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
Q9NP90 UniProt NPD GO	RAB9B_HUMAN	Ras-related protein Rab-9B (Rab-9L) (RAB9-like protein)	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		300285		201
Q39222 UniProt NPD GO	RB11B_ARATH	Ras-related protein Rab11	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				216
Q40521 UniProt NPD GO	RB11B_TOBAC	Ras-related protein Rab11B	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				217
Q40194 UniProt NPD GO	RB11D_LOTJA	Ras-related protein Rab11D	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				218
P34139 UniProt NPD GO	RAB1A_DICDI	Ras-related protein Rab1A	0.01	-	cyt	0					167
Q01111 UniProt NPD GO	YPT3_NICPL	Ras-related protein YPT3	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				218
P21586 UniProt NPD GO	RKGG_CARCR	Rathke gland glycoprotein (Fragment)	0.01	-		0	Secreted protein				15
Q8R4C6 UniProt NPD GO	RAMP1_CAVPO	Receptor activity-modifying protein 1 precursor	0.01	-	exc	2 *	Membrane; single-pass type I membrane protein (By similarity)				148
Q9JJ73 UniProt NPD GO	RAMP3_RAT	Receptor activity-modifying protein 3 precursor	0.01	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				147
O60896 UniProt NPD GO	RAMP3_HUMAN	Receptor activity-modifying protein 3 precursor (CRLR activity-modifying protein 3) (Calcitonin-rece ...	0.01	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] lysosome [TAS] plasma membrane [TAS]	605155		148
Q5RE33 UniProt NPD GO	REEP5_PONPY	Receptor expression-enhancing protein 5 (Polyposis locus protein 1 homolog)	0.01	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				189
Q60870 UniProt NPD GO	REEP5_MOUSE	Receptor expression-enhancing protein 5 (Polyposis locus protein 1 homolog) (TB2 protein homolog) (G ...	0.01	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				185
Q32LG5 UniProt NPD GO	REEP6_BOVIN	Receptor expression-enhancing protein 6	0.01	-	mit	2 *	Membrane; multi-pass membrane protein (By similarity)				185
Q5XI60 UniProt NPD GO	REEP6_RAT	Receptor expression-enhancing protein 6 (Polyposis locus protein 1-like 1)	0.01	-	end	3 *	Membrane; multi-pass membrane protein (By similarity). Cytoplasmic; in a punctate pattern				211
Q9JM62 UniProt NPD GO	REEP6_MOUSE	Receptor expression-enhancing protein 6 (Polyposis locus protein 1-like 1) (TB2 protein-like 1)	0.01	-	mit	3 *	Membrane; multi-pass membrane protein (By similarity)				201
Q26324 UniProt NPD GO	RPCH_CARMA	Red pigment-concentrating prohormone precursor [Contains: Red pigment-concentrating hormone (RPCH); ...	0.01	-	exc	1 *	Secreted protein				110
Q95170 UniProt NPD GO	OPSR_CAPHI	Red-sensitive opsin (Red cone photoreceptor pigment)	0.01	-	end	7	Membrane; multi-pass membrane protein				364
O18913 UniProt NPD GO	OPSR_FELCA	Red-sensitive opsin (Red cone photoreceptor pigment)	0.01	-	end	7	Membrane; multi-pass membrane protein				364
O18914 UniProt NPD GO	OPSR_CANFA	Red-sensitive opsin (Red cone photoreceptor pigment) (Fragment)	0.01	-	end	6 *	Membrane; multi-pass membrane protein				273
O18912 UniProt NPD GO	OPSR_HORSE	Red-sensitive opsin (Red cone photoreceptor pigment) (Fragment)	0.01	-	end	6 *	Membrane; multi-pass membrane protein				273
Q9N117 UniProt NPD GO	RELN_BOVIN	Reelin (EC 3.4.21.-) (Fragment)	0.01	-	cyt	0	Secreted protein (By similarity)				52
Q15493 UniProt NPD GO	RGN_HUMAN	Regucalcin (RC) (Senescence marker protein 30) (SMP-30)	0.01	-	nuc	0	Cytoplasm (By similarity)		300212		299
Q62795 UniProt NPD GO	NPT1_RAT	Renal sodium-dependent phosphate transport protein 1 (Sodium/phosphate cotransporter 1) (Na(+)/PI co ...	0.01	-	end	11 *	Membrane; multi-pass membrane protein				465
Q92374 UniProt NPD GO	RFA3_SCHPO	Replication factor-A protein 3 (Single-stranded DNA-binding protein P12 subunit)	0.01	-	cyt	0	Nucleus				104
Q9CQ71 UniProt NPD GO	RFA3_MOUSE	Replication protein A 14 kDa subunit (RP-A) (RF-A) (Replication factor-A protein 3) (p14)	0.01	-	cyt	0	Nucleus (By similarity)				121
Q9ES97 UniProt NPD GO	RTN3_MOUSE	Reticulon-3	0.01	-	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				237
Q924D0 UniProt NPD GO	RT4I1_MOUSE	Reticulon-4-interacting protein 1, mitochondrial precursor (NOGO-interacting mitochondrial protein)	0.01	-	mit	0	Mitochondrion				396
P00352 UniProt NPD GO	AL1A1_HUMAN	Retinal dehydrogenase 1 (EC 1.2.1.36) (RalDH1) (RALDH 1) (Aldehyde dehydrogenase family 1 member A1) ...	0.01	-	cyt	0	Cytoplasm	cytoplasm [TAS]	100640		500
Q8HYE4 UniProt NPD GO	AL1A1_MACFA	Retinal dehydrogenase 1 (EC 1.2.1.36) (RalDH1) (RALDH 1) (Aldehyde dehydrogenase family 1 member A1) ...	0.01	-	cyt	0	Cytoplasm (By similarity)				500
P51647 UniProt NPD GO	AL1A1_RAT	Retinal dehydrogenase 1 (EC 1.2.1.36) (RalDH1) (RALDH 1) (Aldehyde dehydrogenase family 1 member A1) ...	0.01	-	cyt	0	Cytoplasm				500
Q9YGX2 UniProt NPD GO	RPE65_CHICK	Retinal pigment epithelium-specific 65 kDa protein	0.01	-	cyt	0					533
O55057 UniProt NPD GO	PDE6D_MOUSE	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase delta-subunit (EC 3.1.4.17) (GMP ...	0.01	-	nuc	0					150
Q95142 UniProt NPD GO	PDE6D_BOVIN	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (EC 3.1.4.17) (GMP ...	0.01	-	nuc	0					150
Q9XT54 UniProt NPD GO	PDE6D_CANFA	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (EC 3.1.4.17) (GMP ...	0.01	-	nuc	0					150
Q920A5 UniProt NPD GO	RISC_MOUSE	Retinoid-inducible serine carboxypeptidase precursor (EC 3.4.16.-) (Serine carboxypeptidase 1)	0.01	-	exc	1 *	Secreted protein (Potential)				452
Q8TC12 UniProt NPD GO	RDH11_HUMAN	Retinol dehydrogenase 11 (EC 1.1.1.-) (Retinal reductase 1) (RalR1) (Prostate short-chain dehydrogen ...	0.01	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein	intracellular [ISS]	607849		318
P59837 UniProt NPD GO	RDH12_BOVIN	Retinol dehydrogenase 12 (EC 1.1.1.-) (Double substrate specificity short chain dehydrogenase/reduct ...	0.01	-	nuc	1 *		intracellular [ISS]			316
P09455 UniProt NPD GO	RET1_HUMAN	Retinol-binding protein I, cellular (Cellular retinol-binding protein) (CRBP)	0.01	-	cyt	0	Cytoplasm		180260		134
P02696 UniProt NPD GO	RET1_RAT	Retinol-binding protein I, cellular (Cellular retinol-binding protein) (CRBP)	0.01	-	cyt	0	Cytoplasm			1MX8	134
Q00915 UniProt NPD GO	RET1_MOUSE	Retinol-binding protein I, cellular (Cellular retinol-binding protein) (CRBP) (mCRBPI)	0.01	-	cyt	0	Cytoplasm				134
Q00017 UniProt NPD GO	RHA1_ASPAC	Rhamnogalacturonan acetylesterase precursor (EC 3.1.1.-) (RGAE)	0.01	-	end	0				1PP4	250
P84107 UniProt NPD GO	RHG_RAT	Rho-GTPase-activating protein (Fragment)	0.01	-		0					9
P08946 UniProt NPD GO	LITR_PHYRO	Rhodei-litorin	0.01	-		0	Secreted protein				9
P56514 UniProt NPD GO	OPSD_BUFBU	Rhodopsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				354
Q17292 UniProt NPD GO	OPSD_CAMAB	Rhodopsin	0.01	-	end	7	Membrane; multi-pass membrane protein				378
Q17296 UniProt NPD GO	OPSD_CATBO	Rhodopsin	0.01	-	end	7	Membrane; multi-pass membrane protein				378
P22328 UniProt NPD GO	OPSD_CHICK	Rhodopsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				351
P28681 UniProt NPD GO	OPSD_CRIGR	Rhodopsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				348
O62791 UniProt NPD GO	OPSD_DELDE	Rhodopsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				348
Q769E8 UniProt NPD GO	OPSD_GALCR	Rhodopsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				348

You are viewing entries 91151 to 91200 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.