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
P81167 UniProt NPD GO	PA2B_MICNI	Phospholipase A2 (EC 3.1.1.4) (Nigroxin B) (Phosphatidylcholine 2-acylhydrolase)	0.00	-	nuc	0	Secreted protein				118
P18999 UniProt NPD GO	PA2_DABRU	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.00	-	cyt	0	Secreted protein				22
Q7LZQ6 UniProt NPD GO	PA2D_BUNFA	Phospholipase A2 13 (EC 3.1.1.4) (Phospholipase A2 XIII) (Cytotoxin XIII) (Phosphatidylcholine 2-acy ...	0.00	-	cyt	0	Secreted protein				31
P59171 UniProt NPD GO	PA25_ECHOC	Phospholipase A2 5 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.00	-	exc	1 *	Secreted protein (By similarity)				138
O42191 UniProt NPD GO	PA27_AGKHP	Phospholipase A2 A (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.00	-	cyt	0	Secreted protein (By similarity)				124
O42190 UniProt NPD GO	PA26_AGKHP	Phospholipase A2 BA2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.00	-	nuc	0	Secreted protein (By similarity)				124
Q910A0 UniProt NPD GO	PA23_ECHCO	Phospholipase A2 EC3 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.00	-	end	0	Secreted protein (By similarity)				138
P31100 UniProt NPD GO	PA27_DABRU	Phospholipase A2 RV-7 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Phospholipase A2 ...	0.00	-	end	0	Secreted protein			1OQS	138
Q9PRT7 UniProt NPD GO	PA24_BOTAS	Phospholipase A2 homolog 4 (Myotoxin IV) (Fragment)	0.00	-	cyt	0	Secreted protein				23
Q8UVZ7 UniProt NPD GO	PA2H_CROAT	Phospholipase A2 homolog Cax-K49 precursor	0.00	-	exc	0	Secreted protein				137
P82142 UniProt NPD GO	PLIA_AGKBL	Phospholipase A2 inhibitor subunit A (PLI-A)	0.00	-	cyt	0	Secreted protein				147
P21755 UniProt NPD GO	PLIA_TRIFL	Phospholipase A2 inhibitor subunit A (PLI-A)	0.00	-	cyt	0	Secreted protein				147
P21756 UniProt NPD GO	PLIB_TRIFL	Phospholipase A2 inhibitor subunit B (PLI-B)	0.00	-	cyt	0	Secreted protein				147
P25072 UniProt NPD GO	PA21B_MICFM	Phospholipase A2 isozyme 1 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.00	-		0	Secreted protein				12
P00602 UniProt NPD GO	PA21B_NAJMO	Phospholipase A2 isozyme CM-I (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.00	-	cyt	0	Secreted protein				118
Q9PWR6 UniProt NPD GO	PA27_VIPPA	Phospholipase A2 isozyme VP7 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.00	-	mit	0	Secreted protein (By similarity)				138
Q98996 UniProt NPD GO	PA2A_VIPPA	Phospholipase A2 isozyme acidic VpaPLA2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) ...	0.00	-	mit	0	Secreted protein				138
Q92147 UniProt NPD GO	PA2P_TRIFL	Phospholipase A2 isozyme pgPLA 1b/pgPLA 2b precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrola ...	0.00	-	mit	0	Secreted protein (By similarity)				138
Q8JIY9 UniProt NPD GO	PA2_TRIJE	Phospholipase A2 jerdoxin precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.00	-	end	0	Secreted protein (By similarity)				138
P82895 UniProt NPD GO	PA24_TRIST	Phospholipase A2, acid 4 (EC 3.1.1.4) (PA2-IV) (PLA2-IV) (Phosphatidylcholine 2-acylhydrolase) (Frag ...	0.00	-	cyt	0	Secreted protein				24
P14418 UniProt NPD GO	PA21B_AGKHP	Phospholipase A2, acidic (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.00	-	cyt	0	Secreted protein			1PSJ	124
Q7LZQ4 UniProt NPD GO	PA2A_AGKCA	Phospholipase A2, acidic (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.00	-	cyt	0	Secreted protein				124
Q910A1 UniProt NPD GO	PA2_VIPAA	Phospholipase A2, ammodytin I1 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (amdI1)	0.00	-	mit	0	Secreted protein (By similarity)				138
P14424 UniProt NPD GO	PA2B_VIPAA	Phospholipase A2, ammodytoxin B precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.00	-	mit	1 *	Secreted protein				138
P31859 UniProt NPD GO	PA2B_VIPBO	Phospholipase A2, basic (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.00	-		0	Secreted protein				12
O70325 UniProt NPD GO	GPX41_MOUSE	Phospholipid hydroperoxide glutathione peroxidase, mitochondrial precursor (EC 1.11.1.12) (PHGPx) (G ...	0.00	-	exc	0	Mitochondrion. Cytoplasm	cytosol [IDA] mitochondrial inner membrane [IDA] mitochondrion [IDA] nuclear envelope [IDA] nucleus [IDA]			197
P36970 UniProt NPD GO	GPX41_RAT	Phospholipid hydroperoxide glutathione peroxidase, mitochondrial precursor (EC 1.11.1.12) (PHGPx) (G ...	0.00	-	exc	0	Mitochondrion. Cytoplasm				197
P36969 UniProt NPD GO	GPX4_HUMAN	Phospholipid hydroperoxide glutathione peroxidase, mitochondrial precursor (EC 1.11.1.12) (PHGPx) (G ...	0.00	-	exc	0	Mitochondrion. Cytoplasm	mitochondrion [TAS]	138322		197
P36968 UniProt NPD GO	GPX4_PIG	Phospholipid hydroperoxide glutathione peroxidase, mitochondrial precursor (EC 1.11.1.12) (PHGPx) (G ...	0.00	-	exc	0	Mitochondrion. Cytoplasm				197
Q9N2J2 UniProt NPD GO	GPX4_BOVIN	Phospholipid hydroperoxide glutathione peroxidase, mitochondrial precursor (EC 1.11.1.12) (PHGPx) (G ...	0.00	-	exc	0	Mitochondrion (By similarity). Cytoplasm (By similarity)				197
Q4AEG9 UniProt NPD GO	GPX4_CEBAP	Phospholipid hydroperoxide glutathione peroxidase, mitochondrial precursor (EC 1.11.1.12) (PHGPx) (G ...	0.00	-	exc	0	Mitochondrion (By similarity). Cytoplasm (By similarity)				197
Q4AEH1 UniProt NPD GO	GPX4_HYLLA	Phospholipid hydroperoxide glutathione peroxidase, mitochondrial precursor (EC 1.11.1.12) (PHGPx) (G ...	0.00	-	exc	0	Mitochondrion (By similarity). Cytoplasm (By similarity)				197
Q4AEH0 UniProt NPD GO	GPX4_MACFU	Phospholipid hydroperoxide glutathione peroxidase, mitochondrial precursor (EC 1.11.1.12) (PHGPx) (G ...	0.00	-	exc	0	Mitochondrion (By similarity). Cytoplasm (By similarity)				197
Q4AEH2 UniProt NPD GO	GPX4_PONPY	Phospholipid hydroperoxide glutathione peroxidase, mitochondrial precursor (EC 1.11.1.12) (PHGPx) (G ...	0.00	-	exc	0	Mitochondrion (By similarity). Cytoplasm (By similarity)				197
Q08975 UniProt NPD GO	THI21_YEAST	Phosphomethylpyrimidine kinase THI21 (EC 2.7.4.7) (HMP-phosphate kinase) (HMP-P kinase)	0.00	-	cyt	0					551
P52421 UniProt NPD GO	PUR2_VIGUN	Phosphoribosylamine--glycine ligase (EC 6.3.4.13) (GARS) (Glycinamide ribonucleotide synthetase) (Ph ...	0.00	-	cyt	0	Plastid; chloroplast				311
O74197 UniProt NPD GO	PUR6_CANGA	Phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) (AIR carboxylase) (AIRC)	0.00	-	cyt	0					570
Q9C1J4 UniProt NPD GO	PUR7_PICPA	Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) (SAICAR synthetase)	0.00	-	cyt	0					304
P81664 UniProt NPD GO	KPPR_PINPS	Phosphoribulokinase (EC 2.7.1.19) (Phosphopentokinase) (PRKase) (PRK) (Fragments)	0.00	-	cyt	0	Plastid; chloroplast				35
P25933 UniProt NPD GO	KPPR1_SELMI	Phosphoribulokinase, 40 kDa subunit (EC 2.7.1.19) (Phosphopentokinase) (Fragment)	0.00	-		0					14
P25934 UniProt NPD GO	KPPR2_SELMI	Phosphoribulokinase, 41 kDa subunit (EC 2.7.1.19) (Phosphopentokinase) (Fragment)	0.00	-		0					15
Q9Y617 UniProt NPD GO	SERC_HUMAN	Phosphoserine aminotransferase (EC 2.6.1.52) (PSAT)	0.00	-	cyt	0					370
Q99K85 UniProt NPD GO	SERC_MOUSE	Phosphoserine aminotransferase (EC 2.6.1.52) (PSAT) (Endometrial progesterone-induced protein) (EPIP ...	0.00	-	cyt	0					370
P10658 UniProt NPD GO	SERC_RABIT	Phosphoserine aminotransferase (EC 2.6.1.52) (PSAT) (Endometrial progesterone-induced protein) (EPIP ...	0.00	-	cyt	0					370
Q5RB83 UniProt NPD GO	SERB_PONPY	Phosphoserine phosphatase (EC 3.1.3.3) (PSP) (O-phosphoserine phosphohydrolase) (PSPase)	0.00	-	cyt	0					225
P78330 UniProt NPD GO	SERB_HUMAN	Phosphoserine phosphatase (EC 3.1.3.3) (PSP) (O-phosphoserine phosphohydrolase) (PSPase) (L-3-phosph ...	0.00	-	cyt	0			172480	1NNL	225
Q85B27 UniProt NPD GO	PSAA_ANTFO	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.00	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				750
Q8MFA3 UniProt NPD GO	PSAA_PHYPA	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.00	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				750
Q85WX3 UniProt NPD GO	PSAA_PINKO	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.00	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				750
P41639 UniProt NPD GO	PSAA_PINTH	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.00	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				753

You are viewing entries 96401 to 96450 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.