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
P50990 UniProt NPD GO	TCPQ_HUMAN	T-complex protein 1 subunit theta (TCP-1-theta) (CCT-theta) (NY-REN-15 antigen)	0.03	-	mit	0	Cytoplasm				547
P28147 UniProt NPD GO	TBP1_ARATH	TATA-box-binding protein 1 (TATA-box factor 1) (TATA-binding factor 1) (TATA sequence-binding protei ...	0.03	-	mit	0	Nucleus			1VOL	200
P80204 UniProt NPD GO	TGFR1_RAT	TGF-beta receptor type-1 precursor (EC 2.7.11.30) (TGF-beta receptor type I) (TGFR-1) (TGF-beta type ...	0.03	-	end	2 *	Membrane; single-pass type I membrane protein				501
P36897 UniProt NPD GO	TGFR1_HUMAN	TGF-beta receptor type-1 precursor (EC 2.7.11.30) (TGF-beta receptor type I) (TGFR-1) (TGF-beta type ...	0.03	-	end	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	190181	1VJY	503
Q5U4D9 UniProt NPD GO	THOC6_MOUSE	THO complex subunit 6 homolog (WD repeat protein 58)	0.03	-	mit	0					341
Q6AY87 UniProt NPD GO	THOC6_RAT	THO complex subunit 6 homolog (WD repeat protein 58)	0.03	-	mit	0					341
Q9LYT3 UniProt NPD GO	TT12_ARATH	TRANSPARENT TESTA 12 protein	0.03	-	end	12	Vacuole; vacuolar membrane; multi-pass membrane protein (Probable). Tonoplast				507
P81738 UniProt NPD GO	TRP6_LEUMA	Tachykinin-related peptide 6 (LemTRP 6)	0.03	-		0	Secreted protein				10
Q05117 UniProt NPD GO	PPA5_MOUSE	Tartrate-resistant acid phosphatase type 5 precursor (EC 3.1.3.2) (TR-AP) (Tartrate-resistant acid A ...	0.03	-	nuc	0	Lysosome				327
Q646F5 UniProt NPD GO	T2R10_PAPHA	Taste receptor type 2 member 10 (T2R10)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				307
Q7M720 UniProt NPD GO	T2R13_MOUSE	Taste receptor type 2 member 13 (T2R13) (Taste receptor type 2 member 121) (T2R121) (mT2R48)	0.03	-	end	7 *	Cell membrane; multi-pass membrane protein				305
Q9NYW5 UniProt NPD GO	TA2R4_HUMAN	Taste receptor type 2 member 4 (T2R4)	0.03	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]	604869		299
Q646D3 UniProt NPD GO	TA2R4_PANPA	Taste receptor type 2 member 4 (T2R4)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				299
Q646B0 UniProt NPD GO	TA2R4_PANTR	Taste receptor type 2 member 4 (T2R4)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				299
Q645V3 UniProt NPD GO	T2R44_PONPY	Taste receptor type 2 member 44 (T2R44)	0.03	-	end	6 *	Membrane; multi-pass membrane protein				309
P59539 UniProt NPD GO	T2R45_HUMAN	Taste receptor type 2 member 45 (T2R45) (G-protein coupled receptor 59)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				299
P51865 UniProt NPD GO	TDGF1_MOUSE	Teratocarcinoma-derived growth factor precursor (Epidermal growth factor-like Cripto protein) (Cript ...	0.03	-	mit	0		extracellular region [TAS] extrinsic to plasma membrane [IDA]			171
P56587 UniProt NPD GO	TERT_APIME	Tertiapin	0.03	-	nuc	0	Secreted protein			1TER	21
P50695 UniProt NPD GO	RST1_AVESA	Thaumatin-like pathogenesis-related protein 1 precursor	0.03	-	exc	1 *					169
Q9NBW4 UniProt NPD GO	THST_THETS	Therostasin precursor	0.03	-	exc	0	Secreted protein				101
Q5E9T4 UniProt NPD GO	TPK1_BOVIN	Thiamin pyrophosphokinase 1 (EC 2.7.6.2) (Thiamine pyrophosphokinase 1)	0.03	-	cyt	0					243
Q38709 UniProt NPD GO	THI4_ALNGL	Thiazole biosynthetic enzyme, chloroplast precursor (AG6)	0.03	-	cyt	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein				352
Q9NPJ3 UniProt NPD GO	THEM2_HUMAN	Thioesterase superfamily member 2	0.03	-	cyt	0				2H4U	140
Q8H166 UniProt NPD GO	ALEU_ARATH	Thiol protease aleurain precursor (EC 3.4.22.16) (AtALEU) (Senescence-associated gene product 2)	0.03	-	exc	1 *	Vacuole. Predominantly vacuolar. From the Golgi apparatus, transported to the lytic vacuole (LV) in ...				358
Q9SBK8 UniProt NPD GO	THN_BRARP	Thionin precursor [Contains: Thionin; Acidic protein]	0.03	-	nuc	0					133
P29450 UniProt NPD GO	TRXF_PEA	Thioredoxin F-type, chloroplast precursor (TRX-F)	0.03	-	cyt	0	Plastid; chloroplast				182
O65049 UniProt NPD GO	TRXH_PICMA	Thioredoxin H-type (TRX-H)	0.03	-	cyt	0	Cytoplasm (By similarity)				125
Q41864 UniProt NPD GO	TRXM_MAIZE	Thioredoxin M-type, chloroplast precursor (TRX-M)	0.03	-	cyt	0	Plastid; chloroplast (By similarity)				167
Q5E936 UniProt NPD GO	TXD12_BOVIN	Thioredoxin domain-containing protein 12 precursor (EC 1.8.4.2)	0.03	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				172
Q91W90 UniProt NPD GO	TXND5_MOUSE	Thioredoxin domain-containing protein 5 precursor (Thioredoxin-like protein p46) (Endoplasmic reticu ...	0.03	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum lumen [IDA]			417
P51978 UniProt NPD GO	TRXB_NEUCR	Thioredoxin reductase (EC 1.8.1.9)	0.03	-	cyt	0	Cytoplasm (By similarity)				334
P43496 UniProt NPD GO	TRXB_PENCH	Thioredoxin reductase (EC 1.8.1.9)	0.03	-	cyt	0					333
Q8T6Z1 UniProt NPD GO	TRXB_SPIBA	Thioredoxin reductase (EC 1.8.1.9) (L-TrxR) (Fragment)	0.03	-	cyt	0	Cytoplasm (By similarity)				305
P91938 UniProt NPD GO	TRXR1_DROME	Thioredoxin reductase 1, mitochondrial precursor (EC 1.8.1.9) (TrxR-1)	0.03	-	mit	0	Isoform B: Mitochondrion. Isoform A: Cytoplasm	cytoplasm [IDA] mitochondrion [IDA]			596
Q39242 UniProt NPD GO	TRXB2_ARATH	Thioredoxin reductase 2 (EC 1.8.1.9) (NADPH-dependent thioredoxin reductase 2) (NTR 2)	0.03	-	mit	0	Cytoplasm				383
P38816 UniProt NPD GO	TRXB2_YEAST	Thioredoxin reductase 2, mitochondrial precursor (EC 1.8.1.9)	0.03	-	mit	0	Mitochondrion	mitochondrion [IDA]			342
Q6HA24 UniProt NPD GO	TRXB_KLULA	Thioredoxin reductase, mitochondrial precursor (EC 1.8.1.9)	0.03	-	mit	0	Mitochondrion (Potential)				349
Q58DA7 UniProt NPD GO	TXNL2_BOVIN	Thioredoxin-like protein 2	0.03	-	cyt	0	Cytoplasm; cell cortex (By similarity). Under the plasma membrane. After PMA stimulation, TXNL2/PICO ...				334
Q9JLZ1 UniProt NPD GO	TXNL2_RAT	Thioredoxin-like protein 2 (PKC-interacting cousin of thioredoxin) (PKCq-interacting protein) (PKC-t ...	0.03	-	mit	0	Cytoplasm; cell cortex (By similarity). Under the plasma membrane. After PMA stimulation, TXNL2/PICO ...				337
P52196 UniProt NPD GO	THTR_MOUSE	Thiosulfate sulfurtransferase (EC 2.8.1.1) (Rhodanese)	0.03	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA] mitochondrion [IDA]			296
Q06684 UniProt NPD GO	THBI_RHOPR	Thrombin inhibitor rhodniin	0.03	-	nuc	0	Secreted protein			1TBR	103
O49292 UniProt NPD GO	TL30_ARATH	Thylakoid lumenal 29.8 kDa protein, chloroplast precursor	0.03	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				274
O93603 UniProt NPD GO	TRFR_CHICK	Thyrotropin-releasing hormone receptor (TRH-R) (Thyroliberin receptor)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				395
P79696 UniProt NPD GO	TWHH_CARAU	Tiggy-winkle hedgehog protein (Fragment)	0.03	-	cyt	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				53
O13212 UniProt NPD GO	TWHH_DANFR	Tiggy-winkle hedgehog protein (Fragment)	0.03	-	cyt	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				53
P79715 UniProt NPD GO	TWHH_DANKE	Tiggy-winkle hedgehog protein (Fragment)	0.03	-	cyt	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				53
O13253 UniProt NPD GO	TWHH_DEVPA	Tiggy-winkle hedgehog protein (Fragment)	0.03	-	cyt	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				53
P79855 UniProt NPD GO	TWHH_PUNTE	Tiggy-winkle hedgehog protein (Fragment)	0.03	-	cyt	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				53
P13726 UniProt NPD GO	TF_HUMAN	Tissue factor precursor (TF) (Coagulation factor III) (Thromboplastin) (CD142 antigen)	0.03	-	nuc	1 *	Membrane; single-pass type I membrane protein	integral to membrane [TAS] plasma membrane [NAS]	134390	2HFT	295
Q8R1J9 UniProt NPD GO	TOR2A_MOUSE	Torsin-2A precursor (Torsin family 2 member A)	0.03	-	exc	1 *	Secreted protein (Probable)				321

You are viewing entries 81801 to 81850 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.