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
Q8STF2 UniProt NPD GO	Y104_ENCCU	Hypothetical protein ECU01_0040/ECU01_1570/ECU04_0050/ECU05_0020/ ECU08_2130/ECU10_1880	0.63	-	mit	0					204
Q09531 UniProt NPD GO	YQP4_CAEEL	Hypothetical protein F07F6.4 in chromosome III	0.63	-	nuc	0					529
P34518 UniProt NPD GO	YM42_CAEEL	Hypothetical protein K11H3.2	0.63	-	nuc	0					228
P34565 UniProt NPD GO	YNV2_CAEEL	Hypothetical protein T16H12.2	0.63	-	nuc	0					181
O95373 UniProt NPD GO	IPO7_HUMAN	Importin-7 (Imp7) (Ran-binding protein 7) (RanBP7)	0.63	-	cyt	0	Cytoplasm. Nucleus	nuclear pore [TAS] soluble fraction [TAS]	605586		1038
P58166 UniProt NPD GO	INHBE_HUMAN	Inhibin beta E chain precursor (Activin beta-E chain)	0.63	+	exc	0	Secreted protein (By similarity)				350
Q12345 UniProt NPD GO	IES3_YEAST	Ino eighty subunit 3	0.63	-	nuc	0	Nucleus	INO80 complex [IPI] nucleus [IDA]			250
P17105 UniProt NPD GO	IP3KA_RAT	Inositol-trisphosphate 3-kinase A (EC 2.7.1.127) (Inositol 1,4,5-trisphosphate 3-kinase A) (IP3K A) ...	0.63	-	nuc	0				1TZD	459
Q80ZG2 UniProt NPD GO	IP3KC_RAT	Inositol-trisphosphate 3-kinase C (EC 2.7.1.127) (Inositol 1,4,5-trisphosphate 3-kinase C) (IP3K-C)	0.63	-	nuc	0	Nucleus. Cytoplasm. Shuttles actively between nucleus and cytoplasm with both nuclear import and nuc ...				678
P50212 UniProt NPD GO	ISL2B_ONCTS	Insulin gene enhancer protein ISL-2B (Islet-2B) (Fragment)	0.63	+	nuc	0	Nucleus				340
P05007 UniProt NPD GO	IFNAA_BOVIN	Interferon alpha-A precursor	0.63	-	mit	1 *	Secreted protein				189
P23906 UniProt NPD GO	IRF2_MOUSE	Interferon regulatory factor 2 (IRF-2)	0.63	-	nuc	0	Nucleus			2IRF	349
Q9N0Y2 UniProt NPD GO	MX2_CANFA	Interferon-induced GTP-binding protein Mx2	0.63	-	nuc	0	Cytoplasm (By similarity)				711
P19182 UniProt NPD GO	IFRD1_MOUSE	Interferon-related developmental regulator 1 (Nerve growth factor-inducible protein PC4) (TPA-induce ...	0.63	-	nuc	0		nucleus [IDA]			449
Q9HBE4 UniProt NPD GO	IL21_HUMAN	Interleukin-21 precursor (IL-21) (Za11)	0.63	-	nuc	0	Secreted protein	extracellular space [NAS]	605384		155
P48998 UniProt NPD GO	INVO_RAT	Involucrin	0.63	-	nuc	0	Cytoplasm. Constituent of the scaffolding of the cornified envelope				568
Q9C075 UniProt NPD GO	K1C23_HUMAN	Keratin, type I cytoskeletal 23 (Cytokeratin-23) (CK-23) (Keratin-23) (K23)	0.63	-	nuc	0			606194		422
P22023 UniProt NPD GO	KRE5_YEAST	Killer toxin-resistance protein 5 precursor	0.63	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [TAS]			1365
P46822 UniProt NPD GO	KLC_CAEEL	Kinesin light chain (KLC)	0.63	-	nuc	0					540
P46875 UniProt NPD GO	ATK3_ARATH	Kinesin-3 (Kinesin-like protein C)	0.63	-	nuc	0					754
Q5JT82 UniProt NPD GO	KLF17_HUMAN	Krueppel-like factor 17 (Zinc finger protein 393)	0.63	-	nuc	0	Nucleus (Potential)		609602		389
Q9Y5W3 UniProt NPD GO	KLF2_HUMAN	Krueppel-like factor 2 (Lung krueppel-like factor)	0.63	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]	602016		355
Q16992 UniProt NPD GO	LWA_ANTEL	LWamide neuropeptides precursor [Contains: LWamide I; Metamorphosin A (LWamide II) (MMA); LWamide II ...	0.63	-	exc	0	Secreted protein				514
P87058 UniProt NPD GO	LAH1_SCHPO	La protein homolog (La ribonucleoprotein) (La autoantigen homolog)	0.63	+	nuc	0	Nucleus (Probable)	nucleus [IDA]			298
P05692 UniProt NPD GO	LEGJ_PEA	Legumin J precursor [Contains: Legumin J alpha chain (Legumin J acidic chain); Legumin J beta chain ...	0.63	-	exc	0					503
P05190 UniProt NPD GO	LEGB4_VICFA	Legumin type B precursor [Contains: Legumin type B alpha chain (Legumin type B acidic chain); Legumi ...	0.63	-	exc	0					484
Q8N6Y2 UniProt NPD GO	LRC17_HUMAN	Leucine-rich repeat-containing protein 17 precursor (p37NB)	0.63	-	nuc	0					441
Q9DAP0 UniProt NPD GO	LRC46_MOUSE	Leucine-rich repeat-containing protein 46	0.63	-	nuc	0					323
Q6P1C6 UniProt NPD GO	LRIG3_MOUSE	Leucine-rich repeats and immunoglobulin-like domains protein 3 precursor	0.63	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				1117
P15702 UniProt NPD GO	LEUK_MOUSE	Leukosialin precursor (Leukocyte sialoglycoprotein) (Sialophorin) (Ly-48) (B cell differentiation an ...	0.63	+	exc	1	Membrane; single-pass type I membrane protein	basement membrane [IDA] external side of plasma membrane [IDA] integral to plasma membrane [IDA] uropod [IDA]			395
P50541 UniProt NPD GO	MXI1_BRARE	MAX-interacting protein 1 (Protein MXI1)	0.63	-	nuc	0	Nucleus				243
P09603 UniProt NPD GO	CSF1_HUMAN	Macrophage colony-stimulating factor 1 precursor (CSF-1) (MCSF) (M-CSF) (Lanimostim)	0.63	-	exc	1	Cell membrane; single-pass membrane protein (By similarity). Processed form: Secreted protein; extra ...	membrane [NAS]	120420	1HMC	554
Q9H000 UniProt NPD GO	MKRN2_HUMAN	Makorin-2 (RING finger protein 62)	0.63	-	nuc	0		intracellular [IEP]	608426		416
Q6EIJ6 UniProt NPD GO	MATK_ADADI	Maturase K (Intron maturase)	0.63	-	cyt	0	Plastid; chloroplast				504
Q9TKR9 UniProt NPD GO	MATK_AUSBL	Maturase K (Intron maturase)	0.63	-	cyt	0	Plastid; chloroplast				506
Q9MVW4 UniProt NPD GO	MATK_CRYJA	Maturase K (Intron maturase)	0.63	-	cyt	0	Plastid; chloroplast				507
Q7YN83 UniProt NPD GO	MATK_DIOVR	Maturase K (Intron maturase)	0.63	-	cyt	0	Plastid; chloroplast				503
Q9GHB1 UniProt NPD GO	MATK_EICCR	Maturase K (Intron maturase)	0.63	-	cyt	0	Plastid; chloroplast				504
Q8MEX3 UniProt NPD GO	MATK_EPHSI	Maturase K (Intron maturase)	0.63	-	mit	1	Plastid; chloroplast				531
Q8MET5 UniProt NPD GO	MATK_EUCUL	Maturase K (Intron maturase)	0.63	-	nuc	0	Plastid; chloroplast				509
Q8GVA0 UniProt NPD GO	MATK_GALEW	Maturase K (Intron maturase)	0.63	-	cyt	0	Plastid; chloroplast				520
Q8GV94 UniProt NPD GO	MATK_GALNI	Maturase K (Intron maturase)	0.63	-	cyt	0	Plastid; chloroplast				516
Q6BDG1 UniProt NPD GO	MATK_KETDA	Maturase K (Intron maturase)	0.63	-	nuc	0	Plastid; chloroplast				519
Q7YJG2 UniProt NPD GO	MATK_KNIUV	Maturase K (Intron maturase)	0.63	-	nuc	0	Plastid; chloroplast				521
Q8MCR5 UniProt NPD GO	MATK_LENER	Maturase K (Intron maturase)	0.63	-	cyt	0	Plastid; chloroplast				507
Q8MCP5 UniProt NPD GO	MATK_MELAB	Maturase K (Intron maturase)	0.63	-	nuc	0	Plastid; chloroplast				506
Q8MCP4 UniProt NPD GO	MATK_MELID	Maturase K (Intron maturase)	0.63	-	nuc	0	Plastid; chloroplast				506
Q6EW67 UniProt NPD GO	MATK_NYMAL	Maturase K (Intron maturase)	0.63	-	cyt	0	Plastid; chloroplast				507
O98637 UniProt NPD GO	MATK_NYMOD	Maturase K (Intron maturase)	0.63	-	cyt	0	Plastid; chloroplast				509
Q6EIJ4 UniProt NPD GO	MATK_PACAQ	Maturase K (Intron maturase)	0.63	-	cyt	0	Plastid; chloroplast				504

You are viewing entries 17451 to 17500 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.