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
Q04516 UniProt NPD GO	YMI7_YEAST	Uncharacterized oxidoreductase YML087C (EC 1.-.-.-)	0.06	-	cyt	2 *	Membrane; multi-pass membrane protein (Potential)				312
Q4WCX9 UniProt NPD GO	YA280_ASPFU	Uncharacterized protein Afu6g02800 precursor	0.06	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				242
Q8VD62 UniProt NPD GO	CK068_MOUSE	Uncharacterized protein C11orf68 homolog (Basophilic leukemia expressed protein Bles03) (Protein WF- ...	0.06	-	cyt	0					251
Q8N6I4 UniProt NPD GO	CN109_HUMAN	Uncharacterized protein C14orf109	0.06	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				131
Q5R694 UniProt NPD GO	CN162_PONPY	Uncharacterized protein C14orf162 homolog	0.06	-	mit	0					89
Q9P1J3 UniProt NPD GO	CN167_HUMAN	Uncharacterized protein C14orf167	0.06	-	nuc	0					65
Q2KIJ2 UniProt NPD GO	CA156_BOVIN	Uncharacterized protein C1orf156 homolog	0.06	-	cyt	0					373
Q5T1J6 UniProt NPD GO	CT091_HUMAN	Uncharacterized protein C20orf91	0.06	-	mit	0					154
Q8TCX9 UniProt NPD GO	CU041_HUMAN	Uncharacterized protein C21orf41	0.06	-	cyt	0					40
O13989 UniProt NPD GO	YEG7_SCHPO	Uncharacterized protein C26H5.07c precursor	0.06	-	end	8 *	Membrane; multi-pass membrane protein				505
Q8TDM3 UniProt NPD GO	CB012_HUMAN	Uncharacterized protein C2orf12 (Cervical cancer oncogene 4) (HCC-4)	0.06	-	nuc	0					56
Q8WU43 UniProt NPD GO	CB015_HUMAN	Uncharacterized protein C2orf15	0.06	-	nuc	0					125
Q5RKH7 UniProt NPD GO	CB018_RAT	Uncharacterized protein C2orf18 homolog precursor	0.06	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				372
Q60534 UniProt NPD GO	CF105_MESAU	Uncharacterized protein C6orf105 homolog (Androgen-dependent expressed protein FAR-17a)	0.06	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				231
P25575 UniProt NPD GO	YCE6_YEAST	Uncharacterized protein YCL046W	0.06	-	cyt	0					107
Q07589 UniProt NPD GO	YD144_YEAST	Uncharacterized protein YDL144C	0.06	-	mit	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			356
Q07651 UniProt NPD GO	YD222_YEAST	Uncharacterized protein YDL222C	0.06	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	cell cortex [IDA] mitochondrion [IDA]			309
Q03193 UniProt NPD GO	YD090_YEAST	Uncharacterized protein YDR090C	0.06	-	end	6 *	Cell membrane; multi-pass membrane protein (Potential)				310
Q7LHD1 UniProt NPD GO	YD134_YEAST	Uncharacterized protein YDR134C precursor	0.06	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor				136
P40006 UniProt NPD GO	YEA1_YEAST	Uncharacterized protein YEL001C precursor	0.06	-	end	1		endoplasmic reticulum [IDA]			225
Q3E817 UniProt NPD GO	YF041_YEAST	Uncharacterized protein YFL041W-A	0.06	-	cyt	0					63
Q3E739 UniProt NPD GO	YI021_YEAST	Uncharacterized protein YIR021W-A	0.06	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				70
P46992 UniProt NPD GO	YJR1_YEAST	Uncharacterized protein YJL171C precursor	0.06	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	cell wall (sensu Fungi) [IDA] mitochondrion [IDA]			396
Q12155 UniProt NPD GO	YL050_YEAST	Uncharacterized protein YLR050C	0.06	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			161
Q8TGS9 UniProt NPD GO	YM001_YEAST	Uncharacterized protein YMR001C-A	0.06	-	nuc	0					76
P53981 UniProt NPD GO	YNB0_YEAST	Uncharacterized protein YNL010W	0.06	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			241
P53949 UniProt NPD GO	YNF6_YEAST	Uncharacterized protein YNL056W	0.06	-	cyt	0		cytoplasm [IDA]			197
P40342 UniProt NPD GO	YN81_YEAST	Uncharacterized protein YNR004W	0.06	-	cyt	0		nucleolus [IDA]			146
P82037 UniProt NPD GO	UPE61_UPEIN	Uperin-6.1	0.06	-	nuc	0	Secreted protein				30
Q26998 UniProt NPD GO	UPP_TOXGO	Uracil phosphoribosyltransferase (EC 2.4.2.9) (UMP pyrophosphorylase) (UPRTase) (UPRT)	0.06	-	cyt	0				1UPU	244
Q8VHL0 UniProt NPD GO	UT1_MOUSE	Urea transporter, erythrocyte (Urea transporter B) (UT-B)	0.06	-	end	9	Membrane; multi-pass membrane protein	integral to membrane [TAS]			384
Q8MHW6 UniProt NPD GO	URIC_MACFA	Uricase (EC 1.7.3.3) (Urate oxidase)	0.06	-	nuc	0	Peroxisome				303
Q8MKJ3 UniProt NPD GO	URIC_MACMU	Uricase (EC 1.7.3.3) (Urate oxidase)	0.06	-	nuc	0	Peroxisome				303
P25689 UniProt NPD GO	URIC_PAPHA	Uricase (EC 1.7.3.3) (Urate oxidase)	0.06	-	nuc	0	Peroxisome				303
Q01637 UniProt NPD GO	PYR5_DROME	Uridine 5'-monophosphate synthase (UMP synthase) (Rudimentary-like protein) [Includes: Orotate phosp ...	0.06	-	cyt	0					493
Q42942 UniProt NPD GO	PYR5_TOBAC	Uridine 5'-monophosphate synthase (UMP synthase) [Includes: Orotate phosphoribosyltransferase (EC 2. ...	0.06	-	cyt	0					461
Q04179 UniProt NPD GO	URH1_YEAST	Uridine nucleosidase (EC 3.2.2.3) (Uridine ribohydrolase)	0.06	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			378
Q9V595 UniProt NPD GO	DCUP_DROME	Uroporphyrinogen decarboxylase (EC 4.1.1.37) (URO-D) (UPD)	0.06	-	nuc	0	Cytoplasm				356
Q75EU0 UniProt NPD GO	VA0E_ASHGO	Vacuolar ATP synthase subunit e (EC 3.6.3.14) (V-ATPase e subunit) (Vacuolar proton pump e subunit)	0.06	-	end	2 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				72
P93026 UniProt NPD GO	VSR1_ARATH	Vacuolar sorting receptor 1 precursor (AtVSR1) (Epidermal growth factor receptor-like protein 1) (At ...	0.06	-	end	1	Membrane; single-pass type I membrane protein. Associated to the Golgi apparatus, mostly on the tran ...				623
Q9FYH7 UniProt NPD GO	VSR6_ARATH	Vacuolar sorting receptor 6 precursor (AtVSR6) (Epidermal growth factor receptor-like protein 6) (At ...	0.06	-	end	2 *					622
P41815 UniProt NPD GO	BAP3_YEAST	Valine amino-acid permease (Branched-chain amino-acid permease 3)	0.06	-	end	12	Membrane; multi-pass membrane protein (Probable)	mitochondrion [IDA]			604
P49053 UniProt NPD GO	PRXC_CURIN	Vanadium chloroperoxidase (EC 1.11.1.10) (VCPO) (Vanadium chloride peroxidase)	0.06	-	cyt	0	Secreted protein			1VNS	609
P39089 UniProt NPD GO	VIP_DIDMA	Vasoactive intestinal peptide (VIP) (Vasoactive intestinal polypeptide)	0.06	-	nuc	0	Secreted protein				28
P09684 UniProt NPD GO	VIP_GADMO	Vasoactive intestinal peptide (VIP) (Vasoactive intestinal polypeptide) (Fragment)	0.06	-	nuc	0	Secreted protein				25
O77808 UniProt NPD GO	V2R_CANFA	Vasopressin V2 receptor (Renal-type arginine vasopressin receptor) (Antidiuretic hormone receptor) ( ...	0.06	-	end	7 *	Membrane; multi-pass membrane protein				370
P69128 UniProt NPD GO	OXYT_CYPCA	Vasotocin	0.06	-		0	Secreted protein				9
P69129 UniProt NPD GO	OXYT_PETMA	Vasotocin	0.06	-		0	Secreted protein				9
Q05108 UniProt NPD GO	VA5_DOLAR	Venom allergen 5 (Antigen 5) (Ag5) (Allergen Dol a 5) (Dol a V)	0.06	-	nuc	0	Secreted protein. Venom reservoirs				203
P81656 UniProt NPD GO	VA5_POLDO	Venom allergen 5 (Antigen 5) (Ag5) (Allergen Pol d 5)	0.06	-	nuc	0	Secreted protein. Venom reservoirs				206

You are viewing entries 73451 to 73500 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.