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
P05718 UniProt NPD GO	CYB_VICFA	Cytochrome b	0.01	-	end	9 *					392
Q9B6D0 UniProt NPD GO	CYB_YARLI	Cytochrome b	0.01	-	end	8 *					385
P92845 UniProt NPD GO	CYB_AGKCO	Cytochrome b (Fragment)	0.01	-	end	5 *					214
P92852 UniProt NPD GO	CYB_AGKHA	Cytochrome b (Fragment)	0.01	-	end	5 *					214
Q31684 UniProt NPD GO	CYB_ANOCU	Cytochrome b (Fragment)	0.01	-	end	3 *					134
P92846 UniProt NPD GO	CYB_BOTAT	Cytochrome b (Fragment)	0.01	-	end	5 *					214
P92849 UniProt NPD GO	CYB_BOTSC	Cytochrome b (Fragment)	0.01	-	end	5 *					214
P82049 UniProt NPD GO	CYB_CERNA	Cytochrome b (Fragment)	0.01	-	end	4 *					154
P82048 UniProt NPD GO	CYB_CERNH	Cytochrome b (Fragment)	0.01	-	end	4 *					154
P82047 UniProt NPD GO	CYB_CERNN	Cytochrome b (Fragment)	0.01	-	end	4 *					149
P82046 UniProt NPD GO	CYB_CERNP	Cytochrome b (Fragment)	0.01	-	end	4 *					154
P82045 UniProt NPD GO	CYB_CERNT	Cytochrome b (Fragment)	0.01	-	end	4 *					153
Q34254 UniProt NPD GO	CYB_CHISL	Cytochrome b (Fragment)	0.01	-	end	3 *					134
Q34260 UniProt NPD GO	CYB_CHITR	Cytochrome b (Fragment)	0.01	-	end	3 *					134
P69219 UniProt NPD GO	CYB_CICCE	Cytochrome b (Fragment)	0.01	-	cyt	1 *					79
P69220 UniProt NPD GO	CYB_CICCT	Cytochrome b (Fragment)	0.01	-	cyt	1 *					79
P69221 UniProt NPD GO	CYB_CICLA	Cytochrome b (Fragment)	0.01	-	cyt	1 *					79
P16366 UniProt NPD GO	CYB_CICNI	Cytochrome b (Fragment)	0.01	-	cyt	1 *					79
P92850 UniProt NPD GO	CYB_CROAT	Cytochrome b (Fragment)	0.01	-	end	5 *					214
Q95776 UniProt NPD GO	CYB_CROVV	Cytochrome b (Fragment)	0.01	-	mit	3 *					128
P87416 UniProt NPD GO	CYB_ELASE	Cytochrome b (Fragment)	0.01	-	end	5 *					214
P29666 UniProt NPD GO	CYB_GOMVA	Cytochrome b (Fragment)	0.01	-	exc	3 *					95
P16367 UniProt NPD GO	CYB_JULRE	Cytochrome b (Fragment)	0.01	-	cyt	1 *					79
P29668 UniProt NPD GO	CYB_MEGAT	Cytochrome b (Fragment)	0.01	-	exc	3 *					102
Q36291 UniProt NPD GO	CYB_MORKA	Cytochrome b (Fragment)	0.01	-	end	3 *					176
Q35117 UniProt NPD GO	CYB_NYCAU	Cytochrome b (Fragment)	0.01	-	end	4 *					176
Q36572 UniProt NPD GO	CYB_NYCHU	Cytochrome b (Fragment)	0.01	-	end	3 *					176
P29669 UniProt NPD GO	CYB_POLSX	Cytochrome b (Fragment)	0.01	-	end	3 *					100
P29670 UniProt NPD GO	CYB_POMNI	Cytochrome b (Fragment)	0.01	-	nuc	2 *					85
P16362 UniProt NPD GO	CYB_POMSU	Cytochrome b (Fragment)	0.01	-	cyt	1 *					79
P29640 UniProt NPD GO	CYB_PTIPL	Cytochrome b (Fragment)	0.01	-	end	8 *					308
P29672 UniProt NPD GO	CYB_SCAPL	Cytochrome b (Fragment)	0.01	-	end	3 *					98
P29641 UniProt NPD GO	CYB_SCYMA	Cytochrome b (Fragment)	0.01	-	end	8 *					308
Q35994 UniProt NPD GO	CYB_TADBR	Cytochrome b (Fragment)	0.01	-	end	4 *					176
P29642 UniProt NPD GO	CYB_THRDO	Cytochrome b (Fragment)	0.01	-	end	8 *					308
P00163 UniProt NPD GO	CYB_YEAST	Cytochrome b (Ubiquinol-cytochrome-c reductase complex cytochrome b subunit) (Complex III subunit CY ...	0.01	-	end	9 *		respiratory chain complex III (sensu Eukary... [IDA]		1P84	385
O04354 UniProt NPD GO	CYB5_BOROF	Cytochrome b5	0.01	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				132
P40934 UniProt NPD GO	CYB5_BRAOB	Cytochrome b5	0.01	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				134
Q874I5 UniProt NPD GO	CYB5_CANTR	Cytochrome b5	0.01	-	cyt	1					129
P00174 UniProt NPD GO	CYB5_CHICK	Cytochrome b5	0.01	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				138
P49097 UniProt NPD GO	CYB5_CUSRE	Cytochrome b5	0.01	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				135
P49100 UniProt NPD GO	CYB5_ORYSA	Cytochrome b5	0.01	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				137
P00169 UniProt NPD GO	CYB5_RABIT	Cytochrome b5	0.01	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...			1DO9	133
P49098 UniProt NPD GO	CYB5_TOBAC	Cytochrome b5	0.01	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				136
P49096 UniProt NPD GO	CYB5_MUSDO	Cytochrome b5 (CYTB5)	0.01	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				134
Q42342 UniProt NPD GO	CYB51_ARATH	Cytochrome b5 isoform 1	0.01	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				134
P04166 UniProt NPD GO	CYB5B_RAT	Cytochrome b5 type B precursor (Cytochrome b5 outer mitochondrial membrane isoform)	0.01	-	cyt	1	Mitochondrion; mitochondrial outer membrane			1LJ0	146
Q85C42 UniProt NPD GO	PSBE_ANTFO	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
Q8M9W8 UniProt NPD GO	PSBE_CHAGL	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P56309 UniProt NPD GO	PSBE_CHLVU	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.01	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				83

You are viewing entries 87601 to 87650 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.