HHsearch alignment for GI: 254780143 and conserved domain: pfam04561
>pfam04561 RNA_pol_Rpb2_2 RNA polymerase Rpb2, domain 2. RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Probab=100.00 E-value=2.3e-34 Score=265.39 Aligned_cols=177 Identities=31% Similarity=0.494 Sum_probs=142.3
Q ss_pred CCCCEEECCCCCCCCCCCCEEEEEEEECCCCCEEEEEECCCCEEEEEECCCCCHHHHHHHHHCCCCHH-HHHHHHCCCEE
Q ss_conf 27852120234651577856799998118872368997589829999718787039989988099847-99997387405
Q gi|254780143|r 159 RSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSE-EILSTFYPKIV 237 (1386)
Q Consensus 159 RSPGVyf~~~k~k~~~s~k~~ysa~IIP~RGSwLe~e~d~kd~iyvrIdr~rKIPi~ilLrALG~ssd-eIl~~f~~~~~ 237 (1386)
T Consensus 1 RSPGvy~~~~~~~~--~~~~~y~a~iip~rG~Wl~~e~d~~~~~~v~idr~~kiPi~ilLrALG~~sd~eIl~~i~~~~~ 78 (180)
T pfam04561 1 RSNGIYVEKELDKN--GIGATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREILDRLCYDFN 78 (180)
T ss_pred CCCCEEEECCCCCC--CCCCEEEEEEECCCCCCEEEEECCCCEEEEEECCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCC
T ss_conf 99946852243788--8851688999238987179998689879999778775239999999768988999998444420
Q ss_pred EEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCEEECCCCHHHHHHHHHHHHCCCCCCCCCHHHHCCCCCCCCCCCCCC
Q ss_conf 77306731023545666421012232112445845440221020799887876360001026677347410000136667
Q gi|254780143|r 238 YSQRGDFWCFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGET 317 (1386)
Q Consensus 238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l~~~~~~~~~~d~~~ 317 (1386)
T Consensus 79 ~~~~---------------------------------------------------------------------------- 82 (180)
T pfam04561 79 DPQM---------------------------------------------------------------------------- 82 (180)
T ss_pred CHHH----------------------------------------------------------------------------
T ss_conf 0778----------------------------------------------------------------------------
Q ss_pred CEEEEECCCCCCHHHHHHHHHCCCCCEEEEEECCCCCCCCCCHHHHCCCCCCHHHHHHHHHHHH--CCCCCCHHHHHHHH
Q ss_conf 7699962345998999999865654102442024445520000011023458899999988760--57763104568888
Q gi|254780143|r 318 GEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVM--RPGDVSTFSVAESM 395 (1386)
Q Consensus 318 gei~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~d~~~~~~eAl~~I~k~l--r~~~~~~~~~~~~~ 395 (1386)
T Consensus 83 ---------------~~---------------------~~~~~~~~~~~~~t~~~Al~~i~~~~~~~~~~~~~~~~a~~- 125 (180)
T pfam04561 83 ---------------LE---------------------LLKPELEEAENIYTQEEALDYIGKGFYLRRGEEPRLQRARE- 125 (180)
T ss_pred ---------------HH---------------------HHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHHH-
T ss_conf ---------------99---------------------98899987167899999999999884247899844999999-
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCCCCCCHHCCCCCCC
Q ss_conf 6202453023334555577765420366776770661899888898887630487643440101533233
Q gi|254780143|r 396 FNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVR 465 (1386)
Q Consensus 396 ~~~~~~~~~~y~l~~vgr~~~n~~l~~~~~~~~~~Lt~~d~~~~i~~L~~l~~g~~~~DdiDhlgnkRvr 465 (1386)
T Consensus 126 ---------------~l~~~ln~kLg~~~~~~~~~lt~~di~~~i~~Li~l~~g~~~~DDiDhlgNRRvR 180 (180)
T pfam04561 126 ---------------ILYSNLNKHLGLNEPFENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 180 (180)
T ss_pred ---------------HHHHHCCCCCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf ---------------9875031126888887765757999999999999985399999767665466689