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
O14793 UniProt NPD GO	GDF8_HUMAN	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.38	+	cyt	0	Secreted protein		601788		375
O18831 UniProt NPD GO	GDF8_PIG	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.38	+	mit	0	Secreted protein (By similarity)				375
Q6DTL9 UniProt NPD GO	GDF8_VULVU	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.38	+	mit	0	Secreted protein (By similarity)				375
P38523 UniProt NPD GO	GRPE_YEAST	GrpE protein homolog, mitochondrial precursor	0.38	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA] mitochondrion [IDA] presequence translocase-associated import m... [IPI]			228
P48604 UniProt NPD GO	GRPE_DROME	GrpE protein homolog, mitochondrial precursor (dRoe1)	0.38	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				213
P16894 UniProt NPD GO	GPA1_DICDI	Guanine nucleotide-binding protein alpha-1 subunit (G alpha-1)	0.38	-	nuc	0					356
Q6CHP5 UniProt NPD GO	GBG_YARLI	Guanine nucleotide-binding protein subunit gamma	0.38	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				108
P52785 UniProt NPD GO	GUC2E_MOUSE	Guanylyl cyclase GC-E precursor (EC 4.6.1.2) (Guanylate cyclase 2E)	0.38	-	end	2	Membrane; single-pass type I membrane protein	membrane fraction [TAS]			1108
P14431 UniProt NPD GO	HA19_MOUSE	H-2 class I histocompatibility antigen, Q9 alpha chain precursor (Fragment)	0.38	-	exc	0	Membrane; single-pass type I membrane protein				200
P14432 UniProt NPD GO	HA1T_MOUSE	H-2 class I histocompatibility antigen, TLA(B) alpha chain precursor (MHC thymus leukemia antigen)	0.38	-	end	1	Membrane; single-pass type I membrane protein				384
P63118 UniProt NPD GO	GAH2_HUMAN	HERV-H_3q26 provirus ancestral Gag polyprotein (Gag polyprotein)	0.38	-	nuc	0	Cell membrane (Potential)				214
P16189 UniProt NPD GO	1A31_HUMAN	HLA class I histocompatibility antigen, A-31 alpha chain precursor (MHC class I antigen A*31)	0.38	-	end	1 *	Membrane; single-pass type I membrane protein		142800		365
P16190 UniProt NPD GO	1A33_HUMAN	HLA class I histocompatibility antigen, A-33 alpha chain precursor (MHC class I antigen A*33) (Aw-33 ...	0.38	-	end	1 *	Membrane; single-pass type I membrane protein		142800		365
P30459 UniProt NPD GO	1A74_HUMAN	HLA class I histocompatibility antigen, A-74 alpha chain precursor (MHC class I antigen A*74) (Aw-74 ...	0.38	-	end	1	Membrane; single-pass type I membrane protein		142800		365
P30486 UniProt NPD GO	1B48_HUMAN	HLA class I histocompatibility antigen, B-48 alpha chain precursor (MHC class I antigen B*48) (Bw-48 ...	0.38	-	end	1	Membrane; single-pass type I membrane protein		142830		362
P01889 UniProt NPD GO	1B07_HUMAN	HLA class I histocompatibility antigen, B-7 alpha chain precursor (MHC class I antigen B*7)	0.38	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	142830		362
P30508 UniProt NPD GO	1C12_HUMAN	HLA class I histocompatibility antigen, Cw-12 alpha chain precursor (MHC class I antigen Cw*12)	0.38	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	142840		366
P30510 UniProt NPD GO	1C14_HUMAN	HLA class I histocompatibility antigen, Cw-14 alpha chain precursor (MHC class I antigen Cw*14)	0.38	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	142840		366
Q27975 UniProt NPD GO	HS70A_BOVIN	Heat shock 70 kDa protein 1A (HSP70.1)	0.38	-	cyt	0					641
Q27965 UniProt NPD GO	HS70B_BOVIN	Heat shock 70 kDa protein 1B (HSP70.2)	0.38	-	cyt	0					641
P46587 UniProt NPD GO	HSP72_CANAL	Heat shock protein SSA2	0.38	-	cyt	0	Cytoplasm. Cell wall				644
Q9DAM3 UniProt NPD GO	HSPB9_MOUSE	Heat-shock protein beta-9 (HspB9)	0.38	-	nuc	0					168
Q09118 UniProt NPD GO	HBEGF_CERAE	Heparin-binding EGF-like growth factor precursor (HB-EGF) (HBEGF) (Diphtheria toxin receptor) (DT-R) ...	0.38	-	end	1	Precursor form: Cell membrane; single-pass type I membrane protein (By similarity). Mature form: Sec ...				208
Q9XSK7 UniProt NPD GO	HDGF_BOVIN	Hepatoma-derived growth factor (HDGF)	0.38	-	nuc	0	Cytoplasm (By similarity)				239
Q7M733 UniProt NPD GO	HPS6_RAT	Hermansky-Pudlak syndrome 6 protein homolog (Ruby-eye protein homolog) (Ruby-eye-like protein) (Ru)	0.38	-	mit	0					809
P51992 UniProt NPD GO	RO32_XENLA	Heterogeneous nuclear ribonucleoprotein A3 homolog 2 (hnRNP A3(B))	0.38	+	cyt	0	Nucleus (By similarity). Component of ribonucleosomes (By similarity)				385
O60812 UniProt NPD GO	HNRCL_HUMAN	Heterogeneous nuclear ribonucleoprotein C-like 1 (hnRNP core protein C-like 1)	0.38	-	nuc	0	Nucleus (By similarity). Component of ribonucleosomes (By similarity)				293
O88569 UniProt NPD GO	ROA2_MOUSE	Heterogeneous nuclear ribonucleoproteins A2/B1 (hnRNP A2 / hnRNP B1)	0.38	+	cyt	0	Nucleus. Component of ribonucleosomes	spliceosome complex [ISS]			341
P23444 UniProt NPD GO	H1_MAIZE	Histone H1	0.38	-	nuc	0	Nucleus				245
P35066 UniProt NPD GO	H2A_TRYCR	Histone H2A	0.38	-	nuc	0	Nucleus				135
P27893 UniProt NPD GO	H2B_LEIEN	Histone H2B	0.38	-	mit	0	Nucleus				111
Q99285 UniProt NPD GO	H2B_PEA	Histone H2B (Fragments)	0.38	+	nuc	0	Nucleus				119
P13281 UniProt NPD GO	H2BS1_ECHES	Histone H2B.1, sperm (Fragment)	0.38	-	nuc	0	Nucleus				25
P02310 UniProt NPD GO	H41_TETPY	Histone H4, major	0.38	-	nuc	0	Nucleus (By similarity)				102
Q12341 UniProt NPD GO	HAT1_YEAST	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.38	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] histone acetyltransferase complex [IPI] nucleus [IDA]		1BOB	374
Q3T022 UniProt NPD GO	SAP18_BOVIN	Histone deacetylase complex subunit SAP18 (Sin3-associated polypeptide, 18 kDa) (Sin3-associated pol ...	0.38	-	nuc	0					153
P15858 UniProt NPD GO	EMS_APIME	Homeobox protein H40 (Fragment)	0.38	+	nuc	0	Nucleus (Probable)				74
P09638 UniProt NPD GO	HXB2_SALSA	Homeobox protein Hox-B2 (S6) (Fragment)	0.38	+	nuc	0	Nucleus				60
Q99P31 UniProt NPD GO	HPBP1_MOUSE	Hsp70-binding protein 1 (HspBP1) (Heat shock protein-binding protein 1) (Hsp70-interacting protein 1 ...	0.38	-	nuc	0					357
P53302 UniProt NPD GO	YG47_YEAST	Hypothetical 13.4 kDa protein in BUB1-HIP1 intergenic region	0.38	-	nuc	0					121
P40000 UniProt NPD GO	YEB0_YEAST	Hypothetical 13.5 kDa protein in GLC3-GCN4 intergenic region	0.38	-	nuc	1					116
P32633 UniProt NPD GO	YED3_YEAST	Hypothetical 16.1 kDa protein in HYP2-MCM3 intergenic region	0.38	+	end	2 *	Membrane; multi-pass membrane protein (Potential)				139
P47053 UniProt NPD GO	YJE3_YEAST	Hypothetical 29.2 kDa protein in GYP6-MHP1 intergenic region	0.38	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA]			257
P48279 UniProt NPD GO	YCF39_CYAPA	Hypothetical 36.4 kDa protein ycf39	0.38	-	cyt	0	Plastid; cyanelle				321
P51203 UniProt NPD GO	YCF55_PORPU	Hypothetical 37.8 kDa protein ycf55 (ORF320)	0.38	-	cyt	0	Plastid; chloroplast				320
P09753 UniProt NPD GO	YCX1_CHLMO	Hypothetical 38.5 kDa protein in psbA intron 1	0.38	-	nuc	0	Plastid; chloroplast				345
P38780 UniProt NPD GO	YHL4_YEAST	Hypothetical 41.1 kDa protein in CUP1-CPR2 intergenic region	0.38	-	cyt	0					354
P53324 UniProt NPD GO	YG5J_YEAST	Hypothetical 48.5 kDa protein in APL6-MES1 intergenic region	0.38	-	nuc	1 *		endoplasmic reticulum [IDA]			424
P51363 UniProt NPD GO	YCF44_PORPU	Hypothetical 50.2 kDa protein ycf44 (ORF437)	0.38	-	end	4 *	Plastid; chloroplast				437
Q03236 UniProt NPD GO	YM49_YEAST	Hypothetical 50.3 kDa protein in HSC82-GCV2 intergenic region	0.38	-	cyt	3	Membrane; multi-pass membrane protein (Potential)				431

You are viewing entries 33451 to 33500 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.