HHsearch alignment for GI: 254780589 and conserved domain: pfam03734

>pfam03734 YkuD L,D-transpeptidase catalytic domain. This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. This gives bacteria resistance to beta-lactam antibiotics that inhibit PBPs which usually carry out the cross-linking reaction. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue. Several members of this family contain peptidoglycan binding domains. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.
Probab=99.59  E-value=6.4e-15  Score=112.42  Aligned_cols=103  Identities=25%  Similarity=0.354  Sum_probs=87.5

Q ss_pred             EEEEEECCCCEE-EEEEECCCCCEEEEEEEEECCCCCCCCCHHCCCCCCCCCEEEEEEECCCCCCCCCCEEEECCCCCHH
Q ss_conf             799998378699-9986078896689998652132389887010178747507999840125875765214207998988
Q gi|254780589|r   52 TVIRIFKNENIL-EIWKRNVDAEYVLLKEYKICAWSGTFGPKIETGDEQAPEGFYYIGWNNLNPNSKYFLSINIGFPNEF  130 (239)
Q Consensus        52 i~Irv~K~e~~L-el~~~~~~g~~~l~ktY~Ic~~sg~lGpK~~eGD~kTPEG~Y~i~~~~~np~S~y~ls~~i~YPN~~  130 (239)
T Consensus         2 ~~I~Vd~~~~~l~~~~~~g-----~~v~~~~vs~G---------~~~~~TP~G~~~i~~k~~~~~~~~~~~~~~~~~~~~   67 (122)
T pfam03734         2 RVIVVDLSEQRLLLLYENG-----KLVLTYPVSVG---------RGDTPTPLGTFTITEKVENPTWAPGPGNGLGYVKFL   67 (122)
T ss_pred             CEEEEECCCCEEEEEEECC-----EEEEEEEEEEC---------CCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCC
T ss_conf             2999989438999997599-----99999778858---------899988665699899875884578675554687655


Q ss_pred             HHHCCCCCCCEEECCC----------CCCCCCEEECHHHHHHHHHHHH
Q ss_conf             9972999882687167----------7866718706466999999999
Q gi|254780589|r  131 DKAHNRTGADLMIHGE----------CASAGCYAMNNKQMQEIYAIVR  168 (239)
Q Consensus       131 Dr~~grtG~~I~IHG~----------~~S~GC~amtd~~i~EIy~~v~  168 (239)
T Consensus        68 ~~~~~~~~~~i~iH~~~~~~~~~~g~~~ShGCIrl~~~d~~~l~~~v~  115 (122)
T pfam03734        68 DPWAFPNGGGIYIHGTGTPDLFSGGAPRSHGCIRLSNEDAKELYDWVL  115 (122)
T ss_pred             CEEEECCCCCEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCC
T ss_conf             246872798438966888842247984677601579999999997099