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
P01612 UniProt NPD GO	KV1T_HUMAN	Ig kappa chain V-I region Mev	0.27	-	nuc	0		extracellular region [NAS]			109
P01623 UniProt NPD GO	KV3E_HUMAN	Ig kappa chain V-III region WOL	0.27	-	nuc	0		extracellular region [NAS]			109
P01874 UniProt NPD GO	MUC_CANFA	Ig mu chain C region	0.27	-	cyt	0					450
P01871 UniProt NPD GO	MUC_HUMAN	Ig mu chain C region	0.27	-	nuc	0		membrane fraction [NAS]	147020		454
P06337 UniProt NPD GO	MUC_MESAU	Ig mu chain C region	0.27	-	nuc	0					454
Q99N28 UniProt NPD GO	IGS4B_MOUSE	Immunoglobulin superfamily member 4B precursor (Nectin-like protein 1) (Necl-1) (TSLC1-like protein ...	0.27	-	end	1	Cell membrane; cell-cell junction; single-pass type I membrane protein. Localized at the cell-cell a ...	intercellular junction [IDA]			396
Q7ZV50 UniProt NPD GO	IAG2_BRARE	Implantation-associated protein homolog precursor	0.27	-	end	4	Membrane; multi-pass membrane protein (Potential)				328
O81829 UniProt NPD GO	GH35_ARATH	Indole-3-acetic acid-amido synthetase GH3.5 (EC 6.3.2.-) (Auxin-responsive GH3-like protein 5) (AtGH ...	0.27	-	cyt	0					612
Q80V72 UniProt NPD GO	IP6K2_MOUSE	Inositol hexakisphosphate kinase 2 (EC 2.7.4.21) (InsP6 kinase 2) (Inositol hexakisphosphate kinase ...	0.27	-	mit	0	Nucleus (By similarity)	nucleus [IDA]			448
O97477 UniProt NPD GO	INO1_DROME	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.27	-	nuc	0	Cytoplasm (By similarity)				565
Q93YN9 UniProt NPD GO	IPPK_ARATH	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.27	-	nuc	0					451
Q9Y6M1 UniProt NPD GO	IF2B2_HUMAN	Insulin-like growth factor 2 mRNA-binding protein 2 (IGF-II mRNA-binding protein 2) (IMP-2) (Hepatoc ...	0.27	-	cyt	0	Cytoplasm (Probable)	cytoplasm [TAS]	608289	2CQH	556
P49705 UniProt NPD GO	IBP2_CHICK	Insulin-like growth factor-binding protein 2 precursor (IGFBP-2) (IBP-2) (IGF-binding protein 2)	0.27	-	nuc	0	Secreted protein				311
Q28893 UniProt NPD GO	IBP4_SHEEP	Insulin-like growth factor-binding protein 4 (IGFBP-4) (IBP-4) (IGF-binding protein 4)	0.27	-	nuc	0	Secreted protein				237
P56199 UniProt NPD GO	ITA1_HUMAN	Integrin alpha-1 (Laminin and collagen receptor) (VLA-1) (CD49a antigen)	0.27	-	cyt	1	Membrane; single-pass type I membrane protein	integrin complex [TAS]	192968	1QCY	1151
P24063 UniProt NPD GO	ITAL_MOUSE	Integrin alpha-L precursor (Leukocyte adhesion glycoprotein LFA-1 alpha chain) (LFA-1A) (Leukocyte f ...	0.27	-	end	1	Membrane; single-pass type I membrane protein				1163
Q9GLP0 UniProt NPD GO	ITB1_PIG	Integrin beta-1 precursor (Fibronectin receptor subunit beta) (Integrin VLA-4 subunit beta) (CD29 an ...	0.27	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				798
Q8SQB8 UniProt NPD GO	ITB6_BOVIN	Integrin beta-6 precursor	0.27	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				788
P18564 UniProt NPD GO	ITB6_HUMAN	Integrin beta-6 precursor	0.27	-	nuc	1	Membrane; single-pass type I membrane protein	integrin complex [TAS]	147558	1LH9	788
P26013 UniProt NPD GO	ITB8_RABIT	Integrin beta-8 precursor	0.27	-	exc	1	Membrane; single-pass type I membrane protein				768
Q9XSQ6 UniProt NPD GO	IL12A_HORSE	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.27	-	exc	0	Secreted protein				222
Q96PD4 UniProt NPD GO	IL17F_HUMAN	Interleukin-17F precursor (IL-17F) (Interleukin-24) (IL-24) (Cytokine ML-1)	0.27	-	nuc	0	Secreted protein	extracellular region [NAS]	606496	1JPY	153
P47966 UniProt NPD GO	IL4_MERUN	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.27	-	exc	0	Secreted protein				143
Q08125 UniProt NPD GO	IL5_RAT	Interleukin-5 precursor (IL-5) (T-cell replacing factor) (TRF) (B-cell growth factor II) (BCGF-II) ( ...	0.27	-	exc	0	Secreted protein				132
P52173 UniProt NPD GO	IL5_BOVIN	Interleukin-5 precursor (IL-5) (T-cell replacing factor) (TRF) (Eosinophil differentiation factor)	0.27	-	end	0	Secreted protein				134
P41693 UniProt NPD GO	IL6_MUSVI	Interleukin-6 (IL-6) (Fragment)	0.27	-	nuc	0	Secreted protein				125
Q9XT80 UniProt NPD GO	IL6_DELLE	Interleukin-6 precursor (IL-6)	0.27	-	exc	0	Secreted protein				208
Q5I6E3 UniProt NPD GO	IL6_MACTH	Interleukin-6 precursor (IL-6)	0.27	-	exc	1 *	Secreted protein	extracellular region [ISS] extracellular space [ISS]			212
Q01114 UniProt NPD GO	IL9R_MOUSE	Interleukin-9 receptor precursor (IL-9R) (CD129 antigen)	0.27	-	nuc	1	Cell membrane; single-pass type I membrane protein. Secreted protein				468
P93110 UniProt NPD GO	ACEA_CUCMA	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.27	-	exc	0	Glyoxysome				576
Q9H478 UniProt NPD GO	KCQ1D_HUMAN	KCNQ1 downstream neighbor protein (Beckwith-Wiedemann region transcript protein)	0.27	-	nuc	0					68
Q6UW63 UniProt NPD GO	KDEL1_HUMAN	KDEL motif-containing protein 1 precursor	0.27	-	end	0	Endoplasmic reticulum; Endoplasmic reticulum lumen (By similarity)				502
Q7JIG6 UniProt NPD GO	KLK15_SAGOE	Kallikrein-15 precursor (EC 3.4.21.-)	0.27	-	exc	0	Secreted protein (Probable)				255
Q9Y337 UniProt NPD GO	KLK5_HUMAN	Kallikrein-5 precursor (EC 3.4.21.-) (Stratum corneum tryptic enzyme) (Kallikrein-like protein 2) (K ...	0.27	-	exc	1 *	Secreted protein	extracellular region [NAS] extracellular space [TAS]	605643		293
Q28441 UniProt NPD GO	CASK_HIPAM	Kappa-casein (Fragment)	0.27	-	nuc	0	Secreted protein				145
Q28451 UniProt NPD GO	CASK_LAMGU	Kappa-casein (Fragment)	0.27	-	nuc	0	Secreted protein				125
P79139 UniProt NPD GO	CASK_CAMDR	Kappa-casein precursor	0.27	-	exc	0	Secreted protein				182
Q53G59 UniProt NPD GO	KLH12_HUMAN	Kelch-like protein 12 (CUL3-interacting protein 1)	0.27	-	cyt	0					568
Q8BZM0 UniProt NPD GO	KLH12_MOUSE	Kelch-like protein 12 (CUL3-interacting protein 1)	0.27	-	cyt	0					568
Q8R2H4 UniProt NPD GO	KLH12_RAT	Kelch-like protein 12 (CUL3-interacting protein 1)	0.27	-	cyt	0					568
Q53GT1 UniProt NPD GO	KLH22_HUMAN	Kelch-like protein 22	0.27	-	cyt	0					634
Q99JN2 UniProt NPD GO	KLH22_MOUSE	Kelch-like protein 22	0.27	-	cyt	0					634
O42235 UniProt NPD GO	KERA_CHICK	Keratocan precursor (KTN) (Keratan sulfate proteoglycan keratocan)	0.27	-	exc	0	Secreted protein; extracellular space; extracellular matrix				353
P83556 UniProt NPD GO	KI3L1_RAT	Killer cell immunoglobulin-like receptor 3DL1 precursor	0.27	-	gol	1	Membrane; single-pass type I membrane protein				422
P21581 UniProt NPD GO	SCF_RAT	Kit ligand precursor (C-kit ligand) (Stem cell factor) (SCF) (Mast cell growth factor) (MGF) (Hemato ...	0.27	-	cyt	1	Isoform 1, isoform 2: Cell membrane; single-pass type I membrane protein (By similarity). Processed ...				273
Q5NVE1 UniProt NPD GO	ADPPT_PONPY	L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase (EC 2.7.8.-) (4'-phosphopa ...	0.27	-	mit	0	Cytoplasm (By similarity)				309
O24467 UniProt NPD GO	LE14B_PRUAR	LEC14B homolog	0.27	-	nuc	0					475
P14755 UniProt NPD GO	CRYL1_RABIT	Lambda-crystallin	0.27	-	mit	0					319
Q9XSW9 UniProt NPD GO	LEP_SMICR	Leptin precursor (Obesity factor)	0.27	-	end	0	Secreted protein (Probable)				167
O75473 UniProt NPD GO	LGR5_HUMAN	Leucine-rich repeat-containing G-protein coupled receptor 5 precursor (Orphan G-protein coupled rece ...	0.27	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	606667		907

You are viewing entries 43301 to 43350 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.