HHsearch alignment for GI: 254780870 and conserved domain: TIGR00442

>TIGR00442 hisS histidyl-tRNA synthetase; InterPro: IPR015807 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 . Histidyl-tRNA synthetase (6.1.1.21 from EC) is an alpha2 dimer that belongs to class IIa. Every completed genome includes a histidyl-tRNA synthetase. Apparent second copies from Bacillus subtilis, Synechocystis sp., and Aquifex aeolicus are slightly shorter, more closely related to each other than to other hisS proteins, and not demonstrated to act as histidyl-tRNA synthetases (see IPR004517 from INTERPRO). The regulatory protein kinase GCN2 of Saccharomyces cerevisiae (YDR283c), and related proteins from other species designated eIF-2 alpha kinase, have a domain closely related to histidyl-tRNA synthetase that may serve to detect and respond to uncharged tRNA(his), an indicator of amino acid starvation, but these regulatory proteins are not orthologous.; GO: 0000166 nucleotide binding, 0004821 histidine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006427 histidyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=100.00  E-value=7.9e-35  Score=239.61  Aligned_cols=388  Identities=19%  Similarity=0.279  Sum_probs=244.1

Q ss_pred             ECCCCCHHCCCCHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHH-CCC-CHHHHHHHCCHHHCCCCCCEECCCCC
Q ss_conf             0038811104316999999999999999866988973575124689877-197-31122221040213786200034555
Q gi|254780870|r   34 QHSKGIYSWLPLGQKALDNVNAIIREEQNRTGAIEMSVPTLQSADLWVE-SGR-YDSYGKEMLRLADRNDKAMIYGPTHE  111 (449)
Q Consensus        34 ~~~~G~~~~lP~G~~i~~~le~~~r~~~~~~G~~ei~tP~l~~~eL~~~-SGh-~d~~~~em~~~~d~~~~~~~LrP~~~  111 (449)
T Consensus         5 ~~~~G~~d~~p~~~~~~~~~~~~~~~~~~~~g~~~~~~P~~e~~~~~~~~~~~~~~~~~~~~y~f~d~~~~~~~lrp~~t   84 (446)
T TIGR00442         5 QKPRGTKDWLPGELVYRQWIEAKLRSVLESYGYSEIRTPIFEYTELFARGIGKSGDEVEKELYTFKDKGGRDLALRPELT   84 (446)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHEEEECCCCCEEEECCCHH
T ss_conf             23455200254157899999999999997517720012114445666530253013344443012127884144222003


Q ss_pred             CCCCCCHHHCCCCC-CCCCEEEEECCCCCCCCCCCC-CCCCCCEEEEEEECCEECCCHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             43101100001342-013402641465334566767-5434531668740422118868879999999998741111006
Q gi|254780870|r  112 EVMTDIFRSHIKSY-RNLPFTFYQIQLKFRDELRPR-FGVMRSREFLMKDAYSFDLTPEGSKHSYNKMFVSYLRIFHRLG  189 (449)
Q Consensus       112 e~~~~i~~~~~~SY-r~LPlr~y~ig~~fR~E~rp~-~GL~R~ReF~q~D~~~F~~~~e~~~~e~~~~~~~~~~i~~~lg  189 (449)
T Consensus        85 ~~~~r~~~~~~~~~~~~~p~~~~~~g~~~r~e-~p~~~g--r~r~f~~~~~~~~G~~~~~~~~~---~~~~~~~~~~~~g  158 (446)
T TIGR00442        85 APVVRLVAENKLLLPANKPLRLYYIGPVFRYE-RPQLKG--RYREFWQFGCEVIGSESPLADAE---VLSLAVEGLKALG  158 (446)
T ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEEECHHHCC-CHHHHC--CHHHHHHCCEEEECCCCCHHHHH---HHHHHHHHHHHHC
T ss_conf             68999998754310467642432320101022-412301--01133211504643665203689---9999999898607


Q ss_pred             CHH-HHHHHCCHHCCCCHHHHHHHHCC--CC-----CCEEEECCCCC---CCCCCHHHCCHHHHHCCCCC--CCCCCCCC
Q ss_conf             201-22331100101311334345468--67-----70143101003---47764111220121001122--00013632
Q gi|254780870|r  190 LKS-IPMRAESGPIGGDLSHEFIVLAD--TG-----ETQVFCSKDFM---DFPIPSENTDFDDIISLNSI--VEQWTAPY  256 (449)
Q Consensus       190 l~~-~~v~~~~~~ig~~~s~e~~~~~~--~~-----e~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~--~~~~~~~~  256 (449)
T Consensus       159 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (446)
T TIGR00442       159 LEGHFKLKLNHLGILEGILEYRGALEEDVYLTPIKDKLDKDDQERLEEELTNPLRILDEKVDELLELLKLKGAPEILDYL  238 (446)
T ss_pred             CCCEEEEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             66327887413001456666521102345665666662301156789987654432122245677776325622578888


Q ss_pred             CC-----------CHHH-CHHHHHCCC-----CCCCEEEEEEEEC--CCEEEC-----CCCCCCCCEEEEE---CCCCCC
Q ss_conf             12-----------0110-002330358-----7655243211115--814422-----3112230115896---477772
Q gi|254780870|r  257 AA-----------TSDV-HNEKLFDSL-----PENKRVSARGIEV--GHIFYF-----GTKYSLPMSATFK---GADGKD  309 (449)
Q Consensus       257 ~~-----------~~d~-~~~~~~d~l-----~~~~~~~~~~ie~--~~~f~l-----G~~ys~~~~~~~~---~~~g~~  309 (449)
T Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~rGldyy~g~~~e~~~~~~~~~~~~~~GG~yd~l~~~~~~~  318 (446)
T TIGR00442       239 DELLDESEGHFEGLKDLEELFQLLEDLGIDDLYELNLGLARGLDYYTGTVFEIVTNALGAQGTVCGGGRYDNLVEEFGGP  318 (446)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCHHHHHHHHHCCEEEEEECCCCCCCCCEECCCCHHHHHHHHCCC
T ss_conf             88741235788899899999999865054210220511331001111323443101124321000465101256650675


Q ss_pred             CCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCHHHCCCC----CEEEECCCCHHHHHHHHHHHHHHHHHC--CCEEEEEC
Q ss_conf             323366634474300233221023211111363320321----102421788799999999999999986--98799975
Q gi|254780870|r  310 HYVQMGSYGIGAMRVVAAVIESSHDGKGIIWPDSVAPFK----ISLINIKAHDQVCRDACEKIYARLSKV--GCDVFWDD  383 (449)
Q Consensus       310 ~~~~~g~~giG~~R~~~alle~~~d~~g~~wP~~iaP~~----v~Iipi~~~~~~~~~~A~~i~~~Lr~~--Gi~v~~D~  383 (449)
T Consensus       319 ~~~~~G-~~~g~~r~~~~~~~~~~~-----~~~~-~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~g~~~~~~~  388 (446)
T TIGR00442       319 PTPAVG-FAFGLERLINLLDAEKPS-----FPLA-KVVDARVFVLVVGLG---EEALPEALRLAEKLREALPGISAELYP  388 (446)
T ss_pred             CCCCCH-HHHHHHHHHHHHHHHHHH-----HCCC-CCCCCEEEEEEEECC---HHHHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             454100-233089999987565431-----0000-111110257786064---245789999999998733785168852


Q ss_pred             C--CCCHHHHHHHHHHCCCCEEEEECCCHHHCCEEEEEECCCC-CEEEEEHHHHHHH
Q ss_conf             8--9797086787874899889998624023571899998999-7878619999999
Q gi|254780870|r  384 M--GEQIGSQFAVADLLGFPLQVIVGSKFVSDSKVEIKHRLTG-IREDMSLEEVINY  437 (449)
Q Consensus       384 r--~~~iGkK~~~Ad~~gip~~iiiG~~el~~~~Vtir~r~tg-~q~~v~l~eli~~  437 (449)
T Consensus       389 ~~~~~~~~~~~~~a~~~g~~~~~~~G~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~  445 (446)
T TIGR00442       389 KNNGRKLKKQFSYADKLGARFAVVLGEEELKEGKVTVKDLETGFEQTTLALDELIDI  445 (446)
T ss_pred             CCCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEHHHHHHHHHHHHHHHHHHHC
T ss_conf             211001345554564348548998453100134122012231245677757877512