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
Q36675 UniProt NPD GO	COX3_PLAVI	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.04	-	end	7 *					263
O46586 UniProt NPD GO	COX41_PERPO	Cytochrome c oxidase subunit 4 isoform 1 (EC 1.9.3.1) (Cytochrome c oxidase subunit IV isoform 1) (C ...	0.04	-	nuc	1	Mitochondrion; mitochondrial inner membrane				137
P92505 UniProt NPD GO	CYC2_ASCSU	Cytochrome c type-2	0.04	-	nuc	0	Mitochondrion; mitochondrial matrix				108
Q8UUR3 UniProt NPD GO	CYGB_BRARE	Cytoglobin	0.04	-	mit	0	Cytoplasm (By similarity)				174
Q9CX80 UniProt NPD GO	CYGB_MOUSE	Cytoglobin (Histoglobin) (HGb)	0.04	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS]			190
Q921A4 UniProt NPD GO	CYGB_RAT	Cytoglobin (Histoglobin) (HGb) (Stellate cell activation-associated protein)	0.04	-	cyt	0	Cytoplasm	cytoplasm [NAS]			190
Q9FUJ1 UniProt NPD GO	CKX7_ARATH	Cytokinin dehydrogenase 7 (EC 1.5.99.12) (Cytokinin oxidase 7) (CKO7) (AtCKX7) (AtCKX5)	0.04	-	cyt	0				2EXR	524
P83774 UniProt NPD GO	CAP1_CANAL	Cytoplasmic antigenic protein 1 (Fragments)	0.04	-	nuc	0	Cytoplasm				52
Q6PH37 UniProt NPD GO	ST1S1_BRARE	Cytosolic sulfotransferase 1 (EC 2.8.2.-) (SULT1 ST1)	0.04	-	cyt	0	Cytoplasm	cytoplasm [NAS]			299
P01448 UniProt NPD GO	CX1_NAJME	Cytotoxin 1 (Cytotoxin V-II-1) (Toxin V(II)1)	0.04	-	nuc	0	Secreted protein				60
P01471 UniProt NPD GO	CX1_HEMHA	Cytotoxin 1 (Hemolytic protein 12B)	0.04	-	nuc	0	Secreted protein				61
P01473 UniProt NPD GO	CX3_NAJME	Cytotoxin 3 (Component 3.20)	0.04	-	nuc	0	Secreted protein				61
P01458 UniProt NPD GO	CX3_NAJNI	Cytotoxin 3 (Toxin V-II-3)	0.04	-	nuc	0	Secreted protein				60
P21728 UniProt NPD GO	DRD1_HUMAN	D(1A) dopamine receptor	0.04	-	end	7 *	Cell membrane; multi-pass membrane protein. Endoplasmic reticulum; endoplasmic reticulum membrane; m ...	cell [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	126449	1OZ5	446
O77680 UniProt NPD GO	DRD1_MACMU	D(1A) dopamine receptor	0.04	-	end	7 *	Cell membrane; multi-pass membrane protein. Endoplasmic reticulum; endoplasmic reticulum membrane; m ...				446
P50130 UniProt NPD GO	DRD1_PIG	D(1A) dopamine receptor	0.04	-	end	7 *	Cell membrane; multi-pass membrane protein. Endoplasmic reticulum; endoplasmic reticulum membrane; m ...				446
Q8BLD9 UniProt NPD GO	DRD5_MOUSE	D(1B) dopamine receptor (D(5) dopamine receptor)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				478
O08651 UniProt NPD GO	SERA_RAT	D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (3-PGDH)	0.04	-	cyt	0					532
Q61753 UniProt NPD GO	SERA_MOUSE	D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (3-PGDH) (A10)	0.04	-	cyt	0					532
P50167 UniProt NPD GO	ARDH_PICST	D-arabinitol 2-dehydrogenase [ribulose-forming] (EC 1.1.1.250) (ARDH)	0.04	-	mit	0					278
P29147 UniProt NPD GO	BDH_RAT	D-beta-hydroxybutyrate dehydrogenase, mitochondrial precursor (EC 1.1.1.30) (BDH) (3-hydroxybutyrate ...	0.04	-	mit	0	Mitochondrion; mitochondrial matrix				343
O18756 UniProt NPD GO	GLCE_BOVIN	D-glucuronyl C5 epimerase (EC 5.1.3.-) (Heparin/heparan sulfate:glucuronic acid C5 epimerase)	0.04	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	Golgi apparatus [ISS]			617
P46681 UniProt NPD GO	DLD2_YEAST	D-lactate dehydrogenase [cytochrome] 2, mitochondrial precursor (EC 1.1.2.4) (D-lactate ferricytochr ...	0.04	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			530
Q6CW48 UniProt NPD GO	DAD1_KLULA	DASH complex subunit DAD1 (Outer kinetochore protein DAD1)	0.04	-	cyt	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				95
Q12223 UniProt NPD GO	RAD59_YEAST	DNA repair protein RAD59	0.04	-	nuc	0	Nucleus	nucleus [IGI]			238
P38902 UniProt NPD GO	RPB11_YEAST	DNA-directed RNA polymerase II 13.6 kDa polypeptide (EC 2.7.7.6) (B13.6)	0.04	-	cyt	0	Nucleus	DNA-directed RNA polymerase II, core complex [TAS]		2B8K	120
P16370 UniProt NPD GO	RPB3_YEAST	DNA-directed RNA polymerase II 45 kDa polypeptide (EC 2.7.7.6) (B44.5)	0.04	-	nuc	0	Nucleus	DNA-directed RNA polymerase II, core complex [TAS]		2B8K	318
Q9TLV2 UniProt NPD GO	RPOA_CYACA	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.04	-	cyt	0	Plastid; chloroplast				310
O94616 UniProt NPD GO	RPC5_SCHPO	DNA-directed RNA polymerases I and III 40 kDa polypeptide (EC 2.7.7.6) (AC40)	0.04	-	mit	0	Nucleus				348
P07703 UniProt NPD GO	RPC5_YEAST	DNA-directed RNA polymerases I and III 40 kDa polypeptide (EC 2.7.7.6) (AC40) (C37)	0.04	-	cyt	0	Nucleus	DNA-directed RNA polymerase I complex [TAS] DNA-directed RNA polymerase III complex [TAS]			335
P21793 UniProt NPD GO	PGS2_BOVIN	Decorin precursor (Bone proteoglycan II) (PG-S2)	0.04	-	nuc	0	Secreted protein; extracellular space; extracellular matrix			1XKU	360
O46542 UniProt NPD GO	PGS2_HORSE	Decorin precursor (Bone proteoglycan II) (PG-S2) (Dermatan sulfate proteoglycan II) (DS-PGII)	0.04	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
Q6C0B6 UniProt NPD GO	DCN1_YARLI	Defective in cullin neddylation protein 1	0.04	-	cyt	0					240
P81603 UniProt NPD GO	DEFC_AEDAE	Defensin-C precursor	0.04	-	exc	1 *	Secreted protein				99
Q3U0B3 UniProt NPD GO	DHR11_MOUSE	Dehydrogenase/reductase SDR family member 11 precursor (EC 1.-.-.-)	0.04	-	mit	1 *	Secreted protein (Potential)				260
Q8VBZ0 UniProt NPD GO	DHRSX_MOUSE	Dehydrogenase/reductase SDR family member on chromosome X homolog precursor (EC 1.1.-.-) (SCAD famil ...	0.04	-	end	1 *					280
Q01447 UniProt NPD GO	ERG24_FUSSO	Delta(14)-sterol reductase (EC 1.3.1.70) (C-14 sterol reductase) (Sterol C14-reductase)	0.04	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				485
P38670 UniProt NPD GO	ERG24_NEUCR	Delta(14)-sterol reductase (EC 1.3.1.70) (C-14 sterol reductase) (Sterol C14-reductase)	0.04	-	end	8 *	Membrane; multi-pass membrane protein (Probable)				490
Q8WMV1 UniProt NPD GO	ERG24_BOVIN	Delta(14)-sterol reductase (EC 1.3.1.70) (C-14 sterol reductase) (Sterol C14-reductase) (Delta14-SR) ...	0.04	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				418
Q9DEX7 UniProt NPD GO	FADS_BRARE	Delta-5/delta-6 fatty acid desaturase (EC 1.14.19.-)	0.04	-	cyt	3					444
Q9LMI3 UniProt NPD GO	ADSL5_ARATH	Delta-9 desaturase-like 5 protein (EC 1.14.19.-)	0.04	-	mit	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				299
P10518 UniProt NPD GO	HEM2_MOUSE	Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) (Porphobilinogen synthase) (ALADH)	0.04	-	mit	0					330
P06214 UniProt NPD GO	HEM2_RAT	Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) (Porphobilinogen synthase) (ALADH)	0.04	-	mit	0					330
Q17778 UniProt NPD GO	NUC1_CAEEL	Deoxyribonuclease-2 precursor (EC 3.1.22.1) (Deoxyribonuclease II) (DNase II)	0.04	-	exc	0					375
P43058 UniProt NPD GO	DUT_CANAL	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) (dUTPase) (dUTP pyrophosphatase)	0.04	-	cyt	0					159
Q8T3T0 UniProt NPD GO	SIXA1_MESMA	Depressant insect toxin BmK ITa1 precursor	0.04	-	exc	0	Secreted protein (By similarity)				85
Q9D8K3 UniProt NPD GO	DERL3_MOUSE	Derlin-3 (Degradation in endoplasmic reticulum protein 3) (Der1-like protein 3) (Protein IZP6)	0.04	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				228
O93221 UniProt NPD GO	DMS1_AGAAN	Dermaseptin AA-1-1 precursor	0.04	-	exc	0	Secreted protein				77
P80282 UniProt NPD GO	DMS1_PHYBI	Dermaseptin BI precursor (Dermaseptin B1)	0.04	-	exc	0	Secreted protein				78
Q90ZK3 UniProt NPD GO	DRG1_PHYBI	Dermaseptin DRG1 precursor (Dermaseptin-1)	0.04	-	exc	0	Secreted protein (Probable)				81

You are viewing entries 76801 to 76850 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.