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
P56676 UniProt NPD GO	TXH1_ORNHU	Huwentoxin-1 precursor (Huwentoxin-I) (HwTx-I)	0.03	-	end	1 *	Secreted protein			1QK6	81
P68422 UniProt NPD GO	TXH8_ORNHU	Huwentoxin-8 (Huwentoxin-VIII) (HwTx-VIII)	0.03	-	nuc	0	Secreted protein				35
Q95058 UniProt NPD GO	CH60_TRIVA	Hydrogenosomal chaperonin HSP60 (Protein Cpn60) (groEL protein) (Heat shock protein 60)	0.03	-	cyt	0	Hydrogenosome				470
P49072 UniProt NPD GO	HYP1_AGABI	Hydrophobin-1 precursor (Hydrophobin-A)	0.03	-	end	0	Secreted protein				112
P49073 UniProt NPD GO	HYP2_AGABI	Hydrophobin-2 precursor (Hydrophobin-C)	0.03	-	end	0	Secreted protein (By similarity)				115
Q9AR73 UniProt NPD GO	HQGT_RAUSE	Hydroquinone glucosyltransferase (EC 2.4.1.218) (Arbutin synthase)	0.03	-	cyt	0					470
P15616 UniProt NPD GO	YM15_PARTE	Hypothetical 10.3 kDa protein (ORF15)	0.03	-	cyt	0					85
P40488 UniProt NPD GO	YIK2_YEAST	Hypothetical 11.3 kDa protein in MOB1-SGA1 intergenic region	0.03	-	cyt	0					101
P37825 UniProt NPD GO	YCX5_CHLRE	Hypothetical 11.4 kDa protein in trnR-chlB intergenic region (ORF101)	0.03	-	cyt	0	Plastid; chloroplast				101
Q9MVP1 UniProt NPD GO	YCF20_CYACA	Hypothetical 11.5 kDa protein ycf20	0.03	-	mit	3 *	Plastid; chloroplast				101
P51214 UniProt NPD GO	YCF20_PORPU	Hypothetical 11.9 kDa protein ycf20 (ORF108)	0.03	-	end	2 *	Plastid; chloroplast				108
P36443 UniProt NPD GO	YCX6_CHLRE	Hypothetical 12.3 kDa protein in petA-petD intergenic region (ORF102)	0.03	-	cyt	0	Plastid; chloroplast				112
P47003 UniProt NPD GO	YJP2_YEAST	Hypothetical 13.7 kDa protein in INO1-IDS2 intergenic region	0.03	-	nuc	1					119
P47038 UniProt NPD GO	YJG4_YEAST	Hypothetical 13.9 kDa protein in SMC3-MRPL8 intergenic region	0.03	-	nuc	0					131
P43624 UniProt NPD GO	YFM6_YEAST	Hypothetical 14.0 kDa protein in HXK1 3'region	0.03	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				122
P47010 UniProt NPD GO	YJO2_YEAST	Hypothetical 14.8 kDa protein in MPI2-YAK1 intergenic region	0.03	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				130
Q03579 UniProt NPD GO	YM8W_YEAST	Hypothetical 17.2 kDa protein in PRC1-ADE4 intergenic region	0.03	-	mit	1 *		endoplasmic reticulum [IDA] endoplasmic reticulum membrane [IDA] nuclear envelope [IDA]			150
P51273 UniProt NPD GO	YCF36_PORPU	Hypothetical 19.2 kDa protein ycf36 (ORF165)	0.03	-	end	2 *	Plastid; chloroplast				165
P43543 UniProt NPD GO	YFG1_YEAST	Hypothetical 25.2 kDa protein in SNZ3-COS4 intergenic region and in SNZ2-COS1 intergenic region	0.03	-	cyt	0					225
Q04018 UniProt NPD GO	YM79_YEAST	Hypothetical 37.4 kDa protein in ZRC1-FAA4 intergenic region	0.03	-	exc	1 *					355
P03885 UniProt NPD GO	YMCF_EMENI	Hypothetical 5.6 kDa protein in COX1 intron (URF-F)	0.03	-	cyt	1 *					48
P51282 UniProt NPD GO	YCXG_PORPU	Hypothetical 7.6 kDa protein in ycf45-accB intergenic region (ORF65)	0.03	-	cyt	0	Plastid; chloroplast				65
O96799 UniProt NPD GO	YCF47_SKECO	Hypothetical 7.7 kDa protein ycf47	0.03	-	end	2 *	Plastid; chloroplast				69
P49542 UniProt NPD GO	YCF47_ODOSI	Hypothetical 8.4 kDa protein ycf47 (ORF74)	0.03	-	end	2 *	Plastid; chloroplast				74
P11673 UniProt NPD GO	YCX1_OENBE	Hypothetical 8.5 kDa protein (ORF B72)	0.03	-	cyt	1 *	Plastid; chloroplast				72
P49535 UniProt NPD GO	YCF40_ODOSI	Hypothetical 8.5 kDa protein ycf40 (ORF73)	0.03	-	cyt	0	Plastid; chloroplast				73
Q86I95 UniProt NPD GO	FA18_DICDI	Hypothetical FAM18-like protein	0.03	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				198
O94404 UniProt NPD GO	YJ3C_SCHPO	Hypothetical UPF0135 protein C126.12 in chromosome III	0.03	-	mit	0					278
Q9W1Y1 UniProt NPD GO	U172_DROME	Hypothetical UPF0172 protein CG3501	0.03	-	cyt	0					203
O43073 UniProt NPD GO	YGW2_SCHPO	Hypothetical UPF0220 protein C8D2.02c in chromosome II	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			170
P34368 UniProt NPD GO	YLJ5_CAEEL	Hypothetical calcium-binding protein C50C3.5	0.03	-	cyt	0					202
P05467 UniProt NPD GO	YKP1_KLULA	Hypothetical killer plasmid pGKl-2 protein 1	0.03	-	cyt	0					224
P34255 UniProt NPD GO	YKA3_CAEEL	Hypothetical protein B0303.3 in chromosome III	0.03	-	mit	0					448
Q10937 UniProt NPD GO	YWS1_CAEEL	Hypothetical protein B0310.1	0.03	-	end	4	Membrane; multi-pass membrane protein (Potential)				228
Q03561 UniProt NPD GO	YKD3_CAEEL	Hypothetical protein B0464.3	0.03	-	nuc	1 *					82
P42172 UniProt NPD GO	YKL5_CAEEL	Hypothetical protein C03C10.5	0.03	-	cyt	0					68
Q11124 UniProt NPD GO	YX13_CAEEL	Hypothetical protein C03F11.3 in chromosome X	0.03	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				563
Q10092 UniProt NPD GO	YAOD_SCHPO	Hypothetical protein C11D3.13 in chromosome I	0.03	-	mit	0					222
Q09875 UniProt NPD GO	YAGC_SCHPO	Hypothetical protein C12G12.12 in chromosome I	0.03	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				324
Q09686 UniProt NPD GO	YA14_SCHPO	Hypothetical protein C13C5.04 in chromosome I	0.03	-	cyt	0					248
O13711 UniProt NPD GO	YDZ4_SCHPO	Hypothetical protein C14C4.04 in chromosome I	0.03	-	cyt	0					267
O13729 UniProt NPD GO	YDO9_SCHPO	Hypothetical protein C15A10.09c in chromosome I	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				288
O13827 UniProt NPD GO	YEEB_SCHPO	Hypothetical protein C19A8.11c in chromosome I	0.03	-	cyt	0					246
Q65ZA5 UniProt NPD GO	YFSA_SCHPO	Hypothetical protein C19D5.10c in chromosome I	0.03	-	exc	2 *	Membrane; multi-pass membrane protein (Potential)				87
Q92340 UniProt NPD GO	YDI2_SCHPO	Hypothetical protein C1F8.02c in chromosome I	0.03	-	exc	0	Membrane; multi-pass membrane protein (Potential)				226
O13912 UniProt NPD GO	YDW6_SCHPO	Hypothetical protein C23C11.06c in chromosome I	0.03	-	end	5 *	Membrane; multi-pass membrane protein				535
Q09239 UniProt NPD GO	YQA1_CAEEL	Hypothetical protein C28F5.1	0.03	-	nuc	0					67
O14143 UniProt NPD GO	YEW7_SCHPO	Hypothetical protein C3G6.07 in chromosome I	0.03	-	cyt	0					125
Q03572 UniProt NPD GO	YLF2_CAEEL	Hypothetical protein C40H1.2	0.03	-	mit	0					208
P34364 UniProt NPD GO	YLH0_CAEEL	Hypothetical protein C48B4.10	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				182

You are viewing entries 80251 to 80300 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.