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
Q9NUG6 UniProt NPD GO	PDRG1_HUMAN	p53 and DNA damage-regulated protein 1	0.22	-	cyt	0					133
P59048 UniProt NPD GO	PDRG1_MOUSE	p53 and DNA damage-regulated protein 1	0.22	-	cyt	0					133
Q8J254 UniProt NPD GO	PACC_COLGL	pH-response transcription factor pacC/RIM101 (Fragment)	0.22	-	nuc	0					65
Q3ZBL1 UniProt NPD GO	MTND_BOVIN	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase (EC 1.13.-.-) (Aci-reductone dioxygenase) (ARD) ...	0.21	-	cyt	0	Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity). Nucleus (By similarity ...	cytoplasm [ISS] nucleus [ISS] plasma membrane [ISS]			179
Q9D6Y9 UniProt NPD GO	GLGB_MOUSE	1,4-alpha-glucan branching enzyme (EC 2.4.1.18) (Glycogen branching enzyme) (Brancher enzyme)	0.21	-	cyt	0					702
P93210 UniProt NPD GO	14335_LYCES	14-3-3 protein 5	0.21	-	nuc	0					255
Q26540 UniProt NPD GO	14331_SCHMA	14-3-3 protein homolog 1	0.21	-	cyt	0					252
P93342 UniProt NPD GO	1433A_TOBAC	14-3-3-like protein A	0.21	-	cyt	0					255
P42645 UniProt NPD GO	14335_ARATH	14-3-3-like protein GF14 upsilon (General regulatory factor 5)	0.21	-	nuc	0					268
Q8VCR2 UniProt NPD GO	DHB13_MOUSE	17-beta hydroxysteroid dehydrogenase 13 precursor (EC 1.1.-.-) (Short-chain dehydrogenase/reductase ...	0.21	+	nuc	0	Secreted protein (Potential)				304
Q4N4T9 UniProt NPD GO	P23_THEPA	23 kDa piroplasm membrane protein precursor (p23)	0.21	-	end	2 *	Membrane; single-pass membrane protein (Potential)				229
Q75F44 UniProt NPD GO	RPN8_ASHGO	26S proteasome regulatory subunit RPN8	0.21	-	nuc	0					326
Q43349 UniProt NPD GO	ROC2_ARATH	29 kDa ribonucleoprotein, chloroplast precursor (RNA-binding protein cp29)	0.21	-	mit	0	Plastid; chloroplast				342
P53859 UniProt NPD GO	CSL4_YEAST	3'-5' exoribonuclease CSL4 (EC 3.1.13.-)	0.21	-	cyt	0	Cytoplasm. Nucleus; nucleolus	cytoplasmic exosome (RNase complex) [IDA] nuclear exosome (RNase complex) [IDA]			292
Q74ZM9 UniProt NPD GO	LEU2_ASHGO	3-isopropylmalate dehydratase (EC 4.2.1.33) (Isopropylmalate isomerase) (Alpha-IPM isomerase) (IPMI) ...	0.21	-	cyt	0					776
Q9H0U6 UniProt NPD GO	RM18_HUMAN	39S ribosomal protein L18, mitochondrial precursor (L18mt) (MRP-L18)	0.21	-	mit	0	Mitochondrion	mitochondrial ribosome [NAS]			180
Q90YR4 UniProt NPD GO	RS10_ICTPU	40S ribosomal protein S10	0.21	-	cyt	0	Cytoplasm (By similarity)				166
P63325 UniProt NPD GO	RS10_MOUSE	40S ribosomal protein S10	0.21	-	nuc	0	Cytoplasm				165
Q9AYP4 UniProt NPD GO	RS10_ORYSA	40S ribosomal protein S10	0.21	-	nuc	0	Cytoplasm (By similarity)				183
P63326 UniProt NPD GO	RS10_RAT	40S ribosomal protein S10	0.21	-	nuc	0	Cytoplasm				165
P46784 UniProt NPD GO	RS10B_YEAST	40S ribosomal protein S10-B	0.21	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			105
P93377 UniProt NPD GO	RS14_TOBAC	40S ribosomal protein S14 (Fragment)	0.21	-	nuc	0					66
Q01855 UniProt NPD GO	RS15_YEAST	40S ribosomal protein S15 (S21) (YS21) (RP52) (RIG protein)	0.21	-	mit	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]		1K5X	142
P08636 UniProt NPD GO	RS17_CHICK	40S ribosomal protein S17	0.21	-	nuc	0					134
Q7ZUB2 UniProt NPD GO	RS17_COTJA	40S ribosomal protein S17	0.21	-	nuc	0					134
Q8T5Z4 UniProt NPD GO	RS19_BRABE	40S ribosomal protein S19	0.21	-	cyt	0					147
Q4WI01 UniProt NPD GO	RS21_ASPFU	40S ribosomal protein S21	0.21	-	nuc	0					88
Q4PM64 UniProt NPD GO	RS21_IXOSC	40S ribosomal protein S21	0.21	-	nuc	0					83
Q6PBK3 UniProt NPD GO	RS28_BRARE	40S ribosomal protein S28	0.21	-	nuc	0					69
Q90YP3 UniProt NPD GO	RS28_ICTPU	40S ribosomal protein S28	0.21	-	nuc	0					69
Q40941 UniProt NPD GO	RS4_CHLS6	40S ribosomal protein S4	0.21	-	nuc	0					242
P38982 UniProt NPD GO	RSSA_CRIGR	40S ribosomal protein SA (p40) (34/67 kDa laminin receptor)	0.21	-	mit	0	Cytoplasm				294
P14206 UniProt NPD GO	RSSA_MOUSE	40S ribosomal protein SA (p40) (34/67 kDa laminin receptor)	0.21	-	nuc	0	Cytoplasm	nuclear euchromatin [IDA]			294
P38983 UniProt NPD GO	RSSA_RAT	40S ribosomal protein SA (p40) (34/67 kDa laminin receptor)	0.21	-	mit	0	Cytoplasm				294
P08865 UniProt NPD GO	RSSA_HUMAN	40S ribosomal protein SA (p40) (34/67 kDa laminin receptor) (Colon carcinoma laminin-binding protein ...	0.21	-	mit	0	Cytoplasm	cytoplasm [TAS] nucleus [TAS]	150370		294
P26452 UniProt NPD GO	RSSA_BOVIN	40S ribosomal protein SA (p40) (C10 protein)	0.21	-	mit	0	Cytoplasm				294
Q08682 UniProt NPD GO	RSSAA_ARATH	40S ribosomal protein SA-1 (p40) (Laminin receptor homolog)	0.21	-	cyt	0	Cytoplasm				298
Q5BIS9 UniProt NPD GO	AAKB1_BOVIN	5'-AMP-activated protein kinase subunit beta-1 (AMPK beta-1 chain) (AMPKb)	0.21	-	nuc	0					269
Q9R078 UniProt NPD GO	AAKB1_MOUSE	5'-AMP-activated protein kinase subunit beta-1 (AMPK beta-1 chain) (AMPKb)	0.21	-	nuc	0		nucleus [IDA]			269
P46636 UniProt NPD GO	5HT1B_CRIGR	5-hydroxytryptamine 1B receptor (5-HT-1B) (Serotonin receptor 1B) (5-HT1B)	0.21	-	end	7 *	Membrane; multi-pass membrane protein				386
Q588Y6 UniProt NPD GO	5HT1B_FELCA	5-hydroxytryptamine 1B receptor (5-HT-1B) (Serotonin receptor 1B) (5-HT1B)	0.21	-	end	7 *	Membrane; multi-pass membrane protein				389
P51412 UniProt NPD GO	RK21_ARATH	50S ribosomal protein L21, chloroplast precursor (CL21)	0.21	-	mit	0	Plastid; chloroplast				220
Q16877 UniProt NPD GO	F264_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 (6PF-2-K/Fru-2,6-P2ASE testis-type isozyme) [I ...	0.21	-	mit	0			605320		468
Q5R931 UniProt NPD GO	RL10_PONPY	60S ribosomal protein L10	0.21	-	mit	0					213
Q6PDV7 UniProt NPD GO	RL10_RAT	60S ribosomal protein L10	0.21	-	mit	0					213
Q9XSI3 UniProt NPD GO	RL10_BOVIN	60S ribosomal protein L10 (QM protein homolog)	0.21	-	mit	0					213
Q6ZWV3 UniProt NPD GO	RL10_MOUSE	60S ribosomal protein L10 (QM protein homolog)	0.21	-	mit	0					213
Q29195 UniProt NPD GO	RL10_PIG	60S ribosomal protein L10 (QM protein homolog) (Lamin receptor homolog)	0.21	-	mit	0					213
P27635 UniProt NPD GO	RL10_HUMAN	60S ribosomal protein L10 (QM protein) (Tumor suppressor QM) (Laminin receptor homolog)	0.21	-	mit	0			312173		213
Q8VZB9 UniProt NPD GO	R10A1_ARATH	60S ribosomal protein L10a-1	0.21	+	nuc	0					216

You are viewing entries 49101 to 49150 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.