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
O70443 UniProt NPD GO	GNAZ_MOUSE	Guanine nucleotide-binding protein G(z) subunit alpha (G(x) alpha chain) (Gz-alpha)	0.51	-	mit	0	Membrane; lipid-anchor	heterotrimeric G-protein complex [TAS] membrane fraction [TAS]			354
Q04665 UniProt NPD GO	GPA2_SCHPO	Guanine nucleotide-binding protein alpha-2 subunit (GP2-alpha)	0.51	-	nuc	0		heterotrimeric G-protein complex [TAS]			354
P34043 UniProt NPD GO	GPA5_DICDI	Guanine nucleotide-binding protein alpha-5 subunit (G alpha-5)	0.51	-	nuc	0					347
P54853 UniProt NPD GO	GPA1_CRYNE	Guanine nucleotide-binding protein subunit alpha	0.51	-	nuc	0					431
Q14264 UniProt NPD GO	ENR1_HUMAN	HERV-R_7q21.2 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (ERV3 envelope pro ...	0.51	-	mit	0					604
P40548 UniProt NPD GO	SNL1_YEAST	HSP70 co-chaperone SNL1 (Suppressor of NUP116-C lethal)	0.51	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Nucleus ...	endoplasmic reticulum membrane [IDA] mitochondrion [IDA] nuclear envelope [IDA]			159
Q12329 UniProt NPD GO	HSP42_YEAST	Heat shock protein 42 (42 kDa heat shock protein)	0.51	-	nuc	0		chaperonin-containing T-complex [IPI] cytoplasm [IDA] cytoskeleton [IPI]			375
Q10007 UniProt NPD GO	HLH6_CAEEL	Helix-loop-helix protein 6	0.51	-	nuc	0	Nucleus (Potential)				268
P08581 UniProt NPD GO	MET_HUMAN	Hepatocyte growth factor receptor precursor (EC 2.7.10.1) (HGF receptor) (Scatter factor receptor) ( ...	0.51	-	end	1	Membrane; single-pass type I membrane protein	basal plasma membrane [IDA] integral to plasma membrane [TAS]	164860	2G15	1390
P55317 UniProt NPD GO	HNF3A_HUMAN	Hepatocyte nuclear factor 3-alpha (HNF-3A) (Forkhead box protein A1)	0.51	+	nuc	0	Nucleus		602294		473
P23512 UniProt NPD GO	HNF3A_RAT	Hepatocyte nuclear factor 3-alpha (HNF-3A) (Forkhead box protein A1)	0.51	+	nuc	0	Nucleus	nucleus [IDA]			466
Q8R081 UniProt NPD GO	HNRPL_MOUSE	Heterogeneous nuclear ribonucleoprotein L (hnRNP L)	0.51	+	nuc	0	Nucleus; nucleoplasm (By similarity)	pronucleus [IDA]			555
Q9N2B2 UniProt NPD GO	HRH1_PANTR	Histamine H1 receptor	0.51	-	end	7 *	Membrane; multi-pass membrane protein				487
P27795 UniProt NPD GO	H2B_TRYCR	Histone H2B	0.51	-	nuc	0	Nucleus				112
Q8WNR4 UniProt NPD GO	H2BV_BOVIN	Histone H2B subacrosomal variant (SubH2Bv)	0.51	+	nuc	0	Cytoplasm. Subacrosomal region. Does not localize in nucleus				121
Q6BRG2 UniProt NPD GO	H2B1_DEBHA	Histone H2B.1	0.51	-	nuc	0	Nucleus (By similarity)				129
Q6BKW7 UniProt NPD GO	H2B2_DEBHA	Histone H2B.2	0.51	-	nuc	0	Nucleus (By similarity)				128
Q757N1 UniProt NPD GO	H3_ASHGO	Histone H3	0.51	-	nuc	0	Nucleus (By similarity)				135
P61833 UniProt NPD GO	H3_CANGA	Histone H3	0.51	-	nuc	0	Nucleus (By similarity)				135
Q98RY4 UniProt NPD GO	H3_GUITH	Histone H3	0.51	-	nuc	0	Nucleus (By similarity)				135
P61831 UniProt NPD GO	H3_KLULA	Histone H3	0.51	-	nuc	0	Nucleus (By similarity)				135
P61830 UniProt NPD GO	H3_YEAST	Histone H3	0.51	-	nuc	0	Nucleus	nuclear nucleosome [TAS] nucleus [IDA]		1QSN	135
P61836 UniProt NPD GO	H3_ZYGBA	Histone H3	0.51	-	nuc	0	Nucleus (By similarity)				135
Q6CXW4 UniProt NPD GO	GCN5_KLULA	Histone acetyltransferase GCN5 (EC 2.3.1.48)	0.51	-	nuc	0	Nucleus (By similarity)				516
Q9H4S2 UniProt NPD GO	GSHI_HUMAN	Homeobox protein GSH-1	0.51	+	nuc	0	Nucleus (By similarity)				264
P15857 UniProt NPD GO	HM17_APIME	Homeobox protein H17 (Fragment)	0.51	+	nuc	0	Nucleus (Potential)				79
P28362 UniProt NPD GO	MSX2_CHICK	Homeobox protein MSX-2 (CHOX-8) (GHox-8)	0.51	+	nuc	0	Nucleus				259
P23410 UniProt NPD GO	MSX2_COTJA	Homeobox protein MSX-2 (MSX-1) (QUOX-7)	0.51	+	nuc	0	Nucleus				259
P53771 UniProt NPD GO	BOX5_NOTVI	Homeobox protein box-5 (NVHBOX-5) (Fragment)	0.51	+	nuc	0	Nucleus (Potential)				258
Q18273 UniProt NPD GO	HM43_CAEEL	Homeobox protein ceh-43	0.51	+	nuc	0	Nucleus (Potential)				273
P20270 UniProt NPD GO	HM07_CAEEL	Homeobox protein ceh-7	0.51	+	cyt	0	Nucleus (Probable)				84
P38329 UniProt NPD GO	YB85_YEAST	Hypothetical 124.0 kDa protein in PBP2-ABD1 intergenic region	0.51	-	end	10	Membrane; multi-pass membrane protein (Potential)				1120
P38801 UniProt NPD GO	YHO1_YEAST	Hypothetical 21.0 kDa protein in IRE1-KSP1 intergenic region	0.51	-	nuc	0		nuclear exosome (RNase complex) [IPI]			184
P17960 UniProt NPD GO	YALI_TRYBB	Hypothetical 22 kDa protein in aldolase locus (ORFI)	0.51	-	nuc	0					185
P40572 UniProt NPD GO	YIT6_YEAST	Hypothetical 28.9 kDa protein in SQT1-MET28 intergenic region	0.51	-	exc	0					265
Q04867 UniProt NPD GO	YM91_YEAST	Hypothetical 35.9 kDa protein in NIP1-GLC8 intergenic region	0.51	-	nuc	0		nucleus [IDA]			317
P33757 UniProt NPD GO	YB9A_YEAST	Hypothetical 59.9 kDa protein in ARO4-MRPS5 intergenic region	0.51	-	nuc	0					523
P47041 UniProt NPD GO	YJF8_YEAST	Hypothetical 60.8 kDa protein in BTN1-PEP8 intergenic region	0.51	-	nuc	0		cytoplasm [IDA] TORC 2 complex [IPI]			543
Q96WW2 UniProt NPD GO	YNH6_SCHPO	Hypothetical TPR repeat-containing protein SPBC32H8.06	0.51	-	nuc	0					383
P92562 UniProt NPD GO	M1310_ARATH	Hypothetical mitochondrial protein AtMg01310 (ORF136b)	0.51	-	nuc	0	Mitochondrion (Potential)				136
Q10341 UniProt NPD GO	YBLH_SCHPO	Hypothetical protein C106.17c in chromosome II	0.51	-	mit	0					504
O94542 UniProt NPD GO	YCD2_SCHPO	Hypothetical protein C1322.02 in chromosome III	0.51	-	nuc	0					351
O14115 UniProt NPD GO	YKO1_SCHPO	Hypothetical protein C1786.01c in chromosome I	0.51	-	mit	1					630
Q09853 UniProt NPD GO	YAED_SCHPO	Hypothetical protein C23D3.13c in chromosome I	0.51	-	end	0					1616
Q10068 UniProt NPD GO	YAN2_SCHPO	Hypothetical protein C3H1.02c in chromosome I	0.51	-	cyt	0					1036
O14218 UniProt NPD GO	YDTD_SCHPO	Hypothetical protein C6B12.13 in chromosome I	0.51	-	nuc	0					104
Q10033 UniProt NPD GO	YSI1_CAEEL	Hypothetical protein F15G9.1	0.51	-	nuc	0					279
Q19532 UniProt NPD GO	YTDK_CAEEL	Hypothetical protein F17H10.3 in chromosome X	0.51	-	nuc	0					540
Q19948 UniProt NPD GO	YPP4_CAEEL	Hypothetical protein F32A5.4 precursor	0.51	-	exc	0	Secreted protein (Potential)				243
Q20806 UniProt NPD GO	YXWL_CAEEL	Hypothetical protein F55C10.4	0.51	-	exc	1 *					517

You are viewing entries 24351 to 24400 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.