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
Q96UF2 UniProt NPD GO	G3P2_RHIRA	Glyceraldehyde-3-phosphate dehydrogenase 2 (EC 1.2.1.12) (GAPDH 2)	0.00	-	cyt	0	Cytoplasm (By similarity)				338
P00358 UniProt NPD GO	G3P2_YEAST	Glyceraldehyde-3-phosphate dehydrogenase 2 (EC 1.2.1.12) (GAPDH 2)	0.00	-	mit	0	Cytoplasm	cell wall (sensu Fungi) [IDA] cytoplasm [IDA] lipid particle [IDA]			331
P32809 UniProt NPD GO	G3P2_CAEBR	Glyceraldehyde-3-phosphate dehydrogenase 2 (EC 1.2.1.12) (GAPDH-2)	0.00	-	cyt	0	Cytoplasm				341
P17329 UniProt NPD GO	G3P2_CAEEL	Glyceraldehyde-3-phosphate dehydrogenase 2 (EC 1.2.1.12) (GAPDH-2)	0.00	-	cyt	0	Cytoplasm				341
P17730 UniProt NPD GO	G3P2_TRIKO	Glyceraldehyde-3-phosphate dehydrogenase 2 (EC 1.2.1.12) (GAPDH2)	0.00	-	cyt	0	Cytoplasm				337
P07487 UniProt NPD GO	G3P2_DROME	Glyceraldehyde-3-phosphate dehydrogenase 2 (EC 1.2.1.12) (Glyceraldehyde-3-phosphate dehydrogenase I ...	0.00	-	cyt	0	Cytoplasm				332
O44104 UniProt NPD GO	G3P2_DROPS	Glyceraldehyde-3-phosphate dehydrogenase 2 (EC 1.2.1.12) (Glyceraldehyde-3-phosphate dehydrogenase I ...	0.00	-	cyt	0	Cytoplasm				332
O44105 UniProt NPD GO	G3P2_DROSU	Glyceraldehyde-3-phosphate dehydrogenase 2 (EC 1.2.1.12) (Glyceraldehyde-3-phosphate dehydrogenase I ...	0.00	-	cyt	0	Cytoplasm				304
Q96UF1 UniProt NPD GO	G3P3_RHIRA	Glyceraldehyde-3-phosphate dehydrogenase 3 (EC 1.2.1.12) (GAPDH 3)	0.00	-	cyt	0	Cytoplasm (By similarity)				339
P00359 UniProt NPD GO	G3P3_YEAST	Glyceraldehyde-3-phosphate dehydrogenase 3 (EC 1.2.1.12) (GAPDH 3)	0.00	-	mit	0	Cytoplasm	cell wall (sensu Fungi) [IDA] cytoplasm [IDA] lipid particle [IDA]			331
P17330 UniProt NPD GO	G3P3_CAEEL	Glyceraldehyde-3-phosphate dehydrogenase 3 (EC 1.2.1.12) (GAPDH-3)	0.00	-	cyt	0	Cytoplasm				341
P17331 UniProt NPD GO	G3P4_CAEEL	Glyceraldehyde-3-phosphate dehydrogenase 4 (EC 1.2.1.12) (GAPDH-4)	0.00	-	cyt	0	Cytoplasm				341
P84544 UniProt NPD GO	G3PB_POPEU	Glyceraldehyde-3-phosphate dehydrogenase B (EC 1.2.1.13) (NADP-dependent glyceraldehydephosphate deh ...	0.00	-		0					10
P25857 UniProt NPD GO	G3PB_ARATH	Glyceraldehyde-3-phosphate dehydrogenase B, chloroplast precursor (EC 1.2.1.13) (NADP-dependent glyc ...	0.00	-	mit	0	Plastid; chloroplast; chloroplast membrane; peripheral membrane protein. Plastid; chloroplast; chlor ...				447
P12860 UniProt NPD GO	G3PB_SPIOL	Glyceraldehyde-3-phosphate dehydrogenase B, chloroplast precursor (EC 1.2.1.13) (NADP-dependent glyc ...	0.00	-	mit	0	Plastid; chloroplast				451
P25861 UniProt NPD GO	G3PC_ANTMA	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.00	-	cyt	0	Cytoplasm				337
P25858 UniProt NPD GO	G3PC_ARATH	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.00	-	cyt	0	Cytoplasm				338
P34920 UniProt NPD GO	G3PC_CHOCR	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.00	-	cyt	0	Cytoplasm				335
P34921 UniProt NPD GO	G3PC_DIACA	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.00	-	cyt	0	Cytoplasm				338
Q39769 UniProt NPD GO	G3PC_GINBI	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.00	-	cyt	0	Cytoplasm				340
P54270 UniProt NPD GO	G3PC_GRAVE	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.00	-	cyt	0	Cytoplasm				335
P26520 UniProt NPD GO	G3PC_PETHY	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.00	-	cyt	0	Cytoplasm				337
P34924 UniProt NPD GO	G3PC_PINSY	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.00	-	cyt	0	Cytoplasm				340
P04796 UniProt NPD GO	G3PC_SINAL	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.00	-	cyt	0	Cytoplasm				337
Q41595 UniProt NPD GO	G3PC_TAXBA	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	0.00	-	cyt	0	Cytoplasm				340
P09094 UniProt NPD GO	G3PC_TOBAC	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12) (Fragment)	0.00	-	cyt	0	Cytoplasm				326
Q01558 UniProt NPD GO	G3PC_LEIME	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12) (GAPDH)	0.00	-	mit	0	Cytoplasm				330
P08735 UniProt NPD GO	G3PC_MAIZE	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 1 (EC 1.2.1.12)	0.00	-	cyt	0	Cytoplasm				337
Q09054 UniProt NPD GO	G3PD_MAIZE	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 2 (EC 1.2.1.12)	0.00	-	cyt	0	Cytoplasm				337
Q27890 UniProt NPD GO	G3PG_LEIME	Glyceraldehyde-3-phosphate dehydrogenase, glycosomal (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Glycosome			1I33	360
P22513 UniProt NPD GO	G3PG_TRYCR	Glyceraldehyde-3-phosphate dehydrogenase, glycosomal (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Glycosome			1QXS	359
P80534 UniProt NPD GO	G3P1_JACOR	Glyceraldehyde-3-phosphate dehydrogenase, muscle (EC 1.2.1.12) (GAPDH)	0.00	-	cyt	0	Cytoplasm				363
P13443 UniProt NPD GO	DHGY_CUCSA	Glycerate dehydrogenase (EC 1.1.1.29) (NADH-dependent hydroxypyruvate reductase) (HPR) (GDH)	0.00	-	cyt	0	Peroxisome				382
Q14410 UniProt NPD GO	GLPK2_HUMAN	Glycerol kinase, testis specific 2 (EC 2.7.1.30) (ATP:glycerol 3-phosphotransferase) (Glycerokinase) ...	0.00	-	cyt	0	Mitochondrion; mitochondrial outer membrane; peripheral membrane protein; cytoplasmic side (By simil ...	cytoplasm [NAS] mitochondrial outer membrane [NAS]	600148		553
Q9UVF4 UniProt NPD GO	GPD1_YARLI	Glycerol-3-phosphate dehydrogenase [NAD+] 1 (EC 1.1.1.8)	0.00	-	mit	0	Cytoplasm (Probable)				398
Q6ZYA7 UniProt NPD GO	GPD2_PICJA	Glycerol-3-phosphate dehydrogenase [NAD+] 2 (EC 1.1.1.8)	0.00	-	cyt	0					394
Q09845 UniProt NPD GO	GPD2_SCHPO	Glycerol-3-phosphate dehydrogenase [NAD+] 2 (EC 1.1.1.8)	0.00	-	cyt	0	Cytoplasm (Potential)				373
Q27556 UniProt NPD GO	GPDA_DROAE	Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic (EC 1.1.1.8) (GPD-C) (GPDH-C)	0.00	-	cyt	0	Cytoplasm				349
Q27567 UniProt NPD GO	GPDA_DROEZ	Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic (EC 1.1.1.8) (GPD-C) (GPDH-C)	0.00	-	cyt	0	Cytoplasm				349
O97463 UniProt NPD GO	GPDA_DROKA	Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic (EC 1.1.1.8) (GPD-C) (GPDH-C)	0.00	-	cyt	0	Cytoplasm (By similarity)				359
P13706 UniProt NPD GO	GPDA_DROME	Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic (EC 1.1.1.8) (GPD-C) (GPDH-C)	0.00	-	cyt	0	Cytoplasm				363
Q27928 UniProt NPD GO	GPDA_DROPS	Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic (EC 1.1.1.8) (GPD-C) (GPDH-C)	0.00	-	cyt	0	Cytoplasm				353
P07735 UniProt NPD GO	GPDA_DROVI	Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic (EC 1.1.1.8) (GPD-C) (GPDH-C)	0.00	-	cyt	0	Cytoplasm				352
O57656 UniProt NPD GO	GPDA_FUGRU	Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic (EC 1.1.1.8) (GPD-C) (GPDH-C)	0.00	-	cyt	0	Cytoplasm				351
P20821 UniProt NPD GO	GCSH_BOVIN	Glycine cleavage system H protein, mitochondrial precursor	0.00	-	mit	0	Mitochondrion				173
P11183 UniProt NPD GO	GCSH_CHICK	Glycine cleavage system H protein, mitochondrial precursor	0.00	-	mit	0	Mitochondrion				164
P46485 UniProt NPD GO	GCSH_FLATR	Glycine cleavage system H protein, mitochondrial precursor	0.00	-	mit	0	Mitochondrion				165
P23434 UniProt NPD GO	GCSH_HUMAN	Glycine cleavage system H protein, mitochondrial precursor	0.00	-	mit	0	Mitochondrion	glycine cleavage complex [TAS] mitochondrion [TAS]	605899		173
P16048 UniProt NPD GO	GCSH_PEA	Glycine cleavage system H protein, mitochondrial precursor	0.00	-	mit	0	Mitochondrion			1HTP	165
Q39733 UniProt NPD GO	GCSH_FLAAU	Glycine cleavage system H protein, mitochondrial precursor (Fragment)	0.00	-	mit	0	Mitochondrion				143

You are viewing entries 94851 to 94900 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.