HHsearch alignment for GI: 254780260 and conserved domain: TIGR03672

>TIGR03672 rpl4p_arch 50S ribosomal protein L4P. One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.
Probab=100.00  E-value=0  Score=368.47  Aligned_cols=198  Identities=26%  Similarity=0.332  Sum_probs=171.6

Q ss_pred             CEEEEECCCCCEEEEEEECHHHHCCCCCHHHHHHHHHHHHHCCCCC--C---CCCCCCHHHCCCCC---CCCCCCCCCCC
Q ss_conf             6226554688645568609779398766899999999999727886--2---00136212148988---76455887554
Q gi|254780260|r    2 IELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIG--C---SKSKGRSEVAYTGS---KMYVQKGTGRA   73 (207)
Q Consensus         2 m~~~v~~~~g~~~~~i~l~~~vf~~~~~~~li~~~v~~~~~~~R~g--t---a~tk~r~ev~gs~k---K~~~QKGtGrA   73 (207)
T Consensus         1 Mkv~V~~~~G~~~g~ieLp-~VF~~~ir~dli~~~v~~~~an~RQp~g~~~~AG~k~sa~s~g~grg~aR~pR~kgtgra   79 (251)
T TIGR03672         1 MKAKVYDLDGEVVGEIELP-AVFEEPVRPDLIKRAVLAAQTNRLQPYGADPYAGKRTSAESWGSGRGIARVPRIKGGSRA   79 (251)
T ss_pred             CCEEEECCCCCCCCEEECH-HHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCC
T ss_conf             9415977889898478702-754899878999999999998645666767666761142555788774548605288863


Q ss_pred             CCCCCCCCCCCCCCCCCCCCC-CCCCCCCHHHHHHHHHHHHHHHHHH------------CCCE-EEEECCCCCCCCHHHH
Q ss_conf             236531110105774227787-5320000159999999998787650------------5958-9951433787781899
Q gi|254780260|r   74 RHSSKSVSQFRGGGKAFGPVP-IIGVHALPKKVRSLALRHALSDKFC------------SNDI-MVIDNLVSKECKTKYL  139 (207)
Q Consensus        74 R~Gs~rsp~~rgGg~afgp~p-r~~~~klnkK~~~lAl~saLs~k~~------------~~~l-~Vvd~~~~~~~KTK~~  139 (207)
T Consensus        80 ~----~aP~~rGGg~ahgPk~~r~~~~kiNKK~rrlAl~SALsata~~~~v~~Rgh~i~~~~lpiVv~d~~e~~~KTKe~  155 (251)
T TIGR03672        80 A----RVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATADPELVKARGHVFEGDELPIVVVDDFESLKKTKEV  155 (251)
T ss_pred             E----ECCEEECCCCCCCCCCHHHHHHHCCHHHHHHHHHHHHHHHCCHHHHHHCCCCCCCCCCEEEEECCCCCCHHHHHH
T ss_conf             2----265142475456996304544342899999999878873057777873566246664008982443320528999


Q ss_pred             HHHHHHCCC---------------------------CCEEEEECCCCCHHHHHHHCCCCCCEEEEHHCCCHHHHEECCC-
Q ss_conf             998411355---------------------------6327861577517899996278895684240288757100590-
Q gi|254780260|r  140 VTRFRALDL---------------------------SNALIIDGCQLDRNFQLAARNIPNINLLPVQGINVYDILRCSK-  191 (207)
Q Consensus       140 ~~~L~~l~~---------------------------~~~llv~~~~~d~n~~~s~rNi~~v~v~~~~~lnv~dll~~~~-  191 (207)
T Consensus       156 ~~~L~~lgl~~di~r~~~~k~iraGkgkmRgRry~~~k~~LiV~~~-~~~~~ka~RNIpGVdv~~v~~LNv~dLapGg~~  234 (251)
T TIGR03672       156 RELLEALGVYDDIERAKEGKKIRAGKGKMRGRRYKEPKSVLIVVGD-DSGISKAARNLPGVDVVTVNNLNVEHLAPGGHP  234 (251)
T ss_pred             HHHHHHCCCHHHHHHHHHCCCEECCCCCCCCCEEECCCEEEEEECC-CCHHHHHHHCCCCCEEEECCCCCHHHHCCCCCC
T ss_conf             9999985862778988634501157764257300035415999748-712888860799976985487769990778877


Q ss_pred             ---EEEEHHHHHHHHHH
Q ss_conf             ---89849999999997
Q gi|254780260|r  192 ---LVLSKSAIEALEDR  205 (207)
Q Consensus       192 ---iVit~~Ai~~l~e~  205 (207)
T Consensus       235 gRl~i~T~sA~~~l~er  251 (251)
T TIGR03672       235 GRLTVWTESAIEKLEER  251 (251)
T ss_pred             CEEEEEEHHHHHHHHCC
T ss_conf             80899866999987429