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
P69760 UniProt NPD GO	CX6C_CONVC	Conotoxin Vc6.3 precursor	0.00	-	exc	0	Secreted protein				76
P69761 UniProt NPD GO	CX6D_CONVC	Conotoxin Vc6.4 precursor	0.00	-	end	1 *	Secreted protein				81
P69763 UniProt NPD GO	CX6F_CONVC	Conotoxin Vc6.6 precursor	0.00	-	vac	1 *	Secreted protein				76
P69758 UniProt NPD GO	CX6A_CONVC	Conotoxin Vc6a precursor (Conotoxin Vc6.1)	0.00	-	end	1 *	Secreted protein				75
P69759 UniProt NPD GO	CX6B_CONVC	Conotoxin Vc6b precursor (Conotoxin Vc6.2)	0.00	-	vac	0	Secreted protein				77
P0C1C8 UniProt NPD GO	CS7A_CONAF	Conotoxin as7a	0.00	-	nuc	0	Secreted protein				31
P58848 UniProt NPD GO	CX5A_CONAL	Conotoxin au5a	0.00	-		0	Secreted protein				11
Q9BH73 UniProt NPD GO	CXM3A_CONTE	Conotoxin tx3a precursor (Conotoxin Tx3.2)	0.00	-	exc	1 *	Secreted protein				70
P34630 UniProt NPD GO	CUTC_CAEEL	Copper homeostasis protein cutC homolog	0.00	-	mit	0					250
Q9TT99 UniProt NPD GO	ATOX1_CANFA	Copper transport protein ATOX1 (Metal transport protein ATX1)	0.00	-	cyt	0					68
O08997 UniProt NPD GO	ATOX1_MOUSE	Copper transport protein ATOX1 (Metal transport protein ATX1)	0.00	-	nuc	0					68
Q9WUC4 UniProt NPD GO	ATOX1_RAT	Copper transport protein ATOX1 (Metal transport protein ATX1)	0.00	-	cyt	0					68
Q9XT28 UniProt NPD GO	ATOX1_SHEEP	Copper transport protein ATOX1 (Metal transport protein ATX1) (Copper chaperone SAH)	0.00	-	cyt	0					68
Q3T126 UniProt NPD GO	CNIH4_BOVIN	Cornichon homolog 4	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				139
Q9P003 UniProt NPD GO	CNIH4_HUMAN	Cornichon homolog 4	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				139
Q9CX13 UniProt NPD GO	CNIH4_MOUSE	Cornichon homolog 4	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				139
Q5R9M4 UniProt NPD GO	CNIH4_PONPY	Cornichon homolog 4	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				139
Q6P3N5 UniProt NPD GO	CNIH4_XENTR	Cornichon homolog 4	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				139
Q01595 UniProt NPD GO	CCDP_MAIZE	Cortical cell-delineating protein precursor (Root-specific protein ZRP3)	0.00	-	exc	0					129
Q91502 UniProt NPD GO	SC6A8_TORMA	Creatine transporter	0.00	-	end	12 *	Membrane; multi-pass membrane protein (By similarity)				611
P80007 UniProt NPD GO	CRA2_HOMGA	Crustacyanin-A2 subunit	0.00	-	cyt	0	Secreted protein; extracellular space			1GKA	174
P83622 UniProt NPD GO	TXC1D_CUPSA	Cupiennin-1d	0.00	-	cyt	0	Secreted protein				35
Q9HC47 UniProt NPD GO	CTGE1_HUMAN	Cutaneous T-cell lymphoma-associated antigen 1 (cTAGE-1 protein)	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)		608856		74
P80676 UniProt NPD GO	CU02_BLACR	Cuticle protein 2 (Bc-NCP2)	0.00	-	cyt	0					99
P11736 UniProt NPD GO	CU32_LOCMI	Cuticle protein 32 (LM-32) (LM-ACP 32) (Fragment)	0.00	-	cyt	1 *					41
P11737 UniProt NPD GO	CU36_LOCMI	Cuticle protein 36 (LM-36) (LM-ACP 36) (Fragment)	0.00	-	cyt	0					29
P82118 UniProt NPD GO	CUO5_BLACR	Cuticle protein 5 (BcNCP14.6)	0.00	-	mit	1 *					145
P11738 UniProt NPD GO	CU54_LOCMI	Cuticle protein 54 (LM-54) (LM-ACP 54) (Fragment)	0.00	-	cyt	1 *					31
P82120 UniProt NPD GO	CUO7_BLACR	Cuticle protein 7 (BcNCP15.0)	0.00	-	cyt	0					145
P11733 UniProt NPD GO	CU07_LOCMI	Cuticle protein 7 (LM-7) (LM-ACP 7)	0.00	-	cyt	0					131
P11734 UniProt NPD GO	CU08_LOCMI	Cuticle protein 8 (LM-8) (LM-ACP 8)	0.00	-	cyt	0					148
P81581 UniProt NPD GO	CUPC2_CANPG	Cuticle protein CP1243 (CPCP1243)	0.00	-	cyt	0					117
Q94984 UniProt NPD GO	CU15_MANSE	Cuticle protein CP14.6 precursor (MSCP14.6)	0.00	-	exc	0					106
P81585 UniProt NPD GO	CUPC6_CANPG	Cuticle protein CP434 (CPCP434)	0.00	-	cyt	0					43
P81586 UniProt NPD GO	CUPC7_CANPG	Cuticle protein CP459 (CPCP459)	0.00	-	cyt	0					44
P81589 UniProt NPD GO	CUC11_CANPG	Cuticle protein CP575 (CPCP575)	0.00	-	cyt	0					51
P80406 UniProt NPD GO	CUDP_VERCH	Cuticle-degrading protease-like protein (EC 3.4.21.-) (Chymoelastase) (Fragment)	0.00	-		0	Secreted protein				20
P15761 UniProt NPD GO	RR19_CYAPA	Cyanelle 30S ribosomal protein S19	0.00	-	mit	0	Plastid; cyanelle				92
P48124 UniProt NPD GO	RK12_CYAPA	Cyanelle 50S ribosomal protein L12	0.00	-	cyt	0	Plastid; cyanelle				126
P62809 UniProt NPD GO	CPD_WHEAT	Cyclic phosphodiesterase (EC 3.1.4.-) (CPDase) (Fragments)	0.00	-	cyt	0					51
P56872 UniProt NPD GO	CYLA_PSYLO	Cyclopsychotride-A (CPT)	0.00	-	nuc	0					31
P84648 UniProt NPD GO	HYFLB_HYBFL	Cyclotide Hyfl B	0.00	-	nuc	0					32
P82230 UniProt NPD GO	CYO1_VIOOD	Cycloviolacin-O1	0.00	-	nuc	0				1NBJ	30
P58442 UniProt NPD GO	CYO10_VIOOD	Cycloviolacin-O10	0.00	-	nuc	0					30
P58443 UniProt NPD GO	CYO11_VIOOD	Cycloviolacin-O11	0.00	-	nuc	0					31
P83836 UniProt NPD GO	CYO12_VIOOD	Cycloviolacin-O12	0.00	-	nuc	0					29
P58438 UniProt NPD GO	CYO6_VIOOD	Cycloviolacin-O6	0.00	-	nuc	0					31
P58439 UniProt NPD GO	CYO7_VIOOD	Cycloviolacin-O7	0.00	-	nuc	0					30
P58440 UniProt NPD GO	CYO8_VIOOD	Cycloviolacin-O8	0.00	-	nuc	0					30
P84638 UniProt NPD GO	CYVB_LEOCM	Cycloviolin-B	0.00	-	nuc	0					28

You are viewing entries 93251 to 93300 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.