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
Q8R4A8 UniProt NPD GO	GNAS_CRIGR	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.43	-	mit	0	Cell membrane; lipid anchor (By similarity)				394
P63093 UniProt NPD GO	GNAS_MESAU	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.43	-	mit	0	Cell membrane; lipid anchor (By similarity)				394
P63094 UniProt NPD GO	GNAS_MOUSE	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.43	-	mit	0		heterotrimeric G-protein complex [TAS] membrane fraction [IMP]			394
P63095 UniProt NPD GO	GNAS_RAT	Guanine nucleotide-binding protein G(s) subunit alpha (Adenylate cyclase-stimulating G alpha protein ...	0.43	-	mit	0	Cell membrane; lipid anchor (By similarity)				394
P16051 UniProt NPD GO	GPA2_DICDI	Guanine nucleotide-binding protein alpha-2 subunit (G alpha-2)	0.43	-	cyt	0					356
O04279 UniProt NPD GO	GPA2_PEA	Guanine nucleotide-binding protein alpha-2 subunit (GP-alpha-2)	0.43	-	nuc	0					384
Q05424 UniProt NPD GO	GPA2_NEUCR	Guanine nucleotide-binding protein alpha-2 subunit (GP2-alpha)	0.43	-	cyt	0					355
Q9NPE3 UniProt NPD GO	NOLA3_HUMAN	H/ACA ribonucleoprotein complex subunit 3 (Nucleolar protein family A member 3) (snoRNP protein NOP1 ...	0.43	-	nuc	0	Nucleus; nucleolus. Nucleus; nucleoplasm; Cajal body. Also localized to Cajal bodies (coiled bodies) ...	small nucleolar ribonucleoprotein complex [TAS]	606471		64
Q9CQS2 UniProt NPD GO	NOLA3_MOUSE	H/ACA ribonucleoprotein complex subunit 3 (Nucleolar protein family A member 3) (snoRNP protein NOP1 ...	0.43	-	nuc	0	Nucleus; nucleolus (By similarity). Also localized to Cajal bodies (coiled bodies) (By similarity)				64
P30487 UniProt NPD GO	1B49_HUMAN	HLA class I histocompatibility antigen, B-49 alpha chain precursor (MHC class I antigen B*49) (B-21) ...	0.43	-	end	1 *	Membrane; single-pass type I membrane protein		142830		362
Q8LE10 UniProt NPD GO	HA22I_ARATH	HVA22-like protein i (AtHVA22i)	0.43	-	nuc	0					296
Q39818 UniProt NPD GO	HS22M_SOYBN	Heat shock 22 kDa protein, mitochondrial precursor	0.43	-	mit	0	Mitochondrion				211
P87047 UniProt NPD GO	HSP70_PARBR	Heat shock 70 kDa protein	0.43	-	cyt	0					649
P34182 UniProt NPD GO	HRTE_CROAT	Hemorrhagic metalloproteinase HT-E precursor (EC 3.4.24.44) (Atrolysin E) (Hemorrhagic toxin E) [Con ...	0.43	+	nuc	0					478
P97523 UniProt NPD GO	MET_RAT	Hepatocyte growth factor receptor precursor (EC 2.7.10.1) (HGF receptor) (Scatter factor receptor) ( ...	0.43	-	end	1	Membrane; single-pass type I membrane protein				1382
P09651 UniProt NPD GO	ROA1_HUMAN	Heterogeneous nuclear ribonucleoprotein A1 (Helix-destabilizing protein) (Single-strand RNA-binding ...	0.43	+	cyt	0	Nucleus. Cytoplasm. Shuttles continuously between the nucleus and the cytoplasm along with mRNA. Com ...	cytoplasm [TAS] heterogeneous nuclear ribonucleoprotein com... [TAS] nucleoplasm [TAS] spliceosome complex [IDA]	164017	2UP1	371
P30546 UniProt NPD GO	HRH1_BOVIN	Histamine H1 receptor	0.43	-	end	7 *	Membrane; multi-pass membrane protein				491
P07305 UniProt NPD GO	H10_HUMAN	Histone H1.0 (H1(0)) (Histone H1')	0.43	+	nuc	0	Nucleus		142708		193
P02251 UniProt NPD GO	H13_RABIT	Histone H1.3	0.43	-	nuc	0	Nucleus				213
P06892 UniProt NPD GO	H1A_XENLA	Histone H1A	0.43	+	nuc	0	Nucleus				209
Q8J1K2 UniProt NPD GO	H2B_ROSNE	Histone H2B	0.43	-	nuc	0	Nucleus (By similarity)				135
Q5BJA5 UniProt NPD GO	H2B1_BRARE	Histone H2B 1/2	0.43	+	nuc	0	Nucleus				123
P02289 UniProt NPD GO	H2BE_STRPU	Histone H2B, embryonic	0.43	-	nuc	0	Nucleus				123
P48989 UniProt NPD GO	H2B1_CANAL	Histone H2B.1	0.43	+	nuc	0	Nucleus (By similarity)				129
P13282 UniProt NPD GO	H2BS2_ECHES	Histone H2B.2, sperm (Fragment)	0.43	-	mit	0	Nucleus				29
P59226 UniProt NPD GO	H3_ARATH	Histone H3	0.43	-	nuc	0	Nucleus (By similarity)				135
Q6LBE3 UniProt NPD GO	H3_ASPOF	Histone H3	0.43	-	nuc	0	Nucleus (By similarity)				135
Q6LCK1 UniProt NPD GO	H3_BRANA	Histone H3	0.43	-	nuc	0	Nucleus (By similarity)				135
Q6RUR1 UniProt NPD GO	H3_CAPAN	Histone H3	0.43	-	nuc	0	Nucleus (By similarity)				135
P50564 UniProt NPD GO	H3_CHLRE	Histone H3	0.43	-	nuc	0	Nucleus (By similarity)				134
Q71T45 UniProt NPD GO	H3_EUPES	Histone H3	0.43	-	nuc	0	Nucleus (By similarity)				135
Q71V89 UniProt NPD GO	H3_GOSHI	Histone H3	0.43	-	nuc	0	Nucleus (By similarity)				135
P69245 UniProt NPD GO	H3_LOLTE	Histone H3	0.43	-	nuc	0	Nucleus (By similarity)				135
Q71U98 UniProt NPD GO	H3_ORYCO	Histone H3	0.43	-	nuc	0	Nucleus (By similarity)				135
P69247 UniProt NPD GO	H3_ORYSA	Histone H3	0.43	-	nuc	0	Nucleus (By similarity)				135
P69248 UniProt NPD GO	H3_PETCR	Histone H3	0.43	-	nuc	0	Nucleus (By similarity)				135
Q711T2 UniProt NPD GO	H3_PINPS	Histone H3	0.43	-	nuc	0	Nucleus (By similarity)				135
P69246 UniProt NPD GO	H31_MAIZE	Histone H3 type 1	0.43	-	nuc	0	Nucleus (By similarity)				135
Q53X03 UniProt NPD GO	H32_MAIZE	Histone H3 type 2	0.43	-	nuc	0	Nucleus (By similarity)				135
P69244 UniProt NPD GO	H32_MEDSA	Histone H3.2 (Minor histone H3)	0.43	-	nuc	0	Nucleus				135
P59169 UniProt NPD GO	H33_ARATH	Histone H3.3	0.43	-	nuc	0	Nucleus (By similarity)				135
Q71H73 UniProt NPD GO	H33_VITVI	Histone H3.3	0.43	-	nuc	0	Nucleus (By similarity)				135
P06902 UniProt NPD GO	H34_CAIMO	Histone H3.4	0.43	-	nuc	0	Nucleus (By similarity)				135
Q59VF4 UniProt NPD GO	HAT1_CANAL	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.43	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				413
P31316 UniProt NPD GO	GSH2_MOUSE	Homeobox protein GSH-2	0.43	+	nuc	0	Nucleus				305
P09026 UniProt NPD GO	HXB3_MOUSE	Homeobox protein Hox-B3 (Hox-2.7) (MH-23)	0.43	+	nuc	0	Nucleus				433
Q2VL86 UniProt NPD GO	MSX1_SAIBB	Homeobox protein MSX-1 (Msh homeobox 1-like protein)	0.43	+	nuc	0	Nucleus (By similarity)				297
Q03358 UniProt NPD GO	MSX2_MOUSE	Homeobox protein MSX-2 (Hox-8.1)	0.43	+	nuc	0	Nucleus				267
O02734 UniProt NPD GO	HMCS2_PIG	Hydroxymethylglutaryl-CoA synthase, mitochondrial precursor (EC 2.3.3.10) (HMG-CoA synthase) (3-hydr ...	0.43	-	mit	0	Mitochondrion				508
Q9R1Y5 UniProt NPD GO	HIC1_MOUSE	Hypermethylated in cancer 1 protein (Hic-1)	0.43	-	nuc	0	Nucleus (Probable)				892

You are viewing entries 29651 to 29700 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.