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
P04966 UniProt NPD GO	PSAA_MAIZE	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.06	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				751
P49479 UniProt NPD GO	PSAA_ODOSI	Photosystem I P700 chlorophyll a apoprotein A1 (PsaA) (PSI-A)	0.06	-	end	9	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				752
Q00914 UniProt NPD GO	PSAC_CHLRE	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.06	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q9MRI1 UniProt NPD GO	PSAC_GNEGN	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.06	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q9MUM9 UniProt NPD GO	PSAC_MESVI	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.06	-	exc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
O78502 UniProt NPD GO	PSAD_GUITH	Photosystem I reaction center subunit II (Photosystem I 16 kDa polypeptide) (PSI-D)	0.06	-	cyt	0	Plastid; chloroplast				141
Q41228 UniProt NPD GO	PSAEA_NICSY	Photosystem I reaction center subunit IV A, chloroplast precursor (PSI-E A) [Contains: Photosystem I ...	0.06	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				141
P12354 UniProt NPD GO	PSAE_SPIOL	Photosystem I reaction center subunit IV, chloroplast precursor (PSI-E)	0.06	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein				125
O04006 UniProt NPD GO	PSAH_BRARA	Photosystem I reaction center subunit VI, chloroplast precursor (PSI-H) (Light-harvesting complex I ...	0.06	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				145
P22181 UniProt NPD GO	PSAH_ORYSA	Photosystem I reaction center subunit VI, chloroplast precursor (PSI-H) (Light-harvesting complex I ...	0.06	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				142
Q9SUI4 UniProt NPD GO	PSAL_ARATH	Photosystem I reaction center subunit XI, chloroplast precursor (PSI-L) (PSI subunit V)	0.06	-	mit	2	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				219
Q6B8M4 UniProt NPD GO	PSAK_GRATL	Photosystem I reaction center subunit psaK (Photosystem I subunit X) (PSI-K)	0.06	-	nuc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				86
P10900 UniProt NPD GO	PSBB_HORVU	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.06	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
P49511 UniProt NPD GO	PSBI_ODOSI	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.06	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P31591 UniProt NPD GO	PSBN_EUGGR	Photosystem II reaction center N protein	0.06	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				44
P28554 UniProt NPD GO	CRTI_LYCES	Phytoene dehydrogenase, chloroplast precursor (EC 1.14.99.-) (Phytoene desaturase)	0.06	-	nuc	0	Plastid; chloroplast. Plastid; chromoplast				583
Q9M2Y0 UniProt NPD GO	PSK3_ARATH	Phytosulfokines 3 precursor (AtPSK3) [Contains: Phytosulfokine-alpha (PSK-alpha) (Phytosulfokine-a); ...	0.06	-	exc	1 *	Secreted protein				79
P48408 UniProt NPD GO	DPS2_PINST	Pinosylvin synthase 2 (EC 2.3.1.-) (Stilbene synthase 2) (STS 2)	0.06	-	mit	0	Cytoplasm				396
Q9D711 UniProt NPD GO	PIR_MOUSE	Pirin	0.06	-	cyt	0	Nucleus (By similarity)				290
P32903 UniProt NPD GO	PMP1_YEAST	Plasma membrane ATPase proteolipid 1 precursor	0.06	-	mit	1 *	Cell membrane	plasma membrane [IDA]			40
Q7KQM4 UniProt NPD GO	PLM1_PLAF7	Plasmepsin-1 precursor (EC 3.4.23.38) (Aspartic hemoglobinase I) (PfAPG)	0.06	-	mit	1 *	Vacuole (By similarity). Could be first anchored to the membrane through its propeptide before being ...				452
P39898 UniProt NPD GO	PLM1_PLAFA	Plasmepsin-1 precursor (EC 3.4.23.38) (Aspartic hemoglobinase I) (PfAPG)	0.06	-	mit	1 *	Vacuole. Could be first anchored to the membrane through its propeptide before being released			1LDU	452
P33574 UniProt NPD GO	PLMN_PETMA	Plasminogen (EC 3.4.21.7) (Fragments)	0.06	-	cyt	0	Secreted protein				325
P42341 UniProt NPD GO	RR2_CONAM	Plastid 30S ribosomal protein S2 (Fragment)	0.06	-		0	Plastid				11
P58133 UniProt NPD GO	RR3_ASTLO	Plastid 30S ribosomal protein S3	0.06	-	cyt	0	Plastid				219
O99010 UniProt NPD GO	RK12_PROWI	Plastid 50S ribosomal protein L12	0.06	-	cyt	0	Plastid				130
P34771 UniProt NPD GO	RK23_ASTLO	Plastid 50S ribosomal protein L23	0.06	-	cyt	0	Plastid				98
Q6P698 UniProt NPD GO	PLSL_BRARE	Plastin-2 (L-plastin) (Lymphocyte cytosolic plastin 1)	0.06	-	cyt	0	Cytoplasm (By similarity)				624
P20423 UniProt NPD GO	PLAS_ORYSA	Plastocyanin, chloroplast precursor	0.06	-	exc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				154
Q9VXP4 UniProt NPD GO	PA1B2_DROME	Platelet-activating factor acetylhydrolase IB beta homolog	0.06	-	nuc	0					225
Q61206 UniProt NPD GO	PA1B2_MOUSE	Platelet-activating factor acetylhydrolase IB subunit beta (EC 3.1.1.47) (PAF acetylhydrolase 30 kDa ...	0.06	-	cyt	0	Cytoplasm	cytoplasm [IDA]			229
P35366 UniProt NPD GO	PTAFR_MACMU	Platelet-activating factor receptor (PAF-R) (Fragment)	0.06	-	end	5 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS]			208
Q9QYE9 UniProt NPD GO	PKHB1_MOUSE	Pleckstrin homology domain-containing family B member 1 (Pleckstrin homology domain retinal protein ...	0.06	-	cyt	0	Membrane-associated. Highly expressed in the outer segments of photoreceptor cells, both in rods and ...	integral to membrane [IDA]			243
P36985 UniProt NPD GO	TXP11_PLETR	Plectoxin-11 precursor (Plectoxin XI) (PLT-XI) (PLTXI) (Fragment)	0.06	-	exc	0	Secreted protein				79
P69198 UniProt NPD GO	POLC2_BRANA	Polcalcin Bra n 2 (Calcium-binding pollen allergen Bra n 2)	0.06	-	cyt	0					83
P69199 UniProt NPD GO	POLC2_BRARA	Polcalcin Bra r 2 (Calcium-binding pollen allergen Bra r 2)	0.06	-	cyt	0					83
P15151 UniProt NPD GO	PVR_HUMAN	Poliovirus receptor precursor (Nectin-like protein 5) (Necl-5) (CD155 antigen)	0.06	-	end	1	Isoform alpha, isoform delta: Cell membrane; single-pass type I membrane protein. Isoform beta, isof ...	cytoplasm [TAS] extracellular space [TAS] integral to membrane [TAS]	173850	1NN8	417
O64411 UniProt NPD GO	PAO_MAIZE	Polyamine oxidase precursor (EC 1.5.3.11)	0.06	-	cyt	0				1H86	500
Q9Y834 UniProt NPD GO	PGLR1_PENOL	Polygalacturonase 1 precursor (EC 3.2.1.15) (PG 1) (Pectinase 1)	0.06	-	exc	0	Secreted protein				370
Q39766 UniProt NPD GO	PGLR_GOSBA	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.06	-	exc	0					407
O93883 UniProt NPD GO	PGLR_PENGR	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.06	-	vac	0					376
P59936 UniProt NPD GO	KA121_TITSE	Potassium channel toxin alpha-KTx 12.1 (Butantoxin) (BuTX) (TsTX-IV)	0.06	-	nuc	0	Secreted protein			1WT7	40
P0C168 UniProt NPD GO	KA122_TITTR	Potassium channel toxin alpha-KTx 12.2 (Butantoxin) (BuTX) (TtBut)	0.06	-	nuc	0	Secreted protein				40
P0C185 UniProt NPD GO	KA123_TITCO	Potassium channel toxin alpha-KTx 12.3 (Butantoxin-like peptide) (Tco30)	0.06	-	nuc	0	Secreted protein				40
P60233 UniProt NPD GO	KA151_ANDAU	Potassium channel toxin alpha-KTx 15.1 (Peptide Aa1)	0.06	-	nuc	0	Secreted protein				37
Q95NJ8 UniProt NPD GO	KA171_MESMA	Potassium channel toxin alpha-KTx 17.1 precursor (Toxin Kk4) (BmKK4) (Toxin TXKs4)	0.06	-	vac	1 *	Secreted protein			1S8K	55
P60211 UniProt NPD GO	KA181_TITCA	Potassium channel toxin alpha-KTx 18.1 (Toxin Tc32)	0.06	-	nuc	0	Secreted protein	extracellular region [IDA]			35
P59290 UniProt NPD GO	KAX39_BUTOC	Potassium channel toxin alpha-KTx 3.9 (Kaliotoxin-3) (KTX-3)	0.06	-	nuc	0	Secreted protein				37
P80671 UniProt NPD GO	KAX84_LEIQH	Potassium channel toxin alpha-KTx 8.4 (Leiuropeptide-3) (Leiuropeptide III) (LpIII)	0.06	-	nuc	0	Secreted protein				29
Q86QV5 UniProt NPD GO	KGX32_CENEL	Potassium channel toxin gamma-KTx 3.2 (Ergtoxin-like protein 2) (ErgTx2) (CeErg2) (CeErgTx2)	0.06	-	nuc	0	Secreted protein				43

You are viewing entries 72801 to 72850 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.