HHsearch alignment for GI: 254781108 and conserved domain: cd01475

>cd01475 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
Probab=99.82  E-value=1.7e-18  Score=129.39  Aligned_cols=182  Identities=19%  Similarity=0.297  Sum_probs=140.9

Q ss_pred             CCCCCEEEECCCCCCCCCCCCCCCCHHHHHCCCEECCCCCCCCEEEECCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             65431357505566666676663101233102301268876540310134322011255533341000245665541022
Q gi|254781108|r  146 LAISICMVLDVSRSMEDLYLQKHNDNNNMTSNKYLLPPPPKKSFWSKNTTKSKYAPAPAPANRKIDVLIESAGNLVNSIQ  225 (398)
Q Consensus       146 ~~~di~lvlD~SgSm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  225 (398)
T Consensus         1 gplDlvFllD~S~Svg~~---------------------------------------------nF~~~k~Fv~~lv~~f~   35 (224)
T cd01475           1 GPTDLVFLIDSSRSVRPE---------------------------------------------NFELVKQFLNQIIDSLD   35 (224)
T ss_pred             CCEEEEEEEECCCCCCHH---------------------------------------------HHHHHHHHHHHHHHHCC
T ss_conf             974399999488998989---------------------------------------------99999999999998568


Q ss_pred             HCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHCCCC-CCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             0276877652134654126776543112356899999999735778-887445889999999611346666656676666
Q gi|254781108|r  226 KAIQEKKNLSVRIGTIAYNIGIVGNQCTPLSNNLNEVKSRLNKLNP-YENTNTYPAMHHAYRELYNEKESSHNTIGSTRL  304 (398)
Q Consensus       226 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lt~~~~~~~~~I~~l~~-~G~T~~~~gl~~a~~~l~~~~~~~~~~~~~~~~  304 (398)
T Consensus        36 I-----~~~~trVgvv~ys~~~~~~f~l~~~~~k~~l~~aI~~i~~~gggT~Tg~AL~~~~~~~f~~~~G~Rp--~~~~v  108 (224)
T cd01475          36 V-----GPDATRVGLVQYSSTVKQEFPLGRFKSKADLKRAVRRMEYLETGTMTGLAIQYAMNNAFSEAEGARP--GSERV  108 (224)
T ss_pred             C-----CCCCEEEEEEEECCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCC--CCCCC
T ss_conf             7-----9985299999965827899966886788999999986361388446999999999972770239987--55689


Q ss_pred             CEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHCCC--CCEEEECCHHHHHHHHHH
Q ss_conf             516998158877877777663148999999997898899999547975589999985199--818994698999999999
Q gi|254781108|r  305 KKFVIFITDGENSGASAYQNTLNTLQICEYMRNAGMKIYSVAVSAPPEGQDLLRKCTDSS--GQFFAVNDSRELLESFDK  382 (398)
Q Consensus       305 ~k~iillTDG~~~~~~~~~~~~~~~~~c~~~K~~gi~IytIg~~~~~~~~~~l~~cAs~~--~~yy~a~~~~~L~~aF~~  382 (398)
T Consensus       109 pkvlIviTDG~s~D--------~v~~~A~~lr~~GV~ifaVGVg-~-~~~~eL~~IAs~P~~~hvf~v~~F~~l~~l~~~  178 (224)
T cd01475         109 PRVGIVVTDGRPQD--------DVSEVAAKARALGIEMFAVGVG-R-ADEEELREIASEPLADHVFYVEDFSTIEELTKK  178 (224)
T ss_pred             CEEEEEECCCCCCC--------CHHHHHHHHHHCCCEEEEEECC-C-CCHHHHHHHHCCCCHHCEEEECCHHHHHHHHHH
T ss_conf             85999971798766--------3899999999879889999637-4-798999998559737568994798899999999


Q ss_pred             HHHHHHH
Q ss_conf             9998751
Q gi|254781108|r  383 ITDKIQE  389 (398)
Q Consensus       383 I~~~i~~  389 (398)
T Consensus       179 l~~~iC~  185 (224)
T cd01475         179 FQGKICV  185 (224)
T ss_pred             HHHHHCC
T ss_conf             8761189