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
Q64349 UniProt NPD GO	MAL_RAT	Myelin and lymphocyte protein (T-lymphocyte maturation-associated protein) (17 kDa myelin vesicular ...	0.00	-	end	4 *	Membrane; multi-pass membrane protein	lipid raft [IDA] peripheral to membrane of membrane fraction [IDA]			153
P04116 UniProt NPD GO	MYPR_BOVIN	Myelin proteolipid protein (PLP) (Lipophilin)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				276
P23294 UniProt NPD GO	MYPR_CANFA	Myelin proteolipid protein (PLP) (Lipophilin)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				276
P60201 UniProt NPD GO	MYPR_HUMAN	Myelin proteolipid protein (PLP) (Lipophilin)	0.00	-	end	4 *	Membrane; multi-pass membrane protein		312920		276
Q8HXW7 UniProt NPD GO	MYPR_MACFA	Myelin proteolipid protein (PLP) (Lipophilin)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				276
P60202 UniProt NPD GO	MYPR_MOUSE	Myelin proteolipid protein (PLP) (Lipophilin)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				276
P47790 UniProt NPD GO	MYPR_POEGU	Myelin proteolipid protein (PLP) (Lipophilin)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				276
P47789 UniProt NPD GO	MYPR_RABIT	Myelin proteolipid protein (PLP) (Lipophilin)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				276
P60203 UniProt NPD GO	MYPR_RAT	Myelin proteolipid protein (PLP) (Lipophilin)	0.00	-	end	4 *	Membrane; multi-pass membrane protein	compact myelin [IMP] integral to plasma membrane [TAS]			276
P35801 UniProt NPD GO	MYPRA_XENLA	Myelin proteolipid protein A (PLP-A) (Lipophilin-A)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				280
P23290 UniProt NPD GO	MYPRB_XENLA	Myelin proteolipid protein B (PLP-B) (Lipophilin-B)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				280
P84477 UniProt NPD GO	MBSP_CYPCA	Myofibril-bound serine protease (EC 3.4.21.-) (MBSP) (Fragment)	0.00	-	cyt	0	Cytoplasm				22
P84478 UniProt NPD GO	MBSP_SAUUN	Myofibril-bound serine protease (EC 3.4.21.-) (MBSP) (Fragment)	0.00	-	cyt	0	Cytoplasm				22
P84476 UniProt NPD GO	MBSP_SAUWA	Myofibril-bound serine protease (EC 3.4.21.-) (MBSP) (Fragment)	0.00	-		0	Cytoplasm				10
Q6I7B0 UniProt NPD GO	MYG_AUXRO	Myoglobin	0.00	-	cyt	0					146
P02179 UniProt NPD GO	MYG_BALAC	Myoglobin	0.00	-	cyt	0					153
P02180 UniProt NPD GO	MYG_BALPH	Myoglobin	0.00	-	cyt	0					153
P02192 UniProt NPD GO	MYG_BOVIN	Myoglobin	0.00	-	cyt	0				1Z2S	153
Q6VN46 UniProt NPD GO	MYG_BRARE	Myoglobin	0.00	-	cyt	0					146
P63113 UniProt NPD GO	MYG_CANFA	Myoglobin	0.00	-	cyt	0					153
P02191 UniProt NPD GO	MYG_CEREL	Myoglobin	0.00	-	cyt	0					153
Q7T044 UniProt NPD GO	MYG_CHARH	Myoglobin	0.00	-	cyt	0					146
P87497 UniProt NPD GO	MYG_CHIRA	Myoglobin	0.00	-	cyt	0					146
Q9DEP0 UniProt NPD GO	MYG_CRYAN	Myoglobin	0.00	-	cyt	0					146
P20856 UniProt NPD GO	MYG_CTEGU	Myoglobin	0.00	-	cyt	0					153
P68276 UniProt NPD GO	MYG_DELDE	Myoglobin	0.00	-	cyt	0					153
P02174 UniProt NPD GO	MYG_GLOME	Myoglobin	0.00	-	cyt	0					153
Q9DEN9 UniProt NPD GO	MYG_GOBGI	Myoglobin	0.00	-	mit	0					146
P02181 UniProt NPD GO	MYG_INIGE	Myoglobin	0.00	-	cyt	0					153
Q9DGI8 UniProt NPD GO	MYG_KATPE	Myoglobin	0.00	-	cyt	0					145
P02159 UniProt NPD GO	MYG_LYCPI	Myoglobin	0.00	-	cyt	0					153
Q9DGJ1 UniProt NPD GO	MYG_MAKNI	Myoglobin	0.00	-	cyt	0					146
Q9DEN8 UniProt NPD GO	MYG_NOTCO	Myoglobin	0.00	-	cyt	0					146
Q6PL31 UniProt NPD GO	MYG_OCHCU	Myoglobin	0.00	-	mit	0					153
P02173 UniProt NPD GO	MYG_ORCOR	Myoglobin	0.00	-	cyt	0					153
P63114 UniProt NPD GO	MYG_OTOME	Myoglobin	0.00	-	cyt	0					153
P68277 UniProt NPD GO	MYG_PHODA	Myoglobin	0.00	-	cyt	0					153
P68278 UniProt NPD GO	MYG_PHOPH	Myoglobin	0.00	-	cyt	0					153
P02189 UniProt NPD GO	MYG_PIG	Myoglobin	0.00	-	cyt	0				1YCB	153
Q9DEP1 UniProt NPD GO	MYG_PSEGE	Myoglobin	0.00	-	mit	0					146
P02170 UniProt NPD GO	MYG_RABIT	Myoglobin	0.00	-	cyt	0					153
P02190 UniProt NPD GO	MYG_SHEEP	Myoglobin	0.00	-	cyt	0					153
Q701N9 UniProt NPD GO	MYG_TETNG	Myoglobin	0.00	-	mit	0					145
P68279 UniProt NPD GO	MYG_TURTR	Myoglobin	0.00	-	cyt	0					153
P02160 UniProt NPD GO	MYG_VULCH	Myoglobin	0.00	-	cyt	0					153
P49672 UniProt NPD GO	GLB2_ASCSU	Myoglobin (Globin, body wall isoform)	0.00	-	cyt	0	Cytoplasm				153
P51535 UniProt NPD GO	GLB2_NIPBR	Myoglobin (Globin, body wall isoform)	0.00	-	cyt	0	Cytoplasm (By similarity)				154
P53141 UniProt NPD GO	MLC1_YEAST	Myosin light chain 1 (Myosin-2 light chain) (Calmodulin-like myosin light chain MLC1)	0.00	-	cyt	0	Concentrates to sites of polarized growth, namely to the incipient bud site in G1, to the bud tip du ...	actin cap [IPI]		1N2D	149
P02605 UniProt NPD GO	MLE3_CHICK	Myosin light chain 3, skeletal muscle isoform (A2 catalytic) (Alkali myosin light chain 3) (MLC-3) ( ...	0.00	-	cyt	0				1O1G	149
P05978 UniProt NPD GO	MLE3_MOUSE	Myosin light chain 3, skeletal muscle isoform (A2 catalytic) (Alkali myosin light chain 3) (MLC3F)	0.00	-	cyt	0					149

You are viewing entries 95701 to 95750 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.