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
O57385 UniProt NPD GO	PA2H_AGKAC	Phospholipase A2 homolog Dac-K49II precursor	0.03	-	exc	0	Secreted protein (By similarity)			1MG6	138
Q9YGJ7 UniProt NPD GO	PA28_VIPPA	Phospholipase A2 homolog VP8 precursor	0.03	-	mit	1 *	Secreted protein (By similarity)				137
P49121 UniProt NPD GO	PA2M_AGKCL	Phospholipase A2 homolog precursor (Myotoxin)	0.03	-	exc	0	Secreted protein			1S8I	137
P00615 UniProt NPD GO	PA22_OXYSC	Phospholipase A2 homolog, taipoxin beta chain	0.03	-	nuc	0	Secreted protein				118
Q90WA8 UniProt NPD GO	PA22_BUNFA	Phospholipase A2 isozyme 2 precursor (EC 3.1.1.4) (Phospholipase A2 isozyme II) (Phosphatidylcholine ...	0.03	-	exc	0	Secreted protein (By similarity)				145
P00605 UniProt NPD GO	PA23_NAJNG	Phospholipase A2 isozyme 3 (EC 3.1.1.4) (Phospholipase A2 isozyme III) (Phosphatidylcholine 2-acylhy ...	0.03	-	nuc	0	Secreted protein				118
P00627 UniProt NPD GO	PA26_BUNFA	Phospholipase A2 isozyme 6 (EC 3.1.1.4) (Phospholipase A2 isozyme VI) (Toxin VI) (Phosphatidylcholin ...	0.03	-	nuc	0	Secreted protein				118
P00604 UniProt NPD GO	PA23_NAJMO	Phospholipase A2 isozyme CM-III (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.03	-	nuc	0	Secreted protein				118
P14615 UniProt NPD GO	PA2N_BUNFA	Phospholipase A2 isozyme III, neutral (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.03	-	nuc	0	Secreted protein				118
P20250 UniProt NPD GO	PA2G_PSEAU	Phospholipase A2 isozyme PA-1G (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.03	-	nuc	0	Secreted protein				117
P20252 UniProt NPD GO	PA25_PSEAU	Phospholipase A2 isozyme PA-5 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.03	-	nuc	0	Secreted protein				118
P80003 UniProt NPD GO	PA22_HELSU	Phospholipase A2 isozyme PA4 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) [Contains: Phospholi ...	0.03	-	nuc	0	Secreted protein				142
P59264 UniProt NPD GO	PA2A_TRIFL	Phospholipase A2 isozyme PLA-A, basic (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.03	-	mit	0	Secreted protein				122
Q9PUG8 UniProt NPD GO	PA216_AUSSU	Phospholipase A2 isozyme S16-19 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA1 ...	0.03	-	exc	1 *	Secreted protein (By similarity)				152
P08872 UniProt NPD GO	PA2_AIPLA	Phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.03	-	exc	0	Secreted protein				144
P59067 UniProt NPD GO	PA2S_AUSSU	Phospholipase A2, superbin a (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.03	-	mit	0	Secreted protein				62
P59068 UniProt NPD GO	PA2T_AUSSU	Phospholipase A2, superbin b (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.03	-	mit	0	Secreted protein				57
P59069 UniProt NPD GO	PA2U_AUSSU	Phospholipase A2, superbin c (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.03	-	nuc	0	Secreted protein				46
P30811 UniProt NPD GO	PA2C_PSETE	Phospholipase A2, textilotoxin C chain (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.03	-	nuc	0	Secreted protein				118
P52032 UniProt NPD GO	GPX1_ARATH	Phospholipid hydroperoxide glutathione peroxidase 1, chloroplast precursor (EC 1.11.1.12) (PHGPx)	0.03	-	mit	0	Plastid; chloroplast; chloroplast stroma				236
Q8VDG5 UniProt NPD GO	PPCS_MOUSE	Phosphopantothenate--cysteine ligase (EC 6.3.2.5) (Phosphopantothenoylcysteine synthetase) (PPC synt ...	0.03	-	cyt	0					311
P52877 UniProt NPD GO	SERC_SPIOL	Phosphoserine aminotransferase, chloroplast precursor (EC 2.6.1.52) (PSAT)	0.03	-	mit	0	Plastid; chloroplast (Potential)				430
Q99LS3 UniProt NPD GO	SERB_MOUSE	Phosphoserine phosphatase (EC 3.1.3.3) (PSP) (O-phosphoserine phosphohydrolase) (PSPase)	0.03	-	cyt	0					225
P42052 UniProt NPD GO	PSAO_CUCSA	Photosystem 1 reaction center subunit 8 (Photosystem I 17.5 kDa protein) (Fragment)	0.03	-		0	Plastid; chloroplast				15
Q8M9W0 UniProt NPD GO	PSAA_CHAGL	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.03	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				748
P05310 UniProt NPD GO	PSAA_PEA	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.03	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				758
P51284 UniProt NPD GO	PSAA_PORPU	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.03	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				752
P06511 UniProt NPD GO	PSAA_SPIOL	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.03	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				750
Q9MUJ7 UniProt NPD GO	PSAA_ARAAA	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A) (Fragment)	0.03	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				716
Q9MUK0 UniProt NPD GO	PSAA_CYCRE	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A) (Fragment)	0.03	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				717
Q9MUJ9 UniProt NPD GO	PSAA_DRIWI	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A) (Fragment)	0.03	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				717
Q70Y04 UniProt NPD GO	PSAB_AMBTC	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q33332 UniProt NPD GO	PSAB_ANTMA	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
P56767 UniProt NPD GO	PSAB_ARATH	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q8S8X5 UniProt NPD GO	PSAB_ATRBE	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q7YJX3 UniProt NPD GO	PSAB_CALFE	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	9 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
P36492 UniProt NPD GO	PSAB_CHLMO	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	vac	10 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				735
Q9TLQ6 UniProt NPD GO	PSAB_CYACA	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q85FY6 UniProt NPD GO	PSAB_CYAME	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	10 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				732
Q9XQV2 UniProt NPD GO	PSAB_HETTR	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	11	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				776
Q5SD11 UniProt NPD GO	PSAB_HUPLU	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
P58385 UniProt NPD GO	PSAB_LOTJA	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q9TKW1 UniProt NPD GO	PSAB_NEPOL	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q6EW49 UniProt NPD GO	PSAB_NYMAL	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	9 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q68S07 UniProt NPD GO	PSAB_PANGI	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	9 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
P05311 UniProt NPD GO	PSAB_PEA	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	11	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q8MFA2 UniProt NPD GO	PSAB_PHYPA	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	9 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q85WX0 UniProt NPD GO	PSAB_PINKO	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	9 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				734
P41640 UniProt NPD GO	PSAB_PINTH	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	9 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
P06512 UniProt NPD GO	PSAB_SPIOL	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	9 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				734

You are viewing entries 81051 to 81100 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.