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
P61262 UniProt NPD GO	BD01_PAPAN	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.12	-	exc	0	Secreted protein (Potential)				68
O18794 UniProt NPD GO	BD01_MACMU	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1) (RhBD-1)	0.12	-	exc	0	Secreted protein (Potential)				68
Q8R2I8 UniProt NPD GO	BD10_MOUSE	Beta-defensin 10 precursor (Defensin, beta 10) (BD-10) (mBD-10)	0.12	-	mit	0	Secreted protein (By similarity)				73
Q96PH6 UniProt NPD GO	DB118_HUMAN	Beta-defensin 118 precursor (Defensin, beta 118) (Beta-defensin 18) (DEFB-18) (Epididymal secretory ...	0.12	-	nuc	0	Secreted protein		607650		123
Q7Z7B8 UniProt NPD GO	DB128_HUMAN	Beta-defensin 128 precursor (Defensin, beta 128) (Beta-defensin 28) (DEFB-28)	0.12	-	end	0	Secreted protein (Potential)				93
Q8K3U4 UniProt NPD GO	BD36_MOUSE	Beta-defensin 36 precursor (Defensin, beta 36) (BD-36) (mBD-36) (Fragment)	0.12	-	nuc	0	Secreted protein (By similarity)				43
Q60HF6 UniProt NPD GO	BGAL_MACFA	Beta-galactosidase precursor (EC 3.2.1.23) (Lactase) (Acid beta-galactosidase)	0.12	-	exc	0	Lysosome (By similarity)				682
Q15486 UniProt NPD GO	GUSL2_HUMAN	Beta-glucuronidase-like protein SMA3	0.12	-	nuc	0					140
Q15487 UniProt NPD GO	GUSL3_HUMAN	Beta-glucuronidase-like protein SMA4	0.12	-	nuc	0					140
Q9UUZ3 UniProt NPD GO	MANBA_ASPNG	Beta-mannosidase precursor (EC 3.2.1.25) (Mannanase) (Mannase)	0.12	-	end	0	Secreted protein	extracellular region [NAS]			931
Q2HJ40 UniProt NPD GO	BACE1_BOVIN	Beta-secretase 1 precursor (EC 3.4.23.46) (Beta-site APP cleaving enzyme 1) (Beta-site amyloid precu ...	0.12	-	end	1	Membrane; single-pass type I membrane protein				501
P49080 UniProt NPD GO	AKH2_MAIZE	Bifunctional aspartokinase/homoserine dehydrogenase 2, chloroplast precursor (AK-HD 2) (AK-HSDH 2) [ ...	0.12	-	end	0	Plastid; chloroplast				917
P52848 UniProt NPD GO	NDST1_HUMAN	Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 (EC 2.8.2.8) (Glucosaminyl N-deacety ...	0.12	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein		600853	1NST	882
Q9ES38 UniProt NPD GO	S27A5_RAT	Bile acyl-CoA synthetase (EC 6.2.1.7) (BACS) (Bile acid CoA ligase) (BA-CoA ligase) (BAL) (Cholate-- ...	0.12	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				690
Q9PSN3 UniProt NPD GO	VSP2_AGKBI	Bilineobin (EC 3.4.21.-)	0.12	-	cyt	0	Secreted protein				235
P51283 UniProt NPD GO	BCCP_PORPU	Biotin carboxyl carrier protein of acetyl-CoA carboxylase (BCCP)	0.12	-	nuc	0	Plastid; chloroplast				157
P50584 UniProt NPD GO	AP4A_PIG	Bis(5'-nucleosyl)-tetraphosphatase [Asymmetrical] (EC 3.6.1.17) (Diadenosine 5',5'''-P1,P4-tetraphos ...	0.12	-	mit	0					146
Q3T138 UniProt NPD GO	BOLA1_BOVIN	BolA-like protein 1	0.12	-	nuc	0					135
Q8CEI1 UniProt NPD GO	BOLA3_MOUSE	BolA-like protein 3	0.12	-	mit	0					110
Q9M439 UniProt NPD GO	BCAT2_ARATH	Branched-chain-amino-acid aminotransferase 2, chloroplast precursor (EC 2.6.1.42) (Atbcat-2)	0.12	-	mit	0	Plastid; chloroplast				388
O35855 UniProt NPD GO	BCAT2_MOUSE	Branched-chain-amino-acid aminotransferase, mitochondrial precursor (EC 2.6.1.42) (BCAT(m))	0.12	-	cyt	0	Mitochondrion	mitochondrion [IDA]			393
O19098 UniProt NPD GO	BCAT2_PIG	Branched-chain-amino-acid aminotransferase, mitochondrial precursor (EC 2.6.1.42) (BCAT(m)) (Fragmen ...	0.12	-	mit	0	Mitochondrion (By similarity)				31
Q4FCM6 UniProt NPD GO	BURS_MANSE	Bursicon precursor (Bursicon subunit alpha) (Cuticle-tanning hormone)	0.12	-	nuc	0	Secreted protein (By similarity)				156
O00478 UniProt NPD GO	BT3A3_HUMAN	Butyrophilin subfamily 3 member A3 precursor	0.12	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				584
Q9UIR0 UniProt NPD GO	BTNL2_HUMAN	Butyrophilin-like protein 2 precursor (BTL-II)	0.12	-	cyt	0	Secreted protein; extracellular space (Potential)		606000		455
O70355 UniProt NPD GO	BTNL2_MOUSE	Butyrophilin-like protein 2 precursor (Fragment)	0.12	-	mit	0	Secreted protein; extracellular space (Potential)				452
Q9Z2I3 UniProt NPD GO	CCR3_CAVPO	C-C chemokine receptor type 3 (C-C CKR-3) (CC-CKR-3) (CCR-3) (CCR3) (CKR3) (CD193 antigen)	0.12	-	end	7 *	Membrane; multi-pass membrane protein				358
P56492 UniProt NPD GO	CCR3_CERAE	C-C chemokine receptor type 3 (C-C CKR-3) (CC-CKR-3) (CCR-3) (CCR3) (CKR3) (CD193 antigen)	0.12	-	end	7 *	Membrane; multi-pass membrane protein				355
P51677 UniProt NPD GO	CCR3_HUMAN	C-C chemokine receptor type 3 (C-C CKR-3) (CC-CKR-3) (CCR-3) (CCR3) (CKR3) (Eosinophil eotaxin recep ...	0.12	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	601268		355
O88712 UniProt NPD GO	CTBP1_MOUSE	C-terminal-binding protein 1 (EC 1.1.1.-) (CtBP1)	0.12	-	mit	0	Cytoplasm. Nucleus				440
Q9YHU0 UniProt NPD GO	CTBPA_XENLA	C-terminal-binding protein A (CtBP)	0.12	-	mit	0	Nucleus (Potential)				440
Q8IUN9 UniProt NPD GO	CLC10_HUMAN	C-type lectin domain family 10 member A (C-type lectin superfamily member 14) (Macrophage lectin 2) ...	0.12	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)	plasma membrane [TAS]	605999		316
Q67EQ0 UniProt NPD GO	CLC4A_RAT	C-type lectin domain family 4 member A (C-type lectin superfamily member 6) (Dendritic cell inhibito ...	0.12	-	nuc	1 *	Membrane; single-pass type II membrane protein (Probable)				240
Q8AXR2 UniProt NPD GO	ANFC2_ONCMY	C-type natriuretic peptide 2 precursor (C-type natriuretic peptide II) (CNP-22 II)	0.12	-	exc	0	Secreted protein				131
Q9LDI3 UniProt NPD GO	CPK24_ARATH	CBL-interacting serine/threonine-protein kinase 24 (EC 2.7.11.1) (SNF1-related kinase 3.11) (SALT OV ...	0.12	-	end	0					446
O95971 UniProt NPD GO	BY55_HUMAN	CD160 antigen precursor (Natural killer cell receptor BY55)	0.12	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor	anchored to plasma membrane [IDA] plasma membrane [NAS]	604463		181
O43866 UniProt NPD GO	CD5L_HUMAN	CD5 antigen-like precursor (SP-alpha) (CT-2) (IgM-associated peptide)	0.12	-	exc	0	Secreted protein	extracellular region [NAS] extracellular space [TAS]	602592		347
Q8SQA4 UniProt NPD GO	CD97_BOVIN	CD97 antigen precursor	0.12	-	end	7	Membrane; multi-pass membrane protein				734
P34117 UniProt NPD GO	CDC2H_DICDI	CDC2-like serine/threonine-protein kinase CRP (EC 2.7.11.22) (EC 2.7.11.23)	0.12	-	cyt	0					292
Q9N425 UniProt NPD GO	CSN3_CAEEL	COP9 signalosome complex subunit 3 (Signalosome subunit 3)	0.12	-	mit	0	Cytoplasm. Nucleus	signalosome complex [IPI]			501
Q5U2N0 UniProt NPD GO	PYRG2_RAT	CTP synthase 2 (EC 6.3.4.2) (UTP--ammonia ligase 2) (CTP synthetase 2)	0.12	-	cyt	0					586
Q3B7N0 UniProt NPD GO	CAD13_BOVIN	Cadherin-13 precursor	0.12	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				713
Q9R100 UniProt NPD GO	CAD17_MOUSE	Cadherin-17 precursor (Liver-intestine-cadherin) (LI-cadherin) (BILL-cadherin) (P130)	0.12	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]			827
Q9LTB8 UniProt NPD GO	CNBL9_ARATH	Calcineurin B-like protein 9	0.12	-	cyt	0	Cell membrane; lipid-anchor (By similarity)				212
Q6CGE6 UniProt NPD GO	CANB_YARLI	Calcineurin subunit B (Protein phosphatase 2B regulatory subunit) (Calcineurin regulatory subunit)	0.12	+	cyt	0					173
Q9JHG2 UniProt NPD GO	CCP2_MOUSE	Calcipressin-2 (Down syndrome candidate region 1-like protein 1) (Myocyte-enriched calcineurin-inter ...	0.12	-	nuc	0					197
Q5RBC8 UniProt NPD GO	CMC1_PONPY	Calcium-binding mitochondrial carrier protein Aralar1 (Mitochondrial aspartate glutamate carrier 1) ...	0.12	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				678
Q9JLK4 UniProt NPD GO	CABP2_MOUSE	Calcium-binding protein 2 (CaBP2)	0.12	-	nuc	0					215
Q9N1Q8 UniProt NPD GO	CABP5_BOVIN	Calcium-binding protein 5 (CaBP5)	0.12	-	cyt	0					173
Q9NP86 UniProt NPD GO	CABP5_HUMAN	Calcium-binding protein 5 (CaBP5)	0.12	-	cyt	0			607316		173

You are viewing entries 60901 to 60950 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.