HHsearch alignment for GI: 254780784 and conserved domain: TIGR02063
>TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805 This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in Escherichia coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Not included in this entry are shorter, divergent forms from the Chlamydiae and the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans , .; GO: 0003723 RNA binding, 0004518 nuclease activity.
Probab=98.93 E-value=3.3e-09 Score=93.52 Aligned_cols=197 Identities=21% Similarity=0.323 Sum_probs=108.8
Q ss_pred CCCCCCCCCCCCEEEEE--CCCCCEEEECC--C-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCCCC
Q ss_conf 14422013655100100--55651244324--5-365568899999999999999999999984356674--33224487
Q gi|254780784|r 479 ISGDEDHLGHMDFKVAG--TDSGITAMQMD--M-KIGGISENIMVMALQQAKRGRLHILNEMSKVLSESR--LQLGEFTP 551 (699)
Q Consensus 479 I~G~ED~~GdMDFKvaG--T~~GiTa~QmD--i-K~~gi~~~il~~al~~A~~gr~~il~~m~~~~~~~~--~~~~~~ap 551 (699)
T Consensus 518 l~~l~~fl~~lG~~~~~~G~~~~~~P~~~~~~le~~~~~P~~~l~~~~---------lLRsM~qA~Ys~~N~GHFGLa~~ 588 (755)
T TIGR02063 518 LQNLREFLKELGLTLKGGGTSDKIQPKDLQKLLEKVKGRPEEELINTV---------LLRSMQQAKYSPENIGHFGLALE 588 (755)
T ss_pred HHHHHHHHHHCCCEECCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHH---------HHHHHHCCCCCCCCCCCHHHHHC
T ss_conf 999999998718154488888875869999999984088438999999---------99874113117678862104552
Q ss_pred EEEEEEECCCC---------EEEEECCCCHHHHHHH-------HHHCCEEEEECCEEEEEEECCHHHHHHHHHHHHHHC-
Q ss_conf 57999977115---------0000378607799899-------986888998088089999689899999999999852-
Q gi|254780784|r 552 RVEIMAIPPDQ---------IRNVIGMGGKVIRGIV-------EQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSIT- 614 (699)
Q Consensus 552 ~~~~~~i~~~k---------i~~~iG~gG~~ik~i~-------~~~~~~i~i~d~g~v~i~~~~~~~~~~a~~~i~~~~- 614 (699)
T Consensus 589 ~YtHFTSPIRRYPDL~VHRlik~~L~~~~~~~~~~~~l~~~~~~~~~~~l--~~~~-~h~S~~ERrA~~AERd~~d~kka 665 (755)
T TIGR02063 589 YYTHFTSPIRRYPDLIVHRLIKKALFKGENTTKEKETLTEYAKEYLEAKL--EEIA-EHSSKTERRADEAERDVNDWKKA 665 (755)
T ss_pred CCCCCCCCHHCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH--HHHH-HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 75445884210156899999999850788875034222245456427889--9999-86112112155312779999999
Q ss_pred --CCCCCCCEEEEEEEEEEECCEEEECCC-CCCEEEEEEECCCCC-----------CCCHHHHCCCCCEEEEEEEEECC-
Q ss_conf --475468678999999941536998287-971048866314445-----------47855603259889999997868-
Q gi|254780784|r 615 --DVPEVNKIYKGQVVKVMDFGAFVHFCG-ARDGLVHISQLSTER-----------VAKTSDVVKEGDTVWVKLLDFDD- 679 (699)
Q Consensus 615 --~~~e~g~~y~~~v~~i~~fGafve~~~-g~~gl~HiS~l~~~~-----------v~~~~d~~~~Gd~i~vk~~~~d~- 679 (699)
T Consensus 666 eyM~~~iG~~f~G~Is~VT~FG~FVeL~~~~ieGLVhI~~L~dDYY~Fd~~~~~L~G~R~gk~frLGD~v~V~V~~ad~~ 745 (755)
T TIGR02063 666 EYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLD 745 (755)
T ss_pred HHHHHCCCCEEEEEEEEEEEEEEEEEECCCEEEEEEECCCCCCCCCEECCCCCEEEEECCCCEEECCCEEEEEEEEECCC
T ss_conf 99985079688779975662013897367411102632789885630752207886432687372487489999996103
Q ss_pred CCCEEEEE
Q ss_conf 99866687
Q gi|254780784|r 680 RGKIKLSM 687 (699)
Q Consensus 680 ~g~i~lSr 687 (699)
T Consensus 746 ~~~idF~L 753 (755)
T TIGR02063 746 TGKIDFEL 753 (755)
T ss_pred CCEEEEEE
T ss_conf 36698997