HHsearch alignment of GI: 254780406 and MMDB domain: 1k8w_A_80-224

>1k8w_A (A:80-224) TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli}

Probab=90.68  E-value=1.2  Score=23.61  Aligned_cols=66  Identities=12%  Similarity=0.208  Sum_probs=42.5

Q ss_pred             HHHHHHHHCCCEEEE--CCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCC------EEEEEEEEEECCEECC
Q ss_conf             887400000876750--3430364026880799999951842899999998398------6868897587054518
Q gi|254780406|r  159 NLLKKGIVIQGICYG--DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW------KVNRLIRISYGPFQLG  226 (354)
Q Consensus       159 ~~~~~g~~~~~~~~~--~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~------~V~~L~Rv~~G~~~l~  226 (354)
                      +-.++|..++-..-.  --.+.+..-.....++++.-..|-+  ||.++..+|.      .+..|.|+++|+|.|+
T Consensus        72 elAr~G~~~~~~~r~v~I~~~~l~~~~~p~~~~~v~cs~GTY--IRsL~~dig~~Lg~~a~~~~L~Rt~~G~f~l~  145 (145)
T 1k8w_A           72 EYARQGIEVPREARPITVYELLFIRHEGNELELEIHCSKGTY--IRTIIDDLGEKLGCGAHVIYLRRLAVSKYPVE  145 (145)
T ss_dssp             HHHHTTCCCCCCCEEEEEEEEEEEEEETTEEEEEEEECTTCC--HHHHHHHHHHHHTSCEEEEEEEEEEETTCCGG
T ss_pred             HHHHHCCCCCCCCEEEEEEEEEEEECCCCEEEEEEEECCCHH--HHHHHHHHHHHCCCCEEEEEEEEEEECCCCCH
T ss_conf             999756655578366465127984133548999999678458--99999998765089589837898888783803