Saccharomyces cerevisiae Xbp1

Saccharomyces cerevisiae Xbp1

Here is evidence that Xbp1 is a non-canonical APSES domain transcription factor with a long insertion.

It turns out that an entire APSES domain can be defined for Xbp1; it has one 84 amino acid insertion and another 17 amino acid insertion relative to the consensus APSES domains and is therefore split into separate HSPs.. Failure to recognize domain similarity when one or more long indels are present is a frequently encountered problem that automatic algorithms do not address well.

I have included the sequence here, but removed all residues that are inserted relative to the closely related Debaryomyces hansenii orthologue

Mbp1_SACCE      SIMKRKKDDWVNATHILKAA--------NFA------KAKRTRILEKEV--LKETHEKVQGGFGKYQGTWVPLNIAKQLAEK--FSVYD-QLKPLFDF
Xbp1_SACCE      CVIWSHDSGYVFMTGIWRLYQDVMKGLINLP[87]NIKPELRDLICQSYKDFANFTKRIRGGYIKIQGTWLPMEISRLLCLRFCFPIRY-FLVPIFG-

>ref|NP_012165.1|  Xbp1p [Saccharomyces cerevisiae S288c]
Length=647

 GENE ID: 854706 XBP1 | Xbp1p [Saccharomyces cerevisiae S288c]
(Over 10 PubMed links)


                                                         Sort alignments for this subject sequence by:
                                                           E value  Score  Percent identity
                                                           Query start position  Subject start position
 Score = 40.3 bits (93),  Expect = 5e-07, Method: Composition-based stats.
 Identities = 9/22 (41%), Positives = 16/22 (73%), Gaps = 0/22 (0%)

Query  58   ETHEKVQGGFGKYQGTWVPLNI  79
               ++++GG+ K QGTW+P+ I
Sbjct  343  NFTKRIRGGYIKIQGTWLPMEI  364


 Score = 29.9 bits (66),  Expect = 0.001, Method: Composition-based stats.
 Identities = 4/25 (16%), Positives = 9/25 (36%), Gaps = 0/25 (0%)

Query  15   FIHSTGSIMKRKKDDWVNATHILKA  39
             I+    ++      +V  T I + 
Sbjct  187  LINPNNCVIWSHDSGYVFMTGIWRL  211

   

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