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
O94544 UniProt NPD GO	LKHA4_SCHPO	Probable leukotriene A-4 hydrolase (EC 3.3.2.6) (LTA-4 hydrolase) (Leukotriene A(4) hydrolase)	0.28	-	cyt	0	Cytoplasm (By similarity)				612
Q9C2H9 UniProt NPD GO	SYMM_NEUCR	Probable methionyl-tRNA synthetase, mitochondrial (EC 6.1.1.10) (Methionine--tRNA ligase) (MetRS)	0.28	-	mit	0	Mitochondrion; mitochondrial matrix				622
Q9P7X1 UniProt NPD GO	MPPB_SCHPO	Probable mitochondrial-processing peptidase subunit beta, mitochondrial precursor (EC 3.4.24.64) (Be ...	0.28	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				457
Q5Y5T3 UniProt NPD GO	ZDH23_MOUSE	Probable palmitoyltransferase ZDHHC23 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 23) ( ...	0.28	-	end	6	Membrane; multi-pass membrane protein (Potential)				425
P15721 UniProt NPD GO	PEL56_LYCES	Probable pectate lyase P56 precursor (EC 4.2.2.2)	0.28	-	vac	1 *					398
Q9SCX5 UniProt NPD GO	AKT5_ARATH	Probable potassium channel AKT5	0.28	-	end	5	Membrane; multi-pass membrane protein				880
O14250 UniProt NPD GO	PSA1_SCHPO	Probable proteasome subunit alpha type 1 (EC 3.4.25.1)	0.28	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [TAS]			272
Q09878 UniProt NPD GO	MET10_SCHPO	Probable sulfite reductase [NADPH] flavoprotein component (EC 1.8.1.2)	0.28	-	cyt	0					1006
Q6BV30 UniProt NPD GO	ETR2_DEBHA	Probable trans-2-enoyl-CoA reductase 2, mitochondrial precursor (EC 1.3.1.38)	0.28	-	mit	0	Mitochondrion (By similarity)				387
Q6BN11 UniProt NPD GO	MCH1_DEBHA	Probable transporter MCH1	0.28	-	end	10 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				486
Q9Y2Z4 UniProt NPD GO	SYYM_HUMAN	Probable tyrosyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.1) (Tyrosine--tRNA ligase) (TyrR ...	0.28	-	mit	0	Mitochondrion (Potential)	mitochondrion [NAS]			477
Q9VCQ3 UniProt NPD GO	VA0D2_DROME	Probable vacuolar ATP synthase subunit d 2 (EC 3.6.3.14) (V-ATPase d subunit 2) (Vacuolar proton pum ...	0.28	-	cyt	0					350
Q9FT51 UniProt NPD GO	WBC28_ARATH	Probable white-brown complex homolog protein 28	0.28	-	end	5	Membrane; multi-pass membrane protein (By similarity)				737
P79373 UniProt NPD GO	PRGR_MACEU	Progesterone receptor (PR) (Fragment)	0.28	-	nuc	0	Nucleus				180
P51921 UniProt NPD GO	GON3_PAGMA	Progonadoliberin-3 precursor (Progonadoliberin III) [Contains: Gonadoliberin-3 (Gonadoliberin III) ( ...	0.28	-	exc	0	Secreted protein				90
P51923 UniProt NPD GO	GON3_SPAAU	Progonadoliberin-3 precursor (Progonadoliberin III) [Contains: Gonadoliberin-3 (Gonadoliberin III) ( ...	0.28	-	exc	0	Secreted protein				90
Q8R414 UniProt NPD GO	PROK1_RAT	Prokineticin-1 precursor (Endocrine-gland-derived vascular endothelial growth factor) (EG-VEGF)	0.28	-	exc	0	Secreted protein (By similarity)				105
P46403 UniProt NPD GO	PRL_FELCA	Prolactin precursor (PRL)	0.28	-	exc	0	Secreted protein				229
P29234 UniProt NPD GO	PRL_MUSVI	Prolactin precursor (PRL)	0.28	-	exc	0	Secreted protein				229
P01237 UniProt NPD GO	PRL_RAT	Prolactin precursor (PRL)	0.28	-	exc	0	Secreted protein	extracellular region [IDA]			226
P59996 UniProt NPD GO	PCSK9_RAT	Proprotein convertase subtilisin/kexin type 9 precursor (EC 3.4.21.-) (Proprotein convertase PC9) (S ...	0.28	-	exc	0	Secreted protein (By similarity)				691
O97554 UniProt NPD GO	PGH1_RABIT	Prostaglandin G/H synthase 1 precursor (EC 1.14.99.1) (Cyclooxygenase-1) (COX-1) (Prostaglandin-endo ...	0.28	-	nuc	0	Microsome; microsomal membrane; peripheral membrane protein (By similarity)				606
O13268 UniProt NPD GO	PSA7_CHICK	Proteasome subunit alpha type 7 (EC 3.4.25.1) (GPRO-28)	0.28	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				249
Q9Y442 UniProt NPD GO	CV024_HUMAN	Protein C22orf24	0.28	-	nuc	1 *					160
Q9H993 UniProt NPD GO	CF211_HUMAN	Protein C6orf211	0.28	-	cyt	0					441
Q9H330 UniProt NPD GO	CI005_HUMAN	Protein C9orf5 (Protein CG-2)	0.28	-	end	14	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			911
O00622 UniProt NPD GO	CYR61_HUMAN	Protein CYR61 precursor (Cysteine-rich, angiogenic inducer, 61) (Insulin-like growth factor-binding ...	0.28	-	mit	0	Secreted protein		602369		381
P43555 UniProt NPD GO	EMP47_YEAST	Protein EMP47 precursor (47 kDa endomembrane protein) (Endosomal P44 protein)	0.28	-	end	1	Golgi apparatus; Golgi apparatus membrane; single-pass type I membrane protein. Endoplasmic reticulu ...	ER to Golgi transport vesicle [IDA] Golgi apparatus [TAS]		2A71	445
Q502A3 UniProt NPD GO	F100B_BRARE	Protein FAM100B	0.28	-	nuc	0					172
Q921M7 UniProt NPD GO	FA49B_MOUSE	Protein FAM49B	0.28	-	cyt	0					324
Q5BIM9 UniProt NPD GO	GPR89_BOVIN	Protein GPR89A	0.28	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				423
Q8LGD5 UniProt NPD GO	MKS1_ARATH	Protein MKS1 (Protein MAP kinase 4 substrate 1)	0.28	-	nuc	0	Nucleus				222
Q9UN36 UniProt NPD GO	NDRG2_HUMAN	Protein NDRG2 (Protein Syld709613)	0.28	-	cyt	0	Cytoplasm. Cytoplasm; perinuclear region. Perinuclear in neurons	cytosol [NAS]	605272		371
Q6DFS4 UniProt NPD GO	NDRG3_XENTR	Protein NDRG3	0.28	-	cyt	0					387
Q4IEA7 UniProt NPD GO	OS9_GIBZE	Protein OS-9 homolog precursor	0.28	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				512
Q6C3U1 UniProt NPD GO	OS9_YARLI	Protein OS-9 homolog precursor	0.28	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				558
P47065 UniProt NPD GO	PT130_YEAST	Protein PET130	0.28	-	nuc	0	Mitochondrion; mitochondrial matrix (Potential)	mitochondrion [IDA]			347
Q28050 UniProt NPD GO	S10A7_BOVIN	Protein S100-A7 (S100 calcium-binding protein A7) (Allergen Bos d 3) (Dander minor allergen BDA11) ( ...	0.28	-	nuc	0					101
Q74ZD5 UniProt NPD GO	SEY1_ASHGO	Protein SEY1	0.28	-	nuc	1	Membrane; multi-pass membrane protein (Potential)				791
Q6FLC5 UniProt NPD GO	SEY1_CANGA	Protein SEY1	0.28	-	vac	2	Membrane; multi-pass membrane protein (Potential)				783
P31283 UniProt NPD GO	WNT13_XENLA	Protein Wnt-13 (XWnt-13) (XWnt-2) (Fragment)	0.28	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				128
Q9H1J5 UniProt NPD GO	WNT8A_HUMAN	Protein Wnt-8a precursor (Wnt-8d)	0.28	-	nuc	0	Secreted protein; extracellular space; extracellular matrix		606360		355
Q99MI9 UniProt NPD GO	ANMX_CRILO	Protein arginine N-methyltransferase (EC 2.1.1.-)	0.28	-	cyt	0					729
Q4R793 UniProt NPD GO	CI096_MACFA	Protein kinase-like protein C9orf96 homolog	0.28	-	end	0					649
Q10120 UniProt NPD GO	LIN52_CAEEL	Protein lin-52 (Abnormal cell lineage protein 52)	0.28	-	nuc	0					161
Q8BST6 UniProt NPD GO	PELI2_MOUSE	Protein pellino homolog 2 (Pellino-2)	0.28	-	cyt	0					419
Q7SXW4 UniProt NPD GO	POB_BRARE	Protein pob	0.28	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)	Golgi apparatus [IDA] trans-Golgi network transport vesicle [IDA]			261
Q9XZL8 UniProt NPD GO	SRA_DROME	Protein sarah (Protein nebula)	0.28	-	nuc	0					292
Q05360 UniProt NPD GO	WHITE_LUCCU	Protein white	0.28	-	end	6	Membrane; multi-pass membrane protein				677
P46108 UniProt NPD GO	CRK_HUMAN	Proto-oncogene C-crk (P38) (Adapter molecule crk)	0.28	-	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Translocated to the plasma membrane upon c ...	cytoplasm [TAS] nucleus [TAS]	164762	1JU5	304

You are viewing entries 42601 to 42650 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.