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
Q37600 UniProt NPD GO	COX3_PYLLI	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					272
O47696 UniProt NPD GO	COX3_RAPCA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	5 *					261
O47697 UniProt NPD GO	COX3_RAPME	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	5 *					261
P05505 UniProt NPD GO	COX3_RAT	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					260
P80441 UniProt NPD GO	COX3_RHIST	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					281
Q96065 UniProt NPD GO	COX3_RHIUN	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
Q9XLX0 UniProt NPD GO	COX3_SACKL	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					269
Q36860 UniProt NPD GO	COX3_SALSA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
P14058 UniProt NPD GO	COX3_SCHCO	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					268
O21619 UniProt NPD GO	COX3_SHEEP	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	5 *					261
P14853 UniProt NPD GO	COX3_SOYBN	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					265
Q9ZZ48 UniProt NPD GO	COX3_SQUAC	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
P15546 UniProt NPD GO	COX3_STRPU	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	mit	6 *					260
O47690 UniProt NPD GO	COX3_SYNCA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
Q8W9G7 UniProt NPD GO	COX3_TACAC	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
Q4JQI1 UniProt NPD GO	COX3_TETNG	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
Q37679 UniProt NPD GO	COX3_THEAN	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					255
O47685 UniProt NPD GO	COX3_TRAIM	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
O47686 UniProt NPD GO	COX3_TRAOR	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	5 *					261
O47688 UniProt NPD GO	COX3_TRASP	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					261
O47687 UniProt NPD GO	COX3_TRASR	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
O47689 UniProt NPD GO	COX3_TRAST	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					261
Q03227 UniProt NPD GO	COX3_VICFA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	6 *					265
P00419 UniProt NPD GO	COX3_XENLA	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					260
Q9B6D8 UniProt NPD GO	COX3_YARLI	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.00	-	end	7 *					268
Q35826 UniProt NPD GO	COX3_SPOFR	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III) (Fragment)	0.00	-	end	4 *					147
Q6CW24 UniProt NPD GO	CCPR_KLULA	Cytochrome c peroxidase, mitochondrial precursor (EC 1.11.1.5) (CCP)	0.00	-	mit	1 *	Mitochondrion; mitochondrial matrix (By similarity)				346
P29610 UniProt NPD GO	CY12_SOLTU	Cytochrome c1, heme protein, mitochondrial precursor (Clone PC18I) (Fragment)	0.00	-	exc	0	Mitochondrion; mitochondrial intermembrane space				260
P11448 UniProt NPD GO	CYC6_BRYMA	Cytochrome c6 (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553)	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen				88
P83391 UniProt NPD GO	CYC6_CLAGO	Cytochrome c6 (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553)	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen			1LS9	91
P00119 UniProt NPD GO	CYC6_EUGGR	Cytochrome c6 (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553) (Cytochrome c-552)	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen				87
Q09099 UniProt NPD GO	CYC6_MONBR	Cytochrome c6 (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553) (Cytochrome c-552)	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen			1JX8	89
P51200 UniProt NPD GO	CYC6_PORPU	Cytochrome c6 precursor (Soluble cytochrome f) (Cytochrome c553) (Cytochrome c-553)	0.00	-	exc	1 *	Plastid; chloroplast; chloroplast thylakoid lumen (By similarity)				110
P58763 UniProt NPD GO	CKX_WHEAT	Cytokinin dehydrogenase (EC 1.5.99.12) (Cytokinin oxidase) (CKO) (CKX) (Fragment)	0.00	-		0	Membrane. Might be located on membranes				15
P58689 UniProt NPD GO	ACTP1_RADMG	Cytolysin-1 (Cytolysin I) (HMg I) (Magnificalysin I) (Fragment)	0.00	-		0	Secreted protein. Found in nematocyst				20
P58690 UniProt NPD GO	ACTP2_RADMG	Cytolysin-2 (Cytolysin II) (HMg II) (Magnificalysin II) (Fragment)	0.00	-	cyt	0	Secreted protein. Found in nematocyst				22
P83776 UniProt NPD GO	CAP3_CANAL	Cytoplasmic antigenic protein 3 (Fragments)	0.00	-		0	Cytoplasm				19
P83781 UniProt NPD GO	CAP4_CANAL	Cytoplasmic antigenic protein 4 (Fragment)	0.00	-		0	Cytoplasm				8
P28839 UniProt NPD GO	AMPL_PIG	Cytosol aminopeptidase (EC 3.4.11.1) (Leucine aminopeptidase) (LAP) (Leucyl aminopeptidase) (Proline ...	0.00	-	nuc	0	Cytoplasm				36
P60304 UniProt NPD GO	CTX1_NAJAT	Cytotoxin 1 precursor (CTX1) (CTX-1) (Cardiotoxin analog I) (Cardiotoxin 1) (CTX I)	0.00	-	mit	0	Secreted protein			2CDX	81
P01445 UniProt NPD GO	CX2_NAJKA	Cytotoxin 2 (Cytotoxin CM-7A)	0.00	-	nuc	0	Secreted protein				60
Q9DGH9 UniProt NPD GO	CTX2_NAJKA	Cytotoxin 2 precursor	0.00	-	mit	0	Secreted protein				81
P01442 UniProt NPD GO	CTX2_NAJAT	Cytotoxin 2 precursor (Cardiotoxin analog II) (Cardiotoxin 2) (Cardiotoxin 1A) (CTX2) (CTX II) (Ctx- ...	0.00	-	mit	0	Secreted protein			1CRF	81
P24780 UniProt NPD GO	CX3_NAJNA	Cytotoxin 3 (Cytotoxin IIa)	0.00	-	nuc	0	Secreted protein				60
P60301 UniProt NPD GO	CTX3_NAJAT	Cytotoxin 3 precursor (Cardiotoxin 3) (CTX-3) (Cardiotoxin analog III) (CTX III)	0.00	-	mit	0	Secreted protein			2CRT	81
P80245 UniProt NPD GO	CX6_NAJAT	Cytotoxin 6 precursor (Cardiotoxin 6) (CTX6) (Cytotoxin N) (Cardiotoxin N) (Ctx-N) (CTXN)	0.00	-	mit	0	Secreted protein			1UG4	81
P01454 UniProt NPD GO	CX9_NAJHA	Cytotoxin 9 (Toxin CM-2e)	0.00	-	nuc	0	Secreted protein				60
P60303 UniProt NPD GO	CTX4_NAJKA	Cytotoxin IV precursor	0.00	-	mit	0	Secreted protein				81
P60307 UniProt NPD GO	CX5A_NAJAT	Cytotoxin SP15a	0.00	-	nuc	0	Secreted protein				60
P60309 UniProt NPD GO	CX5D_NAJAT	Cytotoxin SP15d	0.00	-	nuc	0	Secreted protein				60

You are viewing entries 94201 to 94250 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.