HHsearch alignment for GI: 254781166 and conserved domain: TIGR01087
>TIGR01087 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase; InterPro: IPR005762 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 (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC) and MurF (6.3.2.10 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 UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD). MurD catalyses the addition of d-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-l-alanine. ; GO: 0005524 ATP binding, 0008764 UDP-N-acetylmuramoylalanine-D-glutamate ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=92.14 E-value=0.51 Score=26.50 Aligned_cols=146 Identities=14% Similarity=0.090 Sum_probs=79.4
Q ss_pred EEEEECCCCCCHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHH-HCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 899948898841799999999988988999848988999999997-1389289998889999999999999999847988
Q gi|254781166|r 12 RGIVLGVANNRSLAWSIAKMCHAAGAKVALTWQGDATKKRIEGLV-EGMDFFMAGHCNVSNSETIDDVFRNLEKEWGTID 90 (284)
Q Consensus 12 ~~iVtGa~g~~GIG~aiA~~la~~Ga~Vvi~~~~~~~~~~~~~~~-~~~~~~~~~~~Dv~~~~~v~~~~~~~~~~~G~iD 90 (284)
T Consensus 1 ~i~i~GlG~-tG~G~a~a~~L~~~g~~~~~~D~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-----------~~~~~~d 68 (476)
T TIGR01087 1 KILILGLGK-TGRGVAVARFLKKKGAEVTVTDDDPEEELERSKGQLKLSEGVVLYTGGKDDL-----------EDLNNAD 68 (476)
T ss_pred CEEEEEECC-CCHHHHHHHHHHHCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEECCCCCC-----------CCCCCCE
T ss_conf 978998675-1078999999997298799998452213431133124556413532675310-----------1233420
Q ss_pred EEEECCCCCCCCCCCCCCCCCCHHHHHHHHCCC--CCHHHHHHHHHHHHHCC--CCCEECCCCCCCCCCCCCHHHHHHHH
Q ss_conf 999627212742125862135899985564026--40232234678874101--22100013332346772012445448
Q gi|254781166|r 91 FLVHAIAFSDKAELTGPYINTTRENFLNTMDVS--VYSFTALAARASSLMNK--GGSMLTLTYLGADKVMPHYNCMGPAK 166 (284)
Q Consensus 91 ~lInnag~~~~~~~~~~~~~~~~e~~~~~~~vn--l~~~~~~~k~~~~~m~~--~G~IInisS~~~~~~~p~~~~Y~asK 166 (284)
T Consensus 69 ~vv~SPGi~~~-----------hp~~~~a~~~g~~v~gd---i~L~~~~~~~~~~~~~~aITGTnG-------------K 121 (476)
T TIGR01087 69 LVVLSPGIPPD-----------HPLVQAAAKRGIPVVGD---IELALRLVDFPEPAKVVAITGTNG-------------K 121 (476)
T ss_pred EEEECCCCCCC-----------CHHHHHHHHCCCEEEEH---HHHHHHHCCCCCCCCEEEEECCCC-------------H
T ss_conf 79978989867-----------77999999669808986---799997415789873799972686-------------0
Q ss_pred HHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCHHHH
Q ss_conf 999999999999827742379985223872694563
Q gi|254781166|r 167 AALQSAVRYLAMDLGRQSGIRVNALSAGPAKTLASS 202 (284)
Q Consensus 167 aai~~ltk~lA~elg~~~gIRVN~I~PG~i~T~~~~ 202 (284)
T Consensus 122 tTTT~L~~~~L~~~G~------~a~~gGNIG~p~L~ 151 (476)
T TIGR01087 122 TTTTSLLYHLLKAAGL------KAVLGGNIGTPALE 151 (476)
T ss_pred HHHHHHHHHHHHHCCC------CEEEECCCCCHHHH
T ss_conf 7999999999984699------77862578812555