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
Q05728 UniProt NPD GO	PUR5_ARATH	Phosphoribosylformylglycinamidine cyclo-ligase, chloroplast precursor (EC 6.3.3.1) (AIRS) (Phosphori ...	0.05	-	mit	0	Plastid; chloroplast				389
P19824 UniProt NPD GO	KPPR_CHLRE	Phosphoribulokinase, chloroplast precursor (EC 2.7.1.19) (Phosphopentokinase) (PRKase) (PRK)	0.05	-	mit	0	Plastid; chloroplast				375
O42282 UniProt NPD GO	RDS2_CHICK	Photoreceptor outer segment membrane glycoprotein 2 (CRDS2)	0.05	-	end	4 *	Membrane; multi-pass membrane protein				364
Q9MUJ6 UniProt NPD GO	PSAA_EQUPA	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A) (Fragment)	0.05	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				719
Q9MUK2 UniProt NPD GO	PSAA_WELMI	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A) (Fragment)	0.05	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				720
P09144 UniProt NPD GO	PSAB_CHLRE	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.05	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				735
P04967 UniProt NPD GO	PSAB_MAIZE	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.05	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				735
Q6ENH5 UniProt NPD GO	PSAB_ORYNI	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.05	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
P12156 UniProt NPD GO	PSAB_ORYSA	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.05	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q9MUN8 UniProt NPD GO	YCF4_MESVI	Photosystem I assembly protein ycf4	0.05	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				187
Q85FH4 UniProt NPD GO	PSAC_ADICA	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q70XW3 UniProt NPD GO	PSAC_AMBTC	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q85AC1 UniProt NPD GO	PSAC_ANTFO	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				81
Q06439 UniProt NPD GO	PSAC_ANTSP	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P62090 UniProt NPD GO	PSAC_ARATH	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P62091 UniProt NPD GO	PSAC_ATRBE	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q7HKX2 UniProt NPD GO	PSAC_CALFE	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q8M9U0 UniProt NPD GO	PSAC_CHAGL	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P56301 UniProt NPD GO	PSAC_CHLVU	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
O19905 UniProt NPD GO	PSAC_CYACA	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q85G47 UniProt NPD GO	PSAC_CYAME	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P31173 UniProt NPD GO	PSAC_CYAPA	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	cyt	0	Plastid; cyanelle; cyanelle thylakoid membrane; peripheral membrane protein; stromal side (By simila ...				80
P62092 UniProt NPD GO	PSAC_LOTJA	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P11601 UniProt NPD GO	PSAC_MAIZE	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q6EVZ9 UniProt NPD GO	PSAC_NYMAL	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P49477 UniProt NPD GO	PSAC_ODOSI	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				81
P62093 UniProt NPD GO	PSAC_OENHO	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P10793 UniProt NPD GO	PSAC_PEA	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q6YXQ2 UniProt NPD GO	PSAC_PHYPA	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				81
Q85WU9 UniProt NPD GO	PSAC_PINKO	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P41649 UniProt NPD GO	PSAC_PINTH	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P51374 UniProt NPD GO	PSAC_PORPU	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P58870 UniProt NPD GO	PSAC_PSINU	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P10098 UniProt NPD GO	PSAC_SPIOL	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P62094 UniProt NPD GO	PSAC_TOBAC	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P42046 UniProt NPD GO	PSAC_CUCSA	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC) (PS ...	0.05	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P51193 UniProt NPD GO	PSAF_PORPU	Photosystem I reaction center subunit III (PSI-F)	0.05	-	vac	2 *	Plastid; chloroplast; chloroplast thylakoid lumen				185
P12352 UniProt NPD GO	PSAE_CHLRE	Photosystem I reaction center subunit IV, chloroplast precursor (PSI-E) (Photosystem I 8.1 kDa prote ...	0.05	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				97
Q9SUI7 UniProt NPD GO	PSAH1_ARATH	Photosystem I reaction center subunit VI-1, chloroplast precursor (PSI-H1)	0.05	-	pox	0	Plastid; chloroplast				145
Q9SUI6 UniProt NPD GO	PSAH2_ARATH	Photosystem I reaction center subunit VI-2, chloroplast precursor (PSI-H1)	0.05	-	mit	0	Plastid; chloroplast				145
P13165 UniProt NPD GO	PSAI_HORVU	Photosystem I reaction center subunit VIII (PSI-I)	0.05	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q41385 UniProt NPD GO	PSAL_SPIOL	Photosystem I reaction center subunit XI, chloroplast precursor (PSI-L) (PSI subunit V)	0.05	-	mit	2	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				216
Q85G61 UniProt NPD GO	PSBY_CYAME	Photosystem II protein Y	0.05	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
P12363 UniProt NPD GO	PSBH_HORVU	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.05	-	gol	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
P24993 UniProt NPD GO	PSBH_MAIZE	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.05	-	gol	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
Q6L373 UniProt NPD GO	PSBH_SACHY	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.05	-	gol	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
Q6ENT5 UniProt NPD GO	PSBH_SACOF	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.05	-	gol	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
Q85FP4 UniProt NPD GO	PSBI_CYAME	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.05	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
Q6B8Q2 UniProt NPD GO	PSBI_GRATL	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.05	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P51236 UniProt NPD GO	PSBI_PORPU	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.05	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38

You are viewing entries 75201 to 75250 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.