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
P62686 UniProt NPD GO	GAK13_HUMAN	HERV-K_1p13.3 provirus ancestral Gag polyprotein (Gag polyprotein)	0.04	-	cyt	0					163
P28068 UniProt NPD GO	2DMB_HUMAN	HLA class II histocompatibility antigen, DM beta chain precursor (MHC class II antigen DMB)	0.04	-	end	1	Endosome; late endosome; late endosomal membrane; single-pass type I membrane protein. Lysosome; lys ...		142856	1HDM	263
P13765 UniProt NPD GO	2DOB_HUMAN	HLA class II histocompatibility antigen, DO beta chain precursor (MHC class II antigen DOB)	0.04	-	nuc	1	Membrane; single-pass type I membrane protein	lysosome [IDA]	142920		273
P04229 UniProt NPD GO	2B11_HUMAN	HLA class II histocompatibility antigen, DRB1-1 beta chain precursor (MHC class I antigen DRB1*1) (D ...	0.04	-	end	1 *	Membrane; single-pass type I membrane protein		142857	1T5X	266
Q30134 UniProt NPD GO	2B18_HUMAN	HLA class II histocompatibility antigen, DRB1-8 beta chain precursor (MHC class I antigen DRB1*8) (D ...	0.04	-	end	2 *	Membrane; single-pass type I membrane protein		142857		266
Q08623 UniProt NPD GO	HDD1A_HUMAN	Haloacid dehalogenase-like hydrolase domain-containing protein 1A (GS1 protein)	0.04	-	cyt	0			306480		214
P56852 UniProt NPD GO	TXHN1_GRASP	Hanatoxin-1 (HaTx1)	0.04	-	cyt	0	Secreted protein			1D1H	35
P56853 UniProt NPD GO	TXHN2_GRASP	Hanatoxin-2 (HaTx2)	0.04	-	cyt	0	Secreted protein				35
P78983 UniProt NPD GO	HSP70_ALTAL	Heat shock 70 kDa protein (Allergen Alt a 3) (Fragment)	0.04	-	nuc	0					152
P48741 UniProt NPD GO	HSP77_HUMAN	Heat shock 70 kDa protein 7 (Heat shock 70 kDa protein B) (Fragment)	0.04	-	cyt	0			140556		247
Q6FJI3 UniProt NPD GO	HSP7F_CANGA	Heat shock protein homolog SSE1	0.04	-	cyt	0	Cytoplasm (By similarity)				694
Q5RAB0 UniProt NPD GO	HSPB8_PONPY	Heat-shock protein beta-8 (HspB8)	0.04	-	nuc	0					196
Q9UJY1 UniProt NPD GO	HSPB8_HUMAN	Heat-shock protein beta-8 (HspB8) (Alpha crystallin C chain) (Small stress protein-like protein HSP2 ...	0.04	-	nuc	0			608014		196
P02242 UniProt NPD GO	HCYE_EURCA	Hemocyanin E chain (HcE)	0.04	-	cyt	0	Secreted protein; extracellular space	extracellular space [ISS]			623
P04253 UniProt NPD GO	HCY2_LIMPO	Hemocyanin II	0.04	-	cyt	0	Secreted protein; extracellular space	extracellular space [IC]		1OXY	628
P82296 UniProt NPD GO	HCY1_HOMAM	Hemocyanin subunit 1 (Fragment)	0.04	-	cyt	0	Secreted protein; extracellular space				31
P84293 UniProt NPD GO	HCY2_CARAE	Hemocyanin subunit 2 (CaeSS2)	0.04	-	cyt	0	Secreted protein; extracellular space				650
P84620 UniProt NPD GO	HCYB_CONCC	Hemocyanin subunit B (CCH-B) (Fragment)	0.04	-		0	Secreted protein; extracellular space				7
Q8T115 UniProt NPD GO	HCYC_SCUCO	Hemocyanin subunit C precursor	0.04	-	cyt	0	Secreted protein; extracellular space	extracellular region [IDA]			673
P82310 UniProt NPD GO	HCYIA_PANJA	Hemocyanin subunit Ia (Fragment)	0.04	-		0	Secreted protein; extracellular space				20
P01954 UniProt NPD GO	HBA_ELEMA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.04	-	cyt	0					141
P01955 UniProt NPD GO	HBA_LOXAF	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.04	-	cyt	0					141
P14390 UniProt NPD GO	HBA_PTEPO	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.04	-	cyt	0					141
P01941 UniProt NPD GO	HBA_TUPGL	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.04	-	cyt	0					141
P02010 UniProt NPD GO	HBA_VIPAS	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.04	-	nuc	0					141
P07035 UniProt NPD GO	HBAD_CHLME	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.04	-	cyt	0					141
P0C0U7 UniProt NPD GO	HBAD_DRYCE	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.04	-	cyt	0					141
P02028 UniProt NPD GO	HBB_CERAE	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.04	-	cyt	0					146
P08259 UniProt NPD GO	HBB_MANSP	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.04	-	cyt	0					146
P02110 UniProt NPD GO	HBB_TACAC	Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin)	0.04	-	cyt	0					146
P19886 UniProt NPD GO	HBD_COLPO	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.04	-	cyt	0					146
P61773 UniProt NPD GO	HBD_GORGO	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.04	-	cyt	0					146
P02042 UniProt NPD GO	HBD_HUMAN	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.04	-	cyt	0		hemoglobin complex [TAS]	142000	1SI4	146
P61774 UniProt NPD GO	HBD_HYLLA	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.04	-	cyt	0					146
P61772 UniProt NPD GO	HBD_PANTR	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.04	-	cyt	0					146
P61775 UniProt NPD GO	HBD_PONPY	Hemoglobin subunit delta (Hemoglobin delta chain) (Delta-globin)	0.04	-	cyt	0					146
P31398 UniProt NPD GO	HEMO_MANSE	Hemolin precursor (P4 protein) (Hemocyte aggregation inhibitor)	0.04	-	vac	0	Secreted protein; extracellular space				413
P80745 UniProt NPD GO	LE06_BIOGL	Hemolymph 65 kDa lectin BG06 (Fragment)	0.04	-		0	Secreted protein				16
Q5R231 UniProt NPD GO	ACTP1_ACTVL	Hemolytic toxin Avt-1 precursor (Avt-I)	0.04	-	mit	0	Secreted protein. Found in nematocyst				226
P20057 UniProt NPD GO	HEMO_CHICK	Hemopexin (Fragment)	0.04	-	nuc	0	Secreted protein				34
P02790 UniProt NPD GO	HEMO_HUMAN	Hemopexin precursor (Beta-1B-glycoprotein)	0.04	-	exc	0	Secreted protein	extracellular region [NAS] extracellular space [TAS]	142290		462
Q9FZP1 UniProt NPD GO	HPSE3_ARATH	Heparanase-like protein 3 precursor (EC 3.2.-.-)	0.04	-	exc	0	Lysosome; lysosomal membrane; peripheral membrane protein (By similarity). Secreted protein (By simi ...				536
P82951 UniProt NPD GO	HEPC_MORCS	Hepcidin precursor	0.04	-	exc	0	Secreted protein			1S6W	85
P33284 UniProt NPD GO	HXK_KLULA	Hexokinase (EC 2.7.1.1)	0.04	-	mit	0					484
Q42525 UniProt NPD GO	HXK1_ARATH	Hexokinase-1 (EC 2.7.1.1)	0.04	-	nuc	1 *	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein (By similarity)				496
P50521 UniProt NPD GO	HXK2_SCHPO	Hexokinase-2 (EC 2.7.1.1)	0.04	-	cyt	0					455
Q2KNB9 UniProt NPD GO	HXK2_ORYSA	Hexokinase-2 (EC 2.7.1.1) (Hexokinase-3)	0.04	-	nuc	0					494
Q9XSZ6 UniProt NPD GO	FCERG_PIG	High affinity immunoglobulin epsilon receptor gamma-subunit precursor (FceRI gamma) (IgE Fc receptor ...	0.04	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				86
P20411 UniProt NPD GO	FCERG_RAT	High affinity immunoglobulin epsilon receptor gamma-subunit precursor (FceRI gamma) (IgE Fc receptor ...	0.04	-	end	1 *	Membrane; single-pass type I membrane protein				86
P55919 UniProt NPD GO	CXCR1_GORGO	High affinity interleukin-8 receptor A (IL-8R A) (IL-8 receptor type 1) (CXCR-1) (CD181 antigen)	0.04	-	end	6 *	Membrane; multi-pass membrane protein				350

You are viewing entries 77201 to 77250 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.