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
P53261 UniProt NPD GO	PESC_YEAST	Pescadillo homolog (Nucleolar protein 7)	0.86	+	mit	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA]			605
Q8TCU6 UniProt NPD GO	PREX1_HUMAN	Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein (P-Rex1 protein)	0.86	-	nuc	0	Cytoplasm; cytosol. Mainly. Cell membrane. Some amount is apparently associated to the plasma membra ...	cytosol [IDA] plasma membrane [TAS]	606905		1659
P32600 UniProt NPD GO	TOR2_YEAST	Phosphatidylinositol 3-kinase TOR2 (EC 2.7.1.137) (PtdIns-3-kinase TOR2) (PI3-kinase TOR2) (PI3K TOR ...	0.86	-	nuc	0		extrinsic to internal side of plasma membrane [IDA] mitochondrion [IDA] plasma membrane [IDA] TORC 1 complex [IPI] TORC 2 complex [IPI] vacuolar membrane [IDA]			2473
P26450 UniProt NPD GO	P85A_MOUSE	Phosphatidylinositol 3-kinase regulatory subunit alpha (PI3-kinase p85-subunit alpha) (PtdIns-3-kina ...	0.86	-	nuc	0		cytoplasm [IDA] cytosol [IDA] membrane [IDA] phosphoinositide 3-kinase complex, class IA [ISS]			724
P78337 UniProt NPD GO	PITX1_HUMAN	Pituitary homeobox 1 (Hindlimb expressed homeobox protein backfoot)	0.86	+	nuc	0	Nucleus		602149		314
P04085 UniProt NPD GO	PDGFA_HUMAN	Platelet-derived growth factor A chain precursor (PDGF A-chain) (Platelet-derived growth factor alph ...	0.86	+	exc	0			173430		211
P30427 UniProt NPD GO	PLEC1_RAT	Plectin-1 (PLTN) (PCN)	0.86	+	nuc	0					4687
Q15149 UniProt NPD GO	PLEC1_HUMAN	Plectin-1 (PLTN) (PCN) (Hemidesmosomal protein 1) (HD1)	0.86	+	nuc	0		plasma membrane [NAS]	131950	1MB8	4684
P51003 UniProt NPD GO	PAPOA_HUMAN	Poly(A) polymerase alpha (EC 2.7.7.19) (PAP) (Polynucleotide adenylyltransferase alpha)	0.86	+	nuc	0	Cytoplasm. Nucleus. The 90 kDa form is nuclear while the 100 kDa and the 106 kDa forms are both nucl ...	cytoplasm [TAS] nucleus [TAS]	605553		744
Q9N4H4 UniProt NPD GO	PME1_CAEEL	Poly(ADP-ribose) polymerase pme-1 (EC 2.4.2.30) (Poly ADP-ribose metabolism enzyme 1)	0.86	+	nuc	0	Nucleus (Probable)				945
Q14721 UniProt NPD GO	KCNB1_HUMAN	Potassium voltage-gated channel subfamily B member 1 (Voltage-gated potassium channel subunit Kv2.1) ...	0.86	-	nuc	5	Membrane; multi-pass membrane protein		600397		858
Q4PFD9 UniProt NPD GO	PRP5_USTMA	Pre-mRNA-processing ATP-dependent RNA helicase PRP5 (EC 3.6.1.-)	0.86	-	nuc	0	Nucleus (By similarity)				1156
Q12309 UniProt NPD GO	CLF1_YEAST	Pre-mRNA-splicing factor CLF1 (Crooked neck-like factor 1) (PRP19-associated complex protein 77) (Sy ...	0.86	-	cyt	0	Nucleus	chromatin [IDA]			687
P53333 UniProt NPD GO	CWC22_YEAST	Pre-mRNA-splicing factor CWC22 (Complexed with CEF1 protein 22)	0.86	-	mit	0	Cytoplasm. Nucleus	spliceosome complex [IPI]			577
Q6FIT9 UniProt NPD GO	PRP45_CANGA	Pre-mRNA-splicing factor PRP45 (Pre-mRNA-processing protein 45)	0.86	-	nuc	0	Nucleus (By similarity)				414
Q7RYH7 UniProt NPD GO	CWC21_NEUCR	Pre-mRNA-splicing factor cwc-21	0.86	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				344
P87126 UniProt NPD GO	CWC2_SCHPO	Pre-mRNA-splicing factor cwc2 (Complexed with cdc5 protein 2) (Pre-mRNA-processing protein 3) (Cell ...	0.86	+	nuc	0	Nucleus (By similarity)	spliceosome complex [IDA]			388
Q8NIZ4 UniProt NPD GO	PRI2_NEUCR	Probable DNA primase large subunit (EC 2.7.7.-)	0.86	-	nuc	0					513
Q95SX7 UniProt NPD GO	RTBS_DROME	Probable RNA-directed DNA polymerase from transposon BS (EC 2.7.7.49) (Reverse transcriptase)	0.86	+	nuc	0					906
O64747 UniProt NPD GO	WRK35_ARATH	Probable WRKY transcription factor 35 (WRKY DNA-binding protein 35)	0.86	-	nuc	0	Nucleus (Probable)				427
Q9LY00 UniProt NPD GO	WRK70_ARATH	Probable WRKY transcription factor 70 (WRKY DNA-binding protein 70)	0.86	+	nuc	0	Nucleus (Probable)				294
Q9C9F0 UniProt NPD GO	WRKY9_ARATH	Probable WRKY transcription factor 9 (WRKY DNA-binding protein 9)	0.86	+	nuc	0	Nucleus (Potential)				374
Q6CNF3 UniProt NPD GO	NDC80_KLULA	Probable kinetochore protein NDC80	0.86	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				673
Q99848 UniProt NPD GO	EBP2_HUMAN	Probable rRNA-processing protein EBP2 (EBNA1-binding protein 2) (Nucleolar protein p40)	0.86	-	nuc	0	Nucleus; nucleolus	membrane fraction [TAS]			306
P29590 UniProt NPD GO	PML_HUMAN	Probable transcription factor PML (Tripartite motif-containing protein 19) (RING finger protein 71)	0.86	-	nuc	0	Nucleus. Localized to PML nuclear bodies	insoluble fraction [IDA] nucleoplasm [IDA] PML body [TAS]	102578	1BOR	882
Q9UT46 UniProt NPD GO	YFR7_SCHPO	Probable transcriptional regulatory protein C821.07c	0.86	+	nuc	0	Nucleus	nucleus [IDA]			497
O00507 UniProt NPD GO	USP9Y_HUMAN	Probable ubiquitin carboxyl-terminal hydrolase FAF-Y (EC 3.1.2.15) (Ubiquitin thioesterase FAF-Y) (U ...	0.86	+	end	0			415000		2555
P04090 UniProt NPD GO	REL2_HUMAN	Prorelaxin H2 precursor [Contains: Relaxin B chain; Relaxin A chain]	0.86	-	exc	0	Secreted protein		179740	6RLX	185
P24642 UniProt NPD GO	PRT2_BUFJA	Protamine-2 (P2)	0.86	+	nuc	0	Nucleus				39
Q8IYW2 UniProt NPD GO	CJ092_HUMAN	Protein C10orf92	0.86	-	nuc	0					876
Q9NYF5 UniProt NPD GO	CE005_HUMAN	Protein C5orf5 (GAP-like protein N61)	0.86	+	nuc	0			609371		915
Q9IAB2 UniProt NPD GO	MTG8R_XENLA	Protein CBFA2T2 (MTG8-like protein) (MTG8-related protein 1)	0.86	-	nuc	0	Nucleus (By similarity)				586
Q5FW14 UniProt NPD GO	CHMP7_XENTR	Protein CHMP7	0.86	+	nuc	0					468
O82804 UniProt NPD GO	ELF3_ARATH	Protein EARLY FLOWERING 3 (Nematode-responsive protein)	0.86	-	nuc	0	Nucleus				695
Q06340 UniProt NPD GO	ESC2_YEAST	Protein ESC2 (Establishes silent chromatin protein 2)	0.86	-	nuc	0	Cytoplasm. Nucleus	nucleus [IDA]			456
Q5RDR5 UniProt NPD GO	FAM5B_PONPY	Protein FAM5B precursor	0.86	-	mit	1 *	Secreted protein (Potential)				783
Q6PBM7 UniProt NPD GO	FA76B_BRARE	Protein FAM76B	0.86	-	nuc	0					328
Q59U11 UniProt NPD GO	GRC3_CANAL	Protein GRC3	0.86	+	nuc	0	Nucleus (By similarity)				686
Q5SZV5 UniProt NPD GO	K0319_MOUSE	Protein KIAA0319 precursor	0.86	-	end	1	Membrane; single-pass type I membrane protein (Potential)				1081
Q9ULL0 UniProt NPD GO	K1210_HUMAN	Protein KIAA1210	0.86	-	nuc	0					1093
P38717 UniProt NPD GO	SIP3_YEAST	Protein SIP3	0.86	-	end	2		nucleus [IPI]			1229
P34226 UniProt NPD GO	SKT5_YEAST	Protein SKT5	0.86	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	bud neck [IDA] incipient bud site [IDA]			696
P23201 UniProt NPD GO	SPA2_YEAST	Protein SPA2	0.86	-	nuc	0	Localizes a sharp patch at the shmoo tip (mating projection) which is the site of polarized cell gro ...	bud neck [IDA] bud tip [IDA] incipient bud site [IDA] mating projection tip [IDA] polarisome [TAS]			1466
Q06160 UniProt NPD GO	SPH1_YEAST	Protein SPH1 (SPA2 homolog 1)	0.86	-	nuc	0	Sites of polarized growth as bud tip, bud neck and mating projection. Hub1 is necessary for the prop ...	bud neck [IDA] bud tip [IDA] incipient bud site [IDA] mating projection [IDA] polarisome [TAS]			661
P38699 UniProt NPD GO	STB5_YEAST	Protein STB5	0.86	-	nuc	0	Nucleus (Probable)	nucleus [IPI]			743
Q6DFP9 UniProt NPD GO	ZN403_XENTR	Protein ZNF403	0.86	-	nuc	0	Cytoplasm (By similarity)				669
Q9US05 UniProt NPD GO	BFR2_SCHPO	Protein bfr2	0.86	-	nuc	0	Nucleus; nucleolus (By similarity)				452
P11420 UniProt NPD GO	DA_DROME	Protein daughterless	0.86	-	nuc	0	Nucleus				710
Q9NYP3 UniProt NPD GO	DONS_HUMAN	Protein downstream neighbor of Son (B17)	0.86	-	nuc	0	Nucleus (By similarity)				566
Q99014 UniProt NPD GO	KPC1_TRIRE	Protein kinase C-like (EC 2.7.11.13)	0.86	-	nuc	0					1139

You are viewing entries 6201 to 6250 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.