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
P51281 UniProt NPD GO	YCF45_PORPU	Hypothetical 64.2 kDa protein ycf45 (ORF565)	0.68	-	nuc	0	Plastid; chloroplast				565
P05511 UniProt NPD GO	YMC6_SCHPO	Hypothetical 91 kDa protein in cob intron	0.68	-	mit	0					807
Q09600 UniProt NPD GO	YRM2_CAEEL	Hypothetical RING finger protein R06F6.2 in chromosome II	0.68	-	nuc	0					950
P22191 UniProt NPD GO	YMC1_SCHPO	Hypothetical cox1 intron-1 45.6 kDa protein (Probable maturase)	0.68	-	nuc	0					384
P34440 UniProt NPD GO	YL82_CAEEL	Hypothetical histone H3-like protein F54C8.2 in chromosome III	0.68	-	nuc	0					261
Q09872 UniProt NPD GO	YAG9_SCHPO	Hypothetical protein C12G12.09 in chromosome I	0.68	-	nuc	0					977
Q10223 UniProt NPD GO	YAZ1_SCHPO	Hypothetical protein C13D6.01 in chromosome I	0.68	-	nuc	0					431
Q9UTM5 UniProt NPD GO	YIJ1_SCHPO	Hypothetical protein C1420.01c in chromosome I	0.68	-	nuc	0					580
O13718 UniProt NPD GO	YDZB_SCHPO	Hypothetical protein C14C4.11 in chromosome I	0.68	-	end	3	Membrane; multi-pass membrane protein (Potential)				734
Q9UTC2 UniProt NPD GO	YIDH_SCHPO	Hypothetical protein C227.17c in chromosome I	0.68	-	nuc	0					121
Q9P7J2 UniProt NPD GO	YJNE_SCHPO	Hypothetical protein C24B10.14c in chromosome III	0.68	-	nuc	0					203
Q92360 UniProt NPD GO	YDHF_SCHPO	Hypothetical protein C6G9.15c in chromosome I	0.68	+	nuc	0					498
Q8SUH9 UniProt NPD GO	Y8K7_ENCCU	Hypothetical protein ECU08_2070	0.68	+	vac	0					619
P34418 UniProt NPD GO	YLZ5_CAEEL	Hypothetical protein F42H10.5	0.68	-	nuc	0					810
P32743 UniProt NPD GO	YNH5_CAEEL	Hypothetical protein R107.5	0.68	-	nuc	0					274
Q09358 UniProt NPD GO	YS03_CAEEL	Hypothetical protein ZK1128.3	0.68	+	nuc	0					360
P46578 UniProt NPD GO	GOP1_CAEEL	Hypothetical protein gop-1	0.68	-	mit	0					892
Q10096 UniProt NPD GO	YAOH_SCHPO	Hypothetical zinc finger protein C11D3.17 in chromosome I	0.68	-	end	0	Nucleus (Potential)				585
Q9W4V8 UniProt NPD GO	TI50C_DROME	Import inner membrane translocase subunit TIM50-C, mitochondrial precursor	0.68	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)	mitochondrial inner membrane presequence tr... [ISS]			428
O14920 UniProt NPD GO	IKKB_HUMAN	Inhibitor of nuclear factor kappa B kinase subunit beta (EC 2.7.11.10) (I-kappa-B-kinase beta) (IkBK ...	0.68	-	nuc	0	Cytoplasm	cytoplasm [NAS]	603258		756
Q6PD10 UniProt NPD GO	IP6K1_MOUSE	Inositol hexaphosphate kinase 1 (EC 2.7.4.21) (InsP6 kinase 1) (Inositol hexakisphosphate kinase 1)	0.68	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			433
Q9ESM0 UniProt NPD GO	IP6K1_RAT	Inositol hexaphosphate kinase 1 (EC 2.7.4.21) (InsP6 kinase 1) (Inositol hexakisphosphate kinase 1)	0.68	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			433
P01581 UniProt NPD GO	IFNG_RAT	Interferon gamma precursor (IFN-gamma)	0.68	-	exc	0	Secreted protein	extracellular region [IMP]			156
P20592 UniProt NPD GO	MX2_HUMAN	Interferon-induced GTP-binding protein Mx2 (Interferon-regulated resistance GTP-binding protein MxB) ...	0.68	-	nuc	0	Cytoplasm	cytoplasm [TAS] nucleus [TAS]	147890		715
Q9Z1X4 UniProt NPD GO	ILF3_MOUSE	Interleukin enhancer-binding factor 3	0.68	-	nuc	0	Nucleus; nucleolus (By similarity)				898
Q9HBG6 UniProt NPD GO	IF122_HUMAN	Intraflagellar transport 122 homolog (WD repeat protein 10)	0.68	-	cyt	0	Cytoplasm		606045		1242
Q61371 UniProt NPD GO	IFT88_MOUSE	Intraflagellar transport 88 homolog (Tetratricopeptide repeat protein 10) (TPR repeat protein 10) (R ...	0.68	-	nuc	0		axoneme [IDA] basal body [IDA]			824
Q63054 UniProt NPD GO	ICA69_RAT	Islet cell autoantigen 1 (69 kDa islet cell autoantigen) (ICA69) (p69) (Islet cell autoantigen p69) ...	0.68	-	nuc	0	Cytoplasm; cytosol (By similarity). Predominantly. Membrane (By similarity). Also exists as a membra ...	cytosol [ISS] Golgi membrane [ISS] secretory granule membrane [ISS] synaptic vesicle membrane [ISS]			480
Q6ZPY7 UniProt NPD GO	JHD2B_MOUSE	JmjC domain-containing histone demethylation protein 2B (EC 1.14.11.-) (Jumonji domain-containing pr ...	0.68	-	nuc	0	Nucleus (By similarity)				1562
Q07834 UniProt NPD GO	YL032_YEAST	KH domain-containing protein YLL032C	0.68	-	nuc	0	Cytoplasm	cytoplasm [IDA]			825
O13359 UniProt NPD GO	KEX2_CANAL	Kexin precursor (EC 3.4.21.61) (KEX2 protease)	0.68	+	end	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type I membrane prot ...				924
P34540 UniProt NPD GO	KINH_CAEEL	Kinesin heavy chain (Uncoordinated protein 116)	0.68	-	nuc	0					815
Q5R581 UniProt NPD GO	KLC1_PONPY	Kinesin light chain 1 (KLC 1)	0.68	-	nuc	0					556
Q8C3Y4 UniProt NPD GO	KNTC1_MOUSE	Kinetochore-associated protein 1	0.68	-	cyt	0					2207
Q99JB0 UniProt NPD GO	KLF7_MOUSE	Krueppel-like factor 7	0.68	-	nuc	0	Nucleus (Probable)				301
P10072 UniProt NPD GO	HKR1_HUMAN	Krueppel-related zinc finger protein 1 (Protein HKR1)	0.68	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	165250		640
Q6P1M3 UniProt NPD GO	L2GL2_HUMAN	Lethal(2) giant larvae protein homolog 2 (HGL)	0.68	-	mit	0	Cytoplasm. Localized in the perinuclear structure and faintly at the cell-cell contacts sites in the ...				1020
Q6CWW0 UniProt NPD GO	LCMT1_KLULA	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) (Protein phosphatase methyltransferase 1)	0.68	-	nuc	0					333
Q6VAM0 UniProt NPD GO	MAD56_ORYSA	MADS-box transcription factor 56 (OsMADS56) (FDRMADS8) (RMADS214)	0.68	-	nuc	0	Nucleus (Probable)				233
Q2V0P1 UniProt NPD GO	MAD58_ORYSA	MADS-box transcription factor 58 (OsMADS58)	0.68	-	nuc	0	Nucleus (Probable)				272
Q9QZ04 UniProt NPD GO	MAGL2_MOUSE	MAGE-like protein 2 (Protein nS7)	0.68	-	nuc	0					490
P87311 UniProt NPD GO	YB2A_SCHPO	MYND-type zinc finger protein C31F10.10c	0.68	-	nuc	0	Nucleus (Potential)				574
Q24747 UniProt NPD GO	EXU_DROVI	Maternal protein exuperantia	0.68	-	nuc	0					486
Q08398 UniProt NPD GO	MTAL1_KLULA	Mating-type protein ALPHA1 (Transcription activator Alpha1p) (MATalpha1 protein)	0.68	-	mit	0	Nucleus (By similarity)				261
Q5J2Z9 UniProt NPD GO	MATK_AMACA	Maturase K (Intron maturase)	0.68	-	nuc	0	Plastid; chloroplast				504
Q5D1C1 UniProt NPD GO	MATK_ASTSI	Maturase K (Intron maturase)	0.68	-	cyt	0	Plastid; chloroplast				508
Q52ZX4 UniProt NPD GO	MATK_BANCU	Maturase K (Intron maturase)	0.68	-	cyt	0	Plastid; chloroplast				509
Q8MA31 UniProt NPD GO	MATK_CAMSI	Maturase K (Intron maturase)	0.68	-	mit	0	Plastid; chloroplast				499
Q8WIV8 UniProt NPD GO	MATK_CAMSS	Maturase K (Intron maturase)	0.68	-	mit	0	Plastid; chloroplast				499
Q5YK50 UniProt NPD GO	MATK_CERSL	Maturase K (Intron maturase)	0.68	-	cyt	0	Plastid; chloroplast				499

You are viewing entries 14751 to 14800 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.