HHsearch alignment for GI: 254780142 and conserved domain: cd02737
>cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain. Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Probab=100.00 E-value=0 Score=485.27 Aligned_cols=351 Identities=16% Similarity=0.109 Sum_probs=200.0
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEEEE-ECCCCCE--EEEECCCCEEEEECCC
Q ss_conf 101460211110078898776420245432221122024014876897211346-5178877--8974276046640677
Q gi|254780142|r 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRNVC-RNSTNDL--ISMGRNTTLQILDMSG 985 (1398)
Q Consensus 909 Ge~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~~~-~n~~~~~--i~vs~~~~~~i~d~~~ 985 (1398)
T Consensus 1 GE~VG~IAAQSIGEPaTQMTLnTFH~agts-------------~vpRlkEIl~~~~~~~~~~~t~~~~l~~~~~~~~~~~ 67 (381)
T cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSLESS-------------PLELLKEVLECRSKSKSKENDRRVILSLHLCKCDHGF 67 (381)
T ss_pred CCCCHHHHHHHCCCHHHCCCCCCCCCCCCC-------------CCHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCHHH
T ss_conf 972126676744727754112251336456-------------6277888863102678999873589840323320116
Q ss_pred CEEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEEC--CCCEEHHHHHCCCCCEEEEEEEHHHC
Q ss_conf 6000000110000135678553225078621354311320246368975312--78320012302368602677510110
Q gi|254780142|r 986 QEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLV--DGISVIESIGESTGIAKRKVIDWRFA 1063 (1398)
Q Consensus 986 ~~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~--~~~~~~~~~~~~t~~~~~~~i~~~~~ 1063 (1398)
T Consensus 68 e~~~~A~~Vk~~IE~ttL~div~~~~I~y~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~d~~~~ 147 (381)
T cd02737 68 EYERAALEVKNHLERVTLEDLATTSMIKYSPQATEAIVGEIGDQLNTKKKGKKKAIFSTSLKITKFSPWVCHFHLDKECQ 147 (381)
T ss_pred HHHHHHHHHHHHHHHEEHHHHHEEEEEEECCCCCCEEEECCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHEEEEECHHHH
T ss_conf 78999999998764137984010899999488662244031889998875555566776653313673021356405451
Q ss_pred CCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCCCHHHHHHHHHC
Q ss_conf 12212385347742778253224788420213778445413676135484222101320245543367732889887525
Q gi|254780142|r 1064 SRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARR 1143 (1398)
Q Consensus 1064 ~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GLPrV~eLFEar~ 1143 (1398)
T Consensus 148 ~--------------------~~~~~---------~-i~~~~~~~~---------------~~~------~~~~l~~l~~ 176 (381)
T cd02737 148 K--------------------LSDGP---------C-LTFSVSKEV---------------SKS------SEELLDVLRD 176 (381)
T ss_pred C--------------------CCCCC---------E-EEEEECCCC---------------CCH------HHHHHHHHHH
T ss_conf 0--------------------24563---------5-999836555---------------700------8999999999
Q ss_pred ---CC-CCCEECCCCCEEEEEE--EC------------CCCEEEEEEECCCCCCEEEEEECCCCEEE-EECCC--EEECC
Q ss_conf ---11-1101113478678633--12------------79449999836898402689813896589-84198--77408
Q gi|254780142|r 1144 ---PK-NHAILAEISGTIRIKR--NY------------KNKSRVVIEPFEDGVEPAEYFIPKNKHFY-LQDGD--HVEKG 1202 (1398)
Q Consensus 1144 ---pk-~~aiisei~Giv~i~~--~~------------~~k~~~vi~~~~~g~~~~e~~ip~~~~l~-v~dgd--~V~~g 1202 (1398)
T Consensus 177 ~i~~~ll~~~ikGi~~i~~v~i~~~~~~~~~~~~~~~~~~~~e~~l~v~~~~~~~----~~~~~~~~~v~~~cl~~ld~V 252 (381)
T cd02737 177 RIIPFLLETVIKGDERIKSVNILWEDSPSTSWVKSVGKSSRGELVLEVTVEESCK----KTRGNAWNVVMDACIPVMDLI 252 (381)
T ss_pred HHHHHHHCCEECCCCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEEEEEEECCCC----CCCCCHHHHHHHHCCCCCCCC
T ss_conf 9875652033458766556999840576543112334577754999998403433----014303566654121223443
Q ss_pred CEEECCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHH
Q ss_conf 64643899999998752799999999999999999809700612560124762861489418864545664106999999
Q gi|254780142|r 1203 DYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEE 1282 (1398)
Q Consensus 1203 d~lt~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~ 1282 (1398)
T Consensus 253 D~~RT~sn~i~ei~~~lGIEaar~~i~~e~~~~~~~~g~~v~~rHl~llad~mt~~G~~~~------i~r~G~~~~~--- 323 (381)
T cd02737 253 DWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVG------LNAKGYKAQR--- 323 (381)
T ss_pred CCCCCEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCEEE------EECCCCCCCC---
T ss_conf 5775230879999997709999999999999999852764218889898887335781677------5330201445---
Q ss_pred HHHHHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCH-HH
Q ss_conf 9999997289875201210000145302310776504025899999974528552366532215507305655354-66
Q gi|254780142|r 1283 LNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGA-IL 1360 (1398)
Q Consensus 1283 ~Nr~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~-f~ 1360 (1398)
T Consensus 324 ------------------------~sv~~~~pl~~asfe~t~~~l~~Aa~~~~~d~~~gvs~~i~~G~~~~~GTG~~Fd 378 (381)
T cd02737 324 ------------------------RSLKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSKFE 378 (381)
T ss_pred ------------------------CCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHCCCCCCCCCCCCEE
T ss_conf ------------------------5554468888854465999999999847977778989987659988888887641