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
P23225 UniProt NPD GO	GLTB_MAIZE	Ferredoxin-dependent glutamate synthase, chloroplast precursor (EC 1.4.7.1) (Fd-GOGAT)	0.12	-	mit	0	Plastid; chloroplast; chloroplast stroma				1616
O78461 UniProt NPD GO	FTRC_GUITH	Ferredoxin-thioredoxin reductase, catalytic chain (EC 1.18.-.-) (FTR-C) (Ferredoxin-thioredoxin redu ...	0.12	-	nuc	0	Plastid; chloroplast				102
P02792 UniProt NPD GO	FRIL_HUMAN	Ferritin light chain (Ferritin L subunit)	0.12	-	cyt	0		ferritin complex [TAS]	606159		174
P48805 UniProt NPD GO	FGF4A_XENLA	Fibroblast growth factor 4-I precursor (FGF-4-I) (HBGF-4-I) (Embryonic fibroblast growth factor I) ( ...	0.12	-	mit	1 *	Secreted protein (Probable)				187
P53603 UniProt NPD GO	FTCD_PIG	Formimidoyltransferase-cyclodeaminase (Formiminotransferase-cyclodeaminase) (FTCD) [Includes: Glutam ...	0.12	-	cyt	0				1QD1	541
Q862A9 UniProt NPD GO	GPBAR_BOVIN	G-protein coupled bile acid receptor 1	0.12	-	end	7 *	Cell membrane; multi-pass membrane protein (By similarity)				329
O95866 UniProt NPD GO	G6B_HUMAN	G6b protein precursor	0.12	-	end	1	Isoform A, isoform B: Cell membrane; single-pass type I membrane protein. Isoform D, isoform E: Endo ...	plasma membrane [IDA]	606520		241
Q06547 UniProt NPD GO	GABP2_HUMAN	GA-binding protein beta chain (GABP subunit beta-2) (GABP-2) (GABP subunit beta-1) (GABPB-1) (Transc ...	0.12	-	cyt	0		nucleus [TAS]	600610		395
Q8TGB2 UniProt NPD GO	GPI7_CANAL	GPI ethanolamine phosphate transferase 2 (EC 2.-.-.-) (Glycosylphosphatidylinositol-anchor biosynthe ...	0.12	-	end	13 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				892
Q6CLN2 UniProt NPD GO	GPI7_KLULA	GPI ethanolamine phosphate transferase 2 (EC 2.-.-.-) (Glycosylphosphatidylinositol-anchor biosynthe ...	0.12	-	end	11 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				787
Q09837 UniProt NPD GO	SMP3_SCHPO	GPI mannosyltransferase 4 (EC 2.4.1.-) (GPI mannosyltransferase IV) (GPI-MT-IV)	0.12	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				533
Q5XI31 UniProt NPD GO	PIGS_RAT	GPI transamidase component PIG-S (Phosphatidylinositol-glycan biosynthesis class S protein)	0.12	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	GPI-anchor transamidase complex [ISS]			554
P50141 UniProt NPD GO	GCH1_CHICK	GTP cyclohydrolase I (EC 3.5.4.16) (GTP-CH-I)	0.12	-	cyt	0					236
Q94465 UniProt NPD GO	GCH1_DICDI	GTP cyclohydrolase I (EC 3.5.4.16) (GTP-CH-I)	0.12	-	cyt	0					232
Q74ZA9 UniProt NPD GO	GSP1_ASHGO	GTP-binding nuclear protein GSP1/Ran	0.12	+	cyt	0	Nucleus (By similarity)				214
Q9P4E9 UniProt NPD GO	GSP1_CANAL	GTP-binding nuclear protein GSP1/Ran	0.12	+	cyt	0	Nucleus (By similarity)				214
Q7RVL0 UniProt NPD GO	GSP1_NEUCR	GTP-binding nuclear protein GSP1/Ran	0.12	+	cyt	0	Nucleus (By similarity)				215
Q8TFK3 UniProt NPD GO	GSP1_YARLI	GTP-binding nuclear protein GSP1/Ran	0.12	+	cyt	0	Nucleus (By similarity)				214
P62825 UniProt NPD GO	RAN_CANFA	GTP-binding nuclear protein Ran (GTPase Ran) (Ras-like protein TC4)	0.12	+	cyt	0	Nucleus. Cytoplasm. Becomes dispersed throughout the cytoplasm during mitosis			3RAN	215
P62827 UniProt NPD GO	RAN_MOUSE	GTP-binding nuclear protein Ran (GTPase Ran) (Ras-like protein TC4)	0.12	+	cyt	0	Nucleus. Cytoplasm. Becomes dispersed throughout the cytoplasm during mitosis				215
P62828 UniProt NPD GO	RAN_RAT	GTP-binding nuclear protein Ran (GTPase Ran) (Ras-like protein TC4)	0.12	+	cyt	0	Nucleus. Cytoplasm. Becomes dispersed throughout the cytoplasm during mitosis			1A2K	215
P52301 UniProt NPD GO	RAN_XENLA	GTP-binding nuclear protein Ran (GTPase Ran) (Ras-like protein TC4)	0.12	+	cyt	0	Nucleus				216
Q6GL85 UniProt NPD GO	RAN_XENTR	GTP-binding nuclear protein Ran (GTPase Ran) (Ras-like protein TC4)	0.12	+	cyt	0	Nucleus				216
P62826 UniProt NPD GO	RAN_HUMAN	GTP-binding nuclear protein Ran (GTPase Ran) (Ras-like protein TC4) (Androgen receptor-associated pr ...	0.12	+	cyt	0	Nucleus. Cytoplasm. Becomes dispersed throughout the cytoplasm during mitosis	cytoplasm [IDA] nuclear pore [NAS]	601179	1RRP	215
P28748 UniProt NPD GO	SPI1_SCHPO	GTP-binding nuclear protein spi1	0.12	+	cyt	0	Nucleus	nucleus [TAS]			216
P36861 UniProt NPD GO	YPTV2_VOLCA	GTP-binding protein yptV2	0.12	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				217
P54804 UniProt NPD GO	GALC_CANFA	Galactocerebrosidase precursor (EC 3.2.1.46) (GALCERase) (Galactosylceramidase) (Galactosylceramide ...	0.12	-	cyt	1 *	Lysosome (By similarity)				669
P54818 UniProt NPD GO	GALC_MOUSE	Galactocerebrosidase precursor (EC 3.2.1.46) (GALCERase) (Galactosylceramidase) (Galactosylceramide ...	0.12	-	cyt	1 *	Lysosome (By similarity)	lysosome [TAS]			668
P16305 UniProt NPD GO	GBRA6_MOUSE	Gamma-aminobutyric-acid receptor alpha-6 subunit precursor (GABA(A) receptor)	0.12	-	end	4	Membrane; multi-pass membrane protein				453
P50571 UniProt NPD GO	GBRB1_MOUSE	Gamma-aminobutyric-acid receptor beta-1 subunit precursor (GABA(A) receptor)	0.12	-	mit	4	Membrane; multi-pass membrane protein				474
Q99MZ4 UniProt NPD GO	GGT4_RAT	Gamma-glutamyltransferase 4 precursor (EC 2.3.2.2) (Gamma-glutamyltranspeptidase 4) (Gamma-glutamylt ...	0.12	-	end	1	Membrane; single-pass type II membrane protein (By similarity)				662
Q14390 UniProt NPD GO	GGTL4_HUMAN	Gamma-glutamyltransferase-like protein 4	0.12	-	cyt	0					252
Q60928 UniProt NPD GO	GGT1_MOUSE	Gamma-glutamyltranspeptidase 1 precursor (EC 2.3.2.2) (Gamma-glutamyltransferase 1) (GGT 1) (CD224 a ...	0.12	-	cyt	1 *	Membrane; single-pass type II membrane protein (By similarity)	integral to plasma membrane [TAS]			568
Q13326 UniProt NPD GO	SGCG_HUMAN	Gamma-sarcoglycan (Gamma-SG) (35 kDa dystrophin-associated glycoprotein) (35DAG)	0.12	-	mit	1 *	Sarcolemma; sarcolemmal membrane; single-pass type II membrane protein (By similarity)	plasma membrane [TAS] sarcoglycan complex [TAS]	608896		290
O08597 UniProt NPD GO	SGCG_MESAU	Gamma-sarcoglycan (Gamma-SG) (35 kDa dystrophin-associated glycoprotein) (35DAG)	0.12	-	mit	1 *	Sarcolemma; sarcolemmal membrane; single-pass type II membrane protein (By similarity)				290
P82348 UniProt NPD GO	SGCG_MOUSE	Gamma-sarcoglycan (Gamma-SG) (35 kDa dystrophin-associated glycoprotein) (35DAG)	0.12	-	mit	1 *	Sarcolemma; sarcolemmal membrane; single-pass type II membrane protein	integral to plasma membrane [TAS] sarcoglycan complex [IDA]			290
Q9VKU7 UniProt NPD GO	GCP4_DROME	Gamma-tubulin complex component 4 homolog (Gamma ring complex protein 75) (dGrip75)	0.12	-	nuc	0	Centrosome (Potential)	gamma-tubulin ring complex [ISS]			650
Q6S9C0 UniProt NPD GO	CXA1_CANFA	Gap junction alpha-1 protein (Connexin-43) (Cx43)	0.12	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				381
P17302 UniProt NPD GO	CXA1_HUMAN	Gap junction alpha-1 protein (Connexin-43) (Cx43) (Gap junction 43 kDa heart protein)	0.12	-	end	4 *	Membrane; multi-pass membrane protein	connexon complex [TAS] integral to plasma membrane [TAS]	186100		381
Q9NTQ9 UniProt NPD GO	CXB4_HUMAN	Gap junction beta-4 protein (Connexin-30.3) (Cx30.3)	0.12	-	end	4 *	Membrane; multi-pass membrane protein	gap junction [NAS]	605425		266
Q5XWD5 UniProt NPD GO	IF_CANFA	Gastric intrinsic factor precursor (Intrinsic factor) (IF) (INF) (Pancreatic intrinsic factor)	0.12	-	exc	0	Secreted protein (By similarity)				417
Q9GMY3 UniProt NPD GO	PEPC_RHIFE	Gastricsin precursor (EC 3.4.23.3) (Pepsinogen C)	0.12	-	vac	0	Secreted protein				389
P68273 UniProt NPD GO	GLUC_CAMDR	Glucagon	0.12	-	nuc	0	Secreted protein (By similarity)				29
P68274 UniProt NPD GO	GLUC_RABIT	Glucagon	0.12	-	nuc	0	Secreted protein (By similarity)				29
P68275 UniProt NPD GO	GLUC_SAISC	Glucagon	0.12	-	nuc	0	Secreted protein (By similarity)				29
Q01412 UniProt NPD GO	E13A_LYCES	Glucan endo-1,3-beta-glucosidase A precursor (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase A) ((1- ...	0.12	-	exc	0	Secreted protein; extracellular space				336
Q04802 UniProt NPD GO	NAG1_CANAL	Glucosamine-6-phosphate isomerase (EC 3.5.99.6) (Glucosamine-6-phosphate deaminase) (GNPDA) (GlcN6P ...	0.12	-	pox	0					248
P00367 UniProt NPD GO	DHE3_HUMAN	Glutamate dehydrogenase 1, mitochondrial precursor (EC 1.4.1.3) (GDH)	0.12	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]	138130	1NR1	558
O81776 UniProt NPD GO	GLR24_ARATH	Glutamate receptor 2.4 precursor (Ligand-gated ion channel 2.4)	0.12	-	end	3	Membrane; multi-pass membrane protein				896
Q84W41 UniProt NPD GO	GLR36_ARATH	Glutamate receptor 3.6 precursor (Ligand-gated ion channel 3.6)	0.12	-	end	3	Membrane; multi-pass membrane protein				903

You are viewing entries 61151 to 61200 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.