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
Q08753 UniProt NPD GO	GLB1_CHLEU	Globin LI637	0.17	-	mit	0	Plastid; chloroplast. Particularly in the pyrenoid and the thylakoid region			1UVX	164
Q7SID0 UniProt NPD GO	GLBF1_EPTBU	Globin-F1	0.17	-	mit	0				1IT3	146
P52911 UniProt NPD GO	EXG2_YEAST	Glucan 1,3-beta-glucosidase 2 precursor (EC 3.2.1.58) (Exo-1,3-beta-glucanase 2)	0.17	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA]			562
P22832 UniProt NPD GO	AMYG_ASPSH	Glucoamylase precursor (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan glucohydrolas ...	0.17	-	exc	0					639
P55243 UniProt NPD GO	GLGL3_SOLTU	Glucose-1-phosphate adenylyltransferase large subunit 3, chloroplast precursor (EC 2.7.7.27) (ADP-gl ...	0.17	-	nuc	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...				483
P15280 UniProt NPD GO	GLGS_ORYSA	Glucose-1-phosphate adenylyltransferase small subunit, chloroplast precursor (EC 2.7.7.27) (ADP-gluc ...	0.17	-	mit	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...	amyloplast [IEP]			483
P30523 UniProt NPD GO	GLGS_WHEAT	Glucose-1-phosphate adenylyltransferase small subunit, chloroplast precursor (EC 2.7.7.27) (ADP-gluc ...	0.17	-	cyt	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...				473
P20228 UniProt NPD GO	DCE_DROME	Glutamate decarboxylase (EC 4.1.1.15) (GAD)	0.17	-	nuc	0					510
P15104 UniProt NPD GO	GLNA_HUMAN	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.17	-	cyt	0	Cytoplasm		610015		372
P09606 UniProt NPD GO	GLNA_RAT	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.17	-	cyt	0	Cytoplasm				372
P93111 UniProt NPD GO	HEM11_CUCSA	Glutamyl-tRNA reductase 1, chloroplast precursor (EC 1.2.1.70) (GluTR)	0.17	-	mit	0	Plastid; chloroplast (By similarity)				552
P80894 UniProt NPD GO	GSTA1_ANTST	Glutathione S-transferase (EC 2.5.1.18) (GST class-alpha)	0.17	-	cyt	0	Cytoplasm (By similarity)				221
P40582 UniProt NPD GO	GST1_YEAST	Glutathione S-transferase I (EC 2.5.1.18) (GST-I)	0.17	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	endoplasmic reticulum [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			234
Q9P6M1 UniProt NPD GO	GST3_SCHPO	Glutathione S-transferase III (EC 2.5.1.18) (GST-III)	0.17	-	cyt	0	Cytoplasm	cytoplasm [IDA]			242
P08010 UniProt NPD GO	GSTM2_RAT	Glutathione S-transferase Mu 2 (EC 2.5.1.18) (GSTM2-2) (Glutathione S-transferase Yb-2) (GST Yb2) (G ...	0.17	-	cyt	0	Cytoplasm			1B4P	217
Q4AEH9 UniProt NPD GO	GPX2_HYLLA	Glutathione peroxidase 2 (EC 1.11.1.9) (GSHPx-2) (GPx-2) (Glutathione peroxidase-gastrointestinal) ( ...	0.17	-	cyt	0	Cytoplasm (By similarity)				190
Q4AEH8 UniProt NPD GO	GPX2_MACFU	Glutathione peroxidase 2 (EC 1.11.1.9) (GSHPx-2) (GPx-2) (Glutathione peroxidase-gastrointestinal) ( ...	0.17	-	cyt	0	Cytoplasm (By similarity)				190
P18283 UniProt NPD GO	GPX2_HUMAN	Glutathione peroxidase 2 (EC 1.11.1.9) (GSHPx-2) (GPx-2) (Glutathione peroxidase-gastrointestinal) ( ...	0.17	-	cyt	0	Cytoplasm. Mainly	cytoplasm [TAS]	138319		190
Q03878 UniProt NPD GO	GRP1_DAUCA	Glycine-rich RNA-binding protein	0.17	+	cyt	0					157
P51138 UniProt NPD GO	MSK2_MEDSA	Glycogen synthase kinase-3 homolog MsK-2 (EC 2.7.11.1)	0.17	-	cyt	0					411
P80051 UniProt NPD GO	GLHA_RANCA	Glycoprotein hormones alpha chain (Anterior pituitary glycoprotein hormones common subunit alpha) (F ...	0.17	-	nuc	0	Secreted protein				97
Q6BJF4 UniProt NPD GO	NMT_DEBHA	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.17	-	cyt	0	Cytoplasm (By similarity)				451
Q98848 UniProt NPD GO	GTHB1_CARAU	Gonadotropin beta-1 subunit precursor (Gonadotropin beta-I chain) (GTH-I-beta) (Follicle-stimulating ...	0.17	-	exc	0	Secreted protein				130
Q8VC88 UniProt NPD GO	GRAN_MOUSE	Grancalcin	0.17	-	cyt	0	Cytoplasm (By similarity). Membrane (By similarity). Attached to membranes and granules (By similari ...	cytosol [TAS]			220
Q29118 UniProt NPD GO	CSF2_PIG	Granulocyte-macrophage colony-stimulating factor precursor (GM-CSF) (Colony-stimulating factor) (CSF ...	0.17	-	mit	0	Secreted protein				144
Q9QXX3 UniProt NPD GO	PA2GX_MOUSE	Group 10 secretory phospholipase A2 precursor (EC 3.1.1.4) (Group X secretory phospholipase A2) (Pho ...	0.17	-	exc	0	Secreted protein				151
Q9QZT3 UniProt NPD GO	PA2GX_RAT	Group 10 secretory phospholipase A2 precursor (EC 3.1.1.4) (Group X secretory phospholipase A2) (Pho ...	0.17	-	exc	0	Secreted protein	extracellular region [TAS]			151
Q9UNK4 UniProt NPD GO	PA2GD_HUMAN	Group IID secretory phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase GII ...	0.17	-	nuc	1 *	Secreted protein (Potential)	extracellular region [TAS]	605630		145
Q63772 UniProt NPD GO	GAS6_RAT	Growth-arrest-specific protein 6 precursor (GAS-6) (Growth-potentiating factor) (GPF)	0.17	-	exc	0	Secreted protein				674
Q99LP6 UniProt NPD GO	GRPE1_MOUSE	GrpE protein homolog 1, mitochondrial precursor (Mt-GrpE#1)	0.17	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			217
P50149 UniProt NPD GO	GNAT2_MOUSE	Guanine nucleotide-binding protein G(t), alpha-2 subunit (Transducin alpha-2 chain)	0.17	-	gol	0		heterotrimeric G-protein complex [TAS] membrane fraction [TAS]			353
P49026 UniProt NPD GO	GBLP_TOBAC	Guanine nucleotide-binding protein subunit beta-like protein	0.17	-	nuc	0					326
O13009 UniProt NPD GO	GUC2B_PIG	Guanylate cyclase activator 2B precursor [Contains: Uroguanylin (UGN)]	0.17	-	exc	1 *	Secreted protein (By similarity)				113
O73762 UniProt NPD GO	GUC1B_RANPI	Guanylyl cyclase-activating protein 2 (GCAP 2) (Guanylate cyclase activator 1B)	0.17	-	cyt	0					196
P33589 UniProt NPD GO	VSPA_LACMU	Gyroxin analog (EC 3.4.21.74) (Thrombin-like enzyme) (Venombin A)	0.17	-	cyt	0	Secreted protein				228
Q6Q547 UniProt NPD GO	NOP10_YEAST	H/ACA ribonucleoprotein complex subunit 3 (Nucleolar protein family A member 3) (snoRNP protein NOP1 ...	0.17	-	nuc	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [IDA]		2AQA	58
P13762 UniProt NPD GO	HB2K_HUMAN	HLA class II histocompatibility antigen, DR-W53 beta chain precursor	0.17	-	end	1	Membrane; single-pass type I membrane protein (Potential)				266
P04232 UniProt NPD GO	HB2T_HUMAN	HLA class II histocompatibility antigen, SB beta chain (Clone PHA-beta) (Fragment)	0.17	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)				181
P08418 UniProt NPD GO	HSP70_SCHMA	Heat shock 70 kDa homolog protein (HSP70) (Major surface antigen)	0.17	-	cyt	0					637
Q08276 UniProt NPD GO	HSP7M_SOLTU	Heat shock 70 kDa protein, mitochondrial precursor	0.17	-	mit	0	Mitochondrion				682
O65719 UniProt NPD GO	HSP73_ARATH	Heat shock cognate 70 kDa protein 3 (Hsc70.3)	0.17	-	cyt	0	Cytoplasm (Probable)				649
Q3T149 UniProt NPD GO	HSPB1_BOVIN	Heat-shock protein beta-1 (HspB1) (Heat shock 27 kDa protein) (HSP 27)	0.17	-	mit	0					201
O13224 UniProt NPD GO	HSPB1_POELU	Heat-shock protein beta-1 (HspB1) (Heat shock 27 kDa protein) (HSP 27)	0.17	-	nuc	0					201
Q8T116 UniProt NPD GO	HCYX_SCUCO	Hemocyanin subunit X precursor	0.17	-	exc	1 *	Secreted protein; extracellular space (By similarity)	extracellular region [ISS]			685
P15167 UniProt NPD GO	HRTD_CROAT	Hemorrhagic metalloproteinase HT-D/HT-C precursor (EC 3.4.24.42) (Atrolysin D/C) (Hemorrhagic toxin ...	0.17	-	mit	0				1HTD	414
Q71RP1 UniProt NPD GO	HPSE_RAT	Heparanase precursor (EC 3.2.-.-) (Endo-glucoronidase) [Contains: Heparanase 8 kDa subunit; Heparana ...	0.17	-	exc	0	Lysosome; lysosomal membrane; peripheral membrane protein (By similarity). Secreted protein (By simi ...				536
P05546 UniProt NPD GO	HEP2_HUMAN	Heparin cofactor 2 precursor (Heparin cofactor II) (HC-II) (Protease inhibitor leuserpin 2) (HLS2)	0.17	-	end	0		extracellular region [NAS]	142360	1JMO	499
P34004 UniProt NPD GO	FGF1_MESAU	Heparin-binding growth factor 1 precursor (HBGF-1) (Acidic fibroblast growth factor) (aFGF)	0.17	-	nuc	0					155
Q8MJ80 UniProt NPD GO	HEPC_PIG	Hepcidin precursor	0.17	-	exc	1 *	Secreted protein				82
Q7T273 UniProt NPD GO	HEPC2_BRARE	Hepcidin precursor 2	0.17	-	exc	1 *	Secreted protein				91

You are viewing entries 54351 to 54400 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.