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
Q66I59 UniProt NPD GO	ASPD_BRARE	Putative L-aspartate dehydrogenase (EC 1.4.1.21)	0.00	-	cyt	0					276
P12806 UniProt NPD GO	PRT1_PICAN	Putative PRT1 protein	0.00	-	cyt	0					220
Q9SZL4 UniProt NPD GO	ATL4N_ARATH	Putative RING-H2 finger protein ATL4N precursor	0.00	-	mit	2 *		anchored to membrane [TAS]			145
Q9UDP3 UniProt NPD GO	S11Y_HUMAN	Putative S100 calcium-binding protein H_NH0456N16.1	0.00	-	cyt	0					104
Q9P5N3 UniProt NPD GO	ALR2_SCHPO	Putative alanine racemase C359.02 (EC 5.1.1.1)	0.00	-	mit	0					370
P81870 UniProt NPD GO	LEAH_PHAVU	Putative alpha-amylase inhibitor (Fragment)	0.00	-	cyt	0					30
Q9FL81 UniProt NPD GO	EXP21_ARATH	Putative alpha-expansin 21 precursor (AtEXPA21) (At-EXP21) (AtEx21) (Ath-ExpAlpha-1.20)	0.00	-	cyt	0	Cell wall; peripheral membrane protein				256
Q9FIZ9 UniProt NPD GO	NIP41_ARATH	Putative aquaporin NIP4.1 (NOD26-like intrinsic protein 4.1)	0.00	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				283
O82598 UniProt NPD GO	TIP13_ARATH	Putative aquaporin TIP1.3 (Tonoplast intrinsic protein 1.3) (Gamma-tonoplast intrinsic protein 3) (G ...	0.00	-	end	7 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				252
Q9FFD0 UniProt NPD GO	PIN8_ARATH	Putative auxin efflux carrier component 8 (AtPIN8)	0.00	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				351
Q8LG89 UniProt NPD GO	BABL_ARATH	Putative basic blue protein precursor (Plantacyanin)	0.00	-	mit	0					129
P81669 UniProt NPD GO	BGAL_PINPS	Putative beta-galactosidase (EC 3.2.1.23) (Lactase) (Fragments)	0.00	-	cyt	0					44
Q9C9W3 UniProt NPD GO	CAMT1_ARATH	Putative caffeoyl-CoA O-methyltransferase At1g67980 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltra ...	0.00	-	cyt	0					232
Q10131 UniProt NPD GO	CEX1_CAEEL	Putative calcium-binding protein cex-1	0.00	-	cyt	0					204
P80532 UniProt NPD GO	CATL3_FASHE	Putative cathepsin L3 (EC 3.4.22.15) (Newly excysted juvenile protein 8) (Fragment)	0.00	-		0	Lysosome (Potential)				19
Q09190 UniProt NPD GO	CDD_SCHPO	Putative cytidine deaminase (EC 3.5.4.5) (Cytidine aminohydrolase) (CDA)	0.00	-	cyt	0					133
O03983 UniProt NPD GO	LEA14_ARATH	Putative desiccation-related protein LEA14	0.00	-	cyt	0				1XO8	151
Q9DCZ9 UniProt NPD GO	APH1C_MOUSE	Putative gamma-secretase subunit APH-1C	0.00	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				258
Q9FMA6 UniProt NPD GO	GL112_ARATH	Putative germin-like protein subfamily 1 member 12 precursor	0.00	-	end	1 *	Secreted protein; extracellular space; apoplast (By similarity)				223
Q9M8X1 UniProt NPD GO	GL12_ARATH	Putative germin-like protein subfamily 1 member 2 precursor	0.00	-	exc	0	Secreted protein; extracellular space; apoplast (By similarity)				229
Q9FMB0 UniProt NPD GO	GL19_ARATH	Putative germin-like protein subfamily 1 member 9 precursor	0.00	-	end	0	Secreted protein; extracellular space; apoplast (By similarity)				222
P84178 UniProt NPD GO	SY1_PHYPO	Putative isoleucyl-tRNA synthetase (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS) (Fragments)	0.00	-	cyt	0					64
P82728 UniProt NPD GO	LCR13_ARATH	Putative low-molecular-weight cysteine-rich protein LCR13 precursor	0.00	-	mit	0					77
P82731 UniProt NPD GO	LCR16_ARATH	Putative low-molecular-weight cysteine-rich protein LCR16 precursor	0.00	-	cyt	0					71
Q9M0F2 UniProt NPD GO	LCR26_ARATH	Putative low-molecular-weight cysteine-rich protein LCR26	0.00	-	cyt	0					65
P82755 UniProt NPD GO	LCR40_ARATH	Putative low-molecular-weight cysteine-rich protein LCR40 precursor	0.00	-	exc	0					74
P82757 UniProt NPD GO	LCR42_ARATH	Putative low-molecular-weight cysteine-rich protein LCR42 precursor	0.00	-	vac	0					77
P82763 UniProt NPD GO	LCR48_ARATH	Putative low-molecular-weight cysteine-rich protein LCR48 precursor	0.00	-	exc	0					80
P82721 UniProt NPD GO	LCR6_ARATH	Putative low-molecular-weight cysteine-rich protein LCR6 precursor	0.00	-	cyt	0					75
P82775 UniProt NPD GO	LCR61_ARATH	Putative low-molecular-weight cysteine-rich protein LCR61 precursor	0.00	-	mit	1 *					78
P82790 UniProt NPD GO	LCR81_ARATH	Putative low-molecular-weight cysteine-rich protein LCR81 precursor	0.00	-	mit	1 *					79
P82793 UniProt NPD GO	LCR84_ARATH	Putative low-molecular-weight cysteine-rich protein LCR84 precursor	0.00	-	exc	0					76
Q9SX55 UniProt NPD GO	TO402_ARATH	Putative mitochondrial import receptor subunit TOM40 homolog 2 (Translocase of outer membrane 40 kDa ...	0.00	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				310
O60361 UniProt NPD GO	NDK8_HUMAN	Putative nucleoside diphosphate kinase (EC 2.7.4.6) (NDK) (NDP kinase)	0.00	-	cyt	0					137
P84718 UniProt NPD GO	PSBO_PINST	Putative oxygen-evolving enhancer protein 1 (OEE1) (33 kDa subunit of oxygen evolving system of phot ...	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				128
O65457 UniProt NPD GO	PEL17_ARATH	Putative pectate lyase 17 precursor (EC 4.2.2.2)	0.00	-	exc	0					394
P56578 UniProt NPD GO	MALF3_MALFU	Putative peroxiredoxin (EC 1.11.1.15) (Thioredoxin reductase) (Allergen Mal f 3) (MF2) (Fragment)	0.00	-	pox	0	Peroxisome (Potential)				166
P51272 UniProt NPD GO	YCF42_PORPU	Putative peroxiredoxin ycf42 (EC 1.11.1.15) (Thioredoxin reductase)	0.00	-	cyt	0	Plastid; chloroplast				199
P14292 UniProt NPD GO	PMPA_CANBO	Putative peroxiredoxin-A (EC 1.11.1.15) (Thioredoxin reductase) (Peroxisomal membrane protein A) (PM ...	0.00	-	pox	0	Peroxisome; peroxisomal membrane; peripheral membrane protein				166
P14293 UniProt NPD GO	PMPB_CANBO	Putative peroxiredoxin-B (EC 1.11.1.15) (Thioredoxin reductase) (Peroxisomal membrane protein B) (PM ...	0.00	-	pox	0	Peroxisome; peroxisomal membrane; peripheral membrane protein				166
Q01116 UniProt NPD GO	PMP20_LIPKO	Putative peroxisomal peroxiredoxin (EC 1.11.1.15) (Thioredoxin reductase)	0.00	-	cyt	0	Peroxisome (Potential)				166
P80525 UniProt NPD GO	PPCK_FASHE	Putative phosphoenolpyruvate carboxykinase [GTP] (EC 4.1.1.32) (Phosphoenolpyruvate carboxylase) (PE ...	0.00	-		0					10
P84731 UniProt NPD GO	PGK_PINST	Putative phosphoglycerate kinase (EC 2.7.2.3) (PS15) (Fragments)	0.00	-	cyt	0					27
Q95P89 UniProt NPD GO	SCS1_MESMA	Putative potassium channel blocker TXKS1 precursor (BmTXKS1)	0.00	-	mit	0	Secreted protein				60
O17271 UniProt NPD GO	HEH1_CAEEL	Putative protein heh-1 precursor	0.00	-	exc	0	Secreted protein (Potential)				154
Q20848 UniProt NPD GO	P5CR_CAEEL	Putative pyrroline-5-carboxylate reductase (EC 1.5.1.2) (P5CR) (P5C reductase)	0.00	-	cyt	0					299
Q12458 UniProt NPD GO	YPR1_YEAST	Putative reductase 1 (EC 1.1.1.-)	0.00	-	mit	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			312
O76206 UniProt NPD GO	RIFK_DROME	Putative riboflavin kinase (EC 2.7.1.26) (ATP:riboflavin 5'-phosphotransferase) (Flavokinase)	0.00	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS]			153
Q8LN49 UniProt NPD GO	RIP5_ORYSA	Putative ripening-related protein 5 precursor	0.00	-	end	0	Secreted protein (Potential)				276
Q19892 UniProt NPD GO	SELT2_CAEEL	Putative selT-like protein F28H7.4 precursor	0.00	-	end	4 *					232

You are viewing entries 97451 to 97500 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.