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
P00342 UniProt NPD GO	LDHC_MOUSE	L-lactate dehydrogenase C chain (EC 1.1.1.27) (LDH-C) (LDH testis subunit) (LDH-X)	0.01	-	cyt	0	Cytoplasm			2LDX	331
P19629 UniProt NPD GO	LDHC_RAT	L-lactate dehydrogenase C chain (EC 1.1.1.27) (LDH-C) (LDH testis subunit) (LDH-X)	0.01	-	cyt	0	Cytoplasm				331
Q29563 UniProt NPD GO	LDHC_VULVU	L-lactate dehydrogenase C chain (EC 1.1.1.27) (LDH-C) (LDH testis subunit) (LDH-X)	0.01	-	mit	0	Cytoplasm (By similarity)				331
Q8VBT2 UniProt NPD GO	SDHL_MOUSE	L-serine dehydratase (EC 4.3.1.17) (L-serine deaminase)	0.01	-	mit	0	Cytoplasm (By similarity)				326
P17324 UniProt NPD GO	SDHL_YEAST	L-serine dehydratase (EC 4.3.1.17) (L-serine deaminase)	0.01	-	cyt	0	Cytoplasm				338
P09367 UniProt NPD GO	SDHL_RAT	L-serine dehydratase/L-threonine deaminase [Includes: L-serine dehydratase (EC 4.3.1.17) (L-serine d ...	0.01	-	mit	0	Cytoplasm			1RSQ	362
Q91X52 UniProt NPD GO	DCXR_MOUSE	L-xylulose reductase (EC 1.1.1.10) (XR) (Dicarbonyl/L-xylulose reductase)	0.01	-	cyt	0	Membrane; peripheral membrane protein (By similarity). Probably recruited to membranes via an intera ...	brush border [IDA] microvillus [IDA]			244
Q920P0 UniProt NPD GO	DCXR_RAT	L-xylulose reductase (EC 1.1.1.10) (XR) (Dicarbonyl/L-xylulose reductase)	0.01	-	cyt	0	Membrane; peripheral membrane protein (By similarity). Probably recruited to membranes via an intera ...				244
Q7Z4W1 UniProt NPD GO	DCXR_HUMAN	L-xylulose reductase (EC 1.1.1.10) (XR) (Dicarbonyl/L-xylulose reductase) (Kidney dicarbonyl reducta ...	0.01	-	cyt	0	Membrane; peripheral membrane protein (By similarity). Probably recruited to membranes via an intera ...		608347	1WNT	244
Q920N9 UniProt NPD GO	DCXR_CAVPO	L-xylulose reductase (EC 1.1.1.10) (XR) (Dicarbonyl/L-xylulose reductase) (Protein P26h)	0.01	-	cyt	0	Membrane; peripheral membrane protein (By similarity). Probably recruited to membranes via an intera ...				244
Q91XV4 UniProt NPD GO	DCXR_MESAU	L-xylulose reductase (EC 1.1.1.10) (XR) (Dicarbonyl/L-xylulose reductase) (Sperm antigen P26h)	0.01	-	cyt	0	Membrane; peripheral membrane protein. Probably recruited to membranes via an interaction with phosp ...				244
P80171 UniProt NPD GO	LASP1_PIG	LIM and SH3 domain protein 1 (LASP-1) (Cysteine-rich peptide ZF-1) (Fragment)	0.01	-	nuc	0	Cytoplasm (By similarity). Associated with the F-actin rich cortical cytoskeleton (By similarity)	cortical actin cytoskeleton [ISS]		1ZFO	30
Q12570 UniProt NPD GO	LAC1_BOTCI	Laccase (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Diphenol oxidase) (Fra ...	0.01	-	nuc	0	Secreted protein (Potential)				486
Q99056 UniProt NPD GO	COPA1_TRAVI	Laccase 5 precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase)	0.01	-	vac	0	Secreted protein				527
Q12717 UniProt NPD GO	LAC5_TRAVE	Laccase 5 precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Diphenol o ...	0.01	-	vac	0	Secreted protein				527
Q01679 UniProt NPD GO	LAC1_PHLRA	Laccase precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Ligninolytic ...	0.01	-	exc	0	Secreted protein				520
P59082 UniProt NPD GO	LFS_ALLCE	Lachrymatory-factor synthase precursor	0.01	-	cyt	0	Vacuole (Probable)				169
Q8H0V3 UniProt NPD GO	LGUL_ARATH	Lactoylglutathione lyase (EC 4.4.1.5) (Methylglyoxalase) (Aldoketomutase) (Glyoxalase I) (Glx I) (Ke ...	0.01	-	cyt	0					185
O04885 UniProt NPD GO	LGUL_BRAJU	Lactoylglutathione lyase (EC 4.4.1.5) (Methylglyoxalase) (Aldoketomutase) (Glyoxalase I) (Glx I) (Ke ...	0.01	-	cyt	0					185
O95278 UniProt NPD GO	EPM2A_HUMAN	Laforin (EC 3.1.3.48) (EC 3.1.3.16) (Lafora PTPase) (LAFPTPase)	0.01	-	mit	0	Cytoplasm. Isoform 1, isoform 2: Endoplasmic reticulum. Cell membrane.Isoform 1 is primarily associa ...	polysome [TAS]	607566		331
Q91XQ2 UniProt NPD GO	EPM2A_RAT	Laforin (EC 3.1.3.48) (EC 3.1.3.16) (Lafora PTPase) (LAFPTPase) (Fragment)	0.01	-	nuc	0	Cytoplasm (By similarity). Endoplasmic reticulum (By similarity). Localizes at the endoplasmic retic ...				327
P58808 UniProt NPD GO	CXL2_CONMR	Lambda-conotoxin CMrVIB precursor (Chi-conotoxin MrIA) (Chi-MrIA) (mr10a)	0.01	-	exc	1 *	Secreted protein				61
P33575 UniProt NPD GO	LAMP_PETMA	Lamprin 0.9 precursor (Cartilage matrix protein)	0.01	-	mit	4 *	Secreted protein; extracellular space; extracellular matrix				139
P33577 UniProt NPD GO	LAMR_PETMA	Lamprin 1.8-10 precursor (Cartilage matrix protein)	0.01	-	mit	3 *	Secreted protein; extracellular space; extracellular matrix				119
Q01774 UniProt NPD GO	LCP34_DROMI	Larval cuticle protein III/IV precursor	0.01	-	exc	0					112
P13229 UniProt NPD GO	CU14_MANSE	Larval cuticle protein LCP-14 precursor	0.01	-	exc	0					125
O02388 UniProt NPD GO	CU22_BOMMO	Larval cuticle protein LCP-22 precursor	0.01	-	end	0					174
P14485 UniProt NPD GO	CUP1_SARBU	Larval cuticle protein SC1 (Fragment)	0.01	-	cyt	0					43
P09355 UniProt NPD GO	LSP_APIME	Larval-specific very high density lipoprotein (VHDL) (Fragment)	0.01	-	cyt	0	Secreted protein; extracellular space				27
P35360 UniProt NPD GO	OPSL_LIMPO	Lateral eye opsin	0.01	-	end	7 *	Membrane; multi-pass membrane protein				376
O88822 UniProt NPD GO	SC5D_MOUSE	Lathosterol oxidase (EC 1.14.21.6) (Lathosterol 5-desaturase) (Delta-7-sterol 5-desaturase) (C-5 ste ...	0.01	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)				299
P84522 UniProt NPD GO	VHL1_VIOHE	Leaf cyclotide 1 (Vhl-1)	0.01	-	nuc	0					31
Q7M3Y0 UniProt NPD GO	SJL1_STIJA	Lectin 1 (Stichopus japonicus lectin 1) (SJL-1)	0.01	-	cyt	0					143
P84821 UniProt NPD GO	LEC_LITSE	Lectin 80 kDa subunit (LsL) (Fragment)	0.01	-		0	Secreted protein; extracellular space	extracellular region [IDA]			15
P04122 UniProt NPD GO	LECB_LATOC	Lectin beta-1 and beta-2 chains	0.01	-	cyt	0				1LOG	181
Q93X49 UniProt NPD GO	LEC_LENCO	Lectin precursor [Contains: Lectin beta chain; Lectin alpha chain]	0.01	-	mit	1 *					275
Q8VXF2 UniProt NPD GO	LEC_LENCT	Lectin precursor [Contains: Lectin beta chain; Lectin alpha chain]	0.01	-	mit	1 *					275
P02867 UniProt NPD GO	LEC_PEA	Lectin precursor [Contains: Lectin beta chain; Lectin alpha chain]	0.01	-	mit	1 *				2LTN	275
P93849 UniProt NPD GO	LGB3_VICFA	Leghemoglobin 49 (VfLb49)	0.01	-	cyt	0					145
Q27673 UniProt NPD GO	GP63_LEIAM	Leishmanolysin precursor (EC 3.4.24.36) (Cell surface protease) (Major surface glycoprotein) (Protei ...	0.01	-	mit	1 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	membrane [NAS]			597
Q6RZ07 UniProt NPD GO	MIP_CAVPO	Lens fiber major intrinsic protein (Aquaporin-0)	0.01	-	end	6 *	Membrane; multi-pass membrane protein				263
P56563 UniProt NPD GO	LMIP_MOUSE	Lens fiber membrane intrinsic protein (MP17) (MP18) (MP19) (MP20)	0.01	-	end	4 *	Membrane; multi-pass membrane protein	tight junction [TAS]			173
P54825 UniProt NPD GO	LMIP_RAT	Lens fiber membrane intrinsic protein (MP17) (MP18) (MP19) (MP20)	0.01	-	end	4 *	Membrane; multi-pass membrane protein				173
O89013 UniProt NPD GO	OBRG_MOUSE	Leptin receptor gene-related protein (OB-R gene-related protein) (OB-RGRP)	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				131
Q9JLS8 UniProt NPD GO	OBRG_RAT	Leptin receptor gene-related protein (OB-R gene-related protein) (OB-RGRP)	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				131
O15243 UniProt NPD GO	OBRG_HUMAN	Leptin receptor gene-related protein (OB-R gene-related protein) (OB-RGRP) (Leptin receptor overlapp ...	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [NAS]			131
P58785 UniProt NPD GO	COW2_CONPU	Leu-contryphan-P	0.01	-		0	Secreted protein				8
P15231 UniProt NPD GO	PHAM_PHAVU	Leucoagglutinating phytohemagglutinin precursor (PHA-L)	0.01	-	exc	0					273
P51091 UniProt NPD GO	LDOX_MALDO	Leucoanthocyanidin dioxygenase (EC 1.14.11.19) (LDOX) (Leucocyanidin oxygenase) (Leucoanthocyanidin ...	0.01	-	cyt	0					357
Q96323 UniProt NPD GO	LDOX_ARATH	Leucoanthocyanidin dioxygenase (EC 1.14.11.19) (LDOX) (Leucocyanidin oxygenase) (Leucoanthocyanidin ...	0.01	-	cyt	0				1GP6	356

You are viewing entries 89351 to 89400 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.