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
Q8N806 UniProt NPD GO	CN130_HUMAN	Uncharacterized protein C14orf130	0.64	+	nuc	0					425
Q8C190 UniProt NPD GO	CP007_MOUSE	Uncharacterized protein C16orf7 homolog (5-day ovary-specific transcript 1 protein)	0.64	-	nuc	0					649
Q5RBH3 UniProt NPD GO	CS021_PONPY	Uncharacterized protein C19orf21 homolog	0.64	-	nuc	0					685
Q2TA11 UniProt NPD GO	CA158_BOVIN	Uncharacterized protein C1orf158 homolog	0.64	-	nuc	0					196
Q9CX62 UniProt NPD GO	CC054_MOUSE	Uncharacterized protein C3orf54 homolog	0.64	-	nuc	0					282
P53124 UniProt NPD GO	YGN4_YEAST	Uncharacterized protein YGL134W	0.64	-	nuc	0		cyclin-dependent protein kinase holoenzyme ... [TAS]			433
Q3E772 UniProt NPD GO	YG169_YEAST	Uncharacterized protein YGR169C-A	0.64	-	nuc	0					92
P40493 UniProt NPD GO	YIJ6_YEAST	Uncharacterized protein YIL096C	0.64	-	nuc	0		nucleolus [IDA] nucleus [IDA]			336
P47019 UniProt NPD GO	YJM2_YEAST	Uncharacterized protein YJL122W	0.64	+	mit	0		nucleus [IDA]			175
Q05881 UniProt NPD GO	YL287_YEAST	Uncharacterized protein YLR287C	0.64	-	cyt	0	Cytoplasm	cytoplasm [IDA]			355
Q07957 UniProt NPD GO	USF1_XENBO	Upstream stimulatory factor 1 (USF) (SPF1) (B1 factor)	0.64	+	nuc	0	Nucleus				307
Q74ZJ6 UniProt NPD GO	BRO1_ASHGO	Vacuolar protein-sorting protein BRO1 (BRO domain-containing protein 1)	0.64	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity)				834
Q753W3 UniProt NPD GO	SNF7_ASHGO	Vacuolar sorting protein SNF7 (Vacuolar protein sorting-associated protein VPS32)	0.64	-	nuc	0	Cytoplasm (By similarity). Endosome; endosomal membrane; peripheral membrane protein (By similarity) ...				237
Q96JC1 UniProt NPD GO	VPS39_HUMAN	Vam6/Vps39-like protein (hVam6p)	0.64	-	cyt	0	Cytoplasm. Lysosome; lysosomal membrane; peripheral membrane protein. Endosome; late endosome; late ...				886
O43915 UniProt NPD GO	VEGFD_HUMAN	Vascular endothelial growth factor D precursor (VEGF-D) (c-fos-induced growth factor) (FIGF)	0.64	-	nuc	0	Secreted protein	extracellular space [TAS]	300091		354
Q8AXB3 UniProt NPD GO	VGFR2_BRARE	Vascular endothelial growth factor receptor 2 precursor (EC 2.7.10.1) (VEGFR-2) (Receptor tyrosine k ...	0.64	-	nuc	0	Membrane; single-pass type I membrane protein (Probable)	integral to membrane [NAS]			1302
P35917 UniProt NPD GO	VGFR3_MOUSE	Vascular endothelial growth factor receptor 3 precursor (EC 2.7.10.1) (VEGFR-3) (Tyrosine-protein ki ...	0.64	-	end	1	Membrane; single-pass type I membrane protein				1363
Q3HXX9 UniProt NPD GO	NGFV2_HOPST	Venom nerve growth factor 2 precursor (vNGF-2)	0.64	-	exc	0	Secreted protein				245
Q3HXY5 UniProt NPD GO	NGFV3_NOTSC	Venom nerve growth factor 3 precursor (vNGF-3)	0.64	-	exc	0	Secreted protein				244
Q9IAX9 UniProt NPD GO	VAX2B_XENLA	Ventral anterior homeobox 2b (Ventral anterior homeobox 3)	0.64	+	nuc	0	Nucleus (By similarity)				294
Q9USL2 UniProt NPD GO	YJK9_SCHPO	Very hypothetical protein C18B5.09c in chromosome III	0.64	-	nuc	0					116
P08438 UniProt NPD GO	VCL_VICFA	Vicilin precursor	0.64	-	exc	0	Protein body. Vacuole. Cotyledonary membrane-bound vacuolar protein bodies				463
P81021 UniProt NPD GO	VIGLN_CHICK	Vigilin	0.64	-	cyt	0	Cytoplasm				1270
Q23989 UniProt NPD GO	QUAI_DROME	Villin-like protein quail	0.64	-	cyt	0					887
P38435 UniProt NPD GO	VKGC_HUMAN	Vitamin K-dependent gamma-carboxylase (EC 6.4.-.-) (Gamma-glutamyl carboxylase) (Vitamin K gamma glu ...	0.64	-	end	5	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to membrane [TAS] membrane fraction [TAS]	277450		758
P18947 UniProt NPD GO	VIT4_CAEEL	Vitellogenin-4 precursor	0.64	-	cyt	0	Secreted protein				1603
P06125 UniProt NPD GO	VIT5_CAEEL	Vitellogenin-5 precursor	0.64	-	exc	0	Secreted protein				1603
Q00975 UniProt NPD GO	CAC1B_HUMAN	Voltage-dependent N-type calcium channel subunit alpha-1B (Voltage-gated calcium channel subunit alp ...	0.64	-	end	21	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]	601012		2339
Q24270 UniProt NPD GO	CAC1D_DROME	Voltage-dependent calcium channel type D alpha-1 subunit (DmCa1D)	0.64	+	end	18	Membrane; multi-pass membrane protein	apical plasma membrane [IDA] basolateral plasma membrane [IDA] voltage-gated calcium channel complex [NAS]			2516
Q8BKW4 UniProt NPD GO	ZCHC4_MOUSE	Zinc finger CCHC domain-containing protein 4	0.64	-	nuc	0					512
Q9P217 UniProt NPD GO	ZSWM5_HUMAN	Zinc finger SWIM domain-containing protein 5	0.64	-	nuc	0					1185
P98169 UniProt NPD GO	ZXDB_HUMAN	Zinc finger X-linked protein ZXDB	0.64	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	300236		803
P15620 UniProt NPD GO	ZN271_MOUSE	Zinc finger protein 271 (Zinc finger protein 35) (Zfp-35)	0.64	-	nuc	0	Nucleus				580
Q9Y2G7 UniProt NPD GO	ZFP30_HUMAN	Zinc finger protein 30 homolog (Zfp-30) (Zinc finger protein 745)	0.64	-	nuc	0	Nucleus (Potential)				519
Q96RE9 UniProt NPD GO	ZN300_HUMAN	Zinc finger protein 300	0.64	-	nuc	0	Nucleus				604
Q8WUU4 UniProt NPD GO	ZN342_HUMAN	Zinc finger protein 342	0.64	-	nuc	0	Nucleus (Probable)				475
P51814 UniProt NPD GO	ZNF41_HUMAN	Zinc finger protein 41	0.64	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	314995		821
Q8TF45 UniProt NPD GO	ZN418_HUMAN	Zinc finger protein 418	0.64	-	nuc	0	Nucleus (Probable)				676
Q8TBC5 UniProt NPD GO	ZN447_HUMAN	Zinc finger protein 447	0.64	-	nuc	0	Nucleus (Potential)				510
Q9BX82 UniProt NPD GO	ZN471_HUMAN	Zinc finger protein 471 (EZFIT-related protein 1)	0.64	-	nuc	0	Nucleus (Potential)				626
Q86XF7 UniProt NPD GO	ZN575_HUMAN	Zinc finger protein 575	0.64	-	nuc	0	Nucleus (Potential)				245
Q8NAF0 UniProt NPD GO	ZN759_HUMAN	Zinc finger protein 579	0.64	+	nuc	0	Nucleus (Potential)				562
Q9UC06 UniProt NPD GO	ZNF70_HUMAN	Zinc finger protein 70 (Zinc finger protein N27C7-1)	0.64	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	194544		446
P47977 UniProt NPD GO	CTH2_YEAST	Zinc finger protein CTH2 (YTIS11 protein)	0.64	-	nuc	0	Nucleus (Potential)	cytoplasm [IDA] nucleus [IDA]			285
P32805 UniProt NPD GO	FZF1_YEAST	Zinc finger protein FZF1 (Sulfite resistance protein 1)	0.64	-	nuc	0	Nucleus (Potential)	nucleus [IC]			299
Q9N2V2 UniProt NPD GO	NAS30_CAEEL	Zinc metalloproteinase nas-30 precursor (EC 3.4.24.21) (Nematode astacin 30)	0.64	+	mit	0					746
P32527 UniProt NPD GO	ZUO1_YEAST	Zuotin (Ribosome-associated complex subunit ZUO1) (J-protein ZUO1) (DnaJ-related protein ZUO1) (Heat ...	0.64	-	nuc	0	Cytoplasm	cytoplasm [IDA] cytosol [NAS] mitochondrion [IDA] ribosome [NAS]			433
Q08493 UniProt NPD GO	PDE4C_HUMAN	cAMP-specific 3',5'-cyclic phosphodiesterase 4C (EC 3.1.4.17) (DPDE1) (PDE21)	0.64	-	nuc	0			600128	1LXU	712
Q03042 UniProt NPD GO	KGP1_DROME	cGMP-dependent protein kinase, isozyme 1 (EC 2.7.11.12) (CGK)	0.64	-	cyt	0					768
Q7Z8R5 UniProt NPD GO	PALI_YARLI	pH-response regulator protein palI/RIM9	0.64	-	end	4 *	Cell membrane; multi-pass membrane protein (By similarity)				728

You are viewing entries 17201 to 17250 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.