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
Q6EYH4 UniProt NPD GO	PSBN_NELLU	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q3C1K1 UniProt NPD GO	PSBN_NICSY	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q33C04 UniProt NPD GO	PSBN_NICTO	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6EW24 UniProt NPD GO	PSBN_NYMAL	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7IW41 UniProt NPD GO	PSBN_NYMOD	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P49515 UniProt NPD GO	PSBN_ODOSI	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6ENE6 UniProt NPD GO	PSBN_ORYNI	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q68RX9 UniProt NPD GO	PSBN_PANGI	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q9XQR4 UniProt NPD GO	PSBN_PEA	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q67HX4 UniProt NPD GO	PSBN_PHOTN	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6EYG3 UniProt NPD GO	PSBN_PHYAM	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7GUC9 UniProt NPD GO	PSBN_PINKO	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P41626 UniProt NPD GO	PSBN_PINTH	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6EYF1 UniProt NPD GO	PSBN_PLAOC	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P51324 UniProt NPD GO	PSBN_PORPU	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q8WHZ5 UniProt NPD GO	PSBN_PSINU	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6L374 UniProt NPD GO	PSBN_SACHY	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6ENT6 UniProt NPD GO	PSBN_SACOF	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q8HS19 UniProt NPD GO	PSBN_SAGLA	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7GZA1 UniProt NPD GO	PSBN_SALEU	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6EYE3 UniProt NPD GO	PSBN_SARHE	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7J186 UniProt NPD GO	PSBN_SAUCE	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q8HS15 UniProt NPD GO	PSBN_SCHCH	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q67HX0 UniProt NPD GO	PSBN_SISMO	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q2MIG0 UniProt NPD GO	PSBN_SOLBU	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q2VEF2 UniProt NPD GO	PSBN_SOLTU	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7HIV8 UniProt NPD GO	PSBN_SPAWA	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6W630 UniProt NPD GO	PSBN_SPHCU	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q71KP7 UniProt NPD GO	PSBN_SPIMX	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P62116 UniProt NPD GO	PSBN_SPIOL	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q32RU3 UniProt NPD GO	PSBN_STAPU	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6EYD5 UniProt NPD GO	PSBN_STEPS	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7YNT5 UniProt NPD GO	PSBN_SUAMA	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7GZA5 UniProt NPD GO	PSBN_TECAU	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q6EYB9 UniProt NPD GO	PSBN_THUPL	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P62114 UniProt NPD GO	PSBN_TOBAC	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7J185 UniProt NPD GO	PSBN_TROAR	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q67I33 UniProt NPD GO	PSBN_TYPAN	Photosystem II reaction center N protein	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q8HS08 UniProt NPD GO	PSBN_WELMI	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q67HS2 UniProt NPD GO	PSBN_YUCGL	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q32RQ4 UniProt NPD GO	PSBN_ZYGCR	Photosystem II reaction center N protein	0.00	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P68859 UniProt NPD GO	PSBN_LOTJA	Photosystem II reaction center N protein (PSII N-protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P68854 UniProt NPD GO	PSBN_MAIZE	Photosystem II reaction center N protein (PSII N-protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P68858 UniProt NPD GO	PSBN_OENAR	Photosystem II reaction center N protein (PSII N-protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P68857 UniProt NPD GO	PSBN_OENHO	Photosystem II reaction center N protein (PSII N-protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P68853 UniProt NPD GO	PSBN_ORYSA	Photosystem II reaction center N protein (PSII N-protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P68860 UniProt NPD GO	PSBN_POPDE	Photosystem II reaction center N protein (PSII N-protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P68856 UniProt NPD GO	PSBN_SECCE	Photosystem II reaction center N protein (PSII N-protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P68855 UniProt NPD GO	PSBN_WHEAT	Photosystem II reaction center N protein (PSII N-protein)	0.00	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q7J1A0 UniProt NPD GO	PSBT_ACOCL	Photosystem II reaction center T protein (PSII-T)	0.00	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35

You are viewing entries 96751 to 96800 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.