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
P30683 UniProt NPD GO	GNAO_LYMST	Guanine nucleotide-binding protein G(o) subunit alpha	0.21	-	cyt	0					353
P04695 UniProt NPD GO	GNAT1_BOVIN	Guanine nucleotide-binding protein G(t), alpha-1 subunit (Transducin alpha-1 chain)	0.21	-	gol	0				1TND	349
P19087 UniProt NPD GO	GNAT2_HUMAN	Guanine nucleotide-binding protein G(t), alpha-2 subunit (Transducin alpha-2 chain)	0.21	-	gol	0		heterotrimeric G-protein complex [NAS]	139340		353
P26308 UniProt NPD GO	GBB1_DROME	Guanine nucleotide-binding protein subunit beta 1	0.21	-	cyt	0					340
Q75BU5 UniProt NPD GO	GBG_ASHGO	Guanine nucleotide-binding protein subunit gamma	0.21	-	nuc	0	Membrane; peripheral membrane protein (By similarity)				90
Q8TGH6 UniProt NPD GO	GDA1_CANAL	Guanosine-diphosphatase (EC 3.6.1.42) (GDPase)	0.21	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				599
P70107 UniProt NPD GO	GUC2B_CAVPO	Guanylate cyclase activator 2B precursor [Contains: Uroguanylin (UGN)]	0.21	-	exc	0	Secreted protein				111
Q28358 UniProt NPD GO	GUC2B_DIDMA	Guanylate cyclase activator 2B precursor [Contains: Uroguanylin (UGN)]	0.21	-	exc	0	Secreted protein				109
O54865 UniProt NPD GO	GCYB1_MOUSE	Guanylate cyclase soluble subunit beta-1 (EC 4.6.1.2) (GCS-beta-1) (Soluble guanylate cyclase small ...	0.21	-	cyt	0	Cytoplasm (By similarity)				620
P22717 UniProt NPD GO	GCYB2_RAT	Guanylate cyclase soluble subunit beta-2 (EC 4.6.1.2) (GCS-beta-2)	0.21	-	cyt	0	Cytoplasm				682
P04223 UniProt NPD GO	HA1K_MOUSE	H-2 class I histocompatibility antigen, K-K alpha chain precursor (H-2K(K))	0.21	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]		1ZT7	369
P06343 UniProt NPD GO	HB2K_MOUSE	H-2 class II histocompatibility antigen, A-K beta chain precursor	0.21	-	end	1	Membrane; single-pass type I membrane protein (Potential)	early endosome [IDA] external side of plasma membrane [IDA] Golgi apparatus [IDA] integral to membrane [IDA] intracellular [IDA] MHC class II protein complex [IDA] multivesicular body [IDA] plasma membrane [IDA]		1JL4	263
P14439 UniProt NPD GO	HA23_MOUSE	H-2 class II histocompatibility antigen, E-U alpha chain (Fragment)	0.21	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)				229
P13747 UniProt NPD GO	HLAE_HUMAN	HLA class I histocompatibility antigen, alpha chain E precursor (MHC class I antigen E)	0.21	-	nuc	1	Membrane; single-pass type I membrane protein		143010	2ESV	358
Q95IT3 UniProt NPD GO	HLAE_PANTR	HLA class I histocompatibility antigen, alpha chain E precursor (MHC class I antigen E)	0.21	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				350
Q07093 UniProt NPD GO	GCYH_DROME	Head-specific guanylate cyclase (EC 4.6.1.2) (Gycalpha99B)	0.21	-	nuc	0	Cytoplasm (Potential)	guanylate cyclase complex, soluble [IDA]			676
P08106 UniProt NPD GO	HSP70_CHICK	Heat shock 70 kDa protein (HSP70)	0.21	-	cyt	0		cell surface [ISS] intracellular [ISS] soluble fraction [IDA]			634
P24629 UniProt NPD GO	HSP71_LYCES	Heat shock cognate 70 kDa protein 1	0.21	-	cyt	0					650
P27322 UniProt NPD GO	HSP72_LYCES	Heat shock cognate 70 kDa protein 2	0.21	-	cyt	0					644
O59838 UniProt NPD GO	HSP7F_SCHPO	Heat shock protein homolog pss1	0.21	-	cyt	0	Cytoplasm				720
Q61699 UniProt NPD GO	HS105_MOUSE	Heat-shock protein 105 kDa (Heat shock-related 100 kDa protein E7I) (HSP-E7I) (Heat shock 110 kDa pr ...	0.21	-	cyt	0	Cytoplasm. Nucleus. Strictly cytoplasmic in neurons				858
Q6DCX5 UniProt NPD GO	HCP1_XENLA	Heme carrier protein 1	0.21	-	end	10 *	Membrane; multi-pass membrane protein (By similarity)				463
Q96QI5 UniProt NPD GO	OST6_HUMAN	Heparan sulfate glucosamine 3-O-sulfotransferase 6 (EC 2.8.2.23) (Heparan sulfate D-glucosaminyl 3-O ...	0.21	-	cyt	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	integral to membrane [ISS]			342
Q8L608 UniProt NPD GO	HPSE2_ARATH	Heparanase-like protein 2 precursor (EC 3.2.-.-)	0.21	-	exc	0	Lysosome; lysosomal membrane; peripheral membrane protein (By similarity). Secreted protein (By simi ...				539
P07867 UniProt NPD GO	LIPH_RAT	Hepatic triacylglycerol lipase precursor (EC 3.1.1.3) (Hepatic lipase) (HL)	0.21	-	end	0	Secreted protein				494
O54947 UniProt NPD GO	TIMD1_RAT	Hepatitis A virus cellular receptor 1 homolog precursor (HAVcr-1) (T cell immunoglobulin and mucin d ...	0.21	-	exc	1	Membrane; single-pass type I membrane protein (Probable)				307
Q02155 UniProt NPD GO	HXK_PLAFA	Hexokinase (EC 2.7.1.1)	0.21	-	nuc	0					493
P52790 UniProt NPD GO	HXK3_HUMAN	Hexokinase-3 (EC 2.7.1.1) (Hexokinase type III) (HK III)	0.21	-	cyt	0		membrane [NAS]	142570		923
Q12300 UniProt NPD GO	RGT2_YEAST	High-affinity glucose transporter RGT2	0.21	-	end	12	Membrane; multi-pass membrane protein	plasma membrane [IMP]			763
Q5R6S5 UniProt NPD GO	HPCL4_PONPY	Hippocalcin-like protein 4	0.21	-	nuc	0					190
Q9UM19 UniProt NPD GO	HPCL4_HUMAN	Hippocalcin-like protein 4 (HLP4)	0.21	-	nuc	0					190
Q8BGZ1 UniProt NPD GO	HPCL4_MOUSE	Hippocalcin-like protein 4 (Neural visinin-like protein 2) (NVP-2)	0.21	-	nuc	0					190
P70187 UniProt NPD GO	HIAT1_MOUSE	Hippocampus abundant transcript 1 protein	0.21	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				490
P12081 UniProt NPD GO	SYH_HUMAN	Histidyl-tRNA synthetase (EC 6.1.1.21) (Histidine--tRNA ligase) (HisRS)	0.21	-	nuc	0	Cytoplasm	cytoplasm [NAS]	142810	1X59	509
P09426 UniProt NPD GO	H1_ANAPL	Histone H1	0.21	+	nuc	0	Nucleus				217
Q4WWC6 UniProt NPD GO	H2A_ASPFU	Histone H2A	0.21	-	nuc	0	Nucleus (By similarity)				132
O13413 UniProt NPD GO	H2A_ASPNG	Histone H2A	0.21	-	nuc	0	Nucleus				133
Q2U5A8 UniProt NPD GO	H2A_ASPOR	Histone H2A	0.21	-	nuc	0	Nucleus (By similarity)				132
P08844 UniProt NPD GO	H2A_EMENI	Histone H2A	0.21	-	nuc	0	Nucleus				131
P27325 UniProt NPD GO	H2A_URECA	Histone H2A	0.21	-	nuc	0	Nucleus				124
P20671 UniProt NPD GO	H2A1D_HUMAN	Histone H2A type 1-D (H2A.3)	0.21	-	nuc	0	Nucleus	nucleosome [NAS]	602792		129
Q8CGP7 UniProt NPD GO	H2A1K_MOUSE	Histone H2A type 1-K	0.21	-	nuc	0	Nucleus				129
Q7L7L0 UniProt NPD GO	H2A3_HUMAN	Histone H2A type 3	0.21	-	nuc	0	Nucleus				129
Q8BFU2 UniProt NPD GO	H2A3_MOUSE	Histone H2A type 3	0.21	-	nuc	0	Nucleus (By similarity)				129
Q4FZT6 UniProt NPD GO	H2A3_RAT	Histone H2A type 3	0.21	-	nuc	0	Nucleus				129
P27891 UniProt NPD GO	H2A1_LEIIN	Histone H2A.1	0.21	-	nuc	1 *	Nucleus				132
P02273 UniProt NPD GO	H2A1_TETPY	Histone H2A.1	0.21	-	nuc	0	Nucleus				137
P35064 UniProt NPD GO	H2A1_TETTH	Histone H2A.1	0.21	-	nuc	0	Nucleus				137
P04911 UniProt NPD GO	H2A1_YEAST	Histone H2A.1	0.21	-	nuc	0	Nucleus	nuclear nucleosome [TAS]		1ID3	131
P40281 UniProt NPD GO	H2A2_PEA	Histone H2A.2	0.21	+	mit	0	Nucleus				149

You are viewing entries 49551 to 49600 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.