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
P50159 UniProt NPD GO	TBP2_MAIZE	TATA-box-binding protein 2 (TATA-box factor 2) (TATA-binding factor 2) (TATA sequence-binding protei ...	0.08	-	mit	0	Nucleus				200
Q02879 UniProt NPD GO	TBP2_WHEAT	TATA-box-binding protein 2 (TATA-box factor 2) (TATA-binding factor 2) (TATA sequence-binding protei ...	0.08	-	cyt	0	Nucleus				201
Q86W42 UniProt NPD GO	THOC6_HUMAN	THO complex subunit 6 homolog (WD repeat protein 58)	0.08	-	mit	0					341
Q9EQZ1 UniProt NPD GO	T22D3_RAT	TSC22 domain family protein 3 (Glucocorticoid-induced leucine zipper protein)	0.08	-	cyt	0					134
P81733 UniProt NPD GO	TRP2_LEUMA	Tachykinin-related peptide 2 (LemTRP 2) [Contains: Tachykinin-related peptide 1 (LemTRP 1)]	0.08	-		0	Secreted protein				17
Q9BN11 UniProt NPD GO	TMTX2_MESTA	Tamulustoxin-2 (TmTX2)	0.08	-	nuc	0	Secreted protein				35
P78581 UniProt NPD GO	TAN_ASPOR	Tannase precursor (EC 3.1.1.20) [Contains: Tannase 33 kDa subunit; Tannase 30 kDa subunit]	0.08	-	mit	0					588
Q49HH9 UniProt NPD GO	TS1R3_CANFA	Taste receptor type 1 member 3 precursor (Sweet taste receptor T1R3)	0.08	-	end	7	Membrane; multi-pass membrane protein				845
Q646D7 UniProt NPD GO	T2R10_PANPA	Taste receptor type 2 member 10 (T2R10)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				307
Q646B5 UniProt NPD GO	T2R10_PANTR	Taste receptor type 2 member 10 (T2R10)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				307
Q9NYW0 UniProt NPD GO	T2R10_HUMAN	Taste receptor type 2 member 10 (T2R10) (Taste receptor family B member 2) (TRB2)	0.08	-	end	8 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	604791		307
Q9JKT4 UniProt NPD GO	TR105_MOUSE	Taste receptor type 2 member 105 (T2R105) (Taste receptor type 2 member 5) (T2R5) (Taste receptor ty ...	0.08	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			300
Q646F7 UniProt NPD GO	T2R13_PAPHA	Taste receptor type 2 member 13 (T2R13)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				303
Q645Y4 UniProt NPD GO	T2R16_GORGO	Taste receptor type 2 member 16 (T2R16)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				291
Q697L6 UniProt NPD GO	T2R38_PANPA	Taste receptor type 2 member 38 (T2R38)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				333
Q697L5 UniProt NPD GO	T2R38_PANTR	Taste receptor type 2 member 38 (T2R38)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				333
Q697L3 UniProt NPD GO	T2R38_PONPY	Taste receptor type 2 member 38 (T2R38)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				333
Q646F1 UniProt NPD GO	TA2R4_PAPHA	Taste receptor type 2 member 4 (T2R4)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				299
Q646B2 UniProt NPD GO	T2R41_PANTR	Taste receptor type 2 member 41 (T2R41)	0.08	-	end	6 *	Membrane; multi-pass membrane protein				307
Q645Z3 UniProt NPD GO	T2R42_GORGO	Taste receptor type 2 member 42 (T2R42) (T2R55)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				299
Q7RTR8 UniProt NPD GO	T2R42_HUMAN	Taste receptor type 2 member 42 (T2R42) (T2R55)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				314
Q5Y4Z2 UniProt NPD GO	T2R42_PANPA	Taste receptor type 2 member 42 (T2R42) (T2R55)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				314
Q646B8 UniProt NPD GO	T2R42_PANTR	Taste receptor type 2 member 42 (T2R42) (T2R55)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				314
Q9JKE9 UniProt NPD GO	TA2R6_RAT	Taste receptor type 2 member 6 (T2R6)	0.08	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			312
Q6PN83 UniProt NPD GO	CX53_CONMR	Tau conotoxin mr5.3 precursor (Gla-MrIV)	0.08	-	exc	0	Secreted protein (By similarity)				64
P79874 UniProt NPD GO	TEMB_RANTE	Temporin-B precursor	0.08	-	exc	0	Secreted protein				61
Q924B5 UniProt NPD GO	TX101_RAT	Testis-expressed protein 101 precursor (Lipid raft-associated glycoprotein TEC-21)	0.08	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor. Associated with lipid rafts	lipid raft [IMP]			250
P43025 UniProt NPD GO	TETN_MOUSE	Tetranectin precursor (TN) (C-type lectin domain family 3 member B) (Plasminogen kringle 4-binding p ...	0.08	-	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [TAS] extracellular space [TAS]			202
P58845 UniProt NPD GO	CXCV_CONTE	Textile convulsant peptide	0.08	-	nuc	0	Secreted protein				23
P02883 UniProt NPD GO	THM1_THADA	Thaumatin-1 (Thaumatin I)	0.08	-	nuc	0	Cytoplasmic vesicle. Thaumatin accumulates in vesicle-like organelles			2BLU	207
P83332 UniProt NPD GO	TLP1_PRUPE	Thaumatin-like protein 1 precursor (PpAZ44)	0.08	-	exc	1 *	Secreted protein (Potential)				246
P41888 UniProt NPD GO	TNR3_SCHPO	Thiamine pyrophosphokinase (EC 2.7.6.2) (TPK) (Thiamine kinase)	0.08	-	cyt	0					569
Q69AB2 UniProt NPD GO	TXND8_MOUSE	Thioredoxin domain-containing protein 8 (Spermatid-specific thioredoxin-3) (Sptrx-3) (Thioredoxin-6) ...	0.08	-	cyt	0	Cytoplasm. Golgi apparatus				127
Q9NNW7 UniProt NPD GO	TRXR2_HUMAN	Thioredoxin reductase 2, mitochondrial precursor (EC 1.8.1.9) (TR3) (TR-beta) (Selenoprotein Z) (Sel ...	0.08	-	mit	0	Mitochondrion	mitochondrion [IEP]	606448		524
Q99757 UniProt NPD GO	THIOM_HUMAN	Thioredoxin, mitochondrial precursor (Mt-Trx) (MTRX) (Thioredoxin-2)	0.08	-	mit	0	Mitochondrion		609063	1W89	166
O64654 UniProt NPD GO	TRXL1_ARATH	Thioredoxin-like 1	0.08	-	nuc	0					275
P42706 UniProt NPD GO	TPO_PIG	Thrombopoietin (Megakaryocyte colony-stimulating factor) (C-MPL ligand) (ML) (Megakaryocyte growth a ...	0.08	-	nuc	0	Secreted protein				26
P21731 UniProt NPD GO	TA2R_HUMAN	Thromboxane A2 receptor (TXA2-R) (Prostanoid TP receptor)	0.08	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	188070	1LBN	369
Q9DET5 UniProt NPD GO	TYBN_COTJA	Thymosin beta	0.08	-	nuc	0	Cytoplasm (By similarity)				44
P26351 UniProt NPD GO	TYB11_ONCMY	Thymosin beta-11	0.08	-	nuc	0	Cytoplasm				41
P62328 UniProt NPD GO	TYB4_HUMAN	Thymosin beta-4 (T beta 4) (Fx) [Contains: Hematopoietic system regulatory peptide (Seraspenide)]	0.08	-	nuc	0	Cytoplasm		300159		43
P62326 UniProt NPD GO	TYB4_BOVIN	Thymosin beta-4 (T beta 4) [Contains: Hematopoietic system regulatory peptide (Seraspenide)]	0.08	-	nuc	0	Cytoplasm				43
P34032 UniProt NPD GO	TYB4_RABIT	Thymosin beta-4 (T beta 4) [Contains: Hematopoietic system regulatory peptide (Seraspenide)]	0.08	-	nuc	0	Cytoplasm				43
P62329 UniProt NPD GO	TYB4_RAT	Thymosin beta-4 (T beta 4) [Contains: Hematopoietic system regulatory peptide (Seraspenide)]	0.08	-	nuc	0	Cytoplasm				43
Q6S9C5 UniProt NPD GO	TYB4_CHILA	Thymosin beta-4 (T beta-4) [Contains: Hematopoietic system regulatory peptide (Seraspenide)]	0.08	-	nuc	0	Cytoplasm (By similarity)				43
P62327 UniProt NPD GO	TYB4_HORSE	Thymosin beta-4 (T beta-4) [Contains: Hematopoietic system regulatory peptide (Seraspenide)]	0.08	-	nuc	0	Cytoplasm				43
Q95274 UniProt NPD GO	TYB4_PIG	Thymosin beta-4 (T beta-4) [Contains: Hematopoietic system regulatory peptide (Seraspenide)]	0.08	-	nuc	0	Cytoplasm (By similarity)				43
Q5R7H8 UniProt NPD GO	TYB4_PONPY	Thymosin beta-4 (T beta-4) [Contains: Hematopoietic system regulatory peptide (Seraspenide)]	0.08	-	nuc	0	Cytoplasm (By similarity)				43
O57340 UniProt NPD GO	TSHB_CHICK	Thyrotropin beta chain precursor (Thyroid-stimulating hormone subunit beta) (TSH-beta) (TSH-B)	0.08	-	exc	0	Secreted protein				134
P30931 UniProt NPD GO	TF_BOVIN	Tissue factor precursor (TF) (Coagulation factor III) (CD142 antigen)	0.08	-	end	2 *	Membrane; single-pass type I membrane protein				292

You are viewing entries 69101 to 69150 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.