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
O81825 UniProt NPD GO	DRL28_ARATH	Putative disease resistance protein At4g27220	0.41	-	mit	0					919
P83292 UniProt NPD GO	G23AB_DROME	Putative gustatory receptor 23a, isoform B	0.41	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			374
O14089 UniProt NPD GO	IMB2_SCHPO	Putative importin beta-2 subunit (Karyopherin beta-2 subunit) (Importin 104) (Transportin) (TRN)	0.41	-	cyt	0	Cytoplasm (By similarity)				910
Q6L438 UniProt NPD GO	R1A6_SOLDE	Putative late blight resistance protein homolog R1A-6	0.41	-	vac	0	Cytoplasm (By similarity)				1247
Q9SAF5 UniProt NPD GO	ALA11_ARATH	Putative phospholipid-transporting ATPase 11 (EC 3.6.3.1) (Aminophospholipid flippase 11)	0.41	-	end	9	Membrane; multi-pass membrane protein				1203
Q7Z4T8 UniProt NPD GO	GLTL5_HUMAN	Putative polypeptide N-acetylgalactosaminyltransferase-like protein 5 (EC 2.4.1.-) (Protein-UDP acet ...	0.41	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				443
Q863D4 UniProt NPD GO	KCNRG_BOVIN	Putative potassium channel regulatory protein (Potassium channel regulator) (Protein CLLD4)	0.41	-	nuc	0					267
P34633 UniProt NPD GO	YOO1_CAEEL	Putative serine/threonine-protein kinase ZK507.1 (EC 2.7.11.1)	0.41	-	nuc	0					331
P34635 UniProt NPD GO	YOO3_CAEEL	Putative serine/threonine-protein kinase ZK507.3 (EC 2.7.11.1)	0.41	-	nuc	0					374
O13879 UniProt NPD GO	YE1F_SCHPO	Putative transporter C1B3.15C	0.41	-	end	11	Membrane; multi-pass membrane protein (Potential)				628
P25639 UniProt NPD GO	YCV1_YEAST	Putative uncharacterized protein YCR061W precursor	0.41	-	end	10 *	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA]			631
Q95KF1 UniProt NPD GO	RN125_MACFA	RING finger protein 125 (EC 6.3.2.-)	0.41	-	nuc	0					231
Q5TM52 UniProt NPD GO	RNF39_MACMU	RING finger protein 39	0.41	-	nuc	0	Cytoplasm (By similarity)				420
Q9H4P4 UniProt NPD GO	RNF41_HUMAN	RING finger protein 41	0.41	-	cyt	0				2GWF	317
Q940Q4 UniProt NPD GO	ATL4K_ARATH	RING-H2 finger protein ATL4K (RING-H2 finger protein ATL13)	0.41	-	nuc	1 *					472
Q5A3Q0 UniProt NPD GO	REXO4_CANAL	RNA exonuclease 4 (EC 3.1.-.-)	0.41	+	nuc	0	Nucleus (By similarity)				285
Q9Y7N2 UniProt NPD GO	MED19_SCHPO	RNA polymerase II mediator complex subunit 19 (RNA polymerase II mediator complex protein rox3)	0.41	-	nuc	0	Nucleus (Probable)	mediator complex [IDA]			138
Q10477 UniProt NPD GO	MED27_SCHPO	RNA polymerase II mediator complex subunit 27 (RNA polymerase II mediator complex protein pmc3)	0.41	-	nuc	0	Nucleus (Potential)				273
Q9JKN6 UniProt NPD GO	NOVA1_MOUSE	RNA-binding protein Nova-1 (Neuro-oncological ventral antigen 1) (Ventral neuron-specific protein 1) ...	0.41	-	nuc	0	Nucleus	nucleus [IC]			493
Q5RCE1 UniProt NPD GO	GDIB_PONPY	Rab GDP dissociation inhibitor beta (Rab GDI beta) (Guanosine diphosphate dissociation inhibitor 2) ...	0.41	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				445
O14715 UniProt NPD GO	RBP23_HUMAN	Ran-binding protein 2-like 3 (RanBP2L3) (Fragment)	0.41	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex (Probable)	nuclear pore [NAS]			755
P28701 UniProt NPD GO	RXRG_CHICK	Retinoic acid receptor RXR-gamma (Retinoid X receptor gamma)	0.41	+	nuc	0	Nucleus				467
P04283 UniProt NPD GO	ENV17_DROME	Retrovirus-related Env polyprotein from copia-like transposable element 17.6	0.41	-	nuc	1					456
Q863K1 UniProt NPD GO	RNAS9_PANTR	Ribonuclease-like protein 9 precursor	0.41	-	mit	0	Secreted protein (Probable)				205
P21524 UniProt NPD GO	RIR1_YEAST	Ribonucleoside-diphosphate reductase large chain 1 (EC 1.17.4.1) (Ribonucleotide reductase large sub ...	0.41	-	cyt	0	Cytoplasm	cytoplasm [IDA] ribonucleoside-diphosphate reductase complex [IDA]		2EUD	888
P07742 UniProt NPD GO	RIR1_MOUSE	Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) (Ribonucleoside-diphosphate reducta ...	0.41	-	nuc	0	Cytoplasm				792
P82231 UniProt NPD GO	RRFC_SPIOL	Ribosome recycling factor, chloroplast precursor (Ribosome-releasing factor, chloroplast) (RRF) (CpF ...	0.41	-	nuc	0	Plastid; chloroplast; chloroplast stroma. The major part was found in the stroma and some protein wa ...				271
Q64131 UniProt NPD GO	RUNX3_MOUSE	Runt-related transcription factor 3 (Core-binding factor, alpha 3 subunit) (CBF-alpha 3) (Acute myel ...	0.41	-	nuc	0	Nucleus	nucleus [IDA]			409
Q4WKH9 UniProt NPD GO	RUVB2_ASPFU	RuvB-like helicase 2 (EC 3.6.1.-)	0.41	-	cyt	0	Nucleus (By similarity)				469
P17841 UniProt NPD GO	SLSG4_BRAOL	S-locus-specific glycoprotein S14 precursor (SLSG-14) (Fragment)	0.41	-	exc	1 *					434
Q8JZW5 UniProt NPD GO	SH2D5_MOUSE	SH2 domain-containing protein 5	0.41	-	mit	0					345
Q96288 UniProt NPD GO	STO_ARATH	Salt-tolerance protein	0.41	-	nuc	0	Nucleus (Potential)				248
P16230 UniProt NPD GO	SRCH_RABIT	Sarcoplasmic reticulum histidine-rich calcium-binding protein precursor	0.41	-	exc	0	Sarcoplasmic reticulum; sarcoplasmic reticulum lumen				852
Q710A1 UniProt NPD GO	SPP24_SALSA	Secreted phosphoprotein 24 precursor (Spp-24) (Secreted phosphoprotein 2)	0.41	-	exc	0	Secreted protein (By similarity)				196
O08623 UniProt NPD GO	SQSTM_RAT	Sequestosome-1 (Ubiquitin-binding protein p62) (Protein kinase C-zeta-interacting protein) (PKC-zeta ...	0.41	-	nuc	0	Cytoplasm. Endosome; late endosome. Localizes to late endosomes. Nucleus. May also localize to the n ...	cytosol [ISS]			439
P07666 UniProt NPD GO	SRYA_DROME	Serendipity locus protein alpha	0.41	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein; cytoplasmic side. Inner membrane-associated a ...	cytosol [IDA] plasma membrane [IDA]			530
Q9D6X6 UniProt NPD GO	PRS23_MOUSE	Serine protease 23 precursor (EC 3.4.21.-)	0.41	-	exc	1 *	Secreted protein (Potential)				382
Q6P4P1 UniProt NPD GO	SPA3A_MOUSE	Serine protease inhibitor A3A precursor (Serpin A3A)	0.41	-	end	1 *	Secreted protein (By similarity)				422
Q9UBE8 UniProt NPD GO	NLK_HUMAN	Serine/threonine kinase NLK (EC 2.7.11.24) (Nemo-like kinase) (Protein LAK1)	0.41	-	nuc	0	Nucleus (By similarity). Predominantly. Cytoplasm (By similarity). A smaller fraction is cytoplasmic ...	nucleus [ISS]	609476		515
Q5Z8Z7 UniProt NPD GO	2ABA_ORYSA	Serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform (PP2A, subunit B, ...	0.41	-	nuc	0					581
Q9Z2W1 UniProt NPD GO	STK25_MOUSE	Serine/threonine-protein kinase 25 (EC 2.7.11.1) (Sterile 20/oxidant stress-response kinase 1) (Ste2 ...	0.41	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus (By similarity). Localizes to the Golgi apparatus (By sim ...				426
P0C198 UniProt NPD GO	CHK1_USTMA	Serine/threonine-protein kinase CHK1 (EC 2.7.11.1) (Checkpoint kinase 1)	0.41	-	nuc	0	Nucleus (By similarity)				662
P11801 UniProt NPD GO	KPSH1_HUMAN	Serine/threonine-protein kinase H1 (EC 2.7.11.1) (PSK-H1)	0.41	-	nuc	0	Localized in the Brefeldin A-sensitive Golgi compartment, at centrosomes, in the nucleus with a some ...		177015		423
O82734 UniProt NPD GO	PP18_ARATH	Serine/threonine-protein phosphatase PP1 isozyme 8 (EC 3.1.3.16)	0.41	-	cyt	0					324
Q09213 UniProt NPD GO	SRE1_CAEEL	Serpentine receptor class epsilon-1 (Protein sre-1)	0.41	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				355
Q9CYP7 UniProt NPD GO	SESN3_MOUSE	Sestrin-3	0.41	-	mit	0					492
Q13507 UniProt NPD GO	TRPC3_HUMAN	Short transient receptor potential channel 3 (TrpC3) (Htrp-3) (Htrp3)	0.41	-	end	8	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]	602345		848
P37107 UniProt NPD GO	SR54C_ARATH	Signal recognition particle 54 kDa protein, chloroplast precursor (SRP54) (54 chloroplast protein) ( ...	0.41	+	mit	0	Plastid; chloroplast; chloroplast stroma				564
Q9DBG7 UniProt NPD GO	SRPR_MOUSE	Signal recognition particle receptor subunit alpha (SR-alpha) (Docking protein alpha) (DP-alpha)	0.41	+	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity). ...				636
P09886 UniProt NPD GO	HS21C_PEA	Small heat shock protein, chloroplast precursor	0.41	-	mit	0	Plastid; chloroplast				232

You are viewing entries 31401 to 31450 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.