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