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
P30582 UniProt NPD GO	CHS2_ASPNG	Chitin synthase 2 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 2) (Class-II chitin synt ...	0.07	-	cyt	0	Cell membrane; multi-pass membrane protein				189
P30591 UniProt NPD GO	CHS2_PHAEX	Chitin synthase 2 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 2) (Class-II chitin synt ...	0.07	-	cyt	0	Cell membrane; multi-pass membrane protein				189
Q7M443 UniProt NPD GO	CHIT2_TULBA	Chitinase 2 (EC 3.2.1.14) (Tulip bulb chitinase-2) (TBC-2)	0.07	-	cyt	0					275
P51802 UniProt NPD GO	CLCKB_RAT	Chloride channel protein ClC-Kb (Chloride channel Kb) (ClC-K2)	0.07	-	end	8 *	Cell membrane; multi-pass membrane protein. Golgi apparatus; Golgi membrane; multi-pass membrane pro ...				687
P04963 UniProt NPD GO	PRXC_CALFU	Chloroperoxidase precursor (EC 1.11.1.10) (Chloride peroxidase) (CPO)	0.07	-	exc	0				2CPO	373
P12360 UniProt NPD GO	CB11_LYCES	Chlorophyll a-b binding protein 6A, chloroplast precursor (LHCI type I CAB-6A) (Light-harvesting com ...	0.07	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				246
Q9XQE1 UniProt NPD GO	RR12_SOLNI	Chloroplast 30S ribosomal protein S12 (Fragment)	0.07	-	mit	0	Plastid; chloroplast				85
Q6EW11 UniProt NPD GO	RR19_NYMAL	Chloroplast 30S ribosomal protein S19	0.07	-	mit	0	Plastid; chloroplast				92
Q6B8W9 UniProt NPD GO	RR5_GRATL	Chloroplast 30S ribosomal protein S5	0.07	-	nuc	0	Plastid; chloroplast				172
P49493 UniProt NPD GO	RR5_ODOSI	Chloroplast 30S ribosomal protein S5	0.07	-	nuc	0	Plastid; chloroplast				185
Q9TL24 UniProt NPD GO	RR8_NEPOL	Chloroplast 30S ribosomal protein S8	0.07	-	cyt	0	Plastid; chloroplast				129
P42340 UniProt NPD GO	RK14_OENAM	Chloroplast 50S ribosomal protein L14 (Fragments)	0.07	-	cyt	0	Plastid; chloroplast				74
Q1XDI5 UniProt NPD GO	RK24_PORYE	Chloroplast 50S ribosomal protein L24	0.07	-	nuc	0	Plastid; chloroplast				116
P49569 UniProt NPD GO	RK3_ODOSI	Chloroplast 50S ribosomal protein L3	0.07	-	cyt	0	Plastid; chloroplast				196
Q68RY5 UniProt NPD GO	RK33_PANGI	Chloroplast 50S ribosomal protein L33	0.07	-	nuc	0	Plastid; chloroplast				66
P28805 UniProt NPD GO	RK33_SPIOL	Chloroplast 50S ribosomal protein L33	0.07	-	nuc	0	Plastid; chloroplast				65
P06393 UniProt NPD GO	RK33_TOBAC	Chloroplast 50S ribosomal protein L33	0.07	-	nuc	0	Plastid; chloroplast				65
P51334 UniProt NPD GO	RK9_PORPU	Chloroplast 50S ribosomal protein L9	0.07	-	nuc	0	Plastid; chloroplast				155
Q39002 UniProt NPD GO	TLC1_ARATH	Chloroplast ADP,ATP carrier protein 1, chloroplast precursor (ADP/ATP translocase 1) (Adenine nucleo ...	0.07	-	end	9	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				624
Q6ENG1 UniProt NPD GO	CEMA_ORYNI	Chloroplast envelope membrane protein	0.07	-	end	4 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				230
P12212 UniProt NPD GO	CEMA_ORYSA	Chloroplast envelope membrane protein	0.07	-	end	4 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				230
P69373 UniProt NPD GO	CEMA_WHEAT	Chloroplast envelope membrane protein	0.07	-	end	4 *	Plastid; chloroplast; chloroplast inner membrane; multi-pass membrane protein (By similarity)				230
Q5IZC8 UniProt NPD GO	TC754_ARATH	Chloroplastic protein TOC75-4 (75 kDa translocon at the outer-envelope-membrane of chloroplasts 4) ( ...	0.07	-	cyt	0	Plastid; chloroplast; chloroplast outer membrane; multi-pass membrane protein				396
O04121 UniProt NPD GO	CHMO_SPIOL	Choline monooxygenase, chloroplast precursor (EC 1.14.15.7)	0.07	-	mit	0	Plastid; chloroplast; chloroplast stroma				439
Q8BY89 UniProt NPD GO	CTL2_MOUSE	Choline transporter-like protein 2 (Solute carrier family 44 member 2)	0.07	-	end	10 *	Membrane; multi-pass membrane protein (By similarity)				704
Q53GD3 UniProt NPD GO	CTL4_HUMAN	Choline transporter-like protein 4 (Solute carrier family 44 member 4)	0.07	+	end	10 *	Membrane; multi-pass membrane protein (By similarity)		606107		710
P21702 UniProt NPD GO	CSH1_RAT	Chorionic somatomammotropin hormone 1 precursor (Placental lactogen I) (PL-I)	0.07	-	exc	0	Secreted protein				230
P83547 UniProt NPD GO	CHY3_PAGMA	Chrysophsin-3	0.07	-		0	Secreted protein				20
Q9N2D2 UniProt NPD GO	CHYM_CALJA	Chymosin precursor (EC 3.4.23.4) (Preprorennin)	0.07	-	mit	0					381
P83039 UniProt NPD GO	ICHY_CAIMO	Chymotrypsin inhibitor (DPCI)	0.07	-	nuc	0	Secreted protein				65
P07481 UniProt NPD GO	ISC3_BOMMO	Chymotrypsin inhibitor SCI-III	0.07	-	nuc	0					63
O64969 UniProt NPD GO	CADH_EUCGL	Cinnamyl alcohol dehydrogenase (EC 1.1.1.195) (CAD)	0.07	-	cyt	0					356
Q42726 UniProt NPD GO	CADH1_EUCGU	Cinnamyl alcohol dehydrogenase 1 (EC 1.1.1.195) (CAD)	0.07	-	cyt	0					354
P31655 UniProt NPD GO	CADH2_EUCGU	Cinnamyl alcohol dehydrogenase 2 (EC 1.1.1.195) (CAD)	0.07	-	cyt	0					356
P42495 UniProt NPD GO	CADH1_ARACO	Cinnamyl-alcohol dehydrogenase 1 (EC 1.1.1.195) (CAD)	0.07	-	cyt	0					360
P00890 UniProt NPD GO	CISY1_YEAST	Citrate synthase, mitochondrial precursor (EC 2.3.3.1)	0.07	-	nuc	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [TAS] mitochondrion [IDA]			479
O80433 UniProt NPD GO	CISY_DAUCA	Citrate synthase, mitochondrial precursor (EC 2.3.3.1)	0.07	-	mit	0	Mitochondrion; mitochondrial matrix				472
P40096 UniProt NPD GO	NCB1_YEAST	Class 2 transcription repressor (NC2)	0.07	-	cyt	0		nucleus [IPI]			142
O88551 UniProt NPD GO	CLD1_MOUSE	Claudin-1	0.07	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein	integral to membrane [NAS] tight junction [IDA]			211
Q9JKD6 UniProt NPD GO	CLD5_RAT	Claudin-5	0.07	-	end	4 *	Cell membrane; cell-cell junction; tight junction; multi-pass membrane protein (By similarity)	integral to membrane [ISS] tight junction [ISS]			218
Q08121 UniProt NPD GO	CLYT_CLYGR	Clytin precursor (Phialidin)	0.07	-	nuc	0					198
P41811 UniProt NPD GO	COPB2_YEAST	Coatomer subunit beta' (Beta'-coat protein) (Beta'-COP)	0.07	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	COPI vesicle coat [IGI]			889
Q9JHH9 UniProt NPD GO	COPZ2_MOUSE	Coatomer subunit zeta-2 (Zeta-2 coat protein) (Zeta-2 COP)	0.07	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...				205
Q8K0Z7 UniProt NPD GO	CCD44_MOUSE	Coiled-coil domain-containing protein 44	0.07	-	mit	0		mitochondrion [IDA]			294
Q91XL7 UniProt NPD GO	COL_SPETR	Colipase precursor	0.07	-	exc	0	Secreted protein				111
O62806 UniProt NPD GO	MMP13_RABIT	Collagenase 3 precursor (EC 3.4.24.-) (Matrix metalloproteinase-13) (MMP-13)	0.07	-	exc	0					471
P23667 UniProt NPD GO	CO3_XENLA	Complement C3 (Fragment)	0.07	-	cyt	0					323
Q9MZE0 UniProt NPD GO	C1QBP_CERAE	Complement component 1 Q subcomponent-binding protein, mitochondrial precursor (Globular head recept ...	0.07	-	mit	0	Mitochondrion; mitochondrial matrix (Probable)				282
Q07021 UniProt NPD GO	C1QBP_HUMAN	Complement component 1 Q subcomponent-binding protein, mitochondrial precursor (Glycoprotein gC1qBP) ...	0.07	-	mit	0	Mitochondrion; mitochondrial matrix	plasma membrane [TAS]	601269	1P32	282
P32038 UniProt NPD GO	CFAD_RAT	Complement factor D precursor (EC 3.4.21.46) (C3 convertase activator) (Properdin factor D) (Adipsin ...	0.07	-	mit	0	Secreted protein				263

You are viewing entries 69701 to 69750 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.