Hello Biostars community!
We are suppose to validate a cluster of orthologous groups (COGs). So I have the following multiple sequence alignment of the COGs:
NP_013713.1 -MSSRKKNILKVIILGDSGVGKTSLMHRYVNDKYSQQYKATIGADFLTKEVTVDGDKVAT
XP_961487.1 -MSSRKKVLLKVIILGDSGVGKTSLMNQYVNKKFSASYKATIGADFLTREVLVD-DRQVT
XP_018243741.1 -MSSRKKVLLKVIILGDSGVGKTSLMNQYVNKKFSASYKATIGADFLTREVLVD-DRQVT
XP_657693.1 -MSSRKKVMLKVIILGDSGVGKTSLMNQYVNKKFSGSYKATIGADFLTKEVLVD-DR---
CCF47966.1 -MASRKKVLLKVIILGDSGVGKTSLMNQYVNKRFSSAYKATIGADFLTREVMVD-DRLVT
XP_018739135.1 -----------------------------MCVRFSAAYKATIGADFLTREVVVD-GRVVT
XP_009269712.1 MPQPKKTVLLKVIILGDSGVGKTSLMNQYVNKRFSNQYKATIGADFLTKEVVVD-DRVVT
XP_012048028.1 -MATRKKHLLKVIILGDSGVGKTSLMNQYVNKRFSTQYKATIGADFLTRELVVD-DRVVT
XP_001828916.1 ----MGRVLLKVIILGDSGVGKTSLMNQYVNKRFSNQYKATIGADFLTKEVMVD-DRLVT
SCV71343.1 -MASRRKVLLKVIILGDSGVGKTSLMNQYVNKRFSNQYKATIGADFLTKEVMVD-DRLVT
NP_596307.1 -MAGKKKHLLKVIILGESGVGKTSIMNQYVNRKFSKDYKATIGADFLTKEVLVD-DKVVT
OLL26130.1 --MTTPKPVYKVIVIGDNGVGKTSLRTRFLYGKFTSSYRATIGADFLTKNINGM-----T
: ::: *:*********:::
NP_983406.1 MQVWDTAGQERFQSLG--VAFYRGADCCVLVYDVTNAKSFENVKSWRDEFLVHANVPSPE
NP_013713.1 MQVWDTAGQERFQSLG--VAFYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANVNSPE
XP_961487.1 MQLWDTAGQERFQSLG--VAFYRGADCCVLVYDVNNSKSFDALDSWRDEFLIQASPRDPD
XP_018243741.1 MQLWDTAGQERFQSLG--VAFYRGADCCVLVYDVNNAKSFEALDSWRDEFLIQASPRDPP
XP_657693.1 -LIWDTAGQERFQSLG--VAFYRGADCCVLVYDVNNSKSFEALDSWRDEFLIQASPRDPE
CCF47966.1 MQLWDTAGQERFQSLG--VAFYRGADCCCLCYDVNNAKSFETLDSWRDEFLIQAAPHDPE
XP_018739135.1 MQLWDTAGQERFQSLG--VAFYRGADCCVLVYDVNNPKSFETLDSWRDEFLIQASPHDPD
XP_009269712.1 IQLWDTAGQERFQSLG--VAFYRGADCCVLVYDVNNAKSFETLDSWRDEFLIQASPQDPV
XP_012048028.1 MQLWDTAGQERFQSLG--VAFYRGADCCVLVYDVNSNKSFEALDGWRDEFLVQASPHDPE
XP_001828916.1 MQLWDTAGQERFQSLG--VAFYRGADCCVLVYDVNSAKSFETLDSWRDEFLIQASPHDPE
SCV71343.1 MQLWDTAGQERFQSLG--VAFYRGADCCVLVYDVNSSKSFETLDSWRDEFLIQASPRDPE
NP_596307.1 LQLWDTAGQERFQSLG--VAFYRGADCCVLVYDVNNSKSFETLDSWRDEFLIQASPSNPE
OLL26130.1 LSIWDTAGQERFNSLGSSNPIFRGTDAAIFVFDSTNASSFASLEKWLTQFLSSSGSPSP-
:*********:*** .::**:*.. : :* .. .** :. * :** : .*
Sorry for the arrangement of the MSA, as I am not sure how to type this in courier here. Anyways as you can see all of them starts with methionine. Is this a good alignment? The protein XP_018739135.1 seems to be a bit shorter than the rest of them.
Thank you very much in advance!
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