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
P80566 UniProt NPD GO	SODC_CHICK	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				153
O94178 UniProt NPD GO	SODC_COLGL	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	nuc	0	Cytoplasm (By similarity)				153
Q9C0N4 UniProt NPD GO	SODC_CRYGA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm (By similarity)				153
P41973 UniProt NPD GO	SODC_DROWI	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				152
P00443 UniProt NPD GO	SODC_HORSE	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				153
P07509 UniProt NPD GO	SODC_NEUCR	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				153
P27082 UniProt NPD GO	SODC_NICPL	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	exc	0	Cytoplasm				151
P24706 UniProt NPD GO	SODC_ONCVO	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				158
Q02610 UniProt NPD GO	SODC_PEA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				151
Q711T9 UniProt NPD GO	SODC_PODAN	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm (By similarity)				153
O04996 UniProt NPD GO	SODC_SOLCS	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	exc	0	Cytoplasm				152
P22233 UniProt NPD GO	SODC_SPIOL	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	exc	0	Cytoplasm				152
P00445 UniProt NPD GO	SODC_YEAST	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm. A small percentage (around 1-5 percent) localizes to the mitochondrial intermembrane spac ...	cytosol [IDA] mitochondrial intermembrane space [IDA]		2JCW	153
Q12548 UniProt NPD GO	SODC_ASPJA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) (Fragment)	0.01	-	nuc	0	Cytoplasm				120
Q95085 UniProt NPD GO	SODC_DROOB	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1) (Fragment)	0.01	-	cyt	0	Cytoplasm				114
P14830 UniProt NPD GO	SODC1_LYCES	Superoxide dismutase [Cu-Zn] 1 (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				151
P93258 UniProt NPD GO	SODC1_MESCR	Superoxide dismutase [Cu-Zn] 1 (EC 1.15.1.1)	0.01	-	exc	0	Cytoplasm				152
P28756 UniProt NPD GO	SODC1_ORYSA	Superoxide dismutase [Cu-Zn] 1 (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				151
Q43779 UniProt NPD GO	SODC2_LYCES	Superoxide dismutase [Cu-Zn] 2 (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				151
P11428 UniProt NPD GO	SODC2_MAIZE	Superoxide dismutase [Cu-Zn] 2 (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				150
P28757 UniProt NPD GO	SODC2_ORYSA	Superoxide dismutase [Cu-Zn] 2 (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				151
P23345 UniProt NPD GO	SODC4_MAIZE	Superoxide dismutase [Cu-Zn] 4A (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				151
P23346 UniProt NPD GO	SODC5_MAIZE	Superoxide dismutase [Cu-Zn] 4AP (EC 1.15.1.1)	0.01	-	cyt	0	Cytoplasm				151
P24707 UniProt NPD GO	SODCP_PINSY	Superoxide dismutase [Cu-Zn], chloroplast (EC 1.15.1.1) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				141
O78310 UniProt NPD GO	SODCP_ARATH	Superoxide dismutase [Cu-Zn], chloroplast precursor (EC 1.15.1.1)	0.01	-	mit	0	Plastid; chloroplast				216
P14831 UniProt NPD GO	SODCP_LYCES	Superoxide dismutase [Cu-Zn], chloroplast precursor (EC 1.15.1.1)	0.01	-	mit	0	Plastid; chloroplast				217
P93407 UniProt NPD GO	SODCP_ORYSA	Superoxide dismutase [Cu-Zn], chloroplast precursor (EC 1.15.1.1)	0.01	-	mit	0	Plastid; chloroplast				211
P11964 UniProt NPD GO	SODCP_PEA	Superoxide dismutase [Cu-Zn], chloroplast precursor (EC 1.15.1.1)	0.01	-	mit	0	Plastid; chloroplast				202
P10792 UniProt NPD GO	SODCP_PETHY	Superoxide dismutase [Cu-Zn], chloroplast precursor (EC 1.15.1.1)	0.01	-	mit	0	Plastid; chloroplast				219
O04997 UniProt NPD GO	SODCP_SOLCS	Superoxide dismutase [Cu-Zn], chloroplast precursor (EC 1.15.1.1)	0.01	-	mit	0	Plastid; chloroplast				220
O65199 UniProt NPD GO	SODCP_VITVI	Superoxide dismutase [Cu-Zn], chloroplast precursor (EC 1.15.1.1)	0.01	-	mit	0	Plastid; chloroplast				212
O65175 UniProt NPD GO	SODCP_ZANAE	Superoxide dismutase [Cu-Zn], chloroplast precursor (EC 1.15.1.1)	0.01	-	mit	0	Plastid; chloroplast				216
P19666 UniProt NPD GO	SODF_TETPY	Superoxide dismutase [Fe] (EC 1.15.1.1)	0.01	-	cyt	0					196
P09233 UniProt NPD GO	SODM1_MAIZE	Superoxide dismutase [Mn] 3.1, mitochondrial precursor (EC 1.15.1.1)	0.01	-	mit	0	Mitochondrion; mitochondrial matrix				235
P28761 UniProt NPD GO	SODM_BRAFL	Superoxide dismutase [Mn], mitochondrial (EC 1.15.1.1) (Fragment)	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix				144
P54712 UniProt NPD GO	SODM_CANFA	Superoxide dismutase [Mn], mitochondrial (EC 1.15.1.1) (Fragment)	0.01	-		0	Mitochondrion; mitochondrial matrix				13
P36215 UniProt NPD GO	SODM_RANCA	Superoxide dismutase [Mn], mitochondrial (EC 1.15.1.1) (Fragment)	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix				23
Q877B6 UniProt NPD GO	SODM_ASPOR	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.01	-	exc	0	Mitochondrion; mitochondrial matrix (By similarity)				210
Q5ABA2 UniProt NPD GO	SVF1_CANAL	Survival factor 1	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				382
Q6FY35 UniProt NPD GO	SVF1_CANGA	Survival factor 1	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				443
Q6BIH2 UniProt NPD GO	SVF1_DEBHA	Survival factor 1	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				376
Q4ICI6 UniProt NPD GO	SVF1_GIBZE	Survival factor 1	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				377
Q6CQY2 UniProt NPD GO	SVF1_KLULA	Survival factor 1	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				403
Q99536 UniProt NPD GO	VAT1_HUMAN	Synaptic vesicle membrane protein VAT-1 homolog (EC 1.-.-.-)	0.01	-	cyt	0		integral to membrane [TAS]	604631		393
Q62465 UniProt NPD GO	VAT1_MOUSE	Synaptic vesicle membrane protein VAT-1 homolog (EC 1.-.-.-)	0.01	-	cyt	0					406
O43760 UniProt NPD GO	SNG2_HUMAN	Synaptogyrin-2 (Cellugyrin)	0.01	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	603926		224
O54980 UniProt NPD GO	SNG2_RAT	Synaptogyrin-2 (Cellugyrin)	0.01	-	end	4 *	Membrane; multi-pass membrane protein				224
P07825 UniProt NPD GO	SYPH_RAT	Synaptophysin (Major synaptic vesicle protein p38)	0.01	-	end	4 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein	integral to synaptic vesicle membrane [TAS] synaptic vesicle [IDA]			307
Q62277 UniProt NPD GO	SYPH_MOUSE	Synaptophysin (Major synaptic vesicle protein p38) (BM89 antigen)	0.01	-	end	3 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)	integral to synaptic vesicle membrane [TAS] synapse [IDA] synaptosome [IDA]			314
Q8TBG9 UniProt NPD GO	SYNPR_HUMAN	Synaptoporin	0.01	-	end	4 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)				265

You are viewing entries 91601 to 91650 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.