [IDA]			102
Q5R601 UniProt NPD GO	VAPA_PONPY	Vesicle-associated membrane protein-associated protein A (VAMP-associated protein A) (VAMP-A) (VAP-A ...	0.24	-	nuc	1	Cell membrane; single-pass type IV membrane protein (By similarity). Intracellular membrane; single- ...				242
Q9P0L0 UniProt NPD GO	VAPA_HUMAN	Vesicle-associated membrane protein-associated protein A (VAMP-associated protein A) (VAMP-A) (VAP-A ...	0.24	-	nuc	1	Cell membrane; single-pass type IV membrane protein. Intracellular membrane; single-pass type IV mem ...		605703		242
P53241 UniProt NPD GO	VHT1_YEAST	Vitamin H transporter (H+/biotin symporter)	0.24	+	end	10	Membrane; multi-pass membrane protein (Potential)	plasma membrane [IDA]			593
Q9EQ43 UniProt NPD GO	V1B10_MOUSE	Vomeronasal type-1 receptor B10	0.24	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				310
Q9HAD4 UniProt NPD GO	WDR41_HUMAN	WD repeat protein 41	0.24	-	mit	0					459
Q8BH57 UniProt NPD GO	WDR48_MOUSE	WD repeat protein 48	0.24	-	nuc	0	Lysosome (By similarity)				676
P25382 UniProt NPD GO	YCW2_YEAST	WD repeat protein YCR072C	0.24	-	nuc	0		nucleolus [IDA]			515
P25680 UniProt NPD GO	TXW10_NAJNI	Weak toxin CM-10	0.24	-	nuc	0	Secreted protein				65
Q5GH22 UniProt NPD GO	XKR2_SMIMA	XK-related protein 2 (X Kell blood group-related, X-linked)	0.24	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				456
Q49LS9 UniProt NPD GO	XKR4_TETNG	XK-related protein 4	0.24	-	end	4	Membrane; multi-pass membrane protein (Potential)				498
Q5GH64 UniProt NPD GO	XKR7_MOUSE	XK-related protein 7	0.24	-	end	8	Membrane; multi-pass membrane protein (Potential)				580
Q5GH56 UniProt NPD GO	XKR7_RAT	XK-related protein 7	0.24	-	end	8	Membrane; multi-pass membrane protein (Potential)				580
Q611X0 UniProt NPD GO	XOL1_CAEBR	XO lethal protein 1 homolog	0.24	-	mit	0					457
Q40082 UniProt NPD GO	XYLA_HORVU	Xylose isomerase (EC 5.3.1.5)	0.24	-	exc	0					479
Q96LD1 UniProt NPD GO	SGCZ_HUMAN	Zeta-sarcoglycan (Zeta-SG) (ZSG1)	0.24	-	mit	1 *	Sarcolemma; sarcolemmal membrane; single-pass type II membrane protein (By similarity)		608113		299
Q5NAW2 UniProt NPD GO	ZFNL1_ORYSA	Zinc finger CCCH domain-containing protein ZFN-like 1	0.24	-	nuc	0	Nucleus (By similarity)				476
Q9BQ24 UniProt NPD GO	ZFY21_HUMAN	Zinc finger FYVE domain-containing protein 21	0.24	-	cyt	0					234
Q9UHR6 UniProt NPD GO	ZNHI2_HUMAN	Zinc finger HIT domain-containing protein 2 (Protein FON)	0.24	-	cyt	0			604575	1X4S	403
Q5TJE2 UniProt NPD GO	ZN297_CANFA	Zinc finger protein 297	0.24	-	nuc	0	Nucleus (Probable)				640
Q9Z0G7 UniProt NPD GO	ZN297_MOUSE	Zinc finger protein 297 (BING1 protein)	0.24	-	nuc	0	Nucleus (Probable)				638
Q19203 UniProt NPD GO	UNC98_CAEEL	Zinc finger protein unc-98 (Uncoordinated protein 98)	0.24	-	nuc	0	Nucleus. Cytoplasm. Localized in body wall muscle M-lines, dense bodies and muscle nuclei				310
O13766 UniProt NPD GO	MDE10_SCHPO	Zinc metalloprotease mde10 precursor (EC 3.4.24.-) (Sporulation protein mde10)	0.24	-	exc	0	Endoplasmic reticulum. Endoplasmic reticulum during meiosis. Located at the spore rim at the end of ...	endoplasmic reticulum membrane [IDA] spore wall (sensu Fungi) [IDA]			512
Q29175 UniProt NPD GO	KE4_PIG	Zinc transporter SLC39A7 (Solute carrier family 39 member 7) (Histidine-rich membrane protein Ke4) ( ...	0.24	-	mit	1 *	Membrane; multi-pass membrane protein (Probable)				155
P20239 UniProt NPD GO	ZP2_MOUSE	Zona pellucida sperm-binding protein 2 precursor (Zona pellucida glycoprotein ZP2) (Zona pellucida p ...	0.24	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				713
O70571 UniProt NPD GO	PDK4_MOUSE	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 4, mitochondrial precursor (EC 2.7.11.2) (Pyruva ...	0.24	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			412
Q04758 UniProt NPD GO	IPKB_MOUSE	cAMP-dependent protein kinase inhibitor beta (PKI-beta) (cAMP-dependent protein kinase inhibitor tes ...	0.24	-	nuc	0					92
Q6BZG7 UniProt NPD GO	KAPR_DEBHA	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.24	-	nuc	0					452
Q9C1C2 UniProt NPD GO	KAPR_GLOLA	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.24	-	cyt	0					391
O14448 UniProt NPD GO	KAPR_MAGGR	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.24	-	cyt	0					390
Q01386 UniProt NPD GO	KAPR_NEUCR	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.24	-	cyt	0					385
P24256 UniProt NPD GO	KAPB2_BOVIN	cAMP-dependent protein kinase, beta-2-catalytic subunit (EC 2.7.11.11) (PKA C-beta-2)	0.24	-	cyt	0					397
Q6BTT1 UniProt NPD GO	YTH1_DEBHA	mRNA 3'-end-processing protein YTH1	0.24	-	nuc	0	Nucleus (By similarity)				223

You are viewing entries 46951 to 47000 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.