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
P08171 UniProt NPD GO	EST6_DROME	Esterase-6 precursor (EC 3.1.1.1) (Est-6) (Carboxylic-ester hydrolase 6) (Carboxylesterase-6)	0.18	-	exc	0	Secreted protein				544
P51657 UniProt NPD GO	DHB1_RAT	Estradiol 17-beta-dehydrogenase 1 (EC 1.1.1.62) (17-beta-HSD 1) (17-beta-hydroxysteroid dehydrogenas ...	0.18	-	nuc	0	Cytoplasm				344
O49230 UniProt NPD GO	ETR1_BRAOL	Ethylene receptor (EC 2.7.13.3)	0.18	-	vac	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				735
P35614 UniProt NPD GO	ERF1Z_ARATH	Eukaryotic peptide chain release factor subunit 1-3 (eRF1-3) (Eukaryotic release factor 1-3) (Omnipo ...	0.18	-	cyt	0	Cytoplasm				435
P06730 UniProt NPD GO	IF4E_HUMAN	Eukaryotic translation initiation factor 4E (eIF4E) (eIF-4E) (mRNA cap-binding protein) (eIF-4F 25 k ...	0.18	-	cyt	0		eukaryotic translation initiation factor 4F... [TAS]	133440	1WKW	217
P63073 UniProt NPD GO	IF4E_MOUSE	Eukaryotic translation initiation factor 4E (eIF4E) (eIF-4E) (mRNA cap-binding protein) (eIF-4F 25 k ...	0.18	-	cyt	0		cytoplasm [IDA]		1L8B	217
P63074 UniProt NPD GO	IF4E_RAT	Eukaryotic translation initiation factor 4E (eIF4E) (eIF-4E) (mRNA cap-binding protein) (eIF-4F 25 k ...	0.18	-	cyt	0					217
Q80VV3 UniProt NPD GO	4EBP3_MOUSE	Eukaryotic translation initiation factor 4E-binding protein 3 (4E-BP3) (eIF4E-binding protein 3)	0.18	-	nuc	0					101
P32911 UniProt NPD GO	SUI1_YEAST	Eukaryotic translation initiation factor eIF-1 (Protein translation factor SUI1)	0.18	-	cyt	0		multi-eIF complex [IDA]			108
Q9UBQ6 UniProt NPD GO	EXTL2_HUMAN	Exostosin-like 2 (EC 2.4.1.223) (Glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltran ...	0.18	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...		602411		330
Q2QLB9 UniProt NPD GO	CAZA2_CALMO	F-actin capping protein alpha-2 subunit (CapZ alpha-2)	0.18	-	nuc	0					285
Q29221 UniProt NPD GO	CAZA2_PIG	F-actin capping protein alpha-2 subunit (CapZ alpha-2)	0.18	-	nuc	0					285
Q8NEZ5 UniProt NPD GO	FBX22_HUMAN	F-box only protein 22 (F-box protein FBX22p44)	0.18	-	cyt	0			609096		403
Q5RF88 UniProt NPD GO	FKBP5_PONPY	FK506-binding protein 5 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase)	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				457
Q9SCY2 UniProt NPD GO	FKBP3_ARATH	FKBP-type peptidyl-prolyl cis-trans isomerase 3, chloroplast precursor (EC 5.2.1.8) (PPIase) (Rotama ...	0.18	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen			1Y0O	208
Q23092 UniProt NPD GO	FABP4_CAEEL	Fatty acid-binding protein homolog 4	0.18	-	nuc	0					145
Q8WT58 UniProt NPD GO	FAR1_ONCDU	Fatty-acid and retinol-binding protein 1 precursor (Od-FAR-1)	0.18	-	gol	0	Secreted protein (By similarity)	extracellular region [ISS]			178
Q8WT59 UniProt NPD GO	FAR1_ONCGU	Fatty-acid and retinol-binding protein 1 precursor (Og-FAR-1)	0.18	-	nuc	0	Secreted protein	extracellular region [IDA]			178
Q8WT57 UniProt NPD GO	FAR1_ONCOC	Fatty-acid and retinol-binding protein 1 precursor (Oo-FAR-1)	0.18	-	nuc	0	Secreted protein	extracellular region [IDA]			178
Q25619 UniProt NPD GO	FAR1_ONCVO	Fatty-acid and retinol-binding protein 1 precursor (Ov-FAR-1) (Ov20) (OvS1) (S1 protein) (OvMBP/11) ...	0.18	-	nuc	0	Secreted protein	extracellular region [IDA]			178
P32791 UniProt NPD GO	FRE1_YEAST	Ferric reductase transmembrane component 1 precursor (EC 1.16.1.7) (Ferric-chelate reductase 1)	0.18	-	end	7 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			686
P02793 UniProt NPD GO	FRIL1_RAT	Ferritin light chain 1 (Ferritin L subunit 1)	0.18	-	cyt	0					182
P35551 UniProt NPD GO	FBRL_SCHPO	Fibrillarin	0.18	+	cyt	0	Nucleus; nucleolus. Fibrillar region of the nucleolus				305
Q9FEF8 UniProt NPD GO	FBRL1_ARATH	Fibrillarin-1 (SKP1-interacting partner 7)	0.18	+	cyt	0	Nucleus; nucleolus. Fibrillar region of the nucleolus				308
Q94AH9 UniProt NPD GO	FBRL2_ARATH	Fibrillarin-2 (Fibrillarin-like protein)	0.18	+	cyt	0	Nucleus; nucleolus (By similarity). Fibrillar region of the nucleolus (By similarity)				320
Q66H07 UniProt NPD GO	FANK1_RAT	Fibronectin type 3 and ankyrin repeat domains 1 protein	0.18	-	cyt	0					344
Q9DAM9 UniProt NPD GO	FANK1_MOUSE	Fibronectin type 3 and ankyrin repeat domains 1 protein (Germ cell-specific gene 1 protein) (GSG1)	0.18	-	cyt	0				1WFU	344
O75636 UniProt NPD GO	FCN3_HUMAN	Ficolin-3 precursor (Collagen/fibrinogen domain-containing protein 3) (Collagen/fibrinogen domain-co ...	0.18	-	mit	0	Secreted protein. Found in blood plasma, bronchus, alveolus and bile duct	extracellular region [NAS] extracellular space [TAS]	604973	1LA5	299
P37120 UniProt NPD GO	C75A2_SOLME	Flavonoid 3',5'-hydroxylase (EC 1.14.13.88) (F3'5'H) (Cytochrome P450 75A2) (CYPLXXVA2) (P-450EG1)	0.18	+	nuc	1 *					513
Q62632 UniProt NPD GO	FSTL1_RAT	Follistatin-related protein 1 precursor (Follistatin-like 1)	0.18	-	exc	0	Secreted protein				306
Q62356 UniProt NPD GO	FSTL1_MOUSE	Follistatin-related protein 1 precursor (Follistatin-like 1) (TGF-beta-inducible protein TSC-36)	0.18	-	exc	0	Secreted protein (Potential)				306
O95954 UniProt NPD GO	FTCD_HUMAN	Formimidoyltransferase-cyclodeaminase (Formiminotransferase-cyclodeaminase) (FTCD) (LCHC1) [Includes ...	0.18	-	cyt	0	Cytoplasm	cytoplasm [TAS]	606806		541
P48544 UniProt NPD GO	IRK5_HUMAN	G protein-activated inward rectifier potassium channel 4 (GIRK4) (Potassium channel, inwardly rectif ...	0.18	-	end	2	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	600734		419
P48545 UniProt NPD GO	IRK5_MOUSE	G protein-activated inward rectifier potassium channel 4 (GIRK4) (Potassium channel, inwardly rectif ...	0.18	-	end	2	Membrane; multi-pass membrane protein				419
O02670 UniProt NPD GO	IRK5_PIG	G protein-activated inward rectifier potassium channel 4 (GIRK4) (Potassium channel, inwardly rectif ...	0.18	-	end	2	Membrane; multi-pass membrane protein				419
Q08301 UniProt NPD GO	CCNB1_CRIGR	G2/mitotic-specific cyclin-B1	0.18	-	mit	0					429
Q9IBG1 UniProt NPD GO	CCNB1_ORYLA	G2/mitotic-specific cyclin-B1	0.18	-	mit	0					404
Q6EV70 UniProt NPD GO	OFUT1_RAT	GDP-fucose protein O-fucosyltransferase 1 precursor (EC 2.4.1.221) (Peptide-O-fucosyltransferase) (O ...	0.18	-	exc	0	Endoplasmic reticulum				395
Q5BAX7 UniProt NPD GO	SMP3_EMENI	GPI mannosyltransferase 4 (EC 2.4.1.-) (GPI mannosyltransferase IV) (GPI-MT-IV)	0.18	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				530
P30793 UniProt NPD GO	GCH1_HUMAN	GTP cyclohydrolase I (EC 3.5.4.16) (GTP-CH-I)	0.18	-	nuc	0			128230	1FB1	250
P36406 UniProt NPD GO	ARD1_HUMAN	GTP-binding protein ARD-1 (ADP-ribosylation factor domain protein 1) (Tripartite motif-containing pr ...	0.18	-	cyt	0	Intracytoplasmic membrane. Golgi apparatus; Golgi membrane. Lysosome; lysosomal membrane. Membrane-a ...	Golgi membrane [IDA] lysosomal membrane [IDA]	601747		574
O95057 UniProt NPD GO	DIRA1_HUMAN	GTP-binding protein Di-Ras1 (Distinct subgroup of the Ras family member 1) (Ras-related inhibitor of ...	0.18	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		607862	2GF0	198
P40908 UniProt NPD GO	GAL7_CRYNE	Galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (Gal-1-P uridylyltransferase) (UDP-glucose-- ...	0.18	-	cyt	0					381
O94766 UniProt NPD GO	B3GA3_HUMAN	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3 (EC 2.4.1.135) (Beta-1,3-glucuro ...	0.18	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	Golgi membrane [NAS] integral to membrane [NAS]	606374	1KWS	335
P56479 UniProt NPD GO	GALR1_MOUSE	Galanin receptor type 1 (GAL1-R) (GALR1)	0.18	+	end	7 *	Membrane; multi-pass membrane protein				348
O88854 UniProt NPD GO	GALR2_MOUSE	Galanin receptor type 2 (GAL2-R) (GALR2)	0.18	-	end	7 *	Membrane; multi-pass membrane protein				371
Q29058 UniProt NPD GO	LEG4_PIG	Galectin-4 (Lactose-binding lectin 4) (L-36 lactose-binding protein) (L36LBP)	0.18	-	cyt	0					323
P56470 UniProt NPD GO	LEG4_HUMAN	Galectin-4 (Lactose-binding lectin 4) (L-36 lactose-binding protein) (L36LBP) (Antigen NY-CO-27)	0.18	-	cyt	0		cytosol [TAS] plasma membrane [TAS]	602518	1X50	323
Q9BLY8 UniProt NPD GO	GBRB_DROSI	Gamma-aminobutyric-acid receptor subunit beta precursor (GABA(A) receptor) (Protein cyclodiene resis ...	0.18	-	end	4	Membrane; multi-pass membrane protein	integral to membrane [ISS]			606
P27352 UniProt NPD GO	IF_HUMAN	Gastric intrinsic factor precursor (Intrinsic factor) (IF) (INF)	0.18	-	exc	0	Secreted protein		609342		417

You are viewing entries 53001 to 53050 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.