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
Q02159 UniProt NPD GO	UBC7_YEAST	Ubiquitin-conjugating enzyme E2-18 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.16	-	nuc	0		endoplasmic reticulum [TAS]		2UCZ	165
O60015 UniProt NPD GO	UBCX_PICAN	Ubiquitin-conjugating enzyme E2-21 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.16	-	mit	0					188
P42748 UniProt NPD GO	UBC4_ARATH	Ubiquitin-conjugating enzyme E2-21 kDa 1 (EC 6.3.2.19) (Ubiquitin-protein ligase 4) (Ubiquitin carri ...	0.16	-	nuc	0					187
P42749 UniProt NPD GO	UBC5_ARATH	Ubiquitin-conjugating enzyme E2-21 kDa 2 (EC 6.3.2.19) (Ubiquitin-protein ligase 5) (Ubiquitin carri ...	0.16	-	cyt	0					185
P55857 UniProt NPD GO	SMT3_ORYSA	Ubiquitin-like protein SMT3	0.16	-	cyt	0					100
Q62885 UniProt NPD GO	UN119_RAT	Unc-119 protein homolog (Retinal protein 4) (RRG4)	0.16	-	nuc	0					240
Q2TAP0 UniProt NPD GO	CJ132_HUMAN	Uncharacterized protein C10orf132	0.16	-	nuc	0					167
Q9NWQ9 UniProt NPD GO	CN119_HUMAN	Uncharacterized protein C14orf119	0.16	-	nuc	0					140
Q9JJ93 UniProt NPD GO	CN119_MOUSE	Uncharacterized protein C14orf119 homolog	0.16	-	nuc	0					142
Q5BK13 UniProt NPD GO	CQ032_RAT	Uncharacterized protein C17orf32 homolog	0.16	-	end	2	Membrane; multi-pass membrane protein (Potential)				208
Q9BR10 UniProt NPD GO	CT165_HUMAN	Uncharacterized protein C20orf165	0.16	-	nuc	0					227
Q9H1P6 UniProt NPD GO	CT085_HUMAN	Uncharacterized protein C20orf85	0.16	-	cyt	0					137
Q8TCU9 UniProt NPD GO	CH016_HUMAN	Uncharacterized protein C8orf16	0.16	-	cyt	0					80
P38332 UniProt NPD GO	YB96_YEAST	Uncharacterized protein YBR246W	0.16	-	cyt	0					387
Q3E837 UniProt NPD GO	YJ052_YEAST	Uncharacterized protein YJL052C-A precursor	0.16	-	nuc	0					39
Q2V2P2 UniProt NPD GO	YK065_YEAST	Uncharacterized protein YKL065W-A	0.16	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				73
P33324 UniProt NPD GO	YKJ1_YEAST	Uncharacterized protein YKL091C	0.16	-	cyt	0		nucleus [IDA]			310
Q3E808 UniProt NPD GO	YN130_YEAST	Uncharacterized protein YNL130C-A, mitochondrial precursor	0.16	-	mit	0	Mitochondrion (Potential)				48
Q3E769 UniProt NPD GO	YO59A_YEAST	Uncharacterized protein YOL159C-A	0.16	-	cyt	0	Cytoplasm	cytoplasm [IDA]			90
Q3E7B4 UniProt NPD GO	YP038_YEAST	Uncharacterized protein YPL038W-A	0.16	-	mit	0					63
P82326 UniProt NPD GO	UT107_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 107) (Fragment)	0.16	-		0	Plastid; chloroplast; chloroplast thylakoid				14
P82338 UniProt NPD GO	UT023_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 23) (Spot 28) (Spot 205) (Fragments)	0.16	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid				45
P22673 UniProt NPD GO	URIC_DROPS	Uricase (EC 1.7.3.3) (Urate oxidase)	0.16	-	mit	0	Peroxisome				346
O44111 UniProt NPD GO	URIC_DROSU	Uricase (EC 1.7.3.3) (Urate oxidase) (Fragment)	0.16	-	mit	0	Peroxisome				339
Q99ML8 UniProt NPD GO	UCN2_MOUSE	Urocortin-2 precursor (Urocortin II) (Ucn II)	0.16	-	mit	0	Secreted protein	extracellular region [ISS]			112
P17255 UniProt NPD GO	VATA_YEAST	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump A ...	0.16	-	nuc	0	Intracytoplasmic membrane. Membranes of various intracellular acidic compartments	hydrogen-transporting ATPase V1 domain [TAS] vacuolar membrane (sensu Fungi) [IDA]		1VDE	1070
P31406 UniProt NPD GO	VATA_SCHPO	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.16	-	nuc	0		vacuolar membrane [TAS]			619
P22550 UniProt NPD GO	VATB_CANTR	Vacuolar ATP synthase subunit B (EC 3.6.3.14) (V-ATPase B subunit) (Vacuolar proton pump B subunit) ...	0.16	-	cyt	0					511
P31407 UniProt NPD GO	VATB1_BOVIN	Vacuolar ATP synthase subunit B, kidney isoform (EC 3.6.3.14) (V-ATPase B1 subunit) (Vacuolar proton ...	0.16	-	nuc	0	Cell membrane. Plasma membrane of the renal intercalated cells				513
P21282 UniProt NPD GO	VATC_BOVIN	Vacuolar ATP synthase subunit C (EC 3.6.3.14) (V-ATPase C subunit) (Vacuolar proton pump C subunit)	0.16	-	cyt	0		proton-transporting two-sector ATPase complex [ISS]			381
Q9SCB9 UniProt NPD GO	VATC_HORVU	Vacuolar ATP synthase subunit C (EC 3.6.3.14) (V-ATPase C subunit) (Vacuolar proton pump C subunit)	0.16	-	cyt	0	Vacuole; vacuolar membrane. Tonoplast				354
Q9Z1G3 UniProt NPD GO	VATC_MOUSE	Vacuolar ATP synthase subunit C (EC 3.6.3.14) (V-ATPase C subunit) (Vacuolar proton pump C subunit)	0.16	-	cyt	0		proton-transporting two-sector ATPase complex [ISS]			381
P32563 UniProt NPD GO	VPH1_YEAST	Vacuolar ATP synthase subunit a, vacuolar isoform (EC 3.6.3.14) (V-ATPase a subunit) (Vacuolar proto ...	0.16	+	end	7	Vacuole; vacuolar membrane; multi-pass membrane protein	hydrogen-transporting ATPase V0 domain [TAS] vacuole [IDA]			839
P56216 UniProt NPD GO	VAOX_PENSI	Vanillyl-alcohol oxidase (EC 1.1.3.38) (Aryl-alcohol oxidase) (4-allylphenol oxidase)	0.16	-	cyt	0	Peroxisome. Cytoplasm			2VAO	560
P32241 UniProt NPD GO	VIPR1_HUMAN	Vasoactive intestinal polypeptide receptor 1 precursor (VIP-R-1) (Pituitary adenylate cyclase-activa ...	0.16	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	192321	1OGT	457
Q91085 UniProt NPD GO	VIPR_MELGA	Vasoactive intestinal polypeptide receptor precursor (VIP-R) (VIP receptor)	0.16	-	end	7	Membrane; multi-pass membrane protein				457
P42992 UniProt NPD GO	NEUV_BUFRE	Vasotocin-neurophysin VT (VT) [Contains: Hydrin-2 (Hydrin II)] (Fragment)	0.16	-	nuc	0					27
P35784 UniProt NPD GO	VA5_VESGE	Venom allergen 5 (Antigen 5) (Ag5) (Allergen Ves g 5) (Ves g V)	0.16	-	nuc	0	Secreted protein. Venom reservoirs				204
P00982 UniProt NPD GO	IVBIK_DENAN	Venom basic protease inhibitor K (Dendrotoxin delta-DaTX) (Toxin C13S1C3)	0.16	-	nuc	0	Secreted protein				57
Q9P7M7 UniProt NPD GO	YIOB_SCHPO	Very hypothetical protein P27G11.11c in chromosome I	0.16	-	nuc	0					73
P25562 UniProt NPD GO	YCC2_YEAST	Very hypothetical protein YCL022C	0.16	-	mit	0					171
P36058 UniProt NPD GO	YKP3_YEAST	Very hypothetical protein YKL153W	0.16	-	cyt	0					169
P01537 UniProt NPD GO	THN1_VISAL	Viscotoxin 1-PS	0.16	-	nuc	0	Secreted protein				46
Q9EP51 UniProt NPD GO	VN1B1_MOUSE	Vomeronasal type-1 receptor B1 (Vomeronasal type-1 receptor A5) (Vomeronasal receptor 2) (Pheromone ...	0.16	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				310
P42783 UniProt NPD GO	WAPP_COCIM	Wall-associated proteinase precursor (EC 3.4.21.-)	0.16	-	cyt	0	Cell wall; peripheral membrane protein				309
P25679 UniProt NPD GO	TXW9A_NAJKA	Weak toxin CM-9a	0.16	-	nuc	0	Secreted protein				64
Q9W6F9 UniProt NPD GO	WIF1_BRARE	Wnt inhibitory factor 1 precursor (WIF-1)	0.16	-	mit	0	Secreted protein				378
O96006 UniProt NPD GO	ZBED1_HUMAN	Zinc finger BED domain-containing protein 1 (dREF homolog) (Putative Ac-like transposable element)	0.16	-	cyt	0	Nucleus. In granular structures	nuclear chromosome [TAS]	300178	2CT5	694
P51502 UniProt NPD GO	ZNF80_CERAE	Zinc finger protein 80	0.16	-	nuc	0	Nucleus (Probable)				213
O13918 UniProt NPD GO	ZHF1_SCHPO	Zinc homeostasis factor 1	0.16	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Nucleus; nuclear ...	endoplasmic reticulum membrane [IDA]			387

You are viewing entries 56451 to 56500 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.