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
P49193 UniProt NPD GO	RALB_TODPA	Retinal-binding protein (RALBP)	0.04	-	cyt	0					342
P82708 UniProt NPD GO	RET5_BOVIN	Retinol-binding protein III, cellular (CRBP-III) (Fragment)	0.04	-	nuc	0	Cytoplasm (By similarity)				42
P43232 UniProt NPD GO	CARP5_RHINI	Rhizopuspepsin-5 precursor (EC 3.4.23.21) (Aspartate protease)	0.04	-	exc	0					392
P17264 UniProt NPD GO	CRO_RANCA	Rho crystallin	0.04	-	cyt	0				1LLG	323
P02532 UniProt NPD GO	CRO_RANTE	Rho crystallin	0.04	-	cyt	0					323
P20466 UniProt NPD GO	RHA3_RHOTO	Rhodotorucin-A peptides type 3 precursor [Contains: Rhodotorucin-A (Rhodotorucine-A)]	0.04	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				47
Q9CWY8 UniProt NPD GO	RNHL_MOUSE	Ribonuclease HI large subunit (EC 3.1.26.4) (RNase HI large subunit) (Ribonuclease H2) (RNase H2)	0.04	-	cyt	0					301
P78346 UniProt NPD GO	RPP30_HUMAN	Ribonuclease P protein subunit p30 (EC 3.1.26.5) (RNaseP protein p30) (RNase P subunit 2)	0.04	-	cyt	0	Nucleus; nucleolus (Potential)	nucleolar ribonuclease P complex [TAS] nucleus [TAS]	606115		268
P81477 UniProt NPD GO	RNPB_PHYPO	Ribonuclease Phyb (EC 3.1.27.-) (RNase Phyb)	0.04	-	cyt	0					180
Q70IB2 UniProt NPD GO	RNS10_BOVIN	Ribonuclease-like protein 10 precursor (Protein Train A) (Fragment)	0.04	-	exc	1 *	Secreted protein (By similarity)				162
Q85G81 UniProt NPD GO	RBL_CYAME	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.04	-	nuc	1	Plastid; chloroplast				488
P23755 UniProt NPD GO	RBL_GALSU	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.04	-	nuc	0	Plastid; chloroplast				493
Q08051 UniProt NPD GO	RBL_PLECA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.04	-	nuc	1	Plastid; chloroplast				488
O98946 UniProt NPD GO	RBS_DETCO	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.04	-	cyt	0	Plastid; chloroplast				139
O98948 UniProt NPD GO	RBS_THANO	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.04	-	cyt	0	Plastid; chloroplast				139
Q39743 UniProt NPD GO	RBS1_FLAPR	Ribulose bisphosphate carboxylase small chain 1, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.04	-	cyt	0	Plastid; chloroplast				173
P26575 UniProt NPD GO	RBSA_SOLTU	Ribulose bisphosphate carboxylase small chain 2A, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.04	-	mit	0	Plastid; chloroplast				180
P26576 UniProt NPD GO	RBSB_SOLTU	Ribulose bisphosphate carboxylase small chain 2B, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.04	-	mit	0	Plastid; chloroplast				180
P26577 UniProt NPD GO	RBSC_SOLTU	Ribulose bisphosphate carboxylase small chain 2C, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.04	-	mit	0	Plastid; chloroplast				180
Q38693 UniProt NPD GO	RBS7_ACECL	Ribulose bisphosphate carboxylase small chain 7, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.04	-	cyt	0	Plastid; chloroplast				183
P18566 UniProt NPD GO	RBS2_ORYSA	Ribulose bisphosphate carboxylase small chain A, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.04	-	cyt	0	Plastid; chloroplast				175
P00871 UniProt NPD GO	RBS1_WHEAT	Ribulose bisphosphate carboxylase small chain PWS4.3, chloroplast precursor (EC 4.1.1.39) (RuBisCO s ...	0.04	-	mit	0	Plastid; chloroplast				174
Q40004 UniProt NPD GO	RBS_HORVU	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.04	-	mit	0	Plastid; chloroplast				174
P10053 UniProt NPD GO	RBS_PINTH	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.04	-	cyt	0	Plastid; chloroplast				171
P18960 UniProt NPD GO	RBS_SILPR	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.04	-	mit	0	Plastid; chloroplast				177
Q41351 UniProt NPD GO	RBS_STELP	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.04	-	mit	0	Plastid; chloroplast				180
P17673 UniProt NPD GO	RBS_TRIRP	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.04	-	cyt	0	Plastid; chloroplast				178
Q43088 UniProt NPD GO	RBCMT_PEA	Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast precu ...	0.04	-	cyt	0	Plastid; chloroplast			1P0Y	489
Q96AT9 UniProt NPD GO	RPE_HUMAN	Ribulose-phosphate 3-epimerase (EC 5.1.3.1) (Ribulose-5-phosphate-3-epimerase)	0.04	-	cyt	0			180480		228
Q5R5Y2 UniProt NPD GO	RPE_PONPY	Ribulose-phosphate 3-epimerase (EC 5.1.3.1) (Ribulose-5-phosphate-3-epimerase)	0.04	-	cyt	0					228
Q8VEE0 UniProt NPD GO	RPE_MOUSE	Ribulose-phosphate 3-epimerase (EC 5.1.3.1) (Ribulose-5-phosphate-epimerase)	0.04	-	cyt	0					228
P17722 UniProt NPD GO	DEFI_APIME	Royalisin precursor (Defensin)	0.04	-	mit	1 *	Secreted protein				95
Q42695 UniProt NPD GO	RUBC_CHLRE	RuBisCO large subunit-binding protein subunit beta-2 (60 kDa chaperonin subunit beta-2) (CPN-60 beta ...	0.04	-	cyt	0	Plastid; chloroplast				259
Q04694 UniProt NPD GO	DCAM_SOLTU	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) (Induced stolen tip pr ...	0.04	-	cyt	0				1MHM	360
Q42829 UniProt NPD GO	DCAM_HORCH	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.04	-	cyt	0					393
Q39676 UniProt NPD GO	DCAM1_DIACA	S-adenosylmethionine decarboxylase proenzyme 1 (EC 4.1.1.50) (AdoMetDC 1) (SamDC 1) [Contains: S-ade ...	0.04	-	cyt	0					381
Q39677 UniProt NPD GO	DCAM2_DIACA	S-adenosylmethionine decarboxylase proenzyme 2 (EC 4.1.1.50) (AdoMetDC 2) (SamDC 2) [Contains: S-ade ...	0.04	-	cyt	0					377
P50304 UniProt NPD GO	METK_ASCIM	S-adenosylmethionine synthetase (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoMet synthetase)	0.04	-	cyt	0					393
P40320 UniProt NPD GO	METK_DROME	S-adenosylmethionine synthetase (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoMet synthetase)	0.04	-	cyt	0					408
Q28281 UniProt NPD GO	ARRS_CANFA	S-arrestin (Retinal S-antigen) (48 kDa protein) (S-AG) (Rod photoreceptor arrestin)	0.04	-	cyt	0					405
P10523 UniProt NPD GO	ARRS_HUMAN	S-arrestin (Retinal S-antigen) (48 kDa protein) (S-AG) (Rod photoreceptor arrestin)	0.04	-	nuc	0			258100		405
O35324 UniProt NPD GO	SH21B_MOUSE	SH2 domain protein 1B (EWS/FLI1-activated transcript 2) (EAT-2)	0.04	-	cyt	0				1I3Z	132
P31530 UniProt NPD GO	SAPC_SARPE	Sapecin-C	0.04	-	cyt	0	Secreted protein				40
P82352 UniProt NPD GO	SSPN_RABIT	Sarcospan	0.04	-	end	4 *	Sarcolemma; sarcolemmal membrane; multi-pass membrane protein. Also found in myotendinous junctions ...				238
Q90WJ9 UniProt NPD GO	SXT2_TAKPA	Saxitoxin and tetrodotoxin-binding protein 2 precursor	0.04	-	end	0	Secreted protein				391
P97943 UniProt NPD GO	SCRB1_RAT	Scavenger receptor class B member 1 (SRB1) (SR-BI)	0.04	-	end	2 *	Cell membrane; multi-pass membrane protein (By similarity). Predominantly localized to cholesterol a ...				509
P02852 UniProt NPD GO	SECP_APIME	Secapin precursor	0.04	-	exc	1 *	Secreted protein				77
P55000 UniProt NPD GO	SLUR1_HUMAN	Secreted Ly-6/uPAR-related protein 1 precursor (SLURP-1) (ARS component B) (ARS(Component B)-81/S) ( ...	0.04	-	exc	0	Secreted protein	extracellular region [NAS]	606119		103
P01280 UniProt NPD GO	SECR_CHICK	Secretin	0.04	-	nuc	0	Secreted protein				27
P46284 UniProt NPD GO	S17P_CHLRE	Sedoheptulose-1,7-bisphosphatase, chloroplast precursor (EC 3.1.3.37) (Sedoheptulose-bisphosphatase) ...	0.04	-	cyt	0	Plastid; chloroplast			1EOY	389

You are viewing entries 78351 to 78400 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.