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
Q6ENV4 UniProt NPD GO	PSAI_SACOF	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
P17228 UniProt NPD GO	PSAI_SPIOL	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				33
P69398 UniProt NPD GO	PSAI_WHEAT	Photosystem I reaction center subunit VIII (PSI-I)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q85FP8 UniProt NPD GO	PSAL_CYAME	Photosystem I reaction center subunit XI (PSI-L) (PSI subunit V)	0.00	-	end	2	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				140
Q6B8P4 UniProt NPD GO	PSAL_GRATL	Photosystem I reaction center subunit XI (PSI-L) (PSI subunit V)	0.00	-	end	2	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				150
Q85AJ9 UniProt NPD GO	PSAM_ANTFO	Photosystem I reaction center subunit XII (PSI-M)	0.00	-	mit	1 *	Plastid; chloroplast				32
P56314 UniProt NPD GO	PSAM_CHLVU	Photosystem I reaction center subunit XII (PSI-M)	0.00	-	nuc	1 *	Plastid; chloroplast				31
Q9TLX5 UniProt NPD GO	PSAM_CYACA	Photosystem I reaction center subunit XII (PSI-M)	0.00	-	mit	1 *	Plastid; chloroplast				30
P48185 UniProt NPD GO	PSAM_CYAPA	Photosystem I reaction center subunit XII (PSI-M)	0.00	-	nuc	1 *	Plastid; cyanelle				31
O78448 UniProt NPD GO	PSAM_GUITH	Photosystem I reaction center subunit XII (PSI-M)	0.00	-	nuc	1 *	Plastid; chloroplast				29
Q9MUS2 UniProt NPD GO	PSAM_MESVI	Photosystem I reaction center subunit XII (PSI-M)	0.00	-	nuc	1 *	Plastid; chloroplast				30
P49487 UniProt NPD GO	PSAM_ODOSI	Photosystem I reaction center subunit XII (PSI-M)	0.00	-	nuc	1 *	Plastid; chloroplast				30
P41601 UniProt NPD GO	PSAM_PINTH	Photosystem I reaction center subunit XII (PSI-M)	0.00	-	nuc	1 *	Plastid; chloroplast				30
P51395 UniProt NPD GO	PSAM_PORPU	Photosystem I reaction center subunit XII (PSI-M)	0.00	-	nuc	1 *	Plastid; chloroplast				30
P51370 UniProt NPD GO	PSAK_PORPU	Photosystem I reaction center subunit psaK (Photosystem I subunit X) (PSI-K)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				86
P42051 UniProt NPD GO	PSAK_CUCSA	Photosystem I reaction center subunit psaK, chloroplast (Photosystem I subunit X) (PSI-K) (Photosyst ...	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				33
P14225 UniProt NPD GO	PSAK_CHLRE	Photosystem I reaction center subunit psaK, chloroplast precursor (Photosystem I subunit X) (PSI-K) ...	0.00	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				113
P12358 UniProt NPD GO	PSBR_WHEAT	Photosystem II 10 kDa polypeptide (Fragment)	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				24
P27202 UniProt NPD GO	PSBR_ARATH	Photosystem II 10 kDa polypeptide, chloroplast precursor	0.00	-	nuc	1	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				140
P49108 UniProt NPD GO	PSBR_BRACM	Photosystem II 10 kDa polypeptide, chloroplast precursor	0.00	-	nuc	1	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				141
Q40163 UniProt NPD GO	PSBR_LYCES	Photosystem II 10 kDa polypeptide, chloroplast precursor	0.00	-	cyt	1	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				138
P06183 UniProt NPD GO	PSBR_SOLTU	Photosystem II 10 kDa polypeptide, chloroplast precursor (Light-inducible tissue-specific ST-LS1 pro ...	0.00	-	cyt	1	Plastid; chloroplast; chloroplast thylakoid membrane. Associated with the photosystem II complex				138
Q08684 UniProt NPD GO	PSBC_CHLEU	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.00	-	cyt	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				461
P10898 UniProt NPD GO	PSBC_CHLRE	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				461
P56308 UniProt NPD GO	PSBC_CHLVU	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.00	-	mit	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
Q9TM46 UniProt NPD GO	PSBC_CYACA	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.00	-	end	8 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				460
P48104 UniProt NPD GO	PSBC_CYAPA	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.00	-	end	5 *	Plastid; cyanelle; cyanelle thylakoid membrane; multi-pass membrane protein (By similarity)				461
P28254 UniProt NPD GO	PSBC_GALSU	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
O78426 UniProt NPD GO	PSBC_GUITH	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.00	-	end	5	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
P49472 UniProt NPD GO	PSBC_ODOSI	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				471
P51356 UniProt NPD GO	PSBC_PORPU	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.00	-	end	6	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				487
P69685 UniProt NPD GO	PSBD_ANTMA	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P56761 UniProt NPD GO	PSBD_ARATH	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P56319 UniProt NPD GO	PSBD_CHLVU	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P48079 UniProt NPD GO	PSBD_CYAPA	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; cyanelle; cyanelle thylakoid membrane; multi-pass membrane protein (By similarity)				352
P28253 UniProt NPD GO	PSBD_GALSU	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				351
P11849 UniProt NPD GO	PSBD_HORVU	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
Q9BBT0 UniProt NPD GO	PSBD_LOTJA	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P48184 UniProt NPD GO	PSBD_MAIZE	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
Q9TL00 UniProt NPD GO	PSBD_NEPOL	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P49478 UniProt NPD GO	PSBD_ODOSI	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				351
Q9MTN1 UniProt NPD GO	PSBD_OENHO	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
Q6ENJ1 UniProt NPD GO	PSBD_ORYNI	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P12095 UniProt NPD GO	PSBD_ORYSA	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P06006 UniProt NPD GO	PSBD_PEA	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P41644 UniProt NPD GO	PSBD_PINTH	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
Q9XQA8 UniProt NPD GO	PSBD_POPDE	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P51357 UniProt NPD GO	PSBD_PORPU	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				351
Q6L3B1 UniProt NPD GO	PSBD_SACHY	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
Q6ENY1 UniProt NPD GO	PSBD_SACOF	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353

You are viewing entries 96501 to 96550 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.