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
P81583 UniProt NPD GO	CUPC4_CANPG	Cuticle protein CP1499 (CPCP1499)	0.02	-	cyt	0					148
P81588 UniProt NPD GO	CUC10_CANPG	Cuticle protein CP498 (CPCP498)	0.02	-	cyt	0					50
Q8X1P1 UniProt NPD GO	CUTI_ERYGR	Cutinase precursor (EC 3.1.1.74) (Cutin hydrolase)	0.02	-	vac	0	Secreted protein (By similarity)				236
P22143 UniProt NPD GO	CYAH_MYRVE	Cyanamide hydratase (EC 4.2.1.69) (Urea hydro-lyase)	0.02	-	cyt	0					244
P48126 UniProt NPD GO	RK11_CYAPA	Cyanelle 50S ribosomal protein L11	0.02	-	cyt	0	Plastid; cyanelle				141
P23405 UniProt NPD GO	RK14_CYAPA	Cyanelle 50S ribosomal protein L14	0.02	-	cyt	0	Plastid; cyanelle				122
Q6ZIX2 UniProt NPD GO	SMT1_ORYSA	Cycloartenol-C-24-methyltransferase 1 (EC 2.1.1.41) (24-sterol C-methyltransferase 1) (Sterol C-meth ...	0.02	-	cyt	0					344
Q9M643 UniProt NPD GO	CCI1_ARATH	Cycloeucalenol cycloisomerase (EC 5.5.1.9) (Cycloeucalenol--obtusifoliol isomerase) (Cyclopropyl ste ...	0.02	-	end	6 *	Membrane; multi-pass membrane protein				280
P58435 UniProt NPD GO	CYO3_VIOOD	Cycloviolacin-O3	0.02	-	nuc	0					30
P58436 UniProt NPD GO	CYO4_VIOOD	Cycloviolacin-O4	0.02	-	nuc	0					29
P84637 UniProt NPD GO	CYVA_LEOCM	Cycloviolin-A	0.02	-	nuc	0					31
P84639 UniProt NPD GO	CYVC_LEOCM	Cycloviolin-C	0.02	-	nuc	0					30
P84640 UniProt NPD GO	CYVD_LEOCM	Cycloviolin-D	0.02	-	nuc	0					30
P82152 UniProt NPD GO	ALL1_CYDPO	Cydiastatin-1	0.02	-		0	Secreted protein				8
P82153 UniProt NPD GO	ALL2_CYDPO	Cydiastatin-2	0.02	-		0	Secreted protein				18
P82154 UniProt NPD GO	ALL3_CYDPO	Cydiastatin-3	0.02	-		0	Secreted protein				8
P82155 UniProt NPD GO	ALL4_CYDPO	Cydiastatin-4	0.02	-		0	Secreted protein				8
P82156 UniProt NPD GO	ALL5_CYDPO	Cydiastatin-5	0.02	-		0	Secreted protein				8
Q8WNR9 UniProt NPD GO	CYTA_FELCA	Cystatin A (Allergen Fel d 3)	0.02	-	cyt	0	Cytoplasm (By similarity)				98
P25417 UniProt NPD GO	CYTB_BOVIN	Cystatin B (Stefin B)	0.02	-	cyt	0	Cytoplasm				98
P35481 UniProt NPD GO	CYT_CYPCA	Cystatin precursor (Ovarian cystatin) (P12)	0.02	-	exc	0					129
P50463 UniProt NPD GO	CSRP3_RAT	Cysteine and glycine-rich protein 3 (Cysteine-rich protein 3) (CRP3) (LIM domain protein, cardiac) ( ...	0.02	-	nuc	0	Nucleus. Cytoplasm. Nuclear, associates with the actin cytoskeleton				194
P05993 UniProt NPD GO	PAPA5_CARPA	Cysteine proteinase (EC 3.4.22.-) (Clone PLBPC13) (Fragment)	0.02	-	cyt	0					96
P04988 UniProt NPD GO	CYSP1_DICDI	Cysteine proteinase 1 precursor (EC 3.4.22.-)	0.02	-	cyt	0	Lysosome				343
P32955 UniProt NPD GO	CYSP2_CARCN	Cysteine proteinase 2 (EC 3.4.22.-) (Cysteine proteinase II) (CC-II) (Fragment)	0.02	-	cyt	0					43
Q10992 UniProt NPD GO	CYTA_HELAN	Cysteine proteinase inhibitor A (Cystatin A) (SCA)	0.02	-	cyt	0					82
P30226 UniProt NPD GO	AFP2_BRANA	Cysteine-rich antifungal protein 2 (AFP2) (Fragment)	0.02	-	nuc	0					23
P84803 UniProt NPD GO	CRV24_NAJKA	Cysteine-rich venom protein 24 (CRVP-24k) (Fragment)	0.02	-	nuc	0	Secreted protein	extracellular region [IDA]			23
Q8T0W0 UniProt NPD GO	CVP6_PIMHY	Cysteine-rich venom protein 6 precursor	0.02	-	exc	0	Secreted protein				77
Q924T9 UniProt NPD GO	CLTR2_RAT	Cysteinyl leukotriene receptor 2 (CysLTR2) (RSBPT32)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				309
Q9WTR6 UniProt NPD GO	XCT_MOUSE	Cystine/glutamate transporter (Amino acid transport system xc-) (xCT)	0.02	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				502
P10634 UniProt NPD GO	CP2DQ_RAT	Cytochrome P450 2D26 (EC 1.14.14.1) (CYPIID26) (P450-DB2) (P450-CMF2) (Debrisoquine 4-hydroxylase)	0.02	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				500
Q9LXM3 UniProt NPD GO	C71BZ_ARATH	Cytochrome P450 71B38 (EC 1.14.-.-)	0.02	-	end	0					500
O23976 UniProt NPD GO	C76B1_HELTU	Cytochrome P450 76B1 (EC 1.14.-.-) (7-ethoxycoumarin O-deethylase) (ECOD) (Phenylurea dealkylase)	0.02	-	nuc	1 *					490
Q8WB03 UniProt NPD GO	CYB_ACISI	Cytochrome b	0.02	-	end	8 *					380
O48010 UniProt NPD GO	CYB_ACRDU	Cytochrome b	0.02	-	end	10 *					372
Q9ZZE3 UniProt NPD GO	CYB_AEGAC	Cytochrome b	0.02	-	end	9 *					380
Q8HF67 UniProt NPD GO	CYB_AERVU	Cytochrome b	0.02	-	end	9 *					380
Q5QFW6 UniProt NPD GO	CYB_AKODA	Cytochrome b	0.02	-	end	9 *					379
P21715 UniProt NPD GO	CYB_AKOJE	Cytochrome b	0.02	-	end	9 *					379
Q33887 UniProt NPD GO	CYB_AKOTB	Cytochrome b	0.02	-	end	9 *					379
Q36319 UniProt NPD GO	CYB_ALERU	Cytochrome b	0.02	-	end	9 *					380
Q5VJ52 UniProt NPD GO	CYB_ALLTR	Cytochrome b	0.02	-	end	9 *					379
O78928 UniProt NPD GO	CYB_AMBCI	Cytochrome b	0.02	-	end	9 *					379
O20434 UniProt NPD GO	CYB_ANTLA	Cytochrome b	0.02	-	end	9 *					381
O63537 UniProt NPD GO	CYB_ANTLE	Cytochrome b	0.02	-	end	9 *					381
O63534 UniProt NPD GO	CYB_ANTMI	Cytochrome b	0.02	-	end	9 *					381
Q33800 UniProt NPD GO	CYB_ANTNA	Cytochrome b	0.02	-	end	9 *					381
O79195 UniProt NPD GO	CYB_APTPA	Cytochrome b	0.02	-	end	9 *					380
Q9ZZE4 UniProt NPD GO	CYB_ASIFL	Cytochrome b	0.02	-	end	9 *					380

You are viewing entries 82901 to 82950 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.