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
P49361 UniProt NPD GO	GCSPA_FLAPR	Glycine dehydrogenase [decarboxylating] A, mitochondrial precursor (EC 1.4.4.2) (Glycine decarboxyla ...	0.22	-	mit	0	Mitochondrion				1037
P09811 UniProt NPD GO	PYGL_RAT	Glycogen phosphorylase, liver form (EC 2.4.1.1)	0.22	-	nuc	0					849
Q06636 UniProt NPD GO	GPI11_YEAST	Glycosylphosphatidylinositol anchor biosynthesis protein 11 (PIGF homolog)	0.22	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IC]			219
O49809 UniProt NPD GO	MFPA_BRANA	Glyoxysomal fatty acid beta-oxidation multifunctional protein MFP-a [Includes: Enoyl-CoA hydratase ( ...	0.22	-	mit	0	Glyoxysome (By similarity)	glyoxysome [ISS]			725
Q91X51 UniProt NPD GO	GR65_MOUSE	Golgi reassembly-stacking protein 1 (Golgi reassembly-stacking protein of 65 kDa) (GRASP65) (Golgi p ...	0.22	-	nuc	0	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; peripherical membrane protein; cytop ...	Golgi apparatus [IDA]			445
Q5EA55 UniProt NPD GO	GOGA7_BOVIN	Golgin subfamily A member 7	0.22	-	nuc	0	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				137
Q7Z5G4 UniProt NPD GO	GOGA7_HUMAN	Golgin subfamily A member 7 (Golgi complex-associated protein of 16 kDa)	0.22	-	nuc	0	Golgi apparatus; Golgi membrane; multi-pass membrane protein		609453		137
P12837 UniProt NPD GO	GTHB_MURCI	Gonadotropin subunit beta (Gonadotropin beta chain)	0.22	-	nuc	0	Secreted protein				113
P28799 UniProt NPD GO	GRN_HUMAN	Granulins precursor (Proepithelin) (PEPI) [Contains: Acrogranin; Paragranulin; Granulin-1 (Granulin ...	0.22	-	exc	0	Secreted protein		138945	1G26	593
O13168 UniProt NPD GO	TLE1_BRARE	Groucho 1 protein (Fragment)	0.22	-	nuc	0	Nucleus (Probable)				535
P11017 UniProt NPD GO	GBB2_BOVIN	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta 2 (Transducin beta chain 2) (G protei ...	0.22	-	cyt	0		heterotrimeric G-protein complex [IDA]			326
P51875 UniProt NPD GO	GNAO_CAEEL	Guanine nucleotide-binding protein G(o) subunit alpha	0.22	-	cyt	0					353
P51877 UniProt NPD GO	GNAO_HELTI	Guanine nucleotide-binding protein G(o) subunit alpha	0.22	-	cyt	0					353
P10825 UniProt NPD GO	GNAO_XENLA	Guanine nucleotide-binding protein G(o) subunit alpha	0.22	-	cyt	0					353
Q20701 UniProt NPD GO	GPA5_CAEEL	Guanine nucleotide-binding protein alpha-5 subunit	0.22	-	nuc	0					385
P49178 UniProt NPD GO	GBB_MAIZE	Guanine nucleotide-binding protein subunit beta	0.22	-	nuc	0					380
P62881 UniProt NPD GO	GBB5_MOUSE	Guanine nucleotide-binding protein subunit beta 5 (Transducin beta chain 5) (Gbeta5)	0.22	-	cyt	0					395
P46800 UniProt NPD GO	GBLP_DICDI	Guanine nucleotide-binding protein subunit beta-like protein	0.22	-	cyt	0					329
P54406 UniProt NPD GO	GBG_CAEEL	Guanine nucleotide-binding protein subunit gamma precursor	0.22	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				62
Q9W497 UniProt NPD GO	GR05A_DROME	Gustatory receptor for trehalose (Trehalose receptor)	0.22	-	end	5	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			444
P01902 UniProt NPD GO	HA1D_MOUSE	H-2 class I histocompatibility antigen, K-D alpha chain precursor (H-2K(D))	0.22	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]		2FWO	368
P01898 UniProt NPD GO	HA10_MOUSE	H-2 class I histocompatibility antigen, Q10 alpha chain precursor	0.22	-	exc	0	Membrane; single-pass type I membrane protein				322
O42043 UniProt NPD GO	ENK7_HUMAN	HERV-K_1q23.3 provirus ancestral Env polyprotein (Envelope polyprotein) (HERV-K18 envelope protein) ...	0.22	-	end	2					560
P13763 UniProt NPD GO	HB2Q_HUMAN	HLA class II histocompatibility antigen, DP(W2) beta chain precursor (SB-2-beta)	0.22	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				258
O95757 UniProt NPD GO	HS74L_HUMAN	Heat shock 70 kDa protein 4L (Osmotic stress protein 94) (Heat shock 70-related protein APG-1)	0.22	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). May translocate to the nucleus after heat shock ...	cytoplasm [ISS] nucleus [ISS]			839
Q75E44 UniProt NPD GO	HSP75_ASHGO	Heat shock protein SSB	0.22	-	cyt	0	Cytoplasm. Associated with translating ribosomes; may bind directly to the nascent polypeptide				612
Q876N3 UniProt NPD GO	HSP75_CANGA	Heat shock protein SSB	0.22	-	cyt	0	Cytoplasm. Associated with translating ribosomes; may bind directly to the nascent polypeptide				612
Q6CQ83 UniProt NPD GO	HSP75_KLULA	Heat shock protein SSB	0.22	-	cyt	0	Cytoplasm. Associated with translating ribosomes; may bind directly to the nascent polypeptide				612
P41770 UniProt NPD GO	HSP75_KLUMA	Heat shock protein SSB	0.22	-	cyt	0	Cytoplasm. Associated with translating ribosomes; may bind directly to the nascent polypeptide				612
Q60446 UniProt NPD GO	HS105_CRIGR	Heat-shock protein 105 kDa (Heat shock 110 kDa protein)	0.22	-	nuc	0	Cytoplasm				858
Q5R606 UniProt NPD GO	HS105_PONPY	Heat-shock protein 105 kDa (Heat shock 110 kDa protein)	0.22	-	cyt	0	Cytoplasm (By similarity)				858
Q66HA8 UniProt NPD GO	HS105_RAT	Heat-shock protein 105 kDa (Heat shock 110 kDa protein)	0.22	-	cyt	0	Cytoplasm (By similarity)				858
Q92598 UniProt NPD GO	HS105_HUMAN	Heat-shock protein 105 kDa (Heat shock 110 kDa protein) (Antigen NY-CO-25)	0.22	-	cyt	0	Cytoplasm	cytoplasm [TAS]			858
Q3T0T5 UniProt NPD GO	HN1_BOVIN	Hematological and neurological expressed 1 protein	0.22	-	nuc	0	Nucleus (By similarity)				153
Q9UK76 UniProt NPD GO	HN1_HUMAN	Hematological and neurological expressed 1 protein (Androgen-regulated protein 2)	0.22	-	nuc	0	Nucleus				153
Q9ESG5 UniProt NPD GO	OST1_RAT	Heparan sulfate glucosamine 3-O-sulfotransferase 1 precursor (EC 2.8.2.23) (Heparan sulfate D-glucos ...	0.22	-	mit	0	Golgi apparatus; Golgi lumen (Probable)				311
Q8VIM0 UniProt NPD GO	TIMD3_MOUSE	Hepatitis A virus cellular receptor 2 homolog precursor (HAVcr-2) (T cell immunoglobulin and mucin d ...	0.22	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				281
P55318 UniProt NPD GO	HNF3G_HUMAN	Hepatocyte nuclear factor 3-gamma (HNF-3G) (Forkhead box protein A3) (Fork head-related protein FKH ...	0.22	+	nuc	0	Nucleus	nucleus [TAS]	602295		350
Q99020 UniProt NPD GO	ROAA_MOUSE	Heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) (CArG-binding factor-A) (CBF-A)	0.22	+	nuc	0	Nucleus (Probable)				285
P05708 UniProt NPD GO	HXK1_RAT	Hexokinase-1 (EC 2.7.1.1) (Hexokinase type I) (HK I) (Brain form hexokinase)	0.22	-	cyt	0	Mitochondrion; mitochondrial outer membrane. Its hydrophobic N-terminal sequence may be involved in ...			1BG3	918
P79945 UniProt NPD GO	PSP24_XENLA	High-affinity lysophosphatidic acid receptor (PSP24)	0.22	-	end	7 *	Membrane; multi-pass membrane protein				372
Q9Y5N1 UniProt NPD GO	HRH3_HUMAN	Histamine H3 receptor (HH3R) (G-protein coupled receptor 97)	0.22	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	604525		445
Q9EST2 UniProt NPD GO	HNMT_CAVPO	Histamine N-methyltransferase (EC 2.1.1.8) (HMT)	0.22	-	mit	0	Cytoplasm (By similarity)				292
Q6VAK4 UniProt NPD GO	HP1_ORYSA	Histidine-containing phosphotransfer protein 1 (OsHP1)	0.22	-	vac	0				1YVI	149
P38635 UniProt NPD GO	HIS9_YEAST	Histidinol-phosphatase (EC 3.1.3.15) (HolPase)	0.22	-	cyt	0		intracellular [TAS]			335
Q2KI84 UniProt NPD GO	SYH_BOVIN	Histidyl-tRNA synthetase (EC 6.1.1.21) (Histidine--tRNA ligase) (HisRS)	0.22	-	nuc	0	Cytoplasm (By similarity)				509
P34183 UniProt NPD GO	SYH_CAEEL	Histidyl-tRNA synthetase (EC 6.1.1.21) (Histidine--tRNA ligase) (HisRS)	0.22	-	mit	0					521
P07178 UniProt NPD GO	SYH_MESAU	Histidyl-tRNA synthetase (EC 6.1.1.21) (Histidine--tRNA ligase) (HisRS)	0.22	-	cyt	0					508
P93422 UniProt NPD GO	SYH_ORYSA	Histidyl-tRNA synthetase (EC 6.1.1.21) (Histidine--tRNA ligase) (HisRS)	0.22	-	cyt	0					788
Q08864 UniProt NPD GO	H11_VOLCA	Histone H1-I	0.22	-	nuc	0	Nucleus				260

You are viewing entries 48451 to 48500 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.