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
Q04742 UniProt NPD GO	EMX1_MOUSE	Homeobox protein EMX1 (Empty spiracles homolog 1) (Empty spiracles-like protein 1) (Fragment)	0.53	+	nuc	0	Nucleus (Probable)				66
Q28599 UniProt NPD GO	HXA5_SHEEP	Homeobox protein Hox-A5 (Fragment)	0.53	+	nuc	0	Nucleus				49
P24344 UniProt NPD GO	HXD13_CHICK	Homeobox protein Hox-D13 (Chox-4.8) (Chox-4G)	0.53	+	nuc	0	Nucleus				301
P43688 UniProt NPD GO	NKX26_MOUSE	Homeobox protein Nkx-2.6 (Homeobox protein NK-2 homolog F)	0.53	-	nuc	0	Nucleus (Probable)				289
Q94398 UniProt NPD GO	HM08_CAEEL	Homeobox protein ceh-8	0.53	+	nuc	0	Nucleus (Potential)				276
P20913 UniProt NPD GO	HM19_XENLA	Homeotic protein NRL-19 (Fragment)	0.53	+	nuc	0	Nucleus				105
P20009 UniProt NPD GO	DLL_DROME	Homeotic protein distal-less (Protein brista)	0.53	+	nuc	0	Nucleus				327
Q90850 UniProt NPD GO	HIC1_CHICK	Hypermethylated in cancer 1 protein (Hic-1) (GammaFBP) (Fragment)	0.53	-	nuc	0	Nucleus (Probable)				676
P25620 UniProt NPD GO	YCR2_YEAST	Hypothetical 13.2 kDa protein in HSP30-PMP1 intergenic region	0.53	-	nuc	0					114
P38305 UniProt NPD GO	YB44_YEAST	Hypothetical 14.2 kDa protein in RIM2-MSI1 intergenic region	0.53	-	nuc	0		cytoplasm [IDA]			123
P38450 UniProt NPD GO	YMF01_MARPO	Hypothetical 19.2 kDa protein in RPS2 3'region (ORF 168)	0.53	-	nuc	1					168
P40218 UniProt NPD GO	YM24_YEAST	Hypothetical 25.9 kDa protein in TIF34-SWP1 intergenic region	0.53	-	mit	0					223
P53234 UniProt NPD GO	YG21_YEAST	Hypothetical 32.2 kDa protein in SCM4-MUP1 intergenic region	0.53	+	nuc	0					283
P47127 UniProt NPD GO	YJ51_YEAST	Hypothetical 44.4 kDa protein in MIR1-STE18 intergenic region	0.53	-	mit	0		mitochondrion [IDA]			394
P46987 UniProt NPD GO	YJS1_YEAST	Hypothetical 69.5 kDa protein in SWE1-ATP12 intergenic region	0.53	-	nuc	0					611
P90859 UniProt NPD GO	YUES_CAEEL	Hypothetical RING finger protein F26E4.11 in chromosome I	0.53	-	end	8 *					564
Q11187 UniProt NPD GO	YPD8_CAEEL	Hypothetical protein C05D11.8	0.53	-	nuc	0					873
P34321 UniProt NPD GO	YKT0_CAEEL	Hypothetical protein C07A9.10	0.53	-	nuc	0					254
P79058 UniProt NPD GO	YF9G_SCHPO	Hypothetical protein C10F6.16 in chromosome I	0.53	-	exc	0					139
O13785 UniProt NPD GO	YEO7_SCHPO	Hypothetical protein C17G6.07c in chromosome I	0.53	-	nuc	1					222
Q10412 UniProt NPD GO	YD87_SCHPO	Hypothetical protein C1F3.07c in chromosome I	0.53	-	nuc	0					403
Q09804 UniProt NPD GO	YAB2_SCHPO	Hypothetical protein C2G11.02 in chromosome I	0.53	-	nuc	0					1318
Q10073 UniProt NPD GO	YAN8_SCHPO	Hypothetical protein C3H1.08c in chromosome I	0.53	-	nuc	1					211
Q9USJ3 UniProt NPD GO	YJ23_SCHPO	Hypothetical protein C4B3.03c in chromosome III precursor	0.53	+	end	5 *	Membrane; multi-pass membrane protein (Potential)				679
P83475 UniProt NPD GO	Y737_DROME	Hypothetical protein CG31737 in chromosome 2	0.53	-	nuc	0					263
Q8SWH4 UniProt NPD GO	Y208_ENCCU	Hypothetical protein ECU02_0080	0.53	-	cyt	0					579
Q8SVF4 UniProt NPD GO	Y608_ENCCU	Hypothetical protein ECU06_0080	0.53	-	cyt	0					580
P34434 UniProt NPD GO	YL54_CAEEL	Hypothetical protein F44E2.4	0.53	-	nuc	0					1283
Q09401 UniProt NPD GO	YRD5_CAEEL	Hypothetical protein K02A2.5 precursor	0.53	-	mit	1 *					91
P34523 UniProt NPD GO	YM62_CAEEL	Hypothetical protein K12H4.2 in chromosome III	0.53	+	mit	0					190
Q8BKC5 UniProt NPD GO	IMB3_MOUSE	Importin beta-3 (Karyopherin beta-3) (Ran-binding protein 5) (RanBP5)	0.53	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				1096
P53067 UniProt NPD GO	IMB5_YEAST	Importin beta-5 subunit (Karyopherin beta-5 subunit) (114 kDa karyopherin)	0.53	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			1004
Q8K2V6 UniProt NPD GO	IPO11_MOUSE	Importin-11 (Imp11) (Ran-binding protein 11) (RanBP11)	0.53	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				975
Q6X2S4 UniProt NPD GO	INHBA_FELCA	Inhibin beta A chain precursor (Activin beta-A chain)	0.53	+	nuc	0	Secreted protein (By similarity)				424
Q4P4C1 UniProt NPD GO	IPPK_USTMA	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.53	-	nuc	0					534
P16611 UniProt NPD GO	IBP3_PIG	Insulin-like growth factor-binding protein 3 precursor (IGFBP-3) (IBP-3) (IGF-binding protein 3)	0.53	-	exc	0	Secreted protein	extracellular region [ISS]			293
Q9D168 UniProt NPD GO	PHF22_MOUSE	Integrator complex subunit 12 (PHD finger protein 22)	0.53	-	nuc	0		integrator complex [ISS]		1WEV	461
Q62470 UniProt NPD GO	ITA3_MOUSE	Integrin alpha-3 precursor (Galactoprotein B3) (GAPB3) (VLA-3 alpha chain) (CD49c antigen) [Contains ...	0.53	-	nuc	2 *	Membrane; single-pass type I membrane protein	basolateral plasma membrane [IDA] synaptosome [IDA]			1053
P26007 UniProt NPD GO	ITA6_CHICK	Integrin alpha-6 precursor (VLA-6) [Contains: Integrin alpha-6 heavy chain; Integrin alpha-6 light c ...	0.53	-	end	1	Membrane; single-pass type I membrane protein				1072
P01562 UniProt NPD GO	IFNA1_HUMAN	Interferon alpha-1/13 precursor (Interferon alpha-D) (LeIF D)	0.53	-	exc	0	Secreted protein		147660		189
Q6XZW6 UniProt NPD GO	IFNB_TACAC	Interferon beta precursor (IFN-beta)	0.53	-	mit	0	Secreted protein				187
P79161 UniProt NPD GO	IL1A_CAPHI	Interleukin-1 alpha precursor (IL-1 alpha)	0.53	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				268
P24710 UniProt NPD GO	INVO_GALCR	Involucrin	0.53	-	exc	0	Cytoplasm. Constituent of the scaffolding of the cornified envelope				384
P14590 UniProt NPD GO	INVO_LEMCA	Involucrin	0.53	-	nuc	0	Cytoplasm. Constituent of the scaffolding of the cornified envelope				450
Q9BZI1 UniProt NPD GO	IRX2_HUMAN	Iroquois-class homeodomain protein IRX-2 (Iroquois homeobox protein 2) (Homeodomain protein IRXA2)	0.53	-	nuc	0	Nucleus (By similarity)		606198		471
Q6IG00 UniProt NPD GO	K2C4_RAT	Keratin, type II cytoskeletal 4 (Cytokeratin-4) (CK-4) (Keratin-4) (K4) (Type II keratin Kb4)	0.53	-	cyt	0		keratin filament [ISS]			536
Q60654 UniProt NPD GO	KLRA7_MOUSE	Killer cell lectin-like receptor 7 (T-cell surface glycoprotein Ly-49G) (Ly49-G antigen) (Lymphocyte ...	0.53	-	nuc	1 *	Membrane; single-pass type II membrane protein	plasma membrane [TAS]			280
P53412 UniProt NPD GO	LHX3_CHICK	LIM/homeobox protein Lhx3 (Homeobox protein LIM-3)	0.53	+	nuc	0	Nucleus (Probable)				395
Q969G2 UniProt NPD GO	LHX4_HUMAN	LIM/homeobox protein Lhx4	0.53	+	nuc	0	Nucleus (Potential)		606606		367
Q32LM6 UniProt NPD GO	LIN7A_BOVIN	LIN-7 homolog A (LIN-7A)	0.53	-	cyt	0	Cell membrane; peripheral membrane protein. Cell membrane; cell-cell junction; peripheral membrane p ...				233

You are viewing entries 23151 to 23200 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.