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
Q61JS7 UniProt NPD GO	TIM50_CAEBR	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.70	-	nuc	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				456
Q874C1 UniProt NPD GO	TIM50_NEUCR	Import inner membrane translocase subunit tim-50, mitochondrial precursor	0.70	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein				540
O14063 UniProt NPD GO	IMA1_SCHPO	Importin subunit alpha (Karyopherin subunit alpha) (Serine-rich RNA polymerase I suppressor protein) ...	0.70	-	nuc	0	Nucleus	nucleus [IDA]			542
P55102 UniProt NPD GO	INHBA_HORSE	Inhibin beta A chain precursor (Activin beta-A chain)	0.70	+	nuc	0	Secreted protein (By similarity)				426
Q9VEZ5 UniProt NPD GO	IKKB_DROME	Inhibitor of nuclear factor kappa B kinase subunit beta (EC 2.7.11.1) (DmIKK-beta) (Immune response ...	0.70	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [IDA]			751
Q14571 UniProt NPD GO	ITPR2_HUMAN	Inositol 1,4,5-trisphosphate receptor type 2 (Type 2 inositol 1,4,5-trisphosphate receptor) (Type 2 ...	0.70	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] plasma membrane [TAS]	600144		2701
Q9Z329 UniProt NPD GO	ITPR2_MOUSE	Inositol 1,4,5-trisphosphate receptor type 2 (Type 2 inositol 1,4,5-trisphosphate receptor) (Type 2 ...	0.70	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				2701
P53408 UniProt NPD GO	ISL2A_ONCTS	Insulin gene enhancer protein ISL-2A (Islet-2A)	0.70	+	nuc	0	Nucleus				358
P24594 UniProt NPD GO	IBP5_RAT	Insulin-like growth factor-binding protein 5 precursor (IGFBP-5) (IBP-5) (IGF-binding protein 5)	0.70	-	exc	0	Secreted protein				271
Q05718 UniProt NPD GO	IBP6_BOVIN	Insulin-like growth factor-binding protein 6 precursor (IGFBP-6) (IBP-6) (IGF-binding protein 6)	0.70	-	exc	0	Secreted protein				237
P05010 UniProt NPD GO	IFNAD_BOVIN	Interferon alpha-D precursor	0.70	-	mit	1 *	Secreted protein				189
Q13099 UniProt NPD GO	IFT88_HUMAN	Intraflagellar transport 88 homolog (Tetratricopeptide repeat protein 10) (TPR repeat protein 10) (R ...	0.70	-	nuc	0			600595		824
Q8K3E5 UniProt NPD GO	AHI1_MOUSE	Jouberin (Abelson helper integration site 1 protein) (AHI-1)	0.70	+	nuc	0					1047
Q9BR39 UniProt NPD GO	JPH2_HUMAN	Junctophilin-2 (Junctophilin type 2) (JP-2)	0.70	+	nuc	1	Cell membrane; peripheral membrane protein (By similarity). Endoplasmic reticulum; endoplasmic retic ...		605267		696
P50090 UniProt NPD GO	KEL2_YEAST	Kelch repeat-containing protein 2	0.70	-	nuc	0		bud neck [IDA] bud tip [IDA] mating projection tip [IDA]			882
P46825 UniProt NPD GO	KLC_LOLPE	Kinesin light chain (KLC)	0.70	-	nuc	0					571
P28743 UniProt NPD GO	KIP2_YEAST	Kinesin-like protein KIP2	0.70	-	mit	0		cytoplasmic microtubule [IDA] kinesin complex [TAS] mitochondrion [IDA]			706
Q8TE12 UniProt NPD GO	LMX1A_HUMAN	LIM homeobox transcription factor 1 alpha (LIM/homeobox protein LMX1A) (LIM-homeobox protein 1.1) (L ...	0.70	-	nuc	0	Nucleus (By similarity)		600298		382
Q9JKU8 UniProt NPD GO	LMX1A_MOUSE	LIM homeobox transcription factor 1 alpha (LIM/homeobox protein LMX1A) (LIM-homeobox protein 1.1) (L ...	0.70	-	nuc	0	Nucleus (By similarity)				382
Q9H2C1 UniProt NPD GO	LHX5_HUMAN	LIM/homeobox protein Lhx5	0.70	+	nuc	0	Nucleus (Probable)		605992		402
P61375 UniProt NPD GO	LHX5_MOUSE	LIM/homeobox protein Lhx5	0.70	+	nuc	0	Nucleus (Probable)				402
P61376 UniProt NPD GO	LHX5_RAT	LIM/homeobox protein Lhx5 (Homeobox protein LIM-2)	0.70	+	nuc	0	Nucleus (Probable)				402
Q21313 UniProt NPD GO	LAML2_CAEEL	Laminin-like protein K08C7.3 precursor	0.70	-	nuc	0					3672
Q5T7P3 UniProt NPD GO	LCE1B_HUMAN	Late cornified envelope protein 1B (Late envelope protein 2) (Small proline-rich-like epidermal diff ...	0.70	-	mit	0					118
Q5RCX2 UniProt NPD GO	L2GL2_PONPY	Lethal(2) giant larvae protein homolog 2	0.70	+	mit	0	Cytoplasm. Localized in the perinuclear structure and faintly at the cell-cell contacts sites in the ...				1019
Q91YU6 UniProt NPD GO	LZTS2_MOUSE	Leucine zipper putative tumor suppressor 2	0.70	-	nuc	0					671
Q9NZU0 UniProt NPD GO	FLRT3_HUMAN	Leucine-rich repeat transmembrane protein FLRT3 precursor (Fibronectin-like domain-containing leucin ...	0.70	-	cyt	1	Membrane; single-pass type I membrane protein (Probable)	extracellular matrix (sensu Metazoa) [NAS] integral to plasma membrane [NAS]	604808		649
Q8K1T1 UniProt NPD GO	LRC25_MOUSE	Leucine-rich repeat-containing protein 25 precursor (Monocyte and plasmacytoid-activated protein)	0.70	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				297
Q9Y546 UniProt NPD GO	LRC42_HUMAN	Leucine-rich repeat-containing protein 42	0.70	-	nuc	0					428
Q5ZI11 UniProt NPD GO	LRC45_CHICK	Leucine-rich repeat-containing protein 45	0.70	-	nuc	0					670
Q5FVQ5 UniProt NPD GO	LAX1_RAT	Lymphocyte transmembrane adapter 1 (Membrane-associated adapter protein LAX)	0.70	+	nuc	1 *	Cell membrane; single-pass type III membrane protein (By similarity)				406
P06652 UniProt NPD GO	MPIP_SCHPO	M-phase inducer phosphatase (EC 3.1.3.48) (Mitosis initiation protein) (P80)	0.70	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			596
Q8VWM8 UniProt NPD GO	M17_MAIZE	MADS-box protein ZMM17	0.70	-	nuc	0	Nucleus (By similarity)				259
Q40700 UniProt NPD GO	MADS1_ORYSA	MADS-box transcription factor 1 (OsMADS1) (Protein LEAFY HULL STERILE1) (Protein SEPALLATA-like)	0.70	-	nuc	0	Nucleus (Probable)				257
Q6Z4G0 UniProt NPD GO	MAD18_ORYSA	MADS-box transcription factor 18 (OsMADS18) (MADS-box protein 2) (OsMADS2) (MADS-box protein 28) (Os ...	0.70	-	nuc	0	Nucleus (By similarity)				249
Q6Q9H6 UniProt NPD GO	MAD34_ORYSA	MADS-box transcription factor 34 (OsMADS34) (RMADS212/RMADS217/RMADS221)	0.70	-	nuc	0	Nucleus (Probable)				239
Q6Q9I1 UniProt NPD GO	MADS7_ORYSA	MADS-box transcription factor 7 (OsMADS7) (Protein AGAMOUS-like 6) (MADS-box protein 45) (OsMADS45) ...	0.70	-	nuc	0	Nucleus (Probable)				249
Q6P7F1 UniProt NPD GO	MPP4_MOUSE	MAGUK p55 subfamily member 4 (Discs large homolog 6) (MDLG6)	0.70	-	nuc	0	Cytoplasm. Localized at photoreceptor synaptic terminals in retina. Localized in rod and cone photor ...				635
Q4TU93 UniProt NPD GO	MRC2_RAT	Macrophage mannose receptor 2 precursor (Endocytic receptor 180) (CD280 antigen)	0.70	-	nuc	1					1480
Q9GHG9 UniProt NPD GO	MATK_ACOCL	Maturase K (Intron maturase)	0.70	-	nuc	0	Plastid; chloroplast				511
O19816 UniProt NPD GO	MATK_ALLCA	Maturase K (Intron maturase)	0.70	-	cyt	0	Plastid; chloroplast				505
Q8HVA1 UniProt NPD GO	MATK_ALPCA	Maturase K (Intron maturase)	0.70	-	cyt	0	Plastid; chloroplast				515
Q8SKV2 UniProt NPD GO	MATK_ALPZE	Maturase K (Intron maturase)	0.70	-	cyt	0	Plastid; chloroplast				515
Q9MV08 UniProt NPD GO	MATK_ANOMA	Maturase K (Intron maturase)	0.70	+	nuc	0	Plastid; chloroplast				510
Q70D30 UniProt NPD GO	MATK_ANTAN	Maturase K (Intron maturase)	0.70	-	cyt	0	Plastid; chloroplast				509
Q70D24 UniProt NPD GO	MATK_ANTVS	Maturase K (Intron maturase)	0.70	-	cyt	0	Plastid; chloroplast				509
Q8WJR4 UniProt NPD GO	MATK_ARUDI	Maturase K (Intron maturase)	0.70	-	nuc	0	Plastid; chloroplast				504
Q7JF70 UniProt NPD GO	MATK_ATRJA	Maturase K (Intron maturase)	0.70	-	cyt	0	Plastid; chloroplast				506
Q6TND0 UniProt NPD GO	MATK_DALWR	Maturase K (Intron maturase)	0.70	-	cyt	0	Plastid; chloroplast				512
Q6LA20 UniProt NPD GO	MATK_DIAEN	Maturase K (Intron maturase)	0.70	-	cyt	0	Plastid; chloroplast				522

You are viewing entries 13801 to 13850 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.