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
O94788 UniProt NPD GO	AL1A2_HUMAN	Retinal dehydrogenase 2 (EC 1.2.1.36) (RalDH2) (RALDH 2) (RALDH(II)) (Retinaldehyde-specific dehydro ...	0.10	-	cyt	0	Cytoplasm		603687		518
Q9ERI6 UniProt NPD GO	RDH14_MOUSE	Retinol dehydrogenase 14 (EC 1.1.1.-) (Alcohol dehydrogenase PAN2)	0.10	-	mit	1 *					334
Q08652 UniProt NPD GO	RET2_MOUSE	Retinol-binding protein II, cellular (CRBP-II)	0.10	-	cyt	0	Cytoplasm				133
P50121 UniProt NPD GO	RET2_PIG	Retinol-binding protein II, cellular (CRBP-II)	0.10	-	mit	0	Cytoplasm				133
Q12434 UniProt NPD GO	GDIR_YEAST	Rho GDP-dissociation inhibitor (Rho GDI)	0.10	-	cyt	0	Cytoplasm	cytosol [IDA]			202
Q8BYP3 UniProt NPD GO	RHOF_MOUSE	Rho-related GTP-binding protein RhoF	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				211
Q8BP97 UniProt NPD GO	RHBD3_MOUSE	Rhomboid domain-containing protein 3	0.10	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				385
O75783 UniProt NPD GO	RHBD1_HUMAN	Rhomboid-related protein 1 (EC 3.4.21.105) (RRP) (Rhomboid-like protein 1)	0.10	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	603264		438
Q8TDE3 UniProt NPD GO	RNAS8_HUMAN	Ribonuclease 8 precursor (EC 3.1.27.-) (RNase 8)	0.10	-	exc	0	Secreted protein (Probable)				154
P24657 UniProt NPD GO	RNTR_TRIVI	Ribonuclease Trv (EC 3.1.27.1) (RNase Trv)	0.10	-	mit	0					234
P67875 UniProt NPD GO	RNMG_ASPFU	Ribonuclease mitogillin precursor (EC 3.1.27.-) (Major allergen Asp f 1) (Asp f I) (Allergen I/a) (I ...	0.10	-	exc	0	Secreted protein				176
P67876 UniProt NPD GO	RNMG_ASPRE	Ribonuclease mitogillin precursor (EC 3.1.27.-) (Restrictocin)	0.10	-	exc	0	Secreted protein			1JBT	176
P33185 UniProt NPD GO	RIP1_BRYDI	Ribosome-inactivating protein bryodin I precursor (EC 3.2.2.22) (rRNA N-glycosidase) (BD1)	0.10	-	exc	0				1BRY	290
P98185 UniProt NPD GO	RIP1_SAPOF	Ribosome-inactivating protein saporin-1 (EC 3.2.2.22) (SAP-1) (SO-4) (rRNA N-glycosidase) (Fragment) ...	0.10	-	nuc	0					40
Q9XGX5 UniProt NPD GO	RBS2_AMAHP	Ribulose bisphosphate carboxylase small chain 2, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.10	-	mit	0	Plastid; chloroplast				184
Q39744 UniProt NPD GO	RBS2_FLAPR	Ribulose bisphosphate carboxylase small chain 2, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.10	-	mit	0	Plastid; chloroplast				178
P22433 UniProt NPD GO	RBS2_NICSY	Ribulose bisphosphate carboxylase small chain S41, chloroplast precursor (EC 4.1.1.39) (RuBisCO smal ...	0.10	-	end	0	Plastid; chloroplast				181
P04715 UniProt NPD GO	RBS2_PETHY	Ribulose bisphosphate carboxylase small chain SSU11A, chloroplast precursor (EC 4.1.1.39) (RuBisCO s ...	0.10	-	mit	0	Plastid; chloroplast				180
Q40460 UniProt NPD GO	RCA1_TOBAC	Ribulose bisphosphate carboxylase/oxygenase activase 1, chloroplast precursor (RuBisCO activase 1) ( ...	0.10	-	cyt	0	Plastid; chloroplast; chloroplast stroma				442
Q7X9A0 UniProt NPD GO	RCA1_LARTR	Ribulose bisphosphate carboxylase/oxygenase activase 1, chloroplast precursor (RuBisCO activase 1) ( ...	0.10	-	mit	0	Plastid; chloroplast; chloroplast stroma (By similarity)				476
Q43843 UniProt NPD GO	RPE_SOLTU	Ribulose-phosphate 3-epimerase, chloroplast precursor (EC 5.1.3.1) (Pentose-5-phosphate 3-epimerase) ...	0.10	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane	thylakoid membrane (sensu Viridiplantae) [ISS]		1RPX	280
P08927 UniProt NPD GO	RUBB_PEA	RuBisCO large subunit-binding protein subunit beta, chloroplast precursor (60 kDa chaperonin subunit ...	0.10	-	mit	0	Plastid; chloroplast				595
Q9Z2J9 UniProt NPD GO	RUNX2_RAT	Runt-related transcription factor 2 (Core-binding factor, alpha 1 subunit) (CBF-alpha 1) (Osteoblast ...	0.10	-	nuc	0	Nucleus (By similarity)				218
Q8AWW7 UniProt NPD GO	RUVB1_BRARE	RuvB-like 1 (EC 3.6.1.-) (Pontin) (zPontin)	0.10	-	cyt	0	Nucleus (By similarity)				456
Q5BBV9 UniProt NPD GO	RUVB1_EMENI	RuvB-like helicase 1 (EC 3.6.1.-)	0.10	-	nuc	0	Nucleus (By similarity)				460
Q6CB52 UniProt NPD GO	RUVB1_YARLI	RuvB-like helicase 1 (EC 3.6.1.-)	0.10	-	nuc	0	Nucleus (By similarity)				453
Q03940 UniProt NPD GO	RUVB1_YEAST	RuvB-like protein 1 (EC 3.6.1.-) (RUVBL1) (TIP49a homolog) (TIP49-homology protein 1)	0.10	-	cyt	0	Nucleus	INO80 complex [IPI] nucleus [IDA] SWR1 complex [IPI]			463
Q96471 UniProt NPD GO	DCAM_IPONI	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.10	-	cyt	0					362
P51478 UniProt NPD GO	ARRS_RANCA	S-arrestin (Retinal S-antigen) (Rod photoreceptor arrestin)	0.10	-	cyt	0					396
P22552 UniProt NPD GO	SLSG1_BRAOA	S-locus-specific glycoprotein BS29-1 precursor	0.10	-	exc	1 *					444
P45816 UniProt NPD GO	SEC14_YARLI	SEC14 cytosolic factor (Phosphatidylinositol/phosphatidylcholine transfer protein) (PI/PC TP)	0.10	-	cyt	0	Golgi apparatus; Golgi membrane; peripheral membrane protein (By similarity)				492
P15983 UniProt NPD GO	HB2D_PIG	SLA class II histocompatibility antigen, DQ haplotype D beta chain precursor	0.10	-	end	1	Membrane; single-pass type I membrane protein (Potential)				258
O94905 UniProt NPD GO	SPFH2_HUMAN	SPFH domain-containing protein 2 precursor	0.10	-	cyt	0	Membrane; peripheral membrane protein (Potential)				339
Q8BFZ9 UniProt NPD GO	SPFH2_MOUSE	SPFH domain-containing protein 2 precursor	0.10	-	cyt	0	Membrane; peripheral membrane protein (Potential)				340
Q5R7C5 UniProt NPD GO	SPFH2_PONPY	SPFH domain-containing protein 2 precursor	0.10	-	cyt	0	Membrane; peripheral membrane protein (Potential)				339
O88506 UniProt NPD GO	STK39_RAT	STE20/SPS1-related proline-alanine-rich protein kinase (EC 2.7.11.1) (Ste-20-related kinase) (Serine ...	0.10	-	mit	0	Cytoplasm (Probable). Nucleus (Probable). Nucleus when caspase-cleaved (Probable)	cytoplasm [IDA] cytoskeleton [IDA]			553
O14983 UniProt NPD GO	AT2A1_HUMAN	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (EC 3.6.3.8) (Calcium pump 1) (SERCA1) (SR Ca(2+ ...	0.10	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...	smooth endoplasmic reticulum [TAS]	601003		1001
Q8R429 UniProt NPD GO	AT2A1_MOUSE	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (EC 3.6.3.8) (Calcium pump 1) (SERCA1) (SR Ca(2+ ...	0.10	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...	sarcoplasmic reticulum [IDA]			994
Q64578 UniProt NPD GO	AT2A1_RAT	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (EC 3.6.3.8) (Calcium pump 1) (SERCA1) (SR Ca(2+ ...	0.10	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...	sarcoplasmic reticulum [TAS]			994
Q7YWA6 UniProt NPD GO	SECP_POLHE	Secapin precursor	0.10	-	exc	1 *	Secreted protein (By similarity)				77
Q8K021 UniProt NPD GO	SCAM1_MOUSE	Secretory carrier-associated membrane protein 1 (Secretory carrier membrane protein 1)	0.10	-	end	4	Membrane; multi-pass membrane protein (By similarity)	synaptic vesicle membrane [IDA] zymogen granule membrane [IDA]			338
O77735 UniProt NPD GO	SCAM1_PIG	Secretory carrier-associated membrane protein 1 (Secretory carrier membrane protein 1)	0.10	-	end	4	Membrane; multi-pass membrane protein				338
P56603 UniProt NPD GO	SCAM1_RAT	Secretory carrier-associated membrane protein 1 (Secretory carrier membrane protein 1) (SCAMP 37)	0.10	-	end	4	Membrane; multi-pass membrane protein				338
Q3SZY3 UniProt NPD GO	PTTG1_BOVIN	Securin (Pituitary tumor-transforming protein 1)	0.10	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				202
P09439 UniProt NPD GO	LOX2_SOYBN	Seed lipoxygenase-2 (EC 1.13.11.12) (L-2)	0.10	-	cyt	0	Cytoplasm				865
P62341 UniProt NPD GO	SELT_HUMAN	Selenoprotein T precursor	0.10	-	end	0			607912		195
P62342 UniProt NPD GO	SELT_MOUSE	Selenoprotein T precursor	0.10	-	end	0					195
P00669 UniProt NPD GO	RNS_BOVIN	Seminal ribonuclease precursor (EC 3.1.27.5) (Seminal RNase) (S-RNase) (Ribonuclease BS-1)	0.10	-	exc	0	Secreted protein			1Y94	150
P52711 UniProt NPD GO	CBP23_HORVU	Serine carboxypeptidase II-3 precursor (EC 3.4.16.6) (CP-MII.3) [Contains: Serine carboxypeptidase I ...	0.10	-	cyt	1 *					516
Q13530 UniProt NPD GO	SERC3_HUMAN	Serine incorporator 3 (Tumor differentially expressed protein 1)	0.10	-	end	11 *	Cell membrane; multi-pass membrane protein (By similarity)	integral to membrane [TAS]	607165		473

You are viewing entries 65201 to 65250 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.