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
P81104 UniProt NPD GO	FKB70_PINPS	70 kDa peptidyl-prolyl isomerase (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (Cyclophilin) (P ...	0.00	-		0					15
P16392 UniProt NPD GO	GRP78_HORSE	78 kDa glucose-regulated protein (GRP 78) (Immunoglobulin heavy chain-binding protein) (BiP) (Fragme ...	0.00	-		0	Endoplasmic reticulum; endoplasmic reticulum lumen				15
Q06931 UniProt NPD GO	ABR17_PEA	ABA-responsive protein ABR17	0.00	-	cyt	0					157
Q06930 UniProt NPD GO	ABR18_PEA	ABA-responsive protein ABR18	0.00	-	cyt	0					158
O77636 UniProt NPD GO	ADA17_PIG	ADAM 17 (EC 3.4.24.86) (A disintegrin and metalloproteinase domain 17) (TNF-alpha-converting enzyme) ...	0.00	-	cyt	0	Membrane; single-pass type I membrane protein (By similarity)				112
Q75A26 UniProt NPD GO	ARF_ASHGO	ADP-ribosylation factor	0.00	-	cyt	0					180
Q96361 UniProt NPD GO	ARF1_BRARP	ADP-ribosylation factor 1	0.00	-	cyt	0					181
P40940 UniProt NPD GO	ARF3_ARATH	ADP-ribosylation factor 3	0.00	-	cyt	0					181
P40994 UniProt NPD GO	ARF3_YEAST	ADP-ribosylation factor 3	0.00	-	cyt	0					182
P38116 UniProt NPD GO	ARL1_YEAST	ADP-ribosylation factor-like protein 1 (Arf-like GTPase 1)	0.00	-	cyt	0	Golgi apparatus	Golgi apparatus [IDA] soluble fraction [IDA]		1MOZ	182
Q6T311 UniProt NPD GO	ARL9_HUMAN	ADP-ribosylation factor-like protein 9	0.00	-	cyt	0					187
Q99145 UniProt NPD GO	HIS1_YARLI	ATP phosphoribosyltransferase (EC 2.4.2.17) (ATP-PRTase) (ATP-PRT)	0.00	-	cyt	0	Cytoplasm (By similarity)				296
P80496 UniProt NPD GO	ATP7_SOLTU	ATP synthase 27 kDa subunit, mitochondrial (EC 3.6.3.14) (Fragment)	0.00	-	cyt	0	Mitochondrion				33
Q85FN2 UniProt NPD GO	ATPH_ADICA	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
P61172 UniProt NPD GO	ATPH_ANTFO	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
Q02851 UniProt NPD GO	ATPH_ANTSP	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				82
P56760 UniProt NPD GO	ATPH_ARATH	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
Q37304 UniProt NPD GO	ATPH_CHLRE	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				82
P56297 UniProt NPD GO	ATPH_CHLVU	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				82
Q9TM30 UniProt NPD GO	ATPH_CYACA	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				82
P48086 UniProt NPD GO	ATPH_CYAPA	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; cyanelle; cyanelle thylakoid membrane; multi-pass membrane protein (By similarity)				81
P10603 UniProt NPD GO	ATPH_EUGGR	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
O78479 UniProt NPD GO	ATPH_GUITH	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				82
P69194 UniProt NPD GO	ATPH_LOTJA	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
P69449 UniProt NPD GO	ATPH_MAIZE	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
P62481 UniProt NPD GO	ATPH_MARPO	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
Q9MUT0 UniProt NPD GO	ATPH_MESVI	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				82
Q9TL14 UniProt NPD GO	ATPH_NEPOL	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				82
Q42969 UniProt NPD GO	ATPH_OCHNE	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				82
Q00824 UniProt NPD GO	ATPH_ODOSI	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				82
P62480 UniProt NPD GO	ATPH_OENHO	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
Q6ENH9 UniProt NPD GO	ATPH_ORYNI	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
P69450 UniProt NPD GO	ATPH_ORYSA	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
P28530 UniProt NPD GO	ATPH_PAVLU	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				83
P08212 UniProt NPD GO	ATPH_PEA	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
P41603 UniProt NPD GO	ATPH_PINTH	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
P51246 UniProt NPD GO	ATPH_PORPU	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				82
Q6L3A2 UniProt NPD GO	ATPH_SACHY	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
Q6ENW8 UniProt NPD GO	ATPH_SACOF	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
P69195 UniProt NPD GO	ATPH_SOYBN	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
P69447 UniProt NPD GO	ATPH_SPIOL	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
P06286 UniProt NPD GO	ATPH_TOBAC	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
P69448 UniProt NPD GO	ATPH_WHEAT	ATP synthase C chain (EC 3.6.3.14) (Lipid-binding protein) (ATPase subunit III)	0.00	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				81
P81451 UniProt NPD GO	ATP19_YEAST	ATP synthase K chain, mitochondrial (EC 3.6.3.14)	0.00	-	cyt	0		proton-transporting ATP synthase complex, c... [IMP]			68
Q37385 UniProt NPD GO	ATP6_ACACA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.00	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				247
P34834 UniProt NPD GO	ATP6_ANOGA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.00	-	end	5 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				226
O47426 UniProt NPD GO	ATP6_BRAFL	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.00	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O21004 UniProt NPD GO	ATP6_BRALA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.00	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
Q31720 UniProt NPD GO	ATP6_BRANA	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.00	-	end	7 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				260
O78684 UniProt NPD GO	ATP6_CARAU	ATP synthase a chain (EC 3.6.3.14) (ATPase protein 6)	0.00	-	end	6 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227

You are viewing entries 92301 to 92350 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.