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
Q3E801 UniProt NPD GO	YJ136_YEAST	Uncharacterized protein YJL136W-A	0.04	-	nuc	0					27
P47095 UniProt NPD GO	YJZ4_YEAST	Uncharacterized protein YJR024C	0.04	-	cyt	0		cytoplasm [IDA]			244
P36068 UniProt NPD GO	YKN0_YEAST	Uncharacterized protein YKL130C	0.04	-	cyt	0		cytoplasm [IDA]		1XLY	246
Q12431 UniProt NPD GO	YL014_YEAST	Uncharacterized protein YLL014W	0.04	-	cyt	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			108
Q3E809 UniProt NPD GO	YM054_YEAST	Uncharacterized protein YML054C-A	0.04	-	cyt	0					52
Q8TGS8 UniProt NPD GO	YM105_YEAST	Uncharacterized protein YMR105W-A	0.04	-	cyt	0					64
Q03262 UniProt NPD GO	YM8L_YEAST	Uncharacterized protein YMR278W	0.04	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			622
P53736 UniProt NPD GO	YN8O_YEAST	Uncharacterized protein YNR040W	0.04	-	nuc	0		mitochondrion [IDA]			256
P52923 UniProt NPD GO	YN9B_YEAST	Uncharacterized protein YNR074C	0.04	-	mit	1 *		mitochondrion [IDA] nucleus [IDA]			378
Q8TGS0 UniProt NPD GO	YO161_YEAST	Uncharacterized protein YOR161C-C	0.04	-	cyt	1 *	Membrane; single-pass membrane protein (Potential)				48
P83438 UniProt NPD GO	UP03_METAN	Unknown 33 kDa protein (Fragment)	0.04	-	cyt	0					21
P31144 UniProt NPD GO	UKA2_HUMAN	Unknown protein from 2D-PAGE of epidermal keratinocytes (Spot 1617) (Fragments)	0.04	-		0					12
P80610 UniProt NPD GO	UC04_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 128) (Fragment)	0.04	-		0					14
P99032 UniProt NPD GO	ULAL_MOUSE	Unknown protein from 2D-PAGE of liver tissue (Spot 2D-0014M9) (Fragment)	0.04	-		0					12
P82340 UniProt NPD GO	UT204_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 204) (Fragment)	0.04	-		0	Plastid; chloroplast; chloroplast thylakoid				14
P09059 UniProt NPD GO	SVF30_VICFA	Unknown seed protein 30.1 precursor (VF30.1)	0.04	-	cyt	0					268
Q9D142 UniProt NPD GO	NUD14_MOUSE	Uridine diphosphate glucose pyrophosphatase (EC 3.6.1.45) (UDPG pyrophosphatase) (UGPPase) (Nucleosi ...	0.04	-	cyt	0	Cytoplasm (By similarity)				222
O95045 UniProt NPD GO	UPP2_HUMAN	Uridine phosphorylase 2 (EC 2.4.2.3) (UrdPase 2) (UPase 2)	0.04	-	nuc	0		cytosol [NAS] type III intermediate filament [IDA]			317
P81828 UniProt NPD GO	UP2_RAT	Urinary protein 2 precursor (RUP-2)	0.04	-	exc	0	Secreted protein				101
Q862Z3 UniProt NPD GO	UROM_CANFA	Uromodulin precursor (Tamm-Horsfall urinary glycoprotein) (THP)	0.04	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity). Secreted protein (By similarity). Secreted ...				642
Q9JKX8 UniProt NPD GO	UPK3A_MOUSE	Uroplakin-3A precursor (Uroplakin III) (UPIII)	0.04	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				287
Q2VPS3 UniProt NPD GO	UTER_BOVIN	Uteroglobin precursor (Secretoglobin family 1A member 1)	0.04	-	exc	0	Secreted protein				91
P02779 UniProt NPD GO	UTER_RABIT	Uteroglobin precursor (Secretoglobin family 1A member 1) (Blastokinin)	0.04	-	exc	0	Secreted protein			2UTG	91
Q920H1 UniProt NPD GO	SG3A2_MOUSE	Uteroglobin-related protein 1 precursor (Secretoglobin family 3A member 2) (Pneumo secretory protein ...	0.04	-	mit	1 *	Secreted protein	extracellular region [IDA]			139
O16109 UniProt NPD GO	VATA_AEDAE	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.04	-	cyt	0					615
Q5TTG1 UniProt NPD GO	VATA_ANOGA	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.04	-	cyt	0					614
Q61VZ4 UniProt NPD GO	VATA_CAEBR	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) (Vacuolar proton pump s ...	0.04	-	cyt	0					606
Q9XXU9 UniProt NPD GO	VATC_CAEEL	Vacuolar ATP synthase subunit C (EC 3.6.3.14) (V-ATPase C subunit) (Vacuolar proton pump C subunit)	0.04	-	cyt	0					384
Q17029 UniProt NPD GO	VATF_ANOGA	Vacuolar ATP synthase subunit F (EC 3.6.3.14) (V-ATPase F subunit) (Vacuolar proton pump F subunit) ...	0.04	-	cyt	0					127
P48836 UniProt NPD GO	VATG_YEAST	Vacuolar ATP synthase subunit G (EC 3.6.3.14) (V-ATPase G subunit) (Vacuolar proton pump G subunit) ...	0.04	-	nuc	0		hydrogen-transporting ATPase V1 domain [TAS]			114
Q769E5 UniProt NPD GO	CAX1A_ORYSA	Vacuolar cation/proton exchanger 1a (Ca(2+)/H(+) exchanger 1a) (OsCAX1a)	0.04	-	end	10	Vacuole; vacuolar membrane; multi-pass membrane protein (Probable). Tonoplast				451
Q5KTQ9 UniProt NPD GO	CAX1C_ORYSA	Vacuolar cation/proton exchanger 1c (Ca(2+)/H(+) exchanger 1c) (OsCAX1c)	0.04	-	end	8	Vacuole; vacuolar membrane; multi-pass membrane protein (Probable). Tonoplast				450
Q08474 UniProt NPD GO	VAM10_YEAST	Vacuolar morphogenesis protein 10	0.04	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein (Probable)	vacuolar membrane [IC]			114
P38759 UniProt NPD GO	PEP11_YEAST	Vacuolar protein sorting 29 (Vesicle protein sorting 29)	0.04	-	nuc	0		endosome [IPI] retromer complex [TAS]			282
P26335 UniProt NPD GO	VSE2_TRYBR	Variant surface glycoprotein ETAT 1.2 precursor (Fragment)	0.04	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. A soluble form is released from ruptured cells by the actio ...				55
P67862 UniProt NPD GO	TXVE_TRIFL	Vascular endothelial growth factor toxin precursor (svVEGF)	0.04	-	mit	0	Secreted protein				146
Q9NY84 UniProt NPD GO	VNN3_HUMAN	Vascular non-inflammatory molecule 3 precursor (Vanin-3)	0.04	-	mit	1 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)		606592		501
Q9QZ25 UniProt NPD GO	VNN3_MOUSE	Vascular non-inflammatory molecule 3 precursor (Vanin-3)	0.04	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				500
P63289 UniProt NPD GO	VIP_CANFA	Vasoactive intestinal peptide (VIP) (Vasoactive intestinal polypeptide)	0.04	-	nuc	0	Secreted protein				28
P63290 UniProt NPD GO	VIP_CAPHI	Vasoactive intestinal peptide (VIP) (Vasoactive intestinal polypeptide)	0.04	-	nuc	0	Secreted protein				28
P84488 UniProt NPD GO	VIP_MACMU	Vasoactive intestinal peptide (VIP) (Vasoactive intestinal polypeptide)	0.04	-	nuc	0	Secreted protein				28
P63291 UniProt NPD GO	VIP_SHEEP	Vasoactive intestinal peptide (VIP) (Vasoactive intestinal polypeptide)	0.04	-	nuc	0	Secreted protein				28
P81657 UniProt NPD GO	VA5_VESMA	Venom allergen 5 (Antigen 5) (Ag5) (Allergen Vesp m 5)	0.04	-	nuc	0	Secreted protein. Venom reservoirs				202
P83230 UniProt NPD GO	VNOC_OXYMI	Venom natriuretic peptide OxsSNPc	0.04	-	nuc	0	Secreted protein	extracellular region [NAS]			39
P83231 UniProt NPD GO	VNOC_OXYSA	Venom natriuretic peptide OxsSNPc	0.04	-	nuc	0	Secreted protein	extracellular region [NAS]			39
Q10219 UniProt NPD GO	YAYC_SCHPO	Very hypothetical protein C4H3.12c in chromosome I	0.04	-	nuc	1 *					101
P40588 UniProt NPD GO	YIW4_YEAST	Very hypothetical protein YIR044C	0.04	-	cyt	0					61
P53957 UniProt NPD GO	YNE3_YEAST	Very hypothetical protein YNL043C	0.04	-	nuc	0					106
Q9DCQ3 UniProt NPD GO	GOT1A_MOUSE	Vesicle transport protein GOT1A (Golgi transport 1 homolog A)	0.04	-	end	4 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				133
Q8VD57 UniProt NPD GO	SFT2B_MOUSE	Vesicle transport protein SFT2B (SFT2 domain-containing protein 2)	0.04	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				159

You are viewing entries 78751 to 78800 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.