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
Q61553 UniProt NPD GO	FSCN1_MOUSE	Fascin (Singed-like protein)	0.23	-	cyt	0		filopodium [IDA]			492
O18728 UniProt NPD GO	FSCN2_BOVIN	Fascin-2 (Retinal fascin)	0.23	-	cyt	0					492
P17663 UniProt NPD GO	FRIH1_XENLA	Ferritin heavy chain 1 (EC 1.16.3.1)	0.23	-	nuc	0					176
Q9BXU8 UniProt NPD GO	FHL17_HUMAN	Ferritin heavy polypeptide-like 17	0.23	-	cyt	1 *			300308		183
P49946 UniProt NPD GO	FRIH_SALSA	Ferritin, heavy subunit (EC 1.16.3.1) (Ferritin H)	0.23	-	nuc	0					177
P07229 UniProt NPD GO	FRI1_RANCA	Ferritin, higher subunit (EC 1.16.3.1) (Ferritin H)	0.23	-	cyt	0				1BG7	175
Q9ESL9 UniProt NPD GO	FGF20_MOUSE	Fibroblast growth factor 20 (FGF-20)	0.23	-	nuc	0	Secreted protein (By similarity)				211
Q9EST9 UniProt NPD GO	FGF20_RAT	Fibroblast growth factor 20 (FGF-20)	0.23	-	nuc	0	Secreted protein (By similarity)				212
Q03142 UniProt NPD GO	FGFR4_MOUSE	Fibroblast growth factor receptor 4 precursor (EC 2.7.10.1) (FGFR-4) (Protein-tyrosine kinase recept ...	0.23	-	end	0	Membrane; single-pass type I membrane protein				799
P12804 UniProt NPD GO	FGL2_MOUSE	Fibroleukin precursor (Fibrinogen-like protein 2) (Prothrombinase) (Cytotoxic T-lymphocyte-specific ...	0.23	-	exc	0	Secreted protein				432
Q75LI2 UniProt NPD GO	FEN1B_ORYSA	Flap endonuclease 1b (EC 3.1.-.-) (OsFEN-1b)	0.23	-	cyt	0	Nucleus (Probable)				412
P41438 UniProt NPD GO	S19A1_MOUSE	Folate transporter 1 (Solute carrier family 19 member 1) (Intestinal folate carrier protein) (IFC-1) ...	0.23	-	end	11 *	Membrane; multi-pass membrane protein (Probable)				512
Q3B7L5 UniProt NPD GO	FLCN_BOVIN	Folliculin	0.23	-	cyt	0					579
Q8QZS3 UniProt NPD GO	FLCN_MOUSE	Folliculin	0.23	-	cyt	0					579
Q28F43 UniProt NPD GO	FOXN2_XENTR	Forkhead box protein N2	0.23	-	nuc	0	Nucleus (Potential)				334
Q5TD97 UniProt NPD GO	FHL5_HUMAN	Four and a half LIM domains protein 5 (FHL-5) (Activator of cAMP-responsive element modulator in tes ...	0.23	-	nuc	0	Nucleus. Nuclei of round and elongated spermatids		605126	1X68	284
P30280 UniProt NPD GO	CCND2_MOUSE	G1/S-specific cyclin-D2	0.23	-	cyt	0					289
P81069 UniProt NPD GO	GABP3_MOUSE	GA-binding protein beta-2-1 chain (GABP subunit beta-2-1) (GABPB2-1)	0.23	-	cyt	0					414
Q6SJE0 UniProt NPD GO	GFRAL_MOUSE	GDNF family receptor alpha-like precursor	0.23	-	nuc	1	Membrane; single-pass membrane protein (Potential)				393
Q9P2T1 UniProt NPD GO	GMPR2_HUMAN	GMP reductase 2 (EC 1.7.1.7) (Guanosine 5'-monophosphate oxidoreductase 2) (Guanosine monophosphate ...	0.23	-	cyt	0				2C6Q	348
Q5A3M6 UniProt NPD GO	MCD4_CANAL	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-)	0.23	-	end	14 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				971
O82653 UniProt NPD GO	ERG_ARATH	GTP-binding protein ERG	0.23	-	mit	0					437
P70224 UniProt NPD GO	GIMA1_MOUSE	GTPase, IMAP family member 1 (Immunity-associated protein 1) (Immune-associated protein 38) (IAP38)	0.23	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein				277
Q9GKK4 UniProt NPD GO	GALK1_CANFA	Galactokinase (EC 2.7.1.6) (Galactose kinase)	0.23	-	nuc	0					392
P51570 UniProt NPD GO	GALK1_HUMAN	Galactokinase (EC 2.7.1.6) (Galactose kinase)	0.23	-	cyt	0		cytoplasm [TAS]	230200	1WUU	392
O97422 UniProt NPD GO	B3GI_DROME	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase I (EC 2.4.1.135) (Beta-1,3-glucuro ...	0.23	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)	Golgi apparatus [NAS]			306
P22466 UniProt NPD GO	GALA_HUMAN	Galanin precursor [Contains: Galanin; Galanin message-associated peptide (GMAP)]	0.23	-	exc	1 *	Secreted protein		137035		123
Q91321 UniProt NPD GO	CRG12_RANCA	Gamma crystallin M1-2 (Gamma M1-2)	0.23	-	nuc	0					177
Q8BHJ7 UniProt NPD GO	GBRA5_MOUSE	Gamma-aminobutyric-acid receptor alpha-5 subunit precursor (GABA(A) receptor)	0.23	-	mit	4	Membrane; multi-pass membrane protein				463
P19969 UniProt NPD GO	GBRA5_RAT	Gamma-aminobutyric-acid receptor alpha-5 subunit precursor (GABA(A) receptor)	0.23	-	mit	4	Membrane; multi-pass membrane protein	plasma membrane [IMP]			464
Q5T442 UniProt NPD GO	CXA12_HUMAN	Gap junction alpha-12 protein (Connexin-47) (Cx47) (Connexin-46.6) (Cx46.6)	0.23	-	end	4 *	Membrane; multi-pass membrane protein		608804		439
P41987 UniProt NPD GO	CXA3_BOVIN	Gap junction alpha-3 protein (Connexin-44) (Cx44)	0.23	-	end	3 *	Membrane; multi-pass membrane protein				406
Q9TU17 UniProt NPD GO	CXA3_SHEEP	Gap junction alpha-3 protein (Connexin-44) (Cx44)	0.23	-	end	3 *	Membrane; multi-pass membrane protein				412
Q00977 UniProt NPD GO	CXB2_MOUSE	Gap junction beta-2 protein (Connexin-26) (Cx26)	0.23	-	end	4 *	Membrane; multi-pass membrane protein	gap junction [IDA]			226
P21994 UniProt NPD GO	CXB2_RAT	Gap junction beta-2 protein (Connexin-26) (Cx26)	0.23	-	end	4 *	Membrane; multi-pass membrane protein				226
P47851 UniProt NPD GO	GRP_SHEEP	Gastrin-releasing peptide precursor (GRP) [Contains: Neuromedin C (GRP-10)]	0.23	-	nuc	0	Secreted protein				134
P56481 UniProt NPD GO	GASR_MOUSE	Gastrin/cholecystokinin type B receptor (CCK-B receptor) (CCK-BR) (Cholecystokinin-2 receptor) (CCK2 ...	0.23	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS] plasma membrane [ISS]			453
Q9CWY4 UniProt NPD GO	GEMI7_MOUSE	Gem-associated protein 7 (Gemin-7)	0.23	-	cyt	0	Nucleus (By similarity). Found both in the nucleoplasm and in nuclear bodies called gems (Gemini of ...	cytoplasm [ISS] nuclear body [ISS] nucleoplasm [ISS]			129
P53048 UniProt NPD GO	MAL11_YEAST	General alpha-glucoside permease (Maltose permease MAL11) (Maltose transport protein MAL11)	0.23	-	end	10	Membrane; multi-pass membrane protein (Potential)	membrane fraction [TAS]			616
P18207 UniProt NPD GO	GLBL_TYLHE	Giant extracellular hemoglobin linker 1 chain	0.23	-	cyt	0					253
Q8RVF5 UniProt NPD GO	GAOX2_ORYSA	Gibberellin 20 oxidase 2 (EC 1.14.11.-) (Gibberellin C-20 oxidase 2) (GA 20-oxidase 2) (Os20ox2) (Se ...	0.23	-	cyt	0					389
Q91875 UniProt NPD GO	FGF9_XENLA	Glia-activating factor precursor (GAF) (Fibroblast growth factor 9) (FGF-9) (HBGF-9) (XFGF-9)	0.23	-	cyt	0	Secreted protein				209
P79695 UniProt NPD GO	GLUC_CARAU	Glucagon precursor [Contains: Glicentin-related polypeptide (GRPP); Glucagon; Glucagon-like peptide] ...	0.23	-	exc	0	Secreted protein				121
P55238 UniProt NPD GO	GLGS_HORVU	Glucose-1-phosphate adenylyltransferase small subunit, chloroplast precursor (EC 2.7.7.27) (ADP-gluc ...	0.23	-	mit	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...				513
O55044 UniProt NPD GO	G6PD_CRIGR	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD)	0.23	-	cyt	0					514
Q42919 UniProt NPD GO	G6PD_MEDSA	Glucose-6-phosphate 1-dehydrogenase, cytoplasmic isoform (EC 1.1.1.49) (G6PD)	0.23	-	mit	0	Cytoplasm				515
P48318 UniProt NPD GO	DCE1_MOUSE	Glutamate decarboxylase 1 (EC 4.1.1.15) (Glutamate decarboxylase, 67 kDa isoform) (GAD-67) (67 kDa g ...	0.23	-	cyt	0		axon [IDA] cytoplasm [IDA] mitochondrion [IDA] synapse [IDA]			593
P48319 UniProt NPD GO	DCE1_PIG	Glutamate decarboxylase 1 (EC 4.1.1.15) (Glutamate decarboxylase, 67 kDa isoform) (GAD-67) (67 kDa g ...	0.23	-	cyt	0					594
Q9Z2W9 UniProt NPD GO	GRIA3_MOUSE	Glutamate receptor 3 precursor (GluR-3) (GluR-C) (GluR-K3) (Glutamate receptor ionotropic, AMPA 3) ( ...	0.23	-	end	3	Membrane; multi-pass membrane protein (Potential)				888
P20478 UniProt NPD GO	GLNA2_DROME	Glutamine synthetase 2 cytoplasmic (EC 6.3.1.2) (Glutamate--ammonia ligase 2)	0.23	-	cyt	0	Cytoplasm				369

You are viewing entries 47351 to 47400 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.