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
Q8N628 UniProt NPD GO	OR2C3_HUMAN	Olfactory receptor 2C3	0.07	-	end	7 *	Membrane; multi-pass membrane protein				319
Q13607 UniProt NPD GO	OR2F1_HUMAN	Olfactory receptor 2F1 (Olfactory receptor-like protein OLF3)	0.07	-	end	7 *	Membrane; multi-pass membrane protein		608497		317
O95006 UniProt NPD GO	OR2F2_HUMAN	Olfactory receptor 2F2 (Olfactory receptor 7-1) (OR7-1) (Olfactory receptor OR7-6)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				317
Q8NGZ4 UniProt NPD GO	OR2G3_HUMAN	Olfactory receptor 2G3 (Olfactory receptor OR1-33)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				309
Q6IEV9 UniProt NPD GO	OR4CB_HUMAN	Olfactory receptor 4C11 (Olfactory receptor OR11-136)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				310
Q8NH54 UniProt NPD GO	O56A3_HUMAN	Olfactory receptor 56A3	0.07	-	end	7 *	Membrane; multi-pass membrane protein				315
Q8NGR4 UniProt NPD GO	OR5C1_HUMAN	Olfactory receptor 5C1 (Olfactory receptor 9-F) (OR9-F)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				320
Q8NGV7 UniProt NPD GO	OR5H2_HUMAN	Olfactory receptor 5H2	0.07	-	end	7 *	Membrane; multi-pass membrane protein				309
Q8NGY3 UniProt NPD GO	OR6K3_HUMAN	Olfactory receptor 6K3	0.07	-	end	5 *	Membrane; multi-pass membrane protein				315
O76099 UniProt NPD GO	OR7C1_HUMAN	Olfactory receptor 7C1 (Olfactory receptor TPCR86)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				320
Q60892 UniProt NPD GO	OLF8_MOUSE	Olfactory receptor 8 (Odorant receptor M64)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				310
Q9FME8 UniProt NPD GO	OPT4_ARATH	Oligopeptide transporter 4 (AtOPT4)	0.07	-	end	14 *	Membrane; multi-pass membrane protein (Probable)				729
Q6FPE8 UniProt NPD GO	RFT1_CANGA	Oligosaccharide translocation protein RFT1	0.07	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				551
P40913 UniProt NPD GO	RFT1_KLULA	Oligosaccharide translocation protein RFT1	0.07	-	end	11 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				556
Q9WUK7 UniProt NPD GO	OPN3_MOUSE	Opsin-3 (Encephalopsin) (Panopsin)	0.07	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [ISS]			400
Q8WV07 UniProt NPD GO	ORAV1_HUMAN	Oral cancer overexpressed protein 1 (Tumor amplified and overexpressed sequence 1)	0.07	-	cyt	0			607224		137
P56717 UniProt NPD GO	OREX_BOVIN	Orexin-A (Hypocretin-1) (Hcrt1)	0.07	-	nuc	0	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Associated with perikaryal rough ...				33
P25513 UniProt NPD GO	ORND_PLAOR	Ornatin-D (Fragment)	0.07	-	nuc	0	Secreted protein				28
O50039 UniProt NPD GO	OTC_ARATH	Ornithine carbamoyltransferase, chloroplast precursor (EC 2.1.3.3) (OTCase) (Ornithine transcarbamyl ...	0.07	-	mit	0	Plastid; chloroplast				375
P56409 UniProt NPD GO	ORNT_ORNMO	Ornithodorin	0.07	-	nuc	0				1TOC	119
P18904 UniProt NPD GO	PYRE_SORMA	Orotate phosphoribosyltransferase (EC 2.4.2.10) (OPRT) (OPRTase)	0.07	-	cyt	0					232
P13649 UniProt NPD GO	PYRF_CANAL	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.07	-	cyt	0					270
Q9Y720 UniProt NPD GO	PYRF_RHIPU	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.07	-	cyt	0					263
Q9GZN6 UniProt NPD GO	S6A16_HUMAN	Orphan sodium- and chloride-dependent neurotransmitter transporter NTT5 (Solute carrier family 6 mem ...	0.07	-	end	10	Membrane; multi-pass membrane protein	intracellular [NAS]	607972		736
Q8K559 UniProt NPD GO	OTOSP_CAVPO	Otospiralin precursor	0.07	-	exc	0	Secreted protein (Probable)				88
P19104 UniProt NPD GO	OVAL_COTJA	Ovalbumin	0.07	-	nuc	0	Secreted protein (By similarity)				382
P01013 UniProt NPD GO	OVALX_CHICK	Ovalbumin-related protein X (Gene X protein) (Fragment)	0.07	-	cyt	0					232
P02789 UniProt NPD GO	TRFE_CHICK	Ovotransferrin precursor (Conalbumin) (Allergen Gal d 3) (Gal d III) (Serum transferrin)	0.07	-	exc	0	Secreted protein			2D3I	705
P26320 UniProt NPD GO	PSBO_SOLTU	Oxygen-evolving enhancer protein 1, chloroplast precursor (OEE1) (33 kDa subunit of oxygen evolving ...	0.07	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				333
Q9S841 UniProt NPD GO	PSBO2_ARATH	Oxygen-evolving enhancer protein 1-2, chloroplast precursor (OEE1) (33 kDa subunit of oxygen evolvin ...	0.07	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				331
P52708 UniProt NPD GO	HNLS_SORBI	P-(S)-hydroxymandelonitrile lyase precursor (EC 4.1.2.11) (Hydroxynitrile lyase) (HNL) [Contains: P- ...	0.07	-	cyt	0					366
Q9UBL9 UniProt NPD GO	P2RX2_HUMAN	P2X purinoceptor 2 (ATP receptor) (P2X2) (Purinergic receptor)	0.07	-	mit	1 *	Membrane; multi-pass membrane protein		600844		471
P43657 UniProt NPD GO	P2RY5_HUMAN	P2Y purinoceptor 5 (P2Y5) (Purinergic receptor 5) (RB intron encoded G-protein coupled receptor)	0.07	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	609239		344
Q3T0X8 UniProt NPD GO	PDZD1_BOVIN	PDZ domain-containing protein 1	0.07	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with pe ...				520
P84645 UniProt NPD GO	PALIC_PALCO	Palicourein	0.07	-	nuc	0				1R1F	37
Q6C520 UniProt NPD GO	AKR1_YARLI	Palmitoyltransferase AKR1 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR1)	0.07	-	end	4	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				702
Q74ZZ2 UniProt NPD GO	SWF1_ASHGO	Palmitoyltransferase SWF1 (EC 2.3.1.-)	0.07	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				326
P11967 UniProt NPD GO	PAHO_STRCA	Pancreatic hormone (Pancreatic polypeptide) (PP)	0.07	-	cyt	0	Secreted protein				36
P17892 UniProt NPD GO	LIPR2_MOUSE	Pancreatic lipase-related protein 2 precursor (EC 3.1.1.3) (Cytotoxic T-lymphocyte lipase)	0.07	-	vac	0	Secreted protein				468
P16233 UniProt NPD GO	LIPP_HUMAN	Pancreatic triacylglycerol lipase precursor (EC 3.1.1.3) (Pancreatic lipase) (PL)	0.07	-	exc	0	Secreted protein		246600	1N8S	465
P29183 UniProt NPD GO	LIPP_HORSE	Pancreatic triacylglycerol lipase precursor (EC 3.1.1.3) (Pancreatic lipase) (PL) (Fragment)	0.07	-	cyt	0	Secreted protein			1HPL	461
P81059 UniProt NPD GO	PEN3B_PENVA	Penaeidin-3b precursor (Pen-3b) (P3-b)	0.07	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				82
Q963D9 UniProt NPD GO	PEN3J_PENVA	Penaeidin-3j precursor (Pen-3j)	0.07	-	mit	0	Cytoplasmic granule. Cytoplasmic granules of hemocytes and to a lesser extent in small granules of h ...				81
P00793 UniProt NPD GO	PEPA_CHICK	Pepsin A precursor (EC 3.4.23.1)	0.07	-	nuc	0					367
P09641 UniProt NPD GO	PYY_MYOSC	Peptide YY-like (PYY)	0.07	-	nuc	0	Secreted protein				36
Q9GK12 UniProt NPD GO	PGRP_CAMDR	Peptidoglycan recognition protein precursor (Peptidoglycan recognition protein short) (PGRP-S)	0.07	-	exc	0	Secreted protein; cytoplasmic granule (By similarity)				193
P08478 UniProt NPD GO	AMD1_XENLA	Peptidyl-glycine alpha-amidating monooxygenase 1 precursor (EC 1.14.17.3) (Peptidyl-glycine alpha-am ...	0.07	-	exc	0					400
Q9C566 UniProt NPD GO	CYP40_ARATH	Peptidyl-prolyl cis-trans isomerase CYP40 (EC 5.2.1.8) (PPIase CYP40) (Rotamase CYP40) (Cyclophilin- ...	0.07	-	cyt	0	Cytoplasm (Probable)				361
Q75A33 UniProt NPD GO	PPID_ASHGO	Peptidyl-prolyl cis-trans isomerase D (EC 5.2.1.8) (PPIase D) (Rotamase D)	0.07	-	cyt	0	Cytoplasm (By similarity)				369
Q5ACI8 UniProt NPD GO	PPID_CANAL	Peptidyl-prolyl cis-trans isomerase D (EC 5.2.1.8) (PPIase D) (Rotamase D)	0.07	-	nuc	0	Cytoplasm (By similarity)				369

You are viewing entries 70601 to 70650 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.