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
P31538 UniProt NPD GO	HME1B_XENLA	Homeobox protein engrailed-1-B (En-1B) (Fragment)	0.79	+	nuc	0	Nucleus (Potential)				171
P09015 UniProt NPD GO	HME2A_BRARE	Homeobox protein engrailed-2a (Zf-En-2) (Eng2)	0.79	+	nuc	0	Nucleus				265
P52906 UniProt NPD GO	UNC30_CAEEL	Homeobox protein unc-30 (Uncoordinated protein 30)	0.79	+	nuc	0	Nucleus				319
P46668 UniProt NPD GO	ATHB6_ARATH	Homeobox-leucine zipper protein ATHB-6 (Homeodomain transcription factor ATHB-6) (HD-ZIP protein ATH ...	0.79	+	exc	0	Nucleus				311
P31264 UniProt NPD GO	HMPB_DROME	Homeotic protein proboscipedia	0.79	+	nuc	0	Nucleus				782
P42858 UniProt NPD GO	HD_HUMAN	Huntingtin (Huntington disease protein) (HD protein)	0.79	+	end	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleus [TAS] soluble fraction [TAS]	143100		3144
P34782 UniProt NPD GO	YCXA_ASTLO	Hypothetical 66.5 kDa protein in trnI-trnV intergenic region (ORF558)	0.79	+	cyt	0	Plastid				558
O20159 UniProt NPD GO	YCX7_CHLVU	Hypothetical 79.7 kDa protein in psaB-ycf62 intergenic region (ORF695)	0.79	+	nuc	0	Plastid; chloroplast				695
P34472 UniProt NPD GO	YMH5_CAEEL	Hypothetical C-type lectin protein F58A4.5 precursor	0.79	-	mit	0					786
P90794 UniProt NPD GO	YRIQ_CAEEL	Hypothetical WD repeat protein D2030.9	0.79	-	nuc	0					571
P34320 UniProt NPD GO	YKT9_CAEEL	Hypothetical protein C07A9.9	0.79	-	nuc	0					161
Q10201 UniProt NPD GO	YBX7_SCHPO	Hypothetical protein C17D1.07c in chromosome II	0.79	-	nuc	0					962
Q09847 UniProt NPD GO	YAE6_SCHPO	Hypothetical protein C23D3.06c in chromosome I	0.79	-	nuc	0		nuclear pore [TAS]			1325
Q09356 UniProt NPD GO	YRZ4_CAEEL	Hypothetical protein T19H5.4	0.79	-	nuc	1					313
Q09663 UniProt NPD GO	YS54_CAEEL	Hypothetical protein ZK673.4	0.79	-	nuc	0					476
Q9BTL4 UniProt NPD GO	IER2_HUMAN	Immediate early response gene 2 protein (Protein ETR101)	0.79	+	nuc	0					223
Q86SU0 UniProt NPD GO	ILDR1_HUMAN	Immunoglobulin-like domain-containing receptor 1 precursor	0.79	-	exc	2 *	Cell membrane; single-pass type I membrane protein. Isoform 5 localizes to cytosol		609739		546
Q80UK8 UniProt NPD GO	INT2_MOUSE	Integrator complex subunit 2 (Int2)	0.79	-	cyt	0	Nucleus; nuclear membrane; single-pass membrane protein (By similarity)				1198
Q9YGB9 UniProt NPD GO	IFNG_ANAPL	Interferon gamma precursor (IFN-gamma)	0.79	-	nuc	1 *	Secreted protein				164
P28333 UniProt NPD GO	IFNG_CEREL	Interferon gamma precursor (IFN-gamma)	0.79	-	exc	0	Secreted protein (By similarity)				166
O35735 UniProt NPD GO	IFNG_MARMO	Interferon gamma precursor (IFN-gamma)	0.79	-	exc	0	Secreted protein				166
P15314 UniProt NPD GO	IRF1_MOUSE	Interferon regulatory factor 1 (IRF-1)	0.79	+	nuc	0	Nucleus	nucleus [IC]		1IF1	329
Q9Y4C1 UniProt NPD GO	JHD2A_HUMAN	JmjC domain-containing histone demethylation protein 2A (EC 1.14.11.-) (Jumonji domain-containing pr ...	0.79	+	nuc	0	Nucleus (Probable)				1321
Q99PS0 UniProt NPD GO	K1C23_MOUSE	Keratin, type I cytoskeletal 23 (Cytokeratin-23) (CK-23) (Keratin-23) (K23)	0.79	-	nuc	0					422
Q86ZC1 UniProt NPD GO	KINH_BOTCI	Kinesin heavy chain	0.79	-	nuc	0					880
O43093 UniProt NPD GO	KINH_SYNRA	Kinesin heavy chain (Synkin)	0.79	-	nuc	0					935
P18105 UniProt NPD GO	NOD_DROME	Kinesin-like protein Nod	0.79	-	nuc	0		kinesin complex [IDA]			666
Q60793 UniProt NPD GO	KLF4_MOUSE	Krueppel-like factor 4 (Gut-enriched krueppel-like factor) (Epithelial zinc-finger protein EZF)	0.79	-	nuc	0	Nucleus	nucleus [NAS]			474
Q9WUH2 UniProt NPD GO	LHX9_MOUSE	LIM/homeobox protein Lhx9	0.79	-	nuc	0	Nucleus (Probable)				388
P46379 UniProt NPD GO	BAT3_HUMAN	Large proline-rich protein BAT3 (HLA-B-associated transcript 3) (Protein G3)	0.79	-	nuc	0			142590		1132
Q2T9W6 UniProt NPD GO	LRRF2_BOVIN	Leucine-rich repeat flightless-interacting protein 2 (LRR FLI-II-interacting protein 2)	0.79	-	nuc	0					400
Q80TE7 UniProt NPD GO	LRRC7_MOUSE	Leucine-rich repeat-containing protein 7 (Protein LAP1) (Densin-180)	0.79	-	nuc	0	Cytoplasm (By similarity)				1490
Q7Y023 UniProt NPD GO	MAD14_ORYSA	MADS-box transcription factor 14 (OsMADS14) (Protein APETALA1-like B) (Protein AGAMOUS-like 10) (FDR ...	0.79	-	nuc	0	Nucleus (Probable)				246
Q7XUN2 UniProt NPD GO	MAD17_ORYSA	MADS-box transcription factor 17 (OsMADS17) (NMADS3) (RMADS213)	0.79	-	nuc	0	Nucleus (Probable)				249
P49137 UniProt NPD GO	MAPK2_HUMAN	MAP kinase-activated protein kinase 2 (EC 2.7.11.1) (MAPK-activated protein kinase 2) (MAPKAP kinase ...	0.79	-	nuc	0		nucleus [TAS]	602006	1NY3	400
P43638 UniProt NPD GO	MHP1_YEAST	MAP-homologous protein 1	0.79	-	nuc	0	Cytoplasm. Cytoplasmic microtubules and mitotic spindles	microtubule [IDA]			1398
Q03141 UniProt NPD GO	MARK3_MOUSE	MAP/microtubule affinity-regulating kinase 3 (EC 2.7.11.1) (MPK-10) (ELKL motif kinase 2)	0.79	-	nuc	0				1UL7	753
P22015 UniProt NPD GO	B1_USTMA	Mating-type locus allele B1 protein	0.79	-	nuc	0	Nucleus				410
P22020 UniProt NPD GO	B6_USTMA	Mating-type locus allele B6 protein	0.79	-	nuc	0	Nucleus				410
Q9NQ76 UniProt NPD GO	MEPE_HUMAN	Matrix extracellular phosphoglycoprotein precursor (Osteoblast/osteocyte factor 45) (OF45)	0.79	-	exc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [TAS]	605912		525
Q9TIS6 UniProt NPD GO	MATK_CASLN	Maturase K (Intron maturase)	0.79	-	pox	0	Plastid				509
Q8WIV4 UniProt NPD GO	MATK_CYRRA	Maturase K (Intron maturase)	0.79	-	cyt	0	Plastid; chloroplast				513
Q717X5 UniProt NPD GO	MATK_LACFR	Maturase K (Intron maturase)	0.79	-	nuc	0	Plastid; chloroplast				504
Q9MUW8 UniProt NPD GO	MATK_PANCA	Maturase K (Intron maturase)	0.79	-	cyt	0	Plastid; chloroplast				513
Q8MCN3 UniProt NPD GO	MATK_TRIFR	Maturase K (Intron maturase)	0.79	-	nuc	0	Plastid; chloroplast				506
Q10336 UniProt NPD GO	MCP6_SCHPO	Meiotic coiled-coil protein 6 (Horsetail movement protein hrs1)	0.79	-	nuc	0	Nucleus. Spindle pole body	spindle pole body [IDA]			327
Q8C5S7 UniProt NPD GO	REC8L_MOUSE	Meiotic recombination protein REC8-like 1 (Cohesin Rec8p)	0.79	+	nuc	0	Nucleus. Localized along chromosome axis, but not chromosome ends	lateral element [IDA] nucleus [IDA]			591
P43364 UniProt NPD GO	MAGAB_HUMAN	Melanoma-associated antigen 11 (MAGE-11 antigen)	0.79	-	mit	0	Nucleus. Cytoplasm		300344		429
P43366 UniProt NPD GO	MAGB1_HUMAN	Melanoma-associated antigen B1 (MAGE-B1 antigen) (MAGE-XP antigen) (DSS-AHC critical interval MAGE s ...	0.79	-	nuc	0			300097		347
Q16819 UniProt NPD GO	MEP1A_HUMAN	Meprin A subunit alpha precursor (EC 3.4.24.18) (Endopeptidase-2) (N-benzoyl-L-tyrosyl-P-amino-benzo ...	0.79	-	exc	2 *	Membrane; single-pass type I membrane protein	extracellular space [TAS] integral to plasma membrane [TAS] soluble fraction [TAS]	600388		746

You are viewing entries 9401 to 9450 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.