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
Q6CP93 UniProt NPD GO	YOP1_KLULA	Protein YOP1	0.01	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				180
Q51VY4 UniProt NPD GO	YOP1_MAGGR	Protein YOP1	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				170
Q12512 UniProt NPD GO	ZPS1_YEAST	Protein ZPS1 precursor	0.01	-	exc	0		cell wall (sensu Fungi) [IDA] vacuole (sensu Fungi) [IDA]			249
O70467 UniProt NPD GO	ANM3_RAT	Protein arginine N-methyltransferase 3 (EC 2.1.1.-) (Heterogeneous nuclear ribonucleoprotein methylt ...	0.01	-	cyt	0	Cytoplasm	cytoplasm [IDA]		1F3L	528
P49858 UniProt NPD GO	CNI_DROME	Protein cornichon	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				144
P52159 UniProt NPD GO	CNI_DROVI	Protein cornichon	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				144
Q17770 UniProt NPD GO	PDI2_CAEEL	Protein disulfide-isomerase 2 precursor (EC 5.3.4.1) (PDI 1) (Prolyl 4-hydroxylase subunit beta)	0.01	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen				493
P29828 UniProt NPD GO	PDI_MEDSA	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI)	0.01	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				512
Q43116 UniProt NPD GO	PDI_RICCO	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI)	0.01	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				498
P52589 UniProt NPD GO	PDI_WHEAT	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI)	0.01	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				515
P09102 UniProt NPD GO	PDIA1_CHICK	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI) (Prolyl 4-hydroxylase subunit beta) (Cellul ...	0.01	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Highly abundant. In some cell types, seems to be ...				515
P34101 UniProt NPD GO	PK1_DICDI	Protein kinase 1 (EC 2.7.11.1) (Fragment)	0.01	-	nuc	0					33
O94472 UniProt NPD GO	PBN1_SCHPO	Protein pbn1	0.01	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...				332
Q7SCY7 UniProt NPD GO	SYM1_NEUCR	Protein sym-1	0.01	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				190
Q9IAY5 UniProt NPD GO	SDOS_CHICK	Protein syndesmos	0.01	-	cyt	0	Intracytoplasmic membrane. Colocalizes with SDC4 in ventral plasma membrane adhesion plaques				313
Q9BRJ7 UniProt NPD GO	SDOS_HUMAN	Protein syndesmos (NUDT16-like protein 1)	0.01	-	mit	0	Cytoplasm (By similarity)				211
P22244 UniProt NPD GO	RIP1_HORVU	Protein synthesis inhibitor I (EC 3.2.2.22) (Ribosome-inactivating protein I) (rRNA N-glycosidase)	0.01	-	mit	0	Starchy endosperm of mature seeds				280
Q9SMP2 UniProt NPD GO	S61G3_ARATH	Protein transport protein SEC61 gamma-3 subunit	0.01	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				69
P35179 UniProt NPD GO	SC61G_YEAST	Protein transport protein SSS1 (Sec61 complex subunit SSS1) (Sec61 complex subunit gamma) (Ssh1 comp ...	0.01	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein	endoplasmic reticulum membrane [IDA] Sec complex-associated translocon complex [TAS]			80
Q85FN5 UniProt NPD GO	YCF12_ADICA	Protein ycf12	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
Q9TLX0 UniProt NPD GO	YCF12_CYACA	Protein ycf12	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				35
Q4G3D2 UniProt NPD GO	YCF12_EMIHU	Protein ycf12	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				34
Q6B8L0 UniProt NPD GO	YCF12_GRATL	Protein ycf12	0.01	-	cyt	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				34
Q1XDA2 UniProt NPD GO	YCF12_PORYE	Protein ycf12	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				34
Q8WI31 UniProt NPD GO	YCF12_PSINU	Protein ycf12	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				33
P51385 UniProt NPD GO	YCF12_PORPU	Protein ycf12 (ORF34)	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast membrane; single-pass membrane protein (Potential)				34
Q65Z59 UniProt NPD GO	YPEL1_CERAE	Protein yippee-like 1	0.01	-	mit	0	Nucleus (By similarity)				119
O60688 UniProt NPD GO	YPEL1_HUMAN	Protein yippee-like 1	0.01	-	mit	0	Nucleus (By similarity)		608082		119
Q9ESC7 UniProt NPD GO	YPEL1_MOUSE	Protein yippee-like 1 (DGL-1) (Mdgl-1)	0.01	-	mit	0	Nucleus				118
Q9DG42 UniProt NPD GO	YPEL1_COTJA	Protein yippee-like 1 (DGL-1) (Qdgl-1)	0.01	-	mit	0					119
Q2YDI3 UniProt NPD GO	YPEL2_BOVIN	Protein yippee-like 2	0.01	-	mit	0	Nucleus; nucleolus (By similarity)				119
Q65Z58 UniProt NPD GO	YPEL2_CERAE	Protein yippee-like 2	0.01	-	mit	0	Nucleus; nucleolus (By similarity)				119
Q96QA6 UniProt NPD GO	YPEL2_HUMAN	Protein yippee-like 2	0.01	-	mit	0	Nucleus; nucleolus		609723		119
Q65Z95 UniProt NPD GO	YPEL2_MOUSE	Protein yippee-like 2	0.01	-	mit	0	Nucleus; nucleolus (By similarity)				119
Q5RDN9 UniProt NPD GO	YPEL2_PONPY	Protein yippee-like 2	0.01	-	mit	0	Nucleus; nucleolus (By similarity)				119
Q9LY56 UniProt NPD GO	YIPL4_ARATH	Protein yippee-like At3g55890	0.01	-	cyt	0					121
Q9W2X7 UniProt NPD GO	YPL1_DROME	Protein yippee-like CG15309	0.01	-	mit	0					114
P15246 UniProt NPD GO	PIMT_BOVIN	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (EC 2.1.1.77) (Protein-beta-aspartate methyl ...	0.01	-	nuc	0	Cytoplasm				226
Q92047 UniProt NPD GO	PIMT_BRARE	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (EC 2.1.1.77) (Protein-beta-aspartate methyl ...	0.01	-	nuc	0	Cytoplasm (By similarity)				227
P22061 UniProt NPD GO	PIMT_HUMAN	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (EC 2.1.1.77) (Protein-beta-aspartate methyl ...	0.01	-	nuc	0	Cytoplasm	endoplasmic reticulum [TAS]	176851	1KR5	226
P23506 UniProt NPD GO	PIMT_MOUSE	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (EC 2.1.1.77) (Protein-beta-aspartate methyl ...	0.01	-	nuc	0	Cytoplasm				226
P80895 UniProt NPD GO	PIMT_PIG	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (EC 2.1.1.77) (Protein-beta-aspartate methyl ...	0.01	-	nuc	0	Cytoplasm				226
P22062 UniProt NPD GO	PIMT_RAT	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (EC 2.1.1.77) (Protein-beta-aspartate methyl ...	0.01	-	nuc	0	Cytoplasm				226
P32584 UniProt NPD GO	STE14_YEAST	Protein-S-isoprenylcysteine O-methyltransferase (EC 2.1.1.100) (Isoprenylcysteine carboxylmethyltran ...	0.01	-	end	5 *	Membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum membrane [IDA]			239
Q9WVM4 UniProt NPD GO	ICMT_RAT	Protein-S-isoprenylcysteine O-methyltransferase (EC 2.1.1.100) (Isoprenylcysteine carboxylmethyltran ...	0.01	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				232
P20015 UniProt NPD GO	PRTT_TRIAL	Proteinase T precursor (EC 3.4.21.-) (Fragment)	0.01	-	cyt	0					293
P82381 UniProt NPD GO	ICI_LINUS	Proteinase inhibitor (LUTI)	0.01	-	cyt	0				1DWM	69
P31608 UniProt NPD GO	IPRA_SAGSA	Proteinase inhibitor A precursor (Double-headed proteinase inhibitor A) (API-A)	0.01	-	exc	0	Secreted protein				181
P01081 UniProt NPD GO	IP2A_SOLTU	Proteinase inhibitor IIA (Fragment)	0.01	-	nuc	0	Secreted protein				45
Q41489 UniProt NPD GO	IP2Y_SOLTU	Proteinase inhibitor type-2 precursor (Proteinase inhibitor type II)	0.01	-	exc	1 *					147

You are viewing entries 90951 to 91000 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.