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
P20117 UniProt NPD GO	PSAD_PEA	Photosystem I reaction center subunit II (Photosystem I 21 kDa subunit) (PSI-D) (Fragment)	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Stromal side (By ...				36
P13193 UniProt NPD GO	PSAF_MAIZE	Photosystem I reaction center subunit III (Light-harvesting complex I 17 kDa protein) (PSI-F) (Fragm ...	0.00	-		0	Plastid; chloroplast; chloroplast thylakoid lumen				20
P42047 UniProt NPD GO	PSAE_CUCSA	Photosystem I reaction center subunit IV (PSI-E) (Photosystem I 19.5 kDa protein) (PS I subunit 6) ( ...	0.00	-		0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				19
Q85FK2 UniProt NPD GO	PSAJ_ADICA	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
Q70XY6 UniProt NPD GO	PSAJ_AMBTC	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
Q8M9Y5 UniProt NPD GO	PSAJ_CHAGL	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
Q9TLW5 UniProt NPD GO	PSAJ_CYACA	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
P48117 UniProt NPD GO	PSAJ_CYAPA	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	mit	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				40
Q6B947 UniProt NPD GO	PSAJ_GRATL	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
O78456 UniProt NPD GO	PSAJ_GUITH	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	vac	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
Q5SD35 UniProt NPD GO	PSAJ_HUPLU	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
Q85V00 UniProt NPD GO	PSAJ_LARDC	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				44
P12191 UniProt NPD GO	PSAJ_MARPO	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
Q9MUP4 UniProt NPD GO	PSAJ_MESVI	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
Q9TKZ8 UniProt NPD GO	PSAJ_NEPOL	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
P49485 UniProt NPD GO	PSAJ_ODOSI	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	exc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				41
Q9MTK3 UniProt NPD GO	PSAJ_OENHO	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	vac	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				43
Q68RY6 UniProt NPD GO	PSAJ_PANGI	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
Q6YXM2 UniProt NPD GO	PSAJ_PHYPA	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				41
P69393 UniProt NPD GO	PSAJ_PICGL	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
P69394 UniProt NPD GO	PSAJ_PICMA	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
P69395 UniProt NPD GO	PSAJ_PICRU	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
P41613 UniProt NPD GO	PSAJ_PINTH	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				44
P51194 UniProt NPD GO	PSAJ_PORPU	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
Q8WI01 UniProt NPD GO	PSAJ_PSINU	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				42
P17230 UniProt NPD GO	PSAJ_SPIOL	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				44
P12193 UniProt NPD GO	PSAJ_TOBAC	Photosystem I reaction center subunit IX (PSI-J)	0.00	-	vac	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				44
P82339 UniProt NPD GO	PSAN_PEA	Photosystem I reaction center subunit N (PSI-N) (Fragment)	0.00	-		0	Plastid; chloroplast; chloroplast thylakoid membrane; lumenal side				14
P42053 UniProt NPD GO	PSAN_CUCSA	Photosystem I reaction center subunit N (Photosystem I 7.6 kDa protein) (PSI-N) (PS I subunit 9A) (F ...	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; lumenal side				24
P42050 UniProt NPD GO	PSAH_CUCSA	Photosystem I reaction center subunit VI, chloroplast (PSI-H) (Photosystem I 7.6 kDa protein) (PS I ...	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				24
Q85FL2 UniProt NPD GO	PSAI_ADICA	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P69396 UniProt NPD GO	PSAI_AEGCR	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q6L603 UniProt NPD GO	PSAI_AEGSP	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P69397 UniProt NPD GO	PSAI_AEGTA	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q85CI4 UniProt NPD GO	PSAI_ANTFO	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q9GDV2 UniProt NPD GO	PSAI_CARCL	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q8M9X5 UniProt NPD GO	PSAI_CHAGL	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q9TM24 UniProt NPD GO	PSAI_CYACA	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P48116 UniProt NPD GO	PSAI_CYAPA	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	cyt	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				35
O78462 UniProt NPD GO	PSAI_GUITH	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q9BBS0 UniProt NPD GO	PSAI_LOTJA	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
P30980 UniProt NPD GO	PSAI_MAIZE	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q9MUQ4 UniProt NPD GO	PSAI_MESVI	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q9TL12 UniProt NPD GO	PSAI_NEPOL	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q9MTL2 UniProt NPD GO	PSAI_OENHO	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q6ENG4 UniProt NPD GO	PSAI_ORYNI	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P12186 UniProt NPD GO	PSAI_ORYSA	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q68RZ6 UniProt NPD GO	PSAI_PANGI	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P51387 UniProt NPD GO	PSAI_PORPU	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q6L390 UniProt NPD GO	PSAI_SACHY	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36

You are viewing entries 96451 to 96500 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.