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
P21143 UniProt NPD GO	LCK4_LEUMA	Leucokinin-4 (Leucokinin IV) (L-IV)	0.01	-		0	Secreted protein				8
P19987 UniProt NPD GO	LCK5_LEUMA	Leucokinin-5 (Leucokinin V) (L-V)	0.01	-		0	Secreted protein				8
P19988 UniProt NPD GO	LCK6_LEUMA	Leucokinin-6 (Leucokinin VI) (L-VI)	0.01	-		0	Secreted protein				8
P21144 UniProt NPD GO	LCMS_LEUMA	Leucomyosuppressin (LMS) (LeM-MS)	0.01	-		0	Secreted protein				10
Q9N0K1 UniProt NPD GO	CD47_BOVIN	Leukocyte surface antigen CD47 precursor (Integrin-associated protein) (IAP)	0.01	-	end	5	Cell membrane; multi-pass membrane protein (By similarity)				303
Q61735 UniProt NPD GO	CD47_MOUSE	Leukocyte surface antigen CD47 precursor (Integrin-associated protein) (IAP)	0.01	-	end	5	Cell membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			303
P97829 UniProt NPD GO	CD47_RAT	Leukocyte surface antigen CD47 precursor (Integrin-associated protein) (IAP)	0.01	-	end	5	Cell membrane; multi-pass membrane protein (By similarity)				303
Q58DM3 UniProt NPD GO	CD53_BOVIN	Leukocyte surface antigen CD53 (Cell surface glycoprotein CD53)	0.01	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				219
P19397 UniProt NPD GO	CD53_HUMAN	Leukocyte surface antigen CD53 (Cell surface glycoprotein CD53) (Tetraspanin-25) (Tspan-25)	0.01	-	end	4 *	Membrane; multi-pass membrane protein	plasma membrane [TAS]	151525		219
P52922 UniProt NPD GO	LKHA4_DICDI	Leukotriene A-4 hydrolase (EC 3.3.2.6) (LTA-4 hydrolase) (Leukotriene A(4) hydrolase) (Fragment)	0.01	-	cyt	0	Cytoplasm (By similarity)				316
P12257 UniProt NPD GO	GUB2_HORVU	Lichenase-2 precursor (EC 3.2.1.73) (Lichenase II) (Endo-beta-1,3-1,4 glucanase II) ((1->3,1->4)-bet ...	0.01	-	cyt	0				1GHR	312
P48110 UniProt NPD GO	CHLL_CYAPA	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.01	-	cyt	0	Plastid; cyanelle				282
Q5SCY9 UniProt NPD GO	CHLL_HUPLU	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) (LI-PO ...	0.01	-	cyt	0	Plastid; chloroplast				292
P37845 UniProt NPD GO	CHLB_EQUAR	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.01	-	cyt	0	Plastid; chloroplast				103
P02744 UniProt NPD GO	LIMU_LIMPO	Limulin (Fragment)	0.01	-	cyt	0					84
Q99156 UniProt NPD GO	LIP1_YARLI	Lipase 1 precursor (EC 3.1.1.3)	0.01	-	cyt	0					486
O46108 UniProt NPD GO	LIP3_DROME	Lipase 3 precursor (EC 3.1.1.-) (DmLip3)	0.01	-	exc	0					394
P60588 UniProt NPD GO	LPP1_PIG	Lipid phosphate phosphohydrolase 1 (EC 3.1.3.4) (Phosphatidic acid phosphatase 2a) (Phosphatidate ph ...	0.01	-		0	Cell membrane; multi-pass membrane protein				15
O43688 UniProt NPD GO	LPP2_HUMAN	Lipid phosphate phosphohydrolase 2 (EC 3.1.3.4) (Phosphatidic acid phosphatase 2c) (Phosphatidate ph ...	0.01	-	end	6 *	Membrane; multi-pass membrane protein	membrane [TAS]	607126		288
P31025 UniProt NPD GO	LCN1_HUMAN	Lipocalin-1 precursor (Von Ebner gland protein) (VEG protein) (Tear prealbumin) (TP) (Tear lipocalin ...	0.01	-	exc	0	Secreted protein		151675	1XKI	176
P84810 UniProt NPD GO	LVP1A_BUTOC	Lipolysis-activating peptide 1-alpha chain precursor (LVP1-alpha)	0.01	-	vac	1 *	Secreted protein	extracellular region [IDA]			91
P08945 UniProt NPD GO	LITO_LITAU	Litorin	0.01	-		0	Secreted protein				9
Q8VCC2 UniProt NPD GO	EST1_MOUSE	Liver carboxylesterase 1 precursor (EC 3.1.1.1) (Acyl coenzyme A:cholesterol acyltransferase) (ES-x) ...	0.01	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity). Microsomal membrane, lumen of en ...				565
Q29550 UniProt NPD GO	EST1_PIG	Liver carboxylesterase precursor (EC 3.1.1.1) (Proline-beta-naphthylamidase)	0.01	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				566
P41491 UniProt NPD GO	LOK1_LOCMI	Locustakinin-1 (Locustakinin I)	0.01	-		0	Secreted protein				6
P22395 UniProt NPD GO	LMT1_LOCMI	Locustamyotropin-1 (Lom-MT-1)	0.01	-		0	Secreted protein				12
P16224 UniProt NPD GO	TKL2_LOCMI	Locustatachykinin-2 (Locustatachykinin II) (TK-II)	0.01	-		0	Secreted protein				10
P38496 UniProt NPD GO	LMA1_LOCMI	Lom-AG-myotropin-1 (Lom-AG-myotropin I) (Accessory gland myotropin I)	0.01	-		0					13
P38497 UniProt NPD GO	LMA2_LOCMI	Lom-AG-myotropin-2 (Lom-AG-myotropin II) (Accessory gland myotropin II)	0.01	-		0					15
P11918 UniProt NPD GO	KLOM_LUMTE	Lombricine kinase (EC 2.7.3.5) (LK) (Fragment)	0.01	-		0					15
P25667 UniProt NPD GO	NXL3_DENPO	Long neurotoxin 3 (Toxin VN2)	0.01	-	nuc	0	Secreted protein				72
P59827 UniProt NPD GO	LPLC4_HUMAN	Long palate, lung and nasal epithelium carcinoma-associated protein 4 (Ligand-binding protein RY2G5) ...	0.01	-	cyt	0	Secreted protein (By similarity)				575
Q05704 UniProt NPD GO	LPLC4_RAT	Long palate, lung and nasal epithelium carcinoma-associated protein 4 (Ligand-binding protein RY2G5) ...	0.01	-	mit	0	Secreted protein (By similarity)				470
P09336 UniProt NPD GO	LP3_BOMMO	Low molecular 30 kDa lipoprotein PBMHPC-19 precursor	0.01	-	exc	0	Secreted protein; extracellular space				254
Q00802 UniProt NPD GO	L301_BOMMO	Low molecular mass 30 kDa lipoprotein 19G1 precursor	0.01	-	exc	0					256
Q00801 UniProt NPD GO	L302_BOMMO	Low molecular mass 30 kDa lipoprotein 21G1 precursor	0.01	-	exc	0					263
P18631 UniProt NPD GO	RAG1_KLULA	Low-affinity glucose transporter (Hexose transporter 1)	0.01	-	end	10	Membrane; multi-pass membrane protein				567
P32465 UniProt NPD GO	HXT1_YEAST	Low-affinity glucose transporter HXT1	0.01	-	end	11	Membrane; multi-pass membrane protein	plasma membrane [IDA]			570
P80089 UniProt NPD GO	BIP_PHAVU	Luminal-binding protein (78 kDa glucose-regulated protein homolog) (GRP 78) (Fragment)	0.01	-		0	Endoplasmic reticulum; endoplasmic reticulum lumen				20
Q03683 UniProt NPD GO	BIP3_TOBAC	Luminal-binding protein 3 (BiP 3) (78 kDa glucose-regulated protein homolog 3) (GRP 78-3) (Fragment) ...	0.01	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum lumen				168
Q29529 UniProt NPD GO	CBR2_PIG	Lung carbonyl reductase [NADPH] (EC 1.1.1.184) (NADPH-dependent carbonyl reductase) (LCR)	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				244
P08074 UniProt NPD GO	CBR2_MOUSE	Lung carbonyl reductase [NADPH] (EC 1.1.1.184) (NADPH-dependent carbonyl reductase) (LCR) (Adipocyte ...	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix			1CYD	244
P61507 UniProt NPD GO	LYT1_HOGCA	Lycotoxin-1 (Lycotoxin I)	0.01	-	pox	0	Secreted protein				25
P80178 UniProt NPD GO	DFAM1_LYMST	Lymna-DF-amide 1	0.01	-		0	Secreted protein				13
P80179 UniProt NPD GO	DFAM2_LYMST	Lymna-DF-amide 2	0.01	-		0	Secreted protein				13
P80180 UniProt NPD GO	DFAM3_LYMST	Lymna-DF-amide 3	0.01	-		0	Secreted protein				13
P80181 UniProt NPD GO	DFAM4_LYMST	Lymna-DF-amide 4	0.01	-		0	Secreted protein				13
P80182 UniProt NPD GO	DFAM5_LYMST	Lymna-DF-amide 5	0.01	-		0	Secreted protein				13
P05486 UniProt NPD GO	CONO_CONGE	Lys-conopressin G	0.01	-		0	Secreted protein				9
O35114 UniProt NPD GO	SCRB2_MOUSE	Lysosome membrane protein 2 (Lysosome membrane protein II) (LIMP II) (Scavenger receptor class B mem ...	0.01	-	end	2 *	Lysosome; lysosomal membrane; multi-pass membrane protein				477

You are viewing entries 89401 to 89450 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.