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
Q96P67 UniProt NPD GO	GPR82_HUMAN	Probable G-protein coupled receptor 82	0.25	-	end	6 *	Membrane; multi-pass membrane protein		606924		336
P60893 UniProt NPD GO	GPR85_HUMAN	Probable G-protein coupled receptor 85 (Super conserved receptor expressed in brain 2)	0.25	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)		605188		370
P60894 UniProt NPD GO	GPR85_MOUSE	Probable G-protein coupled receptor 85 (Super conserved receptor expressed in brain 2)	0.25	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				370
P60895 UniProt NPD GO	GPR85_RAT	Probable G-protein coupled receptor 85 (Super conserved receptor expressed in brain 2) (PKrCx1)	0.25	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				370
Q10907 UniProt NPD GO	YWO4_CAEEL	Probable G-protein coupled receptor AH9.4	0.25	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				364
Q8GYD9 UniProt NPD GO	SDE3_ARATH	Probable RNA helicase SDE3 (EC 3.6.1.-) (Silencing defective protein 3)	0.25	-	nuc	0	Cytoplasm (Probable)				1002
O14352 UniProt NPD GO	LSM4_SCHPO	Probable U6 snRNA-associated Sm-like protein LSm4	0.25	-	nuc	0	Nucleus (Potential)				121
P53051 UniProt NPD GO	MALX3_YEAST	Probable alpha-glucosidase FSP2 (EC 3.2.1.20) (Maltase) (Flocculent-specific protein 2)	0.25	-	cyt	0		mitochondrion [IDA]			589
P50514 UniProt NPD GO	ARLZ_SCHPO	Probable argininosuccinate lyase (EC 4.3.2.1) (Arginosuccinase) (ASAL)	0.25	-	cyt	0					460
Q21286 UniProt NPD GO	YBF7_CAEEL	Probable cation-transporting ATPase K07E3.7 in chromosome X (EC 3.6.3.-)	0.25	-	end	11	Membrane; multi-pass membrane protein				1203
Q8NJJ3 UniProt NPD GO	ATG4_PICPA	Probable cysteine protease ATG4 (EC 3.4.22.-) (Autophagy-related protein 4) (Pexophagy zeocin-resist ...	0.25	-	cyt	0	Cytoplasm (By similarity)				533
Q9V675 UniProt NPD GO	CP6G2_DROME	Probable cytochrome P450 6g2 (EC 1.14.-.-) (CYPVIG2)	0.25	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				519
Q9XV52 UniProt NPD GO	EFGM_CAEEL	Probable elongation factor G, mitochondrial precursor (mEF-G)	0.25	-	nuc	0	Mitochondrion (By similarity)				750
Q9VM33 UniProt NPD GO	EFGM_DROME	Probable elongation factor G, mitochondrial precursor (mEF-G)	0.25	-	nuc	0	Mitochondrion (By similarity)	mitochondrion [NAS]			745
Q9CXN7 UniProt NPD GO	MAWB1_MOUSE	Probable isomerase MAWBP-1 (EC 5.1.-.-)	0.25	-	cyt	0					288
Q5RDP4 UniProt NPD GO	SYLM_PONPY	Probable leucyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.4) (Leucine--tRNA ligase) (LeuRS) ...	0.25	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				903
P13080 UniProt NPD GO	MALT_AEDAE	Probable maltase precursor (EC 3.2.1.20)	0.25	-	nuc	0					579
P53320 UniProt NPD GO	YG5F_YEAST	Probable mitochondrial carrier YGR257C	0.25	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			366
Q9VCI0 UniProt NPD GO	ORN_DROME	Probable oligoribonuclease (EC 3.1.-.-)	0.25	-	mit	0					211
O14228 UniProt NPD GO	PUR4_SCHPO	Probable phosphoribosylformylglycinamidine synthase (EC 6.3.5.3) (FGAM synthase) (FGAMS) (Formylglyc ...	0.25	-	mit	0	Cytoplasm (By similarity)	cytoplasm [IDA]			1323
O14334 UniProt NPD GO	PFD1_SCHPO	Probable prefoldin subunit 1	0.25	-	nuc	0					112
Q9VW56 UniProt NPD GO	PFD6_DROME	Probable prefoldin subunit 6	0.25	-	nuc	0					125
Q9LJI5 UniProt NPD GO	VA0D1_ARATH	Probable vacuolar ATP synthase subunit d 1 (EC 3.6.3.14) (V-ATPase d subunit 1) (Vacuolar proton pum ...	0.25	-	cyt	0					351
Q9LHA4 UniProt NPD GO	VA0D2_ARATH	Probable vacuolar ATP synthase subunit d 2 (EC 3.6.3.14) (V-ATPase d subunit 2) (Vacuolar proton pum ...	0.25	-	cyt	0					351
Q9DG36 UniProt NPD GO	GON2_RANCA	Progonadoliberin-2 precursor (Progonadoliberin II) [Contains: Gonadoliberin-2 (Gonadoliberin II) (LH ...	0.25	-	nuc	1 *	Secreted protein	extracellular region [NAS]			93
O42241 UniProt NPD GO	GON2_ONCMY	Progonadoliberin-2 precursor (Progonadoliberin II) [Contains: Gonadoliberin-2 (Gonadoliberin II) (Lu ...	0.25	-	vac	0	Secreted protein				86
Q8NFJ6 UniProt NPD GO	PKR2_HUMAN	Prokineticin receptor 2 (PK-R2) (G-protein coupled receptor 73-like 1) (GPR73b) (GPRg2)	0.25	+	end	6	Membrane; multi-pass membrane protein		607123		384
P33089 UniProt NPD GO	PRL_BALBO	Prolactin (PRL)	0.25	-	cyt	0	Secreted protein				199
Q28318 UniProt NPD GO	PRL_CAPHI	Prolactin precursor (PRL)	0.25	-	nuc	0	Secreted protein				229
Q9QZL1 UniProt NPD GO	PRL_MICMO	Prolactin precursor (PRL)	0.25	-	exc	0	Secreted protein				225
O46561 UniProt NPD GO	PRLR_SHEEP	Prolactin receptor precursor (PRL-R) (OPR)	0.25	-	exc	2 *	Membrane; single-pass type I membrane protein	cell surface [ISS]			581
P50580 UniProt NPD GO	PA2G4_MOUSE	Proliferation-associated protein 2G4 (Proliferation-associated protein 1) (Protein p38-2G4) (Mpp1) ( ...	0.25	-	cyt	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)				393
P51524 UniProt NPD GO	PF11_PIG	Prophenin-1 precursor (PF-1) (C6) (Fragment)	0.25	-	exc	0	Secreted protein				212
Q29626 UniProt NPD GO	PTGIS_BOVIN	Prostacyclin synthase (EC 5.3.99.4) (Prostaglandin I2 synthase)	0.25	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				500
O16812 UniProt NPD GO	PSA73_DROVI	Proteasome subunit alpha type 7-1B (EC 3.4.25.1) (Testis-specific proteasome 28 kDa subunit 1B)	0.25	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				245
Q8W487 UniProt NPD GO	YB95_ARATH	Protein At2g39795, mitochondrial precursor	0.25	-	mit	0	Mitochondrion; mitochondrial matrix				250
Q8RXW0 UniProt NPD GO	Y3761_ARATH	Protein At3g17611	0.25	-	cyt	0	Membrane; multi-pass membrane protein (Potential)				334
Q96B45 UniProt NPD GO	CJ032_HUMAN	Protein C10orf32	0.25	-	nuc	0					105
Q99J19 UniProt NPD GO	CU051_MOUSE	Protein C21orf51 homolog	0.25	-	mit	1 *					55
Q86T20 UniProt NPD GO	CF001_HUMAN	Protein C6orf1 precursor	0.25	-	mit	0					159
Q96MT4 UniProt NPD GO	CF195_HUMAN	Protein C6orf195	0.25	-	nuc	0					127
Q5RAR5 UniProt NPD GO	CF096_PONPY	Protein C6orf96 homolog	0.25	-	nuc	0					449
Q99J23 UniProt NPD GO	LGP1_MOUSE	Protein D11Lgp1 precursor	0.25	-	end	1 *	Endoplasmic reticulum. Nucleus; nuclear envelope	endoplasmic reticulum [IDA]			532
Q5XGE4 UniProt NPD GO	F100B_XENTR	Protein FAM100B	0.25	-	nuc	0					166
Q6IP57 UniProt NPD GO	F00BA_XENLA	Protein FAM100B-A	0.25	-	nuc	0					166
Q6DD24 UniProt NPD GO	F00BB_XENLA	Protein FAM100B-B	0.25	-	nuc	0					165
Q8BS95 UniProt NPD GO	GPR89_MOUSE	Protein GPR89A	0.25	-	end	9 *	Membrane; multi-pass membrane protein				455
Q9Y302 UniProt NPD GO	GPR89_HUMAN	Protein GPR89A (Putative MAPK-activating protein PM01) (Putative NF-kappa-B-activating protein 90)	0.25	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				455
O60320 UniProt NPD GO	K0574_HUMAN	Protein KIAA0574 (Fragment)	0.25	-	nuc	1 *					405
Q9JK81 UniProt NPD GO	MYG1_MOUSE	Protein MYG1 (Protein Gamm1)	0.25	-	mit	0					380

You are viewing entries 45601 to 45650 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.