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
P69564 UniProt NPD GO	PSBA_GOSHI	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
O78446 UniProt NPD GO	PSBA_GUITH	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				360
Q32389 UniProt NPD GO	PSBA_HETCA	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				360
P05337 UniProt NPD GO	PSBA_HORVU	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P69557 UniProt NPD GO	PSBA_LACSA	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
Q9BBU3 UniProt NPD GO	PSBA_LOTJA	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
O98736 UniProt NPD GO	PSBA_MAGPY	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P48183 UniProt NPD GO	PSBA_MAIZE	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P06402 UniProt NPD GO	PSBA_MARPO	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P04998 UniProt NPD GO	PSBA_MEDSA	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
Q9MUW0 UniProt NPD GO	PSBA_MESVI	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
Q9TL35 UniProt NPD GO	PSBA_NEPOL	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P69561 UniProt NPD GO	PSBA_NICDE	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P69562 UniProt NPD GO	PSBA_NICPL	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P49460 UniProt NPD GO	PSBA_ODOSI	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	mit	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				360
Q6ENJ7 UniProt NPD GO	PSBA_ORYNI	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P12094 UniProt NPD GO	PSBA_ORYSA	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P04999 UniProt NPD GO	PSBA_PETHY	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P50155 UniProt NPD GO	PSBA_PICAB	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P69550 UniProt NPD GO	PSBA_PINCO	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P69551 UniProt NPD GO	PSBA_PINTH	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P36491 UniProt NPD GO	PSBA_POPDE	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P10510 UniProt NPD GO	PSBA_SECCE	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P11848 UniProt NPD GO	PSBA_SINAL	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P69563 UniProt NPD GO	PSBA_SOLNI	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P02957 UniProt NPD GO	PSBA_SOYBN	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P27201 UniProt NPD GO	PSBA_SPIOG	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P69556 UniProt NPD GO	PSBA_TOBAC	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P13910 UniProt NPD GO	PSBA_VICFA	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
Q33282 UniProt NPD GO	PSBA_VIGUN	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P12463 UniProt NPD GO	PSBA_WHEAT	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
Q85C23 UniProt NPD GO	PSBA_ADICA	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1) (PSII D1 pr ...	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
Q85BH5 UniProt NPD GO	PSBA_ANTFO	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1) (PSII D1 pr ...	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P83755 UniProt NPD GO	PSBA_ARATH	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1) (PSII D1 pr ...	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P83756 UniProt NPD GO	PSBA_OENHO	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1) (PSII D1 pr ...	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				352
Q6L3B5 UniProt NPD GO	PSBA_SACHY	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1) (PSII D1 pr ...	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P0C157 UniProt NPD GO	PSBA_SACOF	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1) (PSII D1 pr ...	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P18290 UniProt NPD GO	PSBA_BRANA	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1) (Triazine-r ...	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				353
P06585 UniProt NPD GO	PSBA_PEA	Photosystem Q(B) protein precursor (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P69560 UniProt NPD GO	PSBA_SPIOL	Photosystem Q(B) protein precursor (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.00	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein			1DOP	352
P30943 UniProt NPD GO	PHE2_RHOS2	Phycoerythrin alpha-2 chain, chloroplast precursor	0.00	-	end	1 *	Plastid; chloroplast; chloroplast thylakoid lumen			1XG0	104
Q00433 UniProt NPD GO	PHE3_RHOS2	Phycoerythrin alpha-3 chain, chloroplast precursor	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen			1XG0	128
Q7LZC4 UniProt NPD GO	CAER_PHYSA	Phyllocaerulein	0.00	-		0	Secreted protein				9
P21334 UniProt NPD GO	CRTI_NEUCR	Phytoene dehydrogenase (EC 1.14.99.-) (Phytoene desaturase) (Albino-1 protein)	0.00	-	cyt	1					595
P58261 UniProt NPD GO	PSK_DAUCA	Phytosulfokine-alpha (PSK-alpha) [Contains: Phytosulfokine-beta (PSK-beta)]	0.00	-		0	Secreted protein				5
Q9FEB4 UniProt NPD GO	PSK5_ARATH	Phytosulfokines 5 precursor (AtPSK5) [Contains: Phytosulfokine-alpha (PSK-alpha) (Phytosulfokine-a); ...	0.00	-	exc	0	Secreted protein (By similarity)				77
Q9TWW7 UniProt NPD GO	PDH_PROCL	Pigment-dispersing hormone (PDH)	0.00	-		0	Secreted protein				18
P08871 UniProt NPD GO	PDH_UCAPU	Pigment-dispersing hormone (PDH) (Beta-PDH) (Light-adapting distal retinal pigment hormone) (DRPH)	0.00	-		0	Secreted protein				18
P01209 UniProt NPD GO	PDH_PANBO	Pigment-dispersing hormone (PDH) (Light-adapting distal retinal pigment hormone) (DRPH)	0.00	-		0	Secreted protein				18
P83586 UniProt NPD GO	PDHB_ORCLI	Pigment-dispersing hormone B (PDH B) (Light-adapting distal retinal pigment hormone B) (DRPH B)	0.00	-		0	Secreted protein				18

You are viewing entries 97001 to 97050 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.