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
Q12726 UniProt NPD GO	HOSM_YARLI	Homocitrate synthase, mitochondrial precursor (EC 2.3.3.14)	0.00	-	cyt	0	Mitochondrion				446
Q12122 UniProt NPD GO	HOSM_YEAST	Homocitrate synthase, mitochondrial precursor (EC 2.3.3.14)	0.00	-	cyt	0	Mitochondrion (Potential)	nucleus [IDA]			440
Q92209 UniProt NPD GO	KHSE_CANAL	Homoserine kinase (EC 2.7.1.39) (HSK) (HK) (Fragment)	0.00	-	cyt	0					147
P68420 UniProt NPD GO	TXH6_ORNHU	Huwentoxin-6 (Huwentoxin-VI) (HwTx-VI)	0.00	-	nuc	0	Secreted protein				41
P68423 UniProt NPD GO	TXH9_ORNHU	Huwentoxin-9 (Huwentoxin-IX) (HwTx-IX)	0.00	-	mit	0	Secreted protein				34
Q8H5T6 UniProt NPD GO	LTI6A_ORYSA	Hydrophobic protein LTI6A (Low temperature-induced protein 6A)	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				56
Q6AT93 UniProt NPD GO	LTI6B_ORYSA	Hydrophobic protein LTI6B (Low temperature-induced protein 6B)	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				55
Q9LRI7 UniProt NPD GO	OSR8_ORYSA	Hydrophobic protein OSR8	0.00	-	exc	2 *	Membrane; multi-pass membrane protein (Potential)				72
Q9ZNQ7 UniProt NPD GO	RCI2A_ARATH	Hydrophobic protein RCI2A (Low temperature and salt-responsive protein LTI6A)	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				54
Q9ZNS6 UniProt NPD GO	RCI2B_ARATH	Hydrophobic protein RCI2B (Low temperature and salt-responsive protein LTI6B)	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				54
Q04571 UniProt NPD GO	RODL_NEUCR	Hydrophobin precursor (Rodlet protein) (Clock-controlled gene protein 2) (Blue light-induced protein ...	0.00	-	end	0	Secreted protein			2FMC	108
P79073 UniProt NPD GO	HYP2_TRIRE	Hydrophobin-2 precursor (Hydrophobin II) (HFBII)	0.00	-	vac	0	Spore wall; secreted			2B97	86
Q28333 UniProt NPD GO	GLO2_CALJA	Hydroxyacylglutathione hydrolase (EC 3.1.2.6) (Glyoxalase II) (Glx II) (Germ cell-specific protein)	0.00	-	cyt	0					260
Q8HZJ0 UniProt NPD GO	HIOM_MACMU	Hydroxyindole O-methyltransferase (EC 2.1.1.4) (HIOMT) (Acetylserotonin O-methyltransferase) (ASMT)	0.00	-	cyt	0					345
P08613 UniProt NPD GO	TKN1_KASMA	Hylambates kassinin ([Glu2,Pro5]-kassinin)	0.00	-		0	Secreted protein				12
P84292 UniProt NPD GO	HLP1_HYLPU	Hylaseptin-P1 (HSP1)	0.00	-		0	Secreted protein				14
P84003 UniProt NPD GO	HYB2_HYLBI	Hylin-b2 (Hy-b2)	0.00	-		0	Secreted protein	extracellular region [IDA]			19
P14596 UniProt NPD GO	HTF_TABAT	Hypertrehalosaemic factor (HOTH) (Dipteran corpora cardiaca factor II) (DCC II)	0.00	-		0	Secreted protein				10
P67789 UniProt NPD GO	HTF_TENMO	Hypertrehalosaemic factor (HOTH) (Hypertrehalosaemic neuropeptide)	0.00	-		0	Secreted protein				8
P67790 UniProt NPD GO	HTF_ZOPRU	Hypertrehalosaemic factor (HOTH) (Hypertrehalosaemic neuropeptide)	0.00	-		0	Secreted protein				8
P84261 UniProt NPD GO	HTF1_BLAOR	Hypertrehalosaemic factor 1 (Hypertrehalosaemic factor I) (Hypertrehalosaemic neuropeptide I)	0.00	-		0	Secreted protein				8
P84260 UniProt NPD GO	HTF1_LEPDE	Hypertrehalosaemic factor 1 (Hypertrehalosaemic factor I) (LeD-CC-I)	0.00	-		0	Secreted protein				8
P84259 UniProt NPD GO	HTF1_PERAM	Hypertrehalosaemic factor 1 (Hypertrehalosaemic factor I) (Neuropeptide M-I) (Periplanetin CC-I) (Pe ...	0.00	-		0	Secreted protein				8
P62542 UniProt NPD GO	HTF2_CARMO	Hypertrehalosaemic factor 2 (Hypertrehalosaemic factor II) (HTF-II) (HRTH-II) (Hypertrehalosaemic ne ...	0.00	-		0	Secreted protein				10
P84220 UniProt NPD GO	HTF_BLAGE	Hypertrehalosaemic hormone (HTH) (Hypertrehalosaemic neuropeptide)	0.00	-		0	Secreted protein				10
P84221 UniProt NPD GO	HTF_GROPO	Hypertrehalosaemic hormone (HTH) (Hypertrehalosaemic neuropeptide)	0.00	-		0	Secreted protein				10
P84219 UniProt NPD GO	HTF_LEUMA	Hypertrehalosaemic hormone (HTH) (Hypertrehalosaemic neuropeptide)	0.00	-		0	Secreted protein				10
P84218 UniProt NPD GO	HTF_NAUCI	Hypertrehalosaemic hormone (HTH) (Hypertrehalosaemic neuropeptide)	0.00	-		0	Secreted protein				10
P16353 UniProt NPD GO	HTF_HELZE	Hypertrehalosaemic hormone (HeZ-HRTH)	0.00	-		0	Secreted protein				10
P62543 UniProt NPD GO	HTF_EXTTI	Hypertrehalosaemic neuropeptide	0.00	-		0	Secreted protein				10
P35588 UniProt NPD GO	HYPB_HYPLI	Hypodermin B precursor (EC 3.4.21.-) (HB)	0.00	-	exc	1 *	Secreted protein				256
P84189 UniProt NPD GO	HYT1_TITSE	Hypotensin-1 (Hypotensin I)	0.00	-	nuc	0	Secreted protein				25
P84190 UniProt NPD GO	HYT2_TITSE	Hypotensin-2 (Hypotensin II)	0.00	-	nuc	0	Secreted protein				25
P84191 UniProt NPD GO	HYT3_TITSE	Hypotensin-3 (Hypotensin III)	0.00	-	nuc	0	Secreted protein				24
P84192 UniProt NPD GO	HYT4_TITSE	Hypotensin-4 (Hypotensin IV)	0.00	-	nuc	0	Secreted protein				24
P38460 UniProt NPD GO	YMF17_MARPO	Hypothetical 10.2 kDa protein in RPS1-NAD4L intergenic region (ORF 86A)	0.00	-	mit	2 *					86
P47131 UniProt NPD GO	YJ55_YEAST	Hypothetical 11.3 kDa protein in MIR1-STE18 intergenic region	0.00	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			105
P53948 UniProt NPD GO	YNF7_YEAST	Hypothetical 11.6 kDa protein in ARP5-OMP2 intergenic region	0.00	-	cyt	0					110
P28255 UniProt NPD GO	YCF19_GALSU	Hypothetical 11.6 kDa protein ycf19	0.00	-	end	3 *	Plastid; chloroplast				98
P53213 UniProt NPD GO	YG1E_YEAST	Hypothetical 11.7 kDa protein in VMA7-RPS25A intergenic region	0.00	-	cyt	0					109
P39974 UniProt NPD GO	YEI3_YEAST	Hypothetical 12.0 kDa protein in DLD3 5'region	0.00	-	cyt	0					107
P53190 UniProt NPD GO	YGC4_YEAST	Hypothetical 12.2 kDa protein in PGD1-STT3 intergenic region	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				111
P47092 UniProt NPD GO	YJZ0_YEAST	Hypothetical 12.3 kDa protein in ESS1-MER2 intergenic region	0.00	-	nuc	1					110
P47126 UniProt NPD GO	YJ49_YEAST	Hypothetical 12.6 kDa protein in MIR1-STE18 intergenic region	0.00	-	cyt	0					109
P05722 UniProt NPD GO	YCX2_CHLRE	Hypothetical 12.7 kDa protein in 16S rRNA region	0.00	-	cyt	1 *	Plastid; chloroplast				117
P47020 UniProt NPD GO	YJM0_YEAST	Hypothetical 12.8 kDa protein in POS18-PHO86 intergenic region	0.00	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				107
P25650 UniProt NPD GO	YCX5_YEAST	Hypothetical 13.5 kDa protein in TUP1 3'region	0.00	-	cyt	1					117
P50088 UniProt NPD GO	YG4Z_YEAST	Hypothetical 14.4 kDa protein in YHB1-PFK1 intergenic region	0.00	-	cyt	1 *		mitochondrion [IDA]			129
P53162 UniProt NPD GO	YGG9_YEAST	Hypothetical 16.1 kDa protein in RPB9-ALG2 intergenic region	0.00	-	mit	0					154
P38470 UniProt NPD GO	YMF28_MARPO	Hypothetical 16.2 kDa protein in NAD3-NAD7 intergenic region (ORF 139)	0.00	-	cyt	1					139

You are viewing entries 95151 to 95200 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.