HHsearch alignment for GI: 254780187 and conserved domain: pfam00163

>pfam00163 Ribosomal_S4 Ribosomal protein S4/S9 N-terminal domain. This family includes small ribosomal subunit S9 from prokaryotes and S16 from metazoans. This domain is predicted to bind to ribosomal RNA. This domain is composed of four helices in the known structure. However the domain is discontinuous in sequence and the alignment for this family contains only the first three helices.
Probab=99.95  E-value=2.9e-28  Score=204.04  Aligned_cols=91  Identities=32%  Similarity=0.448  Sum_probs=84.3

Q ss_pred             CCCCCCEEEEEEECCCCCCCCCCC-CHHCCCCCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             764487123520058888888877-00013689987765443--341358999999884855515654799999998753
Q gi|254780187|r    2 SKRESSKHKIDRRIGENLWGRPKS-PVNTRSYGPGLHGQRRK--SKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEAD   78 (206)
Q Consensus         2 ~r~~gpk~K~~RrlG~~l~~~~k~-~~~~r~~~pGqhg~~r~--~k~S~yg~qL~eKQKlr~~YG~~~ekq~~~~~~~A~   78 (206)
T Consensus         1 aRy~GP~~K~~RR~g~~~~~~~~~~~~~~~~~~pg~hg~~~~~~rk~S~Yg~qL~EKQklr~~YG-l~ErQfr~y~~~A~   79 (94)
T pfam00163         1 SRYRGPTLKLPRRLGELPRLTAKTKLAGEYGLRPGQHGWRVKKGRRLSRYLLRLDEKQKLRFFYG-LLERQLRRYGVLAK   79 (94)
T ss_pred             CCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC-HHHHHHHHHHHHHH
T ss_conf             96657554431789998677677767676778999865344576526189887864307999805-30999999999997


Q ss_pred             HCCCCCCHHHHHHHH
Q ss_conf             033443026899999
Q gi|254780187|r   79 RSRGDTSHNLISFLE   93 (206)
Q Consensus        79 ~~~g~t~~~ll~~LE   93 (206)
T Consensus        80 k~~G~TG~~Ll~lLE   94 (94)
T pfam00163        80 KLDGSLGLNLLDLLE   94 (94)
T ss_pred             CCCCCHHHHHHHHHC
T ss_conf             479877999999809