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PR00938

Identifier
BRACHYURY  [View Relations]  [View Alignment]  
Accession
PR00938
No. of Motifs
5
Creation Date
18-SEP-1998  (UPDATE 13-JUN-1999)
Title
Brachyury protein family signature
Database References
PRINTS; PR00937 TBOX
INTERPRO; IPR002070
PDB; 1XBR
SCOP; 1XBR
CATH; 1XBR
Literature References
1. PAPAIOANNOU, V.E. AND SILVER L.M.
The T-box gene family.
BIOESSAYS 20(1) 9-19 (1998).
 
2. WATTLER, S., RUSS, A., EVANS, M. AND NEHLS, M.
A combined analysis of genomic and primary protein structure defines the
phylogenetic realtionship of new members of the T-box family.
GENOMICS 48 24-33 (1998).
 
3. KAVKA, A.I. AND GREEN, J.B.A.
Tales of Tails: Brachyury and the T-box genes.
BIOCHIM.BIOPHYS.ACTA 1333 f73-f84 (1997).
 
4. PAPAIOANNOU, V.E.
T-box family reunion.
TRENDS GENET. 13(6) 212-213 (1997).

Documentation
The T-box gene family is an ancient group of putative transcription
factors that appear to play a critical role in the development of all
animal species.
 
These genes were uncovered on the basis of similarity to the DNA binding
domain [1] of murine Brachyury (T) gene product, which similarity is the
defining feature of the family. The Brachyury gene is named for its
phenotype, which was identified 70 years ago as a mutant mouse strain with
a short blunted tail. The gene, and its paralogues, have become a well-
studied model for the family, and hence much of what is known about the
T-box family is derived from the murine Brachyury gene.
 
Consistent with its nuclear location, Brachyury protein has a sequence-
specific DNA-binding activity and can act as a transcriptional regulator
[2]. Homozygous mutants for the gene undergo extensive developmental
anomalies, thus rendering the mutation lethal [3]. The postulated role of
Brachyury is as a transcription factor, regulating the specification and
differentiation of posterior mesoderm during gastrulation in a dose-
dependent manner [1].
 
Common features shared by T-box family members are, DNA-binding and
transcriptional regulatory activity, a role in development and conserved
expression patterns, most of the known genes in all species being expressed
in mesoderm of mesoderm precursors [4].
 
BRACHYURY is a 5-element fingerprint that provides a signature for the
brachyury family. The fingerprint was derived from an initial alignment 
of 8 sequences: the motifs were drawn from the full alignment length,
including the region characterised as the T-box domain - motif 2 spans
beta-strands 6-8; motif 3 includes strand 13; and motif 4 spans helix 6. 
Two iterations on OWL30.2 were required to reach convergence, at which
point a true set comprising 12 sequences was identified. Several partial
matches were also found: three of these (BRAC_HALRO, S74163 and BYN_DROME)
are brachyury sequences that fail to make significant matches with one or
more motifs; two are fragments (D89442 and SSU91519); and the remaining
two are closely related T-box proteins (TBX6_MOUSE and H15_DROME).
 
An update on SPTR37_9f identified a true set of 11 sequences, and 4
partial matches.
Summary Information
  11 codes involving  5 elements
1 codes involving 4 elements
1 codes involving 3 elements
2 codes involving 2 elements
Composite Feature Index
51111111111
401111
301110
202200
12345
True Positives
BRA1_BRAFL    BRA2_BRAFL    BRAC_BRARE    BRAC_CHICK    
BRAC_HEMPU BRAC_MOUSE BRAC_XENLA O15178
O42100 O57386 TBXT_CHICK
True Positive Partials
Codes involving 4 elements
BRAC_HALRO
Codes involving 3 elements
BYN_DROME
Codes involving 2 elements
H15_DROME TBX6_MOUSE
Sequence Titles
BRA1_BRAFL  BRACHYURY PROTEIN HOMOLOG 1 (AMBRA-1) - BRANCHIOSTOMA FLORIDAE (FLORIDA LANCELET) (AMPHIOXUS). 
BRA2_BRAFL BRACHYURY PROTEIN HOMOLOG 2 (AMBRA-2) - BRANCHIOSTOMA FLORIDAE (FLORIDA LANCELET) (AMPHIOXUS).
BRAC_BRARE BRACHYURY PROTEIN HOMOLOG (T PROTEIN HOMOLOG) (T-BOX PROTEIN ZFT) (ZF- T) - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).
BRAC_CHICK BRACHYURY PROTEIN (T PROTEIN) - GALLUS GALLUS (CHICKEN).
BRAC_HEMPU BRACHYURY PROTEIN HOMOLOG (T PROTEIN) (HPTA) - HEMICENTROTUS PULCHERRIMUS (SEA URCHIN).
BRAC_MOUSE BRACHYURY PROTEIN (T PROTEIN) - MUS MUSCULUS (MOUSE).
BRAC_XENLA BRACHYURY PROTEIN (T PROTEIN) (XBRA) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
O15178 BRACHYURY PROTEIN (T PROTEIN) - HOMO SAPIENS (HUMAN).
O42100 ME-TAM - ORYZIAS LATIPES (MEDAKA FISH).
O57386 BRACHYURY - CYNOPS PYRRHOGASTER (JAPANESE COMMON NEWT).
TBXT_CHICK T-BOX CONTAINING PROTEIN TBXT - GALLUS GALLUS (CHICKEN).

BRAC_HALRO BRACHYURY PROTEIN HOMOLOG (T PROTEIN) (AS-T) - HALOCYNTHIA RORETZI (SEA SQUIRT).

BYN_DROME T-RELATED PROTEIN (TRP) (BRACHYENTERON PROTEIN) - DROSOPHILA MELANOGASTER (FRUIT FLY).

H15_DROME T-BOX PROTEIN H15 - DROSOPHILA MELANOGASTER (FRUIT FLY).
TBX6_MOUSE TBX6 PROTEIN (T-BOX PROTEIN 6) - MUS MUSCULUS (MOUSE).
Scan History
OWL30_2    2  220  NSINGLE    
SPTR37_9f 2 100 NSINGLE
Initial Motifs
Motif 1  width=26
Element Seqn Id St Int Rpt
HLLSAVESEISAGSEKGDPTERDLKV BRA2_BRAFL 12 12 -
HLLSAVESEFQKGSEKGDASERDIKL BRAC_BRARE 12 12 -
HLLSAVESEISAGSEKGDPTERDLKI BRA1_BRAFL 22 22 -
HLLNAVQSEMNRGSEKGDPSEEGLKV BRAC_HEMPU 18 18 -
HLLSAVENELQAGSEKGDPTERELRV HSBRACHYT 19 19 -
HLLSAVESELQAGSEKGDPTERELRV BRAC_CHICK 17 17 -
HLLSAVESELQAGSEKGDPTERELRV BRAC_MOUSE 19 19 -
HLLSAVENELQAGSEKGDPTEKELKV BRAC_XENLA 17 17 -

Motif 2 width=21
Element Seqn Id St Int Rpt
YVNGEWVPGGKPEPSVPSCVY BRA2_BRAFL 97 59 -
YVNGEWVPGGKPEPSVPSCVY BRA1_BRAFL 107 59 -
YVNGEWVPGGKPEPQAPSCVY HSBRACHYT 104 59 -
YVNGEWIPGGKPDGSPPTTAY BRAC_HEMPU 103 59 -
YVNGEWVPGGKPEPQAPSCVY BRAC_CHICK 102 59 -
YVNGEWVPGGKPEPQAPSCVY BRAC_MOUSE 104 59 -
YVNGEWVPGGKPEPQAPSCVY BRAC_XENLA 102 59 -
YVNGEWVPGGKPEPQSPSCVY BRAC_BRARE 97 59 -

Motif 3 width=18
Element Seqn Id St Int Rpt
HKYEPRIHIVRVGGPQRM BRAC_MOUSE 164 39 -
HKYEPRIHIVRVGGPQRM HSBRACHYT 164 39 -
HKYEPRIHIVRVGGPQRM BRAC_CHICK 162 39 -
HKYEPRIHIVRVGGTQRM BRAC_XENLA 162 39 -
HKYEPRIHIVKVGGPDNQ BRA2_BRAFL 158 40 -
HKYEPRIHIVKVGGIQKM BRAC_BRARE 157 39 -
HKYEPRLHIIKVGGPDNQ BRA1_BRAFL 167 39 -
HKYEPRIHIIRVGGREKQ BRAC_HEMPU 163 39 -

Motif 4 width=11
Element Seqn Id St Int Rpt
KAFLDIKDKND BRAC_HEMPU 216 35 -
KAFLDAKERND BRAC_CHICK 213 33 -
KAFLDAKERND BRAC_MOUSE 215 33 -
KAFLDAKERND BRAC_XENLA 213 33 -
KAFLDAKERSD HSBRACHYT 215 33 -
KAFLDAKERND BRA2_BRAFL 211 35 -
KAFLDAKERSD BRAC_BRARE 208 33 -
KAFLDAKERSD BRA1_BRAFL 220 35 -

Motif 5 width=16
Element Seqn Id St Int Rpt
CERYSSLRNHRAAPYP BRAC_BRARE 269 50 -
CDRYGGLRSHRTSPYP BRAC_HEMPU 275 48 -
CERYSPLRNHRSAPYP BRAC_CHICK 275 51 -
CDRYPTLRSHRSSPYP HSBRACHYT 276 50 -
CERYPALRNHRSSPYP BRAC_MOUSE 276 50 -
CERYSSLRNHRSAPYP BRAC_XENLA 274 50 -
CDRYSTLRNHRSAPYP BRA2_BRAFL 270 48 -
CDRYSTLRNHRSAPYP BRA1_BRAFL 278 47 -
Final Motifs
Motif 1  width=26
Element Seqn Id St Int Rpt
HLLSAVESELQAGSEKGDPTERELRV BRAC_CHICK 17 17 -
HLLSAVESELQAGSEKGDPTERELRV BRAC_MOUSE 19 19 -
HLLSAVENELQAGSEKGDPTEKELKV BRAC_XENLA 17 17 -
HLLSAVEHELQAGSEKGDPTERQLKV O57386 21 21 -
HLLSAVENELQAGSEKGDPTERELRV O15178 19 19 -
HLLSAVESEISAGSEKGDPTERDLKV BRA2_BRAFL 12 12 -
HLLSAVESEFQKGSEKGDASERDIKL BRAC_BRARE 12 12 -
HLLSAVESEFQKGSEKGDASERDIKL O42100 12 12 -
HLLSAVESEISAGSEKGDPTERDLKI BRA1_BRAFL 22 22 -
RLLSVVESELRAGRDKGDPTEKQLQV TBXT_CHICK 16 16 -
HLLNAVQSEMNRGSEKGDPSEEGLKV BRAC_HEMPU 18 18 -

Motif 2 width=21
Element Seqn Id St Int Rpt
YVNGEWVPGGKPEPQAPSCVY BRAC_CHICK 102 59 -
YVNGEWVPGGKPEPQAPSCVY BRAC_MOUSE 104 59 -
YVNGEWVPGGKPEPQAPSCVY BRAC_XENLA 102 59 -
YVNGEWVPGGKPEPQVPSCVY O57386 106 59 -
YVNGEWVPGGKPEPQAPSCVY O15178 104 59 -
YVNGEWVPGGKPEPSVPSCVY BRA2_BRAFL 97 59 -
YVNGEWVPGGKPEPQSPSCVY BRAC_BRARE 97 59 -
YVNGEWVPGGKPEPQSPSCVY O42100 97 59 -
YVNGEWVPGGKPEPSVPSCVY BRA1_BRAFL 107 59 -
YVNGEWVPAGKPEPPNHSCVY TBXT_CHICK 101 59 -
YVNGEWIPGGKPDGSPPTTAY BRAC_HEMPU 103 59 -

Motif 3 width=18
Element Seqn Id St Int Rpt
HKYEPRIHIVRVGGPQRM BRAC_CHICK 162 39 -
HKYEPRIHIVRVGGPQRM BRAC_MOUSE 164 39 -
HKYEPRIHIVRVGGTQRM BRAC_XENLA 162 39 -
HKYEPRIHIVRVGGPQRM O57386 166 39 -
HKYEPRIHIVRVGGPQRM O15178 164 39 -
HKYEPRIHIVKVGGPDNQ BRA2_BRAFL 158 40 -
HKYEPRIHIVKVGGIQKM BRAC_BRARE 157 39 -
HKYEPRIHIVKVGGIQKM O42100 157 39 -
HKYEPRLHIIKVGGPDNQ BRA1_BRAFL 167 39 -
HKYEPQVHIVRVGGPHRM TBXT_CHICK 161 39 -
HKYEPRIHIIRVGGREKQ BRAC_HEMPU 163 39 -

Motif 4 width=11
Element Seqn Id St Int Rpt
KAFLDAKERND BRAC_CHICK 213 33 -
KAFLDAKERND BRAC_MOUSE 215 33 -
KAFLDAKERND BRAC_XENLA 213 33 -
KAFLDAKERSD O57386 217 33 -
KAFLDAKERSD O15178 215 33 -
KAFLDAKERND BRA2_BRAFL 211 35 -
KAFLDAKERSD BRAC_BRARE 208 33 -
KAFLDAKERSD O42100 208 33 -
KAFLDAKERSD BRA1_BRAFL 220 35 -
KAFLDAKERNH TBXT_CHICK 212 33 -
KAFLDIKDKND BRAC_HEMPU 216 35 -

Motif 5 width=16
Element Seqn Id St Int Rpt
CERYSPLRNHRSAPYP BRAC_CHICK 275 51 -
CERYPALRNHRSSPYP BRAC_MOUSE 276 50 -
CERYSSLRNHRSAPYP BRAC_XENLA 274 50 -
CERYPSLRNHRSSPYP O57386 279 51 -
CDRYPTLRSHRSSPYP O15178 276 50 -
CDRYSTLRNHRSAPYP BRA2_BRAFL 270 48 -
CERYSSLRNHRAAPYP BRAC_BRARE 269 50 -
CERYSGLRSHRAAPYP O42100 269 50 -
CDRYSTLRNHRSAPYP BRA1_BRAFL 278 47 -
CERYSALRGHRAAPYP TBXT_CHICK 248 25 -
CDRYGGLRSHRTSPYP BRAC_HEMPU 275 48 -