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
O24456 UniProt NPD GO	GBLP_ARATH	Guanine nucleotide-binding protein subunit beta-like protein (WD-40 repeat auxin-dependent protein A ...	0.10	-	cyt	0					327
P06346 UniProt NPD GO	HB2F_MOUSE	H-2 class II histocompatibility antigen, A-F beta chain precursor (Fragment)	0.10	-	end	1	Membrane; single-pass type I membrane protein (Potential)	early endosome [IDA] external side of plasma membrane [IDA] Golgi apparatus [IDA] integral to membrane [IDA] intracellular [IDA] MHC class II protein complex [IDA] multivesicular body [IDA] plasma membrane [IDA]			252
P06342 UniProt NPD GO	HB2Q_MOUSE	H-2 class II histocompatibility antigen, A-Q beta chain precursor	0.10	-	end	1	Membrane; single-pass type I membrane protein (Potential)	early endosome [IDA] external side of plasma membrane [IDA] Golgi apparatus [IDA] integral to membrane [IDA] intracellular [IDA] MHC class II protein complex [IDA] multivesicular body [IDA] plasma membrane [IDA]			265
P18468 UniProt NPD GO	HB2I_MOUSE	H-2 class II histocompatibility antigen, I-A beta chain precursor	0.10	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				264
Q5E950 UniProt NPD GO	NOLA2_BOVIN	H/ACA ribonucleoprotein complex subunit 2 (Nucleolar protein family A member 2)	0.10	-	nuc	0	Nucleus; nucleolus (By similarity). Also localized to Cajal bodies (coiled bodies) (By similarity)				153
Q4R5F0 UniProt NPD GO	HBLD2_MACFA	HESB-like domain-containing protein 2, mitochondrial precursor (Iron sulfur assembly protein IscA)	0.10	-	mit	0	Mitochondrion (By similarity)				129
Q9D924 UniProt NPD GO	HBLD2_MOUSE	HESB-like domain-containing protein 2, mitochondrial precursor (Iron sulfur assembly protein IscA)	0.10	-	mit	0	Mitochondrion (By similarity)				129
Q80W96 UniProt NPD GO	HBLD2_RAT	HESB-like domain-containing protein 2, mitochondrial precursor (Iron sulfur assembly protein IscA)	0.10	-	mit	0	Mitochondrion (By similarity)				129
Q9BUE6 UniProt NPD GO	HBLD2_HUMAN	HESB-like domain-containing protein 2, mitochondrial precursor (Iron sulfur assembly protein IscA) ( ...	0.10	-	mit	0	Mitochondrion				129
P01919 UniProt NPD GO	HB22_HUMAN	HLA class II histocompatibility antigen, DQ(W1.1) beta chain precursor (DQB1*0501)	0.10	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)	membrane [NAS]	604305		261
Q30167 UniProt NPD GO	2B1A_HUMAN	HLA class II histocompatibility antigen, DRB1-10 beta chain precursor (MHC class I antigen DRB1*10) ...	0.10	-	end	2 *	Membrane; single-pass type I membrane protein		142857		266
P05538 UniProt NPD GO	HB2X_HUMAN	HLA class II histocompatibility antigen, DX beta chain precursor	0.10	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)	membrane [NAS]			268
P40621 UniProt NPD GO	HMGL_WHEAT	HMG1/2-like protein	0.10	-	nuc	0	Nucleus (Potential)				161
P22978 UniProt NPD GO	HS6B_DROME	Heat shock protein 67B2	0.10	-	nuc	0					111
P30946 UniProt NPD GO	HS90A_RABIT	Heat shock protein HSP 90-alpha (Fragment)	0.10	-	cyt	0	Cytoplasm				40
P82995 UniProt NPD GO	HS90A_RAT	Heat shock protein HSP 90-alpha (Fragment)	0.10	-		0	Cytoplasm				12
P14602 UniProt NPD GO	HSPB1_MOUSE	Heat-shock protein beta-1 (HspB1) (Heat shock 27 kDa protein) (HSP 27) (Growth-related 25 kDa protei ...	0.10	-	mit	0		contractile fiber [IDA] cytoplasm [IDA] insoluble fraction [IDA] nucleus [IDA] plasma membrane [IDA] soluble fraction [IDA] Z disc [IDA]			209
P04254 UniProt NPD GO	HCYA_PANIN	Hemocyanin A chain	0.10	-	cyt	0	Secreted protein; extracellular space			1HCY	657
P10787 UniProt NPD GO	HCYB_PANIN	Hemocyanin B chain	0.10	-	cyt	0	Secreted protein; extracellular space				657
Q9NFH9 UniProt NPD GO	HCYB_EURCA	Hemocyanin B chain (HcB)	0.10	-	cyt	0	Secreted protein; extracellular space	extracellular space [ISS]			626
P83040 UniProt NPD GO	HCY2E_RAPTH	Hemocyanin type 2 unit e (RtH2-e)	0.10	-	cyt	0	Secreted protein; extracellular space			1LNL	413
P15655 UniProt NPD GO	FGF2_MOUSE	Heparin-binding growth factor 2 precursor (HBGF-2) (Basic fibroblast growth factor) (BFGF) (Prostatr ...	0.10	-	nuc	0		extracellular space [IDA]			154
P13109 UniProt NPD GO	FGF2_RAT	Heparin-binding growth factor 2 precursor (HBGF-2) (Basic fibroblast growth factor) (BFGF) (Prostatr ...	0.10	-	nuc	0					154
P03969 UniProt NPD GO	FGF2_BOVIN	Heparin-binding growth factor 2 precursor (HBGF-2) (Basic fibroblast growth factor) (BFGF) (Prostatr ...	0.10	-	nuc	0					155
P52597 UniProt NPD GO	HNRPF_HUMAN	Heterogeneous nuclear ribonucleoprotein F (hnRNP F) (Nucleolin-like protein mcs94-1)	0.10	-	cyt	0	Nucleus; nucleoplasm	heterogeneous nuclear ribonucleoprotein com... [TAS] nucleus [TAS]	601037		414
Q9VE46 UniProt NPD GO	SC5A7_DROME	High-affinity choline transporter 1	0.10	-	end	13 *	Membrane; multi-pass membrane protein (Probable)	integral to membrane [ISS]			614
P41803 UniProt NPD GO	ELI2_PHYCR	Highly acidic elicitin 20 precursor	0.10	-	exc	0	Secreted protein				123
P40277 UniProt NPD GO	H1C_CHITE	Histone H1C	0.10	-	nuc	0	Nucleus				221
Q9M531 UniProt NPD GO	H2A_EUPES	Histone H2A	0.10	-	cyt	0	Nucleus				153
P09589 UniProt NPD GO	H2A3_LYTPI	Histone H2A, sperm (Fragment)	0.10	-	mit	0	Nucleus				112
P04910 UniProt NPD GO	H2A2_SCHPO	Histone H2A-beta (H2A.2)	0.10	-	nuc	0	Nucleus				130
P49120 UniProt NPD GO	H2B4_MAIZE	Histone H2B.4	0.10	+	nuc	0	Nucleus				136
O22446 UniProt NPD GO	HDAC_ARATH	Histone deacetylase (HD)	0.10	-	cyt	0	Nucleus (By similarity)				501
Q8VH37 UniProt NPD GO	HDAC8_MOUSE	Histone deacetylase 8 (HD8)	0.10	-	cyt	0	Nucleus (By similarity)	cytoplasm [TAS] histone deacetylase complex [TAS] nucleus [TAS]			377
O09173 UniProt NPD GO	HGD_MOUSE	Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (Homogentisicase) (Homogentisate oxygenase) (Homogentis ...	0.10	-	cyt	0					445
P60316 UniProt NPD GO	HOOK3_BOVIN	Hook homolog 3 (Fragment)	0.10	-		0	Cytoplasm (By similarity). Golgi apparatus (By similarity). Associates with the Golgi complex. Enric ...				12
P16386 UniProt NPD GO	LIPS_BOVIN	Hormone-sensitive lipase (EC 3.1.1.79) (HSL) (Fragment)	0.10	-	nuc	0					27
Q8IVG9 UniProt NPD GO	HUNIN_HUMAN	Humanin	0.10	-	nuc	0	Secreted protein		606120	1Y32	24
O76536 UniProt NPD GO	HYAL_STRPU	Hyalin (Fragment)	0.10	-	cyt	0	Secreted protein; extracellular space; extracellular matrix				1200
Q92056 UniProt NPD GO	HIOM_CHICK	Hydroxyindole O-methyltransferase (EC 2.1.1.4) (HIOMT) (Acetylserotonin O-methyltransferase) (ASMT)	0.10	-	cyt	0					346
P54871 UniProt NPD GO	HMCS_CAEEL	Hydroxymethylglutaryl-CoA synthase (EC 2.3.3.10) (HMG-CoA synthase) (3-hydroxy-3-methylglutaryl coen ...	0.10	-	cyt	0					462
P24397 UniProt NPD GO	HY6H_HYONI	Hyoscyamine 6-dioxygenase (EC 1.14.11.11) (Hyoscyamine 6-beta-hydroxylase)	0.10	-	cyt	0					344
P53126 UniProt NPD GO	YGN2_YEAST	Hypothetical 12.2 kDa protein in RPL1B-CEG1 intergenic region	0.10	-	nuc	0					111
P34215 UniProt NPD GO	YBZ4_YEAST	Hypothetical 12.3 kDa protein in SUP1-ADH5 intergenic region	0.10	-	cyt	0					104
Q9MSA1 UniProt NPD GO	YCF83_GALSU	Hypothetical 12.5 kDa protein ycf83 (ORF339)	0.10	-	nuc	0	Plastid; chloroplast				112
P47091 UniProt NPD GO	YJY8_YEAST	Hypothetical 13.3 kDa protein in ESS1-MER2 intergenic region	0.10	-	nuc	0					120
P40001 UniProt NPD GO	YEA8_YEAST	Hypothetical 14.0 kDa protein in GCN4-WBP1 intergenic region	0.10	-	mit	0					126
P53831 UniProt NPD GO	YN25_YEAST	Hypothetical 14.1 kDa protein in SEC21-MRPL10 intergenic region	0.10	-	cyt	0					123
P53887 UniProt NPD GO	YNR1_YEAST	Hypothetical 14.6 kDa protein in RPS3-PSD1 intergenic region	0.10	-	cyt	0					122
P53864 UniProt NPD GO	YNW6_YEAST	Hypothetical 16.0 kDa protein in URE2-SSU72 intergenic region	0.10	-	cyt	0					136

You are viewing entries 64451 to 64500 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.