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