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
P05189 UniProt NPD GO	IPNS_CEPAC	Isopenicillin N synthetase (EC 1.21.3.1) (IPNS) (Isopenicillin N synthase)	0.04	-	cyt	0					338
P05326 UniProt NPD GO	IPNS_EMENI	Isopenicillin N synthetase (EC 1.21.3.1) (IPNS) (Isopenicillin N synthase)	0.04	-	cyt	0				2BU9	331
O00105 UniProt NPD GO	IPUA_ASPNG	Isopullulanase precursor (EC 3.2.1.57)	0.04	-	exc	0	Secreted protein			1WMR	564
Q9FS88 UniProt NPD GO	IVD1_SOLTU	Isovaleryl-CoA dehydrogenase 1, mitochondrial precursor (EC 1.3.99.10) (IVD 1)	0.04	-	mit	0	Mitochondrion (By similarity)				412
P26440 UniProt NPD GO	IVD_HUMAN	Isovaleryl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.10) (IVD)	0.04	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [NAS]	243500	1IVH	423
Q9XT56 UniProt NPD GO	JAM1_BOVIN	Junctional adhesion molecule A precursor (JAM-A) (Junctional adhesion molecule 1) (JAM-1) (CD321 ant ...	0.04	-	end	1 *	Cell membrane; cell-cell junction; tight junction; single-pass type I membrane protein (By similarit ...				298
P19985 UniProt NPD GO	ESTJ_MANSE	Juvenile hormone esterase (EC 3.1.1.59) (JH esterase) (Fragment)	0.04	-		0					15
Q28773 UniProt NPD GO	KLK1_PAPHA	Kallikrein-1 precursor (EC 3.4.21.35) (Tissue kallikrein) (Kidney/pancreas/salivary gland kallikrein ...	0.04	-	exc	0					258
P58921 UniProt NPD GO	CXK4A_CONST	Kappa-A-conotoxin SIVA precursor (Spastic peptide)	0.04	-	exc	0	Secreted protein				69
P41145 UniProt NPD GO	OPRK_HUMAN	Kappa-type opioid receptor (KOR-1)	0.04	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	165196		380
P33534 UniProt NPD GO	OPRK_MOUSE	Kappa-type opioid receptor (KOR-1) (MSL-1)	0.04	-	end	7	Membrane; multi-pass membrane protein				380
Q5E9A7 UniProt NPD GO	KLDC2_BOVIN	Kelch domain-containing protein 2	0.04	-	cyt	0					406
Q6JEL2 UniProt NPD GO	KLH10_HUMAN	Kelch-like protein 10	0.04	-	cyt	0	Cytoplasm (By similarity)		608778		608
Q8NBE8 UniProt NPD GO	KLH23_HUMAN	Kelch-like protein 23	0.04	-	cyt	0					558
Q6GQU2 UniProt NPD GO	KLH23_MOUSE	Kelch-like protein 23	0.04	-	cyt	0					558
Q5RCQ9 UniProt NPD GO	KLH23_PONPY	Kelch-like protein 23	0.04	-	cyt	0					558
Q3LI66 UniProt NPD GO	KRA62_HUMAN	Keratin-associated protein 6-2	0.04	-	cyt	0					62
P97328 UniProt NPD GO	KHK_MOUSE	Ketohexokinase (EC 2.7.1.3) (Hepatic fructokinase)	0.04	-	cyt	0					298
P82685 UniProt NPD GO	KINI1_PERAM	Kinin-1 (Pea-K-1)	0.04	-		0	Secreted protein				8
O13069 UniProt NPD GO	VSP2_BOTJA	Kinin-releasing and fibrinogen-clotting serine proteinase 2 precursor (EC 3.4.21.-) (KN-BJ 2)	0.04	-	exc	0	Secreted protein				257
P10752 UniProt NPD GO	KRX6B_MOUSE	Krox-6.1B+ protein (Fragment)	0.04	-	nuc	0	Nucleus (Potential)				55
Q9TWF8 UniProt NPD GO	KC3_ANESU	Kunitz-type kalicludin-3 (AsKC3) (Kalicludine-3)	0.04	-	nuc	0	Secreted protein. Found in nematocyst				59
P83603 UniProt NPD GO	BMTI2_BOOMI	Kunitz-type serine protease inhibitor BmTI-2 (Fragment)	0.04	-	cyt	0	Secreted protein				25
Q9CR70 UniProt NPD GO	LAGE3_MOUSE	L antigen family member 3 (ITBA2 protein homolog)	0.04	-	nuc	0					148
P27544 UniProt NPD GO	LASS1_HUMAN	LAG1 longevity assurance homolog 1 (UOG-1 protein) (Protein LAG1)	0.04	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...		606919		350
O59896 UniProt NPD GO	LAC1_PYCCI	Laccase precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Ligninolytic ...	0.04	-	exc	1 *	Secreted protein				518
P78722 UniProt NPD GO	LAC2_PODAN	Laccase-2 precursor (EC 1.10.3.2) (Laccase II) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase ...	0.04	-	exc	1 *	Secreted protein				621
Q08431 UniProt NPD GO	MFGM_HUMAN	Lactadherin precursor (Milk fat globule-EGF factor 8) (MFG-E8) (HMFG) (Breast epithelial antigen BA4 ...	0.04	-	mit	0	Membrane; peripheral membrane protein		602281		387
Q9WUA5 UniProt NPD GO	EPM2A_MOUSE	Laforin (EC 3.1.3.48) (EC 3.1.3.16) (Lafora PTPase) (LAFPTPase)	0.04	-	cyt	0	Cytoplasm. Endoplasmic reticulum. Localizes at the endoplasmic reticulum				330
Q8SQ26 UniProt NPD GO	CRYL1_PIG	Lambda-crystallin homolog	0.04	-	mit	0					321
Q9QXW9 UniProt NPD GO	LAT2_MOUSE	Large neutral amino acids transporter small subunit 2 (L-type amino acid transporter 2)	0.04	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				531
Q9WVR6 UniProt NPD GO	LAT2_RAT	Large neutral amino acids transporter small subunit 2 (L-type amino acid transporter 2)	0.04	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				533
Q8SQ30 UniProt NPD GO	LLPB_MACEU	Late lactation protein B precursor (LLP-B)	0.04	-	exc	0	Secreted protein				174
P16349 UniProt NPD GO	LEC_LATSP	Lectin	0.04	-	cyt	0					244
P83511 UniProt NPD GO	LEC_DELRE	Lectin (DRL) (Fragment)	0.04	-		0					16
P07439 UniProt NPD GO	LEC3_MEGRO	Lectin BRA-3 precursor	0.04	-	vac	0					162
P38662 UniProt NPD GO	LECA_DOLLA	Lectin [Contains: Lectin alpha chain; Lectin beta chain]	0.04	-	nuc	0					237
P58906 UniProt NPD GO	LECA_CANBN	Lectin alpha chain [Contains: Lectin beta chain; Lectin gamma chain] (Fragments)	0.04	-	nuc	0					47
Q39527 UniProt NPD GO	LECR_CLALU	Lectin-related protein precursor (CLLRP) (LRPCL) (Fragment)	0.04	-	mit	0					290
P15706 UniProt NPD GO	GP63_LEICH	Leishmanolysin precursor (EC 3.4.24.36) (Cell surface protease) (Major surface glycoprotein) (Protei ...	0.04	-	mit	1 *	Cell membrane; lipid-anchor; GPI-anchor				599
Q8MNZ1 UniProt NPD GO	GP63_LEITR	Leishmanolysin precursor (EC 3.4.24.36) (Cell surface protease) (Major surface glycoprotein) (Protei ...	0.04	-	cyt	2 *					657
P35479 UniProt NPD GO	CPI1_PIG	Leukocyte cysteine proteinase inhibitor 1 (PLCPI) (Stefin D1)	0.04	-	cyt	0	Cytoplasm				103
P13049 UniProt NPD GO	LPK_LEUMA	Leukopyrokinin (LPK) (Lem-PK)	0.04	-		0	Secreted protein				8
P49012 UniProt NPD GO	LIG2_PHACH	Ligninase LG2 precursor (EC 1.11.1.14) (Diarylpropane peroxidase) (Lignin peroxidase)	0.04	-	end	0				1LLP	371
P22394 UniProt NPD GO	LIP2_GEOCN	Lipase 2 precursor (EC 3.1.1.3) (Lipase II) (GCL II)	0.04	-	exc	0	Secreted protein			1THG	563
P32947 UniProt NPD GO	LIP3_CANRU	Lipase 3 precursor (EC 3.1.1.3) (Cholesterol esterase)	0.04	-	exc	0				1LLF	549
O14494 UniProt NPD GO	LPP1_HUMAN	Lipid phosphate phosphohydrolase 1 (EC 3.1.3.4) (Phosphatidic acid phosphatase 2a) (Phosphatidate ph ...	0.04	-	end	6 *	Cell membrane; multi-pass membrane protein	integral to plasma membrane [NAS] membrane fraction [IDA] plasma membrane [TAS]	607124		284
P53395 UniProt NPD GO	ODB2_MOUSE	Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitocho ...	0.04	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			482
Q86UP9 UniProt NPD GO	LHPL3_HUMAN	Lipoma HMGIC fusion partner-like 3 protein	0.04	-	end	4 *	Membrane; multi-pass membrane protein (Potential)		609719		222
Q9CTN8 UniProt NPD GO	LHPL3_MOUSE	Lipoma HMGIC fusion partner-like 3 protein	0.04	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				222

You are viewing entries 77401 to 77450 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.