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
P22831 UniProt NPD GO	SYNPR_RAT	Synaptoporin	0.01	-	end	4 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein	synaptic vesicle membrane [NAS]			265
P37379 UniProt NPD GO	SYU_TORCA	Synuclein	0.01	-	cyt	0	Nucleus				143
P01851 UniProt NPD GO	TCB2_MOUSE	T-cell receptor beta-2 chain C region	0.01	-	cyt	1				1MWA	173
Q9QZZ2 UniProt NPD GO	CD1B1_CAVPO	T-cell surface glycoprotein CD1b1 precursor (CD1-b1 antigen)	0.01	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				333
Q9QZZ1 UniProt NPD GO	CD1B2_CAVPO	T-cell surface glycoprotein CD1b2 precursor (CD1-b2 antigen)	0.01	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				332
P04235 UniProt NPD GO	CD3D_MOUSE	T-cell surface glycoprotein CD3 delta chain precursor (T-cell receptor T3 delta chain)	0.01	-	nuc	1	Membrane; single-pass type I membrane protein	alpha-beta T cell receptor complex [IDA]			173
P26356 UniProt NPD GO	TBP1_WHEAT	TATA-box-binding protein 1 (TATA-box factor 1) (TATA-binding factor 1) (TATA sequence-binding protei ...	0.01	-	cyt	0	Nucleus				233
Q27084 UniProt NPD GO	TAL2_TACTR	Tachylectin-2 precursor (Lectin L10c)	0.01	-	cyt	0	Stored in large secretory granules of hemocytes and secreted upon stimulation by lipopolysaccharides ...			1TL2	255
Q6IV76 UniProt NPD GO	TAZ_ERYPA	Tafazzin	0.01	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				262
Q6IV77 UniProt NPD GO	TAZ_MACMU	Tafazzin	0.01	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				262
Q6IV78 UniProt NPD GO	TAZ_SAISC	Tafazzin	0.01	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				262
Q645Z5 UniProt NPD GO	T2R13_GORGO	Taste receptor type 2 member 13 (T2R13)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				303
Q9NYV9 UniProt NPD GO	T2R13_HUMAN	Taste receptor type 2 member 13 (T2R13) (Taste receptor family B member 3) (TRB3)	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	604792		303
Q67ES2 UniProt NPD GO	TR135_RAT	Taste receptor type 2 member 135 (T2R135) (T2R35) (Taste receptor type 2 member 28) (T2R28)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				321
Q7TQA9 UniProt NPD GO	TR135_MOUSE	Taste receptor type 2 member 135 (T2R135) (Taste receptor type 2 member 35) (T2R35) (mT2r38)	0.01	-	end	6 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			312
Q9JKU1 UniProt NPD GO	T2R19_RAT	Taste receptor type 2 member 19 (T2R19) (Taste receptor type 2 member 1) (T2R1)	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			335
Q645U7 UniProt NPD GO	T2R60_PONPY	Taste receptor type 2 member 60 (T2R60) (T2R56)	0.01	-	end	6 *	Membrane; multi-pass membrane protein				318
P11917 UniProt NPD GO	KTRC_AREMA	Taurocyamine kinase (EC 2.7.3.4) (Fragment)	0.01	-		0					16
O61063 UniProt NPD GO	TCT1_PHYPO	Tectonin-1 (Tectonin I)	0.01	-	cyt	0	Cell surface. Cytoplasmic vesicle; cytoplasmic vesicle membrane. Also bound to inner membrane of cer ...				216
P56276 UniProt NPD GO	MYLK_MELGA	Telokin	0.01	-	cyt	0				1TLK	154
P82883 UniProt NPD GO	TE1CD_RANCL	Temporin-1Cd	0.01	-		0	Secreted protein				13
P82884 UniProt NPD GO	TE1CE_RANCL	Temporin-1Ce	0.01	-		0	Secreted protein				13
P82830 UniProt NPD GO	TE1LA_RANLU	Temporin-1La	0.01	-		0	Secreted protein				13
P82832 UniProt NPD GO	TE1LC_RANLU	Temporin-1Lc	0.01	-		0	Secreted protein				14
Q27023 UniProt NPD GO	DEFI_TENMO	Tenecin-1 precursor	0.01	-	exc	0	Secreted protein				84
P84465 UniProt NPD GO	TPAN1_PANIM	Tetrapandin-1	0.01	-		0	Secreted protein				4
Q96FV3 UniProt NPD GO	TSN17_HUMAN	Tetraspanin-17 (Tspan-17) (Transmembrane 4 superfamily member 17) (Tetraspan protein SB134) (F-box o ...	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	ubiquitin ligase complex [NAS]			263
Q9D7W4 UniProt NPD GO	TSN17_MOUSE	Tetraspanin-17 (Tspan-17) (Transmembrane 4 superfamily member 17) (Tetraspan protein SB134) (F-box o ...	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				270
Q80WR1 UniProt NPD GO	TSN18_MOUSE	Tetraspanin-18 (Tspan-18)	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				248
Q5RAP8 UniProt NPD GO	TSN31_PONPY	Tetraspanin-31 (Tspan-31) (Sarcoma amplified sequence homolog)	0.01	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				210
Q5U1V9 UniProt NPD GO	TSN31_RAT	Tetraspanin-31 (Tspan-31) (Sarcoma amplified sequence homolog)	0.01	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				210
Q9JHH2 UniProt NPD GO	TSN32_MOUSE	Tetraspanin-32 (Protein Phemx) (AML1-regulated transmembrane protein 1)	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS] intracellular [IDA]			256
O70401 UniProt NPD GO	TSN6_MOUSE	Tetraspanin-6 (Tspan-6) (Transmembrane 4 superfamily member 6)	0.01	-	end	4 *	Membrane; multi-pass membrane protein				245
O43657 UniProt NPD GO	TSN6_HUMAN	Tetraspanin-6 (Tspan-6) (Transmembrane 4 superfamily member 6) (T245 protein) (Tetraspanin TM4-D) (A ...	0.01	-	end	4 *	Membrane; multi-pass membrane protein		300191		245
Q7YQK9 UniProt NPD GO	TSN7_PONPY	Tetraspanin-7 (Tspan-7) (Transmembrane 4 superfamily member 2) (CD231 antigen)	0.01	-	end	4 *	Membrane; multi-pass membrane protein				244
Q5R9S6 UniProt NPD GO	TSN8_PONPY	Tetraspanin-8 (Tspan-8)	0.01	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				237
P19075 UniProt NPD GO	TSN8_HUMAN	Tetraspanin-8 (Tspan-8) (Transmembrane 4 superfamily member 3) (Tumor-associated antigen CO-029)	0.01	-	end	4 *	Membrane; multi-pass membrane protein	lysosome [TAS]	600769		237
Q8JZL3 UniProt NPD GO	THTPA_MOUSE	Thiamine-triphosphatase (EC 3.6.1.28) (ThTPase)	0.01	-	nuc	0	Cytoplasm (By similarity)				223
Q8CGV7 UniProt NPD GO	THTPA_RAT	Thiamine-triphosphatase (EC 3.6.1.28) (ThTPase)	0.01	-	nuc	0	Cytoplasm (By similarity)				223
P49570 UniProt NPD GO	THIG_ODOSI	Thiazole biosynthesis protein thiG	0.01	-	cyt	0	Plastid; chloroplast				261
Q41738 UniProt NPD GO	THI41_MAIZE	Thiazole biosynthetic enzyme 1-1, chloroplast precursor	0.01	-	mit	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein				354
Q41739 UniProt NPD GO	THI42_MAIZE	Thiazole biosynthetic enzyme 1-2, chloroplast precursor	0.01	-	mit	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein				354
P40998 UniProt NPD GO	THI2_SCHPO	Thiazole biosynthetic enzyme, mitochondrial precursor	0.01	-	cyt	0	Mitochondrion (Potential)				328
Q9UUZ9 UniProt NPD GO	THI4_ASPOR	Thiazole biosynthetic enzyme, mitochondrial precursor	0.01	-	cyt	0	Mitochondrion (Potential)				327
Q8HX86 UniProt NPD GO	TPMT_CANFA	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.01	-	cyt	0	Cytoplasm (By similarity)				245
Q6EIC1 UniProt NPD GO	TPMT_FELCA	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.01	-	cyt	0	Cytoplasm (By similarity)				245
Q3BCR3 UniProt NPD GO	TPMT_GORGO	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.01	-	cyt	0	Cytoplasm				245
P51580 UniProt NPD GO	TPMT_HUMAN	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.01	-	cyt	0	Cytoplasm		187680	2BZG	245
Q3BCR5 UniProt NPD GO	TPMT_LYCPI	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.01	-	cyt	0	Cytoplasm				245
Q3BCR9 UniProt NPD GO	TPMT_LYNRU	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.01	-	cyt	0	Cytoplasm				245

You are viewing entries 91651 to 91700 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.