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
P55011 UniProt NPD GO	S12A2_HUMAN	Solute carrier family 12 member 2 (Bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1) ...	0.12	-	end	12	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	600840		1212
P46721 UniProt NPD GO	SO1A2_HUMAN	Solute carrier organic anion transporter family member 1A2 (Solute carrier family 21 member 3) (Sodi ...	0.12	-	end	12 *	Membrane; multi-pass membrane protein		602883		670
Q9EP96 UniProt NPD GO	SO1A4_MOUSE	Solute carrier organic anion transporter family member 1A4 (Solute carrier family 21 member 5) (Sodi ...	0.12	-	end	11 *	Membrane; multi-pass membrane protein				670
Q96BD0 UniProt NPD GO	SO4A1_HUMAN	Solute carrier organic anion transporter family member 4A1 (Solute carrier family 21 member 12) (Sod ...	0.12	-	end	11	Membrane; multi-pass membrane protein				722
P01172 UniProt NPD GO	SMS2_ICTPU	Somatostatin-2 precursor (Somatostatin II) [Contains: Somatostatin-22 (SS-22)]	0.12	-	exc	0	Secreted protein				105
Q92008 UniProt NPD GO	SHH_BRARE	Sonic hedgehog A protein precursor (SHHA) (VHH-1) [Contains: Sonic hedgehog A protein N-product; Son ...	0.12	-	mit	1 *	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				418
P79691 UniProt NPD GO	SHH_CARAU	Sonic hedgehog protein (SHH) (Fragments)	0.12	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
P79850 UniProt NPD GO	SHH_PUNTE	Sonic hedgehog protein (SHH) (Fragments)	0.12	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
Q90385 UniProt NPD GO	SHH_CYNPY	Sonic hedgehog protein precursor (SHH) [Contains: Sonic hedgehog protein N-product; Sonic hedgehog p ...	0.12	-	mit	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				432
P84109 UniProt NPD GO	SRBS1_RAT	Sorbin and SH3 domain-containing protein 1 (SH3P12) (Ponsin) (Fragments)	0.12	-	nuc	0	Cell membrane; cell-cell junction; adherens junction. Cell membrane; cell-matrix junction; adherens ...	cell-cell adherens junction [ISS] cell-substrate adherens junction [ISS] lipid raft [ISS] nucleus [ISS] stress fiber [ISS]			35
Q9Y343 UniProt NPD GO	SNX24_HUMAN	Sorting nexin-24	0.12	-	cyt	0					169
Q810K3 UniProt NPD GO	SGPP2_MOUSE	Sphingosine-1-phosphate phosphatase 2 (EC 3.1.3.-) (Sphingosine-1-phosphatase 2) (SPPase2) (Spp2)	0.12	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				354
Q8IWX5 UniProt NPD GO	SGPP2_HUMAN	Sphingosine-1-phosphate phosphatase 2 (EC 3.1.3.-) (Sphingosine-1-phosphatase 2) (SPPase2) (Spp2) (h ...	0.12	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				399
Q923D4 UniProt NPD GO	SF3B5_MOUSE	Splicing factor 3B subunit 5 (SF3b5) (Pre-mRNA-splicing factor SF3b 10 kDa subunit)	0.12	-	nuc	0	Nucleus (By similarity)				86
Q876J2 UniProt NPD GO	SPR1_SACBA	Sporulation-specific glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.12	-	exc	0					445
P32603 UniProt NPD GO	SPR1_YEAST	Sporulation-specific glucan 1,3-beta-glucosidase precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.12	-	mit	0		cell wall (sensu Fungi) [IMP]			445
P02808 UniProt NPD GO	STAT_HUMAN	Statherin precursor	0.12	-	vac	0	Secreted protein	extracellular region [NAS]	184470		62
P35610 UniProt NPD GO	SOAT1_HUMAN	Sterol O-acyltransferase 1 (EC 2.3.1.26) (Cholesterol acyltransferase 1) (Acyl coenzyme A:cholestero ...	0.12	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] membrane [TAS]	102642		550
O77761 UniProt NPD GO	SOAT1_MACFA	Sterol O-acyltransferase 1 (EC 2.3.1.26) (Cholesterol acyltransferase 1) (Acyl coenzyme A:cholestero ...	0.12	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				550
Q876L2 UniProt NPD GO	ARE2_SACBA	Sterol O-acyltransferase 2 (EC 2.3.1.26) (Sterol-ester synthase 2)	0.12	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				650
Q06837 UniProt NPD GO	BNP_NICSY	Stress response protein (Basic protein) (Fragment)	0.12	-	cyt	0	Nucleus (Potential)				57
Q02028 UniProt NPD GO	HSP7S_PEA	Stromal 70 kDa heat shock-related protein, chloroplast precursor	0.12	-	mit	0	Plastid; chloroplast; chloroplast stroma				706
O65351 UniProt NPD GO	SUBL_ARATH	Subtilisin-like protease precursor (EC 3.4.21.-) (Cucumisin-like serine protease)	0.12	-	exc	0	Intracellular spaces and cell wall				757
Q8HXW3 UniProt NPD GO	DHSA_MACFA	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1) (Fp) ...	0.12	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				664
P53598 UniProt NPD GO	SUCA_YEAST	Succinyl-CoA ligase [ADP-forming] subunit alpha, mitochondrial precursor (EC 6.2.1.5) (Succinyl-CoA ...	0.12	-	mit	0	Mitochondrion	mitochondrial nucleoid [IDA] mitochondrion [IDA]			329
Q9WUM5 UniProt NPD GO	SUCA_MOUSE	Succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial precursor (EC 6.2.1.4) (Succinyl-CoA ...	0.12	-	mit	0	Mitochondrion (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			333
P49037 UniProt NPD GO	SUSY_LYCES	Sucrose synthase (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase)	0.12	-	mit	0					805
P31922 UniProt NPD GO	SUS1_HORVU	Sucrose synthase 1 (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase 1)	0.12	-	cyt	0					807
O04249 UniProt NPD GO	STP7_ARATH	Sugar transport protein 7 (Hexose transporter 7)	0.12	-	end	11 *	Membrane; multi-pass membrane protein				513
P78937 UniProt NPD GO	MET3_SCHPO	Sulfate adenylyltransferase (EC 2.7.7.4) (Sulfate adenylate transferase) (SAT) (ATP-sulfurylase)	0.12	-	cyt	0					490
P50225 UniProt NPD GO	ST1A1_HUMAN	Sulfotransferase 1A1 (EC 2.8.2.1) (Aryl sulfotransferase 1) (Phenol sulfotransferase 1) (Phenol-sulf ...	0.12	-	cyt	0	Cytoplasm		171150	2D06	295
O75897 UniProt NPD GO	ST1C2_HUMAN	Sulfotransferase 1C2 (EC 2.8.2.-) (SULT1C) (SULT1C#2)	0.12	-	cyt	0	Cytoplasm		608357	2GWH	302
Q6WG17 UniProt NPD GO	ST6B1_GORGO	Sulfotransferase 6B1 (EC 2.8.2.-)	0.12	-	cyt	0	Cytoplasm (By similarity)				265
Q9P4T6 UniProt NPD GO	SODM_AGABI	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.12	-	mit	0	Mitochondrion; mitochondrial matrix				200
Q24536 UniProt NPD GO	SSL_DROME	Suppressor-of-stellate-like protein (Suste-like protein) (Su(ste)-like)	0.12	-	cyt	0					219
Q5BH63 UniProt NPD GO	SVF1_EMENI	Survival factor 1	0.12	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				546
O76735 UniProt NPD GO	SNG1_CAEEL	Synaptogyrin homolog 1	0.12	-	end	4 *	Membrane; multi-pass membrane protein	synaptic vesicle [IDA]			247
Q9DCP2 UniProt NPD GO	S38A3_MOUSE	System N amino acid transporter 1 (SN1) (N-system amino acid transporter 1) (Solute carrier family 3 ...	0.12	-	end	11	Cell membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			505
P27058 UniProt NPD GO	SYST_LYCES	Systemin precursor	0.12	-	nuc	0	Cytoplasm				200
P01848 UniProt NPD GO	TCA_HUMAN	T-cell receptor alpha chain C region	0.12	-	cyt	0		integral to plasma membrane [NAS]		2BNU	142
Q9XS72 UniProt NPD GO	CD1A_PIG	T-cell surface glycoprotein CD1a precursor (CD1a antigen)	0.12	-	end	1	Membrane; single-pass type I membrane protein				339
P29016 UniProt NPD GO	CD1B_HUMAN	T-cell surface glycoprotein CD1b precursor (CD1b antigen)	0.12	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS] plasma membrane [TAS]	188360	1UQS	333
P23043 UniProt NPD GO	CD1D_SYLFL	T-cell surface glycoprotein CD1d (Leukocyte differentiation-like antigen Ta) (Fragment)	0.12	-	mit	0	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]			275
Q7YRN2 UniProt NPD GO	CD3E_PIG	T-cell surface glycoprotein CD3 epsilon chain precursor	0.12	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				196
P42069 UniProt NPD GO	CD28_RABIT	T-cell-specific surface glycoprotein CD28 precursor	0.12	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]			221
Q6C100 UniProt NPD GO	TCPD_YARLI	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta)	0.12	-	nuc	0	Cytoplasm (Potential)				527
P08932 UniProt NPD GO	KNT2_RAT	T-kininogen 2 precursor (T-kininogen II) (Major acute phase protein) (Alpha-1-MAP) (Thiostatin) [Con ...	0.12	-	exc	0	Secreted protein; extracellular space				430
Q5E9C4 UniProt NPD GO	TBCD7_BOVIN	TBC1 domain family member 7	0.12	-	nuc	0					293
Q18120 UniProt NPD GO	TWK18_CAEEL	TWiK family of potassium channels protein 18	0.12	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				461
O54885 UniProt NPD GO	TYOBP_MOUSE	TYRO protein tyrosine kinase-binding protein precursor (DNAX-activation protein 12) (KAR-associated ...	0.12	-	end	2 *	Membrane; single-pass type I membrane protein				114

You are viewing entries 61951 to 62000 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.