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
P82652 UniProt NPD GO	TIN2_HOPTI	Tigerinin-2	0.01	-		0	Secreted protein				12
P45669 UniProt NPD GO	TTX6_TITSE	Tityustoxin-6 (Tityustoxin VI) (TsTX-VI) (TsTXVI) (Toxin VI) (Ts VI) (Ts4)	0.01	-	nuc	0	Secreted protein				62
Q8LG88 UniProt NPD GO	TDT_ARATH	Tonoplast dicarboxylate transporter (AttDT) (Vacuolar malate transporter) (Sodium-dicarboxylate cotr ...	0.01	-	end	12 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				540
Q9ER39 UniProt NPD GO	TOR1A_MOUSE	Torsin A precursor (Torsin family 1 member A) (Dystonia 1 protein)	0.01	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	cytoplasm [IDA] nucleus [IDA]			333
P68426 UniProt NPD GO	TXT1_ORNHU	Toxin 1 precursor (Toxin-I) (SHT-I)	0.01	-	exc	1 *	Secreted protein (By similarity)				81
P45662 UniProt NPD GO	SCX4_CENNO	Toxin 4 precursor (Toxin II-10) (Cn4) (Toxin CngtV)	0.01	-	mit	0	Secreted protein				87
P45663 UniProt NPD GO	SCX5_CENNO	Toxin 5 precursor (Cn5) (CngtII)	0.01	-	exc	1 *	Secreted protein				87
P60265 UniProt NPD GO	SCX9_CENNO	Toxin 9 (Toxin II-14.4) (Fragment)	0.01	-		0	Secreted protein				14
P0C1F3 UniProt NPD GO	TXA22_ANTEL	Toxin APE 2-2	0.01	-	nuc	0	Secreted protein (Probable). Found in nematocyst (Probable)				47
P61792 UniProt NPD GO	TXU2_HETVE	Toxin AU2	0.01	-	cyt	0	Secreted protein				30
P61790 UniProt NPD GO	TX5B_HETVE	Toxin AU5B	0.01	-	cyt	0	Secreted protein				36
P45664 UniProt NPD GO	SCXX_CENNO	Toxin CngtIII precursor	0.01	-	exc	1 *	Secreted protein				87
P60267 UniProt NPD GO	SCX6_CENSU	Toxin Css VI (CssVI)	0.01	-	cyt	0	Secreted protein				66
Q7YT39 UniProt NPD GO	MTX4_GRASP	Toxin GsMTx-4 precursor (MTx4)	0.01	-	exc	1 *	Secreted protein			1TYK	82
P68411 UniProt NPD GO	SCX2_TITST	Toxin II (TsTX-II) (Tityustoxin II) (Ts2) (Tst2) (Toxin III-8)	0.01	-	cyt	0	Secreted protein				62
P68410 UniProt NPD GO	SCX2_TITSE	Toxin II (TsTX-II) (Tityustoxin II) (Ts2) (Tst2) (Toxin T1-IV) (TsTX-III)	0.01	-	cyt	0	Secreted protein				62
P56609 UniProt NPD GO	SCX2_TITBA	Toxin III-8 (Tb2)	0.01	-	nuc	0	Secreted protein				62
P60311 UniProt NPD GO	KJC3_NAJSP	Toxin KJC3	0.01	-	nuc	0	Secreted protein				60
P61095 UniProt NPD GO	SFI1_SEGFL	Toxin SFI 1 (F5.6)	0.01	-	nuc	0	Secreted protein				46
P61098 UniProt NPD GO	SFI4_SEGFL	Toxin SFI 4	0.01	-	nuc	0	Secreted protein				46
P61099 UniProt NPD GO	SFI5_SEGFL	Toxin SFI 5	0.01	-	nuc	0	Secreted protein				46
P61101 UniProt NPD GO	SFI7_SEGFL	Toxin SFI 7	0.01	-	nuc	0	Secreted protein				46
P61102 UniProt NPD GO	SFI8_SEGFL	Toxin SFI 8	0.01	-	nuc	0	Secreted protein				46
P56854 UniProt NPD GO	TX482_HYSGI	Toxin SNX-482	0.01	-	cyt	0	Secreted protein				41
P60276 UniProt NPD GO	SCXJ_TITBA	Toxin Tb2-II	0.01	-	nuc	0	Secreted protein				62
P84678 UniProt NPD GO	SC31_TITCA	Toxin Tc31 (Fragment)	0.01	-		0	Secreted protein	extracellular region [IDA]			8
P84684 UniProt NPD GO	SC41_TITCA	Toxin Tc41 (Fragment)	0.01	-		0	Secreted protein	extracellular region [IDA]			10
P15226 UniProt NPD GO	SCX7_TITSE	Toxin VII precursor (TsTX-VII) (Tityustoxin VII) (Ts VII) (Toxin II-11) (Toxin III-10) (Ts1) (Toxin ...	0.01	-	mit	0	Secreted protein			1NPI	84
P56611 UniProt NPD GO	SCX7_TITBA	Toxin gamma precursor (Tb1)	0.01	-	mit	0	Secreted protein				84
P56612 UniProt NPD GO	SCX7_TITST	Toxin gamma precursor (Tst1)	0.01	-	mit	0	Secreted protein	extracellular region [IDA]			84
Q5G8B8 UniProt NPD GO	SCX7_TITCO	Toxin gamma-like	0.01	-	nuc	0	Secreted protein				64
Q4LCT3 UniProt NPD GO	TXA1_ANDAU	Toxin-like peptide AaF1CA1 precursor	0.01	-	exc	1 *	Secreted protein (By similarity)	extracellular region [ISS]			80
Q96RJ0 UniProt NPD GO	TAAR1_HUMAN	Trace amine-associated receptor 1 (Trace amine receptor 1) (TaR-1)	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]	609333		339
Q8HZ64 UniProt NPD GO	TAAR1_MACMU	Trace amine-associated receptor 1 (Trace amine receptor 1) (TaR-1)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				338
Q5QD29 UniProt NPD GO	TAAR1_PANTR	Trace amine-associated receptor 1 (Trace amine receptor 1) (TaR-1)	0.01	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				339
Q5QD14 UniProt NPD GO	TAAR5_MOUSE	Trace amine-associated receptor 5	0.01	-	end	7 *	Membrane; multi-pass membrane protein				337
Q5QD23 UniProt NPD GO	TAAR5_RAT	Trace amine-associated receptor 5	0.01	-	end	7 *	Membrane; multi-pass membrane protein				337
Q969N4 UniProt NPD GO	TAAR8_HUMAN	Trace amine-associated receptor 8 (Trace amine receptor 5) (TaR-5) (G-protein coupled receptor 102)	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]	606927		342
Q5QD05 UniProt NPD GO	TAA8C_MOUSE	Trace amine-associated receptor 8c	0.01	-	end	7 *	Membrane; multi-pass membrane protein				344
Q923Y0 UniProt NPD GO	TAA8C_RAT	Trace amine-associated receptor 8c (Trace amine receptor 10) (TaR-10)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				344
Q5QD04 UniProt NPD GO	TAAR9_MOUSE	Trace amine-associated receptor 9	0.01	-	end	7 *	Membrane; multi-pass membrane protein				348
Q923Y6 UniProt NPD GO	TAAR9_RAT	Trace amine-associated receptor 9 (Trace amine receptor 3) (TaR-3)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				338
Q9CQA1 UniProt NPD GO	TPPC5_MOUSE	Trafficking protein particle complex subunit 5	0.01	-	mit	0	Golgi apparatus; cis-Golgi network (By similarity)				188
O75865 UniProt NPD GO	TPC6A_HUMAN	Trafficking protein particle complex subunit 6A	0.01	-	cyt	0	Golgi apparatus; cis-Golgi network (By similarity)			2C0J	159
O42700 UniProt NPD GO	TAL1_SCHPO	Transaldolase (EC 2.2.1.2)	0.01	-	cyt	0					322
P17440 UniProt NPD GO	TAL1_PICJA	Transaldolase-1 (EC 2.2.1.2) (Transaldolase I) (Fragment)	0.01	-		0					9
P17441 UniProt NPD GO	TAL3_PICJA	Transaldolase-3 (EC 2.2.1.2) (Transaldolase III) (Fragment)	0.01	-		0					9
Q3SYX6 UniProt NPD GO	SPT4H_BOVIN	Transcription elongation factor SPT4 (DRB sensitivity-inducing factor small subunit) (DSIF small sub ...	0.01	-	mit	0	Nucleus (By similarity)				117
Q6DGQ0 UniProt NPD GO	SPT4H_BRARE	Transcription elongation factor SPT4 (DRB sensitivity-inducing factor small subunit) (DSIF small sub ...	0.01	-	mit	0	Nucleus (By similarity)				117
Q4R941 UniProt NPD GO	SPT4H_MACFA	Transcription elongation factor SPT4 (DRB sensitivity-inducing factor small subunit) (DSIF small sub ...	0.01	-	mit	0	Nucleus (By similarity)				117

You are viewing entries 91751 to 91800 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.