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
P30983 UniProt NPD GO	GLHA_CTEID	Glycoprotein hormones alpha chain precursor (Gonadotropin alpha chain) (GTH-alpha)	0.03	-	exc	1 *	Secreted protein				118
P37037 UniProt NPD GO	GLHA_HYPMO	Glycoprotein hormones alpha chain precursor (Gonadotropin alpha chain) (GTH-alpha)	0.03	-	exc	1 *	Secreted protein				118
Q74ZU2 UniProt NPD GO	TVP15_ASHGO	Golgi apparatus membrane protein TVP15	0.03	-	end	3 *	Golgi apparatus; Golgi apparatus membrane; multi-pass membrane protein (By similarity)				143
P53192 UniProt NPD GO	GET1_YEAST	Golgi to ER traffic protein 1 (Mitochondrial distribution and morphology protein 39)	0.03	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...	endoplasmic reticulum [IDA] GET complex [IMP]			235
Q96P88 UniProt NPD GO	GNRR2_HUMAN	Gonadotropin-releasing hormone II receptor (Type II GnRH receptor) (GnRH-II-R)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				379
P09842 UniProt NPD GO	SSG1_HORVU	Granule-bound starch synthase 1, chloroplast precursor (EC 2.4.1.242) (Granule-bound starch synthase ...	0.03	-	cyt	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Granule-bound				603
P04713 UniProt NPD GO	SSG1_MAIZE	Granule-bound starch synthase 1, chloroplast precursor (EC 2.4.1.242) (Granule-bound starch synthase ...	0.03	-	cyt	0	Or: Plastid; chloroplast. Granule-bound. Or: Plastid; amyloplast. Granule-bound				605
P28683 UniProt NPD GO	OPSG_CHICK	Green-sensitive opsin (Green cone photoreceptor pigment)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				355
P48076 UniProt NPD GO	PA2GC_MOUSE	Group IIC secretory phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase GII ...	0.03	-	mit	1 *	Secreted protein (Potential)				150
Q2KIX1 UniProt NPD GO	GA45G_BOVIN	Growth arrest and DNA-damage-inducible protein GADD45 gamma	0.03	-	cyt	0					159
Q27913 UniProt NPD GO	GBP_PSESE	Growth-blocking peptide precursor (GBP)	0.03	-	nuc	0				1BQF	143
P84835 UniProt NPD GO	TXG1E_PLEGU	Guangxitoxin-1E (GxTX-1E)	0.03	-	cyt	0	Secreted protein				36
O35969 UniProt NPD GO	GAMT_MOUSE	Guanidinoacetate N-methyltransferase (EC 2.1.1.2)	0.03	-	cyt	0					236
Q9U1X4 UniProt NPD GO	MSS4_CAEEL	Guanine nucleotide exchange factor MSS4 homolog	0.03	-	cyt	0					98
Q9JMF3 UniProt NPD GO	GBG13_MOUSE	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-13 subunit precursor	0.03	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	heterotrimeric G-protein complex [IPI] membrane [TAS]			67
Q61016 UniProt NPD GO	GBG7_MOUSE	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-7 subunit precursor	0.03	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				68
Q10282 UniProt NPD GO	GBB_SCHPO	Guanine nucleotide-binding protein subunit beta	0.03	-	cyt	0		heterotrimeric G-protein complex [TAS]			305
Q7M515 UniProt NPD GO	RNA1_ASPPL	Guanyl-specific ribonuclease Ap1 (EC 3.1.27.3) (RNase Ap1) (ApI)	0.03	-	nuc	0	Secreted protein				104
P00651 UniProt NPD GO	RNT1_ASPOR	Guanyl-specific ribonuclease T1 precursor (EC 3.1.27.3) (RNase T1)	0.03	-	exc	0				9RNT	130
P07736 UniProt NPD GO	RNU1_USTSP	Guanyl-specific ribonuclease U1 (EC 3.1.27.3) (RNase U1)	0.03	-	nuc	0					105
Q39525 UniProt NPD GO	HUP3_CHLKE	H(+)/hexose cotransporter 3	0.03	-	end	12 *	Membrane; multi-pass membrane protein				534
P01908 UniProt NPD GO	HA21_HUMAN	HLA class II histocompatibility antigen, DQ(1) alpha chain precursor (DC-4 alpha chain)	0.03	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				255
P04226 UniProt NPD GO	HA22_HUMAN	HLA class II histocompatibility antigen, DQ(2) alpha chain precursor	0.03	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [NAS]			254
P01909 UniProt NPD GO	HA23_HUMAN	HLA class II histocompatibility antigen, DQ(3) alpha chain precursor (DC-alpha) (HLA-DCA) (HLA-DQA1* ...	0.03	-	end	1	Membrane; single-pass type I membrane protein (Potential)		146880	1S9V	254
P04225 UniProt NPD GO	HA24_HUMAN	HLA class II histocompatibility antigen, DQ(4) alpha chain precursor (DQ-DRW9 alpha chain) (Fragment ...	0.03	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)		146880	1JK8	232
P05536 UniProt NPD GO	HA27_HUMAN	HLA class II histocompatibility antigen, DQ(W3) alpha chain precursor	0.03	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [NAS]			254
P38074 UniProt NPD GO	HMT1_YEAST	HNRNP arginine N-methyltransferase (EC 2.1.1.-) (Protein ODP1)	0.03	-	nuc	0		nucleus [IDA]		1G6Q	348
Q8R3U1 UniProt NPD GO	HRSL3_MOUSE	HRAS-like suppressor 3 (H-rev 107 protein)	0.03	-	nuc	1					162
Q682H0 UniProt NPD GO	HA22F_ARATH	HVA22-like protein f (AtHVA22f)	0.03	-	cyt	2 *	Membrane; multi-pass membrane protein (Potential)				158
P60975 UniProt NPD GO	TXHA5_SELHA	Hainantoxin-5 (Hainantoxin-V) (HnTX-V)	0.03	-	nuc	0	Secreted protein				35
P81161 UniProt NPD GO	HS22M_LYCES	Heat shock 22 kDa protein, mitochondrial (Fragments)	0.03	-	cyt	0	Mitochondrion				56
Q6SJQ8 UniProt NPD GO	HSPB8_MACMU	Heat-shock protein beta-8 (HspB8) (Protein kinase H11)	0.03	-	nuc	0					195
Q6CIK2 UniProt NPD GO	HOT13_KLULA	Helper of Tim protein 13	0.03	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity). Mitochondrion; mitochondrial membr ...				114
O70453 UniProt NPD GO	HMOX3_RAT	Heme oxygenase 3 (EC 1.14.99.3) (HO-3)	0.03	-	cyt	1	Microsome				290
P80096 UniProt NPD GO	HCYC_PANIN	Hemocyanin C chain	0.03	-	cyt	0	Secreted protein; extracellular space				661
P02022 UniProt NPD GO	HBAM_RANCA	Hemoglobin heart muscle subunit alpha-type (Hemoglobin alpha-type chain, heart muscle)	0.03	-	cyt	0					132
P18969 UniProt NPD GO	HBA_AILFU	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.03	-	cyt	0					141
P01963 UniProt NPD GO	HBA_CERSI	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.03	-	cyt	0					141
Q9XSE9 UniProt NPD GO	HBA_EQUPR	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.03	-	cyt	0					141
P02021 UniProt NPD GO	HBA_HETPO	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.03	-	cyt	0					148
P19015 UniProt NPD GO	HBA_HIPAM	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.03	-	cyt	0					141
P01958 UniProt NPD GO	HBA_HORSE	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.03	-	cyt	0				2MHB	141
P26915 UniProt NPD GO	HBA_NASNA	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.03	-	cyt	0					141
P63111 UniProt NPD GO	HBA_PAPAN	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.03	-	cyt	0					141
P63112 UniProt NPD GO	HBA_PAPCY	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.03	-	cyt	0					141
P28780 UniProt NPD GO	HBA_TAPGE	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.03	-	cyt	0					141
P01932 UniProt NPD GO	HBA_THEGE	Hemoglobin subunit alpha (Hemoglobin alpha chain) (Alpha-globin)	0.03	-	cyt	0					141
P01967 UniProt NPD GO	HBA1_BOSMU	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin)	0.03	-	cyt	0					141
Q9TSN7 UniProt NPD GO	HBA1_BUBBU	Hemoglobin subunit alpha-1 (Hemoglobin alpha-1 chain) (Alpha-1-globin) (Ialpha1)	0.03	-	cyt	0					141
P21768 UniProt NPD GO	HBA_MACSI	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin)	0.03	-	cyt	0					141

You are viewing entries 80101 to 80150 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.