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
P28300 UniProt NPD GO	LYOX_HUMAN	Protein-lysine 6-oxidase precursor (EC 1.4.3.13) (Lysyl oxidase)	0.62	-	exc	0	Secreted protein; extracellular space		219100		417
Q2NKY8 UniProt NPD GO	DHX30_BOVIN	Putative ATP-dependent RNA helicase DHX30 (EC 3.6.1.-) (DEAH box protein 30)	0.62	-	mit	0					1220
Q8GX47 UniProt NPD GO	CAP3_ARATH	Putative clathrin assembly protein At4g02650	0.62	-	nuc	0					611
Q95XZ0 UniProt NPD GO	COG4_CAEEL	Putative conserved oligomeric Golgi complex component 4	0.62	-	cyt	0	Golgi apparatus (By similarity)				801
Q9VJD3 UniProt NPD GO	COG5_DROME	Putative conserved oligomeric Golgi complex component 5 (Four way stop protein)	0.62	-	nuc	0	Golgi apparatus (By similarity)				751
P47124 UniProt NPD GO	HOC1_YEAST	Putative glycosyltransferase HOC1 (EC 2.4.-.-) (Mannan polymerase II complex HOC1 subunit) (M-Pol II ...	0.62	-	mit	1 *	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; single-pass type II membrane protein ...	alpha-1,6-mannosyltransferase complex [IDA]			395
O60072 UniProt NPD GO	YBBA_SCHPO	Putative helicase C13G1.10c (EC 3.6.1.-)	0.62	-	cyt	0	Cytoplasm (By similarity)				1935
Q9P7C3 UniProt NPD GO	YKU1_SCHPO	Putative mannosyl-oligosaccharide 1,2-alpha-mannosidase (EC 3.2.1.113) (Man(9)-alpha-mannosidase)	0.62	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				521
Q93425 UniProt NPD GO	RT05_CAEEL	Putative mitochondrial 40S ribosomal protein S5	0.62	-	mit	0	Mitochondrion (Potential)				418
Q9ZVR7 UniProt NPD GO	PSKR_ARATH	Putative phytosulfokine receptor precursor (EC 2.7.11.1) (Phytosulfokine LRR receptor kinase)	0.62	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity)				1008
Q8MRC9 UniProt NPD GO	GALT9_DROME	Putative polypeptide N-acetylgalactosaminyltransferase 9 (EC 2.4.1.41) (Protein-UDP acetylgalactosam ...	0.62	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				650
Q00681 UniProt NPD GO	STCJ_EMENI	Putative sterigmatocystin biosynthesis fatty acid synthase alpha subunit	0.62	-	vac	0					1559
Q27974 UniProt NPD GO	AUXI_BOVIN	Putative tyrosine-protein phosphatase auxilin (EC 3.1.3.48) (DnaJ homolog subfamily C member 6)	0.62	-	nuc	0				1XI5	910
O75061 UniProt NPD GO	AUXI_HUMAN	Putative tyrosine-protein phosphatase auxilin (EC 3.1.3.48) (DnaJ homolog subfamily C member 6)	0.62	-	nuc	0			608375		913
Q09805 UniProt NPD GO	YAB3_SCHPO	Putative vacuolar protein sorting-associated protein C2G11.03c	0.62	-	cyt	0					558
P11345 UniProt NPD GO	RAF1_RAT	RAF proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1) (Raf-1) (C-RAF) (cRaf)	0.62	-	nuc	0		cytosol [TAS] insoluble fraction [IDA]		1RRB	648
Q5ZJ40 UniProt NPD GO	RCOR3_CHICK	REST corepressor 3	0.62	-	nuc	0	Nucleus (By similarity)				378
Q9EPZ8 UniProt NPD GO	RN103_RAT	RING finger protein 103 (Zinc finger protein 103) (Zfp-103) (ADRG34 protein)	0.62	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				682
O15541 UniProt NPD GO	R113A_HUMAN	RING finger protein 113A (Zinc finger protein 183)	0.62	+	nuc	0					343
Q9NTX7 UniProt NPD GO	RN146_HUMAN	RING finger protein 146 (Dactylidin)	0.62	+	nuc	0					359
Q9SK92 UniProt NPD GO	ATL1C_ARATH	RING-H2 finger protein ATL1C precursor (RING-H2 finger protein ATL15)	0.62	-	exc	2 *					381
Q8GW38 UniProt NPD GO	ATL1D_ARATH	RING-H2 finger protein ATL1D	0.62	-	nuc	1					369
Q9LUZ9 UniProt NPD GO	ATL5O_ARATH	RING-H2 finger protein ATL5O	0.62	+	nuc	1 *					308
Q02939 UniProt NPD GO	TFB2_YEAST	RNA polymerase II transcription factor B subunit 2 (RNA polymerase II transcription factor B p52 sub ...	0.62	+	mit	0	Nucleus (By similarity)	nucleotide-excision repair factor 3 complex [TAS] transcription factor TFIIH complex [IDA]			513
Q15042 UniProt NPD GO	RB3GP_HUMAN	Rab3 GTPase-activating protein catalytic subunit (RAB3 GTPase-activating protein 130 kDa subunit) (R ...	0.62	-	cyt	0	Cytoplasm. In neurons, it is enriched in the synaptic soluble fraction	soluble fraction [IDA]	602536		980
Q22670 UniProt NPD GO	RBGPR_CAEEL	Rab3 GTPase-activating protein regulatory subunit (Rab3 GTPase-activating protein 2)	0.62	-	cyt	0	Cytoplasm (Probable)	soluble fraction [ISS]			1307
P11346 UniProt NPD GO	KRAF1_DROME	Raf homolog serine/threonine-protein kinase dRAF-1 (EC 2.7.11.1) (Protein pole-hole)	0.62	-	nuc	0					739
P10586 UniProt NPD GO	PTPRF_HUMAN	Receptor-type tyrosine-protein phosphatase F precursor (EC 3.1.3.48) (LAR protein) (Leukocyte antige ...	0.62	+	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	179590	1LAR	1897
P28827 UniProt NPD GO	PTPRM_HUMAN	Receptor-type tyrosine-protein phosphatase mu precursor (EC 3.1.3.48) (Protein-tyrosine phosphatase ...	0.62	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	176888	2C9A	1452
Q23376 UniProt NPD GO	RGS9_CAEEL	Regulator of G-protein signaling rgs-9	0.62	-	nuc	0					235
O76512 UniProt NPD GO	RENT1_CAEEL	Regulator of nonsense transcripts 1 (EC 3.6.1.-) (ATP-dependent helicase smg-2) (Nonsense mRNA reduc ...	0.62	-	nuc	0	Cytoplasm (Potential)				1069
Q99109 UniProt NPD GO	REP1_USTMA	Repellent protein 1 precursor [Contains: Rep1-1; Rep1-2; Rep1-3; Rep1-4; Rep1-5; Rep1-6; Rep1-7; Rep ...	0.62	-	exc	0	Cell wall	hyphal cell wall [IDA]			652
O97039 UniProt NPD GO	RX_DUGJA	Retinal homeobox protein Rax (DjRax) (Fragment)	0.62	+	nuc	0	Nucleus (By similarity)				268
Q90273 UniProt NPD GO	RARG2_BRARE	Retinoic acid receptor gamma-2 (RAR-gamma-2) (Fragment)	0.62	+	nuc	0	Nucleus	nucleus [NAS]			367
P49788 UniProt NPD GO	TIG1_HUMAN	Retinoic acid receptor responder protein 1 (Tazarotene-induced gene 1 protein) (RAR-responsive prote ...	0.62	-	mit	0	Membrane; single-pass type II membrane protein (Potential)	integral to membrane [TAS]	605090		294
Q9ULJ6 UniProt NPD GO	ZIM10_HUMAN	Retinoic acid-induced protein 17 (PIAS-like protein Zimp10)	0.62	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Cytoplasm		607159		1067
Q6TNR1 UniProt NPD GO	RHPN2_BRARE	Rhophilin-2 (GTP-Rho-binding protein 2)	0.62	-	nuc	0	Cytoplasm (By similarity)				683
Q96DU3 UniProt NPD GO	SLAF6_HUMAN	SLAM family member 6 precursor (NK-T-B-antigen) (NTB-A) (Activating NK receptor)	0.62	-	exc	1	Membrane; single-pass type I membrane protein (Potential)		606446		331
P53783 UniProt NPD GO	SOX1_MOUSE	SOX-1 protein	0.62	+	nuc	1	Nucleus (Probable)				391
Q14515 UniProt NPD GO	SPRL1_HUMAN	SPARC-like protein 1 precursor (High endothelial venule protein) (Hevin) (MAST 9)	0.62	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		606041		664
Q9QX96 UniProt NPD GO	SALL2_MOUSE	Sal-like protein 2 (Spalt-like protein 2) (MSal-2)	0.62	-	nuc	0	Nucleus (Probable)				1004
Q6FHJ7 UniProt NPD GO	SFRP4_HUMAN	Secreted frizzled-related protein 4 precursor (sFRP-4) (Frizzled protein, human endometrium) (FrpHE) ...	0.62	-	exc	0	Secreted protein		606570		346
Q5E9P6 UniProt NPD GO	BSCL2_BOVIN	Seipin (Bernardinelli-Seip congenital lipodystrophy type 2 protein homolog)	0.62	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	integral to endoplasmic reticulum membrane [ISS]			394
O88632 UniProt NPD GO	SEM3F_MOUSE	Semaphorin-3F precursor (Semaphorin IV) (Sema IV)	0.62	-	exc	0	Secreted protein (By similarity)				785
O95084 UniProt NPD GO	PRS23_HUMAN	Serine protease 23 precursor (EC 3.4.21.-) (Putative secreted protein ZSIG13)	0.62	-	exc	0	Secreted protein (Potential)				383
Q5RAJ5 UniProt NPD GO	STK36_PONPY	Serine/threonine-protein kinase 36 (EC 2.7.11.1) (Fused homolog)	0.62	-	end	0	Cytoplasm (By similarity). Low level: Nucleus (By similarity). Low levels also present in the nucleu ...	cytoplasm [ISS] nucleus [ISS]			1315
Q91VJ4 UniProt NPD GO	STK38_MOUSE	Serine/threonine-protein kinase 38 (EC 2.7.11.1) (NDR1 protein kinase) (Nuclear Dbf2-related kinase ...	0.62	-	cyt	0	Nucleus (By similarity)	nucleus [ISS]			465
Q9CQS5 UniProt NPD GO	RIOK2_MOUSE	Serine/threonine-protein kinase RIO2 (EC 2.7.11.1) (RIO kinase 2)	0.62	-	nuc	0					547
Q90ZY4 UniProt NPD GO	SBK1_BRARE	Serine/threonine-protein kinase SBK1 (EC 2.7.11.1) (SH3-binding kinase 1) (Brain-specific protein ki ...	0.62	-	cyt	0	Cytoplasm (By similarity)				385
P78759 UniProt NPD GO	2AD2_SCHPO	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta 2 isoform (PP2A, B subunit, ...	0.62	-	nuc	0	Cytoplasm. Nucleus	protein phosphatase type 2A complex [TAS]			627

You are viewing entries 18151 to 18200 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.