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
Q96R67 UniProt NPD GO	OR4CC_HUMAN	Olfactory receptor 4C12 (Olfactory receptor OR11-259)	0.03	-	end	6 *	Membrane; multi-pass membrane protein				309
Q8NGC6 UniProt NPD GO	OR4KH_HUMAN	Olfactory receptor 4K17	0.03	-	end	7 *	Membrane; multi-pass membrane protein				312
Q96R72 UniProt NPD GO	OR4K3_HUMAN	Olfactory receptor 4K3	0.03	-	end	7 *	Membrane; multi-pass membrane protein				315
Q8NGB6 UniProt NPD GO	OR4M2_HUMAN	Olfactory receptor 4M2	0.03	-	end	6 *	Membrane; multi-pass membrane protein				313
Q8IXE1 UniProt NPD GO	OR4N5_HUMAN	Olfactory receptor 4N5 (Olfactory receptor OR14-33)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				308
Q8VG09 UniProt NPD GO	OL502_MOUSE	Olfactory receptor 502 (Olfactory receptor 204-8)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				314
Q8NGJ6 UniProt NPD GO	O51A4_HUMAN	Olfactory receptor 51A4	0.03	-	end	7 *	Membrane; multi-pass membrane protein				313
Q9H344 UniProt NPD GO	O51I2_HUMAN	Olfactory receptor 51I2 (Odorant receptor HOR5'beta12) (Olfactory receptor OR11-38)	0.03	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			312
Q8NH57 UniProt NPD GO	O52P1_HUMAN	Olfactory receptor 52P1	0.03	-	end	7 *	Membrane; multi-pass membrane protein				321
Q8NH76 UniProt NPD GO	O56B4_HUMAN	Olfactory receptor 56B4	0.03	-	end	7 *	Membrane; multi-pass membrane protein				319
Q8NGK9 UniProt NPD GO	OR5DG_HUMAN	Olfactory receptor 5D16	0.03	-	end	7 *	Membrane; multi-pass membrane protein				328
Q8NH18 UniProt NPD GO	OR5J2_HUMAN	Olfactory receptor 5J2 (Olfactory receptor OR11-266)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				312
Q8NGP6 UniProt NPD GO	OR5M8_HUMAN	Olfactory receptor 5M8 (Olfactory receptor OR11-194)	0.03	-	end	6 *	Membrane; multi-pass membrane protein				311
Q8WZ92 UniProt NPD GO	OR5P2_HUMAN	Olfactory receptor 5P2 (Olfactory receptor-like protein JCG3)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				322
Q8NG75 UniProt NPD GO	OR5T1_HUMAN	Olfactory receptor 5T1 (Olfactory receptor OR11-179)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				326
Q8NGY2 UniProt NPD GO	OR6K2_HUMAN	Olfactory receptor 6K2	0.03	-	end	6 *	Membrane; multi-pass membrane protein				324
O60412 UniProt NPD GO	OR7C2_HUMAN	Olfactory receptor 7C2 (Olfactory receptor 19-18) (OR19-18)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				320
Q8NH51 UniProt NPD GO	OR8K3_HUMAN	Olfactory receptor 8K3	0.03	-	end	6 *	Membrane; multi-pass membrane protein				312
Q8VF76 UniProt NPD GO	OL998_MOUSE	Olfactory receptor 998 (Olfactory receptor 175-5)	0.03	-	end	6 *	Membrane; multi-pass membrane protein				314
P37067 UniProt NPD GO	OLF1_CHICK	Olfactory receptor-like protein COR1	0.03	-	end	7 *	Membrane; multi-pass membrane protein				318
P37068 UniProt NPD GO	OLF2_CHICK	Olfactory receptor-like protein COR2	0.03	-	end	5 *	Membrane; multi-pass membrane protein				312
P37069 UniProt NPD GO	OLF3_CHICK	Olfactory receptor-like protein COR3	0.03	-	end	7 *	Membrane; multi-pass membrane protein				318
P37071 UniProt NPD GO	OLF5_CHICK	Olfactory receptor-like protein COR5	0.03	-	end	6 *	Membrane; multi-pass membrane protein				312
Q9SUA4 UniProt NPD GO	OPT5_ARATH	Oligopeptide transporter 5 (AtOPT5)	0.03	-	end	14	Membrane; multi-pass membrane protein (Probable)				753
O82485 UniProt NPD GO	OPT7_ARATH	Oligopeptide transporter 7 (AtOPT7)	0.03	-	end	14	Membrane; multi-pass membrane protein (Probable)				766
P46310 UniProt NPD GO	FAD3C_ARATH	Omega-3 fatty acid desaturase, chloroplast precursor (EC 1.14.19.-)	0.03	-	nuc	3	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein				446
P48621 UniProt NPD GO	FAD3C_SOYBN	Omega-3 fatty acid desaturase, chloroplast precursor (EC 1.14.19.-)	0.03	-	nuc	3	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (Probable)				453
P32291 UniProt NPD GO	FAD3E_PHAAU	Omega-3 fatty acid desaturase, endoplasmic reticulum (EC 1.14.19.-) (Indole-3-acetic acid-induced pr ...	0.03	-	mit	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				380
P48631 UniProt NPD GO	FD6E2_SOYBN	Omega-6 fatty acid desaturase, endoplasmic reticulum isozyme 2 (EC 1.14.19.-)	0.03	-	mit	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				383
P15970 UniProt NPD GO	TOG1B_AGEAP	Omega-agatoxin-1B (Omega-agatoxin IB) (Omega-Aga-IB) (Fragment)	0.03	-	nuc	0	Secreted protein				36
P60590 UniProt NPD GO	WGRTX_GRASP	Omega-grammotoxin SIA (Omega-GrTx SIA) (Omega-GsTx SIA) (Omega-GTX SIA)	0.03	-	nuc	0	Secreted protein			1KOZ	36
P28680 UniProt NPD GO	OPS3_DROPS	Opsin Rh3 (Inner R7 photoreceptor cells opsin)	0.03	-	end	7	Membrane; multi-pass membrane protein				382
Q9UW81 UniProt NPD GO	NOP1_NEUCR	Opsin-1 (NR)	0.03	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			304
Q9W6A8 UniProt NPD GO	OP1S2_BRARE	Opsin-1, short-wave-sensitive 2 (Blue-sensitive opsin) (Blue cone photoreceptor pigment) (Opsin SWS- ...	0.03	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			354
Q26495 UniProt NPD GO	OPS2_SCHGR	Opsin-2	0.03	-	end	7 *	Membrane; multi-pass membrane protein				380
Q6AY78 UniProt NPD GO	ORCT2_RAT	Organic cation transporter-like protein 2 (Solute carrier family 22 member 18)	0.03	-	end	9 *	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Localized at the a ...				404
P27119 UniProt NPD GO	DCOR_MUSPA	Ornithine decarboxylase (EC 4.1.1.17) (ODC)	0.03	-	cyt	0					461
P27121 UniProt NPD GO	DCOR_NEUCR	Ornithine decarboxylase (EC 4.1.1.17) (ODC)	0.03	-	cyt	0					484
P09057 UniProt NPD GO	DCOR_RAT	Ornithine decarboxylase (EC 4.1.1.17) (ODC)	0.03	-	cyt	0					461
Q9I8S4 UniProt NPD GO	DCOR2_XENLA	Ornithine decarboxylase 2 (EC 4.1.1.17) (ODC 2) (xODC2)	0.03	-	cyt	0					456
O95190 UniProt NPD GO	OAZ2_HUMAN	Ornithine decarboxylase antizyme 2 (ODC-Az 2) (AZ2)	0.03	-	cyt	0			604152		189
O08608 UniProt NPD GO	OAZ2_MOUSE	Ornithine decarboxylase antizyme 2 (ODC-Az 2) (AZ2) (Seizure-related protein 15)	0.03	-	cyt	0					189
Q6BY69 UniProt NPD GO	PYRF_DEBHA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.03	-	cyt	0					267
Q9C131 UniProt NPD GO	PYRF_PARBR	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.03	-	mit	0					285
O94127 UniProt NPD GO	PYRF_PICJA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.03	-	cyt	0					266
P80781 UniProt NPD GO	OLP_TOBAC	Osmotin-like protein (Fragment)	0.03	-		0	Cell wall				15
Q41350 UniProt NPD GO	OLP1_LYCES	Osmotin-like protein precursor	0.03	-	exc	0	Cell wall (Potential)				252
P25871 UniProt NPD GO	OLPA_TOBAC	Osmotin-like protein precursor (Pathogenesis-related protein PR-5d)	0.03	-	vac	1 *				1AUN	251
P83489 UniProt NPD GO	OSTC_BISPR	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.03	-	cyt	0	Secreted protein	extracellular region [ISS]			49
P02819 UniProt NPD GO	OSTC_MACFA	Osteocalcin (Gamma-carboxyglutamic acid-containing protein) (Bone Gla-protein) (BGP)	0.03	-	cyt	0	Secreted protein				49

You are viewing entries 80851 to 80900 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.