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
P43599 UniProt NPD GO	YFI8_YEAST	Uncharacterized protein YFR018C	0.02	-	exc	0					363
Q8TGT8 UniProt NPD GO	YG174_YEAST	Uncharacterized protein YGR174W-A	0.02	-	cyt	0					28
Q3E705 UniProt NPD GO	YG271_YEAST	Uncharacterized protein YGR271C-A	0.02	-	cyt	0	Nucleus; nucleolus	nucleolus [IDA]			63
Q3E7Z5 UniProt NPD GO	YI002_YEAST	Uncharacterized protein YIL002W-A	0.02	-	nuc	0					69
Q2V2P3 UniProt NPD GO	YK023_YEAST	Uncharacterized protein YKL023C-A	0.02	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				75
Q07951 UniProt NPD GO	YL021_YEAST	Uncharacterized protein YLR021W	0.02	-	cyt	0					179
P53964 UniProt NPD GO	YND3_YEAST	Uncharacterized protein YNL033W precursor	0.02	-	end	2 *					284
Q3E841 UniProt NPD GO	YN034_YEAST	Uncharacterized protein YNR034W-A	0.02	-	cyt	0	Cytoplasm	cytoplasm [IDA]			98
Q3E805 UniProt NPD GO	YO376_YEAST	Uncharacterized protein YOR376W-A	0.02	-	cyt	0					51
Q10085 UniProt NPD GO	YAO6_SCHPO	Uncharacterized transporter C11D3.06	0.02	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				455
Q03697 UniProt NPD GO	YMD8_YEAST	Uncharacterized transporter YML038C	0.02	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				442
Q9ZUX4 UniProt NPD GO	UMP2_ARATH	Unknown mitochondrial protein At2g27730	0.02	-	nuc	1	Mitochondrion				113
Q9FMV1 UniProt NPD GO	UMP7_ARATH	Unknown mitochondrial protein At5g63510	0.02	-	nuc	0	Mitochondrion				252
P83898 UniProt NPD GO	NF03_NAEFO	Unknown protein NF003 from 2D-PAGE (Fragment)	0.02	-		0					20
P83889 UniProt NPD GO	NF09_NAEFO	Unknown protein NF009 from 2D-PAGE (Fragment)	0.02	-		0					20
P83598 UniProt NPD GO	NF16_NAEFO	Unknown protein NF016 from 2D-PAGE (Fragment)	0.02	-	cyt	0					23
P83729 UniProt NPD GO	NF41_NAEFO	Unknown protein NF041 from 2D-PAGE (Fragment)	0.02	-		0					15
P83599 UniProt NPD GO	NL16_NAELO	Unknown protein NLV016 from 2D-PAGE (Fragment)	0.02	-	cyt	0					23
P80614 UniProt NPD GO	UC08_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 159) (Fragment)	0.02	-		0					15
P80622 UniProt NPD GO	UC16_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 308) (Fragment)	0.02	-		0					15
P80642 UniProt NPD GO	UC36_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 415) (Fragments)	0.02	-	cyt	0					52
P80630 UniProt NPD GO	UC24_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 447) (Fragment)	0.02	-		0					7
P38639 UniProt NPD GO	UF01_MOUSE	Unknown protein from 2D-PAGE of fibroblasts (P19) (Fragment)	0.02	-		0					5
P31929 UniProt NPD GO	ULAD_HUMAN	Unknown protein from 2D-PAGE of liver tissue (Spot 106) (Fragment)	0.02	-		0					9
P31933 UniProt NPD GO	ULAG_HUMAN	Unknown protein from 2D-PAGE of liver tissue (Spot 118) (Fragment)	0.02	-		0					11
P99031 UniProt NPD GO	ULAK_MOUSE	Unknown protein from 2D-PAGE of liver tissue (Spot 2D-0014LD) (Fragment)	0.02	-		0					9
P30091 UniProt NPD GO	UPA5_HUMAN	Unknown protein from 2D-PAGE of plasma (Spot 13) (Fragment)	0.02	-		0					10
P82342 UniProt NPD GO	UT123_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 123) (Fragment)	0.02	-		0	Plastid; chloroplast; chloroplast thylakoid				12
P33413 UniProt NPD GO	DUR3_YEAST	Urea active transporter	0.02	-	end	15 *	Membrane; multi-pass membrane protein	plasma membrane [IMP]			735
Q15849 UniProt NPD GO	UT2_HUMAN	Urea transporter, kidney	0.02	-	end	8	Membrane; multi-pass membrane protein	integral to membrane [TAS] membrane fraction [TAS]	601611		397
Q62668 UniProt NPD GO	UT2_RAT	Urea transporter, kidney	0.02	-	end	8	Membrane; multi-pass membrane protein				397
P08298 UniProt NPD GO	UREA_SOYBN	Urease (EC 3.5.1.5) (Urea amidohydrolase) (Fragment)	0.02	-	cyt	0					129
Q07307 UniProt NPD GO	UAPA_EMENI	Uric acid-xanthine permease (UAPA transporter)	0.02	-	end	12	Membrane; multi-pass membrane protein				574
P34798 UniProt NPD GO	URIC1_CANLI	Uricase-2 isozyme 1 (EC 1.7.3.3) (Uricase II clone pcClNUO-01) (Urate oxidase)	0.02	-	pox	0	Peroxisome (By similarity)				308
P04670 UniProt NPD GO	URIC1_SOYBN	Uricase-2 isozyme 1 (EC 1.7.3.3) (Uricase II isozyme 1) (Urate oxidase) (Nodulin 35) (N-35) (Nodule- ...	0.02	-	pox	0	Peroxisome				309
P34799 UniProt NPD GO	URIC2_CANLI	Uricase-2 isozyme 2 (EC 1.7.3.3) (Uricase II clone pcClNUO-02) (Urate oxidase)	0.02	-	pox	0	Peroxisome (By similarity)				301
P48733 UniProt NPD GO	UROM_BOVIN	Uromodulin precursor (Tamm-Horsfall urinary glycoprotein) (THP)	0.02	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity). Secreted protein (By similarity). Secreted ...				643
P38573 UniProt NPD GO	UPK1B_BOVIN	Uroplakin-1b (Uroplakin Ib) (UPIb)	0.02	-	end	4 *	Membrane; multi-pass membrane protein	endoplasmic reticulum [IDA] integral to membrane [IDA] plasma membrane [IDA]			259
Q9Z2C6 UniProt NPD GO	UPK1B_MOUSE	Uroplakin-1b (Uroplakin Ib) (UPIb)	0.02	-	end	4 *	Membrane; multi-pass membrane protein				259
Q566D0 UniProt NPD GO	UPK1B_RAT	Uroplakin-1b (Uroplakin Ib) (UPIb)	0.02	-	end	4 *	Membrane; multi-pass membrane protein				259
P30413 UniProt NPD GO	UPK1B_MUSVI	Uroplakin-1b (Uroplakin Ib) (UPIb) (TI 1 protein)	0.02	-	end	4 *	Membrane; multi-pass membrane protein				259
O75841 UniProt NPD GO	UPK1B_HUMAN	Uroplakin-1b (Uroplakin Ib) (UPIb) (Tetraspanin-20) (Tspan-20)	0.02	-	end	4 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	602380		259
P38575 UniProt NPD GO	UPK2_MOUSE	Uroplakin-2 precursor (UP 2) (Uroplakin II) (UPII)	0.02	-	end	1 *	Membrane; single-pass type I membrane protein (Potential). Heterodimer formation with Uroplakin Ia i ...				184
Q42967 UniProt NPD GO	DCUP_TOBAC	Uroporphyrinogen decarboxylase, chloroplast precursor (EC 4.1.1.37) (URO-D) (UPD)	0.02	-	mit	0	Plastid; chloroplast			1J93	391
P04561 UniProt NPD GO	UTS2B_CYPCA	Urotensin II-beta (UII-beta) (U-II-beta)	0.02	-		0	Secreted protein				12
P81022 UniProt NPD GO	UTS2_POLSP	Urotensin-2 (Urotensin II) (U-II) (UII)	0.02	-		0	Secreted protein				12
P04559 UniProt NPD GO	UTS2B_CATCO	Urotensin-2B (Urotensin IIB) (U-IIB) (UIIB)	0.02	-		0	Secreted protein				12
Q65C83 UniProt NPD GO	UTER_NEOAS	Uteroglobin precursor (Secretoglobin family 1A member 1) (Clara cell secretory protein)	0.02	-	exc	0	Secreted protein				93
Q920D7 UniProt NPD GO	SG3A1_MOUSE	Uteroglobin-related protein 2 precursor (Cytokine HIN-1) (High in normal-1) (Secretoglobin family 3A ...	0.02	-	exc	0	Secreted protein (By similarity)				104
P04477 UniProt NPD GO	ESG1_TRYBB	VSG expression site-associated protein 117A precursor (ESAG protein)	0.02	-	cyt	0					325

You are viewing entries 86151 to 86200 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.