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
Q59ZG8 UniProt NPD GO	DAD2_CANAL	DASH complex subunit DAD2 (Outer kinetochore protein DAD2)	0.10	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				125
Q93ZG7 UniProt NPD GO	RH38_ARATH	DEAD-box ATP-dependent RNA helicase 38 (EC 3.6.1.-) (Protein CRYOPHYTE) (Low expression of osmotical ...	0.10	-	cyt	0	Cytoplasm. Nucleus				496
Q8W4E1 UniProt NPD GO	RH47_ARATH	DEAD-box ATP-dependent RNA helicase 47 (EC 3.6.1.-)	0.10	-	mit	0					551
Q9ST59 UniProt NPD GO	RHT1_WHEAT	DELLA protein RHT-1 (Reduced height protein 1) (Protein Rht-B1/Rht-D1)	0.10	-	cyt	0	Nucleus (By similarity)				623
P32761 UniProt NPD GO	DNE1_CHLEU	DNA endonuclease I-CeuI (EC 3.1.-.-) (23S rRNA intron 1 protein)	0.10	-	cyt	0	Plastid; chloroplast			2EX5	218
Q13216 UniProt NPD GO	ERCC8_HUMAN	DNA excision repair protein ERCC-8 (Cockayne syndrome WD repeat protein CSA)	0.10	-	cyt	0	Nucleus (Probable)	nuclear matrix [IDA] nucleotide-excision repair complex [IDA] nucleus [IDA]	609412		396
O14593 UniProt NPD GO	RFXK_HUMAN	DNA-binding protein RFXANK (Regulatory factor X subunit B) (RFX-B) (Ankyrin repeat family A protein ...	0.10	-	cyt	0	Nucleus		603200		260
Q6DCB7 UniProt NPD GO	DND1_XENLA	Dead end protein homolog 1	0.10	-	nuc	0					371
P82172 UniProt NPD GO	DLP1_ORNAN	Defensin-like peptide 1 (DLP-1)	0.10	-	nuc	0	Secreted protein	extracellular region [IDA]		1B8W	42
Q9GKX2 UniProt NPD GO	DHRS4_RABIT	Dehydrogenase/reductase SDR family member 4 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase/NADP- ...	0.10	-	mit	0	Peroxisome	mitochondrion [ISS]			260
O04015 UniProt NPD GO	P5CS_ACTCH	Delta 1-pyrroline-5-carboxylate synthetase (P5CS) [Includes: Glutamate 5-kinase (EC 2.7.2.11) (Gamma ...	0.10	-	nuc	0					717
Q96480 UniProt NPD GO	P5CS_LYCES	Delta 1-pyrroline-5-carboxylate synthetase (P5CS) [Includes: Glutamate 5-kinase (EC 2.7.2.11) (Gamma ...	0.10	-	nuc	0					717
Q9SFH9 UniProt NPD GO	HEM2_ARATH	Delta-aminolevulinic acid dehydratase, chloroplast precursor (EC 4.2.1.24) (Porphobilinogen synthase ...	0.10	-	mit	0	Plastid; chloroplast (By similarity)				430
P97281 UniProt NPD GO	SGCD_MESAU	Delta-sarcoglycan (SG-delta) (35 kDa dystrophin-associated glycoprotein) (35DAG)	0.10	-	mit	1 *	Sarcolemma; sarcolemmal membrane; single-pass type II membrane protein (By similarity)				289
P82347 UniProt NPD GO	SGCD_MOUSE	Delta-sarcoglycan (SG-delta) (35 kDa dystrophin-associated glycoprotein) (35DAG)	0.10	-	mit	1 *	Sarcolemma; sarcolemmal membrane; single-pass type II membrane protein	integral to plasma membrane [TAS] sarcoglycan complex [IDA]			289
Q13011 UniProt NPD GO	ECH1_HUMAN	Delta3,5-delta2,4-dienoyl-CoA isomerase, mitochondrial precursor (EC 5.3.3.-)	0.10	-	pox	0	Mitochondrion (By similarity). Peroxisome (By similarity)	peroxisome [TAS]	600696		328
O42446 UniProt NPD GO	DNAS1_OREMO	Deoxyribonuclease-1 precursor (EC 3.1.21.1) (Deoxyribonuclease I) (DNase I)	0.10	-	end	1 *	Secretory protein, stored in zymogen granules and found in the nuclear envelope (By similarity)				284
O18998 UniProt NPD GO	DNAS1_RABIT	Deoxyribonuclease-1 precursor (EC 3.1.21.1) (Deoxyribonuclease I) (DNase I)	0.10	-	end	0	Secretory protein, stored in zymogen granules and found in the nuclear envelope (By similarity)				281
O93454 UniProt NPD GO	DMS4_PACDA	Dermaseptin PD-3-6 precursor	0.10	-	exc	0	Secreted protein				71
P14720 UniProt NPD GO	DFRA_PETHY	Dihydroflavonol-4-reductase (EC 1.1.1.219) (DFR) (Dihydrokaempferol 4-reductase)	0.10	-	cyt	2 *					380
O00087 UniProt NPD GO	DLDH_SCHPO	Dihydrolipoyl dehydrogenase, mitochondrial precursor (EC 1.8.1.4) (DLDH) (Dihydrolipoamide dehydroge ...	0.10	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				511
Q9D2G2 UniProt NPD GO	ODO2_MOUSE	Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, m ...	0.10	-	mit	0	Mitochondrion (By similarity)				454
Q8HZ70 UniProt NPD GO	FMO2_PANTR	Dimethylaniline monooxygenase [N-oxide-forming] 2 (EC 1.14.13.8) (Pulmonary flavin-containing monoox ...	0.10	-	end	1	Microsome				534
P36367 UniProt NPD GO	FMO4_RABIT	Dimethylaniline monooxygenase [N-oxide-forming] 4 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.10	-	cyt	0	Microsome				554
Q8K4C0 UniProt NPD GO	FMO5_RAT	Dimethylaniline monooxygenase [N-oxide-forming] 5 (EC 1.14.13.8) (Hepatic flavin-containing monooxyg ...	0.10	-	end	1	Microsome				532
P43477 UniProt NPD GO	DPEP1_SHEEP	Dipeptidase 1 precursor (EC 3.4.13.19) (Microsomal dipeptidase)	0.10	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. Brush border membrane				410
Q9UHL4 UniProt NPD GO	DPP2_HUMAN	Dipeptidyl-peptidase 2 precursor (EC 3.4.14.2) (Dipeptidyl-peptidase II) (DPP II) (Dipeptidyl aminop ...	0.10	-	end	0	Lysosome. Cytoplasmic vesicle				492
Q9EPB1 UniProt NPD GO	DPP2_RAT	Dipeptidyl-peptidase 2 precursor (EC 3.4.14.2) (Dipeptidyl-peptidase II) (DPP II) (Dipeptidyl aminop ...	0.10	-	end	0	Lysosome	cytosol [IMP]			500
Q59NX9 UniProt NPD GO	DPH5_CANAL	Diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.10	-	cyt	0	Cytoplasm (By similarity)				299
P21858 UniProt NPD GO	DISI_AGKHA	Disintegrin halysin (Platelet aggregation activation inhibitor)	0.10	-	nuc	0	Secreted protein				71
O14466 UniProt NPD GO	DPM1_SCHPO	Dolichol-phosphate mannosyltransferase (EC 2.4.1.83) (Dolichol-phosphate mannose synthase) (Dolichyl ...	0.10	-	cyt	0	Endoplasmic reticulum				236
P25235 UniProt NPD GO	RIB2_RAT	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 63 kDa subunit precursor (EC 2.4.1.11 ...	0.10	-	end	3	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	oligosaccharyl transferase complex [ISS]			631
Q9DBG6 UniProt NPD GO	RPN2_MOUSE	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 63 kDa subunit precursor (EC 2.4.1.11 ...	0.10	-	end	3	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				631
P04843 UniProt NPD GO	RIB1_HUMAN	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kDa subunit precursor (EC 2.4.1.11 ...	0.10	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	oligosaccharyl transferase complex [TAS]	180470		607
P83758 UniProt NPD GO	DMT3A_BRARE	Doublesex- and mab-3-related transcription factor 3a (Dmrt7a) (Fragment)	0.10	-	nuc	0	Nucleus (Potential)				31
Q5BIP9 UniProt NPD GO	DUS18_BOVIN	Dual specificity protein phosphatase 18 (EC 3.1.3.48) (EC 3.1.3.16)	0.10	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				188
Q9DAJ5 UniProt NPD GO	DLC2B_MOUSE	Dynein light chain 2B, cytoplasmic	0.10	-	cyt	0	Cytoplasm	cytoplasmic dynein complex [ISS]			96
P38820 UniProt NPD GO	UBA4_YEAST	E1-like URM1 activator protein (Ubiquitin-like protein activator 4)	0.10	-	cyt	0	Cytoplasm	cytoplasm [IDA]			440
P41048 UniProt NPD GO	EFH51_TRYCR	EF-hand protein 5 variant 1 (EFH5) (Calmodulin-ubiquitin-associated protein CUB2.65)	0.10	-	cyt	0					208
P41049 UniProt NPD GO	EFH52_TRYCR	EF-hand protein 5 variant 2 (EFH5) (Calmodulin-ubiquitin-associated protein CUB2.8)	0.10	-	cyt	0					208
P70372 UniProt NPD GO	ELAV1_MOUSE	ELAV-like protein 1 (Hu-antigen R) (HuR) (Elav-like generic protein) (MelG)	0.10	-	cyt	0					326
Q07108 UniProt NPD GO	CD69_HUMAN	Early activation antigen CD69 (Early T-cell activation antigen p60) (GP32/28) (Leu-23) (MLR-3) (EA1) ...	0.10	-	cyt	1 *	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS]	107273	1FM5	199
Q9Y5L3 UniProt NPD GO	ENP2_HUMAN	Ectonucleoside triphosphate diphosphohydrolase 2 (EC 3.6.1.-) (NTPDase2) (Ecto-ATPase) (CD39 antigen ...	0.10	-	end	2 *	Membrane; multi-pass membrane protein (Potential)		602012		495
P19448 UniProt NPD GO	ELYS_HALCO	Egg-lysin precursor (Sperm-lysin)	0.10	-	exc	0					155
Q91UZ4 UniProt NPD GO	EGLN3_MOUSE	Egl nine homolog 3 (EC 1.14.11.-) (Hypoxia-inducible factor prolyl hydroxylase 3) (HIF-prolyl hydrox ...	0.10	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				239
P05303 UniProt NPD GO	EF12_DROME	Elongation factor 1-alpha (EF-1-alpha)	0.10	-	cyt	0	Cytoplasm				462
P19039 UniProt NPD GO	EF1A_APIME	Elongation factor 1-alpha (EF-1-alpha)	0.10	-	cyt	0	Cytoplasm				461
Q00080 UniProt NPD GO	EF1A_PLAFK	Elongation factor 1-alpha (EF-1-alpha)	0.10	-	cyt	0	Cytoplasm				443
Q01520 UniProt NPD GO	EF1A_PODAN	Elongation factor 1-alpha (EF-1-alpha)	0.10	-	cyt	0	Cytoplasm				460
Q01765 UniProt NPD GO	EF1A_PODCU	Elongation factor 1-alpha (EF-1-alpha)	0.10	-	cyt	0	Cytoplasm				461

You are viewing entries 64251 to 64300 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.