HHsearch alignment for GI: 254780562 and conserved domain: TIGR00090

>TIGR00090 TIGR00090 iojap homolog; InterPro: IPR004394 The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. Maize has two RNA polymerases in plastids, but the plastid-encoded one, similar to bacterial RNA polymerases, is missing in iojap mutants. The role of iojap in chloroplast development, and the role of its bacterial orthologs modeled here, is unclear..

Probab=99.74  E-value=2.7e-18  Score=120.20  Aligned_cols=63  Identities=38%  Similarity=0.508  Sum_probs=58.2

Q ss_pred             HHHHHHHHHHHHHHH-HHCCCCCEEEEEECCCCCCHHCEEEEEEECCHHHHHHHHHHHHHHHHHC
Q ss_conf             799999999999999-8436863498980488872000878895188689999999999999743
Q gi|254780562|r   13 ADHLDSCIATVMECL-KELKAEDICHIENTSLRSLICDNMVIVSGRSTKHVASIADNLISYLKKK   76 (77)
Q Consensus        13 ~~~~~~~l~~i~~~l-~dkKa~dI~~ldv~~~~s~~~D~fVIatg~S~rhv~Aia~~v~~~lk~~   76 (77)
T Consensus        24 aPate~~i~~i~~~~CdekkA~Di~~ld~~-~~s~l~d~~iICTG~S~~qV~aiaD~~~~~~~~~   87 (155)
T TIGR00090        24 APATEKLIETIAAALCDEKKAEDIVHLDVE-GVSYLADYFIICTGTSSKQVLAIADNIKKQLKEA   87 (155)
T ss_pred             CCCHHHHHHHHHHHHHCCCCCCCEEEEEEC-CCCEEECCCEEEECCHHHHHHHHHHHHHHHHHHH
T ss_conf             860245899999986125676625887205-8742112203330672789999999999999986