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
Q8N136 UniProt NPD GO	WDR69_HUMAN	WD repeat protein 69	0.15	-	cyt	0					415
Q6X7J5 UniProt NPD GO	WOX8_ARATH	WUSCHEL-related homeobox 8	0.15	-	cyt	0	Nucleus (By similarity)				325
P42717 UniProt NPD GO	BRK_PARID	Waspkinin	0.15	-		0	Secreted protein. Venom reservoirs				13
P01415 UniProt NPD GO	TXW2_NAJHH	Weak toxin CM-2	0.15	-	nuc	0	Secreted protein				61
P82935 UniProt NPD GO	TXWW_NAJKA	Weak tryptophan-containing neurotoxin (WTX)	0.15	-	nuc	0	Secreted protein				65
Q5GH68 UniProt NPD GO	XKR2_MOUSE	XK-related protein 2 (X Kell blood group-related, X-linked)	0.15	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				449
Q95333 UniProt NPD GO	XPP2_PIG	Xaa-Pro aminopeptidase 2 precursor (EC 3.4.11.9) (X-Pro aminopeptidase 2) (Membrane-bound aminopepti ...	0.15	-	vac	0	Cell membrane; lipid-anchor; GPI-anchor				673
Q502M5 UniProt NPD GO	YJDC_BRARE	YjeF domain-containing protein 1 (LSM16 protein homolog)	0.15	-	nuc	0					507
Q06731 UniProt NPD GO	ZN33B_HUMAN	Zinc finger protein 33B (Fragment)	0.15	-	nuc	0	Nucleus (Potential)	nucleus [NAS]			34
Q9H963 UniProt NPD GO	ZN702_HUMAN	Zinc finger protein 702	0.15	-	nuc	0	Nucleus (Potential)				129
Q22396 UniProt NPD GO	NAS20_CAEEL	Zinc metalloproteinase nas-20 precursor (EC 3.4.24.21) (Nematode astacin 20)	0.15	-	exc	0	Secreted protein (Potential)				379
P55112 UniProt NPD GO	NAS4_CAEEL	Zinc metalloproteinase nas-4 precursor (EC 3.4.24.21) (Nematode astacin 4)	0.15	-	exc	1 *	Secreted protein (Potential)				315
Q805F4 UniProt NPD GO	DISB_AGKPI	Zinc metalloproteinase piscivostatin-beta precursor (EC 3.4.24.-) [Contains: Disintegrin piscivostat ...	0.15	-	nuc	0	Secreted protein				483
Q62720 UniProt NPD GO	ZNT1_RAT	Zinc transporter 1 (ZnT-1) (Solute carrier family 30 member 1)	0.15	-	end	6 *	Cell membrane; multi-pass membrane protein (Probable). Localized on the basolateral surface of the e ...	integral to membrane [IDA] plasma membrane [IDA]			507
O08569 UniProt NPD GO	ZP3R_CAVPO	Zona pellucida 3 receptor precursor (Acrosomal matrix component 67) (Protein AM67) (p67)	0.15	-	nuc	0	Acrosome; acrosomal lumen. Sperm acrosomal matrix. Restricted to the M1 domain of the apical segment ...	acrosomal matrix [IDA]			533
Q90641 UniProt NPD GO	IPKA_CHICK	cAMP-dependent protein kinase inhibitor alpha (PKI-alpha) (cAMP-dependent protein kinase inhibitor, ...	0.15	-	nuc	0					75
Q5E9A4 UniProt NPD GO	RAE1L_BOVIN	mRNA-associated protein mrnp 41 (Rae1 protein homolog)	0.15	-	exc	0	Cytoplasm (By similarity). Nucleus (By similarity)				368
P78406 UniProt NPD GO	RAE1L_HUMAN	mRNA-associated protein mrnp 41 (Rae1 protein homolog)	0.15	-	exc	0	Cytoplasm. Nucleus	cytoplasm [TAS] cytoskeleton [TAS] nuclear outer membrane [TAS] nuclear pore [TAS] nucleus [TAS]	603343		368
Q8J256 UniProt NPD GO	PACC_PENEC	pH-response transcription factor pacC/RIM101 (Fragment)	0.15	-	nuc	0					70
Q874A5 UniProt NPD GO	PACC_PENEN	pH-response transcription factor pacC/RIM101 (Fragment)	0.15	-	nuc	0					47
Q9LSS3 UniProt NPD GO	SEN22_ARATH	tRNA-splicing endonuclease subunit Sen2-2 (EC 3.1.27.9) (AtSen2) (tRNA-intron endonuclease Sen2-2)	0.15	-	cyt	0	Nucleus (By similarity)				250
O74687 UniProt NPD GO	GEL1_ASPFU	1,3-beta-glucanosyltransferase gel1 precursor (EC 2.4.1.-) (Glucan elongating glucanosyltransferase ...	0.14	-	nuc	1	Cell membrane; lipid-anchor; GPI-anchor				452
Q08047 UniProt NPD GO	GLGB_MAIZE	1,4-alpha-glucan branching enzyme IIB, chloroplast precursor (EC 2.4.1.18) (Starch branching enzyme ...	0.14	-	cyt	0	Plastid; chloroplast. Plastid; amyloplast				799
Q28C60 UniProt NPD GO	PLCG_XENTR	1-acyl-sn-glycerol-3-phosphate acyltransferase eta (EC 2.3.1.51) (1-AGP acyltransferase 7) (1-AGPAT ...	0.14	-	cyt	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				522
P62261 UniProt NPD GO	1433E_BOVIN	14-3-3 protein epsilon (14-3-3E)	0.14	-	cyt	0	Cytoplasm (By similarity)				255
Q5ZMT0 UniProt NPD GO	1433E_CHICK	14-3-3 protein epsilon (14-3-3E)	0.14	-	cyt	0	Cytoplasm (By similarity)				255
P62258 UniProt NPD GO	1433E_HUMAN	14-3-3 protein epsilon (14-3-3E)	0.14	-	cyt	0	Cytoplasm (By similarity)		605066	2BR9	255
P62259 UniProt NPD GO	1433E_MOUSE	14-3-3 protein epsilon (14-3-3E)	0.14	-	cyt	0	Cytoplasm (By similarity)				255
P62260 UniProt NPD GO	1433E_RAT	14-3-3 protein epsilon (14-3-3E) (Mitochondrial import stimulation factor L subunit) (MSF L)	0.14	-	cyt	0	Cytoplasm (By similarity)				255
P62262 UniProt NPD GO	1433E_SHEEP	14-3-3 protein epsilon (14-3-3E) (Protein kinase C inhibitor protein 1) (KCIP-1)	0.14	-	cyt	0	Cytoplasm (By similarity)				255
Q24902 UniProt NPD GO	14331_ECHMU	14-3-3 protein homolog 1 (Emma14-3-3.1)	0.14	-	nuc	0					244
Q96451 UniProt NPD GO	1433B_SOYBN	14-3-3-like protein B (SGF14B) (Fragment)	0.14	-	cyt	0					247
P02815 UniProt NPD GO	SG16_MOUSE	16.5 kDa submandibular gland glycoprotein precursor (Salivary protein 1)	0.14	-	exc	0	Secreted protein; extracellular space (Probable)				138
P51379 UniProt NPD GO	GPMI_PORPU	2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.1) (Phosphoglyceromutase) (BPG ...	0.14	-	cyt	0	Plastid; chloroplast				534
Q6Y1R5 UniProt NPD GO	OXGR1_RAT	2-oxoglutarate receptor 1 (Alpha-ketoglutarate receptor 1) (G-protein coupled receptor 80) (P2Y puri ...	0.14	-	end	7 *	Membrane; multi-pass membrane protein				337
P81097 UniProt NPD GO	OLEOX_BRANA	20 kDa pollen coat protein (Fragment)	0.14	-		0					17
O18413 UniProt NPD GO	PRS8_DROME	26S protease regulatory subunit 8	0.14	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)	proteasome regulatory particle (sensu Eukar... [IDA]			405
P38764 UniProt NPD GO	RPN1_YEAST	26S proteasome regulatory subunit RPN1 (Proteasome non-ATPase subunit 1)	0.14	-	nuc	0		cytoplasm [IDA] endoplasmic reticulum [IDA] nucleus [IDA] proteasome regulatory particle, base subcom... [IPI]			992
P41878 UniProt NPD GO	RPN11_SCHPO	26S proteasome regulatory subunit rpn11 (Protein pad1)	0.14	-	cyt	0		nucleus [TAS] proteasome complex (sensu Eukaryota) [IPI]			308
O74440 UniProt NPD GO	RPN8_SCHPO	26S proteasome regulatory subunit rpn8	0.14	-	cyt	0		nucleus [TAS]			324
P22071 UniProt NPD GO	3BHS1_RAT	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type I (3Beta-HSD I) [Includes: 3-beta-hyd ...	0.14	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...				372
P29057 UniProt NPD GO	HMDH1_HEVBR	3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 (EC 1.1.1.34) (HMG-CoA reductase 1)	0.14	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Mitochondrion; m ...				575
Q9XEL8 UniProt NPD GO	HMDH2_CAPAN	3-hydroxy-3-methylglutaryl-coenzyme A reductase 2 (EC 1.1.1.34) (HMG-CoA reductase 2)	0.14	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				604
Q41437 UniProt NPD GO	HMDH2_SOLTU	3-hydroxy-3-methylglutaryl-coenzyme A reductase 2 (EC 1.1.1.34) (HMG-CoA reductase 2) (HMG2.2)	0.14	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				595
P17279 UniProt NPD GO	LEU2_RHIRA	3-isopropylmalate dehydratase (EC 4.2.1.33) (Isopropylmalate isomerase) (Alpha-IPM isomerase) (IPMI) ...	0.14	-	cyt	0					644
Q12452 UniProt NPD GO	ERG27_YEAST	3-keto-steroid reductase (EC 1.1.1.270)	0.14	-	cyt	0	Endoplasmic reticulum; peripheral membrane protein. And in lipid particles	endoplasmic reticulum [IDA] endoplasmic reticulum membrane [IDA] mitochondrial outer membrane [IDA]			347
Q8VCH0 UniProt NPD GO	THIKB_MOUSE	3-ketoacyl-CoA thiolase B, peroxisomal precursor (EC 2.3.1.16) (Beta-ketothiolase B) (Acetyl-CoA acy ...	0.14	-	nuc	0	Peroxisome (By similarity)				424
P07871 UniProt NPD GO	THIKB_RAT	3-ketoacyl-CoA thiolase B, peroxisomal precursor (EC 2.3.1.16) (Beta-ketothiolase B) (Acetyl-CoA acy ...	0.14	-	nuc	0	Peroxisome				424
Q6CE86 UniProt NPD GO	TSC10_YARLI	3-ketodihydrosphingosine reductase TSC10 (EC 1.1.1.102) (3-dehydrosphinganine reductase) (KDS reduct ...	0.14	-	end	3 *	Endoplasmic reticulum (By similarity)				372
Q93X62 UniProt NPD GO	FABG1_BRANA	3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplast precursor (EC 1.1.1.100) (3-ketoacyl-acyl ...	0.14	-	mit	0	Plastid; chloroplast (By similarity). And non-photosynthetic plastids (By similarity)			1EDO	320

You are viewing entries 57851 to 57900 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.