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
Q96JZ2 UniProt NPD GO	HSH2D_HUMAN	Hematopoietic SH2 domain-containing protein (Hematopoietic SH2 protein) (Adaptor in lymphocytes of u ...	0.52	-	nuc	0	Cytoplasm. Nucleus		608349	2CS0	352
Q2QLF1 UniProt NPD GO	MET_PANTR	Hepatocyte growth factor receptor precursor (EC 2.7.10.1) (HGF receptor) (Scatter factor receptor) ( ...	0.52	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1390
P29227 UniProt NPD GO	HP1_DROVI	Heterochromatin protein 1 (HP1)	0.52	+	nuc	0	Nucleus				213
P61979 UniProt NPD GO	HNRPK_MOUSE	Heterogeneous nuclear ribonucleoprotein K	0.52	+	nuc	0	Cytoplasm (By similarity). Nucleus; nucleoplasm (By similarity)				463
P61980 UniProt NPD GO	HNRPK_RAT	Heterogeneous nuclear ribonucleoprotein K (dC stretch-binding protein) (CSBP)	0.52	+	nuc	0	Cytoplasm (By similarity). Nucleus; nucleoplasm (By similarity)				463
O19049 UniProt NPD GO	HNRPK_RABIT	Heterogeneous nuclear ribonucleoprotein K (hnRNP K)	0.52	+	nuc	0	Cytoplasm (By similarity). Nucleus; nucleoplasm (By similarity)				463
P61978 UniProt NPD GO	HNRPK_HUMAN	Heterogeneous nuclear ribonucleoprotein K (hnRNP K) (Transformation up-regulated nuclear protein) (T ...	0.52	+	nuc	0	Cytoplasm. Nucleus; nucleoplasm		600712	1ZZK	463
P14866 UniProt NPD GO	HNRPL_HUMAN	Heterogeneous nuclear ribonucleoprotein L (hnRNP L)	0.52	+	nuc	0	Nucleus; nucleoplasm	heterogeneous nuclear ribonucleoprotein com... [TAS] nucleoplasm [TAS]	603083		558
P35367 UniProt NPD GO	HRH1_HUMAN	Histamine H1 receptor	0.52	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600167		487
Q94555 UniProt NPD GO	H12_DROVI	Histone H1.2	0.52	+	nuc	0	Nucleus				250
Q7Z9J4 UniProt NPD GO	H2B_AJECA	Histone H2B	0.52	-	nuc	0	Nucleus (By similarity)				137
Q5KMT4 UniProt NPD GO	H2B_CRYNE	Histone H2B	0.52	-	nuc	0	Nucleus				138
Q7M400 UniProt NPD GO	H2B_TETPY	Histone H2B	0.52	-	nuc	0	Nucleus				120
Q6PC60 UniProt NPD GO	H2B3_BRARE	Histone H2B 3	0.52	+	nuc	0	Nucleus				125
Q8CGP2 UniProt NPD GO	H2B1P_MOUSE	Histone H2B type 1-P	0.52	+	nuc	0	Nucleus				125
Q74ZL5 UniProt NPD GO	H2B1_ASHGO	Histone H2B.1	0.52	-	nuc	0	Nucleus (By similarity)				131
P08993 UniProt NPD GO	H2B1_TETTH	Histone H2B.1 (H2B-1)	0.52	-	nuc	0	Nucleus. Macronuclei				121
Q9HDN1 UniProt NPD GO	H3_MORAP	Histone H3	0.52	-	nuc	0	Nucleus (By similarity)				135
P09988 UniProt NPD GO	H31_SCHPO	Histone H3.1/H3.2	0.52	-	nuc	0	Nucleus (By similarity)				135
P10651 UniProt NPD GO	H33_SCHPO	Histone H3.3	0.52	-	nuc	0	Nucleus (By similarity)				135
Q8WZM0 UniProt NPD GO	GCN5_YARLI	Histone acetyltransferase GCN5 (EC 2.3.1.48)	0.52	-	nuc	0	Nucleus (By similarity)				464
Q8BY71 UniProt NPD GO	HAT1_MOUSE	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.52	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear in S-phase cells and cytoplasmic (By sim ...				416
O97670 UniProt NPD GO	HESX1_RABIT	Homeobox expressed in ES cells 1 (Homeobox protein ANF) (Fragment)	0.52	+	nuc	0	Nucleus (By similarity)				175
Q9W6D8 UniProt NPD GO	BARX1_CHICK	Homeobox protein BarH-like 1 (Fragment)	0.52	+	nuc	0	Nucleus (Probable)				207
Q9QZW9 UniProt NPD GO	HLXB9_MOUSE	Homeobox protein HB9	0.52	+	nuc	0	Nucleus (By similarity)				404
Q93352 UniProt NPD GO	HM36_CAEEL	Homeobox protein ceh-36	0.52	-	nuc	0	Nucleus (Probable)				254
P47012 UniProt NPD GO	YJN5_YEAST	Hypothetical 12.4 kDa protein in RPS21B-MRS3 intergenic region	0.52	-	nuc	0					105
P38808 UniProt NPD GO	YHP5_YEAST	Hypothetical 16.7 kDa protein in HXT1-HXT5 intergenic region	0.52	+	nuc	0					144
P53214 UniProt NPD GO	YG1F_YEAST	Hypothetical 57.5 kDa protein in VMA7-RPS25A intergenic region	0.52	-	exc	1					551
P43549 UniProt NPD GO	YFF4_YEAST	Hypothetical 70.5 kDa protein in AGP3-DAK3 intergenic region	0.52	+	nuc	6	Membrane; multi-pass membrane protein (Probable)				646
Q9MTM6 UniProt NPD GO	YCX9_OENHO	Hypothetical 9.7 kDa protein in trnC-rpoB intergenic region (ORF84)	0.52	+	nuc	0	Plastid; chloroplast				84
P0C0V6 UniProt NPD GO	Y1985_EMENI	Hypothetical protein AN1985	0.52	-	nuc	0					352
Q10060 UniProt NPD GO	YAM5_SCHPO	Hypothetical protein C1F5.05c in chromosome I	0.52	-	nuc	0					151
Q09798 UniProt NPD GO	YAA4_SCHPO	Hypothetical protein C22G7.04 in chromosome I	0.52	-	nuc	0					1115
P34349 UniProt NPD GO	YK83_CAEEL	Hypothetical protein C30A5.3	0.52	-	nuc	0					223
Q20680 UniProt NPD GO	YT32_CAEEL	Hypothetical protein F52H3.2 in chromosome II	0.52	-	mit	0					638
Q4HWB3 UniProt NPD GO	YA745_GIBZE	Hypothetical protein FG10745	0.52	-	nuc	0					351
P34622 UniProt NPD GO	YO86_CAEEL	Hypothetical protein ZK1236.6	0.52	-	nuc	0					206
P34646 UniProt NPD GO	YOQ8_CAEEL	Hypothetical protein ZK512.8	0.52	-	nuc	0					171
Q09378 UniProt NPD GO	YS56_CAEEL	Hypothetical protein ZK673.6	0.52	-	nuc	0					284
O18304 UniProt NPD GO	YHS5_CAEEL	Hypothetical protein ZK849.5 in chromosome I	0.52	-	end	3 *					411
P41248 UniProt NPD GO	YMF19_HELAN	Hypothetical protein ymf19 (ORFB)	0.52	-	nuc	1 *	Mitochondrion (Potential)				159
P01854 UniProt NPD GO	IGHE_HUMAN	Ig epsilon chain C region	0.52	-	nuc	0			147180	1O0V	428
O22478 UniProt NPD GO	IMA_LYCES	Importin subunit alpha (Karyopherin subunit alpha) (KAP alpha)	0.52	-	mit	0	Cytoplasm (By similarity)				527
P08069 UniProt NPD GO	IGF1R_HUMAN	Insulin-like growth factor 1 receptor precursor (EC 2.7.10.1) (Insulin-like growth factor I receptor ...	0.52	+	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [IC]	147370	1P4O	1367
P26006 UniProt NPD GO	ITA3_HUMAN	Integrin alpha-3 precursor (Galactoprotein B3) (GAPB3) (VLA-3 alpha chain) (FRP-2) (CD49c antigen) [ ...	0.52	-	end	2 *	Membrane; single-pass type I membrane protein	integrin complex [TAS]	605025		1066
P38570 UniProt NPD GO	ITAE_HUMAN	Integrin alpha-E precursor (Mucosal lymphocyte 1 antigen) (HML-1 antigen) (Integrin alpha-IEL) (CD10 ...	0.52	-	end	1 *	Membrane; single-pass type I membrane protein	integrin complex [TAS]	604682		1179
P01571 UniProt NPD GO	IFN17_HUMAN	Interferon alpha-17 precursor (Interferon alpha-I') (Interferon alpha-T) (Interferon alpha-88)	0.52	-	nuc	0	Secreted protein		147583		189
P08831 UniProt NPD GO	IL1A_BOVIN	Interleukin-1 alpha precursor (IL-1 alpha)	0.52	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				268
Q28579 UniProt NPD GO	IL1A_SHEEP	Interleukin-1 alpha precursor (IL-1 alpha)	0.52	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				268

You are viewing entries 23751 to 23800 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.