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
Q27666 UniProt NPD GO	SODC_HAECO	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				159
P81926 UniProt NPD GO	SODC_HALRO	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				151
Q07796 UniProt NPD GO	SODC_IPOBA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	exc	0	Cytoplasm				151
Q6T3B0 UniProt NPD GO	SODC_PAESI	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm (By similarity)				153
O22668 UniProt NPD GO	SODC_PANGI	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	vac	0	Cytoplasm				152
O49073 UniProt NPD GO	SODC_PAUKA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				152
P04178 UniProt NPD GO	SODC_PIG	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				152
P11418 UniProt NPD GO	SODC_PRIGL	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				152
P09212 UniProt NPD GO	SODC_RABIT	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				152
Q01137 UniProt NPD GO	SODC_SCHMA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm			1TO5	153
P28758 UniProt NPD GO	SODC_SCHPO	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				154
P09670 UniProt NPD GO	SODC_SHEEP	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				151
Q7M1R5 UniProt NPD GO	SODC_SOYBN	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	mit	0	Cytoplasm (By similarity)				152
P03946 UniProt NPD GO	SODC_XIPGL	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				151
O65174 UniProt NPD GO	SODC_ZANAE	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				152
P80740 UniProt NPD GO	SODC_OLEEU	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) (Allergen Ole e 5) (Ole e V) (Fragment)	0.00	-	cyt	0					29
P54407 UniProt NPD GO	SODC_DROBS	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) (Fragment)	0.00	-	cyt	0	Cytoplasm (By similarity)				145
Q95081 UniProt NPD GO	SODC_DROMD	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) (Fragment)	0.00	-	cyt	0	Cytoplasm				114
Q95079 UniProt NPD GO	SODC_DROMI	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) (Fragment)	0.00	-	cyt	0	Cytoplasm				114
Q95087 UniProt NPD GO	SODC_DROPB	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) (Fragment)	0.00	-	cyt	0	Cytoplasm				114
Q95088 UniProt NPD GO	SODC_DROPE	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) (Fragment)	0.00	-	cyt	0	Cytoplasm				114
Q95095 UniProt NPD GO	SODC_DROTO	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) (Fragment)	0.00	-	cyt	0	Cytoplasm				114
P34936 UniProt NPD GO	SODC_HORVU	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) (Fragment)	0.00	-	cyt	0	Cytoplasm				21
P81036 UniProt NPD GO	SODC_LAMCR	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) (Fragment)	0.00	-	cyt	0	Cytoplasm				138
P83129 UniProt NPD GO	SODC_PAROL	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) (Fragment)	0.00	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [TAS]			25
P23417 UniProt NPD GO	SODC_RANCA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) (Fragment)	0.00	-	cyt	0	Cytoplasm				24
P81163 UniProt NPD GO	SODC_STRHE	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) (Fragments)	0.00	-	cyt	0	Cytoplasm (By similarity)				31
Q42611 UniProt NPD GO	SODC1_BRAJU	Superoxide dismutase [Cu-Zn] 1 (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				151
O42724 UniProt NPD GO	SODC1_DEBHA	Superoxide dismutase [Cu-Zn] 1 (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				153
Q42612 UniProt NPD GO	SODC2_BRAJU	Superoxide dismutase [Cu-Zn] 2 (EC 1.15.1.1)	0.00	-	cyt	0	Cytoplasm				151
P82902 UniProt NPD GO	SODC2_DEBHA	Superoxide dismutase [Cu-Zn] 2 (EC 1.15.1.1) (Fragments)	0.00	-	cyt	0	Cytoplasm				52
P29428 UniProt NPD GO	SODC2_PICAB	Superoxide dismutase [Cu-Zn] 2 (EC 1.15.1.1) (Superoxide dismutase [Cu-Zn] II) (SOD II) (Fragment)	0.00	-	cyt	0	Cytoplasm				21
P13926 UniProt NPD GO	SODC1_XENLA	Superoxide dismutase [Cu-Zn] A (EC 1.15.1.1) (xSODA)	0.00	-	cyt	0	Cytoplasm				150
P15107 UniProt NPD GO	SODC2_XENLA	Superoxide dismutase [Cu-Zn] B (EC 1.15.1.1) (xSODB)	0.00	-	cyt	0	Cytoplasm			1XSO	150
P29427 UniProt NPD GO	SODCP_PICAB	Superoxide dismutase [Cu-Zn], chloroplast (EC 1.15.1.1) (SOD I) (Fragment)	0.00	-	exc	0	Plastid; chloroplast				23
P21276 UniProt NPD GO	SODF_ARATH	Superoxide dismutase [Fe], chloroplast precursor (EC 1.15.1.1)	0.00	-	cyt	0	Plastid; chloroplast; chloroplast membrane				212
P83289 UniProt NPD GO	SODM_ARTDA	Superoxide dismutase [Mn/Fe] (EC 1.15.1.1) (Fragment)	0.00	-		0					13
P28524 UniProt NPD GO	SODM_HORVU	Superoxide dismutase [Mn], mitochondrial (EC 1.15.1.1) (Fragment)	0.00	-		0	Mitochondrion; mitochondrial matrix				20
P28765 UniProt NPD GO	SODM_PALVU	Superoxide dismutase [Mn], mitochondrial (EC 1.15.1.1) (Fragment)	0.00	-	cyt	0	Mitochondrion; mitochondrial matrix				144
Q42684 UniProt NPD GO	SODM_CHLRE	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.00	-	nuc	0	Mitochondrion; mitochondrial matrix (By similarity)				218
O17528 UniProt NPD GO	SEL9_CAEEL	Suppressor/enhancer of lin-12 protein 9 precursor	0.00	-	end	2 *	Type I membrane protein. Golgi-derived coatomer-coated vesicles	ER to Golgi transport vesicle membrane [NAS]			203
P81545 UniProt NPD GO	SP34_DICMU	Surface protein P34 (Fragment)	0.00	-		0	Macrocyst primary wall				10
O57590 UniProt NPD GO	SURF4_FUGRU	Surfeit locus protein 4	0.00	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				269
O15260 UniProt NPD GO	SURF4_HUMAN	Surfeit locus protein 4	0.00	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	ER-Golgi intermediate compartment [IDA]	185660		269
Q64310 UniProt NPD GO	SURF4_MOUSE	Surfeit locus protein 4	0.00	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				269
O18405 UniProt NPD GO	SURF4_DROME	Surfeit locus protein 4 homolog	0.00	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				270
Q755L7 UniProt NPD GO	SVF1_ASHGO	Survival factor 1	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				385
P0C1R2 UniProt NPD GO	SYLV_PROSY	Sylverin	0.00	-	nuc	0	Secreted protein				22
O09117 UniProt NPD GO	SYPL1_MOUSE	Synaptophysin-like protein 1 (Pantophysin)	0.00	-	end	3	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein. Cytoplasmic transpor ...	membrane [IDA] secretory granule [IDA]			261
P17696 UniProt NPD GO	TSYL_DENAN	Synergistic-like venom protein precursor	0.00	-	mit	1 *	Secreted protein				86

You are viewing entries 98151 to 98200 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.