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
P51221 UniProt NPD GO	PETL_PORPU	Cytochrome b6-f complex subunit 6 (Cytochrome b6-f complex subunit VI) (Cytochrome b6-f complex subu ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q3ZJ65 UniProt NPD GO	PETL_PSEAK	Cytochrome b6-f complex subunit 6 (Cytochrome b6-f complex subunit VI) (Cytochrome b6-f complex subu ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q8WI03 UniProt NPD GO	PETL_PSINU	Cytochrome b6-f complex subunit 6 (Cytochrome b6-f complex subunit VI) (Cytochrome b6-f complex subu ...	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q2PMR6 UniProt NPD GO	PETL_SOYBN	Cytochrome b6-f complex subunit 6 (Cytochrome b6-f complex subunit VI) (Cytochrome b6-f complex subu ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q32RT4 UniProt NPD GO	PETL_STAPU	Cytochrome b6-f complex subunit 6 (Cytochrome b6-f complex subunit VI) (Cytochrome b6-f complex subu ...	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q5K3S2 UniProt NPD GO	PETL_VITVI	Cytochrome b6-f complex subunit 6 (Cytochrome b6-f complex subunit VI) (Cytochrome b6-f complex subu ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q9TLR5 UniProt NPD GO	PETM_CYACA	Cytochrome b6-f complex subunit 7 (Cytochrome b6-f complex subunit VII) (Cytochrome b6-f complex sub ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q85FX8 UniProt NPD GO	PETM_CYAME	Cytochrome b6-f complex subunit 7 (Cytochrome b6-f complex subunit VII) (Cytochrome b6-f complex sub ...	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				32
O78499 UniProt NPD GO	PETM_GUITH	Cytochrome b6-f complex subunit 7 (Cytochrome b6-f complex subunit VII) (Cytochrome b6-f complex sub ...	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				32
P49531 UniProt NPD GO	PETM_ODOSI	Cytochrome b6-f complex subunit 7 (Cytochrome b6-f complex subunit VII) (Cytochrome b6-f complex sub ...	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
P51275 UniProt NPD GO	PETM_PORPU	Cytochrome b6-f complex subunit 7 (Cytochrome b6-f complex subunit VII) (Cytochrome b6-f complex sub ...	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				32
O96810 UniProt NPD GO	PETM_SKECO	Cytochrome b6-f complex subunit 7 (Cytochrome b6-f complex subunit VII) (Cytochrome b6-f complex sub ...	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				25
P80883 UniProt NPD GO	PETM_SPIOL	Cytochrome b6-f complex subunit 7 (Cytochrome b6-f complex subunit VII) (Cytochrome b6-f complex sub ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q85FM5 UniProt NPD GO	PETN_ADICA	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q8MA13 UniProt NPD GO	PETN_CHAGL	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q5IHI1 UniProt NPD GO	PETN_CRYJA	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
P48258 UniProt NPD GO	PETN_CYAPA	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	mit	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				29
Q6B8U0 UniProt NPD GO	PETN_GRATL	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				33
O78498 UniProt NPD GO	PETN_GUITH	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q5SCY5 UniProt NPD GO	PETN_HUPLU	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q33302 UniProt NPD GO	PETN_MAIZE	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
P12177 UniProt NPD GO	PETN_MARPO	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q9MUS4 UniProt NPD GO	PETN_MESVI	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q9TL01 UniProt NPD GO	PETN_NEPOL	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				30
P49527 UniProt NPD GO	PETN_ODOSI	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
P41611 UniProt NPD GO	PETN_PINTH	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
P51276 UniProt NPD GO	PETN_PORPU	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
Q8WI23 UniProt NPD GO	PETN_PSINU	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
O96807 UniProt NPD GO	PETN_SKECO	Cytochrome b6-f complex subunit 8 (Cytochrome b6-f complex subunit VIII) (Cytochrome b6-f complex su ...	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				29
P0C1D4 UniProt NPD GO	PETN_CHLRE	Cytochrome b6-f complex subunit 8, chloroplast precursor (Cytochrome b6-f complex subunit VIII) (Cyt ...	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein			1Q90	36
P00078 UniProt NPD GO	CYC_CRIFA	Cytochrome c	0.00	-	cyt	0	Mitochondrion; mitochondrial matrix				113
P00077 UniProt NPD GO	CYC_CRION	Cytochrome c	0.00	-	cyt	0	Mitochondrion; mitochondrial matrix				112
P18822 UniProt NPD GO	CYC_TRYBB	Cytochrome c (Fragments)	0.00	-	cyt	0	Mitochondrion; mitochondrial matrix				93
P56315 UniProt NPD GO	CCSA_CHLVU	Cytochrome c biogenesis protein ccsA	0.00	-	end	8 *	Plastid; chloroplast				315
P31565 UniProt NPD GO	CCSA_OENBE	Cytochrome c biogenesis protein ccsA (Fragment)	0.00	-	mit	2 *	Plastid; chloroplast				65
P80983 UniProt NPD GO	COX81_THUOB	Cytochrome c oxidase polypeptide VIII-1 (EC 1.9.3.1) (Fragment)	0.00	-		0	Mitochondrion; mitochondrial inner membrane				20
Q8SQ79 UniProt NPD GO	COX82_GORGO	Cytochrome c oxidase polypeptide VIII-liver, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.00	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				69
P80337 UniProt NPD GO	COX81_SHEEP	Cytochrome c oxidase polypeptide VIII-liver/heart (EC 1.9.3.1) (Cytochrome c oxidase subunit 8-1) (F ...	0.00	-		0	Mitochondrion; mitochondrial inner membrane				10
P80335 UniProt NPD GO	COX81_ONCMY	Cytochrome c oxidase polypeptide VIII-liver/heart (EC 1.9.3.1) (Fragment)	0.00	-		0	Mitochondrion; mitochondrial inner membrane				20
P10176 UniProt NPD GO	COX82_HUMAN	Cytochrome c oxidase polypeptide VIII-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.00	-	mit	1 *	Mitochondrion; mitochondrial inner membrane		123870		69
Q862Z9 UniProt NPD GO	COX82_HYLAG	Cytochrome c oxidase polypeptide VIII-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.00	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				69
P60181 UniProt NPD GO	COX82_PANPA	Cytochrome c oxidase polypeptide VIII-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.00	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				69
P60182 UniProt NPD GO	COX82_PANTR	Cytochrome c oxidase polypeptide VIII-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.00	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				69
P60183 UniProt NPD GO	COX82_PONPY	Cytochrome c oxidase polypeptide VIII-liver/heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome ...	0.00	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane				69
P80979 UniProt NPD GO	COX7A_THUOB	Cytochrome c oxidase polypeptide VIIa (EC 1.9.3.1) (Fragment)	0.00	-		0	Mitochondrion; mitochondrial inner membrane				15
P80332 UniProt NPD GO	CX7A2_ONCMY	Cytochrome c oxidase polypeptide VIIa-heart (EC 1.9.3.1) (Fragment)	0.00	-		0	Mitochondrion; mitochondrial inner membrane				10
Q9TRZ8 UniProt NPD GO	CX7A1_CANFA	Cytochrome c oxidase polypeptide VIIa-heart, mitochondrial (EC 1.9.3.1) (Cytochrome c oxidase subuni ...	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane				23
P80333 UniProt NPD GO	CX7A1_ONCMY	Cytochrome c oxidase polypeptide VIIa-liver (EC 1.9.3.1) (VIIIC) (Fragment)	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane				23
Q9TR29 UniProt NPD GO	CX7A2_CANFA	Cytochrome c oxidase polypeptide VIIa-liver/heart, mitochondrial (EC 1.9.3.1) (Cytochrome c oxidase ...	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane				29
Q9TR30 UniProt NPD GO	CX7A2_SHEEP	Cytochrome c oxidase polypeptide VIIa-liver/heart, mitochondrial (EC 1.9.3.1) (Cytochrome c oxidase ...	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane				24

You are viewing entries 94001 to 94050 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.