MDL test case: Chromo shadow family, Z=2.0

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Partitioning defined by patterns:

  1. DmHP1_A DvHP1_A HuHP1_A MoMOD1_A MoMOD2_A PcHET1_A PcHET2_A
  2. HuHP1_B MoMOD1_B MoMOD2_B PcHET1_B
  3. DmPc MoMOD3 SmPAJ26 Pf0131C CfTENV
  4. HuMG44 MoCHD1_A ScYEZ4_A ScYEZ4_B Ce29H12
  5. DmHP1_B DvHP1_B PcHET2_B SpSWI6_B
  6. CeYO82 DmSuv39 FoSKPY CeYK9A3
  7. SpSWI6_A CeT9A58 MgGRH MgMAGGY
  8. MoCHD1_B

Does this correspond to the tree?

The first set corresponds roughly to the set that Rein Aasland has called the ``classical chromo domains linked to chromo shadow domains'', and the second set corresponds to a relatively dense subtree/subset within what he calles ``chromo shadow domains''. The third and fourth are sets of sequences with no obvious relationship from the reported NJ tree, while the fifth is the rest of the ``chromo shadow domains'' (the ones not included in set 2). Sets 6 and 7 have no obvious relationship in the tree.

Patterns covering the set:

  1. DmHP1_A DvHP1_A HuHP1_A MoMOD1_A MoMOD2_A PcHET1_A PcHET2_A 
    93.29485 130.61278 
E-x(0,1)-E-E-[FY]-x-V-E-K-[IV]-[IL]-D-[KR]-R-x(3,4)-G-x-V-x-Y-x-L-K-W-K-G-[FY]-x-[ED]-x-[HED]-N-T-W-E-P-x(2)-N-x-[ED]-C-x-[ED]-L-[IL]
Occurences: 11(7)
             DmHP1_A:     4-    52:   aee EEEEYAVEKIIDRRVRKGKVEYYLKWKGYPETENTWEPENNLDCQDLIQ qyeas
             DmHP1_A:     5-    53:  aeee EEEYAVEKIIDRRVRKGKVEYYLKWKGYPETENTWEPENNLDCQDLIQQ yeasr
             DvHP1_A:     4-    52:   aee EEEEYAVEKILDRRVRKGKVEYYLKWKGYAETENTWEPEGNLDCQDLIQ qyels
             DvHP1_A:     5-    53:  aeee EEEYAVEKILDRRVRKGKVEYYLKWKGYAETENTWEPEGNLDCQDLIQQ yelsr
             HuHP1_A:     5-    53:  ssed EEEYVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNLDCPELISE fmkky
            MoMOD1_A:     4-    52:   lee EEEEYVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIA eflqs
            MoMOD1_A:     5-    53:  leee EEEYVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAE flqsq
            MoMOD2_A:     4-    52:   eea EPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIE dflns
            PcHET1_A:     4-    52:   sgs EEEEYVVEKIIDKRTVNGKVQYFLKWKGYDESENTWEPHENLECPELIA eferk
            PcHET1_A:     5-    53:  sgse EEEYVVEKIIDKRTVNGKVQYFLKWKGYDESENTWEPHENLECPELIAE ferkw
            PcHET2_A:     5-    53:  vpav EEEFIVEKILDKRTEPDGSVRYLLKWKGYGDEDNTWEPPENMDCEDLLE efekk
  2. HuHP1_B MoMOD1_B MoMOD2_B PcHET1_B 
    82.39683 164.79366  
I-I-G-A-T-D-x(0,1)-S-x(0,1)-G-[ED]-L-M-F-L-M-K-W-[KE]-x-[TS]-D-E-A-D-L-V-x-[AS]-x-[ED]-A-x(2)-K-C-P-Q-[ILV]-[IV]-I-x-F-Y-E-[KE]-[HR]-L-T-W
Occurences: 4(4)
             HuHP1_B:    13-    62: lepek IIGATDSCGDLMFLMKWKDTDEADLVLAKEANVKCPQIVIAFYEERLTWH aype
            MoMOD1_B:    13-    62: leper IIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWH syps
            MoMOD2_B:    13-    62: ldper IIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLTWH scpe
            PcHET1_B:    13-    62: lkper IIGATDTSGELMFLMKWEGTDEADLVRSVDARTKCPQLIIEFYEKHLTWN nase
  3. DmPc MoMOD3 SmPAJ26 Pf0131C CfTENV 
    40.14603 66.91005 
K-x(4,5)-G-x(2,3)-Y-x-[LV]-K-W-[KR]-G-[YW]-[SDN]-x(3)-N-[TS]-W-E-P-[ER]-x-N-[IL]
Occurences: 5(5)
                DmPc:    16-    46: ekiiq KRVKKGVVEYRVKWKGWNQRYNTWEPEVNIL drrli
              MoMOD3:    16-    46: ecils KRLRKGKLEYLVKWRGWSSKHNSWEPEENIL dprll
             SmPAJ26:    14-    44: vekil KVRIRNGRKEYFLKWKGYSEEDNTWEPEENL cpdli
             Pf0131C:    13-    41: dilei KKKKNGFIYLVKWKGYSDDENTWEPESNL
              CfTENV:    12-    42: efeve KILDKKGQRYLVKWKGYDESENTWEPRINLA ncyql
  4. HuMG44 MoCHD1_A ScYEZ4_A ScYEZ4_B Ce29H12 
    25.66752 42.77919 
Y-x(0,2)-L-[IV]-K-W-x(6)-[HE]-x-T-W-E-x(3)-[TSDN]-[IL]-x(9)-[HKD]
Occurences: 6(5)
              HuMG44:    23-    55: ireqe YYLVKWRGYPDSESTWEPRQNLKCVRILKQFHK dlere
              HuMG44:    24-    56: reqey YLVKWRGYPDSESTWEPRQNLKCVRILKQFHKD lerel
            MoCHD1_A:    26-    58: kgdiq YLIKWKGWSHIHNTWETEETLKQQNVRGMKKLD nykkk
            ScYEZ4_A:    24-    56: ncken YEFLIKWTDESHLHNTWETYESIGQVRGLKRLD nyckq
            ScYEZ4_B:    30-    62: tsqlq YLVKWRRLNYDEATWENATDIVKLAPEQVKHFQ nrens
             Ce29H12:    24-    56: flesn YFFLVKWLGYGNKEMTWEPESNIPDSVYLYEYK klnnm
  5. DmHP1_B DvHP1_B PcHET2_B SpSWI6_B 
    18.91922 37.83844 
L-x(8,9)-A-x(8,9)-N-x(3)-P-x(3)-[IL]-x-[FY]-Y-E-x-[HR]-L
Occurences: 4(4)
             DmHP1_B:    26-    61: grltf LIQFKGVDQAEMVPSSVANEKIPRMVIHFYEERLSW ysdne
             DvHP1_B:    26-    61: grltf LIQFKGVDQAEMVPSTVANVKIPQMVIRFYEERLSW ysdne
            PcHET2_B:    25-    60: gslkf LMKWEGIERATFVLAKEANIVCPQLVIDYYESRLQL fdpkm
            SpSWI6_B:    28-    63: kddgt LEIYLTWKNGAISHHPSTITNKKCPQKMLQFYESHL tfren
  6. CeYO82 DmSuv39 FoSKPY CeYK9A3 
    15.83123 31.66245 
W-x(2)-[YW]-x-[HED]-x-[HE]-N-[TS]-W-E-x(4)-[ILV]
Occurences: 4(4)
              CeYO82:    29-    45: efyik WLGYDHTHNSWEPKENI vdptl
             DmSuv39:    29-    45: vffvk WLGYHDSENTWESLANV adcae
              FoSKPY:    29-    45: eylik WKNYPENENTWEPPKHL vnaqr
             CeYK9A3:     2-    18:     k WTGWSHLHNTWESENSL almna
  7. SpSWI6_A CeT9A58 MgGRH MgMAGGY 
    14.66756 29.33512 
E-x(4)-[YWH]-x-V-x(3)-L-x(5,6)-R-x(2)-G-x(0,1)-G-x-[EDR]
            SpSWI6_A:     3-    28:    ee EEEDEYVVEKVLKHRMARKGGGYEYL lkweg
             CeT9A58:    11-    36: eifev EKILAHKVTDNLLVLQVRWLGYGADE dtwep
               MgGRH:     3-    28:    tg EPEEVWAVEAILAAKNRRGRGGGRQV lvkwq
             MgMAGGY:     3-    28:    ev EGEREYEVEEILDSFWETRGRGGRRL kyivr
  8. MoCHD1_B 
    ddlhkqyqiveriiahsnkqsaaglpdyyckwqglpysecswedgaliskkfqtcideyfsrnqskttpfk

Page compiled by: Inge Jonassen.

Chromo Test Set MDL.