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
P04629 UniProt NPD GO	NTRK1_HUMAN	High affinity nerve growth factor receptor precursor (EC 2.7.10.1) (Neurotrophic tyrosine kinase rec ...	0.13	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Endocytosed to the endosomes upo ...	cytoplasm [ISS] integral to plasma membrane [TAS]	164970	1WWW	796
Q5R632 UniProt NPD GO	HPCL1_PONPY	Hippocalcin-like protein 1	0.13	-	nuc	0					192
P42324 UniProt NPD GO	HPCL1_CHICK	Hippocalcin-like protein 1 (Rem-1 protein)	0.13	-	nuc	0					192
P26631 UniProt NPD GO	ITHP_HIRMA	Hirullin P18 (Thrombin inhibitor hirullin P18) (Hirudin P18)	0.13	-	nuc	0	Secreted protein			1THR	62
P40262 UniProt NPD GO	H1E_CHIPA	Histone H1E	0.13	-	nuc	0	Nucleus				235
P02264 UniProt NPD GO	H2A_ONCMY	Histone H2A	0.13	-	mit	0	Nucleus. A secreted form has been detected in skin secretions				127
Q6PV61 UniProt NPD GO	H2A_PENVA	Histone H2A	0.13	-	mit	0	Nucleus	nucleosome [ISS]			122
P40282 UniProt NPD GO	H2A_PLAFA	Histone H2A	0.13	-	nuc	0	Nucleus				132
Q4WE68 UniProt NPD GO	H2AZ_ASPFU	Histone H2A.Z	0.13	-	cyt	0	Nucleus (By similarity)				138
Q5AUJ1 UniProt NPD GO	H2AZ_EMENI	Histone H2A.Z	0.13	-	nuc	0	Nucleus (By similarity)				136
Q8MTV8 UniProt NPD GO	H4_APLCA	Histone H4	0.13	-	cyt	0	Nucleus (By similarity)				102
P91890 UniProt NPD GO	H4_TRICD	Histone H4	0.13	-	cyt	0	Nucleus (By similarity)				102
P49775 UniProt NPD GO	HNT2_YEAST	Hit family protein 2	0.13	-	mit	0		cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA]			217
Q9UT74 UniProt NPD GO	LYS4_SCHPO	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.13	-	cyt	0	Mitochondrion (By similarity)				721
Q9FUN0 UniProt NPD GO	HMT1_MAIZE	Homocysteine S-methyltransferase 1 (EC 2.1.1.10) (S-methylmethionine:homocysteine methyltransferase ...	0.13	-	cyt	0					323
P10915 UniProt NPD GO	HPLN1_HUMAN	Hyaluronan and proteoglycan link protein 1 precursor (Proteoglycan link protein) (Cartilage link pro ...	0.13	-	exc	0		extracellular matrix (sensu Metazoa) [TAS]	115435		354
Q12320 UniProt NPD GO	GLO4_YEAST	Hydroxyacylglutathione hydrolase, mitochondrial precursor (EC 3.1.2.6) (Glyoxalase II) (Glx II)	0.13	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA] mitochondrion [IDA]			285
P13704 UniProt NPD GO	HMCS1_CRIGR	Hydroxymethylglutaryl-CoA synthase, cytoplasmic (EC 2.3.3.10) (HMG-CoA synthase) (3-hydroxy-3-methyl ...	0.13	-	cyt	0	Cytoplasm				520
Q10416 UniProt NPD GO	HYTA_APIME	Hymenoptaecin precursor	0.13	-	exc	0					129
Q01572 UniProt NPD GO	YCX1_PAVLU	Hypothetical 10.9 kDa protein in secA 5'region	0.13	-	mit	1 *	Plastid; chloroplast				93
P38223 UniProt NPD GO	YBO2_YEAST	Hypothetical 11.5 kDa protein in RPL4A-HMT1 intergenic region	0.13	-	cyt	0					100
P47080 UniProt NPD GO	YJA7_YEAST	Hypothetical 11.9 kDa protein in CCT8-CTK2 intergenic region	0.13	-	mit	1					104
P40326 UniProt NPD GO	YG5N_YEAST	Hypothetical 12.3 kDa protein in FOL2-YTA7 intergenic region	0.13	-	mit	0					108
P36031 UniProt NPD GO	YKW3_YEAST	Hypothetical 13.1 kDa protein in FRE2 5'region	0.13	-	cyt	0					110
P25563 UniProt NPD GO	YCC3_YEAST	Hypothetical 13.5 kDa protein in AGP1-LEU2 intergenic region	0.13	-	mit	2 *					115
P53300 UniProt NPD GO	YG45_YEAST	Hypothetical 13.6 kDa protein in RNR4-QCR9 intergenic region	0.13	-	nuc	0					117
P47146 UniProt NPD GO	YJ78_YEAST	Hypothetical 14.2 kDa protein in SOD1-CPA2 intergenic region	0.13	-	cyt	0					123
P36079 UniProt NPD GO	YKI3_YEAST	Hypothetical 23.7 kDa protein in MDH1-VMA5 intergenic region	0.13	-	end	5 *					204
P47044 UniProt NPD GO	YJF5_YEAST	Hypothetical 26.9 kDa protein in BTN1-PEP8 intergenic region	0.13	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			245
P38430 UniProt NPD GO	YM8C_YEAST	Hypothetical 36.1 kDa protein in TPS3-IPP2 intergenic region (ORF3)	0.13	-	cyt	0					313
P47173 UniProt NPD GO	YJ9J_YEAST	Hypothetical 39.7 kDa protein in HOM6-PMT4 intergenic region	0.13	-	nuc	0					342
Q03795 UniProt NPD GO	YM30_YEAST	Hypothetical 60.0 kDa protein in IMP1-HLJ1 intergenic region	0.13	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				547
P08974 UniProt NPD GO	YCF15_SPIOL	Hypothetical 7.5 kDa protein ycf15 (ORF 63)	0.13	-	nuc	0	Plastid; chloroplast				63
P38469 UniProt NPD GO	YMF27_MARPO	Hypothetical 7.9 kDa protein in NAD6-NAD3 intergenic region (ORF 69)	0.13	-	cyt	0					69
Q00865 UniProt NPD GO	YCX1_PINTH	Hypothetical 9.7 kDa protein in chlB-trnK intergenic region (ORF 83)	0.13	-	nuc	0	Plastid; chloroplast				83
P53795 UniProt NPD GO	YHIT_CAEEL	Hypothetical HIT-like protein F21C3.3	0.13	-	cyt	0					130
P04219 UniProt NPD GO	HYIG_MOUSE	Hypothetical Ig-region protein	0.13	-	mit	0		B cell receptor complex [IDA] external side of plasma membrane [IDA] immunoglobulin complex, circulating [IDA] perinuclear region [IDA]			140
P43541 UniProt NPD GO	YFG3_YEAST	Hypothetical UPF0320 protein YFL063W	0.13	-	mit	0					151
Q93847 UniProt NPD GO	YZLL_CAEEL	Hypothetical WD repeat protein K04G11.4	0.13	-	nuc	0					395
P51384 UniProt NPD GO	YCXQ_PORPU	Hypothetical monothiol glutaredoxin in trpA-ycf12 intergenic region (ORF107)	0.13	-	cyt	0	Plastid; chloroplast				107
P0C042 UniProt NPD GO	Y4597_ARATH	Hypothetical protein At4g15970	0.13	-	mit	0					367
Q11097 UniProt NPD GO	YWZ7_CAEEL	Hypothetical protein C02B8.7	0.13	-	nuc	0					52
Q9P7F5 UniProt NPD GO	YKY9_SCHPO	Hypothetical protein C1142.09 in chromosome I	0.13	-	cyt	0					115
O60082 UniProt NPD GO	YQK8_SCHPO	Hypothetical protein C1494.08c in chromosome III	0.13	-	cyt	0					274
Q10323 UniProt NPD GO	YD6B_SCHPO	Hypothetical protein C17G8.11c in chromosome I	0.13	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				356
Q09802 UniProt NPD GO	YAAB_SCHPO	Hypothetical protein C22G7.11c in chromosome I	0.13	-	nuc	0					140
Q9Y7K7 UniProt NPD GO	YGI5_SCHPO	Hypothetical protein C2A9.05c in chromosome II	0.13	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				219
Q10211 UniProt NPD GO	YAY3_SCHPO	Hypothetical protein C4H3.03c in chromosome I	0.13	-	cyt	0	Membrane; multi-pass membrane protein (Potential)				649
Q09888 UniProt NPD GO	YC9E_SCHPO	Hypothetical protein C584.14 in chromosome III	0.13	-	cyt	0					431
Q8ST97 UniProt NPD GO	Y107_ENCCU	Hypothetical protein ECU01_0070/ECU01_1540/ECU02_1570/ECU04_0080/ ECU08_2100	0.13	-	end	7 *					254

You are viewing entries 59801 to 59850 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.