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
P01354 UniProt NPD GO	GAST_FELCA	Gastrin precursor [Contains: Big gastrin (Gastrin 34) (G34); Gastrin]	0.18	-	exc	0	Secreted protein				104
P32239 UniProt NPD GO	GASR_HUMAN	Gastrin/cholecystokinin type B receptor (CCK-B receptor) (CCK-BR) (Cholecystokinin-2 receptor) (CCK2 ...	0.18	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	118445	1L4T	447
Q2KHW8 UniProt NPD GO	GEMI6_BOVIN	Gem-associated protein 6 (Gemin-6)	0.18	-	nuc	0	Nucleus. Found both in the nucleoplasm and in nuclear bodies called gems (Gemini of Cajal bodies) th ...				166
Q9UKN8 UniProt NPD GO	TF3C4_HUMAN	General transcription factor 3C polypeptide 4 (EC 2.3.1.48) (Transcription factor IIIC subunit delta ...	0.18	-	nuc	0	Nucleus	transcription factor TFIIIC complex [TAS]	604892		822
Q90W22 UniProt NPD GO	GHRL_RANCA	Ghrelin precursor [Contains: Ghrelin-27; Ghrelin-28]	0.18	-	exc	1 *	Secreted protein				114
O49561 UniProt NPD GO	G2OX8_ARATH	Gibberellin 2-beta-dioxygenase 8 (EC 1.14.11.13) (Gibberellin 2-beta-hydroxylase 8) (Gibberellin 2-o ...	0.18	-	cyt	0					293
Q9H2C0 UniProt NPD GO	GAN_HUMAN	Gigaxonin (Kelch-like protein 16)	0.18	-	cyt	0		neurofilament [NAS]	605379		597
Q9ERL7 UniProt NPD GO	GMFG_MOUSE	Glia maturation factor gamma (GMF-gamma)	0.18	+	cyt	0				1WFS	142
P31371 UniProt NPD GO	FGF9_HUMAN	Glia-activating factor precursor (GAF) (Fibroblast growth factor 9) (FGF-9) (HBGF-9)	0.18	-	cyt	0	Secreted protein	extracellular space [TAS]	600921	1IHK	208
P23063 UniProt NPD GO	GLUCL_HYDCO	Glucagon-like peptide (GLP)	0.18	-	nuc	0	Secreted protein				38
P07683 UniProt NPD GO	AMYG_RHIOR	Glucoamylase 1 precursor (EC 3.2.1.3) (Gluc 1) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan gl ...	0.18	-	exc	0					604
Q92407 UniProt NPD GO	HXKG_ASPNG	Glucokinase (EC 2.7.1.2) (Glucose kinase) (GLK)	0.18	-	cyt	0					495
P97324 UniProt NPD GO	G6PD2_MOUSE	Glucose-6-phosphate 1-dehydrogenase 2 (EC 1.1.1.49) (G6PD)	0.18	-	cyt	0					512
Q00612 UniProt NPD GO	G6PD1_MOUSE	Glucose-6-phosphate 1-dehydrogenase X (EC 1.1.1.49) (G6PD)	0.18	-	cyt	0					514
Q5R7S7 UniProt NPD GO	DCE1_PONPY	Glutamate decarboxylase 1 (EC 4.1.1.15)	0.18	-	cyt	0					594
Q9LV72 UniProt NPD GO	GLR12_ARATH	Glutamate receptor 1.2 precursor (Ligand-gated ion channel 1.2)	0.18	-	end	5 *	Membrane; multi-pass membrane protein				867
P48058 UniProt NPD GO	GRIA4_HUMAN	Glutamate receptor 4 precursor (GluR-4) (GluR4) (GluR-D) (Glutamate receptor ionotropic, AMPA 4) (AM ...	0.18	-	end	4 *	Membrane; multi-pass membrane protein	plasma membrane [TAS]	138246		902
P15103 UniProt NPD GO	GLNA_BOVIN	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.18	-	cyt	0	Cytoplasm (By similarity)				372
Q8HZM5 UniProt NPD GO	GLNA_CANFA	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.18	-	cyt	0	Cytoplasm (By similarity)				372
P04773 UniProt NPD GO	GLNA_CRIGR	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.18	-	cyt	0	Cytoplasm (By similarity)				372
Q4R7U3 UniProt NPD GO	GLNA_MACFA	Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)	0.18	-	cyt	0	Cytoplasm (By similarity)				373
P47897 UniProt NPD GO	SYQ_HUMAN	Glutaminyl-tRNA synthetase (EC 6.1.1.18) (Glutamine--tRNA ligase) (GlnRS)	0.18	-	cyt	0	Cytoplasm		603727		775
Q9FEA2 UniProt NPD GO	SYE_ARATH	Glutamyl-tRNA synthetase (EC 6.1.1.17) (Glutamate--tRNA ligase) (GluRS)	0.18	+	cyt	0		chloroplast [IDA] mitochondrion [IDA]			570
P12309 UniProt NPD GO	GLRX1_PIG	Glutaredoxin-1 (Thioltransferase-1) (TTase-1)	0.18	-	cyt	0	Cytoplasm			1KTE	105
P12864 UniProt NPD GO	GLRX1_RABIT	Glutaredoxin-1 (Thioltransferase-1) (TTase-1)	0.18	-	cyt	0	Cytoplasm				106
Q923X4 UniProt NPD GO	GLRX2_MOUSE	Glutaredoxin-2, mitochondrial precursor	0.18	-	mit	0	Isoform 1: Mitochondrion. Isoform 2: Nucleus	mitochondrion [ISS] nucleus [ISS]			156
Q8HXX8 UniProt NPD GO	GCDH_MACFA	Glutaryl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.7) (GCD)	0.18	-	mit	0	Mitochondrion; mitochondrial matrix				438
P46426 UniProt NPD GO	GSTP_DIRIM	Glutathione S-transferase (EC 2.5.1.18) (GST class-pi)	0.18	-	cyt	0					208
P46433 UniProt NPD GO	GSTT4_MUSDO	Glutathione S-transferase 4 (EC 2.5.1.18) (GST class-theta)	0.18	-	cyt	0					210
P28801 UniProt NPD GO	GSTP1_BOVIN	Glutathione S-transferase P (EC 2.5.1.18) (GST class-pi)	0.18	-	cyt	0					209
P04903 UniProt NPD GO	GSTA2_RAT	Glutathione S-transferase alpha-2 (EC 2.5.1.18) (Glutathione S-transferase Ya-2) (GST Ya2) (GST 1b-1 ...	0.18	-	nuc	0	Cytoplasm				221
P48640 UniProt NPD GO	GSHRP_SOYBN	Glutathione reductase, chloroplast precursor (EC 1.8.1.7) (GR) (GRase)	0.18	-	mit	0	Plastid; chloroplast (Potential)				544
Q5EAC2 UniProt NPD GO	GSHB_BOVIN	Glutathione synthetase (EC 6.3.2.3) (Glutathione synthase) (GSH synthetase) (GSH-S)	0.18	-	cyt	0					474
Q9LMM0 UniProt NPD GO	GPAT4_ARATH	Glycerol-3-phosphate acyltransferase 4 (EC 2.3.1.15) (AtGPAT4)	0.18	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				503
Q9GJS9 UniProt NPD GO	GLRB_BOVIN	Glycine receptor beta chain precursor (Glycine receptor 58 kDa subunit)	0.18	+	end	4	Membrane; multi-pass membrane protein				497
P48167 UniProt NPD GO	GLRB_HUMAN	Glycine receptor beta chain precursor (Glycine receptor 58 kDa subunit)	0.18	+	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	138492		497
P14220 UniProt NPD GO	GLP_MOUSE	Glycophorin	0.18	-	nuc	1	Membrane; single-pass type III membrane protein	external side of plasma membrane [IDA] integral to plasma membrane [IDA]			168
P55808 UniProt NPD GO	XG_HUMAN	Glycoprotein Xg precursor (Protein PBDX)	0.18	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)	membrane [NAS]	314700		180
P12836 UniProt NPD GO	GLHA_MURCI	Glycoprotein hormones alpha chain (Gonadotropin alpha chain) (GTH-alpha)	0.18	-	nuc	0	Secreted protein				93
P27794 UniProt NPD GO	GLHA_ANGAN	Glycoprotein hormones alpha chain precursor (Gonadotropin alpha chain) (GTH-alpha)	0.18	-	exc	0	Secreted protein				117
Q9LSG3 UniProt NPD GO	QUA1_ARATH	Glycosyltransferase QUASIMODO1 (EC 2.4.1.-)	0.18	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				559
P48253 UniProt NPD GO	GTHB2_ONCMA	Gonadotropin beta-2 subunit precursor (Gonadotropin beta-II chain) (GTH-II-beta)	0.18	-	cyt	0	Secreted protein				142
P48317 UniProt NPD GO	GA45A_RAT	Growth arrest and DNA-damage-inducible protein GADD45 alpha (DNA-damage-inducible transcript 1) (DDI ...	0.18	-	cyt	0					165
Q6FPH2 UniProt NPD GO	GRPE_CANGA	GrpE protein homolog, mitochondrial precursor	0.18	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				231
Q5RDY7 UniProt NPD GO	GBB5_PONPY	Guanine nucleotide-binding protein subunit beta 5 (Transducin beta chain 5) (Gbeta5)	0.18	-	cyt	0					353
Q6PNB6 UniProt NPD GO	GBB5_RABIT	Guanine nucleotide-binding protein subunit beta 5 (Transducin beta chain 5) (Gbeta5)	0.18	-	cyt	0					353
P62882 UniProt NPD GO	GBB5_RAT	Guanine nucleotide-binding protein subunit beta 5 (Transducin beta chain 5) (Gbeta5)	0.18	-	cyt	0					353
Q80ZD0 UniProt NPD GO	GBB5_TAMST	Guanine nucleotide-binding protein subunit beta 5 (Transducin beta chain 5) (Gbeta5)	0.18	-	cyt	0					353
O24076 UniProt NPD GO	GBLP_MEDSA	Guanine nucleotide-binding protein subunit beta-like protein	0.18	-	cyt	0					325
Q6CPB4 UniProt NPD GO	GBG_KLULA	Guanine nucleotide-binding protein subunit gamma	0.18	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				90

You are viewing entries 53051 to 53100 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.