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
P06835 UniProt NPD GO	BGLS_HANAN	Beta-glucosidase precursor (EC 3.2.1.21) (Gentiobiase) (Cellobiase) (Beta-D-glucoside glucohydrolase ...	0.06	-	cyt	0					825
Q86M34 UniProt NPD GO	HEXB_ENTHI	Beta-hexosaminidase beta chain precursor (EC 3.2.1.52) (N-acetyl-beta-glucosaminidase) (Beta-GlcNAca ...	0.06	-	exc	0	Cytoplasmic granule				565
O13152 UniProt NPD GO	KRFJ_CHICK	Beta-keratin-related protein	0.06	-	nuc	0					108
P67975 UniProt NPD GO	LACB_OVIMU	Beta-lactoglobulin (Beta-LG)	0.06	-	nuc	0					162
P02755 UniProt NPD GO	LACB_BUBBU	Beta-lactoglobulin precursor (Beta-LG)	0.06	-	nuc	0	Secreted protein				180
Q28767 UniProt NPD GO	MSMB_PAPAN	Beta-microseminoprotein precursor (Prostate secreted seminal plasma protein) (Prostate secretory pro ...	0.06	-	exc	1 *	Secreted protein. Sperm surface (By similarity)				114
Q9Y5Z0 UniProt NPD GO	BACE2_HUMAN	Beta-secretase 2 precursor (EC 3.4.23.45) (Beta-site APP-cleaving enzyme 2) (Aspartyl protease 1) (A ...	0.06	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS] membrane fraction [TAS]	605668		518
P56533 UniProt NPD GO	BADH_GADCA	Betaine aldehyde dehydrogenase (EC 1.2.1.8) (BADH)	0.06	-	cyt	0				1BPW	503
Q7TQ49 UniProt NPD GO	GLCNE_CRIGR	Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (UDP-GlcNAc-2-epimerase/ ...	0.06	-	cyt	0	Cytoplasm (By similarity)				722
Q91WG8 UniProt NPD GO	GLCNE_MOUSE	Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (UDP-GlcNAc-2-epimerase/ ...	0.06	-	cyt	0	Cytoplasm (By similarity)				722
O35826 UniProt NPD GO	GLCNE_RAT	Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (UDP-GlcNAc-2-epimerase/ ...	0.06	-	cyt	0	Cytoplasm	cytosol [IDA]			722
P81241 UniProt NPD GO	CHLY_CARPA	Bifunctional chitinase/lysozyme [Includes: Chitinase (EC 3.2.1.14); Lysozyme (EC 3.2.1.17)] (Fragmen ...	0.06	-	nuc	0	Secreted protein; extracellular space				25
P18155 UniProt NPD GO	MTDC_MOUSE	Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial precursor [Includ ...	0.06	-	mit	0	Mitochondrion				350
Q14032 UniProt NPD GO	BAAT_HUMAN	Bile acid CoA:amino acid N-acyltransferase (EC 2.3.1.65) (BAT) (BACAT) (Glycine N-choloyltransferase ...	0.06	-	cyt	0	Cytoplasm	cytoplasm [TAS] cytosol [TAS]	607748		418
O19918 UniProt NPD GO	BCCP_CYACA	Biotin carboxyl carrier protein of acetyl-CoA carboxylase (BCCP)	0.06	-	nuc	0	Plastid; chloroplast				152
P84211 UniProt NPD GO	BOML2_BOMVA	Bombesin-like peptide 2	0.06	-		0	Secreted protein	extracellular region [IDA]			13
Q17192 UniProt NPD GO	BXA1_BOMMO	Bombyxin A-1 precursor (BBX-A1) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin A-1 B ...	0.06	-	mit	0	Secreted protein				92
P26730 UniProt NPD GO	BXA7_BOMMO	Bombyxin A-7 precursor (BBX-A7) (4K-prothoracicotropic hormone) (4K-PTTH) [Contains: Bombyxin A-7 B ...	0.06	-	vac	0	Secreted protein				92
P84825 UniProt NPD GO	BRK1_ASCTR	Bradykinin	0.06	-		0	Secreted protein	extracellular region [IDA]			9
P68515 UniProt NPD GO	BPP1_BOTIN	Bradykinin-potentiating peptide S3,1 (13A) (Angiotensin-converting enzyme inhibitor)	0.06	-		0					13
P30422 UniProt NPD GO	BPP2_BOTIN	Bradykinin-potentiating peptide S4,3,1 (10C) (Angiotensin-converting enzyme inhibitor)	0.06	-		0					10
P68516 UniProt NPD GO	BPP1_BOTJA	Bradykinin-potentiating peptide V-9 (Angiotensin-converting enzyme inhibitor V-9)	0.06	-		0					13
P63030 UniProt NPD GO	BR44L_MOUSE	Brain protein 44-like protein	0.06	-	nuc	0		mitochondrial inner membrane [IDA]			109
P63031 UniProt NPD GO	BR44L_RAT	Brain protein 44-like protein (Apoptosis-regulating basic protein)	0.06	-	nuc	0					109
Q922D8 UniProt NPD GO	C1TC_MOUSE	C-1-tetrahydrofolate synthase, cytoplasmic (C1-THF synthase) [Includes: Methylenetetrahydrofolate de ...	0.06	-	nuc	0	Cytoplasm (By similarity)				934
P27653 UniProt NPD GO	C1TC_RAT	C-1-tetrahydrofolate synthase, cytoplasmic (C1-THF synthase) [Includes: Methylenetetrahydrofolate de ...	0.06	-	cyt	0	Cytoplasm				934
Q9UUH4 UniProt NPD GO	ERG25_SCHPO	C-4 methylsterol oxidase (EC 1.14.13.72) (Methylsterol monooxygenase)	0.06	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Probable)				300
O54814 UniProt NPD GO	CCR3_RAT	C-C chemokine receptor type 3 (C-C CKR-3) (CC-CKR-3) (CCR-3) (CCR3) (CKR3) (CD193 antigen)	0.06	-	end	7 *	Membrane; multi-pass membrane protein	cytoplasm [IDA]			359
Q8MJW8 UniProt NPD GO	CCR4_CANFA	C-C chemokine receptor type 4 (C-C CKR-4) (CC-CKR-4) (CCR-4) (CCR4)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				360
Q2HJ17 UniProt NPD GO	CCR5_BOVIN	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				352
P49682 UniProt NPD GO	CXCR3_HUMAN	C-X-C chemokine receptor type 3 (CXC-R3) (CXCR-3) (Interferon-inducible protein 10 receptor) (IP-10 ...	0.06	-	end	7	Membrane; multi-pass membrane protein	cytoplasm [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	300574		368
Q9N0Z0 UniProt NPD GO	CXCR6_CERTO	C-X-C chemokine receptor type 6 (CXC-R6) (CXCR-6) (G-protein coupled receptor bonzo) (G-protein coup ...	0.06	-	end	7 *	Membrane; multi-pass membrane protein				343
Q69FH1 UniProt NPD GO	CLC4D_RAT	C-type lectin domain family 4 member D (C-type lectin superfamily member 8)	0.06	-	nuc	1 *	Membrane; single-pass type II membrane protein (Probable)				218
Q9Z2H6 UniProt NPD GO	CLC4D_MOUSE	C-type lectin domain family 4 member D (C-type lectin superfamily member 8) (Macrophage-restricted C ...	0.06	-	nuc	1 *	Membrane; single-pass type II membrane protein (Probable)				219
Q9P296 UniProt NPD GO	C5ARL_HUMAN	C5a anaphylatoxin chemotactic receptor C5L2 (G-protein coupled receptor 77)	0.06	-	end	7 *	Membrane; multi-pass membrane protein		609949		337
Q63064 UniProt NPD GO	CD52_RAT	CAMPATH-1 antigen precursor (Lymphocyte differentiation antigen B7) (CD52 antigen) (CDw52)	0.06	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				96
Q90460 UniProt NPD GO	CD166_BRARE	CD166 antigen homolog precursor (Activated leukocyte-cell adhesion molecule) (Neurolin) (DM-GRASP ho ...	0.06	-	end	2 *	Membrane; single-pass type I membrane protein				564
Q8VE98 UniProt NPD GO	CD276_MOUSE	CD276 antigen precursor (Costimulatory molecule) (B7 homolog 3) (B7-H3)	0.06	-	end	1	Membrane; single-pass type I membrane protein (Probable)	external side of plasma membrane [IDA]			316
Q7TPB4 UniProt NPD GO	CD276_RAT	CD276 antigen precursor (Costimulatory molecule) (B7 homolog 3) (B7-H3)	0.06	-	end	1	Membrane; single-pass type I membrane protein (Probable)				316
Q5ZPR3 UniProt NPD GO	CD276_HUMAN	CD276 antigen precursor (Costimulatory molecule) (B7 homolog 3) (B7-H3) (4Ig-B7-H3)	0.06	-	end	1	Membrane; single-pass type I membrane protein (Probable)		605715		534
P46657 UniProt NPD GO	CD59_CALSQ	CD59 glycoprotein precursor (Membrane attack complex inhibition factor) (MACIF) (MAC-inhibitory prot ...	0.06	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				128
Q9NL55 UniProt NPD GO	CHHL_BOMMO	CHH-like protein precursor (BmCHHL)	0.06	-	mit	0	Secreted protein				110
Q60E70 UniProt NPD GO	COBL3_ORYSA	COBRA-like 3 protein precursor (BRITTLE CULM1-like 4 protein)	0.06	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				457
Q7Z4G1 UniProt NPD GO	COMD6_HUMAN	COMM domain-containing protein 6	0.06	-	cyt	0					85
P38123 UniProt NPD GO	SWD3_YEAST	COMPASS component SWD3 (Complex proteins associated with SET1 protein SWD3) (Set1C component SWD3)	0.06	-	cyt	0	Nucleus (Probable)	COMPASS complex [IPI]			315
Q7RXX8 UniProt NPD GO	CSN5_NEUCR	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	0.06	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				336
P68395 UniProt NPD GO	CSN7_BRAOL	COP9 signalosome complex subunit 7 (CSN complex subunit 7) (FUSCA protein 5) (FUSCA5) (Fragments)	0.06	-	cyt	0	Cytoplasm. Nucleus				71
Q7RZV2 UniProt NPD GO	PYRG_NEUCR	CTP synthase (EC 6.3.4.2) (UTP--ammonia ligase) (CTP synthetase)	0.06	-	cyt	0					568
P55287 UniProt NPD GO	CAD11_HUMAN	Cadherin-11 precursor (Osteoblast-cadherin) (OB-cadherin) (OSF-4)	0.06	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]	600023		796
Q41720 UniProt NPD GO	CAMT_ZINEL	Caffeoyl-CoA O-methyltransferase (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltransferase) (CCoAMT) ...	0.06	-	cyt	0					245

You are viewing entries 71651 to 71700 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.