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
Q20EY4 UniProt NPD GO	YCF12_OLTVI	Protein ycf12	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
Q9MS78 UniProt NPD GO	YCF12_PHAAC	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				31
P61051 UniProt NPD GO	YCF12_PHYPA	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
Q3ZJ17 UniProt NPD GO	YCF12_PSEAK	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				34
Q1KVW3 UniProt NPD GO	YCF12_SCEOB	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
O96797 UniProt NPD GO	YCF12_SKECO	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				34
Q32RW9 UniProt NPD GO	YCF12_STAPU	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
Q32RP1 UniProt NPD GO	YCF12_ZYGCR	Protein ycf12	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
P31560 UniProt NPD GO	YCF12_MARPO	Protein ycf12 (ORF33)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
P41600 UniProt NPD GO	YCF12_PINTH	Protein ycf12 (ORF33)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
P49529 UniProt NPD GO	YCF12_ODOSI	Protein ycf12 (ORF34)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				34
Q8M9Z7 UniProt NPD GO	YCF12_CHAGL	Protein ycf12 (RF12)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
Q9MUS3 UniProt NPD GO	YCF12_MESVI	Protein ycf12 (RF12)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
Q9TKY6 UniProt NPD GO	YCF12_NEPOL	Protein ycf12 (RF12)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
P59234 UniProt NPD GO	YIPL_SOLTU	Protein yippee-like	0.00	-	cyt	0					129
Q9SR97 UniProt NPD GO	YIPL1_ARATH	Protein yippee-like At3g08990	0.00	-	cyt	0					128
Q9C777 UniProt NPD GO	YIPL3_ARATH	Protein yippee-like At3g11230	0.00	-	cyt	0					129
Q4WTW3 UniProt NPD GO	YOP1_ASPFU	Protein yop1	0.00	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				169
Q5BB01 UniProt NPD GO	YOP1_EMENI	Protein yop1	0.00	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				169
Q42539 UniProt NPD GO	PIMT_ARATH	Protein-L-isoaspartate O-methyltransferase (EC 2.1.1.77) (Protein-beta-aspartate methyltransferase) ...	0.00	-	cyt	0	Cytoplasm				230
O60725 UniProt NPD GO	ICMT_HUMAN	Protein-S-isoprenylcysteine O-methyltransferase (EC 2.1.1.100) (Isoprenylcysteine carboxylmethyltran ...	0.00	-	mit	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] membrane fraction [TAS]	605851		284
Q9EQK7 UniProt NPD GO	ICMT_MOUSE	Protein-S-isoprenylcysteine O-methyltransferase (EC 2.1.1.100) (Isoprenylcysteine carboxylmethyltran ...	0.00	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				283
Q66GT5 UniProt NPD GO	PTPM1_MOUSE	Protein-tyrosine phosphatase mitochondrial 1, mitochondrial precursor (EC 3.1.3.48) (EC 3.1.3.16) (P ...	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane. Associated with the inner membrane				193
P84033 UniProt NPD GO	PN47_PHONI	Proteinase PN47 (EC 3.4.-.-) (Fragment)	0.00	-	cyt	0	Secreted protein				39
Q00783 UniProt NPD GO	ICI1_SOLTU	Proteinase inhibitor 1 precursor (Proteinase inhibitor I)	0.00	-	vac	0					107
Q43652 UniProt NPD GO	IP27_SOLTU	Proteinase inhibitor type-2 CM7 precursor (Proteinase inhibitor type II CM7)	0.00	-	mit	1 *					154
Q41435 UniProt NPD GO	IP2T_SOLTU	Proteinase inhibitor type-2 T precursor (Proteinase inhibitor type II T)	0.00	-	exc	1 *					147
Q40561 UniProt NPD GO	IP21_TOBAC	Proteinase inhibitor type-2 precursor (Proteinase inhibitor type II)	0.00	-	exc	1 *					197
P36963 UniProt NPD GO	DMA_SQUAC	Proteolipid protein DM alpha	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				245
P36965 UniProt NPD GO	DMG_SQUAC	Proteolipid protein DM gamma	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				246
Q01621 UniProt NPD GO	LCK_RAT	Proto-oncogene tyrosine-protein kinase LCK (EC 2.7.10.2) (p56-LCK) (Lymphocyte cell-specific protein ...	0.00	-		0	Cytoplasm (By similarity). Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Present in ...				17
P69437 UniProt NPD GO	PROTO_AGEPP	Protonectin	0.00	-		0	Secreted protein				12
P0C1R1 UniProt NPD GO	PROTO_PROSY	Protonectin	0.00	-		0	Secreted protein				12
Q12335 UniProt NPD GO	PST2_YEAST	Protoplast secreted protein 2 precursor	0.00	-	cyt	0	Secreted protein	cytoplasm [IDA] mitochondrion [IDA]			198
P83188 UniProt NPD GO	PS1_PSEPD	Pseudin-1	0.00	-	cyt	0	Secreted protein				24
P83189 UniProt NPD GO	PS2_PSEPD	Pseudin-2	0.00	-	cyt	0	Secreted protein				24
P83190 UniProt NPD GO	PS3_PSEPD	Pseudin-3	0.00	-	cyt	0	Secreted protein				23
P83191 UniProt NPD GO	PS4_PSEPD	Pseudin-4	0.00	-	cyt	0	Secreted protein				23
P29532 UniProt NPD GO	GERP_WHEAT	Pseudogermin (Fragment)	0.00	-	cyt	0	Cell wall. Component of the walls of the mature, ungerminated embryos				21
P84460 UniProt NPD GO	PHCY_LIODE	Pseudohemocyanin (Fragment)	0.00	-		0					12
P84768 UniProt NPD GO	PHCY_LIOHO	Pseudohemocyanin (Fragment)	0.00	-		0					12
P22397 UniProt NPD GO	PSPC_CANFA	Pulmonary surfactant-associated protein C (SP-C) (Pulmonary surfactant-associated proteolipid SPL(Va ...	0.00	-	gol	1 *	Secreted protein; extracellular space				34
P15785 UniProt NPD GO	PSPC_PIG	Pulmonary surfactant-associated protein C (SP-C) (Pulmonary surfactant-associated proteolipid SPL(Va ...	0.00	-	mit	1 *	Secreted protein; extracellular space			1SPF	35
P55152 UniProt NPD GO	PSPC_MACMU	Pulmonary surfactant-associated protein C precursor (SP-C) (Pulmonary surfactant-associated proteoli ...	0.00	-	gol	1 *	Secreted protein; extracellular space				191
P00491 UniProt NPD GO	PNPH_HUMAN	Purine nucleoside phosphorylase (EC 2.4.2.1) (Inosine phosphorylase) (PNP)	0.00	-	cyt	0			164050	2A0Y	289
P82867 UniProt NPD GO	SB18_MAIZE	Putative 18 kDa spermidine-binding protein (Fragment)	0.00	-		0	Microsome; microsomal membrane	microsome [NAS]			20
Q9USJ1 UniProt NPD GO	THTM_SCHPO	Putative 3-mercaptopyruvate sulfurtransferase (EC 2.8.1.2) (MST)	0.00	-	cyt	0					298
O02058 UniProt NPD GO	PTPS_CAEEL	Putative 6-pyruvoyl tetrahydrobiopterin synthase (EC 4.2.3.12) (PTPS) (PTP synthase)	0.00	-	cyt	0				2G64	140
P84723 UniProt NPD GO	CLPP_PINST	Putative ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp) (PS7/PS12 ...	0.00	-	cyt	0	Plastid; chloroplast (By similarity)				80
Q9BW83 UniProt NPD GO	RAYL_HUMAN	Putative GTP-binding protein RAY-like (Rab-like protein 4)	0.00	-	cyt	0					186

You are viewing entries 97401 to 97450 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.