HHsearch alignment for GI: 254780722 and conserved domain: COG1955

>COG1955 FlaJ Archaeal flagella assembly protein J [Cell motility and secretion / Intracellular trafficking and secretion].
Probab=99.19  E-value=2.4e-08  Score=70.51  Aligned_cols=119  Identities=18%  Similarity=0.242  Sum_probs=100.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH-CCCHHHHHHHHHHHHH-HCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf             999999999999999999999995699989999999992-4842899999999986-30388889999977534873479
Q gi|254780722|r    5 IKKRTAKFLDDFPNALDIIVRSVRAGLPVSDAVAVIVGQ-SSDPVRSEFRRVIETQ-HLGLSLSESISRMVRYMPLQEVS   82 (187)
Q Consensus         5 ~~~R~~~~~~~l~~~l~~l~~~l~aG~sl~~Al~~~a~~-~~~~l~~e~~~i~~~~-~~G~~~~~al~~~~~~~~~~~~~   82 (187)
T Consensus        43 ~d~k~~~in~~l~f~lt~m~~LsTs~i~r~~If~~ls~~~eyg~~~~~f~kI~~L~~~Wgy~~a~Ac~~iA~k~~~~~l~  122 (527)
T COG1955          43 RDSKKNRINSDLLFFLTYMASLSTSDIPRDDIFRILSRKEEYGPLRKEFRKIYNLVDKWGYSLAEACRFIAKKTPSEILA  122 (527)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHHHHH
T ss_conf             26777521312699999999996069988999999654152124899999999999986845689999998609679999


Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999874257468999999999999999999999986
Q gi|254780722|r   83 FFSTVISVQSQLGGNLSEALANLSRILRDRKNMKAKVQALS  123 (187)
Q Consensus        83 ~~~~~l~~~~~~gg~~~~~L~~la~~~~~~~~~~~~~~~~~  123 (187)
T Consensus       123 dfL~Rla~ai~sGe~~~eFl~~E~~~~~~~y~~~Yer~LeS  163 (527)
T COG1955         123 DFLDRLAYALDSGEDLKEFLEREQDTTMDEYETEYERALES  163 (527)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999987742587379999999999999999999999988