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
Q8AYM7 UniProt NPD GO	OPSG3_BRARE	Green-sensitive opsin-3 (Green cone photoreceptor pigment 3) (Opsin-1, medium-wave-sensitive 3) (Ops ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein				349
Q9W6A6 UniProt NPD GO	OPSG4_BRARE	Green-sensitive opsin-4 (Green cone photoreceptor pigment 4) (Opsin-1, medium-wave-sensitive 4) (Ops ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			349
Q9WTQ7 UniProt NPD GO	GA45G_RAT	Growth arrest and DNA-damage-inducible protein GADD45 gamma	0.01	-	cyt	0					159
O95257 UniProt NPD GO	GA45G_HUMAN	Growth arrest and DNA-damage-inducible protein GADD45 gamma (Cytokine-responsive protein CR6)	0.01	-	cyt	0			604949		159
Q9Z111 UniProt NPD GO	GA45G_MOUSE	Growth arrest and DNA-damage-inducible protein GADD45 gamma (Cytokine-responsive protein CR6)	0.01	-	cyt	0		nucleus [TAS]			159
P84863 UniProt NPD GO	PENT_ANTYA	Growth-suppressing pentapeptide	0.01	-		0					5
P46443 UniProt NPD GO	GUAM_HIRNI	Guamerin	0.01	-	nuc	0	Secreted protein				57
Q6PBF6 UniProt NPD GO	GAMT_XENTR	Guanidinoacetate N-methyltransferase (EC 2.1.1.2)	0.01	-	cyt	0					232
Q7ZXG7 UniProt NPD GO	GAMTA_XENLA	Guanidinoacetate N-methyltransferase A (EC 2.1.1.2)	0.01	-	cyt	0					233
Q5HZ68 UniProt NPD GO	GAMTB_XENLA	Guanidinoacetate N-methyltransferase B (EC 2.1.1.2)	0.01	-	cyt	0					233
Q9R111 UniProt NPD GO	GUAD_MOUSE	Guanine deaminase (EC 3.5.4.3) (Guanase) (Guanine aminase) (Guanine aminohydrolase) (GAH)	0.01	-	vac	0					454
Q9Y2T3 UniProt NPD GO	GUAD_HUMAN	Guanine deaminase (EC 3.5.4.3) (Guanase) (Guanine aminase) (Guanine aminohydrolase) (GAH) (p51-nedas ...	0.01	-	cyt	0		intracellular [TAS]	139260		454
Q9P2W3 UniProt NPD GO	GBG13_HUMAN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-13 subunit precursor	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		607298		67
P50154 UniProt NPD GO	GBGT2_BOVIN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-T2 subunit precursor (G gamma-C) (G-gamma-8) ...	0.01	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				69
O14610 UniProt NPD GO	GBGT2_HUMAN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-T2 subunit precursor (G gamma-C) (G-gamma-8) ...	0.01	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	extracellular region [NAS] heterotrimeric G-protein complex [NAS]	603655		69
O97564 UniProt NPD GO	GBGT2_CANFA	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-T2 subunit precursor (G gamma-C) (Tgamma c)	0.01	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				69
P02698 UniProt NPD GO	GBG1_BOVIN	Guanine nucleotide-binding protein G(T) gamma-T1 subunit precursor (Transducin gamma chain)	0.01	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)			2TRC	73
P49027 UniProt NPD GO	GBLP_ORYSA	Guanine nucleotide-binding protein subunit beta-like protein (GPB-LR) (RWD)	0.01	-	cyt	0					334
P38011 UniProt NPD GO	GBLP_YEAST	Guanine nucleotide-binding protein subunit beta-like protein (Receptor of activated protein kinase C ...	0.01	-	cyt	0	Cytoplasm	cytoplasm [IDA] cytosolic small ribosomal subunit (sensu Eu... [IDA]		1TRJ	318
P00653 UniProt NPD GO	RNMS_ASPSA	Guanyl-specific ribonuclease Ms (EC 3.1.27.3) (RNase Ms)	0.01	-	cyt	0				1RMS	105
P55936 UniProt NPD GO	GUC2A_DIDMA	Guanylin (Guanylate cyclase activator 2A)	0.01	-		0	Secreted protein				15
Q02747 UniProt NPD GO	GUC2A_HUMAN	Guanylin precursor (Guanylate cyclase activator 2A) (Guanylate cyclase-activating protein 1) (Gap-I) ...	0.01	-	exc	1 *	Secreted protein	extracellular region [NAS]	139392	1O8R	115
P15686 UniProt NPD GO	HUP1_CHLKE	H(+)/hexose cotransporter 1	0.01	-	end	12 *	Membrane; multi-pass membrane protein				534
P62687 UniProt NPD GO	GAK14_HUMAN	HERV-K_16p3.3 provirus ancestral Gag polyprotein (Gag polyprotein)	0.01	-	cyt	0					119
P61568 UniProt NPD GO	ENK13_HUMAN	HERV-K_1p13.3 provirus ancestral Env polyprotein (Envelope polyprotein) [Includes: Truncated surface ...	0.01	-	cyt	0					191
Q5NVQ1 UniProt NPD GO	HIG1A_PONPY	HIG1 domain family member 1A	0.01	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				93
Q9Y241 UniProt NPD GO	HIG1A_HUMAN	HIG1 domain family member 1A (Hypoxia-inducible gene 1 protein)	0.01	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				93
P28067 UniProt NPD GO	2DMA_HUMAN	HLA class II histocompatibility antigen, DM alpha chain precursor (MHC class II antigen DMA)	0.01	-	cyt	1	Endosome; late endosome; late endosomal membrane; single-pass type I membrane protein. Lysosome; lys ...		142855	1HDM	261
P06340 UniProt NPD GO	2DOA_HUMAN	HLA class II histocompatibility antigen, DO alpha chain precursor (MHC class II antigen DOA) (MHC DZ ...	0.01	-	nuc	1	Membrane; single-pass type I membrane protein	plasma membrane [TAS]	142930		250
P01907 UniProt NPD GO	HA25_HUMAN	HLA class II histocompatibility antigen, DQ(5) alpha chain precursor (DC-1 alpha chain)	0.01	-	end	1	Membrane; single-pass type I membrane protein (Potential)				255
Q9HDD0 UniProt NPD GO	HRSL1_HUMAN	HRAS-like suppressor	0.01	-	cyt	0			606487		168
Q9NWW9 UniProt NPD GO	HRSL2_HUMAN	HRAS-like suppressor 2	0.01	-	cyt	1					162
Q9FED2 UniProt NPD GO	HA22E_ARATH	HVA22-like protein e (AtHVA22e)	0.01	-	cyt	3 *	Membrane; multi-pass membrane protein (Potential)				116
Q6NLY8 UniProt NPD GO	HA22K_ARATH	HVA22-like protein k (AtHVA22k)	0.01	-	cyt	0					200
P84286 UniProt NPD GO	HPOR_APLCA	Haemoporin (Fragment)	0.01	-		0	Secreted protein				20
P83705 UniProt NPD GO	HLOA_HALAU	Halocidin subunit A	0.01	-		0	Secreted protein	extracellular region [IC]			18
P83706 UniProt NPD GO	HLOB_HALAU	Halocidin subunit B	0.01	-		0	Secreted protein	extracellular region [IC]			15
Q60574 UniProt NPD GO	HPT_MUSCR	Haptoglobin precursor [Contains: Haptoglobin alpha chain; Haptoglobin beta chain]	0.01	-	end	0	Secreted protein (By similarity)				347
Q62558 UniProt NPD GO	HPT_MUSSA	Haptoglobin precursor [Contains: Haptoglobin alpha chain; Haptoglobin beta chain]	0.01	-	end	0	Secreted protein (By similarity)				347
P19007 UniProt NPD GO	HPT_RABIT	Haptoglobin precursor [Contains: Haptoglobin alpha chain; Haptoglobin beta chain]	0.01	-	exc	0	Secreted protein				347
P18694 UniProt NPD GO	HSP72_USTMA	Heat shock 70 kDa protein 2 (Fragment)	0.01	-	cyt	0					90
P55938 UniProt NPD GO	HSP71_LEITA	Heat shock 70-related protein 1, mitochondrial (Fragment)	0.01	-	cyt	0	Mitochondrion				22
P84588 UniProt NPD GO	HSP7D_RAT	Heat shock cognate 71 kDa protein 2 (Fragment)	0.01	-		0	Nucleus; nucleoplasm; nuclear matrix				13
Q00398 UniProt NPD GO	AG19_COCIM	Heat-stable 19 kDa antigen precursor (CS-AG)	0.01	-	exc	0	Secreted protein				181
P83425 UniProt NPD GO	HIP_MYTED	Heavy metal-binding protein HIP	0.01	-	cyt	0	Secreted protein				213
Q9NRV9 UniProt NPD GO	HEBP1_HUMAN	Heme-binding protein 1 (p22HBP)	0.01	-	cyt	0	Cytoplasm		605826		189
P23543 UniProt NPD GO	HEMTA_LINRE	Hemerythrin alpha chain	0.01	-	cyt	0					117
P22764 UniProt NPD GO	HEMTA_LINUN	Hemerythrin alpha chain	0.01	-	cyt	0					117
Q9NH76 UniProt NPD GO	HEMTL_NAEFO	Hemerythrin-like protein	0.01	-	cyt	0					119
Q10583 UniProt NPD GO	HCYA_MEGCR	Hemocyanin A chain (KLH-A) (Fragment)	0.01	-		0	Secreted protein; extracellular space				14

You are viewing entries 88601 to 88650 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.