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
Q9HCP6 UniProt NPD GO	GUP1_HUMAN	Glycerol uptake/transporter homolog	0.02	-	end	8 *	Membrane; multi-pass membrane protein (Potential)	cytoplasm [NAS]	608116		504
Q9D1G3 UniProt NPD GO	GUP1_MOUSE	Glycerol uptake/transporter homolog	0.02	-	end	8 *	Membrane; multi-pass membrane protein (Potential)	cytoplasm [ISS]			503
Q759G5 UniProt NPD GO	GPD_ASHGO	Glycerol-3-phosphate dehydrogenase [NAD+] (EC 1.1.1.8)	0.02	-	nuc	0					424
Q7Z8E7 UniProt NPD GO	GPD_COLGL	Glycerol-3-phosphate dehydrogenase [NAD+] (EC 1.1.1.8)	0.02	-	cyt	0					420
Q9HGY1 UniProt NPD GO	GPD2_ZYGRO	Glycerol-3-phosphate dehydrogenase [NAD+] 2 (EC 1.1.1.8)	0.02	-	cyt	0	Cytoplasm (Potential)				389
Q39732 UniProt NPD GO	GCSH_FLAAN	Glycine cleavage system H protein, mitochondrial precursor	0.02	-	mit	0	Mitochondrion				162
P49359 UniProt NPD GO	GCSH_FLAPR	Glycine cleavage system H protein, mitochondrial precursor	0.02	-	mit	0	Mitochondrion				162
O22535 UniProt NPD GO	GCSH_ORYSA	Glycine cleavage system H protein, mitochondrial precursor	0.02	-	mit	0	Mitochondrion (By similarity). Cytoplasm. Also cytoplasmic				164
Q9U616 UniProt NPD GO	GCSH_DROME	Glycine cleavage system H protein, mitochondrial precursor (Protein pumpless)	0.02	-	mit	0	Mitochondrion (By similarity)				165
P17816 UniProt NPD GO	GRP1_HORVU	Glycine-rich cell wall structural protein precursor	0.02	-	vac	1 *					200
P68265 UniProt NPD GO	GLTP_BOVIN	Glycolipid transfer protein (GLTP)	0.02	-	cyt	0	Cytoplasm (By similarity)			2BV7	208
Q9JL62 UniProt NPD GO	GLTP_MOUSE	Glycolipid transfer protein (GLTP)	0.02	-	mit	0	Cytoplasm (By similarity)	membrane [ISS]			208
P68266 UniProt NPD GO	GLTP_PIG	Glycolipid transfer protein (GLTP)	0.02	-	cyt	0	Cytoplasm (By similarity)				208
Q28914 UniProt NPD GO	GLPB_PANTR	Glycophorin B precursor (CD235b antigen)	0.02	-	end	2 *	Membrane; single-pass type I membrane protein				123
Q28915 UniProt NPD GO	GLPE_PANTR	Glycophorin E precursor	0.02	-	end	2 *	Membrane; single-pass type I membrane protein				78
Q925Q4 UniProt NPD GO	GPHA2_RAT	Glycoprotein hormone alpha-2 precursor (Thyrostimulin subunit alpha)	0.02	-	vac	0	Secreted protein (By similarity)				130
Q3YC03 UniProt NPD GO	GLHA_SAIBB	Glycoprotein hormones alpha chain precursor (Anterior pituitary glycoprotein hormones common subunit ...	0.02	-	exc	1 *	Secreted protein				120
P55320 UniProt NPD GO	GIH_HOMAM	Gonad-inhibiting hormone precursor (GIH) (Vitellogenesis-inhibiting hormone) (VIH)	0.02	-	mit	1 *	Secreted protein				112
P81749 UniProt NPD GO	GON1_CLUPA	Gonadoliberin-1 (Gonadoliberin I) (Gonadotropin-releasing hormone I) (GnRH-I) (LH-RH) (Luliberin I)	0.02	-		0	Secreted protein				10
P30948 UniProt NPD GO	GON3_PETMA	Gonadoliberin-3 (Gonadoliberin III) (Gonadotropin-releasing hormone III) (GnRH-III) (Luliberin III)	0.02	-		0	Secreted protein				10
Q9YGK3 UniProt NPD GO	GTHB1_ANGJA	Gonadotropin beta-1 subunit precursor (Gonadotropin beta-I chain) (GTH-I-beta)	0.02	-	exc	0	Secreted protein				127
P30972 UniProt NPD GO	GTHB2_FUNHE	Gonadotropin beta-2 subunit precursor (Gonadotropin beta-II chain) (GTH-II-beta)	0.02	-	exc	0	Secreted protein				136
Q9NHA8 UniProt NPD GO	BGBP3_DROME	Gram-negative bacteria-binding protein 3 precursor	0.02	-	exc	1 *	Secreted protein (By similarity)	extracellular region [ISS]			490
Q43784 UniProt NPD GO	SSG1_MANES	Granule-bound starch synthase 1, chloroplast precursor (EC 2.4.1.242) (Granule-bound starch synthase ...	0.02	-	cyt	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Granule-bound				608
Q00775 UniProt NPD GO	SSG1_SOLTU	Granule-bound starch synthase 1, chloroplast precursor (EC 2.4.1.242) (Granule-bound starch synthase ...	0.02	-	mit	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Granule-bound				607
Q43134 UniProt NPD GO	SSG1_SORBI	Granule-bound starch synthase 1, chloroplast precursor (EC 2.4.1.242) (Granule-bound starch synthase ...	0.02	-	cyt	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Granule-bound				608
P27736 UniProt NPD GO	SSG1_WHEAT	Granule-bound starch synthase 1, chloroplast precursor (EC 2.4.1.242) (Granule-bound starch synthase ...	0.02	-	cyt	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Granule-bound				615
Q7YRZ7 UniProt NPD GO	GRAA_BOVIN	Granzyme A precursor (EC 3.4.21.78)	0.02	-	mit	0	Secreted protein; cytoplasmic granule (By similarity). Cytoplasmic granules of cytolytic T-lymphocyt ...				258
Q06606 UniProt NPD GO	GRZ2_RAT	Granzyme-like protein 2 precursor (EC 3.4.21.-) (GLP-2) (Granzyme-like protein II) (GLP II) (Mast ce ...	0.02	-	end	0					248
P04001 UniProt NPD GO	OPSG_HUMAN	Green-sensitive opsin (Green cone photoreceptor pigment)	0.02	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	303800	1KPW	364
P87366 UniProt NPD GO	OPSG_ORYLA	Green-sensitive opsin (Green cone photoreceptor pigment) (KFH-G)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				345
Q9R024 UniProt NPD GO	OPSG_CAVPO	Green-sensitive opsin (Green cone photoreceptor pigment) (Medium wavelength-sensitive cone opsin)	0.02	-	end	7	Membrane; multi-pass membrane protein				364
O18910 UniProt NPD GO	OPSG_RABIT	Green-sensitive opsin (Green cone photoreceptor pigment) (Medium wavelength-sensitive cone opsin)	0.02	-	end	7	Membrane; multi-pass membrane protein				364
O35476 UniProt NPD GO	OPSG_RAT	Green-sensitive opsin (Green cone photoreceptor pigment) (Medium wavelength-sensitive cone opsin)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				359
O35599 UniProt NPD GO	OPSG_MOUSE	Green-sensitive opsin (Green cone photoreceptor pigment) (Medium wavelength-sensitive cone opsin) (M ...	0.02	-	end	7 *	Membrane; multi-pass membrane protein	photoreceptor outer segment [IDA]			359
P22331 UniProt NPD GO	OPSG2_ASTFA	Green-sensitive opsin-2 (Green cone photoreceptor pigment 2)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				353
P39878 UniProt NPD GO	PA2GC_RAT	Group IIC secretory phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase GII ...	0.02	-	end	1 *	Secreted protein (Potential)				150
Q9H3K2 UniProt NPD GO	GHITM_HUMAN	Growth hormone-inducible transmembrane protein (Dermal papilla-derived protein 2) (Transmembrane BAX ...	0.02	-	end	6	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			345
P33581 UniProt NPD GO	GHR4_RAT	Growth hormone-related protein 4 (Fragment)	0.02	-	cyt	0	Secreted protein				32
P34999 UniProt NPD GO	GHRHR_PIG	Growth hormone-releasing hormone receptor precursor (GHRH receptor) (GRF receptor) (GRFR)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				423
P01157 UniProt NPD GO	GRWM_HUMAN	Growth-modulating peptide	0.02	-		0					3
P84836 UniProt NPD GO	TXG1D_PLEGU	Guangxitoxin-1D (GxTX-1D)	0.02	-	cyt	0	Secreted protein				36
P84837 UniProt NPD GO	TXG2_PLEGU	Guangxitoxin-2 (GxTX-2)	0.02	-	nuc	0	Secreted protein				33
Q71N41 UniProt NPD GO	GAMT_BRARE	Guanidinoacetate N-methyltransferase (EC 2.1.1.2)	0.02	-	cyt	0					234
Q14353 UniProt NPD GO	GAMT_HUMAN	Guanidinoacetate N-methyltransferase (EC 2.1.1.2)	0.02	-	cyt	0			601240	1ZX0	236
P63210 UniProt NPD GO	GBG1_CANFA	Guanine nucleotide-binding protein G(T) gamma-T1 subunit precursor (Transducin gamma chain)	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				73
P63211 UniProt NPD GO	GBG1_HUMAN	Guanine nucleotide-binding protein G(T) gamma-T1 subunit precursor (Transducin gamma chain)	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		189970		73
Q61012 UniProt NPD GO	GBG1_MOUSE	Guanine nucleotide-binding protein G(T) gamma-T1 subunit precursor (Transducin gamma chain)	0.02	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				73
P69103 UniProt NPD GO	GBLP_TRYBB	Guanine nucleotide-binding protein subunit beta-like protein (Activated protein kinase C receptor ho ...	0.02	-	cyt	0					318
P69104 UniProt NPD GO	GBLP_TRYBR	Guanine nucleotide-binding protein subunit beta-like protein (Activated protein kinase C receptor ho ...	0.02	-	cyt	0					318

You are viewing entries 83651 to 83700 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.