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
P10267 UniProt NPD GO	ENK10_HUMAN	HERV-K_5q33.3 provirus ancestral Env polyprotein (Envelope polyprotein) (HERV-K10 envelope protein) ...	0.29	-	end	2					587
P03989 UniProt NPD GO	1B27_HUMAN	HLA class I histocompatibility antigen, B-27 alpha chain precursor (MHC class I antigen B*27)	0.29	-	end	1	Membrane; single-pass type I membrane protein	membrane fraction [TAS]	106300	2BST	362
P30485 UniProt NPD GO	1B47_HUMAN	HLA class I histocompatibility antigen, B-47 alpha chain precursor (MHC class I antigen B*47) (Bw-47 ...	0.29	-	end	1 *	Membrane; single-pass type I membrane protein		142830		362
Q00423 UniProt NPD GO	HMGYA_SOYBN	HMG-Y-related protein A (SB16A protein)	0.29	-	nuc	0	Nucleus (Potential)				176
P46254 UniProt NPD GO	HS22M_PEA	Heat shock 22 kDa protein, mitochondrial precursor	0.29	-	mit	0	Mitochondrion				202
P34933 UniProt NPD GO	HSP73_BOVIN	Heat shock 70 kDa protein 3	0.29	-	cyt	0					631
P09446 UniProt NPD GO	HSP7A_CAEEL	Heat shock 70 kDa protein A	0.29	-	cyt	0					640
P22953 UniProt NPD GO	HSP71_ARATH	Heat shock cognate 70 kDa protein 1 (Hsc70.1)	0.29	-	cyt	0	Cytoplasm (Probable)				651
Q9W6Y1 UniProt NPD GO	HSP7C_ORYLA	Heat shock cognate 71 kDa protein (Hsc70.1)	0.29	-	cyt	0					686
P97825 UniProt NPD GO	HN1_MOUSE	Hematological and neurological expressed 1 protein	0.29	-	nuc	0	Nucleus (By similarity)				153
O14792 UniProt NPD GO	OST1_HUMAN	Heparan sulfate glucosamine 3-O-sulfotransferase 1 precursor (EC 2.8.2.23) (Heparan sulfate D-glucos ...	0.29	-	cyt	0	Golgi apparatus; Golgi lumen (Probable)	Golgi lumen [TAS] integral to membrane [TAS]	603244	1ZRH	307
Q5U9D2 UniProt NPD GO	HEPC_CANFA	Hepcidin precursor	0.29	-	exc	1 *	Secreted protein				85
Q9GL42 UniProt NPD GO	HFE_DICSU	Hereditary hemochromatosis protein homolog precursor	0.29	-	end	1	Membrane; single-pass type I membrane protein				348
P70387 UniProt NPD GO	HFE_MOUSE	Hereditary hemochromatosis protein homolog precursor	0.29	-	end	1 *	Membrane; single-pass type I membrane protein				359
P07909 UniProt NPD GO	ROA1_DROME	Heterogeneous nuclear ribonucleoprotein A1 (hnRNP core protein A1-A) (PEN repeat clone P9)	0.29	-	cyt	0		ribonucleoprotein complex [IDA]			365
P21522 UniProt NPD GO	ROA1_SCHAM	Heterogeneous nuclear ribonucleoprotein A1, A2/B1 homolog	0.29	+	cyt	0					342
P52272 UniProt NPD GO	HNRPM_HUMAN	Heterogeneous nuclear ribonucleoprotein M (hnRNP M)	0.29	-	cyt	0	Nucleus; nucleolus	integral to plasma membrane [TAS] spliceosome complex [IDA]	160994		729
Q3TRM8 UniProt NPD GO	HXK3_MOUSE	Hexokinase-3 (EC 2.7.1.1) (Hexokinase type III) (HK III)	0.29	-	cyt	0					922
Q91009 UniProt NPD GO	NTRK1_CHICK	High affinity nerve growth factor receptor precursor (EC 2.7.10.1) (Neurotrophic tyrosine kinase rec ...	0.29	-	nuc	0	Membrane; single-pass type I membrane protein				778
P54772 UniProt NPD GO	DCHS_LYCES	Histidine decarboxylase (EC 4.1.1.22) (HDC) (TOM92)	0.29	-	cyt	0					413
P43275 UniProt NPD GO	H11_MOUSE	Histone H1.1 (H1 VAR.3) (H1a)	0.29	+	nuc	0	Nucleus				212
P40268 UniProt NPD GO	H1C2_TRYCR	Histone H1.C2	0.29	+	nuc	0					97
P93354 UniProt NPD GO	H2B_TOBAC	Histone H2B	0.29	-	nuc	0	Nucleus				145
P81198 UniProt NPD GO	H34_STYLE	Histone H3-4 (Fragment)	0.29	-	nuc	0	Nucleus (By similarity)				112
P84048 UniProt NPD GO	H4_ACRAS	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
P84047 UniProt NPD GO	H4_ASEAQ	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [NAS]			102
P62784 UniProt NPD GO	H4_CAEEL	Histone H4	0.29	-	cyt	0	Nucleus				102
P62800 UniProt NPD GO	H4_CAIMO	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
Q7KQD1 UniProt NPD GO	H4_CHAVR	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
P62801 UniProt NPD GO	H4_CHICK	Histone H4	0.29	-	cyt	0	Nucleus	nucleosome [ISS]		2HIO	102
P84046 UniProt NPD GO	H4_CHITH	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [NAS]			102
P91882 UniProt NPD GO	H4_DIAPU	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)				102
P84041 UniProt NPD GO	H4_DROER	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
P84042 UniProt NPD GO	H4_DROHY	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
Q76FE7 UniProt NPD GO	H4_DROMA	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
P84040 UniProt NPD GO	H4_DROME	Histone H4	0.29	-	cyt	0	Nucleus	nucleosome [IDA] RCAF complex [IDA]			102
Q76FF1 UniProt NPD GO	H4_DROOR	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
Q76FD9 UniProt NPD GO	H4_DROSE	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
P84043 UniProt NPD GO	H4_DROSI	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
Q76FF5 UniProt NPD GO	H4_DROTE	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
P84044 UniProt NPD GO	H4_DROYA	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
P62776 UniProt NPD GO	H4_HOLTU	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)				102
P62805 UniProt NPD GO	H4_HUMAN	Histone H4	0.29	-	cyt	0	Nucleus	nucleosome [TAS]	142750	2CV5	102
P62782 UniProt NPD GO	H4_LYTPI	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)				102
P62806 UniProt NPD GO	H4_MOUSE	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]		1F66	102
P84049 UniProt NPD GO	H4_MYRRU	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
Q6WV73 UniProt NPD GO	H4_MYTCA	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
Q7K8C0 UniProt NPD GO	H4_MYTED	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
Q6WV90 UniProt NPD GO	H4_MYTGA	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
Q6WV72 UniProt NPD GO	H4_MYTTR	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102

You are viewing entries 41301 to 41350 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.