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
Q3T0F5 UniProt NPD GO	RAB7_BOVIN	Ras-related protein Rab-7	0.12	-	cyt	0	Endosome; late endosome. Lysosome (By similarity). Phagosome (By similarity). Found on late lysosome ...				207
Q9JIW9 UniProt NPD GO	RALB_MOUSE	Ras-related protein Ral-B	0.12	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				206
Q5QGT7 UniProt NPD GO	RTP2_HUMAN	Receptor-transporting protein 2	0.12	-	nuc	1	Cell membrane; single-pass type III membrane protein (By similarity). Effective cell surface express ...	cell surface [IDA]	609138		225
P35243 UniProt NPD GO	RECO_HUMAN	Recoverin (Cancer-associated retinopathy protein) (Protein CAR)	0.12	-	cyt	0			179618		199
P42854 UniProt NPD GO	REG3G_RAT	Regenerating islet-derived protein 3 gamma precursor (Reg III-gamma) (Pancreatitis-associated protei ...	0.12	-	exc	0	Secreted protein				174
Q6AXS4 UniProt NPD GO	RENR_RAT	Renin receptor precursor (Renin/prorenin receptor) (ATPase, H+-transporting, lysosomal accessory pro ...	0.12	-	end	1	Membrane; single-pass type I membrane protein (Potential)				350
P06281 UniProt NPD GO	RENI1_MOUSE	Renin-1 precursor (EC 3.4.23.15) (Angiotensinogenase) (Kidney renin)	0.12	-	mit	1 *	Secreted protein (By similarity). Membrane (By similarity). Associated to membranes via binding to A ...	extracellular space [IDA]			402
Q63528 UniProt NPD GO	RFA2_RAT	Replication protein A 32 kDa subunit (RP-A) (RF-A) (Replication factor-A protein 2) (p32)	0.12	-	nuc	0	Nucleus. Also present in PML nuclear bodies. Redistributes to discrete nuclear foci upon DNA damage ...				270
Q62148 UniProt NPD GO	AL1A2_MOUSE	Retinal dehydrogenase 2 (EC 1.2.1.36) (RalDH2) (RALDH 2) (RALDH(II)) (Retinaldehyde-specific dehydro ...	0.12	-	cyt	0	Cytoplasm				518
Q63639 UniProt NPD GO	AL1A2_RAT	Retinal dehydrogenase 2 (EC 1.2.1.36) (RalDH2) (RALDH 2) (RALDH(II)) (Retinaldehyde-specific dehydro ...	0.12	-	cyt	0	Cytoplasm	cytosol [IDA]		1BI9	518
Q9HB40 UniProt NPD GO	RISC_HUMAN	Retinoid-inducible serine carboxypeptidase precursor (EC 3.4.16.-) (Serine carboxypeptidase 1)	0.12	-	gol	0	Secreted protein (Potential)				452
Q99PT1 UniProt NPD GO	GDIR_MOUSE	Rho GDP-dissociation inhibitor 1 (Rho GDI 1) (Rho-GDI alpha) (GDI-1)	0.12	-	cyt	0	Cytoplasm (By similarity)	immunological synapse [IDA]			203
P84097 UniProt NPD GO	RHOG_CRICR	Rho-related GTP-binding protein RhoG precursor	0.12	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				191
P84095 UniProt NPD GO	RHOG_HUMAN	Rho-related GTP-binding protein RhoG precursor	0.12	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		179505		191
P84096 UniProt NPD GO	RHOG_MOUSE	Rho-related GTP-binding protein RhoG precursor (Sid 10750)	0.12	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				191
O16005 UniProt NPD GO	OPSD_SEPOF	Rhodopsin	0.12	-	end	6 *	Membrane; multi-pass membrane protein				464
Q969G6 UniProt NPD GO	RIFK_HUMAN	Riboflavin kinase (EC 2.7.1.26) (ATP:riboflavin 5'-phosphotransferase) (Flavokinase)	0.12	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [NAS]		1Q9S	162
O60930 UniProt NPD GO	RNH1_HUMAN	Ribonuclease H1 (EC 3.1.26.4) (RNase H1) (Ribonuclease H type II)	0.12	-	mit	0	Cytoplasm (Potential)		604123		286
O75818 UniProt NPD GO	RPP40_HUMAN	Ribonuclease P protein subunit p40 (EC 3.1.26.5) (RNaseP protein p40) (RNase P subunit 1)	0.12	-	nuc	0	Nucleus; nucleolus (Potential)	nucleolar ribonuclease P complex [TAS] nucleus [TAS]	606117		302
O80325 UniProt NPD GO	RNS7_PYRPY	Ribonuclease S-7 precursor (EC 3.1.27.1) (S7-RNase)	0.12	-	nuc	1 *					226
Q5AK94 UniProt NPD GO	RNY1A_CANAL	Ribonuclease T2-like 1-A precursor (EC 3.1.27.1) (RNase T2-like A)	0.12	-	exc	0	Secreted protein (By similarity)				399
P61823 UniProt NPD GO	RNAS1_BOVIN	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.12	-	exc	0	Secreted protein			9RSA	150
Q9QYX3 UniProt NPD GO	RNAS1_MUSPA	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.12	-	exc	0	Secreted protein				149
Q9WUV4 UniProt NPD GO	RNAS1_NIVCR	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.12	-	exc	0	Secreted protein				149
P38291 UniProt NPD GO	POP7_YEAST	Ribonucleases P/MRP protein subunit POP7 (EC 3.1.26.5) (RNases P/MRP 15.8 kDa subunit) (RNA-processi ...	0.12	-	mit	0	Nucleus (Potential)	nucleolar ribonuclease P complex [IDA] ribonuclease MRP complex [IDA]			140
P27560 UniProt NPD GO	RIP3_SAPOF	Ribosome-inactivating protein saporin-3 (EC 3.2.2.22) (SAP-3) (SO-3) (rRNA N-glycosidase) (Fragment) ...	0.12	-	cyt	0					236
Q9XGX4 UniProt NPD GO	RBS3_AMAHP	Ribulose bisphosphate carboxylase small chain 3, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.12	-	mit	0	Plastid; chloroplast				180
Q96542 UniProt NPD GO	RBS_BETVE	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.12	-	mit	0	Plastid; chloroplast				182
P17537 UniProt NPD GO	RBS_CHLMO	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.12	-	mit	0	Plastid; chloroplast				168
Q42822 UniProt NPD GO	RBS_GLYTO	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.12	-	cyt	0	Plastid; chloroplast				178
P16881 UniProt NPD GO	RBS_EUGGR	Ribulose bisphosphate carboxylase small chains, chloroplast precursor (EC 4.1.1.39) (RuBisCO small s ...	0.12	-	end	2 *	Plastid; chloroplast				1273
Q8SRP6 UniProt NPD GO	RPE_ENCCU	Ribulose-phosphate 3-epimerase (EC 5.1.3.1) (Pentose-5-phosphate 3-epimerase) (PPE) (RPE)	0.12	-	cyt	0					217
P34794 UniProt NPD GO	RUB2_BRANA	RuBisCO large subunit-binding protein subunit alpha, chloroplast precursor (60 kDa chaperonin subuni ...	0.12	-	mit	0	Plastid; chloroplast				583
Q5A0W7 UniProt NPD GO	RUVB1_CANAL	RuvB-like helicase 1 (EC 3.6.1.-)	0.12	-	cyt	0	Nucleus (By similarity)				458
Q9AXE3 UniProt NPD GO	DCAM_DAUCA	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.12	-	cyt	0					361
Q9M4D8 UniProt NPD GO	DCAM_VICFA	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.12	-	cyt	0					353
Q08986 UniProt NPD GO	SAM3_YEAST	S-adenosylmethionine permease SAM3 (S-adenosylmethionine metabolism protein 3)	0.12	-	end	11	Membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum	plasma membrane [IMP]			587
Q9NRG4 UniProt NPD GO	SMYD2_HUMAN	SET and MYND domain-containing protein 2 (HSKM-B)	0.12	-	cyt	0					433
Q8BMC3 UniProt NPD GO	SHC2_MOUSE	SHC-transforming protein 2 (SH2 domain protein C2) (Src homology 2 domain-containing-transforming pr ...	0.12	-	cyt	0					548
Q93084 UniProt NPD GO	AT2A3_HUMAN	Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 (EC 3.6.3.8) (Calcium pump 3) (SERCA3) (SR Ca(2+ ...	0.12	-	end	7	Nucleus; nuclear membrane; multi-pass membrane protein. Endoplasmic reticulum; endoplasmic reticulum ...	integral to plasma membrane [TAS] sarcoplasmic reticulum [IDA]	601929		1043
Q7YWB0 UniProt NPD GO	SECP_APICC	Secapin precursor	0.12	-	exc	1 *	Secreted protein (By similarity)				77
Q7YWA9 UniProt NPD GO	SECP_VESMC	Secapin precursor	0.12	-	exc	1 *	Secreted protein (By similarity)				77
P47872 UniProt NPD GO	SCTR_HUMAN	Secretin receptor precursor (SCT-R)	0.12	-	end	5	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	182098		440
P81121 UniProt NPD GO	SP1_HORSE	Seminal plasma protein HSP-1	0.12	-	nuc	0	Secreted protein				120
Q9M099 UniProt NPD GO	BRS1_ARATH	Serine carboxypeptidase 2 precursor (EC 3.4.16.6) (Serine carboxypeptidase II) (Carboxypeptidase D) ...	0.12	-	exc	0	Secreted protein (Probable)				465
O62585 UniProt NPD GO	GLYC_ENCCU	Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) (Serine methylase) (Glycine hydroxymethyltra ...	0.12	-	cyt	0	Cytoplasm (Probable)				460
O35453 UniProt NPD GO	HEPS_MOUSE	Serine protease hepsin (EC 3.4.21.-) [Contains: Serine protease hepsin non-catalytic chain; Serine p ...	0.12	-	cyt	1 *	Membrane; single-pass type II membrane protein	plasma membrane [IDA]			436
P09005 UniProt NPD GO	SPI21_RAT	Serine protease inhibitor 2.1 (SPI-2.1) (Fragment)	0.12	-	cyt	0					214
P34953 UniProt NPD GO	IPK2_MACFA	Serine protease inhibitor Kazal-type 2 precursor (Acrosin-trypsin inhibitor)	0.12	-	exc	1 *	Secreted protein				81
O43930 UniProt NPD GO	PRKY_HUMAN	Serine/threonine-protein kinase PRKY (EC 2.7.11.1)	0.12	-	cyt	0			400008		277

You are viewing entries 61851 to 61900 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.