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
Q5R9M7 UniProt NPD GO	RB11A_PONPY	Ras-related protein Rab-11A	0.11	-	cyt	0	Cell membrane; peripheral membrane protein (By similarity). Endosome; recycling endosome; recycling ...				215
P62490 UniProt NPD GO	RB11A_CANFA	Ras-related protein Rab-11A (Rab-11)	0.11	-	cyt	0	Cell membrane; peripheral membrane protein (By similarity). Endosome; recycling endosome; recycling ...				215
P62492 UniProt NPD GO	RB11A_MOUSE	Ras-related protein Rab-11A (Rab-11)	0.11	-	cyt	0	Cell membrane; peripheral membrane protein (By similarity). Endosome; recycling endosome; recycling ...				215
P62493 UniProt NPD GO	RB11A_RABIT	Ras-related protein Rab-11A (Rab-11)	0.11	-	cyt	0	Cell membrane; peripheral membrane protein (By similarity). Endosome; recycling endosome; recycling ...				215
P62494 UniProt NPD GO	RB11A_RAT	Ras-related protein Rab-11A (Rab-11) (24KG)	0.11	-	cyt	0	Cell membrane; peripheral membrane protein (By similarity). Endosome; recycling endosome; recycling ...				215
P62491 UniProt NPD GO	RB11A_HUMAN	Ras-related protein Rab-11A (Rab-11) (YL8)	0.11	-	cyt	0	Cell membrane; peripheral membrane protein. Endosome; recycling endosome; recycling endosomal membra ...	Golgi trans face [IDA]	605570	1YZK	215
Q2HJH2 UniProt NPD GO	RAB1B_BOVIN	Ras-related protein Rab-1B	0.11	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				201
Q05975 UniProt NPD GO	RAB2_LYMST	Ras-related protein Rab-2	0.11	-	cyt	0	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				212
P35282 UniProt NPD GO	RAB21_MOUSE	Ras-related protein Rab-21 (Rab-12)	0.11	-	cyt	0	Golgi apparatus; Golgi membrane; lipid-anchor (By similarity)				221
Q29RR0 UniProt NPD GO	RAB26_BOVIN	Ras-related protein Rab-26	0.11	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				256
Q99P58 UniProt NPD GO	RB27B_MOUSE	Ras-related protein Rab-27B	0.11	-	cyt	0	Membrane; lipid-anchor (By similarity)				217
P53994 UniProt NPD GO	RAB2A_MOUSE	Ras-related protein Rab-2A	0.11	-	cyt	0	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...	Golgi apparatus [IDA]			212
Q01971 UniProt NPD GO	RAB2A_RABIT	Ras-related protein Rab-2A	0.11	-	cyt	0	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				212
P05712 UniProt NPD GO	RAB2A_RAT	Ras-related protein Rab-2A	0.11	-	cyt	0	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				212
O35963 UniProt NPD GO	RB33B_MOUSE	Ras-related protein Rab-33B	0.11	-	nuc	0	Golgi apparatus; Golgi membrane; lipid-anchor			1Z06	229
Q8BHD0 UniProt NPD GO	RB39A_MOUSE	Ras-related protein Rab-39A (Rab-39)	0.11	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				217
P34140 UniProt NPD GO	RAB1B_DICDI	Ras-related protein Rab1B (Fragment)	0.11	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				199
Q41640 UniProt NPD GO	RAB7_VIGAC	Ras-related protein Rab7	0.11	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				206
Q8R4C5 UniProt NPD GO	RAMP2_CAVPO	Receptor activity-modifying protein 2 precursor	0.11	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				157
Q8R4C4 UniProt NPD GO	RAMP3_CAVPO	Receptor activity-modifying protein 3 precursor	0.11	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				146
Q80ZI2 UniProt NPD GO	RTP2_MOUSE	Receptor-transporting protein 2	0.11	-	nuc	1	Cell membrane; single-pass type III membrane protein. Effective cell surface expression depends upon ...				223
P21457 UniProt NPD GO	RECO_BOVIN	Recoverin (p26)	0.11	-	cyt	0				1REC	201
Q9MTQ6 UniProt NPD GO	RCCR_HORVU	Red chlorophyll catabolite reductase (EC 1.-.-.-) (RCC reductase) (HvRCCR) (Fragment)	0.11	-	cyt	0	Plastid; chloroplast; chloroplast stroma				205
P22329 UniProt NPD GO	OPSR_CHICK	Red-sensitive opsin (Red cone photoreceptor pigment) (Iodopsin)	0.11	-	end	7	Membrane; multi-pass membrane protein				362
O93344 UniProt NPD GO	AL1A2_CHICK	Retinal dehydrogenase 2 (EC 1.2.1.36) (RalDH2) (RALDH 2) (RALDH(II)) (Retinaldehyde-specific dehydro ...	0.11	-	cyt	0	Cytoplasm				518
Q9I8W8 UniProt NPD GO	AL1A2_POEGU	Retinal dehydrogenase 2 (EC 1.2.1.36) (RalDH2) (RALDH 2) (RALDH(II)) (Retinaldehyde-specific dehydro ...	0.11	-	cyt	0	Cytoplasm				517
Q8NFJ5 UniProt NPD GO	RAI3_HUMAN	Retinoic acid-induced protein 3 (G-protein coupled receptor family C group 5 member A) (Retinoic aci ...	0.11	-	end	7 *	Cell membrane; multi-pass membrane protein. Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi ...	integral to plasma membrane [TAS]	604138		357
Q9EPC5 UniProt NPD GO	RET7_MOUSE	Retinoid-binding protein 7 (Cellular retinoic acid-binding protein 4) (CRBP4) (Cellular retinoic aci ...	0.11	-	cyt	0	Cytoplasm (By similarity)				134
P11370 UniProt NPD GO	ENV2_MOUSE	Retrovirus-related Env polyprotein from Fv-4 locus	0.11	-	end	1					679
P10602 UniProt NPD GO	CARP1_RHINI	Rhizopuspepsin-1 precursor (EC 3.4.23.21) (Aspartate protease)	0.11	-	exc	0					389
P09241 UniProt NPD GO	OPSD_OCTDO	Rhodopsin	0.11	-	end	6 *	Membrane; multi-pass membrane protein				455
Q8VC82 UniProt NPD GO	RHBD1_MOUSE	Rhomboid-related protein 1 (EC 3.4.21.105) (RRP) (Rhomboid-like protein 1)	0.11	-	end	7	Membrane; multi-pass membrane protein (Probable)				373
P25800 UniProt NPD GO	RBTN1_HUMAN	Rhombotin-1 (Cysteine-rich protein TTG-1) (T-cell translocation protein 1) (LIM-only protein 1)	0.11	-	cyt	0	Nucleus (By similarity)		186921		156
P08904 UniProt NPD GO	RNAS6_BOVIN	Ribonuclease K6 precursor (EC 3.1.27.-) (RNase K6) (K6b) (RNase K2)	0.11	-	vac	0	Lysosome (Probable). Matrix of eosinophil's large specific granule				154
Q5BJI6 UniProt NPD GO	POP5_BRARE	Ribonuclease P/MRP protein subunit POP5 (EC 3.1.26.5)	0.11	-	cyt	0	Nucleus; nucleolus (By similarity)				169
P08056 UniProt NPD GO	RNRH_RHINI	Ribonuclease Rh precursor (EC 3.1.27.1) (RNase Rh)	0.11	-	exc	0				1BOL	238
P16414 UniProt NPD GO	RNAS1_SPAEH	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.11	-	nuc	0	Secreted protein				125
Q8VD89 UniProt NPD GO	RNS1G_RAT	Ribonuclease pancreatic gamma-type precursor (EC 3.1.27.5) (RNase 1 gamma)	0.11	-	exc	0	Secreted protein (By similarity)				152
Q9WUS2 UniProt NPD GO	RNAS1_GERNI	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.11	-	exc	0	Secreted protein				148
P36602 UniProt NPD GO	RIR1_SCHPO	Ribonucleoside-diphosphate reductase large chain (EC 1.17.4.1) (Ribonucleotide reductase)	0.11	-	cyt	0		cytoplasm [TAS] ribonucleoside-diphosphate reductase complex [TAS]			811
O46310 UniProt NPD GO	RIR2_LEIAM	Ribonucleoside-diphosphate reductase small chain (EC 1.17.4.1) (Ribonucleotide reductase small subun ...	0.11	-	cyt	0					345
P35184 UniProt NPD GO	SQT1_YEAST	Ribosome assembly protein SQT1	0.11	-	cyt	0		cytoplasm [IDA] cytosol [IDA] cytosolic ribosome (sensu Eukaryota) [IDA]			431
P24312 UniProt NPD GO	RBL_CYAPA	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) (RuBisCO large subunit)	0.11	-	cyt	0	Plastid; cyanelle				475
Q41406 UniProt NPD GO	RBL2_SYMSP	Ribulose bisphosphate carboxylase precursor (EC 4.1.1.39) (RuBisCO) [Contains: Ribulose bisphosphate ...	0.11	-	cyt	0	Plastid; chloroplast (Probable). In this organism the plastid is the result of a secondary endosymbi ...				1501
P24007 UniProt NPD GO	RBS_PYRPY	Ribulose bisphosphate carboxylase small chain, chloroplast precursor (EC 4.1.1.39) (RuBisCO small su ...	0.11	-	cyt	0	Plastid; chloroplast				183
Q7X999 UniProt NPD GO	RCA2_LARTR	Ribulose bisphosphate carboxylase/oxygenase activase 2, chloroplast precursor (RuBisCO activase 2) ( ...	0.11	-	mit	0	Plastid; chloroplast; chloroplast stroma (By similarity)				435
Q43157 UniProt NPD GO	RPE_SPIOL	Ribulose-phosphate 3-epimerase, chloroplast precursor (EC 5.1.3.1) (Pentose-5-phosphate 3-epimerase) ...	0.11	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane	thylakoid membrane (sensu Viridiplantae) [IDA]			285
P21240 UniProt NPD GO	RUBB_ARATH	RuBisCO large subunit-binding protein subunit beta, chloroplast precursor (60 kDa chaperonin subunit ...	0.11	-	cyt	0	Plastid; chloroplast; chloroplast stroma				600
Q750R1 UniProt NPD GO	RUVB1_ASHGO	RuvB-like helicase 1 (EC 3.6.1.-)	0.11	-	cyt	0	Nucleus (By similarity)				459
P13822 UniProt NPD GO	SANT_PLAFP	S-antigen protein (Fragment)	0.11	-	nuc	0	Parasitophorous vacuole				76

You are viewing entries 63451 to 63500 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.