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
Q14957 UniProt NPD GO	NMDE3_HUMAN	Glutamate [NMDA] receptor subunit epsilon 3 precursor (N-methyl D-aspartate receptor subtype 2C) (NR ...	0.13	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	138254		1233
Q42472 UniProt NPD GO	DCE2_ARATH	Glutamate decarboxylase 2 (EC 4.1.1.15) (GAD 2)	0.13	-	cyt	0					494
Q64HZ8 UniProt NPD GO	DHE4_PANTR	Glutamate dehydrogenase 2, mitochondrial precursor (EC 1.4.1.3) (GDH)	0.13	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				558
Q13002 UniProt NPD GO	GRIK2_HUMAN	Glutamate receptor, ionotropic kainate 2 precursor (Glutamate receptor 6) (GluR-6) (GluR6) (Excitato ...	0.13	-	end	3	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	138244		908
P15102 UniProt NPD GO	GLNA4_PHAVU	Glutamine synthetase leaf isozyme, chloroplast precursor (EC 6.3.1.2) (Isozyme delta) (Glutamate--am ...	0.13	-	mit	0	Plastid; chloroplast				429
Q12438 UniProt NPD GO	YD010_YEAST	Glutaredoxin-like protein YDL010W precursor	0.13	-	nuc	1 *	Vacuole	vacuole (sensu Fungi) [IDA]			231
P42860 UniProt NPD GO	GSTT1_LUCCU	Glutathione S-transferase 1-1 (EC 2.5.1.18) (GST class-theta)	0.13	-	cyt	0					208
P30104 UniProt NPD GO	GSTT1_DROER	Glutathione S-transferase 1-1 (EC 2.5.1.18) (GST class-theta) (Fragment)	0.13	-	mit	0					200
P30106 UniProt NPD GO	GSTT1_DROSE	Glutathione S-transferase 1-1 (EC 2.5.1.18) (GST class-theta) (Fragment)	0.13	-	mit	0					200
P31671 UniProt NPD GO	GST28_FASHE	Glutathione S-transferase 26 kDa 7 (EC 2.5.1.18) (GST7) (FH7) (GST class-mu)	0.13	-	cyt	0					217
P26697 UniProt NPD GO	GSTA3_CHICK	Glutathione S-transferase 3 (EC 2.5.1.18) (GST-CL3) (GST class-alpha)	0.13	-	cyt	0	Cytoplasm			1VF4	228
Q7RTV2 UniProt NPD GO	GSTA5_HUMAN	Glutathione S-transferase A5-5 (EC 2.5.1.18) (GST class-alpha)	0.13	-	nuc	0	Cytoplasm (By similarity)		607605		222
Q9TSM4 UniProt NPD GO	GSTM2_MACFA	Glutathione S-transferase Mu 2 (EC 2.5.1.18) (GSTM2-2) (GST class-mu 2)	0.13	-	cyt	0	Cytoplasm				217
Q9BEB0 UniProt NPD GO	GSTM2_MACFU	Glutathione S-transferase Mu 2 (EC 2.5.1.18) (GSTM2-2) (GST class-mu 2)	0.13	-	cyt	0	Cytoplasm				217
O15770 UniProt NPD GO	GSHR_PLAF7	Glutathione reductase (EC 1.8.1.7) (GR) (GRase)	0.13	-	cyt	0	Cytoplasm (By similarity)				499
Q94655 UniProt NPD GO	GSHR_PLAFK	Glutathione reductase (EC 1.8.1.7) (GR) (GRase)	0.13	-	cyt	0	Cytoplasm			1ONF	499
Q9H4Y5 UniProt NPD GO	GSTO2_HUMAN	Glutathione transferase omega-2 (EC 2.5.1.18) (GSTO-2)	0.13	-	cyt	0					243
Q9D964 UniProt NPD GO	GATM_MOUSE	Glycine amidinotransferase, mitochondrial precursor (EC 2.1.4.1) (L-arginine:glycine amidinotransfer ...	0.13	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)	mitochondrion [IDA]			423
P50442 UniProt NPD GO	GATM_RAT	Glycine amidinotransferase, mitochondrial precursor (EC 2.1.4.1) (L-arginine:glycine amidinotransfer ...	0.13	-	mit	0	Mitochondrion; mitochondrial inner membrane				423
P37705 UniProt NPD GO	GRP3_DAUCA	Glycine-rich protein A3	0.13	-	nuc	0					195
Q925Q5 UniProt NPD GO	GPHA2_MOUSE	Glycoprotein hormone alpha-2 precursor (Thyrostimulin subunit alpha)	0.13	-	exc	0	Secreted protein (By similarity)				128
O46642 UniProt NPD GO	GLHA_EQUBU	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.13	-	exc	0	Secreted protein				120
O74234 UniProt NPD GO	NMT_CANGA	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.13	-	cyt	0	Cytoplasm				451
Q5K7E9 UniProt NPD GO	NMT_CRYNE	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.13	-	cyt	0	Cytoplasm (By similarity)				493
P34809 UniProt NPD GO	NMT_CRYNV	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.13	-	cyt	0	Cytoplasm				491
P48251 UniProt NPD GO	GTHB2_CORAU	Gonadotropin beta-2 subunit precursor (Gonadotropin beta-II chain) (GTH-II-beta)	0.13	-	exc	0	Secreted protein				142
P10256 UniProt NPD GO	GTHB2_ONCKE	Gonadotropin beta-2 subunit precursor (Gonadotropin beta-II chain) (GTH-II-beta)	0.13	-	exc	0	Secreted protein				142
P24523 UniProt NPD GO	GA45A_CRIGR	Growth arrest and DNA-damage-inducible protein GADD45 alpha (DNA-damage-inducible transcript 1) (DDI ...	0.13	-	cyt	0					165
P48316 UniProt NPD GO	GA45A_MOUSE	Growth arrest and DNA-damage-inducible protein GADD45 alpha (DNA-damage-inducible transcript 1) (DDI ...	0.13	-	cyt	0		nucleus [TAS]			165
O43047 UniProt NPD GO	GRPE_SCHPO	GrpE protein homolog, mitochondrial precursor	0.13	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				223
P50151 UniProt NPD GO	GBG10_HUMAN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-10 subunit precursor	0.13	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		604389		68
Q9NFZ2 UniProt NPD GO	GBGE_CALVI	Guanine nucleotide-binding protein gamma-e subunit precursor	0.13	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				72
P04230 UniProt NPD GO	HB21_MOUSE	H-2 class II histocompatibility antigen, E-B beta chain precursor	0.13	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				264
Q7ZVE0 UniProt NPD GO	NOLA1_BRARE	H/ACA ribonucleoprotein complex subunit 1 (Nucleolar protein family A member 1)	0.13	+	cyt	0	Nucleus; nucleolus (By similarity)				226
Q7KVQ0 UniProt NPD GO	NOLA1_DROME	H/ACA ribonucleoprotein complex subunit 1-like protein (GCR 101 snRNP)	0.13	+	cyt	0	Nucleus; nucleolus (By similarity)	small nucleolar ribonucleoprotein complex [ISS]			237
Q9CRB2 UniProt NPD GO	NOLA2_MOUSE	H/ACA ribonucleoprotein complex subunit 2 (Nucleolar protein family A member 2) (snoRNP protein NHP2 ...	0.13	-	nuc	0	Nucleus; nucleolus (By similarity). Also localized to Cajal bodies (coiled bodies) (By similarity)	small nucleolar ribonucleoprotein complex [ISS]			153
Q4QRC6 UniProt NPD GO	HBLD2_BRARE	HESB-like domain-containing protein 2, mitochondrial precursor (Iron sulfur assembly protein IscA)	0.13	-	mit	0	Mitochondrion (By similarity)				129
P16121 UniProt NPD GO	HSP70_LUPPO	Heat shock 70 kDa protein (Fragment)	0.13	-	nuc	0					257
P12795 UniProt NPD GO	HSP70_SCHJA	Heat shock 70 kDa protein (HSP70) (Fragment)	0.13	-	nuc	0					198
P12398 UniProt NPD GO	HSP77_YEAST	Heat shock protein SSC1, mitochondrial precursor (mtHSP70) (Endonuclease SceI 75 kDa subunit) (Endo. ...	0.13	-	mit	0	Mitochondrion; mitochondrial matrix. Nucleus. Detected also in the nucleus after heat shock	mitochondrial inner membrane [IDA] mitochondrial nucleoid [IDA] mitochondrion [IDA] presequence translocase-associated import m... [IPI]			654
Q12988 UniProt NPD GO	HSPB3_HUMAN	Heat-shock protein beta-3 (HspB3) (Heat shock 17 kDa protein)	0.13	-	nuc	0			604624		150
P56825 UniProt NPD GO	HCYE_SEPOF	Hemocyanin, units E and F (Fragments)	0.13	-	nuc	0					208
P09106 UniProt NPD GO	HBAT_PAPAN	Hemoglobin subunit theta-1 (Hemoglobin theta-1 chain) (Theta-1-globin)	0.13	-	cyt	0					141
P48800 UniProt NPD GO	FGF2_CHICK	Heparin-binding growth factor 2 precursor (HBGF-2) (Basic fibroblast growth factor) (BFGF)	0.13	-	cyt	0					158
P09038 UniProt NPD GO	FGF2_HUMAN	Heparin-binding growth factor 2 precursor (HBGF-2) (Basic fibroblast growth factor) (BFGF) (Prostatr ...	0.13	-	nuc	0		extracellular region [TAS] extracellular space [TAS]	134920	4FGF	155
O46559 UniProt NPD GO	LIPH_RABIT	Hepatic triacylglycerol lipase precursor (EC 3.1.1.3) (Hepatic lipase) (HL)	0.13	-	mit	0	Secreted protein (By similarity)				499
Q96D42 UniProt NPD GO	TIMD1_HUMAN	Hepatitis A virus cellular receptor 1 precursor (HAVcr-1) (T cell immunoglobulin and mucin domain-co ...	0.13	-	end	1	Membrane; single-pass type I membrane protein (Probable)		606518		359
P31942 UniProt NPD GO	HNRH3_HUMAN	Heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) (hnRNP 2H9)	0.13	-	cyt	0	Nucleus	heterogeneous nuclear ribonucleoprotein com... [NAS] nucleus [TAS]	602324		346
P12319 UniProt NPD GO	FCERA_HUMAN	High affinity immunoglobulin epsilon receptor alpha-subunit precursor (FcERI) (IgE Fc receptor, alph ...	0.13	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	147140	1RPQ	257
P12371 UniProt NPD GO	FCERA_RAT	High affinity immunoglobulin epsilon receptor alpha-subunit precursor (FcERI) (IgE Fc receptor, alph ...	0.13	-	end	1 *	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein				245

You are viewing entries 59751 to 59800 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.