HHsearch alignment for GI: 254781004 and conserved domain: TIGR00408

>TIGR00408 proS_fam_I prolyl-tRNA synthetase; InterPro: IPR004499 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 is a class II tRNA synthetase and is recognized by IPR002314 from INTERPRO, which recognises tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi (Lyme desease spirochete). The other family, IPR004500 from INTERPRO, includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis sp. (strain PCC6803), and one of the two prolyl-tRNA synthetases of Saccharomyces cerevisiae (Baker's yeast).; 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=468.41  Aligned_cols=359  Identities=22%  Similarity=0.358  Sum_probs=310.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCEEEECCCCCCEEEEECCHHHHHHHHHHHHHHHHHC--------------------CCEE
Q ss_conf             99999975320088754114404422678743565010789999999999988768--------------------9638
Q gi|254781004|r  234 YLYFLEESEKRDHRKLAREMDLFHIAEDGSGVIFWHRKGWKIFQTLISYMRRKIKD--------------------DYEE  293 (652)
Q Consensus       234 ~~~~~eea~~rdHr~lg~~~~lf~~~~~~~G~~~wlP~G~~i~~~ie~~ir~~~~~--------------------G~~e  293 (652)
T Consensus        12 Y~~il~kAel~d~R------------ypVKG~~v~~P~g~~iw~~iq~~~~~~~~~~~~~~~~~L~~F~P~~~~~Y~h~~   79 (533)
T TIGR00408        12 YDQILQKAELIDYR------------YPVKGCYVFLPYGFKIWENIQKILRDKLDEIKLKDKVILKKFIPIESLPYGHEE   79 (533)
T ss_pred             HHHHHHCCEEEEEC------------CCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHH
T ss_conf             89987305576641------------760103784598778999999999999987643546766405677777777001


Q ss_pred             EECCCCCCCCCCCC-CCCCCCCCCCCCEEECCCCCCCCCCEEEECCCCHHHHHHHHHHCCCCHHHCCHHHHHHEEEECCC
Q ss_conf             55543244310001-12100125554201001456777823774343125777765201222231043200010001278
Q gi|254781004|r  294 INTPQVLDQHLWQQ-SGHWDSYRANMFAVKCADDTIKDLRTFALKPMNCPGHVAVFNHGLKSYRELPVRLAEFGSVYRNE  372 (652)
Q Consensus       294 V~tP~l~~~~Lw~~-SGh~~~y~~~mf~~~~~~~~~~~~~~~~LkPmncp~h~~i~~~~~~SYrdLPlrl~e~~~~~R~E  372 (652)
T Consensus        80 v~fP~L~p~~~L~KEk~HikGF~pEv~wi~~-~G~~~L~~pLaLRPTSEt~~y~m~~kWv~sy~DLPlk~nQw~~vfR~E  158 (533)
T TIGR00408        80 VYFPMLIPESELEKEKDHIKGFEPEVYWITH-GGLKKLDEPLALRPTSETAMYNMYKKWVKSYRDLPLKINQWVNVFRYE  158 (533)
T ss_pred             EECCCCCCHHHHHHHCCCCCCCCCHHHHEEC-CCCCCCCCCCEECCCCHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECC
T ss_conf             0056445255786321356885840021010-377724675012586178887657878512158876898435889802


Q ss_pred             CCCCCEEEEECCCCC-CCCCEE-ECCHHHHHHHHHHHHHHHHHHHH-HHCCCCCEECCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             764520001056353-344210-10537678878999999887665-521332100014653112586035778999999
Q gi|254781004|r  373 PSGSLHGLMRVRGFT-QDDAHV-FCTKEQMFNECLKIHNLIISIYK-DFGFEKIMVKLSTRPEKRVGSDALWDDAENIMK  449 (652)
Q Consensus       373 ~sg~l~GL~R~ReF~-~~Dah~-F~~~eq~~~e~~~~~~~~~~v~~-~~g~~~~~~~ls~~~~~~~g~~~~~~~ae~~l~  449 (652)
T Consensus       159 ~kHT-RPflR~rEf~twqE~HT~H~t~~eAee~v~~~~~~Yk~f~~~~LaIP~~~-g~k~E~eKFaGA~~T~--------  228 (533)
T TIGR00408       159 KKHT-RPFLRTREFLTWQEAHTAHATAEEAEEEVLKALDLYKEFIENLLAIPYFV-GRKSEKEKFAGAEYTW--------  228 (533)
T ss_pred             CCCC-CCCHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEE-ECCCCCCCCCCCCCCE--------
T ss_conf             1787-86102333210100013143777889999999998899975028864687-1488755478876223--------


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCC-HHHHCCCCCCCEEEEECCCEEEEEEEEECCC
Q ss_conf             999850212125667520555555455432110021103310012110-1110223467416731797213799640341
Q gi|254781004|r  450 GVLDTIKNSSQDRINTGVLLGEGAFYGPKFEYILKDAIGRDWQCGTIQ-VDFNLPSRFNAFYVNSHSEKCHPVMIHRAVF  528 (652)
Q Consensus       450 ~~l~~~~~~~~~~~~~~~~~g~~afygpkid~~~~d~~gr~~~~~tiq-~df~~p~~f~l~y~~~dg~~~~pvmihr~~~  528 (652)
T Consensus       229 ----------------------------~~e~imP-DgG~~LQ~ATsH~LGqnF~K~F~i~fe~p~Gs~~~~~~ayq~s~  279 (533)
T TIGR00408       229 ----------------------------TFETIMP-DGGRTLQIATSHDLGQNFAKTFDIKFENPTGSDMDKVYAYQTSY  279 (533)
T ss_pred             ----------------------------EEEEECC-CCCEEHHHHHHHHHHCCCEEEEEEEEECCCCCCCCCCCCEECCC
T ss_conf             ----------------------------5675247-76500122121133035402036788778889764101001013


Q ss_pred             HHHHHHHHHHHHHH----CCCCCCCCCCEEEEEEE-C----C-----HHHHHHHHHHHHHHHHCCCEEEEECCCC-CCCH
Q ss_conf             03789999999973----87088733780899985-7----9-----6689999999999998798899975896-6367
Q gi|254781004|r  529 GSIERFIGIMIENF----KGNLPLWLSPIQAIVTT-I----T-----SSAVEYAQEIANLLKSHHLSIETDFRNE-TINY  593 (652)
Q Consensus       529 Gs~eR~ia~liE~~----~g~~P~wLAP~QV~Iip-i----~-----e~~~eya~~i~~~L~~~girV~~Ddr~~-~~G~  593 (652)
T Consensus       280 G~StR~igali~~HsD~~GLVLPp~vAp~Qvv~~Pv~IFkK~s~E~~~~~~e~a~~v~~~Lk~~~iRv~~D~~~~~~pG~  359 (533)
T TIGR00408       280 GISTRVIGALILIHSDEKGLVLPPRVAPIQVVIIPVIIFKKKSDEENKKVMELARKVEDKLKKLGIRVHLDKRDNYRPGK  359 (533)
T ss_pred             CHHHHHHHHEEEEECCCCCCCCCCCCCCEEEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCC
T ss_conf             35788754500012267775167012733589998677558752147789999999998773041007970355753231


Q ss_pred             HHHHHHHCCCCEEEEECHHHHHCCCEEEEECCCCC--EEEECHHHHHHH-HHHH
Q ss_conf             66655434898899987425325818999889886--633429999999-9873
Q gi|254781004|r  594 KIREHSIKKIPIIIICGDKEASERSIGIRRFGSTT--TQKVSLLDAIPI-LTKE  644 (652)
Q Consensus       594 Kir~a~l~giP~~ivIG~ke~e~~~Vtir~R~~~~--~~~i~lee~i~~-l~~e  644 (652)
T Consensus       360 kf~~~E~kGiPlR~evGP~D~~~n~~~~~rR~~~~kfK~~~~~~~L~~~k~~~~  413 (533)
T TIGR00408       360 KFSKWELKGIPLRLEVGPNDIEKNIVVVSRRDTKRKFKYQVSLDELEERKVVEL  413 (533)
T ss_pred             HHHCCCEEECCEEEEECCCCCCCCEEEEEEECCCCEEEEEEEHHHHHHHHHHHH
T ss_conf             320453330426998777510437689999617713557720545446789999