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
P81879 UniProt NPD GO	SMS2_PIAME	Somatostatin-2 (Somatostatin II) (Fragment)	0.09	-	nuc	0	Secreted protein				57
O42179 UniProt NPD GO	SSRL_FUGRU	Somatostatin-like receptor F_48D10.1	0.09	-	end	5	Membrane; multi-pass membrane protein (By similarity)				289
Q91035 UniProt NPD GO	SHH_CHICK	Sonic hedgehog protein precursor (SHH) [Contains: Sonic hedgehog protein N-product; Sonic hedgehog p ...	0.09	-	nuc	1 *	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				425
Q9Y6Z9 UniProt NPD GO	SOU1_SCHPO	Sorbitol utilization protein sou1 (EC 1.1.-.-)	0.09	-	cyt	0					255
Q9CRB0 UniProt NPD GO	SNX24_MOUSE	Sorting nexin-24	0.09	-	cyt	0					169
Q5U2S5 UniProt NPD GO	SNX24_RAT	Sorting nexin-24	0.09	-	cyt	0					169
Q9GU58 UniProt NPD GO	CX9A_CONTE	Spasmodic peptide tx9a precursor (Pi-conotoxin TxIXA)	0.09	-	exc	1 *	Secreted protein				88
P83045 UniProt NPD GO	SMA1_LOXIN	Sphingomyelinase P1 precursor (EC 3.1.4.41) (SMase P1) (Dermonecrotic protein 1) (LiD1)	0.09	-	exc	0	Secreted protein				315
Q9Z0U9 UniProt NPD GO	EDG3_MOUSE	Sphingosine 1-phosphate receptor Edg-3 (S1P receptor Edg-3) (Endothelial differentiation G-protein c ...	0.09	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			378
Q9BX95 UniProt NPD GO	SGPP1_HUMAN	Sphingosine-1-phosphate phosphatase 1 (EC 3.1.3.-) (Sphingosine-1-phosphatase 1) (SPPase1) (Spp1) (h ...	0.09	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				441
P83411 UniProt NPD GO	SDMI_SPOLI	Spodomicin	0.09	-	nuc	0	Secreted protein				40
Q03029 UniProt NPD GO	SPO19_YEAST	Sporulation-specific protein 19 precursor	0.09	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)	cell wall (sensu Fungi) [IDA]			223
Q38737 UniProt NPD GO	FIL1_ANTMA	Stamen-specific protein FIL1 precursor	0.09	-	exc	0					99
O97676 UniProt NPD GO	SRBP1_PIG	Sterol regulatory element-binding protein 1 (SREBP-1) (Sterol regulatory element-binding transcripti ...	0.09	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				144
Q20363 UniProt NPD GO	SIP1_CAEEL	Stress-induced protein 1	0.09	-	cyt	0					159
P83762 UniProt NPD GO	MUCSM_CANFA	Submaxillary mucin (CSM) (Fragment)	0.09	-	nuc	0	Secreted protein				89
P51144 UniProt NPD GO	NK2R_MESAU	Substance-K receptor (SKR) (Neurokinin A receptor) (NK-2 receptor) (NK-2R) (Tachykinin receptor 2)	0.09	-	end	7 *	Membrane; multi-pass membrane protein				384
P30547 UniProt NPD GO	NK1R_CAVPO	Substance-P receptor (SPR) (NK-1 receptor) (NK-1R) (Tachykinin receptor 1)	0.09	-	end	7 *	Membrane; multi-pass membrane protein				407
P14600 UniProt NPD GO	NK1R_RAT	Substance-P receptor (SPR) (NK-1 receptor) (NK-1R) (Tachykinin receptor 1)	0.09	-	end	7 *	Membrane; multi-pass membrane protein				407
Q750S6 UniProt NPD GO	DHSD_ASHGO	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (CybS) (Suc ...	0.09	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				171
Q09508 UniProt NPD GO	DHSA_CAEEL	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1) (FP) ...	0.09	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)	mitochondrial inner membrane [ISS]			646
Q8K2B3 UniProt NPD GO	DHSA_MOUSE	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1) (Fp) ...	0.09	-	nuc	0	Mitochondrion; mitochondrial inner membrane (By similarity)	mitochondrial inner membrane [IDA]			664
O74882 UniProt NPD GO	SDH3_SCHPO	Succinate dehydrogenase cytochrome B subunit, mitochondrial precursor	0.09	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				180
P13086 UniProt NPD GO	SUCA_RAT	Succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial precursor (EC 6.2.1.4) (Succinyl-CoA ...	0.09	-	mit	0	Mitochondrion				333
P53399 UniProt NPD GO	SUCA1_TRIVA	Succinyl-CoA ligase [GDP-forming] subunit alpha-1, mitochondrial precursor (EC 6.2.1.4) (Succinyl-Co ...	0.09	-	cyt	0	Hydrogenosome				309
P53401 UniProt NPD GO	SUCA3_TRIVA	Succinyl-CoA ligase [GDP-forming] subunit alpha-3, mitochondrial precursor (EC 6.2.1.4) (Succinyl-Co ...	0.09	-	cyt	0	Hydrogenosome				309
P30298 UniProt NPD GO	SUS1_ORYSA	Sucrose synthase 1 (EC 2.4.1.13) (Sucrose synthase 2) (Sucrose-UDP glucosyltransferase 1)	0.09	-	nuc	0					808
O24301 UniProt NPD GO	SUS2_PEA	Sucrose synthase 2 (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase 2)	0.09	-	cyt	0					809
Q41607 UniProt NPD GO	SUS2_TULGE	Sucrose synthase 2 (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase 2)	0.09	-	mit	0					820
Q8GW61 UniProt NPD GO	STP14_ARATH	Sugar transport protein 14 (Hexose transporter 14)	0.09	-	end	11 *	Membrane; multi-pass membrane protein				504
Q93Y91 UniProt NPD GO	STP5_ARATH	Sugar transport protein 5 (Hexose transporter 5)	0.09	-	end	12 *	Membrane; multi-pass membrane protein				506
Q8BPG6 UniProt NPD GO	SUMF2_MOUSE	Sulfatase-modifying factor 2 precursor (C-alpha-formyglycine-generating enzyme 2)	0.09	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum [IDA]			308
Q9BYN0 UniProt NPD GO	SRXN1_HUMAN	Sulfiredoxin-1 (EC 1.8.98.2)	0.09	-	cyt	0	Cytoplasm	cytosol [IDA]		1YZS	137
Q9S850 UniProt NPD GO	SUOX_ARATH	Sulfite oxidase (EC 1.8.3.1) (Moco-containing protein AtMCP) (At-SO) (AtSOX)	0.09	-	cyt	0	Peroxisome	mitochondrion [IDA]		1OGP	393
Q07116 UniProt NPD GO	SUOX_RAT	Sulfite oxidase, mitochondrial precursor (EC 1.8.3.1)	0.09	-	cyt	0	Mitochondrion; mitochondrial intermembrane space				488
Q6WG18 UniProt NPD GO	ST6B1_PANTR	Sulfotransferase 6B1 (EC 2.8.2.-)	0.09	-	cyt	0	Cytoplasm (By similarity)				265
P36214 UniProt NPD GO	SODCP_POPTM	Superoxide dismutase [Cu-Zn], chloroplast precursor (EC 1.15.1.1)	0.09	-	mit	0	Plastid; chloroplast				201
P41977 UniProt NPD GO	SODM2_CAEEL	Superoxide dismutase [Mn] 2, mitochondrial precursor (EC 1.15.1.1)	0.09	-	mit	0	Mitochondrion; mitochondrial matrix				218
Q3MSU9 UniProt NPD GO	SODB_ASPNG	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.09	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				210
Q9XS41 UniProt NPD GO	SODM_HORSE	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1) (Mn-SOD)	0.09	-	mit	0	Mitochondrion; mitochondrial matrix				222
Q7L1I2 UniProt NPD GO	SV2B_HUMAN	Synaptic vesicle glycoprotein 2B	0.09	-	end	12	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein. Associated with synaptic-l ...		185861		683
Q05940 UniProt NPD GO	VMAT2_HUMAN	Synaptic vesicular amine transporter (Monoamine transporter) (Vesicular amine transporter 2) (VAT2) ...	0.09	-	end	11 *	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	193001		514
Q16563 UniProt NPD GO	SYPL1_HUMAN	Synaptophysin-like protein 1 (Pantophysin)	0.09	-	end	3	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein (By similarity). Cyto ...	integral to plasma membrane [TAS]			259
P49414 UniProt NPD GO	SDC2_XENLA	Syndecan-2 precursor (SYND2) (Xsyn-2)	0.09	-	end	1	Membrane; single-pass type I membrane protein				191
Q29268 UniProt NPD GO	STXB2_PIG	Syntaxin-binding protein 2 (UNC-18 homolog 2) (UNC-18B) (Fragment)	0.09	-	cyt	0					118
Q93646 UniProt NPD GO	SNT1_CAEEL	Syntrophin-1	0.09	-	cyt	0	Membrane; peripheral membrane protein (By similarity)	dystrophin-associated glycoprotein complex [IMP]			440
Q5XNS0 UniProt NPD GO	TBX19_CANFA	T-box transcription factor TBX19 (T-box protein 19)	0.09	-	nuc	0	Nucleus (Potential)				445
O35975 UniProt NPD GO	NAR2B_MOUSE	T-cell ecto-ADP-ribosyltransferase 2 precursor (EC 2.4.2.31) (T-cell NAD(P)(+)--arginine ADP-ribosyl ...	0.09	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	extrinsic to plasma membrane [TAS] membrane [TAS]			289
Q5YB65 UniProt NPD GO	CD1B_AOTNA	T-cell surface glycoprotein CD1b precursor (CD1b antigen)	0.09	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				333
P27597 UniProt NPD GO	CD3E_CANFA	T-cell surface glycoprotein CD3 epsilon chain precursor	0.09	-	end	1	Membrane; single-pass type I membrane protein				202

You are viewing entries 67101 to 67150 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.