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
P02276 UniProt NPD GO	H2A2_WHEAT	Histone H2A.2.1	0.21	-	nuc	0	Nucleus				151
P54345 UniProt NPD GO	H2B2_CHLRE	Histone H2B.2 (H2B-II)	0.21	-	nuc	0	Nucleus				155
P16867 UniProt NPD GO	H2B3_VOLCA	Histone H2B.3 (H2B-III)	0.21	-	nuc	0	Nucleus				156
P54347 UniProt NPD GO	H2B4_CHLRE	Histone H2B.4 (H2B-IV)	0.21	-	nuc	0	Nucleus				152
O94244 UniProt NPD GO	HAT2_SCHPO	Histone acetyltransferase type B subunit 2 (EC 2.3.1.48)	0.21	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	Mis6-Sim4 complex [TAS]			430
P55924 UniProt NPD GO	BCD_DROSU	Homeotic protein bicoid (Fragment)	0.21	-	nuc	0	Nucleus				95
Q9Y5Z7 UniProt NPD GO	HCFC2_HUMAN	Host cell factor 2 (HCF-2) (C2 factor)	0.21	-	mit	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]	607926		792
P82960 UniProt NPD GO	TXH22_ORNHU	Huwentoxin-2 form 2 (Huwentoxin-II) (HwTx-II)	0.21	-	nuc	0	Secreted protein				37
P13563 UniProt NPD GO	HAS1_XENLA	Hyaluronan synthase 1 (EC 2.4.1.212) (Hyaluronate synthase 1) (Hyaluronic acid synthase 1) (HA synth ...	0.21	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				588
P46666 UniProt NPD GO	YCF15_MAIZE	Hypothetical 11.6 kDa protein ycf15 (ORF 99)	0.21	-	mit	0	Plastid; chloroplast				99
P47062 UniProt NPD GO	YJC8_YEAST	Hypothetical 12.9 kDa protein in MAD2-RNR2 intergenic region	0.21	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				111
P35727 UniProt NPD GO	YKG1_YEAST	Hypothetical 13.5 kDa protein in MSN4-FBA1 intergenic region	0.21	-	nuc	0		endosome [IDA]			113
P53186 UniProt NPD GO	YGD4_YEAST	Hypothetical 13.6 kDa protein in MIG1-AGA2 intergenic region	0.21	-	mit	0					121
P38258 UniProt NPD GO	YBU9_YEAST	Hypothetical 14.8 kDa protein in VPS15-YMC2 intergenic region	0.21	-	mit	2 *					127
P32859 UniProt NPD GO	YKD6_YEAST	Hypothetical 14.9 kDa protein in PTM1-IXR1 intergenic region	0.21	-	cyt	0					130
P38752 UniProt NPD GO	YHA5_YEAST	Hypothetical 15.4 kDa protein in STE20-MRP4 intergenic region	0.21	-	mit	0					130
P51208 UniProt NPD GO	YCF56_PORPU	Hypothetical 29.5 kDa protein ycf56 (ORF263)	0.21	-	nuc	0	Plastid; chloroplast				263
P36040 UniProt NPD GO	YKU6_YEAST	Hypothetical 30.7 kDa protein in STE6-LOS1 intergenic region	0.21	-	cyt	0		cytoplasm [IDA]			267
O19888 UniProt NPD GO	YCF55_CYACA	Hypothetical 36.5 kDa protein ycf55	0.21	-	end	1	Plastid; chloroplast				308
P40215 UniProt NPD GO	YM23_YEAST	Hypothetical 62.8 kDa protein in RPS16A-TIF34 intergenic region	0.21	-	mit	0		mitochondrion [IDA]			560
Q96WW0 UniProt NPD GO	YNH9_SCHPO	Hypothetical WD repeat protein C32H8.09 in chromosome II	0.21	-	mit	0					483
P92516 UniProt NPD GO	M750_ARATH	Hypothetical mitochondrial protein AtMg00750 (ORF119)	0.21	-	cyt	0	Mitochondrion (Potential)				119
P92521 UniProt NPD GO	M840_ARATH	Hypothetical mitochondrial protein AtMg00840 (ORF121b)	0.21	-	nuc	0	Mitochondrion (Potential)				121
Q10094 UniProt NPD GO	YAOF_SCHPO	Hypothetical protein C11D3.15 in chromosome I	0.21	-	cyt	0					1317
O14330 UniProt NPD GO	YB7F_SCHPO	Hypothetical protein C16E9.15 in chromosome II	0.21	-	nuc	0					75
Q10347 UniProt NPD GO	YDA5_SCHPO	Hypothetical protein C1F12.05 in chromosome I	0.21	-	nuc	0					377
O13964 UniProt NPD GO	YE44_SCHPO	Hypothetical protein C24C9.04 in chromosome I	0.21	-	nuc	0					121
Q8SW84 UniProt NPD GO	Y302_ENCCU	Hypothetical protein ECU03_0020	0.21	-	end	6 *					269
Q8SW79 UniProt NPD GO	Y308_ENCCU	Hypothetical protein ECU03_0080	0.21	-	end	5 *					225
Q8SU91 UniProt NPD GO	YAI6_ENCCU	Hypothetical protein ECU10_1860	0.21	-	cyt	0					218
Q20624 UniProt NPD GO	YL71_CAEEL	Hypothetical protein F49E2.1 in chromosome X	0.21	-	mit	0					600
Q9JHJ8 UniProt NPD GO	ICOSL_MOUSE	ICOS ligand precursor (B7 homolog 2) (B7-H2) (B7-like protein Gl50) (B7-related protein 1) (B7RP-1) ...	0.21	-	end	2 *	Membrane; single-pass type I membrane protein	extracellular region [IDA] integral to membrane [NAS]			322
P01596 UniProt NPD GO	KV1D_HUMAN	Ig kappa chain V-I region CAR	0.21	-	nuc	0		extracellular region [NAS]			107
P01605 UniProt NPD GO	KV1M_HUMAN	Ig kappa chain V-I region Lay	0.21	-	nuc	0		extracellular region [NAS]			108
P01670 UniProt NPD GO	KV3R_MOUSE	Ig kappa chain V-III region PC 6684	0.21	-	mit	0					111
P20763 UniProt NPD GO	LAC_CHICK	Ig lambda chain C region	0.21	-	nuc	0					103
P21250 UniProt NPD GO	API_ONCVO	Immunodominant antigen Ov33-3 precursor	0.21	+	exc	0	Secreted protein				235
P24071 UniProt NPD GO	FCAR_HUMAN	Immunoglobulin alpha Fc receptor precursor (IgA Fc receptor) (CD89 antigen)	0.21	-	end	0	Isoform A.1, isoform A.2, isoform A.3: Cell membrane; single-pass type I membrane protein. Isoform B ...	integral to plasma membrane [TAS] plasma membrane [TAS]	147045	1UCT	287
Q63ZR0 UniProt NPD GO	IAG2_XENLA	Implantation-associated protein homolog precursor	0.21	-	end	4	Membrane; multi-pass membrane protein (Potential)				329
Q10297 UniProt NPD GO	IMB5_SCHPO	Importin beta-5 subunit (Karyopherin beta-5 subunit) (114 kDa karyopherin)	0.21	-	nuc	0	Nucleus	nucleus [IDA]			986
Q91YE6 UniProt NPD GO	IPO9_MOUSE	Importin-9 (Importin 9a) (Imp9a) (Importin 9b) (Imp9b) (Ran-binding protein 9) (RanBP9)	0.21	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS]			1040
Q18581 UniProt NPD GO	ACN1_CAEEL	Inactive angiotensin-converting enzyme-related protein precursor (ACE-like non-metallopeptidase prot ...	0.21	-	exc	0					906
Q7YR73 UniProt NPD GO	ICOS_CANFA	Inducible T-cell co-stimulator precursor (Activation-inducible lymphocyte immunomediatory molecule) ...	0.21	-	end	1	Membrane; single-pass type I membrane protein (Potential)				208
Q9R1T7 UniProt NPD GO	ICOS_RAT	Inducible T-cell co-stimulator precursor (Activation-inducible lymphocyte immunomediatory molecule) ...	0.21	-	end	1	Membrane; single-pass type I membrane protein (Potential)				200
P07994 UniProt NPD GO	INHA_BOVIN	Inhibin alpha chain precursor	0.21	-	exc	0	Secreted protein	extracellular region [ISS]			360
Q99NI4 UniProt NPD GO	IPMK_RAT	Inositol polyphosphate multikinase (EC 2.7.1.151) (Inositol 1,3,4,6-tetrakisphosphate 5-kinase)	0.21	-	cyt	0	Nucleus (By similarity)				396
O80568 UniProt NPD GO	ITPK4_ARATH	Inositol-tetrakisphosphate 1-kinase 4 (EC 2.7.1.134) (Inositol-triphosphate 5/6-kinase 4) (EC 2.7.1. ...	0.21	-	cyt	0					488
O97937 UniProt NPD GO	INSL3_CALJA	Insulin-like 3 precursor (Leydig insulin-like peptide) (Ley-I-L) (Relaxin-like factor) [Contains: In ...	0.21	-	exc	0	Secreted protein				131
P35858 UniProt NPD GO	ALS_HUMAN	Insulin-like growth factor-binding protein complex acid labile chain precursor (ALS)	0.21	-	exc	0	Secreted protein; extracellular space	extracellular region [NAS] extracellular space [TAS] soluble fraction [TAS]	601489		605
Q9QUM0 UniProt NPD GO	ITA2B_MOUSE	Integrin alpha-IIb precursor (Platelet membrane glycoprotein IIb) (GPalpha IIb) (GPIIb) (CD41 antige ...	0.21	-	end	1	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA] focal adhesion [IDA]			1033

You are viewing entries 49601 to 49650 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.