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
P50461 UniProt NPD GO	CSRP3_HUMAN	Cysteine and glycine-rich protein 3 (Cysteine-rich protein 3) (CRP3) (LIM domain protein, cardiac) ( ...	0.03	-	nuc	0	Nucleus (Potential). Cytoplasm. Nuclear, associates with the actin cytoskeleton (Potential)		607482		194
P24744 UniProt NPD GO	CPI2_SOLTU	Cysteine protease inhibitor 2 (PKI-2) (Fragment)	0.03	-	cyt	0					25
P58602 UniProt NPD GO	CPI4_SOLTU	Cysteine protease inhibitor 4 (PCPI-23) (Fragment)	0.03	-	cyt	0	Vacuole (By similarity)				22
P32954 UniProt NPD GO	CYSP1_CARCN	Cysteine proteinase 1 (EC 3.4.22.-) (Cysteine proteinase I) (CC-I) (Fragment)	0.03	-	cyt	0					43
Q05094 UniProt NPD GO	CYSP2_LEIPI	Cysteine proteinase 2 precursor (EC 3.4.22.-) (Amastigote cysteine proteinase A-2)	0.03	-	exc	1 *	Lysosome. Associated with megasome, a unique lysosomal organelle found in intracellular amastigotes ...				444
P36400 UniProt NPD GO	LMCPB_LEIME	Cysteine proteinase B precursor (EC 3.4.22.-)	0.03	-	exc	1 *					443
P82474 UniProt NPD GO	CPGP2_ZINOF	Cysteine proteinase GP-II (EC 3.4.22.-)	0.03	-	mit	0				1CQD	221
Q06445 UniProt NPD GO	CYTI_VIGUN	Cysteine proteinase inhibitor (Cystatin)	0.03	-	cyt	0					97
Q10993 UniProt NPD GO	CYTB_HELAN	Cysteine proteinase inhibitor B (Cystatin B) (SCB)	0.03	-	cyt	0					101
Q43317 UniProt NPD GO	CYSK_CITLA	Cysteine synthase (EC 2.5.1.47) (Beta-pyrazolylalanine synthase) (Beta-PA/CSase) (EC 2.5.1.51) (L-mi ...	0.03	-	cyt	0	Cytoplasm (By similarity)				325
Q00834 UniProt NPD GO	CYSK_SPIOL	Cysteine synthase (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserine (Thiol)-lyase) (CSase ...	0.03	-	mit	0	Cytoplasm				325
P50867 UniProt NPD GO	CYSK_EMENI	Cysteine synthase (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserine (Thiol)-lyase) (CSase ...	0.03	-	mit	0					371
P84538 UniProt NPD GO	CYSK_POPEU	Cysteine synthase (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserine (Thiol)-lyase) (CSase ...	0.03	-	nuc	0	Cytoplasm (By similarity)				29
P31300 UniProt NPD GO	CYSKP_CAPAN	Cysteine synthase, chloroplast precursor (EC 2.5.1.47) (O-acetylserine sulfhydrylase) (O-acetylserin ...	0.03	-	cyt	0	Plastid; chloroplast; chloroplast stroma. Plastid; chromoplast				374
P69240 UniProt NPD GO	AFP1_BRANA	Cysteine-rich antifungal protein 1 (AFP1) (Fragment)	0.03	-	nuc	0	Secreted protein (By similarity)				44
P30227 UniProt NPD GO	AFP1_BRARA	Cysteine-rich antifungal protein 1 (AFP1) (Fragment)	0.03	-	nuc	0					27
P30231 UniProt NPD GO	AFP1_SINAL	Cysteine-rich antifungal protein 1 (AFP1) (M1)	0.03	-	nuc	0				1AYJ	51
Q56K04 UniProt NPD GO	CRIP1_BOVIN	Cysteine-rich protein 1	0.03	-	nuc	0					76
P63254 UniProt NPD GO	CRIP1_MOUSE	Cysteine-rich protein 1 (Cysteine-rich intestinal protein) (CRIP)	0.03	-	nuc	0					76
P63255 UniProt NPD GO	CRIP1_RAT	Cysteine-rich protein 1 (Cysteine-rich intestinal protein) (CRIP)	0.03	-	nuc	0				1IML	76
P50238 UniProt NPD GO	CRIP1_HUMAN	Cysteine-rich protein 1 (Cysteine-rich intestinal protein) (CRIP) (Cysteine-rich heart protein) (hCR ...	0.03	-	nuc	0		cytoplasm [TAS]	123875		76
P12020 UniProt NPD GO	CRIS1_RAT	Cysteine-rich secretory protein 1 precursor (Sperm-coating glycoprotein) (SCP) (Acidic epididymal gl ...	0.03	-	exc	0	Secreted protein				246
Q8T0W5 UniProt NPD GO	CVP1_PIMHY	Cysteine-rich venom protein 1 precursor	0.03	-	mit	0	Secreted protein				85
P16496 UniProt NPD GO	CP52C_CANMA	Cytochrome P450 52A3 (EC 1.14.14.-) (CYPLIIA3) (Alkane-inducible P450-ALK1-A) (P450-CM1) (CYP52A3-A) ...	0.03	-	mit	1 *					522
Q9GQM9 UniProt NPD GO	CP6L1_BLAGE	Cytochrome P450 6l1 (EC 1.14.-.-) (CYPVIL1)	0.03	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				503
Q9LTL8 UniProt NPD GO	C71BO_ARATH	Cytochrome P450 71B24 (EC 1.14.-.-)	0.03	-	end	0					498
O48012 UniProt NPD GO	CYB_ACRMA	Cytochrome b	0.03	-	end	10 *					372
Q8SJB6 UniProt NPD GO	CYB_ACRTE	Cytochrome b	0.03	-	end	9 *					384
Q8LZ97 UniProt NPD GO	CYB_AEQTE	Cytochrome b	0.03	-	end	9 *					378
Q36311 UniProt NPD GO	CYB_ALEGR	Cytochrome b	0.03	-	end	9 *					380
Q8HLD2 UniProt NPD GO	CYB_ALLNG	Cytochrome b	0.03	-	end	9 *					380
P34844 UniProt NPD GO	CYB_ANOGA	Cytochrome b	0.03	-	end	9 *					378
P33501 UniProt NPD GO	CYB_ANOQU	Cytochrome b	0.03	-	end	10 *					378
P34845 UniProt NPD GO	CYB_APILI	Cytochrome b	0.03	-	end	9 *					383
Q36976 UniProt NPD GO	CYB_APTAU	Cytochrome b	0.03	-	end	9 *					379
Q9MLL3 UniProt NPD GO	CYB_AUSSU	Cytochrome b	0.03	-	end	10 *					367
Q9MIX8 UniProt NPD GO	CYB_BRARE	Cytochrome b	0.03	-	end	9 *					380
O48023 UniProt NPD GO	CYB_CANAS	Cytochrome b	0.03	-	end	10 *					371
O48025 UniProt NPD GO	CYB_CANCA	Cytochrome b	0.03	-	end	10 *					371
O78690 UniProt NPD GO	CYB_CARAU	Cytochrome b	0.03	-	end	9 *					380
Q9TDL2 UniProt NPD GO	CYB_CEPCM	Cytochrome b	0.03	-	end	9 *					379
Q9TDL3 UniProt NPD GO	CYB_CEPEU	Cytochrome b	0.03	-	end	9 *					379
Q9TDL5 UniProt NPD GO	CYB_CEPHA	Cytochrome b	0.03	-	end	9 *					379
Q9TDL4 UniProt NPD GO	CYB_CEPHE	Cytochrome b	0.03	-	end	9 *					379
Q94TI3 UniProt NPD GO	CYB_CHASL	Cytochrome b	0.03	-	end	9 *					378
P18946 UniProt NPD GO	CYB_CHICK	Cytochrome b	0.03	-	end	9 *				3BCC	380
Q9B9F5 UniProt NPD GO	CYB_CHROW	Cytochrome b	0.03	-	end	9 *					379
Q8SGQ9 UniProt NPD GO	CYB_CLAFC	Cytochrome b	0.03	-	end	9 *					392
P35075 UniProt NPD GO	CYB_COTJA	Cytochrome b	0.03	-	end	9 *					380
P34197 UniProt NPD GO	CYB_CROLA	Cytochrome b	0.03	-	end	9 *					380

You are viewing entries 79501 to 79550 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.