HHsearch alignment for GI: 254780870 and conserved domain: TIGR00443

>TIGR00443 hisS_second histidyl-tRNA synthetase 2, putative; InterPro: IPR004517 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 (see IPR004516 from INTERPRO). Every completed genome includes a histidyl-tRNA synthetase. Apparent second copies from Bacillus subtilis, Synechocystis spp., 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. 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. An unusual feature is that this putative second HisS is shorter at the C-terminus. It shows greater similarity to archaeal HisS than to other bacterial HisS. There is reason by analogy to suspect this second HisS may have a function other than (or in addition to) ligating His to its tRNA: the protein kinase DGCN2 of Drosophila has a C-terminal domain related to HisS that appears to detect uncharged tRNA(his), an indicator of amino acid starvation, and respond by phosphorylating eIF-2alpha.; GO: 0000105 histidine biosynthetic process, 0005737 cytoplasm.
Probab=98.64  E-value=4.3e-08  Score=70.59  Aligned_cols=160  Identities=17%  Similarity=0.102  Sum_probs=123.0

Q ss_pred             CEECCCCCHHCCCCHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCCHHHHHHHCCHHHCC-CCCCEECCCC
Q ss_conf             200038811104316999999999999999866988973575124689877197311222210402137-8620003455
Q gi|254780870|r   32 IHQHSKGIYSWLPLGQKALDNVNAIIREEQNRTGAIEMSVPTLQSADLWVESGRYDSYGKEMLRLADRN-DKAMIYGPTH  110 (449)
Q Consensus        32 i~~~~~G~~~~lP~G~~i~~~le~~~r~~~~~~G~~ei~tP~l~~~eL~~~SGh~d~~~~em~~~~d~~-~~~~~LrP~~  110 (449)
T Consensus         2 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~d~~~~~~~~l~~~~   79 (414)
T TIGR00443         2 KFEPPAGERDLLPGEYELKKKINKKLTDLFDKWGYQFIETSTLEWYDTLGLGG--AIGAKELIKLLDSGTGGTLGLRPDL   79 (414)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHCCCCCCHHHHHHHCC--CCCHHHHHEEECCCCCCCEEECCCC
T ss_conf             66655540344456777888998899999986140121013221123332101--1000021000003455402112220


Q ss_pred             CCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCEEEEEEECCEECCCHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             54310110000134201340264146533456676754345316687404221188688799999999987411110062
Q gi|254780870|r  111 EEVMTDIFRSHIKSYRNLPFTFYQIQLKFRDELRPRFGVMRSREFLMKDAYSFDLTPEGSKHSYNKMFVSYLRIFHRLGL  190 (449)
Q Consensus       111 ~e~~~~i~~~~~~SYr~LPlr~y~ig~~fR~E~rp~~GL~R~ReF~q~D~~~F~~~~e~~~~e~~~~~~~~~~i~~~lgl  190 (449)
T Consensus        80 ~~~~~~~~~~~~~~~-~~p~~~~~~~~~~~~~p~~~~g--~~~~~~~~g~~l~~~~~~~~d~~~---~~~~~~~l~~~gl  153 (414)
T TIGR00443        80 TGPIARAAVSKLLDN-GLPERVGYFANVFRLPPEGYGG--RGFEFLQAGVELLGDGGVLADAEV---LLLLTGCLKSLGL  153 (414)
T ss_pred             HHHHHHHHHHHHHHC-CCCHHHHHHHHHHCCCCCCCCC--CCCHHHHHHHHHHCCCCCHHHHHH---HHHHHHHHHHCCC
T ss_conf             146889999887623-6611332221110267533456--541234420232103430125789---9999998863150


Q ss_pred             HHHHHHHCC
Q ss_conf             012233110
Q gi|254780870|r  191 KSIPMRAES  199 (449)
Q Consensus       191 ~~~~v~~~~  199 (449)
T Consensus       154 ~~~~~~~~~  162 (414)
T TIGR00443       154 ADWKLILGH  162 (414)
T ss_pred             HHHHHHHHC
T ss_conf             134555410