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
Q13492 UniProt NPD GO	PICAL_HUMAN	Phosphatidylinositol-binding clathrin assembly protein (Clathrin assembly lymphoid myeloid leukemia ...	0.47	-	nuc	0	Cell membrane. Clathrin-coated areas of the plasma membrane. Golgi apparatus. Colocalized with clath ...	coated pit [IDA]	603025		652
P80576 UniProt NPD GO	AROF_NEUCR	Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) (Phospho-2-keto-3-deoxyheptonate aldolase) ...	0.47	-	nuc	0					481
Q00218 UniProt NPD GO	AROG_ARATH	Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplast precursor (EC 2.5.1.54) (Phospho-2-keto-3 ...	0.47	-	mit	0	Plastid; chloroplast				507
Q9QXZ7 UniProt NPD GO	NR2E3_MOUSE	Photoreceptor-specific nuclear receptor (Retina-specific nuclear receptor)	0.47	-	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			395
P42497 UniProt NPD GO	PHYD_ARATH	Phytochrome D	0.47	-	cyt	0					1164
P05402 UniProt NPD GO	PRP1_BOVIN	Placental prolactin-related protein 1 precursor (PRC-I) (bPRCI)	0.47	-	nuc	0	Secreted protein				238
P00747 UniProt NPD GO	PLMN_HUMAN	Plasminogen precursor (EC 3.4.21.7) [Contains: Plasmin heavy chain A; Activation peptide; Angiostati ...	0.47	-	nuc	0	Secreted protein	extracellular space [TAS]	173350	5HPG	810
P08567 UniProt NPD GO	PLEK_HUMAN	Pleckstrin (Platelet p47 protein)	0.47	-	cyt	0			173570	2CSO	350
Q8K4G9 UniProt NPD GO	PODO_RAT	Podocin	0.47	-	nuc	1	Membrane; multi-pass membrane protein				383
Q7ZYB4 UniProt NPD GO	PAIP1_XENLA	Polyadenylate-binding protein-interacting protein 1 (Poly(A)-binding protein-interacting protein 1) ...	0.47	-	nuc	0	Cytoplasm (Probable)	cytoplasm [ISS]			463
Q59WJ4 UniProt NPD GO	PFS2_CANAL	Polyadenylation factor subunit 2	0.47	-	nuc	0	Nucleus (By similarity)				543
Q6P9S7 UniProt NPD GO	GLT10_MOUSE	Polypeptide N-acetylgalactosaminyltransferase 10 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltran ...	0.47	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				603
Q6P6V1 UniProt NPD GO	GLT11_RAT	Polypeptide N-acetylgalactosaminyltransferase 11 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltran ...	0.47	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				608
Q9BEA0 UniProt NPD GO	EGF_CANFA	Pro-epidermal growth factor precursor (EGF) [Contains: Epidermal growth factor]	0.47	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1216
O17071 UniProt NPD GO	PRS10_CAEEL	Probable 26S protease regulatory subunit S10B (Proteasome regulatory particle ATPase-like protein 4) ...	0.47	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				406
P34388 UniProt NPD GO	RT09_CAEEL	Probable 40S ribosomal protein S9, mitochondrial precursor	0.47	-	mit	0	Mitochondrion (Potential)				392
Q9NXZ2 UniProt NPD GO	DDX43_HUMAN	Probable ATP-dependent RNA helicase DDX43 (EC 3.6.1.-) (DEAD box protein 43) (DEAD box protein HAGE) ...	0.47	-	mit	0			606286		648
Q96PE1 UniProt NPD GO	GP124_HUMAN	Probable G-protein coupled receptor 124 precursor (Tumor endothelial marker 5)	0.47	-	end	6	Membrane; multi-pass membrane protein	integral to membrane [TAS]	606823		1331
Q6X632 UniProt NPD GO	GPR75_MOUSE	Probable G-protein coupled receptor 75	0.47	-	end	7 *	Membrane; multi-pass membrane protein				540
Q08925 UniProt NPD GO	YP184_YEAST	Probable RNA-binding protein YPL184C	0.47	-	nuc	0		cytoplasm [IDA]			612
Q9VGB5 UniProt NPD GO	CP135_DROME	Probable cytochrome P450 313a5 (EC 1.14.-.-) (CYPCCCXIIIA5)	0.47	+	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				487
Q9D0D4 UniProt NPD GO	DIMH_MOUSE	Probable dimethyladenosine transferase (EC 2.1.1.-) (S-adenosylmethionine-6-N',N'-adenosyl(rRNA) dim ...	0.47	-	nuc	0	Nucleus; nucleolus (By similarity)				313
Q9FKZ2 UniProt NPD GO	DRL41_ARATH	Probable disease resistance protein At5g66890	0.47	-	nuc	0					415
Q9CA71 UniProt NPD GO	FUT3_ARATH	Probable fucosyltransferase 3 (EC 2.4.1.-) (AtFUT3)	0.47	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				493
Q5N941 UniProt NPD GO	DMI1_ORYSA	Probable ion channel DMI1, chloroplast precursor	0.47	-	end	2	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				965
Q03829 UniProt NPD GO	YM39_YEAST	Probable mitochondrial carrier YMR166C	0.47	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				368
O94659 UniProt NPD GO	NOG1_SCHPO	Probable nucleolar GTP-binding protein 1	0.47	-	nuc	0	Nucleus; nucleolus (By similarity)				642
Q9ZUT8 UniProt NPD GO	PDR5_ARATH	Probable pleiotropic drug resistance protein 5	0.47	-	end	13	Membrane; multi-pass membrane protein (By similarity)				1413
Q9YGV6 UniProt NPD GO	PRL_PAROL	Prolactin precursor (PRL)	0.47	-	exc	0	Secreted protein				211
P16924 UniProt NPD GO	P4HA1_CHICK	Prolyl 4-hydroxylase alpha-1 subunit (EC 1.14.11.2) (4-PH alpha-1) (Procollagen-proline,2-oxoglutara ...	0.47	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen				516
P11680 UniProt NPD GO	PROP_MOUSE	Properdin precursor (Factor P)	0.47	-	nuc	0	Secreted protein				464
Q9FL12 UniProt NPD GO	DEGP9_ARATH	Protease Do-like 9 (EC 3.4.21.-)	0.47	-	nuc	0					592
Q59LC9 UniProt NPD GO	AF9_CANAL	Protein AF-9 homolog	0.47	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				254
P29311 UniProt NPD GO	BMH1_YEAST	Protein BMH1	0.47	-	nuc	0		nucleus [IDA]			266
Q8C008 UniProt NPD GO	CT012_MOUSE	Protein C20orf12 homolog	0.47	-	nuc	0					778
Q5T280 UniProt NPD GO	CI114_HUMAN	Protein C9orf114	0.47	-	cyt	0					376
Q9H2J1 UniProt NPD GO	CI037_HUMAN	Protein C9orf37	0.47	-	nuc	0					206
Q9H5U8 UniProt NPD GO	CX045_HUMAN	Protein CXorf45	0.47	-	nuc	0					459
Q9I8W6 UniProt NPD GO	EURL_CHICK	Protein EURL	0.47	-	nuc	0					293
Q6UWF7 UniProt NPD GO	FA55D_HUMAN	Protein FAM55D precursor	0.47	-	mit	1 *	Secreted protein (Potential)				544
Q94DE2 UniProt NPD GO	G10A_ORYSA	Protein G10 homolog 1	0.47	-	nuc	0	Nucleus (Potential)				145
Q9DCV6 UniProt NPD GO	K0141_MOUSE	Protein KIAA0141	0.47	-	mit	0					510
Q8BK67 UniProt NPD GO	RCC2_MOUSE	Protein RCC2	0.47	-	cyt	0	Nucleus; nucleolus (By similarity). Appears in the nucleus at G2, then concentrates at the inner cen ...				520
Q08446 UniProt NPD GO	SGT1_YEAST	Protein SGT1 (Suppressor of G2 allele of SKP1)	0.47	-	nuc	0		ubiquitin ligase complex [IDA]			395
P40073 UniProt NPD GO	SSU81_YEAST	Protein SSU81 (SHO1 osmosensor)	0.47	-	mit	4 *	Membrane; multi-pass membrane protein (Potential)	mating projection tip [IDA]			367
Q9Y5U2 UniProt NPD GO	TSSC4_HUMAN	Protein TSSC4 (Tumor-suppressing subchromosomal transferable fragment candidate gene 4 protein) (Tum ...	0.47	-	nuc	0			603852		329
P34888 UniProt NPD GO	WNT1_CAEEL	Protein Wnt-1 precursor	0.47	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix				372
Q24739 UniProt NPD GO	BROWN_DROVI	Protein brown	0.47	-	end	6	Membrane; multi-pass membrane protein				668
Q61644 UniProt NPD GO	PACN1_MOUSE	Protein kinase C and casein kinase substrate in neurons protein 1	0.47	-	nuc	0	Cytoplasm (By similarity). Colocalizes with dynamin I at vesicular structures in the cell body and n ...	COPI-coated vesicle [IDA] cytoplasm [IDA]			441
P36047 UniProt NPD GO	SDS22_YEAST	Protein phosphatase 1 regulatory subunit SDS22	0.47	-	nuc	0	Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]			338

You are viewing entries 27151 to 27200 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.