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
Q8IWA0 UniProt NPD GO	WDR75_HUMAN	WD repeat protein 75	0.25	-	nuc	0	Nucleus; nucleolus				830
Q99PP0 UniProt NPD GO	WISP1_RAT	WNT1-inducible signaling pathway protein 1 precursor (WISP-1) (ELM-1)	0.25	-	mit	1 *	Secreted protein (By similarity)				367
P12253 UniProt NPD GO	DHR21_ORYSA	Water stress-inducible protein Rab21	0.25	-	nuc	0	Cytoplasm				172
Q9W6F8 UniProt NPD GO	WIF1_XENLA	Wnt inhibitory factor 1 precursor (WIF-1)	0.25	-	exc	0	Secreted protein				374
P56695 UniProt NPD GO	WFS1_MOUSE	Wolframin	0.25	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				890
P80457 UniProt NPD GO	XDH_BOVIN	Xanthine dehydrogenase/oxidase [Includes: Xanthine dehydrogenase (EC 1.17.1.4) (XD); Xanthine oxidas ...	0.25	-	cyt	0	Peroxisome			1VDV	1331
Q38857 UniProt NPD GO	XTH22_ARATH	Xyloglucan endotransglucosylase/hydrolase protein 22 precursor (EC 2.4.1.207) (At-XTH22) (XTH-22) (T ...	0.25	-	exc	0	Secreted protein; extracellular space; apoplast (Probable)				284
P05815 UniProt NPD GO	ZEAV_MAIZE	Zein-alpha B49 (22 kDa zein B49) (Fragment)	0.25	-	nuc	0					122
Q9H0C1 UniProt NPD GO	ZMY12_HUMAN	Zinc finger MYND domain-containing protein 12	0.25	-	nuc	0					365
O75346 UniProt NPD GO	ZN253_HUMAN	Zinc finger protein 253 (Bone marrow zinc finger 1) (BMZF-1)	0.25	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	606954		275
Q21179 UniProt NPD GO	NAS18_CAEEL	Zinc metalloproteinase nas-18 precursor (EC 3.4.24.21) (Nematode astacin 18)	0.25	-	nuc	0	Secreted protein (Potential)				410
P42099 UniProt NPD GO	ZP2_PIG	Zona pellucida sperm-binding protein 2 precursor (Zona pellucida glycoprotein ZP2) (Zona pellucida p ...	0.25	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				716
Q75AM2 UniProt NPD GO	KAPR_ASHGO	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.25	-	cyt	0					458
P36600 UniProt NPD GO	KAPR_SCHPO	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.25	-	cyt	0					412
P18154 UniProt NPD GO	M3L_DICDI	cAMP-regulated M3L protein (Fragment)	0.25	-	nuc	0					256
Q9UTD1 UniProt NPD GO	YTH1_SCHPO	mRNA 3'-end-processing protein yth1	0.25	-	nuc	0	Nucleus (By similarity)				170
Q9LLY4 UniProt NPD GO	LPAT1_BRANA	1-acyl-sn-glycerol-3-phosphate acyltransferase 1, chloroplast precursor (EC 2.3.1.51)	0.24	-	end	2	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein				344
Q643R3 UniProt NPD GO	PLCG_HUMAN	1-acyl-sn-glycerol-3-phosphate acyltransferase eta (EC 2.3.1.51) (1-AGP acyltransferase 7) (1-AGPAT ...	0.24	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				524
Q04917 UniProt NPD GO	1433F_HUMAN	14-3-3 protein eta (Protein AS1)	0.24	-	nuc	0		cytoplasm [ISS]	113508	2C74	245
P31947 UniProt NPD GO	1433S_HUMAN	14-3-3 protein sigma (Stratifin) (Epithelial cell marker protein 1)	0.24	-	nuc	0	Or: Cytoplasm. Or: Secreted protein. May be secreted by a non-classical secretory pathway	cytoplasm [TAS] extracellular space [TAS]	601290	1YZ5	248
Q41246 UniProt NPD GO	1433_TOBAC	14-3-3-like protein	0.24	-	cyt	0					251
Q96450 UniProt NPD GO	1433A_SOYBN	14-3-3-like protein A (SGF14A)	0.24	-	cyt	0					257
P42653 UniProt NPD GO	1433A_VICFA	14-3-3-like protein A (VFA-1433A)	0.24	-	nuc	0					261
P48349 UniProt NPD GO	14336_ARATH	14-3-3-like protein GF14 lambda (General regulatory factor 6) (14-3-3-like protein RCI2) (14-3-3-lik ...	0.24	-	cyt	0					248
O04019 UniProt NPD GO	PRS6A_ARATH	26S protease regulatory subunit 6A homolog (TAT-binding protein homolog 1) (TBP-1)	0.24	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				419
P33299 UniProt NPD GO	PRS7_YEAST	26S protease regulatory subunit 7 homolog (Protein CIM5) (TAT-binding homolog 3)	0.24	-	nuc	0	Cytoplasm (Potential). Nucleus (Potential)	proteasome regulatory particle, base subcom... [IPI]			467
P56701 UniProt NPD GO	PSD2_BOVIN	26S proteasome non-ATPase regulatory subunit 2 (26S proteasome regulatory subunit RPN1) (26S proteas ...	0.24	-	nuc	0					99
Q15008 UniProt NPD GO	PSD6_HUMAN	26S proteasome non-ATPase regulatory subunit 6 (26S proteasome regulatory subunit S10) (p42A) (Prote ...	0.24	-	cyt	0		proteasome complex (sensu Eukaryota) [NAS]			389
O15235 UniProt NPD GO	RT12_HUMAN	28S ribosomal protein S12, mitochondrial precursor (S12mt) (MRP-S12) (MT-RPS12)	0.24	-	mit	0	Mitochondrion	mitochondrial ribosome [TAS]	603021		138
P55251 UniProt NPD GO	LEU2_RHIPU	3-isopropylmalate dehydratase (EC 4.2.1.33) (Isopropylmalate isomerase) (Alpha-IPM isomerase) (IPMI) ...	0.24	-	cyt	0					755
P93832 UniProt NPD GO	LEU32_ARATH	3-isopropylmalate dehydrogenase 2, chloroplast precursor (EC 1.1.1.85) (Beta-IPM dehydrogenase 2) (I ...	0.24	-	mit	0	Plastid; chloroplast (By similarity)				405
P39525 UniProt NPD GO	CEM1_YEAST	3-oxoacyl-[acyl-carrier-protein] synthase homolog (EC 2.3.1.41) (Beta-ketoacyl-ACP synthase homolog) ...	0.24	-	mit	0	Mitochondrion (Potential)	mitochondrion [TAS]			442
P56686 UniProt NPD GO	DEF4_ANDAU	4 kDa defensin	0.24	-	mit	0	Secreted protein				37
Q06801 UniProt NPD GO	DPEP_SOLTU	4-alpha-glucanotransferase, chloroplast precursor (EC 2.4.1.25) (Amylomaltase) (Disproportionating e ...	0.24	-	mit	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast			1X1N	576
Q08112 UniProt NPD GO	RS151_ARATH	40S ribosomal protein S15-1	0.24	-	cyt	0	Cytoplasm				152
P49215 UniProt NPD GO	RS17_LYCES	40S ribosomal protein S17	0.24	-	nuc	0					143
Q9SS17 UniProt NPD GO	RS24_ARATH	40S ribosomal protein S24	0.24	-	mit	0					133
Q6PBI5 UniProt NPD GO	RS25_BRARE	40S ribosomal protein S25	0.24	-	nuc	0					124
P52821 UniProt NPD GO	RS25_CAEEL	40S ribosomal protein S25	0.24	+	nuc	0					117
Q56JX6 UniProt NPD GO	RS28_BOVIN	40S ribosomal protein S28	0.24	-	mit	0					69
P62857 UniProt NPD GO	RS28_HUMAN	40S ribosomal protein S28	0.24	-	mit	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	603685		69
P62858 UniProt NPD GO	RS28_MOUSE	40S ribosomal protein S28	0.24	-	mit	0					69
Q6QAT1 UniProt NPD GO	RS28_PIG	40S ribosomal protein S28	0.24	-	mit	0					69
P62859 UniProt NPD GO	RS28_RAT	40S ribosomal protein S28	0.24	-	mit	0					69
Q8SS73 UniProt NPD GO	RS29_ENCCU	40S ribosomal protein S29	0.24	-	mit	0					55
Q7XYB0 UniProt NPD GO	RS29_GRIJA	40S ribosomal protein S29	0.24	-	nuc	0					56
P48152 UniProt NPD GO	RS3_CAEEL	40S ribosomal protein S3	0.24	-	cyt	0					247
P05750 UniProt NPD GO	RS3_YEAST	40S ribosomal protein S3 (YS3) (RP13)	0.24	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]		1K5X	239
O42952 UniProt NPD GO	RS30_SCHPO	40S ribosomal protein S30	0.24	-	nuc	0					61
Q12087 UniProt NPD GO	RS30_YEAST	40S ribosomal protein S30	0.24	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			62

You are viewing entries 45901 to 45950 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.