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
P47803 UniProt NPD GO	RGR_BOVIN	RPE-retinal G protein-coupled receptor	0.02	-	end	6 *	Membrane; multi-pass membrane protein				291
P47804 UniProt NPD GO	RGR_HUMAN	RPE-retinal G protein-coupled receptor	0.02	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600342		291
P20037 UniProt NPD GO	HA2B_RAT	RT1 class II histocompatibility antigen, B alpha chain precursor	0.02	-	end	1	Membrane; single-pass type I membrane protein (Potential)				256
P83719 UniProt NPD GO	RACYT_RANTE	Ranacyclin-T precursor	0.02	-	exc	0	Secreted protein (By similarity)	extracellular region [ISS]			62
P82741 UniProt NPD GO	RAN1_RANCA	Ranatuerin-1	0.02	-	cyt	0	Secreted protein				25
P82875 UniProt NPD GO	RAN1C_RANCL	Ranatuerin-1C	0.02	-	cyt	0	Secreted protein				25
P82740 UniProt NPD GO	RA1T_RANTE	Ranatuerin-1T (Brevinin-2T)	0.02	-	cyt	0	Secreted protein				33
P41924 UniProt NPD GO	RYL1_YARLI	Ras-like GTP-binding protein RYL1	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				203
Q91079 UniProt NPD GO	RAS_LIMLI	Ras-like protein (Fragment)	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side. Inner surface of plasma membrane				93
P80236 UniProt NPD GO	RAC1_CAVPO	Ras-related C3 botulinum toxin substrate 1 (p21-Rac1) (Sigma 1 component protein p22) (Fragment)	0.02	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein				77
P24409 UniProt NPD GO	RAB10_CANFA	Ras-related protein Rab-10	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				200
Q5ZLG1 UniProt NPD GO	RAB18_CHICK	Ras-related protein Rab-18	0.02	-	cyt	0					206
Q5EB77 UniProt NPD GO	RAB18_RAT	Ras-related protein Rab-18	0.02	-	cyt	0					206
Q05976 UniProt NPD GO	RB18A_LYMST	Ras-related protein Rab-18A	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				202
Q58DW6 UniProt NPD GO	RAB25_BOVIN	Ras-related protein Rab-25	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				213
P57735 UniProt NPD GO	RAB25_HUMAN	Ras-related protein Rab-25 (CATX-8)	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				213
P57729 UniProt NPD GO	RAB38_HUMAN	Ras-related protein Rab-38 (Antigen NY-MEL-1)	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		606281		211
Q9CZT8 UniProt NPD GO	RAB3B_MOUSE	Ras-related protein Rab-3B	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	synaptic vesicle [IDA]			219
P48554 UniProt NPD GO	RAC2_DROME	Ras-related protein Rac2	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				192
O14462 UniProt NPD GO	SEC4_CANAL	Ras-related protein SEC4	0.02	-	cyt	0	Secretory vesicle; secretory vesicle membrane; lipid-anchor; cytoplasmic side (By similarity). Cell ...				210
P21587 UniProt NPD GO	RKGG_LEPKE	Rathke gland glycoprotein (Fragment)	0.02	-	cyt	0	Secreted protein				30
Q29RM3 UniProt NPD GO	REEP5_BOVIN	Receptor expression-enhancing protein 5	0.02	-	mit	2 *	Membrane; multi-pass membrane protein (By similarity)				189
Q00765 UniProt NPD GO	REEP5_HUMAN	Receptor expression-enhancing protein 5 (Polyposis locus protein 1) (TB2 protein)	0.02	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]	125265		189
Q9U6Y8 UniProt NPD GO	RFP_DISSP	Red fluorescent protein drFP583 (DsRed)	0.02	-	cyt	0				1ZGQ	225
Q23757 UniProt NPD GO	RPCH_CALSI	Red pigment-concentrating prohormone precursor [Contains: Red pigment-concentrating hormone (RPCH); ...	0.02	-	exc	1 *	Secreted protein				109
Q9BGI7 UniProt NPD GO	OPSR_BOVIN	Red-sensitive opsin (Red cone photoreceptor pigment)	0.02	-	end	7	Membrane; multi-pass membrane protein				364
P04000 UniProt NPD GO	OPSR_HUMAN	Red-sensitive opsin (Red cone photoreceptor pigment)	0.02	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	303900	1KPX	364
Q64374 UniProt NPD GO	RGN_MOUSE	Regucalcin (RC) (Senescence marker protein 30) (SMP-30)	0.02	-	nuc	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			299
Q03336 UniProt NPD GO	RGN_RAT	Regucalcin (RC) (Senescence marker protein 30) (SMP-30)	0.02	-	cyt	0	Cytoplasm				299
Q8BFS3 UniProt NPD GO	REL3_RAT	Relaxin-3 precursor (Prorelaxin R3) (Insulin-like peptide INSL7) (Insulin-like peptide 7) [Contains: ...	0.02	-	exc	0	Secreted protein				140
Q9NSD7 UniProt NPD GO	RL3R1_HUMAN	Relaxin-3 receptor 1 (RLN3 receptor 1) (Relaxin family peptide receptor 3) (Somatostatin- and angiot ...	0.02	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	609445		469
Q28722 UniProt NPD GO	NPT1_RABIT	Renal sodium-dependent phosphate transport protein 1 (Sodium/phosphate cotransporter 1) (Na(+)/PI co ...	0.02	-	end	10 *	Membrane; multi-pass membrane protein				465
Q14916 UniProt NPD GO	NPT1_HUMAN	Renal sodium-dependent phosphate transport protein 1 (Sodium/phosphate cotransporter 1) (Na(+)/PI co ...	0.02	-	end	10 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	182308		465
P81134 UniProt NPD GO	RENR_BOVIN	Renin receptor (Renin/prorenin receptor) (ATPase H(+)-transporting lysosomal accessory protein 2) (A ...	0.02	-	cyt	0	Membrane; single-pass type I membrane protein (Potential)				30
Q13156 UniProt NPD GO	RFA4_HUMAN	Replication protein A 30 kDa subunit (RP-A) (RF-A) (Replication factor-A protein 4) (p30)	0.02	-	cyt	0	Nucleus	DNA replication factor A complex [TAS]			261
Q762I5 UniProt NPD GO	RSN_BOVIN	Resistin precursor	0.02	-	cyt	0	Secreted protein (By similarity)				109
P48644 UniProt NPD GO	AL1A1_BOVIN	Retinal dehydrogenase 1 (EC 1.2.1.36) (RalDH1) (RALDH 1) (Aldehyde dehydrogenase family 1 member A1) ...	0.02	-	cyt	0	Cytoplasm				500
P15437 UniProt NPD GO	AL1A1_HORSE	Retinal dehydrogenase 1 (EC 1.2.1.36) (RalDH1) (RALDH 1) (Aldehyde dehydrogenase family 1 member A1) ...	0.02	-	cyt	0	Cytoplasm				500
P51977 UniProt NPD GO	AL1A1_SHEEP	Retinal dehydrogenase 1 (EC 1.2.1.36) (RalDH1) (RALDH 1) (Aldehyde dehydrogenase family 1 member A1) ...	0.02	-	cyt	0	Cytoplasm			1BXS	500
Q8AXN9 UniProt NPD GO	RPE65_CYNPY	Retinal pigment epithelium-specific 65 kDa protein	0.02	-	cyt	0					532
O43924 UniProt NPD GO	PDE6D_HUMAN	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (EC 3.1.4.17) (GMP ...	0.02	-	nuc	0			602676	1KSJ	150
Q02094 UniProt NPD GO	RHAG_HUMAN	Rhesus blood group-associated glycoprotein (Rhesus blood group-associated ammonia channel) (Erythroc ...	0.02	-	end	11 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [NAS]	268150		409
Q9TU03 UniProt NPD GO	GDIS_BOVIN	Rho GDP-dissociation inhibitor 2 (Rho GDI 2) (Rho-GDI beta) (Ly-GDI) (D4-GDP-dissociation inhibitor) ...	0.02	-	cyt	0	Cytoplasm				199
Q99819 UniProt NPD GO	GDIT_HUMAN	Rho GDP-dissociation inhibitor 3 (Rho GDI 3) (Rho-GDI gamma)	0.02	-	mit	0	Cytoplasm	cytoplasmic membrane-bound vesicle [TAS]	602844		225
P62746 UniProt NPD GO	RHOB_MOUSE	Rho-related GTP-binding protein RhoB precursor	0.02	-	cyt	0	Endosome; late endosome; late endosomal membrane; lipid-anchor. Late endosomal membrane (geranylgera ...	endosome membrane [ISS] nucleus [IDA] plasma membrane [ISS]			196
P62747 UniProt NPD GO	RHOB_RAT	Rho-related GTP-binding protein RhoB precursor	0.02	-	cyt	0	Endosome; late endosome; late endosomal membrane; lipid-anchor (By similarity). Late endosomal membr ...	endosome membrane [ISS] nucleus [ISS] plasma membrane [ISS]			196
P62745 UniProt NPD GO	RHOB_HUMAN	Rho-related GTP-binding protein RhoB precursor (H6)	0.02	-	cyt	0	Endosome; late endosome; late endosomal membrane; lipid-anchor. Late endosomal membrane (geranylgera ...	endosome membrane [IDA] nucleus [ISS] plasma membrane [IDA]	165370	2FV8	196
O00212 UniProt NPD GO	RHOD_HUMAN	Rho-related GTP-binding protein RhoD precursor (Rho-related protein HP1) (RhoHP1)	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		605781		210
P41590 UniProt NPD GO	OPSD_ASTFA	Rhodopsin	0.02	-	end	7 *	Membrane; multi-pass membrane protein				352
O93441 UniProt NPD GO	OPSD_GALML	Rhodopsin	0.02	-	end	7 *	Membrane; multi-pass membrane protein				354

You are viewing entries 85551 to 85600 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.