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
Q4R6W2 UniProt NPD GO	TM55B_MACFA	Transmembrane protein 55B (EC 3.1.3.-) (Type I phosphatidylinositol 4,5-bisphosphate 4-phosphatase) ...	0.21	-	nuc	2	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity). Lysos ...				284
Q9Y5L0 UniProt NPD GO	TNPO3_HUMAN	Transportin-3 (Transportin-SR) (TRN-SR) (Importin-12)	0.21	-	cyt	0	Cytoplasm. Nucleus				975
Q8MMG9 UniProt NPD GO	TREA_PIMHY	Trehalase precursor (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.21	-	exc	1 *	Secreted protein				585
Q8NIG9 UniProt NPD GO	TRI5_FUSCU	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.21	-	cyt	0					375
Q00835 UniProt NPD GO	TRI5_FUSPO	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.21	-	cyt	0					377
P13513 UniProt NPD GO	TRI5_FUSSP	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.21	-	cyt	0				2AET	374
O46629 UniProt NPD GO	ECHB_BOVIN	Trifunctional enzyme subunit beta, mitochondrial precursor (TP-beta) [Includes: 3-ketoacyl-CoA thiol ...	0.21	-	mit	0	Mitochondrion; mitochondrial matrix				475
Q99NH8 UniProt NPD GO	TREM2_MOUSE	Triggering receptor expressed on myeloid cells 2 precursor (Triggering receptor expressed on monocyt ...	0.21	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein (Potential). Isoform 2: Secreted prote ...				227
Q91ZW6 UniProt NPD GO	TMLH_RAT	Trimethyllysine dioxygenase, mitochondrial precursor (EC 1.14.11.8) (Epsilon-trimethyllysine 2-oxogl ...	0.21	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			405
Q28201 UniProt NPD GO	TKDP1_BOVIN	Trophoblast Kunitz domain protein 1 precursor (TKDP-1)	0.21	-	exc	0	Secreted protein				351
Q5M7S9 UniProt NPD GO	TSK_XENTR	Tsukushi precursor (Leucine-rich repeat-containing protein 54)	0.21	-	exc	0	Secreted protein (Potential)				350
Q4WA70 UniProt NPD GO	TBB_ASPFU	Tubulin beta chain (Beta tubulin)	0.21	-	cyt	0					448
P08562 UniProt NPD GO	TBB_TRYCR	Tubulin beta chain (Beta tubulin)	0.21	-	cyt	0					442
Q9N2N6 UniProt NPD GO	TBB_EUPFO	Tubulin beta chain (Beta-tubulin)	0.21	-	cyt	0					444
P12456 UniProt NPD GO	TBB1_CAEEL	Tubulin beta-1 chain (Beta-1 tubulin)	0.21	-	cyt	0		neuron projection [IDA]			441
P46263 UniProt NPD GO	TBB1_SOLTU	Tubulin beta-1 chain (Beta-1 tubulin)	0.21	-	cyt	0					451
P46264 UniProt NPD GO	TBB2_SOLTU	Tubulin beta-2 chain (Beta-2 tubulin)	0.21	-	cyt	0					452
P50260 UniProt NPD GO	TBB2_PORPU	Tubulin beta-2 chain (Beta-2 tubulin) (Fragment)	0.21	-	cyt	0					423
Q9ZRB0 UniProt NPD GO	TBB3_WHEAT	Tubulin beta-3 chain (Beta-3 tubulin)	0.21	-	cyt	0					445
P29515 UniProt NPD GO	TBB7_ARATH	Tubulin beta-7 chain (Beta-7 tubulin)	0.21	-	cyt	0					449
P53378 UniProt NPD GO	TBG_YEAST	Tubulin gamma chain (Gamma tubulin)	0.21	-	nuc	0	Nucleus. Is present in the spindle pole body	gamma-tubulin complex (sensu Saccharomyces) [IPI] inner plaque of spindle pole body [IDA] outer plaque of spindle pole body [IDA]			473
P54404 UniProt NPD GO	TBG2_EUPCR	Tubulin gamma-2 chain (Gamma-2 tubulin)	0.21	-	cyt	0					462
O88472 UniProt NPD GO	TNR17_MOUSE	Tumor necrosis factor receptor superfamily member 17 (B-cell maturation protein)	0.21	-	nuc	1 *	Membrane; single-pass type III membrane protein (Probable)				185
Q969Z4 UniProt NPD GO	TR19L_HUMAN	Tumor necrosis factor receptor superfamily member 19L precursor (Receptor expressed in lymphoid tiss ...	0.21	-	exc	1	Membrane; single-pass type I membrane protein (Probable)				430
P28205 UniProt NPD GO	PTP13_STYPL	Tyrosine-protein phosphatase 13 (EC 3.1.3.48) (Fragment)	0.21	-	cyt	0					114
P28201 UniProt NPD GO	PTP9_STYPL	Tyrosine-protein phosphatase 9 (EC 3.1.3.48) (Fragment)	0.21	-	cyt	0					111
Q8VC85 UniProt NPD GO	LSM1_MOUSE	U6 snRNA-associated Sm-like protein LSm1	0.21	-	cyt	0	Nucleus (Potential)				133
P56558 UniProt NPD GO	OGT1_RAT	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (EC 2.4.1.-) (O-Glc ...	0.21	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)	cytosol [ISS] nucleus [ISS]			1036
Q9Y284 UniProt NPD GO	CG140_HUMAN	UPF0139 protein CGI-140	0.21	-	nuc	1 *	Membrane; multi-pass membrane protein (Potential)				106
Q2M2T6 UniProt NPD GO	CG140_BOVIN	UPF0139 protein CGI-140 homolog	0.21	-	nuc	1 *	Membrane; multi-pass membrane protein (Potential)				106
Q6ZWX0 UniProt NPD GO	CG140_MOUSE	UPF0139 protein CGI-140 homolog	0.21	-	nuc	1 *	Membrane; multi-pass membrane protein (Potential)				106
Q6Q7K0 UniProt NPD GO	CG140_PIG	UPF0139 protein CGI-140 homolog	0.21	-	nuc	1 *	Membrane; multi-pass membrane protein (Potential)				106
Q9VSH9 UniProt NPD GO	U183_DROME	UPF0183 protein CG7083	0.21	-	cyt	0					438
P58686 UniProt NPD GO	CI016_MOUSE	UPF0184 protein C9orf16 homolog	0.21	-	nuc	0					83
Q99382 UniProt NPD GO	YL065_YEAST	UPF0372 protein YLR065C	0.21	-	mit	4 *	Membrane; multi-pass membrane protein (Potential)				181
Q5M9I5 UniProt NPD GO	UCRH_RAT	Ubiquinol-cytochrome c reductase complex 11 kDa protein, mitochondrial precursor (EC 1.10.2.2) (Mito ...	0.21	-	nuc	0	Mitochondrion; mitochondrial inner membrane (By similarity)				89
Q6C3K7 UniProt NPD GO	UCR7_YARLI	Ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2) (Complex III subunit VII)	0.21	-	cyt	0	Mitochondrion; mitochondrial inner membrane (Potential)				128
P13117 UniProt NPD GO	UBIQ_NEUCR	Ubiquitin	0.21	-	nuc	0	Cytoplasm. Nucleus				76
P63072 UniProt NPD GO	UBD_MOUSE	Ubiquitin D (Ubiquitin-like protein FAT10) (Diubiquitin)	0.21	-	nuc	0					162
Q5KN22 UniProt NPD GO	UBC2_CRYNE	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC2) (Ubiquitin carrier p ...	0.21	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				169
P25867 UniProt NPD GO	UBCD1_DROME	Ubiquitin-conjugating enzyme E2-17 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.21	-	nuc	0					147
P42743 UniProt NPD GO	UBCY_ARATH	Ubiquitin-conjugating enzyme E2-18 kDa (EC 6.3.2.19) (Ubiquitin-conjugating enzyme 15) (Ubiquitin-pr ...	0.21	-	mit	0					161
P0C154 UniProt NPD GO	Y0679_EMENI	Uncharacterized protein AN0679	0.21	-	nuc	0					251
Q8BR63 UniProt NPD GO	CN024_MOUSE	Uncharacterized protein C14orf24 homolog	0.21	-	cyt	0					207
Q96FQ7 UniProt NPD GO	CR018_HUMAN	Uncharacterized protein C18orf18	0.21	-	nuc	0					95
Q66H33 UniProt NPD GO	CC038_RAT	Uncharacterized protein C3orf38 homolog	0.21	-	cyt	0					348
Q07541 UniProt NPD GO	YD121_YEAST	Uncharacterized protein YDL121C	0.21	-	vac	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (Potenti ...	endoplasmic reticulum [IDA]			149
P47013 UniProt NPD GO	YJN4_YEAST	Uncharacterized protein YJL134W	0.21	-	vac	6	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			409
P39543 UniProt NPD GO	YJT2_YEAST	Uncharacterized protein YJL192C precursor	0.21	-	end	0		endoplasmic reticulum [IDA] integral to membrane of membrane fraction [IDA]			234
P42844 UniProt NPD GO	YN50_YEAST	Uncharacterized protein YNL310C	0.21	-	mit	0		mitochondrial matrix [IDA] mitochondrion [IDA]			205

You are viewing entries 50151 to 50200 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.