This page supplies supplementary material for the manuscript

"The Brix domain protein family - a key to the ribosomal biogenesis pathway"
by Frank Eisenhaber, Christian Wechselberger, Guenther Kreil

Acknowledgements to:
M. Breitenbach, F.M. Jantsch, G. Lepperdinger
for sharing experimental data with respect to Brix and yol077c with us prior to publication, for discussion of the sequence analysis results and for carefully reading the manuscript.

You might want to know: Sequences and alignments fasta-file with the X. laevis Brix sequence (AF319877) Members of the Brix domain protein superfamily The search history of the Brix domain superfamily and its internal structure fasta-file of Brix Domain Proteins Clustal-formatted grand alignment of Brix proteins The same alignment in postscript and colour HMMs and domain locations The HMM for global domain searches The HMM for local/fragmented domain searches The domain boundaries for Brix domain proteins (hmmsearch output) Reference for HMM: Eddy SR. Profile hidden Markov models. Bioinformatics. 1998;14(9):755-63. Compositions and sequence lengths Charged AA in the regions flanking the Brix domain Length of Brix domain proteins supplementary information kindly supplied by Mensur Dlakic (University Michigan - Medical School) from June 12th, 2001 another alignment of Brix proteins in color this alignment in MSF format the corresponding HMM for global domain searches the corresponding HMM for fragmented domain searches the search output from SWISS-ALL

Features of four Brix domain proteins with unusually large sequence length in their family indicating possible gene prediction or genome assembly inaccuracies:

The length of proteins in the Peter Pan family and in group 1 of hypothetical proteins is typically <475 residues (346-475 residues and 295-434 residues respectively). But four proteins (all of them are hypothetical, conceptual translations of genomic sequences) have an extraordinary length of ~700 residues.

• CAB77212 [unidentified organism, sequence with similarity to human emb|CAB99252.1] (Peter Pan family II)

  Beginning with residue ~450 (up to the C-terminus), a seven TM region with sequence similarity to GPCRs starts. None of the other Brix domain proteins has TM regions.

   predicted TM regions
   450 470
   492 512
   526 546
   567 587
   625 645
   667 687
   729 749
  
  PFAM:
  7tm_1: domain 1 of 1, from 465 to 693: score 116.8, E = 4.5e-36
                     *->GNlLVilvilrtkklr..tptnifilNLAvADLLflltlppwalyyl
                         N+L+++ ++  +k r+  p+ +f + LAv+DLL +ltlpp a+y +
    UI_emb|CAB   465    SNGLALYRFSI-RKQRpwHPAVVFSVQLAVSDLLCALTLPPLAAYLY 510
  
                     vggsedWpfGsalCklvtaldvvnmyaSillLtaISiDRYlAIvhPlryr
                          +W +G+a C+l  +l+++n+  S+ ++t+IS+ RYl IvhP+ +r
    UI_emb|CAB   511 PP--KHWRYGEAACRLERFLFTCNLLGSVIFITCISLNRYLGIVHPFFAR 558
  
                     rrrtsprrAkvvillvWvlalllslPpllfswvktveegngtln......
                     ++ + p++A++v+++ Wvla+ll++P l fs +k+++  +  +++ +  +
    UI_emb|CAB   559 SHLR-PKHAWAVSAAGWVLAALLAMPTLSFSHLKRPPQQG--AGncsvar 605
  
                     .vnvtvClidfpeestasvstwlrsyvllstlvgFllPllvilvcYtrIl
                     ++  + Cl + +++      + +r+y l++  +g  lPll+ l +Y+
    UI_emb|CAB   606 pEACIKCLGTADHGL-----AAYRAYSLVLAGLGCGLPLLLTLAAYGALG 650
  
                     rtlr...........kaaktllvvvvvFvlCWlPyfivllldt<-*
                     r++ ++++ +  ++ ++a +++  v + + + +Py+i+ +l++
    UI_emb|CAB   651 RAVLrspgmtvaeklRVAALVASGVALYASSYVPYHIMRVLNV    693
  

• T32923 [C. elegans] (Peter Pan family II)

  Beginning with sequence position ~470, this protein has an unusually compositioned, long low complexity regions with almost monotonous repeats of FRGG (translation of a non-coding region ?).

  low complexity regions: SEG 12 2.2 2.5
  >gi|7505687|pir||T32923 hypothetical protein K09H9.6 - Caenorhabditis elegans^Agi|2804465|gb|AAB97575.1| (AF043700) contains similarity to human RNA-binding protein FUS/TLS (SW:Q28009) [Caenorhabditis elegans]
  
                                    1-1    M
                      kmkkgkkqrk    2-11
                                   12-32   SGAHNRGNVDALSQKDALYHQ
                  ekfvkklqkqkfle   33-46
                                   47-86   NKEIELARQPHCLVIHRGDVGKYVKGLESD
                                           LRNLVEPNTA
                    knlkilkrnnik   87-98
                                   99-384  DFIVNGAVLGVTNMMVLTSSDASLQLRMMR
                                           FSQGPTLSFKVKQYSLARHVVNCQKRPVAT
                                           DKLFKSSPLVVMNGFGDGTQKHLSLVQTFI
                                           QNMFPSINVDTIQLGNLKRCLIVSYDEETD
                                           EIQMRHFAIRVVASGLNKSVKKLMQAEKTM
                                           GKNIPNLSTYKDISDYFLNPGQFRIRTKLN
                                           FSNINHKIIIKKYSIYLNFPSFSSPGQLSD
                                           SEFEGDQQEVELPQDISEGRGCGVGQKSNV
                                           RLHEIGPRLTLELVKIEEGIDEGEVLYHKH
                                           NAKTPDELIKLRAHMD
                kkkqmkkrreqeseqr  385-400
                                  401-477  VIRRLTIVKEQQDAEEAEVKAIRENAARKQ
                                           AAATGQVEEVENQKEKDREIAMNRERDLKR
                                           ANEEWGTSEASKRPRYE
  dsrggfrggfrgrgedrggfrgrggdrggf  478-608
  rgrdrdgggfrgrsvdrggfrggggdrggf
  rgrssdrggdrggfrgrsgdrdggfrggfg
  grggggfrggdrggfrgrgggggfrggrgg
                     drgggfrggrr
  

• P45073 [C. elegans] (family III/group 1 of hypothetical proteins)

  Within the N-terminal ~300 residues, this protein has a region with some similarity to the AAA+ ATPase module (detected with IMPALA and the signalling domain library of L. Aravind, E=3e-04, and with PFAM, E=0.15, see comments for the somewhat shorter T19409).

• T19409 [C. elegans] (family III/group 1 of hypothetical proteins)

  Within the N-terminal ~300 residues, this protein has a region with some similarity to the AAA+ ATPase module (detected with IMPALA and the signalling domain library of L. Aravind, E=3-04, and with PFAM, E=0.15).

  IMPALA: AAA AAA+ ATPase Module
            Length = 298
  
   Score = 35.0 bits (79), Expect = 3e-04
   Identities = 32/193 (16%), Positives = 32/193 (16%), Gaps = 14/193 (7%)
  
  Query: 95  RKPLVLSFHGYTGSGKNYVAEIIANNTFRLGLRSTFVQHIVATNDFPDKNKLEEYQVELR 154
  
  Sbjct: 78  AQPKGVLLYGPPGTGKTLLARAVAHHTDC---------TFIRVSGSELVQKFIGEGARMV 128
  
  Query: 155 NRILTTVQKCQRSIFIFDEADKLPEQLLGAIKPFLDYYSTISGVDFRRSIFILLSNKGGG 214
  
  Sbjct: 129 RELFVMAREHAPSIIFMDEIDSIGSRLEGGSGGDSEVQRTMLELLNQLDGFEATKN---- 184
  
  Query: 215 EIARITKEQYESGYPREQLRLEAFERELMNFSYNEKGGLQMSELISNHLIDHFVPFLPLQ 274
  
  Sbjct: 185 -IKVIMATNRIDILDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKI 243
  
  Query: 275 REHVRSCVGAYLR 287
  
  Sbjct: 244 AELMPGASGAEVK 256
  
  PFAM: AAA              1/1      99   287 ..     1   216 []   -25.3     0.15
  AAA: domain 1 of 1, from 99 to 287: score -25.3, E = 0.15
                     *->gvLLyGPPGtGKTlLAkavAkelg......vpfisisg......sel
                         + ++G  G+GK  +A+++A+ + + + ++  +  i ++++ ++
    CE_pir|T19    99    VLSFHGYTGSGKNYVAEIIANNTFrlglrsTFVQHIVAtndfpdKNK 145
  
                     vskyvGesekrvralfelArkslkkaaPspiiFIDEiDalapkRgdegdv
                     +++y  e + r+  + ++  +s        i ++DE+D+l  +
    CE_pir|T19   146 LEEYQVELRNRILTTVQKCQRS--------IFIFDEADKLPEQ------- 180
  
                     servvnqLLtemDLerigfekhylr..vsdvvDlsgviviaaTNrpdlld
                            LL  +      f ++y++ ++   vD+++ i+i+ +N  +  +
    CE_pir|T19   181 -------LLGAIK----PFLDYYSTisG---VDFRRSIFILLSNKGGGEI 216
  
                     paLlrpGRfdrrievplPdeeerleIlkihlkkmplalc..qerselakd
                     + +       ++ e ++P e+ rle +++ l ++  +++++  +sel ++
    CE_pir|T19   217 ARITK-----EQYESGYPREQLRLEAFERELMNFSYNEKggLQMSELISN 261
  
                     vdldelakelArrtpgfsgadlaa..lcreAalralr<-*
                     + +d+           f+     +++++r    + lr
    CE_pir|T19   262 HLIDH-----------FVPFLPLQreHVRSCVGAYLR    287