Question: Cogs validation: good alignment?
0
gravatar for c.clarido
12 months ago by
c.clarido40
Netherlands/Rotterdam/Leiden University (Applied Science)
c.clarido40 wrote:

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!

student msa cogs alignment • 318 views
ADD COMMENTlink modified 12 months ago by lieven.sterck4.2k • written 12 months ago by c.clarido40
2

There is no need to SHOUT IN YOUR TITLE. This will not give your question a higher priority. I have adapted your title.

ADD REPLYlink written 12 months ago by WouterDeCoster37k
1

Please use the formatting bar (especially the code option) to present your post better (done for this post). There are no separate fonts on Biostars. Formatting bar

ADD REPLYlink written 12 months ago by genomax64k
1

XP* accessions are derived from automated annotation pipelines and may not have strong experimental support.

ADD REPLYlink written 12 months ago by genomax64k
0
gravatar for lieven.sterck
12 months ago by
lieven.sterck4.2k
VIB, Ghent, Belgium
lieven.sterck4.2k wrote:

Yes that indeed looks like a 'good alignment'. The sequence OLL26130.1 seems to be a bit of an outlier in this dataset though, so depending on what your purpose of this question is you might consider removing that one. You will notice that when you do so you will increase the number of * in the bottom line indicating that the sequences are quite similar

ADD COMMENTlink modified 12 months ago • written 12 months ago by lieven.sterck4.2k
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