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
Q9Y871 UniProt NPD GO	FAEB_PIREQ	Feruloyl esterase B precursor (EC 3.1.1.73) (Ferulic acid esterase B) (Esterase A) (EstA) (Cinnamoyl ...	0.10	-	vac	0	Secreted protein	extracellular region [IDA]			536
P14539 UniProt NPD GO	FIBB_TAPTE	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.10	-		0	Secreted protein				19
Q14314 UniProt NPD GO	FGL2_HUMAN	Fibroleukin precursor (Fibrinogen-like protein 2) (pT49)	0.10	-	cyt	0	Secreted protein	fibrinogen complex [TAS]	605351		439
P52835 UniProt NPD GO	F3ST_FLABI	Flavonol 3-sulfotransferase (EC 2.8.2.-) (F3-ST)	0.10	-	cyt	0	Cytoplasm				312
Q9EQC7 UniProt NPD GO	FSTL3_MOUSE	Follistatin-related protein 3 precursor (Follistatin-like 3) (Follistatin-related gene protein)	0.10	-	exc	0	Secreted protein (Probable)	extracellular space [IDA]			256
Q3SZB7 UniProt NPD GO	F16P1_BOVIN	Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase 1) (FBPa ...	0.10	-	cyt	0					337
P09199 UniProt NPD GO	F16P1_SHEEP	Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase 1) (FBPa ...	0.10	-	cyt	0					336
P05064 UniProt NPD GO	ALDOA_MOUSE	Fructose-bisphosphate aldolase A (EC 4.1.2.13) (Muscle-type aldolase) (Aldolase 1)	0.10	-	cyt	0					363
P04075 UniProt NPD GO	ALDOA_HUMAN	Fructose-bisphosphate aldolase A (EC 4.1.2.13) (Muscle-type aldolase) (Lung cancer antigen NY-LU-1)	0.10	-	cyt	0			103850	4ALD	363
Q9I927 UniProt NPD GO	FUCL5_ANGJA	Fucolectin-5 precursor	0.10	-	exc	0	Secreted protein	extracellular space [IDA]			189
Q40301 UniProt NPD GO	FCPE_MACPY	Fucoxanthin-chlorophyll a-c binding protein E, chloroplast precursor	0.10	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. FCPs are probably ...				212
Q40300 UniProt NPD GO	FCPF_MACPY	Fucoxanthin-chlorophyll a-c binding protein F, chloroplast precursor (Fragment)	0.10	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. FCPs are probably ...				211
P30278 UniProt NPD GO	CCNB2_MEDSA	G2/mitotic-specific cyclin-2 (B-like cyclin) (CycMs2) (Fragment)	0.10	-	cyt	0					328
P04397 UniProt NPD GO	GAL10_YEAST	GAL10 bifunctional protein [Includes: UDP-glucose 4-epimerase (EC 5.1.3.2) (Galactowaldenase); Aldos ...	0.10	-	cyt	0				1Z45	699
P40107 UniProt NPD GO	GOG5_YEAST	GDP-mannose transporter	0.10	-	end	9 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein	Golgi apparatus [IDA] mitochondrion [IDA]			337
P36959 UniProt NPD GO	GMPR1_HUMAN	GMP reductase 1 (EC 1.7.1.7) (Guanosine 5'-monophosphate oxidoreductase 1) (Guanosine monophosphate ...	0.10	-	cyt	0			139265	2BWG	345
Q9DCZ1 UniProt NPD GO	GMPR1_MOUSE	GMP reductase 1 (EC 1.7.1.7) (Guanosine 5'-monophosphate oxidoreductase 1) (Guanosine monophosphate ...	0.10	-	cyt	0					345
Q9Z244 UniProt NPD GO	GMPR1_RAT	GMP reductase 1 (EC 1.7.1.7) (Guanosine 5'-monophosphate oxidoreductase 1) (Guanosine monophosphate ...	0.10	-	cyt	0					345
Q757X5 UniProt NPD GO	MCD4_ASHGO	GPI ethanolamine phosphate transferase 1 (EC 2.-.-.-)	0.10	-	end	14 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				925
Q4WDM5 UniProt NPD GO	GPI7_ASPFU	GPI ethanolamine phosphate transferase 2 (EC 2.-.-.-) (Glycosylphosphatidylinositol-anchor biosynthe ...	0.10	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				767
P40367 UniProt NPD GO	GPI7_YEAST	GPI ethanolamine phosphate transferase 2 (EC 2.-.-.-) (Glycosylphosphatidylinositol-anchor biosynthe ...	0.10	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Membrane; multi- ...	integral to endoplasmic reticulum membrane [IDA] integral to plasma membrane [IDA]			830
Q04174 UniProt NPD GO	SMP3_YEAST	GPI mannosyltransferase 4 (EC 2.4.1.-) (GPI mannosyltransferase IV) (GPI-MT-IV)	0.10	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum [TAS]			516
Q6FLH2 UniProt NPD GO	GWT1_CANGA	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.10	-	end	13 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				486
Q19980 UniProt NPD GO	GCH1_CAEEL	GTP cyclohydrolase I (EC 3.5.4.16) (GTP-CH-I)	0.10	-	mit	0					223
P51596 UniProt NPD GO	GCH1_ONCMY	GTP cyclohydrolase I (EC 3.5.4.16) (GTP-CH-I) (Fragment)	0.10	-	cyt	0					225
P38544 UniProt NPD GO	RAN_ONCVO	GTP-binding nuclear protein Ran (GTPase Ran) (Ras-like protein TC4)	0.10	+	cyt	0	Nucleus (By similarity)				215
Q61820 UniProt NPD GO	RANT_MOUSE	GTP-binding nuclear protein Ran, testis-specific isoform	0.10	+	cyt	0	Nucleus				216
Q39570 UniProt NPD GO	YPTC4_CHLRE	GTP-binding protein YPTC4	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				213
P17609 UniProt NPD GO	YPT2_SCHPO	GTP-binding protein ypt2 (SEC4 homolog)	0.10	+	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				200
P36863 UniProt NPD GO	YPTV4_VOLCA	GTP-binding protein yptV4 (RAB2 homolog)	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				213
Q7TN89 UniProt NPD GO	RASE_MOUSE	GTPase ERas precursor (E-Ras) (Embryonic stem cell-expressed Ras)	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity)				227
P12825 UniProt NPD GO	RASN_CAVPO	GTPase NRas precursor (Transforming protein N-Ras)	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Golgi apparatus; Golgi membrane; lipi ...				189
P01111 UniProt NPD GO	RASN_HUMAN	GTPase NRas precursor (Transforming protein N-Ras)	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side. Golgi apparatus; Golgi membrane; lipid-anchor. Shuttl ...		607785		189
P08556 UniProt NPD GO	RASN_MOUSE	GTPase NRas precursor (Transforming protein N-Ras)	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Golgi apparatus; Golgi membrane; lipi ...	membrane fraction [IDA]			189
Q5RD87 UniProt NPD GO	RASN_PONPY	GTPase NRas precursor (Transforming protein N-Ras)	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Golgi apparatus; Golgi membrane; lipi ...				189
Q04970 UniProt NPD GO	RASN_RAT	GTPase NRas precursor (Transforming protein N-Ras)	0.10	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Golgi apparatus; Golgi membrane; lipi ...				189
Q99MI6 UniProt NPD GO	GIMA3_MOUSE	GTPase, IMAP family member 3 (Immunity-associated nucleotide 4 protein)	0.10	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein	mitochondrial outer membrane [IDA]			301
P81830 UniProt NPD GO	MLB1_VISAL	Galactose-specific lectin I B chain (MLB) (ML-I B)	0.10	-	cyt	0				2MLL	264
Q9JL15 UniProt NPD GO	LEG8_MOUSE	Galectin-8 (LGALS-8)	0.10	-	cyt	0	Cytoplasm				316
P08220 UniProt NPD GO	GBRB1_BOVIN	Gamma-aminobutyric-acid receptor beta-1 subunit precursor (GABA(A) receptor)	0.10	-	mit	4	Membrane; multi-pass membrane protein				474
Q9R0Y8 UniProt NPD GO	GBRG1_MOUSE	Gamma-aminobutyric-acid receptor gamma-1 subunit precursor (GABA(A) receptor)	0.10	-	end	4	Membrane; multi-pass membrane protein				465
P23574 UniProt NPD GO	GBRG1_RAT	Gamma-aminobutyric-acid receptor gamma-1 subunit precursor (GABA(A) receptor)	0.10	-	end	4	Membrane; multi-pass membrane protein				465
P60592 UniProt NPD GO	PIG2_LACMU	Gamma-phospholipase A2 inhibitor LNF2 precursor	0.10	-	nuc	0	Secreted protein				200
Q86BE9 UniProt NPD GO	PEN2_DROME	Gamma-secretase subunit pen-2 (Presenilin enhancer protein 2)	0.10	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				101
P23242 UniProt NPD GO	CXA1_MOUSE	Gap junction alpha-1 protein (Connexin-43) (Cx43) (Gap junction 43 kDa heart protein)	0.10	-	end	4 *	Membrane; multi-pass membrane protein	cell junction [IDA] gap junction [IDA]			381
P18246 UniProt NPD GO	CXA1_BOVIN	Gap junction alpha-1 protein (Connexin-43) (Cx43) (Vascular smooth muscle connexin-43)	0.10	-	end	4 *	Membrane; multi-pass membrane protein				382
Q03190 UniProt NPD GO	CXA4_RAT	Gap junction alpha-4 protein (Connexin-37) (Cx37)	0.10	-	end	4 *	Membrane; multi-pass membrane protein	gap junction [TAS]			332
P08983 UniProt NPD GO	CXB1_XENLA	Gap junction beta-1 protein (Connexin-30) (Cx30)	0.10	-	end	4 *	Membrane; multi-pass membrane protein				264
P28232 UniProt NPD GO	CXB5_RAT	Gap junction beta-5 protein (Connexin-31.1) (Cx31.1)	0.10	-	end	4 *	Membrane; multi-pass membrane protein				271
P29007 UniProt NPD GO	GRP_BOMOR	Gastrin-releasing peptide precursor (GRP-29) [Contains: Neuromedin C (GRP-10); C-terminal extension ...	0.10	-	exc	0	Secreted protein				155

You are viewing entries 64351 to 64400 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.