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
P02187 UniProt NPD GO	MYG_LOXAF	Myoglobin	0.01	-	cyt	0					153
P02150 UniProt NPD GO	MYG_MACFA	Myoglobin	0.01	-	cyt	0					153
P02194 UniProt NPD GO	MYG_MACRU	Myoglobin	0.01	-	cyt	0					153
P02178 UniProt NPD GO	MYG_MEGNO	Myoglobin	0.01	-	cyt	0					153
P32428 UniProt NPD GO	MYG_ONDZI	Myoglobin	0.01	-	cyt	0					153
P02196 UniProt NPD GO	MYG_ORNAN	Myoglobin	0.01	-	cyt	0					153
P02145 UniProt NPD GO	MYG_PANTR	Myoglobin	0.01	-	cyt	0					153
P68084 UniProt NPD GO	MYG_PAPAN	Myoglobin	0.01	-	cyt	0					153
P02148 UniProt NPD GO	MYG_PONPY	Myoglobin	0.01	-	mit	0					153
P02155 UniProt NPD GO	MYG_SAISC	Myoglobin	0.01	-	cyt	0					153
Q9DGJ0 UniProt NPD GO	MYG_SARCH	Myoglobin	0.01	-	cyt	0					146
Q9DGI9 UniProt NPD GO	MYG_SCOJP	Myoglobin	0.01	-	cyt	0					146
P68085 UniProt NPD GO	MYG_SEMEN	Myoglobin	0.01	-	cyt	0					153
P02195 UniProt NPD GO	MYG_TACAC	Myoglobin	0.01	-	cyt	0					153
Q9DGJ2 UniProt NPD GO	MYG_THUAA	Myoglobin	0.01	-	cyt	0					146
P02205 UniProt NPD GO	MYG_THUAL	Myoglobin	0.01	-	cyt	0				1MYT	146
Q76G09 UniProt NPD GO	MYG_THUOB	Myoglobin	0.01	-	cyt	0					146
P68189 UniProt NPD GO	MYG_THUTH	Myoglobin	0.01	-	cyt	0					146
P68190 UniProt NPD GO	MYG_THUTO	Myoglobin	0.01	-	cyt	0					146
P02165 UniProt NPD GO	MYG_TUPGL	Myoglobin	0.01	-	cyt	0					153
Q7M3C1 UniProt NPD GO	MYG_AILME	Myoglobin (Fragment)	0.01	-	cyt	0					96
P15160 UniProt NPD GO	GLB_PARCA	Myoglobin (Hemoglobin)	0.01	-	mit	0				1UVY	116
P27687 UniProt NPD GO	HEMT2_PHAGO	Myohemerythrin-2 (MHR 2) (Fragment)	0.01	-	cyt	0					31
P54696 UniProt NPD GO	MYOH_DICDI	Myosin IH heavy chain (Fragment)	0.01	-	cyt	0					99
P07291 UniProt NPD GO	MLE_AEQIR	Myosin essential light chain, striated adductor muscle (E-LC) (Sulfhydryl light chain) (SHLC)	0.01	-	cyt	0				1WDC	156
P82159 UniProt NPD GO	MLE1_MUGCA	Myosin light chain 1, skeletal muscle isoform (A1 catalytic) (Alkali) (LC-1) (LC1)	0.01	-	cyt	0					186
P02603 UniProt NPD GO	MLE3_RABIT	Myosin light chain 3, skeletal muscle isoform (A2 catalytic) (Alkali myosin light chain 3) (MLC3F)	0.01	-	cyt	0					149
P82160 UniProt NPD GO	MLE3_MUGCA	Myosin light chain 3, skeletal muscle isoform (A2 catalytic) (Alkali) (LC-3) (LC3)	0.01	-	cyt	0					148
Q09196 UniProt NPD GO	MLR4_SCHPO	Myosin regulatory light chain cdc4	0.01	-	cyt	0	Cytoplasm	myosin II [IDA]		1GGW	141
Q17133 UniProt NPD GO	MLE_BRAFL	Myosin, essential light chain (Myosin light chain alkali)	0.01	-	cyt	0					149
P07290 UniProt NPD GO	MLE_PATYE	Myosin, essential light chain, adductor muscle (Sulfhydryl light chain) (SHLC)	0.01	-	cyt	0					156
P42984 UniProt NPD GO	MNP1_LEPDE	Myotropic neuropeptide 1 (Led-MNP-I)	0.01	-		0					7
P82103 UniProt NPD GO	MYNA_MYTGA	Myticin-A precursor	0.01	-	mit	0	Secreted protein				96
P38680 UniProt NPD GO	MTR_NEUCR	N amino acid transport system protein (Methyltryptophan resistance protein)	0.01	-	end	11	Membrane; multi-pass membrane protein				470
P30918 UniProt NPD GO	ASPG_PIG	N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase (EC 3.5.1.26) (Glycosylasparaginase) (Aspartylglucos ...	0.01	-	cyt	0	Lysosome				34
P30919 UniProt NPD GO	ASPG_RAT	N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase precursor (EC 3.5.1.26) (Glycosylasparaginase) (Aspa ...	0.01	-	end	0	Lysosome				345
P83451 UniProt NPD GO	ASPG_ASOTA	N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase (EC 3.5.1.26) (Glycosylasparaginase) (Aspartylglucos ...	0.01	-	cyt	1 *	Secreted protein				40
Q4R6C4 UniProt NPD GO	ASPG_MACFA	N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase precursor (EC 3.5.1.26) (Glycosylasparaginase) (Aspa ...	0.01	-	exc	0	Lysosome (By similarity)				346
P00721 UniProt NPD GO	LYS_CHASP	N,O-diacetylmuramidase (EC 3.2.1.-) (Lysozyme CH)	0.01	-	cyt	0	Secreted protein; extracellular space				211
P43073 UniProt NPD GO	TRPF_CANAL	N-(5'-phosphoribosyl)anthranilate isomerase (EC 5.3.1.24) (PRAI)	0.01	-	mit	0					225
Q5XQP9 UniProt NPD GO	TRPF_SACKU	N-(5'-phosphoribosyl)anthranilate isomerase (EC 5.3.1.24) (PRAI)	0.01	-	mit	0					226
P36230 UniProt NPD GO	LECA_IRIHO	N-acetyl-D-galactosamine-binding lectin subunit A (EC 3.2.2.22) (A-disaccharide-binding lectin subun ...	0.01	-	cyt	0					28
P36231 UniProt NPD GO	LECB_IRIHO	N-acetyl-D-galactosamine-binding lectin subunit B (A-disaccharide-binding lectin subunit B) (Fragmen ...	0.01	-		0					20
O18921 UniProt NPD GO	RENBP_CANFA	N-acylglucosamine 2-epimerase (EC 5.1.3.8) (GlcNAc 2-epimerase) (N-acetyl-D-glucosamine 2-epimerase) ...	0.01	-	cyt	0					35
Q03920 UniProt NPD GO	MTQ2_YEAST	N5-glutamine methyltransferase MTQ2 (EC 2.1.1.-)	0.01	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			221
O74237 UniProt NPD GO	XYL1_CANTE	NAD(P)H-dependent D-xylose reductase (EC 1.1.1.-) (XR)	0.01	-	cyt	0				1Z9A	322
P31867 UniProt NPD GO	XYL1_PICST	NAD(P)H-dependent D-xylose reductase (EC 1.1.1.-) (XR)	0.01	-	cyt	0					318
Q31792 UniProt NPD GO	NU3C_ANTFO	NAD(P)H-quinone oxidoreductase chain 3, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 3) (N ...	0.01	-	end	3 *	Plastid; chloroplast				120
P06259 UniProt NPD GO	NU3C_MARPO	NAD(P)H-quinone oxidoreductase chain 3, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 3) (N ...	0.01	-	end	3 *	Plastid; chloroplast				120
Q32905 UniProt NPD GO	NU5C_PEA	NAD(P)H-quinone oxidoreductase chain 5, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 5) (N ...	0.01	-	end	3 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				124

You are viewing entries 89651 to 89700 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.