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
P30830 UniProt NPD GO	RBL_PERAE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid; chloroplast				477
P34915 UniProt NPD GO	RBL_PHYPA	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid; chloroplast				475
Q6L391 UniProt NPD GO	RBL_SACHY	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid; chloroplast				476
Q6ENV5 UniProt NPD GO	RBL_SACOF	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid; chloroplast				476
P48716 UniProt NPD GO	RBL_SPIMX	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.02	-	cyt	0	Plastid; chloroplast				475
P25829 UniProt NPD GO	RBL_CALUS	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.02	-	cyt	0	Plastid; chloroplast				467
P28259 UniProt NPD GO	RBL_DRYSU	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.02	-	cyt	0	Plastid; chloroplast				471
P31189 UniProt NPD GO	RBL_HIPRI	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.02	-	cyt	0	Plastid; chloroplast				449
Q32397 UniProt NPD GO	RBL_HYDFO	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.02	-	cyt	0	Plastid; chloroplast				453
P92306 UniProt NPD GO	RBL_IRIEN	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.02	-	cyt	0	Plastid; chloroplast				469
P25836 UniProt NPD GO	RBL_SERRE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.02	-	cyt	0	Plastid; chloroplast				467
Q33062 UniProt NPD GO	RBL_SHEAR	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.02	-	cyt	0	Plastid; chloroplast				453
Q36800 UniProt NPD GO	RBL_STRLC	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit) (Fragm ...	0.02	-	cyt	0	Plastid; chloroplast				459
P13951 UniProt NPD GO	RBS_SINAL	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast				82
P10796 UniProt NPD GO	RBS1B_ARATH	Ribulose bisphosphate carboxylase small chain 1B, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.02	-	mit	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein. Plastid; chloroplast; chlor ...				181
Q43832 UniProt NPD GO	RBS2_SPIOL	Ribulose bisphosphate carboxylase small chain 2, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.02	-	mit	0	Plastid; chloroplast			1UZD	180
P07179 UniProt NPD GO	RBS2A_LYCES	Ribulose bisphosphate carboxylase small chain 2A, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.02	-	mit	0	Plastid; chloroplast				180
P07689 UniProt NPD GO	RBS3_PEA	Ribulose bisphosphate carboxylase small chain 3A, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.02	-	cyt	0	Plastid; chloroplast				180
P00869 UniProt NPD GO	RBS2_PEA	Ribulose bisphosphate carboxylase small chain 3C, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.02	-	cyt	0	Plastid; chloroplast				180
P07398 UniProt NPD GO	RBS3_WHEAT	Ribulose bisphosphate carboxylase small chain clone 512 (EC 4.1.1.39) (RuBisCO small subunit) (Fragm ...	0.02	-	cyt	0	Plastid; chloroplast				113
P08474 UniProt NPD GO	RBS_CUCSA	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.02	-	mit	0	Plastid; chloroplast				189
Q40250 UniProt NPD GO	RBS_LACSA	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.02	-	mit	0	Plastid; chloroplast				181
O14105 UniProt NPD GO	RPE_SCHPO	Ribulose-phosphate 3-epimerase (EC 5.1.3.1) (Pentose-5-phosphate 3-epimerase) (PPE) (RPE)	0.02	-	cyt	0					228
P46969 UniProt NPD GO	RPE_YEAST	Ribulose-phosphate 3-epimerase (EC 5.1.3.1) (Pentose-5-phosphate 3-epimerase) (PPE) (RPE)	0.02	-	cyt	0	Cytoplasm	cytosol [TAS]			238
Q9ZTP5 UniProt NPD GO	RPE_ORYSA	Ribulose-phosphate 3-epimerase, chloroplast precursor (EC 5.1.3.1) (Pentose-5-phosphate 3-epimerase) ...	0.02	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane (By similarity)				274
P15252 UniProt NPD GO	REF_HEVBR	Rubber elongation factor protein (REF) (Allergen Hev b 1)	0.02	-	cyt	0	Cytoplasm (Probable). Tightly bound on latex small rubber particles				137
O24215 UniProt NPD GO	DCAM_ORYSA	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.02	-	cyt	0					398
P34039 UniProt NPD GO	DCAM_ACACA	S-adenosylmethionine decarboxylase subunit alpha (EC 4.1.1.50) (AdoMetDC) (SamDC) (Fragment)	0.02	-		0					19
P50300 UniProt NPD GO	METK_PINBN	S-adenosylmethionine synthetase (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoMet synthetase)	0.02	-	cyt	0					393
P17562 UniProt NPD GO	METL_ARATH	S-adenosylmethionine synthetase 2 (EC 2.5.1.6) (Methionine adenosyltransferase 2) (AdoMet synthetase ...	0.02	-	cyt	0					393
P93438 UniProt NPD GO	METL_ORYSA	S-adenosylmethionine synthetase 2 (EC 2.5.1.6) (Methionine adenosyltransferase 2) (AdoMet synthetase ...	0.02	-	cyt	0					394
Q96553 UniProt NPD GO	METM_CATRO	S-adenosylmethionine synthetase 3 (EC 2.5.1.6) (Methionine adenosyltransferase 3) (AdoMet synthetase ...	0.02	-	cyt	0					390
P13444 UniProt NPD GO	METK1_RAT	S-adenosylmethionine synthetase isoform type-1 (EC 2.5.1.6) (Methionine adenosyltransferase 1) (AdoM ...	0.02	-	cyt	0				1QM4	397
P18298 UniProt NPD GO	METK2_RAT	S-adenosylmethionine synthetase isoform type-2 (EC 2.5.1.6) (Methionine adenosyltransferase 2) (AdoM ...	0.02	-	cyt	0					395
P46576 UniProt NPD GO	SAM50_CAEEL	SAM50-like protein gop-3 (Gro-1 operon protein 3)	0.02	-	mit	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				434
O93390 UniProt NPD GO	SPRC_COTJA	SPARC precursor (Secreted protein acidic and rich in cysteine) (Osteonectin) (ON)	0.02	-	exc	0					298
P09486 UniProt NPD GO	SPRC_HUMAN	SPARC precursor (Secreted protein acidic and rich in cysteine) (Osteonectin) (ON) (Basement-membrane ...	0.02	-	exc	0		extracellular matrix (sensu Metazoa) [TAS] extracellular region [NAS]	182120	1SRA	303
P16975 UniProt NPD GO	SPRC_RAT	SPARC precursor (Secreted protein acidic and rich in cysteine) (Osteonectin) (ON) (Basement-membrane ...	0.02	-	exc	0					302
P36378 UniProt NPD GO	SPRC_XENLA	SPARC precursor (Secreted protein acidic and rich in cysteine) (Osteonectin) (ON) (Basement-membrane ...	0.02	-	exc	0					300
P04745 UniProt NPD GO	AMYS_HUMAN	Salivary alpha-amylase precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase)	0.02	-	pox	0	Secreted protein		104700	1Z32	511
P81369 UniProt NPD GO	SAL1_ONCMY	Salmocidin-1 (Fragment)	0.02	-		0	Secreted protein				15
P82240 UniProt NPD GO	SAL3_ONCMY	Salmocidin-3 (Fragment)	0.02	-		0	Secreted protein				16
P83649 UniProt NPD GO	SRS1_ORYSA	Salt-stress root protein RS1	0.02	-	cyt	0					204
P02637 UniProt NPD GO	SCP_PATYE	Sarcoplasmic calcium-binding protein (SCP)	0.02	-	cyt	0					176
P04572 UniProt NPD GO	SCP_PERVT	Sarcoplasmic calcium-binding protein (SCP)	0.02	-	cyt	0					174
Q8WTV0 UniProt NPD GO	SCRB1_HUMAN	Scavenger receptor class B member 1 (SRB1) (SR-BI) (CD36 antigen-like 1) (CD36 and LIMPII analogous ...	0.02	-	end	2 *	Cell membrane; multi-pass membrane protein. Predominantly localized to cholesterol and sphingomyelin ...	plasma membrane [TAS]	601040		552
P56221 UniProt NPD GO	SCYD_MAGGR	Scytalone dehydratase (EC 4.2.1.94)	0.02	-	cyt	0				7STD	172
Q9JL59 UniProt NPD GO	SCTM1_MOUSE	Secreted and transmembrane protein 1 precursor	0.02	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Secreted protein (By similarity) ...				212
P84876 UniProt NPD GO	SPF1_PYTHP	Secreted protein F1 (Fragment)	0.02	-		0	Secreted protein				15
Q01883 UniProt NPD GO	RA17_ORYSA	Seed allergenic protein RA17 precursor	0.02	-	exc	1 *	Secreted protein				162

You are viewing entries 85651 to 85700 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.