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
P81736 UniProt NPD GO	TRP4_LEUMA	Tachykinin-related peptide 4 (LemTRP 4)	0.04	-		0	Secreted protein				9
P81739 UniProt NPD GO	TRP7_LEUMA	Tachykinin-related peptide 7 (LemTRP 7)	0.04	-		0	Secreted protein				10
P81740 UniProt NPD GO	TRP8_LEUMA	Tachykinin-related peptide 8 (LemTRP 8)	0.04	-		0	Secreted protein				10
Q645V1 UniProt NPD GO	T2R13_PONPY	Taste receptor type 2 member 13 (T2R13)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				303
Q9JKT7 UniProt NPD GO	T2R13_RAT	Taste receptor type 2 member 13 (T2R13) (Taste receptor type 2 member 7) (T2R7)	0.04	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			305
P59529 UniProt NPD GO	T2R16_MOUSE	Taste receptor type 2 member 16 (T2R16) (T2R18) (Candidate taste receptor mt2r40)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				299
Q4VHE7 UniProt NPD GO	T2R38_RAT	Taste receptor type 2 member 38 (T2R38) (Taste receptor type 2 member 26) (T2R26)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				331
Q645Y8 UniProt NPD GO	TA2R4_GORGO	Taste receptor type 2 member 4 (T2R4)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				299
Q645U4 UniProt NPD GO	TA2R4_PONPY	Taste receptor type 2 member 4 (T2R4)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				299
Q645U6 UniProt NPD GO	T2R41_PONPY	Taste receptor type 2 member 41 (T2R41)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				307
Q5Y500 UniProt NPD GO	T2R43_PANPA	Taste receptor type 2 member 43 (T2R43)	0.04	-	end	6 *	Membrane; multi-pass membrane protein				309
Q646B4 UniProt NPD GO	T2R43_PANTR	Taste receptor type 2 member 43 (T2R43)	0.04	-	end	6 *	Membrane; multi-pass membrane protein				309
Q646F8 UniProt NPD GO	T2R43_PAPHA	Taste receptor type 2 member 43 (T2R43)	0.04	-	end	6 *	Membrane; multi-pass membrane protein				308
Q646B9 UniProt NPD GO	T2R44_PANTR	Taste receptor type 2 member 44 (T2R44)	0.04	-	end	6 *	Membrane; multi-pass membrane protein				309
Q645T4 UniProt NPD GO	T2R46_MACMU	Taste receptor type 2 member 46 (T2R46)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				308
Q646G0 UniProt NPD GO	T2R46_PAPHA	Taste receptor type 2 member 46 (T2R46)	0.04	-	end	6 *	Membrane; multi-pass membrane protein				309
Q646E2 UniProt NPD GO	T2R47_PANPA	Taste receptor type 2 member 47 (T2R47)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				319
Q645V4 UniProt NPD GO	T2R47_PONPY	Taste receptor type 2 member 47 (T2R47)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				319
Q645Z9 UniProt NPD GO	T2R48_GORGO	Taste receptor type 2 member 48 (T2R48)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				299
P59542 UniProt NPD GO	T2R48_HUMAN	Taste receptor type 2 member 48 (T2R48)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				299
Q5Y4Z5 UniProt NPD GO	T2R48_PANPA	Taste receptor type 2 member 48 (T2R48)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				299
Q646E6 UniProt NPD GO	TA2R5_PAPHA	Taste receptor type 2 member 5 (T2R5)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				299
P59530 UniProt NPD GO	TA2R6_MOUSE	Taste receptor type 2 member 6 (T2R6) (Taste receptor type 2 member 30) (T2R30) (STC 7-4) (T2R42)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				312
P79875 UniProt NPD GO	TEMG_RANTE	Temporin-G precursor	0.04	-	exc	0	Secreted protein				61
O14609 UniProt NPD GO	XKRY_HUMAN	Testis-specific XK-related protein, Y-linked	0.04	-	end	3 *	Membrane; multi-pass membrane protein (Potential)		400015		159
Q11098 UniProt NPD GO	TSP17_CAEEL	Tetraspanin-17	0.04	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				243
P82885 UniProt NPD GO	THAI_NAJKA	Thaicobrin	0.04	-	cyt	0	Secreted protein				108
P50696 UniProt NPD GO	RST2_AVESA	Thaumatin-like pathogenesis-related protein 2 precursor	0.04	-	exc	1 *					169
P50697 UniProt NPD GO	RST3_AVESA	Thaumatin-like pathogenesis-related protein 3 precursor	0.04	-	exc	1 *					169
P50698 UniProt NPD GO	RST4_AVESA	Thaumatin-like pathogenesis-related protein 4 precursor	0.04	-	exc	1 *					169
P84334 UniProt NPD GO	TLP_CASDI	Thaumatin-like protein (Fragment)	0.04	-		0	Secreted protein				17
P83959 UniProt NPD GO	TLP_PHAVU	Thaumatin-like protein (Fragment)	0.04	-	cyt	0	Secreted protein				30
O23787 UniProt NPD GO	THI4_CITSI	Thiazole biosynthetic enzyme, chloroplast precursor	0.04	-	cyt	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein (By similarity)				356
Q9UVF8 UniProt NPD GO	THI4_UROFA	Thiazole biosynthetic enzyme, mitochondrial precursor	0.04	-	cyt	0	Mitochondrion (Potential)				338
P23617 UniProt NPD GO	THI4_FUSSH	Thiazole biosynthetic enzyme, mitochondrial precursor (Stress-inducible protein sti35)	0.04	-	cyt	0	Mitochondrion (Potential)				324
Q42838 UniProt NPD GO	THN7_HORVU	Thionin BTH7 precursor [Contains: Thionin BTH7; Acidic protein]	0.04	-	nuc	0	Secreted protein (Potential)				137
Q42597 UniProt NPD GO	THN22_ARATH	Thionin-2.2 precursor [Contains: Thionin-2.2; Acidic protein]	0.04	-	exc	0	Secreted protein (Potential)				134
Q9ZP20 UniProt NPD GO	TRXM_ORYSA	Thioredoxin M-type, chloroplast precursor (TRX-M)	0.04	-	nuc	0	Plastid; chloroplast (By similarity)				172
P07591 UniProt NPD GO	TRXM_SPIOL	Thioredoxin M-type, chloroplast precursor (TRX-M) [Contains: Thioredoxin M-type Mc; Thioredoxin M-ty ...	0.04	-	mit	0	Plastid; chloroplast			1GL8	181
Q498E0 UniProt NPD GO	TXD12_RAT	Thioredoxin domain-containing protein 12 precursor (EC 1.8.4.2)	0.04	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				170
Q86XW9 UniProt NPD GO	TXND6_HUMAN	Thioredoxin domain-containing protein 6 (Thioredoxin-like protein 2) (Txl-2)	0.04	-	cyt	0	Cytoplasm (By similarity). Associated with microtubules. Detected in cilia of lung epithelium, and a ...				330
P29509 UniProt NPD GO	TRXB1_YEAST	Thioredoxin reductase 1 (EC 1.8.1.9)	0.04	-	cyt	0	Cytoplasm	cytoplasm [TAS]			318
Q9MYY8 UniProt NPD GO	TRXR1_PIG	Thioredoxin reductase 1, cytoplasmic (EC 1.8.1.9) (TR) (TR1)	0.04	-	cyt	0	Cytoplasm (By similarity)				499
Q5NVA2 UniProt NPD GO	TRXR1_PONPY	Thioredoxin reductase 1, cytoplasmic (EC 1.8.1.9) (TR) (TR1)	0.04	-	cyt	0	Cytoplasm (By similarity)				499
Q09433 UniProt NPD GO	THIO1_CAEEL	Thioredoxin-1	0.04	-	mit	0					115
Q9CQM9 UniProt NPD GO	TXNL2_MOUSE	Thioredoxin-like protein 2 (PKC-interacting cousin of thioredoxin) (PKC-theta-interacting protein) ( ...	0.04	-	mit	0	Cytoplasm; cell cortex (By similarity). Under the plasma membrane. After PMA stimulation, TXNL2/PICO ...			1WIK	337
P46635 UniProt NPD GO	THTR_CRIGR	Thiosulfate sulfurtransferase (EC 2.8.1.1) (Rhodanese)	0.04	-	mit	0	Mitochondrion; mitochondrial matrix				296
Q39469 UniProt NPD GO	THD1_CICAR	Threonine dehydratase biosynthetic, chloroplast precursor (EC 4.3.1.19) (Threonine deaminase) (TD)	0.04	-	mit	0	Plastid; chloroplast (By similarity)				590
Q9BY10 UniProt NPD GO	TSCOT_HUMAN	Thymic stromal cotransporter homolog	0.04	-	end	11	Cell membrane; multi-pass membrane protein (By similarity)	integral to membrane [NAS]	608956		475
P45351 UniProt NPD GO	TYSY_CRYNE	Thymidylate synthase (EC 2.1.1.45) (TS) (TSase)	0.04	-	cyt	0				2AAZ	317

You are viewing entries 78551 to 78600 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.