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
P22467 UniProt NPD GO	MYOA_DICDI	Myosin IA heavy chain (Myosin-like protein abmA)	0.73	-	nuc	0					994
O00159 UniProt NPD GO	MYO1C_HUMAN	Myosin Ic (Myosin I beta) (MMI-beta) (MMIb)	0.73	-	cyt	0		unconventional myosin [TAS]	606538		1028
P27742 UniProt NPD GO	ACVS_EMENI	N-(5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine synthase (EC 6.3.2.26) (Delta-(L-alpha-aminoadip ...	0.73	-	end	0					3770
Q8CCN1 UniProt NPD GO	NAL10_MOUSE	NACHT, LRR and PYD-containing protein 10	0.73	+	cyt	0					673
O76041 UniProt NPD GO	NEBL_HUMAN	Nebulette (Actin-binding Z-disk protein)	0.73	-	nuc	0			605491		1014
Q8K1S2 UniProt NPD GO	UNC5D_MOUSE	Netrin receptor UNC5D precursor (Unc-5 homolog D) (Unc-5 homolog 4)	0.73	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				956
Q96SB3 UniProt NPD GO	NEB2_HUMAN	Neurabin-2 (Neurabin-II) (Spinophilin) (Protein phosphatase 1 regulatory subunit 9B)	0.73	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Enriched at synapse and cadherin-based cell-cell ...	cytoplasm [IDA] nucleoplasm [IMP] protein phosphatase type 1 complex [TAS]	603325		815
Q4VYC8 UniProt NPD GO	NSP1_MEDTR	Nodulation signaling pathway 1 protein	0.73	-	nuc	0	Nucleus				554
Q6GQD0 UniProt NPD GO	NBP1B_XENLA	Nuclear cap-binding protein subunit 1-B	0.73	+	mit	0	Nucleus (By similarity)				791
P98150 UniProt NPD GO	NFKB2_CHICK	Nuclear factor NF-kappa-B p100 subunit (Nuclear factor NF-kappa-B p97 subunit) (DNA-binding factor K ...	0.73	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear, but also found in the cytoplasm in an i ...				906
Q9N4B8 UniProt NPD GO	NHR41_CAEEL	Nuclear hormone receptor family member nhr-41	0.73	-	nuc	0	Nucleus (Potential)				615
P41933 UniProt NPD GO	ODR7_CAEEL	Nuclear hormone receptor family member odr-7 (Odorant response abnormal protein 7)	0.73	-	nuc	0	Or: Nucleus (Probable). Or: Cytoplasm; perinuclear region (Probable)				457
P52590 UniProt NPD GO	NU107_RAT	Nuclear pore complex protein Nup107 (Nucleoporin Nup107) (107 kDa nucleoporin) (p105)	0.73	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity). Located on both the cytoplasmic and ...	nuclear pore [ISS]			926
Q498U4 UniProt NPD GO	HCC1_RAT	Nuclear protein Hcc-1	0.73	+	nuc	0	Nucleus (By similarity)				209
Q9N1A7 UniProt NPD GO	STP2_PANTR	Nuclear transition protein 2 (TP-2) (TP2) (Fragment)	0.73	+	mit	0	Nucleus (By similarity)				133
P21573 UniProt NPD GO	YBOX1_XENLA	Nuclease sensitive element-binding protein 1 (Y-box-binding protein 1) (Y-box transcription factor)	0.73	+	nuc	0	Cytoplasm. Nucleus. Shuttles between nucleus and cytoplasm. Predominantly cytoplasmic in proliferati ...				303
Q28618 UniProt NPD GO	YBOX1_RABIT	Nuclease sensitive element-binding protein 1 (Y-box-binding protein 1) (Y-box transcription factor) ...	0.73	+	nuc	0	Cytoplasm. Nucleus. Shuttles between nucleus and cytoplasm. Predominantly cytoplasmic in proliferati ...				323
Q9C3Z4 UniProt NPD GO	NOG2_PNECA	Nucleolar GTP-binding protein 2 (Binding-inducible GTPase)	0.73	-	nuc	0	Nucleus; nucleolus (By similarity)				483
P34077 UniProt NPD GO	NIC96_YEAST	Nucleoporin NIC96 (Nuclear pore protein NIC96) (96 kDa nucleoporin-interacting component)	0.73	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Symmetric dis ...	nuclear pore [IDA]			839
P32499 UniProt NPD GO	NUP2_YEAST	Nucleoporin NUP2 (Nuclear pore protein NUP2) (p95)	0.73	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; nucleoplasmic side	mitochondrion [IDA] nuclear chromatin [IDA] nuclear pore [IDA]		2C1T	720
P22736 UniProt NPD GO	NR4A1_HUMAN	Orphan nuclear receptor NR4A1 (Orphan nuclear receptor HMR) (Early response protein NAK1) (TR3 orpha ...	0.73	-	nuc	0	Nucleus		139139	2GBD	598
P12813 UniProt NPD GO	NR4A1_MOUSE	Orphan nuclear receptor NR4A1 (Orphan nuclear receptor HMR) (Nuclear hormone receptor NUR/77) (N10 n ...	0.73	-	nuc	0	Nucleus	nucleus [IDA]			601
P51666 UniProt NPD GO	NR4A1_CANFA	Orphan nuclear receptor NR4A1 (Orphan nuclear receptor HMR) (Orphan nuclear receptor NGFI-B)	0.73	-	nuc	0	Nucleus				598
Q9DAG9 UniProt NPD GO	PHF7_MOUSE	PHD finger protein 7 (Protein NYD-SP6)	0.73	-	nuc	0	Nucleus (By similarity)			1WEQ	307
Q8LDQ4 UniProt NPD GO	TAP46_ARATH	PP2A regulatory subunit TAP46 (2A phosphatase-associated protein of 46 kDa)	0.73	-	nuc	0					405
P23758 UniProt NPD GO	POXN_DROME	Paired box pox-neuro protein (Paired box neuronal protein)	0.73	-	nuc	0	Nucleus				425
P55864 UniProt NPD GO	PAX6_XENLA	Paired box protein Pax-6	0.73	+	nuc	0	Nucleus				422
P60571 UniProt NPD GO	PANX2_RAT	Pannexin-2	0.73	-	nuc	4 *	Membrane; multi-pass membrane protein (Potential)	gap junction [IMP]			664
Q5ZLM0 UniProt NPD GO	CDC73_CHICK	Parafibromin (Cell division cycle protein 73 homolog)	0.73	-	nuc	0	Nucleus (By similarity)				531
Q98UF7 UniProt NPD GO	PCX1_FUGRU	Pecanex-like protein 1 (Pecanex homolog)	0.73	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				1703
Q8NEB9 UniProt NPD GO	PK3C3_HUMAN	Phosphatidylinositol 3-kinase catalytic subunit type 3 (EC 2.7.1.137) (PtdIns-3-kinase type 3) (PI3- ...	0.73	-	cyt	0			602609		887
Q5I6B8 UniProt NPD GO	PI51C_RAT	Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma (EC 2.7.1.68) (Phosphatidylinositol-4-phospha ...	0.73	-	nuc	0	Cell membrane; cytoplasmic side. Cytoplasmic, associated with the plasma membrane. Detected in focal ...				688
O14939 UniProt NPD GO	PLD2_HUMAN	Phospholipase D2 (EC 3.1.4.4) (PLD 2) (Choline phosphatase 2) (Phosphatidylcholine-hydrolyzing phosp ...	0.73	-	mit	0	Membrane; peripheral membrane protein (By similarity)	plasma membrane [TAS]	602384		933
Q96J94 UniProt NPD GO	PIWL1_HUMAN	Piwi-like protein 1	0.73	+	mit	0	Intracytoplasmic membrane; peripheral membrane protein		605571		861
Q13835 UniProt NPD GO	PKP1_HUMAN	Plakophilin-1 (Band-6 protein) (B6P)	0.73	-	nuc	0	Nucleus. Isoform 1 is also associated with desmosomes	desmosome [NAS] intermediate filament [TAS] nucleus [NAS]	601975	1XM9	747
P28576 UniProt NPD GO	PDGFA_RAT	Platelet-derived growth factor A chain precursor (PDGF A-chain) (Platelet-derived growth factor alph ...	0.73	-	exc	0					204
Q9ERS4 UniProt NPD GO	PKHA3_MOUSE	Pleckstrin homology domain-containing family A member 3 (Phosphoinositol 4-phosphate adaptor protein ...	0.73	-	nuc	0	Cytoplasm (Probable). Membrane; peripheral membrane protein (Probable)				297
Q8VC98 UniProt NPD GO	PKHA4_MOUSE	Pleckstrin homology domain-containing family A member 4 (Phosphoinositol 3-phosphate-binding protein ...	0.73	-	mit	0	Cytoplasm (Probable). Membrane; peripheral membrane protein (Probable)				588
Q9Z0V1 UniProt NPD GO	KCND3_MOUSE	Potassium voltage-gated channel subfamily D member 3 (Voltage-gated potassium channel subunit Kv4.3) ...	0.73	-	end	6	Membrane; multi-pass membrane protein				655
O73925 UniProt NPD GO	KCNQ1_SQUAC	Potassium voltage-gated channel subfamily KQT member 1 (Voltage-gated potassium channel subunit Kv7. ...	0.73	-	end	6	Membrane; multi-pass membrane protein				660
Q5KNF8 UniProt NPD GO	PRP28_CRYNE	Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 (EC 3.6.1.-)	0.73	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				738
Q6CT49 UniProt NPD GO	PRP28_KLULA	Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 (EC 3.6.1.-)	0.73	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				539
P46947 UniProt NPD GO	CWC26_YEAST	Pre-mRNA-splicing factor CWC26 (Complexed with CEF1 protein 26) (Bud site selection protein 13) (Syn ...	0.73	-	nuc	0	Cytoplasm. Nucleus	nucleus [IDA]			266
Q51LA6 UniProt NPD GO	SLU7_MAGGR	Pre-mRNA-splicing factor SLU7	0.73	-	nuc	0	Nucleus (By similarity)				474
Q9VVN2 UniProt NPD GO	RT26_DROME	Probable 28S ribosomal protein S26, mitochondrial precursor (MRP-S26)	0.73	+	nuc	0	Mitochondrion (By similarity)				225
Q84NP7 UniProt NPD GO	AMPD_ORYSA	Probable AMP deaminase (EC 3.5.4.6)	0.73	-	nuc	1 *	Membrane; single-pass membrane protein. Might be associated with the inner mitochondrial membrane (B ...				815
Q8K301 UniProt NPD GO	DDX52_MOUSE	Probable ATP-dependent RNA helicase DDX52 (EC 3.6.1.-) (DEAD box protein 52) (ATP-dependent RNA heli ...	0.73	+	cyt	0	Nucleus; nucleolus (By similarity)				598
Q9C8S9 UniProt NPD GO	RH48_ARATH	Probable DEAD-box ATP-dependent RNA helicase 48 (EC 3.6.1.-)	0.73	-	nuc	0					798
Q5RD78 UniProt NPD GO	HECD2_PONPY	Probable E3 ubiquitin-protein ligase HECTD2 (HECT domain-containing protein 2)	0.73	-	cyt	0					776
Q4P3D8 UniProt NPD GO	TAH18_USTMA	Probable NADPH reductase TAH18 (EC 1.-.-.-)	0.73	-	mit	0					616

You are viewing entries 12401 to 12450 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.