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
P41797 UniProt NPD GO	HSP71_CANAL	Heat shock protein SSA1	0.35	-	cyt	0	Cytoplasm. Cell wall				655
Q5BK20 UniProt NPD GO	HN1L_RAT	Hematological and neurological expressed 1-like protein (HN1-like protein)	0.35	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				190
P28906 UniProt NPD GO	CD34_HUMAN	Hematopoietic progenitor cell antigen CD34 precursor	0.35	-	nuc	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IC]	142230		385
O61363 UniProt NPD GO	HCYG_OCTDO	Hemocyanin G-type, units Oda to Odg	0.35	-	nuc	0				1JS8	2896
P11150 UniProt NPD GO	LIPH_HUMAN	Hepatic triacylglycerol lipase precursor (EC 3.1.1.3) (Hepatic lipase) (HL)	0.35	-	mit	0	Secreted protein		151670		499
P51990 UniProt NPD GO	RO22_XENLA	Heterogeneous nuclear ribonucleoprotein A2 homolog 2 (hnRNP A2(B))	0.35	+	cyt	0	Nucleus. Component of ribonucleosomes				358
P17132 UniProt NPD GO	HNRPC_RAT	Heterogeneous nuclear ribonucleoprotein C (hnRNP C) (hnRNP core protein C) (Fragment)	0.35	-	nuc	0	Nucleus (By similarity). Component of ribonucleosomes (By similarity)				158
P07029 UniProt NPD GO	HNRU2_HUMAN	Heterogeneous nuclear ribonucleoprotein UP2 (Fragment)	0.35	-	nuc	0		heterogeneous nuclear ribonucleoprotein com... [NAS]			225
Q05783 UniProt NPD GO	HMGD_DROME	High mobility group protein D (HMG-D)	0.35	-	nuc	0	Nucleus	nuclear chromatin [IDA]		1QRV	112
P26569 UniProt NPD GO	H12_ARATH	Histone H1.2	0.35	-	nuc	0	Nucleus				273
P15866 UniProt NPD GO	H1C1_XENLA	Histone H1C (Clone XLHW2)	0.35	+	nuc	0	Nucleus				216
P40284 UniProt NPD GO	H2B_ENTIV	Histone H2B	0.35	-	nuc	0	Nucleus				134
O97484 UniProt NPD GO	H2B_EUPCR	Histone H2B	0.35	-	nuc	0	Nucleus (By similarity)				113
P81202 UniProt NPD GO	H38_STYLE	Histone H3-8 (Fragment)	0.35	-	nuc	0	Nucleus (By similarity)				113
Q76MU7 UniProt NPD GO	H4_ASPOR	Histone H4	0.35	-	cyt	0	Nucleus (By similarity)				102
Q6ZXX3 UniProt NPD GO	H4_USTMA	Histone H4	0.35	-	cyt	0	Nucleus (By similarity)				102
P69151 UniProt NPD GO	H42_TETPY	Histone H4, minor	0.35	-	nuc	0	Nucleus (By similarity)				102
P69152 UniProt NPD GO	H42_TETTH	Histone H4, minor	0.35	-	nuc	0	Nucleus (By similarity)				102
P23750 UniProt NPD GO	H41_EMENI	Histone H4.1	0.35	-	cyt	0	Nucleus (By similarity)				102
Q756G9 UniProt NPD GO	GCN5_ASHGO	Histone acetyltransferase GCN5 (EC 2.3.1.48)	0.35	-	nuc	0	Nucleus (By similarity)				452
Q5KNS9 UniProt NPD GO	HAT1_CRYNE	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.35	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				416
O24591 UniProt NPD GO	HD2A_MAIZE	Histone deacetylase 2a (HD2a) (Zm-HD2a) (Nucleolar histone deacetylase HD2-p39)	0.35	-	nuc	0	Nucleus; nucleolus				307
P53547 UniProt NPD GO	HM01_CAEEL	Homeobox protein ceh-1 (Fragment)	0.35	+	nuc	0	Nucleus (Potential)				132
Q15011 UniProt NPD GO	HERPU_HUMAN	Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (Methy ...	0.35	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IDA]	608070	1WGD	391
Q61191 UniProt NPD GO	HCFC1_MOUSE	Host cell factor (HCF) (HCF-1) (C1 factor) [Contains: HCF N-terminal chain 1; HCF N-terminal chain 2 ...	0.35	-	nuc	0	Nucleus. Cytoplasm. Nuclear in general, but uniquely cytoplasmic in trigeminal ganglia, becoming nuc ...	cytoplasm [IDA] nucleus [IDA]			2045
P53869 UniProt NPD GO	YNV1_YEAST	Hypothetical 10.6 kDa protein in PEX17-MER1 intergenic region	0.35	-	mit	0		mitochondrion [IDA]			86
P38311 UniProt NPD GO	YB59_YEAST	Hypothetical 12.1 kDa protein in DUR1,2-NGR1 intergenic region	0.35	-	nuc	1 *					105
P40062 UniProt NPD GO	YES7_YEAST	Hypothetical 12.7 kDa protein in RAD51-UBP9 intergenic region	0.35	-	mit	0					109
P53880 UniProt NPD GO	YNR9_YEAST	Hypothetical 17.6 kDa protein in NPR1-RPS3 intergenic region	0.35	-	mit	2 *					145
P38472 UniProt NPD GO	YMF30_MARPO	Hypothetical 22.6 kDa protein in COX3-NAD1 intergenic region (ORF 196)	0.35	-	nuc	0					196
P17958 UniProt NPD GO	YALV_TRYBB	Hypothetical 25.6 kDa protein in aldolase locus (ORFV)	0.35	-	nuc	0					232
P51239 UniProt NPD GO	YCXE_PORPU	Hypothetical 33.6 kDa protein in ycf39-ycf24 intergenic region (ORF287)	0.35	-	end	5 *	Plastid; chloroplast				287
P34617 UniProt NPD GO	YO81_CAEEL	Hypothetical GTP-binding protein ZK1236.1 in chromosome III	0.35	+	mit	0					645
Q10355 UniProt NPD GO	YDB2_SCHPO	Hypothetical RNA-binding protein C22E12.02 in chromosome I	0.35	-	nuc	0					219
Q09218 UniProt NPD GO	YP69_CAEEL	Hypothetical protein B0495.9	0.35	-	end	2	Membrane; multi-pass membrane protein (Potential)				267
P34319 UniProt NPD GO	YKT8_CAEEL	Hypothetical protein C07A9.8 in chromosome III	0.35	+	mit	4	Membrane; multi-pass membrane protein (Potential)				453
Q09817 UniProt NPD GO	YAC3_SCHPO	Hypothetical protein C16C9.03 in chromosome I	0.35	-	cyt	0					498
O94435 UniProt NPD GO	YFI1_SCHPO	Hypothetical protein C22H12.01c in chromosome I	0.35	-	cyt	0					234
Q09727 UniProt NPD GO	YA48_SCHPO	Hypothetical protein C31A2.08 in chromosome I	0.35	-	mit	0					161
Q09289 UniProt NPD GO	YQK7_CAEEL	Hypothetical protein C56G2.7	0.35	-	nuc	0					374
Q9U1M2 UniProt NPD GO	Y33B_DROME	Hypothetical protein CG32795 in chromosome 1	0.35	-	end	6					387
Q8STE0 UniProt NPD GO	Y108_ENCCU	Hypothetical protein ECU01_0080/ECU01_1530/ECU02_1560/ECU04_0090/ ECU08_0010/ECU08_2090	0.35	-	mit	0					331
Q10034 UniProt NPD GO	YSI2_CAEEL	Hypothetical protein F15G9.2	0.35	-	nuc	0					153
Q10037 UniProt NPD GO	YSI5_CAEEL	Hypothetical protein F15G9.5	0.35	-	exc	0	Membrane; multi-pass membrane protein (Potential)				272
Q09568 UniProt NPD GO	YR86_CAEEL	Hypothetical protein F48E8.6 in chromosome III	0.35	-	nuc	0					817
P34510 UniProt NPD GO	YMX2_CAEEL	Hypothetical protein K06H7.2	0.35	-	nuc	0					406
P34496 UniProt NPD GO	YNA1_CAEEL	Hypothetical protein PAR2.1 in chromosome III	0.35	-	mit	0					170
P82627 UniProt NPD GO	SCRL8_ARATH	Hypothetical protein SCRL8 precursor	0.35	-	exc	1 *					89
P45964 UniProt NPD GO	YNZ4_CAEEL	Hypothetical protein T09A5.4	0.35	-	cyt	0					297
Q09372 UniProt NPD GO	YS44_CAEEL	Hypothetical protein ZK177.4	0.35	-	mit	0					655

You are viewing entries 35901 to 35950 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.