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
P18757 UniProt NPD GO	CGL_RAT	Cystathionine gamma-lyase (EC 4.4.1.1) (Gamma-cystathionase) (Probasin-related antigen) (PRB-RA)	0.06	-	cyt	0	Cytoplasm				398
Q28986 UniProt NPD GO	CYTA5_PIG	Cystatin A5 (Stefin A5)	0.06	-	cyt	0	Cytoplasm				103
P21460 UniProt NPD GO	CYTC_MOUSE	Cystatin C precursor (Cystatin 3)	0.06	-	exc	0					140
Q3SZU4 UniProt NPD GO	CDO1_BOVIN	Cysteine dioxygenase type 1 (EC 1.13.11.20) (Cysteine dioxygenase type I) (CDO) (CDO-I)	0.06	-	nuc	0					200
Q6PZ02 UniProt NPD GO	ATG4B_CHICK	Cysteine protease ATG4B (EC 3.4.22.-) (Autophagy-related protein 4 homolog B) (Autophagy-related cys ...	0.06	-	cyt	0	Cytoplasm (Probable)				393
P35591 UniProt NPD GO	CYSP1_LEIPI	Cysteine proteinase 1 precursor (EC 3.4.22.-) (Amastigote cysteine proteinase A-1)	0.06	-	end	1 *					354
P25804 UniProt NPD GO	CYSP_PEA	Cysteine proteinase 15A precursor (EC 3.4.22.-) (Turgor-responsive protein 15A)	0.06	-	exc	0					363
Q06964 UniProt NPD GO	CPP3_ENTHI	Cysteine proteinase 3 precursor (EC 3.4.22.-) (Cysteine proteinase ACP3) (Fragment)	0.06	-	cyt	0	Secreted protein; extracellular space				308
P32957 UniProt NPD GO	CYSP4_CARCN	Cysteine proteinase 4 (EC 3.4.22.-) (Cysteine proteinase IV) (CC-IV) (Fragment)	0.06	-	cyt	0					43
P25775 UniProt NPD GO	LMCPA_LEIME	Cysteine proteinase A precursor (EC 3.4.22.-)	0.06	-	end	1 *					354
Q6Q6R5 UniProt NPD GO	CRIP3_HUMAN	Cysteine-rich protein 3 (CRP3) (Chromosome 6 LIM-only protein) (h6LIMo)	0.06	-	nuc	0	Cytoplasm (By similarity)				217
Q03650 UniProt NPD GO	CRAM_TRYBB	Cysteine-rich, acidic integral membrane protein precursor	0.06	-	nuc	1	Cell surface. Concentrated in the flagellar pocket				945
P57758 UniProt NPD GO	CTNS_ARATH	Cystinosin homolog	0.06	-	end	7 *	Lysosome; lysosomal membrane; multi-pass membrane protein (By similarity)				270
O57525 UniProt NPD GO	CP17A_RANDY	Cytochrome P450 17A1 (EC 1.14.99.9) (CYPXVII) (P450-C17) (P450c17) (Steroid 17-alpha-hydroxylase/17, ...	0.06	-	nuc	0					519
Q69FB6 UniProt NPD GO	CP19A_LAGAC	Cytochrome P450 19A1 (EC 1.14.14.1) (Aromatase) (CYPXIX) (Estrogen synthetase) (P-450AROM)	0.06	-	cyt	2 *	Membrane; peripheral membrane protein				503
P20814 UniProt NPD GO	CP2CD_RAT	Cytochrome P450 2C13, male-specific (EC 1.14.14.1) (CYPIIC13) (P450-G) (P-450g) (UT-5)	0.06	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				490
P56594 UniProt NPD GO	CP2CL_CANFA	Cytochrome P450 2C21 (EC 1.14.14.1) (CYPIIC21) (DM1-1) (Fragment)	0.06	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				487
O93297 UniProt NPD GO	CP2K4_ONCMY	Cytochrome P450 2K4 (EC 1.14.14.1) (CYPIIK4)	0.06	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				504
P05183 UniProt NPD GO	CP3A2_RAT	Cytochrome P450 3A2 (EC 1.14.14.1) (CYPIIIA2) (P450-PCN2) (P450/6-beta-A) (Testosterone 6-beta-hydro ...	0.06	-	nuc	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				504
Q12599 UniProt NPD GO	NOR2_CYLTO	Cytochrome P450 55A3 (EC 1.14.-.-) (Cytochrome P450NOR2)	0.06	-	mit	1					408
P24465 UniProt NPD GO	C71A1_PERAE	Cytochrome P450 71A1 (EC 1.14.-.-) (CYPLXXIA1) (ARP-2)	0.06	-	vac	1 *	Microsome; microsomal membrane; single-pass membrane protein				471
Q9SAB6 UniProt NPD GO	C71AI_ARATH	Cytochrome P450 71A18 (EC 1.14.-.-)	0.06	-	nuc	0					497
Q9LIP5 UniProt NPD GO	C71BW_ARATH	Cytochrome P450 71B35 (EC 1.14.-.-)	0.06	+	mit	2 *					500
Q96514 UniProt NPD GO	C71B7_ARATH	Cytochrome P450 71B7 (EC 1.14.-.-)	0.06	-	vac	1 *					504
Q6F4F5 UniProt NPD GO	C724B_ORYSA	Cytochrome P450 724B1 (EC 1.14.-.-) (OsDWARF11) (Dwarf protein 11)	0.06	-	nuc	1 *					480
Q7XU38 UniProt NPD GO	C87A3_ORYSA	Cytochrome P450 87A3 (EC 1.14.-.-)	0.06	-	end	2 *	Cytoplasmic vesicle (Probable). Associated with vesicular membranes (Probable)				514
Q5VJ59 UniProt NPD GO	CYB_AVAOC	Cytochrome b	0.06	-	end	9 *					379
Q9MLJ8 UniProt NPD GO	CYB_BUNFA	Cytochrome b	0.06	-	end	8 *					370
O48027 UniProt NPD GO	CYB_CASDU	Cytochrome b	0.06	-	end	9 *					371
O48041 UniProt NPD GO	CYB_EPIAN	Cytochrome b	0.06	-	end	10 *					370
P00156 UniProt NPD GO	CYB_HUMAN	Cytochrome b	0.06	-	end	9 *		respiratory chain complex III (sensu Eukary... [NAS]	535000		380
Q9MLK6 UniProt NPD GO	CYB_HYDSE	Cytochrome b	0.06	-	end	8 *					372
Q9MLL6 UniProt NPD GO	CYB_MATBI	Cytochrome b	0.06	-	end	8 *					374
O79213 UniProt NPD GO	CYB_OCETR	Cytochrome b	0.06	-	end	9 *					380
O21205 UniProt NPD GO	CYB_PHAAS	Cytochrome b	0.06	-	end	9 *					380
Q60720 UniProt NPD GO	CY561_MOUSE	Cytochrome b561 (Cytochrome b-561)	0.06	-	end	6 *	Secretory vesicle; secretory vesicle membrane; multi-pass membrane protein (By similarity). Secretor ...				250
Q7XYM4 UniProt NPD GO	UCRIA_CHLS6	Cytochrome b6-f complex iron-sulfur subunit, chloroplast precursor (EC 1.10.99.1) (Rieske iron-sulfu ...	0.06	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein. The transmembran ...				252
Q69GY7 UniProt NPD GO	UCRIA_SOLTU	Cytochrome b6-f complex iron-sulfur subunit, chloroplast precursor (EC 1.10.99.1) (Rieske iron-sulfu ...	0.06	-	mit	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein. The transmembran ...				230
P56205 UniProt NPD GO	CYC_ASPNG	Cytochrome c	0.06	-	cyt	0	Mitochondrion; mitochondrial matrix				111
P62772 UniProt NPD GO	CYC_BRANA	Cytochrome c	0.06	-	nuc	0	Mitochondrion; mitochondrial matrix				111
P62773 UniProt NPD GO	CYC_BRAOL	Cytochrome c	0.06	-	nuc	0	Mitochondrion; mitochondrial matrix				111
O22642 UniProt NPD GO	CYC_FRIAG	Cytochrome c	0.06	-	nuc	0	Mitochondrion; mitochondrial matrix				112
P00031 UniProt NPD GO	CYC_MACMA	Cytochrome c	0.06	-	cyt	0	Mitochondrion; mitochondrial matrix				104
P00013 UniProt NPD GO	CYC_MINSC	Cytochrome c	0.06	-	cyt	0	Mitochondrion; mitochondrial matrix	cytosol [ISS] mitochondrial intermembrane space [ISS]			104
P00055 UniProt NPD GO	CYC_ORYSA	Cytochrome c	0.06	-	nuc	0	Mitochondrion; mitochondrial matrix			1CCR	111
P59218 UniProt NPD GO	CYC_ROSNE	Cytochrome c	0.06	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				108
Q7YR71 UniProt NPD GO	CYC_TRACR	Cytochrome c	0.06	-	nuc	0	Mitochondrion; mitochondrial matrix	cytosol [ISS] mitochondrial intermembrane space [ISS]			104
O21243 UniProt NPD GO	COXZ_RECAM	Cytochrome c oxidase assembly protein ctaG	0.06	-	mit	1 *					182
Q9UTF6 UniProt NPD GO	COX6_SCHPO	Cytochrome c oxidase polypeptide VI, mitochondrial precursor (EC 1.9.3.1)	0.06	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				140
P61904 UniProt NPD GO	COX81_CANFA	Cytochrome c oxidase polypeptide VIII-heart (EC 1.9.3.1) (Cytochrome c oxidase subunit 8-1) (Fragmen ...	0.06	-		0	Mitochondrion; mitochondrial inner membrane				10

You are viewing entries 71851 to 71900 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.