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
P98106 UniProt NPD GO	LYAM3_RAT	P-selectin precursor (Granule membrane protein 140) (GMP-140) (PADGEM) (Leukocyte-endothelial cell a ...	0.70	-	nuc	1	Membrane; single-pass type I membrane protein				768
Q8IYB4 UniProt NPD GO	PEX5R_HUMAN	PEX5-related protein (Peroxin-5-related protein) (Pex5Rp) (PEX5-like protein) (PEX2-related protein) ...	0.70	-	nuc	0	Cytoplasm. Some fraction is membrane associated via its interaction with RAB8B (By similarity)				626
P54278 UniProt NPD GO	PMS2_HUMAN	PMS1 protein homolog 2 (DNA mismatch repair protein PMS2)	0.70	-	nuc	0	Nucleus	nucleus [TAS]	276300	1H7U	862
Q5KAB3 UniProt NPD GO	CWC27_CRYNE	Peptidyl-prolyl isomerase CWC27 (EC 5.2.1.8)	0.70	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				491
P48736 UniProt NPD GO	PK3CG_HUMAN	Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform (EC 2.7.1.153) (PI3-k ...	0.70	-	cyt	0			601232	2CHZ	1102
Q5CZZ9 UniProt NPD GO	PI51B_RAT	Phosphatidylinositol-4-phosphate 5-kinase type-1 beta (EC 2.7.1.68) (Phosphatidylinositol-4-phosphat ...	0.70	-	nuc	0	Intracytoplasmic membrane (By similarity). Associated with membranes (By similarity)				539
Q01648 UniProt NPD GO	CAPP1_FLATR	Phosphoenolpyruvate carboxylase (EC 4.1.1.31) (PEPCase) (PEPC)	0.70	-	nuc	0	Cytoplasm				967
Q13393 UniProt NPD GO	PLD1_HUMAN	Phospholipase D1 (EC 3.1.4.4) (PLD 1) (Choline phosphatase 1) (Phosphatidylcholine-hydrolyzing phosp ...	0.70	-	cyt	0	Cytoplasm; perinuclear region (By similarity). Endoplasmic reticulum (By similarity). Golgi apparatu ...	endosome [IDA] Golgi apparatus [IDA] membrane [TAS]	602382		1074
Q6P767 UniProt NPD GO	PTTG_RAT	Pituitary tumor-transforming gene 1 protein-interacting protein precursor (Pituitary tumor-transform ...	0.70	-	end	2 *	Cell membrane; single-pass type I membrane protein (By similarity). Cytoplasm (By similarity). Nucle ...				174
Q9Y4D7 UniProt NPD GO	PLXD1_HUMAN	Plexin-D1 precursor	0.70	-	end	1			604282		1925
Q9D2N8 UniProt NPD GO	GLTL2_MOUSE	Polypeptide N-acetylgalactosaminyltransferase-like protein 2 (EC 2.4.1.41) (Protein-UDP acetylgalact ...	0.70	+	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				638
Q6ZPR4 UniProt NPD GO	KCNT1_MOUSE	Potassium channel subfamily T member 1	0.70	-	end	7	Membrane; multi-pass membrane protein (Potential)				1224
Q6CQI2 UniProt NPD GO	CWC15_KLULA	Pre-mRNA-splicing factor CWC15	0.70	-	nuc	0	Nucleus (Probable)				187
Q59W50 UniProt NPD GO	CWC2_CANAL	Pre-mRNA-splicing factor CWC2	0.70	-	nuc	0	Nucleus (By similarity)				363
Q4PEZ0 UniProt NPD GO	ISY1_USTMA	Pre-mRNA-splicing factor ISY1	0.70	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				351
P32639 UniProt NPD GO	BRR2_YEAST	Pre-mRNA-splicing helicase BRR2 (EC 3.6.1.-) (Protein Snu246)	0.70	-	nuc	0	Nucleus (Potential)	snRNP U5 [IPI] U4/U6 x U5 tri-snRNP complex [IDA]			2163
Q9D0R4 UniProt NPD GO	DDX56_MOUSE	Probable ATP-dependent RNA helicase DDX56 (EC 3.6.1.-) (DEAD box protein 56) (ATP-dependent 61 kDa n ...	0.70	+	cyt	0	Nucleus; nucleolus (By similarity)	nucleolus [IDA]			546
Q5U5R9 UniProt NPD GO	HECD2_HUMAN	Probable E3 ubiquitin-protein ligase HECTD2 (HECT domain-containing protein 2)	0.70	-	cyt	0					776
Q8IWK6 UniProt NPD GO	GP125_HUMAN	Probable G-protein coupled receptor 125 precursor	0.70	-	end	8 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]			1321
P53316 UniProt NPD GO	YG5B_YEAST	Probable RNA-binding protein YGR250C	0.70	-	nuc	0		cytoplasm [IDA]			781
O43027 UniProt NPD GO	RGA6_SCHPO	Probable Rho-GTPase-activating protein 6	0.70	+	nuc	0					733
P91303 UniProt NPD GO	VATG_CAEEL	Probable Vacuolar ATP synthase subunit G (EC 3.6.3.14) (V-ATPase G subunit) (Vacuolar proton pump G ...	0.70	-	nuc	0					126
Q9HE88 UniProt NPD GO	SEC8_NEUCR	Probable exocyst complex component sec8	0.70	-	nuc	0					1111
Q4I0J6 UniProt NPD GO	NDC80_GIBZE	Probable kinetochore protein NDC80	0.70	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				726
Q5BH14 UniProt NPD GO	NUF2_EMENI	Probable kinetochore protein nuf2	0.70	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				463
Q8VYB1 UniProt NPD GO	SOH1_ARATH	Probable mediator complex subunit SOH1	0.70	+	nuc	0	Nucleus (Potential)				196
O59721 UniProt NPD GO	PUS4_SCHPO	Probable tRNA pseudouridine synthase 4 (EC 5.4.99.-) (tRNA pseudouridine 55 synthase) (Psi55 synthas ...	0.70	-	nuc	0	Nucleus (By similarity). Mitochondrion (By similarity)				407
Q8AYI2 UniProt NPD GO	PRGR_RANDY	Progesterone receptor (PR) (dyPR)	0.70	+	nuc	0	Nucleus. Predominantly				711
P97814 UniProt NPD GO	PPIP1_MOUSE	Proline-serine-threonine phosphatase-interacting protein 1 (PEST phosphatase-interacting protein 1)	0.70	-	nuc	0	Cytoplasm. Colocalized with the cortical actin cytoskeleton during interphase, lamellipodia and acti ...	contractile ring [IDA] stress fiber [IDA]			415
Q8K305 UniProt NPD GO	CA048_MOUSE	Protein C1orf48 homolog	0.70	-	cyt	0	Nucleus (By similarity). Associated with the kinetochore (By similarity)				281
P81408 UniProt NPD GO	COTE1_HUMAN	Protein COTE1	0.70	-	mit	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			669
Q756K3 UniProt NPD GO	ESC2_ASHGO	Protein ESC2 (Establishes silent chromatin protein 2)	0.70	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				407
Q5NVP3 UniProt NPD GO	F107A_PONPY	Protein FAM107A	0.70	-	nuc	0	Nucleus (By similarity)				144
Q8BUP8 UniProt NPD GO	FA43A_MOUSE	Protein FAM43A	0.70	-	nuc	0					424
P32464 UniProt NPD GO	HYM1_YEAST	Protein HYM1	0.70	-	nuc	0		bud [IDA] incipient bud site [IDA] intracellular [IDA] mating projection tip [IDA]			399
Q14156 UniProt NPD GO	K0143_HUMAN	Protein KIAA0143 (Fragment)	0.70	-	mit	0	Membrane; multi-pass membrane protein (Potential)				885
Q9D786 UniProt NPD GO	K0841_MOUSE	Protein KIAA0841	0.70	-	nuc	0					619
Q6P5B0 UniProt NPD GO	K0690_MOUSE	Protein Kiaa0690	0.70	+	end	0	Nucleus; nucleolus (By similarity)				1295
P24720 UniProt NPD GO	MNE1_YEAST	Protein MNE1	0.70	-	nuc	0		mitochondrion [IDA]			663
P39927 UniProt NPD GO	PTI1_YEAST	Protein PTI1	0.70	-	nuc	0	Nucleus	mRNA cleavage and polyadenylation specifici... [IPI] nucleus [IDA]			425
P40528 UniProt NPD GO	SYG1_YEAST	Protein SYG1	0.70	-	end	5	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA] plasma membrane [IDA]			902
Q24239 UniProt NPD GO	ANGEL_DROME	Protein angel (Angel 39) (ANG39)	0.70	+	mit	0					354
Q96SW2 UniProt NPD GO	CRBN_HUMAN	Protein cereblon	0.70	-	nuc	0			609262		442
Q23985 UniProt NPD GO	DTX_DROME	Protein deltex	0.70	+	nuc	0	Cytoplasm	cytoplasm [IDA]		2A90	738
Q24746 UniProt NPD GO	NEUR_DROVI	Protein neuralized	0.70	+	nuc	0	Nucleus (Potential)	plasma membrane [ISS]			747
P40139 UniProt NPD GO	NG2_DROME	Protein new-glue 2 precursor (NG-2)	0.70	+	nuc	0	Secreted protein (Potential)				112
P40797 UniProt NPD GO	PNUT_DROME	Protein peanut	0.70	+	nuc	0	Localized to the cleavage furrow of dividing cells during cytokinesis and to the intercellular bridg ...	ring canal (sensu Insecta) [NAS]			539
Q9V9W8 UniProt NPD GO	PYGO_DROME	Protein pygopus (Protein gammy legs)	0.70	+	nuc	0	Nucleus	nucleus [NAS]			815
O60183 UniProt NPD GO	SAT1_SCHPO	Protein sat1	0.70	-	cyt	0					550
P38736 UniProt NPD GO	GOS1_YEAST	Protein transport protein GOS1 (Golgi SNARE protein 1) (Golgi SNAP receptor complex member 1)	0.70	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein	integral to membrane [NAS]			223

You are viewing entries 13901 to 13950 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.