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
Q3BCR0 UniProt NPD GO	TPMT_PANLE	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.01	-	cyt	0	Cytoplasm				245
Q3BCR1 UniProt NPD GO	TPMT_PANPR	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.01	-	cyt	0	Cytoplasm				245
Q3BCR2 UniProt NPD GO	TPMT_PANTI	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.01	-	cyt	0	Cytoplasm				245
Q3BCR8 UniProt NPD GO	TPMT_PANTR	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.01	-	cyt	0	Cytoplasm				245
O97680 UniProt NPD GO	THIO_BOVIN	Thioredoxin	0.01	-	mit	0	Cytoplasm (By similarity)				104
Q9BDJ3 UniProt NPD GO	THIO_CALJA	Thioredoxin	0.01	-	mit	0	Cytoplasm (By similarity)				104
P08629 UniProt NPD GO	THIO_CHICK	Thioredoxin	0.01	-	cyt	0	Cytoplasm (By similarity)				104
O96952 UniProt NPD GO	THIO_GEOCY	Thioredoxin	0.01	-	cyt	0	Cytoplasm (By similarity)				106
O97508 UniProt NPD GO	THIO_HORSE	Thioredoxin	0.01	-	cyt	0	Cytoplasm (By similarity)				104
P29451 UniProt NPD GO	THIO_MACMU	Thioredoxin	0.01	-	mit	0	Cytoplasm (By similarity)				104
Q98TX1 UniProt NPD GO	THIO_OPHHA	Thioredoxin	0.01	-	mit	0					104
P82460 UniProt NPD GO	THIO_PIG	Thioredoxin	0.01	-	mit	0	Cytoplasm (By similarity)				104
Q5R9M3 UniProt NPD GO	THIO_PONPY	Thioredoxin	0.01	-	mit	0	Cytoplasm (By similarity)				105
P08628 UniProt NPD GO	THIO_RABIT	Thioredoxin	0.01	-	mit	0	Cytoplasm				104
P11232 UniProt NPD GO	THIO_RAT	Thioredoxin	0.01	-	cyt	0	Cytoplasm (By similarity)				104
P50413 UniProt NPD GO	THIO_SHEEP	Thioredoxin	0.01	-	mit	0	Cytoplasm (By similarity)				104
P10639 UniProt NPD GO	THIO_MOUSE	Thioredoxin (ATL-derived factor) (ADF)	0.01	-	cyt	0	Cytoplasm	mitochondrion [IDA]			104
P10599 UniProt NPD GO	THIO_HUMAN	Thioredoxin (ATL-derived factor) (ADF) (Surface-associated sulphydryl protein) (SASP)	0.01	-	mit	0	Cytoplasm		187700	4TRX	104
P99505 UniProt NPD GO	THIO_CANFA	Thioredoxin (Fragment)	0.01	-		0	Cytoplasm (By similarity)				20
O81332 UniProt NPD GO	TRXF_MESCR	Thioredoxin F-type, chloroplast precursor (TRX-F)	0.01	-	mit	0	Plastid; chloroplast (By similarity)				191
O64432 UniProt NPD GO	TRXH_BRARA	Thioredoxin H-type (TRX-H)	0.01	-	cyt	0	Cytoplasm (By similarity)				123
P68176 UniProt NPD GO	TRXH_BRAOL	Thioredoxin H-type (TRX-H) (Pollen coat protein)	0.01	-	cyt	0	Cytoplasm (By similarity)				123
P68177 UniProt NPD GO	TRXH1_BRANA	Thioredoxin H-type 1 (TRX-H-1)	0.01	-	cyt	0	Cytoplasm (By similarity)				123
P29449 UniProt NPD GO	TRXH1_TOBAC	Thioredoxin H-type 1 (TRX-H1)	0.01	-	cyt	0	Cytoplasm (By similarity)				126
Q39362 UniProt NPD GO	TRXH2_BRANA	Thioredoxin H-type 2 (TRX-H-2)	0.01	-	cyt	0	Cytoplasm (By similarity)				119
P22217 UniProt NPD GO	TRX1_YEAST	Thioredoxin I (TR-I) (Thioredoxin 2)	0.01	-	cyt	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein. Nucleus	cytosol [IDA] vacuole (sensu Fungi) [IPI]			102
P23400 UniProt NPD GO	TRXM_CHLRE	Thioredoxin M-type, chloroplast precursor (TRX-M) (Thioredoxin CH2)	0.01	-	mit	0	Plastid; chloroplast (By similarity)			1DBY	140
Q8T6C4 UniProt NPD GO	TDX_ECHGR	Thioredoxin peroxidase (EC 1.11.1.15) (Peroxiredoxin) (Thioredoxin-dependent peroxide reductase) (TP ...	0.01	-	cyt	0	Cytoplasm (By similarity)				193
Q17172 UniProt NPD GO	TDX2_BRUMA	Thioredoxin peroxidase 2 (EC 1.11.1.15) (Peroxiredoxin 2) (Thioredoxin-dependent peroxide reductase ...	0.01	-	cyt	0	Cytoplasm (By similarity)				199
Q7Z7S3 UniProt NPD GO	TRXB_PNECA	Thioredoxin reductase (EC 1.8.1.9)	0.01	-	cyt	0	Cytoplasm (By similarity)				325
Q8J0U0 UniProt NPD GO	TRXB_PNEJI	Thioredoxin reductase (EC 1.8.1.9)	0.01	-	cyt	0	Cytoplasm (By similarity)				327
Q39243 UniProt NPD GO	TRXB1_ARATH	Thioredoxin reductase 1 (EC 1.8.1.9) (NADPH-dependent thioredoxin reductase 1) (NTR 1)	0.01	-	cyt	0	Cytoplasm			1VDC	333
P29446 UniProt NPD GO	THIO2_DICDI	Thioredoxin-2 (Fragment)	0.01	-	mit	0					88
P29447 UniProt NPD GO	THIO3_DICDI	Thioredoxin-3	0.01	-	cyt	0					104
Q8IFW4 UniProt NPD GO	THIOT_DROME	Thioredoxin-T (ThioredoxinT)	0.01	-	cyt	0	Nucleus. Specifically associated with the Y chromosome loops	Y chromosome [IDA]			157
P30048 UniProt NPD GO	PRDX3_HUMAN	Thioredoxin-dependent peroxide reductase, mitochondrial precursor (EC 1.11.1.15) (Peroxiredoxin-3) ( ...	0.01	-	mit	0	Mitochondrion		604769		256
Q8TFM8 UniProt NPD GO	THIO_FUSCU	Thioredoxin-like protein (Allergen Fus c 2)	0.01	-	cyt	0					121
O76003 UniProt NPD GO	TXNL2_HUMAN	Thioredoxin-like protein 2 (PKC-interacting cousin of thioredoxin) (PKC-theta-interacting protein) ( ...	0.01	-	cyt	0	Cytoplasm; cell cortex. Under the plasma membrane. After PMA stimulation, TXNL2/PICOT and PRKCQ/PKC- ...				335
P83876 UniProt NPD GO	TXN4A_HUMAN	Thioredoxin-like protein 4A (Thioredoxin-like U5 snRNP protein U5-15kD) (Spliceosomal U5 snRNP-speci ...	0.01	-	cyt	0	Nucleus	spliceosome complex [TAS]		1SYX	142
P83877 UniProt NPD GO	TXN4A_MOUSE	Thioredoxin-like protein 4A (Thioredoxin-like U5 snRNP protein U5-15kD) (Spliceosomal U5 snRNP-speci ...	0.01	-	cyt	0	Nucleus (By similarity)	snRNP U5 [TAS] spliceosome complex [ISS]			142
Q5REA8 UniProt NPD GO	TXNL5_PONPY	Thioredoxin-like protein 5	0.01	-	cyt	0	Cytoplasm (By similarity)				123
Q9BRA2 UniProt NPD GO	TXNL5_HUMAN	Thioredoxin-like protein 5 (14 kDa thioredoxin-related protein) (TRP14) (Protein 42-9-9)	0.01	-	cyt	0	Cytoplasm			1WOU	123
P25324 UniProt NPD GO	THTR_CHICK	Thiosulfate sulfurtransferase (EC 2.8.1.1) (Rhodanese)	0.01	-	mit	0	Mitochondrion; mitochondrial matrix				289
Q16762 UniProt NPD GO	THTR_HUMAN	Thiosulfate sulfurtransferase (EC 2.8.1.1) (Rhodanese)	0.01	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [NAS]	180370		296
P24329 UniProt NPD GO	THTR_RAT	Thiosulfate sulfurtransferase (EC 2.8.1.1) (Rhodanese)	0.01	-	mit	0	Mitochondrion; mitochondrial matrix				296
P25306 UniProt NPD GO	THD1_LYCES	Threonine dehydratase biosynthetic, chloroplast precursor (EC 4.3.1.19) (Threonine deaminase) (TD)	0.01	-	mit	0	Plastid; chloroplast				595
P82682 UniProt NPD GO	TL14_SPIOL	Thylakoid lumenal 14.7 kDa protein (P14.7) (Fragment)	0.01	-		0	Plastid; chloroplast; chloroplast thylakoid lumen				20
P81760 UniProt NPD GO	TL17_ARATH	Thylakoid lumenal 17.4 kDa protein, chloroplast precursor (P17.4)	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				236
Q8LCA1 UniProt NPD GO	TMP14_ARATH	Thylakoid membrane phosphoprotein 14 kDa, chloroplast precursor	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane				174
P01222 UniProt NPD GO	TSHB_HUMAN	Thyrotropin beta chain precursor (Thyroid-stimulating hormone subunit beta) (TSH-beta) (TSH-B) (Thyr ...	0.01	-	exc	0	Secreted protein		275100		138

You are viewing entries 91701 to 91750 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.