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
O62605 UniProt NPD GO	SI25_GALME	Fibrohexamerin precursor (25 kDa silk glycoprotein) (p25)	0.27	-	exc	0	Secreted protein				218
P32768 UniProt NPD GO	FLO1_YEAST	Flocculation protein FLO1 precursor (Flocculin-1)	0.27	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor; extracellular side (Probable)	cell wall (sensu Fungi) [IDA]			1537
Q05685 UniProt NPD GO	FOLR2_MOUSE	Folate receptor beta precursor (FR-beta) (Folate receptor 2) (Folate-binding protein 2)	0.27	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	membrane fraction [TAS]			251
P19883 UniProt NPD GO	FST_HUMAN	Follistatin precursor (FS) (Activin-binding protein)	0.27	-	exc	0	Secreted protein	extracellular region [NAS]	136470	2B0U	344
Q9QXD6 UniProt NPD GO	F16P1_MOUSE	Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) (D-fructose-1,6-bisphosphate 1-phosphohydrolase 1) (FBPa ...	0.27	-	cyt	0					337
Q7Z2X7 UniProt NPD GO	GGEE2_HUMAN	G antigen family E member 2 (Prostate-associated gene 2 protein) (PAGE-2)	0.27	-	nuc	0					111
P50755 UniProt NPD GO	CCND1_XENLA	G1/S-specific cyclin-D1	0.27	-	cyt	0					291
P14785 UniProt NPD GO	CCNA_DROME	G2/mitotic-specific cyclin-A	0.27	-	cyt	0		cytoplasm [IDA] fusome [TAS] nucleus [IDA] spectrosome [TAS]			491
P13952 UniProt NPD GO	CCNB_SPISO	G2/mitotic-specific cyclin-B	0.27	-	nuc	0					428
Q9JJI6 UniProt NPD GO	PIGO_MOUSE	GPI ethanolamine phosphate transferase 3 (EC 2.-.-.-) (Phosphatidylinositol-glycan biosynthesis clas ...	0.27	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IDA]			1093
Q8MT80 UniProt NPD GO	PIGZ_DROME	GPI mannosyltransferase 4 (EC 2.4.1.-) (GPI mannosyltransferase IV) (GPI-MT-IV)	0.27	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				696
Q4KRV1 UniProt NPD GO	GPI8_PIG	GPI-anchor transamidase precursor (EC 3.-.-.-) (GPI transamidase) (Phosphatidylinositol-glycan biosy ...	0.27	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...	endoplasmic reticulum lumen [ISS] GPI-anchor transamidase complex [ISS]			395
Q5KBA2 UniProt NPD GO	GWT1_CRYNE	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.27	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				598
Q873N0 UniProt NPD GO	GWT1_CRYNV	GPI-anchored wall transfer protein 1 (EC 2.3.-.-)	0.27	-	end	11 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				598
O75616 UniProt NPD GO	ERAL_HUMAN	GTP-binding protein era homolog (hERA) (ERA-W) (Conserved ERA-like GTPase) (CEGA)	0.27	-	mit	0			607435		437
Q9CW73 UniProt NPD GO	B3GA1_MOUSE	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 (EC 2.4.1.135) (Beta-1,3-glucuro ...	0.27	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				334
Q5CB04 UniProt NPD GO	B3GA1_PANTR	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 (EC 2.4.1.135) (Beta-1,3-glucuro ...	0.27	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				332
O00182 UniProt NPD GO	LEG9_HUMAN	Galectin-9 (HOM-HD-21) (Ecalectin)	0.27	-	cyt	0			601879		355
P48649 UniProt NPD GO	CRGM2_CHICO	Gamma crystallin M2 (Gamma-M2)	0.27	-	nuc	0					175
Q06254 UniProt NPD GO	CRG1_XENLA	Gamma crystallin-1 (Gamma crystallin I) (Gamma-1-CRY)	0.27	-	nuc	0					175
Q8QZW7 UniProt NPD GO	GBRP_MOUSE	Gamma-aminobutyric-acid receptor pi subunit precursor (GABA(A) receptor)	0.27	-	end	4	Membrane; multi-pass membrane protein (By similarity)				440
P50573 UniProt NPD GO	GBRR3_RAT	Gamma-aminobutyric-acid receptor rho-3 subunit precursor (GABA(A) receptor)	0.27	-	end	4	Membrane; multi-pass membrane protein				464
O64405 UniProt NPD GO	TPSD5_ABIGR	Gamma-humulene synthase (EC 4.2.3.-) (Agfghum)	0.27	-	cyt	0	Cytoplasm (Probable)				593
Q29101 UniProt NPD GO	CXA1_PIG	Gap junction alpha-1 protein (Connexin-43) (Cx43) (Fragment)	0.27	-	nuc	0	Membrane; multi-pass membrane protein				92
P28236 UniProt NPD GO	CXA8_MOUSE	Gap junction alpha-8 protein (Connexin-50) (Cx50) (Lens fiber protein MP70)	0.27	-	end	4 *	Membrane; multi-pass membrane protein				439
O02372 UniProt NPD GO	OB76A_DROME	General odorant-binding protein lush precursor	0.27	-	exc	1 *	Secreted protein	extracellular region [IDA]		1OOI	153
P53609 UniProt NPD GO	PGT1_HUMAN	Geranylgeranyl transferase type-1 subunit beta (EC 2.5.1.59) (Geranylgeranyl transferase type I subu ...	0.27	-	cyt	0		CAAX-protein geranylgeranyltransferase complex [TAS]	602031		377
O88873 UniProt NPD GO	GMEB2_RAT	Glucocorticoid modulatory element-binding protein 2 (GMEB-2)	0.27	-	cyt	0	Nucleus. Cytoplasm. May be also cytoplasmic				529
P12300 UniProt NPD GO	GLGL3_WHEAT	Glucose-1-phosphate adenylyltransferase large subunit, chloroplast precursor (EC 2.7.7.27) (ADP-gluc ...	0.27	-	mit	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...				500
P55232 UniProt NPD GO	GLGS_BETVU	Glucose-1-phosphate adenylyltransferase small subunit, chloroplast precursor (EC 2.7.7.27) (ADP-gluc ...	0.27	-	cyt	0	Plastid; chloroplast. Found in the chloroplast in leaf. Plastid; amyloplast. Found in the plastid in ...				489
Q27638 UniProt NPD GO	G6PD_DROYA	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD) (Fragment)	0.27	-	cyt	0					518
P15588 UniProt NPD GO	G6PD_DIDMA	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD) (Fragments)	0.27	-	cyt	0					191
P12646 UniProt NPD GO	G6PD_DROME	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) (G6PD) (Zwischenferment)	0.27	-	cyt	0					524
O24357 UniProt NPD GO	G6PDC_SPIOL	Glucose-6-phosphate 1-dehydrogenase, chloroplast precursor (EC 1.1.1.49) (G6PD)	0.27	-	cyt	0	Plastid; chloroplast (By similarity)				574
Q9FJI5 UniProt NPD GO	G6PD6_ARATH	Glucose-6-phosphate 1-dehydrogenase, cytoplasmic isoform 2 (EC 1.1.1.49) (G6PD6) (G6PDH6)	0.27	-	mit	0	Cytoplasm				515
Q3ZBF0 UniProt NPD GO	NADE1_BOVIN	Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) (NAD(+) synthase [glutamine-hydrolyzing]) (NAD(+) ...	0.27	-	cyt	0					706
P19639 UniProt NPD GO	GSTM4_MOUSE	Glutathione S-transferase Mu 3 (EC 2.5.1.18) (GST class-mu 3) (Glutathione S-transferase GT9.3)	0.27	-	cyt	0	Cytoplasm				217
P48637 UniProt NPD GO	GSHB_HUMAN	Glutathione synthetase (EC 6.3.2.3) (Glutathione synthase) (GSH synthetase) (GSH-S)	0.27	-	cyt	0			231900	2HGS	474
P46416 UniProt NPD GO	GSHB_ARATH	Glutathione synthetase, chloroplast precursor (EC 6.3.2.3) (Glutathione synthase) (GSH synthetase) ( ...	0.27	-	mit	0	Plastid; chloroplast				539
P35574 UniProt NPD GO	GDE_RABIT	Glycogen debranching enzyme (Glycogen debrancher) [Includes: 4-alpha-glucanotransferase (EC 2.4.1.25 ...	0.27	-	cyt	0					1555
P49841 UniProt NPD GO	GSK3B_HUMAN	Glycogen synthase kinase-3 beta (EC 2.7.11.26) (GSK-3 beta)	0.27	-	nuc	0			605004	1UV5	420
Q08271 UniProt NPD GO	GAS4_YEAST	Glycolipid-anchored surface protein 4 precursor	0.27	-	end	1	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cell wall (sensu Fungi) [IDA]			471
Q8CFZ4 UniProt NPD GO	GPC3_MOUSE	Glypican-3 precursor	0.27	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				579
Q28575 UniProt NPD GO	GHR_SHEEP	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.27	-	nuc	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...				634
Q8TAA5 UniProt NPD GO	GRPE2_HUMAN	GrpE protein homolog 2, mitochondrial precursor (Mt-GrpE#2)	0.27	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				225
Q6TMK6 UniProt NPD GO	GBB1_CRIGR	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta 1 (Transducin beta chain 1)	0.27	-	cyt	0					339
Q5R5W8 UniProt NPD GO	GBB1_PONPY	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta 1 (Transducin beta chain 1)	0.27	-	cyt	0					339
Q4VT42 UniProt NPD GO	GPA10_CAEBR	Guanine nucleotide-binding protein alpha-10 subunit	0.27	-	cyt	0					356
Q20636 UniProt NPD GO	GBB2_CAEEL	Guanine nucleotide-binding protein subunit beta 2	0.27	-	cyt	0					356
Q9P7M5 UniProt NPD GO	NOP10_SCHPO	H/ACA ribonucleoprotein complex subunit 3 (Nucleolar protein family A member 3) (snoRNP protein nop1 ...	0.27	-	nuc	0	Nucleus; nucleolus (By similarity)				64

You are viewing entries 43201 to 43250 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.