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
P91964 UniProt NPD GO	PDH2_PENVA	Pigment-dispersing hormone type 2 precursor [Contains: PDH precursor-related peptide (PPRD); Pigment ...	0.02	-	exc	1 *	Secreted protein (By similarity)				80
Q68Y22 UniProt NPD GO	MYR4_MYRBA	Pilosulin-4 precursor	0.02	-	mit	1 *	Secreted protein				84
P38364 UniProt NPD GO	PID6_FUSSO	Pisatin demethylase (EC 1.14.-.-) (Cytochrome P450 57A2)	0.02	-	nuc	1 *					506
Q8TCE9 UniProt NPD GO	PPL13_HUMAN	Placental protein 13-like (Charcot-Leyden crystal protein 2) (CLC2) (Galectin-14)	0.02	-	cyt	0	Nucleus		607260		139
O74837 UniProt NPD GO	PMP31_SCHPO	Plasma membrane proteolipid 31	0.02	-	end	2 *	Cell membrane; multi-pass membrane protein (Potential)				105
P18902 UniProt NPD GO	RETBP_BOVIN	Plasma retinol-binding protein (PRBP) (RBP)	0.02	-	cyt	0	Secreted protein			1KT7	183
P41263 UniProt NPD GO	RETBP_CHICK	Plasma retinol-binding protein precursor (PRBP)	0.02	-	exc	0	Secreted protein			1IIU	196
P83169 UniProt NPD GO	PLMN_STRCA	Plasminogen (EC 3.4.21.7) (Fragments)	0.02	-	cyt	0	Secreted protein				33
P80009 UniProt NPD GO	PLMN_CANFA	Plasminogen (EC 3.4.21.7) [Contains: Plasmin heavy chain A; Plasmin light chain B] (Fragment)	0.02	-	nuc	0	Secreted protein				333
P14757 UniProt NPD GO	RK5_ASTLO	Plastid 50S ribosomal protein L5	0.02	-	cyt	0	Plastid				179
P00287 UniProt NPD GO	PLAS_PHAVU	Plastocyanin	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...			9PCY	99
Q9SXW9 UniProt NPD GO	PLAS_PHYPA	Plastocyanin, chloroplast precursor	0.02	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				168
Q53I06 UniProt NPD GO	PLECT_PSENR	Plectasin precursor	0.02	-	vac	0	Secreted protein (Probable)			1ZFU	95
Q95152 UniProt NPD GO	PDPN_CANFA	Podoplanin precursor (Glycoprotein 38) (Gp38) (Mucin-type membrane protein Gp40)	0.02	-	end	1	Membrane; single-pass type I membrane protein. Localized to actin-rich microvilli and plasma membran ...	filopodium [ISS] lamellipodium [ISS] plasma membrane [ISS] ruffle [ISS]			169
P94092 UniProt NPD GO	POLC7_CYNDA	Polcalcin Cyn d 7 (Calcium-binding pollen allergen Cyn d 7) (Calcium-binding protein B1)	0.02	-	cyt	0					80
O82040 UniProt NPD GO	POLC7_PHLPR	Polcalcin Phl p 7 (Calcium-binding pollen allergen Phl p 7) (P7)	0.02	-	cyt	0				1K9U	78
P27761 UniProt NPD GO	MPA13_AMBAR	Pollen allergen Amb a 1.3 precursor (Antigen E) (Antigen Amb a I)	0.02	-	exc	0					397
P28744 UniProt NPD GO	MPA14_AMBAR	Pollen allergen Amb a 1.4 precursor (Antigen E) (Antigen Amb a I)	0.02	-	exc	0					392
P02878 UniProt NPD GO	MPAA5_AMBEL	Pollen allergen Amb a 5 (Amb a V) (Allergen Ra5)	0.02	-	nuc	0					45
P22286 UniProt NPD GO	MPA93_POAPR	Pollen allergen KBG 60 precursor (Pollen allergen Poa p 9) (Poa p IX)	0.02	-	end	1 *					307
P43215 UniProt NPD GO	MPAP6_PHLPR	Pollen allergen Phl p 6 precursor (Phl p VI)	0.02	-	end	0				1NLX	132
Q9Y833 UniProt NPD GO	PGLR2_PENOL	Polygalacturonase 2 precursor (EC 3.2.1.15) (PG 2) (Pectinase 2)	0.02	-	end	0	Secreted protein				380
P41736 UniProt NPD GO	POTX_PARCV	Poneratoxin (Pac-TX) (PoTX)	0.02	-	nuc	0	Secreted protein			1G92	25
P82414 UniProt NPD GO	PCG1_PACGO	Ponericin-G1	0.02	-	cyt	0	Secreted protein				30
P82416 UniProt NPD GO	PCG3_PACGO	Ponericin-G3	0.02	-	cyt	0	Secreted protein				30
P82417 UniProt NPD GO	PCG4_PACGO	Ponericin-G4	0.02	-	cyt	0	Secreted protein				29
Q9D8F3 UniProt NPD GO	PEVR2_MOUSE	Porcine endogenous retrovirus A receptor 2 homolog precursor (PERV-A receptor 2 homolog) (Protein GP ...	0.02	-	end	11 *	Membrane; multi-pass membrane protein				450
P81897 UniProt NPD GO	TXAEK_ACTEQ	Potassium channel toxin Aek	0.02	-	nuc	0	Secreted protein. Found in nematocyst				36
P24663 UniProt NPD GO	KAX13_MESTA	Potassium channel toxin alpha-KTx 1.3 (Iberiotoxin) (IbTx)	0.02	-	cyt	0	Secreted protein				37
P08815 UniProt NPD GO	KAX21_CENNO	Potassium channel toxin alpha-KTx 2.1 (Noxiustoxin) (NTx) (Toxin II.11)	0.02	-	nuc	0	Secreted protein			1SXM	39
P0C165 UniProt NPD GO	KAX2C_CENEL	Potassium channel toxin alpha-KTx 2.12 (Toxin Ce5)	0.02	-	nuc	0	Secreted protein				39
P0C161 UniProt NPD GO	KAX28_CENEL	Potassium channel toxin alpha-KTx 2.8 (Toxin Ce1)	0.02	-	nuc	0	Secreted protein				39
P0C162 UniProt NPD GO	KAX29_CENEL	Potassium channel toxin alpha-KTx 2.9 (Toxin Ce2)	0.02	-	nuc	0	Secreted protein				39
P46110 UniProt NPD GO	KAX34_LEIQH	Potassium channel toxin alpha-KTx 3.4 (Agitoxin-1) (AGTX-1) (AgTx1) (Leiurotoxin-2) (Leiurotoxin II) ...	0.02	-	nuc	0	Secreted protein				38
P55896 UniProt NPD GO	KAX37_ORTSC	Potassium channel toxin alpha-KTx 3.7 (Toxin OsK1) (OsK-1)	0.02	-	nuc	0	Secreted protein			1SCO	38
P46114 UniProt NPD GO	KAX41_TITSE	Potassium channel toxin alpha-KTx 4.1 (Tityustoxin K-alpha) (TsTX-K-alpha) (TSK4) (Toxin II-9)	0.02	-	nuc	0	Secreted protein			1HP2	37
P60210 UniProt NPD GO	KAX44_TITCA	Potassium channel toxin alpha-KTx 4.4 (Toxin Tc30)	0.02	-	nuc	0	Secreted protein	extracellular region [IDA]			37
P80670 UniProt NPD GO	KAX83_LEIQH	Potassium channel toxin alpha-KTx 8.3 (Leiuropeptide-2) (Leiuropeptide II) (LpII)	0.02	-	nuc	0	Secreted protein				29
Q29079 UniProt NPD GO	PAG2_PIG	Pregnancy-associated glycoprotein 2 precursor (EC 3.4.23.-) (PAG 2)	0.02	-	exc	0	Secreted protein; extracellular space				420
P83496 UniProt NPD GO	PA66D_SHEEP	Pregnancy-associated glycoprotein 66d (EC 3.4.23.-) (ovPAG 66d) (Fragment)	0.02	-		0					10
P46249 UniProt NPD GO	SECY_CYACA	Preprotein translocase secY subunit	0.02	-	end	9	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				410
P51297 UniProt NPD GO	SECY_PORPU	Preprotein translocase secY subunit	0.02	-	end	8 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				411
P49810 UniProt NPD GO	PSN2_HUMAN	Presenilin-2 (EC 3.4.23.-) (PS-2) (STM-2) (E5-1) (AD3LP) (AD5) [Contains: Presenilin-2 NTF subunit; ...	0.02	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum [IDA] Golgi apparatus [IDA] integral to nuclear inner membrane [TAS] integral to plasma membrane [IDA] kinetochore [TAS]	606889		448
O62692 UniProt NPD GO	MCHL1_PANPA	Pro-MCH variant (Fragment)	0.02	-	nuc	0					62
O62693 UniProt NPD GO	MCHL1_PANTR	Pro-MCH variant (Fragment)	0.02	-	nuc	0					62
Q8WWG1 UniProt NPD GO	NRG4_HUMAN	Pro-neuregulin-4, membrane-bound isoform (Pro-NRG4) [Contains: Neuregulin-4 (NRG-4)]	0.02	-	nuc	1	Pro-neuregulin-4, membrane-bound isoform: Cell membrane; single-pass type I membrane protein (By sim ...				115
P62499 UniProt NPD GO	SEM1_ASHGO	Probable 26 proteasome complex subunit SEM1	0.02	-	nuc	0					69
Q9VM46 UniProt NPD GO	SEM1_DROME	Probable 26 proteasome complex subunit sem1	0.02	-	cyt	0		proteasome complex (sensu Eukaryota) [ISS]			79
Q9FL96 UniProt NPD GO	SEM12_ARATH	Probable 26 proteasome complex subunit sem1-2	0.02	-	cyt	0					73
P50086 UniProt NPD GO	PSDA_YEAST	Probable 26S proteasome regulatory subunit p28 (Proteasome non-ATPase subunit 6)	0.02	-	cyt	0		proteasome regulatory particle (sensu Eukar... [IDA]		1WG0	228

You are viewing entries 85101 to 85150 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.