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