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
P55854 UniProt NPD GO	SUMO3_HUMAN	Small ubiquitin-related modifier 3 precursor (SUMO-3) (Ubiquitin-like protein SMT3A) (SMT3 homolog 1 ...	0.27	-	nuc	0	Cytoplasm	kinetochore [TAS]	602231	1U4A	103
P24797 UniProt NPD GO	AT1A2_CHICK	Sodium/potassium-transporting ATPase alpha-2 chain (EC 3.6.3.9) (Sodium pump 2) (Na+/K+ ATPase 2)	0.27	-	end	8	Membrane; multi-pass membrane protein	microsome [ISS] sodium:potassium-exchanging ATPase complex [ISS]			1017
Q6DNF4 UniProt NPD GO	GCY36_CAEEL	Soluble guanylate cyclase gcy-36 (EC 4.6.1.2)	0.27	-	cyt	0	Cytoplasm (By similarity)				675
Q7XE48 UniProt NPD GO	SSY21_ORYSA	Soluble starch synthase 2-1, chloroplast precursor (EC 2.4.1.21) (Soluble starch synthase II-1)	0.27	-	mit	0	Or: Plastid; amyloplast. Or: Plastid; chloroplast. Amyloplast or chloroplast, granule-bound and solu ...				749
Q9GMU6 UniProt NPD GO	SO1C1_MACFA	Solute carrier organic anion transporter family member 1C1 (Solute carrier family 21 member 14)	0.27	-	end	8	Membrane; multi-pass membrane protein				602
P61278 UniProt NPD GO	SMS_HUMAN	Somatostatin precursor (Growth hormone release-inhibiting factor) [Contains: Somatostatin-28; Somato ...	0.27	-	exc	0	Secreted protein		182450	1P2W	116
P60041 UniProt NPD GO	SMS_MOUSE	Somatostatin precursor [Contains: Antrin; Somatostatin-28; Somatostatin-14]	0.27	-	exc	0	Secreted protein				116
P60042 UniProt NPD GO	SMS_RAT	Somatostatin precursor [Contains: Antrin; Somatostatin-28; Somatostatin-14]	0.27	-	exc	0	Secreted protein				116
P26917 UniProt NPD GO	SMS_BOVIN	Somatostatin precursor [Contains: Somatostatin-28; Somatostatin-14]	0.27	-	exc	0	Secreted protein				116
P61279 UniProt NPD GO	SMS_MACFA	Somatostatin precursor [Contains: Somatostatin-28; Somatostatin-14]	0.27	-	exc	0	Secreted protein				116
P01168 UniProt NPD GO	SMS_PIG	Somatostatin precursor [Contains: Somatostatin-28; Somatostatin-14]	0.27	-	exc	0	Secreted protein				116
O46688 UniProt NPD GO	SMS_SHEEP	Somatostatin precursor [Contains: Somatostatin-28; Somatostatin-14]	0.27	-	exc	0	Secreted protein				116
P34993 UniProt NPD GO	SSR2_BOVIN	Somatostatin receptor type 2 (SS2R) (SRIF-1)	0.27	-	vac	7 *	Membrane; multi-pass membrane protein				368
P30874 UniProt NPD GO	SSR2_HUMAN	Somatostatin receptor type 2 (SS2R) (SRIF-1)	0.27	-	vac	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	182452		369
Q659Q8 UniProt NPD GO	SOMA_BALPH	Somatotropin precursor (Growth hormone)	0.27	-	exc	0	Secreted protein (By similarity)				216
P67931 UniProt NPD GO	SOMA_CAPHI	Somatotropin precursor (Growth hormone)	0.27	-	exc	1 *	Secreted protein				217
P08998 UniProt NPD GO	SOMA_CHICK	Somatotropin precursor (Growth hormone)	0.27	-	end	0	Secreted protein				216
P34744 UniProt NPD GO	SOMA_ESOLU	Somatotropin precursor (Growth hormone)	0.27	-	exc	0	Secreted protein				209
P67930 UniProt NPD GO	SOMA_SHEEP	Somatotropin precursor (Growth hormone)	0.27	-	exc	1 *	Secreted protein				217
O70615 UniProt NPD GO	SOMA_SPAEH	Somatotropin precursor (Growth hormone)	0.27	-	exc	0	Secreted protein				216
Q9PWG3 UniProt NPD GO	SOMA_STRCA	Somatotropin precursor (Growth hormone)	0.27	-	cyt	0	Secreted protein				217
Q64674 UniProt NPD GO	SPEE_MOUSE	Spermidine synthase (EC 2.5.1.16) (Putrescine aminopropyltransferase) (SPDSY)	0.27	-	cyt	0					302
P54643 UniProt NPD GO	SP87_DICDI	Spore coat protein SP87 precursor (PL3 protein)	0.27	-	exc	0	Accumulates specifically in regulated secretory vesicles of prespore cells (prespore vesicles). The ...				677
P14328 UniProt NPD GO	SP96_DICDI	Spore coat protein SP96	0.27	-	exc	0	Outer layer of the coat matrix and interspore matrix				600
Q7KZF4 UniProt NPD GO	SND1_HUMAN	Staphylococcal nuclease domain-containing protein 1 (p100 co-activator) (100 kDa coactivator) (EBNA2 ...	0.27	-	cyt	0	Cytoplasm. Nucleus. In IL-4 stimulated cells colocalizes with STAT6 in the nucleus	nucleus [TAS]	602181		910
Q61900 UniProt NPD GO	SMR1_MOUSE	Submaxillary gland androgen-regulated protein 1 precursor (Salivary protein MSG1)	0.27	-	nuc	0	Secreted protein				147
O49845 UniProt NPD GO	SUS2_DAUCA	Sucrose synthase isoform II (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase 2) (Susy*Dc2)	0.27	-	cyt	0					801
Q02596 UniProt NPD GO	SGP50_MOUSE	Sulfated 50 kDa glycoprotein precursor (SGP50) (Endothelial ligand FOR L-selectin) (Glycosylation-de ...	0.27	-	exc	0	Associated with the lumenal surface of the high endothelial venules of peripheral lymph nodes				151
P60877 UniProt NPD GO	SNP25_MACMU	Synaptosomal-associated protein 25 (SNAP-25) (Synaptosomal-associated 25 kDa protein)	0.27	-	nuc	0					206
Q5R1X1 UniProt NPD GO	SNP25_PANTR	Synaptosomal-associated protein 25 (SNAP-25) (Synaptosomal-associated 25 kDa protein)	0.27	-	nuc	0					206
P60878 UniProt NPD GO	SNP25_CHICK	Synaptosomal-associated protein 25 (SNAP-25) (Synaptosomal-associated 25 kDa protein) (Super protein ...	0.27	-	nuc	0					206
P60880 UniProt NPD GO	SNP25_HUMAN	Synaptosomal-associated protein 25 (SNAP-25) (Synaptosomal-associated 25 kDa protein) (Super protein ...	0.27	-	nuc	0			600322	1XTG	206
P60879 UniProt NPD GO	SNP25_MOUSE	Synaptosomal-associated protein 25 (SNAP-25) (Synaptosomal-associated 25 kDa protein) (Super protein ...	0.27	-	nuc	0		plasma membrane [TAS]		2BU0	206
P60881 UniProt NPD GO	SNP25_RAT	Synaptosomal-associated protein 25 (SNAP-25) (Synaptosomal-associated 25 kDa protein) (Super protein ...	0.27	-	nuc	0				1URQ	206
P36978 UniProt NPD GO	SN25B_CARAU	Synaptosomal-associated protein 25B (SNAP-25B)	0.27	-	nuc	0	Complexed with macromolecular elements of the nerve terminal				203
Q5R4J5 UniProt NPD GO	SYT1_PONPY	Synaptotagmin-1 (Synaptotagmin I) (SytI)	0.27	-	nuc	1	Synaptic vesicles and chromaffin granules				419
P43407 UniProt NPD GO	SDC2_MOUSE	Syndecan-2 precursor (SYND2) (Fibroglycan) (Heparan sulfate proteoglycan core protein) (HSPG)	0.27	-	end	1	Membrane; single-pass type I membrane protein				202
Q8I3H7 UniProt NPD GO	TIP_PLAF7	T-cell immunomodulatory protein homolog precursor	0.27	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				719
P11609 UniProt NPD GO	CD1D1_MOUSE	T-cell surface glycoprotein CD1d1 precursor (CD1.1 antigen)	0.27	-	end	1	Membrane; single-pass type I membrane protein	early endosome [IDA] external side of plasma membrane [IDA] integral to plasma membrane [ISS] late endosome [IDA] lysosome [IDA]		2FIK	336
Q9QZY5 UniProt NPD GO	CD1E_CAVPO	T-cell surface glycoprotein CD1e precursor (CD1e antigen)	0.27	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				390
P11942 UniProt NPD GO	CD3G_MOUSE	T-cell surface glycoprotein CD3 gamma chain precursor (T-cell receptor T3 gamma chain)	0.27	-	end	1	Membrane; single-pass type I membrane protein	alpha-beta T cell receptor complex [IDA] integral to plasma membrane [ISS]		1JBJ	182
P05541 UniProt NPD GO	CD8B_RAT	T-cell surface glycoprotein CD8 beta chain precursor (CD8 antigen 37 kDa chain) (OX-8 membrane antig ...	0.27	-	end	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			208
P62500 UniProt NPD GO	T22D1_MOUSE	TSC22 domain family protein 1 (Transforming growth factor beta-1-induced transcript 4 protein) (Regu ...	0.27	-	nuc	0	Cytoplasm. Nucleus				143
P62501 UniProt NPD GO	T22D1_RAT	TSC22 domain family protein 1 (Transforming growth factor beta-1-induced transcript 4 protein) (Regu ...	0.27	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				143
Q67ES0 UniProt NPD GO	TR140_RAT	Taste receptor type 2 member 140 (T2R140) (Taste receptor type 2 member 31) (T2R31)	0.27	-	end	7 *	Membrane; multi-pass membrane protein				312
Q9JKF0 UniProt NPD GO	T2R23_RAT	Taste receptor type 2 member 23 (T2R23) (Taste receptor type 2 member 2) (T2R2)	0.27	+	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			333
Q4R9E0 UniProt NPD GO	TECT3_MACFA	Tectonic-3 precursor	0.27	-	end	0	Membrane; single-pass type I membrane protein (Potential)				608
O14599 UniProt NPD GO	VCY2_HUMAN	Testis-specific basic protein Y 2 (Variably charged protein Y 2)	0.27	-	mit	0			400013		106
Q5BK48 UniProt NPD GO	TTC5_RAT	Tetratricopeptide repeat protein 5 (TPR repeat protein 5)	0.27	-	cyt	0					440
Q9SEU7 UniProt NPD GO	TRXM3_ARATH	Thioredoxin M-type 3, chloroplast precursor (TRX-M3)	0.27	-	mit	0	Plastid; chloroplast (By similarity)				173

You are viewing entries 43701 to 43750 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.