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
P26246 UniProt NPD GO	CYST_MARPO	Probable sulfate transport system permease protein cysT	0.01	-	end	7 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Probable)				288
Q9MUL9 UniProt NPD GO	CYST_MESVI	Probable sulfate transport system permease protein cysT	0.01	-	end	6 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Probable)				269
Q94LW6 UniProt NPD GO	SUT35_ARATH	Probable sulfate transporter 3.5	0.01	-	end	10	Membrane; multi-pass membrane protein (Potential)				634
P81082 UniProt NPD GO	SODCP_PINPS	Probable superoxide dismutase [Cu-Zn], chloroplast (EC 1.15.1.1) (Water stress-responsive protein 15 ...	0.01	-		0	Plastid; chloroplast				15
Q8VZK8 UniProt NPD GO	THN23_ARATH	Probable thionin-2.3 precursor [Contains: Probable thionin-2.3; Acidic protein]	0.01	-	nuc	0	Secreted protein (Potential)				135
P34605 UniProt NPD GO	TPPC3_CAEEL	Probable trafficking protein particle complex subunit 3	0.01	-	nuc	0	Golgi apparatus; cis-Golgi network (By similarity)				181
Q9XXC8 UniProt NPD GO	MECR2_CAEEL	Probable trans-2-enoyl-CoA reductase 2, mitochondrial precursor (EC 1.3.1.38)	0.01	-	mit	0	Mitochondrion (By similarity)				346
Q8LCU7 UniProt NPD GO	MECR_ARATH	Probable trans-2-enoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.38)	0.01	-	cyt	0	Mitochondrion	mitochondrion [IDA]			375
Q9V6U9 UniProt NPD GO	MECR_DROME	Probable trans-2-enoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.38)	0.01	-	mit	0	Mitochondrion (By similarity)	mitochondrion [ISS]			357
Q61E22 UniProt NPD GO	UFM1_CAEBR	Probable ubiquitin-fold modifier 1 precursor	0.01	-	cyt	0					93
P34661 UniProt NPD GO	UFM1_CAEEL	Probable ubiquitin-fold modifier 1 precursor	0.01	-	cyt	0				1L7Y	94
Q94EY2 UniProt NPD GO	UFM1_CHLRE	Probable ubiquitin-fold modifier 1 precursor (Protein PR46A)	0.01	-	cyt	0					96
Q23680 UniProt NPD GO	VATF_CAEEL	Probable vacuolar ATP synthase subunit F (EC 3.6.3.14) (V-ATPase F subunit) (Vacuolar proton pump F ...	0.01	-	cyt	0					121
Q21752 UniProt NPD GO	VDAC_CAEEL	Probable voltage-dependent anion-selective channel	0.01	-	nuc	0	Mitochondrion; mitochondrial outer membrane (By similarity)				283
P18764 UniProt NPD GO	PARA_TRYBB	Procyclic form-specific polypeptide A-alpha precursor (Procyclin A-alpha) (PARP A-alpha)	0.01	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor				114
P09791 UniProt NPD GO	PARB_TRYBB	Procyclic form-specific polypeptide A-beta precursor (Procyclin) (PARP A-beta)	0.01	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor				129
P14043 UniProt NPD GO	PROA_TRYBB	Procyclic form-specific polypeptide precursor (Procyclin) (PARP)	0.01	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor				115
Q6QEJ7 UniProt NPD GO	PROF_APIME	Profilin	0.01	-	cyt	0					126
P39825 UniProt NPD GO	PROF_SCHPO	Profilin	0.01	-	cyt	0		actin cortical patch [TAS] contractile ring (sensu Fungi) [IDA]			127
Q9U0E6 UniProt NPD GO	PROF_SUBDO	Profilin	0.01	-	cyt	0					140
Q26734 UniProt NPD GO	PROF_TRYBB	Profilin	0.01	-	cyt	0					150
P84177 UniProt NPD GO	PROF1_CITSI	Profilin (Allergen Cit s 2) (Fragment)	0.01	-		0					10
Q8GT39 UniProt NPD GO	PROF_PRUPE	Profilin (Allergen Pru p 4.02)	0.01	-	cyt	0					131
P25816 UniProt NPD GO	PROF_BETVE	Profilin (Pollen allergen Bet v 2) (Bet v II)	0.01	-	cyt	0				1CQA	133
O04725 UniProt NPD GO	PROF_CYNDA	Profilin (Pollen allergen Cyn d 12)	0.01	-	cyt	0					131
O81982 UniProt NPD GO	PROF_HELAN	Profilin (Pollen allergen Hel a 2)	0.01	-	mit	0					133
O49894 UniProt NPD GO	PROF_MERAN	Profilin (Pollen allergen Mer a 1)	0.01	-	cyt	0					133
Q9XW16 UniProt NPD GO	PROF1_CAEEL	Profilin-1	0.01	-	cyt	0					132
P52184 UniProt NPD GO	PROF1_HORVU	Profilin-1	0.01	-	cyt	0					131
Q41344 UniProt NPD GO	PROF1_LYCES	Profilin-1	0.01	-	mit	0					133
P49232 UniProt NPD GO	PROF1_WHEAT	Profilin-1 (Fragment)	0.01	-	cyt	0					138
Q8H2C9 UniProt NPD GO	PROF1_ARTVU	Profilin-1 (Pollen allergen Art v 4.01)	0.01	-	cyt	0					132
P35079 UniProt NPD GO	PROF1_PHLPR	Profilin-1 (Pollen allergen Phl p 12) (Phl p 11)	0.01	-	cyt	0					131
P02584 UniProt NPD GO	PROF1_BOVIN	Profilin-1 (Profilin I)	0.01	-	cyt	0				2BTF	139
P07737 UniProt NPD GO	PROF1_HUMAN	Profilin-1 (Profilin I)	0.01	-	cyt	0			176610	1PFL	139
P62962 UniProt NPD GO	PROF1_MOUSE	Profilin-1 (Profilin I)	0.01	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			139
P62963 UniProt NPD GO	PROF1_RAT	Profilin-1 (Profilin I)	0.01	-	cyt	0					139
P35081 UniProt NPD GO	PROF1_MAIZE	Profilin-1 (ZmPRO1)	0.01	-	cyt	0					131
P49233 UniProt NPD GO	PROF2_WHEAT	Profilin-2	0.01	-	cyt	0					141
Q9XF41 UniProt NPD GO	PROF2_MALDO	Profilin-2 (GD4-2) (Pollen allergen Mal d 4.0201)	0.01	-	cyt	0					131
O65810 UniProt NPD GO	PROF2_SOYBN	Profilin-2 (GmPRO2) (Allergen Gly m 3.0102)	0.01	-	cyt	0					131
Q8H2C8 UniProt NPD GO	PROF2_ARTVU	Profilin-2 (Pollen allergen Art v 4.02)	0.01	-	mit	0					132
P35080 UniProt NPD GO	PROF2_HUMAN	Profilin-2 (Profilin II)	0.01	-	cyt	0		actin cytoskeleton [NAS]	176590	1D1J	139
Q9JJV2 UniProt NPD GO	PROF2_MOUSE	Profilin-2 (Profilin II)	0.01	-	cyt	0					139
Q5R4E2 UniProt NPD GO	PROF2_PONPY	Profilin-2 (Profilin II)	0.01	-	cyt	0					139
Q9EPC6 UniProt NPD GO	PROF2_RAT	Profilin-2 (Profilin II)	0.01	-	cyt	0					139
Q09430 UniProt NPD GO	PROF2_BOVIN	Profilin-2 (Profilin II) (Fragment)	0.01	-	cyt	0					111
Q64LH0 UniProt NPD GO	PROF3_AMBAR	Profilin-3 (Pollen allergen D03)	0.01	-	cyt	0					133
Q9M7N0 UniProt NPD GO	PROF3_HEVBR	Profilin-3 (Pollen allergen Hev b 8.0201)	0.01	-	cyt	0					131
P35083 UniProt NPD GO	PROF3_MAIZE	Profilin-3 (ZmPRO3)	0.01	-	cyt	0					131

You are viewing entries 90801 to 90850 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.