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
Q2HJF2 UniProt NPD GO	FXL22_BOVIN	F-box/LRR-repeat protein 22 (F-box and leucine-rich repeat protein 22)	0.38	-	nuc	0					226
Q4IJU0 UniProt NPD GO	POB3_GIBZE	FACT complex subunit POB3 (Facilitates chromatin transcription complex subunit POB3)	0.38	+	mit	0	Nucleus (By similarity)				569
Q6CWD7 UniProt NPD GO	POB3_KLULA	FACT complex subunit POB3 (Facilitates chromatin transcription complex subunit POB3)	0.38	+	nuc	0	Nucleus (By similarity)				555
Q04636 UniProt NPD GO	POB3_YEAST	FACT complex subunit POB3 (Facilitates chromatin transcription complex subunit POB3)	0.38	+	cyt	0	Nucleus. Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci	FACT complex [IDA] nucleus [IPI]		2GCL	552
P50448 UniProt NPD GO	F12AI_BOVIN	Factor XIIa inhibitor precursor (XIIaINH)	0.38	-	end	0					468
P50652 UniProt NPD GO	FANCC_MOUSE	Fanconi anemia group C protein homolog (Protein FACC)	0.38	-	cyt	0	Nucleus (By similarity). Major form. Cytoplasm (By similarity). Minor form				591
P05369 UniProt NPD GO	FPPS_RAT	Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) (Choleste ...	0.38	-	mit	0	Cytoplasm				353
Q10289 UniProt NPD GO	FAS2_SCHPO	Fatty acid synthase subunit alpha (EC 2.3.1.86) (p190/210) [Includes: Acyl carrier; 3-oxoacyl-[acyl- ...	0.38	-	nuc	0		fatty acid synthase complex [IDA]			1842
Q9V9S8 UniProt NPD GO	HEMH_DROME	Ferrochelatase, mitochondrial precursor (EC 4.99.1.1) (Protoheme ferro-lyase) (Heme synthetase)	0.38	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side (By similarity ...				384
P02678 UniProt NPD GO	FIBB_PETMA	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragments)	0.38	-	nuc	0	Secreted protein			1N73	477
P29251 UniProt NPD GO	FAS_PNECA	Folic acid synthesis protein [Includes: Dihydroneopterin aldolase (EC 4.1.2.25) (DHNA) (FASA) (FASB) ...	0.38	-	cyt	0					740
Q9YHV4 UniProt NPD GO	FST_BRARE	Follistatin precursor (FS) (Activin-binding protein)	0.38	-	exc	0					322
Q14192 UniProt NPD GO	FHL2_HUMAN	Four and a half LIM domains protein 2 (FHL-2) (Skeletal muscle LIM-protein 3) (SLIM 3) (LIM-domain p ...	0.38	-	nuc	0	Cytoplasm. Nucleus	nucleus [TAS]	602633	1X4L	279
Q13643 UniProt NPD GO	FHL3_HUMAN	Four and a half LIM domains protein 3 (FHL-3) (Skeletal muscle LIM-protein 2) (SLIM 2)	0.38	-	nuc	0			602790	2CUQ	280
O77438 UniProt NPD GO	FRIZ3_DROME	Frizzled-3 precursor (dFz3)	0.38	-	end	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			581
Q9NBW1 UniProt NPD GO	FRIZ4_DROME	Frizzled-4 precursor (dFz4)	0.38	-	end	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			705
P23188 UniProt NPD GO	FURIN_MOUSE	Furin precursor (EC 3.4.21.75) (Paired basic amino acid residue cleaving enzyme) (PACE) (Dibasic-pro ...	0.38	-	end	2 *	Golgi apparatus; trans-Golgi network. Seems to be localized intracellularly to the trans Golgi netwo ...	early endosome [TAS] integral to membrane [TAS] trans-Golgi network transport vesicle membrane [TAS]		1P8J	793
P23377 UniProt NPD GO	FURIN_RAT	Furin precursor (EC 3.4.21.75) (Paired basic amino acid residue cleaving enzyme) (PACE) (Dibasic-pro ...	0.38	-	end	2 *	Golgi apparatus; trans-Golgi network. Seems to be localized intracellularly to the trans Golgi netwo ...				793
Q13066 UniProt NPD GO	GAGE2_HUMAN	G antigen 2 (GAGE-2)	0.38	-	nuc	0			604244		116
Q9UEU5 UniProt NPD GO	GAGE8_HUMAN	G antigen 8 (GAGE-8)	0.38	-	nuc	0					116
Q5NVJ6 UniProt NPD GO	IRK6_PONPY	G protein-activated inward rectifier potassium channel 2 (GIRK2) (Potassium channel, inwardly rectif ...	0.38	-	end	2	Membrane; multi-pass membrane protein				423
Q9DG96 UniProt NPD GO	CCNB2_ORYLU	G2/mitotic-specific cyclin-B2	0.38	-	cyt	0					386
P43424 UniProt NPD GO	GALT_RAT	Galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (Gal-1-P uridylyltransferase) (UDP-glucose-- ...	0.38	-	cyt	0					379
Q06433 UniProt NPD GO	GAL80_KLULA	Galactose/lactose metabolism regulatory protein GAL80	0.38	-	mit	0					457
Q8HYJ5 UniProt NPD GO	FUT3_PONPY	Galactoside 3(4)-L-fucosyltransferase (EC 2.4.1.65) (Blood group Lewis alpha-4-fucosyltransferase) ( ...	0.38	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				372
Q9JHE4 UniProt NPD GO	G3ST1_MOUSE	Galactosylceramide sulfotransferase (EC 2.8.2.11) (GalCer sulfotransferase) (Cerebroside sulfotransf ...	0.38	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi membrane [TAS]			423
P10066 UniProt NPD GO	CRGB_RAT	Gamma crystallin B (Gamma crystallin 1-2)	0.38	-	nuc	0					174
Q9CXV3 UniProt NPD GO	CRGF_MOUSE	Gamma crystallin F	0.38	-	cyt	0					173
Q5RF21 UniProt NPD GO	GBRL1_PONPY	Gamma-aminobutyric acid receptor-associated protein-like 1 (GABA(A) receptor-associated protein-like ...	0.38	-	nuc	0					117
P22300 UniProt NPD GO	GBRG2_BOVIN	Gamma-aminobutyric-acid receptor gamma-2 subunit precursor (GABA(A) receptor)	0.38	-	end	4	Membrane; multi-pass membrane protein				475
Q9JLF1 UniProt NPD GO	GBRT_MOUSE	Gamma-aminobutyric-acid receptor theta subunit precursor (GABA(A) receptor)	0.38	-	end	4	Membrane; multi-pass membrane protein				638
P21292 UniProt NPD GO	GDBX_WHEAT	Gamma-gliadin precursor	0.38	-	nuc	0					302
Q2HJ66 UniProt NPD GO	CXA7_BOVIN	Gap junction alpha-7 protein	0.38	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				396
Q9D8T2 UniProt NPD GO	GSDC1_MOUSE	Gasdermin domain-containing protein 1	0.38	-	cyt	0					487
P80111 UniProt NPD GO	ANTR_RANCA	Gastrin/cholecystokinin-like peptide precursor (Antral peptide)	0.38	-	exc	0					102
P55229 UniProt NPD GO	GLGL1_ARATH	Glucose-1-phosphate adenylyltransferase large subunit 1, chloroplast precursor (EC 2.7.7.27) (ADP-gl ...	0.38	-	mit	0	Plastid; chloroplast				522
P48826 UniProt NPD GO	G6PD_ASPNG	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD)	0.38	-	cyt	0					510
O00091 UniProt NPD GO	G6PD_SCHPO	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD)	0.38	-	cyt	0					500
Q03460 UniProt NPD GO	GLSN_MEDSA	Glutamate synthase [NADH], chloroplast precursor (EC 1.4.1.14) (NADH-GOGAT)	0.38	-	mit	0	Plastid; amyloplast (Potential)				2194
P16315 UniProt NPD GO	GLTC_WHEAT	Glutenin, low molecular weight subunit PTDUCD1 precursor	0.38	-	exc	0					295
P27472 UniProt NPD GO	GYS2_YEAST	Glycogen [starch] synthase isoform 2 (EC 2.4.1.11)	0.38	-	cyt	0		cytoplasm [IDA]			704
O18751 UniProt NPD GO	PYGM_SHEEP	Glycogen phosphorylase, muscle form (EC 2.4.1.1) (Myophosphorylase)	0.38	-	nuc	0					841
Q9LJK1 UniProt NPD GO	FUT11_ARATH	Glycoprotein 3-alpha-L-fucosyltransferase A (EC 2.4.1.214) (Core alpha-(1,3)-fucosyltransferase) (Fu ...	0.38	-	mit	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...	Golgi apparatus [TAS]			501
P78333 UniProt NPD GO	GPC5_HUMAN	Glypican-5 precursor	0.38	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	integral to plasma membrane [TAS]	602446		572
Q9H772 UniProt NPD GO	GREM2_HUMAN	Gremlin-2 precursor (Cysteine knot superfamily 1, BMP antagonist 2) (Protein related to DAN and cerb ...	0.38	-	exc	0	Secreted protein (Probable)		608832		168
P58757 UniProt NPD GO	SOM2_PANTR	Growth hormone variant precursor (GH-V) (Placenta-specific growth hormone) (Growth hormone 2)	0.38	-	exc	0	Secreted protein				217
Q9UK05 UniProt NPD GO	GDF2_HUMAN	Growth/differentiation factor 2 precursor (GDF-2) (Bone morphogenetic protein 9) (BMP-9)	0.38	-	mit	0	Secreted protein		605120	1ZKZ	429
Q6J1J2 UniProt NPD GO	GDF8_ALOLA	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.38	+	mit	0	Secreted protein (By similarity)				375
Q6UKZ8 UniProt NPD GO	GDF8_CANFA	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.38	+	mit	0	Secreted protein (By similarity)				375
Q5USV9 UniProt NPD GO	GDF8_CAPIB	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.38	+	nuc	0	Secreted protein (By similarity)				375

You are viewing entries 33401 to 33450 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.