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
P84464 UniProt NPD GO	TPAN2_PANIM	Tetrapandin-2	0.02	-		0	Secreted protein				4
Q9CQ88 UniProt NPD GO	TSN31_MOUSE	Tetraspanin-31 (Tspan-31) (Sarcoma amplified sequence homolog)	0.02	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				210
Q12999 UniProt NPD GO	TSN31_HUMAN	Tetraspanin-31 (Tspan-31) (Sarcoma amplified sequence)	0.02	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	181035		210
Q5XHG6 UniProt NPD GO	TS31A_XENLA	Tetraspanin-31 A (Tspan-31 A) (Sarcoma amplified sequence homolog A)	0.02	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				212
Q62283 UniProt NPD GO	TSN7_MOUSE	Tetraspanin-7 (Tspan-7) (Transmembrane 4 superfamily member 2) (Cell surface glycoprotein A15) (PE31 ...	0.02	-	end	4 *	Membrane; multi-pass membrane protein				249
P41732 UniProt NPD GO	TSN7_HUMAN	Tetraspanin-7 (Tspan-7) (Transmembrane 4 superfamily member 2) (Cell surface glycoprotein A15) (T-ce ...	0.02	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	300210		249
P81370 UniProt NPD GO	TLP_ACTDE	Thaumatin-like protein (Fragment)	0.02	-	cyt	0					29
Q9FSG7 UniProt NPD GO	TP1A_MALDO	Thaumatin-like protein 1a precursor (Allergen Mal d 2) (Mdtl1) (Pathogenesis-related protein 5a) (PR ...	0.02	-	exc	0	Secreted protein (Potential)				246
P83336 UniProt NPD GO	TP1B_MALDO	Thaumatin-like protein 1b (Pathogenesis-related protein 5b) (PR-5b) (Fragment)	0.02	-	nuc	0	Secreted protein				212
P81955 UniProt NPD GO	TLP6_CHRCO	Thaumatin-like protein 6 (CTLP6) (Fragment)	0.02	-	cyt	0					35
P31110 UniProt NPD GO	TLP_ORYSA	Thaumatin-like protein precursor	0.02	-	exc	1 *	Secreted protein (Potential)				177
P21381 UniProt NPD GO	THPA_THADA	Thaumatopain (EC 3.4.22.-) (Fragment)	0.02	-	nuc	0					35
Q9H3S4 UniProt NPD GO	TPK1_HUMAN	Thiamin pyrophosphokinase 1 (EC 2.7.6.2) (Thiamine pyrophosphokinase 1) (hTPK1) (Placental protein 2 ...	0.02	-	cyt	0			606370		243
Q9R0M5 UniProt NPD GO	TPK1_MOUSE	Thiamin pyrophosphokinase 1 (EC 2.7.6.2) (Thiamine pyrophosphokinase 1) (mTPK1)	0.02	-	cyt	0				1IG3	243
O60779 UniProt NPD GO	S19A2_HUMAN	Thiamine transporter 1 (ThTr-1) (ThTr1) (Thiamine carrier 1) (TC1) (Solute carrier family 19 member ...	0.02	-	end	12 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	603941		497
Q38814 UniProt NPD GO	THI4_ARATH	Thiazole biosynthetic enzyme, chloroplast precursor (ARA6)	0.02	-	mit	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein			1RP0	349
Q9CQR4 UniProt NPD GO	THEM2_MOUSE	Thioesterase superfamily member 2	0.02	-	cyt	0		mitochondrion [IDA]		2CY9	140
Q8RWQ9 UniProt NPD GO	ALEUL_ARATH	Thiol protease aleurain-like precursor (EC 3.4.22.16)	0.02	-	exc	0					358
O55060 UniProt NPD GO	TPMT_MOUSE	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.02	-	cyt	0	Cytoplasm				240
Q9QX22 UniProt NPD GO	TPMT_MUSSP	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.02	-	cyt	0	Cytoplasm				240
O48897 UniProt NPD GO	TRXF_BRANA	Thioredoxin F-type, chloroplast precursor (TRX-F)	0.02	-	mit	0	Plastid; chloroplast (By similarity)				182
Q43636 UniProt NPD GO	TRXH_RICCO	Thioredoxin H-type (TRX-H)	0.02	-	mit	0	Cytoplasm (By similarity)				118
P29448 UniProt NPD GO	TRXH1_ARATH	Thioredoxin H-type 1 (TRX-H-1)	0.02	-	cyt	0	Cytoplasm (By similarity)			1XFL	114
Q07090 UniProt NPD GO	TRXH2_TOBAC	Thioredoxin H-type 2 (TRX-H2)	0.02	-	cyt	0	Cytoplasm (By similarity)				118
P48384 UniProt NPD GO	TRXM_PEA	Thioredoxin M-type, chloroplast precursor (TRX-M)	0.02	-	mit	0	Plastid; chloroplast (By similarity)				172
Q26695 UniProt NPD GO	TDX_TRYBR	Thioredoxin peroxidase (EC 1.11.1.15) (Peroxiredoxin) (Thioredoxin-dependent peroxide reductase) (Th ...	0.02	-	cyt	0	Cytoplasm (By similarity)				199
Q6FR39 UniProt NPD GO	TRXB_CANGA	Thioredoxin reductase (EC 1.8.1.9)	0.02	-	cyt	0	Cytoplasm (By similarity)				319
Q9JMH6 UniProt NPD GO	TRXR1_MOUSE	Thioredoxin reductase 1, cytoplasmic (EC 1.8.1.9) (TR) (TR1)	0.02	-	mit	0	Cytoplasm	cytosol [IDA]			499
O89049 UniProt NPD GO	TRXR1_RAT	Thioredoxin reductase 1, cytoplasmic (EC 1.8.1.9) (TR) (TR1) (NADPH-dependent thioredoxin reductase) ...	0.02	-	cyt	0	Cytoplasm (By similarity)			1H6V	498
Q9VNT5 UniProt NPD GO	TRXR2_DROME	Thioredoxin reductase 2, mitochondrial precursor (EC 1.8.1.9) (TrxR-2)	0.02	-	mit	0	Mitochondrion				516
P97493 UniProt NPD GO	THIOM_MOUSE	Thioredoxin, mitochondrial precursor (Mt-Trx) (MTRX) (Thioredoxin-2)	0.02	-	mit	0	Mitochondrion	mitochondrion [IDA]			166
P97615 UniProt NPD GO	THIOM_RAT	Thioredoxin, mitochondrial precursor (Mt-Trx) (MTRX) (Thioredoxin-2)	0.02	-	mit	0	Mitochondrion				166
P29445 UniProt NPD GO	THIO1_DICDI	Thioredoxin-1	0.02	-	mit	0					105
P25372 UniProt NPD GO	TRX3_YEAST	Thioredoxin-3, mitochondrial precursor	0.02	-	mit	0	Mitochondrion	mitochondrion [IDA]			127
Q8LDI5 UniProt NPD GO	TRXL4_ARATH	Thioredoxin-like 4	0.02	-	cyt	0					118
Q8BUH1 UniProt NPD GO	TXN4B_MOUSE	Thioredoxin-like protein 4B	0.02	-	nuc	0	Nucleus (By similarity)				149
P82657 UniProt NPD GO	TL11_SPIOL	Thylakoid lumenal 11 kDa protein (P11) (Fragment)	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen				22
P82799 UniProt NPD GO	TL19_SPIOL	Thylakoid lumenal 18.4 kDa protein (P18.4) (Fragment)	0.02	-		0	Plastid; chloroplast; chloroplast thylakoid lumen				20
P01255 UniProt NPD GO	THYF_PIG	Thymic factor	0.02	-		0					9
O96720 UniProt NPD GO	KITH_ENCCU	Thymidine kinase (EC 2.7.1.21)	0.02	-	mit	0					212
P09768 UniProt NPD GO	KITH_CRIGR	Thymidine kinase, cytosolic (EC 2.7.1.21)	0.02	-	cyt	0	Cytoplasm				234
P04183 UniProt NPD GO	KITH_HUMAN	Thymidine kinase, cytosolic (EC 2.7.1.21)	0.02	-	cyt	0	Cytoplasm		188300	1XBT	234
P04184 UniProt NPD GO	KITH_MOUSE	Thymidine kinase, cytosolic (EC 2.7.1.21)	0.02	-	cyt	0	Cytoplasm				233
P27158 UniProt NPD GO	KITH_RAT	Thymidine kinase, cytosolic (EC 2.7.1.21) (Fragment)	0.02	-	cyt	0	Cytoplasm				121
O96650 UniProt NPD GO	TYSY_ASCSU	Thymidylate synthase (EC 2.1.1.45) (TS) (TSase)	0.02	-	cyt	0					294
P62970 UniProt NPD GO	TRH_BOMOR	Thyroliberin (Thyrotropin-releasing hormone) (TRH) (Thyrotropin-releasing factor) (TRF) (TSH-releasi ...	0.02	-		0	Secreted protein				3
P62971 UniProt NPD GO	TRH_NOTVI	Thyroliberin (Thyrotropin-releasing hormone) (TRH) (Thyrotropin-releasing factor) (TRF) (TSH-releasi ...	0.02	-		0	Secreted protein				3
P62968 UniProt NPD GO	TRH_PIG	Thyroliberin (Thyrotropin-releasing hormone) (TRH) (Thyrotropin-releasing factor) (TRF) (TSH-releasi ...	0.02	-		0	Secreted protein				3
P62969 UniProt NPD GO	TRH_SHEEP	Thyroliberin (Thyrotropin-releasing hormone) (TRH) (Thyrotropin-releasing factor) (TRF) (TSH-releasi ...	0.02	-		0	Secreted protein				3
Q62590 UniProt NPD GO	TSHB_PHOSU	Thyrotropin beta chain (Thyroid-stimulating hormone subunit beta) (TSH-beta) (TSH-B) (Fragment)	0.02	-	nuc	0	Secreted protein				101

You are viewing entries 85901 to 85950 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.