Query psy3022
Match_columns 258
No_of_seqs 174 out of 1095
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 23:32:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3022.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3022hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK14977 bifunctional DNA-dire 100.0 2.5E-70 5.5E-75 579.0 16.1 230 2-231 719-1075(1321)
2 KOG0261|consensus 100.0 5.6E-70 1.2E-74 547.3 11.5 236 2-239 740-1130(1386)
3 KOG0260|consensus 100.0 2.2E-65 4.7E-70 521.7 14.3 236 2-237 706-1156(1605)
4 KOG0262|consensus 100.0 2.4E-61 5.2E-66 493.8 8.6 217 6-224 862-1239(1640)
5 TIGR02386 rpoC_TIGR DNA-direct 100.0 4.4E-50 9.5E-55 418.1 11.2 170 5-196 644-931 (1140)
6 PRK14906 DNA-directed RNA poly 100.0 5.4E-50 1.2E-54 420.1 8.9 159 6-185 757-1022(1460)
7 PRK00566 DNA-directed RNA poly 100.0 3.4E-49 7.4E-54 411.8 8.8 166 6-196 654-934 (1156)
8 PRK14844 bifunctional DNA-dire 100.0 6.4E-49 1.4E-53 426.3 9.3 220 7-247 2107-2461(2836)
9 PRK09603 bifunctional DNA-dire 100.0 5.5E-47 1.2E-51 412.3 12.3 143 6-169 2052-2309(2890)
10 CHL00117 rpoC2 RNA polymerase 100.0 1.6E-44 3.6E-49 381.8 9.5 222 3-248 92-454 (1364)
11 PRK02597 rpoC2 DNA-directed RN 100.0 2.9E-43 6.2E-48 370.1 10.2 153 8-181 90-362 (1331)
12 TIGR02388 rpoC2_cyan DNA-direc 100.0 1.1E-42 2.3E-47 363.4 8.9 157 3-181 85-360 (1227)
13 PF04998 RNA_pol_Rpb1_5: RNA p 100.0 6.3E-42 1.4E-46 305.0 3.0 111 101-211 1-145 (277)
14 TIGR02390 RNA_pol_rpoA1 DNA-di 100.0 3E-40 6.4E-45 340.9 10.7 129 2-130 686-814 (868)
15 PRK08566 DNA-directed RNA poly 100.0 3.9E-40 8.5E-45 340.5 10.0 130 2-131 691-820 (882)
16 cd02584 RNAP_II_Rpb1_C Largest 100.0 1.6E-33 3.5E-38 270.2 6.1 102 133-234 23-127 (410)
17 TIGR02389 RNA_pol_rpoA2 DNA-di 100.0 4.5E-33 9.7E-38 263.8 5.3 97 133-229 40-137 (367)
18 cd02736 RNAP_III_Rpc1_C Larges 100.0 1.2E-32 2.7E-37 255.0 6.1 105 133-239 6-113 (300)
19 cd06528 RNAP_A'' A'' subunit o 100.0 3.4E-32 7.3E-37 257.7 6.0 100 133-232 36-136 (363)
20 PRK04309 DNA-directed RNA poly 100.0 1.5E-31 3.2E-36 254.8 7.2 100 133-232 55-155 (383)
21 cd02735 RNAP_I_Rpa1_C Largest 100.0 1.2E-31 2.5E-36 249.4 4.6 90 133-224 6-96 (309)
22 PRK14897 unknown domain/DNA-di 100.0 1.1E-31 2.4E-36 261.4 3.3 92 133-224 178-269 (509)
23 PF05000 RNA_pol_Rpb1_4: RNA p 99.9 3.1E-26 6.7E-31 183.1 7.3 93 2-94 16-108 (108)
24 cd02737 RNAP_IV_NRPD1_C Larges 99.9 1.1E-25 2.5E-30 214.3 3.7 100 137-242 1-111 (381)
25 COG0086 RpoC DNA-directed RNA 99.8 8.3E-22 1.8E-26 202.5 3.9 123 2-131 629-752 (808)
26 cd02655 RNAP_beta'_C Largest s 99.7 1.8E-18 3.8E-23 152.9 1.3 52 133-185 2-53 (204)
27 PRK14898 DNA-directed RNA poly 99.6 1.3E-16 2.8E-21 165.6 3.1 74 151-224 539-612 (858)
28 cd00630 RNAP_largest_subunit_C 99.5 9.2E-15 2E-19 124.7 1.6 48 137-184 1-48 (158)
29 COG0086 RpoC DNA-directed RNA 98.3 6.6E-07 1.4E-11 93.2 5.0 109 133-242 410-521 (808)
30 PRK14898 DNA-directed RNA poly 98.1 7E-07 1.5E-11 93.7 0.0 27 132-158 52-78 (858)
31 PF03323 GerA: Bacillus/Clostr 56.2 3.5 7.6E-05 41.1 -0.2 79 144-224 116-202 (470)
32 PF15278 Sec3_C_2: Sec3 exocys 32.2 39 0.00085 25.9 2.2 23 33-55 63-85 (86)
33 TIGR02388 rpoC2_cyan DNA-direc 21.4 34 0.00073 38.3 0.3 31 156-186 963-993 (1227)
No 1
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=100.00 E-value=2.5e-70 Score=579.00 Aligned_cols=230 Identities=39% Similarity=0.678 Sum_probs=220.2
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChhhHHhhcCCCcChhhHHHHHhhhcccccC--------CcccCCCC
Q psy3022 2 LALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVE--------GKRIPFGF 73 (258)
Q Consensus 2 ~~~~~~~E~~v~~~l~~~~~~~~~~~~~~~~~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~~~--------G~ri~~~~ 73 (258)
++.+|++|.+++++|+++|+++++.+.++++++|++++|+.||||||+.|++||++|||||.++ |+|||.+|
T Consensus 719 ~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~l~~Mv~SGAKGS~~Ni~Qi~~~lGQQ~ve~~~~~~~~G~Ri~~~~ 798 (1321)
T PRK14977 719 MKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTGGRLHEGY 798 (1321)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHhhcccccCHHHHHHHHhccccccccccccccCCCCCCcCCC
Confidence 5788999999999999999999999999999999999999999999999999999999999999 99999999
Q ss_pred CCCCCCCCcCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccCC-----------------------
Q psy3022 74 RKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETAC----------------------- 130 (258)
Q Consensus 74 ~~r~lp~f~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG~----------------------- 130 (258)
++|+||||.++|.+|+++|||.|||++||+|.|||||||||||||+|||||||+|||
T Consensus 799 ~~RtLPhF~~~d~~p~a~GfV~nsFl~GL~P~EfFFHaM~GREGLiDTAVKTA~SGYLQRrLvk~lEDl~v~YD~TVR~s 878 (1321)
T PRK14977 799 KDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDP 878 (1321)
T ss_pred CCCcCCCCCCCCCCcccccchhhhhcCCCCHHHHHHHhhcccccccccccccCcCchhHHHHHHHhcceEEecCCeEEeC
Confidence 999999999999999999999999999999999999999999999999999999991
Q ss_pred -------------------------C------------------------------------------------------
Q psy3022 131 -------------------------N------------------------------------------------------ 131 (258)
Q Consensus 131 -------------------------~------------------------------------------------------ 131 (258)
+
T Consensus 879 ~g~iiQF~YGeDG~d~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 958 (1321)
T PRK14977 879 HGHIIQFKFGEDGIDPQKLDHGEAFNLERIIEKQKIEDRGKGASKDEIEELAKEYTKTFNANLPKLLADAIHGAELKEDE 958 (1321)
T ss_pred CCCEEEEeecCCCcCHHHhccCCcccHHHHHHHhhhhccccCCCHHHHHHHHHHHHHhhhhhhHHHHHHHHHHcCCCHHH
Confidence 0
Q ss_pred --------------CccCCCchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhhccCCCCCeEEEEec
Q psy3022 132 --------------AKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLT 197 (258)
Q Consensus 132 --------------~~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~~~~~t~~~~v~L~ 197 (258)
..++||||||++||||||||+|||||||||+||+++++||+|+|||+||++++++++||.|+++|.
T Consensus 959 ~~~~~~~~~~~~~~~~~~pGe~VG~iaAQSiGEP~TQmTLnTFH~AGv~~~nvt~GvpRl~Eii~a~k~~~tp~m~~~l~ 1038 (1321)
T PRK14977 959 LEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLD 1038 (1321)
T ss_pred HHHHHHHHHHHHHhcccCCcccchhhhhhhccCceeeecccccccccccccCcccCccchHHhhhcccCCCCCeEEEEeC
Confidence 027899999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcchhcHHHHHHHhccccceeccceeE---EEEcCCC
Q psy3022 198 GQAARDAEKAKNVLCRLEHTTLRKVLY---IILRPAT 231 (258)
Q Consensus 198 ~~~~~~~~~a~~v~~~L~~~~l~~v~~---I~ydp~~ 231 (258)
+++..+++.|+.++.+|++++|++++. +.|||+.
T Consensus 1039 ~~~~~~~~~a~~v~~~ie~~~l~~~~~~~~i~~~~~~ 1075 (1321)
T PRK14977 1039 DECKEDIEKAIEIARNLKELKVRALIADSAIDNANEI 1075 (1321)
T ss_pred CcccchHHHHHHHHhheeeeEHHHhhhheEeeccCCc
Confidence 987778899999999999999999987 7788764
No 2
>KOG0261|consensus
Probab=100.00 E-value=5.6e-70 Score=547.26 Aligned_cols=236 Identities=50% Similarity=0.775 Sum_probs=223.9
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChhhHHhhcCCCcChhhHHHHHhhhcccccCCcccCCCCCCCCCCCC
Q psy3022 2 LALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHF 81 (258)
Q Consensus 2 ~~~~~~~E~~v~~~l~~~~~~~~~~~~~~~~~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~~~G~ri~~~~~~r~lp~f 81 (258)
++.+|++|++|..+||.+|++++++|+..|++.|+.++|+.+|||||..|++||++|+|||.+.|.|+|.||.+|+||||
T Consensus 740 ~~~eetLEa~I~~~Ls~IRe~~G~~C~~eL~~~NsPliMa~CGSKGS~INiSQMvACVGQQ~ISG~RvPdGf~dRsLPHF 819 (1386)
T KOG0261|consen 740 CNEEETLEAEILSELSTIREEAGKICIRELHPRNSPLIMALCGSKGSKINISQMVACVGQQIISGHRVPDGFEDRSLPHF 819 (1386)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccChHHHHHhcCCCCcccHHHHHHHhhhhhhcCCcCCCccccccCccc
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccCC-------------------------------
Q psy3022 82 IKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETAC------------------------------- 130 (258)
Q Consensus 82 ~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG~------------------------------- 130 (258)
.+.+..|.++|||.|||+.||+|.|||||+|+|||||+|||||||++||
T Consensus 820 ~r~Sk~P~aKGFV~NSFySGLTptEFfFHtm~GREGLVDTAVKTAETGYMqRRLmK~LEDL~~~YDgTVR~s~~~vvqF~ 899 (1386)
T KOG0261|consen 820 ERHSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKSLEDLSVQYDGTVRNSNGDVVQFT 899 (1386)
T ss_pred cccCCCccccchhhhhcccCCCchhhheeecccccchhhhhhhhhhhhhHHHHHHHHHHHHHHhhcCceecCCCcEEEEe
Confidence 9999999999999999999999999999999999999999999999990
Q ss_pred --------------------------------------------------------------------------------
Q psy3022 131 -------------------------------------------------------------------------------- 130 (258)
Q Consensus 131 -------------------------------------------------------------------------------- 130 (258)
T Consensus 900 YG~DglDPa~mEg~~~pv~f~r~~~~~~~~~~~~~~~~l~~~el~e~~~~~l~~~f~~~~~~F~~~~~~~i~~~~~~~~~ 979 (1386)
T KOG0261|consen 900 YGGDGLDPAMMEGKDQPVNFNRVFDHAKAIFPHRHDPPLSSEELDETLEEELLRKFTEKGDPFVHELREFIASLSKKIKK 979 (1386)
T ss_pred ecCCCCChhhhcCCCCchhHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence
Q ss_pred -----------------------------------------CCccCCCchhhhhhhhccCChhhhhhhhccccCCccccc
Q psy3022 131 -----------------------------------------NAKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKN 169 (258)
Q Consensus 131 -----------------------------------------~~~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~ 169 (258)
..+++||.+||.|||||||||+|||||+|||+|||+++|
T Consensus 980 ~~~~~~d~~~~~~~~~~~~~~~~~t~kql~~f~~~~~~ky~~a~~EpGTavGAi~aQSIGEPGTQMTLKTFHFAGVASMN 1059 (1386)
T KOG0261|consen 980 LQDKYGDECGPKFCPDLLYQISRLTEKQLEKFVERCLDKYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMN 1059 (1386)
T ss_pred HhhhcccccCCccCccceeeeeeccHHHHHHHHHHHHHHHHhhhcCCcchhhhhhcccCCCCCceeeeeeeeecceeeee
Confidence 002799999999999999999999999999999999999
Q ss_pred cccCccccchhhhhccCCCCCeEEEEecCcchhcHHHHHHHhccccceeccceeE---EEEcCCCceeEEEec
Q psy3022 170 VTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVLY---IILRPATHYQVELIS 239 (258)
Q Consensus 170 v~~g~~rl~eil~~~~~~~t~~~~v~L~~~~~~~~~~a~~v~~~L~~~~l~~v~~---I~ydp~~~~~i~~~~ 239 (258)
+|+|+||++||+||+|+++||.++..|.++ .++..|+.|+.||++++|+||++ .-|-|+.++..-.++
T Consensus 1060 iTlGVPRIkEIINAsk~ISTPIItA~L~n~--~d~~~Ar~VKgRiEKt~L~dv~~yieeV~~p~~~fl~i~vd 1130 (1386)
T KOG0261|consen 1060 ITLGVPRIKEIINASKTISTPIITAELENP--HDERSARVVKGRIEKTTLGDVCSYIEEVYGPDSCFLLIRVD 1130 (1386)
T ss_pred eccCcchHHHHHhhhcccCccceeeeecCc--hhHHHHHHHhhhhhhhhHHHHHHHHHHHhCCcceEEEEEec
Confidence 999999999999999999999999999987 57889999999999999999988 568888877654443
No 3
>KOG0260|consensus
Probab=100.00 E-value=2.2e-65 Score=521.66 Aligned_cols=236 Identities=77% Similarity=1.116 Sum_probs=226.4
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChhhHHhhcCCCcChhhHHHHHhhhcccccCCcccCCCCCCCCCCCC
Q psy3022 2 LALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHF 81 (258)
Q Consensus 2 ~~~~~~~E~~v~~~l~~~~~~~~~~~~~~~~~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~~~G~ri~~~~~~r~lp~f 81 (258)
||+.|+||.+++.+||++|++++...++++++.|++..|+.+|||||..|++|+++|+|||+++|+|||+||.+|+||||
T Consensus 706 ~tlretfe~~v~~vlndArd~~gssA~~sl~esNn~k~Mv~aGSKGs~inisQ~saCVGqQnVEgkrIpFGF~~Rtlphf 785 (1605)
T KOG0260|consen 706 RTLRETFENKVNRVLNDARDKSGSSAQKSLSESNNFKTMVVAGSKGSFINISQVSACVGQQNVEGKRIPFGFPKRTLPHF 785 (1605)
T ss_pred hhHHHHHHHHHHHHHHHHHHhhhhHHHhhhhhcccHHHHHhhcCCCcceehhhhhhhhccccccccccccCCCccccccc
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccCC-------------------------------
Q psy3022 82 IKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETAC------------------------------- 130 (258)
Q Consensus 82 ~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG~------------------------------- 130 (258)
.++|++|+++|||+|||+.||+|+|||||||+|||||||||+|||++|+
T Consensus 786 ~kDdysPesrGfVENSyL~GLtP~EfFfHamggREglidtavktaEtGyiqRRL~kameDimv~yDgTVRNs~gqviQf~ 865 (1605)
T KOG0260|consen 786 SKDDYSPESRGFVENSYLTGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLMKAMEDIMVAYDGTVRNSLGQVIQFK 865 (1605)
T ss_pred ccCCCCccccceeecccccCCCHHHHHHHHhcccchhhhhhhcccccchHHHHHHHHHHHHHhhcCcceecccceeEEEE
Confidence 9999999999999999999999999999999999999999999999990
Q ss_pred --------------------------------------------------------------------------------
Q psy3022 131 -------------------------------------------------------------------------------- 130 (258)
Q Consensus 131 -------------------------------------------------------------------------------- 130 (258)
T Consensus 866 YGeDG~d~~~vE~q~~~~l~~~~a~f~~~~~~d~ld~~~~~~~~~~~~e~~~~~~l~~lle~e~~~l~~dr~~l~~i~~~ 945 (1605)
T KOG0260|consen 866 YGEDGLDGHPVEFQNGETLGSLNACFESEFAYDALDEPISLSSEEVVNEISELLKLQNLLECEYKKLVRDRRVLLYIFEY 945 (1605)
T ss_pred eccCccccceeeccccccccchHHHHHhhhhhhhhcCcccchhhhHhhhhhhhHHHHHHHHHHHHhhhhhhhhhhhhccc
Confidence
Q ss_pred ---------C----------------------------------------------------------------------
Q psy3022 131 ---------N---------------------------------------------------------------------- 131 (258)
Q Consensus 131 ---------~---------------------------------------------------------------------- 131 (258)
+
T Consensus 946 g~~k~~lp~n~~r~I~Na~~~f~~~~r~~t~l~~~~v~~g~~~l~e~l~iv~g~~~~sraqrl~~~lLrs~l~~krv~~e 1025 (1605)
T KOG0260|consen 946 GDAKWPLPENLQRIIWNALKKFSIDERKPTDLIPFKVVKGVKELAEKLVIVRGEDYISRAQRLFNILLRSTLATKRVLEE 1025 (1605)
T ss_pred CCcccccchhHHHHHHHHHhhcccccccccccchhhhhhhhhhhhheeEEeeCchhHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 0
Q ss_pred ---------------------CccCCCchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhhccCCCCC
Q psy3022 132 ---------------------AKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAP 190 (258)
Q Consensus 132 ---------------------~~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~~~~~t~ 190 (258)
..+.|||.||.+||||||||+|||||||||.||+++.|||+|+|||+||+|.+|+.|+|
T Consensus 1026 ~rls~eaf~w~~~~Ie~~f~qa~a~pgemvg~lAaqsvgePatqmTlntfh~aGVssknVt~gvprlkei~Nv~k~~ktp 1105 (1605)
T KOG0260|consen 1026 YRLSSEAFEWVLGEIEARFLQAEASPGEMVGALAAQSVGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEIINVAKNAKTP 1105 (1605)
T ss_pred hcccHHHHHHHhhhhhhheeeeecCccchHhHHHHHHhCCchhhcccchhcccceeeeeeeccCcchhhhhhhhccCCCc
Confidence 02899999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEecCcchhcHHHHHHHhccccceeccceeE---EEEcCCCcee-EEE
Q psy3022 191 SLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVLY---IILRPATHYQ-VEL 237 (258)
Q Consensus 191 ~~~v~L~~~~~~~~~~a~~v~~~L~~~~l~~v~~---I~ydp~~~~~-i~~ 237 (258)
+++|+|..+.+++.+.|+.++.+|+++++.+++. |+|||++..+ |.+
T Consensus 1106 sLtV~l~g~~~k~~e~ak~v~~~le~ttl~~vt~~t~i~ydpdp~~tvI~e 1156 (1605)
T KOG0260|consen 1106 SLTVYLTGEAAKDNEWAKLVQCCLEHTTLKDVTRATEIYYDPDPQSTVIDE 1156 (1605)
T ss_pred eEEEEecchhhcchHHHHHHhhhcccccHHhhhccCcceecCCCcceeecc
Confidence 9999999988899999999999999999999977 9999998653 443
No 4
>KOG0262|consensus
Probab=100.00 E-value=2.4e-61 Score=493.77 Aligned_cols=217 Identities=45% Similarity=0.708 Sum_probs=199.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh----cCCCChhhHHhhcCCCcChhhHHHHHhhhcccccCCcccCCCCCCCCCCCC
Q psy3022 6 QTFENQVNRILNDARDKTGGSAKKS----LTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHF 81 (258)
Q Consensus 6 ~~~E~~v~~~l~~~~~~~~~~~~~~----~~~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~~~G~ri~~~~~~r~lp~f 81 (258)
..+....-+.+|...+++.+.|... ..|.|++..|+.||||||.+|++||+++||||.++|+|+|.+.+|++||||
T Consensus 862 ~~LD~~~k~~~n~~ts~I~~~cvP~GLlk~FP~N~mqlM~~SGAKGS~VN~~QISclLGQqeLEGkRvPlMvSGKtLPsF 941 (1640)
T KOG0262|consen 862 AMLDRVMKSELNGYTSEIVKKCVPDGLLKKFPENNMQLMIQSGAKGSNVNTSQISCLLGQQELEGKRVPLMVSGKTLPSF 941 (1640)
T ss_pred HHHHHHHHHHHhhhhHHHHhhhccchhhhcCCcchHHHHHHhcCCcccccHHHHHHhhhhHhhcCCccceeecCCccCCc
Confidence 3455666777888888888877765 247899999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccCC-------------------------------
Q psy3022 82 IKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETAC------------------------------- 130 (258)
Q Consensus 82 ~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG~------------------------------- 130 (258)
.+++.+|.+.|||.+.|+.|+.|+|||||||||||||||||||||+|||
T Consensus 942 ~p~e~spraGGfI~~RFlTGi~PqeyfFHCMAGREGLIDTAVKTSRSGYLQRCLiKhLEgl~V~YD~TVRDsDgsvVQF~ 1021 (1640)
T KOG0262|consen 942 APYETSPRAGGFIDGRFLTGIKPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVHYDLTVRDSDGSVVQFM 1021 (1640)
T ss_pred CCCCCCCCCCCcccceeecCCCchHHhhhhhccccchhhhHHhcccchHHHHHHHHhhhhcEEeccceEEcCCCcEEEEe
Confidence 9999999999999999999999999999999999999999999999990
Q ss_pred ----------------------CC--------------------------------------------------------
Q psy3022 131 ----------------------NA-------------------------------------------------------- 132 (258)
Q Consensus 131 ----------------------~~-------------------------------------------------------- 132 (258)
|.
T Consensus 1022 YGEDglDitKssfl~~~~f~~~Ny~avl~~~~~~~v~s~~d~~~a~~~~k~i~kw~kk~~w~~~~k~~~cpdpv~~k~~p 1101 (1640)
T KOG0262|consen 1022 YGEDGLDITKSSFLNKKEFPTDNYEAVLLKYKSESVLSAFDIKKASKYIKKILKWKKKHMWFELDKKIACPDPVLAKYNP 1101 (1640)
T ss_pred ecCccccccHHhhcchhhhhhhhHHHHHhhhChHHHhhhhhhHHHHHHHHHHHHHHhhhccchhhcccCCCChhhhhcch
Confidence 00
Q ss_pred -----------------------------------------------ccCCCchhhhhhhhccCChhhhhhhhccccCCc
Q psy3022 133 -----------------------------------------------KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGV 165 (258)
Q Consensus 133 -----------------------------------------------~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~ 165 (258)
.++||||||+|||||||||.|||||||||+||.
T Consensus 1102 ~~y~gsvsekf~~~i~~f~~~~~k~~~s~~~~~~~lr~ll~~K~~~SLa~PGE~VGvlAAQSIGEPSTQMTLNTFHfAGr 1181 (1640)
T KOG0262|consen 1102 DKYLGSVSEKFRKKIDDFDDENAKKEKSEEPSEEKLRRLLQLKYIRSLADPGEPVGVLAAQSIGEPSTQMTLNTFHFAGR 1181 (1640)
T ss_pred hhhhccccHHHHHHHHHHHHHhhhhhccccchHHHHHHHHHHHHHHHhcCCCCcceeeeecccCCCcceeehhheeeccc
Confidence 289999999999999999999999999999999
Q ss_pred cccccccCccccchhhh-hccCCCCCeEEEEecCcchhcHHHHHHHhccccceeccceeE
Q psy3022 166 SSKNVTLGVPRLKEIIN-ISKKPKAPSLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVLY 224 (258)
Q Consensus 166 ~~~~v~~g~~rl~eil~-~~~~~~t~~~~v~L~~~~~~~~~~a~~v~~~L~~~~l~~v~~ 224 (258)
+++|||+|+|||+|||. ||++++||+|++++.+. .+.++|..+..+|.+++|++|.+
T Consensus 1182 GemNVTLGIPRLREIlMtASanIkTP~mt~pi~~g--~s~~ra~~i~~~l~rV~L~evlk 1239 (1640)
T KOG0262|consen 1182 GEMNVTLGIPRLREILMTASANIKTPSMTVPIKNG--VSDERADDITKELRRVTLKEVLK 1239 (1640)
T ss_pred cceeeeecchHHHHHHHHHhhccCCCceeeeccCC--ccHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999997 78999999999999886 45688999999999999999866
No 5
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form. Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.
Probab=100.00 E-value=4.4e-50 Score=418.10 Aligned_cols=170 Identities=34% Similarity=0.555 Sum_probs=150.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcCC----CChhhHHhhcCCCcChhhHHHHHhhhcccc-cCCcccCCCCCCCCCC
Q psy3022 5 KQTFENQVNRILNDARDKTGGSAKKSLTE----YNNLKAMVVAGSKGSNINISQVIACVGQQN-VEGKRIPFGFRKRTLP 79 (258)
Q Consensus 5 ~~~~E~~v~~~l~~~~~~~~~~~~~~~~~----~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~-~~G~ri~~~~~~r~lp 79 (258)
.+++|.++.++|+++++++++.+++++++ .|++++|+.||||||+.|++||+||+|||. ..| |++|
T Consensus 644 ~~er~~kvi~iw~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~SGARGS~~ni~QL~GmrGlma~p~G---------rii~ 714 (1140)
T TIGR02386 644 DEERYRKVVSIWSETKDKVTDAMMKLLKKDTYKFNPIFMMADSGARGNISQFRQLAGMRGLMAKPSG---------DIIE 714 (1140)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCcHhhhhhcccccCHHHHHHHHhCCCcccCCCC---------Cccc
Confidence 35688999999999999999999999986 599999999999999999999999999996 233 5555
Q ss_pred CCcCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccC-------------------CCC--------
Q psy3022 80 HFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETA-------------------CNA-------- 132 (258)
Q Consensus 80 ~f~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG-------------------~~~-------- 132 (258)
+ ||.|||++||+|.|||||||||||||+|||+|||+|| |++
T Consensus 715 ~------------PI~ssF~eGLtp~EyF~st~GaRkGLiDTAlKTAdSGYLtRRLVdv~qDviV~~dDCgT~~gi~v~~ 782 (1140)
T TIGR02386 715 L------------PIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEEGIEVEA 782 (1140)
T ss_pred c------------chhhccccCCCHHHHhhhccchhccccchheeecccceeeeehhhhhcceEEEeCCCCCCCCEEEEE
Confidence 4 5999999999999999999999999999999999999 210
Q ss_pred --------------------------------------------------------------------------------
Q psy3022 133 -------------------------------------------------------------------------------- 132 (258)
Q Consensus 133 -------------------------------------------------------------------------------- 132 (258)
T Consensus 783 ~~~~~~~~i~~l~~ri~GR~~~~di~~~~~~~~i~~~~~~i~~~~~~~i~~~~i~~v~iRS~ltC~s~~gvC~~CYG~~L 862 (1140)
T TIGR02386 783 IVEGKDEIIESLKDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYGRDL 862 (1140)
T ss_pred eecCCceEEeehhheeEEEEEhhheEeCCCCcEEEeCCCCcCHHHHHHHHHcCCCEEEecCCeeeCCCCCCccccCCCcc
Confidence
Q ss_pred ----ccCCCchhhhhhhhccCChhhhhhhhccccCCcccc--ccccCccccchhhhhccCCCCCeEEEEe
Q psy3022 133 ----KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSK--NVTLGVPRLKEIINISKKPKAPSLTVFL 196 (258)
Q Consensus 133 ----~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~--~v~~g~~rl~eil~~~~~~~t~~~~v~L 196 (258)
.|++|||||||||||||||||||||||||+||+++. ++|.|+||++|+++|+ +++.+.+...+
T Consensus 863 a~~~~V~~GeaVGiiAAQSIGEPGTQLTmRTFHtGGv~~~~~DIT~GlpRv~elfear-~p~~~a~iae~ 931 (1140)
T TIGR02386 863 ATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASGDITQGLPRVKELFEAR-TPKDKAVIAEV 931 (1140)
T ss_pred cCCcEecccccceeEeeeecCCCcchhehhheeeccccccccccccCchhhhhhhhcc-cCCCceEEEec
Confidence 289999999999999999999999999999999986 9999999999999985 44444444333
No 6
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=100.00 E-value=5.4e-50 Score=420.08 Aligned_cols=159 Identities=33% Similarity=0.569 Sum_probs=148.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcCCCChhhHHhhcCCCcChhhHHHHHhhhcccc-cCCcccCCCCCCCCCCCCcCC
Q psy3022 6 QTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQN-VEGKRIPFGFRKRTLPHFIKD 84 (258)
Q Consensus 6 ~~~E~~v~~~l~~~~~~~~~~~~~~~~~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~-~~G~ri~~~~~~r~lp~f~~~ 84 (258)
+++|.+|+++|+++++++++.+++++++.|++++|++||||||..|++||+||+|||. .+|++++
T Consensus 757 ~Er~~kVi~iw~~a~d~v~~~~~~~l~~~N~i~mMa~SGARGS~~QI~QLaGmRGlma~p~G~iIe-------------- 822 (1460)
T PRK14906 757 RERHKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIID-------------- 822 (1460)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcccCCCeEeeeeccCcccHHHHHHHHhcccceecCCCCccc--------------
Confidence 4568999999999999999999999999999999999999999999999999999984 6887663
Q ss_pred CCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccC-------------------CCC-------------
Q psy3022 85 DYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETA-------------------CNA------------- 132 (258)
Q Consensus 85 ~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG-------------------~~~------------- 132 (258)
.||+|||++||+|.|||||||||||||+|||+|||+|| |++
T Consensus 823 -------~PI~SnFrEGLt~~EyFiSt~GaRKGL~DTALKTAdSGYLTRRLVdVaQDViV~e~DCgT~~Gi~v~~~~~~~ 895 (1460)
T PRK14906 823 -------LPIKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREEDCGTDEGVTYPLVKPKG 895 (1460)
T ss_pred -------cccccccccCCCHHHHHHHcccccchhhhhhhhccccchHHHHHHHhhhheEEEeccCCCCCCEEEEEeeccc
Confidence 25999999999999999999999999999999999999 211
Q ss_pred --------------------------------------------------------------------------ccCCCc
Q psy3022 133 --------------------------------------------------------------------------KCAPGE 138 (258)
Q Consensus 133 --------------------------------------------------------------------------~v~~Ge 138 (258)
.|+.||
T Consensus 896 ~l~~ri~GR~~~~di~~~~g~~i~~~~~~I~~~~~~~~i~~~gi~~v~iRS~ltC~s~~gvC~kCYG~dLatg~~V~iGe 975 (1460)
T PRK14906 896 DVDTNLIGRCLLEDVCDPNGEVLLSAGDYIESMDDLKRLVEAGVTKVQIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGT 975 (1460)
T ss_pred chhheeeeEEEHhhhcCCCCCEEEeCCCeeCcHHHHHHHHHCCCCEEEEeCCeeECCCCCChhhCcCCcccCCcEecccc
Confidence 289999
Q ss_pred hhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhhcc
Q psy3022 139 MVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISK 185 (258)
Q Consensus 139 ~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~~ 185 (258)
||||||||||||||||+||||||+||+++.++|.|+||+.|+++|++
T Consensus 976 aVGiIAAQSIGEPGTQLTMRTFHtGGv~~~dit~GLpRv~eLfEar~ 1022 (1460)
T PRK14906 976 AVGIIAAQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAELFEARK 1022 (1460)
T ss_pred ceeeeeeeecCCCcceeeeeeeecccccccccccCcchhhhheeecc
Confidence 99999999999999999999999999999999999999999999864
No 7
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=3.4e-49 Score=411.83 Aligned_cols=166 Identities=37% Similarity=0.602 Sum_probs=148.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcCC----CChhhHHhhcCCCcChhhHHHHHhhhcccc-cCCcccCCCCCCCCCCC
Q psy3022 6 QTFENQVNRILNDARDKTGGSAKKSLTE----YNNLKAMVVAGSKGSNINISQVIACVGQQN-VEGKRIPFGFRKRTLPH 80 (258)
Q Consensus 6 ~~~E~~v~~~l~~~~~~~~~~~~~~~~~----~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~-~~G~ri~~~~~~r~lp~ 80 (258)
++++.++.++|+++++++++.+++++++ +|++++|+.||||||+.|++||+||+|||. .+|+.++
T Consensus 654 ~er~~kvi~~w~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~SGARGS~~ni~QL~GmrGlma~p~G~iie---------- 723 (1156)
T PRK00566 654 GERYNKVIDIWSKATDEVAKAMMKNLSKDQESFNPIYMMADSGARGSASQIRQLAGMRGLMAKPSGEIIE---------- 723 (1156)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhCccccCCCCChheeeeccCCcCHHHHHHHHhhcCccccCCCCEee----------
Confidence 4567999999999999999999999986 899999999999999999999999999994 6666553
Q ss_pred CcCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccC-------------------CCC---------
Q psy3022 81 FIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETA-------------------CNA--------- 132 (258)
Q Consensus 81 f~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG-------------------~~~--------- 132 (258)
.||.|||++||+|.|||||||||||||+|||||||+|| |++
T Consensus 724 -----------~pI~ssFreGLt~~EyFfst~GaRkGLiDTALKTAdSGYLtRRLVdvaqDviV~~~DCgT~~gi~~~~~ 792 (1156)
T PRK00566 724 -----------TPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCGTDRGIEVTAI 792 (1156)
T ss_pred -----------hhhhhhhhcCCCHHHHhhcCcchhhcccchheeeccceeeehhHHHhhCceEEEECCCCCcCCEEEEEe
Confidence 26999999999999999999999999999999999999 211
Q ss_pred --------------------------------------------------------------------------------
Q psy3022 133 -------------------------------------------------------------------------------- 132 (258)
Q Consensus 133 -------------------------------------------------------------------------------- 132 (258)
T Consensus 793 ~~~~~~i~~l~~~~~GR~~~~di~~~~t~~~i~~~~~~i~~~~~~~i~~~~i~~v~iRS~ltC~s~~gvC~~CYG~~La~ 872 (1156)
T PRK00566 793 IEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVCAKCYGRDLAT 872 (1156)
T ss_pred ccCCEEEeEhhheeEeEEEhhheecCCCCcEEEcCCCccCHHHHHHHHHcCCCEEEEcCCeeecCCCcccHhhhCccccC
Confidence
Q ss_pred --ccCCCchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhhccCCCCCeEEEEe
Q psy3022 133 --KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFL 196 (258)
Q Consensus 133 --~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~~~~~t~~~~v~L 196 (258)
.|+.||||||||||||||||||+||||||+||+ ++|.|+||+.|+++| ++++.+.+...+
T Consensus 873 ~~~v~iGeaVGiIAAQSIGEPGTQLTmRTFHtGGv---dIT~Glprv~elfea-r~pk~~a~ise~ 934 (1156)
T PRK00566 873 GKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV---DITGGLPRVAELFEA-RKPKGPAIIAEI 934 (1156)
T ss_pred CCCcccCcceeEEeeeecCCCccceeeeeeeecce---eccCCccchhhheee-ccCCCceEEEec
Confidence 289999999999999999999999999999999 899999999999998 455555444443
No 8
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=100.00 E-value=6.4e-49 Score=426.32 Aligned_cols=220 Identities=29% Similarity=0.364 Sum_probs=187.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcC------CCChhhHHhhcCCCcChhhHHHHHhhhcccc-cCCcccCCCCCCCCCC
Q psy3022 7 TFENQVNRILNDARDKTGGSAKKSLT------EYNNLKAMVVAGSKGSNINISQVIACVGQQN-VEGKRIPFGFRKRTLP 79 (258)
Q Consensus 7 ~~E~~v~~~l~~~~~~~~~~~~~~~~------~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~-~~G~ri~~~~~~r~lp 79 (258)
.++.++.++|+++++++++.+++.++ +.|++++|++||||||+.|++|++||+||+. .+|..+
T Consensus 2107 Er~~kvi~iW~~~~d~v~~~~~~~l~~~~~~~~~N~i~mMa~SGARGS~sQI~QLaGmRGLmakp~G~iI---------- 2176 (2836)
T PRK14844 2107 ERYNKVIDEWSKCTDMIANDMLKAISIYDGNSKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTKPSGEII---------- 2176 (2836)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhccccCCCCceeeeecccCccCHHHHHHHHhcceeeecCCCCee----------
Confidence 48899999999999999999998773 4799999999999999999999999999985 355543
Q ss_pred CCcCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccC-------------------CCC--------
Q psy3022 80 HFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETA-------------------CNA-------- 132 (258)
Q Consensus 80 ~f~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG-------------------~~~-------- 132 (258)
..+|.|||++||+|.|||||||||||||+|||+|||+|| |++
T Consensus 2177 -----------e~PI~SNFrEGLsv~EyFiSt~GaRKGL~DTALKTAdSGYLTRRLVDVaQDviI~e~DCgT~~Gi~v~~ 2245 (2836)
T PRK14844 2177 -----------ETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKTKNGLVVRA 2245 (2836)
T ss_pred -----------ecchhhhhccCCCHHHhhhhccccccchhhhhhhcccccchhhhhhhhhceEEEEecccCCCCceEEEE
Confidence 245999999999999999999999999999999999999 211
Q ss_pred --------------------------------------------------------------------------------
Q psy3022 133 -------------------------------------------------------------------------------- 132 (258)
Q Consensus 133 -------------------------------------------------------------------------------- 132 (258)
T Consensus 2246 ~~~~~~~i~~L~~ri~GR~~a~di~~p~t~~~i~~~~~~I~~~~~~~i~~~gi~~v~IRS~ltC~s~~gvC~~CYG~~La 2325 (2836)
T PRK14844 2246 TVEGSTIVASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCEISPGVCSLCYGRDLA 2325 (2836)
T ss_pred eccCCeEEeEhhheeEEEEEHhHeEcCCCCCEEEeCCCccCHHHHHHHHHcCCCEEEEcCCeeECCCCCChhhccCcccc
Confidence
Q ss_pred ---ccCCCchhhhhhhhccCChhhhhhhhccccCCcccccc--------ccCccccchhhhhccCCC-----CCeEEEEe
Q psy3022 133 ---KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNV--------TLGVPRLKEIINISKKPK-----APSLTVFL 196 (258)
Q Consensus 133 ---~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v--------~~g~~rl~eil~~~~~~~-----t~~~~v~L 196 (258)
.|+.||||||||||||||||||+||||||+||+++..+ ..|..++.+.....++.+ ++...+.+
T Consensus 2326 ~~~~V~iGeaVGiIAAQSIGEPGTQLTMRTFHtGGvas~~~~~~~i~~~~~G~v~~~~~~~v~~~~g~~iv~sr~~~~~i 2405 (2836)
T PRK14844 2326 TGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRGVESSNIIASINAKIKLNNSNIIIDKNGNKIVISRSCEVVL 2405 (2836)
T ss_pred CCCcccccccceeeeecccCCCcceeeeeheeeccccccccccceeEeccCceEEeccceeEEcCCCcEEEEecccEEEE
Confidence 28999999999999999999999999999999986543 358888887655544444 35556667
Q ss_pred cCcchhcHHHHHHHh-ccccceeccceeE----EEEcCCCceeEEEeccceeeeee
Q psy3022 197 TGQAARDAEKAKNVL-CRLEHTTLRKVLY----IILRPATHYQVELISGARRVASL 247 (258)
Q Consensus 197 ~~~~~~~~~~a~~v~-~~L~~~~l~~v~~----I~ydp~~~~~i~~~~G~~~~~~~ 247 (258)
.+..+...+.++.++ +.|..-+.+.|.. .+|||++.|++++.+|.++|.-+
T Consensus 2406 ~d~~g~~~~~~~i~yga~l~v~~g~~V~~g~~la~wdp~~~piisE~~G~v~f~d~ 2461 (2836)
T PRK14844 2406 IDSLGSEKLKHSVPYGAKLYVDEGGSVKIGDKVAEWDPYTLPIITEKTGTVSYQDL 2461 (2836)
T ss_pred EecCCcEEEEEecccccEEEecCCCEecCCCEEEEEcCCCcceEeecceEEEEEEE
Confidence 666566677777777 8888888888877 89999999999999999999765
No 9
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=100.00 E-value=5.5e-47 Score=412.35 Aligned_cols=143 Identities=36% Similarity=0.562 Sum_probs=127.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcC----CCChhhHHhhcCCCcChhhHHHHHhhhcccc-cCCcccCCCCCCCCCCC
Q psy3022 6 QTFENQVNRILNDARDKTGGSAKKSLT----EYNNLKAMVVAGSKGSNINISQVIACVGQQN-VEGKRIPFGFRKRTLPH 80 (258)
Q Consensus 6 ~~~E~~v~~~l~~~~~~~~~~~~~~~~----~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~-~~G~ri~~~~~~r~lp~ 80 (258)
++.+.++.++|+++++++++.+++++. +.|++++|+.||||||..|++||+||+|||. .+|..+
T Consensus 2052 ~Er~~kvid~w~~~~d~v~~~~~~~l~~~~~~~N~i~mMa~SGARGS~~NI~QLaGmrGqMakp~G~ii----------- 2120 (2890)
T PRK09603 2052 QERYNKIIDTWTEVNDKMSKEMMTAIAKDKEGFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSII----------- 2120 (2890)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCcHHHHHhccccccHHHHHHHHHcCCcEECCCCCcc-----------
Confidence 357899999999999999999998885 4699999999999999999999999999985 233322
Q ss_pred CcCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccC-------------------CCC---------
Q psy3022 81 FIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETA-------------------CNA--------- 132 (258)
Q Consensus 81 f~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG-------------------~~~--------- 132 (258)
..+|.|||++||+|.|||||||||||||+|||||||+|| |++
T Consensus 2121 ----------e~PI~snFrEGLtp~EyFfst~GaRKGLiDTALKTAdSGYLTRRLVdvaQDviI~e~DCgT~~Gi~v~~~ 2190 (2890)
T PRK09603 2121 ----------ETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEITDI 2190 (2890)
T ss_pred ----------cChhhcCcccCCCHHHHHHhccccccchhhhhhhccccchhhhhHHHhhcceEEEeccCCCCCCeEEEEe
Confidence 235899999999999999999999999999999999999 211
Q ss_pred --------------------------------------------------------------------------------
Q psy3022 133 -------------------------------------------------------------------------------- 132 (258)
Q Consensus 133 -------------------------------------------------------------------------------- 132 (258)
T Consensus 2191 ~~~~~~i~~l~~ri~GR~~~~di~~p~t~~~i~~~~~~I~~~~~~~i~~~gi~~v~iRS~LtC~s~~gvC~~CYG~dLa~ 2270 (2890)
T PRK09603 2191 AVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITIRTPVTCKAPKGVCAKCYGLNLGE 2270 (2890)
T ss_pred ecCCeeecchhheeeeEEEHhheEcCCCCcEEEcCCcCcCHHHHHHHHHcCCCEEEEcCcceecCCCcChhhhcCCcccC
Confidence
Q ss_pred --ccCCCchhhhhhhhccCChhhhhhhhccccCCccccc
Q psy3022 133 --KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKN 169 (258)
Q Consensus 133 --~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~ 169 (258)
.|+.|||||||||||||||||||||||||+||+++..
T Consensus 2271 g~~V~iGeaVGiIAAQSIGEPGTQLTMRTFHtGGvas~~ 2309 (2890)
T PRK09603 2271 GKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRS 2309 (2890)
T ss_pred CCCccCCceeeEEeecccCCCccccchhhheeccccccc
Confidence 2899999999999999999999999999999998753
No 10
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=100.00 E-value=1.6e-44 Score=381.83 Aligned_cols=222 Identities=24% Similarity=0.335 Sum_probs=169.1
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHhhc---CCCChhhHHhhcCCCcChhhHHHHHhhhcccc-cCCcccCCCCCCCCC
Q psy3022 3 ALKQTFENQVNRILNDARDKTGGSAKKSL---TEYNNLKAMVVAGSKGSNINISQVIACVGQQN-VEGKRIPFGFRKRTL 78 (258)
Q Consensus 3 ~~~~~~E~~v~~~l~~~~~~~~~~~~~~~---~~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~-~~G~ri~~~~~~r~l 78 (258)
|..|.++ ++.++|+++.+.+.+.+++.+ +++|++++|+.||||||+.|++|++|++|++. ..|+++. +
T Consensus 92 t~~er~~-~~i~~w~~~~~~l~~~~~~~~~~~d~~N~v~mMa~SGARGn~sQi~qLvGmRGlma~p~G~iI~-------~ 163 (1364)
T CHL00117 92 HAVEKLR-QSIEIWYATSEYLKQEMNPNFRMTDPLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQIID-------L 163 (1364)
T ss_pred CHHHHHH-HHHHHHHHHHHHHHHHHHHhhccCCCCCcHhhhhhccCcccHHHHHHHhcccceeeCCCCcEee-------c
Confidence 4555554 455688887777777666664 56899999999999999999999999999874 5676662 2
Q ss_pred CCCcCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccC-------------------CCC-------
Q psy3022 79 PHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETA-------------------CNA------- 132 (258)
Q Consensus 79 p~f~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG-------------------~~~------- 132 (258)
+|.+||++||+|.|||||||||||||+|||+|||+|| |++
T Consensus 164 --------------PI~snFreGLs~~EyFis~~GaRkGLvDTAlkTAdSGYLtRRLVdv~qdviV~~~dCgt~~gi~~~ 229 (1364)
T CHL00117 164 --------------PIQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVS 229 (1364)
T ss_pred --------------chhhhhhcCCCHHHhheeccccccchhhcceecccccchhhHHHhhhccEEEEeccCCCCCCEEEE
Confidence 2999999999999999999999999999999999999 211
Q ss_pred --------------------------------------------------------------------------------
Q psy3022 133 -------------------------------------------------------------------------------- 132 (258)
Q Consensus 133 -------------------------------------------------------------------------------- 132 (258)
T Consensus 230 ~~~~~~~~~~l~~rl~GRv~~~di~~~~~~i~~~n~~I~~~~~~~i~~~~~~~v~iRSpltC~~~~~vC~~CYG~~la~~ 309 (1364)
T CHL00117 230 PRNGMMIERILIQTLIGRVLADDIYIGSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHG 309 (1364)
T ss_pred EecCCeEEeEecceeEEEEEhhhEEeCCEEEEeCCCCcCHHHHHHHHHcCCCEEEEeCCcccccHHHHHHHHhCcccccC
Confidence
Q ss_pred -ccCCCchhhhhhhhccCChhhhhhhhccccCCccccccc-------cCccccchhhh-hccCCC-CCe------EEEEe
Q psy3022 133 -KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVT-------LGVPRLKEIIN-ISKKPK-APS------LTVFL 196 (258)
Q Consensus 133 -~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~-------~g~~rl~eil~-~~~~~~-t~~------~~v~L 196 (258)
.|+.||||||||||||||||||+||||||+||+++..+. .|..++.+-+. ..+... .+. ..+.+
T Consensus 310 ~lV~~GeaVGiiAaQSIGEPGTQLTmRTFH~GGv~t~~~~~~i~a~~~G~i~~~~~~~~~~rt~~g~~~~~~~~~~~~~i 389 (1364)
T CHL00117 310 DLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGVFTGGTAEQVRAPFNGKIKFNEDLVHPTRTRHGHPAFLCKIDLYVTI 389 (1364)
T ss_pred cccChhhhhhhhhhhccCCCchhhhhhhhhhcccccccceeeEEeccCeEEEEecceeeEEeCcCCEEEEEEecceEEEE
Confidence 289999999999999999999999999999999986554 39999988432 222222 111 11112
Q ss_pred cCcchhcHHHHHHHh-ccccceeccceeE----EEEcCCC----------ceeEEEeccceeeeeee
Q psy3022 197 TGQAARDAEKAKNVL-CRLEHTTLRKVLY----IILRPAT----------HYQVELISGARRVASLR 248 (258)
Q Consensus 197 ~~~~~~~~~~a~~v~-~~L~~~~l~~v~~----I~ydp~~----------~~~i~~~~G~~~~~~~~ 248 (258)
.. +.....+..++ ..|..-+.+.|.. .+|||++ .+++++.+|.+.|.-+-
T Consensus 390 ~~--~~~~~~~~ip~gs~l~v~~g~~V~~~q~iae~~~~~~~~~~~e~~~~~i~s~~~G~v~~~~~~ 454 (1364)
T CHL00117 390 ES--EDIIHNVNIPPKSLLLVQNDQYVESEQVIAEIRAGTSTLNFKEKVRKHIYSDSEGEMHWSTDV 454 (1364)
T ss_pred eC--CCeEEEEEeCCCCEEEEeCcCEEcCCCEEEEECCCCcccccccccceeEEEcCCcEEEccccc
Confidence 11 12223344444 5666666666655 8999988 79999999999998753
No 11
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=100.00 E-value=2.9e-43 Score=370.11 Aligned_cols=153 Identities=31% Similarity=0.555 Sum_probs=138.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcC---CCChhhHHhhcCCCcChhhHHHHHhhhcccc-cCCcccCCCCCCCCCCCCcC
Q psy3022 8 FENQVNRILNDARDKTGGSAKKSLT---EYNNLKAMVVAGSKGSNINISQVIACVGQQN-VEGKRIPFGFRKRTLPHFIK 83 (258)
Q Consensus 8 ~E~~v~~~l~~~~~~~~~~~~~~~~---~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~-~~G~ri~~~~~~r~lp~f~~ 83 (258)
.+.++.++|+++++++.+.+.+++. +.|++++|+.||||||+.|+.|++|++|++. .+|+.+ .+|
T Consensus 90 r~~kvi~~w~~t~e~l~~~~~~~~~~~dp~N~v~mMa~SGARGN~sQI~QLvGmRGLma~p~G~ii-------~lP---- 158 (1331)
T PRK02597 90 RFQKVIDTWNETNERLKDEVVKNFRQNDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEII-------DLP---- 158 (1331)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcHHHHhhccCCccHHHHHHHhcchhhccCCCCcEE-------ecc----
Confidence 3489999999999999999999984 5899999999999999999999999999995 577665 233
Q ss_pred CCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccC-------------------CCC------------
Q psy3022 84 DDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETA-------------------CNA------------ 132 (258)
Q Consensus 84 ~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG-------------------~~~------------ 132 (258)
|+|||++||+|.|||||||||||||+|||||||+|| |++
T Consensus 159 ----------I~snFrEGLs~~EyFis~~GaRKGLvDTAlKTAdSGYLTRRLVdv~QDviVre~DCgT~~gi~~~~~~~~ 228 (1331)
T PRK02597 159 ----------IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDG 228 (1331)
T ss_pred ----------hhhhhhcCCCHHHhheeccccccchhhcceecccchhHHHHHHHhhcceEEEecCCCCCCCEEEEEEecC
Confidence 999999999999999999999999999999999999 211
Q ss_pred ------------------------------------------------------------------------------cc
Q psy3022 133 ------------------------------------------------------------------------------KC 134 (258)
Q Consensus 133 ------------------------------------------------------------------------------~v 134 (258)
.|
T Consensus 229 ~~~i~~l~~rl~GR~~~~~i~~~~~~~i~~~n~~i~~~~~~~i~~~~~~~v~iRspltC~s~~gvC~~CYG~~la~~~lv 308 (1331)
T PRK02597 229 DRVLIPLGDRLLGRVLAEDVVDPEGEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLV 308 (1331)
T ss_pred CEEEeEehheeEEEEEhhHeeCCCCCEEEeCCCCcCHHHHHHHHHcCCCEEEEECCEEecCCCCchhhccCcchhcCccc
Confidence 28
Q ss_pred CCCchhhhhhhhccCChhhhhhhhccccCCccccccc-------cCccccchhh
Q psy3022 135 APGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVT-------LGVPRLKEII 181 (258)
Q Consensus 135 ~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~-------~g~~rl~eil 181 (258)
+.||||||||||||||||||+||||||+||+++.+++ .|++++.|-+
T Consensus 309 ~lGeaVGiiAaQSIGEPGTQLTmRTFHtGGv~~~~~~~~i~~~~~G~i~~~~~~ 362 (1331)
T PRK02597 309 DLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSPFAGTVEFGKKL 362 (1331)
T ss_pred chhhhhhhhhhccccCCcchhehhhhhhccccccccceeEEeccCeEEEEecCC
Confidence 9999999999999999999999999999999988877 8999999955
No 12
>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.
Probab=100.00 E-value=1.1e-42 Score=363.40 Aligned_cols=157 Identities=31% Similarity=0.547 Sum_probs=135.8
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHhhc---CCCChhhHHhhcCCCcChhhHHHHHhhhcccc-cCCcccCCCCCCCCC
Q psy3022 3 ALKQTFENQVNRILNDARDKTGGSAKKSL---TEYNNLKAMVVAGSKGSNINISQVIACVGQQN-VEGKRIPFGFRKRTL 78 (258)
Q Consensus 3 ~~~~~~E~~v~~~l~~~~~~~~~~~~~~~---~~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~-~~G~ri~~~~~~r~l 78 (258)
|..|.++ ++.++|+++++.+.+.+.+++ ++.|++++|+.||||||+.|++|++|++|+|. .+|+++. |
T Consensus 85 t~~Er~~-~ii~~w~~t~e~~~~~~~~~~~~~d~~N~v~mMa~SGARGNisQi~QLvGmrGlma~p~G~ii~-------l 156 (1227)
T TIGR02388 85 TEVERFQ-KVIDTWNGTNEELKDEVVNNFRQTDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIID-------L 156 (1227)
T ss_pred cchhhHH-HHHHHHHHHHHHHHHHHHHhhhhcCCCCcHHHHhhccCcccHHHHHHHhcchheecCCCCcEee-------c
Confidence 3445554 788999999999999999985 57899999999999999999999999999995 6777652 3
Q ss_pred CCCcCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccC-------------------CCC-------
Q psy3022 79 PHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETA-------------------CNA------- 132 (258)
Q Consensus 79 p~f~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG-------------------~~~------- 132 (258)
| |++||++||+|.|||||||||||||+|||||||+|| |++
T Consensus 157 P--------------I~snFreGLt~~EyF~sa~GaRkGLvDTAlKTAdSGYLTRRLVdv~qDviV~~~DCgT~~gi~v~ 222 (1227)
T TIGR02388 157 P--------------IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVR 222 (1227)
T ss_pred c--------------chhhhhcCCCHHHhheeccccccchhhcceeccccchHHHHHHHhhceEEEEEcCCCCCCCEEEE
Confidence 4 999999999999999999999999999999999999 211
Q ss_pred --------------------------------------------------------------------------------
Q psy3022 133 -------------------------------------------------------------------------------- 132 (258)
Q Consensus 133 -------------------------------------------------------------------------------- 132 (258)
T Consensus 223 ~~~~~~~~~~l~~rl~GRv~~~di~~~~~~~i~~~n~~I~~~~~~~i~~~~~~~v~iRspltC~s~~~vC~~CYG~~la~ 302 (1227)
T TIGR02388 223 AMTEGDKKISLGDRLLGRLVAEDVLHPEGEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAH 302 (1227)
T ss_pred EeeCCCeEeEhhheeEeeeEHhHeECCCCcEEEeCCCccCHHHHHHHHHcCCCEEEEeCcceecchhhHhHhccCCcccc
Confidence
Q ss_pred --ccCCCchhhhhhhhccCChhhhhhhhccccCCccccccc-------cCccccchhh
Q psy3022 133 --KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVT-------LGVPRLKEII 181 (258)
Q Consensus 133 --~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~-------~g~~rl~eil 181 (258)
.|+.|||||+|||||||||||||||||||+||+++..+. .|..++.+-+
T Consensus 303 ~~lV~lGeaVGiiAaQSIGEPGTQLTmRTFHtGGv~t~~~~~~i~~~~~g~i~~~~~~ 360 (1227)
T TIGR02388 303 AHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSKIDGTVEFGKKL 360 (1227)
T ss_pred CcEechhhhhhhhhhhccCCcchhhhhhhhhhccccccceeeeEEeccCEEEEEccCC
Confidence 289999999999999999999999999999999975432 3666665544
No 13
>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 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, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=100.00 E-value=6.3e-42 Score=305.05 Aligned_cols=111 Identities=62% Similarity=0.911 Sum_probs=95.7
Q ss_pred CCChhHHHHhhcccchhhhhhhhhccccCCC----------------------------------CccCCCchhhhhhhh
Q psy3022 101 GLTPSEFFFHAMGGREGLIDTAVKTAETACN----------------------------------AKCAPGEMVGALAAQ 146 (258)
Q Consensus 101 GL~p~EfFfHa~~gRegliDtavkTa~sG~~----------------------------------~~v~~Ge~VG~iaAq 146 (258)
||+|.|||||||+|||||+|||+|||+|||- ..|+||||||+||||
T Consensus 1 Gl~~~e~f~~~~~~R~gl~dta~kTa~sGyl~R~lv~~~~~~~v~~~~~~~~~~~~i~~~~~~~~~~v~~Ge~VGiiaAQ 80 (277)
T PF04998_consen 1 GLTPTEYFFHCMGGREGLIDTAVKTADSGYLQRRLVKVLEDLIVRYDDCVRNSGGSIIQFIYGEDGLVEPGEAVGIIAAQ 80 (277)
T ss_dssp C-THHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHTTHEEETTSEEESTTSEEEESSCTTTSB--TTSBHHHHHHH
T ss_pred CcCHHHHHHHHhcccccccccceeeeccccchhhhhhccceEEEEEcCccccccceeeecccccccccCccccchhhhhc
Confidence 8999999999999999999999999999920 157999999999999
Q ss_pred ccCChhhhhhhhccccCCccccccccCccccchhhhhccCCCCCeEEEEecCcchhcHHHHHHHh
Q psy3022 147 SLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVL 211 (258)
Q Consensus 147 sigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~~~~~t~~~~v~L~~~~~~~~~~a~~v~ 211 (258)
|||||+|||||||||+||+++.++++|+||++|++++++++++|.+.++.........+....+.
T Consensus 81 SIGEP~TQ~TL~TFH~aG~~~~~vt~giprl~eii~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 145 (277)
T PF04998_consen 81 SIGEPGTQMTLRTFHTAGVASKNVTQGIPRLKEIINASKKIKTPIITVYGKKKIISEKKKIKIIR 145 (277)
T ss_dssp HHHCHGCCSHHSCTSSSCSSTSSCSSSHHHHHHHHTTCSSSSSEEEEECSCSSECSSSHHHHHHH
T ss_pred hhcchhHHhhhcccccCceeeecccccceeeccccccccccccceEEeecccceecccccceEEE
Confidence 99999999999999999999999999999999999999999999998888776433444444443
No 14
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=100.00 E-value=3e-40 Score=340.88 Aligned_cols=129 Identities=48% Similarity=0.803 Sum_probs=126.9
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChhhHHhhcCCCcChhhHHHHHhhhcccccCCcccCCCCCCCCCCCC
Q psy3022 2 LALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHF 81 (258)
Q Consensus 2 ~~~~~~~E~~v~~~l~~~~~~~~~~~~~~~~~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~~~G~ri~~~~~~r~lp~f 81 (258)
+|++|++|.+++++|+++|+++++++.+.++++|++.+|+.||||||+.|++||++|||||.++|+|||.+|++|+||||
T Consensus 686 ~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~~~~M~~sGsKGS~~Ni~Qi~~~lGQQ~~~g~ri~~~~~~rtlp~f 765 (868)
T TIGR02390 686 RTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHF 765 (868)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhhhccCCcccccHHHHHhccCccccCCCcCccccccCCCCCC
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccCC
Q psy3022 82 IKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETAC 130 (258)
Q Consensus 82 ~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG~ 130 (258)
.++|..|+++|||.|||++||+|.|||||||||||||+|||||||+|||
T Consensus 766 ~~~d~~~~~~GfV~~sF~~GL~p~EfFfH~m~gReGLiDTAvKTa~sGY 814 (868)
T TIGR02390 766 KKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGY 814 (868)
T ss_pred CCCCCCcccCceecccccCCCCHHHHHHHHhhhccccccccccccccch
Confidence 9999999999999999999999999999999999999999999999995
No 15
>PRK08566 DNA-directed RNA polymerase subunit A'; Validated
Probab=100.00 E-value=3.9e-40 Score=340.55 Aligned_cols=130 Identities=52% Similarity=0.852 Sum_probs=127.2
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChhhHHhhcCCCcChhhHHHHHhhhcccccCCcccCCCCCCCCCCCC
Q psy3022 2 LALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHF 81 (258)
Q Consensus 2 ~~~~~~~E~~v~~~l~~~~~~~~~~~~~~~~~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~~~G~ri~~~~~~r~lp~f 81 (258)
+|.+|++|.+++++|+++|+++++++.++++++|++.+|+.||||||+.|++||++|+|||.++|+|+|++|++|+||||
T Consensus 691 ~~~~~~~e~~i~~~l~~~r~~~~~~~~~~l~~~N~~~~M~~SGsKGS~~N~~Qi~~~lGqQ~~~g~ri~~~~~~rtLP~f 770 (882)
T PRK08566 691 RTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHF 770 (882)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcceeeeccccccCHHHHHHHHhccCceecCCCcCccCccCccCCCC
Confidence 57889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccCCC
Q psy3022 82 IKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETACN 131 (258)
Q Consensus 82 ~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG~~ 131 (258)
.++|.+++++|||.|||++||+|.|||||||||||||+|||||||+|||-
T Consensus 771 ~~~d~~~~~~GfV~~sF~~GL~p~EfffH~m~GReGliDTAvkTa~sGYl 820 (882)
T PRK08566 771 KPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYM 820 (882)
T ss_pred CCCCCCcccCceeeccccCCCCHHHHHHHHhhhcccccccceeeccCccc
Confidence 99999999999999999999999999999999999999999999999953
No 16
>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain. RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Probab=99.98 E-value=1.6e-33 Score=270.19 Aligned_cols=102 Identities=66% Similarity=0.926 Sum_probs=97.8
Q ss_pred ccCCCchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhhccCCCCCeEEEEecCcchhcHHHHHHHhc
Q psy3022 133 KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLC 212 (258)
Q Consensus 133 ~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~~~~~t~~~~v~L~~~~~~~~~~a~~v~~ 212 (258)
.++|||+||++||||||||+|||||||||+||++++|||+|+|||+||+|++|+++||.|+++|.+++..++++|+.++.
T Consensus 23 ~~~~ge~vg~~aaQSiGEP~TQmTLnTFH~AGVas~NVTlGVPRLkEIInasK~ikTP~~tv~L~~~~~~d~~~A~~v~~ 102 (410)
T cd02584 23 LVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTPSLTVYLEPGFAKDEEKAKKIQS 102 (410)
T ss_pred hcCCCCCcchhhhhhcCCchhcccccccccccccccccccCccchHHHhhcccCCCCCeEEEEecCcccchHHHHHHHHh
Confidence 47999999999999999999999999999999999999999999999999999999999999999988788999999999
Q ss_pred cccceeccceeE---EEEcCCCcee
Q psy3022 213 RLEHTTLRKVLY---IILRPATHYQ 234 (258)
Q Consensus 213 ~L~~~~l~~v~~---I~ydp~~~~~ 234 (258)
+|++++|++++. +.|||+..++
T Consensus 103 ~IE~t~l~dv~~~~~i~ydp~~~~~ 127 (410)
T cd02584 103 RLEHTTLKDVTAATEIYYDPDPQNT 127 (410)
T ss_pred heeEeEHHHhhhheEEEecCcccce
Confidence 999999999987 8999988754
No 17
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=99.97 E-value=4.5e-33 Score=263.82 Aligned_cols=97 Identities=49% Similarity=0.773 Sum_probs=91.7
Q ss_pred ccCCCchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhhccCCCCCeEEEEecCcchhcHHHHHHHhc
Q psy3022 133 KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLC 212 (258)
Q Consensus 133 ~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~~~~~t~~~~v~L~~~~~~~~~~a~~v~~ 212 (258)
.++|||+||++||||||||+|||||||||+||++++|||+|+|||+||+|++|+++||+++++|.+++..+++.|+.++.
T Consensus 40 lv~PGeaVG~IAAQSIGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEIINa~k~i~TP~~ti~L~~~~~~~~~~a~~v~~ 119 (367)
T TIGR02389 40 LIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKTPSTPSMTIYLEDEYEKDREKAEEVAK 119 (367)
T ss_pred cCCCccccchhhhhhcCCccccccccccccccccccCccccchhHHHHhhcccCCCCCeEEEEecCcchhhHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999988788999999999
Q ss_pred cccceeccceeE-EEEcC
Q psy3022 213 RLEHTTLRKVLY-IILRP 229 (258)
Q Consensus 213 ~L~~~~l~~v~~-I~ydp 229 (258)
+|+.++|++++. ++++.
T Consensus 120 ~iE~t~l~dv~~~~~~~~ 137 (367)
T TIGR02389 120 KIEATKLEDVAKDISIDL 137 (367)
T ss_pred HhhheeHHHHHhhhheec
Confidence 999999999987 44443
No 18
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=99.97 E-value=1.2e-32 Score=254.96 Aligned_cols=105 Identities=51% Similarity=0.735 Sum_probs=97.4
Q ss_pred ccCCCchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhhccCCCCCeEEEEecCcchhcHHHHHHHhc
Q psy3022 133 KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLC 212 (258)
Q Consensus 133 ~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~~~~~t~~~~v~L~~~~~~~~~~a~~v~~ 212 (258)
.++||||||++||||||||+|||||||||+||+++++||+|+|||+||+|++|+++||.++++|.+. .++++|+.++.
T Consensus 6 ~v~pGe~vG~iaaQsiGEp~TQmTL~TFH~aGv~~~nvtlGvPRlkEIinasK~~~TP~~ti~l~~~--~~~~~a~~v~~ 83 (300)
T cd02736 6 KVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLEND--RDEKSARIVKG 83 (300)
T ss_pred ccCCCccchhhhhhhcCCccccccccccccccccccccccCchHHHHHHhcccCCCCCeEEEEecCc--ccHHHHHHHHH
Confidence 5799999999999999999999999999999999999999999999999999999999999999884 58999999999
Q ss_pred cccceeccceeE---EEEcCCCceeEEEec
Q psy3022 213 RLEHTTLRKVLY---IILRPATHYQVELIS 239 (258)
Q Consensus 213 ~L~~~~l~~v~~---I~ydp~~~~~i~~~~ 239 (258)
+||+++|+|++. +.|||+...+.-..+
T Consensus 84 ~ie~t~l~di~~~~~~~~~p~~~~~~i~~d 113 (300)
T cd02736 84 RIEKTYLGEVASYIEEVYSPDDCYILIKLD 113 (300)
T ss_pred HHhhccHHHhhhheEEEEcCCCceEEEEec
Confidence 999999999987 889999877654433
No 19
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=99.97 E-value=3.4e-32 Score=257.70 Aligned_cols=100 Identities=48% Similarity=0.735 Sum_probs=94.7
Q ss_pred ccCCCchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhhccCCCCCeEEEEecCcchhcHHHHHHHhc
Q psy3022 133 KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLC 212 (258)
Q Consensus 133 ~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~~~~~t~~~~v~L~~~~~~~~~~a~~v~~ 212 (258)
.++||||||++||||||||+|||||||||+||++++|||+|+|||+||+|++|+++||.|+++|.+++..+++.|+.++.
T Consensus 36 ~~~~Ge~vG~iaAQSiGEP~TQMTLnTFH~AGVas~nVTlGVPRlkEIIna~K~i~TP~mti~L~~~~~~~~~~a~~v~~ 115 (363)
T cd06528 36 LIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKEPSTPTMTIYLEEEYKYDREKAEEVAR 115 (363)
T ss_pred hhccCccccceeeeecCccceecccccccccccccccCccccccHHHHhhcccCCCCceEEEEecCcchhhHHHHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999987788999999999
Q ss_pred cccceeccceeE-EEEcCCCc
Q psy3022 213 RLEHTTLRKVLY-IILRPATH 232 (258)
Q Consensus 213 ~L~~~~l~~v~~-I~ydp~~~ 232 (258)
+||+++|++++. ++.||...
T Consensus 116 ~iE~t~l~di~~~~~i~~~~~ 136 (363)
T cd06528 116 KIEETTLENLAEDISIDLFNM 136 (363)
T ss_pred hhceeEHHHhhhheEEeccCc
Confidence 999999999988 77777654
No 20
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=99.97 E-value=1.5e-31 Score=254.85 Aligned_cols=100 Identities=49% Similarity=0.751 Sum_probs=94.7
Q ss_pred ccCCCchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhhccCCCCCeEEEEecCcchhcHHHHHHHhc
Q psy3022 133 KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLC 212 (258)
Q Consensus 133 ~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~~~~~t~~~~v~L~~~~~~~~~~a~~v~~ 212 (258)
.++||||||++||||||||+|||||||||+||++++|||+|+|||+||+|++|+++||.++++|.+++..++++|+.++.
T Consensus 55 ~v~pGe~VG~iaAQsIGEP~TQMTL~TFH~AGva~~nVTlGvPRlkEIina~K~~~TP~~tv~L~~~~~~d~~~a~~v~~ 134 (383)
T PRK04309 55 LVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKEPSTPMMTIYLKDEYAYDREKAEEVAR 134 (383)
T ss_pred hcCCCCccchhhhhhccchhhhcccccccccCccccCcccCchhHHHHHhcccCCCCCeEEEEecCcccccHHHHHHHHh
Confidence 47999999999999999999999999999999999999999999999999999999999999999887778999999999
Q ss_pred cccceeccceeE-EEEcCCCc
Q psy3022 213 RLEHTTLRKVLY-IILRPATH 232 (258)
Q Consensus 213 ~L~~~~l~~v~~-I~ydp~~~ 232 (258)
+|++++|++++. ++.|+...
T Consensus 135 ~iE~t~L~~v~~~i~~~~~~~ 155 (383)
T PRK04309 135 KIEATTLENLAKDISVDLANM 155 (383)
T ss_pred heeeeEHhhhhhheEeccCCc
Confidence 999999999997 77777654
No 21
>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain. RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=99.97 E-value=1.2e-31 Score=249.43 Aligned_cols=90 Identities=56% Similarity=0.788 Sum_probs=85.1
Q ss_pred ccCCCchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhh-hhccCCCCCeEEEEecCcchhcHHHHHHHh
Q psy3022 133 KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEII-NISKKPKAPSLTVFLTGQAARDAEKAKNVL 211 (258)
Q Consensus 133 ~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil-~~~~~~~t~~~~v~L~~~~~~~~~~a~~v~ 211 (258)
.++||||||++||||||||+|||||||||+||++++|||+|+|||+||+ +|+|+++||.|+++|.+++ +.++|+.++
T Consensus 6 lv~PGE~VG~iaAQSIGEPsTQMTLnTFH~AGv~~~nVTlGvPRL~EIi~~Ask~i~TP~m~v~l~~~~--~~~~a~~~~ 83 (309)
T cd02735 6 LVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKNIKTPSMTLPLKNGK--SAERAETLK 83 (309)
T ss_pred cCCCCcccchhhhhccCCcccccccccccccCccccccccccccHHHHHhhhccCCCCCeEEEEecCch--hHHHHHHHH
Confidence 5899999999999999999999999999999999999999999999998 6899999999999999874 346899999
Q ss_pred ccccceeccceeE
Q psy3022 212 CRLEHTTLRKVLY 224 (258)
Q Consensus 212 ~~L~~~~l~~v~~ 224 (258)
.+|++++|+||+.
T Consensus 84 ~~ie~~~l~dv~~ 96 (309)
T cd02735 84 KRLSRVTLSDVVE 96 (309)
T ss_pred hheeEeEHHHhhh
Confidence 9999999999987
No 22
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=99.97 E-value=1.1e-31 Score=261.44 Aligned_cols=92 Identities=50% Similarity=0.786 Sum_probs=89.5
Q ss_pred ccCCCchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhhccCCCCCeEEEEecCcchhcHHHHHHHhc
Q psy3022 133 KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLC 212 (258)
Q Consensus 133 ~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~~~~~t~~~~v~L~~~~~~~~~~a~~v~~ 212 (258)
.++|||+||++||||||||+|||||||||+||++++|||+|+|||+||+|++|+++||+|+++|.+++..+++.|+.++.
T Consensus 178 ~v~pGE~VG~IAAQSIGEP~TQMTLnTFH~AGVas~NVTlGVPRLkEIINa~K~isTP~mtiyL~~~~~~d~e~A~~V~~ 257 (509)
T PRK14897 178 RVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARKKPSTPTMTIYLKKDYREDEEKVREVAK 257 (509)
T ss_pred ccCCCCCcchhhhhhhCCccccccccccccccccccccccCcchhHHHhhcccCCCCceEEEEecCcccccHHHHHHHHh
Confidence 58999999999999999999999999999999999999999999999999999999999999999888789999999999
Q ss_pred cccceeccceeE
Q psy3022 213 RLEHTTLRKVLY 224 (258)
Q Consensus 213 ~L~~~~l~~v~~ 224 (258)
+|+.++|++|+.
T Consensus 258 ~IE~ttL~dv~~ 269 (509)
T PRK14897 258 KIENTTLIDVAD 269 (509)
T ss_pred hheeeEHHHHHH
Confidence 999999999977
No 23
>PF05000 RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; InterPro: IPR007083 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 entry, domain 4, represents the funnel domain. The funnel domain contains the binding site for some elongation factors [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Q 3HKZ_I 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2Y0S_W 3IYD_D 3LU0_D ....
Probab=99.93 E-value=3.1e-26 Score=183.09 Aligned_cols=93 Identities=54% Similarity=0.825 Sum_probs=83.7
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChhhHHhhcCCCcChhhHHHHHhhhcccccCCcccCCCCCCCCCCCC
Q psy3022 2 LALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHF 81 (258)
Q Consensus 2 ~~~~~~~E~~v~~~l~~~~~~~~~~~~~~~~~~N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~~~G~ri~~~~~~r~lp~f 81 (258)
++.++.+|..+.++|+++++++++++.++++.+|++++|++||||||+.|++||+||+|||.++|+|++.++.+|+||||
T Consensus 16 ~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~N~l~~M~~SGaKGs~~ni~Qi~g~lGqq~~~g~ri~~~~~~Rtlp~f 95 (108)
T PF05000_consen 16 KTYEETFEQKINKILNKVRDEIGKIIKKNLPFNNSLLIMINSGAKGSMSNISQISGCLGQQSVEGKRIPRGFSGRTLPHF 95 (108)
T ss_dssp CHHHHHHHHHHHHHHHHCCHHHHHHHHHCSTTTSHHHHHHHSSSS--HHHHHHHHST-EEEEETTSES--SSTTCSSTTS
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHhhhhccCCCCHHHHHHHHHHHHHhhccccccccCCCCCcCCCc
Confidence 57889999999999999999999999999998899999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCcccccc
Q psy3022 82 IKDDYGPESRGFV 94 (258)
Q Consensus 82 ~~~~~~~~~~GfI 94 (258)
.+.+..|+++|||
T Consensus 96 ~~~~~~~~~~GFI 108 (108)
T PF05000_consen 96 KPFDESPESRGFI 108 (108)
T ss_dssp -SS-SSTTTTTEE
T ss_pred CCCCCCcccCCCC
Confidence 9999999999998
No 24
>cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain. Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Probab=99.91 E-value=1.1e-25 Score=214.32 Aligned_cols=100 Identities=28% Similarity=0.306 Sum_probs=87.4
Q ss_pred CchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhh--ccCCCCCeEEEEecCc---chhc---HHHHH
Q psy3022 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINI--SKKPKAPSLTVFLTGQ---AARD---AEKAK 208 (258)
Q Consensus 137 Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~--~~~~~t~~~~v~L~~~---~~~~---~~~a~ 208 (258)
|||||+|||||||||+|||||+|||++|++ +||||||||++ ++++|+|+++|+|... |.+. +++|+
T Consensus 1 GE~VG~LAAqSIgEPAtQmtLntfh~agvs------~vprLKEiLn~~~~~~~ktps~~v~L~~~~~~~~~~~~~~~~a~ 74 (381)
T cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSLESS------PLELLKEVLECRSKSKSKENDRRVILSLHLCKCDHGFEYERAAL 74 (381)
T ss_pred CCcchhHHHhhhcchHHHhhhccchhcCCc------cHHHHHHHhcccccCCCCCCCEEEEEeccccccccchHHHHHHH
Confidence 899999999999999999999999999996 49999999999 6779999999999851 3222 67899
Q ss_pred HHhccccceeccceeE---EEEcCCCceeEEEeccce
Q psy3022 209 NVLCRLEHTTLRKVLY---IILRPATHYQVELISGAR 242 (258)
Q Consensus 209 ~v~~~L~~~~l~~v~~---I~ydp~~~~~i~~~~G~~ 242 (258)
.|+++|++++|++++. |+|||+....+.+.++..
T Consensus 75 ~Vq~~Le~~tL~~v~~~~~I~Ydp~~~~t~i~~d~~~ 111 (381)
T cd02737 75 EVKNHLERVTLEDLATTSMIKYSPQATEAIVGEIGDQ 111 (381)
T ss_pred HHHHHhhhccHHHhhheEEEEECCCcccccccccHHH
Confidence 9999999999999977 999999887766655543
No 25
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=99.84 E-value=8.3e-22 Score=202.54 Aligned_cols=123 Identities=31% Similarity=0.377 Sum_probs=108.4
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHhhcCCC-ChhhHHhhcCCCcChhhHHHHHhhhcccccCCcccCCCCCCCCCCC
Q psy3022 2 LALKQTFENQVNRILNDARDKTGGSAKKSLTEY-NNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPH 80 (258)
Q Consensus 2 ~~~~~~~E~~v~~~l~~~~~~~~~~~~~~~~~~-N~l~~M~~SGsKGs~~nl~Q~~g~lGqQ~~~G~ri~~~~~~r~lp~ 80 (258)
+++.+.+|.++++++++++.+..+...++...+ |.+.+|..+||+| |+.|+..++|||.+.|++++.+ ++||
T Consensus 629 ~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~~~~~i~~m~~~Gs~~---n~sq~~~~iG~~gv~g~r~~~~----~~~~ 701 (808)
T COG0086 629 NNIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARM---NISQIVQLIGQQGVMGEKISVL----ARAA 701 (808)
T ss_pred CCeEEEeehHHHHHHHHHHHHHHhhhHHhcCCcchhHHHHhhhhhcc---CHHHHHHHhhhheeeccCCCcc----cccc
Confidence 356677889999999999999999988887776 5655555555555 7788888999999999999877 8999
Q ss_pred CcCCCCCCcccccccccCcCCCChhHHHHhhcccchhhhhhhhhccccCCC
Q psy3022 81 FIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETACN 131 (258)
Q Consensus 81 f~~~~~~~~~~GfI~~sf~~GL~p~EfFfHa~~gRegliDtavkTa~sG~~ 131 (258)
|.+.+..+++.|||.+||++||+|.|||||+|+||+||+|||+|||+||+-
T Consensus 702 Fe~~~~~~~a~~~i~s~f~eGLt~~e~f~~~~ggR~GlvDTA~KTa~sGYl 752 (808)
T COG0086 702 FEVTVKHLEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADSGYL 752 (808)
T ss_pred cccccccceeeeeeecccCCCCCcceEEeecCccccchHHHhhhhcccCcc
Confidence 999999999999999999999999999999999999999999999999953
No 26
>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain. Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Probab=99.71 E-value=1.8e-18 Score=152.86 Aligned_cols=52 Identities=48% Similarity=0.822 Sum_probs=49.5
Q ss_pred ccCCCchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhhcc
Q psy3022 133 KCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISK 185 (258)
Q Consensus 133 ~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~~ 185 (258)
.|+|||+||++||||||||+|||||||||.+|+++ ++++|+||++|++++++
T Consensus 2 ~~~~g~~vg~~aaqsigep~tq~t~~tfh~~g~~~-dIt~Glprv~el~e~r~ 53 (204)
T cd02655 2 LVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT-DITQGLPRVEELFEARK 53 (204)
T ss_pred ccCcccccchhhhhhcCCCccccccchhhhccccc-ccccccHHHHHHHHhhc
Confidence 37899999999999999999999999999999985 89999999999999988
No 27
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=99.62 E-value=1.3e-16 Score=165.65 Aligned_cols=74 Identities=46% Similarity=0.688 Sum_probs=70.8
Q ss_pred hhhhhhhhccccCCccccccccCccccchhhhhccCCCCCeEEEEecCcchhcHHHHHHHhccccceeccceeE
Q psy3022 151 PATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVLY 224 (258)
Q Consensus 151 p~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~~~~~t~~~~v~L~~~~~~~~~~a~~v~~~L~~~~l~~v~~ 224 (258)
=.|||||||||+||++++|||+|+|||+||++++|+++||+|+++|.+++..++++|+.++.+|++++|++|+.
T Consensus 539 iv~~~~LnTFH~AGv~~~nVTlGvPRL~EIinask~i~TP~m~i~l~~~~~~~~~~a~~v~~~ie~~~L~dv~~ 612 (858)
T PRK14898 539 VVTHNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVAT 612 (858)
T ss_pred EeeccccceeeccCccccccccCCchHHHHhcccCCCCCceEEEEECCCccchHHHHHHHHhheeeEEHHHHHH
Confidence 46999999999999999999999999999999999999999999999987778899999999999999999987
No 28
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe
Probab=99.48 E-value=9.2e-15 Score=124.73 Aligned_cols=48 Identities=77% Similarity=1.135 Sum_probs=46.9
Q ss_pred CchhhhhhhhccCChhhhhhhhccccCCccccccccCccccchhhhhc
Q psy3022 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINIS 184 (258)
Q Consensus 137 Ge~VG~iaAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~rl~eil~~~ 184 (258)
|||||++||||||||+||+||+|||+.|+.+.++|+|+||++++++++
T Consensus 1 g~~~g~~a~~~~~~p~~~~tl~t~~~~~~~~~~~t~~~pk~~~~~~~~ 48 (158)
T cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48 (158)
T ss_pred CCcchhhhhhhcCCCccchhhhhhhhccccccccccCCccchhhcccc
Confidence 899999999999999999999999999999999999999999999886
No 29
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=98.29 E-value=6.6e-07 Score=93.22 Aligned_cols=109 Identities=29% Similarity=0.342 Sum_probs=96.0
Q ss_pred ccCCCchhhhhhhhccCChhhhhhhhccccCC--ccccccccCccccchhhhhccCCCCCeEEEEecCcchhcHHHHHHH
Q psy3022 133 KCAPGEMVGALAAQSLGEPATQMTLNTFHFAG--VSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNV 210 (258)
Q Consensus 133 ~v~~Ge~VG~iaAqsigEp~TQ~tl~tFH~aG--~~~~~v~~g~~rl~eil~~~~~~~t~~~~v~L~~~~~~~~~~a~~v 210 (258)
...++..+|..+|||+++|+|||++.|||.|| ++..+.+.+.+++-++.++ +.++++.+++++.+.+..+.+.+..+
T Consensus 410 M~~Hvp~s~ea~AEa~~lm~tq~nilsP~~Ggpiv~~~qD~v~g~ylLt~~d~-~~~~~~~~ei~l~~~~~~~~e~~~ai 488 (808)
T COG0086 410 MAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDA-KLPSTPVGEIYLKDEYADDREKAEAI 488 (808)
T ss_pred hhccccchHHHHHHHHHhhccccccccCCCCCceEeecceEEeccEEEEEecc-cCCCCcceEEEeccccccchhhhHHH
Confidence 47899999999999999999999999999999 8888899999999999988 88999999999987777778999999
Q ss_pred hccccceeccceeE-EEEcCCCceeEEEeccce
Q psy3022 211 LCRLEHTTLRKVLY-IILRPATHYQVELISGAR 242 (258)
Q Consensus 211 ~~~L~~~~l~~v~~-I~ydp~~~~~i~~~~G~~ 242 (258)
.+.+...+++.+++ +..+.....++...++.+
T Consensus 489 ~~~~~~~~~k~i~~~i~~~~~~~~i~~t~~~~~ 521 (808)
T COG0086 489 AKKIELTTGKVIVSTISPDLAELSIIVTTDGRR 521 (808)
T ss_pred hcccceeeeeEEEEEeeccCCcceEEEecchhh
Confidence 99999999999998 777766566665555543
No 30
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=98.08 E-value=7e-07 Score=93.66 Aligned_cols=27 Identities=59% Similarity=0.774 Sum_probs=25.0
Q ss_pred CccCCCchhhhhhhhccCChhhhhhhh
Q psy3022 132 AKCAPGEMVGALAAQSLGEPATQMTLN 158 (258)
Q Consensus 132 ~~v~~Ge~VG~iaAqsigEp~TQ~tl~ 158 (258)
.+|+|||+||++||||||||+|||||.
T Consensus 52 a~vepge~vG~~aaqsi~~~~~~~~~~ 78 (858)
T PRK14898 52 ALVEPYEAVGIVAAQSIGEPGTQMSLP 78 (858)
T ss_pred CCCCCCceeeeeeehhcCCCCccccCC
Confidence 468999999999999999999999874
No 31
>PF03323 GerA: Bacillus/Clostridium GerA spore germination protein; InterPro: IPR004995 Dormant Bacillus subtilis spores germinate in the presence of particular nutrients called germinants. The spores are thought to recognise germinants through receptor proteins encoded by the gerA family of operons, which includes gerA, gerB, and gerK. The GerA proteins are predicted to be membrane associated.; GO: 0009847 spore germination, 0016021 integral to membrane
Probab=56.17 E-value=3.5 Score=41.06 Aligned_cols=79 Identities=25% Similarity=0.345 Sum_probs=59.8
Q ss_pred hhhccCChhhhhhhhccccCCccccccccCccc-------cc-hhhhhccCCCCCeEEEEecCcchhcHHHHHHHhcccc
Q psy3022 144 AAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPR-------LK-EIINISKKPKAPSLTVFLTGQAARDAEKAKNVLCRLE 215 (258)
Q Consensus 144 aAqsigEp~TQ~tl~tFH~aG~~~~~v~~g~~r-------l~-eil~~~~~~~t~~~~v~L~~~~~~~~~~a~~v~~~L~ 215 (258)
...||.||.|+-+++-.|-|=+-..+++.++.| |+ |.+...+..+|....+|+.+- -+.+-.+++++||+
T Consensus 116 ~~RsI~EP~tE~~vrGprdgFvE~l~~Ni~LIRrriksp~L~ve~~~iG~~s~T~Vai~Yi~~i--a~~~~v~~v~~rl~ 193 (470)
T PF03323_consen 116 PKRSIEEPETESVVRGPRDGFVESLDTNIALIRRRIKSPNLKVETFTIGERSKTKVAILYIEGI--ADPEIVQEVKQRLE 193 (470)
T ss_pred CCCCCCCCCCccccccchhcccccHHHHHHHHHHhcCCCceEEEeeecccccCceEEEEEecCC--CCHHHHHHHHHHHh
Confidence 378999999999999999875555555555432 22 334445667788889999876 47888999999999
Q ss_pred ceeccceeE
Q psy3022 216 HTTLRKVLY 224 (258)
Q Consensus 216 ~~~l~~v~~ 224 (258)
.++.+.+..
T Consensus 194 ~i~~d~i~~ 202 (470)
T PF03323_consen 194 SIKIDGILD 202 (470)
T ss_pred cCCcceecC
Confidence 999988855
No 32
>PF15278 Sec3_C_2: Sec3 exocyst complex subunit
Probab=32.18 E-value=39 Score=25.95 Aligned_cols=23 Identities=26% Similarity=0.198 Sum_probs=19.1
Q ss_pred CCChhhHHhhcCCCcChhhHHHH
Q psy3022 33 EYNNLKAMVVAGSKGSNINISQV 55 (258)
Q Consensus 33 ~~N~l~~M~~SGsKGs~~nl~Q~ 55 (258)
..=+++-|-.||+-|...|+-|+
T Consensus 63 STiNL~S~~LS~~L~~VIN~EQQ 85 (86)
T PF15278_consen 63 STINLFSMSLSTVLNDVINMEQQ 85 (86)
T ss_pred hHHHHHHHHHHHHhhcccccccC
Confidence 44568889999999999998874
No 33
>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.
Probab=21.45 E-value=34 Score=38.29 Aligned_cols=31 Identities=23% Similarity=0.534 Sum_probs=23.3
Q ss_pred hhhccccCCccccccccCccccchhhhhccC
Q psy3022 156 TLNTFHFAGVSSKNVTLGVPRLKEIINISKK 186 (258)
Q Consensus 156 tl~tFH~aG~~~~~v~~g~~rl~eil~~~~~ 186 (258)
||-+|-+--.-+.|+++|+||+.|+++|++.
T Consensus 963 ~L~~l~~er~ktgDI~qGLPrveellEaR~~ 993 (1227)
T TIGR02388 963 NLALLVFERAKTGDIVQGLPRIEELLEARKP 993 (1227)
T ss_pred EEEEEEeeecccCccccCchhHHHHHhccCC
Confidence 4555555444556899999999999999864
Done!