STIR
 SUPERFAMILY

 1fyv
 

Supplementary material for the publication:
"The STIR domain superfamily (SEFIR, TIR)
in signal transduction, development and immunity" Trends Biochem Sci. 2003 May;28(5):226-9, PMID: 12765832
Novatchkova M, Leibbrandt A, Werzowa J,
Neubüser A and Eisenhaber F

 


   fasta of SEF, chicken sequence
   fasta of bacterial STIR proteins
    -> graphical representation of the Pfam domains with a E value below 0.1 contained in those proteins
   fasta of one archeal protein with similarity to the SEFIR domain of BAB83481.
    The protein obtains an E value of 0.002 in a blast with orf22/BAB83481, and is collected significantly in the psi-blast using orf22/BAB83481.
    The conservation is not focused around the box1 and 2.
   fasta of eukaryotic STIR proteins
    A group of fungal proteins shows distant similarity to the TIR domain and is also collected with significant E values in orf22/BAB83481 psi-blast searches.
    The conservation is not focused around the box1 and 2.
  • fasta of viridiplantae STIR proteins
    -> graphical representation of the Pfam domains with a E value below 0.1 contained in those proteins (png)

  • fasta of metazoan STIR proteins
    • breakdown of the proteins to the different taxonomic groups: nematoda, protostomia/arthropoda, deuterostomia (echinodermata and chordata)
    • fasta of Toll/TLR family
      -> graphical representation of the Pfam domains with a E value below 0.1 contained in those proteins
    • fasta of IL1-R/IL18-R family
      -> graphical representation of the Pfam domains with a E value below 0.1 contained in those proteins
    • fasta of non-Toll/TLR, non-IL1-R/IL18-R proteins
      -> graphical representation of the Pfam domains with a E value below 0.1 contained in those proteins
      • fasta of SEF, orthologs
      • fasta of SEF/IL17-R family

Collection of some SE/IR family using the full chicken SEF sequence as a starting point. Simple BLAST search of full length cSEF against the NRDB.
Collection of the STIR superfamily using chicken SEF as a starting point.
-BLAST search of chicken SEF (310-450) against the NRDB.
  • round 1
  • round 2
  • round 3

    -> This search reveals a weak similarity of the proximal region of chicken SEF (residues 310-450) to small bacterial proteins with a N-terminal TIR domain (BAB83481 and NP_662351). The similarities of the SEF/IL17R membrane proximal domain to these proteins is below conventionally used PSI-BLAST thresholds and are thus indicative of homology, but the significance has to be supported further. A reciprocal psi-blast allowed us to support the similarity of BAB83481 (aligns to 80.7% of the CD TIR domain) to SEFIR proteins and to collect the STIR family.

-BLAST search of BAB83481 (1-150) against the NRDB.

The STIR SUPERFAMILY was collected using saturated blast starting with the residues 1-150 from BAB83481.

The STIR protein family is represented by

  • bacterial (fa)
  • plantal (fa)
  • and metazoan (fa) sequences in NRDB.

    The STIR SUPERFAMILY protein set (fasta with too short sequences being excluded) was used to build a multiple sequence alignment (pdf).
    A protein set made non-redundant with a cut off of 50% identity was used to construct a HMM.
    A subset including SEFIR proteins only was used to construct a SEFIR specific HMM.

    •  

       Chicken SEF (cSEF) was isolated in a screen for FGF4/8 regulated genes in chicken facial mesenchyme. A summary on the initial experimental functional analysis of chicken SEF is published on the web.