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
Q8BW00 UniProt NPD GO	PTH_MOUSE	Probable peptidyl-tRNA hydrolase (EC 3.1.1.29) (PTH)	0.18	-	mit	0					204
O74806 UniProt NPD GO	PTH_SCHPO	Probable peptidyl-tRNA hydrolase (EC 3.1.1.29) (PTH)	0.18	-	nuc	0					218
Q8CFI5 UniProt NPD GO	SYPM_MOUSE	Probable prolyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.15) (Proline--tRNA ligase) (ProRS ...	0.18	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				475
P20346 UniProt NPD GO	P322_SOLTU	Probable protease inhibitor P322 precursor	0.18	-	mit	0					74
Q9XX15 UniProt NPD GO	NEP1_CAEEL	Probable ribosome biogenesis protein nep-1	0.18	-	cyt	0	Nucleus; nucleolus (By similarity)				231
Q9VAL0 UniProt NPD GO	SPCS1_DROME	Probable signal peptidase complex subunit 1 (EC 3.4.-.-) (Microsomal signal peptidase 12 kDa subunit ...	0.18	+	end	2 *	Membrane; multi-pass membrane protein (Potential)				98
P48259 UniProt NPD GO	YCF27_CYAPA	Probable transcriptional regulator ycf27 (OmpR-like protein)	0.18	-	cyt	0	Plastid; cyanelle				239
Q96TW9 UniProt NPD GO	MCH1_HANAN	Probable transporter MCH1	0.18	-	end	10 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				489
P39709 UniProt NPD GO	SEO1_YEAST	Probable transporter SEO1	0.18	-	end	12	Membrane; multi-pass membrane protein				593
P34462 UniProt NPD GO	VATD_CAEEL	Probable vacuolar ATP synthase subunit D (EC 3.6.3.14) (V-ATPase D subunit) (Vacuolar proton pump D ...	0.18	-	cyt	0					257
Q8RU33 UniProt NPD GO	VA0D_ORYSA	Probable vacuolar ATP synthase subunit d (EC 3.6.3.14) (V-ATPase d subunit) (Vacuolar proton pump su ...	0.18	-	cyt	0					351
O77588 UniProt NPD GO	PLOD1_BOVIN	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 precursor (EC 1.14.11.4) (Lysyl hydroxylase 1) (LH ...	0.18	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum cisterna; peripheral ...				726
P55247 UniProt NPD GO	GON1_MACMU	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.18	-	nuc	0	Secreted protein				67
Q8K458 UniProt NPD GO	PKR2_MOUSE	Prokineticin receptor 2 (PK-R2) (G-protein coupled receptor 73-like 1)	0.18	+	end	6	Membrane; multi-pass membrane protein				381
P04768 UniProt NPD GO	PLF2_MOUSE	Proliferin-2 precursor (Mitogen-regulated protein 2)	0.18	-	mit	0	Secreted protein				224
Q10576 UniProt NPD GO	P4HA1_CAEEL	Prolyl 4-hydroxylase alpha-1 subunit precursor (EC 1.14.11.2) (4-PH alpha-1) (Procollagen-proline,2- ...	0.18	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen	cell [IDA]			559
Q612F5 UniProt NPD GO	PCCA_CAEBR	Propionyl-CoA carboxylase alpha chain, mitochondrial precursor (EC 6.4.1.3) (PCCase subunit alpha) ( ...	0.18	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				738
Q8NBP7 UniProt NPD GO	PCSK9_HUMAN	Proprotein convertase subtilisin/kexin type 9 precursor (EC 3.4.21.-) (Proprotein convertase PC9) (S ...	0.18	-	exc	0	Secreted protein		607786		692
Q9P2B2 UniProt NPD GO	FPRP_HUMAN	Prostaglandin F2 receptor negative regulator precursor (Prostaglandin F2-alpha receptor regulatory p ...	0.18	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...		601204		879
O09114 UniProt NPD GO	PTGDS_MOUSE	Prostaglandin-H2 D-isomerase precursor (EC 5.3.99.2) (Lipocalin-type prostaglandin-D synthase) (Glut ...	0.18	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Detected on rough endoplasmic re ...	extracellular region [IDA] Golgi apparatus [ISS] nuclear envelope [ISS] rough endoplasmic reticulum [ISS]			189
P52427 UniProt NPD GO	PSA4_SPIOL	Proteasome subunit alpha type 4 (EC 3.4.25.1) (20S proteasome alpha subunit C) (20S proteasome subun ...	0.18	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				250
Q94561 UniProt NPD GO	PSA5_ENTHI	Proteasome subunit alpha type 5 (EC 3.4.25.1)	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				247
P28070 UniProt NPD GO	PSB4_HUMAN	Proteasome subunit beta type 4 precursor (EC 3.4.25.1) (Proteasome beta chain) (Macropain beta chain ...	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [TAS] proteasome complex (sensu Eukaryota) [TAS]	602177		264
Q7L4S7 UniProt NPD GO	ARMX6_HUMAN	Protein ARMCX6	0.18	-	end	1 *					300
Q8IVU9 UniProt NPD GO	CJ107_HUMAN	Protein C10orf107	0.18	-	mit	0					208
Q96D05 UniProt NPD GO	CJ035_HUMAN	Protein C10orf35	0.18	-	nuc	1					121
Q8C525 UniProt NPD GO	CC059_MOUSE	Protein C3orf59 homolog	0.18	-	cyt	0					428
Q9H6K1 UniProt NPD GO	CF106_HUMAN	Protein C6orf106	0.18	-	nuc	0					298
Q4R526 UniProt NPD GO	CF211_MACFA	Protein C6orf211 homolog	0.18	-	cyt	0					441
Q8N4H5 UniProt NPD GO	CI105_HUMAN	Protein C9orf105	0.18	-	cyt	0					51
Q5R676 UniProt NPD GO	CI105_PONPY	Protein C9orf105 homolog	0.18	-	cyt	0					51
Q6AYM9 UniProt NPD GO	CLN8_RAT	Protein CLN8	0.18	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				288
Q9D1F3 UniProt NPD GO	CX040_MOUSE	Protein CXorf40 homolog	0.18	-	cyt	0					157
Q3T0U7 UniProt NPD GO	FA96A_BOVIN	Protein FAM96A	0.18	-	mit	0					160
Q66IG4 UniProt NPD GO	NDRG1_XENTR	Protein NDRG1	0.18	-	nuc	0					395
Q7ZY73 UniProt NPD GO	NDRG2_XENLA	Protein NDRG2	0.18	-	cyt	0	Cytoplasm (By similarity)				360
Q6P9X9 UniProt NPD GO	PARM1_RAT	Protein PARM-1 precursor (Prostatic androgen-repressed message 1 protein) (Castration-induced prosta ...	0.18	-	mit	1	Membrane; single-pass type I membrane protein (Potential)				296
Q90372 UniProt NPD GO	QNR71_COTJA	Protein QNR-71 precursor	0.18	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				559
P82641 UniProt NPD GO	SCR22_ARATH	Protein SCRL22 precursor	0.18	-	exc	0					96
P78699 UniProt NPD GO	SOM1_KLULA	Protein SOM1, mitochondrial precursor	0.18	-	nuc	0	Mitochondrion; mitochondrial inner membrane (Potential)				71
Q12254 UniProt NPD GO	SVS1_YEAST	Protein SVS1 precursor	0.18	-	exc	0		cell wall (sensu Fungi) [IDA] vacuole (sensu Fungi) [IDA]			260
Q6PL24 UniProt NPD GO	TMED8_HUMAN	Protein TMED8	0.18	-	nuc	0					325
Q8K2T4 UniProt NPD GO	U655_MOUSE	Protein UNQ655/PRO1286 homolog precursor	0.18	-	mit	1 *	Secreted protein (By similarity)				89
P23202 UniProt NPD GO	URE2_YEAST	Protein URE2	0.18	-	nuc	0		cytosol [IDA] soluble fraction [IDA]		1HQO	354
Q2QLG1 UniProt NPD GO	WNT2_CALJA	Protein Wnt-2 precursor	0.18	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
Q2QL76 UniProt NPD GO	WNT2_DIDMA	Protein Wnt-2 precursor	0.18	-	end	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
Q2QL96 UniProt NPD GO	WNT2_MONDO	Protein Wnt-2 precursor	0.18	-	end	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
P41221 UniProt NPD GO	WNT5A_HUMAN	Protein Wnt-5a precursor	0.18	-	vac	1 *	Secreted protein; extracellular space; extracellular matrix	extracellular space [TAS] soluble fraction [TAS]	164975		365
P31286 UniProt NPD GO	WNT5A_XENLA	Protein Wnt-5a precursor (XWnt-5a)	0.18	-	exc	0	Secreted protein; extracellular space; extracellular matrix				380
Q92050 UniProt NPD GO	WNT5B_BRARE	Protein Wnt-5b precursor	0.18	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [NAS]			363

You are viewing entries 53501 to 53550 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.