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
P22771 UniProt NPD GO	GLRA2_RAT	Glycine receptor alpha-2* chain precursor (Neonatal isoform) (Glycine receptor strychnine-binding su ...	0.49	-	end	4	Membrane; multi-pass membrane protein				452
P13834 UniProt NPD GO	GYS1_RABIT	Glycogen [starch] synthase, muscle (EC 2.4.1.11)	0.49	-	cyt	0					734
Q8CAL5 UniProt NPD GO	GPC5_MOUSE	Glypican-5 precursor	0.49	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				572
Q9ERE4 UniProt NPD GO	GOLP3_RAT	Golgi phosphoprotein 3 (Coat-protein GPP34) (Trans-Golgi protein GMx33)	0.49	-	mit	0	Cytoplasm. Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein				298
P20718 UniProt NPD GO	GRAH_HUMAN	Granzyme H precursor (EC 3.4.21.-) (Cytotoxic T-lymphocyte proteinase) (Cathepsin G-like 2) (CTSGL2) ...	0.49	-	end	0	Cytoplasmic granule. Cytoplasmic granules of cytolytic T-lymphocytes	cytoplasm [NAS]	116831	1LXV	246
P79194 UniProt NPD GO	GHR_MACMU	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.49	-	nuc	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...				638
P49083 UniProt NPD GO	GPA1_ORYSA	Guanine nucleotide-binding protein alpha-1 subunit (GP-alpha-1) (Protein Dwarf1)	0.49	-	mit	0		heterotrimeric G-protein complex [IDA]			380
Q9JID2 UniProt NPD GO	GNA11_RAT	Guanine nucleotide-binding protein alpha-11 subunit	0.49	-	cyt	0					359
O42784 UniProt NPD GO	GPA1_COLTR	Guanine nucleotide-binding protein subunit alpha	0.49	-	cyt	0					352
Q757V8 UniProt NPD GO	GAR1_ASHGO	H/ACA ribonucleoprotein complex subunit 1 (snoRNP protein GAR1)	0.49	+	cyt	0	Nucleus; nucleolus (By similarity)				212
P61577 UniProt NPD GO	REC15_HUMAN	HERV-K_3q21.2 provirus Rec protein (HERV-K(I) Np9 protein)	0.49	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity). Shuttles between the nucleus and the ...				105
P40619 UniProt NPD GO	HMGL_IPONI	HMG1/2-like protein	0.49	-	nuc	0	Nucleus (Potential)				144
P04809 UniProt NPD GO	HSP83_DROPS	Heat shock protein 83 (HSP 82)	0.49	-	cyt	0	Cytoplasm	centrosome [ISS]			717
P23897 UniProt NPD GO	GUC2C_RAT	Heat-stable enterotoxin receptor precursor (GC-C) (Intestinal guanylate cyclase) (EC 4.6.1.2) (STA r ...	0.49	-	nuc	1	Membrane; single-pass type I membrane protein				1072
P25092 UniProt NPD GO	GUC2C_HUMAN	Heat-stable enterotoxin receptor precursor (GC-C) (Intestinal guanylate cyclase) (EC 4.6.1.2) (STA r ...	0.49	-	end	2	Membrane; single-pass type I membrane protein		601330		1073
Q15477 UniProt NPD GO	SKIV2_HUMAN	Helicase SKI2W (EC 3.6.1.-) (Helicase-like protein) (HLP)	0.49	-	nuc	0	Nucleus (Potential)		600478		1246
P82942 UniProt NPD GO	KAOU_NAJKA	Hemorrhagic metalloproteinase kaouthiagin (EC 3.4.24.-)	0.49	-	nuc	0					401
Q9Y261 UniProt NPD GO	HNF3B_HUMAN	Hepatocyte nuclear factor 3-beta (HNF-3B) (Forkhead box protein A2)	0.49	+	nuc	0	Nucleus		600288		457
P40618 UniProt NPD GO	HMGB3_CHICK	High mobility group protein B3 (High mobility group protein 4) (HMG-4) (High mobility group protein ...	0.49	+	nuc	0	Nucleus				201
O15347 UniProt NPD GO	HMGB3_HUMAN	High mobility group protein B3 (High mobility group protein 4) (HMG-4) (High mobility group protein ...	0.49	+	nuc	0	Nucleus (By similarity)		300193		199
P70174 UniProt NPD GO	HRH1_MOUSE	Histamine H1 receptor	0.49	-	end	7 *	Membrane; multi-pass membrane protein				488
Q9N2B0 UniProt NPD GO	HRH1_PONPY	Histamine H1 receptor	0.49	-	end	7 *	Membrane; multi-pass membrane protein				487
P02293 UniProt NPD GO	H2B1_YEAST	Histone H2B.1 (Suppressor of Ty protein 12)	0.49	+	nuc	0	Nucleus	nuclear nucleosome [IDA]			130
P08898 UniProt NPD GO	H3_CAEEL	Histone H3	0.49	-	nuc	0	Nucleus (By similarity)				135
P84230 UniProt NPD GO	H3_CAIMO	Histone H3	0.49	-	nuc	0	Nucleus (By similarity)				135
P84236 UniProt NPD GO	H3_DROHY	Histone H3	0.49	-	nuc	0	Nucleus (By similarity)				135
P02299 UniProt NPD GO	H3_DROME	Histone H3	0.49	-	nuc	0	Nucleus (By similarity)	nucleosome [TAS] RCAF complex [IDA]		1KNE	135
P84231 UniProt NPD GO	H3_ICTBU	Histone H3	0.49	-	nuc	0	Nucleus				135
P84234 UniProt NPD GO	H3_ONCMY	Histone H3	0.49	-	nuc	0	Nucleus				135
P84235 UniProt NPD GO	H3_PLADU	Histone H3	0.49	-	nuc	0	Nucleus (By similarity)				135
P84232 UniProt NPD GO	H3_PORAF	Histone H3	0.49	-	nuc	0	Nucleus				135
P84237 UniProt NPD GO	H3_TIGCA	Histone H3	0.49	-	nuc	0	Nucleus (By similarity)				135
P84239 UniProt NPD GO	H3_URECA	Histone H3	0.49	-	nuc	0	Nucleus (By similarity)				135
P84238 UniProt NPD GO	H3_CHITH	Histone H3 (H3)	0.49	-	nuc	0	Nucleus (By similarity)				135
P84229 UniProt NPD GO	H31_CHICK	Histone H3 (Histone H3 class I)	0.49	-	nuc	0	Nucleus			2HIO	135
P69071 UniProt NPD GO	H3_DERIM	Histone H3, embryonic	0.49	-	nuc	0	Nucleus (By similarity)				135
P69072 UniProt NPD GO	H3_LYTPI	Histone H3, embryonic	0.49	-	nuc	0	Nucleus (By similarity)				135
P69073 UniProt NPD GO	H3_PARLI	Histone H3, embryonic	0.49	-	nuc	0	Nucleus (By similarity)				135
P69074 UniProt NPD GO	H3_PISBR	Histone H3, embryonic	0.49	-	nuc	0	Nucleus (By similarity)				135
P69075 UniProt NPD GO	H3_PISOC	Histone H3, embryonic	0.49	-	nuc	0	Nucleus (By similarity)				135
P69076 UniProt NPD GO	H3_PSAMI	Histone H3, embryonic	0.49	-	nuc	0	Nucleus (By similarity)				135
P69077 UniProt NPD GO	H3_PYCHE	Histone H3, embryonic	0.49	-	nuc	0	Nucleus (By similarity)				135
P69078 UniProt NPD GO	H3_SOLST	Histone H3, embryonic	0.49	-	nuc	0	Nucleus (By similarity)				135
P69079 UniProt NPD GO	H3_STRDR	Histone H3, embryonic	0.49	-	nuc	0	Nucleus (By similarity)				135
P06352 UniProt NPD GO	H3_STRPU	Histone H3, embryonic	0.49	-	nuc	0	Nucleus (By similarity)				135
P84233 UniProt NPD GO	H31_XENLA	Histone H3.1	0.49	-	nuc	0	Nucleus			2F8N	135
P84227 UniProt NPD GO	H32_BOVIN	Histone H3.2	0.49	-	nuc	0	Nucleus				135
P84228 UniProt NPD GO	H32_MOUSE	Histone H3.2	0.49	-	nuc	0	Nucleus				135
P84243 UniProt NPD GO	H33_HUMAN	Histone H3.3	0.49	-	nuc	0	Nucleus	nucleosome [ISS]	601128		135
P84244 UniProt NPD GO	H33_MOUSE	Histone H3.3	0.49	-	nuc	0	Nucleus	Barr body [IDA] nucleosome [ISS]			135

You are viewing entries 25601 to 25650 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.