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
P56535 UniProt NPD GO	UHA3_CANFA	Unknown protein from 2D-PAGE of heart tissue (Spot 7520) (Fragment)	0.00	-		0					13
P56573 UniProt NPD GO	UH05_RAT	Unknown protein from 2D-PAGE of heart tissue (Spot P5) (Fragment)	0.00	-		0					10
P31934 UniProt NPD GO	ULAH_HUMAN	Unknown protein from 2D-PAGE of liver tissue (Spot 94) (Fragment)	0.00	-		0					9
P81670 UniProt NPD GO	UN03_PINPS	Unknown protein from 2D-PAGE of needles (N140) (Fragments)	0.00	-	cyt	0					53
P81667 UniProt NPD GO	UN02_PINPS	Unknown protein from 2D-PAGE of needles (N55) (Fragments)	0.00	-		0					13
P30088 UniProt NPD GO	UPA2_HUMAN	Unknown protein from 2D-PAGE of plasma (Spot 10) (Fragment)	0.00	-		0					10
P30089 UniProt NPD GO	UPA3_HUMAN	Unknown protein from 2D-PAGE of plasma (Spot 11) (Fragment)	0.00	-		0					9
P30093 UniProt NPD GO	UPA7_HUMAN	Unknown protein from 2D-PAGE of plasma (Spot 18) (Fragment)	0.00	-		0					9
P30094 UniProt NPD GO	UPA8_HUMAN	Unknown protein from 2D-PAGE of plasma (Spot 34) (Fragment)	0.00	-		0					10
P30096 UniProt NPD GO	UPA10_HUMAN	Unknown protein from 2D-PAGE of plasma (Spot 36) (Fragment)	0.00	-		0					8
P34990 UniProt NPD GO	URA7_HUMAN	Unknown protein from 2D-PAGE of red blood cells (Spot 2D-006HO) (Fragment)	0.00	-		0					10
P82323 UniProt NPD GO	UT104_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 104) (Fragments)	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid				31
P82327 UniProt NPD GO	UT108_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 108) (Fragment)	0.00	-		0	Plastid; chloroplast; chloroplast thylakoid				14
P82329 UniProt NPD GO	UT111_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 111) (Fragment)	0.00	-		0	Plastid; chloroplast; chloroplast thylakoid				12
P82335 UniProt NPD GO	UT119_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 119) (Fragment)	0.00	-		0	Plastid; chloroplast; chloroplast thylakoid				14
P82336 UniProt NPD GO	UT125_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 125) (Fragment)	0.00	-		0	Plastid; chloroplast; chloroplast thylakoid				11
Q3ZBI7 UniProt NPD GO	USMG5_BOVIN	Up-regulated during skeletal muscle growth protein 5	0.00	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				58
Q96IX5 UniProt NPD GO	USMG5_HUMAN	Up-regulated during skeletal muscle growth protein 5 (HCV F-transactivated protein 2)	0.00	-	cyt	1 *	Membrane; single-pass membrane protein (Potential)				58
P82027 UniProt NPD GO	UPE21_UPEIN	Uperin-2.1	0.00	-		0	Secreted protein				19
P82028 UniProt NPD GO	UPE22_UPEIN	Uperin-2.2	0.00	-		0	Secreted protein				19
P82029 UniProt NPD GO	UPE23_UPEIN	Uperin-2.3	0.00	-		0	Secreted protein				19
P82030 UniProt NPD GO	UPE24_UPEIN	Uperin-2.4	0.00	-		0	Secreted protein				19
P82031 UniProt NPD GO	UPE25_UPEIN	Uperin-2.5	0.00	-		0	Secreted protein				19
P82095 UniProt NPD GO	UPE26_UPEMJ	Uperin-2.6	0.00	-		0	Secreted protein				19
P82039 UniProt NPD GO	UPE27_UPEMJ	Uperin-2.7	0.00	-		0	Secreted protein				19
P82040 UniProt NPD GO	UPE28_UPEMJ	Uperin-2.8	0.00	-		0	Secreted protein				19
P82034 UniProt NPD GO	UPE33_UPEIN	Uperin-3.3	0.00	-		0	Secreted protein				17
P82043 UniProt NPD GO	UPE36_UPEMJ	Uperin-3.6	0.00	-		0	Secreted protein				17
P93394 UniProt NPD GO	UPP_TOBAC	Uracil phosphoribosyltransferase (EC 2.4.2.9) (UMP pyrophosphorylase) (UPRTase)	0.00	-	cyt	0					224
Q9ZPR6 UniProt NPD GO	UPS3_ARATH	Ureide permease 3 (AtUPS3)	0.00	-	end	8 *	Membrane; multi-pass membrane protein (Probable)				344
P32459 UniProt NPD GO	ALLA_YEAST	Ureidoglycolate hydrolase (EC 3.5.3.19)	0.00	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				195
P02729 UniProt NPD GO	GLUR_HUMAN	Urine glycopeptide	0.00	-		0		extracellular region [NAS]			8
O00526 UniProt NPD GO	UPK2_HUMAN	Uroplakin-2 precursor (UP 2) (Uroplakin II) (UPII)	0.00	-	end	1 *	Membrane; single-pass type I membrane protein (Potential). Heterodimer formation with Uroplakin Ia i ...	integral to plasma membrane [TAS]			184
Q95L04 UniProt NPD GO	UPK2_PIG	Uroplakin-2 precursor (UP 2) (Uroplakin II) (UPII)	0.00	-	end	1 *	Membrane; single-pass type I membrane protein (Potential). Heterodimer formation with Uroplakin Ia i ...				184
P58418 UniProt NPD GO	USH3A_HUMAN	Usher syndrome type-3 protein	0.00	-	end	2 *	Membrane; multi-pass membrane protein (Potential)		606397		120
Q96PL1 UniProt NPD GO	SG3A2_HUMAN	Uteroglobin-related protein 1 precursor (Secretoglobin family 3A member 2) (Pneumo secretory protein ...	0.00	-	cyt	0	Secreted protein		606531		93
Q96QR1 UniProt NPD GO	SG3A1_HUMAN	Uteroglobin-related protein 2 precursor (Cytokine HIN-1) (High in normal-1) (Secretoglobin family 3A ...	0.00	-	vac	0	Secreted protein	extracellular region [NAS]	606500		104
Q17046 UniProt NPD GO	VATL_ASCSU	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				161
Q00607 UniProt NPD GO	VATL_CANTR	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				160
P55277 UniProt NPD GO	VATL_HELVI	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				156
P27449 UniProt NPD GO	VATL_HUMAN	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein	integral to membrane [TAS]	108745		155
Q26250 UniProt NPD GO	VATL_NEPNO	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				159
P31413 UniProt NPD GO	VATL_NEUCR	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14)	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				161
Q03105 UniProt NPD GO	VATL_TORMA	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14) (15 kDa mediatophore protein)	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein				154
Q41773 UniProt NPD GO	VATL_MAIZE	Vacuolar ATP synthase 16 kDa proteolipid subunit (EC 3.6.3.14) (V-ATPase 16 kDa proteolipid subunit) ...	0.00	-	end	3 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				109
Q21898 UniProt NPD GO	VATL1_CAEEL	Vacuolar ATP synthase 16 kDa proteolipid subunit 1 (EC 3.6.3.14)	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein	integral to membrane [NAS]			169
Q755G4 UniProt NPD GO	VATL2_ASHGO	Vacuolar ATP synthase 16 kDa proteolipid subunit 2 (EC 3.6.3.14) (Proteolipid protein VMA11)	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				164
Q6FUY5 UniProt NPD GO	VATL2_CANGA	Vacuolar ATP synthase 16 kDa proteolipid subunit 2 (EC 3.6.3.14) (Proteolipid protein VMA11)	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				164
Q6BSB9 UniProt NPD GO	VATL2_DEBHA	Vacuolar ATP synthase 16 kDa proteolipid subunit 2 (EC 3.6.3.14) (Proteolipid protein VMA11)	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				163
Q6CT28 UniProt NPD GO	VATL2_KLULA	Vacuolar ATP synthase 16 kDa proteolipid subunit 2 (EC 3.6.3.14) (Proteolipid protein VMA11)	0.00	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				165

You are viewing entries 98601 to 98650 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.