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
Q9HDB8 UniProt NPD GO	ENK8_HUMAN	HERV-K_3q12.3 provirus ancestral Env polyprotein (Envelope polyprotein) (HERV-K(II) envelope protein ...	0.11	-	nuc	0					245
P02518 UniProt NPD GO	HSP27_DROME	Heat shock protein 27	0.11	-	nuc	0					213
P11500 UniProt NPD GO	HSP90_RABIT	Heat shock protein HSP 90 (Eukaryotic peptide initiation factor 2 kinase, alpha-chain-associated pho ...	0.11	-	cyt	0					46
Q07160 UniProt NPD GO	HSP20_NIPBR	Heat shock protein homolog (HSP20)	0.11	-	cyt	0					172
Q99PR8 UniProt NPD GO	HSPB2_MOUSE	Heat-shock protein beta-2 (HspB2)	0.11	-	cyt	0		soluble fraction [IDA]			182
Q9Y5Z4 UniProt NPD GO	HEBP2_HUMAN	Heme-binding protein 2 (Protein SOUL) (Placental protein 23) (PP23)	0.11	-	nuc	0	Cytoplasm (By similarity)		605609		205
Q7M419 UniProt NPD GO	GLBB_OLIMA	Hemoglobin, extracellular, major globin chain b	0.11	-	cyt	0	Secreted protein			2D2N	140
Q9PSN7 UniProt NPD GO	HRT1_CRORU	Hemorrhagic metalloproteinase HT-1 (EC 3.4.24.-) (Hemorrhagic toxin I) (Fragment)	0.11	-	nuc	0	Secreted protein				216
Q6YGZ1 UniProt NPD GO	HPSE_MOUSE	Heparanase precursor (EC 3.2.-.-) (Endo-glucoronidase) [Contains: Heparanase 8 kDa subunit; Heparana ...	0.11	-	exc	0	Lysosome; lysosomal membrane; peripheral membrane protein (By similarity). Secreted protein (By simi ...	extracellular matrix (sensu Metazoa) [TAS]			535
Q9N1S8 UniProt NPD GO	FGF1_CAPCA	Heparin-binding growth factor 1 (HBGF-1) (Fibroblast growth factor 1) (FGF-1) (Acidic fibroblast gro ...	0.11	-	nuc	0					106
Q7M303 UniProt NPD GO	FGF1_SHEEP	Heparin-binding growth factor 1 precursor (HBGF-1) (Acidic fibroblast growth factor) (aFGF)	0.11	-	nuc	0					155
P0C0K5 UniProt NPD GO	TIMD3_RAT	Hepatitis A virus cellular receptor 2 homolog (HAVcr-2) (T cell immunoglobulin and mucin domain-cont ...	0.11	-	nuc	0	Membrane; single-pass type I membrane protein (Potential)				164
P42833 UniProt NPD GO	HXT14_YEAST	Hexose transporter HXT14	0.11	-	end	12	Membrane; multi-pass membrane protein	mitochondrion [IDA]			540
P40886 UniProt NPD GO	HXT8_YEAST	Hexose transporter HXT8	0.11	-	end	10	Membrane; multi-pass membrane protein (Probable)				569
P23585 UniProt NPD GO	HXT2_YEAST	High-affinity glucose transporter HXT2	0.11	-	end	12 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			541
P21895 UniProt NPD GO	H1_CHITH	Histone H1	0.11	-	nuc	0	Nucleus				231
Q19743 UniProt NPD GO	H13_CAEEL	Histone H1.3 (Histone H1-like protein 3)	0.11	+	nuc	0	Nucleus (By similarity)				207
P04909 UniProt NPD GO	H2A1_SCHPO	Histone H2A-alpha (H2A.1)	0.11	-	nuc	0	Nucleus				131
P48003 UniProt NPD GO	H2AZ_SCHPO	Histone H2A.Z	0.11	-	cyt	0	Nucleus				171
Q32LA7 UniProt NPD GO	H2AV_BOVIN	Histone H2AV (H2A.F/Z)	0.11	-	mit	0	Nucleus (By similarity)				127
Q71PD7 UniProt NPD GO	H2AV_BRARE	Histone H2AV (H2A.F/Z)	0.11	-	mit	0	Nucleus				127
P02272 UniProt NPD GO	H2AV_CHICK	Histone H2AV (H2A.F/Z)	0.11	-	mit	0	Nucleus				127
Q71UI9 UniProt NPD GO	H2AV_HUMAN	Histone H2AV (H2A.F/Z)	0.11	-	mit	0	Nucleus (By similarity)				127
Q3THW5 UniProt NPD GO	H2AV_MOUSE	Histone H2AV (H2A.F/Z)	0.11	-	mit	0	Nucleus (By similarity)				127
Q6Y237 UniProt NPD GO	H2AV_PAGMA	Histone H2AV (H2A.F/Z)	0.11	-	mit	0	Nucleus (By similarity)				127
O62695 UniProt NPD GO	H2AV_RABIT	Histone H2AV (H2A.F/Z)	0.11	-	nuc	0	Nucleus (By similarity)				127
Q6GM74 UniProt NPD GO	H2AV_XENLA	Histone H2AV (H2A.F/Z)	0.11	-	mit	0	Nucleus (By similarity)				127
Q5BJ65 UniProt NPD GO	H2AV_XENTR	Histone H2AV (H2A.F/Z)	0.11	-	mit	0	Nucleus (By similarity)				127
P54348 UniProt NPD GO	H2B5_MAIZE	Histone H2B.5 (H2B)	0.11	+	nuc	0	Nucleus				153
Q6FXI8 UniProt NPD GO	HAT2_CANGA	Histone acetyltransferase type B subunit 2 (EC 2.3.1.48)	0.11	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				419
P56523 UniProt NPD GO	CLR3_SCHPO	Histone deacetylase clr3 (Cryptic loci regulator 3)	0.11	-	cyt	0	Nucleus (By similarity)	nucleolar chromatin [IDA]			687
Q7M426 UniProt NPD GO	DEF1_HOLDI	Holotricin-1	0.11	-	nuc	0	Secreted protein				43
Q64201 UniProt NPD GO	OTX2_RAT	Homeobox protein OTX2 (Fragment)	0.11	-	nuc	0	Nucleus (Probable)				70
Q6C791 UniProt NPD GO	LYS4_YARLI	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.11	-	mit	0	Mitochondrion (By similarity)				687
Q9SDL7 UniProt NPD GO	HMT1_ARATH	Homocysteine S-methyltransferase 1 (EC 2.1.1.10) (S-methylmethionine:homocysteine methyltransferase ...	0.11	-	cyt	0					326
Q9M1W4 UniProt NPD GO	HMT2_ARATH	Homocysteine S-methyltransferase 2 (EC 2.1.1.10) (S-methylmethionine:homocysteine methyltransferase ...	0.11	+	cyt	0					333
Q5VRH4 UniProt NPD GO	HGD_ORYSA	Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (Homogentisicase) (Homogentisate oxygenase) (Homogentis ...	0.11	-	cyt	0					470
P68425 UniProt NPD GO	TXH11_ORNHU	Huwentoxin-11 (Huwentoxin-XI) (HwTx-XI)	0.11	-	nuc	0	Secreted protein				55
Q80WM5 UniProt NPD GO	HPLN3_MOUSE	Hyaluronan and proteoglycan link protein 3 precursor (Link protein 3)	0.11	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				359
O57425 UniProt NPD GO	HAS3_CHICK	Hyaluronan synthase 3 (EC 2.4.1.212) (Hyaluronate synthase 3) (Hyaluronic acid synthase 3) (HA synth ...	0.11	-	end	3	Membrane; multi-pass membrane protein (Probable)				190
O57426 UniProt NPD GO	HAS3_XENLA	Hyaluronan synthase 3 (EC 2.4.1.212) (Hyaluronate synthase 3) (Hyaluronic acid synthase 3) (HA synth ...	0.11	-	end	3	Membrane; multi-pass membrane protein (Probable)				190
Q91ZJ9 UniProt NPD GO	HYAL1_MOUSE	Hyaluronidase-1 precursor (EC 3.2.1.35) (Hyal-1) (Hyaluronoglucosaminidase-1)	0.11	-	mit	0	Secreted protein (By similarity). Lysosome (By similarity)				462
P54839 UniProt NPD GO	HMCS_YEAST	Hydroxymethylglutaryl-CoA synthase (EC 2.3.3.10) (HMG-CoA synthase) (3-hydroxy-3-methylglutaryl coen ...	0.11	-	mit	0					491
Q8JZK9 UniProt NPD GO	HMCS1_MOUSE	Hydroxymethylglutaryl-CoA synthase, cytoplasmic (EC 2.3.3.10) (HMG-CoA synthase) (3-hydroxy-3-methyl ...	0.11	-	cyt	0	Cytoplasm (By similarity)				520
P22368 UniProt NPD GO	YPC6_CLAPU	Hypothetical 11.4 kDa protein (ORF6)	0.11	-	mit	0	Membrane; peripheral membrane protein (Potential)				103
P47184 UniProt NPD GO	YJ9V_YEAST	Hypothetical 13.9 kDa protein in THI11-HXT16 intergenic region	0.11	-	nuc	0					120
P38214 UniProt NPD GO	YBM2_YEAST	Hypothetical 16.1 kDa protein in IPP1-TTP1 intergenic region	0.11	-	nuc	0					139
P28626 UniProt NPD GO	YM26_YEAST	Hypothetical 16.9 kDa protein in IMP1-HLJ1 intergenic region (RF435)	0.11	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				145
P38267 UniProt NPD GO	YBW3_YEAST	Hypothetical 18.1 kDa protein in CYC8-RAD16 intergenic region	0.11	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				160
P34775 UniProt NPD GO	YCY1_ASTLO	Hypothetical 20.0 kDa protein in rps2-rps9 intergenic region (ORF162)	0.11	-	cyt	0	Plastid				162

You are viewing entries 62801 to 62850 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.