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
Q5ZJJ8 UniProt NPD GO	UBCP1_CHICK	Ubiquitin-like domain-containing CTD phosphatase 1 (EC 3.1.3.16)	0.05	-	cyt	0	Nucleus (By similarity)				318
P34277 UniProt NPD GO	YKJ3_CAEEL	Uncharacterized GST-like protein C02D5.3 (EC 2.5.1.-)	0.05	-	cyt	0					537
Q9I859 UniProt NPD GO	CK075_FUGRU	Uncharacterized protein C11orf75 homolog (Protein FN5)	0.05	-	mit	1 *					59
Q96N68 UniProt NPD GO	CR015_HUMAN	Uncharacterized protein C18orf15	0.05	-	end	1					181
Q8CEL2 UniProt NPD GO	CT026_MOUSE	Uncharacterized protein C20orf26 homolog (Fragment)	0.05	-	mit	0					399
Q9H0H9 UniProt NPD GO	CB014_HUMAN	Uncharacterized protein C2orf14	0.05	-	nuc	0					118
Q8VE96 UniProt NPD GO	CB018_MOUSE	Uncharacterized protein C2orf18 homolog precursor	0.05	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				372
P40011 UniProt NPD GO	YEK0_YEAST	Uncharacterized protein YER010C	0.05	-	cyt	0				2C5Q	234
P40027 UniProt NPD GO	YEM9_YEAST	Uncharacterized protein YER039C	0.05	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				249
P47181 UniProt NPD GO	YJ9S_YEAST	Uncharacterized protein YJR154W	0.05	-	cyt	0	Cytoplasm	cytoplasm [IDA]			346
Q8TGT1 UniProt NPD GO	YL406_YEAST	Uncharacterized protein YLR406C-A precursor	0.05	-	mit	1 *					49
P53747 UniProt NPD GO	YN8Z_YEAST	Uncharacterized protein YNR061C	0.05	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			219
Q8TGJ2 UniProt NPD GO	YN075_YEAST	Uncharacterized protein YNR075C-A	0.05	-	nuc	0					30
Q08232 UniProt NPD GO	YO073_YEAST	Uncharacterized protein YOL073C	0.05	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				322
Q3E7Y9 UniProt NPD GO	YO097_YEAST	Uncharacterized protein YOL097W-A	0.05	-	cyt	0					61
Q8TGS1 UniProt NPD GO	YO032_YEAST	Uncharacterized protein YOR032W-A	0.05	-	exc	2 *	Membrane; multi-pass membrane protein (Potential)				66
Q06537 UniProt NPD GO	YP153_YEAST	Uncharacterized protein YPR153W	0.05	-	nuc	3 *	Membrane; multi-pass membrane protein (Potential)				144
P38716 UniProt NPD GO	YHR2_YEAST	Uncharacterized trans-sulfuration enzyme YHR112C	0.05	-	cyt	0		cytoplasm [IDA]			378
Q21190 UniProt NPD GO	UNC1_CAEEL	Uncoordinated protein 1 (Protein unc-1)	0.05	-	nuc	2 *					285
P83439 UniProt NPD GO	UP02_METAN	Unknown 70 kDa protein (Fragment)	0.05	-		0					15
P34938 UniProt NPD GO	UE15_HORVU	Unknown endosperm protein E-15/E-16/E-17 (Fragment)	0.05	-		0					15
P83440 UniProt NPD GO	UP01_METAN	Unknown protein (Fragment)	0.05	-		0					15
P80632 UniProt NPD GO	UC26_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 907) (Fragment)	0.05	-		0					8
P82332 UniProt NPD GO	UT115_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 115) (Fragments)	0.05	-		0	Plastid; chloroplast; chloroplast thylakoid				14
O65583 UniProt NPD GO	UPP_ARATH	Uracil phosphoribosyltransferase (EC 2.4.2.9) (UMP pyrophosphorylase) (UPRTase)	0.05	-	nuc	0					198
Q42586 UniProt NPD GO	PYR5_ARATH	Uridine 5'-monophosphate synthase (UMP synthase) [Includes: Orotate phosphoribosyltransferase (EC 2. ...	0.05	-	cyt	0					476
P53385 UniProt NPD GO	HUTU_TRIRP	Urocanate hydratase (EC 4.2.1.49) (Urocanase) (Imidazolonepropionate hydrolase)	0.05	-	cyt	0					564
Q5R5C1 UniProt NPD GO	UROM_PONPY	Uromodulin precursor	0.05	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity). Secreted protein (By similarity). Secreted ...				641
P07911 UniProt NPD GO	UROM_HUMAN	Uromodulin precursor (Tamm-Horsfall urinary glycoprotein) (THP)	0.05	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor. Secreted protein. Secreted after cleavage in the urine	extrinsic to membrane [TAS]	609886		640
Q42855 UniProt NPD GO	DCUP_HORVU	Uroporphyrinogen decarboxylase (EC 4.1.1.37) (URO-D) (UPD) (Fragment)	0.05	-	cyt	0	Plastid; chloroplast				330
P49220 UniProt NPD GO	UR2R_BOVIN	Urotensin II receptor (UR-II-R) (G-protein coupled receptor 14) (G-protein coupled sensory epithelia ...	0.05	-	end	7	Membrane; multi-pass membrane protein				384
Q8MKG2 UniProt NPD GO	UTER_HORSE	Uteroglobin precursor (Secretoglobin family 1A member 1)	0.05	-	exc	0	Secreted protein				91
O23654 UniProt NPD GO	VATA_ARATH	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.05	-	nuc	0					623
Q9UVJ8 UniProt NPD GO	VATA_ASHGO	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.05	-	nuc	0					617
Q39442 UniProt NPD GO	VATA_BETVU	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.05	-	nuc	0					623
Q9SM09 UniProt NPD GO	VATA_CITUN	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.05	-	cyt	0					623
P09469 UniProt NPD GO	VATA_DAUCA	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.05	-	cyt	0					623
P31405 UniProt NPD GO	VATA_GOSHI	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.05	-	cyt	0					623
Q39291 UniProt NPD GO	VATA_BRANA	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.05	-	nuc	0					623
Q9XW92 UniProt NPD GO	VATA_CAEEL	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.05	-	cyt	0					605
Q38676 UniProt NPD GO	VATA1_ACEAT	Vacuolar ATP synthase catalytic subunit A isoform 1 (EC 3.6.3.14) (V-ATPase subunit A 1) (Vacuolar p ...	0.05	-	cyt	0					613
Q38677 UniProt NPD GO	VATA2_ACEAT	Vacuolar ATP synthase catalytic subunit A isoform 2 (EC 3.6.3.14) (V-ATPase subunit A 2) (Vacuolar p ...	0.05	-	cyt	0					613
Q04237 UniProt NPD GO	VATA1_PSINU	Vacuolar ATP synthase catalytic subunit A, isoform 1 (EC 3.6.3.14) (Fragment)	0.05	-	cyt	0					30
Q04239 UniProt NPD GO	VATA2_PSINU	Vacuolar ATP synthase catalytic subunit A, isoform 2 (EC 3.6.3.14) (Fragment)	0.05	-	cyt	0					30
O94072 UniProt NPD GO	VATE_CANAL	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit)	0.05	-	cyt	0					226
Q9I8H3 UniProt NPD GO	VATF_XENLA	Vacuolar ATP synthase subunit F (EC 3.6.3.14) (V-ATPase F subunit) (Vacuolar proton pump F subunit) ...	0.05	-	cyt	0					110
Q5K8S8 UniProt NPD GO	VA0E_CRYNE	Vacuolar ATP synthase subunit e (EC 3.6.3.14) (V-ATPase e subunit) (Vacuolar proton pump e subunit)	0.05	-	nuc	2 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				71
O80977 UniProt NPD GO	VSR3_ARATH	Vacuolar sorting receptor 3 precursor (AtVSR3) (Epidermal growth factor receptor-like protein 2a) (A ...	0.05	-	end	1					628
P09685 UniProt NPD GO	VIP_SCYCA	Vasoactive intestinal peptide (VIP) (Vasoactive intestinal polypeptide)	0.05	-	nuc	0	Secreted protein				28
Q7M428 UniProt NPD GO	NEU3_EPTST	Vasotocin-neurophysin VT precursor [Contains: Vasotocin (VT); Neurophysin VT]	0.05	-	exc	0	Secreted protein				161

You are viewing entries 75901 to 75950 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.