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
P30064 UniProt NPD GO	ACCD_EPIVI	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.54	+	nuc	0	Plastid				493
Q8R2S9 UniProt NPD GO	ARP8_MOUSE	Actin-related protein 8	0.54	-	cyt	0					624
Q8N3C0 UniProt NPD GO	HELC1_HUMAN	Activating signal cointegrator 1 complex subunit 3 (EC 3.6.1.-) (ASC-1 complex subunit p200) (Trip4 ...	0.54	-	nuc	0	Cytoplasm				2202
Q99424 UniProt NPD GO	ACOX2_HUMAN	Acyl-coenzyme A oxidase 2, peroxisomal (EC 1.17.99.3) (3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-ch ...	0.54	-	pox	0	Peroxisome	peroxisome [NAS]	601641		681
Q8K1E6 UniProt NPD GO	ALKB3_MOUSE	Alkylated repair protein alkB homolog 3	0.54	-	nuc	0					286
Q5XIC8 UniProt NPD GO	ALKB3_RAT	Alkylated repair protein alkB homolog 3	0.54	-	mit	0					295
P97259 UniProt NPD GO	MGAT5_CRIGR	Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V (EC 2.4.1.155) (Mannoside ac ...	0.54	+	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				740
O88327 UniProt NPD GO	CTNL1_MOUSE	Alpha-catulin (Catenin alpha-like protein 1) (Alpha-catenin-related protein) (ACRP)	0.54	-	nuc	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein (By similarity)				731
Q15389 UniProt NPD GO	ANGP1_HUMAN	Angiopoietin-1 precursor (ANG-1)	0.54	-	exc	0	Secreted protein		601667		498
O08538 UniProt NPD GO	ANGP1_MOUSE	Angiopoietin-1 precursor (ANG-1)	0.54	-	nuc	0	Secreted protein				498
O18920 UniProt NPD GO	ANGP1_BOVIN	Angiopoietin-1 precursor (ANG-1) (Fragment)	0.54	-	mit	0	Secreted protein				481
P13808 UniProt NPD GO	B3A2_MOUSE	Anion exchange protein 2 (Non-erythroid band 3-like protein) (AE2 anion exchanger) (Solute carrier f ...	0.54	-	end	11	Membrane; multi-pass membrane protein				1237
Q5SUE8 UniProt NPD GO	ANR40_MOUSE	Ankyrin repeat domain-containing protein 40	0.54	-	nuc	0					363
Q7M2U8 UniProt NPD GO	APOE_SHEEP	Apolipoprotein E precursor (Apo-E)	0.54	-	exc	0	Secreted protein				316
O35841 UniProt NPD GO	API5_MOUSE	Apoptosis inhibitor 5 (API-5) (AAC-11)	0.54	-	cyt	0	Nucleus (By similarity). Mainly. Cytoplasm (By similarity)	spliceosome complex [IDA]			504
Q7Z2E3 UniProt NPD GO	APTX_HUMAN	Aprataxin (Forkhead-associated domain histidine triad-like protein) (FHA-HIT)	0.54	+	cyt	0	Nucleus. Upon genotoxic stress, it colocalizes with XRCC1 at sites of DNA damage		607426		356
Q9D7A8 UniProt NPD GO	ARMC1_MOUSE	Armadillo repeat-containing protein 1	0.54	-	nuc	0					282
Q4WVD0 UniProt NPD GO	ATG18_ASPFU	Autophagy-related protein 18	0.54	-	nuc	0	Membrane-associated. Peripheral membrane protein of pre-autophagosomal structure (PAS) and vacuole ( ...				436
Q5KGQ2 UniProt NPD GO	ATG18_CRYNE	Autophagy-related protein 18	0.54	-	nuc	0	Membrane-associated. Peripheral membrane protein of pre-autophagosomal structure (PAS) and vacuole ( ...				423
Q6TGJ4 UniProt NPD GO	ATG9_CRYGA	Autophagy-related protein 9	0.54	+	end	6 *	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...				751
Q9ZTX9 UniProt NPD GO	ARFD_ARATH	Auxin response factor 4	0.54	-	nuc	0	Nucleus				788
P34611 UniProt NPD GO	NCL1_CAEEL	B-box type zinc-finger protein ncl-1	0.54	-	nuc	0	Cytoplasm				851
P37707 UniProt NPD GO	B2_DAUCA	B2 protein	0.54	-	nuc	0					207
O76612 UniProt NPD GO	BAT47_CAEEL	BTB and MATH domain-containing protein 47	0.54	-	nuc	0					683
P58545 UniProt NPD GO	BTBD3_MOUSE	BTB/POZ domain-containing protein 3	0.54	+	cyt	0					532
Q9Y597 UniProt NPD GO	KCTD3_HUMAN	BTB/POZ domain-containing protein KCTD3 (NY-REN-45 antigen)	0.54	-	nuc	0					815
Q9QWK5 UniProt NPD GO	BIR1A_MOUSE	Baculoviral IAP repeat-containing protein 1a (Neuronal apoptosis inhibitory protein 1)	0.54	-	nuc	0					1403
Q13489 UniProt NPD GO	BIRC3_HUMAN	Baculoviral IAP repeat-containing protein 3 (Inhibitor of apoptosis protein 1) (HIAP1) (HIAP-1) (C-I ...	0.54	-	nuc	0	Cytoplasm (Potential)		601721		604
Q64124 UniProt NPD GO	SCX_MOUSE	Basic helix-loop-helix transcription factor scleraxis	0.54	-	nuc	0	Nucleus (By similarity)				207
Q4A1L5 UniProt NPD GO	BCN1_PIG	Beclin-1	0.54	-	cyt	0	Cytoplasm (Potential). Golgi apparatus; Golgi membrane; peripheral membrane protein. Expressed in de ...				448
Q86Z14 UniProt NPD GO	KLOTB_HUMAN	Beta klotho (BetaKlotho) (Klotho beta-like protein)	0.54	-	end	1	Membrane; single-pass type III membrane protein (Potential)				1044
O43825 UniProt NPD GO	B3GT2_HUMAN	Beta-1,3-galactosyltransferase 2 (EC 2.4.1.-) (Beta-1,3-GalTase 2) (Beta3Gal-T2) (UDP-galactose:2-ac ...	0.54	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)		603018		422
Q5R5Y3 UniProt NPD GO	B3GT2_PONPY	Beta-1,3-galactosyltransferase 2 (EC 2.4.1.-) (Beta-1,3-GalTase 2) (Beta3Gal-T2) (UDP-galactose:2-ac ...	0.54	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)				422
P01213 UniProt NPD GO	PDYN_HUMAN	Beta-neoendorphin-dynorphin precursor (Proenkephalin B) (Preprodynorphin) [Contains: Beta-neoendorph ...	0.54	-	exc	0	Secreted protein	plasma membrane [IDA]	131340		254
Q9EQW8 UniProt NPD GO	NDST4_MOUSE	Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 4 (EC 2.8.2.8) (Glucosaminyl N-deacety ...	0.54	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				872
P24608 UniProt NPD GO	BIND_ARBPU	Bindin precursor	0.54	-	nuc	0	Acrosome; acrosomal lumen				480
Q90752 UniProt NPD GO	BMP4_CHICK	Bone morphogenetic protein 4 precursor (BMP-4)	0.54	-	exc	0	Secreted protein (By similarity)				405
Q9VLD6 UniProt NPD GO	BOREA_DROME	Borealin (Borealin-related)	0.54	-	nuc	0	Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metaphase and then ...				315
Q00676 UniProt NPD GO	LUQ1_APLCA	Bradykinin-like neuropeptide precursor	0.54	-	exc	0	Secreted protein				146
P39873 UniProt NPD GO	RNBR_BOVIN	Brain ribonuclease precursor (EC 3.1.27.-) (BRB)	0.54	-	exc	1 *	Secreted protein				167
P53841 UniProt NPD GO	BSC4_YEAST	Bypass of stop codon protein 4	0.54	-	nuc	0					131
Q9WVI9 UniProt NPD GO	JIP1_MOUSE	C-jun-amino-terminal kinase-interacting protein 1 (JNK-interacting protein 1) (JIP-1) (JNK MAP kinas ...	0.54	-	nuc	0	Cytoplasm (By similarity). Accumulates in cell surface projections. Cytoplasm; perinuclear region (B ...	cytoplasm [IEP] neuron projection [IDA]		1UKI	707
Q9R237 UniProt NPD GO	JIP1_RAT	C-jun-amino-terminal kinase-interacting protein 1 (JNK-interacting protein 1) (JIP-1) (JNK MAP kinas ...	0.54	-	nuc	0	Cytoplasm (By similarity). Accumulates in cell surface projections. Cytoplasm; perinuclear region (B ...	cytoplasm [IEP]		2FPF	708
Q09316 UniProt NPD GO	CK5P1_CAEEL	CDK5RAP1-like protein	0.54	-	mit	0					547
P30686 UniProt NPD GO	1C01_PANTR	CHLA class I histocompatibility antigen, C alpha chain precursor	0.54	-	end	1	Membrane; single-pass type I membrane protein				366
Q6IR75 UniProt NPD GO	CSN2_XENLA	COP9 signalosome complex subunit 2 (Signalosome subunit 2) (Fragment)	0.54	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				441
P46962 UniProt NPD GO	CTK2_YEAST	CTD kinase subunit beta (CTD kinase 38 kDa subunit) (CTDK-I subunit beta)	0.54	-	mit	0	Nucleus	nucleus [IPI]			323
Q9Y6N8 UniProt NPD GO	CAD10_HUMAN	Cadherin-10 precursor (T2-cadherin)	0.54	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]	604555		788
Q9ULB5 UniProt NPD GO	CADH7_HUMAN	Cadherin-7 precursor	0.54	+	end	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]	605806		785
O74982 UniProt NPD GO	CID2_SCHPO	Caffeine-induced death protein 2	0.54	-	nuc	0					167

You are viewing entries 22351 to 22400 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.