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
P30108 UniProt NPD GO	GSTT1_DROYA	Glutathione S-transferase 1-1 (EC 2.5.1.18) (GST class-theta) (Fragment)	0.14	-	mit	0					200
P30568 UniProt NPD GO	GSTA_PLEPL	Glutathione S-transferase A (EC 2.5.1.18) (GST-A) (GST class-theta)	0.14	-	nuc	0	Cytoplasm				225
Q16772 UniProt NPD GO	GSTA3_HUMAN	Glutathione S-transferase A3-3 (EC 2.5.1.18) (GST class-alpha)	0.14	-	cyt	0	Cytoplasm		605449	1TDI	222
P46439 UniProt NPD GO	GSTM5_HUMAN	Glutathione S-transferase Mu 5 (EC 2.5.1.18) (GSTM5-5) (GST class-mu 5)	0.14	-	cyt	0	Cytoplasm		138385		217
P30712 UniProt NPD GO	GSTT2_HUMAN	Glutathione S-transferase theta-2 (EC 2.5.1.18) (GST class-theta-2)	0.14	-	mit	0	Cytoplasm		600437	3LJR	243
Q4AEH7 UniProt NPD GO	GPX2_CEBAP	Glutathione peroxidase 2 (EC 1.11.1.9) (GSHPx-2) (GPx-2) (Glutathione peroxidase-gastrointestinal) ( ...	0.14	-	cyt	0	Cytoplasm (By similarity)				190
P80461 UniProt NPD GO	GSHRP_TOBAC	Glutathione reductase, chloroplast precursor (EC 1.8.1.7) (GR) (GRase) (Fragment)	0.14	-	mit	0	Plastid; chloroplast				557
Q03250 UniProt NPD GO	GRP7_ARATH	Glycine-rich RNA-binding protein 7	0.14	+	cyt	0					176
P49310 UniProt NPD GO	GRP1_SINAL	Glycine-rich RNA-binding protein GRP1A	0.14	+	cyt	0	Nucleus				166
Q75EY7 UniProt NPD GO	GPI11_ASHGO	Glycosylphosphatidylinositol anchor biosynthesis protein 11	0.14	-	mit	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				217
Q9UVX3 UniProt NPD GO	NMT_ASPFU	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.14	-	cyt	0	Cytoplasm				492
Q9H8Y8 UniProt NPD GO	GORS2_HUMAN	Golgi reassembly-stacking protein 2 (GRS2) (Golgi reassembly-stacking protein of 55 kDa) (GRASP55) ( ...	0.14	-	nuc	0	Golgi apparatus; Golgi membrane; lipid-anchor		608693		451
Q5RD32 UniProt NPD GO	GOPC_PONPY	Golgi-associated PDZ and coiled-coil motif-containing protein	0.14	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein (By similari ...				462
P27767 UniProt NPD GO	GTHB2_ANGAN	Gonadotropin beta-2 subunit precursor (Gonadotropin beta-II chain) (GTH-II-beta)	0.14	-	nuc	1 *	Secreted protein				140
P07732 UniProt NPD GO	GTHB2_ONCTS	Gonadotropin beta-2 subunit precursor (Gonadotropin beta-II chain) (GTH-II-beta)	0.14	-	exc	0	Secreted protein				142
P48749 UniProt NPD GO	CSF2_CANFA	Granulocyte-macrophage colony-stimulating factor precursor (GM-CSF) (Colony-stimulating factor) (CSF ...	0.14	-	mit	0	Secreted protein				144
Q06605 UniProt NPD GO	GRZ1_RAT	Granzyme-like protein 1 precursor (EC 3.4.21.-) (GLP-1) (Granzyme-like protein I) (GLP I)	0.14	-	exc	0					248
Q9CXP8 UniProt NPD GO	GBG10_MOUSE	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-10 subunit precursor	0.14	-	exc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				68
P31006 UniProt NPD GO	KGUA_PIG	Guanylate kinase (EC 2.7.4.8) (GMP kinase)	0.14	-	nuc	0					197
P14430 UniProt NPD GO	HA18_MOUSE	H-2 class I histocompatibility antigen, Q8 alpha chain precursor	0.14	-	exc	0	Membrane; single-pass type I membrane protein				326
P06345 UniProt NPD GO	HB2S_MOUSE	H-2 class II histocompatibility antigen, A-S beta chain precursor	0.14	-	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]			263
Q5RJV1 UniProt NPD GO	NOLA1_XENTR	H/ACA ribonucleoprotein complex subunit 1-like protein	0.14	+	cyt	0	Nucleus; nucleolus (By similarity)				218
P01920 UniProt NPD GO	HB24_HUMAN	HLA class II histocompatibility antigen, DQ(3) beta chain precursor (Clone II-102)	0.14	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)			1JK8	261
P02515 UniProt NPD GO	HSP22_DROME	Heat shock protein 22	0.14	-	nuc	0					174
O16087 UniProt NPD GO	HSP83_DROMI	Heat shock protein 83 (HSP 82) (Fragment)	0.14	-	cyt	0	Cytoplasm	centrosome [ISS]			269
P83175 UniProt NPD GO	HCYB_CANPG	Hemocyanin subunit B (Fragment)	0.14	-	nuc	0	Secreted protein; extracellular space				37
Q5NVQ3 UniProt NPD GO	FGF1_PONPY	Heparin-binding growth factor 1 precursor (HBGF-1) (Acidic fibroblast growth factor) (aFGF)	0.14	-	nuc	0					155
P20002 UniProt NPD GO	FGF1_PIG	Heparin-binding growth factor 1 precursor (HBGF-1) (Acidic fibroblast growth factor) (aFGF) (Alpha-e ...	0.14	-	nuc	0					152
P05230 UniProt NPD GO	FGF1_HUMAN	Heparin-binding growth factor 1 precursor (HBGF-1) (Acidic fibroblast growth factor) (aFGF) (Beta-en ...	0.14	-	nuc	0			131220	2AXM	155
P52789 UniProt NPD GO	HXK2_HUMAN	Hexokinase-2 (EC 2.7.1.1) (Hexokinase type II) (HK II) (Muscle form hexokinase)	0.14	-	cyt	0	Mitochondrion; mitochondrial outer membrane. Its hydrophobic N-terminal sequence may be involved in ...	mitochondrial outer membrane [NAS]	601125		917
Q1WM16 UniProt NPD GO	HXK7_ORYSA	Hexokinase-7 (EC 2.7.1.1) (Hexokinase-6)	0.14	-	cyt	0	Cytoplasm (Probable)				463
Q2KNB7 UniProt NPD GO	HXK9_ORYSA	Hexokinase-9 (EC 2.7.1.1) (Hexokinase-5)	0.14	-	nuc	1 *	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein (By similarity)				502
P41804 UniProt NPD GO	ELI3_PHYCR	Highly acidic elicitin 26 precursor	0.14	-	nuc	0	Secreted protein				123
P29104 UniProt NPD GO	HPCL4_BOVIN	Hippocalcin-like protein 4 (Neurocalcin beta) (Fragment)	0.14	-	cyt	0					165
P28512 UniProt NPD GO	ITH6_HIRMA	Hirudin P6	0.14	-	nuc	0	Secreted protein				63
Q12670 UniProt NPD GO	HIS2_SACBA	Histidine biosynthesis trifunctional protein [Includes: Phosphoribosyl-AMP cyclohydrolase (EC 3.5.4. ...	0.14	-	cyt	0					799
O82030 UniProt NPD GO	HIS8_TOBAC	Histidinol-phosphate aminotransferase, chloroplast precursor (EC 2.6.1.9) (Imidazole acetol-phosphat ...	0.14	-	cyt	0	Plastid; chloroplast (Potential)				413
P02255 UniProt NPD GO	H1_DROME	Histone H1	0.14	+	nuc	0	Nucleus				256
Q07134 UniProt NPD GO	H1O_CHITH	Histone H1, orphon	0.14	+	nuc	0	Nucleus				244
Q08865 UniProt NPD GO	H12_VOLCA	Histone H1-II	0.14	-	nuc	0	Nucleus				240
P40278 UniProt NPD GO	H1E_CHITE	Histone H1E	0.14	-	nuc	0	Nucleus				237
Q6WV66 UniProt NPD GO	H2A_MYTCA	Histone H2A	0.14	-	nuc	0	Nucleus				124
Q6WV69 UniProt NPD GO	H2A_MYTCH	Histone H2A	0.14	-	nuc	0	Nucleus				124
Q8I0T3 UniProt NPD GO	H2A_MYTED	Histone H2A	0.14	-	nuc	0	Nucleus				124
Q6WV88 UniProt NPD GO	H2A_MYTGA	Histone H2A	0.14	-	nuc	0	Nucleus				124
Q6WV67 UniProt NPD GO	H2A_MYTTR	Histone H2A	0.14	-	nuc	0	Nucleus				124
P06898 UniProt NPD GO	H2A2_XENLA	Histone H2A type 2	0.14	-	nuc	0	Nucleus				129
P69140 UniProt NPD GO	H2A_PARAN	Histone H2A, gonadal	0.14	-	nuc	0	Nucleus				125
P35065 UniProt NPD GO	H2A2_TETTH	Histone H2A.2	0.14	-	nuc	0	Nucleus				132
Q6BQE9 UniProt NPD GO	H2AZ_DEBHA	Histone H2A.Z	0.14	-	nuc	0	Nucleus (By similarity)				131

You are viewing entries 58401 to 58450 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.