HHsearch alignment for GI: 254780709 and conserved domain: TIGR01085

>TIGR01085 murE UDP-N-acetylmuramyl-tripeptide synthetases; InterPro: IPR005761 The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages: (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer. Stage two involves four key Mur ligase enzymes: MurC ( from EC) , MurD ( from EC) , MurE ( from EC) and MurF ( from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales . This entry represents DP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligases (MurE; from EC). An exception is found with Staphylococcus aureus, in which diaminopimelate is replaced by lysine in the peptidoglycan and MurE is ( from EC). The Mycobacteria, part of the closest neighbouring branch outside of the low-GC Gram-positive bacteria, use diaminopimelate.; GO: 0005524 ATP binding, 0016881 acid-amino acid ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=96.44  E-value=0.0046  Score=41.78  Aligned_cols=79  Identities=19%  Similarity=0.208  Sum_probs=52.5

Q ss_conf             2311354444-42478999999985226742677434512456889999975303532122358661245-422899996
Q Consensus       113 vil~vG~nG~-GKTTT~aKLA~~~~~~g~kV~lva~DtfR~aA~eQL~~~a~~~~v~~~~~~~~~dp~~v-~~~a~~~a~  190 (321)
T Consensus        87 ~l~viGvTGTNGKTtt~~li~~~l~~~G~~tgliGT~g~~~~g~-~~~~~~~----------~~TTP~~~~~q~~L~~~~  155 (494)
T ss_conf             51689997128744899999999986797089986545304776-3126655----------567997189999999999

Q ss_pred             HHCCCEEEEECC
Q ss_conf             514875998654
Q gi|254780709|r  191 AKKVDVLIIDTA  202 (321)
Q Consensus       191 ~~~~DvvliDTA  202 (321)
T Consensus       156 ~~g~~~~v~EvS  167 (494)
T TIGR01085       156 EAGAQYAVMEVS  167 (494)
T ss_pred             HCCCCEEEEEEE
T ss_conf             659979999863