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
Q93086 UniProt NPD GO	P2RX5_HUMAN	P2X purinoceptor 5 (ATP receptor) (P2X5) (Purinergic receptor)	0.03	-	cyt	1 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	602836		421
P51578 UniProt NPD GO	P2RX5_RAT	P2X purinoceptor 5 (ATP receptor) (P2X5) (Purinergic receptor)	0.03	-	end	2 *	Membrane; multi-pass membrane protein				455
O35811 UniProt NPD GO	P2RY4_RAT	P2Y purinoceptor 4 (P2Y4)	0.03	-	end	6 *	Membrane; multi-pass membrane protein	apical plasma membrane [IDA] basolateral plasma membrane [IDA]			361
P58826 UniProt NPD GO	P2RY4_CRIGR	P2Y purinoceptor 4 (P2Y4) (P2Y4 metabotropic purinergic receptor) (Fragment)	0.03	-	end	3 *	Membrane; multi-pass membrane protein				165
Q9JJ40 UniProt NPD GO	PDZD1_RAT	PDZ domain-containing protein 1 (Na/Pi cotransporter C-terminal-associated protein) (NaPi-Cap1) (Na( ...	0.03	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Associated with peripheral membranes. Localizes to ...				523
Q8C6U2 UniProt NPD GO	PQLC3_MOUSE	PQ loop repeat-containing protein 3 precursor	0.03	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				202
P50897 UniProt NPD GO	PPT1_HUMAN	Palmitoyl-protein thioesterase 1 precursor (EC 3.1.2.22) (PPT-1) (Palmitoyl-protein hydrolase 1)	0.03	-	exc	0	Lysosome		600722		306
Q6CRV3 UniProt NPD GO	PFA5_KLULA	Palmitoyltransferase PFA5 (EC 2.3.1.-) (Protein fatty acyltransferase 5)	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				349
Q5FWL7 UniProt NPD GO	ZDH15_XENLA	Palmitoyltransferase ZDHHC15 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 15 homolog) (D ...	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				338
Q8BGJ0 UniProt NPD GO	ZDH15_MOUSE	Palmitoyltransferase ZDHHC15 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 15) (DHHC-15)	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				337
Q2TGJ4 UniProt NPD GO	ZDH15_RAT	Palmitoyltransferase ZDHHC15 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 15) (DHHC-15)	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				337
P00997 UniProt NPD GO	IPK1_SHEEP	Pancreatic secretory trypsin inhibitor	0.03	-	nuc	0	Secreted protein				56
O95497 UniProt NPD GO	VNN1_HUMAN	Pantetheinase precursor (EC 3.5.1.92) (Pantetheine hydrolase) (Vascular non-inflammatory molecule 1) ...	0.03	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)		603570		513
Q9H999 UniProt NPD GO	PANK3_HUMAN	Pantothenate kinase 3 (EC 2.7.1.33) (Pantothenic acid kinase 3) (hPanK3)	0.03	-	cyt	0	Cytoplasm (Probable)		606161		370
Q8R2W9 UniProt NPD GO	PANK3_MOUSE	Pantothenate kinase 3 (EC 2.7.1.33) (Pantothenic acid kinase 3) (mPanK3)	0.03	-	cyt	0	Cytoplasm (Probable)				370
P00784 UniProt NPD GO	PAPA1_CARPA	Papain precursor (EC 3.4.22.2) (Papaya proteinase I) (PPI) (Allergen Car p 1)	0.03	-	end	1 *				9PAP	345
P30252 UniProt NPD GO	PAP2_HELVI	Paralytic peptide 2 (Paralytic peptide II) (PP II)	0.03	-	nuc	0					23
P30254 UniProt NPD GO	PAP2_MANSE	Paralytic peptide 2 (Paralytic peptide II) (PP II)	0.03	-	cyt	0					23
P30257 UniProt NPD GO	PAP3_SPOEX	Paralytic peptide 3 (Paralytic peptide III) (PP III)	0.03	-	cyt	0					23
Q91V95 UniProt NPD GO	PTHR2_MOUSE	Parathyroid hormone receptor precursor (PTH2 receptor)	0.03	-	end	4	Membrane; multi-pass membrane protein				546
Q566B2 UniProt NPD GO	PBURS_BOMMO	Partner of bursicon precursor (Bursicon subunit beta)	0.03	-	gol	0	Secreted protein (By similarity)				137
P02614 UniProt NPD GO	PRVB_GRAGE	Parvalbumin beta	0.03	-	cyt	0					108
P35792 UniProt NPD GO	PR12_HORVU	Pathogenesis-related protein PRB1-2 precursor	0.03	-	exc	0					164
P81295 UniProt NPD GO	PRR3_JUNAS	Pathogenesis-related protein precursor (Pollen allergen Jun a 3)	0.03	-	exc	0				1KUR	225
Q00645 UniProt NPD GO	PELA_EMENI	Pectate lyase precursor (EC 4.2.2.2)	0.03	-	end	0	Secreted protein (Potential)				326
Q43043 UniProt NPD GO	PME_PETIN	Pectinesterase precursor (EC 3.1.1.11) (Pectin methylesterase) (PE)	0.03	-	cyt	0					374
Q42920 UniProt NPD GO	PME_MEDSA	Pectinesterase precursor (EC 3.1.1.11) (Pectin methylesterase) (PE) (P65)	0.03	-	cyt	0					447
P80578 UniProt NPD GO	PEDI_HYDAT	Pedin	0.03	-		0					13
P81057 UniProt NPD GO	PEN2A_PENVA	Penaeidin-2a precursor (Pen-2a) (Pen-2) (P2)	0.03	-	end	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				72
P56272 UniProt NPD GO	PEP2B_GADMO	Pepsin IIB (EC 3.4.23.-)	0.03	-	mit	0				1AM5	324
P81626 UniProt NPD GO	AKHX_LOCMI	Peptide hormone	0.03	-		0	Secreted protein				10
Q9UJ68 UniProt NPD GO	MSRA_HUMAN	Peptide methionine sulfoxide reductase (EC 1.8.4.6) (Protein-methionine-S-oxide reductase) (PMSR) (P ...	0.03	-	mit	0			601250		235
O88593 UniProt NPD GO	PGRP_MOUSE	Peptidoglycan recognition protein precursor (Peptidoglycan recognition protein short) (PGRP-S) (Cyto ...	0.03	-	exc	0	Exists in both soluble and membrane-associated forms				182
Q70PU1 UniProt NPD GO	PGSC2_DROSI	Peptidoglycan-recognition protein-SC2 precursor (EC 3.5.1.28)	0.03	-	exc	1 *	Secreted protein (Potential)	extracellular region [ISS]			184
P25007 UniProt NPD GO	PPIA_DROME	Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin) (Cyclosporin A-bi ...	0.03	-	mit	0	Cytoplasm				227
Q8X166 UniProt NPD GO	PPIB_ASPNG	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase B) (Rotamase B)	0.03	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				212
P80311 UniProt NPD GO	PPIB_BOVIN	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin B) (S- ...	0.03	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen				208
P23284 UniProt NPD GO	PPIB_HUMAN	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin B) (S- ...	0.03	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [TAS] endoplasmic reticulum lumen [NAS]	123841	1CYN	208
P24369 UniProt NPD GO	PPIB_MOUSE	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin B) (S- ...	0.03	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				208
P0C1H9 UniProt NPD GO	PPIB1_RHIOR	Peptidyl-prolyl cis-trans isomerase B1 precursor (EC 5.2.1.8) (PPIase B1) (Rotamase B1)	0.03	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				209
P45877 UniProt NPD GO	PPIC_HUMAN	Peptidyl-prolyl cis-trans isomerase C (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin C)	0.03	-	vac	1 *	Cytoplasm	cytoplasm [TAS]	123842	2ESL	212
Q42406 UniProt NPD GO	CP18D_ARATH	Peptidyl-prolyl cis-trans isomerase CYP18-4 (EC 5.2.1.8) (PPIase CYP18-4) (Rotamase cyclophilin-5) ( ...	0.03	-	cyt	0	Cytoplasm (Probable)				172
Q4WCM6 UniProt NPD GO	PPIH_ASPFU	Peptidyl-prolyl cis-trans isomerase H (EC 5.2.1.8) (PPIase H) (Rotamase H)	0.03	-	cyt	0	Nucleus (By similarity)				181
Q4I665 UniProt NPD GO	PIN4_GIBZE	Peptidyl-prolyl cis-trans isomerase PIN4 (EC 5.2.1.8) (PPIase PIN4) (Parvulin PIN4)	0.03	-	cyt	0					133
P30404 UniProt NPD GO	PPIF_BOVIN	Peptidyl-prolyl cis-trans isomerase, mitochondrial precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclo ...	0.03	-	mit	0	Mitochondrion; mitochondrial matrix				209
Q8X191 UniProt NPD GO	PPIL1_ASPNG	Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8) (PPIase) (Rotamase)	0.03	-	cyt	0					162
Q5E992 UniProt NPD GO	PPIL1_BOVIN	Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8) (PPIase) (Rotamase)	0.03	-	cyt	0					166
Q5ASQ0 UniProt NPD GO	PPIL1_EMENI	Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8) (PPIase) (Rotamase)	0.03	-	cyt	0					162
Q9Y3C6 UniProt NPD GO	PPIL1_HUMAN	Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8) (PPIase) (Rotamase)	0.03	-	cyt	0			601301	1XWN	166
Q6MWS8 UniProt NPD GO	PPIL3_NEUCR	Peptidyl-prolyl cis-trans isomerase-like 3 (EC 5.2.1.8) (PPIase) (Rotamase)	0.03	-	cyt	0					167

You are viewing entries 80951 to 81000 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.