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
P27014 UniProt NPD GO	SCRY2_OCTVU	S-crystallin 2	0.43	-	nuc	0					215
Q25626 UniProt NPD GO	SCRY3_OCTVU	S-crystallin 3	0.43	-	nuc	0					215
P57086 UniProt NPD GO	SCND1_HUMAN	SCAN domain-containing protein 1	0.43	-	nuc	0	Nucleus (Potential)	nucleus [ISS]			179
Q96IW2 UniProt NPD GO	SHD_HUMAN	SH2 domain-containing adapter protein D	0.43	-	nuc	0					340
P97306 UniProt NPD GO	STAC_MOUSE	SH3 and cysteine-rich domain-containing protein (SRC homology 3 and cysteine-rich domain protein)	0.43	-	nuc	0	Cytoplasm				403
Q640F2 UniProt NPD GO	SHCBB_XENLA	SHC SH2 domain-binding protein 1 homolog B	0.43	-	mit	0					698
P23327 UniProt NPD GO	SRCH_HUMAN	Sarcoplasmic reticulum histidine-rich calcium-binding protein precursor	0.43	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen		142705		699
Q13103 UniProt NPD GO	SPP24_HUMAN	Secreted phosphoprotein 24 precursor (Spp-24) (Secreted phosphoprotein 2)	0.43	-	nuc	0	Secreted protein		602637		211
O95754 UniProt NPD GO	SEM4F_HUMAN	Semaphorin-4F precursor (Semaphorin W) (Sema W) (Semaphorin M) (Sema M)	0.43	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS] plasma membrane [TAS]	603706		770
Q9QUR8 UniProt NPD GO	SEM7A_MOUSE	Semaphorin-7A precursor (Semaphorin L) (Sema L) (Semaphorin K1) (Sema K1) (CD108 antigen) (CDw108)	0.43	-	nuc	1	Cell membrane; lipid-anchor; GPI-anchor				664
Q64337 UniProt NPD GO	SQSTM_MOUSE	Sequestosome-1 (Ubiquitin-binding protein p62) (STONE14)	0.43	-	nuc	0	Cytoplasm. In cardiac muscles localizes to the sarcomeric band. Localizes to late endosomes. May als ...	cytosol [ISS]			442
Q39247 UniProt NPD GO	2ABB_ARATH	Serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform (PP2A, subunit B, b ...	0.43	-	nuc	0					501
Q9UQB9 UniProt NPD GO	AURKC_HUMAN	Serine/threonine-protein kinase 13 (EC 2.7.11.1) (Aurora/Ipl1/Eg2 protein 2) (Aurora/Ipl1-related ki ...	0.43	-	cyt	0	Centrosome. Localized to centrosome from anaphase to cytokinesis	centrosome [TAS] nucleus [TAS]	603495		309
Q6DE87 UniProt NPD GO	CHK1_XENLA	Serine/threonine-protein kinase Chk1 (EC 2.7.11.1) (xChk1 protein)	0.43	-	cyt	0	Cytoplasm. Nucleus				474
Q00536 UniProt NPD GO	PCTK1_HUMAN	Serine/threonine-protein kinase PCTAIRE-1 (EC 2.7.11.22) (PCTAIRE-motif protein kinase 1)	0.43	-	nuc	0			311550		496
Q96BR1 UniProt NPD GO	SGK3_HUMAN	Serine/threonine-protein kinase Sgk3 (EC 2.7.11.1) (Serum/glucocorticoid-regulated kinase 3) (Serum/ ...	0.43	-	cyt	0	Cytoplasmic vesicle (By similarity). Endosome; early endosome (By similarity). Localized in vesicle- ...		607591		496
Q17941 UniProt NPD GO	AKT1_CAEEL	Serine/threonine-protein kinase akt-1 (EC 2.7.11.1) (Protein kinase B akt-1) (PKB akt-1)	0.43	-	nuc	0		intracellular [IDA]			541
Q9Z2E3 UniProt NPD GO	ERN2_MOUSE	Serine/threonine-protein kinase/endoribonuclease IRE2 precursor (Inositol-requiring protein 2) (IRE1 ...	0.43	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein				911
Q6CYH1 UniProt NPD GO	PTPA1_KLULA	Serine/threonine-protein phosphatase 2A activator 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.43	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				353
P48457 UniProt NPD GO	PP2B_EMENI	Serine/threonine-protein phosphatase 2B catalytic subunit (EC 3.1.3.16) (Calmodulin-dependent calcin ...	0.43	-	cyt	0					530
O82733 UniProt NPD GO	PP17_ARATH	Serine/threonine-protein phosphatase PP1 isozyme 7 (EC 3.1.3.16)	0.43	-	cyt	0					331
P23880 UniProt NPD GO	PP12_SCHPO	Serine/threonine-protein phosphatase PP1-2 (EC 3.1.3.16) (Suppressor protein SDS21)	0.43	-	cyt	0					322
P36394 UniProt NPD GO	SRY_RAT	Sex-determining region Y protein (Testis-determining factor) (Fragment)	0.43	-	nuc	0	Nucleus				121
Q9Y210 UniProt NPD GO	TRPC6_HUMAN	Short transient receptor potential channel 6 (TrpC6)	0.43	-	end	6	Membrane; multi-pass membrane protein (Probable)	plasma membrane [TAS]	603965		931
Q943Z6 UniProt NPD GO	SRP19_ARATH	Signal recognition particle 19 kDa protein (SRP19)	0.43	-	nuc	0	Cytoplasm				145
P47017 UniProt NPD GO	LSM1_YEAST	Sm-like protein LSm1 (SPB8 protein)	0.43	-	nuc	0	Nucleus. Cytoplasm	cytoplasmic mRNA processing body [IDA] mRNA cap complex [IPI]			172
O60721 UniProt NPD GO	NCKX1_HUMAN	Sodium/potassium/calcium exchanger 1 (Na(+)/K(+)/Ca(2+)-exchange protein 1) (Retinal rod Na-Ca+K exc ...	0.43	-	end	11 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS] outer membrane [NAS]	603617		1099
Q60549 UniProt NPD GO	SLIB_MESAU	Somatoliberin precursor (Growth hormone-releasing factor) (GRF) (Growth hormone-releasing hormone) ( ...	0.43	-	nuc	0	Secreted protein				107
P01170 UniProt NPD GO	SMS2_LOPAM	Somatostatin-2 precursor (Somatostatin II) [Contains: [Tyr7,Gly10]-somatostatin-14; [Tyr13,Gly16]-so ...	0.43	-	exc	0	Secreted protein				125
Q01282 UniProt NPD GO	SOMA_ACABU	Somatotropin precursor (Growth hormone)	0.43	-	exc	0	Secreted protein				204
P45654 UniProt NPD GO	SOMA_ACALA	Somatotropin precursor (Growth hormone)	0.43	-	exc	0	Secreted protein				204
P24363 UniProt NPD GO	SOMA_CARDE	Somatotropin precursor (Growth hormone)	0.43	-	nuc	0	Secreted protein				206
P29971 UniProt NPD GO	SOMA_SPAAU	Somatotropin precursor (Growth hormone)	0.43	-	exc	0	Secreted protein				204
Q10916 UniProt NPD GO	ASM1_CAEEL	Sphingomyelin phosphodiesterase 1 precursor (EC 3.1.4.12) (Acid sphingomyelinase 1)	0.43	-	mit	0	Secreted protein	extracellular region [IDA]			564
P70114 UniProt NPD GO	STAR_MESAU	Steroidogenic acute regulatory protein, mitochondrial precursor (StAR) (StARD1)	0.43	-	mit	0	Mitochondrion			1ILJ	284
P92208 UniProt NPD GO	JNK_DROME	Stress-activated protein kinase JNK (EC 2.7.11.24) (dJNK) (Protein basket)	0.43	-	cyt	0	Cytoplasm (By similarity)				372
P21912 UniProt NPD GO	DHSB_HUMAN	Succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (EC 1.3.5.1) (Ip) ...	0.43	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [TAS]	185470		280
P25604 UniProt NPD GO	STP22_YEAST	Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease (Vacuo ...	0.43	-	nuc	0	Cytoplasm. Endosome	endosome [IDA] ESCRT I complex [IDA]		2F6M	385
Q8C6N3 UniProt NPD GO	SYT15_MOUSE	Synaptotagmin-15 (Synaptotagmin XV) (SytXV)	0.43	-	mit	1 *	Membrane; single-pass type III membrane protein	integral to membrane of membrane fraction [IDA]			418
Q9NPQ8 UniProt NPD GO	RIC8A_HUMAN	Synembryn-A (Protein Ric-8A)	0.43	-	nuc	0	Cytoplasm (By similarity)		609146		530
Q9JKK1 UniProt NPD GO	STX6_MOUSE	Syntaxin-6	0.43	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				255
Q63635 UniProt NPD GO	STX6_RAT	Syntaxin-6	0.43	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)	Golgi apparatus [IDA]		1LVF	255
P17542 UniProt NPD GO	TAL1_HUMAN	T-cell acute lymphocytic leukemia-1 protein (TAL-1 protein) (Stem cell protein) (T-cell leukemia/lym ...	0.43	-	nuc	0			187040		331
P46630 UniProt NPD GO	CD4_RABIT	T-cell surface glycoprotein CD4 precursor (T-cell surface antigen T4/Leu-3)	0.43	-	end	2 *	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			459
P33706 UniProt NPD GO	CD8A_CANFA	T-cell surface glycoprotein CD8 alpha chain precursor (CD8a antigen)	0.43	-	end	2	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			239
Q9HBG7 UniProt NPD GO	LY9_HUMAN	T-lymphocyte surface antigen Ly-9 precursor (Lymphocyte antigen 9) (Cell-surface molecule Ly-9) (CD2 ...	0.43	+	end	1	Membrane; single-pass type I membrane protein		600684		655
P53361 UniProt NPD GO	TBP_SPOFR	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.43	-	nuc	0	Nucleus				307
O45211 UniProt NPD GO	TBP_BOMMO	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (Tr ...	0.43	-	nuc	0	Nucleus				307
Q10438 UniProt NPD GO	YDE4_SCHPO	TTL domain-containing protein C12B10.04	0.43	-	nuc	0					403
P10039 UniProt NPD GO	TENA_CHICK	Tenascin precursor (TN) (Hexabrachion) (Cytotactin) (Neuronectin) (GMEM) (JI) (Miotendinous antigen) ...	0.43	-	nuc	0	Secreted protein; extracellular space; extracellular matrix			1QR4	1808

You are viewing entries 30001 to 30050 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.