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
O49203 UniProt NPD GO	NDK3_ARATH	Nucleoside diphosphate kinase III, chloroplast/mitochondrial precursor (EC 2.7.4.6) (NDK III) (NDP k ...	0.08	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen. Mitochondrion; mitochondrial intermembrane space				238
Q9CR24 UniProt NPD GO	NUDT8_MOUSE	Nucleoside diphosphate-linked moiety X motif 8, mitochondrial precursor (EC 3.6.1.-) (Nudix motif 8) ...	0.08	-	mit	0	Mitochondrion	mitochondrion [IDA]			210
Q93ZY7 UniProt NPD GO	NUD12_ARATH	Nudix hydrolase 12, mitochondrial precursor (EC 3.6.1.-) (AtNUDT12)	0.08	-	cyt	0	Mitochondrion (Potential)				203
Q23236 UniProt NPD GO	NDX3_CAEEL	Nudix hydrolase 3 (EC 3.6.1.-)	0.08	-	cyt	0					188
P29527 UniProt NPD GO	OLEO6_GOSHI	Oleosin 18.2 kDa	0.08	-	end	3 *	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface (By similarity)				168
Q60883 UniProt NPD GO	OLF10_MOUSE	Olfactory receptor 10 (Odorant receptor L45)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				311
Q8VFK1 UniProt NPD GO	O1009_MOUSE	Olfactory receptor 1009 (Olfactory receptor 175-3)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				314
Q8VFL9 UniProt NPD GO	O1086_MOUSE	Olfactory receptor 1086 (Olfactory receptor 179-2)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				310
Q96KK4 UniProt NPD GO	O10C1_HUMAN	Olfactory receptor 10C1 (Hs6M1-17)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				312
P30954 UniProt NPD GO	O10J1_HUMAN	Olfactory receptor 10J1 (Olfactory receptor-like protein HGMP07J) (Olfactory receptor OR1-26)	0.08	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			320
Q8NGY7 UniProt NPD GO	O10J6_HUMAN	Olfactory receptor 10J6	0.08	-	end	6 *	Membrane; multi-pass membrane protein				276
Q8NGC1 UniProt NPD GO	O11G2_HUMAN	Olfactory receptor 11G2	0.08	-	end	7 *	Membrane; multi-pass membrane protein				311
P23273 UniProt NPD GO	O1500_RAT	Olfactory receptor 1500 (Olfactory receptor-like protein I14)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				312
Q9TU94 UniProt NPD GO	OR1E1_GORGO	Olfactory receptor 1E1	0.08	-	end	6 *	Membrane; multi-pass membrane protein				314
Q9TUA9 UniProt NPD GO	OR1E1_PANTR	Olfactory receptor 1E1	0.08	-	end	6 *	Membrane; multi-pass membrane protein				314
Q8NGR2 UniProt NPD GO	OR1L6_HUMAN	Olfactory receptor 1L6	0.08	-	end	7 *	Membrane; multi-pass membrane protein				311
Q96R47 UniProt NPD GO	O2A14_HUMAN	Olfactory receptor 2A14 (OST182)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				310
Q8NGT9 UniProt NPD GO	O2A42_HUMAN	Olfactory receptor 2A42	0.08	-	end	6 *	Membrane; multi-pass membrane protein				310
Q8NGE2 UniProt NPD GO	O2AP1_HUMAN	Olfactory receptor 2AP1 (Olfactory receptor OR12-9)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				309
Q8NGZ5 UniProt NPD GO	OR2G2_HUMAN	Olfactory receptor 2G2 (Olfactory receptor OR1-32)	0.08	-	end	6 *	Membrane; multi-pass membrane protein				317
Q5TZ20 UniProt NPD GO	OR2G6_HUMAN	Olfactory receptor 2G6	0.08	-	end	7 *	Membrane; multi-pass membrane protein				316
Q8N349 UniProt NPD GO	OR2LD_HUMAN	Olfactory receptor 2L13	0.08	-	end	7 *	Membrane; multi-pass membrane protein				312
Q8NGZ9 UniProt NPD GO	O2T10_HUMAN	Olfactory receptor 2T10 (Olfactory receptor OR1-64)	0.08	-	end	6 *	Membrane; multi-pass membrane protein				312
Q8NH01 UniProt NPD GO	O2T11_HUMAN	Olfactory receptor 2T11 (Olfactory receptor OR1-65)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				316
Q8NG76 UniProt NPD GO	O2T33_HUMAN	Olfactory receptor 2T33 (Olfactory receptor OR1-56)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				320
Q6IEZ7 UniProt NPD GO	OR2T5_HUMAN	Olfactory receptor 2T5 (Olfactory receptor OR1-62)	0.08	-	end	6 *	Membrane; multi-pass membrane protein				315
Q8NGC2 UniProt NPD GO	OR4E2_HUMAN	Olfactory receptor 4E2 (Olfactory receptor OR14-42)	0.08	-	end	6 *	Membrane; multi-pass membrane protein				313
Q8NGI1 UniProt NPD GO	O56B2_HUMAN	Olfactory receptor 56B2	0.08	-	end	5 *	Membrane; multi-pass membrane protein				322
Q8NH89 UniProt NPD GO	O5AK3_HUMAN	Olfactory receptor 5AK3	0.08	-	end	7 *	Membrane; multi-pass membrane protein				298
Q8NGP3 UniProt NPD GO	OR5M9_HUMAN	Olfactory receptor 5M9 (Olfactory receptor OR11-190)	0.08	-	end	6 *	Membrane; multi-pass membrane protein				310
Q8NGE1 UniProt NPD GO	OR6C4_HUMAN	Olfactory receptor 6C4	0.08	-	end	7 *	Membrane; multi-pass membrane protein				309
O14581 UniProt NPD GO	OR7AH_HUMAN	Olfactory receptor 7A17	0.08	-	end	7 *	Membrane; multi-pass membrane protein				309
Q8NG99 UniProt NPD GO	OR7G2_HUMAN	Olfactory receptor 7G2 (Olfactory receptor 19-13) (OR19-13) (OST260)	0.08	-	end	8 *	Membrane; multi-pass membrane protein				324
Q95154 UniProt NPD GO	OLF1_CANFA	Olfactory receptor-like protein OLF1	0.08	-	end	7 *	Membrane; multi-pass membrane protein				311
Q95157 UniProt NPD GO	OLF4_CANFA	Olfactory receptor-like protein OLF4	0.08	-	end	7 *	Membrane; multi-pass membrane protein				309
Q9ES07 UniProt NPD GO	S15A2_MOUSE	Oligopeptide transporter, kidney isoform (Peptide transporter 2) (Kidney H(+)/peptide cotransporter) ...	0.08	-	end	11	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA] membrane fraction [IDA]			729
P46029 UniProt NPD GO	S15A2_RABIT	Oligopeptide transporter, kidney isoform (Peptide transporter 2) (Kidney H(+)/peptide cotransporter) ...	0.08	-	end	11	Membrane; multi-pass membrane protein				729
Q63424 UniProt NPD GO	S15A2_RAT	Oligopeptide transporter, kidney isoform (Peptide transporter 2) (Kidney H(+)/peptide cotransporter) ...	0.08	-	end	11	Membrane; multi-pass membrane protein				729
P51574 UniProt NPD GO	S15A1_RAT	Oligopeptide transporter, small intestine isoform (Peptide transporter 1) (Intestinal H(+)/peptide c ...	0.08	-	end	11 *	Membrane; multi-pass membrane protein				710
P48625 UniProt NPD GO	FAD3E_SOYBN	Omega-3 fatty acid desaturase, endoplasmic reticulum (EC 1.14.19.-)	0.08	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				380
P58916 UniProt NPD GO	CXO7A_CONCN	Omega-conotoxin CnVIIA	0.08	-	nuc	0	Secreted protein				27
P84093 UniProt NPD GO	TOPC5_PHONI	Omega-phonetoxin PNTx22C5 (Fragment)	0.08	-	nuc	0	Secreted protein				80
P22085 UniProt NPD GO	CYTX_ONCVO	Onchocystatin precursor (Cysteine proteinase inhibitor OV7)	0.08	-	vac	0					162
P32930 UniProt NPD GO	ONCO_HUMAN	Oncomodulin (OM) (Parvalbumin beta)	0.08	-	cyt	0			164795	1TTX	108
P08255 UniProt NPD GO	OPS4_DROME	Opsin Rh4 (Inner R7 photoreceptor cells opsin)	0.08	-	end	7	Membrane; multi-pass membrane protein				378
P29404 UniProt NPD GO	OPS4_DROPS	Opsin Rh4 (Inner R7 photoreceptor cells opsin)	0.08	-	end	7	Membrane; multi-pass membrane protein				380
Q9H015 UniProt NPD GO	S22A4_HUMAN	Organic cation/carnitine transporter 1 (Solute carrier family 22 member 4) (Ergothioneine transporte ...	0.08	-	end	11 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	604190		551
O70594 UniProt NPD GO	S22A5_RAT	Organic cation/carnitine transporter 2 (Solute carrier family 22 member 5) (High-affinity sodium-dep ...	0.08	-	end	11 *	Membrane; multi-pass membrane protein				557
Q9WTN6 UniProt NPD GO	OCTN3_MOUSE	Organic cation/carnitine transporter 3 (Solute carrier family 22 member 21) (Solute carrier family 2 ...	0.08	-	end	10 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein	intrinsic to peroxisomal membrane [IDA]			564
P25510 UniProt NPD GO	ORN3_PLAOR	Ornatin-A3	0.08	-	nuc	0	Secreted protein				41

You are viewing entries 68551 to 68600 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.