HHsearch alignment for GI: 254780487 and conserved domain: cd01121
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=95.24 E-value=0.24 Score=27.88 Aligned_cols=145 Identities=18% Similarity=0.208 Sum_probs=80.2
Q ss_pred EEEEECCCCCCCHHHHHHHHHHHHHCCCCC-CEECCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHCC
Q ss_conf 299983589874799999999998404861-2013887380689999985578731144300145103478899985023
Q gi|254780487|r 4 RLVIVGTDTSVGKTIFASALVHALNAYYWK-PIQSGMYEETDSKTIHRIGRIPKSHIIPEKWKLRTPASPHLAAEIDGVI 82 (217)
Q Consensus 4 ~i~I~GT~t~vGKT~vs~~L~~~l~~~~~K-Pv~~G~~~~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (217)
T Consensus 83 SvvLlgGePGIGKSTLLLQia~~la~~~~~vLYvSG--EES~~QIk~RA~RLg~~~~--~l~l~set~le~Il~~----- 153 (372)
T cd01121 83 SVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSG--EESPEQIKLRADRLGISTE--NLYLLAETNLEDILAS----- 153 (372)
T ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEC--HHHHHHHHHHHHHHCCCCC--CCEEEECCCHHHHHHH-----
T ss_conf 179982599886889999999999863993899824--5678999989998587887--7278843569999999-----
Q ss_pred CHHHHHHHHHHCCEEEEECCCCCCCCCCCC------------CCHHHHHHHHCCCEEEEECC-CCCHH------HHHHHH
Q ss_conf 507886422328879992276555667675------------30899999747944897057-76504------579999
Q gi|254780487|r 83 IDPATINPPDINDSIIIEGIGGLLVPLTTE------------YLFIDLIERWQFPIILCART-SLGTI------NHSLLS 143 (217)
Q Consensus 83 i~~~~~~~~~~~D~viIEGagg~~~~~~~~------------~~~~dla~~l~~~vILV~~~-~~g~i------~~~~l~ 143 (217)
T Consensus 154 ----i--~~~kP~~lIIDSIQT~~~~~~~s~pGsvsQVReca~~L~~~AK~~~i~~~lVGHVTK~G~iAGPkvLEHmVDt 227 (372)
T cd01121 154 ----I--EELKPDLVIIDSIQTVYSSELTSAPGSVSQVRECTAELMRFAKERNIPIFIVGHVTKEGSIAGPKVLEHMVDT 227 (372)
T ss_pred ----H--HHHCCCEEEEECHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCCCCHHHEEEEEE
T ss_conf ----9--9719988999562202037767799878999999999999998619739999876268863774031002136
Q ss_pred HHHHH---HCCCEEEEEEECCCC
Q ss_conf 99998---479907999976977
Q gi|254780487|r 144 LETLR---NRNINIIGIAFIGDS 163 (217)
Q Consensus 144 ~~~~~---~~g~~i~GiIlN~~~ 163 (217)
T Consensus 228 Vl~fEgd~~~~~R~LR~~KNRFG 250 (372)
T cd01121 228 VLYFEGDRHSEYRILRSVKNRFG 250 (372)
T ss_pred EEEECCCCCCCEEEEEEECCCCC
T ss_conf 88751577655035674115677