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
Q4X136 UniProt NPD GO	NPC2_ASPFU	Phosphatidylglycerol/phosphatidylinositol transfer protein precursor (PG/PI-TP)	0.02	-	exc	0					175
Q6BV42 UniProt NPD GO	NPC2_DEBHA	Phosphatidylglycerol/phosphatidylinositol transfer protein precursor (PG/PI-TP)	0.02	-	exc	0					196
Q5B0Q1 UniProt NPD GO	NPC2_EMENI	Phosphatidylglycerol/phosphatidylinositol transfer protein precursor (PG/PI-TP)	0.02	-	end	0					169
Q6CNE0 UniProt NPD GO	NPC2_KLULA	Phosphatidylglycerol/phosphatidylinositol transfer protein precursor (PG/PI-TP)	0.02	-	exc	0					173
P62651 UniProt NPD GO	ERI1_YEAST	Phosphatidylinositol N-acetylglucosaminyltransferase ERI1 subunit (Endoplasmic reticulum-associated ...	0.02	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IDA] glycosylphosphatidylinositol-N-acetylglucos... [IPI]			68
P0C1N9 UniProt NPD GO	PIGY_BOVIN	Phosphatidylinositol N-acetylglucosaminyltransferase subunit Y (Phosphatidylinositol-glycan biosynth ...	0.02	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				71
Q6ZDQ1 UniProt NPD GO	AGM1_ORYSA	Phosphoacetylglucosamine mutase (EC 5.4.2.3) (PAGM) (Acetylglucosamine phosphomutase) (N-acetylgluco ...	0.02	-	cyt	0					562
P15396 UniProt NPD GO	PPD1_BOVIN	Phosphodiesterase 1 (EC 3.1.4.1) (Phosphodiesterase I) (5'-exonuclease) (5'-nucleotide phosphodieste ...	0.02	-	cyt	0					61
Q7RVS9 UniProt NPD GO	PPCK_NEUCR	Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49)	0.02	-	cyt	0					561
P29190 UniProt NPD GO	PPCK_HAECO	Phosphoenolpyruvate carboxykinase [GTP] (EC 4.1.1.32) (Phosphoenolpyruvate carboxylase) (PEPCK)	0.02	-	cyt	0					619
P22130 UniProt NPD GO	PPCK_NEOFR	Phosphoenolpyruvate carboxykinase [GTP] (EC 4.1.1.32) (Phosphoenolpyruvate carboxylase) (PEPCK)	0.02	-	cyt	0					608
Q9SNX2 UniProt NPD GO	PGMC_BROIN	Phosphoglucomutase, cytoplasmic (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.02	-	cyt	0	Cytoplasm (By similarity)				581
O94123 UniProt NPD GO	PGK_AGABI	Phosphoglycerate kinase (EC 2.7.2.3)	0.02	-	cyt	0	Cytoplasm				416
P41756 UniProt NPD GO	PGK_ASPOR	Phosphoglycerate kinase (EC 2.7.2.3)	0.02	-	nuc	0	Cytoplasm (By similarity)				417
O02609 UniProt NPD GO	PGK_OXYNO	Phosphoglycerate kinase (EC 2.7.2.3)	0.02	-	cyt	0					419
P09188 UniProt NPD GO	PGK_PENCH	Phosphoglycerate kinase (EC 2.7.2.3)	0.02	-	nuc	0	Cytoplasm (By similarity)				415
O00869 UniProt NPD GO	PGK_PARPR	Phosphoglycerate kinase (EC 2.7.2.3) (Fragment)	0.02	-	cyt	0					367
Q3T0P6 UniProt NPD GO	PGK1_BOVIN	Phosphoglycerate kinase 1 (EC 2.7.2.3)	0.02	-	nuc	0	Cytoplasm (By similarity)				416
P50310 UniProt NPD GO	PGK1_CRIGR	Phosphoglycerate kinase 1 (EC 2.7.2.3)	0.02	-	nuc	0	Cytoplasm (By similarity)				416
P00559 UniProt NPD GO	PGK1_HORSE	Phosphoglycerate kinase 1 (EC 2.7.2.3)	0.02	-	cyt	0	Cytoplasm			2PGK	416
Q60HD8 UniProt NPD GO	PGK1_MACFA	Phosphoglycerate kinase 1 (EC 2.7.2.3)	0.02	-	nuc	0	Cytoplasm (By similarity)				416
P09411 UniProt NPD GO	PGK1_MOUSE	Phosphoglycerate kinase 1 (EC 2.7.2.3)	0.02	-	nuc	0	Cytoplasm (By similarity)				416
Q7SIB7 UniProt NPD GO	PGK1_PIG	Phosphoglycerate kinase 1 (EC 2.7.2.3)	0.02	-	nuc	0	Cytoplasm			1VJD	416
Q5NVB5 UniProt NPD GO	PGK1_PONPY	Phosphoglycerate kinase 1 (EC 2.7.2.3)	0.02	-	nuc	0	Cytoplasm (By similarity)				416
P16617 UniProt NPD GO	PGK1_RAT	Phosphoglycerate kinase 1 (EC 2.7.2.3)	0.02	-	nuc	0	Cytoplasm (By similarity)				416
P00558 UniProt NPD GO	PGK1_HUMAN	Phosphoglycerate kinase 1 (EC 2.7.2.3) (Primer recognition protein 2) (PRP 2)	0.02	-	nuc	0	Cytoplasm		311800		416
P29406 UniProt NPD GO	PGK2_RHINI	Phosphoglycerate kinase 2 (EC 2.7.2.3)	0.02	-	cyt	0	Cytoplasm (By similarity)				417
Q42961 UniProt NPD GO	PGKH_TOBAC	Phosphoglycerate kinase, chloroplast precursor (EC 2.7.2.3)	0.02	-	mit	0	Plastid; chloroplast				481
P12783 UniProt NPD GO	PGKY_WHEAT	Phosphoglycerate kinase, cytosolic (EC 2.7.2.3)	0.02	-	mit	0	Cytoplasm				401
Q27684 UniProt NPD GO	PGKB_LEIME	Phosphoglycerate kinase, cytosolic (EC 2.7.2.3) (Phosphoglycerate kinase B)	0.02	-	cyt	0	Cytoplasm				417
Q27683 UniProt NPD GO	PGKB_LEIMA	Phosphoglycerate kinase, cytosolic (EC 2.7.2.3) (Phosphoglycerate kinase B) (cPGK)	0.02	-	nuc	0	Cytoplasm				417
Q8MIF7 UniProt NPD GO	PGK2_HORSE	Phosphoglycerate kinase, testis specific (EC 2.7.2.3)	0.02	-	nuc	0	Cytoplasm (By similarity)				416
P07205 UniProt NPD GO	PGK2_HUMAN	Phosphoglycerate kinase, testis specific (EC 2.7.2.3)	0.02	-	nuc	0	Cytoplasm (By similarity)	cytosol [NAS]	172270		416
P82612 UniProt NPD GO	PMGY_CANAL	Phosphoglycerate mutase (EC 5.4.2.1) (Phosphoglyceromutase) (PGAM) (MPGM) (BPG-dependent PGAM) (Frag ...	0.02	-	cyt	0	Cytoplasm				41
P83009 UniProt NPD GO	PLMS_LAMNA	Phospholemman-like protein (PLMS) (Fragment)	0.02	-		0	Microsome; microsomal membrane; single-pass type I membrane protein	microsome [IDA]			13
P14556 UniProt NPD GO	PA2_NAJPA	Phospholipase A2 (EC 3.1.1.4) (Nigexine) (Phosphatidylcholine 2-acylhydrolase)	0.02	-	nuc	0	Secreted protein				118
P81166 UniProt NPD GO	PA2A_MICNI	Phospholipase A2 (EC 3.1.1.4) (Nigroxin A) (Phosphatidylcholine 2-acylhydrolase)	0.02	-	nuc	0	Secreted protein				118
Q7M4I6 UniProt NPD GO	PA2_MEGPE	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.02	-	cyt	0	Secreted protein (By similarity)				136
P59066 UniProt NPD GO	PA2_AUSSU	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.02	-		0	Secreted protein				17
P59170 UniProt NPD GO	PA24_ECHCS	Phospholipase A2 4 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.02	-	nuc	0	Secreted protein (By similarity)				139
O42189 UniProt NPD GO	PA25_AGKHP	Phospholipase A2 BA1 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.02	-	nuc	0	Secreted protein (By similarity)				124
Q90ZZ9 UniProt NPD GO	PA21_ECHCO	Phospholipase A2 EC1 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.02	-	nuc	0	Secreted protein (By similarity)				138
Q9PVF3 UniProt NPD GO	PA2F_AGKRH	Phospholipase A2 homolog G6K49 precursor (CRV/TMV/DAV-K49)	0.02	-	exc	0	Secreted protein (By similarity)				138
P24644 UniProt NPD GO	PA21B_MATBI	Phospholipase A2 isozyme 1 (EC 3.1.1.4) (Phospholipase A2 isozyme I) (Phosphatidylcholine 2-acylhydr ...	0.02	-	cyt	0	Secreted protein				38
P00611 UniProt NPD GO	PA21B_LATSE	Phospholipase A2 isozyme 1 precursor (EC 3.1.1.4) (Phospholipase A2 isozyme I) (Phosphatidylcholine ...	0.02	-	exc	1 *	Secreted protein				145
P81478 UniProt NPD GO	PA22_TRIGA	Phospholipase A2 isozyme 2 (EC 3.1.1.4) (Phospholipase A2 isozyme II) (Phosphatidylcholine 2-acylhyd ...	0.02	-	nuc	0	Secreted protein				122
P07037 UniProt NPD GO	PA22_ASPSC	Phospholipase A2 isozyme CM-II (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.02	-	nuc	0	Secreted protein				119
P20251 UniProt NPD GO	PA23_PSEAU	Phospholipase A2 isozyme PA-3 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.02	-	nuc	0	Secreted protein				118
P06860 UniProt NPD GO	PA2X_TRIFL	Phospholipase A2 isozyme PL-X (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.02	-	mit	0	Secreted protein				122
P59265 UniProt NPD GO	PA2B_TRIFL	Phospholipase A2 isozyme PLA-B, basic (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.02	-	mit	0	Secreted protein				122

You are viewing entries 84951 to 85000 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.