HHsearch alignment for GI: 254780680 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=99.07  E-value=2.2e-10  Score=97.93  Aligned_cols=230  Identities=21%  Similarity=0.253  Sum_probs=181.0

Q ss_pred             HCCCCCEEECCHHHHHHHHHHHHHHHHHHHHCC-CCEEHHHHHCC-HHHHHHHHHCHHHHH---HHHHHHH----CCEEC
Q ss_conf             216753010564889999999999986223203-20212356202-788986551422476---7764310----00231
Q gi|254780680|r  159 LSGARFSVLTGHLAHLERALGQFMIDLHTSEHG-YTEVSAPLLVR-DEAMYGTGQIPKFAD---DMFCTTD----GRWLI  229 (430)
Q Consensus       159 vsGsrF~~Lkg~~A~Le~ALi~y~ld~~~~~~G-y~~v~~P~lv~-~~~~~gtG~lp~f~~---~~y~~~d----~l~Li  229 (430)
T Consensus        35 ~~~SGlY~~LPL~~rVL~Kv~~ivree-M~~~GGA~E~~lp~~~~la~LW~~SGRW~~YG~seGELl~lkDR~~r~f~Lg  113 (620)
T TIGR00409        35 RLGSGLYNWLPLGLRVLKKVENIVREE-MNKDGGAIEVLLPALQPLAELWQESGRWDTYGPSEGELLRLKDRKGREFVLG  113 (620)
T ss_pred             ECCCCHHHHHHHHHHHHHHHHHHHHHH-HCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEECCCCCCCCC
T ss_conf             243414456578999999889999986-2267853346676677899987540753246865433667652688873567


Q ss_pred             CCCCCHHHHHHHHHCCCHHHHCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCC-CHHHHHHHHHHHHHH
Q ss_conf             3454114544534205955504208853221078843355434321222210200212127865-014578989999999
Q gi|254780680|r  230 PTSEVSLTNLYSHEIIESKSLPLRFTTLAPSFRSEAGSAGRDTRGMLRQHQFWKCELVSITREE-DSFTEHERMLSCAEE  308 (430)
Q Consensus       230 ~TaEvpL~~~~~~~~l~~~~LPik~~~~s~cfR~EaGs~GkdtrGl~RvHQF~KVE~~~~~~pe-~S~~~~e~~~~~~~~  308 (430)
T Consensus       114 pT~EEvIT~l~~~~i~SYKqLP~~lYQI~tKFRDEiRPRF----Gl~RgREFiMKDAYSFH~~~ESL~~ty~~m~~aY~~  189 (620)
T TIGR00409       114 PTHEEVITDLVRNEIKSYKQLPLNLYQIQTKFRDEIRPRF----GLLRGREFIMKDAYSFHSDEESLDATYQKMDQAYSN  189 (620)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCEECCCCCCCCCCCCCC----CCCCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             8665568999999875453068301004512144204887----600012323024255447876799998899999999


Q ss_pred             HHHHHCCHHH-HCCCCCHH-CCCHHHEEEEEEEECCCCCCEEEEEEECCCCCHHHHHCCCEEE-------CCCCCCCCEE
Q ss_conf             9998410675-30378011-7844340241011010048332375310210076453268473-------3899841010
Q gi|254780680|r  309 ILKRLDLHYR-VVSLCTGD-LGFSACKTYDLEVWLAGQNLYREISSCSTCGNFQSRRMNSRYR-------DPNSKSLKFT  379 (430)
Q Consensus       309 i~~~L~lpyR-vv~~~sgd-lg~~a~~~~DiE~w~P~~~~y~Ev~S~Snc~D~QsrRl~iry~-------~~~~~~~~~~  379 (430)
T Consensus       190 IF~rlGldFR~iV~ADSGdaIGG~~S~EF~vL~----~~GEDti~~~~h~~dyaAlNiE~A~~~~~~~P~~~~~~~~~~~  265 (620)
T TIGR00409       190 IFSRLGLDFRPIVQADSGDAIGGSASHEFMVLA----ESGEDTIVYSDHESDYAALNIELAEALKPGEPRNAPTAELKKV  265 (620)
T ss_pred             HHHHCCCCCCEEEEECCCCCCCCCCCHHHHHHH----HCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCCCCHHHCCCCC
T ss_conf             998658982106871578757888625678866----4589617886257651232367776425788750113314454


Q ss_pred             EEECCCHHHHHHHHHHHHHHCCCC
Q ss_conf             420043228999999998834689
Q gi|254780680|r  380 HTLNGSGVAVGRCLIAILENYLNA  403 (430)
Q Consensus       380 htlNgt~~A~~R~l~ailEn~q~~  403 (430)
T Consensus       266 ~tPN~~t------i~~~~~~f~~~  283 (620)
T TIGR00409       266 DTPNTKT------IAELVEFFNLP  283 (620)
T ss_pred             CCCCCHH------HHHHHHHHCCC
T ss_conf             7744111------89999986788