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
Q6XHI1 UniProt NPD GO	THIO2_DROYA	Thioredoxin-2	0.00	-	mit	0					106
Q9V429 UniProt NPD GO	THIO2_DROME	Thioredoxin-2 (DmTrx-2)	0.00	-	mit	0				1XWC	114
Q6DBT3 UniProt NPD GO	TXNL5_BRARE	Thioredoxin-like protein 5	0.00	-	cyt	0	Cytoplasm (By similarity)				123
Q9CQM5 UniProt NPD GO	TXNL5_MOUSE	Thioredoxin-like protein 5 (14 kDa thioredoxin-related protein) (TRP14) (Protein 42-9-9)	0.00	-	cyt	0	Cytoplasm (By similarity)			1V9W	123
P00586 UniProt NPD GO	THTR_BOVIN	Thiosulfate sulfurtransferase (EC 2.8.1.1) (Rhodanese)	0.00	-	mit	0	Mitochondrion; mitochondrial matrix			2ORA	296
Q39129 UniProt NPD GO	STR16_ARATH	Thiosulfate sulfurtransferase (EC 2.8.1.1) (Rhodanese) (Senescence-associated protein) (Sulfurtransf ...	0.00	-	cyt	0	Plastid; chloroplast			1TQ1	120
P31212 UniProt NPD GO	THD1_SOLTU	Threonine dehydratase biosynthetic (EC 4.3.1.19) (Threonine deaminase) (TD) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast				359
O42615 UniProt NPD GO	THDH_ARXAD	Threonine dehydratase, mitochondrial precursor (EC 4.3.1.19) (Threonine deaminase)	0.00	-	nuc	0	Mitochondrion				550
P84122 UniProt NPD GO	THRB_SALSA	Thrombin (EC 3.4.21.5) [Contains: Thrombin light chain; Thrombin heavy chain] (Fragments)	0.00	-	cyt	0	Secreted protein				36
P84026 UniProt NPD GO	THBI_BOTJA	Thrombin inhibitor subunit 1 (Thrombin inhibitor subunit I) (Fragment)	0.00	-		0	Secreted protein				15
P82681 UniProt NPD GO	TL13_SPIOL	Thylakoid lumenal 13.8 kDa protein (P13.8) (Fragment)	0.00	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid lumen				21
P82537 UniProt NPD GO	TL1X_SPIOL	Thylakoid lumenal 17 kDa protein (P17) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen				30
P82796 UniProt NPD GO	TL22_SPIOL	Thylakoid lumenal 22 kDa protein (P22) (Fragment)	0.00	-		0	Plastid; chloroplast; chloroplast thylakoid lumen				20
P82671 UniProt NPD GO	TL09_SPIOL	Thylakoid lumenal 9 kDa protein (P9) (Fragment)	0.00	-		0	Plastid; chloroplast; chloroplast thylakoid lumen				17
Q9I980 UniProt NPD GO	TYB10_TORMA	Thymosin beta-10 (Thymb10)	0.00	-	nuc	0	Cytoplasm (By similarity)				43
Q52R90 UniProt NPD GO	TSHB_FELCA	Thyrotropin beta chain precursor (Thyroid-stimulating hormone beta subunit) (TSH-beta) (TSH-B)	0.00	-	mit	0	Secreted protein				138
P82653 UniProt NPD GO	TIN3_HOPTI	Tigerinin-3	0.00	-		0	Secreted protein				12
P82654 UniProt NPD GO	TIN4_HOPTI	Tigerinin-4	0.00	-		0	Secreted protein				11
P46115 UniProt NPD GO	SCXV_TITSE	Tityustoxin-5 (Tityustoxin V) (TsTX-V) (TsTXV) (Toxin V) (Ts V)	0.00	-	nuc	0	Secreted protein				64
P43318 UniProt NPD GO	PA2_RHONO	Toxic phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.00	-	cyt	0	Secreted protein. Found in nematocyst				32
Q9TWL1 UniProt NPD GO	SCX7_CENNO	Toxin 7 (Toxin II-13.3) (Fragment)	0.00	-	cyt	0	Secreted protein				55
Q9TWL0 UniProt NPD GO	SCX8_CENNO	Toxin 8 (Toxin II-13.4) (Fragment)	0.00	-	cyt	0	Secreted protein				62
P69943 UniProt NPD GO	AETX1_ANEER	Toxin AETX-1 (AETX I)	0.00	-	cyt	0	Secreted protein. Found in nematocyst				47
P61541 UniProt NPD GO	APT1_ANTEL	Toxin APETx1	0.00	-	cyt	0	Secreted protein (Probable). Found in nematocyst (Probable)			1WQK	42
O77091 UniProt NPD GO	SIXP_MESMA	Toxin BmK IT-AP precursor (Insect toxin analgesic peptide) (Bm33-I)	0.00	-	cyt	0	Secreted protein			1T0Z	90
Q95P69 UniProt NPD GO	SCAA_MESMA	Toxin BmKT precursor (BmK T) (Antitumor-analgesic peptide) (AGAP)	0.00	-	exc	0	Secreted protein (By similarity)				85
P84509 UniProt NPD GO	TX3_CERCR	Toxin CcoTx3	0.00	-	cyt	0	Secreted protein	extracellular space [IDA]			39
P61094 UniProt NPD GO	SFIF_SEGFL	Toxin F5.5 (Fragment)	0.00	-		0	Secreted protein				18
P56608 UniProt NPD GO	SCX1_TITBA	Toxin IV-5 (Tb3)	0.00	-	cyt	0	Secreted protein				62
P01496 UniProt NPD GO	SCX1_TITSE	Toxin IV-5 precursor (Ts3) (Tityustoxin) (Fragment)	0.00	-	exc	0	Secreted protein				80
P61791 UniProt NPD GO	TXJ1_HETVE	Toxin KJ1	0.00	-	cyt	0	Secreted protein				29
P61229 UniProt NPD GO	TX4B_PHONI	Toxin Pn4B precursor	0.00	-	exc	0	Secreted protein (By similarity)				85
P61096 UniProt NPD GO	SFI2_SEGFL	Toxin SFI 2 (F5.7)	0.00	-	nuc	0	Secreted protein				46
P61097 UniProt NPD GO	SFI3_SEGFL	Toxin SFI 3	0.00	-	nuc	0	Secreted protein				46
P61100 UniProt NPD GO	SFI6_SEGFL	Toxin SFI 6	0.00	-	nuc	0	Secreted protein				46
P84676 UniProt NPD GO	SC27_TITCA	Toxin Tc27 (Fragment)	0.00	-		0	Secreted protein	extracellular region [IDA]			10
P84677 UniProt NPD GO	SC29_TITCA	Toxin Tc29 (Fragment)	0.00	-		0	Secreted protein	extracellular region [IDA]			8
P84682 UniProt NPD GO	SC39_TITCA	Toxin Tc39 (Fragment)	0.00	-		0	Secreted protein	extracellular region [IDA]			10
P84685 UniProt NPD GO	SC43_TITCA	Toxin Tc43 (Fragment)	0.00	-		0	Secreted protein	extracellular region [IDA]			10
P60214 UniProt NPD GO	SC49B_TITCA	Toxin Tc49b	0.00	-	cyt	0	Secreted protein	extracellular region [IDA]			64
P84688 UniProt NPD GO	SC50_TITCA	Toxin Tc50 (Fragment)	0.00	-		0	Secreted protein	extracellular region [IDA]			10
P60215 UniProt NPD GO	SC54_TITCA	Toxin Tc54 (Fragment)	0.00	-	nuc	0	Secreted protein	extracellular region [IDA]			28
P84689 UniProt NPD GO	SC56_TITCA	Toxin Tc56 (Fragment)	0.00	-		0	Secreted protein	extracellular region [IDA]			10
P84690 UniProt NPD GO	SC58_TITCA	Toxin Tc58 (Fragment)	0.00	-		0	Secreted protein	extracellular region [IDA]			10
P84693 UniProt NPD GO	SC66_TITCA	Toxin Tc66 (Fragment)	0.00	-		0	Secreted protein	extracellular region [IDA]			10
P84694 UniProt NPD GO	SC83_TITCA	Toxin Tc83 (Fragment)	0.00	-		0	Secreted protein	extracellular region [IDA]			10
P60260 UniProt NPD GO	SCX1_TITDI	Toxin TdII-1 (Fragment)	0.00	-	cyt	0	Secreted protein				26
P60261 UniProt NPD GO	SCX2_TITDI	Toxin TdII-2 (Fragment)	0.00	-		0	Secreted protein				13
P60262 UniProt NPD GO	SCX3_TITDI	Toxin TdII-3 (Fragment)	0.00	-	cyt	0	Secreted protein				29
Q5QD13 UniProt NPD GO	TAAR6_MOUSE	Trace amine-associated receptor 6	0.00	-	end	7 *	Membrane; multi-pass membrane protein				345

You are viewing entries 98301 to 98350 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.