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
Q9WVA9 UniProt NPD GO	NPFF_RAT	FMRFamide-related peptides precursor [Contains: Neuropeptide SF (NPSF); Neuropeptide FF (NPFF); Neur ...	0.25	-	exc	0	Secreted protein				114
Q99369 UniProt NPD GO	FSH3_YEAST	Family of serine hydrolases 3 (EC 3.1.-.-)	0.25	-	cyt	0					266
P15090 UniProt NPD GO	FABPA_HUMAN	Fatty acid-binding protein, adipocyte (AFABP) (Adipocyte lipid-binding protein) (ALBP) (A-FABP)	0.25	-	cyt	0	Cytoplasm (Potential)	cytoplasm [TAS] soluble fraction [TAS]	600434	1TOW	131
Q99P60 UniProt NPD GO	FABPA_SPETR	Fatty acid-binding protein, adipocyte (AFABP) (Adipocyte lipid-binding protein) (ALBP) (A-FABP)	0.25	-	cyt	0	Cytoplasm (By similarity)				131
P38500 UniProt NPD GO	NIR_BETVE	Ferredoxin--nitrite reductase, chloroplast precursor (EC 1.7.7.1)	0.25	-	mit	0	Plastid; chloroplast (By similarity)				583
Q42997 UniProt NPD GO	NIR_ORYSA	Ferredoxin--nitrite reductase, chloroplast precursor (EC 1.7.7.1)	0.25	-	mit	0	Plastid; chloroplast (Probable)				596
P51375 UniProt NPD GO	GLTB_PORPU	Ferredoxin-dependent glutamate synthase (EC 1.4.7.1) (Fd-GOGAT)	0.25	-	cyt	0	Plastid; chloroplast; chloroplast stroma				1538
P08267 UniProt NPD GO	FRIH_CHICK	Ferritin heavy chain (EC 1.16.3.1) (Ferritin H subunit)	0.25	-	nuc	0		plasma membrane [ISS]			179
P42043 UniProt NPD GO	HEMH1_ARATH	Ferrochelatase-1, chloroplast/mitochondrial precursor (EC 4.99.1.1) (Ferrochelatase I) (Protoheme fe ...	0.25	-	cyt	1	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein. Plastid; chloroplast; chlor ...				466
O15520 UniProt NPD GO	FGF10_HUMAN	Fibroblast growth factor 10 precursor (FGF-10) (Keratinocyte growth factor 2)	0.25	-	exc	1 *	Secreted protein (Potential)	cell surface [NAS] extracellular space [TAS] nucleus [IDA]	602115	1NUN	208
Q03364 UniProt NPD GO	FGFR2_XENLA	Fibroblast growth factor receptor 2 precursor (EC 2.7.10.1) (FGFR-2)	0.25	-	end	2	Membrane; single-pass type I membrane protein				813
Q9SXQ6 UniProt NPD GO	FEN1A_ORYSA	Flap endonuclease 1a (EC 3.1.-.-) (OsFEN-1a)	0.25	-	cyt	0	Nucleus (Probable)				380
Q16595 UniProt NPD GO	FRDA_HUMAN	Frataxin, mitochondrial precursor (Friedreich ataxia protein) (Fxn) [Contains: Frataxin intermediate ...	0.25	-	mit	0	Mitochondrion. Mitochondrial and extramitochondrial	mitochondrion [TAS]	229300	1EKG	210
Q9PWH2 UniProt NPD GO	FZD10_CHICK	Frizzled-10 precursor (Fz-10) (cFz-10)	0.25	+	end	7	Membrane; multi-pass membrane protein				585
O14772 UniProt NPD GO	FPGT_HUMAN	Fucose-1-phosphate guanylyltransferase (EC 2.7.7.30) (GDP-L-fucose pyrophosphorylase) (GDP-L-fucose ...	0.25	-	cyt	0	Cytoplasm	cytoplasm [TAS]	603609		594
P11613 UniProt NPD GO	RDC1_CANFA	G-protein coupled receptor RDC1 (Chemokine orphan receptor 1)	0.25	-	end	7 *	Membrane; multi-pass membrane protein				362
Q64HP0 UniProt NPD GO	CCND1_CANFA	G1/S-specific cyclin-D1	0.25	-	cyt	0					295
P25322 UniProt NPD GO	CCND1_MOUSE	G1/S-specific cyclin-D1	0.25	-	cyt	0		cyclin-dependent protein kinase holoenzyme ... [IPI] cytosol [IDA] nucleus [IDA]			295
P34801 UniProt NPD GO	CCN2_ANTMA	G2/mitotic-specific cyclin-2	0.25	-	cyt	1					441
Q9DGA0 UniProt NPD GO	CCNB1_ORYJA	G2/mitotic-specific cyclin-B1	0.25	-	mit	0					401
P32073 UniProt NPD GO	GUAA_DICDI	GMP synthase [glutamine-hydrolyzing] (EC 6.3.5.2) (Glutamine amidotransferase) (GMP synthetase)	0.25	-	mit	0					718
Q75C82 UniProt NPD GO	GPI14_ASHGO	GPI mannosyltransferase 1 (EC 2.4.1.-) (GPI mannosyltransferase I) (GPI-MT-I) (Glycosylphosphatidyli ...	0.25	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				397
Q7SXZ1 UniProt NPD GO	PIGB_BRARE	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Phosphatidylinosi ...	0.25	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				536
Q873N2 UniProt NPD GO	GWT1_CANAL	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.25	-	end	11 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				485
O75474 UniProt NPD GO	FRAT2_HUMAN	GSK-3-binding protein FRAT2 (Frat-2)	0.25	-	nuc	0			605006		233
Q91Z61 UniProt NPD GO	DIRA1_MOUSE	GTP-binding protein Di-Ras1 (Distinct subgroup of the Ras family member 1) (Small GTP-binding tumor ...	0.25	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				198
Q91320 UniProt NPD GO	CRG11_RANCA	Gamma crystallin M1-1 (Gamma M1-1)	0.25	-	nuc	0					177
P20236 UniProt NPD GO	GBRA3_RAT	Gamma-aminobutyric-acid receptor alpha-3 subunit precursor (GABA(A) receptor)	0.25	-	end	4 *	Membrane; multi-pass membrane protein	plasma membrane [IMP]			493
O00591 UniProt NPD GO	GBRP_HUMAN	Gamma-aminobutyric-acid receptor pi subunit precursor (GABA(A) receptor)	0.25	-	mit	4	Membrane; multi-pass membrane protein		602729		440
O09028 UniProt NPD GO	GBRP_RAT	Gamma-aminobutyric-acid receptor pi subunit precursor (GABA(A) receptor)	0.25	-	end	4	Membrane; multi-pass membrane protein				440
Q9UN88 UniProt NPD GO	GBRT_HUMAN	Gamma-aminobutyric-acid receptor theta subunit precursor (GABA(A) receptor)	0.25	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	300349		632
P16863 UniProt NPD GO	CXA1_XENLA	Gap junction alpha-1 protein (Connexin-43) (Cx43)	0.25	-	end	4 *	Membrane; multi-pass membrane protein				378
P36381 UniProt NPD GO	CXA8_CHICK	Gap junction alpha-8 protein (Connexin-45.6) (Cx45.6)	0.25	-	end	4 *	Membrane; multi-pass membrane protein				399
P43218 UniProt NPD GO	GIPR_MESAU	Gastric inhibitory polypeptide receptor precursor (GIP-R) (Glucose-dependent insulinotropic polypept ...	0.25	-	end	5	Membrane; multi-pass membrane protein				462
P43219 UniProt NPD GO	GIPR_RAT	Gastric inhibitory polypeptide receptor precursor (GIP-R) (Glucose-dependent insulinotropic polypept ...	0.25	-	end	5	Membrane; multi-pass membrane protein				455
P01350 UniProt NPD GO	GAST_HUMAN	Gastrin precursor [Contains: Gastrin 71 (Component I); Gastrin 52 (G52); Big gastrin (Gastrin 34) (G ...	0.25	-	exc	0	Secreted protein		137250		101
P07492 UniProt NPD GO	GRP_HUMAN	Gastrin-releasing peptide precursor (GRP) [Contains: Neuromedin C (GRP-10)]	0.25	-	nuc	0	Secreted protein	extracellular space [IDA]	137260		148
P18716 UniProt NPD GO	ZG28_XENLA	Gastrula zinc finger protein XLCGF28.1 (Fragment)	0.25	-	nuc	0	Nucleus (Potential)				252
P18731 UniProt NPD GO	ZG62_XENLA	Gastrula zinc finger protein XLCGF62.1 (Fragment)	0.25	-	nuc	0	Nucleus (Potential)				169
Q07171 UniProt NPD GO	GELS_DROME	Gelsolin precursor	0.25	-	cyt	0	Isoform 2: Cytoplasm. Isoform 1: Secreted protein	actin filament [IDA] cytosol [IEP] extracellular region [IEP]			798
P18208 UniProt NPD GO	GLBM_TYLHE	Giant extracellular hemoglobin linker 2 chain	0.25	-	cyt	0					236
P09566 UniProt NPD GO	GLUC_LEPSP	Glucagon precursor [Contains: Glucagon; Glucagon-36 (Oxyntomodulin); Glucagon-like peptide] (Fragmen ...	0.25	-	cyt	0	Secreted protein				78
O74799 UniProt NPD GO	EXG3_SCHPO	Glucan 1,3-beta-glucosidase 3 (EC 3.2.1.58) (Exo-1,3-beta-glucanase)	0.25	-	cyt	0					464
Q14397 UniProt NPD GO	GCKR_HUMAN	Glucokinase regulatory protein (Glucokinase regulator)	0.25	-	mit	0			600842		625
P55241 UniProt NPD GO	GLGL1_MAIZE	Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplast precursor (EC 2.7.7.27) (ADP-gl ...	0.25	-	cyt	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...				516
Q43839 UniProt NPD GO	G6PDC_SOLTU	Glucose-6-phosphate 1-dehydrogenase, chloroplast precursor (EC 1.1.1.49) (G6PD)	0.25	-	mit	0	Plastid; chloroplast				577
Q9SHV1 UniProt NPD GO	GLR22_ARATH	Glutamate receptor 2.2 precursor (Ligand-gated ion channel 2.2)	0.25	-	end	4	Membrane; multi-pass membrane protein				920
Q9SHV2 UniProt NPD GO	GLR23_ARATH	Glutamate receptor 2.3 precursor (Ligand-gated ion channel 2.3)	0.25	-	end	4	Membrane; multi-pass membrane protein				895
O15217 UniProt NPD GO	GSTA4_HUMAN	Glutathione S-transferase A4-4 (EC 2.5.1.18) (GST class-alpha)	0.25	-	cyt	0	Cytoplasm		605450	1GUM	222
P48774 UniProt NPD GO	GSTM5_MOUSE	Glutathione S-transferase Mu 5 (EC 2.5.1.18) (GST class-mu 5) (Fibrous sheath component 2) (Fsc2)	0.25	-	cyt	0	Cytoplasm				224

You are viewing entries 45201 to 45250 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.