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
Q4G3B3 UniProt NPD GO	PETM_EMIHU	Cytochrome b6-f complex subunit 7 (Cytochrome b6-f complex subunit VII) (Cytochrome b6-f complex sub ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				32
Q42496 UniProt NPD GO	PETM_CHLRE	Cytochrome b6-f complex subunit 7, chloroplast precursor (Cytochrome b6-f complex subunit VII) (Cyto ...	0.01	-	mit	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein			1Q90	99
Q70Y10 UniProt NPD GO	PETN_AMBTC	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q85A91 UniProt NPD GO	PETN_ANTFO	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q7GQG6 UniProt NPD GO	PETN_ARAEL	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
P61039 UniProt NPD GO	PETN_ARATH	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q7FNT1 UniProt NPD GO	PETN_ATRBE	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q7HKY0 UniProt NPD GO	PETN_CALFE	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q9TLR6 UniProt NPD GO	PETN_CYACA	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q85FX7 UniProt NPD GO	PETN_CYAME	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q56P15 UniProt NPD GO	PETN_LACSA	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
P61040 UniProt NPD GO	PETN_LOTJA	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q6EW55 UniProt NPD GO	PETN_NYMAL	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				32
P61041 UniProt NPD GO	PETN_OENHO	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q6ENI5 UniProt NPD GO	PETN_ORYNI	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
P61042 UniProt NPD GO	PETN_ORYSA	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q7GQE8 UniProt NPD GO	PETN_PANGI	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q7GQD2 UniProt NPD GO	PETN_PANQU	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q5IBK4 UniProt NPD GO	PETN_PLALA	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q6L3A8 UniProt NPD GO	PETN_SACHY	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q6ENX4 UniProt NPD GO	PETN_SACOF	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
P61045 UniProt NPD GO	PETN_SPIOL	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
P61046 UniProt NPD GO	PETN_TOBAC	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				29
P61047 UniProt NPD GO	PETN_WHEAT	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.01	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
P19974 UniProt NPD GO	CYC_CAEEL	Cytochrome c	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix				110
P00076 UniProt NPD GO	CYC_EUGGR	Cytochrome c	0.01	-	nuc	0	Mitochondrion; mitochondrial matrix				102
P22342 UniProt NPD GO	CYC_EUGVI	Cytochrome c	0.01	-	nuc	0	Mitochondrion; mitochondrial matrix				102
P00056 UniProt NPD GO	CYC_MAIZE	Cytochrome c	0.01	-	nuc	0	Mitochondrion; mitochondrial matrix				111
P00079 UniProt NPD GO	CYC_TETPY	Cytochrome c	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix				109
P22554 UniProt NPD GO	CCSA_GUITH	Cytochrome c biogenesis protein ccsA	0.01	-	end	8 *	Plastid; chloroplast				301
Q9MUM3 UniProt NPD GO	CCSA_MESVI	Cytochrome c biogenesis protein ccsA	0.01	-	end	8 *	Plastid; chloroplast				305
P80327 UniProt NPD GO	COX4_ONCMY	Cytochrome c oxidase polypeptide 4 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide IV) (Fragments)	0.01	-		0	Mitochondrion; mitochondrial inner membrane				19
P80984 UniProt NPD GO	COX82_THUOB	Cytochrome c oxidase polypeptide VIII-2 (EC 1.9.3.1) (Fragment)	0.01	-		0	Mitochondrion; mitochondrial inner membrane				19
P48772 UniProt NPD GO	COX81_MOUSE	Cytochrome c oxidase polypeptide VIII-heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.01	-	mit	1 *	Mitochondrion; mitochondrial inner membrane				70
P80336 UniProt NPD GO	COX81_RABIT	Cytochrome c oxidase polypeptide VIII-liver/heart (EC 1.9.3.1) (Cytochrome c oxidase subunit 8-1) (F ...	0.01	-		0	Mitochondrion; mitochondrial inner membrane				10
Q8SPI5 UniProt NPD GO	COX82_MACFA	Cytochrome c oxidase polypeptide VIII-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.01	-	nuc	0	Mitochondrion; mitochondrial inner membrane				69
Q863G9 UniProt NPD GO	COX82_PAPAN	Cytochrome c oxidase polypeptide VIII-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.01	-	nuc	0	Mitochondrion; mitochondrial inner membrane				69
Q8SQ78 UniProt NPD GO	COX82_PAPHA	Cytochrome c oxidase polypeptide VIII-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.01	-	nuc	0	Mitochondrion; mitochondrial inner membrane				69
Q862Z8 UniProt NPD GO	COX82_THEGE	Cytochrome c oxidase polypeptide VIII-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.01	-	nuc	0	Mitochondrion; mitochondrial inner membrane				69
Q9TR28 UniProt NPD GO	CX7A1_SHEEP	Cytochrome c oxidase polypeptide VIIa-heart, mitochondrial (EC 1.9.3.1) (Cytochrome c oxidase subuni ...	0.01	-	nuc	0	Mitochondrion; mitochondrial inner membrane				29
P80980 UniProt NPD GO	COXN_THUOB	Cytochrome c oxidase polypeptide VIIb-heart (EC 1.9.3.1) (Fragment)	0.01	-		0					20
P80432 UniProt NPD GO	COX7C_RAT	Cytochrome c oxidase polypeptide VIIc, mitochondrial (EC 1.9.3.1) (VIIIA) (Fragment)	0.01	-		0					10
P80975 UniProt NPD GO	CX6A1_THUOB	Cytochrome c oxidase polypeptide VIa (EC 1.9.3.1) (Fragment)	0.01	-		0	Mitochondrion; mitochondrial inner membrane				9
P43023 UniProt NPD GO	CX6A2_MOUSE	Cytochrome c oxidase polypeptide VIa-heart, mitochondrial precursor (EC 1.9.3.1) (COXVIAH)	0.01	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA]			97
P12074 UniProt NPD GO	CX6A1_HUMAN	Cytochrome c oxidase polypeptide VIa-liver, mitochondrial precursor (EC 1.9.3.1)	0.01	-	mit	1 *	Mitochondrion; mitochondrial inner membrane		602072		109
P80331 UniProt NPD GO	COX6C_ONCMY	Cytochrome c oxidase polypeptide VIc (EC 1.9.3.1) (Fragment)	0.01	-		0	Mitochondrion; mitochondrial inner membrane				10
P55954 UniProt NPD GO	COX5A_CAEEL	Cytochrome c oxidase polypeptide Va, mitochondrial precursor (EC 1.9.3.1)	0.01	-	mit	0	Mitochondrion; mitochondrial inner membrane				174
P80973 UniProt NPD GO	COXC_THUOB	Cytochrome c oxidase polypeptide Va-2 (EC 1.9.3.1) (Fragment)	0.01	-	cyt	0	Mitochondrion; mitochondrial inner membrane				24
P80329 UniProt NPD GO	CX5B1_ONCMY	Cytochrome c oxidase polypeptide Vb-heart (EC 1.9.3.1) (Fragment)	0.01	-		0	Mitochondrion; mitochondrial inner membrane				20
P68540 UniProt NPD GO	COX1_AEGCO	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.01	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				524

You are viewing entries 87851 to 87900 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.