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
P27057 UniProt NPD GO	GAST1_LYCES	GAST1 protein precursor	0.39	-	exc	0	Secreted protein				112
Q9Y2G5 UniProt NPD GO	OFUT2_HUMAN	GDP-fucose protein O-fucosyltransferase 2 precursor (EC 2.4.1.221) (Peptide-O-fucosyltransferase) (O ...	0.39	-	exc	0	Endoplasmic reticulum (By similarity)				429
Q5R6L8 UniProt NPD GO	GPI8_PONPY	GPI-anchor transamidase precursor (EC 3.-.-.-) (GPI transamidase) (Phosphatidylinositol-glycan biosy ...	0.39	-	end	1 *		GPI-anchor transamidase complex [ISS]			395
Q13588 UniProt NPD GO	GRAP_HUMAN	GRB2-related adapter protein	0.39	-	cyt	0		cytoplasm [TAS]	604330		217
P55043 UniProt NPD GO	RAD_RAT	GTP-binding protein RAD (RAS associated with diabetes) (RAD1)	0.39	-	cyt	0					306
Q05889 UniProt NPD GO	LPG1_LEIDO	Galactofuranosyl glycosyltransferase (EC 2.4.1.-)	0.39	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein				434
Q96UI1 UniProt NPD GO	GAL7_TRIRE	Galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) (Gal-1-P uridylyltransferase) (UDP-glucose-- ...	0.39	-	nuc	0					382
O19058 UniProt NPD GO	FUT3_PANTR	Galactoside 3(4)-L-fucosyltransferase (EC 2.4.1.65) (Blood group Lewis alpha-4-fucosyltransferase) ( ...	0.39	-	mit	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				372
Q6K1E7 UniProt NPD GO	GGNB1_MOUSE	Gametogenetin-binding protein 1	0.39	-	mit	0	Cytoplasm. Membrane; peripheral membrane protein. Golgi apparatus	Golgi apparatus [IDA] plasma membrane [IDA]			370
P02526 UniProt NPD GO	CRGB_BOVIN	Gamma crystallin B (Gamma crystallin II)	0.39	-	nuc	0				4GCR	174
P10043 UniProt NPD GO	CRGM1_CYPCA	Gamma crystallin M1 (Gamma-M1)	0.39	-	nuc	0					177
Q91724 UniProt NPD GO	CRG2_XENLA	Gamma crystallin-2 (Gamma crystallin II) (Gamma-2-CRY)	0.39	-	nuc	0					175
P31644 UniProt NPD GO	GBRA5_HUMAN	Gamma-aminobutyric-acid receptor alpha-5 subunit precursor (GABA(A) receptor)	0.39	-	mit	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	137142		462
Q95K09 UniProt NPD GO	GCP5_MACFA	Gamma-tubulin complex component 5 (GCP-5) (Fragment)	0.39	-	cyt	0	Centrosome (By similarity)	gamma-tubulin ring complex [ISS]			725
P28229 UniProt NPD GO	CXA7_MOUSE	Gap junction alpha-7 protein (Connexin-45) (Cx45)	0.39	-	end	4 *	Membrane; multi-pass membrane protein	gap junction [IDA]			396
P01278 UniProt NPD GO	GLUC1_LOPAM	Glucagon-1 precursor (Glucagon I) [Contains: Glicentin-related polypeptide (GRPP); Glucagon-1 (Gluca ...	0.39	-	exc	0	Secreted protein				124
P04092 UniProt NPD GO	GLUC2_LOPAM	Glucagon-2 precursor (Glucagon II) [Contains: Glicentin-related polypeptide (GRPP); Glucagon-2 (Gluc ...	0.39	-	exc	0	Secreted protein				122
Q91756 UniProt NPD GO	GLRK_XENLA	Glutamate receptor U1 precursor (XENU1) (Unitary non-NMDA glutamate receptor subunit 1)	0.39	-	end	3	Membrane; multi-pass membrane protein				479
Q12680 UniProt NPD GO	GLT1_YEAST	Glutamate synthase [NADPH] precursor (EC 1.4.1.13) (NADPH-GOGAT)	0.39	-	nuc	0		glutamate synthase complex [IPI] mitochondrion [IDA]			2144
Q711T7 UniProt NPD GO	NADE1_MOUSE	Glutamine-dependent NAD(+) synthetase (EC 6.3.5.1) (NAD(+) synthase [glutamine-hydrolyzing]) (NAD(+) ...	0.39	-	mit	0					725
P52780 UniProt NPD GO	SYQ_LUPLU	Glutaminyl-tRNA synthetase (EC 6.1.1.18) (Glutamine--tRNA ligase) (GlnRS)	0.39	-	cyt	0					794
P14614 UniProt NPD GO	GLUB4_ORYSA	Glutelin type-B 4 precursor [Contains: Glutelin type-B 4 acidic chain; Glutelin type-B 4 basic chain ...	0.39	-	exc	0					500
Q6ERU3 UniProt NPD GO	GLUB5_ORYSA	Glutelin type-B 5 precursor [Contains: Glutelin type-B 5 acidic chain; Glutelin type-B 5 basic chain ...	0.39	-	exc	0					500
P08489 UniProt NPD GO	GLT4_WHEAT	Glutenin, high molecular weight subunit PW212 precursor	0.39	-	exc	1 *					838
P79334 UniProt NPD GO	PYGM_BOVIN	Glycogen phosphorylase, muscle form (EC 2.4.1.1) (Myophosphorylase)	0.39	-	nuc	0					841
Q8HXW4 UniProt NPD GO	PYGM_MACFA	Glycogen phosphorylase, muscle form (EC 2.4.1.1) (Myophosphorylase)	0.39	-	cyt	0					841
P00489 UniProt NPD GO	PYGM_RABIT	Glycogen phosphorylase, muscle form (EC 2.4.1.1) (Myophosphorylase)	0.39	-	nuc	0				9GPB	842
Q75EK2 UniProt NPD GO	NMT_ASHGO	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) (Peptide N-myristoyltransferase) (Myristoyl-C ...	0.39	-	nuc	0	Cytoplasm (By similarity)				452
P32236 UniProt NPD GO	GNRHR_BOVIN	Gonadotropin-releasing hormone receptor (GnRH receptor) (GnRH-R)	0.39	+	end	7 *	Membrane; multi-pass membrane protein				328
Q9TU69 UniProt NPD GO	GHR_CANFA	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.39	-	nuc	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...				638
Q8UWD9 UniProt NPD GO	GDF8_ANSAN	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.39	+	cyt	0	Secreted protein (By similarity)				375
Q9GM97 UniProt NPD GO	GDF8_HORSE	Growth/differentiation factor 8 precursor (GDF-8) (Myostatin)	0.39	+	mit	0	Secreted protein (By similarity)				375
P38403 UniProt NPD GO	GNAI3_CAVPO	Guanine nucleotide-binding protein G(k) subunit alpha (G(i) alpha-3)	0.39	-	cyt	0					353
P49084 UniProt NPD GO	GPA1_SOYBN	Guanine nucleotide-binding protein alpha-1 subunit (GP-alpha-1)	0.39	-	nuc	0					385
Q9BIG2 UniProt NPD GO	GPA14_CAEEL	Guanine nucleotide-binding protein alpha-14 subunit	0.39	-	mit	0					368
Q61DE0 UniProt NPD GO	GPA15_CAEBR	Guanine nucleotide-binding protein alpha-15 subunit	0.39	-	nuc	0					356
Q4VT31 UniProt NPD GO	GPA6_CAEBR	Guanine nucleotide-binding protein alpha-6 subunit	0.39	-	nuc	0					366
Q6FSB0 UniProt NPD GO	GAR1_CANGA	H/ACA ribonucleoprotein complex subunit 1 (snoRNP protein GAR1)	0.39	-	cyt	0	Nucleus; nucleolus (By similarity)				222
Q9NX77 UniProt NPD GO	ENK14_HUMAN	HERV-K_16p3.3 provirus ancestral Env polyprotein (Envelope polyprotein) [Contains: Surface protein ( ...	0.39	-	end	2					482
Q9UKH8 UniProt NPD GO	GAK9_HUMAN	HERV-K_5q13.3 provirus ancestral Gag polyprotein (Gag polyprotein) (HERV-K104 Gag protein) [Contains ...	0.39	-	cyt	0					177
P63128 UniProt NPD GO	POK4_HUMAN	HERV-K_6q14.1 provirus ancestral Pol protein (HERV-K109 Pol protein) (HERV-K(C6) Pol protein)	0.39	-	cyt	0					194
P60509 UniProt NPD GO	ERB1_HUMAN	HERV-R(b)_3p24.3 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (HERV-R(b) Env ...	0.39	-	end	1 *					514
O95081 UniProt NPD GO	HRBL_HUMAN	HIV-1 Rev-binding protein-like protein (Rev/Rex activation domain-binding protein related) (RAB-R)	0.39	-	nuc	0			604019		481
P30450 UniProt NPD GO	1A26_HUMAN	HLA class I histocompatibility antigen, A-26 alpha chain precursor (MHC class I antigen A*26)	0.39	-	end	1	Membrane; single-pass type I membrane protein		142800		365
P30456 UniProt NPD GO	1A43_HUMAN	HLA class I histocompatibility antigen, A-43 alpha chain precursor (MHC class I antigen A*43) (Aw-43 ...	0.39	-	end	1	Membrane; single-pass type I membrane protein		142800		365
P30457 UniProt NPD GO	1A66_HUMAN	HLA class I histocompatibility antigen, A-66 alpha chain precursor (MHC class I antigen A*66) (Aw-66 ...	0.39	-	end	1	Membrane; single-pass type I membrane protein		142800		365
Q29960 UniProt NPD GO	1C16_HUMAN	HLA class I histocompatibility antigen, Cw-16 alpha chain precursor (MHC class I antigen Cw*16)	0.39	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein		142840		366
Q29865 UniProt NPD GO	1C18_HUMAN	HLA class I histocompatibility antigen, Cw-18 alpha chain precursor (MHC class I antigen Cw*18)	0.39	-	end	1	Membrane; single-pass type I membrane protein		142840		366
P30504 UniProt NPD GO	1C04_HUMAN	HLA class I histocompatibility antigen, Cw-4 alpha chain precursor (MHC class I antigen Cw*4)	0.39	-	end	1	Membrane; single-pass type I membrane protein		142840	1QQD	366
Q29963 UniProt NPD GO	1C06_HUMAN	HLA class I histocompatibility antigen, Cw-6 alpha chain precursor (MHC class I antigen Cw*6)	0.39	-	end	1	Membrane; single-pass type I membrane protein		142840		366

You are viewing entries 32601 to 32650 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.