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
Q6RI85 UniProt NPD GO	PGK2_PIG	Phosphoglycerate kinase, testis specific (EC 2.7.2.3)	0.04	-	nuc	0	Cytoplasm (By similarity)				416
P25113 UniProt NPD GO	PGAM1_RAT	Phosphoglycerate mutase 1 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (Phosphoglycerate mutase isozyme B ...	0.04	-	cyt	0					253
P53357 UniProt NPD GO	PA12_DOLMA	Phospholipase A1 2 (EC 3.1.1.32) (EC 3.1.1.4) (Allergen Dol m 1.02) (Dol m I)	0.04	-	cyt	0					303
P84651 UniProt NPD GO	PA2_LACMU	Phospholipase A2 (EC 3.1.1.4) (LMPA1) (Phosphatidylcholine 2-acylhydrolase)	0.04	-	cyt	0	Secreted protein				122
Q9I8F8 UniProt NPD GO	PA2_BOTPC	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.04	-	cyt	0	Secreted protein (By similarity)				122
P20258 UniProt NPD GO	PA2A_PSEPO	Phospholipase A2 (EC 3.1.1.4) (Pseudexin A chain) (Phosphatidylcholine 2-acylhydrolase)	0.04	-	nuc	0	Secreted protein				117
Q91506 UniProt NPD GO	PA21B_TRIMU	Phospholipase A2 1 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.04	-	nuc	0	Secreted protein (By similarity)				122
Q9I837 UniProt NPD GO	PA2G_LATSE	Phospholipase A2 GL1-1 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (cPm09)	0.04	-	exc	1 *	Secreted protein (By similarity)				145
Q9DF52 UniProt NPD GO	PA2K_BUNCE	Phospholipase A2 KPA2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.04	-	nuc	0	Secreted protein			1PO8	145
Q9PVE9 UniProt NPD GO	PA2C_AGKRH	Phospholipase A2 S1E6-c precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.04	-	exc	0	Secreted protein (By similarity)				139
Q9I846 UniProt NPD GO	PA2B_LATSE	Phospholipase A2 cL038 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.04	-	exc	1 *	Secreted protein (By similarity)				145
Q9I845 UniProt NPD GO	PA2C_LATSE	Phospholipase A2 cPt09 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.04	-	exc	1 *	Secreted protein (By similarity)				145
Q9IAT9 UniProt NPD GO	PA2H_BOTNE	Phospholipase A2 homolog (Fragment)	0.04	-	nuc	0	Secreted protein (By similarity)			1PC9	119
P82950 UniProt NPD GO	PA2H_ATRNM	Phospholipase A2 homolog (Myotoxin II)	0.04	-	nuc	0	Secreted protein				121
Q90249 UniProt NPD GO	PA2H_BOTJR	Phospholipase A2 homolog 1 (Bothropstoxin I) (BthTX-I) (BtxtxI)	0.04	-	nuc	0	Secreted protein				121
P24605 UniProt NPD GO	PA22_BOTAS	Phospholipase A2 homolog 2 (Myotoxin II)	0.04	-	nuc	0	Secreted protein			1Y4L	121
P82287 UniProt NPD GO	PA22_BOTPI	Phospholipase A2 homolog 2 (Piratoxin-II) (PrTX-II)	0.04	-	nuc	0	Secreted protein			1QLL	121
P17935 UniProt NPD GO	PA2L_VIPAA	Phospholipase A2 homolog, ammodytin L precursor	0.04	-	exc	0	Secreted protein				138
P81165 UniProt NPD GO	PA22_CERGO	Phospholipase A2 homolog, myotoxin II (GODMT-II)	0.04	-	nuc	0	Secreted protein			1GOD	121
Q7LZI1 UniProt NPD GO	PA2I_NAJKA	Phospholipase A2 inhibitor 31 kDa subunit	0.04	-	nuc	0	Secreted protein				188
P82143 UniProt NPD GO	PLIGB_AGKBL	Phospholipase A2 inhibitor subunit gamma B precursor (PLI-gamma B) (Phospholipase A2 inhibitor gamma ...	0.04	-	exc	0	Secreted protein				200
Q90WA7 UniProt NPD GO	PA21B_BUNFA	Phospholipase A2 isozyme 1 precursor (EC 3.1.1.4) (Phospholipase A2 isozyme I) (Phosphatidylcholine ...	0.04	-	exc	0	Secreted protein (By similarity)				145
P21791 UniProt NPD GO	PA22_MICNI	Phospholipase A2 isozyme 2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.04	-	nuc	0	Secreted protein				28
P24645 UniProt NPD GO	PA22_MATBI	Phospholipase A2 isozyme 2 (EC 3.1.1.4) (Phospholipase A2 isozyme II) (Phosphatidylcholine 2-acylhyd ...	0.04	-	cyt	0	Secreted protein				38
P20254 UniProt NPD GO	PA20_PSEAU	Phospholipase A2 isozyme PA-10A (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.04	-	nuc	0	Secreted protein				118
P20253 UniProt NPD GO	PA29_PSEAU	Phospholipase A2 isozyme PA-9C (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.04	-	nuc	0	Secreted protein				118
P24293 UniProt NPD GO	PA21B_ERIMA	Phospholipase A2 isozyme PLA-1 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.04	-	nuc	0	Secreted protein				121
Q8JFG0 UniProt NPD GO	PA21B_VIPAP	Phospholipase A2, B chain precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Vaspin B cha ...	0.04	-	mit	0	Secreted protein (By similarity)				138
P15445 UniProt NPD GO	PA2_NAJNA	Phospholipase A2, acidic (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.04	-	nuc	0	Secreted protein			1PSH	119
P80966 UniProt NPD GO	PA21B_OPHHA	Phospholipase A2, acidic 1 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (APLA2-1) (O ...	0.04	-	exc	0	Secreted protein			1GP7	151
P58464 UniProt NPD GO	PA23_BOTPI	Phospholipase A2-3 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Piratoxin-III) (PrTX-III) (MP ...	0.04	-	nuc	0	Secreted protein			1GMZ	120
P31353 UniProt NPD GO	PMM_CANAL	Phosphomannomutase (EC 5.4.2.8) (PMM)	0.04	-	cyt	0	Cytoplasm				252
Q08224 UniProt NPD GO	THI20_YEAST	Phosphomethylpyrimidine kinase THI20 (EC 2.7.4.7) (HMP-phosphate kinase) (HMP-P kinase)	0.04	-	cyt	0					551
Q9UUK7 UniProt NPD GO	PUR3_SCHPO	Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) (GART) (GAR transformylase) (5'-phosphoribo ...	0.04	-	end	0					207
Q6B8U6 UniProt NPD GO	PSAA_GRATL	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.04	-	end	11	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				752
O78508 UniProt NPD GO	PSAA_GUITH	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.04	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				752
Q6ENH4 UniProt NPD GO	PSAA_ORYNI	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.04	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
P12155 UniProt NPD GO	PSAA_ORYSA	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.04	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
Q6L398 UniProt NPD GO	PSAA_SACHY	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.04	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
Q6ENW3 UniProt NPD GO	PSAA_SACOF	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.04	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
Q9T2L6 UniProt NPD GO	PSAA_SORBI	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.04	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
Q85FM0 UniProt NPD GO	PSAB_ADICA	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.04	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				734
Q85AV8 UniProt NPD GO	PSAB_ANTFO	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.04	-	end	9 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				734
P56342 UniProt NPD GO	PSAB_CHLVU	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.04	-	end	11	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
P19431 UniProt NPD GO	PSAB_EUGGR	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.04	-	end	12 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q6B8U7 UniProt NPD GO	PSAB_GRATL	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.04	-	end	9 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q9MUR7 UniProt NPD GO	PSAB_MESVI	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.04	-	end	12 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q9MTN7 UniProt NPD GO	PSAB_OENHO	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.04	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
P51285 UniProt NPD GO	PSAB_PORPU	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.04	-	end	10 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q6L399 UniProt NPD GO	PSAB_SACHY	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.04	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734

You are viewing entries 77901 to 77950 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.