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
Q864S7 UniProt NPD GO	SOMA_BOSMU	Somatotropin precursor (Growth hormone)	0.28	-	exc	1 *	Secreted protein				217
P01246 UniProt NPD GO	SOMA_BOVIN	Somatotropin precursor (Growth hormone)	0.28	-	exc	1 *	Secreted protein			1BST	217
P33711 UniProt NPD GO	SOMA_CANFA	Somatotropin precursor (Growth hormone)	0.28	-	exc	0	Secreted protein				216
P56437 UniProt NPD GO	SOMA_CEREL	Somatotropin precursor (Growth hormone)	0.28	-	exc	0	Secreted protein				217
P79885 UniProt NPD GO	SOMA_LEPOS	Somatotropin precursor (Growth hormone)	0.28	-	cyt	1 *	Secreted protein				211
Q07221 UniProt NPD GO	SOMA_ONCTS	Somatotropin precursor (Growth hormone)	0.28	-	nuc	0	Secreted protein				210
P10813 UniProt NPD GO	SOMA_RANCA	Somatotropin precursor (Growth hormone)	0.28	-	mit	0	Secreted protein				215
Q7SH92 UniProt NPD GO	SNX3_NEUCR	Sorting nexin-3	0.28	-	cyt	0	Cytoplasm (By similarity)				142
Q15506 UniProt NPD GO	SP17_HUMAN	Sperm surface protein Sp17 (Sperm autoantigenic protein 17) (Sperm protein 17) (Sp17-1)	0.28	+	nuc	0	Membrane; peripheral membrane protein (Potential)		608621		151
Q92206 UniProt NPD GO	ERG1_CANAL	Squalene monooxygenase (EC 1.14.99.7) (Squalene epoxidase) (SE)	0.28	-	end	2	Microsome; microsomal membrane; multi-pass membrane protein				496
P52019 UniProt NPD GO	ERG1_MOUSE	Squalene monooxygenase (EC 1.14.99.7) (Squalene epoxidase) (SE)	0.28	-	end	1 *	Microsome; microsomal membrane; multi-pass membrane protein				572
Q9NQZ5 UniProt NPD GO	STAR7_HUMAN	StAR-related lipid transfer protein 7 (StARD7) (START domain-containing protein 7) (Protein GTT1)	0.28	-	cyt	0					295
Q78PY7 UniProt NPD GO	SND1_MOUSE	Staphylococcal nuclease domain-containing protein 1 (p100 co-activator) (100 kDa coactivator)	0.28	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). In IL-4 stimulated cells colocalizes with STAT6 ...				910
Q966Y3 UniProt NPD GO	JNK_SUBDO	Stress-activated protein kinase JNK (EC 2.7.11.24)	0.28	-	cyt	0					361
Q8WQG9 UniProt NPD GO	JNK1_CAEEL	Stress-activated protein kinase jnk-1 (EC 2.7.11.24)	0.28	-	cyt	0					463
O35400 UniProt NPD GO	ST2B1_MOUSE	Sulfotransferase family cytosolic 2B member 1 (EC 2.8.2.2) (Sulfotransferase 2B1) (Sulfotransferase ...	0.28	-	cyt	0	Cytoplasm (By similarity)				338
P21978 UniProt NPD GO	GP46_LEIAM	Surface membrane glycoprotein GP46/M-2 precursor	0.28	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor				476
P36976 UniProt NPD GO	SNP25_TORMA	Synaptosomal-associated protein 25 (SNAP-25) (Synaptosomal-associated 25 kDa protein)	0.28	-	nuc	0	Complexed with macromolecular elements of the nerve terminal				210
Q946Y7 UniProt NPD GO	SYP61_ARATH	Syntaxin-61 (AtSYP61) (Osmotic stress-sensitive mutant 1)	0.28	+	nuc	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type IV membrane pro ...				245
Q28288 UniProt NPD GO	STXB2_CANFA	Syntaxin-binding protein 2 (Unc-18 homolog 2) (Unc-18B) (Unc18-2)	0.28	-	cyt	0					593
Q15833 UniProt NPD GO	STXB2_HUMAN	Syntaxin-binding protein 2 (Unc-18 homolog 2) (Unc-18B) (Unc18-2)	0.28	-	cyt	0			601717		593
Q16559 UniProt NPD GO	TAL2_HUMAN	T-cell acute lymphocytic leukemia-2 protein (TAL-2 protein)	0.28	-	nuc	0			186855		108
Q7RRM4 UniProt NPD GO	TIP_PLAYO	T-cell immunomodulatory protein homolog precursor	0.28	-	end	1	Membrane; single-pass type I membrane protein (Potential)				701
P80318 UniProt NPD GO	TCPG_MOUSE	T-complex protein 1 subunit gamma (TCP-1-gamma) (CCT-gamma) (Matricin) (mTRiC-P5)	0.28	-	cyt	0	Cytoplasm	chaperonin-containing T-complex [IDA]		1GN1	545
Q8VD76 UniProt NPD GO	TF2H3_MOUSE	TFIIH basal transcription factor complex p34 subunit (Basic transcription factor 2 34 kDa subunit) ( ...	0.28	-	cyt	0	Nucleus (By similarity)				309
Q03167 UniProt NPD GO	TGBR3_HUMAN	TGF-beta receptor type III precursor (TGFR-3) (Transforming growth factor beta receptor III) (Betagl ...	0.28	-	end	1	Secreted protein. Secreted protein; extracellular space. Cell membrane; single-pass type I membrane ...	integral to membrane [TAS]	600742		850
Q5NVM3 UniProt NPD GO	THA10_PONPY	THAP domain-containing protein 10	0.28	-	nuc	0					264
P34410 UniProt NPD GO	TWK7_CAEEL	TWiK family of potassium channels protein 7	0.28	-	end	6	Membrane; multi-pass membrane protein (Potential)				557
Q70YC4 UniProt NPD GO	TALAN_HUMAN	Talanin	0.28	-	nuc	0			607818		216
Q9JKE8 UniProt NPD GO	TR110_RAT	Taste receptor type 2 member 110 (T2R110) (Taste receptor type 2 member 10) (T2R10)	0.28	+	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			333
P59528 UniProt NPD GO	T2R23_MOUSE	Taste receptor type 2 member 23 (T2R23) (STC9-2)	0.28	+	end	7 *	Membrane; multi-pass membrane protein				333
P38866 UniProt NPD GO	FMO1_YEAST	Thiol-specific monooxygenase (EC 1.14.13.-) (Flavin-dependent monooxygenase)	0.28	-	cyt	0		endoplasmic reticulum membrane [IDA]			432
Q5R5P3 UniProt NPD GO	THNSL_PONPY	Threonine synthase-like 1	0.28	-	cyt	0					743
P35443 UniProt NPD GO	TSP4_HUMAN	Thrombospondin-4 precursor	0.28	-	exc	0		extracellular matrix (sensu Metazoa) [TAS]	600715		961
Q9QZ06 UniProt NPD GO	TOLIP_MOUSE	Toll-interacting protein	0.28	-	cyt	0	Cytoplasm (Probable)	interleukin-1 receptor complex [ISS] interleukin-18 receptor complex [ISS]			274
Q9ER38 UniProt NPD GO	TOR3A_MOUSE	Torsin-3A precursor (Torsin family 3 member A) (ATP-dependent interferon-responsive protein)	0.28	-	exc	0	Cytoplasm. Endoplasmic reticulum (By similarity)				385
P81694 UniProt NPD GO	TXC1_CUPSA	Toxin CSTX-1 [Contains: Toxin CSTX-2a; Toxin CSTX-2b]	0.28	-	nuc	0	Secreted protein				74
P13742 UniProt NPD GO	REP2_ZYGFE	Trans-acting factor C (REP2)	0.28	-	cyt	0					200
O81928 UniProt NPD GO	TCMO_CICAR	Trans-cinnamate 4-monooxygenase (EC 1.14.13.11) (Cinnamic acid 4-hydroxylase) (CA4H) (C4H) (P450C4H) ...	0.28	-	end	0					505
Q9R0D6 UniProt NPD GO	TCO2_RAT	Transcobalamin-2 precursor (Transcobalamin II) (TCII) (TC II)	0.28	-	mit	0	Secreted protein				427
Q18885 UniProt NPD GO	BTF3_CAEEL	Transcription factor BTF3 homolog (Inhibitor of cell death 1)	0.28	-	nuc	0	Nucleus (Probable)				161
Q9SS44 UniProt NPD GO	TF2B2_ARATH	Transcription initiation factor IIB-2 (General transcription factor TFIIB-2) (AtTFIIB2)	0.28	-	nuc	0	Nucleus				312
Q9HBA0 UniProt NPD GO	TRPV4_HUMAN	Transient receptor potential cation channel subfamily V member 4 (TrpV4) (osm-9-like TRP channel 4) ...	0.28	+	end	6	Membrane; multi-pass membrane protein (Probable)	plasma membrane [IDA]	605427		871
Q94KR7 UniProt NPD GO	IF1C_SOYBN	Translation initiation factor IF-1, chloroplast precursor	0.28	-	nuc	0	Plastid; chloroplast				138
Q9XEK9 UniProt NPD GO	IF2C_EUGGR	Translation initiation factor IF-2, chloroplast (Fragment)	0.28	-	nuc	0	Plastid; chloroplast				822
Q62818 UniProt NPD GO	EI2BB_RAT	Translation initiation factor eIF-2B subunit beta (eIF-2B GDP-GTP exchange factor subunit beta)	0.28	-	cyt	0		eukaryotic translation initiation factor 2B... [TAS]			351
P47823 UniProt NPD GO	EI2BE_RABIT	Translation initiation factor eIF-2B subunit epsilon (eIF-2B GDP-GTP exchange factor subunit epsilon ...	0.28	-	cyt	0					721
Q6BI99 UniProt NPD GO	SEC62_DEBHA	Translocation protein SEC62	0.28	-	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				278
Q9QYM9 UniProt NPD GO	TEFF2_MOUSE	Transmembrane protein with EGF-like and two follistatin-like domains 2 precursor (Tomoregulin) (TR)	0.28	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				374
Q9C029 UniProt NPD GO	TRIM7_HUMAN	Tripartite motif-containing protein 7 (Glycogenin-interacting protein) (RING finger protein 90)	0.28	-	cyt	0			609315		511

You are viewing entries 42751 to 42800 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.