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
Q6CUB5 UniProt NPD GO	PFA4_KLULA	Palmitoyltransferase PFA4 (EC 2.3.1.-) (Protein fatty acyltransferase 4)	0.12	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				377
Q6C7Q0 UniProt NPD GO	PFA4_YARLI	Palmitoyltransferase PFA4 (EC 2.3.1.-) (Protein fatty acyltransferase 4)	0.12	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				342
Q9VHS7 UniProt NPD GO	COQ2_DROME	Para-hydroxybenzoate--polyprenyltransferase, mitochondrial precursor (EC 2.5.1.-) (PHB:polyprenyltra ...	0.12	-	end	5	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)	DNA-directed RNA polymerase I complex [ISS] DNA-directed RNA polymerase III complex [ISS] mitochondrial inner membrane [ISS]			392
Q10252 UniProt NPD GO	COQ2_SCHPO	Para-hydroxybenzoate--polyprenyltransferase, mitochondrial precursor (EC 2.5.1.-) (PHB:polyprenyltra ...	0.12	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			358
P47244 UniProt NPD GO	PARF_PARTE	Parafusin	0.12	-	cyt	0	Cytoplasm			1KFQ	584
P15478 UniProt NPD GO	PAT5_SOLTU	Patatin T5 precursor (Potato tuber protein)	0.12	-	mit	1 *					386
Q96575 UniProt NPD GO	PME22_LYCES	Pectinesterase-2 precursor (EC 3.1.1.11) (Pectin methylesterase 2) (PE 2)	0.12	-	mit	1 *	Cell wall				550
O04887 UniProt NPD GO	PME2_CITSI	Pectinesterase-2 precursor (EC 3.1.1.11) (Pectin methylesterase) (PE)	0.12	-	exc	0					510
Q963C8 UniProt NPD GO	PEN3F_PENVA	Penaeidin-3f precursor (Pen-3f)	0.12	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				82
P49263 UniProt NPD GO	PXN1_XENLA	Pentraxin fusion protein precursor	0.12	-	mit	0					416
Q9GMY6 UniProt NPD GO	PEPA_CANFA	Pepsin A precursor (EC 3.4.23.1)	0.12	-	exc	0	Secreted protein				386
P81497 UniProt NPD GO	PEPA_SUNMU	Pepsin A precursor (EC 3.4.23.1)	0.12	-	exc	0	Secreted protein				387
Q5KFV5 UniProt NPD GO	PPID_CRYNE	Peptidyl-prolyl cis-trans isomerase D (EC 5.2.1.8) (PPIase D) (Rotamase D)	0.12	-	cyt	0	Cytoplasm (By similarity)				375
P08399 UniProt NPD GO	PHXR5_MOUSE	Per-hexamer repeat protein 5	0.12	-	cyt	0					672
O48677 UniProt NPD GO	PER6_ARATH	Peroxidase 6 precursor (EC 1.11.1.7) (Atperox P6)	0.12	-	exc	0	Secreted protein (By similarity)				326
P11466 UniProt NPD GO	OCTC_RAT	Peroxisomal carnitine O-octanoyltransferase (EC 2.3.1.137) (COT)	0.12	-	cyt	0	Peroxisome (Potential)				612
O70597 UniProt NPD GO	PX11A_RAT	Peroxisomal membrane protein 11A (Peroxin-11A) (Peroxisomal biogenesis factor 11A) (PEX11alpha) (Pex ...	0.12	-	cyt	1	Peroxisome; peroxisomal membrane; multi-pass membrane protein	peroxisomal membrane [IDA]			246
P59382 UniProt NPD GO	PXMP4_RAT	Peroxisomal membrane protein 4 (24 kDa peroxisomal intrinsic membrane protein)	0.12	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein				211
P78980 UniProt NPD GO	PEX16_YARLI	Peroxisomal membrane protein PEX16 (Peroxin-16)	0.12	-	nuc	0	Peroxisome; peroxisomal membrane; peripheral membrane protein; matrix side				391
P01858 UniProt NPD GO	TUFT_HUMAN	Phagocytosis-stimulating peptide (Tuftsin)	0.12	-		0					4
P15245 UniProt NPD GO	PH2M_TRICU	Phenol 2-monooxygenase (EC 1.14.13.7) (Phenol hydroxylase)	0.12	-	cyt	0	Cytoplasm			1FOH	664
P26600 UniProt NPD GO	PAL5_LYCES	Phenylalanine ammonia-lyase (EC 4.3.1.5) (PAL)	0.12	-	nuc	0	Cytoplasm (Probable)				721
O49835 UniProt NPD GO	PAL1_LITER	Phenylalanine ammonia-lyase 1 (EC 4.3.1.5) (PAL-1)	0.12	-	nuc	0	Cytoplasm (Probable)				710
Q99063 UniProt NPD GO	PRA1_USTHO	Pheromone receptor 1	0.12	-	end	7 *	Membrane; multi-pass membrane protein				359
P53811 UniProt NPD GO	PIPNB_MOUSE	Phosphatidylinositol transfer protein beta isoform (PtdIns transfer protein beta) (PtdInsTP) (PI-TP- ...	0.12	-	cyt	0	Cytoplasm. Golgi apparatus				270
Q5R6F0 UniProt NPD GO	PIPNB_PONPY	Phosphatidylinositol transfer protein beta isoform (PtdIns transfer protein beta) (PtdInsTP) (PI-TP- ...	0.12	-	cyt	0	Cytoplasm (By similarity)				271
Q8C398 UniProt NPD GO	PIGW_MOUSE	Phosphatidylinositol-glycan biosynthesis class W protein (EC 2.3.-.-) (PIG-W)	0.12	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				503
P38628 UniProt NPD GO	AGM1_YEAST	Phosphoacetylglucosamine mutase (EC 5.4.2.3) (PAGM) (Acetylglucosamine phosphomutase) (N-acetylgluco ...	0.12	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			557
P08891 UniProt NPD GO	PGKA_TRYBB	Phosphoglycerate kinase A (EC 2.7.2.3) (PGK A allele 2)	0.12	-	cyt	0	Not known				505
P07377 UniProt NPD GO	PGKB_TRYBB	Phosphoglycerate kinase, cytosolic (EC 2.7.2.3) (Phosphoglycerate kinase B) (PGK B allele 2)	0.12	-	cyt	0	Cytoplasm				421
Q3SZ62 UniProt NPD GO	PGAM1_BOVIN	Phosphoglycerate mutase 1 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (Phosphoglycerate mutase isozyme B ...	0.12	-	cyt	0					253
P15259 UniProt NPD GO	PGAM2_HUMAN	Phosphoglycerate mutase 2 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (Phosphoglycerate mutase isozyme M ...	0.12	-	cyt	0			261670		252
P00608 UniProt NPD GO	PA22_NOTSC	Phospholipase A2 (EC 3.1.1.4) (Notexin) (Phosphatidylcholine 2-acylhydrolase)	0.12	-	nuc	0	Secreted protein			1AE7	119
P21789 UniProt NPD GO	PA2_CERCE	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.12	-	nuc	0	Secreted protein				120
Q8UUI1 UniProt NPD GO	PA25_LATLA	Phospholipase A2 PC17 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.12	-	exc	1 *	Secreted protein (By similarity)				145
P00596 UniProt NPD GO	PA21_NAJKA	Phospholipase A2 isozyme 1 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (NnkPLA-I) ( ...	0.12	-	exc	0	Secreted protein				146
P25498 UniProt NPD GO	PA21B_NAJOX	Phospholipase A2 isozyme E (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.12	-	nuc	0	Secreted protein				119
Q8JFG2 UniProt NPD GO	PA2H_LATSE	Phospholipase A2 pkP2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.12	-	exc	1 *	Secreted protein (By similarity)				152
P04055 UniProt NPD GO	PA21B_RAT	Phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Group IB phospholipas ...	0.12	-	exc	0	Secreted protein				146
Q9PTA1 UniProt NPD GO	PA2A_BUNMU	Phospholipase A2, beta bungarotoxin A-AL1 chain precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhy ...	0.12	-	nuc	0	Secreted protein (By similarity)				138
Q90251 UniProt NPD GO	PA26_BUNMU	Phospholipase A2, beta bungarotoxin A6 chain precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydro ...	0.12	-	nuc	0	Secreted protein (By similarity)				137
P56788 UniProt NPD GO	YCF4_ARATH	Photosystem I assembly protein ycf4	0.12	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
P12207 UniProt NPD GO	YCF4_TOBAC	Photosystem I assembly protein ycf4	0.12	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
Q9T4W8 UniProt NPD GO	PSAD_CYAPA	Photosystem I reaction center subunit II, cyanelle precursor (Photosystem I 20 kDa subunit) (PSI-D)	0.12	-	mit	0	Plastid; cyanelle; cyanelle thylakoid membrane; peripheral membrane protein; stromal side (By simila ...				220
Q9SA56 UniProt NPD GO	PSAD2_ARATH	Photosystem I reaction center subunit II-2, chloroplast precursor (Photosystem I 20 kDa subunit 2) ( ...	0.12	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Stromal side (By ...	thylakoid membrane (sensu Viridiplantae) [IDA]			204
Q9TLW6 UniProt NPD GO	PSAF_CYACA	Photosystem I reaction center subunit III (PSI-F)	0.12	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid lumen				187
P23816 UniProt NPD GO	PH62_CHRSP	Phycocyanin-645 alpha-2 chain (PC-645)	0.12	-	nuc	0					80
Q9ZTN9 UniProt NPD GO	CRTI_ORYSA	Phytoene dehydrogenase, chloroplast precursor (EC 1.14.99.-) (Phytoene desaturase)	0.12	-	nuc	0	Plastid; chloroplast. Plastid; chromoplast				578
P70205 UniProt NPD GO	PACR_MOUSE	Pituitary adenylate cyclase-activating polypeptide type I receptor precursor (PACAP type I receptor) ...	0.12	-	end	7 *	Membrane; multi-pass membrane protein				496
O54831 UniProt NPD GO	PRLPF_MOUSE	Placental prolactin-like protein F precursor (PRL-like protein F) (PLP-F)	0.12	-	cyt	0	Secreted protein (By similarity)				253

You are viewing entries 61601 to 61650 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.