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
P07284 UniProt NPD GO	SYSC_YEAST	Seryl-tRNA synthetase, cytoplasmic (EC 6.1.1.11) (Serine--tRNA ligase) (SerRS)	0.24	-	mit	0	Cytoplasm	cytoplasm [IDA]			462
Q4R6P7 UniProt NPD GO	SESN1_MACFA	Sestrin-1	0.24	-	nuc	0	Nucleus (By similarity)				492
Q9Y6P5 UniProt NPD GO	SESN1_HUMAN	Sestrin-1 (p53-regulated protein PA26)	0.24	-	nuc	0	Nucleus	nucleus [TAS]	606103		492
P04278 UniProt NPD GO	SHBG_HUMAN	Sex hormone-binding globulin precursor (SHBG) (Sex steroid-binding protein) (SBP) (Testis-specific a ...	0.24	-	end	0	Secreted protein (By similarity). In testis, it is synthesized by the Sertoli cells, secreted into t ...	extracellular region [NAS]	182205	1LHW	402
P25494 UniProt NPD GO	NXS1_HYDCY	Short neurotoxin 1 (Hydrophitoxin a)	0.24	-	nuc	0	Secreted protein				60
P37108 UniProt NPD GO	SRP14_HUMAN	Signal recognition particle 14 kDa protein (SRP14) (18 kDa Alu RNA-binding protein)	0.24	-	nuc	0	Cytoplasm	cytoplasm [TAS] signal recognition particle (sensu Eukaryota) [TAS]	600708	1RY1	136
Q6FP52 UniProt NPD GO	SEC65_CANGA	Signal recognition particle SEC65 subunit	0.24	-	nuc	0	Cytoplasm (By similarity)				264
P29478 UniProt NPD GO	SEC65_YEAST	Signal recognition particle subunit SEC65	0.24	-	nuc	0	Cytoplasm (By similarity)	signal recognition particle (sensu Eukaryota) [IDA]			273
Q13291 UniProt NPD GO	SLAF1_HUMAN	Signaling lymphocytic activation molecule precursor (IPO-3) (CD150 antigen) (CDw150)	0.24	+	exc	2 *	Cell membrane; single-pass type I membrane protein. Present on the surface of B-cells and T-cells		603492	1M27	335
Q68Y88 UniProt NPD GO	CCL13_CANFA	Small inducible cytokine A13 precursor (CCL13) (Monocyte chemotactic protein 4) (MCP-4) (Monocyte ch ...	0.24	-	exc	0	Secreted protein (By similarity)				98
P14844 UniProt NPD GO	CCL2_RAT	Small inducible cytokine A2 precursor (CCL2) (Monocyte chemotactic protein 1) (MCP-1) (Monocyte chem ...	0.24	-	exc	0	Secreted protein	cytoplasm [IDA]			148
Q8SQB1 UniProt NPD GO	CCL20_BOVIN	Small inducible cytokine A20 precursor (CCL20) (Macrophage inflammatory protein 3 alpha) (MIP-3-alph ...	0.24	-	exc	0	Secreted protein (By similarity)				96
P80075 UniProt NPD GO	CCL8_HUMAN	Small inducible cytokine A8 precursor (CCL8) (Monocyte chemotactic protein 2) (MCP-2) (Monocyte chem ...	0.24	-	exc	0	Secreted protein		602283	1ESR	99
P35325 UniProt NPD GO	SPR2B_HUMAN	Small proline-rich protein 2B (SPR-2B)	0.24	-	nuc	0	Cytoplasm	cornified envelope [NAS] cytoplasm [NAS]	182268		72
P22531 UniProt NPD GO	SPR2E_HUMAN	Small proline-rich protein 2E (SPR-2E) (Small proline-rich protein II) (SPR-II)	0.24	-	nuc	0	Cytoplasm	cornified envelope [NAS] cytoplasm [IDA]			72
Q96RM1 UniProt NPD GO	SPR2F_HUMAN	Small proline-rich protein 2F (SPR-2F)	0.24	-	nuc	0	Cytoplasm (By similarity)	cornified envelope [NAS]			72
O70559 UniProt NPD GO	SPR2H_MOUSE	Small proline-rich protein 2H	0.24	-	nuc	0	Cytoplasm (By similarity)	cornified envelope [NAS]			108
O70560 UniProt NPD GO	SPR2I_MOUSE	Small proline-rich protein 2I	0.24	-	nuc	0	Cytoplasm (By similarity)	cornified envelope [NAS]			76
P05025 UniProt NPD GO	AT1A_TORCA	Sodium/potassium-transporting ATPase alpha chain precursor (EC 3.6.3.9) (Sodium pump alpha chain) (N ...	0.24	-	end	10	Membrane; multi-pass membrane protein				1022
P25489 UniProt NPD GO	AT1A1_CATCO	Sodium/potassium-transporting ATPase alpha-1 chain precursor (EC 3.6.3.9) (Sodium pump 1) (Na+/K+ AT ...	0.24	-	end	8	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [ISS]			1027
P50993 UniProt NPD GO	AT1A2_HUMAN	Sodium/potassium-transporting ATPase alpha-2 chain precursor (EC 3.6.3.9) (Sodium pump 2) (Na+/K+ AT ...	0.24	-	end	8	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [ISS]	602481		1020
Q6PIE5 UniProt NPD GO	AT1A2_MOUSE	Sodium/potassium-transporting ATPase alpha-2 chain precursor (EC 3.6.3.9) (Sodium pump 2) (Na+/K+ AT ...	0.24	-	end	8	Membrane; multi-pass membrane protein	microsome [IDA]			1020
P06686 UniProt NPD GO	AT1A2_RAT	Sodium/potassium-transporting ATPase alpha-2 chain precursor (EC 3.6.3.9) (Sodium pump 2) (Na+/K+ AT ...	0.24	-	end	8	Membrane; multi-pass membrane protein	plasma membrane [IMP] sodium:potassium-exchanging ATPase complex [ISS]			1020
Q9IAL7 UniProt NPD GO	NCKX2_CHICK	Sodium/potassium/calcium exchanger 2 precursor (Na(+)/K(+)/Ca(2+)-exchange protein 2) (Retinal cone ...	0.24	-	end	11 *	Membrane; multi-pass membrane protein				651
Q6Z2T8 UniProt NPD GO	SSY22_ORYSA	Soluble starch synthase 2-2, chloroplast precursor (EC 2.4.1.21) (Soluble starch synthase II-2)	0.24	-	mit	0	Or: Plastid; amyloplast. Or: Plastid; chloroplast. Amyloplast or chloroplast, granule-bound and solu ...				694
O95528 UniProt NPD GO	GTR10_HUMAN	Solute carrier family 2, facilitated glucose transporter member 10 (Glucose transporter type 10)	0.24	-	end	12 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	606145		541
P45641 UniProt NPD GO	SOML_HIPHI	Somatolactin precursor (SL)	0.24	-	end	0	Secreted protein				230
Q9I9H4 UniProt NPD GO	SOML_TETMU	Somatolactin precursor (SL)	0.24	-	nuc	0	Secreted protein				229
Q9YGH5 UniProt NPD GO	SMS1A_CARAU	Somatostatin IA precursor [Contains: Somatostatin-26; Somatostatin-14]	0.24	-	exc	0	Secreted protein				114
P33092 UniProt NPD GO	SOMA_BALBO	Somatotropin (Growth hormone)	0.24	-	cyt	0	Secreted protein				190
P09538 UniProt NPD GO	SOMA1_ONCMY	Somatotropin 1 precursor (Growth hormone 1)	0.24	-	exc	0	Secreted protein				210
Q9GKA1 UniProt NPD GO	SOMA_GALSE	Somatotropin precursor (Growth hormone)	0.24	-	exc	0	Secreted protein				217
Q9GMB2 UniProt NPD GO	SOMA_NYCPY	Somatotropin precursor (Growth hormone)	0.24	-	exc	0	Secreted protein				217
P07064 UniProt NPD GO	SOMA_ONCKE	Somatotropin precursor (Growth hormone)	0.24	-	exc	0	Secreted protein				210
Q91222 UniProt NPD GO	SOMA1_ONCNE	Somatotropin-1 precursor (Somatotropin I) (Growth hormone I)	0.24	-	exc	0	Secreted protein				210
P26774 UniProt NPD GO	SOMA2_ACIGU	Somatotropin-2 (Somatotropin II) (Growth hormone II)	0.24	-	mit	0	Secreted protein				190
Q4I1H6 UniProt NPD GO	SNX3_GIBZE	Sorting nexin-3	0.24	-	cyt	0	Cytoplasm (By similarity)				157
O19021 UniProt NPD GO	SP17_MACFA	Sperm surface protein Sp17 (Sperm autoantigenic protein 17)	0.24	+	nuc	0	Membrane; peripheral membrane protein (Potential)				151
Q9JKM5 UniProt NPD GO	EDG8_RAT	Sphingosine 1-phosphate receptor Edg-8 (Endothelial differentiation sphingolipid G-protein-coupled r ...	0.24	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IDA]			400
P22698 UniProt NPD GO	SPG7_DICDI	Spore germination protein 270-11	0.24	-	exc	1 *					532
Q14534 UniProt NPD GO	ERG1_HUMAN	Squalene monooxygenase (EC 1.14.99.7) (Squalene epoxidase) (SE)	0.24	-	end	6 *	Microsome; microsomal membrane; multi-pass membrane protein	microsome [NAS]	602019		574
Q7KV13 UniProt NPD GO	STEL2_DROME	Stellate protein CG33237	0.24	-	nuc	0		cytoplasm [ISS] nucleus [ISS] protein kinase CK2 complex [ISS]			171
P15021 UniProt NPD GO	STEL5_DROME	Stellate protein CG33240/CG33245	0.24	-	nuc	0		cytoplasm [IDA] nucleus [IDA] protein kinase CK2 complex [ISS]			172
Q7KV17 UniProt NPD GO	STEL6_DROME	Stellate protein CG33241	0.24	-	nuc	0		cytoplasm [ISS] nucleus [ISS] protein kinase CK2 complex [ISS]			171
Q7KV19 UniProt NPD GO	STEL7_DROME	Stellate protein CG33243	0.24	-	nuc	0		cytoplasm [ISS] nucleus [ISS] protein kinase CK2 complex [ISS]			171
Q9DEB4 UniProt NPD GO	STAR_ONCMY	Steroidogenic acute regulatory protein, mitochondrial precursor (StAR) (StARD1)	0.24	-	cyt	0	Mitochondrion (By similarity)				287
P33295 UniProt NPD GO	PEPC_ASPNG	Subtilisin-like serine protease pepC precursor (EC 3.4.21.-)	0.24	-	vac	0					533
Q920N7 UniProt NPD GO	SYT12_MOUSE	Synaptotagmin-12 (Synaptotagmin XII) (SytXII)	0.24	-	nuc	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)				421
Q61A92 UniProt NPD GO	RIC8_CAEBR	Synembryn (Resistance to inhibitors of cholinesterase protein 8)	0.24	-	cyt	0	Cytoplasm; cell cortex (By similarity). Localizes to the cell cortex (By similarity)				567
O60499 UniProt NPD GO	STX10_HUMAN	Syntaxin-10 (Syn10)	0.24	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (Potential)	Golgi membrane [TAS]	603765		249

You are viewing entries 46851 to 46900 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.