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
P01038 UniProt NPD GO	CYT_CHICK	Cystatin precursor (Egg-white cystatin)	0.05	-	end	1 *				1YVB	139
Q80ZN5 UniProt NPD GO	CST13_MOUSE	Cystatin-13 precursor (Cystatin T)	0.05	-	cyt	0	Secreted protein (Potential). Ref.1: Cytoplasm				141
Q32LE9 UniProt NPD GO	CSRP2_BOVIN	Cysteine and glycine-rich protein 2 (Cysteine-rich protein 2) (CRP2)	0.05	-	nuc	0	Nucleus (By similarity)				192
P97314 UniProt NPD GO	CSRP2_MOUSE	Cysteine and glycine-rich protein 2 (Cysteine-rich protein 2) (CRP2) (Double LIM protein 1) (DLP-1)	0.05	-	nuc	0	Nucleus (By similarity)				192
Q62908 UniProt NPD GO	CSRP2_RAT	Cysteine and glycine-rich protein 2 (Cysteine-rich protein 2) (CRP2) (Smooth muscle cell LIM protein ...	0.05	-	nuc	0	Nucleus	nucleus [IDA]			192
Q16527 UniProt NPD GO	CSRP2_HUMAN	Cysteine and glycine-rich protein 2 (Cysteine-rich protein 2) (CRP2) (Smooth muscle cell LIM protein ...	0.05	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]	601871		192
Q23894 UniProt NPD GO	CYSP3_DICDI	Cysteine proteinase 3 (EC 3.4.22.-) (Cysteine proteinase II) (Fragment)	0.05	-	nuc	0	Lysosome (Potential)				151
P25251 UniProt NPD GO	CYSP4_BRANA	Cysteine proteinase COT44 precursor (EC 3.4.22.-) (Fragment)	0.05	-	cyt	0					328
P25249 UniProt NPD GO	CYSP1_HORVU	Cysteine proteinase EP-B 1 precursor (EC 3.4.22.-)	0.05	-	exc	0					371
P25250 UniProt NPD GO	CYSP2_HORVU	Cysteine proteinase EP-B 2 precursor (EC 3.4.22.-)	0.05	-	exc	0					373
P82473 UniProt NPD GO	CPGP1_ZINOF	Cysteine proteinase GP-I (EC 3.4.22.-)	0.05	-	cyt	0					221
P30228 UniProt NPD GO	AFP2_BRARA	Cysteine-rich antifungal protein 2 (AFP2) (Fragment)	0.05	-	nuc	0					27
P30232 UniProt NPD GO	AFP2A_SINAL	Cysteine-rich antifungal protein 2A (AFP2A) (M2A)	0.05	-	nuc	0					51
O19010 UniProt NPD GO	CRIS3_HORSE	Cysteine-rich secretory protein 3 precursor (CRISP-3)	0.05	-	exc	0	Secreted protein (By similarity). In neutrophils, localized in specific granules (By similarity)	extracellular matrix (sensu Metazoa) [ISS] extracellular region [ISS] specific granule [ISS]			245
Q9UPY5 UniProt NPD GO	XCT_HUMAN	Cystine/glutamate transporter (Amino acid transport system xc-) (xCT) (Calcium channel blocker resis ...	0.05	-	end	12 *	Membrane; multi-pass membrane protein (Probable)	integral to membrane [TAS]	607933		501
Q9NYL5 UniProt NPD GO	CP39A_HUMAN	Cytochrome P450 39A1 (EC 1.14.13.99) (24-hydroxycholesterol 7-alpha-hydroxylase) (Oxysterol 7-alpha- ...	0.05	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [TAS]	605994		469
Q43068 UniProt NPD GO	C82A1_PEA	Cytochrome P450 82A1 (EC 1.14.-.-) (CYPLXXXII) (Fragment)	0.05	-	nuc	1 *					544
O48014 UniProt NPD GO	CYB_ANISC	Cytochrome b	0.05	-	end	9 *					371
Q2Y067 UniProt NPD GO	CYB_AOTIN	Cytochrome b	0.05	-	end	9 *					379
Q9MLJ9 UniProt NPD GO	CYB_BOUAN	Cytochrome b	0.05	-	end	8 *					372
Q9B205 UniProt NPD GO	CYB_CAICR	Cytochrome b	0.05	-	end	9 *					383
Q9MLD7 UniProt NPD GO	CYB_CALKE	Cytochrome b	0.05	-	end	8 *					371
Q9MLD6 UniProt NPD GO	CYB_CALMC	Cytochrome b	0.05	-	end	8 *					371
Q8SJL3 UniProt NPD GO	CYB_CLEMA	Cytochrome b	0.05	-	end	9 *					379
Q9MLJ6 UniProt NPD GO	CYB_DENPO	Cytochrome b	0.05	-	end	9 *					372
Q9MLK9 UniProt NPD GO	CYB_DRYCO	Cytochrome b	0.05	-	end	9 *					371
Q9MLK8 UniProt NPD GO	CYB_ELANI	Cytochrome b	0.05	-	end	8 *					371
Q36368 UniProt NPD GO	CYB_ERIEU	Cytochrome b	0.05	-	end	9 *					379
Q9MLJ4 UniProt NPD GO	CYB_LATCO	Cytochrome b	0.05	-	end	8 *					371
P92658 UniProt NPD GO	CYB_MAMPR	Cytochrome b	0.05	-	end	9 *					378
Q9T7L5 UniProt NPD GO	CYB_MICXA	Cytochrome b	0.05	-	end	9 *					380
Q9MLK1 UniProt NPD GO	CYB_NAJNI	Cytochrome b	0.05	-	end	8 *					372
Q9MLJ2 UniProt NPD GO	CYB_NOTAT	Cytochrome b	0.05	-	end	8 *					368
Q9MLI6 UniProt NPD GO	CYB_OPHHA	Cytochrome b	0.05	-	end	8 *					372
Q9T9W4 UniProt NPD GO	CYB_PANPA	Cytochrome b	0.05	-	end	9 *					380
O79680 UniProt NPD GO	CYB_PELSU	Cytochrome b	0.05	-	end	9 *					380
O21224 UniProt NPD GO	CYB_POLPL	Cytochrome b	0.05	-	end	9 *					380
O48111 UniProt NPD GO	CYB_PYTSE	Cytochrome b	0.05	-	end	10 *					371
Q8LWP6 UniProt NPD GO	CYB_RANSI	Cytochrome b	0.05	-	end	8 *					380
Q9TF20 UniProt NPD GO	CYB_SPEWA	Cytochrome b	0.05	-	end	9 *					379
Q8SJK8 UniProt NPD GO	CYB_TERCO	Cytochrome b	0.05	-	end	9 *					379
Q8SJK7 UniProt NPD GO	CYB_TERNE	Cytochrome b	0.05	-	end	9 *					379
Q9MLK3 UniProt NPD GO	CYB_TOXPR	Cytochrome b	0.05	-	end	8 *					371
P21713 UniProt NPD GO	CYB_AKOAN	Cytochrome b (Fragment)	0.05	-	end	6 *					267
Q95MN4 UniProt NPD GO	CY24A_RABIT	Cytochrome b-245 light chain (p22 phagocyte B-cytochrome) (Neutrophil cytochrome b 22 kDa polypeptid ...	0.05	-	end	2 *					193
P00171 UniProt NPD GO	CYB5_BOVIN	Cytochrome b5	0.05	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...			1U9U	133
Q6EW36 UniProt NPD GO	PSBE_NYMAL	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.05	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				82
P05334 UniProt NPD GO	PSBF_EUGGR	Cytochrome b559 beta subunit (PSII reaction center subunit VI)	0.05	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				41
Q03367 UniProt NPD GO	PSBF_CAPAN	Cytochrome b559 beta subunit (PSII reaction center subunit VI) (Fragment)	0.05	-		0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				10
P30361 UniProt NPD GO	UCRIA_TOBAC	Cytochrome b6-f complex iron-sulfur subunit 1, chloroplast precursor (EC 1.10.99.1) (Rieske iron-sul ...	0.05	-	mit	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein. The transmembran ...				228

You are viewing entries 74151 to 74200 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.