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
P22006 UniProt NPD GO	SVS2_RAT	Seminal vesicle secretory protein 2 precursor (Seminal vesicle secretory protein II) (SVS II)	0.52	-	nuc	0					414
Q9ZQY6 UniProt NPD GO	2A5D_ARATH	Serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B' delta isoform (PP2A, B' subunit ...	0.52	-	nuc	0		cytoplasm [IDA] nucleolus [IDA]			477
O75385 UniProt NPD GO	ULK1_HUMAN	Serine/threonine-protein kinase ULK1 (EC 2.7.11.1) (Unc-51-like kinase 1)	0.52	-	nuc	0			603168		1050
P18961 UniProt NPD GO	YPK2_YEAST	Serine/threonine-protein kinase YPK2/YKR2 (EC 2.7.11.1)	0.52	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			677
Q9N3Z3 UniProt NPD GO	CHK1_CAEEL	Serine/threonine-protein kinase chk-1 (EC 2.7.11.1)	0.52	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				503
Q9P7J8 UniProt NPD GO	GAD8_SCHPO	Serine/threonine-protein kinase gad8 (EC 2.7.11.1)	0.52	-	mit	0					569
O42626 UniProt NPD GO	NRC2_NEUCR	Serine/threonine-protein kinase nrc-2 (EC 2.7.11.1) (Nonrepressible conidiation protein 2)	0.52	-	nuc	0					623
Q10056 UniProt NPD GO	SHK2_SCHPO	Serine/threonine-protein kinase shk2 (EC 2.7.11.1)	0.52	-	nuc	0					589
Q58CN8 UniProt NPD GO	SESN2_BOVIN	Sestrin-2	0.52	-	cyt	0					499
Q10572 UniProt NPD GO	FOX1_CAEEL	Sex determination protein fox-1 (Feminizing locus on X protein 1)	0.52	-	nuc	0	Nucleus (Potential)				415
O55063 UniProt NPD GO	SRY_APOAG	Sex-determining region Y protein (Testis-determining factor) (Fragment)	0.52	-	nuc	0	Nucleus				57
O55062 UniProt NPD GO	SRY_APOFL	Sex-determining region Y protein (Testis-determining factor) (Fragment)	0.52	-	nuc	0	Nucleus				57
O97859 UniProt NPD GO	NEUR3_BOVIN	Sialidase-3 (EC 3.2.1.18) (Membrane sialidase) (Ganglioside sialidase) (N-acetyl-alpha-neuraminidase ...	0.52	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				428
O75920 UniProt NPD GO	SERF1_HUMAN	Small EDRK-rich factor 1a	0.52	-	nuc	1			603011		110
O43927 UniProt NPD GO	SCYBD_HUMAN	Small inducible cytokine B13 precursor (CXCL13) (B lymphocyte chemoattractant) (CXC chemokine BLC) ( ...	0.52	-	exc	0	Secreted protein	soluble fraction [TAS]	605149		109
O42224 UniProt NPD GO	SMO_CHICK	Smoothened homolog precursor (SMO) (Fragment)	0.52	+	end	6	Membrane; multi-pass membrane protein				794
Q15036 UniProt NPD GO	SNX17_HUMAN	Sorting nexin-17	0.52	-	cyt	0	Cytoplasm. Endosome; early endosome. Associated with early endosomes	early endosome [IDA] Golgi apparatus [IDA] membrane [NAS]	605963		470
Q6AYS6 UniProt NPD GO	SNX17_RAT	Sorting nexin-17	0.52	-	cyt	0	Cytoplasm (By similarity). Endosome; early endosome (By similarity). Associated with early endosomes ...				470
O94291 UniProt NPD GO	SNX3_SCHPO	Sorting nexin-3	0.52	-	nuc	0	Cytoplasm (By similarity)				143
Q9XZV1 UniProt NPD GO	SWP1_ENCCU	Spore wall protein 1 precursor	0.52	-	exc	0					450
Q03441 UniProt NPD GO	RMD1_YEAST	Sporulation protein RMD1	0.52	-	nuc	1	Cytoplasm	cytoplasm [IDA]			430
Q8R4U0 UniProt NPD GO	STAB2_MOUSE	Stabilin-2 precursor [Contains: Short form stabilin-2]	0.52	-	exc	1	Cell membrane; single-pass type I membrane protein (By similarity)	external side of plasma membrane [ISS]			2559
Q80VJ2 UniProt NPD GO	SRA1_MOUSE	Steroid receptor RNA activator 1 (Steroid receptor RNA activator protein) (SRAP)	0.52	-	nuc	0	Nucleus. Cytoplasm (By similarity)	nucleus [ISS] ribonucleoprotein complex [ISS] transcription factor complex [IDA]			220
Q8LBZ7 UniProt NPD GO	DHSB1_ARATH	Succinate dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial precursor (EC 1.3.5.1) (IP ...	0.52	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA]			279
P39015 UniProt NPD GO	STM1_YEAST	Suppressor protein STM1 (GU4 nucleic-binding protein 2) (G4p2 protein) (Triplex-binding protein 1) ( ...	0.52	-	nuc	0	Cytoplasm. Nucleus. Cytoplasm; perinuclear region. Concentrated in the perinuclear region	cytoplasm [IDA] cytosolic ribosome (sensu Eukaryota) [IDA] nuclear telomere cap complex [IGI]			272
Q9R0N3 UniProt NPD GO	SYT11_MOUSE	Synaptotagmin-11 (Synaptotagmin XI) (SytXI)	0.52	+	nuc	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [IDA]			430
O00445 UniProt NPD GO	SYT5_HUMAN	Synaptotagmin-5 (Synaptotagmin V) (SytV)	0.52	+	nuc	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity). Endosome; ...		600782		386
P70452 UniProt NPD GO	STX4_MOUSE	Syntaxin-4	0.52	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)	cytoplasm [IDA] plasma membrane [IDA]			298
Q08850 UniProt NPD GO	STX4_RAT	Syntaxin-4	0.52	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)				298
Q12846 UniProt NPD GO	STX4_HUMAN	Syntaxin-4 (NY-REN-31 antigen)	0.52	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)	membrane [TAS]	186591		297
P06127 UniProt NPD GO	CD5_HUMAN	T-cell surface glycoprotein CD5 precursor (Lymphocyte antigen T1/Leu-1)	0.52	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS] plasma membrane [IDA]	153340		495
P30434 UniProt NPD GO	CD8B_PONPY	T-cell surface glycoprotein CD8 beta chain precursor (CD8b antigen)	0.52	-	end	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			210
Q9Y6J9 UniProt NPD GO	TAF6L_HUMAN	TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L (PCAF-ass ...	0.52	-	cyt	0	Nucleus	histone deacetylase complex [TAS]	602946		622
Q9NHP5 UniProt NPD GO	TBP_DROVI	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (Tr ...	0.52	-	nuc	0	Nucleus (By similarity)				349
Q92117 UniProt NPD GO	TBP_TRIFL	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (Tr ...	0.52	+	nuc	0	Nucleus				300
Q92146 UniProt NPD GO	TBP_TRIGA	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (Tr ...	0.52	+	nuc	0	Nucleus				302
P41842 UniProt NPD GO	YO91_CAEEL	TPR repeat-containing protein T20B12.1	0.52	-	cyt	0					787
O15482 UniProt NPD GO	TEX28_HUMAN	Testis-specific protein TEX28	0.52	-	nuc	1		integral to membrane [NAS]	300092		410
P52888 UniProt NPD GO	MEPD_HUMAN	Thimet oligopeptidase (EC 3.4.24.15) (Endopeptidase 24.15) (MP78)	0.52	-	cyt	0	Cytoplasm		601117	1S4B	688
Q8N427 UniProt NPD GO	TXND3_HUMAN	Thioredoxin domain-containing protein 3 (Spermatid-specific thioredoxin-2) (Sptrx-2) (NM23-H8)	0.52	-	cyt	0	Cytoplasm		607421		588
Q10587 UniProt NPD GO	TEF_HUMAN	Thyrotroph embryonic factor	0.52	+	nuc	0	Nucleus		188595		303
Q9MYW3 UniProt NPD GO	TLR4_HORSE	Toll-like receptor 4 precursor (CD284 antigen)	0.52	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	lipopolysaccharide receptor complex [ISS]			843
Q921P9 UniProt NPD GO	TCAL1_MOUSE	Transcription elongation factor A protein-like 1 (TCEA-like protein 1) (Transcription elongation fac ...	0.52	-	nuc	0	Nucleus (By similarity)				165
Q5PPP3 UniProt NPD GO	TCAL1_RAT	Transcription elongation factor A protein-like 1 (TCEA-like protein 1) (Transcription elongation fac ...	0.52	-	nuc	0	Nucleus (By similarity)				165
O13936 UniProt NPD GO	SPT5_SCHPO	Transcription elongation factor spt5 (Chromatin elongation factor spt5)	0.52	-	nuc	0	Nucleus				990
P05552 UniProt NPD GO	ADF1_DROME	Transcription factor Adf-1 (ADH distal factor 1)	0.52	+	nuc	0	Nucleus	nucleus [IDA]			253
Q06831 UniProt NPD GO	SOX4_MOUSE	Transcription factor SOX-4	0.52	-	nuc	0	Nucleus	nucleus [IDA]			440
Q6NZA9 UniProt NPD GO	TAF9B_MOUSE	Transcription initiation factor TFIID subunit 9B (Transcription initiation factor TFIID subunit 9-li ...	0.52	-	nuc	0	Nucleus (By similarity)				249
Q9R099 UniProt NPD GO	TBL2_MOUSE	Transducin beta-like 2 protein	0.52	-	nuc	1 *					442
Q9Y4P3 UniProt NPD GO	TBL2_HUMAN	Transducin beta-like 2 protein (WS beta-transducin repeats protein) (WS-betaTRP) (Williams-Beuren sy ...	0.52	-	nuc	1 *			605842		447

You are viewing entries 24001 to 24050 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.