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
P34274 UniProt NPD GO	YO29_CAEEL	Hypothetical protein ZK688.9	0.26	-	mit	0					281
P25351 UniProt NPD GO	YCR3_YEAST	Hypothetical transport protein YCR023C	0.26	-	end	10 *	Membrane; multi-pass membrane protein (Probable)				611
P25601 UniProt NPD GO	YCH5_YEAST	Hypothetical transposon Ty5-1 protein YCL075W	0.26	-	nuc	0					146
P01609 UniProt NPD GO	KV1Q_HUMAN	Ig kappa chain V-I region Scw	0.26	-	nuc	0		extracellular region [NAS]			108
P01638 UniProt NPD GO	KV5F_MOUSE	Ig kappa chain V-V region L6 precursor (Fragment)	0.26	-	exc	0					115
P01642 UniProt NPD GO	KV5I_MOUSE	Ig kappa chain V-V region L7 precursor (Fragment)	0.26	-	exc	0				1J1X	115
P03988 UniProt NPD GO	MUC_RABIT	Ig mu chain C region secreted form	0.26	-	nuc	0	Secreted protein (Probable)				458
P04220 UniProt NPD GO	MUCB_HUMAN	Ig mu heavy chain disease protein (BOT)	0.26	-	nuc	0		membrane fraction [NAS]			391
P83977 UniProt NPD GO	IGNAR_GINCI	IgNAR transmembrane form NE (Fragment)	0.26	-	mit	0					95
Q19969 UniProt NPD GO	IMA3_CAEEL	Importin alpha-3 subunit (Karyopherin alpha-3 subunit)	0.26	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IEP] nuclear pore [IMP]			514
P33046 UniProt NPD GO	INDC_BOVIN	Indolicidin precursor (Cathelicidin-4)	0.26	-	mit	1 *	Secreted protein			1QXQ	144
P04088 UniProt NPD GO	INHBB_PIG	Inhibin beta B chain precursor (Activin beta-B chain)	0.26	-	end	0	Secreted protein	extracellular region [ISS]			407
Q9VWL5 UniProt NPD GO	INX5_DROME	Innexin inx5	0.26	-	end	3	Membrane; multi-pass membrane protein (Potential)	gap junction [IEP] integral to membrane [NAS]			419
P60268 UniProt NPD GO	SCX3_BUTEU	Insectotoxin-I3 (BeI3)	0.26	-	nuc	0	Secreted protein				36
Q5SF07 UniProt NPD GO	IF2B2_MOUSE	Insulin-like growth factor 2 mRNA-binding protein 2 (IGF-II mRNA-binding protein 2) (IMP-2)	0.26	-	cyt	0	Cytoplasm (Probable)				592
Q5RB68 UniProt NPD GO	IF2B2_PONPY	Insulin-like growth factor 2 mRNA-binding protein 2 (IGF-II mRNA-binding protein 2) (IMP-2)	0.26	-	cyt	0	Cytoplasm (Probable)				556
Q90326 UniProt NPD GO	IGF1B_CYPCA	Insulin-like growth factor I, juvenile form precursor	0.26	-	nuc	0	Secreted protein				161
P17301 UniProt NPD GO	ITA2_HUMAN	Integrin alpha-2 precursor (Platelet membrane glycoprotein Ia) (GPIa) (Collagen receptor) (VLA-2 alp ...	0.26	-	end	1 *	Membrane; single-pass type I membrane protein	integrin complex [TAS] plasma membrane [TAS]	192974	1V7P	1181
P32592 UniProt NPD GO	ITB2_BOVIN	Integrin beta-2 precursor (Cell surface adhesion glycoproteins LFA-1/CR3/p150,95 subunit beta) (Comp ...	0.26	-	end	1	Membrane; single-pass type I membrane protein				769
P05107 UniProt NPD GO	ITB2_HUMAN	Integrin beta-2 precursor (Cell surface adhesion glycoproteins LFA-1/CR3/p150,95 subunit beta) (Comp ...	0.26	-	end	1	Membrane; single-pass type I membrane protein	integrin complex [NAS]	116920	1YUK	769
O54890 UniProt NPD GO	ITB3_MOUSE	Integrin beta-3 precursor (Platelet membrane glycoprotein IIIa) (GPIIIa) (CD61 antigen)	0.26	-	exc	1 *	Membrane; single-pass type I membrane protein	external side of plasma membrane [IDA]			787
Q5NKV9 UniProt NPD GO	ICAM1_GORGO	Intercellular adhesion molecule 1 precursor (ICAM-1)	0.26	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				532
Q16552 UniProt NPD GO	IL17_HUMAN	Interleukin-17A precursor (IL-17A) (IL-17) (Cytotoxic T-lymphocyte-associated antigen 8) (CTLA-8)	0.26	-	exc	0	Secreted protein	extracellular space [TAS]	603149		155
Q08081 UniProt NPD GO	IL2_MERUN	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.26	-	exc	0	Secreted protein				155
Q14213 UniProt NPD GO	IL27B_HUMAN	Interleukin-27 beta chain precursor (IL-27B) (Epstein-Barr virus-induced gene 3 protein) (EBV-induce ...	0.26	-	mit	0	Secreted protein	extracellular space [TAS] plasma membrane [TAS]	605816		229
P48093 UniProt NPD GO	IL5_MACMU	Interleukin-5 precursor (IL-5) (T-cell replacing factor) (TRF) (Eosinophil differentiation factor)	0.26	-	exc	0	Secreted protein				134
Q28586 UniProt NPD GO	IL5_SHEEP	Interleukin-5 precursor (IL-5) (T-cell replacing factor) (TRF) (Eosinophil differentiation factor)	0.26	-	end	0	Secreted protein				132
P26893 UniProt NPD GO	IL6_PIG	Interleukin-6 precursor (IL-6)	0.26	-	exc	0	Secreted protein				212
P20014 UniProt NPD GO	ACEA_CANTR	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.26	-	cyt	0	Peroxisome				550
Q8J232 UniProt NPD GO	ACEA_MAGGR	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.26	-	cyt	0	Peroxisome (By similarity)				547
O42493 UniProt NPD GO	NEUI_FUGRU	Isoticin-neurophysin IT 1 precursor [Contains: Isotocin (IT); Neurophysin IT 1]	0.26	-	exc	1 *					155
P57087 UniProt NPD GO	JAM2_HUMAN	Junctional adhesion molecule B precursor (JAM-B) (Junctional adhesion molecule 2) (Vascular endothel ...	0.26	-	nuc	1	Cell membrane; cell-cell junction; tight junction; single-pass type I membrane protein (By similarit ...	integral to plasma membrane [NAS]	606870		298
P50420 UniProt NPD GO	CASK_CAPSU	Kappa-casein precursor	0.26	-	exc	0	Secreted protein				192
Q9NR64 UniProt NPD GO	KLHL1_HUMAN	Kelch-like protein 1	0.26	-	cyt	0	Cytoplasm	cytoplasm [NAS]	605332		748
Q5U374 UniProt NPD GO	KLH12_BRARE	Kelch-like protein 12	0.26	-	cyt	0					564
Q53HC5 UniProt NPD GO	KLH26_HUMAN	Kelch-like protein 26	0.26	-	nuc	0					615
Q9DE66 UniProt NPD GO	KERA_COTJA	Keratocan precursor (KTN) (Keratan sulfate proteoglycan keratocan)	0.26	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				353
Q14953 UniProt NPD GO	KI2S5_HUMAN	Killer cell immunoglobulin-like receptor 2DS5 precursor (MHC class I NK cell receptor) (Natural kill ...	0.26	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	604956		304
P47149 UniProt NPD GO	NNF1_YEAST	Kinetochore-associated protein NNF1	0.26	-	nuc	0	Nucleus. Associated with the kinetochore	kinetochore [IDA] MIND complex [IDA] spindle pole [IDA]			201
Q09108 UniProt NPD GO	SCF_CHICK	Kit ligand precursor (C-kit ligand) (Stem cell factor) (SCF) (Mast cell growth factor) (MGF)	0.26	-	exc	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				287
Q74Z24 UniProt NPD GO	LYS5_ASHGO	L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase (EC 2.7.8.-) (AASD-PPT)	0.26	-	cyt	0					276
Q9C8V8 UniProt NPD GO	LBD5_ARATH	LOB domain-containing protein 5	0.26	-	nuc	0					122
P83790 UniProt NPD GO	LED2_PHYAM	Lectin-D2 (PL-D2)	0.26	-	nuc	0				1ULN	82
Q588F9 UniProt NPD GO	LEP_ORYLA	Leptin precursor	0.26	-	nuc	0	Secreted protein (Probable)				155
Q28504 UniProt NPD GO	LEP_MACMU	Leptin precursor (Obesity factor)	0.26	-	end	0	Secreted protein (Probable)				167
P13503 UniProt NPD GO	SYLM_SACDO	Leucyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.4) (Leucine--tRNA ligase) (LeuRS)	0.26	-	mit	0	Mitochondrion; mitochondrial matrix				894
P29376 UniProt NPD GO	LTK_HUMAN	Leukocyte tyrosine kinase receptor precursor (EC 2.7.10.1) (Protein tyrosine kinase 1)	0.26	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS] soluble fraction [TAS]	151520		864
Q6YXN5 UniProt NPD GO	CHLB_PHYPA	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.26	-	cyt	0	Plastid; chloroplast				510
Q85X76 UniProt NPD GO	CHLB_PINKO	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.26	-	cyt	0	Plastid; chloroplast				510
Q9T4F6 UniProt NPD GO	CHLN_NEPOL	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.26	-	cyt	0	Plastid; chloroplast				431

You are viewing entries 44301 to 44350 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.