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
P17572 UniProt NPD GO	PRL_MELGA	Prolactin precursor (PRL)	0.14	-	exc	0	Secreted protein				229
Q13258 UniProt NPD GO	PD2R_HUMAN	Prostaglandin D2 receptor (Prostanoid DP receptor) (PGD receptor)	0.14	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	604687		359
Q8BJR6 UniProt NPD GO	PRS27_MOUSE	Protease serine 27 precursor (EC 3.4.21.-) (Marapsin) (Pancreasin)	0.14	-	exc	0	Secreted protein (By similarity)				328
Q8TAA3 UniProt NPD GO	PSA7L_HUMAN	Proteasome subunit alpha type 7-like (EC 3.4.25.1)	0.14	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				256
Q9R1P3 UniProt NPD GO	PSB2_MOUSE	Proteasome subunit beta type 2 (EC 3.4.25.1) (Proteasome component C7-I) (Macropain subunit C7-I) (M ...	0.14	-	cyt	0	Cytoplasm. Nucleus				201
P40307 UniProt NPD GO	PSB2_RAT	Proteasome subunit beta type 2 (EC 3.4.25.1) (Proteasome component C7-I) (Macropain subunit C7-I) (M ...	0.14	-	cyt	0	Cytoplasm. Nucleus				201
Q6CF24 UniProt NPD GO	AF9_YARLI	Protein AF-9 homolog	0.14	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				202
Q6FX19 UniProt NPD GO	BUR2_CANGA	Protein BUR2	0.14	-	cyt	0	Nucleus (By similarity)				357
Q8BH93 UniProt NPD GO	CN032_MOUSE	Protein C14orf32 homolog	0.14	-	nuc	0					241
Q9Y312 UniProt NPD GO	CT004_HUMAN	Protein C20orf4	0.14	-	cyt	0					384
Q96HW9 UniProt NPD GO	CU124_HUMAN	Protein C21orf124	0.14	-	nuc	0					162
Q8TCZ7 UniProt NPD GO	CU074_HUMAN	Protein C21orf74	0.14	-	nuc	0					72
P59088 UniProt NPD GO	CU085_HUMAN	Protein C21orf85 precursor	0.14	-	end	2 *					96
P59090 UniProt NPD GO	CU090_HUMAN	Protein C21orf90	0.14	-	nuc	0					65
Q8R2U4 UniProt NPD GO	CI032_MOUSE	Protein C9orf32 homolog	0.14	-	cyt	0					222
Q5BJX0 UniProt NPD GO	CI032_RAT	Protein C9orf32 homolog	0.14	-	cyt	0					222
Q8C353 UniProt NPD GO	CI071_MOUSE	Protein C9orf71 homolog	0.14	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				183
O44400 UniProt NPD GO	F37C4_CAEEL	Protein F37C4.5	0.14	+	cyt	0					555
Q52KP5 UniProt NPD GO	FA55D_MOUSE	Protein FAM55D precursor	0.14	-	mit	1 *	Secreted protein (Potential)				543
Q8TBR7 UniProt NPD GO	FA57A_HUMAN	Protein FAM57A (CT120 protein)	0.14	-	end	7 *	Cell membrane; multi-pass membrane protein				257
Q9S746 UniProt NPD GO	HTH_ARATH	Protein HOTHEAD precursor (Protein ADHESION OF CALYX EDGES)	0.14	-	end	0					594
Q00747 UniProt NPD GO	LE25_LYCES	Protein LE25	0.14	-	nuc	0					88
Q640Z1 UniProt NPD GO	NDR4A_XENLA	Protein NDRG4-A	0.14	-	end	0					390
Q6DJD3 UniProt NPD GO	NDR4B_XENLA	Protein NDRG4-B	0.14	-	cyt	0					367
Q9UTC8 UniProt NPD GO	OS9_SCHPO	Protein OS-9 homolog precursor	0.14	-	cyt	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				322
Q25423 UniProt NPD GO	P18_LEITA	Protein P18, mitochondrial precursor	0.14	-	mit	0	Mitochondrion; mitochondrial inner membrane				187
Q01889 UniProt NPD GO	PAG1_TRYBB	Protein PAG1 precursor	0.14	-	gol	0	Cell membrane; lipid-anchor; GPI-anchor				405
P07091 UniProt NPD GO	S10A4_MOUSE	Protein S100-A4 (S100 calcium-binding protein A4) (Metastasin) (Protein Mts1) (Metastatic cell prote ...	0.14	-	cyt	0					101
P82624 UniProt NPD GO	SCRL5_ARATH	Protein SCRL5 precursor	0.14	-	exc	0					97
P40472 UniProt NPD GO	SIM1_YEAST	Protein SIM1 precursor	0.14	-	nuc	0		cell wall (sensu Fungi) [IDA]			475
Q07549 UniProt NPD GO	SNA4_YEAST	Protein SNA4	0.14	-	exc	2 *	Vacuole; vacuolar membrane; multi-pass membrane protein (Potential)	vacuolar membrane (sensu Fungi) [IDA]			140
P32579 UniProt NPD GO	SUA5_YEAST	Protein SUA5	0.14	-	nuc	0		cytoplasm [IDA]			426
Q59Q43 UniProt NPD GO	SYM1_CANAL	Protein SYM1	0.14	-	mit	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				195
Q5M8I4 UniProt NPD GO	TSSC1_XENTR	Protein TSSC1	0.14	-	cyt	0					387
P28100 UniProt NPD GO	WNT1_ALOVU	Protein Wnt-1 (Fragment)	0.14	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				126
P28112 UniProt NPD GO	WNT10_EPTST	Protein Wnt-10 (Fragment)	0.14	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				113
P56704 UniProt NPD GO	WNT3A_HUMAN	Protein Wnt-3a precursor	0.14	-	exc	0	Secreted protein; extracellular space; extracellular matrix	extracellular region [NAS]	606359		352
P28102 UniProt NPD GO	WNT3B_ALOVU	Protein Wnt-3b (Fragment)	0.14	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
P49355 UniProt NPD GO	PFTB_BOVIN	Protein farnesyltransferase subunit beta (EC 2.5.1.58) (CAAX farnesyltransferase subunit beta) (RAS ...	0.14	-	cyt	0					437
P49356 UniProt NPD GO	PFTB_HUMAN	Protein farnesyltransferase subunit beta (EC 2.5.1.58) (CAAX farnesyltransferase subunit beta) (RAS ...	0.14	-	cyt	0			134636	1TN6	437
Q8K2I1 UniProt NPD GO	PFTB_MOUSE	Protein farnesyltransferase subunit beta (EC 2.5.1.58) (CAAX farnesyltransferase subunit beta) (RAS ...	0.14	-	cyt	0					437
Q02029 UniProt NPD GO	HUNB_EUSPL	Protein hunchback (Fragment)	0.14	-	nuc	0	Nucleus (Probable)				56
P36982 UniProt NPD GO	PP2C_LEICH	Protein phosphatase 2C (EC 3.1.3.16) (PP2C)	0.14	-	cyt	0					406
O04719 UniProt NPD GO	PP2C2_ARATH	Protein phosphatase 2C ABI2 (EC 3.1.3.16) (PP2C) (Abscisic acid-insensitive 2)	0.14	-	cyt	0					423
P38797 UniProt NPD GO	PP2C7_YEAST	Protein phosphatase 2C homolog 7 (EC 3.1.3.16) (PP2C-7)	0.14	-	mit	1 *	Mitochondrion	mitochondrion [IDA]			374
Q96WY0 UniProt NPD GO	RHOC_EMENI	Protein rhoC (Rho3 protein homolog)	0.14	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				230
P42678 UniProt NPD GO	SUI1_ANOGA	Protein translation factor SUI1 homolog	0.14	-	cyt	0					110
P23606 UniProt NPD GO	TGM1_RAT	Protein-glutamine gamma-glutamyltransferase K (EC 2.3.2.13) (Transglutaminase K) (TGase K) (TGK) (TG ...	0.14	-	cyt	0	Membrane; peripheral membrane protein				824
P23653 UniProt NPD GO	PRTR_TRIAL	Proteinase R precursor (EC 3.4.21.-)	0.14	-	exc	0					387
P06240 UniProt NPD GO	LCK_MOUSE	Proto-oncogene tyrosine-protein kinase LCK (EC 2.7.10.2) (p56-LCK) (Lymphocyte cell-specific protein ...	0.14	-	cyt	0	Cytoplasm. Cell membrane; lipid-anchor; cytoplasmic side. Present in lipid rafts in an unactive form ...	lipid raft [ISS] pericentriolar material [ISS] plasma membrane [ISS]			508

You are viewing entries 58901 to 58950 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.