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
P28507 UniProt NPD GO	ITHG_HIRME	Hirudin IIIA	0.02	-	nuc	0	Secreted protein			1TOM	65
P01050 UniProt NPD GO	ITH1_HIRME	Hirudin variant-1 (Lepirudin)	0.02	-	nuc	0	Secreted protein			6HIR	65
P09945 UniProt NPD GO	ITH3_HIRME	Hirudin variant-2 precursor (Fragment)	0.02	-	nuc	0	Secreted protein			4HTC	72
Q01984 UniProt NPD GO	HNMT_RAT	Histamine N-methyltransferase (EC 2.1.1.8) (HMT)	0.02	-	mit	0	Cytoplasm				294
P24226 UniProt NPD GO	HISX_BRAOC	Histidinol dehydrogenase, chloroplast precursor (EC 1.1.1.23) (HDH)	0.02	-	mit	0	Plastid; chloroplast				469
Q5NAY4 UniProt NPD GO	HISX_ORYSA	Histidinol dehydrogenase, chloroplast precursor (EC 1.1.1.23) (HDH)	0.02	-	mit	0	Plastid; chloroplast (By similarity)				473
P07172 UniProt NPD GO	HIS8_YEAST	Histidinol-phosphate aminotransferase (EC 2.6.1.9) (Imidazole acetol-phosphate transaminase)	0.02	-	cyt	0		intracellular [TAS]			385
Q8SSG3 UniProt NPD GO	H2A_ENCCU	Histone H2A	0.02	-	nuc	0	Nucleus				128
Q75DX9 UniProt NPD GO	LYS4_ASHGO	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.02	-	mit	0	Mitochondrion (By similarity)				686
Q6BM98 UniProt NPD GO	LYS4_DEBHA	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.02	-	mit	0	Mitochondrion (By similarity)				688
Q6CT61 UniProt NPD GO	LYS4_KLULA	Homoaconitase, mitochondrial precursor (EC 4.2.1.36) (Homoaconitate hydratase)	0.02	-	mit	0	Mitochondrion (By similarity)				693
Q9SC13 UniProt NPD GO	HSS1_SENVE	Homospermidine synthase 1 (EC 2.5.1.45)	0.02	-	cyt	0					370
Q86C51 UniProt NPD GO	TXL1_ORNHU	Huwenlectin-1 precursor (Huwenlectin-I) (SHL-I) (SHLP-I)	0.02	-	exc	0	Secreted protein			1QK7	83
P61103 UniProt NPD GO	TXH3_ORNHU	Huwentoxin-3 precursor (Huwentoxin-III) (HwTx-III) [Contains: Mutant of huwentoxin-3 (Mutant of huwe ...	0.02	-	exc	0	Secreted protein				87
Q86LR2 UniProt NPD GO	HLYS1_CHLVR	Hydralysin-1	0.02	-	cyt	0	Secreted protein	extracellular region [IDA]			243
Q564A5 UniProt NPD GO	HLYS2_CHLVR	Hydralysin-2	0.02	-	cyt	0	Secreted protein (By similarity)	extracellular region [IDA]			243
Q52SK6 UniProt NPD GO	HLYS3_CHLVR	Hydralysin-3	0.02	-	nuc	0	Secreted protein (By similarity)				217
O13300 UniProt NPD GO	HYP3_AGABI	Hydrophobin-3 precursor	0.02	-	end	2 *	Secreted protein				119
P52752 UniProt NPD GO	SSGA_METAN	Hydrophobin-like protein ssgA precursor	0.02	-	exc	0					96
Q9WU19 UniProt NPD GO	HAOX1_MOUSE	Hydroxyacid oxidase 1 (EC 1.1.3.15) (HAOX1) (Glycolate oxidase) (GOX)	0.02	-	cyt	0	Peroxisome				370
Q99KB8 UniProt NPD GO	GLO2_MOUSE	Hydroxyacylglutathione hydrolase (EC 3.1.2.6) (Glyoxalase II) (Glx II)	0.02	-	cyt	0					260
O35952 UniProt NPD GO	GLO2_RAT	Hydroxyacylglutathione hydrolase (EC 3.1.2.6) (Glyoxalase II) (Glx II) (Round spermatid protein RSP2 ...	0.02	-	cyt	0					260
P08614 UniProt NPD GO	TKN2_KASMA	Hylambatin	0.02	-		0	Secreted protein				12
Q17128 UniProt NPD GO	HTF_BLADI	Hypertrehalosaemic prohormone precursor [Contains: Hypertrehalosaemic hormone (HTH) (Hypertrehalosae ...	0.02	-	exc	1 *	Secreted protein				72
P01155 UniProt NPD GO	HY14_PIG	Hypothalamic tetradecapeptide	0.02	-		0					14
P47066 UniProt NPD GO	YJC2_YEAST	Hypothetical 11.5 kDa protein in PET130-CCT3 intergenic region	0.02	-	mit	0					102
P53160 UniProt NPD GO	YGH4_YEAST	Hypothetical 11.5 kDa protein in RPL7A-HSF1 intergenic region	0.02	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				108
P38192 UniProt NPD GO	YBE8_YEAST	Hypothetical 12.4 kDa protein in SEC17-QCR1 intergenic region	0.02	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				103
P43608 UniProt NPD GO	YFK5_YEAST	Hypothetical 12.5 kDa protein in PHO4-CDC26 intergenic region	0.02	-	mit	2	Membrane; multi-pass membrane protein (Potential)				114
Q9MUL5 UniProt NPD GO	YCF20_MESVI	Hypothetical 13.0 kDa protein ycf20 (RF20)	0.02	-	end	3 *	Plastid; chloroplast				116
P36050 UniProt NPD GO	YKQ9_YEAST	Hypothetical 14.2 kDa protein in MRPL38-MRP49 intergenic region	0.02	-	nuc	0					127
O78438 UniProt NPD GO	YCF35_GUITH	Hypothetical 15.1 kDa protein ycf35	0.02	-	cyt	0	Plastid; chloroplast				128
P51213 UniProt NPD GO	YCF35_PORPU	Hypothetical 15.1 kDa protein ycf35 (ORF128)	0.02	-	cyt	0	Plastid; chloroplast				128
P68513 UniProt NPD GO	YMX1_BRANA	Hypothetical 16.0 kDa protein (ORF138)	0.02	-	nuc	1 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				138
O78501 UniProt NPD GO	YCF36_GUITH	Hypothetical 18.4 kDa protein ycf36	0.02	-	end	3 *	Plastid; chloroplast				155
P48276 UniProt NPD GO	YCF36_CYAPA	Hypothetical 18.6 kDa protein ycf36	0.02	-	end	3 *	Plastid; cyanelle				159
P22375 UniProt NPD GO	YPA2_ASCIM	Hypothetical 19.7 kDa protein (ORF2)	0.02	-	end	4 *					167
O20162 UniProt NPD GO	YCX8_CHLVU	Hypothetical 20.1 kDa protein in psaB-ycf62 intergenic region (ORF177)	0.02	-	cyt	0	Plastid; chloroplast				177
Q04231 UniProt NPD GO	YMB1_YEAST	Hypothetical 20.3 kDa protein in ERV25-SPT5 intergenic region	0.02	-	nuc	0		nucleus [IDA]			177
P38812 UniProt NPD GO	YHQ0_YEAST	Hypothetical 20.9 kDa protein in HXT5-NRK1 intergenic region	0.02	-	cyt	0					185
P43600 UniProt NPD GO	YFJ0_YEAST	Hypothetical 25.7 kDa protein in FAB1-PES4 intergenic region	0.02	-	vac	0					232
P39975 UniProt NPD GO	YEI2_YEAST	Hypothetical 26.8 kDa protein in DLD3 5'region	0.02	-	cyt	0					231
Q03219 UniProt NPD GO	YM44_YEAST	Hypothetical 31.1 kDa protein in SIP18-SPT21 intergenic region	0.02	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			274
P23501 UniProt NPD GO	YK33_YEAST	Hypothetical 46.5 kDa protein in MRS4-DYN1 intergenic region	0.02	-	end	5	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			404
Q05131 UniProt NPD GO	YMS4_YEAST	Hypothetical 48.4 kDa protein in ARP9-IMP2 intergenic region	0.02	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				434
P47159 UniProt NPD GO	YJ94_YEAST	Hypothetical 49.7 kDa protein in RPS5-ZMS1 intergenic region	0.02	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				448
P49828 UniProt NPD GO	YCX2_ODOSI	Hypothetical 5.5 kDa protein in ccsA-rps6 intergenic region (ORF46)	0.02	-	nuc	0	Plastid; chloroplast				46
P48367 UniProt NPD GO	YCF17_CYAPA	Hypothetical 5.5 kDa protein ycf17	0.02	-	mit	0	Plastid; cyanelle				49
P34774 UniProt NPD GO	YCX1_ASTLO	Hypothetical 7.2 kDa protein in rps2-rps9 intergenic region (ORF57)	0.02	-	mit	1 *	Plastid				57
P51233 UniProt NPD GO	YCXA_PORPU	Hypothetical 7.5 kDa protein in cemA-psbI intergenic region (ORF62)	0.02	-	mit	1 *	Plastid; chloroplast				62

You are viewing entries 83901 to 83950 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.