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
Q19061 UniProt NPD GO	SRD59_CAEEL	Serpentine receptor class delta-59 (Protein srd-59)	0.32	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				325
P49971 UniProt NPD GO	SR541_LYCES	Signal recognition particle 54 kDa protein 1 (SRP54)	0.32	-	cyt	0	Cytoplasm				496
Q9BWW4 UniProt NPD GO	SSBP3_HUMAN	Single-stranded DNA-binding protein 3 (Sequence-specific single-stranded-DNA-binding protein)	0.32	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]	607390		388
Q9D032 UniProt NPD GO	SSBP3_MOUSE	Single-stranded DNA-binding protein 3 (Sequence-specific single-stranded-DNA-binding protein) (Lck-a ...	0.32	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			388
Q9GL50 UniProt NPD GO	STEA1_PIG	Six transmembrane epithelial antigen of prostate 1 (Six transmembrane endothelial antigen of PAEC)	0.32	-	end	5	Membrane; multi-pass membrane protein (Potential)				338
Q96EQ0 UniProt NPD GO	SGTB_HUMAN	Small glutamine-rich tetratricopeptide repeat-containing protein B (Small glutamine-rich protein wit ...	0.32	-	nuc	0					304
P35500 UniProt NPD GO	SCNA_DROME	Sodium channel protein para (Protein paralytic)	0.32	+	end	21	Membrane; multi-pass membrane protein	plasma membrane [NAS]			2131
Q6QIY3 UniProt NPD GO	SC10A_MOUSE	Sodium channel protein type 10 subunit alpha (Sodium channel protein type X subunit alpha) (Voltage- ...	0.32	-	end	20	Membrane; multi-pass membrane protein (By similarity). It can be translocated to the extracellular m ...				1958
Q9NPD5 UniProt NPD GO	SO1B3_HUMAN	Solute carrier organic anion transporter family member 1B3 (Solute carrier family 21 member 8) (Orga ...	0.32	-	end	11 *	Cell membrane; basal cell membrane; multi-pass membrane protein. Cell membrane; lateral cell membran ...	integral to plasma membrane [TAS]	605495		702
P20362 UniProt NPD GO	SOML_PAROL	Somatolactin precursor (SL)	0.32	-	end	0	Secreted protein				231
P54863 UniProt NPD GO	SOML1_SPAAU	Somatolactin-1 precursor (SL)	0.32	-	mit	0	Secreted protein				231
P01169 UniProt NPD GO	SMS1_LOPAM	Somatostatin-1 precursor (Somatostatin I) [Contains: Somatostatin-14]	0.32	-	exc	1 *	Secreted protein				121
Q91194 UniProt NPD GO	SMS2_ONCMY	Somatostatin-2 precursor (Somatostatin II) [Contains: [Tyr21,Gly24]-somatostatin-28; [Tyr7,Gly10]-so ...	0.32	-	nuc	0	Secreted protein				115
P37885 UniProt NPD GO	SOMA_LAMPA	Somatotropin (Growth hormone)	0.32	-	mit	0	Secreted protein				190
O73849 UniProt NPD GO	SOMA_BUFMA	Somatotropin precursor (Growth hormone)	0.32	-	nuc	0	Secreted protein				213
P53969 UniProt NPD GO	SAM50_YEAST	Sorting assembly machinery 50 kDa subunit (TOB complex 55 kDa subunit)	0.32	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)	mitochondrial sorting and assembly machiner... [IDA] mitochondrion [IDA]			484
Q96L92 UniProt NPD GO	SNX27_HUMAN	Sorting nexin-27	0.32	-	cyt	0					435
Q7ZT42 UniProt NPD GO	SND1_BRARE	Staphylococcal nuclease domain-containing protein 1 (p100 co-activator) (100 kDa coactivator) (4SNc- ...	0.32	-	cyt	0	Cytoplasm				897
P38647 UniProt NPD GO	GRP75_MOUSE	Stress-70 protein, mitochondrial precursor (75 kDa glucose-regulated protein) (GRP 75) (Peptide-bind ...	0.32	-	mit	0	Mitochondrion	cytoplasm [TAS] mitochondrion [IDA]			679
O55123 UniProt NPD GO	MMP10_MOUSE	Stromelysin-2 precursor (EC 3.4.24.22) (Matrix metalloproteinase-10) (MMP-10) (Transin-2) (SL-2)	0.32	-	mit	0					476
Q499S5 UniProt NPD GO	MMP11_RAT	Stromelysin-3 precursor (EC 3.4.24.-) (ST3) (SL-3) (Matrix metalloproteinase-11) (MMP-11)	0.32	+	nuc	1 *					491
O93309 UniProt NPD GO	SMC3_XENLA	Structural maintenance of chromosome 3 (Fragment)	0.32	-	cyt	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. During pr ...				234
P21911 UniProt NPD GO	DHSB_SCHPO	Succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (EC 1.3.5.1) (IP)	0.32	-	nuc	0	Mitochondrion; mitochondrial inner membrane				252
Q09803 UniProt NPD GO	VPS4_SCHPO	Suppressor protein of bem1/bed5 double mutants	0.32	-	nuc	0					432
Q9QXU2 UniProt NPD GO	SURF1_RAT	Surfeit locus protein 1	0.32	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				306
Q6BSL0 UniProt NPD GO	YKT6_DEBHA	Synaptobrevin homolog YKT6	0.32	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				200
P46096 UniProt NPD GO	SYT1_MOUSE	Synaptotagmin-1 (Synaptotagmin I) (SytI) (p65)	0.32	-	nuc	1	Synaptic vesicles and chromaffin granules	neuron projection [IDA] plasma membrane [TAS] presynaptic membrane [IDA] secretory granule [IDA] synaptic vesicle membrane [IDA]			421
P21707 UniProt NPD GO	SYT1_RAT	Synaptotagmin-1 (Synaptotagmin I) (SytI) (p65)	0.32	-	nuc	1	Synaptic vesicles and chromaffin granules	cytoplasm [IDA] synaptic vesicle membrane [TAS]		1UOW	421
Q45TX8 UniProt NPD GO	RIC8A_XENLA	Synembryn-A (Protein Ric-8A)	0.32	-	mit	0	Cytoplasm (By similarity)				539
Q9SVC2 UniProt NPD GO	SY122_ARATH	Syntaxin-122 (AtSYP122) (Synt4)	0.32	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				341
Q62753 UniProt NPD GO	STXB2_RAT	Syntaxin-binding protein 2 (Unc-18 homolog 2) (Unc-18B) (Unc18-2)	0.32	-	cyt	0					594
P17981 UniProt NPD GO	NAR2A_MOUSE	T-cell ecto-ADP-ribosyltransferase 1 precursor (EC 2.4.2.31) (T-cell NAD(P)(+)--arginine ADP-ribosyl ...	0.32	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor				287
Q9JJX7 UniProt NPD GO	TTRAP_MOUSE	TRAF and TNF receptor-associated protein	0.32	+	cyt	0	Nucleus (By similarity)				370
Q675B7 UniProt NPD GO	TR136_RAT	Taste receptor type 2 member 136 (T2R136) (Taste receptor type 2 member 40) (T2R40)	0.32	-	end	7 *	Membrane; multi-pass membrane protein				330
Q646D6 UniProt NPD GO	TA2R7_PANPA	Taste receptor type 2 member 7 (T2R7)	0.32	-	end	7 *	Membrane; multi-pass membrane protein				325
Q646C4 UniProt NPD GO	TA2R7_PANTR	Taste receptor type 2 member 7 (T2R7) (Fragment)	0.32	-	end	7 *	Membrane; multi-pass membrane protein				319
Q8R2Q6 UniProt NPD GO	TECT3_MOUSE	Tectonic-3 precursor	0.32	-	exc	0	Membrane; single-pass type I membrane protein (Potential)				595
P24821 UniProt NPD GO	TENA_HUMAN	Tenascin precursor (TN) (Hexabrachion) (Cytotactin) (Neuronectin) (GMEM) (JI) (Miotendinous antigen) ...	0.32	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix		187380	1TEN	2201
P13385 UniProt NPD GO	TDGF1_HUMAN	Teratocarcinoma-derived growth factor 1 precursor (Epidermal growth factor-like cripto protein CR1) ...	0.32	-	mit	1 *		cell surface [IDA] extrinsic to plasma membrane [ISS]	187395		188
P51864 UniProt NPD GO	TDGF2_HUMAN	Teratocarcinoma-derived growth factor 2 (Epidermal growth factor-like cripto protein CR3) (Cripto-3 ...	0.32	-	nuc	1 *			187395		188
P90666 UniProt NPD GO	TXND3_ANTCR	Thioredoxin domain-containing protein 3 homolog (Intermediate chain 1)	0.32	-	nuc	0					837
Q11183 UniProt NPD GO	TXND9_CAEEL	Thioredoxin domain-containing protein 9 homolog	0.32	-	cyt	0					208
Q9Z1T2 UniProt NPD GO	TSP4_MOUSE	Thrombospondin-4 precursor	0.32	-	mit	0					963
Q9HFW3 UniProt NPD GO	TRF5_ASHGO	Topoisomerase 1-related protein TRF5	0.32	-	nuc	0					626
Q96K17 UniProt NPD GO	BT3L4_HUMAN	Transcription factor BTF3 homolog 4 (Basic transcription factor 3-like 4)	0.32	-	nuc	0					158
Q9CQH7 UniProt NPD GO	BT3L4_MOUSE	Transcription factor BTF3 homolog 4 (Basic transcription factor 3-like 4)	0.32	-	nuc	0					158
Q15542 UniProt NPD GO	TAF5_HUMAN	Transcription initiation factor TFIID subunit 5 (Transcription initiation factor TFIID 100 kDa subun ...	0.32	+	nuc	0	Nucleus	transcription factor TFIID complex [IDA]	601787		800
P38956 UniProt NPD GO	SNF11_YEAST	Transcription regulatory protein SNF11 (SWI/SNF complex component SNF11)	0.32	-	nuc	0	Nucleus (Probable)	SWI/SNF complex [TAS]			169
O00292 UniProt NPD GO	TGFB4_HUMAN	Transforming growth factor beta-4 precursor (TGF-beta-4) (Endometrial bleeding-associated factor) (L ...	0.32	-	cyt	0	Secreted protein		601877		366
Q697L1 UniProt NPD GO	TRPV1_CANFA	Transient receptor potential cation channel subfamily V member 1 (TrpV1) (osm-9-like TRP channel 1) ...	0.32	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)				840

You are viewing entries 38951 to 39000 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.