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
P35775 UniProt NPD GO	VA2_SOLIN	Venom allergen 2 precursor (Venom allergen II) (Allergen Sol i 2) (Sol i II)	0.05	-	exc	0					138
Q05109 UniProt NPD GO	VA5_POLAN	Venom allergen 5 precursor (Antigen 5) (Ag5) (Allergen Pol a 5) (Pol a V) (Fragment)	0.05	-	nuc	0	Secreted protein. Venom reservoirs				209
P82966 UniProt NPD GO	IVBIC_OPHHA	Venom chymotrypsin inhibitor	0.05	-	mit	0	Secreted protein	extracellular region [NAS]			58
P82957 UniProt NPD GO	DM43_DIDMR	Venom metalloproteinase inhibitor DM43	0.05	-	cyt	0					291
P83224 UniProt NPD GO	VNOA_OXYMI	Venom natriuretic peptide OxsSNPa	0.05	-	nuc	0	Secreted protein	extracellular region [NAS]			35
P83226 UniProt NPD GO	VNOA_OXYSA	Venom natriuretic peptide OxsSNPa	0.05	-	nuc	0	Secreted protein	extracellular region [NAS]			35
P83225 UniProt NPD GO	VNOA_OXYSC	Venom natriuretic peptide OxsSNPa	0.05	-	nuc	0	Secreted protein	extracellular region [NAS]			35
P83227 UniProt NPD GO	VNOB_OXYMI	Venom natriuretic peptide OxsSNPb	0.05	-	nuc	0	Secreted protein	extracellular region [NAS]			35
P83229 UniProt NPD GO	VNOB_OXYSA	Venom natriuretic peptide OxsSNPb	0.05	-	nuc	0	Secreted protein	extracellular region [NAS]			35
P83228 UniProt NPD GO	VNOB_OXYSC	Venom natriuretic peptide OxsSNPb	0.05	-	nuc	0	Secreted protein	extracellular region [NAS]			35
O13062 UniProt NPD GO	VSPC_TRIGA	Venom serine proteinase 2C precursor (EC 3.4.21.-)	0.05	-	exc	0	Secreted protein				257
P24541 UniProt NPD GO	IVBIT_ERIMA	Venom trypsin inhibitor	0.05	-	nuc	0	Secreted protein				62
P20229 UniProt NPD GO	IVBIT_NAJNA	Venom trypsin inhibitor	0.05	-	nuc	0	Secreted protein				57
P93292 UniProt NPD GO	M280_ARATH	Very hypothetical mitochondrial protein AtMg00280 (ORF110a)	0.05	-	cyt	0	Mitochondrion (Potential)				110
Q9C0X2 UniProt NPD GO	YB7J_SCHPO	Very hypothetical protein C16E9.19 in chromosome II	0.05	-	cyt	0					101
P25652 UniProt NPD GO	YCX7_YEAST	Very hypothetical protein YCR087W	0.05	-	end	3					171
Q04838 UniProt NPD GO	YM88_YEAST	Very hypothetical protein YMR254C	0.05	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				102
P18965 UniProt NPD GO	VSPG_DABRU	Vipera russelli proteinase RVV-V gamma (EC 3.4.21.95) (Factor V-activating proteinase gamma) (Snake ...	0.05	-	cyt	0	Secreted protein				236
O35214 UniProt NPD GO	OPSX_MOUSE	Visual pigment-like receptor peropsin	0.05	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				337
Q28380 UniProt NPD GO	PROC_HORSE	Vitamin K-dependent protein C (EC 3.4.21.69) (Autoprothrombin IIA) (Anticoagulant protein C) (Blood ...	0.05	-	mit	0					157
P11449 UniProt NPD GO	VTU1_DROME	Vitelline membrane protein Vm26Aa precursor (Protein TU-2) (Protein SV17.5)	0.05	-	exc	0					141
Q06521 UniProt NPD GO	VTU3_DROME	Vitelline membrane protein Vm34Ca precursor	0.05	-	nuc	0					119
P83627 UniProt NPD GO	VIH_ARMVU	Vitellogenesis-inhibiting hormone (VIH)	0.05	-	nuc	0	Secreted protein	extracellular region [IC]			83
O70578 UniProt NPD GO	CCG1_MOUSE	Voltage-dependent calcium channel gamma-1 subunit (Dihydropyridine-sensitive L-type, skeletal muscle ...	0.05	-	end	4 *	Membrane; multi-pass membrane protein				223
Q8WXS4 UniProt NPD GO	CCGL_HUMAN	Voltage-dependent calcium channel gamma-like subunit (Neuronal voltage-gated calcium channel gamma-l ...	0.05	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				192
Q7Z5H5 UniProt NPD GO	VN1R4_HUMAN	Vomeronasal type-1 receptor 4 (V1r-like receptor 4) (hGPCR27)	0.05	-	end	5 *	Membrane; multi-pass membrane protein				301
Q7ZUX3 UniProt NPD GO	WIPI4_BRARE	WD repeat domain phosphoinositide-interacting protein 4 (WIPI-4) (WD repeat protein 45)	0.05	-	cyt	0					358
Q9W7F2 UniProt NPD GO	WDR1_XENLA	WD repeat protein 1 (Actin-interacting protein 1) (XAIP1)	0.05	-	cyt	0					608
P54686 UniProt NPD GO	WD42_DICDI	WD repeat protein 2	0.05	-	cyt	0					597
P01400 UniProt NPD GO	TXW4_NAJME	Weak toxin S4C11	0.05	-	nuc	0	Secreted protein				65
O64392 UniProt NPD GO	WHW1_WHEAT	Wheatwin-1 precursor (Pathogenesis-related protein 4a) (Protein 0.14)	0.05	-	exc	0				1C2Z	146
O64393 UniProt NPD GO	WHW2_WHEAT	Wheatwin-2 precursor (Pathogenesis-related protein 4b)	0.05	-	exc	0					148
P87252 UniProt NPD GO	HEX1_NEUCR	Woronin body major protein precursor	0.05	-	cyt	0	Peroxisome. Woronin bodies			1KHI	176
Q8LDW9 UniProt NPD GO	XTH9_ARATH	Xyloglucan endotransglucosylase/hydrolase protein 9 precursor (EC 2.4.1.207) (At-XTH9) (XTH-9)	0.05	-	cyt	0	Secreted protein; extracellular space; apoplast (Probable)				290
Q3SYZ6 UniProt NPD GO	XYLB_BOVIN	Xylulose kinase (EC 2.7.1.17) (Xylulokinase)	0.05	-	cyt	0					490
Q40412 UniProt NPD GO	ABA2_NICPL	Zeaxanthin epoxidase, chloroplast precursor (EC 1.14.13.90)	0.05	-	mit	1	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein. Plastid; chloroplast; chlor ...				663
O49901 UniProt NPD GO	ZDS_NARPS	Zeta-carotene desaturase, chloroplast precursor (EC 1.14.99.30) (Carotene 7,8-desaturase)	0.05	-	mit	0	Plastid; chloroplast. Plastid; chromoplast				574
Q8VEB6 UniProt NPD GO	RNZ1_MOUSE	Zinc phosphodiesterase ELAC protein 1 (EC 3.1.26.11) (Ribonuclease Z 1) (RNase Z 1) (tRNase Z 1) (tR ...	0.05	-	cyt	0	Nucleus (Probable)				362
Q99726 UniProt NPD GO	ZNT3_HUMAN	Zinc transporter 3 (ZnT-3) (Solute carrier family 30 member 3)	0.05	-	end	4	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (Probable)	endosome [TAS] integral to plasma membrane [TAS] membrane fraction [TAS] synaptic vesicle [TAS]	602878		388
P97441 UniProt NPD GO	ZNT3_MOUSE	Zinc transporter 3 (ZnT-3) (Solute carrier family 30 member 3)	0.05	-	end	6	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (Probable)				388
Q6P5W5 UniProt NPD GO	S39A4_HUMAN	Zinc transporter ZIP4 precursor (Solute carrier family 39 member 4)	0.05	-	end	7 *	Cell membrane; multi-pass membrane protein. Endosome; recycling endosome; recycling endosomal membra ...		607059		647
Q78IQ7 UniProt NPD GO	S39A4_MOUSE	Zinc transporter ZIP4 precursor (Solute carrier family 39 member 4) (Activated in W/Wv mouse stomach ...	0.05	-	end	6	Cell membrane; multi-pass membrane protein. Endosome; recycling endosome; recycling endosomal membra ...	apical plasma membrane [IDA] cytoplasmic membrane-bound vesicle [IDA] endosome [IDA] plasma membrane [IDA]			660
P97708 UniProt NPD GO	ZP3_RAT	Zona pellucida sperm-binding protein 3 precursor (Zona pellucida glycoprotein ZP3) (Zona pellucida g ...	0.05	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				424
Q6X786 UniProt NPD GO	ZPBP2_MOUSE	Zona pellucida-binding protein 2 precursor	0.05	-	mit	0	Secreted protein (By similarity)				326
Q8CJD3 UniProt NPD GO	ZG16_RAT	Zymogen granule membrane protein 16 precursor (Zymogen granule protein 16) (Secretory lectin ZG16)	0.05	-	exc	0	Secreted protein. Stored in zymogen granules	zymogen granule membrane [IDA]			167
P83058 UniProt NPD GO	KNL3_BOMVA	[Thr6]-bradykinin	0.05	-		0	Secreted protein				9
P83659 UniProt NPD GO	KNL3_CYPDO	[Thr6]-bradykinin	0.05	-		0	Secreted protein	extracellular space [IDA]			9
P84497 UniProt NPD GO	KNL3_TRASC	[Thr6]-bradykinin	0.05	-		0	Secreted protein				9
P21137 UniProt NPD GO	KAPC_CAEEL	cAMP-dependent protein kinase catalytic subunit (EC 2.7.11.11) (PKA C)	0.05	-	cyt	0					404
Q9Y2B9 UniProt NPD GO	IPKG_HUMAN	cAMP-dependent protein kinase inhibitor gamma (PKI-gamma)	0.05	-	nuc	0			604932		76

You are viewing entries 75951 to 76000 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.