Cytoplasmic Protein >

Field: a cytoplasmic protein in the TCA cycle Author: genbank Date: Wed Nov 05 17:12:01 UTC 2014 < cytoplasmic protein > Field: gene_products Author: genbank Date: Wed Nov 05 17:12:01 UTC 2014 Cytoplasmic protein Field: note Author: genbank Date: Wed Nov 05 17:12:01 UTC 2014 Upon using the BLASTp tool, it was seen that the protein showed similarities to others that were already identified which was citrate synthase with relatives being P. torridus and S.todakaii. All the other hits were hypothetical and were therefore not recorded. Blast under swisprot showed the same protein, citrate synthase, with only one different family member being T. acidophilum. The CDD database showed no significant COG hits. The TIGRFAM and PFAM showed two significant hits being citrate synthase_II-2 methylcitrate synthase and cit_synth_I both of which have the function of citrate synthase. SignalP showed an extremely low probability for probable cleavage sites. TMHMM showed no significant transmembrane helices. LipoP showed less than 4 putative cleavage sites predicted. PSORT-B showed very high scores for a probability that the protein exists in the cytoplasm with a cytoplasmic score of 9.65. Under the Phobius database showed compelling evidence that the protein sequence lacks a transmembrane helix, leading to the conclusion that the protein is most likely in the cytoplasm. In the alternative open reading frame, there were no alternative reading frames seen but the Shine Dalgo sequence was found upstream to the start codon indicative of a normal start codon with no alternative ORF. In duplication and degredation, no paralogs and psuedogenes were found. In the horizontal gene transfer, there were close relatives (archaic) like Sulfolobus sp. and Metallosphaera sp. According to the gene context, the gene seems to be similar to distant organisms but it is not probably in an operon. The GC difference between the gene and genome was less than 10% (2.8%). For RNA, Rfam test showed no results indicative that the gene has no RNA functions. Field: discussion Author: genbank Date: Wed Nov 05 17:12:01 UTC 2014 If a protein is to be found in the cytoplasm, it requires hydrophilic, charged and aliphatic amino acid residues (eg isoleucine, histidine etc). In the PEPSTAT database, there were significant amounts of these residues in high amounts (Lysine, leucine etc) which is a strong indication of the protein being in the cytoplasm as they are hydrophilic. TMHMM and Phobius showed that there were no transmembrane protein with SignalP giving a low probability of a signal peptide. In the additional tools (PsortB and LipoP), there was a high probability that the protein is in the cytoplasm. Citrate synthase is found in all organisms both big and small that are Aerobic and Anaerobic. This is due to the fact that they need citrate synthase to catalyse the creation of citrate using the precursors Oxaloacetate and Acetyl CoA. This is ,basically, the start of the TCA cycle where the organism produces energy and other products that can feed into other cycles (eg Electron transport chain). Ferroplasma acidarmanus would use citrate synthase to make citrate for its TCA cycle to produce energy.

Conclusion: According to the findings, the gene OID 638393996 codes for citrate synthase used to make citrate.

Field: literature_links Author: genbank Date: Wed Nov 05 17:12:01 UTC 2014 1. Russell, R., J., Hough, D., W., Danson, M., J., Taylor, G., L. (1994). The crystal structure of citrate synthase from thermophilic archaeon, Thermoplasma acidophilum. Structure, 2(12), 1157- 67. 2. Champe, P., C., & Harvey, R., A. (1994). TCA cycle. Biochemistry. Philidelphia: J.B. Lippincott.

Field: synonyms Author: genbank Date: Wed Nov 05 17:12:01 UTC 2014 IMG OID 638393996, cytoplasmic protein, CP004145

Field: gene_coordinates Author: genbank Date: Wed Nov 05 17:12:01 UTC 2014 Coordinate Low: 290593 Coordinate High: 291717 Strand: Forward The gene OID 638393996, located at the locus 290593..291717 (+) (GeniACT) or 97215..98339 (IMG) and codes for 1125 bp, (374 amino acid sequences) with an isoelectric point of 5.64485. The gene caller identified an SD sequence upstream of the start codon. No alternative ORFs were detected.