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
Q9CYN9 UniProt NPD GO	RENR_MOUSE	Renin receptor precursor (Renin/prorenin receptor) (ATPase H(+)-transporting lysosomal accessory pro ...	0.06	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				350
P52289 UniProt NPD GO	PPA5_KLULA	Repressible acid phosphatase precursor (EC 3.1.3.2)	0.06	-	exc	0	Secreted protein				469
Q812C9 UniProt NPD GO	AOC2_MOUSE	Retina-specific copper amine oxidase precursor (EC 1.4.3.6) (RAO) (Amine oxidase [copper-containing] ...	0.06	-	exc	1 *					757
Q96NR8 UniProt NPD GO	RDH12_HUMAN	Retinol dehydrogenase 12 (EC 1.1.1.-) (All-trans and 9-cis retinol dehydrogenase)	0.06	-	nuc	0		intracellular [IDA]	608830		316
P50170 UniProt NPD GO	RDH2_RAT	Retinol dehydrogenase 2 (EC 1.1.1.105) (Retinol dehydrogenase type II) (RODH II) (29 k-protein)	0.06	-	mit	0	Microsome				317
P82980 UniProt NPD GO	RET5_HUMAN	Retinol-binding protein III, cellular (CRBP-III) (HRBPiso)	0.06	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [NAS]		1GGL	134
P10399 UniProt NPD GO	POL1_CHICK	Retrovirus-related Pol polyprotein [Includes: Reverse transcriptase (EC 2.7.7.49); Endonuclease] (Fr ...	0.06	-	mit	0				1M0C	246
Q03699 UniProt NPD GO	CARP3_RHINI	Rhizopuspepsin-3 precursor (EC 3.4.23.21) (Aspartate protease)	0.06	-	mit	0					391
P52565 UniProt NPD GO	GDIR_HUMAN	Rho GDP-dissociation inhibitor 1 (Rho GDI 1) (Rho-GDI alpha)	0.06	-	cyt	0	Cytoplasm	cytoskeleton [TAS]	601925	2BXW	203
P81398 UniProt NPD GO	RHCB_AGKRH	Rhodocetin subunit beta	0.06	-	cyt	0	Secreted protein			1SB2	129
P07907 UniProt NPD GO	RHA1_RHOTO	Rhodotorucin-A peptides type 1 precursor [Contains: Rhodotorucin-A (Rhodotorucine-A)]	0.06	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				62
P20465 UniProt NPD GO	RHA2_RHOTO	Rhodotorucin-A peptides type 2 precursor [Contains: Rhodotorucin-A (Rhodotorucine-A)]	0.06	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				77
P00654 UniProt NPD GO	RNU2_USTSP	Ribonuclease U2 (EC 3.1.27.4) (RNase U2)	0.06	-	nuc	0				1RTU	114
P00655 UniProt NPD GO	RNAS_ASPGI	Ribonuclease alpha-sarcin precursor (EC 3.1.27.10) (rRNA endonuclease)	0.06	-	exc	0	Secreted protein			1R4Y	177
Q9WUS3 UniProt NPD GO	RNAS1_LEOED	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.06	-	exc	0	Secreted protein				149
Q9WUX4 UniProt NPD GO	RNAS1_TATKG	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.06	-	exc	0	Secreted protein				148
Q5GAM0 UniProt NPD GO	RNS10_RAT	Ribonuclease-like protein 10 precursor (Protein Train A)	0.06	-	exc	1 *	Secreted protein (By similarity)				212
P38620 UniProt NPD GO	KPR2_YEAST	Ribose-phosphate pyrophosphokinase 2 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase 2)	0.06	-	cyt	0		cytoplasm [IDA]			318
Q41389 UniProt NPD GO	RIP5_SAPOF	Ribosome-inactivating protein saporin-5 (EC 3.2.2.22) (SAP-5) (rRNA N-glycosidase)	0.06	-	cyt	0					253
Q41391 UniProt NPD GO	RIP7_SAPOF	Ribosome-inactivating protein saporin-7 (EC 3.2.2.22) (SO-7) (SAP-7) (rRNA N-glycosidase)	0.06	-	cyt	0					253
P48070 UniProt NPD GO	RBL_EUGGE	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.06	-	cyt	0	Plastid; chloroplast				436
P30828 UniProt NPD GO	RBL_MAGLA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit) (Fragment)	0.06	-	cyt	0	Plastid; chloroplast				253
P30401 UniProt NPD GO	RBL_CUSRE	Ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) (RuBisCO large subunit)	0.06	-	cyt	0	Plastid				498
P51227 UniProt NPD GO	RBS_PORPU	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.06	-	cyt	0	Plastid; chloroplast				138
P10795 UniProt NPD GO	RBS1A_ARATH	Ribulose bisphosphate carboxylase small chain 1A, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.06	-	mit	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein. Plastid; chloroplast; chlor ...				180
Q39747 UniProt NPD GO	RBS5_FLAPR	Ribulose bisphosphate carboxylase small chain 5, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.06	-	cyt	0	Plastid; chloroplast				173
Q39749 UniProt NPD GO	RBS7_FLAPR	Ribulose bisphosphate carboxylase small chain 7, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.06	-	cyt	0	Plastid; chloroplast				173
P69250 UniProt NPD GO	RBS1_NICSY	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.06	-	mit	0	Plastid; chloroplast				180
Q38793 UniProt NPD GO	RBS_AEGTA	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.06	-	mit	0	Plastid; chloroplast				175
O65349 UniProt NPD GO	RBS_CAPAN	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.06	-	mit	0	Plastid; chloroplast				187
P07089 UniProt NPD GO	RBS_FLATR	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.06	-	cyt	0	Plastid; chloroplast				173
Q42915 UniProt NPD GO	RBS_MANES	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.06	-	mit	0	Plastid; chloroplast				182
P69249 UniProt NPD GO	RBS_TOBAC	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.06	-	mit	0	Plastid; chloroplast			4RUB	180
P10896 UniProt NPD GO	RCA_ARATH	Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA)	0.06	-	cyt	0	Plastid; chloroplast; chloroplast stroma				474
Q01587 UniProt NPD GO	RCA_CUCSA	Ribulose bisphosphate carboxylase/oxygenase activase, chloroplast precursor (RuBisCO activase) (RA)	0.06	-	mit	0	Plastid; chloroplast; chloroplast stroma				413
Q9SE42 UniProt NPD GO	RPE1_ORYSA	Ribulose-phosphate 3-epimerase, cytoplasmic isoform (EC 5.1.3.1) (Ribulose-5-phosphate-epimerase) (C ...	0.06	-	cyt	0	Cytoplasm			1H1Z	228
P32958 UniProt NPD GO	ROM1_MOUSE	Rod outer segment membrane protein 1 (ROSP1)	0.06	-	end	4 *	Membrane; multi-pass membrane protein				351
P08926 UniProt NPD GO	RUBA_PEA	RuBisCO large subunit-binding protein subunit alpha, chloroplast precursor (60 kDa chaperonin subuni ...	0.06	-	mit	0	Plastid; chloroplast				587
P21239 UniProt NPD GO	RUB1_BRANA	RuBisCO large subunit-binding protein subunit alpha, chloroplast precursor (60 kDa chaperonin subuni ...	0.06	-	cyt	0	Plastid; chloroplast				546
P21241 UniProt NPD GO	RUBB_BRANA	RuBisCO large subunit-binding protein subunit beta, chloroplast precursor (60 kDa chaperonin subunit ...	0.06	-	cyt	0	Plastid; chloroplast				588
Q4ICA8 UniProt NPD GO	RUVB1_GIBZE	RuvB-like helicase 1 (EC 3.6.1.-)	0.06	-	nuc	0	Nucleus (By similarity)				458
P00633 UniProt NPD GO	SAST_ANAPL	S-acyl fatty acid synthase thioesterase, medium chain (EC 3.1.2.14) (Thioesterase II)	0.06	-	mit	0					251
O80402 UniProt NPD GO	DCAM_NICSY	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.06	-	mit	0					361
Q95032 UniProt NPD GO	METK_ACACA	S-adenosylmethionine synthetase (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoMet synthetase)	0.06	-	cyt	0					388
O60198 UniProt NPD GO	METK_SCHPO	S-adenosylmethionine synthetase (EC 2.5.1.6) (Methionine adenosyltransferase) (AdoMet synthetase)	0.06	-	cyt	0					382
Q00266 UniProt NPD GO	METK1_HUMAN	S-adenosylmethionine synthetase isoform type-1 (EC 2.5.1.6) (Methionine adenosyltransferase 1) (AdoM ...	0.06	-	cyt	0			250850		395
P08168 UniProt NPD GO	ARRS_BOVIN	S-arrestin (Retinal S-antigen) (48 kDa protein) (S-AG) (Rod photoreceptor arrestin) [Contains: S-arr ...	0.06	-	cyt	0				1CF1	404
P22551 UniProt NPD GO	SLSG0_BRAOA	S-locus-specific glycoprotein precursor	0.06	-	exc	1 *					444
P55735 UniProt NPD GO	SEC13_HUMAN	SEC13-related protein (SEC13-like protein 1)	0.06	-	cyt	0			600152		321
Q9D1M0 UniProt NPD GO	SEC13_MOUSE	SEC13-related protein (SEC13-like protein 1)	0.06	-	cyt	0					321

You are viewing entries 73101 to 73150 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.