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
Q9YGW9 UniProt NPD GO	NXS2_LATLA	Short neurotoxin VAN-10 precursor	0.26	-	nuc	0	Secreted protein				83
Q9BQP9 UniProt NPD GO	SPLC3_HUMAN	Short palate, lung and nasal epithelium carcinoma-associated protein 3 precursor	0.26	-	exc	0					210
O15467 UniProt NPD GO	CCL16_HUMAN	Small inducible cytokine A16 precursor (CCL16) (IL-10-inducible chemokine) (Chemokine LEC) (Liver-ex ...	0.26	-	exc	0	Secreted protein		601394		120
P10148 UniProt NPD GO	CCL2_MOUSE	Small inducible cytokine A2 precursor (CCL2) (Monocyte chemotactic protein 1) (MCP-1) (Monocyte chem ...	0.26	-	exc	0	Secreted protein				148
P10147 UniProt NPD GO	CCL3_HUMAN	Small inducible cytokine A3 precursor (CCL3) (Macrophage inflammatory protein 1-alpha) (MIP-1-alpha) ...	0.26	-	exc	0	Secreted protein	soluble fraction [TAS]	182283	1B53	92
O70555 UniProt NPD GO	SPR2D_MOUSE	Small proline-rich protein 2D	0.26	-	nuc	0	Cytoplasm (By similarity)	cornified envelope [NAS]			85
P61955 UniProt NPD GO	SUMO2_BOVIN	Small ubiquitin-related modifier 2 precursor (SUMO-2) (Ubiquitin-like protein SMT3B) (SMT3 homolog 2 ...	0.26	-	nuc	0					95
P61957 UniProt NPD GO	SUMO2_MOUSE	Small ubiquitin-related modifier 2 precursor (SUMO-2) (Ubiquitin-like protein SMT3B) (SMT3 homolog 2 ...	0.26	-	nuc	0					95
P61959 UniProt NPD GO	SUMO2_RAT	Small ubiquitin-related modifier 2 precursor (SUMO-2) (Ubiquitin-like protein SMT3B) (SMT3 homolog 2 ...	0.26	-	nuc	0					95
P61956 UniProt NPD GO	SUMO2_HUMAN	Small ubiquitin-related modifier 2 precursor (SUMO-2) (Ubiquitin-like protein SMT3B) (SMT3 homolog 2 ...	0.26	-	nuc	0	Nucleus. Nuclear bodies		603042	2D07	95
Q6LDZ8 UniProt NPD GO	SUMO2_CRIGR	Small ubiquitin-related modifier 2 precursor (SUMO-2) (Ubiquitin-like protein SMT3B) (SMT3 homolog 2 ...	0.26	-	nuc	0					95
P61958 UniProt NPD GO	SUMO2_PIG	Small ubiquitin-related modifier 2 precursor (SUMO-2) (Ubiquitin-like protein SMT3B) (SMT3 homolog 2 ...	0.26	-	nuc	0					95
P51143 UniProt NPD GO	SC6A2_BOVIN	Sodium-dependent noradrenaline transporter (Norepinephrine transporter) (NET)	0.26	-	end	12	Membrane; multi-pass membrane protein				615
P58312 UniProt NPD GO	AT1A3_OREMO	Sodium/potassium-transporting ATPase alpha-3 chain (EC 3.6.3.9) (Sodium pump 3) (Na+/K+ ATPase 3) (A ...	0.26	-	end	8	Membrane; multi-pass membrane protein				1010
Q9QYE2 UniProt NPD GO	SO1A6_RAT	Solute carrier organic anion transporter family member 1A6 (Solute carrier family 21 member 13) (Kid ...	0.26	-	end	10 *	Membrane; multi-pass membrane protein				670
Q9EPZ7 UniProt NPD GO	SO1C1_RAT	Solute carrier organic anion transporter family member 1C1 (Solute carrier family 21 member 14) (Blo ...	0.26	-	end	10	Membrane; multi-pass membrane protein				716
Q9YGK7 UniProt NPD GO	SOML_SCIOC	Somatolactin precursor (SL)	0.26	-	mit	0	Secreted protein				231
Q9PWG4 UniProt NPD GO	SOML_SIGGU	Somatolactin precursor (SL)	0.26	-	exc	0	Secreted protein				231
P45642 UniProt NPD GO	SOML_SOLSE	Somatolactin precursor (SL)	0.26	-	mit	0	Secreted protein				230
P01287 UniProt NPD GO	SLIB_PIG	Somatoliberin (Growth hormone-releasing factor) (GRF) (Growth hormone-releasing hormone) (GHRH)	0.26	-	nuc	0	Secreted protein				44
P31391 UniProt NPD GO	SSR4_HUMAN	Somatostatin receptor type 4 (SS4R)	0.26	-	vac	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	182454		388
O08858 UniProt NPD GO	SSR5_MOUSE	Somatostatin receptor type 5 (SS5R)	0.26	-	end	7 *	Membrane; multi-pass membrane protein				362
P12856 UniProt NPD GO	SOMA2_XENLA	Somatotropin B precursor (Growth hormone B) (GH-B)	0.26	-	end	0	Secreted protein				208
P10607 UniProt NPD GO	SOMA_ONCKI	Somatotropin precursor (Growth hormone)	0.26	-	nuc	0	Secreted protein				210
O70493 UniProt NPD GO	SNX12_MOUSE	Sorting nexin-12 (SDP8 protein)	0.26	-	cyt	0					165
Q91YJ2 UniProt NPD GO	SNX4_MOUSE	Sorting nexin-4	0.26	-	cyt	0					450
O43791 UniProt NPD GO	SPOP_HUMAN	Speckle-type POZ protein	0.26	+	cyt	0	Nucleus	nucleus [TAS]	602650	2CR2	374
Q6ZWS8 UniProt NPD GO	SPOP_MOUSE	Speckle-type POZ protein (PDX-1 C-terminal-interacting factor 1) (PCIF1)	0.26	+	cyt	0	Nucleus				374
Q8N7G0 UniProt NPD GO	SPRM1_HUMAN	Sperm 1 POU-domain transcription factor (SPRM-1)	0.26	-	nuc	0	Nucleus (By similarity)				328
Q10579 UniProt NPD GO	SPE26_CAEEL	Spermatocyte protein spe-26	0.26	-	cyt	0					570
P83430 UniProt NPD GO	SPHE2_APTPA	Spheniscin-2 (Sphe-2) (pBD-2)	0.26	-	mit	0	Secreted protein			1UT3	38
O95977 UniProt NPD GO	EDG6_HUMAN	Sphingosine 1-phosphate receptor Edg-6 (S1P receptor Edg-6) (Endothelial differentiation G-protein c ...	0.26	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	603751		384
Q08143 UniProt NPD GO	SMR2_PODAN	Sporulation minus regulator 2	0.26	-	cyt	0	Nucleus				288
Q93XK2 UniProt NPD GO	STSYN_PEA	Stachyose synthase precursor (EC 2.4.1.67) (Galactinol--raffinose galactosyltransferase)	0.26	-	cyt	0	Cytoplasm (Potential)	cytoplasm [NAS]			853
P42933 UniProt NPD GO	SPG5_YEAST	Stationary phase protein 5	0.26	-	mit	0					373
Q19958 UniProt NPD GO	STO2_CAEEL	Stomatin-2	0.26	-	mit	1					314
O09133 UniProt NPD GO	SMR2A_MOUSE	Submaxillary gland androgen-regulated protein 2, isoform alpha precursor (Salivary protein MSG2, iso ...	0.26	-	exc	0	Secreted protein (Probable)				150
Q75CI4 UniProt NPD GO	DHSB_ASHGO	Succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (EC 1.3.5.1) (IP)	0.26	-	nuc	0	Mitochondrion; mitochondrial inner membrane				261
Q80VR3 UniProt NPD GO	ST1C1_MOUSE	Sulfotransferase 1C1 (EC 2.8.2.-) (Phenol sulfotransferase)	0.26	-	cyt	0	Cytoplasm	cytoplasm [IDA]			304
P78539 UniProt NPD GO	SRPX_HUMAN	Sushi repeat-containing protein SRPX precursor	0.26	-	exc	0	Possibly surface of photoreceptor cell	cell surface [IEP] membrane [TAS]	300187		464
Q7L0J3 UniProt NPD GO	SV2A_HUMAN	Synaptic vesicle glycoprotein 2A	0.26	-	end	12	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein. Enriched in chromaffin gra ...		185860		742
Q4R4X3 UniProt NPD GO	SV2A_MACFA	Synaptic vesicle glycoprotein 2A	0.26	-	end	11	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein. Enriched in chromaffin gra ...				742
Q5R4L9 UniProt NPD GO	SV2A_PONPY	Synaptic vesicle glycoprotein 2A	0.26	-	end	12	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein. Enriched in chromaffin gra ...				742
Q29397 UniProt NPD GO	SV2A_BOVIN	Synaptic vesicle glycoprotein 2A (p87)	0.26	-	end	12	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein. Enriched in chromaffin gra ...				742
P26261 UniProt NPD GO	SDC3_CHICK	Syndecan-3 precursor	0.26	-	exc	1	Membrane; single-pass type I membrane protein				405
P11610 UniProt NPD GO	CD1D2_MOUSE	T-cell surface glycoprotein CD1d2 precursor (CD1.2 antigen)	0.26	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA] integral to plasma membrane [ISS]			336
P12612 UniProt NPD GO	TCPA_YEAST	T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha)	0.26	-	cyt	0	Cytoplasm	chaperonin-containing T-complex [IPI] cytoplasm [TAS] cytoskeleton [TAS]			559
P42070 UniProt NPD GO	CD80_RABIT	T-lymphocyte activation antigen CD80 precursor (Activation B7-1 antigen)	0.26	-	end	1	Membrane; single-pass type I membrane protein				299
P32085 UniProt NPD GO	TBP_CAEEL	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.26	-	nuc	0	Nucleus				340
Q9UNN4 UniProt NPD GO	TF2AY_HUMAN	TFIIA-alpha and beta-like factor (General transcription factor II A, 1-like factor)	0.26	-	nuc	0	Nucleus		605358		478

You are viewing entries 44701 to 44750 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.