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
Q6ENW4 UniProt NPD GO	PSAB_SACOF	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.04	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
P58386 UniProt NPD GO	PSAB_WHEAT	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.04	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q9BBR9 UniProt NPD GO	YCF4_LOTJA	Photosystem I assembly protein ycf4	0.04	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				200
P31556 UniProt NPD GO	PSAC_EUGGR	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.04	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q6B8M0 UniProt NPD GO	PSAC_GRATL	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.04	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
O78443 UniProt NPD GO	PSAC_GUITH	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.04	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P06251 UniProt NPD GO	PSAC_MARPO	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.04	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q9TKV9 UniProt NPD GO	PSAC_NEPOL	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.04	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q85X26 UniProt NPD GO	PSAI_PINKO	Photosystem I reaction center subunit VIII (PSI-I)	0.04	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				56
Q8HB52 UniProt NPD GO	PSBC_ABIAL	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.04	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
P41643 UniProt NPD GO	PSBC_PINTH	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.04	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
P06007 UniProt NPD GO	PSBD_CHLRE	Photosystem II D2 protein (Photosystem Q(A) protein) (PSII D2 protein)	0.04	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				352
P56307 UniProt NPD GO	PSBB_CHLVU	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.04	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
O19928 UniProt NPD GO	PSBB_CYACA	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.04	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				509
O78511 UniProt NPD GO	PSBB_GUITH	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.04	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				509
P49471 UniProt NPD GO	PSBB_ODOSI	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.04	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				509
P51322 UniProt NPD GO	PSBB_PORPU	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.04	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				509
P80470 UniProt NPD GO	PSBY_SPIOL	Photosystem II core complex proteins psbY, chloroplast precursor (L-arginine-metabolizing enzyme) (L ...	0.04	-	end	4	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				199
P49543 UniProt NPD GO	PSBY_ODOSI	Photosystem II protein Y	0.04	-	vac	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q7YJU9 UniProt NPD GO	PSBH_CALFE	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
Q71KQ7 UniProt NPD GO	PSBH_COLOB	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				78
P69554 UniProt NPD GO	PSBH_SECCE	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.04	-	gol	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
P69555 UniProt NPD GO	PSBH_WHEAT	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.04	-	gol	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
Q85CN1 UniProt NPD GO	PSBI_ANTFO	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.04	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				36
Q6B8Y6 UniProt NPD GO	PSBN_GRATL	Photosystem II reaction center N protein	0.04	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				43
P55967 UniProt NPD GO	PSBW_WHEAT	Photosystem II reaction center W protein (PSII 6.1 kDa protein) (Fragment)	0.04	-		0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				20
P61230 UniProt NPD GO	TXP1_PARSR	Phrixotoxin-1 (PaTX1)	0.04	-	cyt	0	Secreted protein			1V7F	29
P81565 UniProt NPD GO	PHYB_PHYBI	Phylloxin precursor	0.04	-	exc	0	Secreted protein				64
P42210 UniProt NPD GO	ASPR_HORVU	Phytepsin precursor (EC 3.4.23.40) (Aspartic proteinase) [Contains: Phytepsin 32 kDa subunit; Phytep ...	0.04	-	end	0	Vacuole			1QDM	508
Q9LMY9 UniProt NPD GO	PSK1_ARATH	Phytosulfokines 1 precursor (AtPSK1) [Contains: Phytosulfokine-alpha (PSK-alpha) (Phytosulfokine-a); ...	0.04	-	exc	1 *	Secreted protein (By similarity)				87
Q9FS10 UniProt NPD GO	PSK_ASPOF	Phytosulfokines precursor [Contains: Phytosulfokine-alpha (PSK-alpha) (Phytosulfokine-a); Phytosulfo ...	0.04	-	exc	0	Secreted protein				75
Q06202 UniProt NPD GO	PDH_CARMA	Pigment-dispersing hormone precursor [Contains: PDH precursor-related peptide (PRPP); Pigment-disper ...	0.04	-	exc	1 *	Secreted protein				78
P21128 UniProt NPD GO	PP11_HUMAN	Placental protein 11 precursor (EC 3.4.21.-) (PP11)	0.04	-	exc	0		cytoplasm [IDA] extracellular region [TAS] extracellular space [TAS] plasma membrane [TAS]	606720		369
Q6AYS4 UniProt NPD GO	FUCO2_RAT	Plasma alpha-L-fucosidase precursor (EC 3.2.1.51) (Alpha-L-fucosidase 2) (Alpha-L-fucoside fucohydro ...	0.04	-	end	0	Secreted protein (Probable)				459
P46925 UniProt NPD GO	PLM2_PLAFA	Plasmepsin-2 precursor (EC 3.4.23.39) (Aspartic hemoglobinase II) (PFAPD)	0.04	-	mit	1 *	Vacuole			2BJU	453
P58138 UniProt NPD GO	RK12_ASTLO	Plastid 50S ribosomal protein L12	0.04	-	nuc	0	Plastid				138
P82277 UniProt NPD GO	RRP2_SPIOL	Plastid-specific 30S ribosomal protein 2, chloroplast precursor (PSRP-2)	0.04	-	mit	0	Plastid; chloroplast				260
Q99K51 UniProt NPD GO	PLST_MOUSE	Plastin-3 (T-plastin)	0.04	-	cyt	0	Cytoplasm (By similarity)				627
Q63598 UniProt NPD GO	PLST_RAT	Plastin-3 (T-plastin)	0.04	-	cyt	0	Cytoplasm				627
P00299 UniProt NPD GO	PLAS1_POPNI	Plastocyanin A, chloroplast precursor	0.04	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...			6PCY	168
P16671 UniProt NPD GO	CD36_HUMAN	Platelet glycoprotein 4 (Platelet glycoprotein IV) (GPIV) (Glycoprotein IIIb) (GPIIIB) (Leukocyte di ...	0.04	-	end	2 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	608404		471
Q9WU68 UniProt NPD GO	PKHB1_RAT	Pleckstrin homology domain-containing family B member 1 (Evectin-1)	0.04	-	mit	0	Membrane-associated. Highly expressed in the outer segments of photoreceptor cells, both in rods and ...				223
P36988 UniProt NPD GO	TXP14_PLETR	Plectoxin-14 (Plectoxin XIV) (PLT-XIV) (PLTXIV)	0.04	-	nuc	0	Secreted protein				46
P27759 UniProt NPD GO	MPA11_AMBAR	Pollen allergen Amb a 1.1 precursor (Antigen E) (AgE) (Antigen Amb a I)	0.04	-	exc	0					396
P43175 UniProt NPD GO	MPA5B_AMBPS	Pollen allergen Amb p 5b precursor (Amb p Vb)	0.04	-	nuc	0	Secreted protein				77
P81430 UniProt NPD GO	ALL7_OLEEU	Pollen allergen Ole e 7 (Ole e VII) (Fragment)	0.04	-	nuc	0					21
P33050 UniProt NPD GO	PSC13_MAIZE	Pollen-specific protein C13 precursor	0.04	-	vac	0					170
P41750 UniProt NPD GO	PGLRB_ASPFL	Polygalacturonase B precursor (EC 3.2.1.15) (Pectinase) (PGL) (P1/P3)	0.04	-	exc	0					366
P35335 UniProt NPD GO	PGLR_ASPOR	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.04	-	cyt	0					363
P48979 UniProt NPD GO	PGLR_PRUPE	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.04	-	cyt	1 *	Secreted protein				393

You are viewing entries 77951 to 78000 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.