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
Q61390 UniProt NPD GO	TCPW_MOUSE	T-complex protein 1 subunit zeta-2 (TCP-1-zeta-2) (CCT-zeta-2) (Cctz-2)	0.16	-	cyt	0	Cytoplasm				530
Q96KB5 UniProt NPD GO	TOPK_HUMAN	T-lymphokine-activated killer cell-originated protein kinase (EC 2.7.12.2) (T-LAK cell-originated pr ...	0.16	-	nuc	0					322
Q42808 UniProt NPD GO	TBP_SOYBN	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.16	-	mit	0	Nucleus				200
Q9D0K0 UniProt NPD GO	TBCD7_MOUSE	TBC1 domain family member 7	0.16	-	nuc	0					293
P80220 UniProt NPD GO	T22D3_PIG	TSC22 domain family protein 3 (Glucocorticoid-induced leucine zipper protein) (Delta sleep-inducing ...	0.16	-	nuc	0				1DIP	77
Q8WNQ8 UniProt NPD GO	TYOBP_MACMU	TYRO protein tyrosine kinase-binding protein precursor (DNAX-activation protein 12)	0.16	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				113
O15533 UniProt NPD GO	TPSN_HUMAN	Tapasin precursor (TPSN) (TPN) (TAP-binding protein) (TAP-associated protein) (NGS-17)	0.16	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (Probable ...	endoplasmic reticulum [TAS] endoplasmic reticulum membrane [IDA] Golgi membrane [IDA] integral to membrane [TAS] MHC class I peptide loading complex [NAS] microsome [NAS]	601962		448
Q9Z0R7 UniProt NPD GO	TS1R2_RAT	Taste receptor type 1 member 2 precursor (G-protein coupled receptor 71) (Sweet taste receptor T1R2) ...	0.16	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [IC]			843
Q645S5 UniProt NPD GO	T2R39_MACMU	Taste receptor type 2 member 39 (T2R39)	0.16	-	end	7 *	Membrane; multi-pass membrane protein				338
Q646C6 UniProt NPD GO	TA2R9_PANTR	Taste receptor type 2 member 9 (T2R9)	0.16	-	end	8 *	Membrane; multi-pass membrane protein				312
P16458 UniProt NPD GO	TEBB_OXYNO	Telomere-binding protein subunit beta (Telomere-binding protein 41 kDa subunit) (TEBP beta)	0.16	-	nuc	0	Nucleus			1PHJ	385
P82321 UniProt NPD GO	TERN_PSEUS	Termicin	0.16	-	nuc	0	Secreted protein			1MM0	36
Q2QLG8 UniProt NPD GO	TES_CALJA	Testin	0.16	-	nuc	0					421
Q2QLE3 UniProt NPD GO	TES_PIG	Testin	0.16	-	nuc	0					421
P55054 UniProt NPD GO	TLBP_RAT	Testis lipid-binding protein (TLBP) (15 kDa perforatorial protein) (PERF 15)	0.16	-	cyt	0	Cytoplasm (Potential)	acrosome [IDA]			132
Q9BXA6 UniProt NPD GO	TSSK6_HUMAN	Testis-specific serine/threonine-protein kinase 6 (EC 2.7.11.1) (TSSK-6) (Small serine/threonine kin ...	0.16	-	cyt	0					273
Q9R1A9 UniProt NPD GO	TREX2_MOUSE	Three prime repair exonuclease 2 (EC 3.1.11.2) (3'-5' exonuclease TREX2)	0.16	-	cyt	0	Nucleus (Probable)				236
P49746 UniProt NPD GO	TSP3_HUMAN	Thrombospondin-3 precursor	0.16	-	mit	0			188062		956
P82658 UniProt NPD GO	TL19_ARATH	Thylakoid lumenal 19 kDa protein, chloroplast precursor (P19)	0.16	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				229
P45352 UniProt NPD GO	TYSY_RAT	Thymidylate synthase (EC 2.1.1.45) (TS) (TSase)	0.16	-	cyt	0				2TSR	307
P48300 UniProt NPD GO	FUCO_CANFA	Tissue alpha-L-fucosidase precursor (EC 3.2.1.51) (Alpha-L-fucosidase I) (Alpha-L-fucoside fucohydro ...	0.16	-	exc	0	Lysosome				465
Q5QD16 UniProt NPD GO	TAAR3_MOUSE	Trace amine-associated receptor 3	0.16	-	end	7 *	Membrane; multi-pass membrane protein				343
Q5QD24 UniProt NPD GO	TAAR3_RAT	Trace amine-associated receptor 3	0.16	-	end	7 *	Membrane; multi-pass membrane protein				342
P37115 UniProt NPD GO	TCMO_PHAAU	Trans-cinnamate 4-monooxygenase (EC 1.14.13.11) (Cinnamic acid 4-hydroxylase) (CA4H) (C4H) (P450C4H) ...	0.16	-	end	0					505
Q2TBL6 UniProt NPD GO	TALDO_BOVIN	Transaldolase (EC 2.2.1.2)	0.16	-	nuc	0	Cytoplasm (Probable)				337
Q7Z2W7 UniProt NPD GO	TRPM8_HUMAN	Transient receptor potential cation channel subfamily M member 8 (Transient receptor potential-p8) ( ...	0.16	-	end	8	Membrane; multi-pass membrane protein (Probable)		606678		1104
P33315 UniProt NPD GO	TKT2_YEAST	Transketolase 2 (EC 2.2.1.1) (TK 2)	0.16	-	mit	0		cytoplasm [IDA] nucleus [IDA]			681
Q9NR50 UniProt NPD GO	EI2BG_HUMAN	Translation initiation factor eIF-2B subunit gamma (eIF-2B GDP-GTP exchange factor subunit gamma)	0.16	-	cyt	0		cytoplasm [TAS]	606273		452
Q15631 UniProt NPD GO	TSN_HUMAN	Translin	0.16	-	cyt	0	Nucleus	nucleus [TAS]	600575	1J1J	228
Q38906 UniProt NPD GO	TOC34_ARATH	Translocase of chloroplast 34 (EC 3.6.5.-) (34 kDa chloroplast outer envelope protein) (GTP-binding ...	0.16	-	cyt	0	Plastid; chloroplast; chloroplast outer membrane				313
Q01685 UniProt NPD GO	TRAM1_CANFA	Translocation-associated membrane protein 1	0.16	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				373
Q15629 UniProt NPD GO	TRAM1_HUMAN	Translocation-associated membrane protein 1	0.16	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] integral to membrane [TAS]	605190		373
Q8BJZ3 UniProt NPD GO	TMBI1_MOUSE	Transmembrane BAX inhibitor motif-containing protein 1 (RECS1 protein) (Responsive to centrifugal fo ...	0.16	-	end	7	Membrane; multi-pass membrane protein (By similarity)				309
Q7Z7H5 UniProt NPD GO	TMED4_HUMAN	Transmembrane emp24 domain-containing protein 4 precursor	0.16	-	cyt	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				227
O60235 UniProt NPD GO	TM11D_HUMAN	Transmembrane protease, serine 11D precursor (EC 3.4.21.-) (Airway trypsin-like protease) [Contains: ...	0.16	-	mit	1 *	Cell membrane; single-pass type II membrane protein. Processed form: Secreted protein. Activated by ...	extracellular region [TAS] integral to plasma membrane [TAS]	605369		418
P17152 UniProt NPD GO	TMM11_HUMAN	Transmembrane protein 11 (Protein PM1)	0.16	-	mit	0	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [TAS]			192
Q6AYN2 UniProt NPD GO	TMM66_RAT	Transmembrane protein 66 precursor	0.16	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				334
P34502 UniProt NPD GO	TTR1_CAEEL	Transthyretin-like protein 1 precursor	0.16	-	nuc	0	Secreted protein (Potential)				156
Q8NIH3 UniProt NPD GO	TRI5_FUSBO	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.16	-	cyt	0					375
P16340 UniProt NPD GO	PUR2_DROPS	Trifunctional purine biosynthetic protein adenosine-3 [Includes: Phosphoribosylamine--glycine ligase ...	0.16	-	cyt	0					1364
P29144 UniProt NPD GO	TPP2_HUMAN	Tripeptidyl-peptidase 2 (EC 3.4.14.10) (Tripeptidyl-peptidase II) (TPP-II) (Tripeptidyl aminopeptida ...	0.16	-	cyt	0	Cytoplasm	cytoplasm [TAS]	190470		1248
Q64560 UniProt NPD GO	TPP2_RAT	Tripeptidyl-peptidase 2 (EC 3.4.14.10) (Tripeptidyl-peptidase II) (TPP-II) (Tripeptidyl aminopeptida ...	0.16	-	cyt	0	Cytoplasm (By similarity)				1248
Q9Z0L0 UniProt NPD GO	TPBG_MOUSE	Trophoblast glycoprotein precursor (5T4 oncofetal trophoblast glycoprotein) (5T4 oncotrophoblast gly ...	0.16	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				426
P01049 UniProt NPD GO	ITR2_ASCSU	Trypsin inhibitor	0.16	-	nuc	0	Secreted protein				66
Q9TLW8 UniProt NPD GO	TRPA1_CYACA	Tryptophan synthase alpha chain (EC 4.2.1.20)	0.16	-	nuc	0	Plastid; chloroplast				266
P24633 UniProt NPD GO	TBA1_EMENI	Tubulin alpha-1 chain	0.16	-	cyt	0					449
P04689 UniProt NPD GO	TBA2_SCHPO	Tubulin alpha-2 chain	0.16	-	cyt	0		microtubule [TAS]			449
O22348 UniProt NPD GO	TBA2_ELEIN	Tubulin alpha-2 chain (Alpha-2 tubulin)	0.16	-	cyt	0					447
Q04709 UniProt NPD GO	TBB_BABBO	Tubulin beta chain (Beta tubulin)	0.16	-	cyt	0					441
P53374 UniProt NPD GO	TBB_GIBFU	Tubulin beta chain (Beta tubulin)	0.16	-	cyt	0					446

You are viewing entries 56351 to 56400 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.