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
Q5RBN6 UniProt NPD GO	NDRG2_PONPY	Protein NDRG2	0.25	-	cyt	0	Cytoplasm (By similarity)				371
Q90827 UniProt NPD GO	NEL_CHICK	Protein NEL precursor (93 kDa protein)	0.25	-	nuc	0					816
P28686 UniProt NPD GO	NOV_CHICK	Protein NOV precursor (Nephroblastoma overexpressed gene protein)	0.25	-	nuc	0	Secreted protein				351
P33755 UniProt NPD GO	NPL4_YEAST	Protein NPL4	0.25	-	mit	0		endoplasmic reticulum [IDA] nuclear envelope-endoplasmic reticulum network [IDA]			580
Q9Y6A1 UniProt NPD GO	POMT1_HUMAN	Protein O-mannosyl-transferase 1 (EC 2.4.1.109) (Dolichyl-phosphate-mannose--protein mannosyltransfe ...	0.25	-	end	12 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] endoplasmic reticulum membrane [IDA] integral to membrane [TAS]	609308		747
Q99PR0 UniProt NPD GO	POMT1_RAT	Protein O-mannosyl-transferase 1 (EC 2.4.1.109) (Dolichyl-phosphate-mannose--protein mannosyltransfe ...	0.25	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum membrane [ISS]			747
P47033 UniProt NPD GO	PRY3_YEAST	Protein PRY3 (Pathogen related in Sc 3)	0.25	-	nuc	1		cell wall (sensu Fungi) [IDA]			881
Q9H1J7 UniProt NPD GO	WNT5B_HUMAN	Protein Wnt-5b precursor	0.25	-	exc	0	Secreted protein; extracellular space; extracellular matrix		606361		359
Q8N9I9 UniProt NPD GO	DTX3_HUMAN	Protein deltex-3 (Deltex-3) (Deltex3)	0.25	-	nuc	0	Cytoplasm (Probable)				347
P93227 UniProt NPD GO	PFTA_LYCES	Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit (EC 2.5.1.58) (EC 2.5.1.5 ...	0.25	-	nuc	0					346
P31504 UniProt NPD GO	HUNB_APIME	Protein hunchback (Fragment)	0.25	-	nuc	0	Nucleus (Probable)				69
Q99435 UniProt NPD GO	NELL2_HUMAN	Protein kinase C-binding protein NELL2 precursor (NEL-like protein 2) (Nel-related protein 2)	0.25	-	exc	1 *	Secreted protein (By similarity)	extracellular region [NAS]	602320		816
Q9UT08 UniProt NPD GO	2AAA_SCHPO	Protein phosphatase PP2A regulatory subunit A (PR65) (Protein phosphatase 2A 65 kDa regulatory subun ...	0.25	-	cyt	0					590
P48613 UniProt NPD GO	TIPE_DROME	Protein tipE (Temperature-induced paralytic E)	0.25	-	end	1 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			452
P18292 UniProt NPD GO	THRB_RAT	Prothrombin precursor (EC 3.4.21.5) (Coagulation factor II) [Contains: Activation peptide fragment 1 ...	0.25	-	exc	0					617
Q5DRF5 UniProt NPD GO	PCDA1_PANTR	Protocadherin alpha 1 precursor (PCDH-alpha1)	0.25	+	nuc	0	Membrane; single-pass type I membrane protein (By similarity)				950
Q9UN74 UniProt NPD GO	PCDA4_HUMAN	Protocadherin alpha 4 precursor (PCDH-alpha4)	0.25	+	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606310		947
Q9NRJ7 UniProt NPD GO	PCDBG_HUMAN	Protocadherin beta 16 precursor (PCDH-beta16) (Protocadherin 3X)	0.25	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)	integral to membrane [NAS]	606345		776
Q9Y5E7 UniProt NPD GO	PCDB2_HUMAN	Protocadherin beta 2 precursor (PCDH-beta2)	0.25	-	end	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS]	606328		798
Q9Y5H1 UniProt NPD GO	PCDG2_HUMAN	Protocadherin gamma A2 precursor (PCDH-gamma-A2)	0.25	-	end	1	Membrane; single-pass type I membrane protein (By similarity)		606289		932
Q41249 UniProt NPD GO	PORA_CUCSA	Protochlorophyllide reductase, chloroplast precursor (EC 1.3.1.33) (PCR) (NADPH-protochlorophyllide ...	0.25	-	mit	0	Plastid; chloroplast				398
Q9SDT1 UniProt NPD GO	POR_DAUCA	Protochlorophyllide reductase, chloroplast precursor (EC 1.3.1.33) (PCR) (NADPH-protochlorophyllide ...	0.25	-	mit	0	Plastid; chloroplast				398
Q12887 UniProt NPD GO	COX10_HUMAN	Protoheme IX farnesyltransferase, mitochondrial precursor (EC 2.5.1.-) (Heme O synthase)	0.25	-	end	4	Mitochondrion; mitochondrial membrane; multi-pass membrane protein		602125		443
Q921A2 UniProt NPD GO	MYCT_RAT	Proton myo-inositol cotransporter (H(+)-myo-inositol cotransporter) (Hmit)	0.25	-	end	12 *	Membrane; multi-pass membrane protein				618
P40012 UniProt NPD GO	PPOX_YEAST	Protoporphyrinogen oxidase (EC 1.3.3.4) (PPO)	0.25	-	mit	0	Mitochondrion; mitochondrial inner membrane. Bound to the mitochondrial inner membrane with its acti ...	mitochondrion [IDA]			539
P55786 UniProt NPD GO	PSA_HUMAN	Puromycin-sensitive aminopeptidase (EC 3.4.11.-) (PSA)	0.25	-	mit	0	Cytoplasm (Potential). Nucleus (Potential)	cytosol [TAS]	606793		919
Q9SRK6 UniProt NPD GO	R37A1_ARATH	Putative 60S ribosomal protein L37a-1	0.25	-	mit	0					92
Q9FLT8 UniProt NPD GO	ATH16_ARATH	Putative ABC2 homolog 16	0.25	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				917
Q9NSE7 UniProt NPD GO	ABCCD_HUMAN	Putative ATP-binding cassette transporter C13	0.25	-	mit	2		nucleus [NAS]	608835		274
Q84L33 UniProt NPD GO	RD23A_ARATH	Putative DNA repair protein RAD23-1 (RAD23-like protein 1) (AtRAD23-1)	0.25	-	nuc	0	Nucleus (Probable)				371
Q5JRK9 UniProt NPD GO	GGEE3_HUMAN	Putative G antigen family E member 3 (Prostate-associated gene 2B protein) (PAGE-2B)	0.25	-	nuc	0					111
Q9NXG6 UniProt NPD GO	EGLX_HUMAN	Putative HIF-prolyl hydroxylase PH-4 (EC 1.14.11.-) (Hypoxia-inducible factor prolyl 4-hydroxylase)	0.25	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				502
P34541 UniProt NPD GO	YNC8_CAEEL	Putative RNA-binding protein R05D3.8	0.25	-	nuc	0					187
P52892 UniProt NPD GO	ALAT_YEAST	Putative alanine aminotransferase (EC 2.6.1.2) (Glutamic--pyruvic transaminase) (GPT) (Glutamic--ala ...	0.25	-	cyt	0	Cytoplasm (Potential)	cytoplasm [IDA] nucleus [IDA]			507
Q9LY77 UniProt NPD GO	ACA12_ARATH	Putative calcium-transporting ATPase 12, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 12 ...	0.25	-	end	8	Membrane; multi-pass membrane protein				1033
Q10276 UniProt NPD GO	KICH_SCHPO	Putative choline kinase (EC 2.7.1.32)	0.25	-	cyt	0	Cytoplasm (Potential)				456
Q9GUM7 UniProt NPD GO	CPLX1_CAEEL	Putative complexin-1	0.25	-	cyt	0	Cytoplasm; cytosol (By similarity)				143
Q95QT2 UniProt NPD GO	GALC_CAEEL	Putative galactocerebrosidase precursor (EC 3.2.1.46) (GALCERase) (Galactosylceramidase) (Galactosyl ...	0.25	-	mit	0					500
Q9SVS8 UniProt NPD GO	G3OX3_ARATH	Putative gibberellin 3-beta-dioxygenase 3 (EC 1.14.11.15) (Gibberellin 3 beta-hydroxylase 3) (GA 3-o ...	0.25	-	nuc	0					349
P58957 UniProt NPD GO	G39AB_DROME	Putative gustatory receptor 39a, isoform C	0.25	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			381
Q9V969 UniProt NPD GO	GR57A_DROME	Putative gustatory receptor 57a	0.25	-	end	8 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			416
Q8I1F0 UniProt NPD GO	G59B_DROER	Putative gustatory receptor 59b	0.25	-	end	10 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			587
Q6L439 UniProt NPD GO	R1A4_SOLDE	Putative late blight resistance protein homolog R1A-4	0.25	-	cyt	0	Cytoplasm (By similarity)				1096
Q6C2N7 UniProt NPD GO	ATG15_YARLI	Putative lipase ATG15 (EC 3.1.1.3) (Autophagy-related protein 15)	0.25	-	cyt	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				549
Q5A013 UniProt NPD GO	NNT1_CANAL	Putative nicotinamide N-methyltransferase (EC 2.1.1.1)	0.25	-	cyt	0	Cytoplasm (By similarity)				262
P81913 UniProt NPD GO	OR24A_DROME	Putative odorant receptor 24a	0.25	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			387
Q9VUK5 UniProt NPD GO	OR71A_DROME	Putative odorant receptor 71a	0.25	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			378
Q8LA14 UniProt NPD GO	PSK6_ARATH	Putative phytosulfokines 6 precursor (AtPSK6) (AtPSK3_2) [Contains: Phytosulfokine-alpha-like (PSK-a ...	0.25	-	exc	0	Secreted protein (By similarity)				81
Q20351 UniProt NPD GO	TPSB_CAEEL	Putative protein-tyrosine sulfotransferase (EC 2.8.2.20) (Tyrosylprotein sulfotransferase) (TPST)	0.25	-	cyt	0					259
Q9W1K5 UniProt NPD GO	SEST_DROME	Putative sestrin	0.25	-	cyt	0	Nucleus (By similarity)				497

You are viewing entries 45651 to 45700 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.