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
Q9BBT1 UniProt NPD GO	PSBC_LOTJA	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.02	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
Q9MUW1 UniProt NPD GO	PSBC_MESVI	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.02	-	mit	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
Q6ENJ0 UniProt NPD GO	PSBC_ORYNI	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.02	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
P12158 UniProt NPD GO	PSBC_ORYSA	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.02	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
P06004 UniProt NPD GO	PSBC_PEA	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
P0C158 UniProt NPD GO	PSBC_SACHY	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.02	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
Q6ENY0 UniProt NPD GO	PSBC_SACOF	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.02	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
P10804 UniProt NPD GO	PSBC_SECCE	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
P06413 UniProt NPD GO	PSBC_TOBAC	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
P56778 UniProt NPD GO	PSBC_ARATH	Photosystem II 44 kDa reaction center protein precursor (P6 protein) (CP43)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
P06003 UniProt NPD GO	PSBC_SPIOL	Photosystem II 44 kDa reaction center protein precursor (P6 protein) (CP43)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
Q9TM47 UniProt NPD GO	PSBD_CYACA	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				351
Q9MUW2 UniProt NPD GO	PSBD_MESVI	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				354
Q85AI7 UniProt NPD GO	PSBB_ANTFO	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
P56777 UniProt NPD GO	PSBB_ARATH	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
P14813 UniProt NPD GO	PSBB_EUGGR	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
Q9BBQ8 UniProt NPD GO	PSBB_LOTJA	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
P05641 UniProt NPD GO	PSBB_MAIZE	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
P06412 UniProt NPD GO	PSBB_MARPO	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
P19819 UniProt NPD GO	PSBB_OENAR	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
Q9MTJ7 UniProt NPD GO	PSBB_OENHO	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
O03061 UniProt NPD GO	PSBB_POPDE	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				509
Q6L376 UniProt NPD GO	PSBB_SACHY	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				508
Q6ENT8 UniProt NPD GO	PSBB_SACOF	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				508
P06411 UniProt NPD GO	PSBB_TOBAC	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
P04160 UniProt NPD GO	PSBB_SPIOL	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein) (cp47 protein)	0.02	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
Q70XX9 UniProt NPD GO	PSBH_AMBTC	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				73
Q7FNS3 UniProt NPD GO	PSBH_ATRBE	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
Q6EW23 UniProt NPD GO	PSBH_NYMAL	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
Q6YXN1 UniProt NPD GO	PSBH_PHYPA	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.02	-	gol	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				73
P41627 UniProt NPD GO	PSBH_PINTH	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				74
Q36632 UniProt NPD GO	PSBH_POPDE	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
P06415 UniProt NPD GO	PSBH_TOBAC	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
O78471 UniProt NPD GO	PSBI_GUITH	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				38
Q06480 UniProt NPD GO	PSBN_CHLRE	Photosystem II reaction center N protein	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				44
O19926 UniProt NPD GO	PSBN_CYACA	Photosystem II reaction center N protein	0.02	-	exc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q9GF86 UniProt NPD GO	PSBN_GINBI	Photosystem II reaction center N protein	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q9MUV5 UniProt NPD GO	PSBN_MESVI	Photosystem II reaction center N protein	0.02	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
Q3ZJ27 UniProt NPD GO	PSBN_PSEAK	Photosystem II reaction center N protein	0.02	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				44
Q9GF90 UniProt NPD GO	PSBT_DRIWI	Photosystem II reaction center T protein (PSII-T)	0.02	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				35
P69669 UniProt NPD GO	PSBT_HORVU	Photosystem II reaction center T protein (PSII-T)	0.02	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P69676 UniProt NPD GO	PSBT_SECCE	Photosystem II reaction center T protein (PSII-T)	0.02	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P59905 UniProt NPD GO	PSBT_SPIMX	Photosystem II reaction center T protein (PSII-T)	0.02	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				37
P69677 UniProt NPD GO	PSBT_WHEAT	Photosystem II reaction center T protein (PSII-T)	0.02	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P84561 UniProt NPD GO	P2SAF_POPEU	Photosystem II stability/assembly factor (Fragment)	0.02	-	cyt	0	Plastid; chloroplast (By similarity)				26
P24725 UniProt NPD GO	PSBA_GALSU	Photosystem Q(B) protein (32 kDa thylakoid membrane protein) (Photosystem II protein D1)	0.02	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				360
P08610 UniProt NPD GO	TKN_PHYBI	Phyllomedusin	0.02	-		0	Secreted protein				10
Q9AR89 UniProt NPD GO	PSK2_ORYSA	Phytosulfokines 2 precursor [Contains: Phytosulfokine-alpha (PSK-alpha) (Phytosulfokine-a); Phytosul ...	0.02	-	mit	1 *	Secreted protein (By similarity)				119
Q23756 UniProt NPD GO	PDH2_CALSI	Pigment-dispersing hormone 2 precursor [Contains: PDH precursor-related peptide 2; Pigment-dispersin ...	0.02	-	exc	0	Secreted protein				78
P37085 UniProt NPD GO	PDHA_ORCLI	Pigment-dispersing hormone A precursor [Contains: PDH precursor-related peptide (PRPP); Pigment-disp ...	0.02	-	exc	0	Secreted protein				76

You are viewing entries 85051 to 85100 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.