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
Q9H2J7 UniProt NPD GO	S6A15_HUMAN	Orphan sodium- and chloride-dependent neurotransmitter transporter NTT73 (Orphan transporter v7-3) ( ...	0.04	-	end	12	Membrane; multi-pass membrane protein	integral to membrane [NAS]	607971		730
P50703 UniProt NPD GO	OS35_SOLCO	Osmotin-like protein OSML15 precursor (PA15)	0.04	-	exc	0					250
P81455 UniProt NPD GO	OSTC_CANFA	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.04	-	cyt	0	Secreted protein				49
P02821 UniProt NPD GO	OSTC_FELCA	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.04	-	cyt	0	Secreted protein				49
P83473 UniProt NPD GO	OSTC_HALDD	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP) (Fragment)	0.04	-		0	Secreted protein	extracellular matrix [TAS]			19
P84350 UniProt NPD GO	OSTC_PONPY	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP) (Fragment)	0.04	-	cyt	0	Secreted protein				33
Q01501 UniProt NPD GO	VDAC_DICDI	Outer mitochondrial membrane protein porin (Voltage-dependent anion-selective channel protein) (VDAC ...	0.04	-	cyt	0	Mitochondrion; mitochondrial outer membrane				275
P68385 UniProt NPD GO	IOVO_LARMA	Ovomucoid (Fragment)	0.04	-	nuc	0	Secreted protein				54
P68386 UniProt NPD GO	IOVO_LARRI	Ovomucoid (Fragment)	0.04	-	nuc	0	Secreted protein				54
P05561 UniProt NPD GO	IOVO_NOTCI	Ovomucoid (Fragment)	0.04	-	nuc	0	Secreted protein				51
P52250 UniProt NPD GO	IOVO_POLEM	Ovomucoid (Fragment)	0.04	-	nuc	0	Secreted protein				51
P68384 UniProt NPD GO	IOVO_VANSP	Ovomucoid (Fragment)	0.04	-	nuc	0	Secreted protein				54
P46483 UniProt NPD GO	PSBO_EUGGR	Oxygen-evolving enhancer protein 1, chloroplast precursor (OEE1)	0.04	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				338
P14226 UniProt NPD GO	PSBO_PEA	Oxygen-evolving enhancer protein 1, chloroplast precursor (OEE1) (33 kDa subunit of oxygen evolving ...	0.04	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				329
Q40459 UniProt NPD GO	PSBO_TOBAC	Oxygen-evolving enhancer protein 1, chloroplast precursor (OEE1) (33 kDa subunit of oxygen evolving ...	0.04	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				332
Q00434 UniProt NPD GO	PSBP_WHEAT	Oxygen-evolving enhancer protein 2, chloroplast precursor (OEE2) (23 kDa subunit of oxygen evolving ...	0.04	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				258
P83247 UniProt NPD GO	TOP1_OXYKI	Oxyopinin-1 (Oxki1)	0.04	-	nuc	0	Secreted protein	extracellular region [NAS]			48
P29531 UniProt NPD GO	OLEO2_SOYBN	P24 oleosin isoform B (P91)	0.04	-	end	3	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface				223
O70397 UniProt NPD GO	P2RX2_CAVPO	P2X purinoceptor 2 (ATP receptor) (P2X2) (Purinergic receptor)	0.04	-	mit	1 *	Membrane; multi-pass membrane protein				474
O54803 UniProt NPD GO	P2RX6_MOUSE	P2X purinoceptor 6 (ATP receptor) (P2X6) (Purinergic receptor) (P2XM) (Purinergic receptor P2X-like ...	0.04	-	end	1 *	Membrane; multi-pass membrane protein				379
P51579 UniProt NPD GO	P2RX6_RAT	P2X purinoceptor 6 (ATP receptor) (P2X6) (Purinergic receptor) (P2XM) (Purinergic receptor P2X-like ...	0.04	-	end	1 *	Membrane; multi-pass membrane protein				379
Q5ZIK2 UniProt NPD GO	PDZ11_CHICK	PDZ domain-containing protein 11	0.04	-	cyt	0					140
Q9D9G2 UniProt NPD GO	PEBPL_MOUSE	PEBP family protein precursor	0.04	-	exc	0	Secreted protein (Potential)				242
Q8N755 UniProt NPD GO	PQLC3_HUMAN	PQ loop repeat-containing protein 3 precursor	0.04	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				202
Q99134 UniProt NPD GO	PYLA_XENLA	PYLa/PGLa precursor [Contains: PYLa; PGLa]	0.04	-	exc	1 *	Secreted protein				64
P45478 UniProt NPD GO	PPT1_BOVIN	Palmitoyl-protein thioesterase 1 precursor (EC 3.1.2.22) (PPT-1) (Palmitoyl-protein hydrolase 1)	0.04	-	exc	1 *	Lysosome			1EXW	306
Q8HXW6 UniProt NPD GO	PPT1_MACFA	Palmitoyl-protein thioesterase 1 precursor (EC 3.1.2.22) (PPT-1) (Palmitoyl-protein hydrolase 1)	0.04	-	exc	0	Lysosome (By similarity)				306
Q755Y0 UniProt NPD GO	AKR1_ASHGO	Palmitoyltransferase AKR1 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR1)	0.04	-	end	6	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				724
Q5B0V6 UniProt NPD GO	AKR1_EMENI	Palmitoyltransferase akr1 (EC 2.3.1.-) (Ankyrin repeat-containing protein akr1)	0.04	-	end	5	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				737
P00688 UniProt NPD GO	AMYP_MOUSE	Pancreatic alpha-amylase precursor (EC 3.2.1.1) (PA) (1,4-alpha-D-glucan glucanohydrolase)	0.04	-	pox	0	Secreted protein; extracellular space				508
P09656 UniProt NPD GO	IPKX_RAT	Pancreatic secretory trypsin inhibitor II precursor (PSTI-II) (Caltrin) (Calcium transport inhibitor ...	0.04	-	vac	0	Secreted protein				79
Q9BDJ5 UniProt NPD GO	VNN1_PIG	Pantetheinase precursor (EC 3.5.1.92) (Pantetheine hydrolase) (Vascular non-inflammatory molecule 1) ...	0.04	-	end	1 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)				513
Q9FKB3 UniProt NPD GO	PANC_ARATH	Pantoate--beta-alanine ligase (EC 6.3.2.1) (Pantothenate synthetase) (Pantoate-activating enzyme)	0.04	-	cyt	0	Cytoplasm (Potential)				310
P05994 UniProt NPD GO	PAPA4_CARPA	Papaya proteinase 4 precursor (EC 3.4.22.25) (Papaya proteinase IV) (PPIV) (Papaya peptidase B) (Gly ...	0.04	-	mit	0				1GEC	348
P30253 UniProt NPD GO	PAP1_MANSE	Paralytic peptide 1 (Paralytic peptide I) (PP I)	0.04	-	cyt	0				1HRL	23
P30255 UniProt NPD GO	PAP1_SPOEX	Paralytic peptide 1 (Paralytic peptide I) (PP I)	0.04	-	nuc	0					23
P30256 UniProt NPD GO	PAP2_SPOEX	Paralytic peptide 2 (Paralytic peptide II) (PP II)	0.04	-	nuc	0					23
P70555 UniProt NPD GO	PTHR2_RAT	Parathyroid hormone receptor precursor (PTH2 receptor)	0.04	-	end	4	Membrane; multi-pass membrane protein				546
Q63471 UniProt NPD GO	PSP_RAT	Parotid secretory protein precursor (PSP) (Neonatal submandibular gland protein)	0.04	-	end	0	Secreted protein	secretory granule [IDA]			235
P80080 UniProt NPD GO	PRVA_GERSP	Parvalbumin alpha	0.04	-	cyt	0					109
P20472 UniProt NPD GO	PRVA_HUMAN	Parvalbumin alpha	0.04	-	cyt	0			168890	1RK9	109
P02624 UniProt NPD GO	PRVA_RABIT	Parvalbumin alpha	0.04	-	cyt	0					109
P80050 UniProt NPD GO	PRVA_MACFU	Parvalbumin alpha (Parvalbumin, muscle)	0.04	-	cyt	0					109
P80026 UniProt NPD GO	PRVM_CHICK	Parvalbumin, muscle	0.04	-	cyt	0					109
P83834 UniProt NPD GO	PR1_CUCME	Pathogenesis-related protein (PR-1) (Allergen Cuc m 3) (Fragments)	0.04	-	cyt	0					41
Q05968 UniProt NPD GO	PR1_HORVU	Pathogenesis-related protein 1 precursor	0.04	-	exc	0					164
Q08697 UniProt NPD GO	PR1A_LYCES	Pathogenesis-related protein 1A1 precursor (PR-1A1)	0.04	-	exc	0					175
P35793 UniProt NPD GO	PR13_HORVU	Pathogenesis-related protein PRB1-3 precursor (PR-1B) (HV-8)	0.04	-	exc	0					164
Q00374 UniProt NPD GO	PLYA_COLGL	Pectin lyase precursor (EC 4.2.2.10)	0.04	-	exc	0	Secreted protein (Potential)				380
Q962A9 UniProt NPD GO	PEN2D_LITSE	Penaeidin-2d precursor (Pen-2d)	0.04	-	end	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				72

You are viewing entries 77801 to 77850 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.