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
Q92597 UniProt NPD GO	NDRG1_HUMAN	Protein NDRG1 (N-myc downstream-regulated gene 1 protein) (Differentiation-related gene 1 protein) ( ...	0.12	-	cyt	0	Cytoplasm. Nucleus. Cell membrane. Whereas in prostate epithelium and placental chorion it is locate ...		605262		394
Q62433 UniProt NPD GO	NDRG1_MOUSE	Protein NDRG1 (N-myc downstream-regulated gene 1 protein) (Protein Ndr1)	0.12	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				394
Q756T2 UniProt NPD GO	OS9_ASHGO	Protein OS-9 homolog precursor	0.12	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; lumenal side (By ...				421
Q6C938 UniProt NPD GO	PNS1_YARLI	Protein PNS1	0.12	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				571
Q9HCY8 UniProt NPD GO	S10AE_HUMAN	Protein S100-A14 (S100 calcium-binding protein A14) (S114)	0.12	-	nuc	0	Cytoplasm		607986		104
P06702 UniProt NPD GO	S10A9_HUMAN	Protein S100-A9 (S100 calcium-binding protein A9) (Calgranulin-B) (Migration inhibitory factor-relat ...	0.12	-	cyt	0			123886	1XK4	114
P24609 UniProt NPD GO	TAP2_ANTMA	Protein TAP2 precursor	0.12	-	exc	1 *					131
P93003 UniProt NPD GO	TFL1_ARATH	Protein TERMINAL FLOWER 1	0.12	-	cyt	0	Cytoplasm (By similarity)			1WKO	177
Q5RE10 UniProt NPD GO	TSSC1_PONPY	Protein TSSC1	0.12	-	cyt	0					414
P28096 UniProt NPD GO	WNT4_STRPU	Protein Wnt-4 (Fragment)	0.12	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				133
P28117 UniProt NPD GO	WNT5A_EUMSK	Protein Wnt-5a (Fragment)	0.12	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				116
P28138 UniProt NPD GO	WNT7A_PLEJO	Protein Wnt-7a (Fragment)	0.12	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
P56706 UniProt NPD GO	WNT7B_HUMAN	Protein Wnt-7b precursor	0.12	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix	extracellular region [NAS]	601967		349
P28047 UniProt NPD GO	WNT7B_MOUSE	Protein Wnt-7b precursor	0.12	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix				349
P53108 UniProt NPD GO	YIP5_YEAST	Protein YIP5 (YPT-interacting protein 5)	0.12	-	end	4	Membrane; multi-pass membrane protein (Potential)				310
P38079 UniProt NPD GO	YRO2_YEAST	Protein YRO2	0.12	+	end	7 *	Membrane; multi-pass membrane protein	bud [IDA] mitochondrion [IDA]			344
Q29RV1 UniProt NPD GO	PDIA4_BOVIN	Protein disulfide-isomerase A4 precursor (EC 5.3.4.1)	0.12	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				643
Q5R875 UniProt NPD GO	TXD10_PONPY	Protein disulfide-isomerase TXNDC10 precursor (EC 5.3.4.1) (Thioredoxin domain-containing protein 10 ...	0.12	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				454
Q02031 UniProt NPD GO	HUNB_PHOPA	Protein hunchback (Fragment)	0.12	-	nuc	0	Nucleus (Probable)				50
Q01789 UniProt NPD GO	HUNB_PLADU	Protein hunchback (Fragment)	0.12	-	nuc	0	Nucleus (Probable)				50
Q02033 UniProt NPD GO	HUNB_SCHLA	Protein hunchback (Fragment)	0.12	-	nuc	0	Nucleus (Probable)				50
Q5SGD2 UniProt NPD GO	PP2CL_HUMAN	Protein phosphatase 2C isoform epsilon (EC 3.1.3.16) (PP2C-epsilon) (Protein phosphatase 1L) (Protei ...	0.12	-	mit	0	Membrane; single-pass type I membrane protein (Potential)				360
Q96MI6 UniProt NPD GO	PP2CE_HUMAN	Protein phosphatase 2C isoform eta (EC 3.1.3.16) (PP2C-eta) (PP2CE) (Protein phosphatase 1M)	0.12	-	cyt	0	Nucleus (By similarity)	nucleus [ISS]	608979		270
P25416 UniProt NPD GO	QUTG_EMENI	Protein qutG	0.12	-	nuc	0					330
P22126 UniProt NPD GO	RAS1_NEUCR	Protein ras-1	0.12	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				213
P34967 UniProt NPD GO	RIP2_PHYDI	Protein synthesis inhibitor PD-S2 (EC 3.2.2.22) (Ribosome-inactivating protein PD-S2) (rRNA N-glycos ...	0.12	-	nuc	0					265
Q27869 UniProt NPD GO	PIMT_DROME	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (EC 2.1.1.77) (Protein-beta-aspartate methyl ...	0.12	-	nuc	0	Cytoplasm (By similarity)			1R18	226
Q9Y2J8 UniProt NPD GO	PADI2_HUMAN	Protein-arginine deiminase type-2 (EC 3.5.3.15) (Protein-arginine deiminase type II) (Peptidylargini ...	0.12	-	mit	0	Cytoplasm		607935		665
P22735 UniProt NPD GO	TGM1_HUMAN	Protein-glutamine gamma-glutamyltransferase K (EC 2.3.2.13) (Transglutaminase K) (TGase K) (TGK) (TG ...	0.12	-	cyt	0	Membrane; lipid-anchor	cornified envelope [TAS] intrinsic to membrane [IDA]	242300		817
P22758 UniProt NPD GO	TGM1_RABIT	Protein-glutamine gamma-glutamyltransferase K (EC 2.3.2.13) (Transglutaminase K) (TGase K) (TGK) (TG ...	0.12	-	cyt	0	Membrane; peripheral membrane protein				836
P06873 UniProt NPD GO	PRTK_TRIAL	Proteinase K precursor (EC 3.4.21.64) (Tritirachium alkaline proteinase) (Endopeptidase K)	0.12	-	exc	0				3PRK	384
P19221 UniProt NPD GO	THRB_MOUSE	Prothrombin precursor (EC 3.4.21.5) (Coagulation factor II) [Contains: Activation peptide fragment 1 ...	0.12	-	exc	0					618
P13406 UniProt NPD GO	FYN_XENLA	Proto-oncogene tyrosine-protein kinase Fyn (EC 2.7.10.2) (p59-Fyn)	0.12	-	nuc	0					536
Q12866 UniProt NPD GO	MERTK_HUMAN	Proto-oncogene tyrosine-protein kinase MER precursor (EC 2.7.10.1) (C-mer) (Receptor tyrosine kinase ...	0.12	-	end	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS] soluble fraction [TAS]	604705		999
Q63418 UniProt NPD GO	PCDH3_RAT	Protocadherin 3 precursor	0.12	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				797
O80333 UniProt NPD GO	POR_MARPA	Protochlorophyllide reductase, chloroplast precursor (EC 1.3.1.33) (PCR) (NADPH-protochlorophyllide ...	0.12	-	mit	0	Plastid; chloroplast				458
Q75F43 UniProt NPD GO	COX10_ASHGO	Protoheme IX farnesyltransferase, mitochondrial precursor (EC 2.5.1.-) (Heme O synthase)	0.12	-	nuc	4	Mitochondrion; mitochondrial membrane; multi-pass membrane protein				435
Q60HD5 UniProt NPD GO	PPOX_MACFA	Protoporphyrinogen oxidase (EC 1.3.3.4) (PPO)	0.12	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...	intrinsic to mitochondrial inner membrane [ISS] mitochondrial membrane [ISS]			477
P55826 UniProt NPD GO	PPOC_ARATH	Protoporphyrinogen oxidase, chloroplast precursor (EC 1.3.3.4) (PPO)	0.12	-	nuc	0	Plastid; chloroplast (Potential)				537
P48254 UniProt NPD GO	CLPPL_CYAPA	Putative ATP-dependent Clp protease proteolytic subunit-like (Endopeptidase Clp-like)	0.12	-	nuc	0	Plastid; cyanelle				199
Q09964 UniProt NPD GO	YS94_CAEEL	Putative G-protein coupled receptor B0244.4	0.12	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				309
Q9SRL8 UniProt NPD GO	LBD21_ARATH	Putative LOB domain-containing protein 21	0.12	-	mit	0					165
Q10941 UniProt NPD GO	UGT46_CAEEL	Putative UDP-glucuronosyltransferase ugt-46 precursor (EC 2.4.1.17) (UDPGT)	0.12	-	end	1 *					531
Q22181 UniProt NPD GO	UGT56_CAEEL	Putative UDP-glucuronosyltransferase ugt-56 precursor (EC 2.4.1.17) (UDPGT)	0.12	-	end	2 *					524
Q9SZW5 UniProt NPD GO	AHM4_ARATH	Putative cadmium/zinc-transporting ATPase 4 (EC 3.6.3.3) (EC 3.6.3.5)	0.12	-	end	6	Membrane; multi-pass membrane protein				760
Q20781 UniProt NPD GO	CAH1_CAEEL	Putative carbonic anhydrase-like protein 1 precursor	0.12	-	mit	0	Secreted protein (Potential)				365
Q9V4Q0 UniProt NPD GO	GR43B_DROME	Putative chemosensory receptor 43b	0.12	+	end	8 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			430
Q93650 UniProt NPD GO	GLS2_CAEEL	Putative glutaminase F30F8.2 (EC 3.5.1.2) (GLS) (L-glutamine amidohydrolase)	0.12	-	cyt	0					583
P58985 UniProt NPD GO	GR59D_DROME	Putative gustatory receptor 59d	0.12	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			390
Q9W0M2 UniProt NPD GO	GR61A_DROME	Putative gustatory receptor 61a	0.12	-	end	5	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			436

You are viewing entries 61751 to 61800 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.