HHsearch alignment for GI: 254781096 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 (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 DP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligases (MurE; 6.3.2.13 from EC). An exception is found with Staphylococcus aureus, in which diaminopimelate is replaced by lysine in the peptidoglycan and MurE is (6.3.2.7 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=100.00 E-value=0 Score=459.15 Aligned_cols=336 Identities=26% Similarity=0.345 Sum_probs=263.3
Q ss_pred HCCCCCEEEECCCCCCHHHHHHHHHHCCCCCCEEEEECCCCCCCC------------CC-----------CCCCCCCCCH
Q ss_conf 116851587045784047788886403444430575357333331------------00-----------1468542001
Q gi|254781096|r 104 MRCRKSISVSGTHGKTTTTSLIAALLEQGKFDPTVINGGIINSYG------------TN-----------ARIGTSEWIV 160 (474)
Q Consensus 104 ~~~~~~IaVTGTnGKTTTt~ml~~il~~~g~~~~~~~G~~~~~~~------------~~-----------~~~~~~~~~V 160 (474)
T Consensus 85 s~~l~viGvTGTNGKTtt~~li~~~l~~~G~~tg-liGT~g~~~~g~~~~~~~~~~TTP~~~~~q~~L~~~~~~g~~~~v 163 (494)
T TIGR01085 85 SKKLKVIGVTGTNGKTTTTSLIAQLLELLGKKTG-LIGTIGYRLGGNELIKDPASLTTPEALTLQKTLAEMVEAGAQYAV 163 (494)
T ss_pred CCCEEEEEEEECCCCHHHHHHHHHHHHHCCCEEE-EEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCEEE
T ss_conf 5251689997128744899999999986797089-986545304776312665556799718999999999965997999
Q ss_pred HHCCC---CCC--HHHHCCCCCEEEEEEECCCHHHCCHHHHHHHHHHCCCCCCCCC------CCCCCCCCCCHHHHHHHH
Q ss_conf 10232---210--1221185530342220220110002556666430133333322------222223465013454320
Q gi|254781096|r 161 VEADE---SDG--TFIRLPSDIVVVTNIDPEHLDYYGDFNAIRAAFYKFIDNIPFY------GFAVVCMDHPEVRSLIAR 229 (474)
Q Consensus 161 ~E~~e---~~~--s~~~~~P~iaVitNI~~DHld~~~s~e~y~~aK~~i~~~~~~~------g~~vin~Dd~~~~~~~~~ 229 (474)
T Consensus 164 ~EvSSHaL~q~TARV~~~~F~~~vFTNl~~DHLDfHgtmEnY~~aK~~LF~~~~~~~~~~~~~~aV~n~dD~~~~~f~~~ 243 (494)
T TIGR01085 164 MEVSSHALAQGTARVEGVDFDAAVFTNLTRDHLDFHGTMENYFAAKAKLFTELGLKSDRRRARFAVINLDDEYGAQFVKR 243 (494)
T ss_pred EEEEHHHHHCCCCEEECCEEEEEEEECCCHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
T ss_conf 98630124214211102115799960788302340334899999998524400136775356611588645446999861
Q ss_pred CCCCCCCCCCCCCCCCEE--EEEEEECCCC-----CEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf 011123333333222202--2102112584-----201355511344444200002356765433322112100123210
Q gi|254781096|r 230 IQNRKIITYGRHPQADIR--YSNIRKYSGR-----SIFDVSVQGNVTKDLTVIKDLSLPLIGEHNISNACASIAVAYKLG 302 (474)
Q Consensus 230 ~~~~~v~~fg~~~~~d~~--~~~i~~~~~~-----~~f~~~~~~~~~~~~~~~~~~~l~l~G~Hn~~NalaAia~a~~lg 302 (474)
T Consensus 244 ~~~~~-~~~~~~~~A~~R~~~~~~~~~~~~~~~~G~~~~~~~~~g~------~~~~~~~LiG~FNv~N~lAa~a~~~~~g 316 (494)
T TIGR01085 244 LPKDI-TVSAITQKADWRGKAQDIKITDSGYSFEGQSFTFETPAGV------EFKLHTPLIGRFNVYNLLAALATLLHLG 316 (494)
T ss_pred HHHHC-EEEEEEECCCCCCCCCCCHHHCCCCEEEEEEEEEECCCCC------EEEEEECCCHHHHHHHHHHHHHHHHHHC
T ss_conf 02522-5778850421263112401100001034566675246752------0688753613688999999999999733
Q ss_pred -CHHHHHHHHHHCCCCCCCCEEEECCCC-CEEEEEECCCCCCCCHHHHHHHH----CCCCCCCEEEEECCCCH-HH-HHH
Q ss_conf -000001334310000158221101478-60476302445543022233310----13443210333036631-47-888
Q gi|254781096|r 303 -LSSEDVKKGLASFSGIKRRFTLVGVWN-DVHVFDDYGHHPIEISSVLAAVR----QICPRKIIAIHQPHRYS-RL-STL 374 (474)
Q Consensus 303 -i~~e~i~~~L~~f~g~~~R~e~v~~~~-gv~~idDyahnP~~i~atl~al~----~~~~~rii~i~~p~~~s-r~-~~~ 374 (474)
T Consensus 317 g~~~~~~~~~l~~~~gv~GRmE~v~~~~~~f~V~VDYAHTPDaLek~L~~lr~~~~~~~~g~L~~vFGcGGdRDr~KRpl 396 (494)
T TIGR01085 317 GIDLEDIVAALEKLRGVPGRMELVDGGQQKFLVIVDYAHTPDALEKVLRTLRAIKLKHKKGRLIVVFGCGGDRDRGKRPL 396 (494)
T ss_pred CCCHHHHHHHHHHCCCCCCCCEEECCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCHH
T ss_conf 88899999898734899873123027899960799714880589999999999984258982799981578998445758
Q ss_pred HHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHCCC-CCEEEECCHHHHHHHHHHHCCCCCEEEEECCCC
Q ss_conf 99999998618999990866677643238999999999996389-989998898999999998558987999944899
Q gi|254781096|r 375 FDQFSSCFGDADIVLISPVYSAGEKEIPGFSSPELVKNIKLQGH-PQAYYMDSFDHLVSKILAIAEPGDFIIFFGAGN 451 (474)
Q Consensus 375 ~~e~~~~l~~ad~vil~~i~~~~e~~~~g~~~~~l~~~i~~~~~-~~~~~~~~~~eav~~~~~~~~~gDvVL~~GaG~ 451 (474)
T Consensus 397 MG~iA~--~~AD~~ilT~DNPR~Edp~~--I~~Di~~G~~~~~~~~~~~~i~DR~~AI~~Ai~~A~~gD~VLiAGKGH 470 (494)
T TIGR01085 397 MGAIAE--QLADLIILTSDNPRSEDPEQ--IIADILAGISEKEKDKDVVIIADRRQAIRKAISNAKAGDVVLIAGKGH 470 (494)
T ss_pred HHHHHH--HHCCEEEEECCCCCCCCHHH--HHHHHHHHCCCCCCCCCEEEEHHHHHHHHHHHHHHCCCCEEEEECCCC
T ss_conf 999999--82986898368854579799--999999714776667515896017899999998404798899961577