HHsearch alignment for GI: 254780295 and conserved domain: TIGR00071

>TIGR00071 hisT_truA tRNA pseudouridine synthase A; InterPro: IPR001406 Transfer RNA-pseudouridine synthetase contains one atom of zinc essential for its native conformation and tRNA recognition and has a strictly conserved aspartic acid that is likely to be involved in catalysis. It is involved in the formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer-RNAs. Pseudouridine is the most abundant modified nucleoside found in all cellular RNAs.; GO: 0000049 tRNA binding, 0016439 tRNA-pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0008033 tRNA processing.
Probab=100.00  E-value=0  Score=516.48  Aligned_cols=237  Identities=40%  Similarity=0.612  Sum_probs=230.6

Q ss_pred             CEEEEEEEECCCCCEEEEECCCCCCHHHHHHHHHHHHHC-----------CCEEEEECCCCCCCCEEEEEEEEEEECCCC
Q ss_conf             229999997166872004875387788999999999709-----------956999711213861222346886406321
Q gi|254780295|r    2 IRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG-----------EIVVVHGAGRTDSGVHALRQVAHFDLVREW   70 (247)
Q Consensus         2 ~r~~~~i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~~-----------~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~   70 (247)
T Consensus         1 ~kia~~iaY~G~~y~G~Q~QP~~~Tvq~~le~aL~~~~~i~~~nS~~l~~~~~~~~~aGRTDkGVHA~~Qv~sf~~~~~~   80 (326)
T TIGR00071         1 RKIALKIAYDGSNYHGWQRQPNKRTVQGELEKALEKIGKISKENSEDLKKKKIKVISAGRTDKGVHALGQVISFDTPKEI   80 (326)
T ss_pred             CEEEEEEEECCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCEEEEECCCCCCEECCCCEEEEEECCCC
T ss_conf             97899997447665024771888982438999999872024220000421697799943777010105647999861778


Q ss_pred             CCHHHHHH--HHHHHCCCCCCCCCC-CCCCCCCCCCEECCCCE-------------------------------------
Q ss_conf             10468999--998618887654344-32267775500021002-------------------------------------
Q gi|254780295|r   71 VPVILCKA--LNAYLKISDTISILN-LSIVDKQFHARFSAIRR-------------------------------------  110 (247)
Q Consensus        71 ~~~~~~~~--lN~~L~~p~~Irv~~-~~~v~~~FhaR~~a~~R-------------------------------------  110 (247)
T Consensus        81 ~~~~l~~~hvLN~~L--p~dI~v~~~~~~V~~~FhaRf~~~~R~YeYLi~~~~L~g~~~~S~L~R~~~~S~~E~~S~E~W  158 (326)
T TIGR00071        81 PDNKLNAKHVLNALL--PPDIRVKAVLEPVNDNFHARFSAQKRVYEYLIPTFSLIGPKRSSLLYRDVEESKRELESKEVW  158 (326)
T ss_pred             CHHHHHHHHHHHHCC--CCCCEEEEEEEECCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCCHHHH
T ss_conf             755557776664127--455578311120477888684333231212032110378897515665253210113314478


Q ss_pred             ----------------------------------EEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHCCHHEE
Q ss_conf             ----------------------------------2355685244320233321024433333566556567652001100
Q gi|254780295|r  111 ----------------------------------SYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFT  156 (247)
Q Consensus       111 ----------------------------------~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~G~HdF~  156 (247)
T Consensus       159 ~~F~~~~~~~FS~~E~~~~~~~~~~~~~~~~~~~~YrY~~~~~~~~~~~~~-~~~hy~~~ld~~~~~~a~~~~~G~hdF~  237 (326)
T TIGR00071       159 DEFKKDAREKFSTDELEALLDYVQKLRDEDDLVEHYRYILYNEKLPPLLAG-YATHYYSPLDLEKMRAAAKEFLGKHDFS  237 (326)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCHHHHCEEEECCCCCCHHHHH-HHCCCCCHHHHHHHHHHHHHCCCCCCCH
T ss_conf             899987324678789999998400000245424322021205655112342-2202253121899999876313642510


Q ss_pred             EECCCC---CCCCCCCCCCCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCC
Q ss_conf             102456---55333211033111123-33200113158888999999999999999768998889999983588211666
Q gi|254780295|r  157 TFRSIH---CQASSPIRTIDHFDVNS-FGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGP  232 (247)
Q Consensus       157 ~F~~~~---~~~~~~~R~I~~~~v~~-~~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~~~~r~~~~~  232 (247)
T Consensus       238 nF~~~~~~~~~~~~~~R~i~~~~~~~~~~~~~~~~I~G~~FL~~mVR~iV~~l~~~g~~~~~~e~~~~ll~~~~r~~~~~  317 (326)
T TIGR00071       238 NFSKAKGAKSKSRSPVRTISKIKVSEESGEYIIFDIIGNSFLWHMVRKIVGALVLVGRGKLPPEWVQKLLDAKKRELAPT  317 (326)
T ss_pred             HHCCCCCCCCCCCCCEEEEEEEEEEECCCCEEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCC
T ss_conf             01000025677777258898889962588889999885430388899999999997516888899999854677575676


Q ss_pred             CCCCCCCEE
Q ss_conf             369898476
Q gi|254780295|r  233 LAPPEGLYF  241 (247)
Q Consensus       233 ~APa~GL~L  241 (247)
T Consensus       318 ~ap~~gL~L  326 (326)
T TIGR00071       318 TAPANGLYL  326 (326)
T ss_pred             CCCCCCCCC
T ss_conf             887567889