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
P80621 UniProt NPD GO	UC15_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 245) (Fragment)	0.01	-		0					14
P80620 UniProt NPD GO	UC14_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 258) (Fragment)	0.01	-		0					15
P80624 UniProt NPD GO	UC18_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 263) (Fragment)	0.01	-		0					14
P80623 UniProt NPD GO	UC17_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 32) (Fragment)	0.01	-		0					15
P80627 UniProt NPD GO	UC21_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 443) (Fragment)	0.01	-		0					18
P80635 UniProt NPD GO	UC29_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 45) (Fragment)	0.01	-		0					15
P80629 UniProt NPD GO	UC23_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 502) (Fragment)	0.01	-		0					15
P80637 UniProt NPD GO	UC31_MAIZE	Unknown protein from 2D-PAGE of etiolated coleoptile (Spot 67) (Fragments)	0.01	-		0					19
P38644 UniProt NPD GO	UF06_MOUSE	Unknown protein from 2D-PAGE of fibroblasts (P50) (Fragment)	0.01	-		0					8
P40930 UniProt NPD GO	UHA3_HUMAN	Unknown protein from 2D-PAGE of heart (Spot 7513) (Fragment)	0.01	-		0					10
P99503 UniProt NPD GO	UHA1_CANFA	Unknown protein from 2D-PAGE of heart tissue (Spot 11) (Fragment)	0.01	-		0					14
P56572 UniProt NPD GO	UH03_RAT	Unknown protein from 2D-PAGE of heart tissue (Spot P3) (Fragment)	0.01	-		0					12
P83648 UniProt NPD GO	UP07_ORYSA	Unknown protein from 2D-PAGE of leaf (OsL8) (Fragments)	0.01	-		0	Plastid; chloroplast				14
P31931 UniProt NPD GO	ULAE_HUMAN	Unknown protein from 2D-PAGE of liver tissue (Spot 115) (Fragment)	0.01	-		0					9
P81675 UniProt NPD GO	UN06_PINPS	Unknown protein from 2D-PAGE of needles (N141) (Fragment)	0.01	-		0					7
P81673 UniProt NPD GO	UN04_PINPS	Unknown protein from 2D-PAGE of needles (N143) (Fragment)	0.01	-		0					15
P81674 UniProt NPD GO	UN05_PINPS	Unknown protein from 2D-PAGE of needles (N147) (Fragments)	0.01	-		0					20
P30090 UniProt NPD GO	UPA4_HUMAN	Unknown protein from 2D-PAGE of plasma (Spot 12) (Fragment)	0.01	-		0					10
P30092 UniProt NPD GO	UPA6_HUMAN	Unknown protein from 2D-PAGE of plasma (Spot 14) (Fragment)	0.01	-		0					9
P31935 UniProt NPD GO	UPA11_HUMAN	Unknown protein from 2D-PAGE of plasma (Spot 53) (Fragments)	0.01	-		0					16
P32080 UniProt NPD GO	URA6_HUMAN	Unknown protein from 2D-PAGE of red blood cells (Spot 17) (Fragment)	0.01	-		0					10
P82324 UniProt NPD GO	UT105_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 105) (Fragment)	0.01	-		0	Plastid; chloroplast; chloroplast thylakoid				8
P82325 UniProt NPD GO	UT106_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 106) (Fragment)	0.01	-		0	Plastid; chloroplast; chloroplast thylakoid				12
P82328 UniProt NPD GO	UT110_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 110) (Fragment)	0.01	-		0	Plastid; chloroplast; chloroplast thylakoid				12
P82330 UniProt NPD GO	UT112_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 112) (Fragment)	0.01	-		0	Plastid; chloroplast; chloroplast thylakoid				14
P82341 UniProt NPD GO	UT251_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 251) (Fragment)	0.01	-		0	Plastid; chloroplast; chloroplast thylakoid				14
Q78IK2 UniProt NPD GO	USMG5_MOUSE	Up-regulated during skeletal muscle growth protein 5	0.01	-	cyt	1 *	Membrane; single-pass membrane protein (Potential)	mitochondrial inner membrane [IDA]			58
Q9JJW3 UniProt NPD GO	USMG5_RAT	Up-regulated during skeletal muscle growth protein 5 (Diabetes-associated protein in insulin-sensiti ...	0.01	-	cyt	1 *	Membrane; single-pass membrane protein (Potential)				58
P82026 UniProt NPD GO	TKN1_UPEIN	Uperin-1.1	0.01	-		0	Secreted protein				11
P82032 UniProt NPD GO	UPE31_UPEIN	Uperin-3.1	0.01	-		0	Secreted protein				17
P82033 UniProt NPD GO	UPE32_UPEIN	Uperin-3.2	0.01	-		0	Secreted protein				17
P82041 UniProt NPD GO	UPE34_UPEMJ	Uperin-3.4	0.01	-		0	Secreted protein				17
P82042 UniProt NPD GO	UPE35_UPEMJ	Uperin-3.5	0.01	-		0	Secreted protein				17
P82044 UniProt NPD GO	UPE37_UPEMJ	Uperin-3.7	0.01	-		0	Secreted protein				17
P82035 UniProt NPD GO	UPE41_UPEIN	Uperin-4.1	0.01	-		0	Secreted protein				17
P82036 UniProt NPD GO	UPE51_UPEIN	Uperin-5.1	0.01	-		0	Secreted protein				13
P82038 UniProt NPD GO	UPE62_UPEIN	Uperin-6.2	0.01	-	nuc	0	Secreted protein				30
P82050 UniProt NPD GO	UPE71_LITEW	Uperin-7.1 [Contains: Uperin-7.1.1]	0.01	-		0	Secreted protein				13
P08612 UniProt NPD GO	TKN1_UPERU	Uperolein	0.01	-		0	Secreted protein				11
Q10279 UniProt NPD GO	FUR4_SCHPO	Uracil permease	0.01	-	end	10	Membrane; multi-pass membrane protein				581
P05316 UniProt NPD GO	FUR4_YEAST	Uracil permease	0.01	-	end	13	Membrane; multi-pass membrane protein	lipid raft [IDA] plasma membrane [IDA]			633
Q00511 UniProt NPD GO	URIC_ASPFL	Uricase (EC 1.7.3.3) (Urate oxidase)	0.01	-	pox	0	Peroxisome			2FXL	301
P33282 UniProt NPD GO	URIC_EMENI	Uricase (EC 1.7.3.3) (Urate oxidase)	0.01	-	cyt	0	Peroxisome				301
P53763 UniProt NPD GO	URIC_PHAVU	Uricase-2 (EC 1.7.3.3) (Uricase II) (Urate oxidase) (Nodule-specific uricase)	0.01	-	pox	0	Peroxisome				308
O04104 UniProt NPD GO	URIC2_SOYBN	Uricase-2 isozyme 2 (EC 1.7.3.3) (Uricase II isozyme 2) (Urate oxidase) (Nodulin 35) (N-35) (Non-sym ...	0.01	-	pox	0	Peroxisome				309
P83121 UniProt NPD GO	UP3_RAT	Urinary protein 3 precursor (RUP-3)	0.01	-	vac	0	Secreted protein				101
P01147 UniProt NPD GO	UTS2_GILMI	Urotensin-2 (Urotensin II) (U-II) (UII)	0.01	-		0	Secreted protein				12
P35490 UniProt NPD GO	UTS2_SCYCA	Urotensin-2 (Urotensin II) (U-II) (UII)	0.01	-		0	Secreted protein				12
P04558 UniProt NPD GO	UTS2A_CATCO	Urotensin-2A (Urotensin IIA) (U-IIA) (UIIA)	0.01	-		0	Secreted protein				12
P04478 UniProt NPD GO	ESG2_TRYBB	VSG expression site-associated protein 221A precursor (ESAG protein)	0.01	-	mit	0					329

You are viewing entries 92001 to 92050 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.