Ðåêîíñòðóêöèÿ ôèëîãåíèè


Çàäàíèå 1

 òàáëèöå 1 ïîêàç ñïèñîê áàêòåðèé, êîòîðûå ÿ èñïîëüçîâàë äëÿ âûïîëíåíèÿ ýòîãî ïðàêòèêóìà, è èõ òàêñîíîìèÿ.
Òàáëèöà 1. Îòîáðàííûå áàêòåðèè
Îðãàíèçì Îðãàíèçàöèÿ Öàðñòâî Òèï Êëàññ Îòðÿä Ñåìåéñòâî Ðîä è íèæå
Rhizobium etli cellular organisms  Bacteria  Proteobacteria  Alphaproteobacteria  Rhizobiales  Rhizobiaceae  Rhizobium/Agrobacterium group
Rhodobacter sphaeroides cellular organisms  Bacteria  Proteobacteria  Alphaproteobacteria  Rhodobacterales  Rhodobacteraceae  Rhodobacter
Burkholderia cenocepacia cellular organisms  Bacteria  Proteobacteria  Betaproteobacteria  Burkholderiales  Burkholderiaceae  Burkholderia
Ralstonia solanacearum cellular organisms  Bacteria  Proteobacteria  Betaproteobacteria  Burkholderiales  Burkholderiaceae  Ralstonia
Escherichia coli cellular organisms  Bacteria  Proteobacteria  Gammaproteobacteria  Enterobacterales  Enterobacteriaceae  Escherichia
Salmonella typhimurium cellular organisms  Bacteria  Proteobacteria  Gammaproteobacteria  Enterobacterales  Enterobacteriaceae  Salmonella
Pasteurella multocida cellular organisms  Bacteria  Proteobacteria  Gammaproteobacteria  Pasteurellales  Pasteurellaceae  Pasteurella


Ìíîþ áûëî âûáðàí áåëîê Ýíîëàçà (ENO) - ôåðìåíò, ó÷àñòâóþùèé â ïðåäïîñëåäíåì ýòàïå ãëèêîëèçà. Ýíîëàçà êàòàëèçèðóåò ïåðåõîä 2-ôîñôî-D-ãëèöåðèíîâîé êèñëîòû â ôîñôîåíîëïèðóâàò. Ïðè ýòîì îò 2-ôîñôî-D-ãëèöåðàòà îòùåïëÿåòñÿ îäíà ìîëåêóëà âîäû.

Çàäàíèå 2

C ïîìîùüþ áàçû "Uniprot", áûë ïîëó÷åíû ôàéë, â êîòîðîè ïðèâåäåííû àìèíîêèñëîòíûå ïîñëåäîâàòåëüíîñòè ýòîãî áåëêà äëÿ êàæäîé áàêòåðèè.
Ïîñëå ýòîãî ÿ âîñïîëüçîâàëñÿ ñåðâåð Muscle íà kodomo, ïîëó÷èë ôàéë ñ âûðîâíÿííûìè ïîëåäîâàòåëüíîñòÿìè.
 ïðîãðàììå "MEGA" èç ïîëó÷åííûõ âûðàâíèâàíèé áûëî ðåêîíñòðóèðîâàíà ôèëîãåíèÿ òðåìÿ ðàçëè÷íûìè ñïîñîáàìè: Maximum Likelyhood, Neighbor-Joining, Minimum-Evolution. Âûðàâíèâàíèÿ ïðèâåäåííûé íèæå.
 
Maximum Likelyhood Tree Neighbor-Joining Tree  Minimum-Evolution Tree Ïðàâèëüíîå äåðåâî

Êàê âèäíî, âñå äåðåâüÿ ïîëíîñòüþ ýäåíòè÷íû ìåæäó ñîáîé è ñ "ïðàâèëüíûì äåðåâîì", ïîëó÷åííîå â pr1.



Çàäàíèå 3

Íåòðèâèàëüíûå âåòâè, îáúåäèíåííûå â ðàçíûå òàêñîíîìè÷åñêèå ãðóïïû:
SALTY, ECOLI - Ñåìåéñòâî  Enterobacteriaceae
RALSO, BURCA - Ñåìåéñòâî  Burkholderiaceae
SALTY, ECOLI ,PASMU - Êëàññ  Gammaproteobacteria
RHIEC, RHOS4 - Êëàññ  Alphaproteobacteria
PASMU, RALSO, BURCA, RHIEC, RHOS4 - Òèï  Proteobacteria
SALTY, ECOLI ,PASMU, RHIEC, RHOS4 - Òèï  Proteobacteria
RALSO, BURCA, RHIEC, RHOS4 - Òèï  Proteobacteria
SALTY, ECOLI, PASMU, RALSO, BURCA - Òèï  Proteobacteria

© Óãîëüêîâ ßðîñëàâ, 2018