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
P69671 UniProt NPD GO	PSBT_MAIZE	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				33
P12182 UniProt NPD GO	PSBT_MARPO	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q9MUV6 UniProt NPD GO	PSBT_MESVI	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q71L95 UniProt NPD GO	PSBT_METGY	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q67HT1 UniProt NPD GO	PSBT_MUSCM	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				33
Q6EYH5 UniProt NPD GO	PSBT_NELLU	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q9TKW5 UniProt NPD GO	PSBT_NEPOL	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q6EW25 UniProt NPD GO	PSBT_NYMAL	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q9MSQ0 UniProt NPD GO	PSBT_NYMOD	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q6ENE7 UniProt NPD GO	PSBT_ORYNI	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
P69674 UniProt NPD GO	PSBT_ORYSA	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q68RY0 UniProt NPD GO	PSBT_PANGI	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				33
Q67HX5 UniProt NPD GO	PSBT_PHOTN	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				33
Q6EYG4 UniProt NPD GO	PSBT_PHYAM	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q85X09 UniProt NPD GO	PSBT_PINKO	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
P41625 UniProt NPD GO	PSBT_PINTH	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q6EYF2 UniProt NPD GO	PSBT_PLAOC	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
P69675 UniProt NPD GO	PSBT_POPDE	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
P51323 UniProt NPD GO	PSBT_PORPU	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				31
Q8HU50 UniProt NPD GO	PSBT_PSINU	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				32
Q6L375 UniProt NPD GO	PSBT_SACHY	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				33
Q6ENT7 UniProt NPD GO	PSBT_SACOF	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				33
Q7HIV9 UniProt NPD GO	PSBT_SAGLA	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				33
Q6EYE4 UniProt NPD GO	PSBT_SARHE	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q9G2D7 UniProt NPD GO	PSBT_SAUCE	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q8HS16 UniProt NPD GO	PSBT_SCHCH	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q67HX1 UniProt NPD GO	PSBT_SISMO	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				33
Q8HS12 UniProt NPD GO	PSBT_SPAWA	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
P61840 UniProt NPD GO	PSBT_SPIOL	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				33
Q71L87 UniProt NPD GO	PSBT_STAER	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q6EYD6 UniProt NPD GO	PSBT_STEPS	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q6EYC4 UniProt NPD GO	PSBT_TAXBR	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q6EYC0 UniProt NPD GO	PSBT_THUPL	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
P12184 UniProt NPD GO	PSBT_TOBAC	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				34
Q9G240 UniProt NPD GO	PSBT_TROAR	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q67I34 UniProt NPD GO	PSBT_TYPAN	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				33
Q8HS09 UniProt NPD GO	PSBT_WELMI	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q67HS3 UniProt NPD GO	PSBT_YUCGL	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				33
Q9MSR2 UniProt NPD GO	PSBT_ZAMFU	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
Q9SPI9 UniProt NPD GO	PSBW_CHLRE	Photosystem II reaction center W protein, chloroplast precursor	0.00	-	mit	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				115
P48266 UniProt NPD GO	PSBX_CYAPA	Photosystem II reaction center X protein	0.00	-	nuc	1 *	Plastid; cyanelle				39
O78455 UniProt NPD GO	PSBX_GUITH	Photosystem II reaction center X protein	0.00	-	mit	1 *	Plastid; chloroplast				39
P49509 UniProt NPD GO	PSBX_ODOSI	Photosystem II reaction center X protein	0.00	-	nuc	1 *	Plastid; chloroplast				38
Q5QA82 UniProt NPD GO	PSBZ_ACOGR	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q85FM4 UniProt NPD GO	PSBZ_ADICA	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q70Y06 UniProt NPD GO	PSBZ_AMBTC	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
P59705 UniProt NPD GO	PSBZ_ANTFO	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
P56790 UniProt NPD GO	PSBZ_ARATH	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
P59706 UniProt NPD GO	PSBZ_ATRBE	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62
Q7YJX5 UniProt NPD GO	PSBZ_CALFE	Photosystem II reaction center Z protein	0.00	-	exc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Associated with t ...				62

You are viewing entries 96851 to 96900 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.