HHsearch alignment for GI: 254780870 and conserved domain: TIGR00409

>TIGR00409 proS_fam_II prolyl-tRNA synthetase; InterPro: IPR004500 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Prolyl-tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form, is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa. This family includes the enzyme from Escherichia coli that contains all three of the conserved consensus motifs characteristic of class II aminoacyl-tRNA synthetases and the enzyme from the spirochete Borrelia burgdorferi.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=850.32  Aligned_cols=439  Identities=44%  Similarity=0.823  Sum_probs=395.1

Q ss_pred             CCCCHHHHHHHHCCCCCCCCCC-HHHHHHHCCCEECCCCCHHCCCCHHHHHHHHHHHHHHHHHHCC-CEEEECCCCCC-H
Q ss_conf             9630678887310711141256-1221353032000388111043169999999999999998669-88973575124-6
Q gi|254780870|r    1 MRRSKYFLPILQENPRDAEIAS-HKLMLRTGMIHQHSKGIYSWLPLGQKALDNVNAIIREEQNRTG-AIEMSVPTLQS-A   77 (449)
Q Consensus         1 m~~s~~~~~~l~~~~~d~~~~~-~~ll~~~g~i~~~~~G~~~~lP~G~~i~~~le~~~r~~~~~~G-~~ei~tP~l~~-~   77 (449)
T Consensus         1 mr~S~~l~~TL~e~P~DA~~~StH~LL~rAGfIR~~~SGlY~~LPL~~rVL~Kv~~ivreeM~~~GGA~E~~lp~~~~la   80 (620)
T TIGR00409         1 MRTSQLLFPTLKETPADAEVKSTHQLLLRAGFIRRLGSGLYNWLPLGLRVLKKVENIVREEMNKDGGAIEVLLPALQPLA   80 (620)
T ss_pred             CCCCCCCCCCCCCCCCCCEECCHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             96553003668888875301112564030164772434144565789999998899999862267853346676677899


Q ss_pred             HHHHHCCCCHHHHH---HHCCHHHCCCCCCEECCCCCCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCEE
Q ss_conf             89877197311222---210402137862000345554310110000134201340264146533456676754345316
Q gi|254780870|r   78 DLWVESGRYDSYGK---EMLRLADRNDKAMIYGPTHEEVMTDIFRSHIKSYRNLPFTFYQIQLKFRDELRPRFGVMRSRE  154 (449)
Q Consensus        78 eL~~~SGh~d~~~~---em~~~~d~~~~~~~LrP~~~e~~~~i~~~~~~SYr~LPlr~y~ig~~fR~E~rp~~GL~R~Re  154 (449)
T Consensus        81 ~LW~~SGRW~~YG~seGELl~lkDR~~r~f~LgpT~EEvIT~l~~~~i~SYKqLP~~lYQI~tKFRDEiRPRFGl~RgRE  160 (620)
T TIGR00409        81 ELWQESGRWDTYGPSEGELLRLKDRKGREFVLGPTHEEVITDLVRNEIKSYKQLPLNLYQIQTKFRDEIRPRFGLLRGRE  160 (620)
T ss_pred             HHHHHCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEECCCCCCCCCCCCCCCCCCCHH
T ss_conf             98754075324686543366765268887356786655689999998754530683010045121442048876000123


Q ss_pred             EEEEECCEECCCHHHHHHHHHHHHHHHHHHHHHCCCHHHH-HHHCCH-HCCCCHHHHHHHHCCCCCCEEEECCCCCCCCC
Q ss_conf             6874042211886887999999999874111100620122-331100-10131133434546867701431010034776
Q gi|254780870|r  155 FLMKDAYSFDLTPEGSKHSYNKMFVSYLRIFHRLGLKSIP-MRAESG-PIGGDLSHEFIVLADTGETQVFCSKDFMDFPI  232 (449)
Q Consensus       155 F~q~D~~~F~~~~e~~~~e~~~~~~~~~~i~~~lgl~~~~-v~~~~~-~ig~~~s~e~~~~~~~~e~~~~~~~~~~~~~~  232 (449)
T Consensus       161 FiMKDAYSFH~~~ESL~~ty~~m~~aY~~IF~rlGldFR~iV~ADSGdaIGG~~S~EF~vL~~~GEDti~~~~h~~dyaA  240 (620)
T TIGR00409       161 FIMKDAYSFHSDEESLDATYQKMDQAYSNIFSRLGLDFRPIVQADSGDAIGGSASHEFMVLAESGEDTIVYSDHESDYAA  240 (620)
T ss_pred             HHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCHHHHHHHHCCCCEEEEECCCCCHHH
T ss_conf             23024255447876799998899999999998658982106871578757888625678866458961788625765123


Q ss_pred             -CHHHCC--------------------------------------------------------------------HHHHH
Q ss_conf             -411122--------------------------------------------------------------------01210
Q gi|254780870|r  233 -PSENTD--------------------------------------------------------------------FDDII  243 (449)
Q Consensus       233 -~~~~~~--------------------------------------------------------------------~~~~~  243 (449)
T Consensus       241 lNiE~A~~~~~~~P~~~~~~~~~~~~tPN~~ti~~~~~~f~~~~~~~~K~ll~ka~~~~~K~~~v~l~vRGD~ielnevK  320 (620)
T TIGR00409       241 LNIELAEALKPGEPRNAPTAELKKVDTPNTKTIAELVEFFNLPAEKVVKTLLVKAVDKSGKEPLVALLVRGDDIELNEVK  320 (620)
T ss_pred             HHHHHHHHHCCCCCCCCHHHCCCCCCCCCCHHHHHHHHHHCCCHHHHHCEEEEEEEECCCCEEEEEEEEECCCCCHHHHC
T ss_conf             23677764257887501133144547744111899999867887683103146665137860688889736701322111


Q ss_pred             CCCCCCCCCCCCCCC-----------------------------------------------------------------
Q ss_conf             011220001363212-----------------------------------------------------------------
Q gi|254780870|r  244 SLNSIVEQWTAPYAA-----------------------------------------------------------------  258 (449)
Q Consensus       244 ~~~~~~~~~~~~~~~-----------------------------------------------------------------  258 (449)
T Consensus       321 ~~n~l-~klaPhy~~~~~le~~~~~~~~~~~~~~~~~~~g~~~~~~sddyiatnkqv~~~~~~~~khvd~iif~~~~~~~  399 (620)
T TIGR00409       321 AKNLL-NKLAPHYLVAQVLELATGEEEIEQKIASKPDLLGPVKINGSDDYIATNKQVFIDIPVLIKHVDQIIFTVALMSD  399 (620)
T ss_pred             CCCCC-CHHCCCHHHCCEEECCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             34662-02134101034011147147999988640675556566653102331013442035666446466212635268


Q ss_pred             --------------------------CHHHCHHHHHC-CCCCCC--EEEEEEEECCCEEECCCCCCCCCEEEEECCCCCC
Q ss_conf             --------------------------01100023303-587655--2432111158144223112230115896477772
Q gi|254780870|r  259 --------------------------TSDVHNEKLFD-SLPENK--RVSARGIEVGHIFYFGTKYSLPMSATFKGADGKD  309 (449)
Q Consensus       259 --------------------------~~d~~~~~~~d-~l~~~~--~~~~~~ie~~~~f~lG~~ys~~~~~~~~~~~g~~  309 (449)
T Consensus       400 f~~~A~~~~~h~~~vn~~~~~~~~~~~~D~r~~~eGDrP~Pdg~G~L~~~~gIEVGHIF~LG~kYS~al~A~f~de~Gk~  479 (620)
T TIGR00409       400 FAAGANADDKHYKNVNWDRDVAIPEVVADIRKVKEGDRPSPDGKGTLKIAKGIEVGHIFKLGTKYSKALKATFLDENGKE  479 (620)
T ss_pred             CCEECCCCCCCEEECCCCCCCCHHHHHHHHHHEEECCCCCCCCCCEEEECCCCEEEEEECCCHHHHHHHCCEEECCCCCC
T ss_conf             50103454565030263100211322200100024777884387405640562341133022033333065564668850


Q ss_pred             C-CCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCHHHCCCCCEEEECCCCH-HHHHHHHHHHHHHHH-----HCCCEEEEE
Q ss_conf             3-233666344743002332210232111113633203211024217887-999999999999999-----869879997
Q gi|254780870|r  310 H-YVQMGSYGIGAMRVVAAVIESSHDGKGIIWPDSVAPFKISLINIKAHD-QVCRDACEKIYARLS-----KVGCDVFWD  382 (449)
Q Consensus       310 ~-~~~~g~~giG~~R~~~alle~~~d~~g~~wP~~iaP~~v~Iipi~~~~-~~~~~~A~~i~~~Lr-----~~Gi~v~~D  382 (449)
T Consensus       480 ~t~~~MGCYGIGVSRl~~Ai~Eq~~D~~G~~WP~~~APy~V~Iv~~N~~~se~~~~~A~~~Y~~L~ndPtm~~g~dvllD  559 (620)
T TIGR00409       480 QTFLTMGCYGIGVSRLVSAIAEQHYDERGIIWPKAIAPYDVVIVVMNMKDSEEQKQLAEEVYSELLNDPTMAQGVDVLLD  559 (620)
T ss_pred             CCEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             25256055571389999999985058786367645388148996178984278999999999985027113653356641


Q ss_pred             CCCCCHHHHHHH--HHHCCCCEEEEECCCHHHCCEEEEEECCCCCEEEEEHHHHHHHHHH
Q ss_conf             589797086787--8748998899986240235718999989997878619999999999
Q gi|254780870|r  383 DMGEQIGSQFAV--ADLLGFPLQVIVGSKFVSDSKVEIKHRLTGIREDMSLEEVINYASH  440 (449)
Q Consensus       383 ~r~~~iGkK~~~--Ad~~gip~~iiiG~~el~~~~Vtir~r~tg~q~~v~l~eli~~i~~  440 (449)
T Consensus       560 DR~ER~Gv~f~Dkl~eLIG~P~~v~~G~~~l~~~~~Ev~~R~~gEk~~i~~~~~~~~~~~  619 (620)
T TIGR00409       560 DRNERAGVKFRDKLSELIGIPLRVVVGKKNLDNGEIEVKKRRNGEKQLIKKDELVEVLEE  619 (620)
T ss_pred             HHHCCCCCCHHHHHHHHCCCCEEEEECCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHC
T ss_conf             010235551566777755987199975621677516898615510457778999998622