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
Q9Y3L5 UniProt NPD GO	RAP2C_HUMAN	Ras-related protein Rap-2c precursor	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				183
Q8BU31 UniProt NPD GO	RAP2C_MOUSE	Ras-related protein Rap-2c precursor	0.09	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				183
Q8BGH4 UniProt NPD GO	REEP1_MOUSE	Receptor expression-enhancing protein 1	0.09	-	nuc	2 *	Cell membrane; multi-pass membrane protein. Cell surface. A small proportion is detected at the cell ...				201
Q26896 UniProt NPD GO	CYAA_TRYCO	Receptor-type adenylate cyclase (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase) (Fragment) ...	0.09	-	end	1	Cell membrane; multi-pass membrane protein (By similarity)				745
Q25263 UniProt NPD GO	CYAB_LEIDO	Receptor-type adenylate cyclase B (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase)	0.09	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				1331
P11953 UniProt NPD GO	RELX_SQUAC	Relaxin [Contains: Relaxin B chain; Relaxin A chain]	0.09	-	nuc	0	Secreted protein				54
P13993 UniProt NPD GO	PRP2_SOYBN	Repetitive proline-rich cell wall protein 2 precursor	0.09	-	exc	0					230
P35250 UniProt NPD GO	RFC2_HUMAN	Replication factor C subunit 2 (Replication factor C 40 kDa subunit) (RF-C 40 kDa subunit) (RFC40) ( ...	0.09	-	nuc	0	Nucleus (Probable)	DNA replication factor C complex [TAS]	600404		354
O94449 UniProt NPD GO	RFC4_SCHPO	Replication factor C subunit 4 (Replication factor C4)	0.09	-	cyt	0	Nucleus (By similarity)	Ctf18 RFC-like complex [TAS] Elg1 RFC-like complex [IDA] Rad17 RFC-like complex [TAS]			342
P26755 UniProt NPD GO	RFA3_YEAST	Replication factor-A protein 3 (RF-A) (Replication protein A 13 kDa subunit)	0.09	-	nuc	0	Nucleus	chromosome, telomeric region [IMP] DNA replication factor A complex [TAS]			122
Q28183 UniProt NPD GO	R157_BOVIN	Retina-specific 15.7 kDa protein	0.09	-	nuc	0					147
Q96R05 UniProt NPD GO	RET7_HUMAN	Retinoid-binding protein 7 (Cellular retinoic acid-binding protein 4) (CRBP4) (Cellular retinoic aci ...	0.09	-	cyt	0	Cytoplasm (By similarity)		608604	1LPJ	134
P50120 UniProt NPD GO	RET2_HUMAN	Retinol-binding protein II, cellular (CRBP-II)	0.09	-	mit	0	Cytoplasm		180280		133
P06768 UniProt NPD GO	RET2_RAT	Retinol-binding protein II, cellular (CRBP-II)	0.09	-	cyt	0	Cytoplasm			1OPB	133
Q5RBM7 UniProt NPD GO	RET5_PONPY	Retinol-binding protein III, cellular (CRBP-III)	0.09	-	cyt	0	Cytoplasm (By similarity)				134
Q00019 UniProt NPD GO	RHGB_ASPAC	Rhamnogalacturonase B precursor (EC 4.2.2.-) (Rhamnogalacturonan lyase) (RGase B) (RHG B)	0.09	-	exc	0				1NKG	527
P84617 UniProt NPD GO	RCAL1_RHEAM	Rheacalcin-1 (RCA-1)	0.09	-	mit	0	Eggshell matrix				135
O76145 UniProt NPD GO	RHIC_ORYRH	Rhinocerosin precursor	0.09	-	cyt	0	Secreted protein				142
P81397 UniProt NPD GO	RHCA_AGKRH	Rhodocetin subunit alpha	0.09	-	nuc	0	Secreted protein			1SB2	133
P58873 UniProt NPD GO	RHBD4_MOUSE	Rhomboid-related protein 4 (EC 3.4.21.105) (Ventrhoid transmembrane protein)	0.09	-	end	6	Membrane; multi-pass membrane protein (Probable)				404
Q924W9 UniProt NPD GO	RBTN1_MOUSE	Rhombotin-1 (Cysteine-rich protein TTG-1) (LIM-only protein 1)	0.09	-	cyt	0	Nucleus				156
P42813 UniProt NPD GO	RNS1_ARATH	Ribonuclease 1 precursor (EC 3.1.27.1)	0.09	-	exc	1 *					230
Q7M438 UniProt NPD GO	RNDI_DICDI	Ribonuclease DdI precursor (EC 3.1.27.1) (RNase DdI)	0.09	-	exc	0	Lysosome				223
Q7M329 UniProt NPD GO	RNT2_PIG	Ribonuclease T2 (EC 3.1.27.-)	0.09	-	cyt	0	Secreted protein (Potential)				200
P49074 UniProt NPD GO	RNCL_ASPCL	Ribonuclease clavin precursor (EC 3.1.27.-)	0.09	-	exc	0					177
P00659 UniProt NPD GO	RNAS1_DAMKO	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.09	-	nuc	0	Secreted protein				124
P14626 UniProt NPD GO	RNASL_RANCA	Ribonuclease, liver (EC 3.1.27.5)	0.09	-	nuc	0	Secreted protein				111
Q12189 UniProt NPD GO	RPIA_YEAST	Ribose-5-phosphate isomerase (EC 5.3.1.6) (Phosphoriboisomerase) (D-ribose-5-phosphate ketol-isomera ...	0.09	-	cyt	0		cytoplasm [IDA] nucleus [IDA]		1XTZ	258
P46585 UniProt NPD GO	KPR1_CANAL	Ribose-phosphate pyrophosphokinase 1 (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase 1)	0.09	-	nuc	0					321
P10666 UniProt NPD GO	KS6AB_XENLA	Ribosomal protein S6 kinase 2 beta (EC 2.7.11.1) (Ribosomal protein S6 kinase II beta) (S6KII-beta) ...	0.09	-	cyt	0					629
P84853 UniProt NPD GO	RIPL1_PHYDI	Ribosome-inactivating protein PD-L1/PD-L2 (EC 3.2.2.22) (rRNA N-glycosidase PD-L1/PD-L2) (Fragment)	0.09	-	nuc	0					45
Q09125 UniProt NPD GO	RBS_PORAE	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.09	-	cyt	0	Plastid; chloroplast				138
P08475 UniProt NPD GO	RBS2_CHLRE	Ribulose bisphosphate carboxylase small chain 2, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.09	-	mit	0	Plastid; chloroplast			1UZH	185
Q39746 UniProt NPD GO	RBS4_FLAPR	Ribulose bisphosphate carboxylase small chain 4, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.09	-	mit	0	Plastid; chloroplast				178
P26573 UniProt NPD GO	RBS8_NICPL	Ribulose bisphosphate carboxylase small chain 8B, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.09	-	mit	0	Plastid; chloroplast				180
P08705 UniProt NPD GO	RBS_HELAN	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.09	-	mit	0	Plastid; chloroplast				178
Q42693 UniProt NPD GO	RUBB_CHLRE	RuBisCO large subunit-binding protein subunit beta-1 (60 kDa chaperonin subunit beta-1) (CPN-60 beta ...	0.09	-	nuc	0	Plastid; chloroplast				435
O65354 UniProt NPD GO	DCAM_HELAN	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.09	-	cyt	0					361
Q9M6K1 UniProt NPD GO	DCAM_IPOBA	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.09	-	cyt	0					362
P20443 UniProt NPD GO	ARRS_MOUSE	S-arrestin (Retinal S-antigen) (48 kDa protein) (S-AG) (Rod photoreceptor arrestin)	0.09	-	cyt	0					403
P51479 UniProt NPD GO	ARRS_RANPI	S-arrestin (Retinal S-antigen) (Rod photoreceptor arrestin)	0.09	-	cyt	0					396
P25554 UniProt NPD GO	SGF29_YEAST	SAGA-associated factor 29 (29 kDa SAGA-associated factor) (SAGA histone acetyltransferase complex 29 ...	0.09	-	cyt	0	Nucleus (Probable)	SAGA complex [IDA]			259
P46250 UniProt NPD GO	SEC14_CANAL	SEC14 cytosolic factor (Phosphatidylinositol/phosphatidylcholine transfer protein) (PI/PC TP)	0.09	-	cyt	0	Golgi apparatus; Golgi membrane; peripheral membrane protein (By similarity)				301
O14796 UniProt NPD GO	SH21B_HUMAN	SH2 domain protein 1B (EWS/FLI1-activated transcript 2) (EAT-2)	0.09	-	nuc	0			608510		132
P15982 UniProt NPD GO	HB2C_PIG	SLA class II histocompatibility antigen, DQ haplotype C beta chain precursor	0.09	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				261
P04110 UniProt NPD GO	SPE2A_STRPU	SPEC 2A protein	0.09	-	cyt	0					150
Q9UEW8 UniProt NPD GO	STK39_HUMAN	STE20/SPS1-related proline-alanine-rich protein kinase (EC 2.7.11.1) (Ste-20-related kinase) (Serine ...	0.09	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable). Nucleus when caspase-cleaved (Probable)	cytoplasm [NAS] nucleus [NAS]	607648		547
P07267 UniProt NPD GO	CARP_YEAST	Saccharopepsin precursor (EC 3.4.23.25) (Aspartate protease) (Proteinase A) (Proteinase YSCA)	0.09	-	exc	0	Vacuole. Lysosome-like vacuoles	mitochondrion [IDA] vacuolar lumen (sensu Fungi) [TAS]		2JXR	405
Q09694 UniProt NPD GO	LYS1_SCHPO	Saccharopine dehydrogenase [NAD+, L-lysine-forming] (EC 1.5.1.7) (Lysine--2-oxoglutarate reductase) ...	0.09	-	nuc	0					368
Q9YGL9 UniProt NPD GO	AT2A3_CHICK	Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 (EC 3.6.3.8) (Calcium pump 3) (SERCA3) (SR Ca(2+ ...	0.09	-	end	8	Nucleus; nuclear membrane; multi-pass membrane protein (By similarity). Endoplasmic reticulum; endop ...				1042

You are viewing entries 67001 to 67050 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.