Query 002296
Match_columns 940
No_of_seqs 167 out of 1770
Neff 6.6
Searched_HMMs 46136
Date Thu Mar 28 20:54:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002296.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002296hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0216 RNA polymerase I, seco 100.0 8E-231 2E-235 1937.1 63.5 895 2-937 5-945 (1111)
2 PRK08565 DNA-directed RNA poly 100.0 9E-202 2E-206 1871.7 79.2 832 9-917 8-924 (1103)
3 KOG0214 RNA polymerase II, sec 100.0 1E-190 3E-195 1621.4 43.3 848 8-917 11-964 (1141)
4 KOG0215 RNA polymerase III, se 100.0 1E-181 3E-186 1527.3 37.3 840 9-917 53-979 (1153)
5 COG0085 RpoB DNA-directed RNA 100.0 1E-171 3E-176 1532.9 55.8 798 6-917 18-897 (1060)
6 cd00653 RNA_pol_B_RPB2 RNA pol 100.0 5E-164 1E-168 1505.5 59.4 656 15-936 1-718 (866)
7 TIGR02013 rpoB DNA-directed RN 100.0 1E-158 3E-163 1463.6 62.9 711 8-913 13-901 (1065)
8 PRK00405 rpoB DNA-directed RNA 100.0 6E-157 1E-161 1456.7 64.8 730 10-917 22-948 (1112)
9 CHL00001 rpoB RNA polymerase b 100.0 5E-154 1E-158 1416.1 61.2 749 7-929 7-899 (1070)
10 CHL00207 rpoB RNA polymerase b 100.0 1E-141 3E-146 1299.2 63.1 753 9-932 4-898 (1077)
11 PRK09603 bifunctional DNA-dire 100.0 2E-129 5E-134 1227.0 58.8 758 10-917 22-1156(2890)
12 PRK14844 bifunctional DNA-dire 100.0 9E-128 2E-132 1208.6 60.4 756 10-917 27-1149(2836)
13 PRK07225 DNA-directed RNA poly 100.0 2E-110 4E-115 983.3 35.7 382 516-917 4-426 (605)
14 TIGR03670 rpoB_arch DNA-direct 100.0 9E-111 2E-115 984.5 33.0 379 519-917 1-420 (599)
15 PRK09606 DNA-directed RNA poly 100.0 6.4E-97 1E-101 864.3 45.6 437 9-504 12-492 (494)
16 PF00562 RNA_pol_Rpb2_6: RNA p 100.0 1.2E-79 2.6E-84 697.4 16.5 272 639-917 1-304 (386)
17 PF04563 RNA_pol_Rpb2_1: RNA p 100.0 2.3E-36 5.1E-41 316.2 13.1 107 14-122 1-149 (203)
18 PF04565 RNA_pol_Rpb2_3: RNA p 99.9 1.8E-27 3.9E-32 204.7 4.9 67 407-473 1-68 (68)
19 PF04561 RNA_pol_Rpb2_2: RNA p 99.8 5.7E-22 1.2E-26 204.5 6.4 174 123-322 1-190 (190)
20 PF04566 RNA_pol_Rpb2_4: RNA p 99.5 1.6E-13 3.4E-18 116.3 9.2 63 519-590 1-63 (63)
21 PF06883 RNA_pol_Rpa2_4: RNA p 99.1 1.3E-10 2.7E-15 96.6 5.7 58 526-583 1-58 (58)
22 PF04567 RNA_pol_Rpb2_5: RNA p 98.4 1.5E-07 3.2E-12 75.7 2.3 40 595-634 7-48 (48)
23 COG0085 RpoB DNA-directed RNA 97.6 7.6E-05 1.6E-09 93.2 6.2 72 627-718 526-597 (1060)
24 KOG0215 RNA polymerase III, se 97.3 0.0001 2.2E-09 87.5 2.1 349 68-477 190-551 (1153)
25 PHA03394 lef-8 DNA-directed RN 95.8 0.012 2.5E-07 71.3 5.8 60 836-898 696-756 (865)
26 KOG0214 RNA polymerase II, sec 94.8 0.012 2.5E-07 71.7 1.4 236 651-904 681-934 (1141)
27 PF14251 DUF4346: Domain of un 50.3 7.7 0.00017 37.2 1.1 13 98-110 11-23 (119)
28 PF04941 LEF-8: Late expressio 47.1 23 0.00049 43.6 4.5 82 486-582 377-459 (748)
29 PF08763 Ca_chan_IQ: Voltage g 29.8 55 0.0012 24.8 2.6 30 893-932 1-30 (35)
30 PF13375 RnfC_N: RnfC Barrel s 26.1 1.9E+02 0.0042 27.2 6.2 52 784-840 45-96 (101)
31 PF13533 Biotin_lipoyl_2: Biot 21.6 57 0.0012 26.3 1.6 16 784-799 17-32 (50)
No 1
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription]
Probab=100.00 E-value=7.8e-231 Score=1937.08 Aligned_cols=895 Identities=52% Similarity=0.864 Sum_probs=840.5
Q ss_pred CCCCcCCccCchhhHHHHHHHHHHHHHHHHHHHH--------------------------------------------HH
Q 002296 2 ARKKSADFEPLRELVRHHIESFDYMLDEGLSEMF--------------------------------------------DH 37 (940)
Q Consensus 2 ~~~~~~~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii--------------------------------------------~e 37 (940)
|+.+-+.++.++.++++|++|||...+.||.... .|
T Consensus 5 ~~k~~p~fp~l~~a~~pHi~sfnal~~~gll~~~v~~~~ek~~~~~g~kis~~ve~i~iakP~l~~~~~ss~~r~lyPaE 84 (1111)
T KOG0216|consen 5 PPKDYPSFPELQDAASPHIDSFNALTNGGLLNAGVAGIAEKVPLKAGDKISMKVESIQIAKPMLSDKVHSSDTRKLYPAE 84 (1111)
T ss_pred CcccCccchhhhhhhhhhhccccchhhhhHHHHHhhchhhhcccccCCceeEEEEEEEecCCCCCccccccccccccchh
Confidence 5666777889999999999999999998887664 89
Q ss_pred HHHcCCeeeeEEEEEEEEEEecCCCceEeeEEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEE
Q 002296 38 CRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFR 117 (940)
Q Consensus 38 cR~r~~TYsa~l~v~i~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr 117 (940)
||+|++||+|.+.|+|.|.+| ++.+......+|.+||||+|++|||.|++++||++++|++.|+||||||||+|||||
T Consensus 85 cRqR~~TY~Gkl~v~v~wsVN--g~~~~~e~~dlG~vPIMlrSklChL~g~sp~eLV~hkEe~~EmGGYFIvNGIEKvIR 162 (1111)
T KOG0216|consen 85 CRQRGLTYKGKLVVRVSWSVN--GGHVVIEKRDLGHVPIMLRSKLCHLNGASPKELVKHKEESSEMGGYFIVNGIEKVIR 162 (1111)
T ss_pred HhhccceecceEEEEEEEEEC--CeeeeeeeeecCccceEEeccccccCCCChHHHhhccCchhhcCcEEEEcChHHhhh
Confidence 999999999999999999999 888888899999999999999999999999999999999999999999999999999
Q ss_pred EEEeccCCccEEEEeccccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHhhHHHhccCCC
Q 002296 118 SVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTN 197 (940)
Q Consensus 118 ~qi~~~~N~~~~~~r~~~~~~~~~~t~~~v~~rs~~~~~~s~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~s 197 (940)
++|+++||+|+++.|++|++||..||+|++++|||++|+++.+++|||+.||.+.++|.++|.+|.+|++++||||...|
T Consensus 163 mLIm~RRNHPiAiIR~Sfk~RG~~yS~yGVsmRcVReDqSsvtn~LHYLnnGtv~~~F~~rK~eylvPv~lILKAL~~ts 242 (1111)
T KOG0216|consen 163 MLIMPRRNHPIAIIRPSFKDRGSSYSDYGVSMRCVREDQSSVTNVLHYLNNGTVMFRFSHRKREYLVPVVLILKALTNTT 242 (1111)
T ss_pred hheeccCCCceEEechhhhhcCCCccccceEEEEeccccccceeEEEEecCCcEEEEEEEeeeeehhhHHHHHHHHhccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcccccchhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhccccccccCCCCccHHHHHHHHHHh
Q 002296 198 DLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRD 277 (940)
Q Consensus 198 D~eI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~i~t~~~al~yig~~fr~~~~~~~~~~~~~~~~~~L~~ 277 (940)
|+|||+.++ +++..++|+.++++.||+++++++++||++|++|||++||+++...+.+++.++|+++|++
T Consensus 243 DeEIf~~lv----------~g~~gdqfl~~rv~~mLr~v~ee~l~trtqcl~yLGs~FRaVl~~v~~~~D~evg~fILr~ 312 (1111)
T KOG0216|consen 243 DEEIFEGLV----------GGDEGDQFLTSRVELMLREVQEENLFTRTQCLQYLGSRFRAVLDFVPEQPDLEVGRFILRE 312 (1111)
T ss_pred HHHHHHHHh----------CCccCceeHHHHHHHHHHHHhhcccccHHHHHHHHhhhhhhhhcCCCCCchHHHHHHHHHh
Confidence 999999997 5777889999999999999999999999999999999999877755568999999999999
Q ss_pred HhccCCCCCcchHHHHHHHHHHHHHhcCCCCCCCCccccccceecccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCc
Q 002296 278 YIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKK 357 (940)
Q Consensus 278 ~ll~Hl~~~~~K~~~L~~MirkLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~ 357 (940)
+++.||+++.+||.+|++|+|||++++.|+|.+||+|+.+|||++++|+|++.+|+|++++|+..++.++++.+.+.+.+
T Consensus 313 ~VlvHLd~~~DKF~lLifmiqKL~slv~ge~~~dnpDs~q~qEil~~ghl~~~~LkEriEe~l~~~~~~vr~~l~~~~~~ 392 (1111)
T KOG0216|consen 313 YVLVHLDSDEDKFNLLIFMIQKLYSLVDGECTPDNPDSPQNQEILLPGHLYGSILKERIEEWLRFISAQVRRDLYKLGFK 392 (1111)
T ss_pred heEEEecccHHHHHHHHHHHHHHHHHhcCCcCCCCCCChhhhhcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999886667
Q ss_pred ccccchHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhhcccccCCccccccccc
Q 002296 358 FDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTS 437 (940)
Q Consensus 358 ~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSh~Rrv~rg~~~~~~K~t~ 437 (940)
.++.+..++++++.+.+ ..|+++|++||||||++++++++++|++|+|++|||+||+|||||||.||||++|++||+|+
T Consensus 393 ~~~~~~~~i~~~~~r~~-~~Ig~~me~fLsTGnl~s~sgldLqQ~sG~tv~AEriNf~RflShFRavhRGa~f~~mrTTt 471 (1111)
T KOG0216|consen 393 EDFLDISAIRKVFMRTN-GNIGRKMEYFLSTGNLVSRSGLDLQQTSGYTVVAERINFYRFLSHFRAVHRGAFFAEMRTTT 471 (1111)
T ss_pred chhHhHHHHHHHHhhcc-ccHHHHHHHHHhcCCeeeccchhhHhhcCcEEehhhhhHHHHHHHHHHHhcccchhheeehh
Confidence 77777778888888776 49999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCccccccCCCCCCccccccccccceeEEeeccCCCCcccccchhhHHHHHHHHhCCCeecCCccccCCCCcce
Q 002296 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVL 517 (940)
Q Consensus 438 vR~Lhps~wGfiCPveTPEG~~cGLvk~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~ 517 (940)
+|||.|++|||+||||||||+||||+||||..|+|++..++.+ .+.++|.++||.|... .... .+..|
T Consensus 472 vRKLlPEsWGFlCPVHTPDG~PCGlLnH~t~~c~I~t~~dd~s----------~ip~~L~~~Gm~p~~~-~~~~-G~~l~ 539 (1111)
T KOG0216|consen 472 VRKLLPESWGFLCPVHTPDGAPCGLLNHMTRTCRIVTRPDDVS----------FIPSILFELGMVPSSH-LVEA-GEPLY 539 (1111)
T ss_pred hHhhCchhhcccccccCCCCCchhHHHhhhhheeEeecCcchh----------hhhHHHHhcCCCchhc-cccC-CCcee
Confidence 9999999999999999999999999999999999999877653 3889999999998732 2222 23479
Q ss_pred EEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCCceEEecCCCceeceEEeccCCCCCCCc
Q 002296 518 SVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQN 597 (940)
Q Consensus 518 ~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~~d~gR~~RPv~~~~~~~~~~~~ 597 (940)
+|++||+++||++.+.+..+++.||++|...+..||.++||+||+.+.+++||++||+|++||++|||.+++.+ .
T Consensus 540 ~VlldGk~vG~~s~~~a~~i~~~lR~~Kv~~p~~iP~~leIg~Vp~s~~gqyPglyi~s~~aR~~RpV~nl~~~-----~ 614 (1111)
T KOG0216|consen 540 PVLLDGKVVGWVSSPLAKKIVDYLRYYKVEAPAVIPNDLEIGYVPTSTNGQYPGLYIFSGPARMIRPVKNLSLD-----S 614 (1111)
T ss_pred EEEECCEEEEeeccHHHHHHHHHHHHHhhcCcccCCCcceEeeeecCCCCCCceeEEecCchhhhhehhccccC-----c
Confidence 99999999999999999999999999999877789999999999999999999999999999999999999887 8
Q ss_pred eeeecccceeeeeeecCCCCCCCCCCCccceecccCCCccccceeecccCCCCCCCccchhhcccccccccccceeEEEe
Q 002296 598 IELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFR 677 (940)
Q Consensus 598 iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~ilsv~AslIPF~~HNqspRn~yq~~M~KQaig~~~~n~~~R 677 (940)
+||||++||++++||+.++++.+.. +||.|++|+.+||++|+||||+||||||||||||||+||+||+|.++|..|
T Consensus 615 ~e~iG~fEQvym~i~~~~~e~~~~v----~th~E~~pt~~ls~~anliP~sD~NQSPRNmYQCQMgKQtmg~p~~a~~~r 690 (1111)
T KOG0216|consen 615 VEWIGPFEQVYMNIAIDPKEIFPDV----TTHVELHPTGILSIVANLIPFSDHNQSPRNMYQCQMGKQTMGTPGHALRTR 690 (1111)
T ss_pred hhhcccHHHhhhhhccchhhcCCCc----ceeEEecccchHhHhhcCccccccCCCchhHHHhhhhhhhcCCccccchhc
Confidence 9999999999999999999998876 899999999999999999999999999999999999999999999999999
Q ss_pred ccCceeeccCCCeeeEeccceeecCCCCCCCCceeEEEEEeccCCCCCceEEEecchhccCcceeeEEEEEEEEeeccCC
Q 002296 678 ADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGN 757 (940)
Q Consensus 678 ~d~~~y~L~~~Q~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~ 757 (940)
+|+|+|+|++||.|+|++..|+.+++|++|.|+||+|||+|||||||||||||||+|+||||+++++||++.++|.++..
T Consensus 691 adnklYrlqt~qsP~vr~~~y~~y~~d~yp~GtNaiVAVisyTgyDMeDAmiiNK~s~eRGf~~G~vykte~i~L~~~~~ 770 (1111)
T KOG0216|consen 691 ADNKLYRLQTPQSPIVRPELYDTYGMDDYPNGTNAIVAVISYTGYDMEDAMIINKSSYERGFAYGTVYKTEKIDLSKKRS 770 (1111)
T ss_pred ccCceEEecCCCCceeecccccccccccCCCCcceEEEEEeecccChhhhhhhchhhhhccccceeEEeeeeechhhccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999876553
Q ss_pred CcCccceeecc-CCCChhhhcccCCCCCcccCcEecCCCcEEEEeecCCCcEEEeeccCCCcEEEEEEEEEecCCCCCce
Q 002296 758 KVDRGQKLFRR-NKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQ 836 (940)
Q Consensus 758 ~~~~~~~~~~~-~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~~~~~~~~~~~~~~~~~~e~g~V~~v~~~~~~~~~~~~ 836 (940)
+ ...|.. |..++ .++||+||+|.+|+++..||++++.++...++++..+|++.|+|+||.|++..++.|+..+
T Consensus 771 r----~~~F~~~p~~~~--~~~ld~dgLP~~G~kl~~~dp~~~y~d~~t~~~~~~~~~~~ep~~vd~vr~~~~~~~~~~k 844 (1111)
T KOG0216|consen 771 R----SKHFGRSPGEPE--LKKLDADGLPSIGQKLEYGDPYYAYFDEETGKTRIKKYHGTEPGIVDEVRVLGNDMGDQEK 844 (1111)
T ss_pred c----eeeeeeCCCCcc--ccccCCCCCCCCcccccCCCcEEEEEcccCCceEEEEecCCCCeeeEEEEEccccCCCccc
Confidence 2 445664 33333 7899999999999999999999999999999999999999999999999999998877668
Q ss_pred EEEEEEeeecCCCcccceeccCCCccEEeeeecCCCcCccCCCCCcCcEEeCCCCccccccHHHHHHHHHHHHHhhchhH
Q 002296 837 KANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVAYMENL 916 (940)
Q Consensus 837 ~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~G~~ 916 (940)
.+.|++|.+|+|.||||||||||||||||+.||.+||||| ++|++||||||||||||||||||++|+||||+||+||++
T Consensus 845 ~~~i~~Ri~R~p~IGDKFsSRhGQKGicS~~wP~~dmPFt-esGm~PDii~NPH~FPSRMTIgM~iEs~AgK~~alhG~~ 923 (1111)
T KOG0216|consen 845 CATITLRIPRNPIIGDKFSSRHGQKGICSQKWPTIDMPFT-ESGMVPDIIINPHAFPSRMTIGMLIESMAGKAGALHGNA 923 (1111)
T ss_pred eEEEEEEecCCCcccchhhhhccccccccccCCCCCCCcc-ccCcCcceeeCCCCCcccccHHHHHHHHhchhhcccccc
Confidence 8999999999999999999999999999999999999999 999999999999999999999999999999999999999
Q ss_pred HHHH-hhhhhhhHHHHHHhhhc
Q 002296 917 WMQH-HLQIQSRKLMEILGLMN 937 (940)
Q Consensus 917 ~~~~-~~~~~~~~~~~~~~~~~ 937 (940)
+|-- |.++.-..|++|||+|-
T Consensus 924 ~Datpf~~~E~~t~~dyfg~~L 945 (1111)
T KOG0216|consen 924 QDATPFIFSEENTAIDYFGEML 945 (1111)
T ss_pred ccCCceeecCcccHHHHHHHHH
Confidence 8332 22233334999999984
No 2
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=100.00 E-value=9.3e-202 Score=1871.74 Aligned_cols=832 Identities=28% Similarity=0.446 Sum_probs=726.2
Q ss_pred ccCchhhHHHHHHHHHHHHHHHHHHHH---------------------------------------HHHHHcCCeeeeEE
Q 002296 9 FEPLRELVRHHIESFDYMLDEGLSEMF---------------------------------------DHCRQAKISYTGKL 49 (940)
Q Consensus 9 ~~~~~~Lv~~hi~SFn~Fi~~gl~~ii---------------------------------------~ecR~r~~TYsa~l 49 (940)
+...++|++|||||||+|+++||++++ +|||+|++||+|+|
T Consensus 8 ~~~~~~Lv~~qidSFn~Fi~~gL~~iv~~~~pI~~~~~~~~L~f~~i~l~~P~~~~~~~~~~~l~P~ecR~r~lTYsa~l 87 (1103)
T PRK08565 8 YFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEIKEADGSERPITPMEARLRNLTYAAPL 87 (1103)
T ss_pred HhcccChHHHHHHHHHHHHHHhHHHHHHhcCCEEecCCCEEEEEEEEEECCCcccccccccCCCCHHHHHhcCCCcceEE
Confidence 456889999999999999999999998 89999999999999
Q ss_pred EEEEEEEEecCCCceEeeEEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeccCCccEE
Q 002296 50 MADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMS 129 (940)
Q Consensus 50 ~v~i~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~~ 129 (940)
+|+|++..+ +.+...+++++|+|||||+|++|||++++++|+++.||||+|+||||||||+|||||+||++++|+|++
T Consensus 88 ~v~i~~~~~--~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~p~D~GGYFIING~ERVI~~q~~~s~n~~~~ 165 (1103)
T PRK08565 88 YLTMIPVEN--GIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVLV 165 (1103)
T ss_pred EEEEEEEEC--CeeeEEEEEEeccCCeEeCCCcccCCCCCHHHHHhcCCCccCCCCeEEECCcEEEEEEEEecCCCEEEE
Confidence 999999765 555566789999999999999999999999999999999999999999999999999999999999988
Q ss_pred EEeccccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHhhHHHhccCCCHHHHHHHhcccc
Q 002296 130 MVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCY 209 (940)
Q Consensus 130 ~~r~~~~~~~~~~t~~~v~~rs~~~~~~s~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~eI~~~i~~~~ 209 (940)
+.+. ++..++.++..+ +.+. ..+.|+.++|+.+|.++++|... +++||+++||||||..||+||++.|..
T Consensus 166 ~~~~----~~~~~~~~a~i~-s~~~-~~~~~~~l~~~~~g~i~~~~~~~--~~~IPi~illkALG~~sD~eI~~~i~~-- 235 (1103)
T PRK08565 166 DKGE----AGSSITHTAKVI-SSRA-GYRAQVTVERRKDGTIYVSFPAV--PGKIPFVILMRALGLETDRDIVYAVSL-- 235 (1103)
T ss_pred EEec----CCCcceEEEEEE-eccC-CCcceEEEEEecCCeEEEEEcCc--ccEeeHHHHHHHcCCCCHHHHHHHhcc--
Confidence 7543 344455444444 4333 33468999999999999999854 457999999999999999999999962
Q ss_pred cchhhcccCCCCChhhHHHHHHHHHHHHhccc-ccHHHHHHHHhccccccccCCCCccHHHHHHHHHHhHhccCCCC---
Q 002296 210 DEKYKKEKGAVGSPLVSERVKIILAEVQDLSL-TTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLND--- 285 (940)
Q Consensus 210 ~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~i-~t~~~al~yig~~fr~~~~~~~~~~~~~~~~~~L~~~ll~Hl~~--- 285 (940)
+..+.+.+...+++. ..+ .|+++|+.|||++|++. .++.++.+.|+++|++++|||++.
T Consensus 236 ------------~~~~~~~l~~~l~~~--~~~~~t~~~al~~ig~~~~~~---~~~~~~~e~~~~~L~~~ll~Hig~~~~ 298 (1103)
T PRK08565 236 ------------DPEIQQELLPSLEQA--SSIAATVEDALDYIGKRVAIG---QPREYRIERAEQILDKYLLPHLGTSPE 298 (1103)
T ss_pred ------------cHHHHHHHHHHHHHh--hccccCHHHHHHHHHHhccCC---CCCccHHHHHHHHHHhhCcccCCCccc
Confidence 111122233333332 235 79999999999999863 345677899999999999999995
Q ss_pred -CcchHHHHHHHHHHHHHhcCCCCCCCCccccccceecccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccccchH
Q 002296 286 -NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLA 364 (940)
Q Consensus 286 -~~~K~~~L~~MirkLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~ 364 (940)
+..|+++|++|++||+.++.|.+.+||+|||+||||+++|+||+.+||+.|+++++.++..+.+.+++ ++.++
T Consensus 299 ~~~~K~~~L~~Mi~kLl~l~~g~~~~DD~D~l~NKRv~l~G~Ll~~~fr~~l~~~~~~ik~~l~~~~~~-~~~~~----- 372 (1103)
T PRK08565 299 DRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYAR-GRKLD----- 372 (1103)
T ss_pred chhHHHHHHHHHHHHHHhhhcCCCCCCCccccCCcEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-cccCC-----
Confidence 34799999999999999999999999999999999999999999999999999999999998877654 33222
Q ss_pred HHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhhcccccCCcccccccccccccCCC
Q 002296 365 NIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPE 444 (940)
Q Consensus 365 ~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSh~Rrv~rg~~~~~~K~t~vR~Lhps 444 (940)
+..+++ ++.||++|++|||||||.+ |++||||+|+|+||+|+|||||||+. ++.+++|.++||+||||
T Consensus 373 -~~~~i~---~~~It~~i~~~~sTGnw~~-------~~sGvSq~ldr~N~l~~lSh~Rrv~s-~~~r~~~~~~vR~Lhps 440 (1103)
T PRK08565 373 -LRAIVR---PDIITERIRHALATGNWVG-------GRTGVSQLLDRTNYLSTLSHLRRVVS-PLSRGQPHFEARDLHGT 440 (1103)
T ss_pred -HHHhcc---cchhhHHHHHHHhcCcccc-------CCcceEEecccCCHHHHHHHHhhccC-CcccCCCCccccccChh
Confidence 333443 3489999999999999975 67999999999999999999999986 46689999999999999
Q ss_pred CccccccCCCCCCccccccccccceeEEeeccCCCCcccccchhhHHHHHHHHhCCCeecCCccccCCCCcceEEEECCE
Q 002296 445 SWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGR 524 (940)
Q Consensus 445 ~wGfiCPveTPEG~~cGLvk~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~~V~lnG~ 524 (940)
||||+||+|||||++||||||||++|+|++..+.+ .|.++|.++|+.++. ++........++|||||+
T Consensus 441 ~wG~iCPveTPEG~~cGLv~~LA~~a~It~~~~~~-----------~i~~~l~~~G~~~~~-~~~~~~~~~~~~V~lnG~ 508 (1103)
T PRK08565 441 QWGRICPFETPEGPNCGLVKNLALMAQISVGVDEE-----------EVEEILYELGVVPVE-EAREEEYISWSRVYLNGR 508 (1103)
T ss_pred hccccCCCCCCCccccchhhhhhcccccccCCChH-----------HHHHHHHHcCCCchh-hcCcccCCCceEEEECCE
Confidence 99999999999999999999999999999876544 588999999998762 232223345699999999
Q ss_pred EEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCCceEEecCCCceeceEEeccCCCC-----------
Q 002296 525 VVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSE----------- 593 (940)
Q Consensus 525 ~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~~d~gR~~RPv~~~~~~~~----------- 593 (940)
|+|+++ ++..+++.||.+||+| .|+.++||.+++. +.+++|+||||+||++|||+++++++.
T Consensus 509 ~iG~~~--~~~~l~~~lR~~Rr~g--~i~~~v~I~~~~~---~~~~~i~I~sd~GRl~RP~~~v~~g~~~~~~~~~~~l~ 581 (1103)
T PRK08565 509 LIGYHP--DGEELAEKIRELRRSG--KISDEVNVAYIET---GEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLK 581 (1103)
T ss_pred EEEEEC--CHHHHHHHHHHHhhcC--CCCCeEEEEEccc---cccceEEEecCCceeeeeEEEEecCceeccHHHHHHhh
Confidence 999984 5899999999999998 6899999988753 568999999999999999999987642
Q ss_pred ----------CCCceeeecccceeeeeeecCCCCCCCCCCCccceecccCCCccccceeecccCCCCCCCccchhhcccc
Q 002296 594 ----------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMA 663 (940)
Q Consensus 594 ----------~~~~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~ilsv~AslIPF~~HNqspRn~yq~~M~ 663 (940)
..|.+||||++||++++||++++++... +||+||+|++|||++||+|||+||||||||||||||+
T Consensus 582 ~~~~~~~~l~~~g~iEyid~~Ee~~~~Ia~~~~~l~~~-----~th~Ei~p~~ilsv~asliPF~~hNqspRn~yq~~M~ 656 (1103)
T PRK08565 582 KGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPE-----HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMA 656 (1103)
T ss_pred ccccchhhHhhcCcEEeeCHHHhcCcEEeccccccCcc-----eeccccCCccccceeeeccCCcccCcccchhhhhhhh
Confidence 1479999999999999999999988554 7999999999999999999999999999999999999
Q ss_pred cccccccceeEEEeccCceeeccCCCeeeEeccceeecCCCCCCCCceeEEEEEeccCCCCCceEEEecchhccCcceee
Q 002296 664 KQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQ 743 (940)
Q Consensus 664 KQaig~~~~n~~~R~d~~~y~L~~~Q~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rG~~~~~ 743 (940)
|||||++++|+.+|.|++.|+|.|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|+||||||++
T Consensus 657 KQa~g~~~~n~~~r~d~~~~~l~~pQ~Plv~t~~~~~~~~~~~p~G~N~iVAv~sy~GYn~EDaiIink~s~~rG~~~s~ 736 (1103)
T PRK08565 657 KQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARST 736 (1103)
T ss_pred hcccccccccceEeecCCcceeecCceeEEEeccccccccccCCCCeeEEEEEEcccCcchHHhhhhhhhhhhcCCceEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEEEeeccCCCcCccceeeccC--CC----ChhhhcccCCCCCcccCcEecCCCcEEEEeecC-------------
Q 002296 744 IYQTETIDLSDDGNKVDRGQKLFRRN--KD----AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKT------------- 804 (940)
Q Consensus 744 ~~~~~~~~~~~~~~~~~~~~~~~~~~--~~----~~~~~~~ld~dGi~~~g~~v~~gd~l~~~~~~~------------- 804 (940)
+|++++++...... +..+.|+.| +. ....+++||+||+|++|++|++||||+||+++.
T Consensus 737 ~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdili~k~~p~~~~~~~~~~~~~~ 813 (1103)
T PRK08565 737 FFRTYETEERKYPG---GQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGL 813 (1103)
T ss_pred EEEEEEEEeeecCC---CCceEEecCCCcccccCchhhhhcCCCCCCcCCCcEEcCCCEEEEEecCCCCCcchhhccccC
Confidence 99999886533211 112345544 11 234579999999999999999999999998762
Q ss_pred -CCcEEEeeccCCCcEEEEEEEEEecCCCCCceEEEEEEeeecCCCcccceeccCCCccEEeeeecCCCcCccCCCCCcC
Q 002296 805 -TNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRP 883 (940)
Q Consensus 805 -~~~~~~~~~~~~e~g~V~~v~~~~~~~~~~~~~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dMPf~~~~G~~p 883 (940)
..++.+++++.+|+|+||+|.++.++++ .+.|+|++|+.|+|+||||||||||||||||++||+|||||| +||++|
T Consensus 814 ~~~~~~s~~~~~~e~g~V~~V~~~~~~~~--~~~vkv~ir~~R~p~iGDKfssRhGqKGv~s~i~~~edmPf~-~~G~~p 890 (1103)
T PRK08565 814 QERRDTSVTVRHGEKGIVDTVLITESPEG--NKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFT-EDGIVP 890 (1103)
T ss_pred CccccceEEecCCCceEEEEEEEEecCCC--cEEEEEEEEEEecCchhhhhhhhccCcceeeeecccccCCcC-CCCCCc
Confidence 2456688999999999999999987654 478999999999999999999999999999999999999999 999999
Q ss_pred cEEeCCCCccccccHHHHHHHHHHHHHhhchhHH
Q 002296 884 DLIINPHAFPSRMTIAMLLESVAAKVVAYMENLW 917 (940)
Q Consensus 884 DiI~NPh~~PSRMtiGql~E~~~gk~~~~~G~~~ 917 (940)
||||||||||||||||||+|+++||||+++|.+.
T Consensus 891 DiI~NPh~~PSRMtiG~l~E~~~gk~~~~~g~~~ 924 (1103)
T PRK08565 891 DLIINPHAIPSRMTVGQLLESIAGKVAALEGRFV 924 (1103)
T ss_pred cEEECCCCCcccccHHHHHHHHHHHHHHhcCcee
Confidence 9999999999999999999999999999999876
No 3
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=100.00 E-value=1.2e-190 Score=1621.43 Aligned_cols=848 Identities=28% Similarity=0.418 Sum_probs=735.1
Q ss_pred CccCchhhHHHHHHHHHHHHHHHHHHHH------------------------------------------------HHHH
Q 002296 8 DFEPLRELVRHHIESFDYMLDEGLSEMF------------------------------------------------DHCR 39 (940)
Q Consensus 8 ~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii------------------------------------------------~ecR 39 (940)
.+...++|+++|++|||.||+.++++|+ +|||
T Consensus 11 ~~f~ekglvrqQldsFdeFiq~~~qeiv~~~p~i~l~~~~qh~~~~~~r~~l~f~qiylskP~~~e~dg~~~~m~p~eAR 90 (1141)
T KOG0214|consen 11 AYFEEKGLVRQQLDSFDEFIQQTLQEIVADSPKIELQDEAQHTQENPARYQLFFEQIYLSKPTHTESDGSTSTMFPNEAR 90 (1141)
T ss_pred hhhcccchHHHHHHHHHHHHHHHHHHHHhcCCCceehhhhhhhccCccceEEEeeeEEEecccccccCCCccccCchhhH
Confidence 3567899999999999999999999998 8999
Q ss_pred HcCCeeeeEEEEEEEEEEecCC---CceEeeEEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEE
Q 002296 40 QAKISYTGKLMADVEFQYLDAG---SPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVF 116 (940)
Q Consensus 40 ~r~~TYsa~l~v~i~~~~~~~~---~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVI 116 (940)
+|++|||+||+|++...+..+. ...+...|+||+||||+||..|.|+++++++|.++||||+|+||||||||+|||+
T Consensus 91 lrnLTYSspLyVd~~k~~~~~~~~~~~~~~qkvfIGkIPiMlrS~~C~l~~~~d~dl~~l~eCp~DqgGyfIINGseKVl 170 (1141)
T KOG0214|consen 91 LRNLTYSSPLYVDATKIVKTSRDEVEDMQEQKVFIGKIPIMLRSSYCLLSGLTDKDLTELGECPYDQGGYFIINGSEKVL 170 (1141)
T ss_pred hhhcccccceEEEeEEEEeeccccccccccceeeEeccceeeehhhhhhcccchhhhhhccCCCcCCCceEEEcCceeee
Confidence 9999999999999998876433 2344678999999999999999999999999999999999999999999999999
Q ss_pred EEEEeccCCccEEEEeccccCCCCcceeeEEEEEeeecCCCce--EEEEEEEe-CC---eEEEEEEeecccccccHhhHH
Q 002296 117 RSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSV--TLKLYYLL-NG---SVRLGFWLQGKEYLLPVGIVL 190 (940)
Q Consensus 117 r~qi~~~~N~~~~~~r~~~~~~~~~~t~~~v~~rs~~~~~~s~--~~~l~y~~-~g---~~~l~~~~~~~~~~IPi~ilL 190 (940)
+.|+.++.|.+.+++. ..+.-.+|..++||+.+..++. ++.+..+. ++ .+...+++.|+ +|||+|||
T Consensus 171 IAQe~matn~vyvf~k-----~~p~~~ay~~EirS~le~~sR~~stl~v~~~ar~~~gq~i~~tlpyikq--eIPI~ilf 243 (1141)
T KOG0214|consen 171 IAQEKMATNIVYVFKK-----AHPGTYAYTGEIRSCLERSSRFISTLSVNMDARAGKGQEIIATLPYIKQ--EIPILILF 243 (1141)
T ss_pred eehhhccCceEEEEec-----CCCCceeEeeeeehhhhccCCCcceeeeeeccccCCCceEEEEeeeecc--cCcEEEEe
Confidence 9999999999888754 3334456778999976654443 33333333 33 34556666666 69999999
Q ss_pred HhccCCCHHHHHHHhcccccchhhcccCCCCChhhHHHHHHHHHHHHh-cccccHHHHHHHHhccccccccCCCCccHHH
Q 002296 191 KALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQD-LSLTTRLQCLQHIGEHFQPVIDGLQSESYYA 269 (940)
Q Consensus 191 kALg~~sD~eI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~-~~i~t~~~al~yig~~fr~~~~~~~~~~~~~ 269 (940)
||||+.+|+||+++|+ ||- +|. ++.+.+..++.+ .-+..++.||+|||++-.. .+..++..++
T Consensus 244 rALG~v~dreILehIc--Yd~---------~D~---em~e~lkpsieeafviq~qn~ALdfig~rga~--~Gvtkekri~ 307 (1141)
T KOG0214|consen 244 RALGFVSDREILEHIC--YDF---------DDA---EMFESLKPSIEEAFVIQEQNVALDFIGQRGAC--IGVTKEKRIK 307 (1141)
T ss_pred hhhcCCccHHHHHhhc--CCC---------CcH---HHHHHhhhhhhhhhhhhhhHHHHHHHHhcCCC--CCCCcchhhH
Confidence 9999999999999998 553 233 344444444443 2467788899999998432 1345677899
Q ss_pred HHHHHHHhHhccCCCCC----cchHHHHHHHHHHHHHhcCCCCCCCCccccccceecccchhHHHHHHHHHHHHHHHHHH
Q 002296 270 VAETVIRDYIFVHLNDN----NDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKK 345 (940)
Q Consensus 270 ~~~~~L~~~ll~Hl~~~----~~K~~~L~~MirkLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~ 345 (940)
+|+++|.+.+|||++.. ..|++||+||+++|+.++.|++.+||+||++|||++++|+||+.+||..|+++++++.+
T Consensus 308 yakdiLqKe~lPhi~~~e~~etkKA~fLGYmi~rlll~aLgRr~~ddRDHfG~KRLDlaGpLLa~lfR~lf~~l~rd~~~ 387 (1141)
T KOG0214|consen 308 YAKEILQKELLPHVGLGEICETKKAYFLGYMVHRLLLAALGRRELDDRDHFGNKRLDLAGPLLAKLFRSLFAKLLRDVTR 387 (1141)
T ss_pred HHHHHHHHHhccccccchhhhhhHHHHHHhhHHHHHHHHcCCCCccchhhccccchhhchhHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999954 48999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcCCcccccchHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhhcccc
Q 002296 346 LIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVH 425 (940)
Q Consensus 346 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSh~Rrv~ 425 (940)
..++.+.+ ++.+++. -++ ..+.||++++|+||||||+.+.. .+..++||||||+|+||+++|||+||++
T Consensus 388 ~mQk~le~-~~dfni~------~ai---ka~iIt~gl~yslaTgnwgdq~k-a~~~ragVsQVLnR~t~~sTLsHlRR~n 456 (1141)
T KOG0214|consen 388 YMQKCLEN-GVDFNIE------LAI---KAKIITNGLNYALATGNWGDQKK-AMQGRAGVSQVLNRLNPLSTLSHLRRTN 456 (1141)
T ss_pred HHHHHHhc-CccceEE------EEE---EeeeecccceeeeccCCccchhH-HhhccccHHHHhccccHHHHHHHHhhcC
Confidence 99999987 4433332 123 24589999999999999986543 4679999999999999999999999999
Q ss_pred cCCcccccccccccccCCCCccccccCCCCCCccccccccccceeEEeeccCCCCcccccchhhHHHHHHHHhCCCeecC
Q 002296 426 RGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSL 505 (940)
Q Consensus 426 rg~~~~~~K~t~vR~Lhps~wGfiCPveTPEG~~cGLvk~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~~g~~~~~ 505 (940)
. +..+++|...||+|||||||++||+|||||++||||||||+||.|+++..+. .|.++|.++|++.+
T Consensus 457 ~-Pigr~GKlAkpRqlHnthwGmvCPaeTPEGqacGLVKNLSLmayIsvGS~~s-----------Pi~EfLeewgmE~l- 523 (1141)
T KOG0214|consen 457 S-PIGRTGKLAKPRQLHNSHWGMVCPAETPEGQACGLVKNLSLMAYISVGSLES-----------PIVEFLEEWGMENL- 523 (1141)
T ss_pred C-ccccccccCCccccCcccceeeccccCCCcceeeccccceEEEEEecCCCcc-----------HHHHHHHHhchhhH-
Confidence 4 5568999999999999999999999999999999999999999999887655 49999999999988
Q ss_pred CccccCCCCcceEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCCceEEecCCCceeceE
Q 002296 506 PKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPV 585 (940)
Q Consensus 506 ~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~~d~gR~~RPv 585 (940)
.++..+...+.++||+||.|+|.+ .+++.+++.||.+||.. .++. |++.+ ++...++++||||+||.+||+
T Consensus 524 e~~~ps~~~datkvfvNG~wvGlh--rdp~~l~~tlr~lRR~~--di~~--Evs~v---RDIr~kE~ri~tDaGR~~rPL 594 (1141)
T KOG0214|consen 524 EEISPSPSPDATKVFVNGVWVGLH--RDPEELVATLKRLRRQF--DIIA--EVSMV---RDIRDKEIRIFTDAGRSLRPL 594 (1141)
T ss_pred hhcCCCcCCCceEEEEcccEEEec--CCHHHHHHHHHHHHHhh--ccch--hhhhh---ccccccceeeeeccCccccce
Confidence 457777778889999999999995 67899999999999986 3333 55555 345678999999999999999
Q ss_pred EeccCCCC------------------------CCCceeeecccceeeeeeecCCCCCCCCCCCccceecccCCCccccce
Q 002296 586 RNISLPSE------------------------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVV 641 (940)
Q Consensus 586 ~~~~~~~~------------------------~~~~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~ilsv~ 641 (940)
+.+++.+. ..|.+||||++|++.++||+.++++......+.||||||||+.|||++
T Consensus 595 liven~~l~~~k~hi~~L~~~~~~~~~w~~lv~~G~ie~idteeEEtvmiam~~~dL~~~~~~~~~THCEiHpsmILgv~ 674 (1141)
T KOG0214|consen 595 LIVENAKLLIKKRHIRALKQSKPNEYRWAHLLSSGEVEYIDTEEEETVMIAMGPKDLAESAYPKTYTHCEIHPSMILGVC 674 (1141)
T ss_pred EEEechhhhhhhHHHHHHhhCchhhcchhhhccccceeeeccchhhhHHHhcCHHHHhhccCCcccccccccHHHhhhhc
Confidence 99988732 258999999999999999999999977444566999999999999999
Q ss_pred eecccCCCCCCCccchhhcccccccccccceeEEEeccCceeeccCCCeeeEeccceeecCCCCCCCCceeEEEEEeccC
Q 002296 642 ANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTG 721 (940)
Q Consensus 642 AslIPF~~HNqspRn~yq~~M~KQaig~~~~n~~~R~d~~~y~L~~~Q~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~G 721 (940)
||+||||||||||||+||++|+|||||.+.+|+..|.|+..|.|+|||+|+|+|+.+++..+.++|+|+|++||++||+|
T Consensus 675 asiIpFpdh~qspr~tYQsa~~kqamg~y~tn~~vR~dtl~~~l~ypqkpl~tt~~~e~l~~~eL~aG~NaiVAi~~~~G 754 (1141)
T KOG0214|consen 675 ASIIPFPDHNQSPRNTYQSAMGKQAMGVYHTNPQVRMDTLAKVLYYPQKPLVTTRAMEYLRFRELPAGQNAIVAIACYSG 754 (1141)
T ss_pred eeeeecCCCCCchHHHHHHHHhhhcceeeeecchhhhhhhhhcccccccchhhHHHHhhhhhhhcccccceEEEEecccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCceEEEecchhccCcceeeEEEEEEEEeeccCCCcCccceeeccCCC------ChhhhcccCCCCCcccCcEecCCC
Q 002296 722 YDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKD------AKSLHSVIDSDGLPYVGQMIHPGE 795 (940)
Q Consensus 722 yn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~ld~dGi~~~g~~v~~gd 795 (940)
||||||||+|+++++||||++.+|++|+.+. ... .....+.|+.|.. ....+++||+||++.+|++|..||
T Consensus 755 YNqEDsvimn~s~v~rg~FrS~~~RsYk~q~--~~~-~~~~ee~~~~~~~~~~~~mr~~~~dkLdddG~i~~G~~vs~~D 831 (1141)
T KOG0214|consen 755 YNQEDSVIMNQSSVDRGLFRSFFIRSYKDQE--HKK-DQGPEEIFEEPPRGEGRGMRNGKYDKLDDDGIIMPGSRVSGGD 831 (1141)
T ss_pred ccHHHHHHHHhhhhhcchhhhhhhhHHHhhh--hhc-ccccccccccccccccccccccccccccccCCccccceeecCC
Confidence 9999999999999999999999999998642 111 2234556666643 234578999999999999999999
Q ss_pred cEEEEeecCC--------------CcEEEeeccCCCcEEEEEEEEEecCCCCCceEEEEEEeeecCCCcccceeccCCCc
Q 002296 796 PYCSIYDKTT--------------NSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQK 861 (940)
Q Consensus 796 ~l~~~~~~~~--------------~~~~~~~~~~~e~g~V~~v~~~~~~~~~~~~~v~i~~r~~R~p~iGDKf~sRHGqK 861 (940)
|++||..+.. +++.++.++.+|.|+||+|.++.|.+ +.+.++|++|+.|.|++|||||||||||
T Consensus 832 v~iGk~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~Givd~V~vt~n~~--G~kF~kv~vr~~ripqiGDKfasrHgqK 909 (1141)
T KOG0214|consen 832 VLIGKTTPQPAKEDESGPEDRLYTKRDHSTKLRHTERGIVDQVWVTKNSE--GPKFVKVRVRQVRIPQIGDKFASRHGQK 909 (1141)
T ss_pred EEeccccCCcccchhccccccccccccceeecccCCcceEEEEEEecCCC--CCceeEEEEeecccccccchhccccccC
Confidence 9999966421 23558888999999999999998775 4588999999999999999999999999
Q ss_pred cEEeeeecCCCcCccCCCCCcCcEEeCCCCccccccHHHHHHHHHHHHHhhchhHH
Q 002296 862 GVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVAYMENLW 917 (940)
Q Consensus 862 Gvvs~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~G~~~ 917 (940)
||||.++++|||||| .+|++|||||||||||||||||||+||++||++|+.|+-.
T Consensus 910 G~ig~~~~qedmpft-~eGi~pDiiiNPhaiPSRmtig~liEc~lgk~~a~~~e~~ 964 (1141)
T KOG0214|consen 910 GTIGITYRQEDMPFT-IEGIVPDIIINPHAIPSRMTIGQLIECLLGKVAAYEGEEG 964 (1141)
T ss_pred ccccceeecCCCCcc-ccCCCcceEECcccCccccchhhhHHHhhhhhhhcccccc
Confidence 999999999999999 9999999999999999999999999999999999998765
No 4
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=100.00 E-value=1.4e-181 Score=1527.30 Aligned_cols=840 Identities=28% Similarity=0.454 Sum_probs=730.5
Q ss_pred ccCchhhHHHHHHHHHHHHHHHHHHHH-----------------------------------------HHHHHcCCeeee
Q 002296 9 FEPLRELVRHHIESFDYMLDEGLSEMF-----------------------------------------DHCRQAKISYTG 47 (940)
Q Consensus 9 ~~~~~~Lv~~hi~SFn~Fi~~gl~~ii-----------------------------------------~ecR~r~~TYsa 47 (940)
+...+|||+||++|||||++++++.|+ +|||+|++||+|
T Consensus 53 flkvkglvkqhldsfnyfv~~~ik~iv~an~~itsd~dp~fylky~dirvg~Ps~~~~~~~~~~~i~p~ecrlrd~tysa 132 (1153)
T KOG0215|consen 53 FLKVKGLVKQHLDSFNYFVDVDIKKIVKANQLITSDVDPSFYLKYLDIRVGKPSIEEGNNVTNDNITPHECRLRDMTYSA 132 (1153)
T ss_pred HHhhhhHHHHHHhhhhhhhhhhHHHHHHhhcccCcCcCchhhheeeeeeccCcchhhccccccccCCchheeehhhhccc
Confidence 456899999999999999999999998 899999999999
Q ss_pred EEEEEEEEEEecCCCceEeeEEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeccCCcc
Q 002296 48 KLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYP 127 (940)
Q Consensus 48 ~l~v~i~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~ 127 (940)
|++|+++++.+ ...+.+.+|.||++|||++|++|+|++.++.++++.+|||.|||||||++|.||||..|++.+.|++
T Consensus 133 ~i~vdieytrg--~~~~~~~~v~igrmpimlrs~rcvl~~~~e~~~a~~~ecpldpggyfiv~G~ekViLiqeqlsknri 210 (1153)
T KOG0215|consen 133 PIYVDIEYTRG--RQIIAKRDVIIGRMPIMLRSSKCVLRGKDEEELARLNECPLDPGGYFIVKGTEKVILIQEQLSKNRI 210 (1153)
T ss_pred ceeEEEEEecC--cceEEecccccccchhhhhccccccCCccHHHHHHhccCCCCCCceeEeccceeEEEehhhhhccCe
Confidence 99999999876 5566688999999999999999999999999999999999999999999999999999999999998
Q ss_pred EEEEeccccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHhhHHHhccCCCHHHHHHHhcc
Q 002296 128 MSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTC 207 (940)
Q Consensus 128 ~~~~r~~~~~~~~~~t~~~v~~rs~~~~~~s~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~eI~~~i~~ 207 (940)
++- . .+++. +.+...|+.....|+|..+ .++|..+++.... ..+||++++|||+|..+|+||.+.++.
T Consensus 211 i~~-~---~k~~~----~~~svtsst~e~kskt~v~--~k~~k~ylk~~~~--~d~ipiviv~ka~g~~sd~ei~~~vg~ 278 (1153)
T KOG0215|consen 211 IVE-E---DKKGN----LQASVTSSTHERKSKTYVT--TKKGKYYLKHNSF--TDDIPIVIVLKAMGLESDQEIVQLVGG 278 (1153)
T ss_pred eec-c---ccCCc----cccccccceeeecceEEEE--eccceeeeehhhh--hccCCEEEEEeeccccchHHHHHHhhc
Confidence 763 1 12332 2344456555666666666 6788877766533 237999999999999999999999972
Q ss_pred cccchhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhccccccccCCCCccHHHHHHHHHHhHhccCCC---
Q 002296 208 CYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLN--- 284 (940)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~i~t~~~al~yig~~fr~~~~~~~~~~~~~~~~~~L~~~ll~Hl~--- 284 (940)
+.++.+....+++++...+++|+.+||+|++.+.+... +...+..+.|..+|...+++|++
T Consensus 279 --------------~~~y~~~~~~s~ee~~~~~v~tqqqal~y~~~kvk~~~--~t~~~~~~e~~~~l~~~~lahv~v~~ 342 (1153)
T KOG0215|consen 279 --------------DSKYQDIFAPSLEECVSLGVYTQQQALEYIGSKVKVKR--GTTPTKDEEALEVLSTTVLAHVPVPD 342 (1153)
T ss_pred --------------chHHHHhhccchhhhhhhhhHHHHHHHHHhhheEEecc--CCCCCchHHHHHHHHhhheeceeccC
Confidence 34566777788999999999999999999999887543 33456678899999999999997
Q ss_pred -CCcchHHHHHHHHHHHHHhcCCCCCCCCccccccceecccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccccch
Q 002296 285 -DNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNL 363 (940)
Q Consensus 285 -~~~~K~~~L~~MirkLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~ 363 (940)
++..|+.|++.|+|+++.+..+.-..||+|+++|||++++|+|++.+|++.|+.++.++++.+.+.+.++.+...++-.
T Consensus 343 ~~~r~K~~yi~~m~rr~~~a~l~~~~~ddrd~~gnkrlelagqllsllfeD~fk~~n~e~k~~~dk~l~k~~ra~~fD~~ 422 (1153)
T KOG0215|consen 343 LNFRMKAIYIGLMVRRVIQAMLNKLAMDDRDYVGNKRLELAGQLLSLLFEDLFKRFNSELKKNIDKILKKPIRAQEFDAL 422 (1153)
T ss_pred CCCcceeehHHHHHHHHHHHHhCcccccchhhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhhhhhHHH
Confidence 5679999999999999999999999999999999999999999999999999999999999999988875554333222
Q ss_pred HHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhhcccccCCcccccccccccccCC
Q 002296 364 ANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLP 443 (940)
Q Consensus 364 ~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSh~Rrv~rg~~~~~~K~t~vR~Lhp 443 (940)
..+. . ..+.||++|.+++|||||..++ |.|.+.|++|||+|++|++.|..+.|++. +|.+++|..+||.|+|
T Consensus 423 ~~~n--~---~~~~it~~l~ra~stgnw~iKr--frmer~gvt~VlsrlSyisaLgmmtri~s-~fektrkvsgprSlq~ 494 (1153)
T KOG0215|consen 423 KHLN--V---RANMITSGLERAISTGNWSIKR--FRMERAGVTQVLSRLSYISALGMMTRINS-QFEKTRKVSGPRSLQP 494 (1153)
T ss_pred HHHH--H---HHHHHHHHHHHHhhcCchHHHH--hhhhhccceeeehhhhhhhhhhhheehhh-hheeehhccCccccCh
Confidence 2221 1 1347999999999999998864 67999999999999999999999999995 7889999999999999
Q ss_pred CCccccccCCCCCCccccccccccceeEEeeccCCCCcccccchhhHHHHHHHHhCCCeecCC-ccccCCCCcceEEEEC
Q 002296 444 ESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLP-KLVKSGPPAVLSVLLD 522 (940)
Q Consensus 444 s~wGfiCPveTPEG~~cGLvk~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~~g~~~~~~-~~~~~~~~~~~~V~ln 522 (940)
||||++||+|||||+.|||+||||++++|+++.+.+ .+...+..+|++.+.. .......++.+.||||
T Consensus 495 sqwgmlcp~dtpegeacglvknlalmthittd~ee~-----------pi~~~~~k~gv~di~~v~~~e~~~~~~~~v~Ln 563 (1153)
T KOG0215|consen 495 SQWGMLCPSDTPEGEACGLVKNLALMTHITTDSEEK-----------PILKLCYKLGVEDIHVVSGRELHTPDSFLVFLN 563 (1153)
T ss_pred hhcccccCCCCCCccccccccchHHHhcccCCCCcc-----------hhHHHHHHhcceeeeeecccccCCCceEEEEec
Confidence 999999999999999999999999999999987666 4889999999987621 1122334567999999
Q ss_pred CEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCCceEEecCCCceeceEEeccCCCC---------
Q 002296 523 GRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSE--------- 593 (940)
Q Consensus 523 G~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~~d~gR~~RPv~~~~~~~~--------- 593 (940)
|.++|.+ ..++.|+..+|.+||+| .|.. |++.+.+.....++|-||.||.|||++.+.++.+
T Consensus 564 g~iig~~--~~~~~~v~~~r~lrr~G--~i~~-----fvsv~~~~~q~~v~i~sdggr~crp~Iiv~~~~~~v~~~h~~e 634 (1153)
T KOG0215|consen 564 GLIIGIT--RRPQYFVNSFRRLRRKG--KIGE-----FVSVFTNTTQRCVYIASDGGRVCRPLIIVDNGRPRVKQHHMDE 634 (1153)
T ss_pred ceeeccc--cchHHHHHHHHHHHHcC--cccc-----eeeeeeeeeeEEEEEecCCCeEeeeEEEEeCCcchhhhhhHHH
Confidence 9999997 46789999999999999 4544 5555555556789999999999999999987743
Q ss_pred ------------CCCceeeecccceeeeeeecCCCCCCCCCCCccceecccCCCccccceeecccCCCCCCCccchhhcc
Q 002296 594 ------------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQ 661 (940)
Q Consensus 594 ------------~~~~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~ilsv~AslIPF~~HNqspRn~yq~~ 661 (940)
..|.|||+|.+|++.++||+.++++.++ +||+||.|..+||++|+|||||+|||||||+|||+
T Consensus 635 l~~g~r~F~DFl~~glvEYLDVNEEND~~Ialye~~I~~~-----TTHLEIEPFTiLGv~AGLIPYPHHNQSPRNTYQCA 709 (1153)
T KOG0215|consen 635 LLDGKRTFDDFLKDGLIEYLDVNEENDSLIALYEEDIGPE-----TTHLEIEPFTILGVVAGLIPYPHHNQSPRNTYQCA 709 (1153)
T ss_pred HHHhhhhHHHHHHhchhheeecccccCceEEechhhcCCC-----cceeeecchhhhhhhccccCCCCCCCCCcchhhhh
Confidence 2589999999999999999999999987 89999999999999999999999999999999999
Q ss_pred cccccccccceeEEEeccCceeeccCCCeeeEeccceeecCCCCCCCCceeEEEEEeccCCCCCceEEEecchhccCcce
Q 002296 662 MAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCH 741 (940)
Q Consensus 662 M~KQaig~~~~n~~~R~d~~~y~L~~~Q~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rG~~~ 741 (940)
|+|||||..++|+..|.|+.+|.|.|||+|+|+|++.+..+++++|+||||.||||||+|||+|||+|+||+|+||||+|
T Consensus 710 MGKQAmG~IaYNQ~~RiDtlmYll~YPq~PmVkTKTIELi~ydKLPAGQNAtVAVMSYSGYDIEDALVLNKsSlDRGfGR 789 (1153)
T KOG0215|consen 710 MGKQAMGAIAYNQKKRIDSLLYLLVYPQRPMVKTKTIELINYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGR 789 (1153)
T ss_pred hhhhhhhhhhhhhhhhHHHHHHHHhcCCCccccceeEEeeccccCCCCCccEEEEEeccCCchhhhhhcccchhccCcce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEEEEEEEEeeccCCCcCccceeeccC----CC--ChhhhcccCCCCCcccCcEecCCCcEEEEeecC-----------
Q 002296 742 GQIYQTETIDLSDDGNKVDRGQKLFRRN----KD--AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKT----------- 804 (940)
Q Consensus 742 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~--~~~~~~~ld~dGi~~~g~~v~~gd~l~~~~~~~----------- 804 (940)
+.+||..+..+....+. . -+.+.-| +. +--..+.||+|||..||..|++|+|++.|--|.
T Consensus 790 C~Vyk~~~~~~kkY~N~--T-~Drimgp~~d~~t~kpi~kh~vLd~DGl~~pG~~V~~~qi~iNK~mP~vt~~~~~~~~~ 866 (1153)
T KOG0215|consen 790 CEVYKKTTTTLKKYANG--T-FDRIMGPQLDPNTRKPIWKHQVLDDDGLATPGERVQPGQIYINKQMPTVTGTSLPGLSA 866 (1153)
T ss_pred EEEEeeeeeeeeecCCC--c-hhhhcccccCCCcCCcchhhcccCcccCCCCccEeccCcEEEeccCCCcccccCCCCCc
Confidence 99999988766433321 0 1111112 22 112357899999999999999999999992211
Q ss_pred ---CCcEEEeeccCCCcEEEEEEEEEecCCCCCceEEEEEEeeecCCCcccceeccCCCccEEeeeecCCCcCccCCCCC
Q 002296 805 ---TNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGM 881 (940)
Q Consensus 805 ---~~~~~~~~~~~~e~g~V~~v~~~~~~~~~~~~~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dMPf~~~~G~ 881 (940)
..+..+..|++.++++||+|.++.+++ +...+|+-+|++|+|++|||||||||||||||.|++||||||. ..||
T Consensus 867 ~~~~Yk~~pitykgpepsyidkVmls~n~~--dq~LIK~llRQTRrPElGDKFSSRHGQKGVcGlIv~QEDMPFn-D~GI 943 (1153)
T KOG0215|consen 867 SQVQYKAVPITYKGPEPSYIDRVMLTSNDE--DQFLIKVLLRQTRRPELGDKFSSRHGQKGVCGLIVQQEDMPFN-DQGI 943 (1153)
T ss_pred cccccccccceecCCCcchhheeEeecCcc--ccHHHHHHHhhccCcccccccccccCCCceeeEEeeccCCCCc-ccCC
Confidence 134558899999999999999999865 3456999999999999999999999999999999999999999 9999
Q ss_pred cCcEEeCCCCccccccHHHHHHHHHHHHHhhchhHH
Q 002296 882 RPDLIINPHAFPSRMTIAMLLESVAAKVVAYMENLW 917 (940)
Q Consensus 882 ~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~G~~~ 917 (940)
+|||||||||||||||||.++|.++||||.+.|.+.
T Consensus 944 cPDiIMNPHGFPSRMTVGK~iELlsGKAGVl~G~~h 979 (1153)
T KOG0215|consen 944 CPDIIMNPHGFPSRMTVGKMIELLSGKAGVLEGTFH 979 (1153)
T ss_pred CcccccCCCCCcccchHHHHHHHhccccceeeeeEe
Confidence 999999999999999999999999999999999885
No 5
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=100.00 E-value=1.5e-171 Score=1532.88 Aligned_cols=798 Identities=24% Similarity=0.332 Sum_probs=674.0
Q ss_pred cCCccCchhhHHHHHHHHHHHHHHHHHHHH------------------------------HHHHHcCCeeeeEEEEEEEE
Q 002296 6 SADFEPLRELVRHHIESFDYMLDEGLSEMF------------------------------DHCRQAKISYTGKLMADVEF 55 (940)
Q Consensus 6 ~~~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii------------------------------~ecR~r~~TYsa~l~v~i~~ 55 (940)
-+.+..+++|+++|++|||+|+.+||++++ .|||+|++||+|||+|++++
T Consensus 18 i~~~~~~p~Lv~~QldSyn~ff~~gLq~i~~~i~PI~~~~~~~~Lef~~~~l~~p~k~~p~EcR~R~lTYsapLyv~lrl 97 (1060)
T COG0085 18 IPEFLDLPNLVEIQLDSYNAFFLEGLQEVFREIFPIESYNGNTELEYGSYRLGEPPKFYPEECRLRGLTYSAPLYVKLRL 97 (1060)
T ss_pred cccccCCccHHHHHHHHHHHHHHHHHHHHHHhcCceecCCCCEEEEEEEEEecCCCCCCHHHHHhcCCccccceEEEEEE
Confidence 345678999999999999999999999999 89999999999999999999
Q ss_pred EEecCCCceEeeEEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeccCCccEEEEeccc
Q 002296 56 QYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSF 135 (940)
Q Consensus 56 ~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~~~~r~~~ 135 (940)
.++..+..++.++|++|+||+||+ ||||||||+||||++|++++||.+|..+..+.
T Consensus 98 v~~~~~e~~k~~eV~iG~iPlMt~------------------------gGyFIINGsERVIVsQ~~rSPgvif~~~~~k~ 153 (1060)
T COG0085 98 VVNETGEEIKEQEVYMGDIPLMTR------------------------GGYFIINGTERVIVSQEHRSPGVIFVEKKDKT 153 (1060)
T ss_pred EECCcccccccceEEeccCcEecC------------------------CcEEEECCeEEEEEEEeecCCCeEEecccccC
Confidence 887322226688999999999998 99999999999999999999997766433211
Q ss_pred cCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHhhHHHhccCCCHHHHHHHhcccccchhhc
Q 002296 136 RDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKK 215 (940)
Q Consensus 136 ~~~~~~~t~~~v~~rs~~~~~~s~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~eI~~~i~~~~~~~~~~ 215 (940)
.+ ...|+...++.|| .|+.+.++.++.+++++..++ +||+++||||||+.||+||++.+.. ++
T Consensus 154 ~~-~~~~~a~vIp~rG-------~wl~~e~d~~d~~~~rId~~r---kiPvtilLRALG~~tDeeI~~~~~~--~~---- 216 (1060)
T COG0085 154 GS-KVLYVARVIPYRG-------SWLEFEFDPKDNLYVRIDRKR---KIPVTILLRALGLETDEEIIEAFGG--DE---- 216 (1060)
T ss_pred Cc-ceEEEEEEecCCc-------ceEEEEEccCccEEEEeeeEE---EeeHHHHHHHhCCCcHHHHHHHhcc--cc----
Confidence 11 2245555554444 489998888899999998765 6999999999999999999999973 10
Q ss_pred ccCCCCChhhHHHHHHHHHHHHhc--ccccHHHHHHHHhccccccccCCCCccHHHHHHHHHHhHhccCCCC--------
Q 002296 216 EKGAVGSPLVSERVKIILAEVQDL--SLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLND-------- 285 (940)
Q Consensus 216 ~~~~~~~~~~~~~~~~ll~~~~~~--~i~t~~~al~yig~~fr~~~~~~~~~~~~~~~~~~L~~~ll~Hl~~-------- 285 (940)
..+.+.....+++++.+.+. .-.+...|++|||++|...........+.++++.++.+.+||||+.
T Consensus 217 ----~~~~~~~~~~~~ll~~~~~~~~~~i~~~~a~~~i~~r~~~~~~~~~~~gR~k~~~~vl~~~~L~hL~~~~~~~~l~ 292 (1060)
T COG0085 217 ----LTDLVPPEGEEALLEIYEEAKGEKITARNALELIGSRVFVVKRYDAKEGRYKRAKYVLDKELLPHLGEAGERYDLS 292 (1060)
T ss_pred ----cccccchHHHHHhHHHHhhccCCCcchHHHHHHHhcccccccccccchhhhhhhhhhhhhhHHhhhcccccccchh
Confidence 01111135667777777644 2233334999999999754321245667899999999999999995
Q ss_pred CcchHHHHHHHHHHHHHhcCCCCCCCCccccccceecccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccccchHH
Q 002296 286 NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLAN 365 (940)
Q Consensus 286 ~~~K~~~L~~MirkLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~ 365 (940)
...|+.+|+.|+++|+.+..|++.+||+|||+||||+++|+||+++||..|.++.+.++.++.+...+
T Consensus 293 ~~~k~~di~~mi~~l~~L~~G~~~~DDiDHlGNKRlrlvGeLl~n~fR~gl~rmer~ikerm~~~~~r------------ 360 (1060)
T COG0085 293 RVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRRLRLVGELLENLFRVGLSRMERDVKERLEKADKR------------ 360 (1060)
T ss_pred hhHHHHHHHHHHHHHHHHhcCCCCCCCCccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh------------
Confidence 23588899999999999999999999999999999999999999999998888888877776654332
Q ss_pred HHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhhcccccCCcccccccccccccCCCC
Q 002296 366 IKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPES 445 (940)
Q Consensus 366 ~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSh~Rrv~rg~~~~~~K~t~vR~Lhps~ 445 (940)
..+. ..+.||.++.+|++||||+ ++||||+++|+||+|.|||+|||++.++.++++.++||+|||||
T Consensus 361 -~~i~---p~dlIn~k~~~Alitgffg---------~sqlSQfmDqtNpLSeLSHkRRIsAlgLsRera~fEvRDvHpTH 427 (1060)
T COG0085 361 -DTLV---PQDLINAKPIHALITGFFG---------RSQLSQFMDQTNPLSELSHKRRLSALGLSRERAGFEVRDVHPTH 427 (1060)
T ss_pred -hccC---chhhcchhHHHHHHhcccc---------ccceeeeeecCChHHhhhhhhceeccCcCccCCCCcccccCccc
Confidence 0011 2357999999999999995 58999999999999999999999996778999999999999999
Q ss_pred ccccccCCCCCCccccccccccceeEEeeccCCCCcccccchhhHHHHHHHH-hCCCeecCCccccCCCCcceEEEECCE
Q 002296 446 WGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLI-GVGMIPSLPKLVKSGPPAVLSVLLDGR 524 (940)
Q Consensus 446 wGfiCPveTPEG~~cGLvk~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~-~~g~~~~~~~~~~~~~~~~~~V~lnG~ 524 (940)
|||+||+|||||+|||||||||++|+|+.....+++ ..+.+. .+|+.++. .++ .....+++||.
T Consensus 428 yGRiCPiETPEGpNiGLI~sLA~~A~Vn~~Gf~etP----------y~kv~~g~~~v~~i~-~l~----~~~~~~~~~~~ 492 (1060)
T COG0085 428 YGRICPIETPEGPNIGLIKSLALYARINEYGFLETP----------YRKVLDGSLVVDEIE-YLS----ADEEDVYVIGQ 492 (1060)
T ss_pred ccccCCCCCCCCcchhHHHHHHHHeEecccCCCCCc----------eEEEEecccccccee-eec----ccccceEEEeE
Confidence 999999999999999999999999999955555534 222222 35565542 111 11267999999
Q ss_pred EEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCCceEEecCCCceeceEEeccCCCC-----------
Q 002296 525 VVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSE----------- 593 (940)
Q Consensus 525 ~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~~d~gR~~RPv~~~~~~~~----------- 593 (940)
++|.++ ++..|++.+|.+|+ + +..++.+. .+...+...-++++.+|.||.+||++.++++..
T Consensus 493 ~~~~~~--~~~~~~~~~~~~R~-~---~~~~~~~~-~~~~~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~l~~~~mqr~~ 565 (1060)
T COG0085 493 ANGTLD--EPGELVEELVECRR-G---GSGEVSVA-DPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGSNMQRQA 565 (1060)
T ss_pred eeeeec--CCCceeeeEEEEee-c---ccccceee-cCccccceeccceEEeccccccCceeEEcCchHhhhhhhhhhhc
Confidence 999874 56889999999997 3 23333332 111122233478999999999999998877631
Q ss_pred -----------CCCceeeecccceeeeeeecCCCCCCCCCCCccceecccCCCccccceeecccCCCCCCCccchhhccc
Q 002296 594 -----------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQM 662 (940)
Q Consensus 594 -----------~~~~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~ilsv~AslIPF~~HNqspRn~yq~~M 662 (940)
+.| +||+++.|+.++.||..+.+ +||+|++|..|++++|++|||++|||||||||||+|
T Consensus 566 ~~l~~~~~~lv~tG-~E~~~a~e~~~~~ia~~~~~---------~~~ve~~~~~I~~~~~~~~~~~~~n~~~~n~~~~~~ 635 (1060)
T COG0085 566 VPLLRTEAPLVGTG-MEYLDAEDSGAAVIAKRPGV---------VTHVEISPIVILGIEASLIPYPEHNQSPYNLYKFAR 635 (1060)
T ss_pred ccccccccccccCC-ceeeccccccceeEeccCCc---------EEEEeeeeeEEEeeccccCCccccCcChHHHHHHhh
Confidence 357 99999999999999999876 799999999999999999999999999999999999
Q ss_pred ccccccccceeEEEeccCceeeccCCCeeeEeccceeecCCCCCCCCceeEEEEEeccCCCCCceEEEecchhccCccee
Q 002296 663 AKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHG 742 (940)
Q Consensus 663 ~KQaig~~~~n~~~R~d~~~y~L~~~Q~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rG~~~~ 742 (940)
+||++|++..|+..|.|+..|.+.|||.|+|.+ +|+|+|+|++||||||+||||||||||||++++||+|++
T Consensus 636 ~~Q~~~~~~~~~~~~~d~~~~~~~~~~~P~~~~--------~e~~~GqN~~VA~m~~~GYn~EDAiiin~~~v~~~~~ts 707 (1060)
T COG0085 636 SNQATGINQRPLVKRGDTVEKGLVYADGPSVDT--------GELALGQNALVAFMPWNGYNYEDAIIISERSVERDLFTS 707 (1060)
T ss_pred hhcccCCCcccceeccccccccceecCCCcccc--------CcccCCceeEEEEecccCcChhHheecccchhhcCCceE
Confidence 999999999999999999999999999999997 899999999999999999999999999999999999999
Q ss_pred eEEEEEEEEeeccCCCcCccceeeccCCCChhhhcccCCCCCcccCcEecCCCcEEEEeecCCC----------------
Q 002296 743 QIYQTETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTN---------------- 806 (940)
Q Consensus 743 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~~~~~~~~---------------- 806 (940)
++|++|.++..+.+. +..+.+.+|+..+..+++||+|||++||++|+.||||+||++|+..
T Consensus 708 ~~~~~~~~~~r~~~~---g~e~~~~iP~~~e~~~~~Lde~Gii~ig~~V~~gdilvgk~tP~~~~~~~~ee~ll~i~~ek 784 (1060)
T COG0085 708 IHIEEYETEARDTKL---GPEEIRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRIFGEK 784 (1060)
T ss_pred EEEEEEeeeeeccCC---CccccccCCCcCHHHHhcCCccCccccccEEcCCCEEEEeeCCCCCCCCCchhhhhccccce
Confidence 999999998655443 3344578899999999999999999999999999999999988742
Q ss_pred -cEEEeeccCCCcEEEEEEEEEecCCCC--CceEEEEEEeeecCCCcccceeccCCCccEEeeeecCCCcCccCCCCCcC
Q 002296 807 -SWRTNSRKGSESVFVDYVAVDMKNSKN--LPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRP 883 (940)
Q Consensus 807 -~~~~~~~~~~e~g~V~~v~~~~~~~~~--~~~~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dMPf~~~~G~~p 883 (940)
++.|++++++++|+|++|.++++++|+ ..+.|||++|+.|.|++|||||||||||||||+|||+|||||+ +||++|
T Consensus 785 ~rdtsl~~~~g~~G~V~~V~~~~~~~~~~g~~~~vkV~v~~~R~~~~GDK~a~RHG~KGVis~i~p~eDMPf~-~~G~~~ 863 (1060)
T COG0085 785 VRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKGVVSKIVPQEDMPFL-EDGTPP 863 (1060)
T ss_pred eeccceeecCCCCeEEEEEEEEeccCCCcCceEEEEEEEEEeccCCccccccccCCCCceeeeecCcccCCcC-CCCCcc
Confidence 246899999999999999999987754 6789999999999999999999999999999999999999999 999999
Q ss_pred cEEeCCCCccccccHHHHHHHHHHHHHhhchhHH
Q 002296 884 DLIINPHAFPSRMTIAMLLESVAAKVVAYMENLW 917 (940)
Q Consensus 884 DiI~NPh~~PSRMtiGql~E~~~gk~~~~~G~~~ 917 (940)
|||+|||||||||||||++|+++||||+++|..+
T Consensus 864 DiilNP~gvPSRM~iGqilE~~lG~a~~~~G~~~ 897 (1060)
T COG0085 864 DIILNPLGVPSRMNIGQILETHLGKAAALLGIPV 897 (1060)
T ss_pred cEEECCCCCCccccHHHHHHHHHHHHHHhcCcee
Confidence 9999999999999999999999999999999886
No 6
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Probab=100.00 E-value=5.3e-164 Score=1505.48 Aligned_cols=656 Identities=33% Similarity=0.536 Sum_probs=560.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHH----------------------------------------HHHHHcCCeeeeEEEEEEE
Q 002296 15 LVRHHIESFDYMLDEGLSEMF----------------------------------------DHCRQAKISYTGKLMADVE 54 (940)
Q Consensus 15 Lv~~hi~SFn~Fi~~gl~~ii----------------------------------------~ecR~r~~TYsa~l~v~i~ 54 (940)
|++||++|||+|+++||++++ +|||+|++||+|+|+|+++
T Consensus 1 Lv~~qi~SFn~Fl~~gl~~ii~~~~~i~~~~~~~~~~l~f~~i~i~~P~~~~~~~~~~l~P~ecRlr~lTYs~~l~v~i~ 80 (866)
T cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEGGVTRKLTPNECRLRDLTYSAPLYVDIR 80 (866)
T ss_pred CchhHHHHHHHHHHHHHHHHHHhcCCeeeccCCCeEEEEEEEEEECCccccccCccccCCHHHHHhhCCccceeEEEEEE
Confidence 689999999999999999997 8999999999999999999
Q ss_pred EEEecCCCce-EeeEEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeccCCccEEEEec
Q 002296 55 FQYLDAGSPV-VRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRS 133 (940)
Q Consensus 55 ~~~~~~~~~~-~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~~~~r~ 133 (940)
++++ +... ..+++.+|+|||||+|++|||++++++|+++.||||.|+||||||||+|||||+||++++|+++++.
T Consensus 81 ~~~~--~~~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~p~d~GGYFIInG~EkVIi~qi~~~~N~~~~~~-- 156 (866)
T cd00653 81 LTVN--DKGKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVED-- 156 (866)
T ss_pred EEEe--cceeEEEEEEEEeeCCcccCcccccccCCCHHHHHhcCCCcccCCCEEEECCceeEEEEEEeccCCeEEEec--
Confidence 9876 4333 5679999999999999999999999999999999999999999999999999999999999998651
Q ss_pred cccCCCCcceeeEEEEEeeecC--CCceEEEEEEEe-CCeEEEEEEeecccccccHhhHHHhccCCCHHHHHHHhccccc
Q 002296 134 SFRDRREGYTDKAVVIRCVRKD--QSSVTLKLYYLL-NGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYD 210 (940)
Q Consensus 134 ~~~~~~~~~t~~~v~~rs~~~~--~~s~~~~l~y~~-~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~eI~~~i~~~~~ 210 (940)
+.. . +....++.... ....|..+..+. .+.++++++..
T Consensus 157 ---~~~-~---~~~~~~s~~~~~~~~~s~~~~~~~~~~~~i~~~i~~~-------------------------------- 197 (866)
T cd00653 157 ---SKG-K---RIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLK-------------------------------- 197 (866)
T ss_pred ---CCC-c---EEEEEEEccCCCcCccEEEEEEEccCCCeEEEEeccc--------------------------------
Confidence 011 0 11222222111 111233332221 12222222110
Q ss_pred chhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhccccccccCCCCccHHHHHHHHHHhHhccCCCCCcchH
Q 002296 211 EKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDNNDKF 290 (940)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~i~t~~~al~yig~~fr~~~~~~~~~~~~~~~~~~L~~~ll~Hl~~~~~K~ 290 (940)
.+++|+.|||++|
T Consensus 198 --------------------------------~~~~al~~ig~~~----------------------------------- 210 (866)
T cd00653 198 --------------------------------RQEEALKYIGKRF----------------------------------- 210 (866)
T ss_pred --------------------------------CHHHHHHHHHHHH-----------------------------------
Confidence 0668999999886
Q ss_pred HHHHHHHHHHHHhcCCCCCCCCccccccceecccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccccchHHHHHHH
Q 002296 291 NLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVM 370 (940)
Q Consensus 291 ~~L~~MirkLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~ 370 (940)
.+|++|++||+.+..|.+.+||+|||+||||+++|+||+.+|++.|+++++.++..+++...+ .+.+. ...++
T Consensus 211 ~~L~~Mi~kLl~~~~g~~~~Dd~D~~~NkRv~~~G~Ll~~lfr~~l~~~~~~~k~~l~~~~~~-~~~~~------~~~~~ 283 (866)
T cd00653 211 EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSK-KKDLT------PQLLI 283 (866)
T ss_pred HHHHHHHHHHHHHhcCCCCCCCchhhhCeEEeeHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc-ccccC------HHHhc
Confidence 789999999999999999999999999999999999999999999999999999998877654 22111 22222
Q ss_pred hcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhhcccccCCcccccccccccccCCCCccccc
Q 002296 371 EKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLC 450 (940)
Q Consensus 371 ~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSh~Rrv~rg~~~~~~K~t~vR~Lhps~wGfiC 450 (940)
+++.||++|++||+||||.++.+ ++|++|+||+|+|+||+++|||+||||+|++++++|+++||+||||||||+|
T Consensus 284 ---~~~~It~~i~~~~~TGnw~~~~~--~~~~~Gvsq~ldr~N~ls~lsh~Rrv~~~~~~~~~k~~~~R~lhps~~G~iC 358 (866)
T cd00653 284 ---NSKPITSGIKEFLATGNWGSKRF--LMQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRIC 358 (866)
T ss_pred ---cchHHHHHHHHHhhcCCcccccc--ccccceEEEEcccCCHHHHHHhhhhcccccccccccCCcccccCcccCCccC
Confidence 24589999999999999998765 7899999999999999999999999999989999999999999999999999
Q ss_pred cCCCCCCccccccccccceeEEeeccCCCCcccccchhhHHHHHHHHhCCCeecCCccccCCCCcceEEEECCEEEeeec
Q 002296 451 PVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIP 530 (940)
Q Consensus 451 PveTPEG~~cGLvk~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~ 530 (940)
|+|||||++||||||||++|+|+
T Consensus 359 PveTPEG~~cGLv~~LA~~a~Is--------------------------------------------------------- 381 (866)
T cd00653 359 PIETPEGENCGLVKNLALMARIS--------------------------------------------------------- 381 (866)
T ss_pred CCCCCCCccccchhhhhceEeee---------------------------------------------------------
Confidence 99999999999999999999882
Q ss_pred CccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCCceEEecCCCceeceEEeccCCCCCCCceeeecccceeeee
Q 002296 531 SSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFME 610 (940)
Q Consensus 531 ~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~~d~gR~~RPv~~~~~~~~~~~~iE~i~~~Eq~~~~ 610 (940)
||++||+++++.
T Consensus 382 ------------------------------------------------Gr~~rP~~~v~~-------------------- 393 (866)
T cd00653 382 ------------------------------------------------GRIERPYRIVEK-------------------- 393 (866)
T ss_pred ------------------------------------------------eEeeeeEEEecc--------------------
Confidence 888999997631
Q ss_pred eecCCCCCCCCCCCccceecccCCCccccceeecccCCCCCCCccchhhcccccccccccceeEEEeccCceeeccCCCe
Q 002296 611 IRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQT 690 (940)
Q Consensus 611 Ia~~~~~~~~~~~~~~~th~EI~p~~ilsv~AslIPF~~HNqspRn~yq~~M~KQaig~~~~n~~~R~d~~~y~L~~~Q~ 690 (940)
.+||+||+|.++||++||+|||+||||||||||||||+|||||++++|+..|.|++.|+|.|||+
T Consensus 394 ---------------~~th~ei~~~~~ls~~asliPf~~hNqspRn~~~~~M~kQa~g~~~~n~~~r~d~~~~~l~~pq~ 458 (866)
T cd00653 394 ---------------EVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQK 458 (866)
T ss_pred ---------------ceEEEEeCccceeeeeeeccCCCCcccccchhhhhcccCCccCchhccccccccchheeeccCCC
Confidence 18999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEeccceeecCCCCCCCCceeEEEEEeccCCCCCceEEEecchhccCcceeeEEEEEEEEeeccCCCcCccceee--cc
Q 002296 691 PIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLF--RR 768 (940)
Q Consensus 691 Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~ 768 (940)
|||.|+.++.++++++|+|+|++||||||+||||||||||||+|+|||||++.+|+++++++...... ..+.+ ..
T Consensus 459 plv~T~~~~~~~~~~~~~G~N~~VAv~~y~Gyn~EDaiiink~s~~rg~~~s~~~~~~~~~~~~~~~~---~~~~~~~~~ 535 (866)
T cd00653 459 PLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNG---PEEITRGDI 535 (866)
T ss_pred CccccchHHHhCCCccCCCceEEEEEeccccccccceeeeehhhhhcCceeEEEEEEEEEEEEecCCC---cceEecCCC
Confidence 99999999999999999999999999999999999999999999999999999999999987543321 11222 23
Q ss_pred CCCChhhhcccCCCCCcccCcEecCCCcEEEEeecCC--------------CcEEEeeccCCCcEEEEEEEEEecC-CCC
Q 002296 769 NKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT--------------NSWRTNSRKGSESVFVDYVAVDMKN-SKN 833 (940)
Q Consensus 769 ~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~~~~~~~--------------~~~~~~~~~~~e~g~V~~v~~~~~~-~~~ 833 (940)
|......+++||+||+|++|++|++||+|+||+++.. .++.+.+++.+++|+|++|.++.+. +.+
T Consensus 536 ~~~~~~~~~~ld~dGi~~~g~~v~~gd~li~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~v~~v~~~~~~~~~~ 615 (866)
T cd00653 536 PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDG 615 (866)
T ss_pred CCCChHHhhccCCCCCcCCCCEecCCCEEEEEecCcccccccccccccCCcceEEEEEecCCCceEEEEEEEeccccCCC
Confidence 4555667899999999999999999999999987642 3567899999999999999998832 113
Q ss_pred CceEEEEEEeeecCCCcccceeccCCCccEEeeeecCCCcCccCCCCCcCcEEeCCCCccccccHHHHHHHHHHHHHhhc
Q 002296 834 LPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVAYM 913 (940)
Q Consensus 834 ~~~~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~ 913 (940)
+...|+|++|+.|+|+||||||||||||||||++||+|||||| +||++|||||||||||||||||||+|+++||+||++
T Consensus 616 ~~~~v~v~~r~~R~p~iGDKfssRhGqKGv~s~i~~~~dmPf~-~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~ 694 (866)
T cd00653 616 GNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFT-EDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALL 694 (866)
T ss_pred CcEEEEEEEeEEecCCcccccccccCCCcEEEEEeccccCCcc-cCCCCCcEEecCCcCcccccHHHHHHHHHHHHHHhc
Confidence 5688999999999999999999999999999999999999999 999999999999999999999999999999999999
Q ss_pred hhHHHHH-hhhhhhhHHHHHHhhh
Q 002296 914 ENLWMQH-HLQIQSRKLMEILGLM 936 (940)
Q Consensus 914 G~~~~~~-~~~~~~~~~~~~~~~~ 936 (940)
|.+++-- |.-.....+.++|+..
T Consensus 695 g~~~d~t~f~~~~~~~~~~~l~~~ 718 (866)
T cd00653 695 GKFGDATPFDGAEEEDISELLGEA 718 (866)
T ss_pred CCcccccccCcchHHHHHHHHHHc
Confidence 9876221 1112334456665543
No 7
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit. This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.
Probab=100.00 E-value=1.5e-158 Score=1463.64 Aligned_cols=711 Identities=21% Similarity=0.338 Sum_probs=586.2
Q ss_pred CccCchhhHHHHHHHHHHHHH----------HHHHHHH-----------------------------HHHHHcCCeeeeE
Q 002296 8 DFEPLRELVRHHIESFDYMLD----------EGLSEMF-----------------------------DHCRQAKISYTGK 48 (940)
Q Consensus 8 ~~~~~~~Lv~~hi~SFn~Fi~----------~gl~~ii-----------------------------~ecR~r~~TYsa~ 48 (940)
.+...++|++||++||||||+ +||++++ +|||+|++||+||
T Consensus 13 ~~~~~p~Lv~~Qi~SFn~FL~~~~~~~~~~~~gL~eii~~~~pI~~~~~~~~l~f~~~~l~~P~~~p~Ear~r~lTYsa~ 92 (1065)
T TIGR02013 13 EVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVEECKERGLTYSAP 92 (1065)
T ss_pred ccccCCCHHHHHHHHHHHHHcCCCcccccccccHHHHHhccCcEEecCCcEEEEEEEEEeCCCCCCHHHHHHhCCCccee
Confidence 445789999999999999999 8999999 9999999999999
Q ss_pred EEEEEEEEEec--CCCceEeeEEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeccCCc
Q 002296 49 LMADVEFQYLD--AGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNY 126 (940)
Q Consensus 49 l~v~i~~~~~~--~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~ 126 (940)
|+|++.+.... ..+++..++|++|+||||++ ||||||||+||||++|+.+++|.
T Consensus 93 l~v~v~l~~~~~~~~~~i~~~~V~iG~iPiMt~------------------------gGyFIINGsERVIV~Qe~rspg~ 148 (1065)
T TIGR02013 93 LKVKLRLINKEEDGTKEIKEQDVYMGDIPLMTD------------------------RGTFIINGAERVVVSQLHRSPGV 148 (1065)
T ss_pred EEEEEEEEEeccCCccceeeeeEEEeCCCccCC------------------------CceEEECCcEEEEEEEeecCCCE
Confidence 99999997541 12355667999999999986 99999999999999999999998
Q ss_pred cEEEEeccccCCC-CcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHhhHHHhccCCCHHHHHHHh
Q 002296 127 PMSMVRSSFRDRR-EGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHL 205 (940)
Q Consensus 127 ~~~~~r~~~~~~~-~~~t~~~v~~rs~~~~~~s~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~eI~~~i 205 (940)
+++.... ..+++ ..| .+.++|.+ ..|+.+.++.++.+|++++..+ +||+++||||||+.+|+||++.+
T Consensus 149 ~~~~~~~-~~~~~~~~~---~a~iis~r----gswl~~e~~~~~~i~v~i~~~~---kIPi~illrALG~~sd~eI~~~i 217 (1065)
T TIGR02013 149 FFSSEKD-THKSGKVLF---SARIIPYR----GSWLEFETDKKDVLYVRIDRKR---KLPATVLLRALGYTIDTLILNRL 217 (1065)
T ss_pred EEEEccc-cCCCCceEE---EEEEEeCC----CCceEEEEecCCeEEEEecCCC---ceeHHHHHHHcCCCcchhhhhhc
Confidence 8776432 11112 233 44555542 4488888888899999988654 69999999999999999999988
Q ss_pred cccccchhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhccccccccCCCCccHHHHHHHHHHhHhcc----
Q 002296 206 TCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFV---- 281 (940)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~i~t~~~al~yig~~fr~~~~~~~~~~~~~~~~~~L~~~ll~---- 281 (940)
+. +.++ ...| .+..+.|+++|+.||++++++. .....+.|+.+|++.+||
T Consensus 218 ~~--------------~~~i----~~~l---~~~~~~~~e~Al~~i~~~~~~g-----~~~~~~~a~~~l~~~f~~~~rY 271 (1065)
T TIGR02013 218 GS--------------GEYI----RNTL---RKDPTNSEEEALVEIYRKLRPG-----EPPTVEAARSLLENLFFDPKRY 271 (1065)
T ss_pred Cc--------------hHHH----HHHH---HhccccCHHHHHHHHHhhcCCC-----CcchHHHHHHHHHHHhcCcccc
Confidence 51 1222 1222 2334789999999999998642 233467899999999987
Q ss_pred ---CCCCC----------------cchHHHHHHHHHHHHHhcCCCCCCCCccccccceecccchhHHHHHHHHHHHHHHH
Q 002296 282 ---HLNDN----------------NDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRK 342 (940)
Q Consensus 282 ---Hl~~~----------------~~K~~~L~~MirkLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~ 342 (940)
|+|.. ..|+++|+ |+++|+.+..|...+||+|||+||||+++|+||+.+|+..|+++.+.
T Consensus 272 ~LghiGr~kln~Kl~~~~~~~~~~l~k~d~l~-mi~~Ll~~~~g~~~~DD~Dhl~NKRvr~aGeLL~~~fr~~l~rl~k~ 350 (1065)
T TIGR02013 272 DLGRVGRYKLNKKLGLDVPEDIGVLTKEDIIA-TIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERI 350 (1065)
T ss_pred cccccchhhhhhhcCcCcCcccceehHHHHHH-HHHHHHHhhcCCCCCcchhhhhccchhhHHHHHHHHHHHHHHHHHHH
Confidence 99921 24888886 99999999999999999999999999999999999999988888877
Q ss_pred HHHHHHHHHHhcCCcccccchHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhhc
Q 002296 343 GKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFR 422 (940)
Q Consensus 343 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSh~R 422 (940)
++..+.+. . .+ .+ .++.++ +++.||+++++||+|| ||||+|+|+||++.|||+|
T Consensus 351 ik~~l~~~-~--~~--~~----~~~~~i---~~~~it~~i~~ff~tg--------------glSQ~Ldr~NpLs~lsh~R 404 (1065)
T TIGR02013 351 VRERMSTQ-D--TD--TL----TPQDLI---NAKPISAAIKEFFGSS--------------QLSQFMDQTNPLAELTHKR 404 (1065)
T ss_pred HHHHhhhc-c--cc--cC----CHHHhc---CccchHHHHHHHhccC--------------CcccccccCCHHHhhhhhc
Confidence 77665432 1 11 11 134454 4568999999999985 9999999999999999999
Q ss_pred ccc---cCCcccccccccccccCCCCccccccCCCCCCccccccccccceeEEeeccCCCCcccccchhhHHHHHHHHhC
Q 002296 423 AVH---RGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGV 499 (940)
Q Consensus 423 rv~---rg~~~~~~K~t~vR~Lhps~wGfiCPveTPEG~~cGLvk~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~~ 499 (940)
|++ +|++.+++|+++||+|||||||||||+|||||++||||+|||++|+|+. +
T Consensus 405 Rlsslgpggl~r~~~~~~~RdlHpShyGrICPiETPEG~n~GLVknLA~~a~i~~------------------------~ 460 (1065)
T TIGR02013 405 RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNE------------------------Y 460 (1065)
T ss_pred eecccCCCCcCccccCCccCccCccccccccCCCCCCCCccccccchhhhcccCc------------------------c
Confidence 999 4567899999999999999999999999999999999999999999962 3
Q ss_pred CCeecCCccccCCCCcceEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCCceEEecCCC
Q 002296 500 GMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPP 579 (940)
Q Consensus 500 g~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~~d~g 579 (940)
|++.. | |.++.||++.
T Consensus 461 G~i~~-P----------~~~V~ng~~~----------------------------------------------------- 476 (1065)
T TIGR02013 461 GFIET-P----------YRKVKDGKVV----------------------------------------------------- 476 (1065)
T ss_pred eEEeC-C----------eEEEECCeEe-----------------------------------------------------
Confidence 44321 1 3333454421
Q ss_pred ceeceEEeccCCCCCCCceeeecccceeeeeeecCCCCCCCCC------------------CCccceecccCCCccccce
Q 002296 580 KFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRR------------------NAFPATHEEIHPTGMLSVV 641 (940)
Q Consensus 580 R~~RPv~~~~~~~~~~~~iE~i~~~Eq~~~~Ia~~~~~~~~~~------------------~~~~~th~EI~p~~ilsv~ 641 (940)
..+.+||++++|++++.||..+.++.... ....+||+||+|.+|||++
T Consensus 477 --------------~~~~i~yl~a~eE~~~~Ia~~~~~l~~~~~~~~~~i~~r~~~~f~~~~~~~vt~~ei~p~~ilsv~ 542 (1065)
T TIGR02013 477 --------------VTDEVDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVA 542 (1065)
T ss_pred --------------ccceeEECChHHhCCcEEEecCcCcCccCccccceeeEEEcCceeecChhHeeEEeeChhhhhhhH
Confidence 01267788888888888887665553210 0124799999999999999
Q ss_pred eecccCCCCCCCccchhhccccccccccc-----------------------------------ceeEEEeccC------
Q 002296 642 ANLTPYSDHNQSPRNMYQCQMAKQTMGFS-----------------------------------VQALKFRADQ------ 680 (940)
Q Consensus 642 AslIPF~~HNqspRn~yq~~M~KQaig~~-----------------------------------~~n~~~R~d~------ 680 (940)
||||||+||||||||||||||||||||+. +.|+..|.|+
T Consensus 543 aslIPFleHNds~R~lmgsnM~kQavpl~~~e~p~VgTg~E~~v~~ds~~~i~a~~~G~v~~v~~~~~~~r~d~~~~~~~ 622 (1065)
T TIGR02013 543 ASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEDEPD 622 (1065)
T ss_pred hhcCCCccccCCcchhhhhhhhhhhhcccccCCCEEEcCcchhhhccccceeEeccCCEEEEEccceEEEEecCCccccc
Confidence 99999999999999999999999999877 8899999995
Q ss_pred ---ceeecc----------CCCeeeEeccce----eecC------CCCCCCCceeEEEEEeccCCCCCceEEEecchhcc
Q 002296 681 ---KLYHLQ----------TPQTPIVRTNTY----TKYG------IDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDR 737 (940)
Q Consensus 681 ---~~y~L~----------~~Q~Plv~t~~~----~~~~------~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~r 737 (940)
+.|.|. |||+|||+|+.+ +.+. ++++|+|+|++||||||+||||||||||||+|+||
T Consensus 623 ~~~~~y~L~~~~~snq~~~~~q~Plv~~~~~v~~~~~l~d~~~~~~~e~~~G~N~~VAvm~y~GYn~EDAiiink~~i~r 702 (1065)
T TIGR02013 623 GGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKD 702 (1065)
T ss_pred ccceEEEeecccccccCceEEeeeeeccCCeEeeeeEecccccccCCcCcCccceEEEEEeeecccccceEEeehhhhcC
Confidence 456654 999999999653 3333 89999999999999999999999999999999999
Q ss_pred CcceeeEEEEEEEEeeccCCCcCccceeec--cCCCChhhhcccCCCCCcccCcEecCCCcEEEEeecCC----------
Q 002296 738 GMCHGQIYQTETIDLSDDGNKVDRGQKLFR--RNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT---------- 805 (940)
Q Consensus 738 G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~~~~~~~---------- 805 (940)
|+|++.+|++|++++...+. ..+.|. .|+.....+++||+||+|++|++|++||||+||+++..
T Consensus 703 g~~~s~~~~~~~~~~~~~~~----g~e~~~~~~p~~~~~~~~~Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~~l 778 (1065)
T TIGR02013 703 DVFTSIHIEEYEVEARDTKL----GPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKL 778 (1065)
T ss_pred CceEEEEEEEEEEEeeccCC----CceEeeccCCCCchhhhhccCCCCCccCccEeCCCCEEEEEecCCcccccChhhhh
Confidence 99999999999998754321 123443 36555567899999999999999999999999987632
Q ss_pred -----------CcEEEeeccCCCcEEEEEEEEEecCCCCC-----ceEEEEEEeeecCCCcccceeccCCCccEEeeeec
Q 002296 806 -----------NSWRTNSRKGSESVFVDYVAVDMKNSKNL-----PQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWP 869 (940)
Q Consensus 806 -----------~~~~~~~~~~~e~g~V~~v~~~~~~~~~~-----~~~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~ 869 (940)
.++.+++++.+++|+||+|.++.+++++. .+.|+|++|+.|+|+||||||||||||||||+|||
T Consensus 779 ~~~~~~~~~~~~~d~s~~~~~~~~g~V~~V~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGDKfasRHGqKGvis~i~~ 858 (1065)
T TIGR02013 779 LRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRKQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILP 858 (1065)
T ss_pred hhhhcccCCccccccceEccCCCCEEEEEEEEEeccCCCccCcCccEEEEEEEeecccccccchhhhcccCceeEEeEec
Confidence 13458899999999999999998766532 46899999999999999999999999999999999
Q ss_pred CCCcCccCCCCCcCcEEeCCCCccccccHHHHHHHHHHHHHhhc
Q 002296 870 DIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVAYM 913 (940)
Q Consensus 870 ~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~ 913 (940)
+|||||| +||++|||||||||||||||||||+|+++||||++.
T Consensus 859 ~eDMPf~-~~G~~pDiIiNPhg~PSRMtiGqllE~~~gka~~~~ 901 (1065)
T TIGR02013 859 IEDMPFL-EDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRL 901 (1065)
T ss_pred CCCCCcc-CCCCCccEEECCCCCcccccHHHHHHHHHHHHHHhc
Confidence 9999999 999999999999999999999999999999999986
No 8
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed
Probab=100.00 E-value=5.8e-157 Score=1456.71 Aligned_cols=730 Identities=21% Similarity=0.319 Sum_probs=584.9
Q ss_pred cCchhhHHHHHHHHHHHH-------HHHHHHHH-----------------------------HHHHHcCCeeeeEEEEEE
Q 002296 10 EPLRELVRHHIESFDYML-------DEGLSEMF-----------------------------DHCRQAKISYTGKLMADV 53 (940)
Q Consensus 10 ~~~~~Lv~~hi~SFn~Fi-------~~gl~~ii-----------------------------~ecR~r~~TYsa~l~v~i 53 (940)
...++|++||++|||||| ++||++++ +|||+|++||+|||+|++
T Consensus 22 ~~~p~Lv~~Qi~SFn~Fl~~~~~~~~~gL~~ii~~~~pI~~~~~~~~l~f~~~~l~~P~~tp~Ear~r~lTYSaplyv~v 101 (1112)
T PRK00405 22 LELPNLLEIQLDSFDWFLQLDVPPEDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPKYDVEECKERGLTYSAPLRVKL 101 (1112)
T ss_pred CCCCCHHHHHHHHHHHHHhcCCcccchhHHHHHHhcCCEEecCCcEEEEEeeeEcCCCCCCHHHHHHhCCCCCeeEEEEE
Confidence 468999999999999999 99999999 999999999999999999
Q ss_pred EEEEecCCCceEeeEEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeccCCccEEEEec
Q 002296 54 EFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRS 133 (940)
Q Consensus 54 ~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~~~~r~ 133 (940)
+++... ++++.+++|++|+||||+ +||||||||+||||++|+++++|.++.....
T Consensus 102 ~l~~~~-~~~i~~~~V~iG~iPiMt------------------------~gGyFIING~ERVIVsQe~rSPg~~~~~~~~ 156 (1112)
T PRK00405 102 RLINKE-TGEIKEQEVYMGDIPLMT------------------------ENGTFIINGTERVIVSQLHRSPGVYFDHDKD 156 (1112)
T ss_pred EEEEec-cCceeeeeEEEecccccc------------------------CCceEEECCeEEEEEEEeecCCCEEEEEecc
Confidence 997541 346667899999999997 4999999999999999999999987765432
Q ss_pred cccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHhhHHHhccCCCHHHHHHHhcccccchh
Q 002296 134 SFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKY 213 (940)
Q Consensus 134 ~~~~~~~~~t~~~v~~rs~~~~~~s~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~eI~~~i~~~~~~~~ 213 (940)
+....+.. |.+.+.+.+ ..|+.+.++.++.+|+++...+ +||+++||||||+ ||+||++.++. +...
T Consensus 157 k~~~~k~~---y~a~Iis~r----Gswl~~e~d~k~~I~vri~~~~---kIPi~iLLrALGl-sd~eIl~~i~~--~~~~ 223 (1112)
T PRK00405 157 KTSSGKLL---YSARIIPYR----GSWLEFEFDPKDILYVRIDRRR---KLPVTVLLRALGY-SDEEILDLFYE--KEEF 223 (1112)
T ss_pred ccCCCcee---EEEEEEECC----CCcEEEEEecCCeEEEEecCCC---cccHHHHHHHcCC-CHHHHHHHhcc--cccc
Confidence 11111222 344555542 3499999898999999998542 7999999999999 99999999962 1111
Q ss_pred h--------cc-cCCCCC--------hhh-------HH-HH-HHHHHHHHhcccccHHHHHHHHhccccccccCCCCccH
Q 002296 214 K--------KE-KGAVGS--------PLV-------SE-RV-KIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESY 267 (940)
Q Consensus 214 ~--------~~-~~~~~~--------~~~-------~~-~~-~~ll~~~~~~~i~t~~~al~yig~~fr~~~~~~~~~~~ 267 (940)
. .. .....+ ..+ .+ .. ..+.+.+.+.++.|+++|+.||++++++. ....
T Consensus 224 ~~~~~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~~~~~i~~~l~~~~~~t~e~Al~~I~k~l~~g-----~~~~ 298 (1112)
T PRK00405 224 GKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITEELDGPYIRNTLEKDPTSSREEALVEIYRRLRPG-----EPPT 298 (1112)
T ss_pred cceeccchHHhcccchhhhhcccccceeeeccCCccchhhhhHHHHHHHhhccccCHHHHHHHHHhhcCCC-----Ccch
Confidence 0 00 000000 000 00 01 12223333345789999999999998642 2334
Q ss_pred HHHHHHHHHhHhc-------cCCCCC-----------cc----hHHHHHHHHHHHHHhcCCCCCCCCccccccceecccc
Q 002296 268 YAVAETVIRDYIF-------VHLNDN-----------ND----KFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPG 325 (940)
Q Consensus 268 ~~~~~~~L~~~ll-------~Hl~~~-----------~~----K~~~L~~MirkLl~~~~g~~~~Dd~D~l~NkRv~l~G 325 (940)
.+.|+.+|++.+| ||+|.. .. +..++++|+++|+.+..|...+||+|||+||||+++|
T Consensus 299 ~e~a~~~l~~~ff~~~rYdL~hiGr~k~nkKl~l~~~~~~~~L~~~d~~~mi~~Ll~l~~g~~~~DDiDhl~NKRvr~aG 378 (1112)
T PRK00405 299 VEAARSLLENLFFDPKRYDLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVG 378 (1112)
T ss_pred HHHHHHHHHHHhcCccccccccCCceecchhcccCcccccccccHHHHHHHHHHHHhhhcccCCCcchhHHhcchhhhHH
Confidence 5679999999886 999941 11 3445699999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccccchHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccce
Q 002296 326 HLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGY 405 (940)
Q Consensus 326 ~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGv 405 (940)
+||+.+|+..|+++.+.++..+... . .+ ++ .++.++ +++.||++|++||+|| ||
T Consensus 379 eLL~~~fr~~~~rl~k~ik~~l~~~--~-~~--~~----~~~~li---n~~~it~~i~~ff~tg--------------gl 432 (1112)
T PRK00405 379 ELLQNQFRIGLSRMERAVRERMSLQ--D-LD--TL----TPQDLI---NAKPVVAAIKEFFGSS--------------QL 432 (1112)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhc--c-cc--cC----CHHHhh---CchhHHHHHHHhhccC--------------Cc
Confidence 9999999988888887776665432 1 11 11 144455 4568999999999985 89
Q ss_pred EEEccccchHHHhhhhcccc---cCCcccccccccccccCCCCccccccCCCCCCccccccccccceeEEeeccCCCCcc
Q 002296 406 TVQAERLNFLRFISFFRAVH---RGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNI 482 (940)
Q Consensus 406 sqvleRln~~~~lSh~Rrv~---rg~~~~~~K~t~vR~Lhps~wGfiCPveTPEG~~cGLvk~LA~~~~Is~~~~~~~~~ 482 (940)
||+++|+|+++.|||+||++ +|++.+++|+++||+|||||||||||+|||||++||||+|||++|+|+
T Consensus 433 SQ~Ldq~NpLselshkRRlss~gpggl~r~~a~~~~R~lH~ShyGriCPiETPEG~n~GLV~nLA~~a~i~--------- 503 (1112)
T PRK00405 433 SQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVN--------- 503 (1112)
T ss_pred ceeeccCCHHHhhhhhceecccCCCCcCccccCCcccccCccccccccCcCCCCCCccccccchhhccccc---------
Confidence 99999999999999999999 467889999999999999999999999999999999999999999997
Q ss_pred cccchhhHHHHHHHHhCCCeecCCccccCCCCcceEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEE
Q 002296 483 RDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVP 562 (940)
Q Consensus 483 ~~~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~ 562 (940)
++|++.. + |.+++||.|..
T Consensus 504 ---------------~~G~~~t-p----------~~~~~nG~~~~----------------------------------- 522 (1112)
T PRK00405 504 ---------------EYGFIET-P----------YRKVVDGKVTD----------------------------------- 522 (1112)
T ss_pred ---------------cCCcccc-c----------eEEEECCeEcc-----------------------------------
Confidence 2465532 2 77889998621
Q ss_pred cCCCCCCCceEEecCCCceeceEEeccCCCCCCCceeeecccceeeeeeecCCCCCCCC------------------CCC
Q 002296 563 LSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGR------------------RNA 624 (940)
Q Consensus 563 ~~~~~~~~~i~i~~d~gR~~RPv~~~~~~~~~~~~iE~i~~~Eq~~~~Ia~~~~~~~~~------------------~~~ 624 (940)
.+||+|++||++..||....++... ...
T Consensus 523 ----------------------------------~i~yl~a~eE~~~~Ia~~~~~l~~~~~~~~~~i~~r~~~e~~~~~~ 568 (1112)
T PRK00405 523 ----------------------------------EIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPP 568 (1112)
T ss_pred ----------------------------------ceEECCHHHhcCcEEEecCcccCCCCcccCceEEEEecCcceeech
Confidence 1334444444444444433332210 001
Q ss_pred ccceecccCCCccccceeecccCCCCCCCccchhhcccccccccccce--------------------------------
Q 002296 625 FPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQ-------------------------------- 672 (940)
Q Consensus 625 ~~~th~EI~p~~ilsv~AslIPF~~HNqspRn~yq~~M~KQaig~~~~-------------------------------- 672 (940)
..+||+||+|.+|+|++||||||+||||||||+|||||||||||+...
T Consensus 569 ~~~~~~~i~p~qi~sv~aslIPFleHnda~R~lmgSnMqrQAvpl~~~~~p~vgTg~e~~~~~ds~~~i~a~~~G~v~~v 648 (1112)
T PRK00405 569 EEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYV 648 (1112)
T ss_pred hhceEEeechhhhceehhhccCcccccCCcchhhhhhhhhhhhhhccccCCeeecCcchhhhhhcchheEeccCCEEEEE
Confidence 237999999999999999999999999999999999999999999877
Q ss_pred ---eEEEec-----------------cCceee-ccCCCeeeEeccce----eec------CCCCCCCCceeEEEEEeccC
Q 002296 673 ---ALKFRA-----------------DQKLYH-LQTPQTPIVRTNTY----TKY------GIDEYPTGTNAIVAVLAYTG 721 (940)
Q Consensus 673 ---n~~~R~-----------------d~~~y~-L~~~Q~Plv~t~~~----~~~------~~~~~~~G~N~~Vav~~y~G 721 (940)
|+..|. |+..++ +.|||+|||+|+.+ +.+ +++++|+|+|++||||||+|
T Consensus 649 ~~~~i~ir~~~~~~~~~~~~~y~L~~~~~sn~~~~~~q~Plv~~~~~v~~g~~lad~~~~~~~e~~~G~N~~VA~~~y~G 728 (1112)
T PRK00405 649 DASRIVVRVEELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNG 728 (1112)
T ss_pred eCCEEEEeecccccCCCCeeEEEecccccccccceeecceeeecCCeEeeccEeecccccCcccccCCcceEEEEEeecc
Confidence 888888 444555 68999999999964 333 68999999999999999999
Q ss_pred CCCCceEEEecchhccCcceeeEEEEEEEEeeccCCCcCccceeec--cCCCChhhhcccCCCCCcccCcEecCCCcEEE
Q 002296 722 YDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFR--RNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCS 799 (940)
Q Consensus 722 yn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~ 799 (940)
|||||||||||+|+|||||++.+|++|.+++..... ..+.+. .|+.....+++||+||||++|++|++||||+|
T Consensus 729 Yn~EDaiiink~si~rg~~~s~~~~~~~~~~~~~~~----~~~~~~~~~p~~~~~~~~~Ld~dGi~~~G~~v~~gDilig 804 (1112)
T PRK00405 729 YNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKL----GPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVG 804 (1112)
T ss_pred cCccceEEEEhhhhccCceEEEEEeeeeeEeeccCC----CceeecccCCCCChHHhhccCCCCCccCccEecCCCEEEE
Confidence 999999999999999999999999999987643321 122333 55555567899999999999999999999999
Q ss_pred EeecCC---------------------CcEEEeeccCCCcEEEEEEEEEec-CCCCC-----ceEEEEEEeeecCCCccc
Q 002296 800 IYDKTT---------------------NSWRTNSRKGSESVFVDYVAVDMK-NSKNL-----PQKANIRFRHTRNPIIGD 852 (940)
Q Consensus 800 ~~~~~~---------------------~~~~~~~~~~~e~g~V~~v~~~~~-~~~~~-----~~~v~i~~r~~R~p~iGD 852 (940)
|++++. .++++++++.+++|+||+|.++.+ .+|+. .+.|+|++|+.|+|+|||
T Consensus 805 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~~~g~V~~v~~~~~~~~~~~~~~~~~~~vkv~ir~~R~p~iGD 884 (1112)
T PRK00405 805 KVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNKLVKVYIAQKRKIQVGD 884 (1112)
T ss_pred EecCCCccccChhhhhhhhhhcccccccccceEEcCCCCCEEEEEEEEeeccccCCccCcCcceEEEEEEeeecccCccc
Confidence 987632 234688999999999999999987 55421 468999999999999999
Q ss_pred ceeccCCCccEEeeeecCCCcCccCCCCCcCcEEeCCCCccccccHHHHHHHHHHHHHhhchhHH
Q 002296 853 KFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVAYMENLW 917 (940)
Q Consensus 853 Kf~sRHGqKGvvs~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~G~~~ 917 (940)
|||||||||||||+|||+|||||+ +||++|||||||||||||||||||+|+++||||++.|.+.
T Consensus 885 KfasRHGqKGvis~i~~~eDMPf~-~~G~~pDiIiNPhg~PSRMtiGql~E~~~gk~~~~~g~~~ 948 (1112)
T PRK00405 885 KMAGRHGNKGVVSRILPVEDMPYL-EDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKF 948 (1112)
T ss_pred chhhccCCceeEEeEeccCCCCcC-CCCCCCcEEECCCCCcccccHHHHHHHHhhHHHHhcCCeE
Confidence 999999999999999999999999 9999999999999999999999999999999999999774
No 9
>CHL00001 rpoB RNA polymerase beta subunit
Probab=100.00 E-value=4.7e-154 Score=1416.13 Aligned_cols=749 Identities=19% Similarity=0.258 Sum_probs=597.4
Q ss_pred CCccCchhhHHHHHHHHHHHHHHHHHHHH-------------------------------HHHHHcCCeeeeEEEEEEEE
Q 002296 7 ADFEPLRELVRHHIESFDYMLDEGLSEMF-------------------------------DHCRQAKISYTGKLMADVEF 55 (940)
Q Consensus 7 ~~~~~~~~Lv~~hi~SFn~Fi~~gl~~ii-------------------------------~ecR~r~~TYsa~l~v~i~~ 55 (940)
.....+++|+++|++||||||++||++++ +|||+|++||+|||+|++.+
T Consensus 7 ~~~~~~P~Lv~~Q~~SF~~Fl~~gL~~i~~~~~pI~~~~~~~~~~~~~~~~~l~~P~~~p~ear~r~lTYsa~l~v~v~l 86 (1070)
T CHL00001 7 EGMSTIPGFNQIQFEGFCRFIDQGLTEELSKFPKIEDTDQEIEFQLFVETYQLVEPLIKERDAVYESLTYSSELYVPAGL 86 (1070)
T ss_pred CCccCCCCHHHHHHHHHHHHHHHhHHHHHHhcCCeECCCCCEEEEEEeCeEEECCCCCCHHHHHHhCCCCCceeEEEEEE
Confidence 34457899999999999999999999999 89999999999999999998
Q ss_pred EEecCCCceEeeEEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeccCCccEEEEeccc
Q 002296 56 QYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSF 135 (940)
Q Consensus 56 ~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~~~~r~~~ 135 (940)
... ..+++.+++|++|+||+| |+||||||||+||||++|+.+++|.++.....
T Consensus 87 ~~~-~~~~i~~~~V~iG~iPlM------------------------t~gG~FIING~ERVIVsQ~~rSpg~~~~~~~~-- 139 (1070)
T CHL00001 87 IWK-KSRDMQEQTVFIGNIPLM------------------------NSLGTFIINGIYRVVINQILRSPGIYYRSELD-- 139 (1070)
T ss_pred EEc-CceeEEEeEEEEecCCcc------------------------CCCcEEEEcCcEEEEEEEEeccCCEEEEEecC--
Confidence 743 234566789999999999 45999999999999999999999988766431
Q ss_pred cCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHhhHHHhccCCCHHHHHHHhcccccchhhc
Q 002296 136 RDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKK 215 (940)
Q Consensus 136 ~~~~~~~t~~~v~~rs~~~~~~s~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~eI~~~i~~~~~~~~~~ 215 (940)
++.+..|++ .+.+.+. .|+.+.++.++.+|++++..+ +||+++||||||+ +|+||++.++ ++
T Consensus 140 ~~~~~~y~a---~iis~rg----swl~~e~d~~~~i~vri~~~~---kiPi~ilLrALG~-sd~eIl~~~~--~~----- 201 (1070)
T CHL00001 140 HNGISVYTG---TIISDWG----GRLELEIDRKARIWARVSRKQ---KISILVLLSAMGL-NLREILDNVC--YP----- 201 (1070)
T ss_pred CCCceeEEE---EEEecCC----CceEEEEecCCeEEEEecCCC---cccHHHHHHHcCC-CHHHHHHHhC--cH-----
Confidence 112233444 4444322 378888888899999988753 7999999999999 5999999985 11
Q ss_pred ccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhccccccccCCCCccHHHHHHHHHHhHhccC------CCCC---
Q 002296 216 EKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVH------LNDN--- 286 (940)
Q Consensus 216 ~~~~~~~~~~~~~~~~ll~~~~~~~i~t~~~al~yig~~fr~~~~~~~~~~~~~~~~~~L~~~ll~H------l~~~--- 286 (940)
+.+..++.+..+..+.|+++|+.||++++... +......+.++.+|.+.+|+| +|..
T Consensus 202 -----------~~l~~~l~~~~~~~~~t~e~Al~~i~~~l~~r---~~~~~~~~~a~~~l~~~ff~~rY~Lg~vGr~~~n 267 (1070)
T CHL00001 202 -----------EIFLSFLNDKEKKKIGSKENAILEFYQQFACV---GGDPVFSESLCKELQKKFFQQRCELGRIGRRNMN 267 (1070)
T ss_pred -----------HHHHHHHHHHhhccccCHHHHHHHHHHhhccC---CCCcchHHHHHHHHHHHhccccccccccCchhhh
Confidence 12233333333346889999999999987321 223445678999999999998 7732
Q ss_pred -c------chHHHH-----HHHHHHHHHhcCCCCCCCCccccccceecccchhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 002296 287 -N------DKFNLL-----IFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENN 354 (940)
Q Consensus 287 -~------~K~~~L-----~~MirkLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~ 354 (940)
. .|+.+| ++|+++|+.+..|....||+|||+||||+++|+||+++||..|+++.+.++..+.+.+++
T Consensus 268 ~kl~~~~~~~~~~L~~~Di~~~i~~Ll~l~~G~~~~DDiDhLgNKRvr~vGeLL~~qfr~~l~r~~r~ik~~m~~~~~~- 346 (1070)
T CHL00001 268 RKLNLDIPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRR- 346 (1070)
T ss_pred hhhcccccccceEecHHHHHHHHHHHHHhhcCCCCccchhHHhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-
Confidence 1 345555 999999999999999999999999999999999999999988888887777777654332
Q ss_pred CCcccccchHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhhcccc---cCCccc
Q 002296 355 GKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVH---RGASFA 431 (940)
Q Consensus 355 ~~~~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSh~Rrv~---rg~~~~ 431 (940)
.+.+ .++.++ ++++||++|++||+| +||||+++|+|+++.|||+||++ +|+..+
T Consensus 347 ~~~~------~~~~li---n~~~It~~ik~ff~t--------------s~LSQflDqtNpLseltHkRRlsslGpgglsr 403 (1070)
T CHL00001 347 KLIP------TPQNLV---TSTPLTTTYESFFGS--------------HPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTG 403 (1070)
T ss_pred cccC------CHHHhh---CcchHHHHHHhhhcC--------------CcceeeeccCCHHHhhhhhhcccccCCCCccc
Confidence 2211 144455 456899999999997 79999999999999999999999 455556
Q ss_pred ccccccccccCCCCccccccCCCCCCccccccccccceeEEeeccCCCCcccccchhhHHHHHHHHhCCCeecCCccccC
Q 002296 432 GLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKS 511 (940)
Q Consensus 432 ~~K~t~vR~Lhps~wGfiCPveTPEG~~cGLvk~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~~g~~~~~~~~~~~ 511 (940)
+++.++||+|||||||||||+|||||++||||++||++|+|+.....+++ |+++ +...+...+ ..++..
T Consensus 404 ~~a~fevRdvHpShyGRICPIETPEG~NiGLI~sLA~~A~In~~GfietP---~~~v-------~~~~~~~~i-~ylsa~ 472 (1070)
T CHL00001 404 RTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESP---FYEI-------SERSKEERM-VYLSPS 472 (1070)
T ss_pred cccCCcccccCccccccccCCCCCCcccccchhhhhhhcccccCCCcccc---eeee-------cccccccee-EEcccc
Confidence 77778999999999999999999999999999999999999976665533 3333 223333322 111111
Q ss_pred CCCcceEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCCceEEecCCCceeceEEeccCC
Q 002296 512 GPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLP 591 (940)
Q Consensus 512 ~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~~d~gR~~RPv~~~~~~ 591 (940)
.++.+.|+ ||.|+|..... ..+. .+ |+..
T Consensus 473 -ee~~~~Ia-~g~~~~~~~~~------------------~~~~-----~~----------------------~~r~---- 501 (1070)
T CHL00001 473 -EDEYYMIA-AGNSLALNQGI------------------QEEQ-----VV----------------------PARY---- 501 (1070)
T ss_pred -ccCceEEE-eCceeeccCCc------------------cccc-----ee----------------------EEEe----
Confidence 24557787 99998742110 0000 00 1110
Q ss_pred CCCCCceeeecccceeeeeeecCCCCCCCCCCCccceecccCCCccccceeecccCCCCCCCccchhhcccccccccccc
Q 002296 592 SEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSV 671 (940)
Q Consensus 592 ~~~~~~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~ilsv~AslIPF~~HNqspRn~yq~~M~KQaig~~~ 671 (940)
-++++.++.. + .||+||+|.+|+|++||||||+||||||||+|||||||||||+..
T Consensus 502 -------------~~e~~~i~~~--~---------i~~~dIsP~qi~svaasLIPFleHndanRalmgsnMqrQAvpll~ 557 (1070)
T CHL00001 502 -------------RQEFLTIAWE--Q---------IHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSR 557 (1070)
T ss_pred -------------cCeEEEEchH--H---------CcEEeeChhhhhhhhhhcCCCccccCcchhhhhhccchhcccccc
Confidence 0224556554 2 599999999999999999999999999999999999999999987
Q ss_pred ee---------EEEec-----------------c-----------C-ceeeccC---------CCeeeEeccceeecC--
Q 002296 672 QA---------LKFRA-----------------D-----------Q-KLYHLQT---------PQTPIVRTNTYTKYG-- 702 (940)
Q Consensus 672 ~n---------~~~R~-----------------d-----------~-~~y~L~~---------~Q~Plv~t~~~~~~~-- 702 (940)
.+ +..|. | + ..|++.| ||||||+++.+...|
T Consensus 558 ~~~p~VgTG~E~~~~~ds~~~i~a~~~G~V~~vd~~~I~i~~~~~~~~y~l~~y~rsnq~t~~~QkPlV~~g~~v~~g~~ 637 (1070)
T CHL00001 558 SEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQI 637 (1070)
T ss_pred CCCCEeecCcchhhhhcccceeEEccCCEEEEEeCCEEEEEcCCCeEEEEeeceeccCCCcccccCCEEecCCEEccCCE
Confidence 76 55555 5 3 3466668 999999999776654
Q ss_pred --------CCCCCCCceeEEEEEeccCCCCCceEEEecchhccCcceeeEEEEEEEEeeccCCCcCccceeec--cCCCC
Q 002296 703 --------IDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFR--RNKDA 772 (940)
Q Consensus 703 --------~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~ 772 (940)
.+++|+|+|++||||||+||||||||||||++++||+|++.+|++|.+++...+. ..+.++ .|+.+
T Consensus 638 ladg~~~~~gel~~G~N~~VA~m~~~GYn~EDAiiin~~~v~~g~~~s~~~~~~~~~~~~~~~----g~e~i~~~~p~~~ 713 (1070)
T CHL00001 638 LADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQ----GPERITKEIPHLE 713 (1070)
T ss_pred eccChhhccccccCCccceeeeeeccccccchhhhhhhhhhcCCceEEEEEeeeeEEEeccCC----CcceEeccCCCCc
Confidence 7999999999999999999999999999999999999999999999988654332 124444 46666
Q ss_pred hhhhcccCCCCCcccCcEecCCCcEEEEeecCC-----------------------CcEEEeeccCCCcEEEEEEEEEec
Q 002296 773 KSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT-----------------------NSWRTNSRKGSESVFVDYVAVDMK 829 (940)
Q Consensus 773 ~~~~~~ld~dGi~~~g~~v~~gd~l~~~~~~~~-----------------------~~~~~~~~~~~e~g~V~~v~~~~~ 829 (940)
+..+++||+||++++|++|++||||+||++++. .++.+++++.+++|+|++|.++..
T Consensus 714 ~~~~~~Ld~dGi~~~G~~v~~gDilvgK~~p~~~~~~~~~~~~~~~~~if~~~~~~~~d~sl~~~~~~~g~V~~v~~~~~ 793 (1070)
T CHL00001 714 AHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQK 793 (1070)
T ss_pred hhhhhccCCCCCccCCcEecCCCEEEEEecCCcccccccCcchhhhhhhhccccCcceeCeEECCCCCceEEEEEEEEec
Confidence 667899999999999999999999999987741 234588888999999999999985
Q ss_pred CCC--CCceEEEEEEeeecCCCcccceeccCCCccEEeeeecCCCcCccCCCCCcCcEEeCCCCccccccHHHHHHHHHH
Q 002296 830 NSK--NLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAA 907 (940)
Q Consensus 830 ~~~--~~~~~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~g 907 (940)
.++ +....|+|++|+.|+|++|||||||||||||||+|||+|||||+ +||++|||||||||||||||||||+|+++|
T Consensus 794 ~~~~~~~~~~vkv~i~~~R~~~vGDK~asRHGqKGvvs~i~~~eDMPf~-~dG~~pDiIlNP~gvPSRMtiGqllE~~~G 872 (1070)
T CHL00001 794 KGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYL-QDGTPVDMVLNPLGVPSRMNVGQIFECLLG 872 (1070)
T ss_pred ccCCCCCcEEEEEEEEEEecCCCCcccccccCCcceEeeeecccCCCcc-cCCCCCceeeccccccccccHHHHHHHHhH
Confidence 322 34678999999999999999999999999999999999999999 999999999999999999999999999999
Q ss_pred HHHhhchhHH-----HHHhhhhhhhHH
Q 002296 908 KVVAYMENLW-----MQHHLQIQSRKL 929 (940)
Q Consensus 908 k~~~~~G~~~-----~~~~~~~~~~~~ 929 (940)
|||++.|.++ ++.+..+.+|++
T Consensus 873 ~a~~~~g~~~~~~pf~~~~~~~~~~~~ 899 (1070)
T CHL00001 873 LAGDLLNRHYRIAPFDERYEQEASRKL 899 (1070)
T ss_pred HHHhhcCceeeeccCCCcchhhhhhhh
Confidence 9999999775 334555666654
No 10
>CHL00207 rpoB RNA polymerase beta subunit; Provisional
Probab=100.00 E-value=1.2e-141 Score=1299.18 Aligned_cols=753 Identities=21% Similarity=0.307 Sum_probs=578.2
Q ss_pred ccCchhhHHHHHHHHHHHHHHHHHHHH-------------------------------HHHHHcCCeeeeEEEEEEEEEE
Q 002296 9 FEPLRELVRHHIESFDYMLDEGLSEMF-------------------------------DHCRQAKISYTGKLMADVEFQY 57 (940)
Q Consensus 9 ~~~~~~Lv~~hi~SFn~Fi~~gl~~ii-------------------------------~ecR~r~~TYsa~l~v~i~~~~ 57 (940)
...+++|++.|++||+||+++||++++ .|||+|++||++||+|++++..
T Consensus 4 ~~~~Pdll~iQ~~SF~~FL~~GL~~~~~~~~pI~~~~~~~~l~~~~~~y~l~~P~~~~~Ea~~r~~TYsa~l~v~~~l~~ 83 (1077)
T CHL00207 4 NFALPDFLEIQRTSFCWFLNEGLNEELNIFSKIFDYTGNLELLLFGKNYKLKYPKYNLLSAKSYDSNYSIQIYLPLKFIN 83 (1077)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHHHHHHHhcCCeECCCCCEEEEEecceEEEcCCCCCHHHHHHhCCccceeEEEEEEEEE
Confidence 456899999999999999999999998 8999999999999999999875
Q ss_pred ecCCCceEeeEEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeccCCccEEEEeccccC
Q 002296 58 LDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRD 137 (940)
Q Consensus 58 ~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~~~~r~~~~~ 137 (940)
. .++++++++|++|+||+|+. +|||||||+||||++|+.++++..+.... .+.
T Consensus 84 ~-~~~~i~~~~V~lG~iPlMT~------------------------~GtFIING~ERViVsQl~RSPGiyf~~~~--~k~ 136 (1077)
T CHL00207 84 L-KTNKIKFINYLIGNLPKMTQ------------------------RGTFIINGLERVIVSQIIRSPGIYFKKEI--KKN 136 (1077)
T ss_pred c-CCceEEEEEEEEeccCccCC------------------------CCEEEEcCceeEEEEEeccCCeEEEEEec--CcC
Confidence 4 24566788999999999985 99999999999999999888874433221 122
Q ss_pred CCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHhhHHHhccCCCHHHHHHHhcccccchhhccc
Q 002296 138 RREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEK 217 (940)
Q Consensus 138 ~~~~~t~~~v~~rs~~~~~~s~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~eI~~~i~~~~~~~~~~~~ 217 (940)
.+..|++..++.||. |+.++++.++.+|++++..+ +||+++||||||+ ||+||++.+..
T Consensus 137 ~~~~y~a~IIp~rGs-------wl~~e~d~k~~i~vridr~r---Kipit~lLrALGl-s~~eIl~~~~~---------- 195 (1077)
T CHL00207 137 SNKIYSATLIPNRGS-------WIKFELDKNKEIWIRIDKNR---KKPLIIFLKALGL-TDQDIYSRLTK---------- 195 (1077)
T ss_pred CceEEEEEEEcCCCc-------eEEEEEcCCCeEEEEecCCc---eeeHHHHHHHhCC-CHHHHHHHHhc----------
Confidence 334688888877773 99999999999999998654 6999999999999 99999998851
Q ss_pred CCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhcccccc---------------ccCCCCccHHHHHHHHHHhHhccC
Q 002296 218 GAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPV---------------IDGLQSESYYAVAETVIRDYIFVH 282 (940)
Q Consensus 218 ~~~~~~~~~~~~~~ll~~~~~~~i~t~~~al~yig~~fr~~---------------~~~~~~~~~~~~~~~~L~~~ll~H 282 (940)
. .+. +.+..++ .+.+..++++|+.+|++++++. ++.+.+|+...+||..|++++-.+
T Consensus 196 ~--~~~---~~~~~~l---~~~~~~~~e~Al~~Iy~~lrp~~~~~~~~a~~~l~~~ff~~~rYdLg~vGR~klN~kl~~~ 267 (1077)
T CHL00207 196 S--EFL---KKLKPIL---LNSNSYTNEEILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLN 267 (1077)
T ss_pred c--chH---HHHHHHH---hccCcccHHHHHHHHHHhcCCCCCccHHHHHHHHHHHhcChhcccccccchhhhhhhccCC
Confidence 0 001 1112222 2235668888999998887652 112344444445555555554444
Q ss_pred CC--CCcchHHHHHHHHHHHHHhcCCCCCCCCccccccceecccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccc
Q 002296 283 LN--DNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDF 360 (940)
Q Consensus 283 l~--~~~~K~~~L~~MirkLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~ 360 (940)
+. ....++..++.|+++|+.+..|....||+|||+||||+++|+||+++|+-. |.++.+.++++++.... -.+
T Consensus 268 ~~~~~~~l~~~Dil~~i~~Li~l~~g~~~~DDiDHL~NRRvrsvGELlq~qfr~g----l~rler~ike~m~~~~~-~~~ 342 (1077)
T CHL00207 268 IPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIG----LKRLERILRNRMTICDI-DSL 342 (1077)
T ss_pred cCccCceecHHHHHHHHHHHHHhhcCCCcccchhhhhcccccchhHHHHHHHHHH----HHHHHHHHHHHhhhccc-ccC
Confidence 32 134567789999999999999999999999999999999999999999854 55555556655553111 011
Q ss_pred cchHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhhcccc---cCCccccccccc
Q 002296 361 FNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVH---RGASFAGLRTTS 437 (940)
Q Consensus 361 ~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSh~Rrv~---rg~~~~~~K~t~ 437 (940)
.+++++ ++++||.+|++||++ +++||.++++|+++.|||+||++ +|++.+++++++
T Consensus 343 ----tp~~li---n~k~lt~~ikeFFgs--------------s~LSQfmDQtNpLselTHKRRlsaLGpGGLsR~ra~fe 401 (1077)
T CHL00207 343 ----SKFNLI---NPKPLIALIREFFGS--------------SQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFA 401 (1077)
T ss_pred ----Chhhcc---cchhHHHHHHHhhcc--------------CCccceecccChHHhhhccceeeccCCCcccccccCCc
Confidence 134444 467999999999985 67788888888889999999999 688889999999
Q ss_pred ccccCCCCccccccCCCCCCccccccccccceeEEeeccCCCCcccccchhhHHHHHHHHhCCCeecCCccccCCCCcce
Q 002296 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVL 517 (940)
Q Consensus 438 vR~Lhps~wGfiCPveTPEG~~cGLvk~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~ 517 (940)
+|++||||||||||+|||||++||||++||++|+|+. +|++.. | |
T Consensus 402 vRdvH~thyGRiCPIETPEG~n~Gli~~la~~~~in~------------------------~Gfiet-P----------y 446 (1077)
T CHL00207 402 VRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINK------------------------FGFIET-P----------F 446 (1077)
T ss_pred ccccCccccccccCCCCCCCcccccccchhhhccccC------------------------CCceeC-c----------e
Confidence 9999999999999999999999999999999999973 566654 3 5
Q ss_pred EEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCCceEEecCCCceeceEEeccCCCCCCCc
Q 002296 518 SVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQN 597 (940)
Q Consensus 518 ~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~~d~gR~~RPv~~~~~~~~~~~~ 597 (940)
..+.||++.- .+ ++ -+| ..+.|-.|+....+ +. ..+.|.+.-..+.++..
T Consensus 447 ~~v~~g~v~~-~~--~i-------~yl--------sa~~e~~~~Ia~~~-----~~-~~~~~~~~~~~v~~r~~------ 496 (1077)
T CHL00207 447 YKVINGKVKK-FG--NP-------IYL--------TADSEDLYRIAPND-----IN-LNKNNYFKKNIIPVRYK------ 496 (1077)
T ss_pred EEEEcCcccc-cC--ce-------eec--------ChHHhcCcEEEecC-----cc-CCCCCcccCCEEEEEEC------
Confidence 5557887521 00 00 011 11111112211111 00 12233333333332211
Q ss_pred eeeecccceeeeeeecCCCCCCCCCCCccceecccCCCccccceeecccCCCCCCCccchhhccccccccccc-------
Q 002296 598 IELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFS------- 670 (940)
Q Consensus 598 iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~ilsv~AslIPF~~HNqspRn~yq~~M~KQaig~~------- 670 (940)
++|..++. ++ .++++++|.+++|++||||||.+||||+|++||||||||||++.
T Consensus 497 --------~ef~~~~~--~~---------v~~~~vsp~Q~~SvaasLIPFLehdDanRaLMGsnMqrQaVPll~~e~p~V 557 (1077)
T CHL00207 497 --------QEFKTVNP--SK---------VDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIV 557 (1077)
T ss_pred --------CcEEEECh--HH---------ceEEEeCcchhcchhhhcCCcccccccchhhhhhccccccccccccCCCeE
Confidence 12222221 11 58999999999999999999999999999999999999999652
Q ss_pred ----------------------------ceeEEEecc---Cceeecc----------CCCeeeEeccceeecC-------
Q 002296 671 ----------------------------VQALKFRAD---QKLYHLQ----------TPQTPIVRTNTYTKYG------- 702 (940)
Q Consensus 671 ----------------------------~~n~~~R~d---~~~y~L~----------~~Q~Plv~t~~~~~~~------- 702 (940)
+..+..|.+ ...|.|. ..|||+|+.+.....|
T Consensus 558 gTg~e~~~a~ds~~~i~a~~~G~v~~v~~~~I~i~~~~~~~~~y~l~~~~rsNq~t~i~qrp~V~~G~~v~~G~iladg~ 637 (1077)
T CHL00207 558 GTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGS 637 (1077)
T ss_pred ECCcchHhhhhcchheEeccCcEEEEecCcEEEEEeCCCceeEEEeccccccccCceeecccccCCCCEEecCCEEecch
Confidence 112233332 2346665 4999999999998766
Q ss_pred ---CCCCCCCceeEEEEEeccCCCCCceEEEecchhccCcceeeEEEEEEEEeeccCCCcCccceeec--cCCCChhhhc
Q 002296 703 ---IDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFR--RNKDAKSLHS 777 (940)
Q Consensus 703 ---~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~ 777 (940)
++|+|+|+|++||||||+||||||||||||++++||+|++.+|++|.+++...+. ..+.|+ .|+..+..++
T Consensus 638 ~~~~~el~lG~N~lVA~m~y~GYN~EDAiiink~~v~rg~f~Si~~~~~~~e~~~~~~----g~e~i~~~~p~~~~~~~~ 713 (1077)
T CHL00207 638 DIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKL----GSEEITRNIPNVSEYSLK 713 (1077)
T ss_pred hccCCcccCCcccEEEEEeeeccccchhhhhhhhhhcCCceEEEEEEEeeeEEeecCC----CceEEeccCCCCChHHhh
Confidence 7999999999999999999999999999999999999999999999987654332 224444 5666666789
Q ss_pred ccCCCCCcccCcEecCCCcEEEEeecCC---------------------CcEEEeeccCCCcEEEEEEEEEecCCCCCc-
Q 002296 778 VIDSDGLPYVGQMIHPGEPYCSIYDKTT---------------------NSWRTNSRKGSESVFVDYVAVDMKNSKNLP- 835 (940)
Q Consensus 778 ~ld~dGi~~~g~~v~~gd~l~~~~~~~~---------------------~~~~~~~~~~~e~g~V~~v~~~~~~~~~~~- 835 (940)
+||+||+|++|++|++||||+||++++. .++.+++++++++|+|++|.++.++++++.
T Consensus 714 ~LD~dGiv~iG~~V~~gDilvgK~tp~~~~~~~~~~~ll~~i~~~~~~~~kd~sl~~~~~~~g~V~~V~~~~~~~~~~~~ 793 (1077)
T CHL00207 714 NLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELK 793 (1077)
T ss_pred ccCccCCCcCCcEeCCCCEEEEEecCccccccChhhhhhhhhhccCCCcceEeEEEcCCCCcEEEEEEEEEecCCCCccc
Confidence 9999999999999999999999987631 246689999999999999999986544332
Q ss_pred ----eEEEEEEeeecCCCcccceeccCCCccEEeeeecCCCcCccCCCCCcCcEEeCCCCccccccHHHHHHHHHHHHHh
Q 002296 836 ----QKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVA 911 (940)
Q Consensus 836 ----~~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~ 911 (940)
..|+|++|+.|+|+||||||||||||||||+|||+|||||+ +||++|||||||||||||||||||+|+++||||+
T Consensus 794 ~~~~~~vkv~i~~~R~p~vGDKfasRHGqKGVvs~i~p~eDMPf~-~dG~~pDiIlNPhg~PSRMtiGqllE~~lGka~~ 872 (1077)
T CHL00207 794 FGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYL-PDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGD 872 (1077)
T ss_pred ccccEEEEEEEEEEecCCcccccccccCCceeEEeeeccCCCCcc-CCCCCccEEECCccccccccHHHHHHHHHHHHHH
Confidence 46999999999999999999999999999999999999999 9999999999999999999999999999999999
Q ss_pred hchhHH-----HHHhhhhhhhHHHHH
Q 002296 912 YMENLW-----MQHHLQIQSRKLMEI 932 (940)
Q Consensus 912 ~~G~~~-----~~~~~~~~~~~~~~~ 932 (940)
+.|..+ .+.+..+.++.+++.
T Consensus 873 ~l~~~~~~tpF~~~~~~~~~~~l~~~ 898 (1077)
T CHL00207 873 NLNKRFKILPFDEMYGSEYSRILINN 898 (1077)
T ss_pred hcCCcEeeccCCCCcHHHHHHHHHhh
Confidence 877554 233455666666643
No 11
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=2.5e-129 Score=1226.97 Aligned_cols=758 Identities=21% Similarity=0.281 Sum_probs=574.7
Q ss_pred cCchhhHHHHHHHHHHHHH------HHHHHHH-----------------------------HHHHHcCCeeeeEEEEEEE
Q 002296 10 EPLRELVRHHIESFDYMLD------EGLSEMF-----------------------------DHCRQAKISYTGKLMADVE 54 (940)
Q Consensus 10 ~~~~~Lv~~hi~SFn~Fi~------~gl~~ii-----------------------------~ecR~r~~TYsa~l~v~i~ 54 (940)
..+|+|++.|.+||+||++ +||++++ .||++|++||++||+|+++
T Consensus 22 ~~iPdLleIQ~~SF~~FLq~~~~~~~GL~e~f~~~fPI~d~~g~~~Lefv~Y~l~~Pk~~~~Ec~~rg~TYsapL~v~~r 101 (2890)
T PRK09603 22 LEVPNLLLLQRDSYDSFLYSKDGKESGIEKVFKSIFPIQDEHNRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVR 101 (2890)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccccHHHHHHhcCCeECCCCcEEEEEEEEEeCCCCCCHHHHHhhCCcccccEEEEEE
Confidence 4689999999999999997 7999998 8999999999999999999
Q ss_pred EEE---ecCCC------ceEeeEEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeccCC
Q 002296 55 FQY---LDAGS------PVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQN 125 (940)
Q Consensus 55 ~~~---~~~~~------~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N 125 (940)
+.+ +..++ ++++++|++|+||+|+. .|+|||||+||||++|++++|+
T Consensus 102 L~~~~~~~~t~~~~~ikeikeq~VylGdiPLMT~------------------------~GTFIING~ERVIVsQL~RSPG 157 (2890)
T PRK09603 102 LILWEKDTKSGEKNGIKDIKEQSIFIREIPLMTE------------------------RTSFIINGVERVVVNQLHRSPG 157 (2890)
T ss_pred EEEeeccccccccccccceEEeeEEEecCCccCC------------------------CceEEEcCceeEEEeeeccCCe
Confidence 975 21122 46788999999999997 8999999999999999999999
Q ss_pred ccEEEEeccccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHhhHHHhccCCCHHHHHHHh
Q 002296 126 YPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHL 205 (940)
Q Consensus 126 ~~~~~~r~~~~~~~~~~t~~~v~~rs~~~~~~s~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~eI~~~i 205 (940)
..|.....+..+.+..|++..++.||. |+.++++.++.+|++++.++ ++|+.+||||||+ |++||++.+
T Consensus 158 VyF~~~~~k~~s~k~lysa~IIP~RGs-------WLefE~D~kd~l~vrIDrkr---Kipit~lLrAlG~-s~edIl~~f 226 (2890)
T PRK09603 158 VIFKEEESSTSLNKLIYTGQIIPDRGS-------WLYFEYDSKDVLYARINKRR---KVPVTILFRAMDY-QKQDIIKMF 226 (2890)
T ss_pred eEEeeccCcCCCCceeEEEEEecCCcc-------eEEEEEcCCCeEEEEEcCcc---eecHHHHHHHhCC-CHHHHHHHh
Confidence 654433221222344599999999985 99999999999999999765 6999999999999 899999977
Q ss_pred ccc-------------ccchhhc-------------------------------ccC-----CC--------------C-
Q 002296 206 TCC-------------YDEKYKK-------------------------------EKG-----AV--------------G- 221 (940)
Q Consensus 206 ~~~-------------~~~~~~~-------------------------------~~~-----~~--------------~- 221 (940)
... +..+... ..+ .. +
T Consensus 227 ~~~~~~~i~~~~~~~~~~~~~l~~~~~~di~d~~g~vlv~~g~rit~~~~~~l~~~g~k~l~~~~~~l~g~~laedivd~ 306 (2890)
T PRK09603 227 YPLVKVRYENDKYLIPFASLDANQRMEFDLKDPQGKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPVMVG 306 (2890)
T ss_pred cccceEEEcccceeecccHHHhcCccceeecccCCCEEEecCccccHHHHHHHHhcCCceeccchhhhcceeeeeeccCc
Confidence 410 0000000 000 00 0
Q ss_pred ChhhHH----HHHHHHHHHHhcc--------------------------------------cccHHHHHHHHhcccccc-
Q 002296 222 SPLVSE----RVKIILAEVQDLS--------------------------------------LTTRLQCLQHIGEHFQPV- 258 (940)
Q Consensus 222 ~~~~~~----~~~~ll~~~~~~~--------------------------------------i~t~~~al~yig~~fr~~- 258 (940)
+..+.+ .-+..++.+.+.+ ..++++|+..|.+++|+.
T Consensus 307 ~Evl~~~~~~Itee~le~i~~~gi~~i~vl~~~~~~~~~~i~~t~~~d~~~~~~~~~t~~~~~~~eeAl~~iyr~lrpge 386 (2890)
T PRK09603 307 KEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSESLKLLKQTEKIDDENALAAIRIHKVMKPGD 386 (2890)
T ss_pred cceeeccCChhcHHHHHHHHHcCCceEEEEeecccccccccccccccccccchhhhhccccccchHHHHHHHHhccCCCC
Confidence 000000 0011122221110 014577888888887651
Q ss_pred --------------ccCCCCccHHHHHHHHHHhHhccCCCC--CcchHHHHHHHHHHHHHhcCCCCCCCCccccccceec
Q 002296 259 --------------IDGLQSESYYAVAETVIRDYIFVHLND--NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEIL 322 (940)
Q Consensus 259 --------------~~~~~~~~~~~~~~~~L~~~ll~Hl~~--~~~K~~~L~~MirkLl~~~~g~~~~Dd~D~l~NkRv~ 322 (940)
++.+.+|+..++||..||+.|-.+... ...-...+...++.|+.+..|....||+|||+||||+
T Consensus 387 p~~~e~A~~l~~~lFFn~~rYdLg~vGR~klN~kL~l~~~~~~~~Lt~~Dil~~i~~li~l~~g~~~~DDiDhL~NRRvr 466 (2890)
T PRK09603 387 PVTTEVAKQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIR 466 (2890)
T ss_pred CCcHHHHHHHHHHHhcCcccccccccchhhhHhhhCCCCCCcccEecchhHHHHHHHHHHHHhCCCCCCcchhhhcchhh
Confidence 345778888899999999999766431 2223345779999999999999999999999999999
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccccchHHHHHHHhcCCCcchHHHHHHHhcccCcccccccccccc
Q 002296 323 LPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQR 402 (940)
Q Consensus 323 l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~ 402 (940)
++|+||+++|+- .|.+|++.++++++......+ .-.++.++ ++++++..+++||+|+.+ +|+|+|+
T Consensus 467 ~vGELl~~qfr~----gl~rler~irerm~~~~~~~~---~~~p~~li---n~k~i~~~ikeFFgssqL----SQfmDQt 532 (2890)
T PRK09603 467 AVGELLANELHS----GLVKMQKTIKDKLTTMSGAFD---SLMPHDLV---NSKMITSTIMEFFMGGQL----SQFMDQT 532 (2890)
T ss_pred hHHHHHHHHHHH----HHHHHHHHHHHHHHhhhcccc---ccChhhhh---ccHHHHHHHHHHhccCch----hhhhccc
Confidence 999999999884 566666666666653111111 11234454 467999999999998654 3556665
Q ss_pred cceEEEccccchHHHhhhhcccc---cCCcccccccccccccCCCCccccccCCCCCCccccccccccceeEEeeccCCC
Q 002296 403 AGYTVQAERLNFLRFISFFRAVH---RGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSR 479 (940)
Q Consensus 403 sGvsqvleRln~~~~lSh~Rrv~---rg~~~~~~K~t~vR~Lhps~wGfiCPveTPEG~~cGLvk~LA~~~~Is~~~~~~ 479 (940)
|++ +.|+|.||++ +|++.++++++++|++||||||||||+|||||+|||||++||.+|+|+
T Consensus 533 NpL----------seltHKRRlSaLGPGGlsr~ra~fevRdVH~shYGRiCPIETPEG~NiGLI~SLa~~a~in------ 596 (2890)
T PRK09603 533 NPL----------SEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVN------ 596 (2890)
T ss_pred Chh----------hhhhhcccccccCCCCccccccCCcccccCcccccccCCCCCCCCCcccchhhhhhheecc------
Confidence 555 4599999999 888889999999999999999999999999999999999999999997
Q ss_pred CcccccchhhHHHHHHHHhCCCeecCCccccCCCCcceEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeE
Q 002296 480 GNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVG 559 (940)
Q Consensus 480 ~~~~~~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~ 559 (940)
++|++.. | |..+.||++...+ .+|- .+.|-.
T Consensus 597 ------------------~~Gfiet-P----------y~kV~~g~v~~~i------------~yls--------a~eE~~ 627 (2890)
T PRK09603 597 ------------------DLGFIEA-P----------YKKVVDGKVVGET------------IYLT--------AIQEDS 627 (2890)
T ss_pred ------------------cCcceec-c----------eEEEecCccccce------------eeeC--------HHHhcC
Confidence 4566654 3 4445788743111 1111 111111
Q ss_pred EEEcCCCCCCCceEEecCCCceeceEEeccCCCCCCCceeeecccceeeeeeecCCCCCCCCCCCccceecccCCCcccc
Q 002296 560 YVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLS 639 (940)
Q Consensus 560 ~v~~~~~~~~~~i~i~~d~gR~~RPv~~~~~~~~~~~~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~ils 639 (940)
|+....+ + ...+.|++....+.++.. +++..++. + ..++++++|.+++|
T Consensus 628 ~~IA~a~-----~-~~~~~~~~~~~~v~~R~~--------------~e~~~~~~--~---------~v~~~dvsp~Q~vS 676 (2890)
T PRK09603 628 HIIAPAS-----T-PIDEEGNILGDLIETRVE--------------GEIVLNEK--S---------KVTLMDLSSSMLVG 676 (2890)
T ss_pred ceEeccC-----C-ccCCCCcccCCeEeEEEC--------------CceEEECh--H---------HceEEEeCccceee
Confidence 2211111 1 112345555544433322 12222221 1 16899999999999
Q ss_pred ceeecccCCCCCCCccchhhccccccccccc-----------------------------------ceeEEEeccC----
Q 002296 640 VVANLTPYSDHNQSPRNMYQCQMAKQTMGFS-----------------------------------VQALKFRADQ---- 680 (940)
Q Consensus 640 v~AslIPF~~HNqspRn~yq~~M~KQaig~~-----------------------------------~~n~~~R~d~---- 680 (940)
++||||||.+||||+|++||||||||||++. +..+.+|.+.
T Consensus 677 vaasLIPFLEhdDAnRALMGSNMQRQAVPLl~~e~piVgTG~E~~va~dSg~~i~a~~~G~V~yvd~~~I~i~~~~~~~~ 756 (2890)
T PRK09603 677 VAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGKEEA 756 (2890)
T ss_pred ehhhcCCccccCccccccccccchhhhhhhccccCCeEecCcchhhhccccceeEecCCeEEEEecCcEEEEEecCCCCc
Confidence 9999999999999999999999999999652 1123343321
Q ss_pred --ceeecc----------CCCeeeEeccceeecC----------CCCCCCCceeEEEEEeccCCCCCceEEEecchhccC
Q 002296 681 --KLYHLQ----------TPQTPIVRTNTYTKYG----------IDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRG 738 (940)
Q Consensus 681 --~~y~L~----------~~Q~Plv~t~~~~~~~----------~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~rG 738 (940)
..|.|. +.|||+|+.+.....| .+|+++|+|++||||||.|||+||||+||++.+..+
T Consensus 757 ~~~~Y~L~Ky~RSNQ~TcinqrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~GYNfEDAIlISERlV~eD 836 (2890)
T PRK09603 757 YIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDD 836 (2890)
T ss_pred eeeEEeeccccccCCCceeeeccEecCCCEeccCCEEecCcccccCeeccCcccEEEEeeeccccCccccccchhhhcCc
Confidence 247775 4999999999998876 599999999999999999999999999999999999
Q ss_pred cceeeEEEEEEEEeeccCCCcCccceeec--cCCCChhhhcccCCCCCcccCcEecCCCcEEEEeecCC-----------
Q 002296 739 MCHGQIYQTETIDLSDDGNKVDRGQKLFR--RNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT----------- 805 (940)
Q Consensus 739 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~~~~~~~----------- 805 (940)
.|+|.+...|.++..+.+. ..+.++ +|+.++...++||++||+++|++|++||||+||++|+.
T Consensus 837 ~fTSIHIee~ei~~r~Tk~----G~EeITrdIPnvse~~l~~LDe~GII~iGa~V~~GDILVGKvTPkge~~~tPEekLL 912 (2890)
T PRK09603 837 IFTSTHIYEKEVDARELKH----GVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLL 912 (2890)
T ss_pred cceEEEEeeeEEEEEecCC----CCcEEeccCCCCCHHHHhcCCCCCCEeeCCEECCCCEEEEeeccCCCCCCChHHHHH
Confidence 8777777777666555442 223333 68888889999999999999999999999999988773
Q ss_pred ----------CcEEEeeccCCCcEEEEEEEEEecC---------------------------------------------
Q 002296 806 ----------NSWRTNSRKGSESVFVDYVAVDMKN--------------------------------------------- 830 (940)
Q Consensus 806 ----------~~~~~~~~~~~e~g~V~~v~~~~~~--------------------------------------------- 830 (940)
.++.|++.+.+..|+|.+|.+++.+
T Consensus 913 raIFGeka~~vkDtSLrvp~G~~G~Vidv~~f~r~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 992 (2890)
T PRK09603 913 RAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDARVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQA 992 (2890)
T ss_pred HHHhcccccccccCceecCCCCcEEEEEEEEecccccchhHHHHHHHHHHHHHHhHhhHHHHHHHHHHHHHhhhhhcccc
Confidence 1355899999999999999998742
Q ss_pred -------------------------------------------------------------------------CCC----
Q 002296 831 -------------------------------------------------------------------------SKN---- 833 (940)
Q Consensus 831 -------------------------------------------------------------------------~~~---- 833 (940)
.|+
T Consensus 993 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~ 1072 (2890)
T PRK09603 993 ILEEPFSHNGKDYKEGDQIPKEEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPN 1072 (2890)
T ss_pred ccccccccccccccccccccHHHHhhCCHHHhhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcCCC
Confidence 011
Q ss_pred -CceEEEEEEeeecCCCcccceeccCCCccEEeeeecCCCcCccCCCCCcCcEEeCCCCccccccHHHHHHHHHHHHHhh
Q 002296 834 -LPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVAY 912 (940)
Q Consensus 834 -~~~~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~ 912 (940)
-.+.|+|++|+.|+|++|||||||||||||||+|||+|||||+ +||++||||+||||||||||||||+|+++||||+.
T Consensus 1073 Gv~~~VkV~ia~kR~~qvGDK~AgRHGnKGViS~I~p~EDMPfl-~dG~~pDIIlNPlGvPSRMnIGQilE~~LG~aa~~ 1151 (2890)
T PRK09603 1073 GVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYT-ADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKE 1151 (2890)
T ss_pred CcceEEEEEEEEeecccccchhhhccCCCeeEEEEEchhcCCCC-CCCCCCcEEECCCCCCccccHHHHHHHHHHHHHHh
Confidence 1357999999999999999999999999999999999999999 99999999999999999999999999999999999
Q ss_pred chhHH
Q 002296 913 MENLW 917 (940)
Q Consensus 913 ~G~~~ 917 (940)
.|..+
T Consensus 1152 lg~~i 1156 (2890)
T PRK09603 1152 FGKQI 1156 (2890)
T ss_pred cCcCh
Confidence 99774
No 12
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=8.6e-128 Score=1208.65 Aligned_cols=756 Identities=20% Similarity=0.294 Sum_probs=581.9
Q ss_pred cCchhhHHHHHHHHHHHHH-----HHHHHHH-----------------------------HHHHHcCCeeeeEEEEEEEE
Q 002296 10 EPLRELVRHHIESFDYMLD-----EGLSEMF-----------------------------DHCRQAKISYTGKLMADVEF 55 (940)
Q Consensus 10 ~~~~~Lv~~hi~SFn~Fi~-----~gl~~ii-----------------------------~ecR~r~~TYsa~l~v~i~~ 55 (940)
..+++|++.|.+||+||++ +||++++ .||++|++||++||+|++++
T Consensus 27 ~~~PdL~~iQ~~Sf~~Fl~~~~~~~GL~~~f~~ifPI~d~~g~~~lefv~y~l~~Pk~~~~Ec~~r~~TYsapl~v~~rL 106 (2836)
T PRK14844 27 DSLLDLVKVQKESYDSFTPKNKGNERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECIKRGITFSAQVIASIRL 106 (2836)
T ss_pred CCCCCHHHHHHHHHHHHhcCCCccccHHHHHHhcCCeECCCCCEEEEEEEEEeCCCCCCHHHHHhcCCcceeeEEEEEEE
Confidence 4689999999999999997 6999998 89999999999999999999
Q ss_pred EEec------------CC----------CceEeeEEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCce
Q 002296 56 QYLD------------AG----------SPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLE 113 (940)
Q Consensus 56 ~~~~------------~~----------~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~E 113 (940)
...+ .+ +++++++|++|+||+|+. .|+|||||+|
T Consensus 107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ikeq~VylGdiPLMT~------------------------~GTFIING~E 162 (2836)
T PRK14844 107 VIMQDGISLDEYKSIKESGDHSKLATVIKSIEEQEVHFCELPMMTD------------------------KGTFIINGVE 162 (2836)
T ss_pred EEeccccccccccccccccccccccccccceeeeeEEEecCCccCC------------------------CeEEEEcCcc
Confidence 7621 11 245678899999999996 8999999999
Q ss_pred eEEEEEEeccCCccEEEEecccc-CCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHhhHHHh
Q 002296 114 RVFRSVILPKQNYPMSMVRSSFR-DRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKA 192 (940)
Q Consensus 114 KVIr~qi~~~~N~~~~~~r~~~~-~~~~~~t~~~v~~rs~~~~~~s~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkA 192 (940)
|||++|++++|+..|.......+ +.+..|++..++.||. |+.++++.++.+|++++.++ ++|+++||||
T Consensus 163 RVIVSQL~RSPGVyF~~~~~kt~~sgk~lysa~IIP~RGs-------WLefE~D~kd~lyvRIDRkR---KiPiT~LLrA 232 (2836)
T PRK14844 163 KVIVSQMHRSPGVFFDSDKGKTYNSGKLIYSARVIPYRGS-------WLDIEFDVKDHLYFRIDRKR---KLPISVLLKA 232 (2836)
T ss_pred eEEEEcceeCCeEEEEcccCcccCCCceeEEEEEecCCcc-------eEEEEEcCCCeEEEEecCCe---eeeHHHHHHH
Confidence 99999999999965543322212 2334799999999985 99999999999999999766 6999999999
Q ss_pred ccCCCHHHHHHHhcccc--cc--hhh-------cccCC--------C---------------------------------
Q 002296 193 LVDTNDLEIFNHLTCCY--DE--KYK-------KEKGA--------V--------------------------------- 220 (940)
Q Consensus 193 Lg~~sD~eI~~~i~~~~--~~--~~~-------~~~~~--------~--------------------------------- 220 (940)
||+ |++||++.+.... .. +.. ...+. .
T Consensus 233 LGl-s~edIL~~F~~~~~~~~~d~~~~~~~~~e~l~g~~~~~Di~d~~g~vlvdkgrrit~~~~krlk~~gvkkl~i~~~ 311 (2836)
T PRK14844 233 LGL-SNNDILDRFYEKIKYIKHKDGWKVPFVPDKFKGVRLPFDLMDVEGNVLLKANVRITSRLAKKLYDNELKEYLVPFD 311 (2836)
T ss_pred hCC-ChHHHHHhhcCceEEEEccCceeeccCHHHHhCCccceeeeccCCCEEEecCccccHHHHHHHHHcccCcccCchH
Confidence 999 8999999774200 00 000 00000 0
Q ss_pred --CChhhH---------------------HHH----------------------HHHHHHHHhcccccHHHHHHHHhccc
Q 002296 221 --GSPLVS---------------------ERV----------------------KIILAEVQDLSLTTRLQCLQHIGEHF 255 (940)
Q Consensus 221 --~~~~~~---------------------~~~----------------------~~ll~~~~~~~i~t~~~al~yig~~f 255 (940)
.+.+++ +.+ ..+...+.+....++++|+..|.+++
T Consensus 312 ~l~g~~LaeDIVD~eTGEiL~eagteIT~e~ik~l~~~gi~~i~~l~~d~~~~~~~i~~tL~~D~~~~~e~Al~eIy~~l 391 (2836)
T PRK14844 312 SICGLFLAEDLIDSASSTKILSAGESIKLEDIKKLELLSIDEISVLNIDNLSVGPYILNTLFLDENMSYQDALYEIYKVL 391 (2836)
T ss_pred hhcCceehhhhcCCCCCeEEEcCCCccCHHHHHHHHHcCCCceeeEeecccccchHHHHHHhhcccccHHHHHHHHHHhc
Confidence 000000 000 01111222234567789999998888
Q ss_pred ccc---------------ccCCCCccHHHHHHHHHHhHhccCCC--CCcchHHHHHHHHHHHHHhcCCCCCCCCcccccc
Q 002296 256 QPV---------------IDGLQSESYYAVAETVIRDYIFVHLN--DNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQN 318 (940)
Q Consensus 256 r~~---------------~~~~~~~~~~~~~~~~L~~~ll~Hl~--~~~~K~~~L~~MirkLl~~~~g~~~~Dd~D~l~N 318 (940)
|+. ++.+.+|+..++||..||++|-.+.. ....-...++.++++|+.+..|....||+|||+|
T Consensus 392 Rpge~~~~e~a~~l~~~~ff~~~~YdLg~vGR~k~N~kl~~~~~~~~~~l~~~Dii~~i~~Li~l~~g~~~~DDiDhL~N 471 (2836)
T PRK14844 392 RPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKLNSYLGLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGN 471 (2836)
T ss_pred CCCCCCcHHHHHHHHHHHhcCccccccccchhhhhhhhhccCCCCCCcEecHHHHHHHHHHHHHHhcCCCcccchhhhhc
Confidence 752 34567888889999999999866532 1223334588999999999999999999999999
Q ss_pred ceecccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccccchHHHHHHHhcCCCcchHHHHHHHhcccCcccccccc
Q 002296 319 QEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLD 398 (940)
Q Consensus 319 kRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~ 398 (940)
|||+++|+||+++|+-.| .++.+.++.+++.... -.+ .++.++ ++++|++++++||+|
T Consensus 472 RRvr~vGeLl~~qfr~gl----~r~~~~i~e~~~~~~~-~~~----~p~~li---n~~~l~~~i~~ff~s---------- 529 (2836)
T PRK14844 472 RRVRSVGEFIENQFRTGL----LKLERAVVDSMSTSSL-DKV----SPSDFI---NPKVLTNVLRDFFNS---------- 529 (2836)
T ss_pred cccchHHHHHHHHHHHHH----HHHHHHHHHHHhhccc-ccc----chhhcc---cchhHHHHHHHHhcc----------
Confidence 999999999999998554 5555555555543111 011 234444 467999999999987
Q ss_pred cccccceEEEccccchHHHhhhhcccc---cCCcccccccccccccCCCCccccccCCCCCCccccccccccceeEEeec
Q 002296 399 LQQRAGYTVQAERLNFLRFISFFRAVH---RGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASY 475 (940)
Q Consensus 399 ~~q~sGvsqvleRln~~~~lSh~Rrv~---rg~~~~~~K~t~vR~Lhps~wGfiCPveTPEG~~cGLvk~LA~~~~Is~~ 475 (940)
+++||.++++|+++.|||+||++ +|++.++++.+++|++||||||+|||+|||||+|||||++||++|+|+
T Consensus 530 ----s~LSQfmDQtNpLseltHkRRlsaLGPGGL~r~~a~fevRdvH~shyGRiCPIETPEG~NiGLI~SLA~yarIn-- 603 (2836)
T PRK14844 530 ----SQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARIN-- 603 (2836)
T ss_pred ----cchhhhccCcChhhhhhhcceecccCCCCcccccCCCcccccCccccccccCCCCCCCCcccchhhhhhheecc--
Confidence 57788888888889999999999 788889999999999999999999999999999999999999999997
Q ss_pred cCCCCcccccchhhHHHHHHHHhCCCeecCCccccCCCCcceEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCC
Q 002296 476 YDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDD 555 (940)
Q Consensus 476 ~~~~~~~~~~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~ 555 (940)
++|++.. | |..+.||++...+ .+|- .+
T Consensus 604 ----------------------~~Gfiet-P----------y~kV~~g~v~~~i------------~yls--------a~ 630 (2836)
T PRK14844 604 ----------------------KYGFIES-P----------YRKVVNRVVTDQI------------EYLS--------AI 630 (2836)
T ss_pred ----------------------CCceEeC-C----------cEEEEcCcCcccc------------cccC--------hH
Confidence 4576654 3 5555788743211 1111 11
Q ss_pred ceeEEEEcCCCCCCCceEEecCCCceeceEEeccCCCCCCCceeeecccceeeeeeecCCCCCCCCCCCccceecccCCC
Q 002296 556 LEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPT 635 (940)
Q Consensus 556 ~ei~~v~~~~~~~~~~i~i~~d~gR~~RPv~~~~~~~~~~~~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~ 635 (940)
.|-.|.....+ + ...+.|++..+.+.++.. ++|..+. +++ .++++++|.
T Consensus 631 ~E~~~~Ia~a~-----~-~~~~~~~~~~~~v~~R~~--------------~ef~~~~--~~~---------v~~~dvsp~ 679 (2836)
T PRK14844 631 DEGLYYIADTS-----A-KLDENNCFVDDMLYCRYA--------------GSFVMVS--SDQ---------VSYIDVSPK 679 (2836)
T ss_pred HhcCcEEEeCC-----c-cCCCCCcccCCeEEEecC--------------CceEEec--HHH---------ceEEEeCcc
Confidence 11122221111 1 113346666665544432 1122221 111 689999999
Q ss_pred ccccceeecccCCCCCCCccchhhccccccccccc-----------------------------------ceeEEEeccC
Q 002296 636 GMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFS-----------------------------------VQALKFRADQ 680 (940)
Q Consensus 636 ~ilsv~AslIPF~~HNqspRn~yq~~M~KQaig~~-----------------------------------~~n~~~R~d~ 680 (940)
+++|++||||||.+||||+|++||||||||||++. +..+.+|.+.
T Consensus 680 Q~~SvaasLIPFLEhdDAnRALMGSNMQRQAVPLl~~e~PiVGTG~E~~vA~DSg~~v~A~~~G~V~yVda~kIvI~~~~ 759 (2836)
T PRK14844 680 QVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRAFD 759 (2836)
T ss_pred hhhhhHhhcCCccccCccccccccccccccccccccCCCCeEecCcchhhhhcccceEEeccCceEEEEcCCEEEEEeCC
Confidence 99999999999999999999999999999999652 1223444422
Q ss_pred ---------ceeecc----------CCCeeeEeccceeecC----------CCCCCCCceeEEEEEeccCCCCCceEEEe
Q 002296 681 ---------KLYHLQ----------TPQTPIVRTNTYTKYG----------IDEYPTGTNAIVAVLAYTGYDMEDAMILN 731 (940)
Q Consensus 681 ---------~~y~L~----------~~Q~Plv~t~~~~~~~----------~~~~~~G~N~~Vav~~y~Gyn~EDaiiin 731 (940)
..|.|. ..|||+|+.+.....| .+|+++|+|++||||||.|||+||||+||
T Consensus 760 ~~~~~~~~~~~Y~L~ky~RSNQ~TcinQrPiV~~Gd~V~kGdilADG~st~~GELALG~NvlVAfmpW~GYNfEDAIliS 839 (2836)
T PRK14844 760 KERVNYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIIS 839 (2836)
T ss_pred CccccccccceEEeccccccccceeeeecceecCCCEeccCCEeccChhhcccccccccceEEEEeccCCcccccccccc
Confidence 247776 4999999999998876 59999999999999999999999999999
Q ss_pred cchhccCcceeeEEEEEEEEeeccCCCcCccceeec--cCCCChhhhcccCCCCCcccCcEecCCCcEEEEeecCC----
Q 002296 732 KSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFR--RNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT---- 805 (940)
Q Consensus 732 k~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~ld~dGi~~~g~~v~~gd~l~~~~~~~~---- 805 (940)
++.+..++|+|.+...|.++..+.+. ..+.++ +|+.++...++||++||+++|++|++|||||||++|+.
T Consensus 840 Erlv~eD~fTSiHIee~ei~~r~Tk~----G~EeITrdIPnv~e~~lr~LDe~GIV~iGa~V~~GDILVGKvtPk~e~~~ 915 (2836)
T PRK14844 840 SEVVKKDLFTSIHIEEFECVVHDTPL----GSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLSL 915 (2836)
T ss_pred hhhccCceeEEEeecceEEEEEeccC----CCceecccCCCCChHHHhcCCCCCCeecCCEECCCCEEEEeecCCCCCCC
Confidence 99999999888887777776655442 223333 68888888999999999999999999999999988763
Q ss_pred -----------------CcEEEeeccCCCcEEEEEEEEEecC--------------------------------------
Q 002296 806 -----------------NSWRTNSRKGSESVFVDYVAVDMKN-------------------------------------- 830 (940)
Q Consensus 806 -----------------~~~~~~~~~~~e~g~V~~v~~~~~~-------------------------------------- 830 (940)
.++.|++.+.+..|+|.+|.+++.+
T Consensus 916 tPEekLL~aIFGek~~~vkdtSLrvp~G~~G~Vidv~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 995 (2836)
T PRK14844 916 PPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYIINVTSEYFYDEL 995 (2836)
T ss_pred CHHHHHHHHHhCCcccccccCceecCCCCCEEEEEEEEEcccccccchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
Confidence 1355899999999999999999753
Q ss_pred ---------------------------------------------------------------CCCC-----ceEEEEEE
Q 002296 831 ---------------------------------------------------------------SKNL-----PQKANIRF 842 (940)
Q Consensus 831 ---------------------------------------------------------------~~~~-----~~~v~i~~ 842 (940)
.|++ .+.|+|++
T Consensus 996 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gdeL~~gv~~~VkVyi 1075 (2836)
T PRK14844 996 KKLLINSGSQDREKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFI 1075 (2836)
T ss_pred hhhhcccccccHHHHhhccHHhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCCCCceEEEEEE
Confidence 1111 25799999
Q ss_pred eeecCCCcccceeccCCCccEEeeeecCCCcCccCCCCCcCcEEeCCCCccccccHHHHHHHHHHHHHhhchhHH
Q 002296 843 RHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVAYMENLW 917 (940)
Q Consensus 843 r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~G~~~ 917 (940)
++.|.++||||+|||||||||||+|+|.|||||+ +||+++|||+||+|+||||||||++|+++|+||...|..+
T Consensus 1076 a~KRkiqvGDKmAGRHGNKGVIS~IlP~eDMPyL-~DGtpvDIvLNPLGVPSRMNvGQilE~hLG~A~~~L~~~~ 1149 (2836)
T PRK14844 1076 AVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYL-EDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKV 1149 (2836)
T ss_pred EEeecCCccccccccCCCCceEeEEcccCCCCcC-CCCCCceEEeCCCCCCccccHHHHHHHHHHHHHhhhhhhh
Confidence 9999999999999999999999999999999999 9999999999999999999999999999999999998543
No 13
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=100.00 E-value=1.6e-110 Score=983.34 Aligned_cols=382 Identities=31% Similarity=0.470 Sum_probs=346.2
Q ss_pred ceEEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCCceEEecCCCceeceEEeccCCCC--
Q 002296 516 VLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSE-- 593 (940)
Q Consensus 516 ~~~V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~~d~gR~~RPv~~~~~~~~-- 593 (940)
.++|||||+|+|+++ ++.+|++.||++||.| .|+.++||.+++. .++|+||||+||++|||+++++++.
T Consensus 4 ~~~VflNG~~vG~~~--~~~~lv~~lR~lRr~g--~i~~~vsI~~~~~-----~~ei~I~tD~GR~~RPl~iv~~g~~~l 74 (605)
T PRK07225 4 KAKVYVNGKLIGTHD--DPEELVEEIREARRSG--EISEEVNVSYKEE-----TNEVIINTDAGRARRPLIVVENGEPLL 74 (605)
T ss_pred ccEEEECCEEEEEEC--CHHHHHHHHHHHHccC--CCCCcEEEEEECC-----CCEEEEEccCCccceeEEEEeCCcccC
Confidence 378999999999984 5899999999999998 5899999987642 4699999999999999999988542
Q ss_pred -------------------CCCceeeecccceeeeeeecCCCCCCCCCCCccceecccCCCccccceeecccCCCCCCCc
Q 002296 594 -------------------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSP 654 (940)
Q Consensus 594 -------------------~~~~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~ilsv~AslIPF~~HNqsp 654 (940)
.+|.|||||++||++++||+.++++... +||+||+|+++||++||+|||+||||||
T Consensus 75 ~~~~~~~l~~~~~~~~dl~~~G~IEyida~EE~~~~IA~~~~~l~~~-----~th~Ei~p~~ilgv~AslIPF~~hNQSP 149 (605)
T PRK07225 75 TEEHIEKLKNGELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEE-----HTHLEIDPSLILGIGAGMIPYPEHNASP 149 (605)
T ss_pred CHHHHHHHHcCCCChHHHHhCCCeeecChhhhcCeEeccchhhhccc-----ccccccCCcceeEEEeeccCCCCCCccc
Confidence 2389999999999999999999888554 7999999999999999999999999999
Q ss_pred cchhhcccccccccccceeEEEeccCceeeccCCCeeeEeccceeecCCCCCCCCceeEEEEEeccCCCCCceEEEecch
Q 002296 655 RNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSS 734 (940)
Q Consensus 655 Rn~yq~~M~KQaig~~~~n~~~R~d~~~y~L~~~Q~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s 734 (940)
||||||||+|||||++++|+..|.|++.|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||||||+|
T Consensus 150 Rn~yq~~M~KQa~g~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~N~iVAvmsy~GYn~EDAiIiNkss 229 (605)
T PRK07225 150 RITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKAS 229 (605)
T ss_pred hhhhhhhhhhcccCccccceeeecCCcccEEeeCCcceEEccchHhhCCCccCCCeeEEEEEECcCCCChhHeeeeehhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccCcceeeEEEEEEEEeeccCCCcCccceeeccCCC------ChhhhcccCCCCCcccCcEecCCCcEEEEeecC----
Q 002296 735 VDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKD------AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKT---- 804 (940)
Q Consensus 735 ~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~ld~dGi~~~g~~v~~gd~l~~~~~~~---- 804 (940)
+||||||+.+|++|+++...... ...+.|..|+. ....+++||+||||++|++|++||||+||..|.
T Consensus 230 idRGlf~s~~~k~~~~~~~~~~~---~~~~~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gdiligk~sp~~~~~ 306 (605)
T PRK07225 230 IERGLGRSHFFRTYEGEERRYPG---GQEDRFEIPDKDVRGYRGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPPRFLE 306 (605)
T ss_pred hhcCceEEEEEEEEEEEeeecCC---CcceEEecCCchhccccChHHhhcCCCCCCccCCCEECCCCEEEEEecCCCCcc
Confidence 99999999999999976533211 12345666642 123579999999999999999999999997652
Q ss_pred ----------CCcEEEeeccCCCcEEEEEEEEEecCCCCCceEEEEEEeeecCCCcccceeccCCCccEEeeeecCCCcC
Q 002296 805 ----------TNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMP 874 (940)
Q Consensus 805 ----------~~~~~~~~~~~~e~g~V~~v~~~~~~~~~~~~~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dMP 874 (940)
..++.+++++.+|+|+||+|.++.+.+| .+.|+|++|+.|+|+||||||||||||||||+|||+||||
T Consensus 307 ~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~--~~~vkv~ir~~R~p~iGDKfssRHGQKGvvs~i~~~eDMP 384 (605)
T PRK07225 307 EPDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEG--SRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMP 384 (605)
T ss_pred chhhhcccccCcceeeEEecCCCcEEEEEEEEEecCCC--CEEEEEEEEEEEeccccchhhhcccCceeEEeEeccccCC
Confidence 1346688999999999999999987654 4789999999999999999999999999999999999999
Q ss_pred ccCCCCCcCcEEeCCCCccccccHHHHHHHHHHHHHhhchhHH
Q 002296 875 FSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVAYMENLW 917 (940)
Q Consensus 875 f~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~G~~~ 917 (940)
|| ++|++|||||||||||||||||||+|+++||+|++.|.++
T Consensus 385 ft-~~G~~PDiIiNPhg~PSRMTiGql~E~~~gk~~~~~g~~~ 426 (605)
T PRK07225 385 FT-ESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRV 426 (605)
T ss_pred cC-CCCCcccEEECcccccccCcHHHHHHHHHHHHHHhcCceE
Confidence 99 9999999999999999999999999999999999999887
No 14
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=100.00 E-value=9e-111 Score=984.54 Aligned_cols=379 Identities=32% Similarity=0.511 Sum_probs=344.0
Q ss_pred EEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCCceEEecCCCceeceEEeccCCCC-----
Q 002296 519 VLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSE----- 593 (940)
Q Consensus 519 V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~~d~gR~~RPv~~~~~~~~----- 593 (940)
|||||+|+|+++ ++.+|++.||.+||.| .|+.++||.+++. .++|+||||+||++|||+++++++.
T Consensus 1 VflNG~~vG~~~--~~~~lv~~LR~lRr~g--~i~~~vsI~~~~~-----~~ei~I~tD~GR~~RPl~iv~~g~l~l~~~ 71 (599)
T TIGR03670 1 VYLNGRLIGYHD--DPEELVEEVRKLRRSG--KLSQEVNVAYYEE-----TNEVYINCDAGRIRRPLIVVENGKPKLTRE 71 (599)
T ss_pred CEECCEEEEEEC--CHHHHHHHHHHHhCcC--CCCCcEEEEEeCC-----CCEEEEEcCCCccceeEEEeeCCCccccHH
Confidence 799999999984 5899999999999998 5899999987743 4899999999999999999988752
Q ss_pred ----------------CCCceeeecccceeeeeeecCCCCCCCCCCCccceecccCCCccccceeecccCCCCCCCccch
Q 002296 594 ----------------ESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNM 657 (940)
Q Consensus 594 ----------------~~~~iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~ilsv~AslIPF~~HNqspRn~ 657 (940)
..|.+||||++||++++||+.++++... +||+||+|+++||++||+|||+|||||||||
T Consensus 72 ~l~~l~~~~~~~~~ll~~G~IEyida~Ee~~~~IA~~~~~l~~~-----~th~Ei~p~~ilgv~AslIPF~~hNqSpRn~ 146 (599)
T TIGR03670 72 HVEKLKEGELTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE-----HTHLEIDPSAILGIIASTIPYPEHNQSPRNT 146 (599)
T ss_pred HHHHHhccCCCHHHHHhcCCeEecCchhhcCeEEecchHHhccC-----cCccccCCcceeeEEeeccCCCCcCcchhhH
Confidence 2478999999999999999999887554 7999999999999999999999999999999
Q ss_pred hhcccccccccccceeEEEeccCceeeccCCCeeeEeccceeecCCCCCCCCceeEEEEEeccCCCCCceEEEecchhcc
Q 002296 658 YQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDR 737 (940)
Q Consensus 658 yq~~M~KQaig~~~~n~~~R~d~~~y~L~~~Q~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiiink~s~~r 737 (940)
|||||+|||||++++|+..|.|++.|+|+|||+|||+|+.++.++++++|+|+||+||||||+|||||||||+||+|+||
T Consensus 147 YQc~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~p~G~N~iVAvmsy~GYn~EDAiIink~si~r 226 (599)
T TIGR03670 147 MGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIER 226 (599)
T ss_pred HHHhhhhccccccccChhhcccccceEEcCCCCceeeeeeHHHhCccccCCCeeEEEEEEcccCcChhHeeeechhhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeeEEEEEEEEeeccCCCcCccceeeccCCC------ChhhhcccCCCCCcccCcEecCCCcEEEEeecC-------
Q 002296 738 GMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKD------AKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKT------- 804 (940)
Q Consensus 738 G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~ld~dGi~~~g~~v~~gd~l~~~~~~~------- 804 (940)
||||+++|++|+++...... ...+.+..|+. .+..+++||+||||++|++|++||||+||+.|.
T Consensus 227 G~f~s~~~~~~~~~~~~~~~---~~~e~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gdiligk~~p~~~~~~~~ 303 (599)
T TIGR03670 227 GLARSTFFRTYEAEERRYPG---GQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPPRFLEELR 303 (599)
T ss_pred CCeEEEEEEEEEEEeeccCC---CCceEEecCCchhccccchhhhccCCCCCCcCCCcEeCCCCEEEEEecCCCCccchh
Confidence 99999999999986533211 12234555532 234579999999999999999999999998752
Q ss_pred -------CCcEEEeeccCCCcEEEEEEEEEecCCCCCceEEEEEEeeecCCCcccceeccCCCccEEeeeecCCCcCccC
Q 002296 805 -------TNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSG 877 (940)
Q Consensus 805 -------~~~~~~~~~~~~e~g~V~~v~~~~~~~~~~~~~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dMPf~~ 877 (940)
..++.+++++.+|+|+||+|.++.++++ .+.|+|++|+.|+|+||||||||||||||||+|||+||||||
T Consensus 304 ~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~--~~~vkv~~r~~R~p~iGDKfssRHGQKGvvs~i~~~eDMPft- 380 (599)
T TIGR03670 304 ELGLVTERRRDTSVTVRHGEKGIVDKVIITETEEG--NKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFT- 380 (599)
T ss_pred hhccccccCceEEEEecCCCcEEEEEEEEEecCCC--cEEEEEEEeeeecCcchhhhhhhccCcceEEeEeccCCCCcC-
Confidence 1346788999999999999999987654 478999999999999999999999999999999999999999
Q ss_pred CCCCcCcEEeCCCCccccccHHHHHHHHHHHHHhhchhHH
Q 002296 878 VTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVAYMENLW 917 (940)
Q Consensus 878 ~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~G~~~ 917 (940)
+||++|||||||||||||||||||+|+++||+|++.|.++
T Consensus 381 ~~G~~pDiIiNPhg~PSRMTiGqllE~~~gk~~~~~g~~~ 420 (599)
T TIGR03670 381 EDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRV 420 (599)
T ss_pred CCCCCCCEEECcccccccccHHHHHHHHHHHHHHhcCCEE
Confidence 9999999999999999999999999999999999999876
No 15
>PRK09606 DNA-directed RNA polymerase subunit B''; Validated
Probab=100.00 E-value=6.4e-97 Score=864.31 Aligned_cols=437 Identities=24% Similarity=0.391 Sum_probs=376.0
Q ss_pred ccCchhhHHHHHHHHHHHHHHHHHHHH----------------------------------------HHHHHcCCeeeeE
Q 002296 9 FEPLRELVRHHIESFDYMLDEGLSEMF----------------------------------------DHCRQAKISYTGK 48 (940)
Q Consensus 9 ~~~~~~Lv~~hi~SFn~Fi~~gl~~ii----------------------------------------~ecR~r~~TYsa~ 48 (940)
+...++|++|||+|||+|+++||++++ +|||+|++||+|+
T Consensus 12 ~~~~~~lv~~qi~SFn~Fi~~gl~~ii~~~~~i~~~~~~~~~l~~~~~~l~~P~~~~~~~~~~~l~P~eaR~r~~TYs~~ 91 (494)
T PRK09606 12 YFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVGKPVVKEADGSEREIYPMEARLRNLTYSAP 91 (494)
T ss_pred HHCCCChHHHHHHHHHHHHHHhHHHHHHhcCCEEEecCCcEEEEEEEEEECCCcccccCCccccCCHHHHHhcCCCccce
Confidence 346789999999999999999999998 7999999999999
Q ss_pred EEEEEEEEEecCCCceEeeEEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeccCCccE
Q 002296 49 LMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPM 128 (940)
Q Consensus 49 l~v~i~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~ 128 (940)
++|+|.+..+ +.+...+++++|+|||||+|++|||++++++|+++.||||+|+||||||||+|||||+|+++++|+++
T Consensus 92 l~v~i~~~~~--~~~~~~~~v~iG~iPiMv~S~~C~L~~~~~~~l~~~~E~~~d~GGyFIING~ErVi~~q~~~~~n~~~ 169 (494)
T PRK09606 92 LYLEMSPVEG--GEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLEDLAPNKIL 169 (494)
T ss_pred EEEEEEEEEC--CCceEEeeEEeccCCeEeccCcccCCCCCHHHHHhcCCCcCCCCCeEEECCCeEEEEEEEeccCCeeE
Confidence 9999999755 44445678999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeccccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHhhHHHhccCCCHHHHHHHhccc
Q 002296 129 SMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCC 208 (940)
Q Consensus 129 ~~~r~~~~~~~~~~t~~~v~~rs~~~~~~s~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~eI~~~i~~~ 208 (940)
++.++.+.++ .| ...+++... ..+.+..++|+.+|.+++++.. .+++||+++||||||..||+||++.|..
T Consensus 170 ~~~~~~~~~~--~~---~~~i~s~~~-~~~~~~~l~~~~~g~i~~~~~~--~~~~iPi~~llkALg~~sd~eI~~~i~~- 240 (494)
T PRK09606 170 VEKDERYGDR--IE---VAKVFSQRR-GYRALVTVERNRDGLLEVSFPS--VPGSIPFVILMRALGLETDEEIVEAVSD- 240 (494)
T ss_pred EEeccCCCcc--ce---EEEEEcccc-cceeeEEEEEecCCeEEEEEcC--ccccccHHHHHHHcCCCCHHHHHHHhCC-
Confidence 9887643321 12 234444322 2344688999999999998865 3457999999999999999999999951
Q ss_pred ccchhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhccccccccCCCCccHHHHHHHHHHhHhccCCCC---
Q 002296 209 YDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLND--- 285 (940)
Q Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~i~t~~~al~yig~~fr~~~~~~~~~~~~~~~~~~L~~~ll~Hl~~--- 285 (940)
+ .++++.++.++++.++.|+++|+.|||++|++. ..+.+..+.|+.+|++++|||+|.
T Consensus 241 ----------~------~~~~~~l~~~~~~~~~~t~~~al~~ig~~~~~~---~~~~~~~~~~~~~l~~~~l~hig~~~~ 301 (494)
T PRK09606 241 ----------D------PEIVKFMLENLEEAEVDTQEEALEYIGKRVAPG---QTKEYRIKRAEYVIDRYLLPHLGVEPE 301 (494)
T ss_pred ----------c------HHHHHHHHHHHHhcccCCHHHHHHHHHHhcCCC---CCcchHHHHHHHHHHHhhhcccCCCcc
Confidence 1 135667777777778999999999999999753 235566789999999999999995
Q ss_pred -CcchHHHHHHHHHHHHHhcCCCCCCCCccccccceecccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccccchH
Q 002296 286 -NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLA 364 (940)
Q Consensus 286 -~~~K~~~L~~MirkLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~ 364 (940)
...|++||++|++||+.++.|.+.+||+|||+||||+++|+||+.+||+.|+++++.++..+++...+ ++..+
T Consensus 302 ~~~~K~~~L~~m~~kLl~~~~g~~~~Dd~D~l~nkRv~~~G~Ll~~~fr~~l~~~~~~~k~~l~~~~~~-~~~~~----- 375 (494)
T PRK09606 302 VRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMR-NRELS----- 375 (494)
T ss_pred hhhHHHHHHHHHHHHHHHHhcCCCCCCCcccccCceeeccchhHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCCC-----
Confidence 34799999999999999999999999999999999999999999999999999999999888776543 33222
Q ss_pred HHHHHHhcCCCcchHHHHHHHhcccCcccccccccccccceEEEccccchHHHhhhhcccccCCcccccccccccccCCC
Q 002296 365 NIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPE 444 (940)
Q Consensus 365 ~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSh~Rrv~rg~~~~~~K~t~vR~Lhps 444 (940)
++.+++ ++.||++|++|||||||.+ +++||||+|+|+||+|+||||||||. ++.+++|.++||+||||
T Consensus 376 -~~~~~~---~~~It~~l~~~~~TGnw~~-------~~~glSq~ldr~N~la~lSh~Rrv~s-~~~r~~~~~~vR~lhps 443 (494)
T PRK09606 376 -IKTAVR---SDVLTERLEHAMATGNWVG-------GRTGVSQLLDRTDYMATLSHLRRVVS-PLSRSQPHFEARDLHPT 443 (494)
T ss_pred -HHHhcC---chhhhHHHHHHhhcccccC-------CCceEEEEccCCCHHHHhhHHHhccC-CccccCccccccccCcc
Confidence 344553 4589999999999999975 46899999999999999999999997 45678899999999999
Q ss_pred CccccccCCCCCCccccccccccceeEEeeccCCCCcccccchhhHHHHHHHHhCCCeec
Q 002296 445 SWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPS 504 (940)
Q Consensus 445 ~wGfiCPveTPEG~~cGLvk~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~~g~~~~ 504 (940)
||||+||||||||++||||||||++|+|+++.+.+ .|.++|.++|+.+.
T Consensus 444 ~~G~iCPveTPEG~~cGLv~~La~~a~V~~~~~~~-----------~i~~~l~~lg~~~~ 492 (494)
T PRK09606 444 QWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEE-----------EVKEILKELGVEPE 492 (494)
T ss_pred cceecccCcCCCCCcccHHHhhhceEEEeCCCChH-----------HHHHHHHHCcCeeC
Confidence 99999999999999999999999999999885433 58899999999865
No 16
>PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerases (2.7.7.6 from EC) catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain represents the hybrid-binding domain and the wall domain []. The hybrid-binding domain binds the nascent RNA strand/template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion []. This domain is also involved in binding to Rpb1 and Rpb3 []. Many of the bacterial members contain large insertions within this domain, which are known as dispensable region 2 (DRII).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_R 3HKZ_B 2PMZ_R 3H0G_B 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B ....
Probab=100.00 E-value=1.2e-79 Score=697.43 Aligned_cols=272 Identities=43% Similarity=0.642 Sum_probs=229.8
Q ss_pred cceeecccCCCCCCCccchhhcccccccccccceeEEEeccCceeeccCCCeeeEecc-ceeecC---------CCCCCC
Q 002296 639 SVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTN-TYTKYG---------IDEYPT 708 (940)
Q Consensus 639 sv~AslIPF~~HNqspRn~yq~~M~KQaig~~~~n~~~R~d~~~y~L~~~Q~Plv~t~-~~~~~~---------~~~~~~ 708 (940)
|++|++|||++||||||++|||||+|||||++.+|+..|.|+.. .|||+|||+|+ .++..+ ++++|+
T Consensus 1 si~As~ipf~~hn~s~R~~~~~~m~kQa~~~y~~~~~~R~d~~~---~~~q~Plv~~~~~~~~~~ilad~~~~~~~e~~~ 77 (386)
T PF00562_consen 1 SIVASLIPFPEHNQSPRNLYQCNMQKQAIGTYSLNKFNRSDQNT---CYPQKPLVKTGDRVEKGQILADGPSTKFGELPL 77 (386)
T ss_dssp -THGGTSSSGGGC-HHHHHHHHHHGCGBCSEEETTTTTS-TSSE---SS-BEESSBSSSTBTTTTECEE-TTECTTTS-S
T ss_pred CEEeCCCCEEEEEcCCcEEEEeCcCCCcccceeeeeeeccCcce---eccccceEEeeccccccCccccccccccccCcc
Confidence 68999999999999999999999999999999999999999988 79999999999 777777 899999
Q ss_pred CceeEEEEEeccCCCCCceEEEecchhccCcceeeEEEEEEEEeeccCCCcCccceeecc-CCCChhhhcccCCCCCccc
Q 002296 709 GTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRR-NKDAKSLHSVIDSDGLPYV 787 (940)
Q Consensus 709 G~N~~Vav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ld~dGi~~~ 787 (940)
|+|++||||||+||||||||||||+|++||||++++|++ .++++.... ....+.+.. |+.....+++||+||||++
T Consensus 78 G~N~iVAvmsy~GYN~EDAiIiNkssv~rG~f~s~~~k~-~~~~~~~~~--g~~e~~~~~~~~~~~~~~~~LD~dGii~~ 154 (386)
T PF00562_consen 78 GQNAIVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHYKT-EIEIRDNKG--GPSEEIFRPIPNVKEYNYSKLDEDGIIKI 154 (386)
T ss_dssp SEEEEEEESBSSSTTTSSEEEEECHHHHTTTTEEEEEEE-EEEEEEETT--SEEBBESS--TSSTSTTGGGBCTTSBB-T
T ss_pred eeeeeEEeeehhcccchhhhhhhhhhhhcCeeeEEEEEE-EeeeecccC--Ccccccccccccchhhhhhhccccccccc
Confidence 999999999999999999999999999999999999999 776644331 111333433 3456677899999999999
Q ss_pred CcEecCCCcEEEEee--------------cCC--CcEEEeeccCCCcEEEEEEEEEecC-----CCCCceEEEEEEeeec
Q 002296 788 GQMIHPGEPYCSIYD--------------KTT--NSWRTNSRKGSESVFVDYVAVDMKN-----SKNLPQKANIRFRHTR 846 (940)
Q Consensus 788 g~~v~~gd~l~~~~~--------------~~~--~~~~~~~~~~~e~g~V~~v~~~~~~-----~~~~~~~v~i~~r~~R 846 (940)
|++|++||+|+||+. .+. ..+.+++++.+|.|+||+|.++.+. ...+...|+|++|+.|
T Consensus 155 G~~v~~gDiligk~~~~~~~~~~~~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~~~~~~~~iki~ir~~R 234 (386)
T PF00562_consen 155 GSRVEKGDILIGKITSPPRFSPLLKKIFGEKNRNYRDTSIKYKSGESGRVDKVIIFSNEKKDTSNNEGYKKIKIRIRSTR 234 (386)
T ss_dssp TCEEETTSEEEEEEESTSC--HHHHHHHHSSSCSEEEEEEES-TT-EEEEEEEEEECCCSSBEEETTCEEEEEEEEEEEE
T ss_pred CcEEecceeEEEEEecccccccchhhccccccccccceeecccccEEeEeccccccccccccccccCcceEEEEEecccc
Confidence 999999999999984 111 3567899999999999999995421 1235789999999999
Q ss_pred CCCcccceeccCCCccEEeeeecCCCcCccCCCCCcCcEEeCCCCccccccHHHHHHHHHHHHHhhchhHH
Q 002296 847 NPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVAYMENLW 917 (940)
Q Consensus 847 ~p~iGDKf~sRHGqKGvvs~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~G~~~ 917 (940)
+|+||||||||||||||||+|||+|||||| ++|++|||||||||||||||||||+|+++||+|++.|.++
T Consensus 235 ~p~iGDKfssRHGqKGVvs~i~~~eDMPft-~~G~~pDiIiNPhgiPSRMtiGqllE~~~g~~~~~~g~~~ 304 (386)
T PF00562_consen 235 RPQIGDKFSSRHGQKGVVSKILPQEDMPFT-EDGIVPDIIINPHGIPSRMTIGQLLESLLGKAGALNGRFV 304 (386)
T ss_dssp E--TTEEEEETTSEEEEEEEEE-TTTSEEE-TTSEB-SEEE-GGGSTTTTBTHHHHHHHHHHHHHHSTCEE
T ss_pred cchhHHHHhhhhcCceEEeeeeccccCccc-cCCCcceeeecccccccccchHHHHhhhhhhhhhccccce
Confidence 999999999999999999999999999999 9999999999999999999999999999999999999876
No 17
>PF04563 RNA_pol_Rpb2_1: RNA polymerase beta subunit; InterPro: IPR007644 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). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain []. The other lobe, RNA polymerase Rpb2, domain 2, is nested within this domain.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_B 3LTI_A 3IYD_C 3LU0_C 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C 3AOH_H ....
Probab=100.00 E-value=2.3e-36 Score=316.16 Aligned_cols=107 Identities=36% Similarity=0.773 Sum_probs=92.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHH-----------------------------------------HHHHHcCCeeeeEEEEE
Q 002296 14 ELVRHHIESFDYMLDEGLSEMF-----------------------------------------DHCRQAKISYTGKLMAD 52 (940)
Q Consensus 14 ~Lv~~hi~SFn~Fi~~gl~~ii-----------------------------------------~ecR~r~~TYsa~l~v~ 52 (940)
||++|||+|||||+++||++++ +|||+|++||+|+++|+
T Consensus 1 ~Lv~~qi~SFn~Fl~~gl~~i~~~~~~i~~~~~~~~~~l~~~~~~i~~P~~~~~~~~~~~l~P~ecR~r~~TYs~~l~v~ 80 (203)
T PF04563_consen 1 GLVKHQIDSFNYFLNNGLKEILKEFPPIEFESSNNRISLKFENIRIGKPTYSESDGRERPLYPRECRLRGLTYSAPLYVD 80 (203)
T ss_dssp TTTHHHHHHHHHHHCTSSHHHHSCSSSCEECCCSTTEEEEEEEEEEESESSEHTTSCEEE--HHHHHHTT-B-EEEEEEE
T ss_pred CchHHHHHHHHHHHHCCCHHHhccCCceEecCCcceEEEEeeEEEEeeeeeccccccccCCCHHHHHhcCCCCCCccceE
Confidence 6899999999999999999998 89999999999999999
Q ss_pred EEEEEecCCC-ceEeeEEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEec
Q 002296 53 VEFQYLDAGS-PVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILP 122 (940)
Q Consensus 53 i~~~~~~~~~-~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~ 122 (940)
|++.++ +. +....++.+|+|||||+|++|||++++++|+++.||||+|+||||||||+|||||+|+++
T Consensus 81 i~~~~~--~~~~~~~~~v~iG~iPiMv~S~~C~L~~~~~~~l~~~~E~~~d~GGYFIInG~EkVi~~q~~~ 149 (203)
T PF04563_consen 81 IELTVN--NKKEIKEQEVFIGKIPIMVRSKRCNLNGLSPKELVQLGECPNDPGGYFIINGSEKVIRMQIMR 149 (203)
T ss_dssp EEEEES--STTEEEESEEEEEEEE-BTTTTTSGGGT--HHHHHHTTS-TT---SSEEETTEEEEE-EEEEE
T ss_pred EEEEee--ccceEEeeEEEEeeCCeEeecceeeCCCCCHHHHHHcCCCCcCCCCEEEECCChhheehhhhh
Confidence 999988 54 677889999999999999999999999999999999999999999999999999999875
No 18
>PF04565 RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; InterPro: IPR007645 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). Domain 3, is also known as the fork domain and is proximal to catalytic site [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_B 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C 3AOH_H 1IW7_M 2O5J_C 2CW0_M ....
Probab=99.94 E-value=1.8e-27 Score=204.69 Aligned_cols=67 Identities=34% Similarity=0.659 Sum_probs=60.7
Q ss_pred EEccccchHHHhhhhccccc-CCcccccccccccccCCCCccccccCCCCCCccccccccccceeEEe
Q 002296 407 VQAERLNFLRFISFFRAVHR-GASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVA 473 (940)
Q Consensus 407 qvleRln~~~~lSh~Rrv~r-g~~~~~~K~t~vR~Lhps~wGfiCPveTPEG~~cGLvk~LA~~~~Is 473 (940)
|+|+|+|++++|||+|||++ |.+++++|.+++|+|||||||||||+|||||++|||+||||++|+||
T Consensus 1 Q~l~r~N~l~~ls~~Rri~~~~~~~~~~~~~~~R~lh~s~~G~iCPveTPEG~~~GLv~~La~~a~I~ 68 (68)
T PF04565_consen 1 QYLDRTNPLSELSHLRRINRLGPLSKESKSTEPRQLHPSQYGRICPVETPEGENCGLVKNLALMARIT 68 (68)
T ss_dssp EE--TSSHHHHHHHHTEEESCSSTSSSSSSSTTTSTTGGGTTTBSSSSS-SSTSTTTEEEBBTT-EE-
T ss_pred CCcccccHHHHHHHHHhcccccccchhhcccccccccccceeEEeecccCCCccEeehheeeeeEEeC
Confidence 78999999999999999998 88889999999999999999999999999999999999999999996
No 19
>PF04561 RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; InterPro: IPR007642 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, a region known as dispensable region 1 (DRI).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_B 3LTI_A 3IYD_C 3LU0_C 2Y0S_R 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C ....
Probab=99.85 E-value=5.7e-22 Score=204.51 Aligned_cols=174 Identities=21% Similarity=0.201 Sum_probs=114.0
Q ss_pred cCCccEEEEeccccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHhhHHHhccCCCHHHHH
Q 002296 123 KQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIF 202 (940)
Q Consensus 123 ~~N~~~~~~r~~~~~~~~~~t~~~v~~rs~~~~~~s~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~eI~ 202 (940)
|+|+|++..+..+......+ ++.....+..|..+.... ..+.+...+..++||+++||||||++||+||+
T Consensus 1 Rsn~i~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~IPi~ilLrALG~~sd~eI~ 70 (190)
T PF04561_consen 1 RSNGIYVEKDKDGNKIIRSV-------RSDIISSRGSWHYLEKDK---KIIIFSRPKKKFKIPIVILLRALGIESDKEII 70 (190)
T ss_dssp ESSSEEEEE-SSSSSCSSCE-------EEEECCSSSEEEEEECET---TTEEEEETTSSSEEEHHHHHHHTT--STCHHH
T ss_pred CCCEEEEEEccCCCCeeEEE-------EeecCCCcceEEEEecCC---cEEEEEEcCcccccceEEeehhhcCcCccccc
Confidence 46888887765443321111 122222333455443332 23345555566789999999999999999999
Q ss_pred HHhcccccchhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhccccccccCCCCccHHHHHHHHH-------
Q 002296 203 NHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVI------- 275 (940)
Q Consensus 203 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~i~t~~~al~yig~~fr~~~~~~~~~~~~~~~~~~L------- 275 (940)
+.|+. .. .........+++.....++.|+++|+.|||++++. ...+....+.++.+|
T Consensus 71 ~~i~~--~~-----------~~~~~~~~~~~~~~~~~~~~t~~~al~~i~~~~~~---~~~~~~~~~~~~~~l~~~y~l~ 134 (190)
T PF04561_consen 71 ELICY--SE-----------EDFEDIEELMLSELEEEEIYTQEQALEYIGKKFRF---RQGKPPKVEEARNFLQKRYDLG 134 (190)
T ss_dssp HHHCC--CS-----------TCHSCSTTTHHHHCCCTSSCSCHHHHHHHHHCCHS---SSSCHCCHCHHHHHHTTCSSTC
T ss_pred ceeec--cc-----------ccccccccccccccccccccccccceeEeccceee---ecccccchhhhhcccccccccc
Confidence 99972 11 11112223355555667899999999999994332 233444556677776
Q ss_pred --HhHhcc-CCCCCcc------hHHHHHHHHHHHHHhcCCCCCCCCccccccceec
Q 002296 276 --RDYIFV-HLNDNND------KFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEIL 322 (940)
Q Consensus 276 --~~~ll~-Hl~~~~~------K~~~L~~MirkLl~~~~g~~~~Dd~D~l~NkRv~ 322 (940)
.+++++ ||+.... |+.+|++|+++|+.++.|.+.+||+|||+||||+
T Consensus 135 ~i~r~~l~~hl~~~~~~~~~~~k~~~l~~m~~~ll~~~~g~~~~Dd~D~l~NkRv~ 190 (190)
T PF04561_consen 135 FIGRYKLNKHLGSDEPNENDRLKAEDLGLMIRKLLKLANGECEPDDRDHLGNKRVR 190 (190)
T ss_dssp CCHHHCCHTTTTSSSSSSSSSCHHHHHHHHHHHHHHHHTTSS-S-STTSCCCEEEE
T ss_pred cccccceeeeeeeeecccccccchhhHHHHHHHHHHHhcCCCCCCCccccCCcCCc
Confidence 466777 9995433 9999999999999999999999999999999995
No 20
>PF04566 RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; InterPro: IPR007646 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). Domain 4, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=99.48 E-value=1.6e-13 Score=116.28 Aligned_cols=63 Identities=24% Similarity=0.371 Sum_probs=54.1
Q ss_pred EEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCCceEEecCCCceeceEEeccC
Q 002296 519 VLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISL 590 (940)
Q Consensus 519 V~lnG~~iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~~d~gR~~RPv~~~~~ 590 (940)
|||||+|+|+++ +|.+|+..||.+||+| .++.+++|.+. ...++|+||||+||++|||+.+++
T Consensus 1 VFlNG~~iG~~~--~p~~l~~~lr~~RR~g--~i~~~vsi~~~-----~~~~ei~I~tD~GR~~RPL~vV~n 63 (63)
T PF04566_consen 1 VFLNGVWIGIHS--DPEELVKTLRNLRRSG--KISKEVSIVYD-----IREKEIRINTDAGRLCRPLFVVEN 63 (63)
T ss_dssp EEETTEEEEEES--SHHHHHHHHHHHHHTT--SS-TTSEEEEE-----TTTTEEEEE-SSCEEEEEEEEESS
T ss_pred CEECCEEEEEEc--CHHHHHHHHHHHhhcc--CCcceeEEEEe-----ccCCEEEEEccCCcccceeEEecC
Confidence 799999999974 7899999999999998 78888888654 457899999999999999998864
No 21
>PF06883 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific domain ; InterPro: IPR009674 This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=99.09 E-value=1.3e-10 Score=96.65 Aligned_cols=58 Identities=48% Similarity=0.940 Sum_probs=55.3
Q ss_pred EeeecCccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcCCCCCCCceEEecCCCceec
Q 002296 526 VGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVR 583 (940)
Q Consensus 526 iG~~~~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~~~~~~~~i~i~~d~gR~~R 583 (940)
|||++++++.++++.||++|..+...||.++||+|++.+.+++||+|||||+++|++|
T Consensus 1 iG~~~~~~a~~~~~~LR~~Kv~~~~~vP~~lEI~~VP~~~~g~yPGLyLft~~aRm~R 58 (58)
T PF06883_consen 1 IGYVSPEEAEQIADQLRYLKVEGEHGVPPTLEIGYVPPSKGGQYPGLYLFTTPARMMR 58 (58)
T ss_pred CceecHHHHHHHHHHHHHHHHcCCCCCCCceEEEEEECCCCCCCCeEEEeCCcccccC
Confidence 5899989999999999999999988899999999999998899999999999999998
No 22
>PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 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). Domain 5, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=98.39 E-value=1.5e-07 Score=75.75 Aligned_cols=40 Identities=25% Similarity=0.185 Sum_probs=29.7
Q ss_pred CCceeeecccceeeeeeecCCCCCC--CCCCCccceecccCC
Q 002296 595 SQNIELIGPFEQVFMEIRCPDGGDG--GRRNAFPATHEEIHP 634 (940)
Q Consensus 595 ~~~iE~i~~~Eq~~~~Ia~~~~~~~--~~~~~~~~th~EI~p 634 (940)
.|.|||||++||++++||++++++. +......||||||||
T Consensus 7 ~G~vE~id~eEEe~~~Iam~~~dl~~~~~~~~~~~TH~EI~P 48 (48)
T PF04567_consen 7 EGVVEYIDAEEEETCMIAMSPEDLESTNEDITHTYTHCEIHP 48 (48)
T ss_dssp TTSEEEEETTTCTT--EESSCCCCCHSGGCCSST-SEEES-G
T ss_pred CCCEEEecchhccccEEEEecccccccCCCCCCccEEEeEeC
Confidence 3599999999999999999998886 222245699999998
No 23
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]
Probab=97.59 E-value=7.6e-05 Score=93.23 Aligned_cols=72 Identities=19% Similarity=0.391 Sum_probs=59.0
Q ss_pred ceecccCCCccccceeecccCCCCCCCccchhhcccccccccccceeEEEeccCceeeccCCCeeeEeccceeecCCCCC
Q 002296 627 ATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEY 706 (940)
Q Consensus 627 ~th~EI~p~~ilsv~AslIPF~~HNqspRn~yq~~M~KQaig~~~~n~~~R~d~~~y~L~~~Q~Plv~t~~~~~~~~~~~ 706 (940)
.+|++++|.++.|+.+++|||.+|++++|.+|+++|+|||+|+ ..+..|+|.|+ ++...-.|
T Consensus 526 ~~~~dv~~~~~~~~~~~~~P~l~~dd~~~~l~~~~mqr~~~~l----------------~~~~~~lv~tG-~E~~~a~e- 587 (1060)
T COG0085 526 VDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGSNMQRQAVPL----------------LRTEAPLVGTG-MEYLDAED- 587 (1060)
T ss_pred ccceeccceEEeccccccCceeEEcCchHhhhhhhhhhhcccc----------------cccccccccCC-ceeecccc-
Confidence 5899999999999999999999999999999999999999993 46899999999 66643211
Q ss_pred CCCceeEEEEEe
Q 002296 707 PTGTNAIVAVLA 718 (940)
Q Consensus 707 ~~G~N~~Vav~~ 718 (940)
-.|++||.-+
T Consensus 588 --~~~~~ia~~~ 597 (1060)
T COG0085 588 --SGAAVIAKRP 597 (1060)
T ss_pred --ccceeEeccC
Confidence 1345555544
No 24
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription]
Probab=97.29 E-value=0.0001 Score=87.54 Aligned_cols=349 Identities=11% Similarity=-0.032 Sum_probs=179.7
Q ss_pred EEeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEEEEEeccCCccEEEEeccccCCCCcceeeEE
Q 002296 68 RFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAV 147 (940)
Q Consensus 68 ~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~D~GGYFIInG~EKVIr~qi~~~~N~~~~~~r~~~~~~~~~~t~~~v 147 (940)
.+..|.-|||+.+.-|.+.+...+ -...|||+.++++||+.++++.+|.++.....++ -.++.++.+ -.+
T Consensus 190 fiv~G~ekViLiqeqlsknrii~~-~~k~~~~~~svtsst~e~kskt~v~~k~~k~ylk-----~~~~~d~ip----ivi 259 (1153)
T KOG0215|consen 190 FIVKGTEKVILIQEQLSKNRIIVE-EDKKGNLQASVTSSTHERKSKTYVTTKKGKYYLK-----HNSFTDDIP----IVI 259 (1153)
T ss_pred eEeccceeEEEehhhhhccCeeec-cccCCccccccccceeeecceEEEEeccceeeee-----hhhhhccCC----EEE
Confidence 577899999999999999999887 6778999999999999999999996664332221 122222221 111
Q ss_pred EEEee--ecCCCceEEEEEEEeCCeEEEEEEeecccccccHhhHHHhccCCCHHHHHHHhcccccchhhcccCCCCChhh
Q 002296 148 VIRCV--RKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLV 225 (940)
Q Consensus 148 ~~rs~--~~~~~s~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~sD~eI~~~i~~~~~~~~~~~~~~~~~~~~ 225 (940)
.+..+ ..|+....+.. .+..+.+.... ....|+.+-+.+. +.-++.+.. .. +...+
T Consensus 260 v~ka~g~~sd~ei~~~vg----~~~~y~~~~~~--s~ee~~~~~v~tq-----qqal~y~~~--kv--k~~~~------- 317 (1153)
T KOG0215|consen 260 VLKAMGLESDQEIVQLVG----GDSKYQDIFAP--SLEECVSLGVYTQ-----QQALEYIGS--KV--KVKRG------- 317 (1153)
T ss_pred EEeeccccchHHHHHHhh----cchHHHHhhcc--chhhhhhhhhHHH-----HHHHHHhhh--eE--EeccC-------
Confidence 11111 01111000000 01101000000 0122332222222 222222210 00 00000
Q ss_pred HHHHHHHHHHHHhcccccHHHHHHHHhccccccccCC-----CCccH-HHHHHHHHHhHhccCCCCC--cchHHHHHHHH
Q 002296 226 SERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGL-----QSESY-YAVAETVIRDYIFVHLNDN--NDKFNLLIFML 297 (940)
Q Consensus 226 ~~~~~~ll~~~~~~~i~t~~~al~yig~~fr~~~~~~-----~~~~~-~~~~~~~L~~~ll~Hl~~~--~~K~~~L~~Mi 297 (940)
....-.++|++.+...+.+..+.+ .+.-. .-..+.++.-.+-+-.-++ .-+-..|-+|.
T Consensus 318 -------------t~~~~~~e~~~~l~~~~lahv~v~~~~~r~K~~yi~~m~rr~~~a~l~~~~~ddrd~~gnkrlelag 384 (1153)
T KOG0215|consen 318 -------------TTPTKDEEALEVLSTTVLAHVPVPDLNFRMKAIYIGLMVRRVIQAMLNKLAMDDRDYVGNKRLELAG 384 (1153)
T ss_pred -------------CCCCchHHHHHHHHhhheeceeccCCCCcceeehHHHHHHHHHHHHhCcccccchhhhccchHHHHH
Confidence 011123356666655443322211 11111 1122222222222222121 12333455555
Q ss_pred HHHHHhcCCCCCCCCccccccceecccchhHHHHHHHHHHHHHHHHHHHHHHHHHhc--CCcccccchHHHHHHHhcCCC
Q 002296 298 QKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENN--GKKFDFFNLANIKKVMEKNPS 375 (940)
Q Consensus 298 rkLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~--~~~~~~~~~~~~~~~~~~~~~ 375 (940)
+ |+.+..+.-..++.+.|++.+-...+.++..++.+.++.+. ..+..+..-+.+. ...+.+ +.++ +.+.
T Consensus 385 q-llsllfeD~fk~~n~e~k~~~dk~l~k~~ra~~fD~~~~~n-~~~~~it~~l~ra~stgnw~i---Krfr--mer~-- 455 (1153)
T KOG0215|consen 385 Q-LLSLLFEDLFKRFNSELKKNIDKILKKPIRAQEFDALKHLN-VRANMITSGLERAISTGNWSI---KRFR--MERA-- 455 (1153)
T ss_pred H-HHHHHHHHHHHHHHHHHHHHHHHHhcchhhhhhhHHHHHHH-HHHHHHHHHHHHHhhcCchHH---HHhh--hhhc--
Confidence 4 45555666667888999999999999988888888887765 4444444444331 111111 1111 0111
Q ss_pred cchHHHHHHHhcccCcccccccccccccceEEEccccchHHHh-hhhcccccCCcccccccccccccCCCCccccccCCC
Q 002296 376 KQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFI-SFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHT 454 (940)
Q Consensus 376 ~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~l-Sh~Rrv~rg~~~~~~K~t~vR~Lhps~wGfiCPveT 454 (940)
.+|+- -+-.|++|... ..-.-++++.++..+..+-+.. |.++.+-+ +-+.....-.+-..+..|+.|||-++
T Consensus 456 -gvt~V--lsrlSyisaLg--mmtri~s~fektrkvsgprSlq~sqwgmlcp--~dtpegeacglvknlalmthittd~e 528 (1153)
T KOG0215|consen 456 -GVTQV--LSRLSYISALG--MMTRINSQFEKTRKVSGPRSLQPSQWGMLCP--SDTPEGEACGLVKNLALMTHITTDSE 528 (1153)
T ss_pred -cceee--ehhhhhhhhhh--hheehhhhheeehhccCccccChhhcccccC--CCCCCccccccccchHHHhcccCCCC
Confidence 12221 12335565321 1113567888877755443322 22222222 23455666789999999999999999
Q ss_pred CCCccccccccccceeEEeeccC
Q 002296 455 PDGEPCGLLNHMTSTCRVASYYD 477 (940)
Q Consensus 455 PEG~~cGLvk~LA~~~~Is~~~~ 477 (940)
|++..|++.|..+...+++....
T Consensus 529 e~pi~~~~~k~gv~di~~v~~~e 551 (1153)
T KOG0215|consen 529 EKPILKLCYKLGVEDIHVVSGRE 551 (1153)
T ss_pred cchhHHHHHHhcceeeeeecccc
Confidence 99999999999999999987744
No 25
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional
Probab=95.84 E-value=0.012 Score=71.30 Aligned_cols=60 Identities=27% Similarity=0.402 Sum_probs=48.1
Q ss_pred eEEEEEEeeecCCCcccceeccCCCccEEeeeecCCCcC-ccCCCCCcCcEEeCCCCccccccH
Q 002296 836 QKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMP-FSGVTGMRPDLIINPHAFPSRMTI 898 (940)
Q Consensus 836 ~~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~dMP-f~~~~G~~pDiI~NPh~~PSRMti 898 (940)
-.+|+++-..=.=-.|=|.||=||||||+.. .||+- |.+|||+.|.|.++|.++-||.|.
T Consensus 696 v~lKl~~Vtst~dLeGlKICgIHGQKGVln~---seDLtew~aeDg~~aQIclSPiSyLsRQtn 756 (865)
T PHA03394 696 VYLKIRLVTSTSDLEGLKICGIHGQKGVLNG---SEDLTEWMAEDGTHAQICLSPISYLSRQTN 756 (865)
T ss_pred EEEEEEEEEEecCcceeEEeeecccccccCC---cchhhhhhccCCCcceEEechHHhhccccc
Confidence 3455555444445579999999999999764 67776 666999999999999999999985
No 26
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription]
Probab=94.78 E-value=0.012 Score=71.70 Aligned_cols=236 Identities=8% Similarity=-0.093 Sum_probs=138.2
Q ss_pred CCCccchhhcccccccccccceeEEEeccCceeeccCCCeeeEeccceeecCCCCCCCCceeEEEEEeccCCCCCceEEE
Q 002296 651 NQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMIL 730 (940)
Q Consensus 651 NqspRn~yq~~M~KQaig~~~~n~~~R~d~~~y~L~~~Q~Plv~t~~~~~~~~~~~~~G~N~~Vav~~y~Gyn~EDaiii 730 (940)
-|.+++.++.-|. |..+-....+..+.+...-.|.+++.++-++......-.-..+.+.++-++.+.+.++..++...-
T Consensus 681 pdh~qspr~tYQs-a~~kqamg~y~tn~~vR~dtl~~~l~ypqkpl~tt~~~e~l~~~eL~aG~NaiVAi~~~~GYNqED 759 (1141)
T KOG0214|consen 681 PDHNQSPRNTYQS-AMGKQAMGVYHTNPQVRMDTLAKVLYYPQKPLVTTRAMEYLRFRELPAGQNAIVAIACYSGYNQED 759 (1141)
T ss_pred CCCCCchHHHHHH-HHhhhcceeeeecchhhhhhhhhcccccccchhhHHHHhhhhhhhcccccceEEEEecccCccHHH
Confidence 3555555555555 222223334444455555555555555555544444334455679999999999999999999999
Q ss_pred ecchhccCcceeeEEEEEEEEeeccCCCcCccceeeccCCCChhhhccc---CCCCCcccCcE--e-cCCCcEEEE-ee-
Q 002296 731 NKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVI---DSDGLPYVGQM--I-HPGEPYCSI-YD- 802 (940)
Q Consensus 731 nk~s~~rG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---d~dGi~~~g~~--v-~~gd~l~~~-~~- 802 (940)
|--..++++.|+. |++..+.-++.+ ..... ...+...++. ...|. +-|.+ + ..|=+-.|. +.
T Consensus 760 svimn~s~v~rg~-FrS~~~RsYk~q----~~~~~----~~~ee~~~~~~~~~~~~m-r~~~~dkLdddG~i~~G~~vs~ 829 (1141)
T KOG0214|consen 760 SVIMNQSSVDRGL-FRSFFIRSYKDQ----EHKKD----QGPEEIFEEPPRGEGRGM-RNGKYDKLDDDGIIMPGSRVSG 829 (1141)
T ss_pred HHHHHhhhhhcch-hhhhhhhHHHhh----hhhcc----cccccccccccccccccc-cccccccccccCCccccceeec
Confidence 9999999998886 455554322211 11100 0111111111 00000 00000 0 011111111 00
Q ss_pred --cCCCcEEEeeccCCCcE--------EEEEEEEEecCCCCCceEEEEEEeeecCCCcccceeccCCCccEEeeeecCCC
Q 002296 803 --KTTNSWRTNSRKGSESV--------FVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDID 872 (940)
Q Consensus 803 --~~~~~~~~~~~~~~e~g--------~V~~v~~~~~~~~~~~~~v~i~~r~~R~p~iGDKf~sRHGqKGvvs~i~~~~d 872 (940)
-.-++.....-+..+.+ +..++.+-.++.| ...+|.++. ++.|+||+.+|++++-+.++-...+
T Consensus 830 ~Dv~iGk~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~G---ivd~V~vt~---n~~G~kF~kv~vr~~ripqiGDKfa 903 (1141)
T KOG0214|consen 830 GDVLIGKTTPQPAKEDESGPEDRLYTKRDHSTKLRHTERG---IVDQVWVTK---NSEGPKFVKVRVRQVRIPQIGDKFA 903 (1141)
T ss_pred CCEEeccccCCcccchhccccccccccccceeecccCCcc---eEEEEEEec---CCCCCceeEEEEeecccccccchhc
Confidence 00112222222222323 5566666555433 334444443 8999999999999999999999999
Q ss_pred cCccCCCCCcCcEEeCCCCccccccHHHHHHH
Q 002296 873 MPFSGVTGMRPDLIINPHAFPSRMTIAMLLES 904 (940)
Q Consensus 873 MPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~ 904 (940)
+++- .-|++++++-+++.-+++|+|-..++.
T Consensus 904 srHg-qKG~ig~~~~qedmpft~eGi~pDiii 934 (1141)
T KOG0214|consen 904 SRHG-QKGTIGITYRQEDMPFTIEGIVPDIII 934 (1141)
T ss_pred cccc-cCccccceeecCCCCccccCCCcceEE
Confidence 9999 999999999999999999999877764
No 27
>PF14251 DUF4346: Domain of unknown function (DUF4346)
Probab=50.30 E-value=7.7 Score=37.16 Aligned_cols=13 Identities=31% Similarity=0.501 Sum_probs=10.7
Q ss_pred cccccCCcEEEEc
Q 002296 98 EEAAEMGGYFILN 110 (940)
Q Consensus 98 E~~~D~GGYFIIn 110 (940)
--..||+|||||.
T Consensus 11 ~i~LDp~GYfiI~ 23 (119)
T PF14251_consen 11 FIDLDPAGYFIIY 23 (119)
T ss_pred ccccCCCccEEEE
Confidence 3457999999997
No 28
>PF04941 LEF-8: Late expression factor 8 (LEF-8); InterPro: IPR007025 Late expression factor 8 (LEF-8) is one of the primary components of RNA polymerase produced by polyhedrosis viruses. LEF-8 shows homology to the second largest subunit of prokaryotic DNA-directed RNA polymerase[].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=47.13 E-value=23 Score=43.60 Aligned_cols=82 Identities=15% Similarity=0.087 Sum_probs=46.2
Q ss_pred chhhHHHHHHHHhCCCeecCCccccCCCCcceEEEECCEEEeeec-CccHHHHHHHHHHHHHhcCCCCCCCceeEEEEcC
Q 002296 486 SKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIP-SSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLS 564 (940)
Q Consensus 486 ~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~~V~lnG~~iG~~~-~~~~~~~~~~lr~~r~~~~~~i~~~~ei~~v~~~ 564 (940)
|.........|.+.|+.....+.......+.+.|-.|.++.-+.- ..+...+.. .+||.. ..+|+.+.
T Consensus 377 Y~~Va~kF~~Li~~~Li~~~~~~~~~~~~~~l~IaFNnRPT~~~C~r~~L~~I~Y---~lKRn~-----~PIElKl~--- 445 (748)
T PF04941_consen 377 YKMVADKFKSLIEKNLIFRNDDENDDNDDDELLIAFNNRPTIYYCRRTDLYKIFY---ELKRNR-----CPIELKLS--- 445 (748)
T ss_pred HHHHHHHHHHHHHcCCceecccccccCCCCeEEEEEcCCCcEEEEehhchHHHHH---HHhccC-----CcEEEEee---
Confidence 455555666777778764322221222345678888988876542 223344444 445432 23677653
Q ss_pred CCCCCCceEEecCCCcee
Q 002296 565 LGGAYPGLYLFTSPPKFV 582 (940)
Q Consensus 565 ~~~~~~~i~i~~d~gR~~ 582 (940)
..-++|+-.+|=+|
T Consensus 446 ----~~ILfVNHHEGMIc 459 (748)
T PF04941_consen 446 ----NNILFVNHHEGMIC 459 (748)
T ss_pred ----CCEEEEecCCceEE
Confidence 24578888888666
No 29
>PF08763 Ca_chan_IQ: Voltage gated calcium channel IQ domain; InterPro: IPR014873 Ca2+ ions are unique in that they not only carry charge but they are also the most widely used of diffusible second messengers. Voltage-dependent Ca2+ channels (VDCC) are a family of molecules that allow cells to couple electrical activity to intracellular Ca2+ signalling. The opening and closing of these channels by depolarizing stimuli, such as action potentials, allows Ca2+ ions to enter neurons down a steep electrochemical gradient, producing transient intracellular Ca2+ signals. Many of the processes that occur in neurons, including transmitter release, gene transcription and metabolism are controlled by Ca2+ influx occurring simultaneously at different cellular locales. The pore is formed by the alpha-1 subunit which incorporates the conduction pore, the voltage sensor and gating apparatus, and the known sites of channel regulation by second messengers, drugs, and toxins []. The activity of this pore is modulated by 4 tightly-coupled subunits: an intracellular beta subunit; a transmembrane gamma subunit; and a disulphide-linked complex of alpha-2 and delta subunits, which are proteolytically cleaved from the same gene product. Properties of the protein including gating voltage-dependence, G protein modulation and kinase susceptibility can be influenced by these subunits. Voltage-gated calcium channels are classified as T, L, N, P, Q and R, and are distinguished by their sensitivity to pharmacological blocks, single-channel conductance kinetics, and voltage-dependence. On the basis of their voltage activation properties, the voltage-gated calcium classes can be further divided into two broad groups: the low (T-type) and high (L, N, P, Q and R-type) threshold-activated channels. The voltage-gated calcium channel alpha 1 subunit contains an IQ domain, named for its isoleucine-glutamine (IQ) motif, which interacts with hydrophobic pockets of Ca2+/calmodulin []. The interaction regulates two self-regulatory calcium dependent feedback mechanisms, calcium dependent inactivation (CDI), and calcium-dependent facilitation (CDF). ; PDB: 3OXQ_F 2F3Z_B 3G43_E 2F3Y_B 2BE6_D 3DVM_B 3BXK_D 2VAY_B 3DVK_B 3BXL_B ....
Probab=29.83 E-value=55 Score=24.83 Aligned_cols=30 Identities=17% Similarity=0.172 Sum_probs=20.1
Q ss_pred cccccHHHHHHHHHHHHHhhchhHHHHHhhhhhhhHHHHH
Q 002296 893 PSRMTIAMLLESVAAKVVAYMENLWMQHHLQIQSRKLMEI 932 (940)
Q Consensus 893 PSRMtiGql~E~~~gk~~~~~G~~~~~~~~~~~~~~~~~~ 932 (940)
++.||||.+.-+++ ++++|.+.++|+.-+.
T Consensus 1 ~d~~TVGK~YAt~l----------I~dyfr~~K~rk~~~~ 30 (35)
T PF08763_consen 1 DDEVTVGKFYATLL----------IQDYFRQFKKRKEQEQ 30 (35)
T ss_dssp ---CCCHHHHHHHH----------HHHHHHHHHHHHHHT-
T ss_pred CCcchhHHHHHHHH----------HHHHHHHHHHHHHHHH
Confidence 46789999876554 4788888888886554
No 30
>PF13375 RnfC_N: RnfC Barrel sandwich hybrid domain
Probab=26.07 E-value=1.9e+02 Score=27.18 Aligned_cols=52 Identities=13% Similarity=0.070 Sum_probs=34.5
Q ss_pred CcccCcEecCCCcEEEEeecCCCcEEEeeccCCCcEEEEEEEEEecCCCCCceEEEE
Q 002296 784 LPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANI 840 (940)
Q Consensus 784 i~~~g~~v~~gd~l~~~~~~~~~~~~~~~~~~~e~g~V~~v~~~~~~~~~~~~~v~i 840 (940)
++++|++|+.|+.|.-. . ..-+...+...+|+|..|.-.....|.....|.|
T Consensus 45 ~V~~Gd~V~~GQ~Ia~~-~----~~~sa~iHAsvSG~V~~I~~~~~~~g~~~~~ivI 96 (101)
T PF13375_consen 45 VVKVGDKVKKGQLIAEA-E----GFLSAPIHASVSGTVTAIEKRPIPHGSKVPAIVI 96 (101)
T ss_pred EEcCCCEEcCCCEEEec-C----CCcEeeEEcCCCeEEEEEeeeEcCCCCCCCEEEE
Confidence 68899999999998532 1 1224445556899999988776655544444433
No 31
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=21.62 E-value=57 Score=26.34 Aligned_cols=16 Identities=19% Similarity=0.223 Sum_probs=14.1
Q ss_pred CcccCcEecCCCcEEE
Q 002296 784 LPYVGQMIHPGEPYCS 799 (940)
Q Consensus 784 i~~~g~~v~~gd~l~~ 799 (940)
.++.|+.|++||+|+-
T Consensus 17 ~V~~G~~VkkGd~L~~ 32 (50)
T PF13533_consen 17 YVKEGQQVKKGDVLLV 32 (50)
T ss_pred EecCCCEEcCCCEEEE
Confidence 4789999999999975
Done!