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Field: <succinyl-CoA synthetase subunit alpha> cytoplasmic protein Author: Jia Yue Liu Date: November 17, 2014 FACI_IFERC00001G1736 The BLASTp showed no conserved class of putative proteins was found. Peptide Statistics with the Search Tool Uniprot showed similarity to the succinyl-CoA synthetase subunit alpha in Picrophilus torridus, Thermoplasm volcanium, Archaeolobus fulgidus DSM 4304, Pseudomonas aeruginosa PAO1. Phylogenetic analysis showed the gene from F. acidarmanus Fer1 was clustering with Thermoplasma and Picophilus. The next closest genes are those from Aciduliprofundum and Methanohalophilus which are the next closest related genomes to the Ferroplasma genome, so there is no evidence to suggest that this gene has recently undergone HGT. SignalP predicted no Probable Signal Peptide found (p<0.450 and 0.570). Therefore no probable cleavage site was predicted. TMHMM predicted no significant transmembrane helix. Expected number of amino acids in TMHs is 220, which is more than 18 aa, indicating high likelihood of protein being located as transmembrane or having a signal peptide. The expected number of amino acids in transmembrane helices in the first 69 aa is 0.02374 aa, which is lower than 10aa, indicating low likelihood of signal peptide at the N terminus. The N-terminus of the protein is predicted (1) to be located extracellularly. The protein was predicted with 96% confidence of being located extracellularly. However, given that no transmembrane helix was predicted, this prediction is most likely not accurate. Phobius also predicted an absence of a transmembrane helix, which indicates that the protein is not directed to the membrane or extracellularly. Psortb and LipoP indicated that the protein is located within the cytoplasm. TIGRFAM and PDB both detected succinate-CoA ligase as their top hit. TIGRFAM further elucidated that the HMM top hit from TIGRFAM describes succinate-CoA ligase as both ADPforming and GDP-forming. Field: discussion Author: genbank Date: Wed Nov 05 17:12:01 UTC 2014 The cellular localization model of OID 638394059 is compliant with the cellular structure and localization of the alpha-subunit of succinyl-CoA synthetase of ortholog from Sulfolobus solfataricus, which forms an acid-labile phosphohistidyl enzyme intermediate during its catalytic cycle [1]. The succinyl-CoA synthetase (EC 6.2.1.5) of Ferroplasma acidarmanus Fer1 is predicted to catalyze the reversible reaction succinyl-CoA + NDP + Pi ↔ succinate + CoA + NTP (N denoting adenosine or guanosine). The enzyme consists of two different subunits, designated α and β. From the data collected, succinyl-CoA synthetase possess a high content of basic, hydrophobic and hydrophilic amino acids. Typically, cytoplasmic proteins possess a high levels of Arginine, Histidine, Isoleucine, Glutamate and Methionine. In addition, there will be a larger proportion of charged, aliphatic, hydrophilic residues. The results of the PEPSTAT predicted that the protein contained 12.27 mol% of Isoleucine, 9.09 mol% of lysine and 4.09 mol% of leucine. There is a low % (0.57%) of cysteine found which is indicative of a cytoplasmic protein. Based on the results of the comparative databases involving cellular localization (PSORT-B, Phobius, LipoP, TMHMM, SignalP), it is believed that the protein is located within the cytoplasm. Hence, it is suggested to be an intracellular protein as previously postulated using the PEPSTATS tool. While the TMHMM postulates that the protein is located extraceullarly, given that no transmembrane helix was predicted, this prediction is most likely not accurate. Based on the results from TMHMM and Phobius, the protein does not contain any transmembrane helices, which complements the theory that the protein is not membrane bound, but rather cytoplasmic. The KEGG, MetaCyc and E.C. databases all corroborate the identity of the query sequence as succinyl-CoA synthetase alpha subunit in Thermoplasma acidophilum. For this gene, no paralogs were found and the gene was not found to be present in any organism outside of the Euryarachaeota Phylum. Therefore, it appears that this gene has not undergone any horizontal gene transfer outside of the archael domain. The most distinct Euryarchaeota containing the gene is the Aciduliprofundum organisms. Analysis of gene neighbourhood COG, indicated that the genes, Succinyl-CoA synthetase alpha and beta subunits are conserved between Aciduliprofundum, Thermoplasma, and Picrophilus organisms. From the phylogentic tree, genes from related organisms such as Thermoplasma, Picrophilus, Ferroplasma are clustered with one another. The Query from Ferroplasma clusters with the best hits from Picrophilus and Thermoplasma. The next closest genes are those from Aciduliprofundum and Methanohalophilus which are the next closest related genomes to the Ferroplasma genome, so there is no evidence to suggest that this gene has recently undergone HGT. Conclusion: Our findings supported a new function for gene OID 638394059 coding the alpha subunit of a succinyl-CoA synthetase in F. acidarmanus Fer1. Field: literature_links Author: genbank Date: Wed Nov 05 17:12:01 UTC 2014 1. Solow, B., Bischoff, K. M., Zylka, M. J., & Kennelly, P. J. (1998). Archaeal phosphoproteins. Identification of a hexosephosphate mutase and the α‐subunit of succinyl‐CoA synthetase in the extreme acidothermophile Sulfolobus solfataricus. Protein science, 7(1), 105-111. Field: synonyms Author: genbank IMG OID 638394059, succinyl-CoA synthetase Field: gene_coordinates Author: genbank The gene OID 638394059 (519bp) is located at locus 1712840..1713694 (+) and codes for 284 amino acids with an isoelectric point of 7.03. The Gene Caller identified one Shine-Dalgarno (SD) sequence upstream of the original start codon. No alternative start codon with SD sequence was manually detected.