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
Q92342 UniProt NPD GO	YDI4_SCHPO	Hypothetical protein C1F8.04c in chromosome I	0.01	-	cyt	0					463
Q10354 UniProt NPD GO	YDB1_SCHPO	Hypothetical protein C22E12.01 in chromosome I	0.01	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				374
P34345 UniProt NPD GO	YK67_CAEEL	Hypothetical protein C29E4.7 in chromosome III	0.01	-	nuc	0					250
Q8IG42 UniProt NPD GO	YK69_CAEEL	Hypothetical protein C29E4.9	0.01	-	nuc	0					74
Q9P7Z4 UniProt NPD GO	YGID_SCHPO	Hypothetical protein C2A9.13 in chromosome II	0.01	-	cyt	0					48
Q9Y7L9 UniProt NPD GO	YGJ8_SCHPO	Hypothetical protein C685.08 in chromosome II	0.01	-	cyt	0					97
Q9URX2 UniProt NPD GO	YLX4_SCHPO	Hypothetical protein C922.04 precursor	0.01	-	end	0					117
Q9VGQ9 UniProt NPD GO	Y701_DROME	Hypothetical protein CG14701	0.01	-	cyt	0					86
Q8SWH5 UniProt NPD GO	Y207_ENCCU	Hypothetical protein ECU02_0070	0.01	-	end	8 *					314
Q8SW75 UniProt NPD GO	Y312_ENCCU	Hypothetical protein ECU03_0120	0.01	-	end	6 *					276
Q8SV58 UniProt NPD GO	Y6G7_ENCCU	Hypothetical protein ECU06_1670	0.01	-	cyt	0					200
Q09315 UniProt NPD GO	YQT3_CAEEL	Hypothetical protein F25B5.3	0.01	-	mit	0					376
Q09551 UniProt NPD GO	YQV1_CAEEL	Hypothetical protein F27E5.1 precursor	0.01	-	exc	0					401
O17883 UniProt NPD GO	YX7O_CAEEL	Hypothetical protein F52F12.7 in chromosome I	0.01	-	cyt	0					241
P50439 UniProt NPD GO	YV59_CAEEL	Hypothetical protein F53A9.9	0.01	-	nuc	0					147
Q21102 UniProt NPD GO	YZ3I_CAEEL	Hypothetical protein K01H12.1 in chromosome IV	0.01	-	cyt	0					80
P32740 UniProt NPD GO	YNH2_CAEEL	Hypothetical protein R107.2 in chromosome III	0.01	-	cyt	0					307
P51073 UniProt NPD GO	RJ39_FRAAN	Hypothetical protein RJ39 (Fragment)	0.01	-	cyt	0					88
P82621 UniProt NPD GO	SCRL2_ARATH	Hypothetical protein SCRL2 precursor	0.01	-	mit	1 *					92
Q22361 UniProt NPD GO	YFR3_CAEEL	Hypothetical protein T09E8.3 in chromosome V	0.01	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				145
Q09359 UniProt NPD GO	YS11_CAEEL	Hypothetical protein ZK1307.1	0.01	-	cyt	0					279
Q09362 UniProt NPD GO	YS14_CAEEL	Hypothetical protein ZK1307.4	0.01	-	nuc	0					115
Q95ZI6 UniProt NPD GO	YOJ9_CAEEL	Hypothetical protein ZK353.9	0.01	-	cyt	0					208
P34674 UniProt NPD GO	YO24_CAEEL	Hypothetical protein ZK688.4	0.01	-	mit	1 *					67
O74486 UniProt NPD GO	WTF19_SCHPO	Hypothetical protein wtf19	0.01	-	end	8	Membrane; multi-pass membrane protein (Potential)				393
Q8TF80 UniProt NPD GO	WTF5_SCHPO	Hypothetical protein wtf5	0.01	-	end	3	Membrane; multi-pass membrane protein (Potential)				269
O78493 UniProt NPD GO	YCF43_GUITH	Hypothetical tatC-like protein ycf43	0.01	-	end	7 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				290
Q6WIT9 UniProt NPD GO	HPRT_CANFA	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) (HGPRT) (HGPRTase)	0.01	-	cyt	0	Cytoplasm (By similarity)				217
P43152 UniProt NPD GO	HPRT_LEIDO	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) (HGPRT) (HGPRTase)	0.01	-	cyt	0	Cytoplasm				211
Q7Z096 UniProt NPD GO	CXI4_CONRA	I-superfamily conotoxin R11.4 precursor (r11c) (Fragment)	0.01	-	nuc	0	Secreted protein				44
P69495 UniProt NPD GO	CXI1_CONIM	I-superfamily conotoxin-1 precursor	0.01	-	exc	1 *	Secreted protein (By similarity)				64
P02733 UniProt NPD GO	ANP3_PSEAM	Ice-structuring protein 3 (ISP 3) (Antifreeze peptide 3)	0.01	-	mit	1 *					37
P12100 UniProt NPD GO	ANP1_PACBR	Ice-structuring protein AB1 (ISP AB1) (Antifreeze peptide AB1)	0.01	-	nuc	0					63
P12101 UniProt NPD GO	ANP2_PACBR	Ice-structuring protein AB2 (ISP AB2) (Antifreeze peptide AB2)	0.01	-	cyt	0					63
Q99013 UniProt NPD GO	ANPB_PSEAM	Ice-structuring protein B precursor (ISP B) (Antifreeze protein B) (HPLC8)	0.01	-	vac	0	Secreted protein; extracellular space	extracellular space [IDA]			82
P19605 UniProt NPD GO	ANPE_MACAM	Ice-structuring protein C10 precursor (ISP C10) (Antifreeze protein C10)	0.01	-	exc	0					87
P19604 UniProt NPD GO	ANPD_MACAM	Ice-structuring protein C7 precursor (ISP C7) (Antifreeze protein C7)	0.01	-	exc	0					87
P20421 UniProt NPD GO	ANP5_MYOAE	Ice-structuring protein GS-5 (ISP GS-5) (Antifreeze peptide GS-5)	0.01	-	nuc	0					33
P20617 UniProt NPD GO	ANP8_MYOAE	Ice-structuring protein GS-8 (ISP GS-8) (Antifreeze peptide GS-8)	0.01	-	cyt	0					40
P24028 UniProt NPD GO	ANP1_LYCPO	Ice-structuring protein LP (ISP LP) (Antifreeze protein LP)	0.01	-	cyt	0					66
P07457 UniProt NPD GO	ANP1_MACAM	Ice-structuring protein SP1-C precursor (ISP SP1-C) (Antifreeze protein SP1-C)	0.01	-	exc	0					87
P19607 UniProt NPD GO	ANP5_MACAM	Ice-structuring protein lambda OP-5 precursor (ISP lambda OP-5) (Antifreeze protein lambda OP-5)	0.01	-	exc	0					87
P01748 UniProt NPD GO	HV04_MOUSE	Ig heavy chain V region 23 precursor	0.01	-	vac	0					117
P18526 UniProt NPD GO	HV55_MOUSE	Ig heavy chain V region 345 precursor	0.01	-	vac	0					117
P18529 UniProt NPD GO	HV58_MOUSE	Ig heavy chain V region 5-76 precursor	0.01	-	exc	0				1I8K	117
P18525 UniProt NPD GO	HV54_MOUSE	Ig heavy chain V region 5-84 precursor	0.01	-	mit	0				1AR1	117
P06330 UniProt NPD GO	HV51_MOUSE	Ig heavy chain V region AC38 205.12	0.01	-	nuc	0					118
P01803 UniProt NPD GO	HV34_MOUSE	Ig heavy chain V region AMPC1	0.01	-	cyt	0					113
P04215 UniProt NPD GO	HV02_HETFR	Ig heavy chain V region HC-3 (Fragment)	0.01	-	cyt	0					89
P01805 UniProt NPD GO	HV01_RAT	Ig heavy chain V region IR2 precursor	0.01	-	mit	0					142

You are viewing entries 89101 to 89150 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.