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
Q6GPQ4 UniProt NPD GO	SMYD5_XENLA	SET and MYND domain-containing protein 5	0.47	-	nuc	0					421
P40652 UniProt NPD GO	MG43_TARMA	SRY-related protein MG43 (Fragment)	0.47	-	nuc	0	Nucleus (Potential)				72
P43554 UniProt NPD GO	SWP82_YEAST	SWI/SNF global transcription activator complex component SWP82	0.47	-	nuc	0	Nucleus	nucleus [IDA] SWI/SNF complex [IDA]			623
O74446 UniProt NPD GO	SIF2_SCHPO	Sad1-interacting factor 2	0.47	-	nuc	2	Nucleus; nuclear envelope; nuclear pore complex				446
P97299 UniProt NPD GO	SFRP2_MOUSE	Secreted frizzled-related protein 2 precursor (sFRP-2) (Secreted apoptosis-related protein 1) (SARP- ...	0.47	-	exc	0	Secreted protein				295
Q8K1I3 UniProt NPD GO	SPP24_MOUSE	Secreted phosphoprotein 24 precursor (Spp-24) (Secreted phosphoprotein 2)	0.47	-	nuc	0	Secreted protein				203
P06602 UniProt NPD GO	EVE_DROME	Segmentation protein even-skipped	0.47	+	nuc	2	Nucleus			1JGG	376
P05995 UniProt NPD GO	SVP1_CAVPO	Seminal vesicle major clotting proteins precursor [Contains: Seminal vesicle protein 1 (SVP-1); Semi ...	0.47	-	exc	0					396
Q13501 UniProt NPD GO	SQSTM_HUMAN	Sequestosome-1 (Phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa) (Ubiquitin-bind ...	0.47	-	nuc	0	Cytoplasm. In cardiac muscles localizes to the sarcomeric band (By similarity). Localizes to late en ...	cytosol [TAS]	601530	1Q02	440
P38147 UniProt NPD GO	CHK1_YEAST	Serine/threonine-protein kinase CHK1 (EC 2.7.11.1) (Checkpoint kinase 1)	0.47	-	mit	0	Nucleus (By similarity)	nucleus [IPI]			527
Q29502 UniProt NPD GO	PAK2_RABIT	Serine/threonine-protein kinase PAK 2 (EC 2.7.11.1) (p21-activated kinase 2) (PAK-2) (Gamma-PAK) (p2 ...	0.47	-	nuc	0					524
Q64303 UniProt NPD GO	PAK2_RAT	Serine/threonine-protein kinase PAK 2 (EC 2.7.11.1) (p21-activated kinase 2) (PAK-2) (Gamma-PAK) (p6 ...	0.47	-	nuc	0					524
P14747 UniProt NPD GO	PP2B2_YEAST	Serine/threonine-protein phosphatase 2B catalytic subunit A2 (EC 3.1.3.16) (Calcineurin A2) (Calmodu ...	0.47	-	nuc	0		calcineurin complex [IPI] cytoplasm [TAS]			604
P58004 UniProt NPD GO	SESN2_HUMAN	Sestrin-2 (Hi95)	0.47	-	cyt	0			607767		480
Q9WVL2 UniProt NPD GO	STAT2_MOUSE	Signal transducer and activator of transcription 2	0.47	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocated into the nucleus upon activation by ...	cytoplasm [IDA] nucleus [IDA]			923
Q14190 UniProt NPD GO	SIM2_HUMAN	Single-minded homolog 2	0.47	-	nuc	0	Nucleus		600892		667
Q9HEQ9 UniProt NPD GO	TCG1_SCHPO	Single-stranded TG1-3 DNA-binding protein	0.47	-	nuc	0	Nucleus (Potential)				348
Q99835 UniProt NPD GO	SMO_HUMAN	Smoothened homolog precursor (SMO) (Gx protein)	0.47	+	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS]	601500		787
P57769 UniProt NPD GO	SNX16_RAT	Sorting nexin-16	0.47	-	nuc	0					344
Q99932 UniProt NPD GO	SPAG8_HUMAN	Sperm-associated antigen 8 (Sperm membrane protein 1) (SMP-1) (HSD-1) (Sperm membrane protein BS-84) ...	0.47	-	nuc	0	Acrosome. Acrosomal region of the head of mature sperm cells		605731		426
Q8K4Z5 UniProt NPD GO	SF3A1_MOUSE	Splicing factor 3 subunit 1 (SF3a120)	0.47	-	nuc	0	Nucleus (By similarity)			1WE7	791
Q07843 UniProt NPD GO	YL033_YEAST	Sporulation protein YLL033W	0.47	-	nuc	0					230
P52020 UniProt NPD GO	ERG1_RAT	Squalene monooxygenase (EC 1.14.99.7) (Squalene epoxidase) (SE)	0.47	-	end	3 *	Microsome; microsomal membrane; multi-pass membrane protein				573
O15524 UniProt NPD GO	SOCS1_HUMAN	Suppressor of cytokine signaling 1 (SOCS-1) (JAK-binding protein) (JAB) (STAT-induced STAT inhibitor ...	0.47	+	nuc	0		cytoplasm [TAS]	603597		211
Q9BEG9 UniProt NPD GO	SOCS3_BOVIN	Suppressor of cytokine signaling 3 (SOCS-3)	0.47	-	nuc	0					229
Q68AM8 UniProt NPD GO	SOCS3_CANFA	Suppressor of cytokine signaling 3 (SOCS-3)	0.47	-	nuc	0					225
Q90X67 UniProt NPD GO	SOCS3_CHICK	Suppressor of cytokine signaling 3 (SOCS-3)	0.47	-	nuc	0					209
Q925B5 UniProt NPD GO	SYT13_RAT	Synaptotagmin-13 (Synaptotagmin XIII) (SytXIII)	0.47	-	nuc	1 *	Membrane; single-pass membrane protein (By similarity)				426
Q80XE1 UniProt NPD GO	RIC8B_MOUSE	Synembryn-B (Protein Ric-8B)	0.47	-	cyt	0	Cytoplasm; cell cortex (By similarity). Localizes to the cell cortex (By similarity)				560
P32854 UniProt NPD GO	PEP12_YEAST	Syntaxin PEP12	0.47	-	cyt	1	Membrane; single-pass type IV membrane protein (Potential)	endosome [IMP] Golgi apparatus [IMP]			288
O70439 UniProt NPD GO	STX7_MOUSE	Syntaxin-7	0.47	-	cyt	1	Endosome; early endosome; early endosomal membrane; single-pass type IV membrane protein (By similar ...			1GL2	260
Q6U7R4 UniProt NPD GO	TIMD4_MOUSE	T-cell immunoglobulin and mucin domain-containing protein 4 precursor (TIMD-4) (T-cell membrane prot ...	0.47	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)				343
Q08340 UniProt NPD GO	CD4_MACNE	T-cell surface glycoprotein CD4 precursor (T-cell surface antigen T4/Leu-3)	0.47	-	end	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			458
P10966 UniProt NPD GO	CD8B_HUMAN	T-cell surface glycoprotein CD8 beta chain precursor (CD8b antigen)	0.47	-	end	1	Cell membrane; single-pass type I membrane protein. Isoform 3: Secreted protein (Probable)	integral to plasma membrane [TAS] plasma membrane [TAS] T cell receptor complex [NAS]	186730		210
P10300 UniProt NPD GO	CD8B_MOUSE	T-cell surface glycoprotein CD8 beta chain precursor (T-cell surface glycoprotein Lyt-3) (T-cell mem ...	0.47	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA] T cell receptor complex [ISS]		2ATP	213
O24160 UniProt NPD GO	TGA21_TOBAC	TGACG-sequence-specific DNA-binding protein TGA-2.1 (TGA2.1)	0.47	-	nuc	0	Nucleus (By similarity)				456
P59924 UniProt NPD GO	THOC1_RAT	THO complex subunit 1 (Tho1) (Nuclear matrix protein p84) (Liver regeneration-related protein LRRG17 ...	0.47	-	cyt	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Nucleus; nucleoplasm; nuclear matrix (By simi ...				343
O12940 UniProt NPD GO	TOM1_CHICK	Target of Myb protein 1 (Tom-1 protein)	0.47	-	nuc	0	Cytoplasm (Probable)				515
Q8BKV0 UniProt NPD GO	TICN3_MOUSE	Testican-3 precursor (SPARC/osteonectin, CWCV, and Kazal-like domains proteoglycan 3)	0.47	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)				436
Q9R1M3 UniProt NPD GO	TSPY1_RAT	Testis-specific Y-encoded protein 1 (rTSPY)	0.47	-	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Also found in nucleus (By similar ...				334
Q96PF2 UniProt NPD GO	TSSK2_HUMAN	Testis-specific serine/threonine-protein kinase 2 (EC 2.7.11.1) (TSSK-2) (Testis-specific kinase 2) ...	0.47	-	nuc	0	Cytoplasm (By similarity)				358
Q9ULT0 UniProt NPD GO	TTC7A_HUMAN	Tetratricopeptide repeat protein 7A (TPR repeat protein 7)	0.47	-	cyt	0			609332		858
Q6P902 UniProt NPD GO	TXND2_MOUSE	Thioredoxin domain-containing protein 2 (Spermatid-specific thioredoxin-1) (Sptrx-1) (Thioredoxin-4) ...	0.47	-	nuc	0	Cytoplasm	flagellum (sensu Eukaryota) [IDA]			515
Q02965 UniProt NPD GO	THB_RANCA	Thyroid hormone receptor beta	0.47	+	cyt	0	Nucleus				373
O54819 UniProt NPD GO	TFPI1_MOUSE	Tissue factor pathway inhibitor precursor (TFPI) (Lipoprotein-associated coagulation inhibitor) (LAC ...	0.47	-	exc	0	Secreted protein				306
Q5I2M8 UniProt NPD GO	TLR9_CANFA	Toll-like receptor 9 precursor (CD289 antigen)	0.47	-	end	0	Membrane; single-pass type I membrane protein (By similarity)				1032
Q99JY4 UniProt NPD GO	TRABD_MOUSE	TraB domain-containing protein	0.47	-	cyt	0					376
P79782 UniProt NPD GO	TCF15_CHICK	Transcription factor 15 (bHLH-EC2 protein) (Paraxis)	0.47	-	nuc	0	Nucleus (By similarity)				183
Q6BEB4 UniProt NPD GO	SP5_HUMAN	Transcription factor Sp5	0.47	-	nuc	0	Nucleus (By similarity)		609391		398
Q8TDD2 UniProt NPD GO	SP7_HUMAN	Transcription factor Sp7 (Zinc finger protein osterix)	0.47	-	nuc	0	Nucleus (By similarity)		606633		431

You are viewing entries 27251 to 27300 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.