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
Q43087 UniProt NPD GO	PYRB2_PEA	Aspartate carbamoyltransferase 2, chloroplast precursor (EC 2.1.3.2) (Aspartate transcarbamylase 2) ...	0.16	-	cyt	0	Plastid; chloroplast				385
P01161 UniProt NPD GO	ANF_RAT	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP) (Prepronatriodilatin) [ ...	0.16	-	exc	1 *	Secreted protein			1T34	152
Q6C044 UniProt NPD GO	ATG18_YARLI	Autophagy-related protein 18	0.16	-	nuc	0	Membrane-associated. Peripheral membrane protein of pre-autophagosomal structure (PAS) and vacuole ( ...				400
Q9S7Z8 UniProt NPD GO	PIN3_ARATH	Auxin efflux carrier component 3 (AtPIN3)	0.16	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				640
P33489 UniProt NPD GO	ABP5_MAIZE	Auxin-binding protein 5 precursor (ABP) (ERABP5) (Fragment)	0.16	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen				150
Q38830 UniProt NPD GO	IAA12_ARATH	Auxin-responsive protein IAA12 (Indoleacetic acid-induced protein 12) (Protein BODENLOS)	0.16	-	mit	0	Nucleus				239
Q38822 UniProt NPD GO	IAA3_ARATH	Auxin-responsive protein IAA3 (Indoleacetic acid-induced protein 3) (Short hypocotyl) (Suppressor of ...	0.16	-	nuc	0	Nucleus (By similarity)				189
Q9C5X0 UniProt NPD GO	IAA34_ARATH	Auxin-responsive protein IAA34 (Indoleacetic acid-induced protein 34)	0.16	-	cyt	0	Nucleus (By similarity)				185
P82251 UniProt NPD GO	BAT1_HUMAN	B(0,+)-type amino acid transporter 1 (B(0,+)AT) (Glycoprotein-associated amino acid transporter b0,+ ...	0.16	-	end	12 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS] plasma membrane [TAS]	604144		487
Q9QXA6 UniProt NPD GO	BAT1_MOUSE	B(0,+)-type amino acid transporter 1 (B(0,+)AT) (Glycoprotein-associated amino acid transporter b0,+ ...	0.16	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				487
Q63604 UniProt NPD GO	NTRK2_RAT	BDNF/NT-3 growth factors receptor precursor (EC 2.7.10.1) (Neurotrophic tyrosine kinase receptor typ ...	0.16	-	nuc	2 *	Membrane; single-pass type I membrane protein				821
P58544 UniProt NPD GO	BTBD1_MOUSE	BTB/POZ domain-containing protein 1 (Glucose signal repressing protein)	0.16	-	nuc	0	Cytoplasm (By similarity). Cytoplasmic bodies (By similarity)				488
Q95M71 UniProt NPD GO	BIRC8_GORGO	Baculoviral IAP repeat-containing protein 8 (Inhibitor of apoptosis-like protein 2) (IAP-like protei ...	0.16	-	cyt	0	Cytoplasm (Probable)				236
Q95M72 UniProt NPD GO	BIRC8_PANTR	Baculoviral IAP repeat-containing protein 8 (Inhibitor of apoptosis-like protein 2) (IAP-like protei ...	0.16	-	cyt	0	Cytoplasm (Probable)				236
P24243 UniProt NPD GO	BRA6_CHITH	Balbiani ring A 67 kDa protein precursor (p67)	0.16	-	exc	0	Secreted protein				453
P02730 UniProt NPD GO	B3AT_HUMAN	Band 3 anion transport protein (Anion exchange protein 1) (AE 1) (Solute carrier family 4 member 1) ...	0.16	-	end	11	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	109270	3BTB	911
Q9FRV1 UniProt NPD GO	CHIA_SECCE	Basic endochitinase A precursor (EC 3.2.1.14) (Rye seed chitinase-a) (RSC-a)	0.16	-	vac	0		extracellular region [IC]			321
P21804 UniProt NPD GO	FGFR1_CHICK	Basic fibroblast growth factor receptor 1 precursor (EC 2.7.10.1)	0.16	-	end	1	Membrane; single-pass type I membrane protein				819
Q4W1I9 UniProt NPD GO	PER2_ZINEL	Basic peroxidase precursor 2 (EC 1.11.1.7) (ZePrx33.44) (ZePrx34.70)	0.16	-	nuc	1 *	Secreted protein (By similarity)				321
Q9D2C7 UniProt NPD GO	BI1_MOUSE	Bax inhibitor 1 (BI-1) (Testis-enhanced gene transcript)	0.16	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				237
P55062 UniProt NPD GO	BI1_RAT	Bax inhibitor 1 (BI-1) (Testis-enhanced gene transcript)	0.16	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				237
Q13323 UniProt NPD GO	BIK_HUMAN	Bcl-2-interacting killer (Apoptosis inducer NBK) (BP4) (BIP1)	0.16	-	cyt	1	Intracytoplasmic membrane; single-pass membrane protein. Around the nuclear envelope, and in cytopla ...		603392		160
Q91315 UniProt NPD GO	CRB11_RANCA	Beta crystallin A1-1	0.16	-	cyt	0					198
P07530 UniProt NPD GO	CRBB1_CHICK	Beta crystallin B1 (Beta-35)	0.16	-	cyt	0					238
Q9N294 UniProt NPD GO	B3GT5_PANPA	Beta-1,3-galactosyltransferase 5 (EC 2.4.1.-) (Beta-1,3-GalTase 5) (Beta3Gal-T5) (b3Gal-T5) (UDP-gal ...	0.16	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				301
Q04714 UniProt NPD GO	B2MG_MUSSP	Beta-2-microglobulin (Fragment)	0.16	-	nuc	0	Secreted protein				92
P01888 UniProt NPD GO	B2MG_BOVIN	Beta-2-microglobulin precursor (Lactollin)	0.16	-	exc	0	Secreted protein			1BMG	118
Q28524 UniProt NPD GO	ADRB3_MACMU	Beta-3 adrenergic receptor (Beta-3 adrenoceptor) (Beta-3 adrenoreceptor)	0.16	-	end	7 *	Membrane; multi-pass membrane protein				418
P26255 UniProt NPD GO	ADRB3_RAT	Beta-3 adrenergic receptor (Beta-3 adrenoceptor) (Beta-3 adrenoreceptor)	0.16	-	end	7 *	Membrane; multi-pass membrane protein				400
P30271 UniProt NPD GO	AMYB_SECCE	Beta-amylase (EC 3.2.1.2) (1,4-alpha-D-glucan maltohydrolase) (Fragment)	0.16	-	cyt	0					222
Q30KQ5 UniProt NPD GO	DB115_HUMAN	Beta-defensin 115 precursor (Defensin, beta 115) (Beta-defensin 15) (DEFB-15)	0.16	-	nuc	1 *	Secreted protein (By similarity)				88
Q9BYW3 UniProt NPD GO	DB126_HUMAN	Beta-defensin 126 precursor (Beta-defensin 26) (DEFB-26) (Epididymal secretory protein 13.2) (ESP13. ...	0.16	-	mit	1 *	Secreted protein	extracellular region [ISS]			111
Q9H1M4 UniProt NPD GO	DB127_HUMAN	Beta-defensin 127 precursor (Defensin, beta 127) (Beta-defensin 27) (DEFB-27)	0.16	-	nuc	0	Secreted protein (Potential)				99
Q9WTL0 UniProt NPD GO	BD03_MOUSE	Beta-defensin 3 precursor (Defensin, beta 3) (BD-3) (mBD-3)	0.16	-	mit	0	Secreted protein				63
P35697 UniProt NPD GO	ELIB_PHYDR	Beta-elicitin DRE-beta	0.16	-	nuc	0	Secreted protein				98
P12265 UniProt NPD GO	BGLR_MOUSE	Beta-glucuronidase precursor (EC 3.2.1.31)	0.16	-	vac	1 *	Lysosome. Endoplasmic reticulum. A small proportion is found in the endoplasmic reticulum				648
P06760 UniProt NPD GO	BGLR_RAT	Beta-glucuronidase precursor (EC 3.2.1.31)	0.16	-	end	1 *	Lysosome				648
P07686 UniProt NPD GO	HEXB_HUMAN	Beta-hexosaminidase beta chain precursor (EC 3.2.1.52) (N-acetyl-beta-glucosaminidase) (Beta-N-acety ...	0.16	-	vac	1 *	Lysosome		268800	1QBD	556
Q03248 UniProt NPD GO	BUP1_RAT	Beta-ureidopropionase (EC 3.5.1.6) (Beta-alanine synthase) (N-carbamoyl-beta-alanine amidohydrolase) ...	0.16	-	cyt	0	Cytoplasm				393
P82286 UniProt NPD GO	BMNL2_BOMVA	Bombinin-like peptides 2 precursor [Contains: Acidic peptide 2-1; Bombinin-like peptide 2 (BLP-2); O ...	0.16	-	end	0	Secreted protein				137
P17734 UniProt NPD GO	IBB_VIGUN	Bowman-Birk type seed trypsin and chymotrypsin inhibitor (BTCI)	0.16	-	nuc	0					83
P28662 UniProt NPD GO	BI3_MOUSE	Brain protein I3	0.16	-	nuc	2					125
P83799 UniProt NPD GO	BUBL_PENBR	Bubble protein	0.16	-	nuc	0	Secreted protein			1UOY	64
Q95NC8 UniProt NPD GO	CCR5_COLPO	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
Q95ND0 UniProt NPD GO	CCR5_ERYPA	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
P56439 UniProt NPD GO	CCR5_GORGO	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
P61755 UniProt NPD GO	CCR5_LOPAT	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
O97975 UniProt NPD GO	CCR5_MACAR	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
P61814 UniProt NPD GO	CCR5_MACFA	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352
P61813 UniProt NPD GO	CCR5_MACMU	C-C chemokine receptor type 5 (C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (CD195 antigen)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				352

You are viewing entries 55351 to 55400 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.