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
P56819 UniProt NPD GO	BACE1_RAT	Beta-secretase 1 precursor (EC 3.4.23.46) (Beta-site APP cleaving enzyme 1) (Beta-site amyloid precu ...	0.10	-	cyt	1	Membrane; single-pass type I membrane protein	endosome [ISS] Golgi apparatus [ISS] integral to membrane [ISS]			501
Q8VC97 UniProt NPD GO	BUP1_MOUSE	Beta-ureidopropionase (EC 3.5.1.6) (Beta-alanine synthase) (N-carbamoyl-beta-alanine amidohydrolase) ...	0.10	-	cyt	0	Cytoplasm (By similarity)				393
P20712 UniProt NPD GO	DRTS_PLACH	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolate reducta ...	0.10	-	cyt	0					583
Q3UHN9 UniProt NPD GO	NDST1_MOUSE	Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 (EC 2.8.2.8) (Glucosaminyl N-deacety ...	0.10	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				882
P38009 UniProt NPD GO	PUR92_YEAST	Bifunctional purine biosynthesis protein ADE17 [Includes: Phosphoribosylaminoimidazolecarboxamide fo ...	0.10	-	cyt	0		cytosol [IDA]			592
Q8CIF4 UniProt NPD GO	BTD_MOUSE	Biotinidase precursor (EC 3.5.1.12)	0.10	-	exc	0	Secreted protein; extracellular space (By similarity)	apical part of cell [IDA] nucleolus [IDA] perikaryon [IDA]			524
Q6ITB1 UniProt NPD GO	IVBI_PSEPO	Blackelin precursor	0.10	-	vac	0	Secreted protein (By similarity)				83
P04562 UniProt NPD GO	BPP_AGKHP	Bradykinin-potentiating peptide (Angiotensin-converting enzyme inhibitor)	0.10	-		0					11
Q9ER10 UniProt NPD GO	BSSP4_MOUSE	Brain-specific serine protease 4 precursor (EC 3.4.21.-) (BSSP-4) (Serine protease 22) (Tryptase eps ...	0.10	-	nuc	0					306
P54690 UniProt NPD GO	BCAT1_RAT	Branched-chain-amino-acid aminotransferase, cytosolic (EC 2.6.1.42) (BCAT(c))	0.10	-	mit	0	Cytoplasm				411
Q5EA40 UniProt NPD GO	BCAT2_BOVIN	Branched-chain-amino-acid aminotransferase, mitochondrial precursor (EC 2.6.1.42) (BCAT(m))	0.10	-	mit	0	Mitochondrion (By similarity)				393
O35854 UniProt NPD GO	BCAT2_RAT	Branched-chain-amino-acid aminotransferase, mitochondrial precursor (EC 2.6.1.42) (BCAT(m))	0.10	-	mit	0	Mitochondrion				393
Q8W0Z7 UniProt NPD GO	BCAL1_ARATH	Branched-chain-amino-acid aminotransferase-like protein 1 (Atbcat-like)	0.10	-	nuc	0					555
Q8TDM0 UniProt NPD GO	BCAS4_HUMAN	Breast carcinoma amplified sequence 4	0.10	-	mit	0	Cytoplasm (Potential)		607471		211
P82268 UniProt NPD GO	BR2TA_RANTE	Brevinin-2Ta precursor	0.10	-	exc	0	Secreted protein				74
P01068 UniProt NPD GO	IBRO_ANACO	Bromelain inhibitor precursor (BI) (Bromein) [Contains: Bromelain inhibitor 1 chain B (BI-I B) (Brom ...	0.10	-	nuc	0				2BI6	246
O97665 UniProt NPD GO	CCR8_MACMU	C-C chemokine receptor type 8 (C-C CKR-8) (CC-CKR-8) (CCR-8)	0.10	-	end	6 *	Membrane; multi-pass membrane protein				356
P32302 UniProt NPD GO	CXCR5_HUMAN	C-X-C chemokine receptor type 5 (CXC-R5) (CXCR-5) (Burkitt lymphoma receptor 1) (Monocyte-derived re ...	0.10	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601613		372
P28558 UniProt NPD GO	PHCB_AGLNE	C-phycocyanin beta chain	0.10	-	nuc	0	Plastid; chloroplast				172
Q6EIG7 UniProt NPD GO	CLC6A_HUMAN	C-type lectin domain family 6 member A (C-type lectin superfamily member 10) (Dendritic cell-associa ...	0.10	-	cyt	1 *	Membrane; single-pass type II membrane protein (Probable)				209
Q9U1H8 UniProt NPD GO	FACE2_DROME	CAAX prenyl protease 2 (EC 3.4.22.-) (Prenyl protein-specific endoprotease 2) (Farnesylated proteins ...	0.10	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				302
Q03530 UniProt NPD GO	RCE1_YEAST	CAAX prenyl protease 2 (EC 3.4.22.-) (Prenyl protein-specific endoprotease 2) (PPSEP 2) (RAS and A-f ...	0.10	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [IDA]			315
Q90304 UniProt NPD GO	CD166_CARAU	CD166 antigen homolog precursor (Activated leukocyte-cell adhesion molecule) (Neurolin) (DM-GRASP ho ...	0.10	-	end	1 *	Membrane; single-pass type I membrane protein				555
O97626 UniProt NPD GO	CD40L_CANFA	CD40 ligand (CD40-L) (Tumor necrosis factor ligand superfamily member 5) (CD154 antigen) [Contains: ...	0.10	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...	integral to membrane [ISS]			260
P27274 UniProt NPD GO	CD59_RAT	CD59 glycoprotein precursor (Membrane attack complex inhibition factor) (MACIF) (MAC-inhibitory prot ...	0.10	-	exc	2 *	Cell membrane; lipid-anchor; GPI-anchor				126
O55186 UniProt NPD GO	CD59A_MOUSE	CD59A glycoprotein precursor (Membrane attack complex inhibition factor) (MACIF) (MAC-inhibitory pro ...	0.10	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor				123
P81033 UniProt NPD GO	CPRP_CANPG	CHH precursor-related peptide (CPRP)	0.10	-	nuc	0	Secreted protein				38
Q494W8 UniProt NPD GO	CRFM7_HUMAN	CHRNA7-FAM7A fusion protein (D-10) (CHRNA7-DR1)	0.10	-	end	5	Membrane; multi-pass membrane protein (By similarity)		609756		412
Q8IZR5 UniProt NPD GO	CKLF4_HUMAN	CKLF-like MARVEL transmembrane domain-containing protein 4 (Chemokine-like factor superfamily member ...	0.10	-	end	4	Membrane; multi-pass membrane protein		607887		234
Q9FME5 UniProt NPD GO	COBL5_ARATH	COBRA-like protein 5 precursor	0.10	-	cyt	0					204
P68357 UniProt NPD GO	CSN6B_BRAOL	COP9 signalosome complex subunit 6b (Signalosome subunit 6b) (Fragments)	0.10	-	nuc	0	Cytoplasm. Nucleus				58
P38627 UniProt NPD GO	URA8_YEAST	CTP synthase 2 (EC 6.3.4.2) (UTP--ammonia ligase 2) (CTP synthetase 2)	0.10	-	cyt	0		cytosol [TAS]			577
Q9WTR5 UniProt NPD GO	CAD13_MOUSE	Cadherin-13 precursor (Truncated-cadherin) (T-cadherin) (T-cad) (Heart-cadherin) (H-cadherin)	0.10	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	external side of plasma membrane [IDA] plasma membrane [IDA]			714
Q7FRS8 UniProt NPD GO	CNB10_ARATH	Calcineurin B-like protein 10	0.10	-	mit	0					256
Q8LEM7 UniProt NPD GO	CNBL3_ARATH	Calcineurin B-like protein 3 (SOS3-like calcium-binding protein 6)	0.10	-	cyt	0					226
O08893 UniProt NPD GO	CALCR_CAVPO	Calcitonin receptor precursor (CT-R)	0.10	-	end	7	Membrane; multi-pass membrane protein				478
Q8CAE3 UniProt NPD GO	KCMB1_MOUSE	Calcium-activated potassium channel subunit beta 1 (Calcium-activated potassium channel, subfamily M ...	0.10	-	end	2 *	Membrane; multi-pass membrane protein				190
Q64566 UniProt NPD GO	AT2C1_RAT	Calcium-transporting ATPase type 2C member 1 (EC 3.6.3.8) (ATPase 2C1) (ATP-dependent Ca(2+) pump PM ...	0.10	-	end	8	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				919
Q64395 UniProt NPD GO	PDE1B_CRIGR	Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (EC 3.1.4.17) (Cam-PDE 1B) ...	0.10	-	mit	0	Cytoplasm (By similarity)				199
Q99895 UniProt NPD GO	CLCR_HUMAN	Caldecrin precursor (EC 3.4.21.2) (Chymotrypsin C)	0.10	-	mit	0			601405		268
Q38858 UniProt NPD GO	CALR2_ARATH	Calreticulin-2 precursor	0.10	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				424
P28871 UniProt NPD GO	CARP2_CANAL	Candidapepsin-2 precursor (EC 3.4.23.24) (Aspartate protease 2) (ACP 2) (Secreted aspartic protease ...	0.10	-	exc	0	Secreted protein			1ZAP	398
P43096 UniProt NPD GO	CARP7_CANAL	Candidapepsin-7 precursor (EC 3.4.23.24) (Aspartate protease 7) (ACP 7) (Secreted aspartic protease ...	0.10	-	exc	0	Secreted protein				588
Q801M1 UniProt NPD GO	CNR1_XENLA	Cannabinoid receptor 1 (CB1) (CB-R)	0.10	-	end	7	Membrane; multi-pass membrane protein (By similarity)				470
Q98894 UniProt NPD GO	CNR1A_FUGRU	Cannabinoid receptor type 1A	0.10	-	end	7	Membrane; multi-pass membrane protein				468
Q9UHJ6 UniProt NPD GO	CARKL_HUMAN	Carbohydrate kinase-like protein (EC 2.7.1.-)	0.10	-	mit	0	Cytoplasm (Potential)		605060		478
Q7M316 UniProt NPD GO	CAH1_GORGO	Carbonic anhydrase 1 (EC 4.2.1.1) (Carbonic anhydrase I) (Carbonate dehydratase I) (CA-I)	0.10	-	nuc	0	Cytoplasm (By similarity)				260
P04069 UniProt NPD GO	CBPB_ASTFL	Carboxypeptidase B (EC 3.4.17.2)	0.10	-	cyt	0	Secreted protein				303
P09955 UniProt NPD GO	CBPB1_PIG	Carboxypeptidase B precursor (EC 3.4.17.2)	0.10	-	end	0	Secreted protein			1ZG9	416
P19223 UniProt NPD GO	CBPB1_RAT	Carboxypeptidase B precursor (EC 3.4.17.2)	0.10	-	exc	0	Secreted protein				415

You are viewing entries 64051 to 64100 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.