HHsearch alignment for GI: 254781115 and conserved domain: TIGR01942

>TIGR01942 pcnB poly(A) polymerase; InterPro: IPR010206 This entry describes the pcnB family of poly(A) polymerases (also known as plasmid copy number protein). These enzymes sequentially add adenosine nucleotides to the 3' end of RNAs, targeting them for degradation by the cell , . This was originally described for anti-sense RNAs, but was later demonstrated for mRNAs as well . Members of this family are as yet limited to the gamma- and beta-proteobacteria, with putative members in the Chlamydiacae and spirochetes. This family has homology to tRNA nucleotidyltransferase.; GO: 0003723 RNA binding, 0004652 polynucleotide adenylyltransferase activity, 0006378 mRNA polyadenylation.
Probab=100.00  E-value=0  Score=463.13  Aligned_cols=224  Identities=31%  Similarity=0.531  Sum_probs=206.2

Q ss_pred             CCHHHHHHHHHHHHCCCEEEEEHHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHHCCCCEECCCCCCCEEEEEECCEEEE
Q ss_conf             99889999999997898599970699888778898608999808989999999876995621343144699998998886
Q gi|254781115|r   11 HDSDLINILSLLNKGEDKSCIVGGAVRDSLMNLSVQDIDIATTILPDRVMRIFSKTRYKVIPTSISYGTIKIICRKKYFD   90 (416)
Q Consensus        11 ~~~~~~~i~~~l~~~g~~~~~VGG~VRD~ll~~~~~DiD~~~~~~~~~~~~~~~~~~~~~~~~~~~~gt~~~~~~~~~~d   90 (416)
T Consensus        14 ~S~~A~~Vv~rL~~AGyqAY~VGG~vRDLlLG~ePKDFDv~T~A~PE~v~~LFRN~R--i--vGRRFrlvHv~fG~~iIE   89 (448)
T TIGR01942        14 FSAHALNVVRRLKKAGYQAYIVGGAVRDLLLGIEPKDFDVATSATPEEVKKLFRNSR--I--VGRRFRLVHVSFGRQIIE   89 (448)
T ss_pred             HHHHHHHHHHHHHHCCEEEEEECCHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHCCE--E--ECCCEEEEEEECCCCEEE
T ss_conf             649999999987007823767231587765479886442127896278998552055--6--404306888815880577


Q ss_pred             EECCCC---CCC-------C---CCCCC-CCCCCHHHHHHCCCCCCCCCCEEECCC-CHHHHHCCCHHHHHHHHHHHCCC
Q ss_conf             421344---667-------6---88743-223320133210447800300200032-10132000068887877764276
Q gi|254781115|r   91 ITTLRS---DLI-------T---DGRYA-KVVFTRDWKADSLRRDFTINALYADQQ-GKVIDYVGGLNDLRNRTIKFIGD  155 (416)
Q Consensus        91 i~~~R~---e~~-------~---~~~~~-~~~~~~~~~eDl~RRDFTINAla~~~~-~~l~Dp~gG~~DL~~~~ir~v~~  155 (416)
T Consensus        90 VaTFR~HHgE~~~Gda~~~~~na~Gri~~DN~YG~-~EEDA~RRDFT~NALYYDP~~e~I~Dy~gG~~Dlk~R~LR~IGD  168 (448)
T TIGR01942        90 VATFRSHHGEDDEGDAKKSSANAEGRILKDNVYGS-LEEDALRRDFTVNALYYDPSKEVILDYVGGVEDLKARRLRLIGD  168 (448)
T ss_pred             EECCCCCCCCCCCCCCHHCCCCCCCCEECCCCCCC-CCCCCCCCCCEECCEECCCCCCEEECCCCCHHHHHCCCCEECCC
T ss_conf             51225546888654210002288632333775301-01033335520421000753256750357678661781010178


Q ss_pred             CCCHHHCCCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf             43100104210033201220136433111100012333321022205776887886421101899999875300233468
Q gi|254781115|r  156 AHHRILEDYLRILRFFRFFAHYGEKNIDSDGLVASIKAKKGLKILSSERIWSEINKLLEAKNPLNAIVHMYNGGIFKEIF  235 (416)
Q Consensus       156 ~~~rf~EDpLRiLRa~RFasrlg~f~id~~t~~ai~~~~~~L~~iS~ERI~~El~KiL~~~~~~~~l~~L~~~gll~~if  235 (416)
T Consensus       169 p~~Ry~EDPVRmLRA~r~~~kl~-f~i~~~t~~pI~~s~~~L~~~p~aRlfeE~~KllfSG~~~~~f~~l~~~~l~~~Lf  247 (448)
T TIGR01942       169 PEERYQEDPVRMLRALRFSSKLE-FTIDEKTAEPIRESAPLLKKIPPARLFEEILKLLFSGKSAILFKMLSEYKLLEPLF  247 (448)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHH
T ss_conf             36531568578999999987722-67898999999998786227897714788999860424899999860565214643


Q ss_pred             CCCCC
Q ss_conf             87010
Q gi|254781115|r  236 LDVQE  240 (416)
Q Consensus       236 pel~~  240 (416)
T Consensus       248 P~~~~  252 (448)
T TIGR01942       248 PSVAK  252 (448)
T ss_pred             HHHHH
T ss_conf             89999