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
Q14409 UniProt NPD GO	GLPK3_HUMAN	Glycerol kinase, testis specific 1 (EC 2.7.1.30) (ATP:glycerol 3-phosphotransferase) (Glycerokinase) ...	0.01	-	cyt	0	Mitochondrion; mitochondrial outer membrane; peripheral membrane protein; cytoplasmic side (By simil ...	cytoplasm [NAS] mitochondrial outer membrane [NAS]	600149		553
Q4PNS1 UniProt NPD GO	GPD_CANTR	Glycerol-3-phosphate dehydrogenase [NAD+] (EC 1.1.1.8)	0.01	-	cyt	0					391
P21695 UniProt NPD GO	GPDA_HUMAN	Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic (EC 1.1.1.8) (GPD-C) (GPDH-C)	0.01	-	cyt	0	Cytoplasm		138420	1X0V	348
P13707 UniProt NPD GO	GPDA_MOUSE	Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic (EC 1.1.1.8) (GPD-C) (GPDH-C)	0.01	-	cyt	0	Cytoplasm	glycerol-3-phosphate dehydrogenase complex [TAS]			348
P08507 UniProt NPD GO	GPDA_RABIT	Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic (EC 1.1.1.8) (GPD-C) (GPDH-C)	0.01	-	cyt	0	Cytoplasm				348
O35077 UniProt NPD GO	GPDA_RAT	Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic (EC 1.1.1.8) (GPD-C) (GPDH-C)	0.01	-	cyt	0	Cytoplasm				348
Q14749 UniProt NPD GO	GNMT_HUMAN	Glycine N-methyltransferase (EC 2.1.1.20)	0.01	-	cyt	0	Cytoplasm		606628	1R74	294
P49360 UniProt NPD GO	GCSH_FLAPU	Glycine cleavage system H protein, mitochondrial precursor (Fragment)	0.01	-	mit	0	Mitochondrion				152
P84560 UniProt NPD GO	GRP1_POPEU	Glycine-rich RNA-binding protein (Fragment)	0.01	-		0					11
P16642 UniProt NPD GO	G24A_DICDI	Glycoprotein 24A (gp24A)	0.01	-	cyt	0	Cell surface				102
P16643 UniProt NPD GO	G24B_DICDI	Glycoprotein 24B (gp24B)	0.01	-	cyt	0	Cell surface				103
P13152 UniProt NPD GO	GLHA1_ONCKE	Glycoprotein hormones alpha chain 1 precursor (Gonadotropin 1 alpha chain) (GTH-alpha) (Fragment)	0.01	-	exc	0	Secreted protein				108
Q3HRV5 UniProt NPD GO	GLHA_AOTNA	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.01	-	exc	1 *	Secreted protein				120
Q4HXT5 UniProt NPD GO	GPI11_GIBZE	Glycosylphosphatidylinositol anchor biosynthesis protein 11	0.01	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				255
Q871U9 UniProt NPD GO	GPI11_NEUCR	Glycosylphosphatidylinositol anchor biosynthesis protein 11	0.01	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				272
Q6C741 UniProt NPD GO	GPI11_YARLI	Glycosylphosphatidylinositol anchor biosynthesis protein 11	0.01	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				223
Q03860 UniProt NPD GO	TVP15_YEAST	Golgi apparatus membrane protein TVP15 (TLG2 compartment vesicle protein 15)	0.01	-	end	3 *	Golgi apparatus; Golgi apparatus membrane; multi-pass membrane protein	integral to Golgi membrane [IDA]			143
P27429 UniProt NPD GO	GONL_SQUAC	Gonadoliberin (Gonadotropin-releasing hormone) (GnRH) (LH-RH) (Luliberin)	0.01	-		0	Secreted protein				10
P37041 UniProt NPD GO	GON1_ALLMI	Gonadoliberin-1 (Gonadoliberin I) (Gonadotropin-releasing hormone I) (GnRH-I) (LH-RH I) (Luliberin I ...	0.01	-		0	Secreted protein				10
P80677 UniProt NPD GO	GON1_CHEPR	Gonadoliberin-1 (Gonadoliberin I) (Gonadotropin-releasing hormone I) (GnRH-I) (Luliberin I)	0.01	-		0	Secreted protein				10
P04378 UniProt NPD GO	GON1_PETMA	Gonadoliberin-1 (Gonadoliberin I) (Gonadotropin-releasing hormone I) (GnRH-I) (Luliberin I)	0.01	-		0	Secreted protein				10
P80678 UniProt NPD GO	GON2_CHEPR	Gonadoliberin-2 (Gonadoliberin II) (Gonadotropin-releasing hormone II) (GnRH-II) (Luliberin II)	0.01	-		0	Secreted protein				10
P68073 UniProt NPD GO	GON2_ALLMI	Gonadoliberin-2 (Gonadoliberin II) (Gonadotropin-releasing hormone II) (GnRH-II) (Luteinizing hormon ...	0.01	-		0	Secreted protein				10
P68072 UniProt NPD GO	GON2_CHICK	Gonadoliberin-2 (Gonadoliberin II) (Gonadotropin-releasing hormone II) (GnRH-II) (Luteinizing hormon ...	0.01	-		0	Secreted protein				10
P68075 UniProt NPD GO	GON2_CLUPA	Gonadoliberin-2 (Gonadoliberin II) (Gonadotropin-releasing hormone II) (GnRH-II) (Luteinizing hormon ...	0.01	-		0	Secreted protein				10
P68076 UniProt NPD GO	GON2_HYDCO	Gonadoliberin-2 (Gonadoliberin II) (Gonadotropin-releasing hormone II) (GnRH-II) (Luteinizing hormon ...	0.01	-		0	Secreted protein				10
P68074 UniProt NPD GO	GON2_SQUAC	Gonadoliberin-2 (Gonadoliberin II) (Gonadotropin-releasing hormone II) (GnRH-II) (Luteinizing hormon ...	0.01	-		0	Secreted protein				10
P69106 UniProt NPD GO	GON3_CLUPA	Gonadoliberin-3 (Gonadoliberin III) (Gonadotropin-releasing hormone III) (GnRH-III) (Luteinizing hor ...	0.01	-		0	Secreted protein				10
P69105 UniProt NPD GO	GON3_ONCKE	Gonadoliberin-3 (Gonadoliberin III) (Gonadotropin-releasing hormone III) (GnRH-III) (Luteinizing hor ...	0.01	-		0	Secreted protein				10
Q91120 UniProt NPD GO	GTHB1_MORSA	Gonadotropin beta-1 subunit precursor (Gonadotropin beta-I chain) (GTH-I-beta)	0.01	-	mit	0	Secreted protein				120
P69845 UniProt NPD GO	GRAA_GRASX	Grammistin Gs A	0.01	-	mit	0	Secreted protein				28
P69839 UniProt NPD GO	GRAB_GRASX	Grammistin Gs B	0.01	-		0	Secreted protein				12
P69846 UniProt NPD GO	GRAC_GRASX	Grammistin Gs C	0.01	-	cyt	0	Secreted protein				26
P69840 UniProt NPD GO	GRAD_GRASX	Grammistin Gs D	0.01	-		0	Secreted protein				13
P69836 UniProt NPD GO	GRAG_GRASX	Grammistin Gs G (Gs 2)	0.01	-	nuc	0	Secreted protein				24
P69842 UniProt NPD GO	GRA1_POGPU	Grammistin Pp 1	0.01	-		0	Secreted protein				13
P69837 UniProt NPD GO	GRA4A_POGPU	Grammistin Pp 4a	0.01	-	nuc	0	Secreted protein				24
P69838 UniProt NPD GO	GRA4B_POGPU	Grammistin Pp 4b	0.01	-	nuc	0	Secreted protein				24
P84766 UniProt NPD GO	SSG1_AEGTS	Granule-bound starch synthase 1 (EC 2.4.1.242) (Granule-bound starch synthase I) (GBSS-I) (Fragment) ...	0.01	-	cyt	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Granule-bound (By similarity)	amyloplast starch grain [ISS] chloroplast starch grain [ISS]			21
P84765 UniProt NPD GO	SSG1_SECCE	Granule-bound starch synthase 1 (EC 2.4.1.242) (Granule-bound starch synthase I) (GBSS-I) (Fragment) ...	0.01	-	cyt	0	Or: Plastid; chloroplast (By similarity). Granule-bound. Or: Plastid; amyloplast (By similarity). Gr ...	amyloplast starch grain [ISS] chloroplast starch grain [ISS]			21
P84633 UniProt NPD GO	SSG1_FAGES	Granule-bound starch synthase 1, chloroplast (EC 2.4.1.242) (Granule-bound starch synthase I) (GBSS- ...	0.01	-	cyt	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Granule-bound (By similarity)				25
Q42857 UniProt NPD GO	SSG1_IPOBA	Granule-bound starch synthase 1, chloroplast precursor (EC 2.4.1.242) (Granule-bound starch synthase ...	0.01	-	cyt	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Granule-bound				608
Q43092 UniProt NPD GO	SSG1_PEA	Granule-bound starch synthase 1, chloroplast precursor (EC 2.4.1.242) (Granule-bound starch synthase ...	0.01	-	cyt	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Granule-bound				603
P58305 UniProt NPD GO	TXGRX_BUNCN	Granulitoxin (GRX) (Fragment)	0.01	-	nuc	0	Secreted protein. Found in nematocyst				21
P42212 UniProt NPD GO	GFP_AEQVI	Green fluorescent protein	0.01	-	cyt	0				2G6E	238
O18911 UniProt NPD GO	OPSG_ODOVI	Green-sensitive opsin (Green cone photoreceptor pigment) (Fragment)	0.01	-	end	6 *	Membrane; multi-pass membrane protein				273
P32311 UniProt NPD GO	OPSG1_CARAU	Green-sensitive opsin-1 (Green cone photoreceptor pigment 1)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				349
Q9W6A5 UniProt NPD GO	OPSG1_BRARE	Green-sensitive opsin-1 (Green cone photoreceptor pigment 1) (Opsin-1, medium-wave-sensitive 1) (Ops ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			349
P32312 UniProt NPD GO	OPSG2_CARAU	Green-sensitive opsin-2 (Green cone photoreceptor pigment 2)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				349
Q8AYM8 UniProt NPD GO	OPSG2_BRARE	Green-sensitive opsin-2 (Green cone photoreceptor pigment 2) (Opsin-1, medium-wave-sensitive 2) (Ops ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein				349

You are viewing entries 88551 to 88600 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.