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
P29308 UniProt NPD GO	1433_SPIOL	14-3-3-like protein (Fragment)	0.25	-	mit	0					220
Q20655 UniProt NPD GO	14332_CAEEL	14-3-3-like protein 2	0.25	-	nuc	0					248
P42643 UniProt NPD GO	14331_ARATH	14-3-3-like protein GF14 chi (General regulatory factor 1)	0.25	-	nuc	0					267
Q01525 UniProt NPD GO	14332_ARATH	14-3-3-like protein GF14 omega (General regulatory factor 2)	0.25	-	cyt	0					259
Q01526 UniProt NPD GO	14332_MAIZE	14-3-3-like protein GF14-12	0.25	-	cyt	0					261
O23894 UniProt NPD GO	PRS6A_BRACM	26S protease regulatory subunit 6A homolog (TAT-binding protein homolog 1) (TBP-1)	0.25	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				424
Q08935 UniProt NPD GO	ROC1_NICSY	29 kDa ribonucleoprotein A, chloroplast precursor (CP29A)	0.25	-	mit	0	Plastid; chloroplast				273
Q9SA14 UniProt NPD GO	LEU31_ARATH	3-isopropylmalate dehydrogenase 1, chloroplast precursor (EC 1.1.1.85) (Beta-IPM dehydrogenase 1) (I ...	0.25	-	cyt	0	Plastid; chloroplast (By similarity)				406
P49244 UniProt NPD GO	FABH1_CUPWR	3-oxoacyl-[acyl-carrier-protein] synthase 3 A, chloroplast precursor (EC 2.3.1.41) (3-oxoacyl-[acyl- ...	0.25	-	mit	0	Plastid; chloroplast				400
P23902 UniProt NPD GO	KASC1_HORVU	3-oxoacyl-[acyl-carrier-protein] synthase I, chloroplast precursor (EC 2.3.1.41) (Beta-ketoacyl-ACP ...	0.25	-	mit	0	Plastid; chloroplast				462
P40920 UniProt NPD GO	HSP30_EMENI	30 kDa heat shock protein	0.25	-	nuc	0					181
Q05904 UniProt NPD GO	SM34_LYTPI	34 kDa spicule matrix protein precursor (LSM34)	0.25	-	exc	0	Secreted protein				335
Q9P0J6 UniProt NPD GO	RM36_HUMAN	39S ribosomal protein L36, mitochondrial precursor (L36mt) (MRP-L36) (BRCA1-interacting protein 1)	0.25	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [NAS]			103
Q8N983 UniProt NPD GO	RM43_HUMAN	39S ribosomal protein L43, mitochondrial precursor (L43mt) (MRP-L43) (Mitochondrial ribosomal protei ...	0.25	-	nuc	0	Mitochondrion	mitochondrial ribosome [NAS]			215
P14010 UniProt NPD GO	GATA_EMENI	4-aminobutyrate aminotransferase (EC 2.6.1.19) (Gamma-amino-N-butyrate transaminase) (GABA transamin ...	0.25	-	mit	0					498
P28189 UniProt NPD GO	RS13_SCHPO	40S ribosomal protein S13	0.25	-	nuc	0					150
Q3T0X6 UniProt NPD GO	RS16_BOVIN	40S ribosomal protein S16	0.25	-	cyt	0					145
O22647 UniProt NPD GO	RS16_FRIAG	40S ribosomal protein S16	0.25	-	cyt	0	Cytoplasm				145
P62249 UniProt NPD GO	RS16_HUMAN	40S ribosomal protein S16	0.25	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	603675		145
P14131 UniProt NPD GO	RS16_MOUSE	40S ribosomal protein S16	0.25	-	cyt	0		small ribosomal subunit [ISS]			145
Q29201 UniProt NPD GO	RS16_PIG	40S ribosomal protein S16	0.25	-	cyt	0		small ribosomal subunit [ISS]			145
P62250 UniProt NPD GO	RS16_RAT	40S ribosomal protein S16	0.25	-	cyt	0		small ribosomal subunit [ISS]			145
O01692 UniProt NPD GO	RS17_CAEEL	40S ribosomal protein S17	0.25	-	nuc	0					130
O94754 UniProt NPD GO	RS18_SCHPO	40S ribosomal protein S18	0.25	-	nuc	0	Cytoplasm				152
Q90YP9 UniProt NPD GO	RS25_ICTPU	40S ribosomal protein S25	0.25	-	nuc	0					124
Q9NB51 UniProt NPD GO	RS29_CULQU	40S ribosomal protein S29	0.25	-	nuc	0					56
Q3T169 UniProt NPD GO	RS3_BOVIN	40S ribosomal protein S3	0.25	-	cyt	0					243
P23396 UniProt NPD GO	RS3_HUMAN	40S ribosomal protein S3	0.25	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	600454	1WH9	243
Q5R465 UniProt NPD GO	RS3_PONPY	40S ribosomal protein S3	0.25	-	cyt	0					243
P05759 UniProt NPD GO	RS37_YEAST	40S ribosomal protein S37 (CEP76) (YS24)	0.25	+	nuc	0		cytoplasm [IDA] cytosolic small ribosomal subunit (sensu Eu... [TAS]			76
Q09781 UniProt NPD GO	RS3A_SCHPO	40S ribosomal protein S3aE-A (S1-A)	0.25	-	nuc	0					251
O24111 UniProt NPD GO	RS5_NICPL	40S ribosomal protein S5 (Fragment)	0.25	-	mit	0					154
O42393 UniProt NPD GO	RAPSN_CHICK	43 kDa receptor-associated protein of the synapse (RAPsyn) (Acetylcholine receptor-associated 43 kDa ...	0.25	-	cyt	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic surface of postsynaptic me ...				411
P09108 UniProt NPD GO	RAPSN_TORCA	43 kDa receptor-associated protein of the synapse (RAPsyn) (Acetylcholine receptor-associated 43 kDa ...	0.25	-	cyt	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic surface of postsynaptic me ...				411
P45894 UniProt NPD GO	AAPK1_CAEEL	5'-AMP-activated protein kinase catalytic subunit alpha-1 (EC 2.7.11.1) (AMP-activated kinase 1)	0.25	-	cyt	0					589
P25114 UniProt NPD GO	F264_RAT	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 (6PF-2-K/Fru-2,6-P2ASE testis-type isozyme) [I ...	0.25	-	mit	0				3BIF	468
Q39724 UniProt NPD GO	RL10_EUGGR	60S ribosomal protein L10	0.25	-	nuc	0					215
Q962U0 UniProt NPD GO	RL13A_SPOFR	60S ribosomal protein L13A	0.25	+	mit	0					204
O43004 UniProt NPD GO	RL16C_SCHPO	60S ribosomal protein L16-C	0.25	-	nuc	0					197
O14339 UniProt NPD GO	RL17A_SCHPO	60S ribosomal protein L17-A	0.25	-	mit	0					187
O59794 UniProt NPD GO	RL17B_SCHPO	60S ribosomal protein L17-B	0.25	-	mit	0					187
O44480 UniProt NPD GO	RL18A_CAEEL	60S ribosomal protein L18a	0.25	-	cyt	0					180
P58372 UniProt NPD GO	RL30_ICTPU	60S ribosomal protein L30	0.25	-	mit	0					115
P45841 UniProt NPD GO	RL31_CHLRE	60S ribosomal protein L31	0.25	-	nuc	0					116
O65071 UniProt NPD GO	RL31_PICMA	60S ribosomal protein L31	0.25	-	cyt	0					120
Q755A7 UniProt NPD GO	RL7_ASHGO	60S ribosomal protein L7	0.25	-	nuc	0					243
P14195 UniProt NPD GO	AAC1_DICDI	AAC-rich mRNA clone AAC1 protein (Fragment)	0.25	-	nuc	0					183
Q84K47 UniProt NPD GO	ATHI_ARATH	ABC2 homolog 1	0.25	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				983
O43506 UniProt NPD GO	ADA20_HUMAN	ADAM 20 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 20)	0.25	-	end	2 *	Membrane; single-pass type I membrane protein		603712		726
O15204 UniProt NPD GO	ADEC1_HUMAN	ADAM DEC1 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain-like protein decysin 1 ...	0.25	-	exc	0	Secreted protein (By similarity)	integral to membrane [NAS]	606393		470

You are viewing entries 44851 to 44900 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.