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
Q9TUG2 UniProt NPD GO	SKI_HORSE	Ski oncogene (C-ski)	0.91	+	nuc	0	Nucleus (By similarity)				730
Q9BX66 UniProt NPD GO	SRBS1_HUMAN	Sorbin and SH3 domain-containing protein 1 (Ponsin) (c-Cbl-associated protein) (CAP) (SH3 domain pro ...	0.91	-	nuc	0	Cell membrane; cell-cell junction; adherens junction. Cell membrane; cell-matrix junction; adherens ...	cell-substrate adherens junction [ISS] lipid raft [ISS] nucleus [IDA] stress fiber [ISS] zonula adherens [TAS]	605264		1292
Q13813 UniProt NPD GO	SPTA2_HUMAN	Spectrin alpha chain, brain (Spectrin, non-erythroid alpha chain) (Alpha-II spectrin) (Fodrin alpha ...	0.91	-	nuc	0		membrane fraction [TAS] spectrin [TAS]	182810		2472
P16086 UniProt NPD GO	SPTA2_RAT	Spectrin alpha chain, brain (Spectrin, non-erythroid alpha chain) (Alpha-II spectrin) (Fodrin alpha ...	0.91	-	nuc	0					2472
P07751 UniProt NPD GO	SPTA2_CHICK	Spectrin alpha chain, brain (Spectrin, non-erythroid alpha chain) (Fodrin alpha chain)	0.91	-	nuc	0				1UUE	2477
Q9QWN8 UniProt NPD GO	SPTN2_RAT	Spectrin beta chain, brain 2 (Spectrin, non-erythroid beta chain 2) (Beta-III spectrin) (SPNB-3) (Be ...	0.91	-	nuc	0		cytoplasm [TAS] nuclear matrix [TAS] spectrin [TAS]			2388
P15508 UniProt NPD GO	SPTB1_MOUSE	Spectrin beta chain, erythrocyte (Beta-I spectrin)	0.91	-	cyt	0		plasma membrane [IDA]			2127
Q60JJ0 UniProt NPD GO	SAS4_CAEBR	Spindle assembly abnormal protein 4	0.91	-	nuc	0	Centrosome (By similarity). Localizes to the centrosome throughout the cell cycle. Localizes to a ti ...				761
Q13435 UniProt NPD GO	SF3B2_HUMAN	Splicing factor 3B subunit 2 (Spliceosome-associated protein 145) (SAP 145) (SF3b150) (Pre-mRNA-spli ...	0.91	+	nuc	0	Nucleus (By similarity)	spliceosome complex [IDA]	605591		872
Q9W770 UniProt NPD GO	SPON1_CHICK	Spondin-1 precursor (F-spondin)	0.91	+	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				802
Q9GLX9 UniProt NPD GO	SPON1_BOVIN	Spondin-1 precursor (F-spondin) (Vascular smooth muscle cell growth-promoting factor)	0.91	+	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				807
Q9HCB6 UniProt NPD GO	SPON1_HUMAN	Spondin-1 precursor (F-spondin) (Vascular smooth muscle cell growth-promoting factor)	0.91	+	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		604989		807
Q12411 UniProt NPD GO	MPC70_YEAST	Sporulation-specific protein 21 (Meiotic plaque component protein 70)	0.91	-	nuc	0	Localizes to prospore membrane. Localizes to the ends of spindle microtubules in cells in meiosis	spindle pole body [IDA]			609
P93015 UniProt NPD GO	SPL3_ARATH	Squamosa promoter-binding-like protein 3	0.91	-	nuc	0	Nucleus (Probable)				131
P83094 UniProt NPD GO	STIM_DROME	Stromal interaction molecule homolog precursor	0.91	-	nuc	1	Cell membrane; single-pass type I membrane protein (Potential)				570
P47037 UniProt NPD GO	SMC3_YEAST	Structural maintenance of chromosome 3 (DA-box protein SMC3)	0.91	-	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. At anapha ...	nuclear cohesin complex [TAS] nucleus [IDA]			1230
Q924W7 UniProt NPD GO	ST5_MOUSE	Suppression of tumorigenicity 5 (DENN domain-containing protein 2B)	0.91	+	nuc	0					1134
Q74Z37 UniProt NPD GO	SEF1_ASHGO	Suppressor protein SEF1 homolog	0.91	+	nuc	0	Nucleus (Potential)				1051
Q9H987 UniProt NPD GO	SYP2L_HUMAN	Synaptopodin 2-like protein	0.91	+	nuc	0	Cytoplasm (By similarity)				977
Q8BWB1 UniProt NPD GO	SYP2L_MOUSE	Synaptopodin 2-like protein	0.91	-	nuc	0	Cytoplasm (By similarity)				975
Q9R0Q1 UniProt NPD GO	SYTL4_MOUSE	Synaptotagmin-like protein 4 (Exophilin-2) (Granuphilin)	0.91	-	nuc	0	Membrane; peripheral membrane protein. Detected close to the plasma membrane and on secretory granul ...	extrinsic to plasma membrane [IDA] secretory granule [IDA]			673
P87377 UniProt NPD GO	VEGT_XENLA	T-box protein VEGT (T-box protein BRAT) (T-box protein antipodean)	0.91	-	nuc	0	Nucleus				455
Q8K2L9 UniProt NPD GO	TAGAP_MOUSE	T-cell activation Rho GTPase-activating protein (T-cell activation GTPase-activating protein)	0.91	+	nuc	0					714
P37998 UniProt NPD GO	CD2_HORSE	T-cell surface antigen CD2 precursor	0.91	-	end	1	Membrane; single-pass type I membrane protein				347
P32333 UniProt NPD GO	MOT1_YEAST	TATA-binding protein-associated factor MOT1 (EC 3.6.1.-) (TBP-associated factor MOT1) (Modifier of t ...	0.91	-	nuc	0	Mitochondrion. Nucleus. Localized on chromatin. Specifically localized to the promoters of the genes ...	mitochondrion [IDA] nuclear chromosome [IDA]			1867
Q86TI0 UniProt NPD GO	TBCD1_HUMAN	TBC1 domain family member 1	0.91	-	nuc	0	Nucleus (By similarity)		609850		1168
Q80YF9 UniProt NPD GO	TCGAP_MOUSE	TC10/CDC42 GTPase-activating protein (Sorting nexin-26)	0.91	-	nuc	0	Translocates to the plasma membrane in response to insulin in adipocytes	cytoplasm [IDA] plasma membrane [IDA]			1305
Q6P3Z3 UniProt NPD GO	THAP4_MOUSE	THAP domain-containing protein 4	0.91	-	nuc	0					569
Q9BT49 UniProt NPD GO	THAP7_HUMAN	THAP domain-containing protein 7	0.91	-	nuc	0			609518		309
Q8RYD9 UniProt NPD GO	TT16_ARATH	TRANSPARENT TESTA 16 protein (Arabidopsis BSISTER MADS-box protein)	0.91	+	nuc	0	Nucleus (By similarity)				252
Q7Z7G0 UniProt NPD GO	TARSH_HUMAN	Target of Nesh-SH3 precursor (Tarsh) (Nesh-binding protein) (NeshBP) (ABI gene family member 3-bindi ...	0.91	-	nuc	1 *			606279		1075
Q6ZSZ6 UniProt NPD GO	TSH1_HUMAN	Teashirt homolog 1 (Serologically defined colon cancer antigen 3) (Antigen NY-CO-33)	0.91	-	nuc	0	Nucleus (Probable)				1077
Q9NXF1 UniProt NPD GO	TEX10_HUMAN	Testis-expressed sequence 10 protein	0.91	+	end	0	Nucleus; nuclear membrane; multi-pass membrane protein. Nucleus; nucleolus				929
P60531 UniProt NPD GO	TSKS_RAT	Testis-specific serine kinase substrate (Testis-specific kinase substrate) (STK22 substrate 1)	0.91	-	nuc	0					585
P04625 UniProt NPD GO	THA_CHICK	Thyroid hormone receptor alpha	0.91	+	nuc	0	Nucleus				408
Q9W6N4 UniProt NPD GO	THA_HIPHI	Thyroid hormone receptor alpha	0.91	+	nuc	0	Nucleus				416
O57606 UniProt NPD GO	THA_NECMA	Thyroid hormone receptor alpha	0.91	+	nuc	0	Nucleus				408
Q90382 UniProt NPD GO	THA_CAIMO	Thyroid hormone receptor alpha (Fragment)	0.91	+	nuc	0	Nucleus				401
Q9HCS4 UniProt NPD GO	TF7L1_HUMAN	Transcription factor 7-like 1 (HMG box transcription factor 3) (TCF-3)	0.91	+	nuc	0	Nucleus	nucleus [NAS]	604652		588
Q9LEZ3 UniProt NPD GO	BIM1_ARATH	Transcription factor BIM1 (BES1-interacting Myc-like protein 1) (Transcription factor EN 126) (AtbHL ...	0.91	-	nuc	0	Nucleus (Probable)				530
Q5EAD3 UniProt NPD GO	NFE2_BOVIN	Transcription factor NF-E2 45 kDa subunit (Nuclear factor, erythroid-derived 2 45 kDa subunit) (p45 ...	0.91	+	nuc	0	Nucleus (By similarity)				374
Q8CGW4 UniProt NPD GO	SOX30_MOUSE	Transcription factor SOX-30	0.91	-	nuc	0	Nucleus (By similarity)				782
P35711 UniProt NPD GO	SOX5_HUMAN	Transcription factor SOX-5	0.91	-	nuc	0	Nucleus (By similarity)		604975		763
P35710 UniProt NPD GO	SOX5_MOUSE	Transcription factor SOX-5	0.91	-	nuc	0	Nucleus			1I11	763
Q04207 UniProt NPD GO	TF65_MOUSE	Transcription factor p65 (Nuclear factor NF-kappa-B p65 subunit)	0.91	+	nuc	0	Nucleus. Cytoplasm. Nuclear, but also found in the cytoplasm in an inactive form complexed to an inh ...	cytoplasm [IDA] nucleus [IDA]		2RAM	549
Q03750 UniProt NPD GO	TAF8_YEAST	Transcription initiation factor TFIID subunit 8 (TBP-associated factor 8) (TBP-associated factor 65 ...	0.91	-	nuc	0	Nucleus	nucleus [IDA] transcription factor TFIID complex [IDA]			510
P38811 UniProt NPD GO	TRA1_YEAST	Transcription-associated protein 1 (p400 kDa component of SAGA)	0.91	-	nuc	0	Nucleus (Probable)	H4/H2A histone acetyltransferase complex [IPI] SLIK (SAGA-like) complex [IPI]			3744
Q9FUY2 UniProt NPD GO	LEUNG_ARATH	Transcriptional corepressor LEUNIG	0.91	-	nuc	0	Nucleus				931
Q8NI51 UniProt NPD GO	BORIS_HUMAN	Transcriptional repressor CTCFL (CCCTC-binding factor) (Brother of the regulator of imprinted sites) ...	0.91	+	nuc	0	Cytoplasm. Nucleus		607022		663
Q9PTQ2 UniProt NPD GO	TGFB1_CYPCA	Transforming growth factor beta-1 precursor (TGF-beta-1)	0.91	-	exc	0	Secreted protein				376

You are viewing entries 3951 to 4000 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.