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
Q6BQR8 UniProt NPD GO	DPB2_DEBHA	DNA polymerase epsilon subunit B (EC 2.7.7.7) (DNA polymerase II subunit B)	0.67	-	nuc	0	Nucleus (By similarity)				669
Q6C4J0 UniProt NPD GO	DPOE_YARLI	DNA polymerase epsilon, catalytic subunit A (EC 2.7.7.7) (DNA polymerase II subunit A)	0.67	-	nuc	0	Nucleus (By similarity)				2183
Q01941 UniProt NPD GO	DPOG_PICPA	DNA polymerase gamma (EC 2.7.7.7) (Mitochondrial DNA polymerase catalytic subunit)	0.67	-	mit	0	Mitochondrion				1012
Q7TQ07 UniProt NPD GO	DPOLN_MOUSE	DNA polymerase nu (EC 2.7.7.7)	0.67	-	cyt	0	Nucleus (By similarity)				864
P54098 UniProt NPD GO	DPOG1_HUMAN	DNA polymerase subunit gamma 1 (EC 2.7.7.7) (Mitochondrial DNA polymerase catalytic subunit) (PolG-a ...	0.67	-	mit	0	Mitochondrion	mitochondrion [TAS]	603041		1239
Q6PFE3 UniProt NPD GO	RA54B_MOUSE	DNA repair and recombination protein RAD54B (EC 3.6.1.-) (RAD54 homolog B)	0.67	-	mit	0	Nucleus (Probable)				886
P38132 UniProt NPD GO	CDC47_YEAST	DNA replication licensing factor CDC47 (Cell division control protein 47)	0.67	-	nuc	0	Nucleus (By similarity)	cytoplasm [IDA] MCM complex [IDA] nucleus [IDA] pre-replicative complex [IDA]			845
Q64399 UniProt NPD GO	TOP2B_CRILO	DNA topoisomerase 2-beta (EC 5.99.1.3) (DNA topoisomerase II, beta isozyme)	0.67	+	nuc	0	Nucleus; nucleolus				1612
Q02880 UniProt NPD GO	TOP2B_HUMAN	DNA topoisomerase 2-beta (EC 5.99.1.3) (DNA topoisomerase II, beta isozyme)	0.67	+	nuc	0	Cytoplasm. Nucleus; nucleolus		126431		1626
Q60611 UniProt NPD GO	SATB1_MOUSE	DNA-binding protein SATB1 (Special AT-rich sequence-binding protein 1)	0.67	-	nuc	0	Nucleus	nuclear heterochromatin [IDA]			764
P58132 UniProt NPD GO	RPOC2_ASTLO	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.67	-	nuc	0	Plastid				817
P06274 UniProt NPD GO	RPOC2_MARPO	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.67	-	nuc	0	Plastid; chloroplast				1386
Q28811 UniProt NPD GO	PHR_POTTR	Deoxyribodipyrimidine photo-lyase (EC 4.1.99.3) (DNA photolyase) (Photoreactivating enzyme)	0.67	+	cyt	0					532
Q04960 UniProt NPD GO	DNJH_CUCSA	DnaJ protein homolog (DNAJ-1)	0.67	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				413
Q9JIM0 UniProt NPD GO	MRE11_RAT	Double-strand break repair protein MRE11A (MRE11 homolog 1) (MRE11 meiotic recombination 11 homolog ...	0.67	-	nuc	0	Nucleus (By similarity). Localizes to discrete nuclear foci after treatment with genotoxic agents (B ...	Mre11 complex [TAS]			706
Q9VQH2 UniProt NPD GO	DUOX_DROME	Dual oxidase (EC 1.6.3.1) (EC 1.11.1.-)	0.67	+	end	6	Membrane; multi-pass membrane protein (Potential)	apical plasma membrane [ISS]			1475
Q39575 UniProt NPD GO	DYHG_CHLRE	Dynein gamma chain, flagellar outer arm	0.67	-	nuc	0	Flagellum				4485
Q9D2N4 UniProt NPD GO	DTNA_MOUSE	Dystrobrevin alpha (Alpha-dystrobrevin)	0.67	-	nuc	0	Cytoplasm	dystrobrevin complex [NAS] microsome [IDA] sarcolemma [TAS] synapse [IDA]			746
Q9Y4J8 UniProt NPD GO	DTNA_HUMAN	Dystrobrevin alpha (Dystrobrevin-alpha) (Dystrophin-related protein 3)	0.67	-	nuc	0	Cytoplasm		606617		743
O23115 UniProt NPD GO	EIL2_ARATH	ETHYLENE-INSENSITIVE3-like 2 protein	0.67	-	nuc	0	Nucleus (By similarity)				518
P34910 UniProt NPD GO	EVI2B_HUMAN	EVI2B protein precursor (Ecotropic viral integration site 2B protein)	0.67	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	158381		448
P43301 UniProt NPD GO	EGR3_RAT	Early growth response protein 3 (EGR-3)	0.67	-	nuc	0	Nucleus (Probable)				387
Q06889 UniProt NPD GO	EGR3_HUMAN	Early growth response protein 3 (EGR-3) (Zinc finger protein pilot)	0.67	-	nuc	0	Nucleus (Probable)		602419		387
Q14641 UniProt NPD GO	INSL4_HUMAN	Early placenta insulin-like peptide precursor (EPIL) (Placentin) (Insulin-like peptide 4) [Contains: ...	0.67	-	exc	0	Secreted protein (By similarity)	extracellular space [TAS] soluble fraction [TAS]	600910		139
P45447 UniProt NPD GO	E78C_DROME	Ecdysone-induced protein 78C (DR-78)	0.67	-	nuc	0	Nucleus (Probable)				866
Q63190 UniProt NPD GO	EMD_RAT	Emerin	0.67	-	nuc	1	Nucleus; nuclear inner membrane; single-pass membrane protein; nucleoplasmic side (By similarity)	integral to membrane [IDA] nuclear envelope [IDA] spindle [IDA]			260
O55196 UniProt NPD GO	ENAM_MOUSE	Enamelin precursor	0.67	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [ISS]			1274
Q09907 UniProt NPD GO	END3_SCHPO	Endonuclease III homolog (EC 4.2.99.18) (DNA-(apurinic or apyrimidinic site) lyase)	0.67	-	nuc	0		nucleus [IDA]			355
P09558 UniProt NPD GO	EDN1_PIG	Endothelin-1 precursor (ET-1) (Preproendothelin-1) (PPET1) [Contains: Big endothelin-1]	0.67	-	nuc	0	Secreted protein				203
O54923 UniProt NPD GO	EXOC6_RAT	Exocyst complex component 6 (Exocyst complex component Sec15A) (Sec15-like 1) (rSec15)	0.67	-	cyt	0					804
P48778 UniProt NPD GO	GOR_PANTR	Exonuclease GOR (EC 3.1.-.-) (Antigen GOR) (RNA exonuclease 1 homolog-like)	0.67	-	nuc	0					427
Q4KLY2 UniProt NPD GO	FBX46_RAT	F-box only protein 46	0.67	-	nuc	0					603
Q6PJ61 UniProt NPD GO	FBX46_HUMAN	F-box only protein 46 (F-box only protein 34-like)	0.67	-	nuc	0			609117		646
Q7Z6J6 UniProt NPD GO	FRMD5_HUMAN	FERM domain-containing protein 5	0.67	-	gol	1	Membrane; single-pass membrane protein (Potential)				570
P42345 UniProt NPD GO	FRAP_HUMAN	FKBP12-rapamycin complex-associated protein (FK506-binding protein 12-rapamycin complex-associated p ...	0.67	-	end	0		cytoplasm [IDA] membrane [IDA] phosphoinositide 3-kinase complex [NAS]	601231	4FAP	2549
P10552 UniProt NPD GO	FMRF_DROME	FMRFamide-related peptides precursor [Contains: FMRFamide A; Corticotropin-releasing factor-like; AA ...	0.67	-	nuc	0	Secreted protein				347
O95073 UniProt NPD GO	FSBP_HUMAN	Fibrinogen silencer-binding protein	0.67	-	nuc	0	Nucleus (Potential)				299
Q92915 UniProt NPD GO	FGF14_HUMAN	Fibroblast growth factor 14 (FGF-14) (Fibroblast growth factor homologous factor 4) (FHF-4)	0.67	-	nuc	0	Nucleus (Probable)		609307		247
P63075 UniProt NPD GO	FGF17_MOUSE	Fibroblast growth factor 17 precursor (FGF-17)	0.67	-	exc	0	Secreted protein (By similarity)				216
P63076 UniProt NPD GO	FGF17_RAT	Fibroblast growth factor 17 precursor (FGF-17)	0.67	-	exc	0	Secreted protein				216
Q52RG8 UniProt NPD GO	FRS3_RAT	Fibroblast growth factor receptor substrate 3 (FGFR substrate 3) (Suc1-associated neurotrophic facto ...	0.67	-	nuc	0	Membrane; lipid-anchor (By similarity)				491
Q02435 UniProt NPD GO	BFSP1_RAT	Filensin (Beaded filament structural protein 1) (Lens fiber cell beaded-filament structural protein ...	0.67	-	nuc	0	Membrane. Cytoplasm. Membrane- and cytoskeleton-associated				617
Q07472 UniProt NPD GO	MADS1_PETHY	Floral homeotic protein PMADS 1 (Green petal homeotic protein)	0.67	-	nuc	0	Nucleus				231
O04425 UniProt NPD GO	FCA_ARATH	Flowering time control protein FCA	0.67	-	nuc	0					747
Q02361 UniProt NPD GO	FD3_DROME	Fork head domain-containing protein FD3	0.67	-	nuc	0	Nucleus				456
Q01167 UniProt NPD GO	FOXK2_HUMAN	Forkhead box protein K2 (Interleukin enhancer-binding factor 1) (Cellular transcription factor ILF-1 ...	0.67	-	mit	0	Nucleus	nucleus [TAS]	147685	2C6Y	655
P97711 UniProt NPD GO	GRK6_RAT	G protein-coupled receptor kinase 6 (EC 2.7.11.16) (G protein-coupled receptor kinase GRK6)	0.67	+	cyt	0	Membrane; lipid-anchor				576
Q8CJ12 UniProt NPD GO	GPR64_MOUSE	G-protein coupled receptor 64 precursor (Epididymis-specific protein 6) (Me6 receptor)	0.67	-	end	7 *	Membrane; multi-pass membrane protein				1009
Q13569 UniProt NPD GO	TDG_HUMAN	G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.-)	0.67	-	nuc	0	Nucleus	nucleoplasm [TAS]	601423	2D07	410
P87049 UniProt NPD GO	CGP1_SCHPO	G1/S-specific cyclin pas1	0.67	-	exc	0					411

You are viewing entries 15201 to 15250 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.