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
O77714 UniProt NPD GO	AQP2_DUGDU	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein				109
P79168 UniProt NPD GO	AQP2_ELEMA	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein				109
O77722 UniProt NPD GO	AQP2_ERIEU	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein				109
P79165 UniProt NPD GO	AQP2_HORSE	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein				109
P79803 UniProt NPD GO	AQP2_MACPR	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein				111
P79200 UniProt NPD GO	AQP2_ORYAF	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein				109
P79229 UniProt NPD GO	AQP2_PROHA	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein				109
P79213 UniProt NPD GO	AQP2_RABIT	Aquaporin-2 (AQP-2) (Aquaporin-CD) (AQP-CD) (Water channel protein for renal collecting duct) (ADH w ...	0.00	-	end	3 *	Membrane; multi-pass membrane protein				109
Q8C4A0 UniProt NPD GO	AQP6_MOUSE	Aquaporin-6 (AQP-6)	0.00	-	nuc	6 *	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS]			293
Q9WTY0 UniProt NPD GO	AQP6_RAT	Aquaporin-6 (AQP-6)	0.00	-	nuc	6 *	Cytoplasmic vesicle; cytoplasmic vesicle membrane; multi-pass membrane protein				276
O54794 UniProt NPD GO	AQP7_MOUSE	Aquaporin-7 (AQP-7)	0.00	-	nuc	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			303
P56403 UniProt NPD GO	AQP7_RAT	Aquaporin-7 (AQP-7)	0.00	-	nuc	6 *	Cell membrane; multi-pass membrane protein. Plasma membrane of spermatids				269
O94778 UniProt NPD GO	AQP8_HUMAN	Aquaporin-8 (AQP-8)	0.00	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	603750		261
P56404 UniProt NPD GO	AQP8_MOUSE	Aquaporin-8 (AQP-8)	0.00	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			261
Q9JJJ3 UniProt NPD GO	AQP9_MOUSE	Aquaporin-9 (AQP-9)	0.00	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS]			295
O43315 UniProt NPD GO	AQP9_HUMAN	Aquaporin-9 (AQP-9) (Small solute channel 1)	0.00	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [ISS]	602914		295
P20292 UniProt NPD GO	FLAP_HUMAN	Arachidonate 5-lipoxygenase-activating protein (FLAP) (MK-886-binding protein)	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)		608557		161
P30355 UniProt NPD GO	FLAP_MOUSE	Arachidonate 5-lipoxygenase-activating protein (FLAP) (MK-886-binding protein)	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				161
P20291 UniProt NPD GO	FLAP_RAT	Arachidonate 5-lipoxygenase-activating protein (FLAP) (MK-886-binding protein)	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	membrane [TAS]			161
P30354 UniProt NPD GO	FLAP_MACMU	Arachidonate 5-lipoxygenase-activating protein (FLAP) (MK-886-binding protein) (Fragment)	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				153
P83572 UniProt NPD GO	ARALA_ARAEL	Aralin A chain (EC 3.2.2.22) (rRNA N-glycosidase) (Fragment)	0.00	-	cyt	0					25
Q12611 UniProt NPD GO	ARGI_EMENI	Arginase (EC 3.5.3.1)	0.00	-	cyt	0					323
P40329 UniProt NPD GO	SYR_RAT	Arginyl-tRNA synthetase (EC 6.1.1.19) (Arginine--tRNA ligase) (ArgRS) (Fragment)	0.00	-		0	Cytoplasm				20
O96567 UniProt NPD GO	DDC_DROSI	Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) (AADC) (DOPA decarboxylase) (DDC)	0.00	-	cyt	0					510
Q32KH9 UniProt NPD GO	ARSG_CANFA	Arylsulfatase G precursor (EC 3.1.6.-) (ASG)	0.00	-	end	0	Endoplasmic reticulum (By similarity)				535
P84071 UniProt NPD GO	ASCL_ALLAS	Ascalin (Fragment)	0.00	-		0					7
P28011 UniProt NPD GO	AAT1_MEDSA	Aspartate aminotransferase 1 (EC 2.6.1.1) (Transaminase A)	0.00	-	cyt	0	Cytoplasm				418
P42999 UniProt NPD GO	OXYA_SQUAC	Aspartocin (Aspargtocin)	0.00	-		0	Secreted protein				9
Q06902 UniProt NPD GO	PEPA_ASPOR	Aspergillopepsin A precursor (EC 3.4.23.18) (Aspergillopepsin O)	0.00	-	mit	0	Secreted protein				404
P84749 UniProt NPD GO	PEP18_ARGAU	Astacin-like peptidase p18 (EC 3.4.24.-) (Fragment)	0.00	-		0					20
P42996 UniProt NPD GO	OXYA_SCYCA	Asvatocin	0.00	-		0	Secreted protein				9
P01513 UniProt NPD GO	ATTE_HYACE	Attacin-E precursor (Immune protein P5) [Contains: Attacin-F]	0.00	-	exc	0	Secreted protein				235
P82386 UniProt NPD GO	AUR11_LITRA	Aurein-1.1	0.00	-		0	Secreted protein				13
P82387 UniProt NPD GO	AUR12_LITRA	Aurein-1.2	0.00	-		0	Secreted protein				13
P69017 UniProt NPD GO	AUR21_LITAU	Aurein-2.1 [Contains: Aurein-2.1.1]	0.00	-		0	Secreted protein				16
P69016 UniProt NPD GO	AUR21_LITRA	Aurein-2.1 [Contains: Aurein-2.1.1]	0.00	-		0	Secreted protein				16
P82389 UniProt NPD GO	AUR22_LITAU	Aurein-2.2 [Contains: Aurein-2.2.1]	0.00	-		0	Secreted protein				16
P82390 UniProt NPD GO	AUR23_LITAU	Aurein-2.3	0.00	-		0	Secreted protein				16
P82391 UniProt NPD GO	AUR24_LITAU	Aurein-2.4 [Contains: Aurein-2.4.1]	0.00	-		0	Secreted protein				16
P69019 UniProt NPD GO	AUR25_LITAU	Aurein-2.5	0.00	-		0	Secreted protein				16
P69018 UniProt NPD GO	AUR25_LITRA	Aurein-2.5	0.00	-		0	Secreted protein				16
P82393 UniProt NPD GO	AUR26_LITRA	Aurein-2.6	0.00	-		0	Secreted protein				16
P82397 UniProt NPD GO	AUR41_LITAU	Aurein-4.1	0.00	-	cyt	0	Secreted protein				23
P69025 UniProt NPD GO	AUR42_LITAU	Aurein-4.2	0.00	-	cyt	0	Secreted protein				23
P69024 UniProt NPD GO	AUR42_LITRA	Aurein-4.2	0.00	-	cyt	0	Secreted protein				23
P82399 UniProt NPD GO	AUR43_LITAU	Aurein-4.3	0.00	-	cyt	0	Secreted protein				23
P69027 UniProt NPD GO	AUR44_LITAU	Aurein-4.4	0.00	-	cyt	0	Secreted protein				23
P69026 UniProt NPD GO	AUR44_LITRA	Aurein-4.4	0.00	-	cyt	0	Secreted protein				23
P69029 UniProt NPD GO	AUR51_LITAU	Aurein-5.1	0.00	-	nuc	0	Secreted protein				25
P69028 UniProt NPD GO	AUR51_LITRA	Aurein-5.1	0.00	-	nuc	0	Secreted protein				25

You are viewing entries 92751 to 92800 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.