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
Q5SD25 UniProt NPD GO	RPOA_HUPLU	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.22	-	cyt	0	Plastid; chloroplast				336
Q6CA26 UniProt NPD GO	RPB5_YARLI	DNA-directed RNA polymerases II 24 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 5)	0.22	-	nuc	0	Nucleus (By similarity)				212
Q91XC8 UniProt NPD GO	DAP1_MOUSE	Death-associated protein 1 (DAP-1)	0.22	-	nuc	0					101
P50704 UniProt NPD GO	DEF6_MOUSE	Defensin-related cryptdin 6/12 precursor	0.22	-	exc	0	Secreted protein				93
P12948 UniProt NPD GO	DHN3_HORVU	Dehydrin DHN3 (B17)	0.22	-	cyt	0					161
P30287 UniProt NPD GO	DHR25_ORYSA	Dehydrin Rab25 (Drought-resistant protein 1) (rDRP1)	0.22	-	nuc	0					228
Q8SQN2 UniProt NPD GO	DHYS_ENCCU	Deoxyhypusine synthase (EC 2.5.1.46) (DHS)	0.22	-	nuc	0					362
P54289 UniProt NPD GO	CAC2D_HUMAN	Dihydropyridine-sensitive L-type calcium channel subunits alpha-2/delta precursor [Contains: L-type ...	0.22	-	end	0	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]	114204		1091
Q6BSY5 UniProt NPD GO	DIM1_DEBHA	Dimethyladenosine transferase (EC 2.1.1.-) (S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltra ...	0.22	-	cyt	0					327
Q9H4A9 UniProt NPD GO	DPEP2_HUMAN	Dipeptidase 2 precursor (EC 3.4.13.19)	0.22	-	end	0	Membrane; lipid-anchor; GPI-anchor (By similarity)		609925		486
O95989 UniProt NPD GO	NUDT3_HUMAN	Diphosphoinositol polyphosphate phosphohydrolase 1 (EC 3.6.1.52) (DIPP-1) (Diadenosine 5',5'''-P1,P6 ...	0.22	-	nuc	0	Cytoplasm (Probable)	intracellular [ISS]	609228	2FVV	172
Q8R2U6 UniProt NPD GO	NUDT4_MOUSE	Diphosphoinositol polyphosphate phosphohydrolase 2 (EC 3.6.1.52) (DIPP-2) (Diadenosine 5',5'''-P1,P6 ...	0.22	-	nuc	0	Cytoplasm (By similarity)	intracellular [ISS]			179
Q99MY2 UniProt NPD GO	NUDT4_RAT	Diphosphoinositol polyphosphate phosphohydrolase 2 (EC 3.6.1.52) (DIPP-2) (rDIPP2) (Diadenosine 5',5 ...	0.22	-	nuc	0	Cytoplasm (By similarity)	intracellular [ISS]			179
Q8NFP7 UniProt NPD GO	NUD10_HUMAN	Diphosphoinositol polyphosphate phosphohydrolase 3 alpha (EC 3.6.1.52) (DIPP-3 alpha) (DIPP3 alpha) ...	0.22	-	cyt	0	Cytoplasm (Probable)	intracellular [ISS]	300527		164
Q75AZ9 UniProt NPD GO	DPH1_ASHGO	Diphthamide biosynthesis protein 1	0.22	-	mit	0	Cytoplasm (By similarity)				426
P18618 UniProt NPD GO	DISI_BOTAT	Disintegrin batroxostatin (Platelet aggregation activation inhibitor)	0.22	-	nuc	0	Secreted protein				71
Q92685 UniProt NPD GO	ALG3_HUMAN	Dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase (EC 2.4.1.-) (Dol-P-Man-dependent alp ...	0.22	+	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)	integral to endoplasmic reticulum membrane [NAS]	608750		438
P34822 UniProt NPD GO	DSL1_CHICK	Dorsalin-1 precursor (DSL-1)	0.22	-	nuc	0	Secreted protein				427
Q9H596 UniProt NPD GO	DUS21_HUMAN	Dual specificity protein phosphatase 21 (EC 3.1.3.48) (EC 3.1.3.16) (Low molecular weight dual speci ...	0.22	-	mit	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			190
Q9NZN4 UniProt NPD GO	EHD2_HUMAN	EH-domain-containing protein 2	0.22	-	nuc	0		nucleus [TAS]	605890		543
P49257 UniProt NPD GO	LMAN1_HUMAN	ERGIC-53 protein precursor (ER-Golgi intermediate compartment 53 kDa protein) (Lectin, mannose-bindi ...	0.22	-	cyt	1	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...	endoplasmic reticulum membrane [TAS] ER-Golgi intermediate compartment [IDA] Golgi membrane [TAS] integral to membrane [TAS]	601567		510
Q41701 UniProt NPD GO	NO12_VICSA	Early nodulin 12 precursor (N-12)	0.22	-	exc	1 *	Cell wall (Potential)				100
Q62630 UniProt NPD GO	EGLN3_RAT	Egl nine homolog 3, mitochondrial precursor (EC 1.14.11.-) (Hypoxia-inducible factor prolyl hydroxyl ...	0.22	-	mit	0	Mitochondrion. Cytoplasm				355
P09445 UniProt NPD GO	EF2_CRIGR	Elongation factor 2 (EF-2)	0.22	-	nuc	0	Cytoplasm				857
Q23716 UniProt NPD GO	EF2_CRYPV	Elongation factor 2 (EF-2)	0.22	-	cyt	0	Cytoplasm (By similarity)				832
P05086 UniProt NPD GO	EF2_MESAU	Elongation factor 2 (EF-2)	0.22	-	nuc	0	Cytoplasm				857
P58252 UniProt NPD GO	EF2_MOUSE	Elongation factor 2 (EF-2)	0.22	-	nuc	0	Cytoplasm				857
P05197 UniProt NPD GO	EF2_RAT	Elongation factor 2 (EF-2)	0.22	-	nuc	0	Cytoplasm				857
Q875Z2 UniProt NPD GO	EF2_SACCA	Elongation factor 2 (EF-2)	0.22	-	cyt	0	Cytoplasm (By similarity)				842
Q9FE64 UniProt NPD GO	EFGM_ORYSA	Elongation factor G, mitochondrial precursor (mEF-G)	0.22	-	nuc	0	Mitochondrion				757
P20075 UniProt NPD GO	LEAD8_DAUCA	Embryonic protein DC-8	0.22	-	nuc	0	Cytoplasm. Cell wall. Cytoplasmic, protein bodies, and cell walls of zygotic embryo and endosperm ti ...				555
Q12667 UniProt NPD GO	XYNA_PIRSP	Endo-1,4-beta-xylanase A precursor (EC 3.2.1.8) (1,4-beta-D-xylan xylanohydrolase) (Xylanase A) (XYL ...	0.22	-	exc	0					625
Q4IPN9 UniProt NPD GO	YSH1_GIBZE	Endoribonuclease YSH1 (EC 3.1.27.-) (mRNA 3'-end-processing protein YSH1)	0.22	-	end	0	Nucleus (By similarity)				864
Q6PBY3 UniProt NPD GO	EDF1_BRARE	Endothelial differentiation-related factor 1 homolog (EDF-1)	0.22	-	nuc	0	Nucleus (By similarity)				146
Q61878 UniProt NPD GO	EMBP_MOUSE	Eosinophil granule major basic protein precursor (MBP) (Proteoglycan 2, bone marrow)	0.22	-	vac	0	Matrix of eosinophil's large specific granule (crystalloid core) (By similarity)				223
P54753 UniProt NPD GO	EPHB3_HUMAN	Ephrin type-B receptor 3 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor HEK-2)	0.22	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	601839		998
P12830 UniProt NPD GO	CADH1_HUMAN	Epithelial-cadherin precursor (E-cadherin) (Uvomorulin) (Cadherin-1) (CAM 120/80) (CD324 antigen) [C ...	0.22	-	end	1	Cell membrane; cell-cell junction; single-pass type I membrane protein. Colocalizes with DLG7 at sit ...	integral to membrane [NAS]	137215	1O6S	882
O46510 UniProt NPD GO	EPB42_BOVIN	Erythrocyte membrane protein band 4.2 (Erythrocyte protein 4.2) (P4.2)	0.22	-	nuc	0	Host: Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity). Cytoplasmic surf ...				686
Q9JLN5 UniProt NPD GO	ERMAP_MOUSE	Erythroid membrane-associated protein precursor	0.22	-	mit	1 *	Cell membrane; single-pass type I membrane protein. Cytoplasm. Also found in the cytoplasm				566
Q867B1 UniProt NPD GO	EPO_HORSE	Erythropoietin precursor	0.22	-	end	0	Secreted protein				192
P07321 UniProt NPD GO	EPO_MOUSE	Erythropoietin precursor	0.22	-	exc	1 *	Secreted protein	extracellular space [IDA]			192
Q922E4 UniProt NPD GO	PCY2_MOUSE	Ethanolamine-phosphate cytidylyltransferase (EC 2.7.7.14) (Phosphorylethanolamine transferase) (CTP: ...	0.22	-	cyt	0					404
Q9ZWA2 UniProt NPD GO	ERF10_ARATH	Ethylene-responsive transcription factor 10 (Ethylene-responsive element-binding factor 10) (EREBP-1 ...	0.22	+	nuc	0	Nucleus (Probable)				245
P55877 UniProt NPD GO	IF1A_SCHPO	Eukaryotic translation initiation factor 1A (EIF-1A) (EIF-4C)	0.22	-	nuc	0					138
Q9P8P3 UniProt NPD GO	GUX1_TRIHA	Exoglucanase 1 precursor (EC 3.2.1.91) (Exoglucanase I) (Exocellobiohydrolase I) (CBHI) (1,4-beta-ce ...	0.22	-	exc	0	Secreted protein				505
Q8IX06 UniProt NPD GO	GOR_HUMAN	Exonuclease GOR (EC 3.1.-.-) (Antigen GOR) (RNA exonuclease 1 homolog-like)	0.22	-	cyt	0					318
Q9CRA8 UniProt NPD GO	EXOS5_MOUSE	Exosome complex exonuclease RRP46 (EC 3.1.13.-) (Ribosomal RNA-processing protein 46) (Exosome compo ...	0.22	-	mit	0	Nucleus; nucleolus (By similarity)				235
Q9QZM8 UniProt NPD GO	FBX17_MOUSE	F-box only protein 17 (F-box only protein 26)	0.22	-	mit	0					286
O94952 UniProt NPD GO	FBX21_HUMAN	F-box only protein 21	0.22	-	cyt	0		ubiquitin ligase complex [NAS]			621
Q8VDH1 UniProt NPD GO	FBX21_MOUSE	F-box only protein 21	0.22	-	cyt	0					627

You are viewing entries 48351 to 48400 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.