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
Q64181 UniProt NPD GO	PROP_CAVPO	Properdin precursor (Factor P)	0.41	-	exc	0	Secreted protein				470
Q78EH2 UniProt NPD GO	PCSK4_RAT	Proprotein convertase subtilisin/kexin type 4 precursor (EC 3.4.21.-) (PC4) (Neuroendocrine converta ...	0.41	+	exc	1 *					678
Q9XT82 UniProt NPD GO	PE2R2_CANFA	Prostaglandin E2 receptor, EP2 subtype (Prostanoid EP2 receptor) (PGE receptor, EP2 subtype)	0.41	-	end	7 *	Membrane; multi-pass membrane protein				361
O62725 UniProt NPD GO	PGH2_MUSVI	Prostaglandin G/H synthase 2 precursor (EC 1.14.99.1) (Cyclooxygenase-2) (COX-2) (Prostaglandin-endo ...	0.41	-	mit	0	Microsome; microsomal membrane; peripheral membrane protein				604
Q05769 UniProt NPD GO	PGH2_MOUSE	Prostaglandin G/H synthase 2 precursor (EC 1.14.99.1) (Cyclooxygenase-2) (COX-2) (Prostaglandin-endo ...	0.41	-	exc	0	Microsome; microsomal membrane; peripheral membrane protein	cytoplasm [IDA]		6COX	604
P22135 UniProt NPD GO	ATP12_YEAST	Protein ATP12, mitochondrial precursor	0.41	-	mit	0	Mitochondrion. Mitochondrial, either as a constituent of the matrix, or in tenous association with t ...	mitochondrial matrix [TAS]			325
Q9WTZ9 UniProt NPD GO	BEX3_MOUSE	Protein BEX3 (Brain-expressed X-linked protein 3 homolog) (p75NTR-associated cell death executor) (N ...	0.41	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the cytoplasm and the nucleus. Associates with replicating mito ...	cytosol [IDA]			124
Q5T742 UniProt NPD GO	CJ025_HUMAN	Protein C10orf25 precursor	0.41	-	exc	0					122
Q8N8W7 UniProt NPD GO	CU123_HUMAN	Protein C21orf123	0.41	-	nuc	0					138
Q9HBI5 UniProt NPD GO	CC014_HUMAN	Protein C3orf14	0.41	-	nuc	0					128
Q9BGQ5 UniProt NPD GO	CI025_MACFA	Protein C9orf25 homolog	0.41	-	nuc	0					165
Q7TPM5 UniProt NPD GO	CI009_MOUSE	Protein C9orf9 homolog	0.41	-	nuc	0					168
P48353 UniProt NPD GO	HLJ1_YEAST	Protein HLJ1	0.41	-	nuc	1		endoplasmic reticulum [IDA] endoplasmic reticulum membrane [IDA]			224
Q91V83 UniProt NPD GO	K0406_MOUSE	Protein KIAA0406 homolog	0.41	-	cyt	0					1085
P38236 UniProt NPD GO	MUM2_YEAST	Protein MUM2 (Muddled meiosis protein 2)	0.41	-	nuc	0		cytoplasm [IDA]			366
P48745 UniProt NPD GO	NOV_HUMAN	Protein NOV homolog precursor (NovH) (Nephroblastoma overexpressed gene protein homolog)	0.41	-	exc	0	Secreted protein		164958		357
Q9VXK0 UniProt NPD GO	NIPSN_DROME	Protein NipSnap	0.41	-	mit	0					273
Q91X88 UniProt NPD GO	PMGT1_MOUSE	Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (EC 2.4.1.-) (POMGnT1)	0.41	-	end	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				660
Q5RCB9 UniProt NPD GO	PMGT1_PONPY	Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (EC 2.4.1.-) (POMGnT1)	0.41	-	end	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				660
P06105 UniProt NPD GO	SC160_YEAST	Protein SCP160 (Protein HX)	0.41	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...	endoplasmic reticulum membrane [IDA] polysome [IDA]			1222
P38987 UniProt NPD GO	TEM1_YEAST	Protein TEM1	0.41	-	nuc	0		spindle pole body [TAS]			245
Q7XAB8 UniProt NPD GO	THF1_SOLTU	Protein THYLAKOID FORMATION1, chloroplast precursor	0.41	-	nuc	0	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein. Plastid; chloroplast ...				293
Q9STE8 UniProt NPD GO	TC753_ARATH	Protein TOC75-3, chloroplast precursor (75 kDa translocon at the outer-envelope-membrane of chloropl ...	0.41	-	mit	0	Plastid; chloroplast; chloroplast outer membrane; multi-pass membrane protein				818
P28092 UniProt NPD GO	WNT7_EVATR	Protein Wnt-7 (Fragment)	0.41	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
Q93098 UniProt NPD GO	WNT8B_HUMAN	Protein Wnt-8b precursor	0.41	-	exc	0	Secreted protein; extracellular space; extracellular matrix		601396		351
P54813 UniProt NPD GO	YME1_CAEEL	Protein YME1 homolog (EC 3.4.24.-)	0.41	-	cyt	0					676
Q5E9L5 UniProt NPD GO	ANM6_BOVIN	Protein arginine N-methyltransferase 6 (EC 2.1.1.-) (Heterogeneous nuclear ribonucleoprotein methylt ...	0.41	-	nuc	0	Nucleus (By similarity)				375
Q24039 UniProt NPD GO	BRO_DROME	Protein brother	0.41	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			213
P51406 UniProt NPD GO	BYS_DROME	Protein bys	0.41	+	cyt	0					436
O74178 UniProt NPD GO	KES1_SCHPO	Protein kes1	0.41	-	nuc	0					388
P23298 UniProt NPD GO	KPCL_MOUSE	Protein kinase C eta type (EC 2.7.11.13) (nPKC-eta) (PKC-L)	0.41	-	cyt	0					683
Q64617 UniProt NPD GO	KPCL_RAT	Protein kinase C eta type (EC 2.7.11.13) (nPKC-eta) (PKC-L)	0.41	-	cyt	0					683
P34722 UniProt NPD GO	KPC1_CAEEL	Protein kinase C-like 1 (EC 2.7.11.13) (PKC) (Tetradecanoyl phorbol acetate-resistant protein 1)	0.41	-	nuc	0					704
Q9URT9 UniProt NPD GO	GSK31_SCHPO	Protein kinase gsk31 (EC 2.7.11.1)	0.41	+	cyt	0					381
Q08470 UniProt NPD GO	L2GL_DROPS	Protein lethal(2) giant larvae (p127)	0.41	-	nuc	0	Or: Cell membrane. Or: Secreted protein; extracellular space; extracellular matrix. Intercellular ma ...				1165
Q09490 UniProt NPD GO	LGG1_CAEEL	Protein lgg-1	0.41	-	nuc	0					123
Q8N485 UniProt NPD GO	LIX1_HUMAN	Protein limb expression 1 homolog	0.41	-	nuc	0					282
O16011 UniProt NPD GO	MBL_DROME	Protein muscleblind (Protein mindmelt)	0.41	-	nuc	1	Nucleus	nucleus [IDA]			297
Q80X73 UniProt NPD GO	PELO_MOUSE	Protein pelota homolog	0.41	-	cyt	0	Nucleus (Potential)				385
O65001 UniProt NPD GO	TE1_MAIZE	Protein terminal ear1	0.41	-	nuc	0					656
Q6CJA0 UniProt NPD GO	SEC22_KLULA	Protein transport protein SEC22	0.41	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)				214
Q12745 UniProt NPD GO	SEC39_YEAST	Protein transport protein SEC39 (Dependent on SLY1-20 protein 3)	0.41	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	endoplasmic reticulum [IDA] nuclear envelope [IDA]			709
P31568 UniProt NPD GO	YCF2_OENPI	Protein ycf2 (Fragment)	0.41	-	cyt	0	Plastid; chloroplast; chloroplast stroma (By similarity)				721
Q9UM07 UniProt NPD GO	PADI4_HUMAN	Protein-arginine deiminase type-4 (EC 3.5.3.15) (Protein-arginine deiminase type IV) (Peptidylargini ...	0.41	-	mit	0	Cytoplasmic granule		180300	1WDA	663
P50118 UniProt NPD GO	MOS_PIG	Proto-oncogene serine/threonine-protein kinase mos (EC 2.7.11.1) (c-mos) (Oocyte maturation factor m ...	0.41	-	mit	0					345
P59468 UniProt NPD GO	LBD24_ARATH	Putative LOB domain-containing protein 24	0.41	-	nuc	0					121
Q9FG21 UniProt NPD GO	ATL5D_ARATH	Putative RING-H2 finger protein ATL5D	0.41	-	nuc	1 *					197
Q7Z4G4 UniProt NPD GO	CF075_HUMAN	Putative RNA methylase C6orf75 (EC 2.1.1.-)	0.41	-	mit	0					463
Q27520 UniProt NPD GO	C13A1_CAEEL	Putative cytochrome P450 CYP13A1 (EC 1.14.-.-)	0.41	-	mit	1 *					519
Q9T6H8 UniProt NPD GO	CCF1_ARATH	Putative cytochrome c biogenesis ccmF N-terminal-like mitochondrial protein	0.41	-	end	4 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				382

You are viewing entries 31351 to 31400 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.