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
Q9VQG4 UniProt NPD GO	COLT_DROME	Congested-like trachea protein	0.07	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				306
P19815 UniProt NPD GO	SPC1D_EMENI	Conidium-specific protein	0.07	-	nuc	0					151
P0C1N5 UniProt NPD GO	CXM36_CONMR	Conotoxin Mr3.6 precursor	0.07	-	exc	1 *	Secreted protein (By similarity)				68
P69768 UniProt NPD GO	CX5D_CONVC	Conotoxin Vc5b precursor (Conotoxin Vc5.4) (Fragment)	0.07	-	exc	0	Secreted protein				55
P08796 UniProt NPD GO	CSA_DICDI	Contact site A protein precursor (CSA) (Membrane-associated glycoprotein gp80) (Cell adhesion molecu ...	0.07	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor. Attached to the membrane by a GPI-anchor that contains a ph ...				514
Q9P232 UniProt NPD GO	CNTN3_HUMAN	Contactin-3 precursor (Brain-derived immunoglobulin superfamily protein 1) (BIG-1) (Plasmacytoma-ass ...	0.07	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)		601325	1WJ3	1028
Q9XYR5 UniProt NPD GO	CONG_CONGE	Contulakin-G precursor (CGX-1160)	0.07	-	cyt	0	Secreted protein				76
P11496 UniProt NPD GO	CORZ_PERAM	Corazonin	0.07	-		0	Secreted protein	extracellular region [IDA]			11
Q8TBE1 UniProt NPD GO	CNIH3_HUMAN	Cornichon homolog 3	0.07	-	cyt	3 *	Membrane; multi-pass membrane protein (Potential)				160
Q6ZWS4 UniProt NPD GO	CNIH3_MOUSE	Cornichon homolog 3	0.07	-	cyt	3 *	Membrane; multi-pass membrane protein (Potential)				160
Q5NVK4 UniProt NPD GO	COR1B_PONPY	Coronin-1B	0.07	-	nuc	0	Localized to the leading edge in fibroblasts, as well as weakly along actin stress fibers (By simila ...				489
P83800 UniProt NPD GO	CHH_ASTFL	Crustacean hyperglycemic hormone (CHH)	0.07	-	cyt	0	Secreted protein				72
P55845 UniProt NPD GO	CHH_PROBO	Crustacean hyperglycemic hormone (CHH)	0.07	-	nuc	0	Secreted protein				72
Q9NGP0 UniProt NPD GO	CHHB_METEN	Crustacean hyperglycemic hormones B precursor (CHH-B) (MeCHH-B) [Contains: CHH precursor-related pep ...	0.07	-	end	0	Secreted protein				113
P19806 UniProt NPD GO	CHHA_HOMAM	Crustacean hyperglycemic hormones isoform A precursor [Contains: CHH precursor-related peptide A (CP ...	0.07	-	cyt	1 *	Secreted protein				134
P34804 UniProt NPD GO	COL40_CAEEL	Cuticle collagen 40	0.07	-	nuc	1 *		extracellular region [NAS]			306
Q17015 UniProt NPD GO	CU01_ANOGA	Cuticle protein (Fragment)	0.07	-	end	0					203
P83357 UniProt NPD GO	CU10_LIMPO	Cuticle protein 10 (LpCP10) (Fragment)	0.07	-	nuc	0					48
P84251 UniProt NPD GO	CU109_IXORI	Cuticle protein 10.9 (Ir-ACP10.9)	0.07	-	nuc	0					102
P80231 UniProt NPD GO	CU67A_LOCMI	Cuticle protein 67, isoform A (LM-67A) (LM-ACP 67A)	0.07	-	mit	2 *					98
P81389 UniProt NPD GO	CU05_HOMAM	Cuticle protein AMP5 (HA-AMP5)	0.07	-	cyt	0					114
P34682 UniProt NPD GO	CUT2_CAEEL	Cuticlin-2 precursor	0.07	-	mit	0	Secreted protein				231
P67877 UniProt NPD GO	GPXC_BRUMA	Cuticular glutathione peroxidase precursor (EC 1.11.1.9) (Cuticular glycoprotein gp29) (Major surfac ...	0.07	-	nuc	0	Secreted protein. Secreted into the cuticle and ultimately released into the medium				223
P67878 UniProt NPD GO	GPXC_BRUPA	Cuticular glutathione peroxidase precursor (EC 1.11.1.9) (Cuticular glycoprotein gp29) (Major surfac ...	0.07	-	nuc	0	Secreted protein. Secreted into the cuticle and ultimately released into the medium				223
P35666 UniProt NPD GO	GPXC_WUCBA	Cuticular glutathione peroxidase precursor (EC 1.11.1.9) (Cuticular glycoprotein gp29) (Major surfac ...	0.07	-	mit	0	Secreted protein. Secreted into the cuticle and ultimately released into the medium				223
Q99174 UniProt NPD GO	CUTI_FUSSC	Cutinase precursor (EC 3.1.1.74) (Cutin hydrolase)	0.07	-	exc	0	Secreted protein				230
Q92161 UniProt NPD GO	CCNA1_CARAU	Cyclin-A1 (Cyclin-A)	0.07	-	cyt	0					391
P35520 UniProt NPD GO	CBS_HUMAN	Cystathionine beta-synthase (EC 4.2.1.22) (Serine sulfhydrase) (Beta-thionase)	0.07	-	end	0	Cytoplasm		236200	1M54	550
Q62426 UniProt NPD GO	CYTB_MOUSE	Cystatin B (Stefin B)	0.07	-	cyt	0	Cytoplasm				98
O89098 UniProt NPD GO	CYTF_MOUSE	Cystatin F precursor (Leukocystatin) (Cystatin-7) (Cystatin-like metastasis-associated protein) (CMA ...	0.07	-	end	0	Secreted protein (Probable)				144
P33404 UniProt NPD GO	CYSP_TRIVA	Cysteine proteinase (EC 3.4.22.-) (Fragment)	0.07	-	cyt	0					22
Q01957 UniProt NPD GO	CPP1_ENTHI	Cysteine proteinase 1 precursor (EC 3.4.22.-)	0.07	-	cyt	0					315
Q91XD7 UniProt NPD GO	CREL1_MOUSE	Cysteine-rich with EGF-like domain protein 1 precursor	0.07	-	end	2	Membrane; multi-pass membrane protein (Potential)				420
Q920A1 UniProt NPD GO	CLTR2_MOUSE	Cysteinyl leukotriene receptor 2 (CysLTR2)	0.07	-	end	7 *	Membrane; multi-pass membrane protein	membrane [IDA]			309
Q95N03 UniProt NPD GO	CLTR2_PIG	Cysteinyl leukotriene receptor 2 (CysLTR2)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				345
Q92148 UniProt NPD GO	CP1A1_MICTO	Cytochrome P450 1A1 (EC 1.14.14.1) (CYPIA1)	0.07	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				515
Q05421 UniProt NPD GO	CP2E1_MOUSE	Cytochrome P450 2E1 (EC 1.14.14.1) (CYPIIE1) (P450-J) (P450-ALC)	0.07	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [IDA]			493
Q92090 UniProt NPD GO	CP2K1_ONCMY	Cytochrome P450 2K1 (EC 1.14.14.1) (CYPIIK1) (P450 LMC2)	0.07	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				504
O70537 UniProt NPD GO	CP3AV_MESAU	Cytochrome P450 3A31 (EC 1.14.14.1) (CYPIIIA31) (P450 SH3A-1)	0.07	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				501
P10613 UniProt NPD GO	CP51_CANAL	Cytochrome P450 51 (EC 1.14.13.70) (CYPLI) (P450-LIA1) (Sterol 14-alpha demethylase) (Lanosterol 14- ...	0.07	-	cyt	2 *					528
Q02315 UniProt NPD GO	CP51_ISSOR	Cytochrome P450 51 (EC 1.14.13.70) (CYPLI) (P450-LIA1) (Sterol 14-alpha demethylase) (Lanosterol 14- ...	0.07	-	cyt	0					414
P16141 UniProt NPD GO	CP52D_CANMA	Cytochrome P450 52A4 (EC 1.14.14.-) (CYPLIIA4) (Alkane-inducible P450-ALK3-A) (P450-CM2)	0.07	-	nuc	2 *					537
Q9STK8 UniProt NPD GO	C71AP_ARATH	Cytochrome P450 71A25 (EC 1.14.-.-)	0.07	-	end	1 *					490
P58050 UniProt NPD GO	C71BD_ARATH	Cytochrome P450 71B13 (EC 1.14.-.-)	0.07	-	end	1 *					496
Q9SAE4 UniProt NPD GO	C71BT_ARATH	Cytochrome P450 71B29 (EC 1.14.-.-)	0.07	-	end	0					490
Q6Z6L1 UniProt NPD GO	C74A3_ORYSA	Cytochrome P450 74A3 (EC 4.2.1.92) (Allene oxide synthase 3) (Hydroperoxide dehydrase 3)	0.07	-	nuc	0					500
O48927 UniProt NPD GO	C78A3_SOYBN	Cytochrome P450 78A3 (EC 1.14.-.-)	0.07	-	nuc	1 *					523
Q9MLI7 UniProt NPD GO	CYB_ACRGR	Cytochrome b	0.07	-	end	10 *					372
Q33629 UniProt NPD GO	CYB_APUAP	Cytochrome b	0.07	-	end	9 *					380
Q6X2M0 UniProt NPD GO	CYB_CARIN	Cytochrome b	0.07	-	end	9 *					379

You are viewing entries 69751 to 69800 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.