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
P70266 UniProt NPD GO	F261_MOUSE	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (6PF-2-K/Fru-2,6-P2ASE liver isozyme) [Include ...	0.00	-	cyt	0		6-phosphofructo-2-kinase/fructose-2,6-bipho... [ISS]			70
P80827 UniProt NPD GO	CWP03_ARATH	60 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				7
P80847 UniProt NPD GO	CWP27_ARATH	60 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				6
P49818 UniProt NPD GO	CH60_CANFA	60 kDa heat shock protein, mitochondrial (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock protein 60) ...	0.00	-		0	Mitochondrion; mitochondrial matrix				13
P31081 UniProt NPD GO	CH60_BOVIN	60 kDa heat shock protein, mitochondrial (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock protein 60) ...	0.00	-	cyt	0	Mitochondrion; mitochondrial matrix				22
Q56K14 UniProt NPD GO	RLA1_BOVIN	60S acidic ribosomal protein P1	0.00	-	cyt	0					114
P18660 UniProt NPD GO	RLA1_CHICK	60S acidic ribosomal protein P1	0.00	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [ISS]			114
P05386 UniProt NPD GO	RLA1_HUMAN	60S acidic ribosomal protein P1	0.00	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]	180520		114
P47955 UniProt NPD GO	RLA1_MOUSE	60S acidic ribosomal protein P1	0.00	-	cyt	0					114
P19944 UniProt NPD GO	RLA1_RAT	60S acidic ribosomal protein P1	0.00	-	cyt	0					114
Q9HGV0 UniProt NPD GO	RLA1_ASPFU	60S acidic ribosomal protein P1 (AfP1)	0.00	-	cyt	0					111
P49148 UniProt NPD GO	RLA1_ALTAL	60S acidic ribosomal protein P1 (Allergen Alt a 12) (Alt a XII)	0.00	-	cyt	0					110
P05318 UniProt NPD GO	RLA1_YEAST	60S acidic ribosomal protein P1-alpha (A1) (L12EIIA)	0.00	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			105
O61463 UniProt NPD GO	RLA2_CRYST	60S acidic ribosomal protein P2	0.00	-	cyt	0					110
P22683 UniProt NPD GO	RLA2_DICDI	60S acidic ribosomal protein P2	0.00	-	mit	0					105
Q9GPU2 UniProt NPD GO	RLA2_EUPRA	60S acidic ribosomal protein P2	0.00	-	exc	0					113
P41099 UniProt NPD GO	RLA2_PARAR	60S acidic ribosomal protein P2	0.00	-	exc	0					114
O44010 UniProt NPD GO	RLA2_LEIBR	60S acidic ribosomal protein P2 (Acidic ribosomal P2 beta protein) (P2B-protein)	0.00	-	cyt	0				1S4H	105
P05389 UniProt NPD GO	RLA2_DROME	60S acidic ribosomal protein P2 (Acidic ribosomal protein RPA1)	0.00	-	cyt	0					113
P05390 UniProt NPD GO	RLA2_WHEAT	60S acidic ribosomal protein P2 (Ribosomal protein 'A') (Fragment)	0.00	-	exc	0					42
P51407 UniProt NPD GO	RLA21_ARATH	60S acidic ribosomal protein P2-1	0.00	-	exc	0					115
Q06382 UniProt NPD GO	RLA3_LEIIN	60S acidic ribosomal protein P2-2	0.00	-	exc	0					111
Q9LH85 UniProt NPD GO	RLA23_ARATH	60S acidic ribosomal protein P2-3	0.00	-	cyt	0					115
Q9LXM8 UniProt NPD GO	RLA24_ARATH	60S acidic ribosomal protein P2-4	0.00	-	exc	0					111
Q9HFQ5 UniProt NPD GO	RLA2_CANAL	60S acidic ribosomal protein P2-A (CaRP2A)	0.00	-	exc	0					108
P08094 UniProt NPD GO	RLA2_SCHPO	60S acidic ribosomal protein P2-alpha (A2) (L40C) (L12EI)	0.00	-	cyt	0					110
P05319 UniProt NPD GO	RLA2_YEAST	60S acidic ribosomal protein P2-alpha (A2) (L44) (L12EIB)	0.00	-	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			106
P46252 UniProt NPD GO	RLA2A_MAIZE	60S acidic ribosomal protein P2A (P2)	0.00	-	exc	0					111
O24415 UniProt NPD GO	RLA2B_MAIZE	60S acidic ribosomal protein P2B	0.00	-	exc	0					113
P56724 UniProt NPD GO	RLA3_ORYSA	60S acidic ribosomal protein P3 (P1/P2-like)	0.00	-	mit	0					118
O24413 UniProt NPD GO	RLA3_MAIZE	60S acidic ribosomal protein P3 (P1/P2-like) (P3A)	0.00	-	mit	1					119
P53875 UniProt NPD GO	RM19_YEAST	60S ribosomal protein L19, mitochondrial precursor (YmL19)	0.00	-	cyt	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			158
Q09668 UniProt NPD GO	RL22_SCHPO	60S ribosomal protein L22	0.00	-	cyt	0					117
P48045 UniProt NPD GO	RL25_KLULA	60S ribosomal protein L25	0.00	-	mit	0					142
P04456 UniProt NPD GO	RL25_YEAST	60S ribosomal protein L25 (YL25) (RP61L)	0.00	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	141
P47831 UniProt NPD GO	RL28_CANAL	60S ribosomal protein L28 (L27A) (L29) (Fragment)	0.00	-	cyt	0					62
Q752U5 UniProt NPD GO	RL30_ASHGO	60S ribosomal protein L30	0.00	-	mit	0					104
Q6FXZ0 UniProt NPD GO	RL30_CANGA	60S ribosomal protein L30	0.00	-	mit	0					105
P38664 UniProt NPD GO	RL30_KLULA	60S ribosomal protein L30 (L32)	0.00	-	mit	0					104
P14120 UniProt NPD GO	RL30_YEAST	60S ribosomal protein L30 (YL32) (RP73)	0.00	-	mit	0		cytoplasm [IDA] cytosolic large ribosomal subunit (sensu Eu... [TAS]		1T0K	104
P53163 UniProt NPD GO	YGG8_YEAST	60S ribosomal protein L7/L12 homolog, mitochondrial precursor	0.00	-	mit	0	Mitochondrion (By similarity)	mitochondrion [IDA]			194
Q9Y221 UniProt NPD GO	NIP7_HUMAN	60S ribosome subunit biogenesis protein NIP7 homolog (KD93)	0.00	-	cyt	0	Nucleus; nucleolus			1T5Y	180
Q9CXK8 UniProt NPD GO	NIP7_MOUSE	60S ribosome subunit biogenesis protein NIP7 homolog (PEachy) (KD93)	0.00	-	cyt	0	Nucleus; nucleolus (By similarity)				180
Q9WV50 UniProt NPD GO	NIP7_RAT	60S ribosome subunit biogenesis protein NIP7 homolog (PEachy) (KD93)	0.00	-	cyt	0	Nucleus; nucleolus (By similarity)				180
P80804 UniProt NPD GO	CWP07_LYCES	62 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				9
P80811 UniProt NPD GO	CWP15_LYCES	62 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				10
P80764 UniProt NPD GO	CWP05_PHAVU	65 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				9
P81188 UniProt NPD GO	ALBU1_TRASC	67 kDa serum albumin (Alb-1) (Fragment)	0.00	-	cyt	0	Secreted protein				40
P81189 UniProt NPD GO	ALBU2_TRASC	68 kDa serum albumin (Alb-2) (Fragment)	0.00	-		0	Secreted protein				15
P80778 UniProt NPD GO	CWP01_TOBAC	70 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				9

You are viewing entries 92251 to 92300 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.