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
Q5XIT0 UniProt NPD GO	CDKL2_RAT	Cyclin-dependent kinase-like 2 (EC 2.7.11.22)	0.38	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				507
Q8BGE6 UniProt NPD GO	ATG4B_MOUSE	Cysteine protease ATG4B (EC 3.4.22.-) (Autophagy-related protein 4 homolog B) (Autophagin-1) (Autoph ...	0.38	-	cyt	0	Cytoplasm (Probable)	cytoplasm [ISS] cytosol [ISS] microtubule associated complex [ISS]			393
P48416 UniProt NPD GO	CP10_LYMST	Cytochrome P450 10 (EC 1.14.-.-) (CYPX)	0.38	-	mit	0					545
Q92095 UniProt NPD GO	CP1A1_OPSTA	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.38	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				521
P10632 UniProt NPD GO	CP2C8_HUMAN	Cytochrome P450 2C8 (EC 1.14.14.1) (CYPIIC8) (P450 form 1) (P450 MP-12/MP-20) (P450 IIC2) (S-mepheny ...	0.38	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	endoplasmic reticulum [NAS] microsome [NAS]	601129	1PQ2	490
Q759W0 UniProt NPD GO	CP51_ASHGO	Cytochrome P450 51 (EC 1.14.13.70) (CYPLI) (P450-LIA1) (Sterol 14-alpha demethylase) (Lanosterol 14- ...	0.38	+	mit	2 *					529
Q43147 UniProt NPD GO	C85A1_LYCES	Cytochrome P450 85A1 (EC 1.14.-.-) (C6-oxidase) (Dwarf protein)	0.38	-	nuc	1 *					464
P58266 UniProt NPD GO	CCSA_WHEAT	Cytochrome c biogenesis protein ccsA	0.38	-	end	6 *	Plastid; chloroplast				322
P04038 UniProt NPD GO	COX6C_BOVIN	Cytochrome c oxidase polypeptide VIc (EC 1.9.3.1) (STA)	0.38	-	mit	1 *	Mitochondrion; mitochondrial inner membrane			2OCC	73
Q91Y94 UniProt NPD GO	COX42_RAT	Cytochrome c oxidase subunit 4 isoform 2, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxidase ...	0.38	-	nuc	1	Mitochondrion; mitochondrial inner membrane	respiratory chain complex IV (sensu Eukaryota) [TAS]			172
Q9D0M3 UniProt NPD GO	CY1_MOUSE	Cytochrome c1, heme protein, mitochondrial precursor (Cytochrome c-1)	0.38	-	mit	1	Mitochondrion; mitochondrial intermembrane space	mitochondrion [IDA]			325
Q24298 UniProt NPD GO	CADE_DROME	DE-cadherin precursor (Protein shotgun)	0.38	-	mit	2 *	Membrane; single-pass type I membrane protein (Potential)	plasma membrane [IDA] zonula adherens [NAS]			1507
Q8LA13 UniProt NPD GO	RH11_ARATH	DEAD-box ATP-dependent RNA helicase 11 (EC 3.6.1.-)	0.38	-	cyt	0					612
Q694C4 UniProt NPD GO	ABC3G_MACNG	DNA dC->dU-editing enzyme APOBEC-3G (EC 3.5.4.-)	0.38	-	mit	0	Cytoplasm (By similarity). Mainly. Nucleus (By similarity). Small amount are found in the nucleus (B ...				383
P05725 UniProt NPD GO	DNE1_CHLRE	DNA endonuclease I-CreI (EC 3.1.-.-) (23S rRNA intron protein)	0.38	-	cyt	0	Plastid; chloroplast			1U0D	163
Q03406 UniProt NPD GO	SLD5_YEAST	DNA replication complex GINS protein SLD5	0.38	-	nuc	0	Nucleus	GINS complex [IPI]			294
Q8M9V7 UniProt NPD GO	RPOA_CHAGL	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.38	-	nuc	0	Plastid; chloroplast				334
Q8WI25 UniProt NPD GO	RPOC1_PSINU	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.38	-	cyt	0	Plastid; chloroplast				674
Q757H7 UniProt NPD GO	RPB5_ASHGO	DNA-directed RNA polymerases II 24 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 5)	0.38	-	cyt	0	Nucleus (By similarity)				215
P50708 UniProt NPD GO	DEF10_MOUSE	Defensin-related cryptdin 10 precursor (Fragment)	0.38	-	exc	0	Secreted protein				92
Q9SYS6 UniProt NPD GO	DRE1C_ARATH	Dehydration-responsive element-binding protein 1C (DREB1C protein) (C-repeat-binding factor 2) (C-re ...	0.38	-	nuc	0	Nucleus (Probable)				216
Q9NZW4 UniProt NPD GO	DSPP_HUMAN	Dentin sialophosphoprotein precursor [Contains: Dentin phosphoprotein (Dentin phosphophoryn) (DPP); ...	0.38	-	nuc	0	Secreted protein	extracellular matrix (sensu Metazoa) [TAS]	605594		1253
Q13609 UniProt NPD GO	DNSL3_HUMAN	Deoxyribonuclease gamma precursor (EC 3.1.21.-) (DNase gamma) (Deoxyribonuclease I-like 3) (DNase I ...	0.38	-	mit	0	Nucleus. May first pass through the ER membrane before being imported in the nucleus		602244		305
Q01107 UniProt NPD GO	DSC1_BOVIN	Desmocollin-1 precursor (Desmosomal glycoprotein 2/3) (DG2/DG3)	0.38	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS]			893
P63036 UniProt NPD GO	DNJA1_RAT	DnaJ homolog subfamily A member 1 (DnaJ-like protein 1)	0.38	-	cyt	0	Membrane; lipid-anchor (Potential)				397
P63037 UniProt NPD GO	DNJA1_MOUSE	DnaJ homolog subfamily A member 1 (Heat shock 40 kDa protein 4) (DnaJ protein homolog 2) (HSJ-2)	0.38	-	cyt	0	Membrane; lipid-anchor (Potential)				397
P31689 UniProt NPD GO	DNJA1_HUMAN	DnaJ homolog subfamily A member 1 (Heat shock 40 kDa protein 4) (DnaJ protein homolog 2) (HSJ-2) (HS ...	0.38	-	cyt	0	Membrane; lipid-anchor (Potential)		602837		397
Q8IS44 UniProt NPD GO	DRD2L_DROME	Dopamine D2-like receptor (DD2R)	0.38	+	end	7	Membrane; multi-pass membrane protein	integral to membrane [NAS]			506
Q14183 UniProt NPD GO	DOC2A_HUMAN	Double C2-like domain-containing protein alpha (Doc2-alpha) (Doc2)	0.38	-	nuc	0	Synaptic vesicle; synaptic vesicle membrane; peripheral membrane protein (Probable). Colocalizes to ...		604567		400
Q91836 UniProt NPD GO	TRBP_XENLA	Double-stranded RNA-binding protein A (XlRBPA)	0.38	-	nuc	0	Cytoplasm. Nucleus			1DI2	298
P45896 UniProt NPD GO	SMA3_CAEEL	Dwarfin sma-3 (MAD protein homolog 2)	0.38	-	nuc	0					393
Q99KJ8 UniProt NPD GO	DCTN2_MOUSE	Dynactin subunit 2 (Dynactin complex 50 kDa subunit) (50 kDa dynein-associated polypeptide) (p50 dyn ...	0.38	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	growth cone [IDA]			401
Q9Y7P1 UniProt NPD GO	ERO12_SCHPO	ERO1-like protein 2 precursor (EC 1.8.4.-) (Endoplasmic oxidoreductin-1-like protein B)	0.38	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side				571
Q9D8N0 UniProt NPD GO	EF1G_MOUSE	Elongation factor 1-gamma (EF-1-gamma) (eEF-1B gamma)	0.38	-	cyt	0					436
P29694 UniProt NPD GO	EF1G_RABIT	Elongation factor 1-gamma (EF-1-gamma) (eEF-1B gamma)	0.38	-	cyt	0					436
Q85FR4 UniProt NPD GO	EFTS_CYAME	Elongation factor Ts (EF-Ts)	0.38	-	cyt	0	Plastid; chloroplast				209
P04568 UniProt NPD GO	EM1_WHEAT	Em protein	0.38	-	nuc	0					93
P08110 UniProt NPD GO	ENPL_CHICK	Endoplasmin precursor (Heat shock protein 90 kDa beta member 1) (Heat shock 108 kDa protein) (HSP108 ...	0.38	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				795
Q98874 UniProt NPD GO	ERH_BRARE	Enhancer of rudimentary homolog	0.38	-	nuc	0					104
P21709 UniProt NPD GO	EPHA1_HUMAN	Ephrin type-A receptor 1 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor EPH)	0.38	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	179610		976
P29318 UniProt NPD GO	EPHA3_CHICK	Ephrin type-A receptor 3 precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor ETK1) (CEK4)	0.38	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]			983
O13097 UniProt NPD GO	EFNB1_XENLA	Ephrin-B1 precursor (EPH-related receptor tyrosine kinase ligand 2) (LERK-2) (ELK ligand) (ELK-L) (X ...	0.38	-	end	1	Membrane; single-pass type I membrane protein				327
Q40470 UniProt NPD GO	IF4A7_TOBAC	Eukaryotic initiation factor 4A-7 (EC 3.6.1.-) (ATP-dependent RNA helicase eIF4A-7) (eIF-4A-7)	0.38	-	cyt	0					413
P56821 UniProt NPD GO	IF39_TOBAC	Eukaryotic translation initiation factor 3 subunit 9 (eIF-3 eta) (eIF3 p110) (eIF3b)	0.38	-	cyt	0					719
O77783 UniProt NPD GO	EXT2_BOVIN	Exostosin-2 (EC 2.4.1.224) (EC 2.4.1.225) (Glucuronosyl-N-acetylglucosaminyl-proteoglycan/N-acetylgl ...	0.38	-	gol	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...	integral to membrane [NAS]			718
Q6P5F9 UniProt NPD GO	XPO1_MOUSE	Exportin-1 (Exp1) (Chromosome region maintenance 1 protein homolog)	0.38	-	cyt	0	Cytoplasm (By similarity). Nucleus; nucleoplasm (By similarity). Nucleus; nucleoplasm; Cajal body (B ...				1071
Q80U96 UniProt NPD GO	XPO1_RAT	Exportin-1 (Exp1) (Chromosome region maintenance 1 protein homolog)	0.38	-	cyt	0	Cytoplasm (By similarity). Nucleus; nucleoplasm (By similarity). Nucleus; nucleoplasm; Cajal body (B ...				1071
Q5RA02 UniProt NPD GO	XPOT_PONPY	Exportin-T (tRNA exportin) (Exportin(tRNA))	0.38	-	cyt	0	Nucleus. Cytoplasm. Nuclear; once bound to tRNA and Ran the complex translocates to the cytoplasm. S ...				962
Q5RDA9 UniProt NPD GO	FBX42_PONPY	F-box only protein 42	0.38	-	nuc	0					717
Q9NXK8 UniProt NPD GO	FXL12_HUMAN	F-box/LRR-repeat protein 12 (F-box and leucine-rich repeat protein 12) (F-box protein FBL12)	0.38	-	cyt	0			609079		326

You are viewing entries 33351 to 33400 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.