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
P46645 UniProt NPD GO	AAT2_ARATH	Aspartate aminotransferase, cytoplasmic isozyme 1 (EC 2.6.1.1) (Transaminase A)	0.01	-	cyt	0	Cytoplasm (Potential)				405
P46646 UniProt NPD GO	AAT4_ARATH	Aspartate aminotransferase, cytoplasmic isozyme 2 (EC 2.6.1.1) (Transaminase A)	0.01	-	cyt	0	Cytoplasm (Potential)				403
P83989 UniProt NPD GO	RACD_ANABR	Aspartate racemase (EC 5.1.1.13) (Fragment)	0.01	-	nuc	0					31
P13663 UniProt NPD GO	DHAS_YEAST	Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (ASA dehydrogenase) (ASA DH)	0.01	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			365
P54958 UniProt NPD GO	ASP2_BLAGE	Aspartic protease Bla g 2 precursor (EC 3.4.23.-) (Allergen Bla g II)	0.01	-	end	0				1YG9	352
Q43646 UniProt NPD GO	API2_SOLTU	Aspartic protease inhibitor 2 precursor (Cathepsin D inhibitor) (CathDinh) (CathIhn)	0.01	-	exc	1 *	Vacuole (By similarity)				220
O04057 UniProt NPD GO	ASPR_CUCPE	Aspartic proteinase precursor (EC 3.4.23.-)	0.01	-	exc	0	Vacuole				513
P50725 UniProt NPD GO	ATTA_TRINI	Attacin-A precursor	0.01	-	exc	0	Secreted protein				254
P69021 UniProt NPD GO	AUR31_LITAU	Aurein-3.1 [Contains: Aurein-3.1.1; Aurein-3.1.2]	0.01	-		0	Secreted protein				17
P69020 UniProt NPD GO	AUR31_LITRA	Aurein-3.1 [Contains: Aurein-3.1.1; Aurein-3.1.2]	0.01	-		0	Secreted protein				17
P69023 UniProt NPD GO	AUR32_LITAU	Aurein-3.2	0.01	-		0	Secreted protein				17
P69022 UniProt NPD GO	AUR32_LITRA	Aurein-3.2	0.01	-		0	Secreted protein				17
P82396 UniProt NPD GO	AUR33_LITRA	Aurein-3.3 [Contains: Aurein-3.3.1]	0.01	-		0	Secreted protein				17
Q757Z8 UniProt NPD GO	ATG27_ASHGO	Autophagy-related protein 27 precursor	0.01	-	nuc	2	Intracytoplasmic membrane; single-pass type I membrane protein (By similarity). Perivacuolar punctat ...				297
P13689 UniProt NPD GO	ABP1_MAIZE	Auxin-binding protein 1 precursor (ABP) (ERABP1)	0.01	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen			1LRH	201
O04011 UniProt NPD GO	ABP20_PRUPE	Auxin-binding protein ABP20 precursor	0.01	-	exc	0	Cell wall				214
P33490 UniProt NPD GO	ABP1_TOBAC	Auxin-binding protein T85 precursor (ABP)	0.01	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				187
O13153 UniProt NPD GO	AVR1_CHICK	Avidin-related protein 1 precursor	0.01	-	exc	0					150
P56735 UniProt NPD GO	AVR6_CHICK	Avidin-related protein 6 precursor	0.01	-	exc	0					150
P56736 UniProt NPD GO	AVR7_CHICK	Avidin-related protein 7 precursor	0.01	-	exc	0					150
Q86Y27 UniProt NPD GO	BAGE5_HUMAN	B melanoma antigen 5 precursor	0.01	-	vac	0					43
P11392 UniProt NPD GO	PHEA_PORCR	B-phycoerythrin alpha chain	0.01	-	cyt	0	Periphery of the rods of the phycobilisome				164
P29947 UniProt NPD GO	PHEA_PORSO	B-phycoerythrin alpha chain	0.01	-	cyt	0	Periphery of the rods of the phycobilisome				164
Q02036 UniProt NPD GO	PHEA_RHOVL	B-phycoerythrin alpha chain	0.01	-	cyt	0	Periphery of the rods of the phycobilisome				164
Q9VLU0 UniProt NPD GO	BAFL_DROME	BAF-like protein CG7380	0.01	-	cyt	0	Nucleus (Potential)	nucleus [NAS]			90
P55269 UniProt NPD GO	BAXD_HUMAN	BAX protein, cytoplasmic isoform delta	0.01	-	end	1	Cytoplasm (Potential)		600040		143
Q9CR40 UniProt NPD GO	BTBD5_MOUSE	BTB/POZ domain-containing protein 5	0.01	-	cyt	0					571
Q8N4F0 UniProt NPD GO	BPIL1_HUMAN	Bactericidal/permeability-increasing protein-like 1 precursor (Long palate, lung and nasal epitheliu ...	0.01	-	exc	1 *	Secreted protein (By similarity)				458
P14662 UniProt NPD GO	CEC2_MANSE	Bactericidin B-2 (Cecropin-like peptide B-2)	0.01	-	nuc	0	Secreted protein				37
P93538 UniProt NPD GO	LECB_SOPJA	Bark lectin precursor (LECSJABG) (Fragment)	0.01	-	exc	0					270
Q03565 UniProt NPD GO	BAF1_CAEEL	Barrier-to-autointegration factor 1	0.01	-	cyt	0	Nucleus (Potential)				89
Q6NTS2 UniProt NPD GO	BAFA_XENLA	Barrier-to-autointegration factor A	0.01	-	cyt	0	Nucleus (By similarity)				90
Q66KV4 UniProt NPD GO	BAFB_XENLA	Barrier-to-autointegration factor B	0.01	-	cyt	0	Nucleus (By similarity)				90
Q32PE7 UniProt NPD GO	BAFL_BOVIN	Barrier-to-autointegration factor-like protein (BAF-L)	0.01	-	cyt	0	Nucleus. Cytoplasm (By similarity)				90
Q8BVR0 UniProt NPD GO	BAFL_MOUSE	Barrier-to-autointegration factor-like protein (BAF-L)	0.01	-	cyt	0	Nucleus. Cytoplasm (By similarity)				90
Q865R3 UniProt NPD GO	BASI_BOVIN	Basigin precursor (EMMPRIN) (CD147 antigen) (Fragment)	0.01	-	mit	1 *	Cell membrane; single-pass type I membrane protein (By similarity). Colocalizes with SLC16A1 and SLC ...				205
Q3C2I0 UniProt NPD GO	B2LA1_BOVIN	Bcl-2-related protein A1	0.01	-	cyt	0	Cytoplasm (By similarity)				175
Q16548 UniProt NPD GO	B2LA1_HUMAN	Bcl-2-related protein A1 (Protein BFL-1) (Hemopoietic-specific early response protein) (Protein GRS) ...	0.01	-	cyt	0	Cytoplasm	intracellular [NAS]	601056		175
O96363 UniProt NPD GO	BGBP_HYPCU	Beta-1,3-glucan-binding protein precursor (BGBP) (Beta-1,3-glucan recognition protein) (BetaGRP) (Gr ...	0.01	-	exc	0	Secreted protein (By similarity)	extracellular region [ISS]			481
P33703 UniProt NPD GO	APOH_CANFA	Beta-2-glycoprotein 1 precursor (Beta-2-glycoprotein I) (Apolipoprotein H) (Apo-H) (B2GPI) (Beta(2)G ...	0.01	-	exc	0	Secreted protein				345
P26644 UniProt NPD GO	APOH_RAT	Beta-2-glycoprotein 1 precursor (Beta-2-glycoprotein I) (Apolipoprotein H) (Apo-H) (B2GPI) (Beta(2)G ...	0.01	-	exc	0	Secreted protein				297
P21612 UniProt NPD GO	B2MG_MELGA	Beta-2-microglobulin	0.01	-	cyt	0	Secreted protein				98
Q9PRF8 UniProt NPD GO	B2MG_ACIBE	Beta-2-microglobulin precursor	0.01	-	mit	0	Secreted protein				122
Q04475 UniProt NPD GO	B2MG_BRARE	Beta-2-microglobulin precursor	0.01	-	end	0	Secreted protein				116
P21611 UniProt NPD GO	B2MG_CHICK	Beta-2-microglobulin precursor	0.01	-	mit	0	Secreted protein				119
P30441 UniProt NPD GO	B2MG_HORSE	Beta-2-microglobulin precursor	0.01	-	end	0	Secreted protein				118
Q8SPW0 UniProt NPD GO	B2MG_MACFA	Beta-2-microglobulin precursor	0.01	-	exc	0	Secreted protein				119
Q864T7 UniProt NPD GO	B2MG_ORNAN	Beta-2-microglobulin precursor	0.01	-	exc	0	Secreted protein				118
Q8AXA0 UniProt NPD GO	B2MG_RAJEG	Beta-2-microglobulin precursor	0.01	-	exc	0	Secreted protein				111
P63068 UniProt NPD GO	B2MG_SAGBB	Beta-2-microglobulin precursor	0.01	-	exc	0	Secreted protein				119

You are viewing entries 86801 to 86850 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.