HHsearch alignment for GI: 254780263 and conserved domain: TIGR00503

>TIGR00503 prfC peptide chain release factor 3; InterPro: IPR004548 Peptide chain release factor 3 increases the formation of ribosomal termination complexes and stimulates activity of RF-1 and RF-2. It binds to guanine nucleotides and has a strong preference for UGA stop codons. This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis sp. (strain PCC 6803), and in Staphylococcus aureus.; GO: 0005525 GTP binding, 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=100.00  E-value=4.8e-42  Score=279.76  Aligned_cols=301  Identities=22%  Similarity=0.317  Sum_probs=210.6

Q ss_pred             EEEEEECCCCCHHHHHHHHHH----------HHHHHHHCCCCCCCCHHHHHCCCEEEEEEEEEECCCEEEEEEECCCCHH
Q ss_conf             999990468988789999998----------7644420013126868698629206378999821990899984787302
Q gi|254780263|r   14 GLSTIGHVDHGKTTLTAAITK----------YYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSHIDCPGHAD   83 (392)
Q Consensus        14 ni~~iGhvd~GKSTL~~~L~~----------~~~~~~~~~~~~D~~~~E~~rGiTi~~~~~~~~~~~~~i~iiD~PGH~~   83 (392)
T Consensus        13 ~FAIISHPDAGKTT~TEK~LLyG~AIQ~AG~VK~r~S~~~A~SDWM~ME~QRGISIT~~VlQF~Y~~~l~NLLDTPGH~D   92 (530)
T TIGR00503        13 TFAIISHPDAGKTTLTEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEMEKQRGISITTSVLQFPYRDCLVNLLDTPGHED   92 (530)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCCEEEEEEEEECCCCCEEECCCCCCCCC
T ss_conf             54366168887424678888742566522441220012212213788750588144412774145774562036858887


Q ss_pred             HHHHHHHHHHCCCCEEEEECCCCCCCCCHHHHHHHHHHCCCCCEEEEECCCCCCC--CHHHHHHCCCCCCEEEEEEEEEE
Q ss_conf             4677987740023314520123443321067788886318760233100233356--12221101232100111014532
Q gi|254780263|r   84 YVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDAVD--DDELLDISEYEIRDLLKEHKYSD  161 (392)
Q Consensus        84 f~~~mi~g~~~~D~ailvVda~~G~~~QT~eh~~l~~~lgi~~iIv~iNKmD~v~--~~~~~~~i~~~i~~~l~~~~~~~  161 (392)
T Consensus        93 FSEDTYRTL~A~D~~~M~IDaAKG~E~~T~KL~EV~RLR~~P-I~TF~NKLDR~~~~P~ELlDEvE~~L~~----~~~~~  167 (530)
T TIGR00503        93 FSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLMEVTRLRDLP-ILTFINKLDRDIRDPLELLDEVENELKI----NCAPI  167 (530)
T ss_pred             CCCHHHHHHHHHHHHEEEHHCCCCHHHHHHHHHHHHHHCCCC-HHHHHHHCCCCCCCHHHHHHHHHHHHCC----CEEEE
T ss_conf             640467999985123001111256123424454201000474-4335232065435537888888877064----11343


Q ss_pred             EEECCCCEEEEE-----------------------------EE--------CCC--------------------------
Q ss_conf             210233114676-----------------------------41--------144--------------------------
Q gi|254780263|r  162 DTPIIRGSALCA-----------------------------LQ--------GTN--------------------------  178 (392)
Q Consensus       162 ~~pii~~sa~~g-----------------------------~~--------~~n--------------------------  178 (392)
T Consensus       168 ~~PIG~G~~F~GVY~~~~~~~yLy~r~G~~~~~~~~~~~~~L~~P~L~~~~G~D~~~~l~dELELv~~A~~EFd~~~~~~  247 (530)
T TIGR00503       168 TYPIGCGKLFKGVYHLLKDEIYLYQRSGTGGTIKAVRVVKGLNNPALDSAVGSDLAQQLRDELELVEGASNEFDLAAFLG  247 (530)
T ss_pred             ECCCCCCCCCHHHHHHHCCEEEEEECCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             05657884311355430140667630588841667777632688015677657899999889999986302456899853


Q ss_pred             ---------CCCCCCCCCCHHHHHHCCCCCCCCC-CC-----------CCCCEECCCCCCCCCCCCCEEEEEEECCCCCC
Q ss_conf             ---------4565212332034431025222210-00-----------01100000001355445430148742453489
Q gi|254780263|r  179 ---------KELGEDSIHALMKAVDTHIPTPQRS-LD-----------APFLMHIEGSCGIEGRGTVVTGCIKRGRIKAG  237 (392)
Q Consensus       179 ---------~~~~~~~~~~Ll~~i~~~~~~p~~~-~~-----------~p~r~~I~~vf~i~g~G~Vv~GrV~sG~l~~G  237 (392)
T Consensus       248 GE~TPVFFG~Al~NFGV~~~L~~l~~~A~~P~~~~~~~~TvE~~~e~FsGFVFK~QANMDPKHRDRvAFlRV~SGKyEK~  327 (530)
T TIGR00503       248 GELTPVFFGTALGNFGVDHFLDGLLQYAPKPEARQSDTRTVEPTEEKFSGFVFKLQANMDPKHRDRVAFLRVVSGKYEKG  327 (530)
T ss_pred             CCCCCEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEECCEEECC
T ss_conf             86463111000101008999999998607888765677540234335442288863379886335057777641346347


Q ss_pred             CEEEEEECCCCCCCEEEECCCC-CCCCCCCCCCCHHHHHHHCCCCCCEEECHHEEECC------CCCCCCEEEEEEEEEE
Q ss_conf             6799950687432125412100-12114432100136664112454322021177326------7776300016899971
Q gi|254780263|r  238 SDVEIIGMGGKKLKVKCTDVEM-FRKKLDEAIAGDNVGLLLRGVNRADVPRGRVVCAP------GSIQEYSRFRASVYIL  310 (392)
Q Consensus       238 d~i~i~p~~~~~~~~kv~si~~-~~~~v~~a~aGd~v~l~Lkgi~~~di~rGdvl~~~------~~~~~~~~f~A~i~il  310 (392)
T Consensus       328 M~~k~~R~gK~V~~S~~~~~~A~~R~~v~~AYaGD~iGL~N----~G~~~IGDT~~~GE~~~f~gIP~F~PELF~~~R~-  402 (530)
T TIGR00503       328 MKLKHVRTGKDVVLSDALTLMAGDREHVEEAYAGDIIGLHN----HGTIQIGDTFTQGEKLKFTGIPNFAPELFRRLRL-  402 (530)
T ss_pred             CEECCCCCCCEEEECCHHHHHHCCHHHHHHCCCCCEEEECC----CCCEEECCCCCCCCEEEECCCCCCCHHHHHHHHC-
T ss_conf             56614213553686323565440212231127776531068----8426747720248656638778866789998621-


Q ss_pred             ECCCCCCCCCCCCCCE
Q ss_conf             0567875555115978
Q gi|254780263|r  311 TASEGGRTTGFMDNYR  326 (392)
Q Consensus       311 ~~~~~~~~~~~~~~~~  326 (392)
T Consensus       403 --~DP~~~K~l~KG~~  416 (530)
T TIGR00503       403 --KDPLKQKQLLKGLV  416 (530)
T ss_pred             --CCCHHHHHHHCCCH
T ss_conf             --38345566550410