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
Q6ENI0 UniProt NPD GO	ATPI_ORYNI	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				247
P12083 UniProt NPD GO	ATPI_ORYSA	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				247
P06452 UniProt NPD GO	ATPI_PEA	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				247
P41604 UniProt NPD GO	ATPI_PINTH	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				248
Q6L3A3 UniProt NPD GO	ATPI_SACHY	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				247
Q6ENW9 UniProt NPD GO	ATPI_SACOF	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				247
P06451 UniProt NPD GO	ATPI_SPIOL	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	4 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				247
P69372 UniProt NPD GO	ATPI_TOBAC	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				247
Q9XPT0 UniProt NPD GO	ATPI_WHEAT	Chloroplast ATP synthase a chain precursor (EC 3.6.3.14) (ATPase subunit IV)	0.00	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				247
P68125 UniProt NPD GO	CCKN_DASVI	Cholecystokinin (CCK)	0.00	-		0					8
P68126 UniProt NPD GO	CCKN_MACEU	Cholecystokinin (CCK)	0.00	-		0					8
Q6MG71 UniProt NPD GO	CTL4_RAT	Choline transporter-like protein 4 (Solute carrier family 44 member 4)	0.00	-	end	10 *	Membrane; multi-pass membrane protein (By similarity)				707
P32749 UniProt NPD GO	CHLE_BOVIN	Cholinesterase (EC 3.1.1.8) (Acylcholine acylhydrolase) (Choline esterase II) (Butyrylcholine estera ...	0.00	-	cyt	0					141
P32751 UniProt NPD GO	CHLE_MACMU	Cholinesterase (EC 3.1.1.8) (Acylcholine acylhydrolase) (Choline esterase II) (Butyrylcholine estera ...	0.00	-	cyt	0					141
P32752 UniProt NPD GO	CHLE_PIG	Cholinesterase (EC 3.1.1.8) (Acylcholine acylhydrolase) (Choline esterase II) (Butyrylcholine estera ...	0.00	-	cyt	0					141
P32753 UniProt NPD GO	CHLE_SHEEP	Cholinesterase (EC 3.1.1.8) (Acylcholine acylhydrolase) (Choline esterase II) (Butyrylcholine estera ...	0.00	-	cyt	0					141
P08826 UniProt NPD GO	CHA1_BOMMO	Chorion class A protein L11 precursor	0.00	-	mit	0					129
P08825 UniProt NPD GO	CHA2_BOMMO	Chorion class A protein L12 precursor	0.00	-	cyt	0					132
P43516 UniProt NPD GO	CHA6_LYMDI	Chorion class A protein Ld12 precursor	0.00	-	exc	0					142
P43517 UniProt NPD GO	CHA7_LYMDI	Chorion class A protein Ld19 precursor	0.00	-	exc	0					142
P0C0U2 UniProt NPD GO	CHA2A_LYMDI	Chorion class A protein Ld2/Ld41 precursor 1	0.00	-	exc	0					140
P0C0U3 UniProt NPD GO	CHA2B_LYMDI	Chorion class A protein Ld2/Ld41 precursor 2	0.00	-	exc	0					140
P43513 UniProt NPD GO	CHA3_LYMDI	Chorion class A protein Ld3/Ld29 precursor	0.00	-	exc	0					146
P43514 UniProt NPD GO	CHA5_LYMDI	Chorion class A protein Ld5 precursor	0.00	-	exc	0					143
P08929 UniProt NPD GO	CHA3_BOMMO	Chorion class A protein M2774 (Fragment)	0.00	-	cyt	0					100
P02846 UniProt NPD GO	CHA1_ANTPO	Chorion class A protein PC292 precursor (Fragment)	0.00	-	mit	0					119
P50602 UniProt NPD GO	CHA8_LYMDI	Chorion class A proteins Ld24 (Fragment)	0.00	-	mit	0					133
P50603 UniProt NPD GO	CHA9_LYMDI	Chorion class A proteins Ld9 (Fragment)	0.00	-	cyt	0					121
P08827 UniProt NPD GO	CHB1_BOMMO	Chorion class B protein L11 precursor	0.00	-	mit	2 *					168
P08828 UniProt NPD GO	CHB2_BOMMO	Chorion class B protein L12 precursor	0.00	-	mit	0					161
P43515 UniProt NPD GO	CHB1_LYMDI	Chorion class B protein Ld10 precursor	0.00	-	mit	0					191
P50604 UniProt NPD GO	CHB2_LYMDI	Chorion class B protein Ld32 precursor (Fragment)	0.00	-	cyt	0					173
P60607 UniProt NPD GO	CHB3_LYMDI	Chorion class B protein Ld34 precursor	0.00	-	mit	0					191
P08916 UniProt NPD GO	CHB7_BOMMO	Chorion class B protein M1768 (Fragment)	0.00	-	cyt	0					126
P08917 UniProt NPD GO	CHB6_BOMMO	Chorion class B protein M2410 (Fragment)	0.00	-	cyt	0					110
P08914 UniProt NPD GO	CHB8_BOMMO	Chorion class B protein M2807 (Fragment)	0.00	-	cyt	0					119
P08915 UniProt NPD GO	CHB3_BOMMO	Chorion class B protein M3A5 (Fragment)	0.00	-	cyt	0					91
P02848 UniProt NPD GO	CHB1_ANTPO	Chorion class B protein PC10 (Fragment)	0.00	-	cyt	0					130
P02847 UniProt NPD GO	CHB4_ANTPO	Chorion class B protein PC401 precursor (Fragment)	0.00	-	mit	0					171
P13531 UniProt NPD GO	CHCA1_BOMMO	Chorion class CA protein ERA.1 precursor	0.00	-	cyt	0					119
Q17212 UniProt NPD GO	CHCA2_BOMMO	Chorion class CA protein ERA.2 precursor	0.00	-	cyt	0					119
P08829 UniProt NPD GO	CHCA4_BOMMO	Chorion class CA protein ERA.4 precursor (M6C11)	0.00	-	cyt	0					121
Q17214 UniProt NPD GO	CHCA5_BOMMO	Chorion class CA protein ERA.5 precursor	0.00	-	mit	0					119
P08830 UniProt NPD GO	CHCB1_BOMMO	Chorion class CB protein M5H4 precursor	0.00	-	end	0					174
P08930 UniProt NPD GO	CHCB2_ANTPO	Chorion class CB protein PC404 (Fragment)	0.00	-	cyt	0					167
P20729 UniProt NPD GO	CHHA3_BOMMO	Chorion class high-cysteine HCA protein 13 precursor (HC-A.13) (Fragment)	0.00	-		0					17
P05688 UniProt NPD GO	CHHB1_BOMMO	Chorion class high-cysteine HCB protein 12 precursor (HC-B.12)	0.00	-	end	0					131
P13532 UniProt NPD GO	CHR1_BOMMO	Chorion protein ERB.1 precursor	0.00	-	exc	0					177
P13425 UniProt NPD GO	CH15_DROGR	Chorion protein S15	0.00	-	vac	1 *					102
P24510 UniProt NPD GO	CH16_DROGR	Chorion protein S16	0.00	-	exc	1 *					142

You are viewing entries 93151 to 93200 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.