GCPred is a webserver for the prediction of adenylyl cyclase functional centers (GCCs) from amino acid sequence. GCC is a novel class of functional centers typically consisting of short 14 amino acids and is found in complex multi-domain proteins. They are different from canonical GC domains hence GCPred is not valid for the prediction of such domains as well as transmembrane regions.
Instructions:
The software takes a single or multiple amino acid sequence and returns predicted GCCs each accompanied by GCC values 0-1, where 1 is closest to the mean of experimentally validated GCCs.
Please enter single letter amino acid codes in FASTA format and select if co-factor binding (Mg
2+/Mn
2+) is required. The amino acid implicated in co-factor binding is found at 0-3 positions downstream of the GCC.
Requirement for Mg
2+/Mn
2+ co-factor
For example
>sp|Q9ZVR7|PSKR1_ARATH Phytosulfokine receptor 1 OS=Arabidopsis thaliana GN=PSKR1 PE=1 SV=4
MRVHRFCVIVIFLTELLCFFYSSESQTTSRCHPHDLEALRDFIAHLEPKP
DGWINSSSSTDCCNWTGITCNSNNTGRVIRLELGNKKLSGKLSESLGKLD
EIRVLNLSRNFIKDSIPLSIFNLKNLQTLDLSSNDLSGGIPTSINLPALQ
SFDLSSNKFNGSLPSHICHNSTQIRVVKLAVNYFAGNFTSGFGKCVLLEH
LCLGMNDLTGNIPEDLFHLKRLNLLGIQENRLSGSLSREIRNLSSLVRLD
VSWNLFSGEIPDVFDELPQLKFFLGQTNGFIGGIPKSLANSPSLNLLNLR
NNSLSGRLMLNCTAMIALNSLDLGTNRFNGRLPENLPDCKRLKNVNLARN
TFHGQVPESFKNFESLSYFSLSNSSLANISSALGILQHCKNLTTLVLTLN
FHGEALPDDSSLHFEKLKVLVVANCRLTGSMPRWLSSSNELQLLDLSWNR
LTGAIPSWIGDFKALFYLDLSNNSFTGEIPKSLTKLESLTSRNISVNEPS
PDFPFFMKRNESARALQYNQIFGFPPTIELGHNNLSGPIWEEFGNLKKLH
VFDLKWNALSGSIPSSLSGMTSLEALDLSNNRLSGSIPVSLQQLSFLSKF
SVAYNNLSGVIPSGGQFQTFPNSSFESNHLCGEHRFPCSEGTESALIKRS
RRSRGGDIGMAIGIAFGSVFLLTLLSLIVLRARRRSGEVDPEIEESESMN
RKELGEIGSKLVVLFQSNDKELSYDDLLDSTNSFDQANIIGCGGFGMVYK
ATLPDGKKVAIKKLSGDCGQIEREFEAEVETLSRAQHPNLVLLRGFCFYK
NDRLLIYSYMENGSLDYWLHERNDGPALLKWKTRLRIAQGAAKGLLYLHE
GCDPHILHRDIKSSNILLDENFNSHLADFGLARLMSPYETHVSTDLVGTL
GYIPPEYGQASVATYKGDVYSFGVVLLELLTDKRPVDMCKPKGCRDLISW
VVKMKHESRASEVFDPLIYSKENDKEMFRVLEIACLCLSENPKQRPTTQQ
LVSWLDDV
If you find GCPred useful for your work, please cite:
Xu N, Fu D, Li S, Wang Y & Wong A (2018). Bioinformatics, DOI: 10.1093/bioinformatics/bty067
GCPred was built based on previous work published in:
Wong A, Tian X, Gehring C & Marondedze C (2018). Comput Struct Biotechnol J, 16 (2018), pp. 70-76
Wheeler J, Wong A, Marondedze C, Arnoud G, Kwezi L et al. (2017). Plant J 91(4), 590-600
Wong A, Gehring C & Irving HR (2015). Front Bioeng Biotechnol 82, 1-8
Wong A & Gehring C (2013). Cell Commun Signal, 11(1), 48
Wong A & Gehring C (2013). Methods Mol Biol, 1016, 195-205, Humana Press
Ludidi N & Gehring C (2003). J Biol Chem 278(8), 6490-6494
This tool is still under development and the GCC values will be revised as new experimental data becomes available. Additional features and improvements are forthcoming.
We also provide a trial service for the prediction of adenylyl cyclase (AC) functional centers. Please click
here to access the ACPred webtool.
Please contact us at alwong@kean.edu if you have any questions or comments.