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
P20698 UniProt NPD GO	PRO7_ORYSA	Prolamin PPROL 17 precursor	0.27	-	exc	0	In rice prolamin accumulates as type I protein body, which originates directly from the endoplasmic ...				156
Q6JHU8 UniProt NPD GO	P3H1_CHICK	Prolyl 3-hydroxylase 1 precursor (EC 1.14.11.7) (Leucine proline-enriched proteoglycan 1 homolog) (L ...	0.27	-	end	0	Endoplasmic reticulum (By similarity)				725
O62664 UniProt NPD GO	PGH1_BOVIN	Prostaglandin G/H synthase 1 (EC 1.14.99.1) (Cyclooxygenase-1) (COX-1) (Prostaglandin-endoperoxide s ...	0.27	-	cyt	0	Microsome; microsomal membrane; peripheral membrane protein				259
Q5REN2 UniProt NPD GO	PSA1_PONPY	Proteasome subunit alpha type 1 (EC 3.4.25.1)	0.27	-	nuc	0	Cytoplasm. Nucleus				263
Q9R1P4 UniProt NPD GO	PSA1_MOUSE	Proteasome subunit alpha type 1 (EC 3.4.25.1) (Proteasome component C2) (Macropain subunit C2) (Mult ...	0.27	-	cyt	0	Cytoplasm. Nucleus				263
P18420 UniProt NPD GO	PSA1_RAT	Proteasome subunit alpha type 1 (EC 3.4.25.1) (Proteasome component C2) (Macropain subunit C2) (Mult ...	0.27	-	cyt	0	Cytoplasm. Nucleus				263
P25786 UniProt NPD GO	PSA1_HUMAN	Proteasome subunit alpha type 1 (EC 3.4.25.1) (Proteasome component C2) (Macropain subunit C2) (Mult ...	0.27	-	cyt	0	Cytoplasm. Nucleus	nucleus [TAS] polysome [TAS] proteasome complex (sensu Eukaryota) [TAS]	602854		263
Q6NN02 UniProt NPD GO	Y4445_ARATH	Protein At4g14450, chloroplast precursor	0.27	-	nuc	0	Plastid; chloroplast (Potential)				125
Q09655 UniProt NPD GO	BAT4_CAEEL	Protein BAT4 homolog	0.27	-	nuc	0					371
Q9VZH1 UniProt NPD GO	CU059_DROME	Protein C21orf59 homolog	0.27	-	cyt	0					291
P59091 UniProt NPD GO	CU093_HUMAN	Protein C21orf93	0.27	-	nuc	0					139
P59093 UniProt NPD GO	CU099_HUMAN	Protein C21orf99	0.27	-	cyt	0					68
O14141 UniProt NPD GO	YEW3_SCHPO	Protein C3G6.03c	0.27	-	cyt	0	Cytoplasm (Potential)				236
Q9D4K4 UniProt NPD GO	CC024_MOUSE	Protein C3orf24 homolog	0.27	-	nuc	0					178
Q6UXA7 UniProt NPD GO	CF015_HUMAN	Protein C6orf15 precursor (Protein STG)	0.27	-	exc	0	Secreted protein (Potential)				325
Q96ET8 UniProt NPD GO	F18B2_HUMAN	Protein FAM18B2	0.27	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				276
Q6DFL2 UniProt NPD GO	FA44B_XENLA	Protein FAM44B	0.27	-	nuc	0					169
Q96DB5 UniProt NPD GO	FA82B_HUMAN	Protein FAM82B	0.27	-	mit	0					314
Q5R8E4 UniProt NPD GO	FA82B_PONPY	Protein FAM82B	0.27	-	mit	0					314
Q9UBU6 UniProt NPD GO	FA8A1_HUMAN	Protein FAM8A1 (Autosomal highly conserved protein)	0.27	-	end	3	Membrane; multi-pass membrane protein (Potential)				413
Q8BUV8 UniProt NPD GO	GP107_MOUSE	Protein GPR107 precursor	0.27	-	end	7	Membrane; multi-pass membrane protein				551
Q9BTD5 UniProt NPD GO	YU01_HUMAN	Protein MGC4604	0.27	-	mit	0					63
Q96AB6 UniProt NPD GO	NTAN1_HUMAN	Protein N-terminal asparagine amidohydrolase (EC 3.5.1.-) (Protein NH2-terminal asparagine deamidase ...	0.27	-	cyt	0	Cytoplasm (By similarity)				309
Q6UX39 UniProt NPD GO	U689_HUMAN	Protein UNQ689/PRO1329 precursor	0.27	-	exc	0	Secreted protein (Probable)				209
P48615 UniProt NPD GO	WNT11_MOUSE	Protein Wnt-11 precursor	0.27	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix				354
Q2QLA5 UniProt NPD GO	WNT2_HORSE	Protein Wnt-2 precursor	0.27	-	mit	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				360
P28120 UniProt NPD GO	WNT52_EPTST	Protein Wnt-5(II) (Fragment)	0.27	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				116
Q9P7E8 UniProt NPD GO	APP1_SCHPO	Protein app1	0.27	-	nuc	0		actin cortical patch [IDA]			857
O78450 UniProt NPD GO	CFXQ_GUITH	Protein cfxQ homolog	0.27	-	cyt	0	Plastid; chloroplast				293
P49826 UniProt NPD GO	CFXQ_ODOSI	Protein cfxQ homolog	0.27	-	cyt	0	Plastid; chloroplast				291
Q12404 UniProt NPD GO	MPD1_YEAST	Protein disulfide-isomerase MPD1 precursor (EC 5.3.4.1)	0.27	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)	vacuole (sensu Fungi) [IDA]			318
Q38920 UniProt NPD GO	PFTB_ARATH	Protein farnesyltransferase subunit beta (EC 2.5.1.58) (CAAX farnesyltransferase subunit beta) (RAS ...	0.27	-	mit	0					404
Q06003 UniProt NPD GO	GOLI_DROME	Protein goliath precursor (Protein g1)	0.27	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)	nucleus [NAS]			461
Q9UUM7 UniProt NPD GO	HOB3_SCHPO	Protein hob3 (Homolog of Bin3)	0.27	-	cyt	0					264
Q25378 UniProt NPD GO	KPC1_LYTPI	Protein kinase C (EC 2.7.11.13)	0.27	-	cyt	0					658
Q05655 UniProt NPD GO	KPCD_HUMAN	Protein kinase C delta type (EC 2.7.11.13) (nPKC-delta)	0.27	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)		176977	1YRK	676
P90980 UniProt NPD GO	KPC2_CAEEL	Protein kinase C-like 2 (EC 2.7.11.13) (PKC2)	0.27	-	nuc	0					682
P31507 UniProt NPD GO	KRUP_APIME	Protein krueppel (Fragment)	0.27	-	nuc	0	Nucleus (Probable)				74
Q4WU12 UniProt NPD GO	PBN1_ASPFU	Protein pbn1	0.27	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...				489
Q2U910 UniProt NPD GO	PBN1_ASPOR	Protein pbn1	0.27	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...				543
Q5BGN7 UniProt NPD GO	PPME1_EMENI	Protein phosphatase methylesterase 1 (EC 3.1.1.-) (PME-1)	0.27	-	cyt	0					407
P45843 UniProt NPD GO	SCRT_DROME	Protein scarlet	0.27	-	end	4	Integral membrane protein; pigment granules within pigment cells and retinula cells of the compound ...				666
O13932 UniProt NPD GO	BET1_SCHPO	Protein transport protein bet1	0.27	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)				117
P47749 UniProt NPD GO	PAR1_XENLA	Proteinase-activated receptor 1 precursor (PAR-1) (Thrombin receptor)	0.27	-	end	8 *	Membrane; multi-pass membrane protein				420
O88689 UniProt NPD GO	PCDA4_MOUSE	Protocadherin alpha 4 precursor (PCDH-alpha4)	0.27	+	nuc	0	Membrane; single-pass membrane protein. Detected in dendrites and synapses	membrane fraction [IDA]		1WUZ	947
Q5DRE6 UniProt NPD GO	PCDA6_PANTR	Protocadherin alpha 6 precursor (PCDH-alpha6)	0.27	+	end	1	Membrane; single-pass type I membrane protein (By similarity)				950
Q5DRE5 UniProt NPD GO	PCDA7_PANTR	Protocadherin alpha 7 precursor (PCDH-alpha7)	0.27	+	nuc	0	Membrane; single-pass type I membrane protein (By similarity)				937
Q9Y5H5 UniProt NPD GO	PCDA9_HUMAN	Protocadherin alpha 9 precursor (PCDH-alpha9)	0.27	+	end	1	Membrane; single-pass type I membrane protein (By similarity)		606315		950
Q5DRE3 UniProt NPD GO	PCDA9_PANTR	Protocadherin alpha 9 precursor (PCDH-alpha9)	0.27	+	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				950
Q5DRD5 UniProt NPD GO	PCDBE_PANTR	Protocadherin beta 14 precursor (PCDH-beta14)	0.27	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				798

You are viewing entries 43551 to 43600 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.