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
P34673 UniProt NPD GO	YO23_CAEEL	Hypothetical protein ZK688.3 in chromosome III	0.02	-	cyt	0					214
Q09618 UniProt NPD GO	YS74_CAEEL	Hypothetical protein ZK892.4 in chromosome III	0.02	-	cyt	0					340
P53716 UniProt NPD GO	YBJ5_CANAL	Hypothetical protein in WHS11 5'region (Fragment)	0.02	-	cyt	0					134
O74420 UniProt NPD GO	WTF13_SCHPO	Hypothetical protein wtf13	0.02	-	end	6	Membrane; multi-pass membrane protein (Potential)				418
O74495 UniProt NPD GO	WTF18_SCHPO	Hypothetical protein wtf18	0.02	-	end	6	Membrane; multi-pass membrane protein (Potential)				402
O74474 UniProt NPD GO	WTF21_SCHPO	Hypothetical protein wtf21	0.02	-	end	5	Membrane; multi-pass membrane protein (Potential)				329
O74564 UniProt NPD GO	WTF9_SCHPO	Hypothetical protein wtf9	0.02	-	end	4	Membrane; multi-pass membrane protein (Potential)				333
Q9W4C5 UniProt NPD GO	Y252_DROME	Hypothetical sodium-dependent transporter CG3252	0.02	-	end	11 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			641
P49538 UniProt NPD GO	YCF43_ODOSI	Hypothetical tatC-like protein ycf43	0.02	-	end	6	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				263
P51321 UniProt NPD GO	YCF38_PORPU	Hypothetical transport permease ycf38 (ORF291)	0.02	-	end	6	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				291
O74492 UniProt NPD GO	YCR4_SCHPO	Hypothetical transthyretin-like protein C285.04 in chromosome III	0.02	-	cyt	0					124
O44578 UniProt NPD GO	TTHY2_CAEEL	Hypothetical transthyretin-like protein ZK697.8 in chromosome V	0.02	-	mit	1 *					190
Q9W719 UniProt NPD GO	HPRT_CHICK	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) (HGPRT) (HGPRTase)	0.02	-	cyt	0	Cytoplasm				218
P00492 UniProt NPD GO	HPRT_HUMAN	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) (HGPRT) (HGPRTase)	0.02	-	cyt	0	Cytoplasm		300322	1Z7G	217
Q6LDD9 UniProt NPD GO	HPRT_MACFA	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) (HGPRT) (HGPRTase)	0.02	-	cyt	0	Cytoplasm (By similarity)				217
P47959 UniProt NPD GO	HPRT_MERUN	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) (HGPRT) (HGPRTase)	0.02	-	cyt	0	Cytoplasm				217
Q45FY6 UniProt NPD GO	HPRT_PIG	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) (HGPRT) (HGPRTase)	0.02	-	nuc	0	Cytoplasm (By similarity)				217
Q9JLS0 UniProt NPD GO	HIG2_MOUSE	Hypoxia-inducible gene 2 protein	0.02	-	mit	1 *					64
Q7Z0A0 UniProt NPD GO	CXI11_CONRA	I-superfamily conotoxin R11.11 precursor (Fragment)	0.02	-	nuc	0	Secreted protein				44
Q7Z093 UniProt NPD GO	CXI17_CONRA	I-superfamily conotoxin R11.17	0.02	-	nuc	0	Secreted protein				46
Q9SWX9 UniProt NPD GO	ILL5_ARATH	IAA-amino acid hydrolase ILR1-like 5 precursor (EC 3.5.1.-)	0.02	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				435
P02732 UniProt NPD GO	ANP3_PAGBO	Ice-structuring glycoprotein 3 (ISGP 3) (Antifreeze glycoprotein 3) (Fragments)	0.02	-	mit	1 *					31
P04002 UniProt NPD GO	ANPA_PSEAM	Ice-structuring protein A precursor (ISP A) (Antifreeze protein A) (HPLC6)	0.02	-	vac	0	Secreted protein; extracellular space	extracellular space [IDA]		1WFB	82
P35753 UniProt NPD GO	ANP3_RHIDE	Ice-structuring protein RD3 (ISP RD3) (Antifreeze peptide RD3)	0.02	-	cyt	0				3RDN	134
P19609 UniProt NPD GO	ANP4_MACAM	Ice-structuring protein SP1(HPLC 4) (ISP SP1(HPLC 4)) (Antifreeze protein SP1(HPLC 4))	0.02	-	cyt	0					63
P19613 UniProt NPD GO	ANPB_MACAM	Ice-structuring protein SP2(HPLC 11) (ISP SP2(HPLC 11)) (Antifreeze protein SP2(HPLC 11))	0.02	-	cyt	0					62
P19608 UniProt NPD GO	ANP2_MACAM	Ice-structuring protein SP2(HPLC1) (ISP SP2(HPLC1)) (Antifreeze protein SP2(HPLC 1))	0.02	-	cyt	0				1OPS	64
P19612 UniProt NPD GO	ANP9_MACAM	Ice-structuring protein SP3(HPLC 9) (ISP SP3(HPLC 9)) (Antifreeze protein SP3(HPLC 9))	0.02	-	cyt	0					64
P19611 UniProt NPD GO	ANP7_MACAM	Ice-structuring protein SP4(HPLC 7) (ISP SP4(HPLC 7)) (Antifreeze protein SP4(HPLC 7))	0.02	-	cyt	0					64
P01750 UniProt NPD GO	HV06_MOUSE	Ig heavy chain V region 102 precursor	0.02	-	exc	0				1QNZ	117
P19180 UniProt NPD GO	HV03_CARAU	Ig heavy chain V region 3 precursor	0.02	-	exc	0					117
P01806 UniProt NPD GO	HV36_MOUSE	Ig heavy chain V region 441 precursor	0.02	-	cyt	0					116
P19181 UniProt NPD GO	HV05_CARAU	Ig heavy chain V region 5A precursor	0.02	-	mit	0					116
P06329 UniProt NPD GO	HV50_MOUSE	Ig heavy chain V region AC38 15.3	0.02	-	cyt	0					120
P01808 UniProt NPD GO	HV38_MOUSE	Ig heavy chain V region T601	0.02	-	cyt	0					119
P06327 UniProt NPD GO	HV52_MOUSE	Ig heavy chain V region VH558 A1/A4 precursor	0.02	-	exc	0					117
P01742 UniProt NPD GO	HV1A_HUMAN	Ig heavy chain V-I region EU	0.02	-	cyt	0		extracellular region [NAS]			117
P23083 UniProt NPD GO	HV1G_HUMAN	Ig heavy chain V-I region V35 precursor	0.02	-	exc	0		extracellular region [NAS]			117
P01760 UniProt NPD GO	HV1D_HUMAN	Ig heavy chain V-I region WOL	0.02	-	cyt	0		extracellular region [NAS]			124
P06331 UniProt NPD GO	HV2I_HUMAN	Ig heavy chain V-II region ARH-77 precursor	0.02	-	end	0		extracellular region [NAS]			146
P01767 UniProt NPD GO	HV3F_HUMAN	Ig heavy chain V-III region BUT	0.02	-	cyt	0		extracellular region [NAS]			115
P80419 UniProt NPD GO	HV3V_HUMAN	Ig heavy chain V-III region GAR	0.02	-	cyt	0		extracellular region [NAS]			118
P01780 UniProt NPD GO	HV3S_HUMAN	Ig heavy chain V-III region JON	0.02	-	cyt	0		extracellular region [NAS]			115
P01775 UniProt NPD GO	HV3N_HUMAN	Ig heavy chain V-III region LAY	0.02	-	cyt	0		extracellular region [NAS]			119
P01774 UniProt NPD GO	HV3M_HUMAN	Ig heavy chain V-III region POM	0.02	-	cyt	0		extracellular region [NAS]			119
P01777 UniProt NPD GO	HV3P_HUMAN	Ig heavy chain V-III region TEI	0.02	-	cyt	0		extracellular region [NAS]			119
P01762 UniProt NPD GO	HV3A_HUMAN	Ig heavy chain V-III region TRO	0.02	-	cyt	1		extracellular region [NAS]			122
P01779 UniProt NPD GO	HV3R_HUMAN	Ig heavy chain V-III region TUR	0.02	-	mit	0		extracellular region [NAS]			116
P01802 UniProt NPD GO	HV33_MOUSE	Ig heavy chain V-III region W3082	0.02	-	cyt	0					115
P01763 UniProt NPD GO	HV3B_HUMAN	Ig heavy chain V-III region WEA	0.02	-	cyt	0		extracellular region [NAS]			114

You are viewing entries 84001 to 84050 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.