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
O16136 UniProt NPD GO	DEF1_STOCA	Defensin-1 precursor	0.01	-	end	1 *	Secreted protein				79
O16137 UniProt NPD GO	DEF2_STOCA	Defensin-2 precursor	0.01	-	vac	0	Secreted protein				97
P83669 UniProt NPD GO	DEFA_ANOCP	Defensin-A	0.01	-	cyt	0	Secreted protein				43
Q08298 UniProt NPD GO	RD22_ARATH	Dehydration-responsive protein RD22 precursor	0.01	-	mit	0					392
Q99L04 UniProt NPD GO	DHRS1_MOUSE	Dehydrogenase/reductase SDR family member 1 (EC 1.1.-.-)	0.01	-	pox	0		mitochondrial inner membrane [IDA]			313
Q71R50 UniProt NPD GO	DHR11_CHICK	Dehydrogenase/reductase SDR family member 11 precursor (EC 1.-.-.-)	0.01	-	mit	0	Secreted protein (Potential)				255
Q9P2X7 UniProt NPD GO	DEC1_HUMAN	Deleted in esophageal cancer 1 (Candidate tumor suppressor CTS9)	0.01	-	cyt	0			604767		70
P01158 UniProt NPD GO	DSIP_RABIT	Delta sleep-inducing peptide (DSIP)	0.01	-		0					9
P78575 UniProt NPD GO	ERG24_ASCIM	Delta(14)-sterol reductase (EC 1.3.1.70) (C-14 sterol reductase) (Sterol C14-reductase)	0.01	-	end	8 *	Membrane; multi-pass membrane protein (Probable)				430
Q09195 UniProt NPD GO	ERG24_SCHPO	Delta(14)-sterol reductase (EC 1.3.1.70) (C-14 sterol reductase) (Sterol C14-reductase)	0.01	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				424
Q08558 UniProt NPD GO	DCI1_YEAST	Delta(3,5)-delta(2,4)-dienoyl-CoA isomerase (EC 5.3.3.-)	0.01	-	mit	0	Peroxisome	peroxisomal matrix [IDA]			271
P78568 UniProt NPD GO	PUT2_AGABI	Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12) (P5C dehydrogenase)	0.01	-	cyt	0	Cytoplasm				546
P78974 UniProt NPD GO	HEM2_SCHPO	Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) (Porphobilinogen synthase) (ALADH)	0.01	-	cyt	0					329
P69749 UniProt NPD GO	CXD6A_CONBU	Delta-conotoxin BVIA (Delta-BVIA)	0.01	-	cyt	0	Secreted protein (By similarity)				27
P60513 UniProt NPD GO	CXD6A_CONER	Delta-conotoxin EVIA (Delta-EVIA)	0.01	-	cyt	0	Secreted protein			1G1Z	32
P58913 UniProt NPD GO	CXD6A_CONPU	Delta-conotoxin PVIA precursor (Lockjaw peptide)	0.01	-	exc	1 *	Secreted protein				81
P24159 UniProt NPD GO	CXDB_CONTE	Delta-conotoxin TxVIB (TxIB)	0.01	-	nuc	0	Secreted protein				27
P79291 UniProt NPD GO	OPRD_PIG	Delta-type opioid receptor (DOR-1) (Fragment)	0.01	-	end	5 *	Membrane; multi-pass membrane protein				228
P07448 UniProt NPD GO	DFTS_RAT	Dentinal fluid transport-stimulating peptide (DFT-stimulating peptide)	0.01	-		0					20
Q9AXR0 UniProt NPD GO	DHYS_LYCES	Deoxyhypusine synthase (EC 2.5.1.46)	0.01	-	cyt	0					381
Q75EW4 UniProt NPD GO	DHYS_ASHGO	Deoxyhypusine synthase (EC 2.5.1.46) (DHS)	0.01	-	cyt	0					382
Q6EWQ6 UniProt NPD GO	DHYS_BOVIN	Deoxyhypusine synthase (EC 2.5.1.46) (DHS)	0.01	-	cyt	0					369
Q6AY53 UniProt NPD GO	DHYS_RAT	Deoxyhypusine synthase (EC 2.5.1.46) (DHS)	0.01	-	cyt	0					369
Q6E4Q0 UniProt NPD GO	DUT_ANTLO	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) (dUTPase) (dUTP pyrophosphatase)	0.01	-	cyt	0					143
Q6FKQ6 UniProt NPD GO	DUT_CANGA	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) (dUTPase) (dUTP pyrophosphatase)	0.01	-	cyt	0					144
Q6CQN7 UniProt NPD GO	DUT_KLULA	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) (dUTPase) (dUTP pyrophosphatase)	0.01	-	cyt	0					148
P33317 UniProt NPD GO	DUT_YEAST	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) (dUTPase) (dUTP pyrophosphatase)	0.01	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			147
Q95WX6 UniProt NPD GO	SIXB_MESMA	Depressant insect neurotoxin BmK ITb precursor	0.01	-	exc	0	Secreted protein				85
Q8I0K7 UniProt NPD GO	SIXI_MESMA	Depressant scorpion toxin BmKIM precursor	0.01	-	exc	0	Secreted protein (By similarity)				85
Q93561 UniProt NPD GO	DERL1_CAEEL	Derlin-1 (DER1-like protein 1) (cDerlin-1) (Coelomocyte uptake defective protein 2)	0.01	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				245
Q99J56 UniProt NPD GO	DERL1_MOUSE	Derlin-1 (Degradation in endoplasmic reticulum protein 1) (Der1-like protein 1)	0.01	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [ISS] integral to endoplasmic reticulum membrane [ISS]			251
Q21997 UniProt NPD GO	DERL2_CAEEL	Derlin-2 (DER1-like protein 2) (cDerlin-2)	0.01	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	integral to endoplasmic reticulum membrane [ISS]			237
P83639 UniProt NPD GO	DDSL_PHYDS	Dermadistinctin-L (DD L)	0.01	-	cyt	0	Secreted protein				28
P83641 UniProt NPD GO	DDQ1_PHYDS	Dermadistinctin-Q1 (DD Q1)	0.01	-	cyt	0	Secreted protein				30
P83637 UniProt NPD GO	DS01_PHYOR	Dermaseptin-01 (DS 01)	0.01	-	cyt	0	Secreted protein				29
P80279 UniProt NPD GO	DMS3_PHYSA	Dermaseptin-3 (DS III)	0.01	-	cyt	0	Secreted protein				30
P80280 UniProt NPD GO	DMS4_PHYSA	Dermaseptin-4 (DS IV)	0.01	-	cyt	0	Secreted protein			2DD6	27
P84523 UniProt NPD GO	DEM_PHYHY	Dermorphin (Hyp-6)	0.01	-		0	Secreted protein				7
P79729 UniProt NPD GO	DHH_BRARE	Desert hedgehog protein (DHH) (Fragment)	0.01	-	cyt	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				88
P46519 UniProt NPD GO	LEA14_SOYBN	Desiccation protectant protein Lea14 homolog	0.01	-	nuc	0					152
P17898 UniProt NPD GO	CPT1_YEAST	Diacylglycerol cholinephosphotransferase (EC 2.7.8.2) (SN-1,2-diacylglycerol cholinephosphotransfera ...	0.01	-	end	8 *	Microsome; microsomal membrane; multi-pass membrane protein				386
Q3T0Q0 UniProt NPD GO	SAT1_BOVIN	Diamine acetyltransferase 1 (EC 2.3.1.57) (Spermidine/spermine N(1)-acetyltransferase 1) (SSAT) (SSA ...	0.01	-	cyt	0	Cytoplasm (By similarity)				171
Q9JHW6 UniProt NPD GO	SAT1_CRIGR	Diamine acetyltransferase 1 (EC 2.3.1.57) (Spermidine/spermine N(1)-acetyltransferase 1) (SSAT) (SSA ...	0.01	-	cyt	0	Cytoplasm (By similarity)				171
P21673 UniProt NPD GO	SAT1_HUMAN	Diamine acetyltransferase 1 (EC 2.3.1.57) (Spermidine/spermine N(1)-acetyltransferase 1) (SSAT) (SSA ...	0.01	-	cyt	0	Cytoplasm		313020	2G3T	171
P48026 UniProt NPD GO	SAT1_MOUSE	Diamine acetyltransferase 1 (EC 2.3.1.57) (Spermidine/spermine N(1)-acetyltransferase 1) (SSAT) (SSA ...	0.01	-	cyt	0	Cytoplasm				171
P49431 UniProt NPD GO	SAT1_MUSSA	Diamine acetyltransferase 1 (EC 2.3.1.57) (Spermidine/spermine N(1)-acetyltransferase 1) (SSAT) (SSA ...	0.01	-	cyt	0	Cytoplasm (Potential)				171
Q28999 UniProt NPD GO	SAT1_PIG	Diamine acetyltransferase 1 (EC 2.3.1.57) (Spermidine/spermine N(1)-acetyltransferase 1) (SSAT) (SSA ...	0.01	-	cyt	0	Cytoplasm (By similarity)				171
P56702 UniProt NPD GO	DBIL5_RAT	Diazepam-binding inhibitor-like 5 (Endozepine-like peptide) (ELP)	0.01	-	cyt	0	Cytoplasm (By similarity)				87
P25784 UniProt NPD GO	CYSP3_HOMAM	Digestive cysteine proteinase 3 precursor (EC 3.4.22.-)	0.01	-	exc	0					321
P24846 UniProt NPD GO	DAPA1_WHEAT	Dihydrodipicolinate synthase 1, chloroplast precursor (EC 4.2.1.52) (DHDPS 1)	0.01	-	mit	0	Plastid; chloroplast				388

You are viewing entries 88051 to 88100 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.