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
P53879 UniProt NPD GO	RHO5_YEAST	Protein RHO5	0.72	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	cytoplasm [IDA] nucleus [IDA]			331
Q9VCE9 UniProt NPD GO	UAS3_DROME	Protein UBASH3A homolog	0.72	-	nuc	0					751
Q4IBN1 UniProt NPD GO	VTS1_GIBZE	Protein VTS1	0.72	-	nuc	0	Cytoplasm (By similarity)				617
Q9Z1K6 UniProt NPD GO	ARI2_MOUSE	Protein ariadne-2 homolog (ARI-2) (Triad1 protein) (UbcM4-interacting protein 48)	0.72	-	nuc	0	Nucleus				492
Q03173 UniProt NPD GO	ENAH_MOUSE	Protein enabled homolog (NPC-derived proline-rich protein 1) (NDPP-1)	0.72	-	nuc	0	Cytoplasm. Targeted to the leading edge of lamellipodia and filopodia by MRL family members. Colocal ...	filopodium [IDA] focal adhesion [IDA] lamellipodium [IDA] stress fiber [IDA]		1EVH	802
P41891 UniProt NPD GO	GAR2_SCHPO	Protein gar2	0.72	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			500
P47997 UniProt NPD GO	G11A_ORYSA	Protein kinase G11A (EC 2.7.11.1)	0.72	-	nuc	0					589
Q9V780 UniProt NPD GO	LAP1_DROME	Protein lap1	0.72	-	nuc	0		adherens junction [ISS]			849
P20154 UniProt NPD GO	LIN11_CAEEL	Protein lin-11 (Abnormal cell lineage protein 11)	0.72	+	nuc	0	Nucleus				405
O43663 UniProt NPD GO	PRC1_HUMAN	Protein regulator of cytokinesis 1	0.72	-	nuc	0	Nucleus. Predominantly localized to the nucleus of interphase cells. Cytoplasm. During mitosis becom ...	nucleus [TAS] spindle microtubule [TAS]	603484		620
Q27350 UniProt NPD GO	SO_DROME	Protein sine oculis	0.72	-	nuc	0	Nucleus				416
P49700 UniProt NPD GO	USP_BOMMO	Protein ultraspiracle homolog (RXR type hormone receptor CF1) (BmCF1)	0.72	+	nuc	0	Nucleus				462
Q9LM83 UniProt NPD GO	WOX10_ARATH	Putative WUSCHEL-related homeobox 10	0.72	+	nuc	0	Nucleus (By similarity)				197
Q9S9N5 UniProt NPD GO	CNGC7_ARATH	Putative cyclic nucleotide-gated ion channel 7 (Cyclic nucleotide- and calmodulin-regulated ion chan ...	0.72	-	end	4	Cell membrane; multi-pass membrane protein (Potential)				738
Q9P7E9 UniProt NPD GO	YDZF_SCHPO	Putative dipeptidyl aminopeptidase C14C4.15c (EC 3.4.14.-)	0.72	+	cyt	1	Vacuole; vacuolar membrane; single-pass type II membrane protein. Lysosome-like vacuoles				853
Q38834 UniProt NPD GO	R13L4_ARATH	Putative disease resistance RPP13-like protein 4	0.72	-	cyt	0					852
O35286 UniProt NPD GO	DHX15_MOUSE	Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 (EC 3.6.1.-) (DEAH box protein 15 ...	0.72	-	nuc	0	Nucleus	minor (U12-dependent) spliceosome complex [ISS]			795
Q9JIR1 UniProt NPD GO	RIMB2_RAT	RIM-binding protein 2 (RIM-BP2)	0.72	-	nuc	0	Synaptic plasma membrane (By similarity)				1049
Q06846 UniProt NPD GO	RP3A_BOVIN	Rabphilin-3A (Exophilin-1)	0.72	-	nuc	0					704
Q53T03 UniProt NPD GO	RBP22_HUMAN	Ran-binding protein 2-like 2 (RanBP2L2)	0.72	-	nuc	0					1765
Q05909 UniProt NPD GO	PTPRG_MOUSE	Receptor-type tyrosine-protein phosphatase gamma precursor (EC 3.1.3.48) (Protein-tyrosine phosphata ...	0.72	-	nuc	1 *	Membrane; single-pass type I membrane protein (Probable)				1442
P79348 UniProt NPD GO	RGS20_BOVIN	Regulator of G-protein signaling 20 (RGS20) (Retina-specific regulator of G-protein signaling) (RET- ...	0.72	-	nuc	0	Membrane; lipid-anchor				374
P47104 UniProt NPD GO	RAV1_YEAST	Regulator of V-ATPase in vacuolar membrane protein 1 (Suppression of the onset of impotence protein ...	0.72	-	nuc	0	Intracytoplasmic membrane. Probably membrane-associated, associates with high density membrane compa ...	cytoplasm [IDA] extrinsic to membrane [IDA] RAVE complex [IPI]			1357
Q24472 UniProt NPD GO	RBF_DROME	Retinoblastoma-family protein	0.72	-	mit	0	Nucleus	chromatin [IDA] Myb complex [IDA] Rb-E2F complex [IDA]			845
P13631 UniProt NPD GO	RARG1_HUMAN	Retinoic acid receptor gamma-1 (RAR-gamma-1)	0.72	+	nuc	0	Nucleus		180190	1FD0	454
P15594 UniProt NPD GO	RTP2_TRYBG	Retrotransposable element SLACS 132 kDa protein (ORF2)	0.72	-	nuc	0					1182
Q8C6B2 UniProt NPD GO	RTKN_MOUSE	Rhotekin	0.72	-	mit	0					564
P53123 UniProt NPD GO	MRM2_YEAST	Ribosomal RNA methyltransferase MRM2, mitochondrial precursor (EC 2.1.1.-) (rRNA(uridine-2'-O-)-meth ...	0.72	-	mit	0	Mitochondrion	mitochondrion [IDA]			320
Q8BLK9 UniProt NPD GO	KS6C1_MOUSE	Ribosomal protein S6 kinase delta-1 (EC 2.7.11.1) (52 kDa ribosomal protein S6 kinase)	0.72	-	nuc	0	Cytoplasm. Membrane. Also found in some small dot-like or ring-shaped early endosome structures (By ...				1056
Q9XVT0 UniProt NPD GO	RRS1_CAEEL	Ribosome biogenesis regulatory protein homolog	0.72	+	nuc	0	Nucleus (By similarity)				333
Q5RJS9 UniProt NPD GO	RPF1_RAT	Ribosome production factor 1 (Ribosome biogenesis protein RPF1) (Brix domain-containing protein 5)	0.72	-	nuc	0	Nucleus; nucleolus (By similarity)	nucleolus [ISS]			345
P53165 UniProt NPD GO	SGF73_YEAST	SAGA-associated factor 73 (73 kDa SAGA-associated factor) (SAGA histone acetyltransferase complex 73 ...	0.72	-	nuc	0	Nucleus (Probable)	SAGA complex [IDA] SLIK (SAGA-like) complex [IPI]			657
Q5QNA6 UniProt NPD GO	SCRL2_ORYSA	SCAR-like protein 2	0.72	-	nuc	0					1334
P53953 UniProt NPD GO	SFB2_YEAST	SED5-binding protein 2 (SEC24-related protein 2)	0.72	-	nuc	0	Cytoplasm (By similarity)	COPII vesicle coat [IPI]			876
O75995 UniProt NPD GO	SLY_HUMAN	SH3 protein expressed in lymphocytes homolog	0.72	-	nuc	0			300441		380
O70143 UniProt NPD GO	SHC3_RAT	SHC-transforming protein 3 (SH2 domain protein C3) (Src homology 2 domain-containing-transforming pr ...	0.72	-	nuc	0					594
Q92529 UniProt NPD GO	SHC3_HUMAN	SHC-transforming protein 3 (SH2 domain protein C3) (Src homology 2 domain-containing-transforming pr ...	0.72	-	nuc	0			605263		594
Q9H156 UniProt NPD GO	SLIK2_HUMAN	SLIT and NTRK-like protein 2 precursor	0.72	-	end	1	Membrane; single-pass membrane protein (Potential)		300561		845
Q24533 UniProt NPD GO	DICH_DROME	SOX-domain protein dichaete (Protein fish-hook)	0.72	+	nuc	0	Nucleus (Potential)	cytoplasm [IDA] nucleus [IDA]			382
Q6DFM1 UniProt NPD GO	SNF5_XENTR	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1	0.72	-	nuc	0	Nucleus (By similarity)				378
Q09877 UniProt NPD GO	SIF3_SCHPO	Sad1-interacting factor 3	0.72	-	nuc	1	Nucleus; nuclear membrane; multi-pass membrane protein				510
Q9DAR7 UniProt NPD GO	DCPS_MOUSE	Scavenger mRNA decapping enzyme DcpS (EC 3.-.-.-) (DCS-1) (Hint-related 7meGMP-directed hydrolase) ( ...	0.72	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)			1VLR	338
Q8K4F7 UniProt NPD GO	DCPS_RAT	Scavenger mRNA decapping enzyme DcpS (EC 3.-.-.-) (DCS-1) (Hint-related 7meGMP-directed hydrolase) ( ...	0.72	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				336
Q5VUG0 UniProt NPD GO	SMBT2_HUMAN	Scm-like with four MBT domains protein 2	0.72	+	nuc	0				1WJR	894
Q5DTW2 UniProt NPD GO	SMBT2_MOUSE	Scm-like with four MBT domains protein 2	0.72	+	mit	0					938
Q62181 UniProt NPD GO	SEM3C_MOUSE	Semaphorin-3C precursor (Semaphorin E) (Sema E)	0.72	-	mit	0	Secreted protein (By similarity)	extracellular space [IDA]			751
Q9W686 UniProt NPD GO	SE3AB_BRARE	Semaphorin-3ab precursor (Semaphorin-1B) (Semaphorin Z1B) (Sema-Z1B)	0.72	-	nuc	0	Secreted protein (By similarity)				778
P18419 UniProt NPD GO	SVP2_MOUSE	Seminal vesicle protein 2 precursor (Seminal vesicle secretory protein IV) (SVS IV)	0.72	-	exc	1 *	Secreted protein; extracellular space				113
P07856 UniProt NPD GO	SERI1_BOMMO	Sericin 1 precursor (Silk gum protein)	0.72	-	nuc	0	Secreted protein				1186
Q05319 UniProt NPD GO	STUB_DROME	Serine proteinase stubble (EC 3.4.21.-) (Protein stubble-stubbloid) [Contains: Serine proteinase stu ...	0.72	-	nuc	1	Membrane; single-pass type II membrane protein				787

You are viewing entries 12951 to 13000 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.