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
Q766C3 UniProt NPD GO	NEP1_NEPGR	Aspartic proteinase nepenthesin-1 precursor (EC 3.4.23.-) (Nepenthesin-I)	0.28	-	nuc	0	Secreted protein (By similarity)				437
P32834 UniProt NPD GO	SXA1_SCHPO	Aspartic proteinase sxa1 precursor (EC 3.4.23.-)	0.28	-	exc	1		cell surface [TAS] plasma membrane [IDA]			533
Q9UBB4 UniProt NPD GO	ATX10_HUMAN	Ataxin-10 (Spinocerebellar ataxia type 10 protein) (Brain protein E46 homolog)	0.28	-	cyt	0			603516		475
Q8BH66 UniProt NPD GO	SPG3A_MOUSE	Atlastin (GTP-binding protein 3) (Guanine nucleotide-binding protein 3)	0.28	-	end	2					558
P07501 UniProt NPD GO	ANF_BOVIN	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP) (Prepronatriodilatin)	0.28	-	exc	0	Secreted protein				152
Q755K1 UniProt NPD GO	ATG3_ASHGO	Autophagy-related protein 3 (Autophagy-related E2-like conjugation enzyme ATG3)	0.28	-	mit	0	Cytoplasm (By similarity)				282
P0C075 UniProt NPD GO	ATG8_CANAL	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier ATG8)	0.28	-	nuc	0	Membrane-associated through a lipid anchor. Cvt vesicles, autophagosomes and vacuolar (By similarity ...				135
Q5B2U9 UniProt NPD GO	ATG8_EMENI	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier atg8)	0.28	-	nuc	0	Membrane-associated through a lipid anchor. Cvt vesicles, autophagosomes and vacuolar (By similarity ...				118
O24542 UniProt NPD GO	AX22D_PHAAU	Auxin-induced protein 22D (Indole-3-acetic acid-induced protein ARG13)	0.28	-	nuc	0	Nucleus (By similarity)				193
P0C129 UniProt NPD GO	IAA27_ORYSA	Auxin-responsive protein IAA27 (Indoleacetic acid-induced protein 27)	0.28	-	nuc	0	Nucleus (By similarity)				143
Q9LDT3 UniProt NPD GO	YAB4_ARATH	Axial regulator YABBY4 (Protein INNER NO OUTER)	0.28	-	nuc	0	Nucleus				231
O35153 UniProt NPD GO	BET1L_MOUSE	BET1-like protein (Vesicle transport protein GOS15) (Golgi SNARE with a size of 15 kDa) (GS15) (GOS- ...	0.28	-	mit	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)	Golgi membrane [IDA]			111
Q8WZ19 UniProt NPD GO	KCD13_HUMAN	BTB/POZ domain-containing protein KCTD13 (Polymerase delta-interacting protein 1) (TNFAIP1-like prot ...	0.28	-	cyt	0	Nucleus		608947		329
O70552 UniProt NPD GO	BTG4_MOUSE	BTG4 protein (PC3b)	0.28	-	nuc	0					250
Q9JHY7 UniProt NPD GO	BIRC5_RAT	Baculoviral IAP repeat-containing protein 5 (Apoptosis inhibitor survivin)	0.28	-	nuc	0	Cytoplasm. Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metapha ...				142
Q5R8P3 UniProt NPD GO	BBS10_PONPY	Bardet-Biedl syndrome 10 protein homolog	0.28	-	end	0					723
Q98SP7 UniProt NPD GO	BBS2_BRARE	Bardet-Biedl syndrome 2 protein homolog	0.28	-	nuc	0					715
P25765 UniProt NPD GO	CHI2_ORYSA	Basic endochitinase 2 precursor (EC 3.2.1.14)	0.28	-	mit	0					336
P02811 UniProt NPD GO	PRPE_HUMAN	Basic proline-rich peptide P-E (IB-9)	0.28	-	nuc	0		extracellular region [NAS]			61
P17790 UniProt NPD GO	BASI_CHICK	Basigin precursor (Blood-brain barrier HT7 antigen) (Neurothelin) (5A11 antigen)	0.28	+	end	2 *	Membrane; single-pass type I membrane protein				388
P26998 UniProt NPD GO	CRBB3_HUMAN	Beta crystallin B3 (Beta-B3-crystallin)	0.28	-	cyt	0			609741		211
P08037 UniProt NPD GO	B4GT1_BOVIN	Beta-1,4-galactosyltransferase 1 (EC 2.4.1.-) (Beta-1,4-GalTase 1) (Beta4Gal-T1) (b4Gal-T1) (UDP-gal ...	0.28	-	nuc	1 *	Isoform Long, isoform Short: Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II ...			2FYD	402
O60512 UniProt NPD GO	B4GT3_HUMAN	Beta-1,4-galactosyltransferase 3 (EC 2.4.1.-) (Beta-1,4-GalTase 3) (Beta4Gal-T3) (b4Gal-T3) (UDP-gal ...	0.28	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Trans cist ...		604014		393
Q5NVN3 UniProt NPD GO	B4GT3_PONPY	Beta-1,4-galactosyltransferase 3 (EC 2.4.1.-) (Beta-1,4-GalTase 3) (Beta4Gal-T3) (b4Gal-T3) (UDP-gal ...	0.28	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				393
Q30KR1 UniProt NPD GO	DB109_HUMAN	Beta-defensin 109 precursor (Defensin, beta 109)	0.28	-	end	0	Secreted protein (By similarity)				87
Q8R2I4 UniProt NPD GO	BD13_MOUSE	Beta-defensin 13 precursor (Defensin, beta 13) (BD-13) (mBD-13)	0.28	-	mit	1 *	Secreted protein (By similarity)				64
Q6AXR4 UniProt NPD GO	HEXB_RAT	Beta-hexosaminidase beta chain precursor (EC 3.2.1.52) (N-acetyl-beta-glucosaminidase) (Beta-N-acety ...	0.28	-	vac	1 *	Lysosome (By similarity)				537
P37142 UniProt NPD GO	AKH_DAUCA	Bifunctional aspartokinase/homoserine dehydrogenase, chloroplast precursor (AK-HD) (AK-HSDH) [Includ ...	0.28	-	mit	0	Plastid; chloroplast				921
P30122 UniProt NPD GO	CEL_BOVIN	Bile salt-activated lipase precursor (EC 3.1.1.3) (EC 3.1.1.13) (BAL) (Bile salt-stimulated lipase) ...	0.28	-	cyt	0		cytoplasm [ISS]		2BCE	597
P29004 UniProt NPD GO	BMNL3_BOMOR	Bombinin-like peptides 3 precursor [Contains: Acidic peptide 1; Bombinin-like peptide 3 (BLP-3); Oct ...	0.28	-	exc	0	Secreted protein				200
Q4V7H8 UniProt NPD GO	BORAA_XENLA	Borealin-A (Dasra-A) (DasraA) (xDasraA) (Cell division cycle-associated protein 8-A)	0.28	+	nuc	0	Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metaphase and then ...				296
P83311 UniProt NPD GO	IBB_PHAAT	Bowman-Birk type proteinase inhibitor (TBPI-B)	0.28	-	nuc	0					80
P82469 UniProt NPD GO	IBB1_DIOGL	Bowman-Birk type proteinase inhibitor 1 (Bowman-Birk type proteinase inhibitor I) (DgTI)	0.28	-	nuc	0					67
P80724 UniProt NPD GO	BASP_BOVIN	Brain acid soluble protein 1 (BASP1 protein) (Neuronal axonal membrane protein NAP-22) (22 kDa neuro ...	0.28	-	nuc	0	Membrane; lipid-anchor. Associated with the membranes of "growth cones" that form the tips of elonga ...				226
Q05175 UniProt NPD GO	BASP_RAT	Brain acid soluble protein 1 (BASP1 protein) (Neuronal axonal membrane protein NAP-22) (22 kDa neuro ...	0.28	-	nuc	0	Membrane; lipid-anchor. Associated with the membranes of "growth cones" that form the tips of elonga ...				219
O97759 UniProt NPD GO	BDNF_AILFU	Brain-derived neurotrophic factor precursor (BDNF)	0.28	-	nuc	0	Secreted protein				247
P23363 UniProt NPD GO	BDNF_RAT	Brain-derived neurotrophic factor precursor (BDNF)	0.28	-	nuc	0	Secreted protein				249
Q02193 UniProt NPD GO	BDNF_XIPMA	Brain-derived neurotrophic factor precursor (BDNF)	0.28	-	mit	0					269
P48539 UniProt NPD GO	PEP19_HUMAN	Brain-specific polypeptide PEP-19 (Brain-specific antigen PCP-4) (Purkinje cell protein 4)	0.28	-	nuc	0			601629		61
Q96GW7 UniProt NPD GO	PGCB_HUMAN	Brevican core protein precursor (Brain-enriched hyaluronan-binding protein) (Protein BEHAB)	0.28	-	vac	0	Isoform 1: Secreted protein; extracellular space; extracellular matrix. Isoform 2: Membrane; lipid-a ...				911
P35350 UniProt NPD GO	CCRL1_BOVIN	C-C chemokine receptor type 11 (C-C CKR-11) (CC-CKR-11) (CCR-11) (CC chemokine receptor-like 1) (Put ...	0.28	+	end	7 *	Membrane; multi-pass membrane protein				350
P17991 UniProt NPD GO	HOR8_HORVU	C-hordein (Clone PC HOR1-3) (Fragment)	0.28	-	nuc	0					72
Q61490 UniProt NPD GO	CD166_MOUSE	CD166 antigen precursor (Activated leukocyte-cell adhesion molecule) (ALCAM) (DM-GRASP protein)	0.28	-	end	1 *	Membrane; single-pass type I membrane protein	axon [IDA] cell soma [IDA] external side of plasma membrane [IDA]			583
Q91ZW8 UniProt NPD GO	C209D_MOUSE	CD209 antigen-like protein D (DC-SIGN-related protein 3) (DC-SIGNR3)	0.28	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)				237
Q9Y6G5 UniProt NPD GO	COMDA_HUMAN	COMM domain-containing protein 10	0.28	-	nuc	0					202
Q8W206 UniProt NPD GO	CSN6A_ARATH	COP9 signalosome complex subunit 6a (Signalosome subunit 6a) (AtCSN6a)	0.28	-	nuc	0	Cytoplasm (Probable). Nucleus (Probable)				317
P33146 UniProt NPD GO	CAD15_MOUSE	Cadherin-15 precursor (Muscle-cadherin) (M-cadherin) (Cadherin-14)	0.28	-	end	1	Membrane; single-pass type I membrane protein				784
P39038 UniProt NPD GO	CADH4_MOUSE	Cadherin-4 precursor (Retinal-cadherin) (R-cadherin) (R-CAD)	0.28	-	end	1	Membrane; single-pass type I membrane protein				913
P04467 UniProt NPD GO	CALB1_BOVIN	Calbindin (Vitamin D-dependent calcium-binding protein, avian-type) (Calbindin D28) (D-28K)	0.28	-	cyt	0					260
O43745 UniProt NPD GO	CHP2_HUMAN	Calcineurin B homologous protein 2 (Hepatocellular carcinoma-associated antigen 520)	0.28	-	cyt	0					195

You are viewing entries 42051 to 42100 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.