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
O60831 UniProt NPD GO	PRAF2_HUMAN	PRA1 family protein 2	0.09	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			178
Q2VL50 UniProt NPD GO	PAX9_PROVC	Paired box protein Pax-9	0.09	-	nuc	0	Nucleus				341
Q9W3C7 UniProt NPD GO	PPT1_DROME	Palmitoyl-protein thioesterase 1 precursor (EC 3.1.2.22) (PPT-1) (Palmitoyl-protein hydrolase 1)	0.09	-	exc	2 *	Lysosome (Probable)				314
Q7S3M5 UniProt NPD GO	AKR1_NEUCR	Palmitoyltransferase AKR1 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR1)	0.09	+	end	5	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				729
Q52T38 UniProt NPD GO	TIP1_ARATH	Palmitoyltransferase TIP1 (EC 2.3.1.-) (Ankyrin repeat-containing S-palmitoyltransferase) (Protein T ...	0.09	-	end	4	Membrane; multi-pass membrane protein (Potential)				620
Q96MV8 UniProt NPD GO	ZDH15_HUMAN	Palmitoyltransferase ZDHHC15 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 15) (DHHC-15)	0.09	-	end	4 *	Membrane; multi-pass membrane protein (Potential)		300577		337
Q5Y5T2 UniProt NPD GO	ZDH18_MOUSE	Palmitoyltransferase ZDHHC18 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 18) (DHHC-18) ...	0.09	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				291
P00689 UniProt NPD GO	AMYP_RAT	Pancreatic alpha-amylase precursor (EC 3.2.1.1) (PA) (1,4-alpha-D-glucan glucanohydrolase)	0.09	-	pox	0	Secreted protein; extracellular space				508
P41335 UniProt NPD GO	PAHO_ERIEU	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.09	-	nuc	0	Secreted protein				36
P41336 UniProt NPD GO	PAHO_RABIT	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.09	-	nuc	0	Secreted protein				36
Q64424 UniProt NPD GO	LIPR2_MYOCO	Pancreatic lipase-related protein 2 precursor (EC 3.1.1.3) (PL-RP2)	0.09	-	exc	0	Secreted protein				470
P09475 UniProt NPD GO	PPY_LOPAM	Pancreatic propolypeptide YG precursor (APY) [Contains: Pancreatic polypeptide YG; Carboxy-terminal ...	0.09	-	nuc	0	Secreted protein				69
Q02157 UniProt NPD GO	LIPP_RABIT	Pancreatic triacylglycerol lipase precursor (EC 3.1.1.3) (Pancreatic lipase) (PL)	0.09	-	vac	0	Secreted protein				465
P27657 UniProt NPD GO	LIPP_RAT	Pancreatic triacylglycerol lipase precursor (EC 3.1.1.3) (Pancreatic lipase) (PL)	0.09	-	exc	0	Secreted protein				465
Q9NVE7 UniProt NPD GO	PANK4_HUMAN	Pantothenate kinase 4 (EC 2.7.1.33) (Pantothenic acid kinase 4) (hPanK4)	0.09	-	cyt	0	Cytoplasm (Probable)		606162		773
P01372 UniProt NPD GO	PPS1_DROFU	Paragonial peptide PS-1 (Paragonial peptide C)	0.09	-	nuc	0	Secreted protein				27
P52212 UniProt NPD GO	PTHY_CANFA	Parathyroid hormone precursor (Parathyrin) (PTH)	0.09	-	mit	0	Secreted protein				115
P49190 UniProt NPD GO	PTHR2_HUMAN	Parathyroid hormone receptor precursor (PTH2 receptor)	0.09	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601469		550
P15476 UniProt NPD GO	PAT1_SOLTU	Patatin B1 precursor (Potato tuber protein) (Fragment)	0.09	-	exc	0					377
P04284 UniProt NPD GO	PR06_LYCES	Pathogenesis-related leaf protein 6 precursor (P6) (Ethylene-induced protein P1) (P14) (P14A) (PR pr ...	0.09	-	vac	0				1CFE	159
P32937 UniProt NPD GO	PR1A_HORVU	Pathogenesis-related protein 1A/1B precursor	0.09	-	exc	1 *					173
Q962B2 UniProt NPD GO	PEN3K_LITSE	Penaeidin-3k precursor (Pen-3k)	0.09	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				75
Q962B1 UniProt NPD GO	PEN3M_LITSE	Penaeidin-3m precursor (Pen-3m)	0.09	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				75
Q962B0 UniProt NPD GO	PEN3N_LITSE	Penaeidin-3n precursor (Pen-3n)	0.09	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				75
P00798 UniProt NPD GO	PENP_PENJA	Penicillopepsin (EC 3.4.23.20) (Peptidase A)	0.09	-	cyt	0				3APP	323
P13636 UniProt NPD GO	PEPA_URSTH	Pepsin A precursor (EC 3.4.23.1) (Fragment)	0.09	-	nuc	0	Secreted protein				60
Q6JQN2 UniProt NPD GO	KN2_MESMA	Peptide BmKn2 precursor	0.09	-	vac	1 *	Secreted protein				70
P0C176 UniProt NPD GO	SCKP3_TITSE	Peptide TsPep3	0.09	-	nuc	0	Secreted protein				29
P29204 UniProt NPD GO	PYY_RANRI	Peptide YY-like (PYY)	0.09	-	nuc	0	Secreted protein				36
P97467 UniProt NPD GO	AMD_MOUSE	Peptidyl-glycine alpha-amidating monooxygenase precursor (EC 1.14.17.3) (PAM)	0.09	-	end	1 *	Secretory granules	cytosol [TAS] integral to plasma membrane [TAS]			979
P14925 UniProt NPD GO	AMD_RAT	Peptidyl-glycine alpha-amidating monooxygenase precursor (EC 1.14.17.3) (PAM)	0.09	-	end	2 *	Secretory granules			3PHM	976
Q6CL78 UniProt NPD GO	PPID_KLULA	Peptidyl-prolyl cis-trans isomerase D (EC 5.2.1.8) (PPIase D) (Rotamase D)	0.09	-	cyt	0	Cytoplasm (By similarity)				372
P0C1I2 UniProt NPD GO	PPIE_RHIOR	Peptidyl-prolyl cis-trans isomerase E (EC 5.2.1.8) (PPIase E) (Rotamase E) (Cyclophilin E)	0.09	-	cyt	0					315
Q27135 UniProt NPD GO	PER_ZAPTU	Period circadian protein (Fragment)	0.09	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				131
O76217 UniProt NPD GO	PE1_ANOGA	Peritrophin-1 precursor (Peritrophin A) (Peritrophic matrix protein 1) (AgAper-1)	0.09	-	exc	0					153
Q9SZE7 UniProt NPD GO	PER51_ARATH	Peroxidase 51 precursor (EC 1.11.1.7) (Atperox P51) (ATP37)	0.09	-	exc	1 *	Secreted protein (By similarity)				329
Q9SY33 UniProt NPD GO	PER7_ARATH	Peroxidase 7 precursor (EC 1.11.1.7) (Atperox P7) (ATP30)	0.09	-	vac	1 *	Secreted protein (By similarity)				349
Q63716 UniProt NPD GO	PRDX1_RAT	Peroxiredoxin-1 (EC 1.11.1.15) (Thioredoxin peroxidase 2) (Thioredoxin-dependent peroxide reductase ...	0.09	-	cyt	0	Cytoplasm			1QQ2	199
P35700 UniProt NPD GO	PRDX1_MOUSE	Peroxiredoxin-1 (EC 1.11.1.15) (Thioredoxin peroxidase 2) (Thioredoxin-dependent peroxide reductase ...	0.09	-	cyt	0	Cytoplasm				199
Q06830 UniProt NPD GO	PRDX1_HUMAN	Peroxiredoxin-1 (EC 1.11.1.15) (Thioredoxin peroxidase 2) (Thioredoxin-dependent peroxide reductase ...	0.09	-	cyt	0	Cytoplasm		176763		199
Q9BGI2 UniProt NPD GO	PRDX4_BOVIN	Peroxiredoxin-4 (EC 1.11.1.15) (Prx-IV)	0.09	-	cyt	0	Cytoplasm (By similarity)				274
P07896 UniProt NPD GO	ECHP_RAT	Peroxisomal bifunctional enzyme (PBE) (PBFE) [Includes: Enoyl-CoA hydratase (EC 4.2.1.17); 3,2-trans ...	0.09	-	pox	0	Peroxisome			1ZCJ	721
Q2KIY1 UniProt NPD GO	PXMP2_BOVIN	Peroxisomal membrane protein 2	0.09	-	mit	4 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein (By similarity)				195
Q9JJW0 UniProt NPD GO	PXMP4_MOUSE	Peroxisomal membrane protein 4 (24 kDa peroxisomal intrinsic membrane protein)	0.09	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein (By similarity)				211
P51659 UniProt NPD GO	DHB4_HUMAN	Peroxisomal multifunctional enzyme type 2 (MFE-2) (D-bifunctional protein) (DBP) (17-beta-hydroxyste ...	0.09	-	pox	0	Peroxisome	peroxisome [TAS]	261515	1S9C	735
P35513 UniProt NPD GO	PAL2_TOBAC	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.09	-	nuc	0	Cytoplasm (Probable)				712
Q92195 UniProt NPD GO	PALY_AGABI	Phenylalanine ammonia-lyase (EC 4.3.1.5) (Fragment)	0.09	-	cyt	0	Cytoplasm (Probable)				142
P12234 UniProt NPD GO	MPCP_BOVIN	Phosphate carrier protein, mitochondrial precursor (PTP) (Solute carrier family 25 member 3)	0.09	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				362
Q08758 UniProt NPD GO	LCAT_PAPAN	Phosphatidylcholine-sterol acyltransferase precursor (EC 2.3.1.43) (Lecithin-cholesterol acyltransfe ...	0.09	-	mit	2 *					440
Q757H2 UniProt NPD GO	CSR1_ASHGO	Phosphatidylinositol transfer protein CSR1	0.09	-	cyt	0	Cytoplasm (By similarity). Endosome (By similarity)				436

You are viewing entries 66701 to 66750 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.