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
Q8TAV4 UniProt NPD GO	STML3_HUMAN	Stomatin-like protein 3	0.03	-	end	1 *	Cell membrane; single-pass type III membrane protein (By similarity). Detected in lipid rafts (By si ...		608327		291
Q41112 UniProt NPD GO	SRP_PHAVU	Stress-related protein (PvSRP)	0.03	-	cyt	0					167
P94111 UniProt NPD GO	STS1_ARATH	Strictosidine synthase 1 precursor (EC 4.3.3.2) (SS-1)	0.03	-	vac	0	Vacuole (By similarity)				335
Q9ESP1 UniProt NPD GO	SDF2L_MOUSE	Stromal cell-derived factor 2-like protein 1 precursor (SDF2-like protein 1)	0.03	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				221
Q9HCN8 UniProt NPD GO	SDF2L_HUMAN	Stromal cell-derived factor 2-like protein 1 precursor (SDF2-like protein 1) (PWP1-interacting prote ...	0.03	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)		607551		221
P28499 UniProt NPD GO	TKNA_ONCMY	Substance P	0.03	-		0	Secreted protein				11
P81712 UniProt NPD GO	ICI1_CANLI	Subtilisin inhibitor CLSI-I	0.03	-	cyt	0	Secreted protein				65
P16063 UniProt NPD GO	ICIB_HORVU	Subtilisin-chymotrypsin inhibitor CI-1B	0.03	-	cyt	0					83
P41956 UniProt NPD GO	C560_CAEEL	Succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor	0.03	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				182
P51650 UniProt NPD GO	SSDH_RAT	Succinate semialdehyde dehydrogenase (EC 1.2.1.24) (NAD(+)-dependent succinic semialdehyde dehydroge ...	0.03	-	cyt	0		mitochondrion [ISS]			488
P51649 UniProt NPD GO	SSDH_HUMAN	Succinate semialdehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.24) (NAD(+)-dependent succin ...	0.03	-	mit	0		mitochondrion [TAS]	271980		535
O82662 UniProt NPD GO	SUCB_ARATH	Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial precursor (EC 6.2.1.4) (Succinyl-CoA syn ...	0.03	-	mit	0	Mitochondrion				421
Q9Z2I8 UniProt NPD GO	SUCB2_MOUSE	Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial precursor (EC 6.2.1.4) (Succinyl-CoA syn ...	0.03	-	cyt	0	Mitochondrion	mitochondrion [IDA]			433
Q94522 UniProt NPD GO	SUCA_DROME	Succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial precursor (EC 6.2.1.4) (Succinyl-CoA ...	0.03	-	nuc	0	Mitochondrion				328
P56729 UniProt NPD GO	SUIS_PIG	Sucrase-isomaltase, intestinal [Contains: Sucrase (EC 3.2.1.48); Isomaltase (EC 3.2.1.10)] (Fragment ...	0.03	-	end	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Brush border (By similarity)				61
Q03411 UniProt NPD GO	SUT_SPIOL	Sucrose transport protein (Sucrose permease) (Sucrose-proton symporter)	0.03	-	end	12 *	Membrane; multi-pass membrane protein				525
Q8R0F3 UniProt NPD GO	SUMF1_MOUSE	Sulfatase-modifying factor 1 precursor (C-alpha-formyglycine-generating enzyme 1)	0.03	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum [IDA]			372
P07850 UniProt NPD GO	SUOX_CHICK	Sulfite oxidase (EC 1.8.3.1)	0.03	-	nuc	0	Mitochondrion; mitochondrial intermembrane space			2A9D	459
Q60HD0 UniProt NPD GO	SUOX_MACFA	Sulfite oxidase, mitochondrial precursor (EC 1.8.3.1)	0.03	-	cyt	0	Mitochondrion; mitochondrial intermembrane space				488
P63046 UniProt NPD GO	ST4A1_MOUSE	Sulfotransferase 4A1 (EC 2.8.2.-) (Brain sulfotransferase-like protein) (mBR-STL) (Nervous system su ...	0.03	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [TAS]			284
P63047 UniProt NPD GO	ST4A1_RAT	Sulfotransferase 4A1 (EC 2.8.2.-) (Brain sulfotransferase-like protein) (rBR-STL) (Nervous system su ...	0.03	-	cyt	0	Cytoplasm				284
Q75DD6 UniProt NPD GO	CCS1_ASHGO	Superoxide dismutase 1 copper chaperone	0.03	-	nuc	0	Cytoplasm (By similarity)				238
Q751L8 UniProt NPD GO	SODC_ASHGO	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.03	-	cyt	0	Cytoplasm (By similarity)				153
Q8HXP8 UniProt NPD GO	SODC_CALJA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.03	-	cyt	0	Cytoplasm (By similarity)				153
Q8HXP9 UniProt NPD GO	SODC_CEBAP	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.03	-	cyt	0	Cytoplasm (By similarity)				153
Q8J0N2 UniProt NPD GO	SODC_CORMI	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.03	-	cyt	0	Cytoplasm (By similarity)				153
Q8HXQ3 UniProt NPD GO	SODC_HYLLA	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.03	-	cyt	0	Cytoplasm (By similarity)				153
P08228 UniProt NPD GO	SODC_MOUSE	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.03	-	cyt	0	Cytoplasm	cytoplasm [TAS] mitochondrion [IDA]			153
Q8J0N3 UniProt NPD GO	SODC_PAETN	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.03	-	cyt	0	Cytoplasm (By similarity)				153
P07632 UniProt NPD GO	SODC_RAT	Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)	0.03	-	cyt	0	Cytoplasm				153
P07505 UniProt NPD GO	SODCP_SPIOL	Superoxide dismutase [Cu-Zn], chloroplast precursor (EC 1.15.1.1)	0.03	-	mit	0	Plastid; chloroplast			1SRD	222
P22302 UniProt NPD GO	SODF_NICPL	Superoxide dismutase [Fe], chloroplast (EC 1.15.1.1) (Fragment)	0.03	-	cyt	0	Plastid; chloroplast				202
Q43008 UniProt NPD GO	SODM_ORYSA	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.03	-	vac	0	Mitochondrion; mitochondrial matrix				231
P41982 UniProt NPD GO	SODM_RABIT	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1) (Fragment)	0.03	-	cyt	0	Mitochondrion; mitochondrial matrix				202
O43761 UniProt NPD GO	SNG3_HUMAN	Synaptogyrin-3	0.03	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	603927		229
Q8R191 UniProt NPD GO	SNG3_MOUSE	Synaptogyrin-3	0.03	-	end	4 *	Membrane; multi-pass membrane protein				229
O89104 UniProt NPD GO	SYPL2_MOUSE	Synaptophysin-like protein 2 (Mitsugumin-29) (Mg29)	0.03	-	end	3 *	Integral membrane protein. Triad junction; the junctional complex between the transverse tubule and ...				264
O62646 UniProt NPD GO	SYPL2_RABIT	Synaptophysin-like protein 2 (Mitsugumin-29) (Mg29)	0.03	-	end	4 *	Integral membrane protein. Triad junction; the junctional complex between the transverse tubule and ...				264
P01410 UniProt NPD GO	TS821_DENAN	Synergistic-type venom protein C8S2, chain 1	0.03	-	nuc	0	Secreted protein				62
Q99JZ0 UniProt NPD GO	SDCB2_MOUSE	Syntenin-2 (Syndecan-binding protein 2)	0.03	-	cyt	0		cytoplasm [ISS] plasma membrane [ISS]			292
P01737 UniProt NPD GO	TVA3_HUMAN	T-cell receptor alpha chain V region PY14 precursor	0.03	-	mit	0		plasma membrane [NAS]		1J8H	135
P01853 UniProt NPD GO	TCC1_MOUSE	T-cell receptor gamma chain C region C10.5	0.03	-	nuc	1					167
P03985 UniProt NPD GO	TCC2_MOUSE	T-cell receptor gamma chain C region C7.5	0.03	-	cyt	1					172
P50157 UniProt NPD GO	TCPA_AMBME	T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha) (Fragment)	0.03	-	cyt	0	Cytoplasm				173
P54410 UniProt NPD GO	TCPH_TETTH	T-complex protein 1 subunit eta (TCP-1-eta) (CCT-eta) (Fragment)	0.03	-	cyt	0	Cytoplasm				353
Q3ZCI9 UniProt NPD GO	TCPQ_BOVIN	T-complex protein 1 subunit theta (TCP-1-theta) (CCT-theta)	0.03	-	mit	0	Cytoplasm (By similarity)				547
Q9N358 UniProt NPD GO	TCPQ_CAEEL	T-complex protein 1 subunit theta (TCP-1-theta) (CCT-theta)	0.03	-	nuc	0	Cytoplasm (By similarity)				581
Q6EE31 UniProt NPD GO	TCPQ_CHICK	T-complex protein 1 subunit theta (TCP-1-theta) (CCT-theta)	0.03	-	mit	0	Cytoplasm (By similarity)				547
P42932 UniProt NPD GO	TCPQ_MOUSE	T-complex protein 1 subunit theta (TCP-1-theta) (CCT-theta)	0.03	-	mit	0	Cytoplasm				547
Q5RAP1 UniProt NPD GO	TCPQ_PONPY	T-complex protein 1 subunit theta (TCP-1-theta) (CCT-theta)	0.03	-	mit	0	Cytoplasm (By similarity)				547

You are viewing entries 81751 to 81800 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.