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
Q8TFG5 UniProt NPD GO	YL53_SCHPO	Very hypothetical protein PB18E9.03c in chromosome I	0.01	-	mit	1 *					44
P45820 UniProt NPD GO	YGR8_YEAST	Very hypothetical protein YGL168W	0.01	-	cyt	1 *		nucleus [IC]			110
P40891 UniProt NPD GO	YJW0_YEAST	Very hypothetical protein YJL220W	0.01	-	end	3 *					150
P53926 UniProt NPD GO	YNL4_YEAST	Very hypothetical protein YNL114C	0.01	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				123
Q5REQ5 UniProt NPD GO	VAMP8_PONPY	Vesicle-associated membrane protein 8 (VAMP-8)	0.01	-	gol	1	Membrane; single-pass type IV membrane protein (Probable)				100
Q9BV40 UniProt NPD GO	VAMP8_HUMAN	Vesicle-associated membrane protein 8 (VAMP-8) (Endobrevin) (EDB)	0.01	-	gol	1	Membrane; single-pass type IV membrane protein (Probable)	early endosome [TAS] membrane fraction [TAS]	603177		100
P34711 UniProt NPD GO	UNC17_CAEEL	Vesicular acetylcholine transporter unc-17 (Uncoordinated protein 17)	0.01	-	end	10 *	Membrane; multi-pass membrane protein	integral to plasma membrane [NAS]			532
Q95KE2 UniProt NPD GO	VIAAT_MACFA	Vesicular inhibitory amino acid transporter (GABA and glycine transporter) (Vesicular GABA transport ...	0.01	-	end	9	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein (By similarity)				525
Q9H598 UniProt NPD GO	VIAAT_HUMAN	Vesicular inhibitory amino acid transporter (GABA and glycine transporter) (Vesicular GABA transport ...	0.01	-	end	9	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein (By similarity)				525
O35633 UniProt NPD GO	VIAAT_MOUSE	Vesicular inhibitory amino acid transporter (GABA and glycine transporter) (Vesicular GABA transport ...	0.01	-	end	9	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [IC]			525
O35458 UniProt NPD GO	VIAAT_RAT	Vesicular inhibitory amino acid transporter (GABA and glycine transporter) (Vesicular GABA transport ...	0.01	-	end	9	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein	integral to membrane [TAS] synapse [IDA]			525
P0C1M2 UniProt NPD GO	CRBLF_VESMG	Vespid chemotactic peptide 5f	0.01	-		0	Secreted protein				13
P28684 UniProt NPD GO	OPSV_CHICK	Violet-sensitive opsin (Violet cone photoreceptor pigment) (Violet cone opsin)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				347
Q07943 UniProt NPD GO	VDP_BOMMO	Vitellin-degrading protease precursor (EC 3.4.21.-) [Contains: Beta-VTN protease; Alpha-VTN protease ...	0.01	-	end	0					264
Q5SXG7 UniProt NPD GO	VMO1_MOUSE	Vitelline membrane outer layer protein 1 homolog precursor	0.01	-	exc	0	Secreted protein (By similarity)				201
P60980 UniProt NPD GO	VSTX1_GRASP	Voltage sensor toxin 1 (VSTX1)	0.01	-	nuc	0	Secreted protein				34
Q99246 UniProt NPD GO	CAC1D_MOUSE	Voltage-dependent L-type calcium channel subunit alpha-1D (Voltage-gated calcium channel subunit alp ...	0.01	-	end	3	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]			281
O73705 UniProt NPD GO	CAC1A_CHICK	Voltage-dependent P/Q-type calcium channel subunit alpha-1A (Voltage-gated calcium channel subunit a ...	0.01	-	end	3 *	Membrane; multi-pass membrane protein				171
Q94920 UniProt NPD GO	VDAC_DROME	Voltage-dependent anion-selective channel (Porin) (DmVDAC)	0.01	-	nuc	0	Mitochondrion; mitochondrial outer membrane	mitochondrial outer membrane [NAS] Nebenkern [IDA]			281
P81004 UniProt NPD GO	VDAC2_XENLA	Voltage-dependent anion-selective channel protein 2 (Outer mitochondrial membrane protein porin)	0.01	-	nuc	0	Mitochondrion; mitochondrial outer membrane (Potential)				282
P81155 UniProt NPD GO	VDAC2_RAT	Voltage-dependent anion-selective channel protein 2 (VDAC-2) (Outer mitochondrial membrane protein p ...	0.01	-	cyt	0	Mitochondrion; mitochondrial outer membrane				295
Q5R7V4 UniProt NPD GO	VDAC3_PONPY	Voltage-dependent anion-selective channel protein 3 (VDAC-3)	0.01	-	cyt	0	Mitochondrion; mitochondrial outer membrane				284
Q9Y277 UniProt NPD GO	VDAC3_HUMAN	Voltage-dependent anion-selective channel protein 3 (VDAC-3) (hVDAC3) (Outer mitochondrial membrane ...	0.01	-	cyt	0	Mitochondrion; mitochondrial outer membrane	mitochondrial outer membrane [TAS]			283
Q60931 UniProt NPD GO	VDAC3_MOUSE	Voltage-dependent anion-selective channel protein 3 (VDAC-3) (mVDAC3) (Outer mitochondrial membrane ...	0.01	-	cyt	0	Mitochondrion; mitochondrial outer membrane	mitochondrial inner membrane [IDA]			283
Q9R1Z0 UniProt NPD GO	VDAC3_RAT	Voltage-dependent anion-selective channel protein 3 (VDAC-3) (rVDAC3) (Outer mitochondrial membrane ...	0.01	-	cyt	0	Mitochondrion; mitochondrial outer membrane	mitochondrial outer membrane [TAS]			283
Q8VHW1 UniProt NPD GO	CCGL_RAT	Voltage-dependent calcium channel gamma-like subunit (Neuronal voltage-gated calcium channel gamma-l ...	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				209
Q62471 UniProt NPD GO	VNS1_MOUSE	Vomeronasal secretory protein 1 precursor (Vomeronasal secretory protein I) (VNSP I) (Lipocalin-3)	0.01	-	exc	0	Secreted protein				182
P20289 UniProt NPD GO	VEGP1_RAT	Von Ebner gland protein 1 precursor (VEG protein 1)	0.01	-	exc	0	Secreted protein				177
O54927 UniProt NPD GO	WSB1_MOUSE	WD repeat and SOCS box-containing protein 1 (WSB-1)	0.01	-	cyt	0					421
Q9H977 UniProt NPD GO	WDR54_HUMAN	WD repeat protein 54	0.01	-	cyt	0					334
Q9R0D8 UniProt NPD GO	WDR54_MOUSE	WD repeat protein 54	0.01	-	mit	0					334
Q4V7A0 UniProt NPD GO	WDR61_RAT	WD repeat protein 61	0.01	-	nuc	0					305
Q9ERF3 UniProt NPD GO	WDR61_MOUSE	WD repeat protein 61 (Meiotic recombination REC14 protein homolog)	0.01	-	nuc	0					305
Q1LV15 UniProt NPD GO	WDR69_BRARE	WD repeat protein 69	0.01	-	cyt	0					418
P35920 UniProt NPD GO	WWA2_ACHFU	WWamide-2	0.01	-		0					7
Q94128 UniProt NPD GO	WRT1_CAEEL	Warthog protein 1 precursor [Contains: Warthog protein 1 N-product; Warthog protein 1 C-product]	0.01	-	exc	1 *	Warthog protein 1: Secreted protein (By similarity). Cell surface (By similarity). Warthog protein 1 ...	extracellular region [NAS] plasma membrane [NAS]			485
P81086 UniProt NPD GO	WSP7_PINPS	Water stress-responsive protein 7 (Fragments)	0.01	-	cyt	0					35
P20144 UniProt NPD GO	WUN1_SOLTU	Wound-induced protein 1	0.01	-	cyt	0					105
P05118 UniProt NPD GO	ICI1_LYCES	Wound-induced proteinase inhibitor 1 precursor (Wound-induced proteinase inhibitor I)	0.01	-	vac	0	Secreted protein				111
P08454 UniProt NPD GO	ICID_SOLTU	Wound-induced proteinase inhibitor 1 precursor (Wound-induced proteinase inhibitor I) (Chymotrypsin ...	0.01	-	exc	0					107
P12955 UniProt NPD GO	PEPD_HUMAN	Xaa-Pro dipeptidase (EC 3.4.13.9) (X-Pro dipeptidase) (Proline dipeptidase) (Prolidase) (Imidodipept ...	0.01	-	cyt	0			170100		492
Q11136 UniProt NPD GO	PEPD_MOUSE	Xaa-Pro dipeptidase (EC 3.4.13.9) (X-Pro dipeptidase) (Proline dipeptidase) (Prolidase) (Imidodipept ...	0.01	-	cyt	0					492
Q9ZSU4 UniProt NPD GO	XTH14_ARATH	Xyloglucan endotransglucosylase/hydrolase protein 14 precursor (EC 2.4.1.207) (At-XTH14) (XTH-14)	0.01	-	end	1 *	Secreted protein; extracellular space; apoplast (Probable)				287
O97764 UniProt NPD GO	QOR_BOVIN	Zeta-crystallin	0.01	-	cyt	0	Cytoplasm				330
Q3ZBU2 UniProt NPD GO	ZCD1_BOVIN	Zinc finger CDGSH domain-containing protein 1	0.01	-	mit	1 *					106
Q91WS0 UniProt NPD GO	ZCD1_MOUSE	Zinc finger CDGSH domain-containing protein 1	0.01	-	mit	1 *		mitochondrion [IDA]			108
O23039 UniProt NPD GO	ZIP5_ARATH	Zinc transporter 5 precursor (ZRT/IRT-like protein 5)	0.01	-	end	9 *	Cell membrane; multi-pass membrane protein (Potential)				360
Q9NY26 UniProt NPD GO	S39A1_HUMAN	Zinc transporter ZIP1 (Zinc-iron-regulated transporter-like) (hZIP1) (Solute carrier family 39 membe ...	0.01	-	end	6 *	Cell membrane; multi-pass membrane protein. Endoplasmic reticulum; endoplasmic reticulum membrane; m ...	integral to membrane [TAS] membrane fraction [TAS]	604740		324
O60844 UniProt NPD GO	ZG16_HUMAN	Zymogen granule membrane protein 16 precursor (Zymogen granule protein 16) (Secretory lectin ZG16)	0.01	-	exc	0	Secreted protein. Stored in zymogen granules (By similarity)				167
P19962 UniProt NPD GO	MOSQ_CLYJA	[Gln6]-mosact	0.01	-		0					10

You are viewing entries 92101 to 92150 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.