Query 016812
Match_columns 382
No_of_seqs 206 out of 1192
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 03:02:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016812.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016812hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1521 RNA polymerase I and I 100.0 5E-116 1E-120 834.5 25.5 323 29-382 1-338 (338)
2 cd07032 RNAP_I_II_AC40 AC40 su 100.0 2.4E-91 5.2E-96 679.5 28.3 275 76-379 1-290 (291)
3 cd07031 RNAP_II_RPB3 RPB3 subu 100.0 7.5E-73 1.6E-77 545.4 25.1 257 76-382 1-263 (265)
4 PRK00783 DNA-directed RNA poly 100.0 3.3E-66 7.2E-71 497.8 23.9 255 76-382 1-260 (263)
5 cd07030 RNAP_D D subunit of Ar 100.0 2.3E-64 5.1E-69 484.0 24.2 254 76-381 1-259 (259)
6 KOG1522 RNA polymerase II, sub 100.0 4.8E-62 1E-66 454.6 19.7 259 73-382 3-266 (285)
7 cd07028 RNAP_RPB3_like RPB3 su 100.0 3.4E-59 7.4E-64 437.2 21.5 206 76-380 1-212 (212)
8 smart00662 RPOLD RNA polymeras 100.0 1.9E-54 4.2E-59 408.2 17.3 221 87-377 1-224 (224)
9 PRK14979 DNA-directed RNA poly 100.0 3.2E-48 6.9E-53 358.3 19.9 183 76-382 4-187 (195)
10 COG0202 RpoA DNA-directed RNA 100.0 5.5E-40 1.2E-44 323.6 10.4 261 76-367 5-298 (317)
11 cd06928 RNAP_alpha_NTD N-termi 100.0 2.8E-34 6.1E-39 269.7 19.3 199 80-376 3-214 (215)
12 PRK05182 DNA-directed RNA poly 100.0 2E-33 4.4E-38 276.7 21.1 209 71-379 2-225 (310)
13 TIGR02027 rpoA DNA-directed RN 100.0 8.1E-31 1.8E-35 257.0 18.8 194 88-379 2-208 (297)
14 PF01000 RNA_pol_A_bac: RNA po 99.9 1.3E-27 2.8E-32 202.6 7.2 105 119-265 1-112 (112)
15 CHL00013 rpoA RNA polymerase a 99.9 5.5E-24 1.2E-28 211.0 18.5 202 75-379 9-223 (327)
16 PF01193 RNA_pol_L: RNA polyme 99.4 1.9E-12 4.1E-17 100.3 6.9 31 88-118 1-31 (66)
17 COG0202 RpoA DNA-directed RNA 99.0 3.6E-09 7.7E-14 105.3 11.7 161 134-380 58-223 (317)
18 cd00460 RNAP_RPB11_RPB3 RPB11 98.9 5.6E-09 1.2E-13 85.1 9.1 35 343-377 52-86 (86)
19 PRK01146 DNA-directed RNA poly 94.6 0.059 1.3E-06 44.1 4.8 38 76-114 1-38 (85)
20 PF13656 RNA_pol_L_2: RNA poly 93.2 0.29 6.4E-06 39.2 6.1 38 344-381 40-77 (77)
21 cd06927 RNAP_L L subunit of Ar 92.7 0.16 3.5E-06 41.3 4.1 33 78-110 1-33 (83)
22 cd07027 RNAP_RPB11_like RPB11 91.7 0.24 5.2E-06 40.3 4.0 33 78-110 1-33 (83)
23 cd07029 RNAP_I_III_AC19 AC19 s 90.2 0.67 1.5E-05 37.9 5.2 37 344-380 48-84 (85)
24 COG1761 RPB11 DNA-directed RNA 89.9 0.55 1.2E-05 39.7 4.6 35 75-109 4-38 (99)
25 cd06927 RNAP_L L subunit of Ar 89.2 0.76 1.7E-05 37.4 4.8 34 345-378 49-82 (83)
26 PRK01146 DNA-directed RNA poly 88.9 0.8 1.7E-05 37.5 4.8 36 344-379 50-85 (85)
27 cd06926 RNAP_II_RPB11 RPB11 su 88.7 1.1 2.3E-05 37.3 5.4 37 344-380 56-92 (93)
28 cd07027 RNAP_RPB11_like RPB11 87.6 1 2.2E-05 36.7 4.5 35 344-378 48-82 (83)
29 cd06926 RNAP_II_RPB11 RPB11 su 82.2 2.1 4.5E-05 35.6 4.1 37 76-113 7-43 (93)
30 COG1761 RPB11 DNA-directed RNA 79.5 4.1 8.9E-05 34.4 5.0 36 344-379 54-89 (99)
31 PRK15449 ferredoxin-like prote 74.2 3.1 6.6E-05 34.9 2.8 50 275-329 22-71 (95)
32 cd07029 RNAP_I_III_AC19 AC19 s 71.3 5 0.00011 32.8 3.4 27 83-109 6-32 (85)
33 PF13656 RNA_pol_L_2: RNA poly 64.8 3.7 7.9E-05 32.9 1.4 30 86-116 1-30 (77)
34 KOG3438 DNA-directed RNA polym 45.0 22 0.00048 30.3 2.9 26 84-109 14-39 (105)
35 COG2440 FixX Ferredoxin-like p 44.5 19 0.00041 30.5 2.4 49 275-325 24-74 (99)
36 KOG3438 DNA-directed RNA polym 38.1 62 0.0013 27.6 4.5 36 344-379 55-90 (105)
37 KOG4392 RNA polymerase, subuni 38.1 79 0.0017 27.5 5.2 38 344-381 68-105 (117)
38 PRK06273 ferredoxin; Provision 29.7 79 0.0017 28.9 4.2 90 288-381 53-150 (165)
39 COG4003 Uncharacterized protei 29.2 6.5 0.00014 32.5 -2.6 41 66-106 2-44 (98)
40 KOG3307 Molybdopterin converti 28.0 21 0.00046 31.6 0.2 43 88-145 50-95 (150)
No 1
>KOG1521 consensus RNA polymerase I and III, subunit RPA40/RPC40 [Transcription]
Probab=100.00 E-value=5.4e-116 Score=834.50 Aligned_cols=323 Identities=59% Similarity=0.922 Sum_probs=310.4
Q ss_pred CcchhhccCeEEeccCCCccccccccCCCCcCCCCCcccchhhccCCceEEEEEecCceEEEEEEccChhhHHHHHHHHH
Q 016812 29 PPHIEFQRTRVQCNLDAPIHTENVMYSGAYASMGVDNSLQLDHFCNNFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILI 108 (382)
Q Consensus 29 ~~~~~~~r~~v~~~~~~~~~~~~~~~~g~~~~~~~d~~~~~~~f~~~~~I~i~~~~~~~~~F~l~Gvd~siaNAlRRILl 108 (382)
|+|++.+|++|++++++|+|++|+||||.|. ++||.|++++|+++|+|.|.+++++.|+|+|+|+|++||||||||||
T Consensus 1 ~~~~~~~~~~v~~~~~~v~~~~s~dfpg~Y~--~~d~~~~~~~f~~~~~V~iv~~~~~~leFDligIda~IANAfRRILi 78 (338)
T KOG1521|consen 1 SAHLERMSTRVVLKEERVTNTTSTDFPGDYV--SEDDQWDLENFKDNFKVDIVSLDEETLEFDLIGIDASIANAFRRILI 78 (338)
T ss_pred ChhhhhhcceeeeccccccccccccCCcchh--cccccccHHHhhhceEEEEEeccCcceeEEEeeccHHHHHHHHHHHH
Confidence 6789999999999999999999999999999 78899999999999999999999999999999999999999999999
Q ss_pred hhCCcceEEEEEEeeCcccccccceeeecccCCCccCCceeeeecccCCCCCC-ceEEEEEEEEeecCCC----------
Q 016812 109 AELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSENDTSNEK-NTIVFKLHVLCERGGP---------- 177 (382)
Q Consensus 109 sEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~~d~~~~~~~~~~d~~~~~-~tv~~~L~v~c~~~~~---------- 177 (382)
|||||||||+|||+||||||||||||||||||||.+||++|+|..+.++..+. +|++|+|+|+|++|+.
T Consensus 79 aEVPtmAiEkVyi~nNTSViqDEvLaHRlGLvPl~aDPrlFe~~~e~d~~~e~~ntlvF~L~VkC~~n~~a~~~~sdpk~ 158 (338)
T KOG1521|consen 79 AEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLVPLRADPRLFEYRSENDEDDEKENTLVFKLNVKCTKNPNAKKDSSDPKE 158 (338)
T ss_pred hhcchhheeeeEEecCccccHHHHHHHhhcCcccccCcchhhccccCCCccCccceEEEEEEeeccCCCCcccCCCChhH
Confidence 99999999999999999999999999999999999999999999987776666 9999999999999842
Q ss_pred ---cceEEcCCceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccccCC-eEEEEeCCCceEEEEEEE
Q 016812 178 ---RLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLD-ITIARLGPGQEIELEAHA 253 (382)
Q Consensus 178 ---~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~i~~v~~-IlIakL~pGQeI~le~~a 253 (382)
|+.|||+|++|.|.|.|.+. |++++++|+++ |+||||||||+|+|+|||
T Consensus 159 Ly~ns~vyS~~~~w~P~g~Q~~~---------------------------f~e~~i~~~~~DILiAkLrPGQEI~le~ha 211 (338)
T KOG1521|consen 159 LYNNSEVYSRDLTWKPKGYQAEI---------------------------FAENPIRPVHDDILIAKLRPGQEIELEAHA 211 (338)
T ss_pred hccCcEEecCcceeccccchhhh---------------------------cccCCccccCcceEEEecCCCCEeeeeeee
Confidence 78999999999999988743 78999999999 999999999999999999
Q ss_pred EecccccccccCccceeeeccccceecccccchhhHHHHhhcCCCceEEeccCCCCceeEEEecCccccccccceecCcc
Q 016812 254 VKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLRCGEE 333 (382)
Q Consensus 254 ~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~a~~l~~~~p~gvi~id~~~~g~~~~~V~~~r~~t~~rec~r~~~~ 333 (382)
+|||||+||||||||||||||||.|.|++++.|++|++|++|||+|||+|++.+ ++++|+|++||+||+||||+| |++
T Consensus 212 vkGIGkdHAKfSPVaTAsYRLlP~I~l~~ei~ge~A~~lqkcfs~gVi~iee~~-~kk~A~Vad~R~dT~sRe~~R-~ee 289 (338)
T KOG1521|consen 212 VKGIGKDHAKFSPVATASYRLLPTIVLLAEIEGEDAERLQKCFSPGVIDIEEMG-GKKRAYVADPRKDTCSREVLR-HEE 289 (338)
T ss_pred ecccCcccccccCcccceeeccceeEecCcccchhHHHHHhhCCCCeEeeecCC-CceEEEecCcccchhhHHHhc-cHH
Confidence 999999999999999999999999999999999999999999999999999875 478999999999999999999 999
Q ss_pred cccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHHhhC
Q 016812 334 WEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITELS 382 (382)
Q Consensus 334 ~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~~L~ 382 (382)
|+++|++++++|||||+|||+|+|+|+.+|.+|+++|+.||+.+.++++
T Consensus 290 ~~d~V~LgrvrdHfIFsvestgal~p~~lf~eavkvle~Kc~al~~~~~ 338 (338)
T KOG1521|consen 290 LKDKVQLGRVRDHFIFSVESTGALKPEVLFEEAVKVLEEKCRALRDEIE 338 (338)
T ss_pred hhhheeeccccceEEEEeecccCCCchhhHHHHHHHHHHHHHHHhhccC
Confidence 9999999999999999999999999999999999999999999998764
No 2
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun
Probab=100.00 E-value=2.4e-91 Score=679.52 Aligned_cols=275 Identities=62% Similarity=0.998 Sum_probs=257.2
Q ss_pred ceEEEEEecCceEEEEEEccChhhHHHHHHHHHhhCCcceEEEEEEeeCcccccccceeeecccCCCccCCceeeeeccc
Q 016812 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSEN 155 (382)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNAlRRILlsEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~~d~~~~~~~~~~ 155 (382)
++|+|++++++.++|+|+|+|+||||||||||||||||||||.|+|++|||+|+|||||||||||||.+|+++|+|+.+|
T Consensus 1 ~~i~i~~~~~~~~~f~l~~~d~s~ANAlRRimiaEVPt~AId~V~i~~NTSvl~DE~lAHRLGLIPL~~d~~~~~~~~~~ 80 (291)
T cd07032 1 FKIEIISLSDEELEFDLIGVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLIPIKADPRLFEYREDS 80 (291)
T ss_pred CeEEEEECCCCEEEEEEecCCHHHHHHHHHHHHhcCcceeEEEEEEEECCccchhHHHHHhhcCceeecCHHHccccccc
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999998774
Q ss_pred -CCCCCCceEEEEEEEEeecCCC-------------cceEEcCCceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCC
Q 016812 156 -DTSNEKNTIVFKLHVLCERGGP-------------RLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDL 221 (382)
Q Consensus 156 -d~~~~~~tv~~~L~v~c~~~~~-------------~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~ 221 (382)
+.+|+.|+|+|+|+|+|++++. +..|||+||+|.|.|.|...
T Consensus 81 ~~~~~~~~~v~f~L~v~c~~~~~~~~~~~~~~~~~~~~~VyS~dl~~~p~g~q~~~------------------------ 136 (291)
T cd07032 81 DDEPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHKVYSGDLKWVPIGSQEKR------------------------ 136 (291)
T ss_pred ccCCCCCcEEEEEEEEEccCCcccccccccccccccccEEECCCCEecCCCccccc------------------------
Confidence 5689999999999999987642 37899999999999987531
Q ss_pred CCCCCCCCccccCC-eEEEEeCCCceEEEEEEEEecccccccccCccceeeeccccceecccccchhhHHHHhhcCCCce
Q 016812 222 LPEFSNNPIRPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNV 300 (382)
Q Consensus 222 ~~~f~~~~i~~v~~-IlIakL~pGQeI~le~~a~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~a~~l~~~~p~gv 300 (382)
|.++++.|+++ |+|+||+|||+|+|+|+|+||+||+||||||||||+|||+|+|+|++++.+++|++|+++||+||
T Consensus 137 ---~~~~~v~~v~~dI~I~kL~~gQ~l~le~~a~kG~Gk~HAKwsPv~ta~yr~~P~I~i~~~~~~~~~~~~~~~cP~~V 213 (291)
T cd07032 137 ---FADNPIRPVHPDILIAKLRPGQEIDLELHCVKGIGKDHAKFSPVATASYRLLPEITLLKPITGEDAEKLQKCFPPGV 213 (291)
T ss_pred ---cCCCCcEEeCCCcEEEEECCCCEEEEEEEEEcCcccccceecCceeEEEEecceEEEcCcCCHHHHHHHHhhCCCcc
Confidence 34677999999 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeccCCCCceeEEEecCccccccccceecCcccccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHH
Q 016812 301 FDIEDIGSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVIT 379 (382)
Q Consensus 301 i~id~~~~g~~~~~V~~~r~~t~~rec~r~~~~~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~ 379 (382)
|++++.+ |.++++|.++++||+||||+| ++++.+.|++++++|||||+|||+|+|+|++||.+|+++|++||+.|++
T Consensus 214 f~i~~~~-~~~~~~V~~~~~ct~crec~~-~~~~~~~V~v~~~~d~fiF~VES~G~l~p~~i~~~Ai~iL~~K~~~l~~ 290 (291)
T cd07032 214 IDIEEVK-GKKKAVVANPRKDTLSREVLR-HEEFKDKVELGRVRDHFIFSIESTGALPPDVLFLEAIKILKEKCRKLLE 290 (291)
T ss_pred EEecccC-CCceEEEcccccCcccHhHhh-hhccCCceeEEEeCCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 9997643 346899999999999999999 8788899999999999999999999999999999999999999999976
No 3
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=100.00 E-value=7.5e-73 Score=545.36 Aligned_cols=257 Identities=35% Similarity=0.472 Sum_probs=217.6
Q ss_pred ceEEEEEecCceEEEEEEccChhhHHHHHHHHHhhCCcceEEEEEEeeCcccccccceeeecccCCCccCC-ceeeee-c
Q 016812 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDP-RLFEYM-S 153 (382)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNAlRRILlsEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~~d~-~~~~~~-~ 153 (382)
++|+|.++++++++|.|+|++++||||||||||||||||||+.|+|++|||+|+|||||||||||||.+++ ..+.+. .
T Consensus 1 p~i~i~~~~~~~~~F~l~~~~~s~aNALRRillsevPt~AI~~V~I~~NtSvl~DE~iaHRlglIPl~~e~~~~~~~~~~ 80 (265)
T cd07031 1 PRVEITELTDDKVKFILENTDLSVANSLRRVMIAEVPTLAIDLVEIEENTSVLHDEFIAHRLGLIPLTSDDVDEFLYYSR 80 (265)
T ss_pred CcEEEEEcCCCEEEEEEEcCcHHHHHHHHHHHHHcCccceEEEEEEecCCcccccceeeeecccCCCccCcHHHHhhhhh
Confidence 46899999999999999999999999999999999999999999999999999999999999999999764 333232 2
Q ss_pred c--cCCCCCCceEEEEEEEEeecCCCcceEEcCCceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCcc
Q 016812 154 E--NDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIR 231 (382)
Q Consensus 154 ~--~d~~~~~~tv~~~L~v~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~i~ 231 (382)
. ++..|+.|+++|+|+++|++++ +..|||+||+|.|.+.|... +.|... +....
T Consensus 81 ~~~~~~~~~~~~v~~~L~v~~~~~~-~~~V~s~Dl~~~~~~~~~~~---------~~pi~~--------------~~~~~ 136 (265)
T cd07031 81 DCDCDEFCDKCSVELTLDVKCTGDQ-TREVTSRDLVSSGPKVNDVV---------PVPIRN--------------DSEDN 136 (265)
T ss_pred hccccCCCCCCeEEEEEEEEeccCC-CceEEHHHcccccccccccC---------Cccccc--------------ccccc
Confidence 2 3345677999999999998765 58999999999876544210 011110 01122
Q ss_pred ccCC-eEEEEeCCCceEEEEEEEEecccccccccCccceeeeccccceecccccchhhHHHHhhcCCCceEEeccCCCCc
Q 016812 232 PMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGK 310 (382)
Q Consensus 232 ~v~~-IlIakL~pGQeI~le~~a~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~a~~l~~~~p~gvi~id~~~~g~ 310 (382)
++++ |+|+||+|||+|+|+|+|+||+||+||||||||||+||++|+|+|+++..+.++
T Consensus 137 ~~~~~i~I~kL~~gq~i~le~~a~kG~Gk~HAKwsPv~~~~y~~~p~i~i~~~~~~~~~--------------------- 195 (265)
T cd07031 137 GEEDGILIVKLRKGQELKLRCIAKKGIGKEHAKWSPTAAVTFEYDPDNALRHTDYWYLE--------------------- 195 (265)
T ss_pred cCCCCeEEEEECCCCEEEEEEEEECCEeccCCEeccceEEEEEEccceEEccccccchh---------------------
Confidence 5678 999999999999999999999999999999999999999999999876543211
Q ss_pred eeEEEecCccccccccceecCc-ccccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHHhhC
Q 016812 311 KRATVAQPRACTLCRECLRCGE-EWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITELS 382 (382)
Q Consensus 311 ~~~~V~~~r~~t~~rec~r~~~-~~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~~L~ 382 (382)
..+++.|++||+|++ +. ++.+.|++++++|||+|+|||+|+|+|++||.+|+++|++||+.|++.|+
T Consensus 196 ----~~~~~~c~~c~~c~~-~~~~~~~~v~i~~~~~~fiF~VES~Gsl~p~~Iv~~Al~iL~~K~~~l~~~l~ 263 (265)
T cd07031 196 ----DEDKEWPKSENACIE-EPPEKDALFDIDAKPDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQLQLS 263 (265)
T ss_pred ----hcccccCchhHHHhh-cccccCCceEEEeeCCEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 127899999999999 53 47889999999999999999999999999999999999999999999874
No 4
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=100.00 E-value=3.3e-66 Score=497.83 Aligned_cols=255 Identities=38% Similarity=0.630 Sum_probs=230.2
Q ss_pred ceEEEEEecCceEEEEEEccChhhHHHHHHHHHhhCCcceEEEEEEeeCcccccccceeeecccCCCccCCceeeeeccc
Q 016812 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSEN 155 (382)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNAlRRILlsEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~~d~~~~~~~~~~ 155 (382)
++|+|.+.++++++|.+.|++++|||||||+||||||||||+.|+|++|||+++||+|||||||||+.++++.++|+.++
T Consensus 1 ~~~~~~~~~~~~~~f~~~g~~~t~~NalRRvlls~vp~~Ai~~v~i~~n~s~~~de~i~hrl~lip~~~~~~~~~~~~~~ 80 (263)
T PRK00783 1 MEIEILELDDRSARFVVEGVTPAFANAIRRAMIADVPTMAIDDVRFYENTSVLFDEILAHRLGLIPLTTDLDKYKPPEEC 80 (263)
T ss_pred CceEEEEcCCcEEEEEEeCCCHHHHHHHHHHHHHcCCeeeEEEEEEEECCcchhHHHHHHhhcCcccccCHHHCCCcccc
Confidence 46899999999999999999999999999999999999999999999999999999999999999999998888887654
Q ss_pred C---CCCCCceEEEEEEEEeecCCCcceEEcCCceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccc
Q 016812 156 D---TSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRP 232 (382)
Q Consensus 156 d---~~~~~~tv~~~L~v~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~i~~ 232 (382)
+ ..|+.|+++|+|+++++ ..|||+||++.| .++.+
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~~-----~~V~a~dl~~~~-------------------------------------~~v~~ 118 (263)
T PRK00783 81 TCEGEGCPDCTVTLSLEVEGP-----KTVYSGDLKSSD-------------------------------------PDVKP 118 (263)
T ss_pred cccCCCCCCcEEEEEEEecCC-----CcEEccccccCC-------------------------------------CCcee
Confidence 3 35778899999999853 689999998621 24789
Q ss_pred cCC-eEEEEeCCCceEEEEEEEEecccccccccCccceeeeccccceecccccchhhHHHHhhcCCCceEEeccCCCCce
Q 016812 233 MLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKK 311 (382)
Q Consensus 233 v~~-IlIakL~pGQeI~le~~a~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~a~~l~~~~p~gvi~id~~~~g~~ 311 (382)
+|| ++|+||++||+|+|+|++.||+||+||||+|+++++||+.|.|.+.+.. ..+..+.+.||.|+|.+++ .
T Consensus 119 v~~~~~I~~L~~~~~l~~e~~~~~G~G~~HAKw~p~~~~~yr~~p~I~i~~~C--~~C~~C~~~CP~~vi~~~~-----~ 191 (263)
T PRK00783 119 VDPNIPIVKLKEGQKLVLEAYARLGRGKEHAKWQPGSACGYKYYPRIEVSEDC--DECEKCVEACPRGVLELKE-----G 191 (263)
T ss_pred cCCCcEEEEeCCCCEEEEEEEEEcCcccccCccCcceEeeecccccccccccC--CchHHHHHhCCccccEecC-----C
Confidence 999 9999999999999999999999999999999999999999999994344 4578899999999999975 2
Q ss_pred eEEEecCcccccccccee-cCcccccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHHhhC
Q 016812 312 RATVAQPRACTLCRECLR-CGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITELS 382 (382)
Q Consensus 312 ~~~V~~~r~~t~~rec~r-~~~~~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~~L~ 382 (382)
.+.+.++..|++|++|++ |. .+.+.+..++++|+|+|||+|+++|++||.+|+++|++||+.|.+.|+
T Consensus 192 ~~~v~~~~~C~~C~~Ci~~CP---~~AI~i~~~~~~~if~vEs~G~l~p~~iv~~A~~~l~~k~~~~~~~~~ 260 (263)
T PRK00783 192 KLVVTDLLNCSLCKLCERACP---GKAIRVSDDENKFIFTVESDGSLPVEEILLEALKILKRKADELIEALE 260 (263)
T ss_pred eEEEeChhhCCCchHHHHhCC---CCceEEEEcCCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 366678899999999998 42 467999999999999999999999999999999999999999998874
No 5
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=100.00 E-value=2.3e-64 Score=484.04 Aligned_cols=254 Identities=40% Similarity=0.686 Sum_probs=226.6
Q ss_pred ceEEEEEecCceEEEEEEccChhhHHHHHHHHHhhCCcceEEEEEEeeCcccccccceeeecccCCCccCCceeeeeccc
Q 016812 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSEN 155 (382)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNAlRRILlsEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~~d~~~~~~~~~~ 155 (382)
++|+|++.++++++|.++|+++++||||||+||||||||||+.|+|++|||+++||+|||||||||+..+...+.+..++
T Consensus 1 ~~~~~~~~~~~~~~f~~~g~~~s~~NalRRills~vp~~Ai~~V~i~~n~s~~~de~i~hrl~~ip~~~e~~~~~~~~~~ 80 (259)
T cd07030 1 MEIEVLELDDDRARFVLEGVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAHRLGLIPLRTDLDLYKYRSEC 80 (259)
T ss_pred CceEEEecCCCEEEEEEeCCCHHHHHHHHHHHHhcCCeeeEEEEEEEeCCchhhHHHHHHhhcCcccccCHHHhcccccc
Confidence 46899999999999999999999999999999999999999999999999999999999999999999775443333332
Q ss_pred ---CCCCCCceEEEEEEEEeecCCCcceEEcCCceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccc
Q 016812 156 ---DTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRP 232 (382)
Q Consensus 156 ---d~~~~~~tv~~~L~v~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~i~~ 232 (382)
...++.|++.|+|+++|+ ..|||+||+|. +..+.|
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~~-----~~v~s~dl~~~-------------------------------------~~~v~~ 118 (259)
T cd07030 81 SCGGAGCPLCTVTLTLSVEGP-----GTVYSGDLKSS-------------------------------------DPDVKP 118 (259)
T ss_pred cccCCCCCCcEEEEEEEccCC-----ceEEccccccC-------------------------------------CCCccc
Confidence 245667999999999875 79999999972 124789
Q ss_pred cCC-eEEEEeCCCceEEEEEEEEecccccccccCccceeeeccccceecccccchhhHHHHhhcCCCceEEeccCCCCce
Q 016812 233 MLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKK 311 (382)
Q Consensus 233 v~~-IlIakL~pGQeI~le~~a~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~a~~l~~~~p~gvi~id~~~~g~~ 311 (382)
+|| |+|+||++||+|+|+++|.||+||+||||+|+++++||++|.|.+.+...+ +.++++.||.|+|.+++ .
T Consensus 119 ~~~~~~I~~l~~~~~l~~~~~~~kg~g~~hakw~p~~~~~yr~~P~i~i~~~C~~--C~~C~~~CP~~vi~~d~-----~ 191 (259)
T cd07030 119 VYDNIPIVKLGKGQKLVLEAYARLGRGKEHAKWQPTTACGYKYYPVIEIDEDCDG--CGKCVEECPRGVLELEE-----G 191 (259)
T ss_pred cCCCcEEEEeCCCCEEEEEEEEecCccCCCCCCCCccEEEEEeecceechhhCCC--hHHHHHhCCccceEccC-----C
Confidence 999 999999999999999999999999999999999999999999998876654 78899999999999864 2
Q ss_pred eEEEecCcccccccccee-cCcccccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHHhh
Q 016812 312 RATVAQPRACTLCRECLR-CGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITEL 381 (382)
Q Consensus 312 ~~~V~~~r~~t~~rec~r-~~~~~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~~L 381 (382)
...+.++..|++|++|.+ |. .+.+++.++.++|+|+|||+|+++|++||.+|+++|++|++.|.+.|
T Consensus 192 ~~~v~~~~~C~~C~~C~~~Cp---~~AI~~~~~~~~~if~vEs~Gsl~p~~il~~A~~~l~~k~~~~~~~~ 259 (259)
T cd07030 192 KVVVEDLEDCSLCKLCERACD---AGAIRVGWDEDRFIFEVESDGSLPPKEILLEALRILKEKADELIEAL 259 (259)
T ss_pred eeEEeChhhCcCchHHHHhCC---CCcEEEEecCCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence 466778999999999998 32 36899999999999999999999999999999999999999998865
No 6
>KOG1522 consensus RNA polymerase II, subunit POLR2C/RPB3 [Transcription]
Probab=100.00 E-value=4.8e-62 Score=454.57 Aligned_cols=259 Identities=34% Similarity=0.510 Sum_probs=205.5
Q ss_pred cCCceEEEEEecCceEEEEEEccChhhHHHHHHHHHhhCCcceEEEEEEeeCcccccccceeeecccCCCccCC-ceeee
Q 016812 73 CNNFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDP-RLFEY 151 (382)
Q Consensus 73 ~~~~~I~i~~~~~~~~~F~l~Gvd~siaNAlRRILlsEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~~d~-~~~~~ 151 (382)
.+.+.|+|.+++++.++|.|.+.|.++||||||+|||||||+||+.|.|.-||||++|||||||||||||.++- ..++|
T Consensus 3 ~~~p~v~I~Elt~d~vkF~L~nTdlsvANsLRRV~iaEvPTiAID~VeIe~NssVL~DEFiAHRLGLIPl~S~~~~~l~y 82 (285)
T KOG1522|consen 3 ANQPTVKIRELTDDNVKFVLSNTDLSVANSLRRVMIAEVPTIAIDLVEIEVNSSVLPDEFIAHRLGLIPLISDRIVELQY 82 (285)
T ss_pred CCCCceEEEecCCCceEEEEecChHHHHHHHHHHHHhcCceeEEEEEEEecccccccHHHHHhhhcceeccchhhhhhhh
Confidence 34578999999999999999999999999999999999999999999999999999999999999999999763 34778
Q ss_pred eccc--CCCCCCceEEEEEEEEeecCCCcceEEcCCceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCC
Q 016812 152 MSEN--DTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNP 229 (382)
Q Consensus 152 ~~~~--d~~~~~~tv~~~L~v~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~ 229 (382)
..+| ++.|+.|+|+|.|+++|+... ...|||+||.. ..|.+.|..++ ++... .
T Consensus 83 trdC~C~~~C~eCSVef~L~~kc~~d~-T~~VtsrDL~s--------------~~~~v~pv~~~---~~~~~-------~ 137 (285)
T KOG1522|consen 83 TRDCECDEFCPECSVEFTLDVKCTDDQ-TRDVTSRDLVS--------------LDPTVTPVDSN---RGSEI-------D 137 (285)
T ss_pred cccCchhccCCcceEEEEEeeeecccc-eeeeehHhhhc--------------cCCcccccccC---CCCcc-------c
Confidence 7655 457999999999999999776 58999999983 23566666642 11110 1
Q ss_pred ccccCC-eEEEEeCCCceEEEEEEEEecccccccccCccceeeeccccceecccccchhhHHHHhhcCCC-ceEEeccCC
Q 016812 230 IRPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPV-NVFDIEDIG 307 (382)
Q Consensus 230 i~~v~~-IlIakL~pGQeI~le~~a~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~a~~l~~~~p~-gvi~id~~~ 307 (382)
....+. |+|+|||+||+|+|+|+|+||+||+||||||+|+++|.|.|+..+.+.........+ ..+|+ ...++++..
T Consensus 138 ~~~e~~gilI~KLRkgQELkLra~akKGigKeHAKWsPta~V~FeYDPdn~lrhT~y~~e~~~~-~Ewp~sk~~e~~~~~ 216 (285)
T KOG1522|consen 138 DDSESKGILIVKLRKGQELKLRAIAKKGIGKEHAKWSPTAAVAFEYDPDNKLRHTLYWFEEDDL-IEWPKSKNSELEEDP 216 (285)
T ss_pred cccccCCcEEEEeecCCceeeeeeecccccccccccCCcceEEEEECccHhhhccCCCccccch-hhCCcccccCCCCCc
Confidence 123345 999999999999999999999999999999999999999999999876543221111 11332 333333211
Q ss_pred CCceeEEEecCccccccccceecCcccccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHHhhC
Q 016812 308 SGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITELS 382 (382)
Q Consensus 308 ~g~~~~~V~~~r~~t~~rec~r~~~~~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~~L~ 382 (382)
+| + ....-...+|+|+|+|||+|+++|.+|+.+|+.+|++|+..+...|+
T Consensus 217 -----------------~e----~----~pyd~~~kpd~F~~~VEs~Gal~~~~iVl~gi~iLk~Kl~~l~~~l~ 266 (285)
T KOG1522|consen 217 -----------------EE----G----APYDPEGKPDKFYFNVESVGALPPSQIVLMGIDILKEKLAALRLALS 266 (285)
T ss_pred -----------------cc----c----CCCCccCCCceEEEEeEecCCCCHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 00 0 11122244699999999999999999999999999999999987664
No 7
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and
Probab=100.00 E-value=3.4e-59 Score=437.19 Aligned_cols=206 Identities=39% Similarity=0.614 Sum_probs=180.3
Q ss_pred ceEEEEEecCceEEEEEEccChhhHHHHHHHHHhhCCcceEEEEEEeeCcccccccceeeecccCCCccCCce---eeee
Q 016812 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRL---FEYM 152 (382)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNAlRRILlsEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~~d~~~---~~~~ 152 (382)
|.|+|.+.++++++|+|+|++++|||||||+|||||||+||+.|+|++|||+++||+|||||||||+..++.+ .+.+
T Consensus 1 ~~i~i~~~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~~AI~~V~I~~NtS~~~DE~iaHrlglIP~~~e~~~~~~~n~k 80 (212)
T cd07028 1 PQVKIREADKDNVDFILSGVDLAMANALRRVMIAEVPTMAVDSVEVETNTSVLADEILAHRLGLIPLQSMDILQLYRSPE 80 (212)
T ss_pred CcEEEEEcCCCEEEEEEEccChhHHHHHHHHHHHcCcceEEEEEEEEcCCCcccceeeeeeeeecccccCcHHHhhhccc
Confidence 4689999999999999999999999999999999999999999999999999999999999999999876432 2223
Q ss_pred cc--cCCCCCCceEEEEEEEEeecCCCcceEEcCCceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCc
Q 016812 153 SE--NDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPI 230 (382)
Q Consensus 153 ~~--~d~~~~~~tv~~~L~v~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~i 230 (382)
.. +...|+.|++.++|+++|+.+. +..|||+||+|.+.|.. ++++
T Consensus 81 ~~~~~~~~~~~~~v~~~l~~~g~~~~-~~~V~s~DL~~~~~~~~--------------------------------~~~v 127 (212)
T cd07028 81 EDCECEDHCDKCSVVLTLQAFAESES-TTNVYSKDLVIVSNLMG--------------------------------RNIG 127 (212)
T ss_pred ccccccccccceeEEEEEEccCCCCC-cceEEHHHcccCCcccc--------------------------------CCCe
Confidence 22 2234566899999999987532 46899999999654421 2458
Q ss_pred cccCC-eEEEEeCCCceEEEEEEEEecccccccccCccceeeeccccceecccccchhhHHHHhhcCCCceEEeccCCCC
Q 016812 231 RPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSG 309 (382)
Q Consensus 231 ~~v~~-IlIakL~pGQeI~le~~a~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~a~~l~~~~p~gvi~id~~~~g 309 (382)
.|++| |+|+||++||+|+|+|+|+||+||+|||||||++++|++.|
T Consensus 128 ~pv~~di~I~kL~~gq~i~le~~~~~G~G~~hAk~sPV~~v~y~~~~--------------------------------- 174 (212)
T cd07028 128 HPIIQDILICKLRKGQEIKLTCVAKKGIGKEHAKFGPVAAIEFRYDP--------------------------------- 174 (212)
T ss_pred EEeCCCcEEEEECCCCEEEEEEEEECCCcCCCCEeCCceEEEEEEEc---------------------------------
Confidence 89999 99999999999999999999999999999999999998765
Q ss_pred ceeEEEecCccccccccceecCcccccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHHh
Q 016812 310 KKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITE 380 (382)
Q Consensus 310 ~~~~~V~~~r~~t~~rec~r~~~~~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~~ 380 (382)
+.|||+|+|||+|+++|++++.+|+++|++|++.|+++
T Consensus 175 ---------------------------------~~d~li~~VeT~Gsi~p~~~l~~A~~iL~~~~~~~~~~ 212 (212)
T cd07028 175 ---------------------------------VADTYIMNVESVGSLPPDQVVVEAIKTLQKKVASILLA 212 (212)
T ss_pred ---------------------------------cCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHhhC
Confidence 14999999999999999999999999999999999863
No 8
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=100.00 E-value=1.9e-54 Score=408.21 Aligned_cols=221 Identities=41% Similarity=0.610 Sum_probs=194.2
Q ss_pred eEEEEEEccChhhHHHHHHHHHhhCCcceEEEEEEeeCcccccccceeeecccCCCccCCceeeeeccc--CCCCCCceE
Q 016812 87 DMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSEN--DTSNEKNTI 164 (382)
Q Consensus 87 ~~~F~l~Gvd~siaNAlRRILlsEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~~d~~~~~~~~~~--d~~~~~~tv 164 (382)
+++|.|.+++.++||||||+||++|||+||+.|+|++|+|.++|||++|||||+||..+.+.+.++..| +..|+.|++
T Consensus 1 ~~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~I~~n~~~v~eev~~~rLnL~pl~~~~~~~~~~~~~~~~~~~~~~~~ 80 (224)
T smart00662 1 RAKFVLEPYGLTLANALRRVLLSSVPGMAVTEVEIEGNTSGVQDEVLAHRLGLKPLASDPDGDEYQRDCECEEGCEKCSV 80 (224)
T ss_pred CeEEEEEcCCchHHHHHHHHHHHcCccceEEEEEEecCCcchhHHHHHHHhCCeeEEEechhccccccccccccCCCceE
Confidence 378999999999999999999999999999999999999999999999999999999876656665433 446888999
Q ss_pred EEEEEEEeecCCCcceEEcCCceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccccCC-eEEEEeCC
Q 016812 165 VFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLD-ITIARLGP 243 (382)
Q Consensus 165 ~~~L~v~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~i~~v~~-IlIakL~p 243 (382)
+++|+++|+ ..|||+||+|.+ ++.+.++|| ++|+||++
T Consensus 81 ~~~L~~~gp-----~~V~a~Dl~~~~------------------------------------~~~v~~vnp~~~I~~L~~ 119 (224)
T smart00662 81 TLTLDVKGP-----GEVTAGDLKSDS------------------------------------DPDVEIVNPDIPIAKLRE 119 (224)
T ss_pred EEEEEEEcC-----CcEEHHHcccCC------------------------------------CCCcEEeCCCcEEEEECC
Confidence 999999985 689999999831 224889999 99999999
Q ss_pred CceEEEEEEEEecccccccccCccceeeeccccceecccccchhhHHHHhhcCCCceEEeccCCCCceeEEEecCccccc
Q 016812 244 GQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTL 323 (382)
Q Consensus 244 GQeI~le~~a~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~a~~l~~~~p~gvi~id~~~~g~~~~~V~~~r~~t~ 323 (382)
||+|+|+++|.||+||+||||+|+++++|++.|.|.++....+.++..+...||.+++..+ |
T Consensus 120 gq~l~~e~~~~~G~G~~hak~~p~~~~~~~~~~~i~id~~~~pv~~v~~~~~~~~~~~~~~----------------~-- 181 (224)
T smart00662 120 GQELELEARAEKGRGYVHAKWSPVSTVEYRYIPRIPVDASFSPVDRVAYQVECPRVVQRTD----------------C-- 181 (224)
T ss_pred CCEEEEEEEEECCcccccCccccccCCCcCcCCEEEECCCCChhhheeeeccCCccceecc----------------c--
Confidence 9999999999999999999999999999999999999987777666667777776654321 5
Q ss_pred cccceecCcccccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHH
Q 016812 324 CRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERV 377 (382)
Q Consensus 324 ~rec~r~~~~~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~ 377 (382)
||||++ + .++|+|+|+|||+|+++|+++|.+|+++|++|++.|
T Consensus 182 ~~~c~~-~----------~~~d~l~f~IeT~G~i~p~~al~~A~~iL~~k~~~~ 224 (224)
T smart00662 182 CRECDE-G----------EEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEAF 224 (224)
T ss_pred chhhhc-c----------CCCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHhhC
Confidence 999998 3 247999999999999999999999999999999764
No 9
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=100.00 E-value=3.2e-48 Score=358.26 Aligned_cols=183 Identities=37% Similarity=0.606 Sum_probs=161.1
Q ss_pred ceEEEEEecCceEEEEEEccChhhHHHHHHHHHhhCCcceEEEEEEeeCcccccccceeeecccCCCccCCceeeeeccc
Q 016812 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSEN 155 (382)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNAlRRILlsEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~~d~~~~~~~~~~ 155 (382)
+++++....++.++|+|+ +++++||||||+|||+|||+||+.|+|++|||+++||++|||||||||+..+ + +.
T Consensus 4 ~~~~~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~V~I~~Nts~~~DEivaHe~~lIpLK~~~--~--~~-- 76 (195)
T PRK14979 4 IKEKEKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIENVYFYENSSSMYDEILAHRLGLIPIKGKP--V--SG-- 76 (195)
T ss_pred cceeeeccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEEEEEecCcccccchheeeeeeeeeeeeee--c--cC--
Confidence 567888889999999999 9999999999999999999999999999999999999999999999998653 1 11
Q ss_pred CCCCCCceEEEEEEEEeecCCCcceEEcCCceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccccCC
Q 016812 156 DTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLD 235 (382)
Q Consensus 156 d~~~~~~tv~~~L~v~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~i~~v~~ 235 (382)
.+++.|+|+++++ +.|||+||+|. .+ .++||
T Consensus 77 -----~~~~~l~L~~~gp-----~~Vta~Di~~~--------------------------------------~~-~ivnp 107 (195)
T PRK14979 77 -----DEVITFTLSKEGP-----CTVYSSDLKSE--------------------------------------NG-EVAFK 107 (195)
T ss_pred -----CCcEEEEEEEeCC-----ceEEHHHcCCC--------------------------------------CC-cccCC
Confidence 3578899998753 78999999871 12 47899
Q ss_pred -eEEEEeCCCceEEEEEEEEecccccccccCccceeeeccccceecccccchhhHHHHhhcCCCceEEeccCCCCceeEE
Q 016812 236 -ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRAT 314 (382)
Q Consensus 236 -IlIakL~pGQeI~le~~a~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~a~~l~~~~p~gvi~id~~~~g~~~~~ 314 (382)
++||+|++||+|+|+|+|.+|+||+||||+|+ .|.|++.
T Consensus 108 di~I~tL~~g~~l~~e~~~~~G~Gy~hAk~~pv-da~y~~~--------------------------------------- 147 (195)
T PRK14979 108 NIPIVKLAEGQKLEIECEALVGTGKIHAKWQPC-NAVYKQI--------------------------------------- 147 (195)
T ss_pred CcEEEEECCCCEEEEEEEEECCCccccccccce-eeEEecC---------------------------------------
Confidence 99999999999999999999999999999994 4555321
Q ss_pred EecCccccccccceecCcccccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHHhhC
Q 016812 315 VAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVITELS 382 (382)
Q Consensus 315 V~~~r~~t~~rec~r~~~~~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~~L~ 382 (382)
+.|+|+|+|||+|+++|++++.+|+++|+++++.|.+.|+
T Consensus 148 ----------------------------~~dkl~leIeTdGsi~P~~al~~Aa~iL~~~l~~~~~~l~ 187 (195)
T PRK14979 148 ----------------------------SNDEVEFKVESFGQMDAEDILRSALEILKNKAEKFLQELE 187 (195)
T ss_pred ----------------------------CCcEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 1489999999999999999999999999999999998774
No 10
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=100.00 E-value=5.5e-40 Score=323.63 Aligned_cols=261 Identities=23% Similarity=0.294 Sum_probs=215.7
Q ss_pred ceEEEEEec----CceEEEEEEccChhhHHHHHHHHHhhCCcceEEEEEEee--C---cc-cccccceeeecccCCCccC
Q 016812 76 FRVEVIRLT----KDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIAN--N---TS-VIQDEVLAHRLGLIPIIVD 145 (382)
Q Consensus 76 ~~I~i~~~~----~~~~~F~l~Gvd~siaNAlRRILlsEVPT~AIe~V~I~~--N---TS-vi~DEvLAHRLGLIPl~~d 145 (382)
..|++.+++ ...++|...|+++++||||||||||+|||+||+.|+|++ | |+ .++|||+||||||+||..+
T Consensus 5 ~~i~i~~~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~V~I~~v~hef~s~~gv~Edvl~~~LnLk~L~~~ 84 (317)
T COG0202 5 KKVKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEIDGVLHEFDSIEGVQEDVLAHRLNLKPLAVK 84 (317)
T ss_pred cceEEEEcccccccEEEEEeeeCCcchhHHHHHHHHHHcCccceEEEEEEeccccccccCcCcHHHHHHHHhcCceeeee
Confidence 348898888 678999999999999999999999999999999999999 3 43 9999999999999999876
Q ss_pred Cc-----eeeeecc--cCCCCCCceEEEEEEEEeecCCC-----------cceEEcCCceecCCCCCCCCCCCCCCCCCC
Q 016812 146 PR-----LFEYMSE--NDTSNEKNTIVFKLHVLCERGGP-----------RLTVKTNELKWLPNGSELPLETKPDSNPSS 207 (382)
Q Consensus 146 ~~-----~~~~~~~--~d~~~~~~tv~~~L~v~c~~~~~-----------~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~ 207 (382)
+. .+.+... |...+..|++.+.|+|.|+...- ...||++|+.|.+.+++.
T Consensus 85 ~~~~~~~~~~~~~~g~g~v~a~d~~~~~~lEv~np~~~ia~~~~~~~l~~~~~V~~G~gyv~~~~~~~------------ 152 (317)
T COG0202 85 LDGDEEVTLELDKEGPGEVTASDITVPLDLEVVNPDHVIATLTEDAKLEMELRVYSGDGYVPAEGNRE------------ 152 (317)
T ss_pred cccccceEEEEeccCCccccHhhcccceeEEEECCCceeeeccCCcceEEEEEEEcCccEeccccccc------------
Confidence 54 2455544 33457889999999999874320 357899999996655442
Q ss_pred CCCcccccCCCCCCCCCCCCCCccccCC-eEEEEeCCCceEEEEEEEEecccccccccCccceeeeccccceecccccch
Q 016812 208 KPRTYTSFSSSQDLLPEFSNNPIRPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVED 286 (382)
Q Consensus 208 ~~~~~~~f~~~q~~~~~f~~~~i~~v~~-IlIakL~pGQeI~le~~a~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~ 286 (382)
.+.++.+... +++++|+++|.+..+++|.+|+|++||||+|+++.+|++.|.+.+...+..
T Consensus 153 ------------------~~~~v~~i~~D~~~spv~kvqy~ve~~r~~~~~~~Dhl~~~~~T~gsi~~~~a~~~aa~il~ 214 (317)
T COG0202 153 ------------------DDPPVGPIAVDAPFSPVRKVQYIVEEARVGQGTDKDHLKWEPETNGSIRPEEALAIAAKILI 214 (317)
T ss_pred ------------------cCCCceeeeCCCceeeeeeceEEEEeEEEeccCCceeEEEEEeeccEeehHHHHHHHHHHHH
Confidence 2456888888 999999999999999999999999999999999999999999988888888
Q ss_pred hhHHHHhhcCCCc-eEEeccCC---CCceeEEEecCccccccccceecCcccccceEEEEEcCEEEEEEEecCcCCHHHH
Q 016812 287 EDAEKLVKTCPVN-VFDIEDIG---SGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETL 362 (382)
Q Consensus 287 ~~a~~l~~~~p~g-vi~id~~~---~g~~~~~V~~~r~~t~~rec~r~~~~~~~~V~l~~~~d~fiF~IEStGsl~P~~i 362 (382)
+++..|+++||.. .+..+... ...-...+.+.+.|+.|++|++ .........+.+..++|+|.|++.|..+++++
T Consensus 215 e~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~I~~l~lsvrs~ncLk-~~~i~~i~~L~~~~e~~l~~v~n~G~ksleEi 293 (317)
T COG0202 215 EHLEVFVELCPKAVEIEEEKPEFPILLVLEAPIDELDLSVRSYNCLK-REGIETIGELVQRTEEELLKVENLGKKSLEEI 293 (317)
T ss_pred HHHHHHHhhccccceeecccccccccccccccccccccceeeehhhc-ccCchhhHHHHhcCHHHHhcccccccCCHHHH
Confidence 9999999999975 33333210 0112347899999999999999 65666666788889999999999999999999
Q ss_pred HHHHH
Q 016812 363 FTEAV 367 (382)
Q Consensus 363 ~~eAi 367 (382)
+..+.
T Consensus 294 ~~kl~ 298 (317)
T COG0202 294 KEKLA 298 (317)
T ss_pred HHHHH
Confidence 94433
No 11
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=100.00 E-value=2.8e-34 Score=269.71 Aligned_cols=199 Identities=26% Similarity=0.355 Sum_probs=161.7
Q ss_pred EEEecCceEEEEE----EccChhhHHHHHHHHHhhCCcceEEEEEEeeCcccccccceeeecccCCCc-cCC-------c
Q 016812 80 VIRLTKDDMEFDL----IGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPII-VDP-------R 147 (382)
Q Consensus 80 i~~~~~~~~~F~l----~Gvd~siaNAlRRILlsEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~-~d~-------~ 147 (382)
+.+.++.+++|.+ .|++.++||||||+||+++|++||+.|.|++| +||||+||+. +|. +
T Consensus 3 ~~~~~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~I~~~---------~He~~~Ipgv~Edv~~IllNlk 73 (215)
T cd06928 3 VENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGV---------LHEFSTIPGVREDVLEILLNLK 73 (215)
T ss_pred eccCCCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEEEccc---------ccccccCCCccccHHHHhhccc
Confidence 3456678999999 58999999999999999999999999999996 7999999996 563 4
Q ss_pred eeeeecccCCCCCCceEEEEEEEEeecCCCcceEEcCCceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCC
Q 016812 148 LFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSN 227 (382)
Q Consensus 148 ~~~~~~~~d~~~~~~tv~~~L~v~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~ 227 (382)
.+.++..|. .|++.++|+++++ +.|||+||++ |
T Consensus 74 ~~~~~~~~~----~~~~~~~l~~~gp-----~~V~a~Di~~-~------------------------------------- 106 (215)
T cd06928 74 EIVFKSDSE----DEPQVLRLKVKGP-----GVVTAADIEL-P------------------------------------- 106 (215)
T ss_pred cEEEEecCC----CceEEEEEEEecC-----eEEEhHhcCc-C-------------------------------------
Confidence 444444332 5789999999864 7999999987 2
Q ss_pred CCccccCC-eEEEEeCCCceEEEEEEEEecccccccccCccceeeeccccceecccccchhhHHHHhhcCCCceEEeccC
Q 016812 228 NPIRPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDI 306 (382)
Q Consensus 228 ~~i~~v~~-IlIakL~pGQeI~le~~a~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~a~~l~~~~p~gvi~id~~ 306 (382)
..++++|| ++||+|++||+|+|+|++.+|+|+.+|+|... ...+.|.|.+|+.
T Consensus 107 ~~i~ivnp~~~IatL~~~~~l~ie~~i~~G~Gy~~~~~~~~--------------------------~~~~~~~~~iDa~ 160 (215)
T cd06928 107 SGVEIVNPDQYIATLTEDASLEMELRIEKGRGYVPAEENKS--------------------------EEKPIGFIPIDAI 160 (215)
T ss_pred CCcEEeCCCcEEEEECCCCEEEEEEEEECcCcceecccccc--------------------------ccCCCceEEeCCC
Confidence 23789999 99999999999999999999999999998630 1135688999876
Q ss_pred CCCceeEEEecCccccccccceecCcccccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHH
Q 016812 307 GSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCER 376 (382)
Q Consensus 307 ~~g~~~~~V~~~r~~t~~rec~r~~~~~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~ 376 (382)
++ +.+++.|..|-.+ +..+.+.|+++|+|||+|+++|++++.+|+++|.++++.
T Consensus 161 f~--------PV~~vny~v~~~~--------~~~~~~~e~L~leI~TnGsi~P~~Al~~A~~il~~~~~~ 214 (215)
T cd06928 161 FS--------PVRKVNYSVESTR--------VGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHFSP 214 (215)
T ss_pred cC--------CeEEEEEEEEEee--------cCCCCCceeEEEEEEECCCCCHHHHHHHHHHHHHHHhhc
Confidence 53 3344444443333 444677899999999999999999999999999998864
No 12
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=100.00 E-value=2e-33 Score=276.67 Aligned_cols=209 Identities=22% Similarity=0.341 Sum_probs=166.6
Q ss_pred hccCCceEEEEEec--CceEEEEEE----ccChhhHHHHHHHHHhhCCcceEEEEEEeeCcccccccceeeecccCCCc-
Q 016812 71 HFCNNFRVEVIRLT--KDDMEFDLI----GIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPII- 143 (382)
Q Consensus 71 ~f~~~~~I~i~~~~--~~~~~F~l~----Gvd~siaNAlRRILlsEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~- 143 (382)
+|.+...+++.+.+ +++++|.+. |++.++||||||+||++||++||+.|.|. .++|||++||+.
T Consensus 2 ~~~~~~~i~~~e~~~~~~~~~F~i~Ple~G~g~tlgNaLRRvLLs~ipg~aI~~VkI~---------gv~hEf~~Ipgv~ 72 (310)
T PRK05182 2 EFLKPQKIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKID---------GVLHEFSTIPGVR 72 (310)
T ss_pred CcccCcEEEEEeccCCCcEEEEEEeccCCCchhHHHHHHHHHHHhcCCeeEEEEEEEc---------ceeeeccccCCcc
Confidence 46676778888876 789999997 99999999999999999999999999994 489999999986
Q ss_pred cCC-------ceeeeecccCCCCCCceEEEEEEEEeecCCCcceEEcCCceecCCCCCCCCCCCCCCCCCCCCCcccccC
Q 016812 144 VDP-------RLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFS 216 (382)
Q Consensus 144 ~d~-------~~~~~~~~~d~~~~~~tv~~~L~v~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~ 216 (382)
+|. +.+.++..| .|++.++|+++++ +.|||+||++ |
T Consensus 73 Edv~eIllNlk~i~~~~~~-----~~~~~~~l~~~gp-----~~VtA~Di~~-~-------------------------- 115 (310)
T PRK05182 73 EDVTEIILNLKGLRLKLHG-----DEPVTLTLSKKGP-----GEVTAGDIET-D-------------------------- 115 (310)
T ss_pred cchhHhhhhhccceeecCC-----CceEEEEEEecCC-----eEEEHHHcCC-C--------------------------
Confidence 552 333343332 2788999999864 7999999987 2
Q ss_pred CCCCCCCCCCCCCccccCC-eEEEEeCCCceEEEEEEEEecccccccccCccceeeeccccceecccccchhhHHHHhhc
Q 016812 217 SSQDLLPEFSNNPIRPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKT 295 (382)
Q Consensus 217 ~~q~~~~~f~~~~i~~v~~-IlIakL~pGQeI~le~~a~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~a~~l~~~ 295 (382)
..++++|| ++||+|++||.|+|+|+|.+|+|+.+|+-.-- .
T Consensus 116 -----------~~v~ivn~d~~IatL~~~~~l~ie~~~~kG~Gy~~~~~~~~---------------------------~ 157 (310)
T PRK05182 116 -----------GDVEIVNPDLVIATLNEGAKLEMELTVERGRGYVPAEENKE---------------------------D 157 (310)
T ss_pred -----------CCcEEeCCCeEEEEECCCCEEEEEEEEECcCCCcccccccc---------------------------c
Confidence 23789999 99999999999999999999999987653210 1
Q ss_pred CCCceEEeccCCCCceeEEEecCccccccccceecCcccccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHH
Q 016812 296 CPVNVFDIEDIGSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCE 375 (382)
Q Consensus 296 ~p~gvi~id~~~~g~~~~~V~~~r~~t~~rec~r~~~~~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~ 375 (382)
.+.|.|.+|+.+ .+.+++.|+.+-.| +....+.|+++|+|||+|+++|.+++.+|+++|++++.
T Consensus 158 ~~~g~i~iDa~f--------~PV~~vny~ve~~~--------~~~~~~~e~L~leI~TnGsi~P~eAl~~A~~iL~~~l~ 221 (310)
T PRK05182 158 APIGRIPVDAIF--------SPVKKVNYTVENTR--------VGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLS 221 (310)
T ss_pred CCcccEEecCCc--------CCccceEEEecccc--------cCCCCcceEEEEEEEECCCCCHHHHHHHHHHHHHHHHH
Confidence 245788887654 34444555544333 34445678999999999999999999999999999999
Q ss_pred HHHH
Q 016812 376 RVIT 379 (382)
Q Consensus 376 ~~~~ 379 (382)
.|.+
T Consensus 222 ~f~~ 225 (310)
T PRK05182 222 VFVD 225 (310)
T ss_pred HHhC
Confidence 8864
No 13
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=99.97 E-value=8.1e-31 Score=256.96 Aligned_cols=194 Identities=26% Similarity=0.352 Sum_probs=155.8
Q ss_pred EEEEEE----ccChhhHHHHHHHHHhhCCcceEEEEEEeeCcccccccceeeecccCCCc-cCC-------ceeeeeccc
Q 016812 88 MEFDLI----GIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPII-VDP-------RLFEYMSEN 155 (382)
Q Consensus 88 ~~F~l~----Gvd~siaNAlRRILlsEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~-~d~-------~~~~~~~~~ 155 (382)
.+|.+. |++.++||||||+||+++|++||..|.|++ ++|++++||+. +|. +.+.++..+
T Consensus 2 ~~f~i~Ple~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~g---------v~HEf~~I~GV~Edv~eIllNlK~i~~~~~~ 72 (297)
T TIGR02027 2 GKFVLEPLERGFGITLGNALRRVLLSSIPGAAITAVKIDG---------VLHEFSTIEGVKEDVTEIILNLKQLVVKSEG 72 (297)
T ss_pred cEEEEecCCCCchhHHHHHHHHHHHhcCCceEEEEEEEcc---------eecccccCCCccccHHHHHhhhhceEEeccC
Confidence 567777 999999999999999999999999999987 89999999986 563 333443333
Q ss_pred CCCCCCceEEEEEEEEeecCCCcceEEcCCceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccccCC
Q 016812 156 DTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLD 235 (382)
Q Consensus 156 d~~~~~~tv~~~L~v~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~i~~v~~ 235 (382)
+ +...++|+++++ +.|||+||+|.|. .+.++||
T Consensus 73 ~-----~~~~~~l~~~gp-----~~VtA~Di~~~p~-------------------------------------~ieivnp 105 (297)
T TIGR02027 73 D-----GERTMTLSKKGP-----GVVTAGDIKAPPG-------------------------------------DVEIVNP 105 (297)
T ss_pred C-----CcEEEEEEEeCC-----EEEEhhhcccCCC-------------------------------------CcEEeCC
Confidence 2 223788888864 8999999997442 3789999
Q ss_pred -eEEEEeCCCceEEEEEEEEecccccccccCccceeeeccccceecccccchhhHHHHhhcCCCceEEeccCCCCceeEE
Q 016812 236 -ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRAT 314 (382)
Q Consensus 236 -IlIakL~pGQeI~le~~a~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~a~~l~~~~p~gvi~id~~~~g~~~~~ 314 (382)
++||+|.+||.|+|++++.+|+|+.+|+-.- ...|+.|.|.+|+.+
T Consensus 106 d~~IatL~~~~~L~iel~i~~G~Gy~~~~~~~--------------------------~~~~~~~~i~iDa~F------- 152 (297)
T TIGR02027 106 DLVIATLTEPADLEIELRVERGRGYVPAEENR--------------------------EEDRPVGVIAVDAIF------- 152 (297)
T ss_pred CeEEEEECCCCEEEEEEEEEcccccCcccccc--------------------------cccCccccccccccc-------
Confidence 9999999999999999999999997654310 013566888888654
Q ss_pred EecCccccccccceecCcccccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHH
Q 016812 315 VAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVIT 379 (382)
Q Consensus 315 V~~~r~~t~~rec~r~~~~~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~ 379 (382)
.+.+++.|+.+..| +....+.|+|+|+|||+|+++|.+++.+|+++|.+++..|.+
T Consensus 153 -sPV~~Vny~ve~~r--------v~~~~~~d~li~eIeT~Gsi~P~~al~~A~~iL~~~~~~~~~ 208 (297)
T TIGR02027 153 -SPVLKVNYEVENTR--------VGQRTDYDKLILEIETNGSITPKDAIAEAAKILIEHLEPFVN 208 (297)
T ss_pred -cCeEEEEEEEeeee--------ccCCccccEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 44566667766665 555567899999999999999999999999999999998864
No 14
>PF01000 RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert domain; InterPro: IPR011262 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 polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha (RpoA) subunit homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. The dimerisation domains differ between the different subunit families. In eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain is comprised of a central insert domain, which interrupts an Rpb11-like domain (IPR009025 from INTERPRO), dividing it into two halves []. In eukaryotic Rpb11 and archaeal L subunits, the insert domain is lacking, leaving the Rpb11-like domain intact and contiguous.; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_O 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3GTK_C 1TWH_C 3HOV_C 3S17_C ....
Probab=99.94 E-value=1.3e-27 Score=202.57 Aligned_cols=105 Identities=36% Similarity=0.509 Sum_probs=87.8
Q ss_pred EEEeeCcccccccceeeecccCCCcc-CC-c-eeeeecc---cCCCCCCceEEEEEEEEeecCCCcceEEcCCceecCCC
Q 016812 119 VLIANNTSVIQDEVLAHRLGLIPIIV-DP-R-LFEYMSE---NDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNG 192 (382)
Q Consensus 119 V~I~~NTSvi~DEvLAHRLGLIPl~~-d~-~-~~~~~~~---~d~~~~~~tv~~~L~v~c~~~~~~~~VyS~DL~~~p~g 192 (382)
|+|++|||+++||++|||||+||+.. |. + ..+++.. +...++.|+++++|+++|+ +.|||+||+|.|
T Consensus 1 v~i~~n~s~~~dE~v~He~~~Ipgv~Edv~~iilnlk~i~~~~~~~~~~~~~~~~L~~~g~-----~~V~a~di~~~~-- 73 (112)
T PF01000_consen 1 VYIYENTSVLPDEGVAHEFGLIPGVSEDVLEIILNLKKIVIDCEEGCDDCSVTFSLKVKGP-----GEVTAGDIKLEP-- 73 (112)
T ss_dssp EEEEEETSSS-HHHHHCHHHBSTCBSSCHHHHHHHHHTT-ESSSSSTTTSEEEEEEEEESS-----SCEEGGGSEESB--
T ss_pred CEEEECCCeeccceeEeccccCCccccchhhhhhcchhhccccccCCCCceEEEEEEecCC-----CccccceeEecC--
Confidence 79999999999999999999999985 42 2 1233322 2456788999999999986 679999999843
Q ss_pred CCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCccccCC-eEEEEeCCCceEEEEEEEEecccccccccC
Q 016812 193 SELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWS 265 (382)
Q Consensus 193 ~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~~~f~~~~i~~v~~-IlIakL~pGQeI~le~~a~KGiGk~HAKws 265 (382)
..++++|| ++||+|++||+|+|+|+|.+|+||+|||||
T Consensus 74 -----------------------------------~~i~ivn~d~~I~tl~~~~~l~~e~~i~~G~Gy~~ak~~ 112 (112)
T PF01000_consen 74 -----------------------------------SGIEIVNPDIYIATLSEGQKLEMELYIEKGRGYVHAKWS 112 (112)
T ss_dssp -----------------------------------TTEEESSTTSEEEEEESSTEEEEEEEEEEEESEECCTS-
T ss_pred -----------------------------------CceEEecCCeEEEEECCCCEEEEEEEEECCCcccccccC
Confidence 24889999 999999999999999999999999999997
No 15
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=99.92 E-value=5.5e-24 Score=210.98 Aligned_cols=202 Identities=18% Similarity=0.169 Sum_probs=155.6
Q ss_pred CceEEEEEecCceEEEEEE----ccChhhHHHHHHHHHhhCCcceEEEEEEeeCcccccccceeeecccCCCc-cCC---
Q 016812 75 NFRVEVIRLTKDDMEFDLI----GIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPII-VDP--- 146 (382)
Q Consensus 75 ~~~I~i~~~~~~~~~F~l~----Gvd~siaNAlRRILlsEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~-~d~--- 146 (382)
....++.+.++.+.+|.+. |++.+|||||||+||+++|++||..|.|.+ +.|.+..||+. +|.
T Consensus 9 ~ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g---------v~hEfs~i~GV~Edv~eI 79 (327)
T CHL00013 9 CVESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG---------VPHEYSTIPGIRESVLEI 79 (327)
T ss_pred ceeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC---------ccccccCCCCcccCHHHH
Confidence 3566777888899999999 677799999999999999999999999976 56999999985 774
Q ss_pred ----ceeeeecccCCCCCCceEEEEEEEEeecCCCcceEEcCCceecCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCC
Q 016812 147 ----RLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLL 222 (382)
Q Consensus 147 ----~~~~~~~~~d~~~~~~tv~~~L~v~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~~~~~~f~~~q~~~ 222 (382)
+.+.++... .....+.|+++++ +.|||+||++ |
T Consensus 80 ilNLK~I~~k~~~-----~~~~~~~l~~~Gp-----~~vtA~Di~~-p-------------------------------- 116 (327)
T CHL00013 80 LLNLKEIVLKSNL-----YGPQKASICVQGP-----KYVTAQDIIL-P-------------------------------- 116 (327)
T ss_pred HHhhhcCeEEccC-----CCcEEEEEEEeCC-----eEEEeeeecc-C--------------------------------
Confidence 223333222 1356788888763 8999999986 2
Q ss_pred CCCCCCCccccCC-eEEEEeCCCceEEEEEEEEecccccccccCccceeeeccccceecccccchhhHHHHhhcCCCceE
Q 016812 223 PEFSNNPIRPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVF 301 (382)
Q Consensus 223 ~~f~~~~i~~v~~-IlIakL~pGQeI~le~~a~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~a~~l~~~~p~gvi 301 (382)
..++++|| .+||+|..|+.|+|++++.+|+|+..|.-.- . ..|+|
T Consensus 117 -----~~ieivnpd~~Iatl~~~~~l~~el~ie~G~GY~~~~~~~----------------------------~-~~g~i 162 (327)
T CHL00013 117 -----PSVEIVDPTQHIATITEPIDLEIELKIEKGRGYRLKTPKN----------------------------F-QDGSF 162 (327)
T ss_pred -----CCeEEeCCCeEEEEeCCCCEEEEEEEEECccCceeccccc----------------------------c-CCCcE
Confidence 23889999 9999999999999999999999986443210 0 23788
Q ss_pred EeccCCCCceeEEEecCccccccccceecCcccccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHH
Q 016812 302 DIEDIGSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVKILEDKCERVIT 379 (382)
Q Consensus 302 ~id~~~~g~~~~~V~~~r~~t~~rec~r~~~~~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~ 379 (382)
.+|+.++ +.+++.|..+-.| +.... .|+++|+|||+|++.|.+++.+|+++|.+.+..|.+
T Consensus 163 ~iDa~Fs--------PV~kVny~Ve~~~--------~~~~~-~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~~ 223 (327)
T CHL00013 163 PIDAVFM--------PVRNVNYSIHSYG--------NGNEK-QEILFLEIWTNGSITPKEALHEASRNLIDLFIPFLH 223 (327)
T ss_pred EeCCCCC--------CeeEEEEEEEEcc--------cCCcc-cceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 8887653 2333333333222 22223 799999999999999999999999999999988754
No 16
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 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 polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=99.35 E-value=1.9e-12 Score=100.25 Aligned_cols=31 Identities=48% Similarity=0.792 Sum_probs=30.2
Q ss_pred EEEEEEccChhhHHHHHHHHHhhCCcceEEE
Q 016812 88 MEFDLIGIDAAIANAFRRILIAELPTMAIEK 118 (382)
Q Consensus 88 ~~F~l~Gvd~siaNAlRRILlsEVPT~AIe~ 118 (382)
++|.+.|.|.++||||||+|+++||++||+.
T Consensus 1 i~~~~~g~~~tl~N~LRr~ll~~vp~~ai~~ 31 (66)
T PF01193_consen 1 IEFLLKGEDHTLGNALRRILLSEVPGVAIDG 31 (66)
T ss_dssp EEEEEESHHHHHHHHHHHHHHSSSEEEEEEE
T ss_pred CEeEEcCCchHHHHHHHHHHHhcCCCceEEe
Confidence 6899999999999999999999999999999
No 17
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=98.98 E-value=3.6e-09 Score=105.29 Aligned_cols=161 Identities=19% Similarity=0.189 Sum_probs=113.6
Q ss_pred eeecccCCCc-cCC--ceeeeecccCCC-CCCceEEEEEEEEeecCCCcceEEcCCceecCCCCCCCCCCCCCCCCCCCC
Q 016812 134 AHRLGLIPII-VDP--RLFEYMSENDTS-NEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKP 209 (382)
Q Consensus 134 AHRLGLIPl~-~d~--~~~~~~~~~d~~-~~~~tv~~~L~v~c~~~~~~~~VyS~DL~~~p~g~q~~~~~~~~~~~~~~~ 209 (382)
.|.+..||.. .|. -.++++.-.-.. .+.. +++++...|. +.||++|+...
T Consensus 58 ~hef~s~~gv~Edvl~~~LnLk~L~~~~~~~~~-~~~~~~~~g~-----g~v~a~d~~~~-------------------- 111 (317)
T COG0202 58 LHEFDSIEGVQEDVLAHRLNLKPLAVKLDGDEE-VTLELDKEGP-----GEVTASDITVP-------------------- 111 (317)
T ss_pred ccccccCcCcHHHHHHHHhcCceeeeecccccc-eEEEEeccCC-----ccccHhhcccc--------------------
Confidence 5888888664 442 122333211000 0011 6788888764 89999999851
Q ss_pred CcccccCCCCCCCCCCCCCCccccCC-eEEEEeCCCceEEEEEEEEecccccccccCccceeeeccccceecccccchhh
Q 016812 210 RTYTSFSSSQDLLPEFSNNPIRPMLD-ITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDED 288 (382)
Q Consensus 210 ~~~~~f~~~q~~~~~f~~~~i~~v~~-IlIakL~pGQeI~le~~a~KGiGk~HAKwsPVata~Yr~~P~i~i~~~i~~~~ 288 (382)
..+..++| ..||+|..|.+|.|++++..|.|+..|--+- ..
T Consensus 112 ------------------~~lEv~np~~~ia~~~~~~~l~~~~~V~~G~gyv~~~~~~------~~-------------- 153 (317)
T COG0202 112 ------------------LDLEVVNPDHVIATLTEDAKLEMELRVYSGDGYVPAEGNR------ED-------------- 153 (317)
T ss_pred ------------------eeEEEECCCceeeeccCCcceEEEEEEEcCccEecccccc------cc--------------
Confidence 23789999 9999999999999999999999976432110 00
Q ss_pred HHHHhhcCCCceEEeccCCCCceeEEEecCccccccccceecCcccccceEEEEEcCEEEEEEEecCcCCHHHHHHHHHH
Q 016812 289 AEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFIFTIESTGALSPETLFTEAVK 368 (382)
Q Consensus 289 a~~l~~~~p~gvi~id~~~~g~~~~~V~~~r~~t~~rec~r~~~~~~~~V~l~~~~d~fiF~IEStGsl~P~~i~~eAik 368 (382)
-.+.+.+..|... ...+++.+-.+..| +.++..+||..|.++|+|++.|++++..|.+
T Consensus 154 ------~~~v~~i~~D~~~--------spv~kvqy~ve~~r--------~~~~~~~Dhl~~~~~T~gsi~~~~a~~~aa~ 211 (317)
T COG0202 154 ------DPPVGPIAVDAPF--------SPVRKVQYIVEEAR--------VGQGTDKDHLKWEPETNGSIRPEEALAIAAK 211 (317)
T ss_pred ------CCCceeeeCCCce--------eeeeeceEEEEeEE--------EeccCCceeEEEEEeeccEeehHHHHHHHHH
Confidence 1244666666533 33444444444444 8899999999999999999999999999999
Q ss_pred HHHHHHHHHHHh
Q 016812 369 ILEDKCERVITE 380 (382)
Q Consensus 369 iL~~K~~~~~~~ 380 (382)
+|.++|..|.+.
T Consensus 212 il~e~~~~~~~~ 223 (317)
T COG0202 212 ILIEHLEVFVEL 223 (317)
T ss_pred HHHHHHHHHHhh
Confidence 999999998763
No 18
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=98.93 E-value=5.6e-09 Score=85.10 Aligned_cols=35 Identities=40% Similarity=0.687 Sum_probs=32.5
Q ss_pred EcCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHH
Q 016812 343 VKDHFIFTIESTGALSPETLFTEAVKILEDKCERV 377 (382)
Q Consensus 343 ~~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~ 377 (382)
+.|+|+|+|||+|+++|.+++.+|+++|+++|+.|
T Consensus 52 ~~d~~~~~VeT~Gs~~P~~al~~Ai~~L~~~~~~~ 86 (86)
T cd00460 52 DEDKFILRIETVGSIPPEEALRRAVEILRKKLEHL 86 (86)
T ss_pred CCCeEEEEEEECCCCCHHHHHHHHHHHHHHHHhhC
Confidence 36899999999999999999999999999999764
No 19
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=94.64 E-value=0.059 Score=44.07 Aligned_cols=38 Identities=18% Similarity=0.472 Sum_probs=33.1
Q ss_pred ceEEEEEecCceEEEEEEccChhhHHHHHHHHHhhCCcc
Q 016812 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTM 114 (382)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNAlRRILlsEVPT~ 114 (382)
|+|+|.+.+++.++|.+.|=|.+++|+||-.|+. -|.+
T Consensus 1 m~ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~-~~~V 38 (85)
T PRK01146 1 MEIKVLEKEDNELELEIEGEDHTLMNLLKEELLE-DPGV 38 (85)
T ss_pred CeEEEEecCCCEEEEEEeCCCchHHHHHHHHHhc-CCCe
Confidence 4789999999999999999999999999999885 3443
No 20
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=93.19 E-value=0.29 Score=39.17 Aligned_cols=38 Identities=21% Similarity=0.455 Sum_probs=34.2
Q ss_pred cCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHHhh
Q 016812 344 KDHFIFTIESTGALSPETLFTEAVKILEDKCERVITEL 381 (382)
Q Consensus 344 ~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~~L 381 (382)
.++..|.|.|+|..+|.++|.+|++-|.+.|+.|.+++
T Consensus 40 ~~~i~l~Iqt~~~~~p~~~l~~a~~~l~~~~~~l~~~F 77 (77)
T PF13656_consen 40 ENKINLRIQTKGGITPIEALKKALEDLIKICEELKKEF 77 (77)
T ss_dssp SSEEEEEEEESTTS-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence 57889999999999999999999999999999998753
No 21
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=92.74 E-value=0.16 Score=41.30 Aligned_cols=33 Identities=21% Similarity=0.497 Sum_probs=27.3
Q ss_pred EEEEEecCceEEEEEEccChhhHHHHHHHHHhh
Q 016812 78 VEVIRLTKDDMEFDLIGIDAAIANAFRRILIAE 110 (382)
Q Consensus 78 I~i~~~~~~~~~F~l~Gvd~siaNAlRRILlsE 110 (382)
|+|++.+++.++|.+.|=|.+++|+||-.|+..
T Consensus 1 ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~~ 33 (83)
T cd06927 1 LKVIEKEDNELELEIEGEDHTLLNLLKEELLRD 33 (83)
T ss_pred CeEEEcCCCEEEEEEeCCCchHHHHHHHHHhcC
Confidence 467788888888888888888888888877764
No 22
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=91.72 E-value=0.24 Score=40.32 Aligned_cols=33 Identities=18% Similarity=0.393 Sum_probs=27.1
Q ss_pred EEEEEecCceEEEEEEccChhhHHHHHHHHHhh
Q 016812 78 VEVIRLTKDDMEFDLIGIDAAIANAFRRILIAE 110 (382)
Q Consensus 78 I~i~~~~~~~~~F~l~Gvd~siaNAlRRILlsE 110 (382)
|+|++.+++.++|.+.|=|.+++|+||-.|+..
T Consensus 1 ~kii~~~~n~~~~~i~~EdHTLgNlLr~~L~~~ 33 (83)
T cd07027 1 LRIISKEKNSVTVEMENEDHTLGNLLREELLKD 33 (83)
T ss_pred CeeEecCCCEEEEEEeCCCchHHHHHHHHHhcC
Confidence 467788888899999998999999998777654
No 23
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=90.21 E-value=0.67 Score=37.89 Aligned_cols=37 Identities=14% Similarity=0.431 Sum_probs=33.8
Q ss_pred cCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHHh
Q 016812 344 KDHFIFTIESTGALSPETLFTEAVKILEDKCERVITE 380 (382)
Q Consensus 344 ~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~~ 380 (382)
.+...|.|.|+|..+|.+++.+|++-|.+.|+.+++.
T Consensus 48 ~~~~~lriqT~~~~~p~~al~~a~~~l~~~~~~~~~~ 84 (85)
T cd07029 48 ENKINLRIQTKGGEPAVDVLKKGLEDLEQICDHILST 84 (85)
T ss_pred CCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 3577899999999999999999999999999999875
No 24
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=89.92 E-value=0.55 Score=39.66 Aligned_cols=35 Identities=20% Similarity=0.499 Sum_probs=31.8
Q ss_pred CceEEEEEecCceEEEEEEccChhhHHHHHHHHHh
Q 016812 75 NFRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIA 109 (382)
Q Consensus 75 ~~~I~i~~~~~~~~~F~l~Gvd~siaNAlRRILls 109 (382)
.+++++.+.++++++|.++|-|.+++|.||-.|+.
T Consensus 4 ~~~l~ii~~~~n~~~i~i~gEdHTL~NlL~~~L~~ 38 (99)
T COG1761 4 EMELRIIKKDDNSLELEIEGEDHTLGNLLREELLK 38 (99)
T ss_pred ceEEEEeccCCCEEEEEEecCCchHHHHHHHHHhC
Confidence 46788889999999999999999999999999886
No 25
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=89.22 E-value=0.76 Score=37.39 Aligned_cols=34 Identities=29% Similarity=0.530 Sum_probs=32.0
Q ss_pred CEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHH
Q 016812 345 DHFIFTIESTGALSPETLFTEAVKILEDKCERVI 378 (382)
Q Consensus 345 d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~ 378 (382)
++..+.|.|+|..+|.+++.+|++-|.+.|+.|+
T Consensus 49 ~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~~~ 82 (83)
T cd06927 49 SNPVLKIKTDGGVDPLEALKEAAKRLIDLCEEFL 82 (83)
T ss_pred CccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 7888999999999999999999999999999886
No 26
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=88.92 E-value=0.8 Score=37.45 Aligned_cols=36 Identities=22% Similarity=0.471 Sum_probs=32.8
Q ss_pred cCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHH
Q 016812 344 KDHFIFTIESTGALSPETLFTEAVKILEDKCERVIT 379 (382)
Q Consensus 344 ~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~ 379 (382)
.++..|.|.|+|..+|.+++.+|++-|.+.|+.|++
T Consensus 50 ~~~~~lrIqt~~~~~p~~al~~a~~~L~~~~~~~~~ 85 (85)
T PRK01146 50 ISNPVLKIKTDGGIDPLEALKEAAKRIIDLCDEFLD 85 (85)
T ss_pred CCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 467889999999999999999999999999998863
No 27
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=88.68 E-value=1.1 Score=37.29 Aligned_cols=37 Identities=16% Similarity=0.330 Sum_probs=33.9
Q ss_pred cCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHHh
Q 016812 344 KDHFIFTIESTGALSPETLFTEAVKILEDKCERVITE 380 (382)
Q Consensus 344 ~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~~ 380 (382)
.+...+.|.|.|+.+|.++|.+|++-|.+.|+.|.+.
T Consensus 56 ~~~~~l~i~t~~~~~p~~al~~a~~~l~~~~~~~~~~ 92 (93)
T cd06926 56 EHKIELRIQTDGSITPKEALKNAITDLISELSLLKEE 92 (93)
T ss_pred CCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 3678899999999999999999999999999999875
No 28
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=87.57 E-value=1 Score=36.70 Aligned_cols=35 Identities=20% Similarity=0.310 Sum_probs=32.0
Q ss_pred cCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHH
Q 016812 344 KDHFIFTIESTGALSPETLFTEAVKILEDKCERVI 378 (382)
Q Consensus 344 ~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~ 378 (382)
.+...|.|.|+|..+|.+++.+|++-|.+.|+.|+
T Consensus 48 ~~~~~lrI~T~~~~~P~~al~~a~~~l~~~~~~l~ 82 (83)
T cd07027 48 IDKIQIRIQTKSGIKPKDALKRAVNKLSKLYEHLG 82 (83)
T ss_pred CCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 36788999999999999999999999999999875
No 29
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=82.18 E-value=2.1 Score=35.57 Aligned_cols=37 Identities=16% Similarity=0.182 Sum_probs=29.4
Q ss_pred ceEEEEEecCceEEEEEEccChhhHHHHHHHHHhhCCc
Q 016812 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPT 113 (382)
Q Consensus 76 ~~I~i~~~~~~~~~F~l~Gvd~siaNAlRRILlsEVPT 113 (382)
..++.....++.++|.+.|=|.++||+||-.|+. -|.
T Consensus 7 v~~~~d~k~~n~~~~~i~~EdHTLgNlLr~~L~~-~~~ 43 (93)
T cd06926 7 ITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLK-DPN 43 (93)
T ss_pred eEEeecCCCCcEEEEEEeCCCchHHHHHHHHHhc-CCC
Confidence 3344444577899999999999999999999887 454
No 30
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=79.51 E-value=4.1 Score=34.44 Aligned_cols=36 Identities=17% Similarity=0.336 Sum_probs=33.8
Q ss_pred cCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHH
Q 016812 344 KDHFIFTIESTGALSPETLFTEAVKILEDKCERVIT 379 (382)
Q Consensus 344 ~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~ 379 (382)
.+++.+.|-+.|.+.|.+++.+|++-+.+.|..|.+
T Consensus 54 ~~~~~i~Ikt~~~~dp~~aL~~A~~~i~~~~~~l~~ 89 (99)
T COG1761 54 IDNPKIRIKTKGGVDPKEALKRAARKILKDLEELLD 89 (99)
T ss_pred CCCceEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 468899999999999999999999999999999987
No 31
>PRK15449 ferredoxin-like protein FixX; Provisional
Probab=74.21 E-value=3.1 Score=34.92 Aligned_cols=50 Identities=30% Similarity=0.583 Sum_probs=36.8
Q ss_pred ccceecccccchhhHHHHhhcCCCceEEeccCCCCceeEEEecCcccccccccee
Q 016812 275 LPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR 329 (382)
Q Consensus 275 ~P~i~i~~~i~~~~a~~l~~~~p~gvi~id~~~~g~~~~~V~~~r~~t~~rec~r 329 (382)
.|+|.|..+......+.+.+.||.|+|..++.+ .++.+...|.-|.-|..
T Consensus 22 ~~HI~i~~~~~~~~~k~C~~aCPagA~~~~e~G-----~V~vd~e~CigCg~C~~ 71 (95)
T PRK15449 22 HPHIVVKADADKQALELLVKACPAGLYKKQDDG-----SVRFDYAGCLECGTCRI 71 (95)
T ss_pred CCcEEEcCCCCchhhhHHHHHCCHhhcEeCCCC-----CEEEcCCCCCcchhhhh
Confidence 478888766544566788999999999875322 34457888999988876
No 32
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a 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. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=71.31 E-value=5 Score=32.77 Aligned_cols=27 Identities=19% Similarity=0.388 Sum_probs=24.6
Q ss_pred ecCceEEEEEEccChhhHHHHHHHHHh
Q 016812 83 LTKDDMEFDLIGIDAAIANAFRRILIA 109 (382)
Q Consensus 83 ~~~~~~~F~l~Gvd~siaNAlRRILls 109 (382)
..++.++|.+.|=|.++||+||-.|+.
T Consensus 6 ~~~n~~~~~i~~EdHTLgNlLr~~L~~ 32 (85)
T cd07029 6 TDESCATFVFYGEDHTLGNSLRYVIMK 32 (85)
T ss_pred CCCCeEEEEEeCCCcchHHHHHHHHhh
Confidence 467799999999999999999999887
No 33
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=64.84 E-value=3.7 Score=32.86 Aligned_cols=30 Identities=23% Similarity=0.581 Sum_probs=22.7
Q ss_pred ceEEEEEEccChhhHHHHHHHHHhhCCcceE
Q 016812 86 DDMEFDLIGIDAAIANAFRRILIAELPTMAI 116 (382)
Q Consensus 86 ~~~~F~l~Gvd~siaNAlRRILlsEVPT~AI 116 (382)
+.++|.+.|=|.++||+||-.|+.. |.+.+
T Consensus 1 n~~~f~i~~EDHTlgNlLr~~L~~~-p~V~f 30 (77)
T PF13656_consen 1 NEITFTIYGEDHTLGNLLRYELLKD-PDVEF 30 (77)
T ss_dssp TEEEEEEES--HHHHHHHHHCCTTS-TTEEE
T ss_pred CeEEEEEeCCCccHHHHHHHHHhhC-CCeEE
Confidence 4689999999999999999988775 54443
No 34
>KOG3438 consensus DNA-directed RNA polymerase, subunit L [Transcription]
Probab=44.97 E-value=22 Score=30.31 Aligned_cols=26 Identities=23% Similarity=0.399 Sum_probs=20.1
Q ss_pred cCceEEEEEEccChhhHHHHHHHHHh
Q 016812 84 TKDDMEFDLIGIDAAIANAFRRILIA 109 (382)
Q Consensus 84 ~~~~~~F~l~Gvd~siaNAlRRILls 109 (382)
+.....|.|..=|.+||||||=+++-
T Consensus 14 d~~~~Tf~~~eEDHTlgNalR~vI~k 39 (105)
T KOG3438|consen 14 DLSSATFQLREEDHTLGNALRYVIMK 39 (105)
T ss_pred CCCceEEEEEecCcchhHHHHHHHhc
Confidence 34567888888888888888887765
No 35
>COG2440 FixX Ferredoxin-like protein [Energy production and conversion]
Probab=44.50 E-value=19 Score=30.48 Aligned_cols=49 Identities=29% Similarity=0.575 Sum_probs=29.2
Q ss_pred ccceecccccchhhHH--HHhhcCCCceEEeccCCCCceeEEEecCccccccc
Q 016812 275 LPEIVLLEDVEDEDAE--KLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCR 325 (382)
Q Consensus 275 ~P~i~i~~~i~~~~a~--~l~~~~p~gvi~id~~~~g~~~~~V~~~r~~t~~r 325 (382)
.|+|.+.++-.-..++ .|...||.|++...+. |+..+....-.-|-.||
T Consensus 24 ~pHI~v~~~~~~~~~~~~~l~~aCPA~~Y~~~~~--g~l~~~yegClECGTCR 74 (99)
T COG2440 24 HPHIIVKDPDDCQECEDKPLIKACPAGCYKLIDD--GKLRFDYEGCLECGTCR 74 (99)
T ss_pred CCcEecCCchhhhhccchhhhhcCCHHHeeECCC--CcEEEeecCeeecccee
Confidence 3788887653333444 7889999999988642 23333333333344443
No 36
>KOG3438 consensus DNA-directed RNA polymerase, subunit L [Transcription]
Probab=38.13 E-value=62 Score=27.65 Aligned_cols=36 Identities=14% Similarity=0.296 Sum_probs=32.1
Q ss_pred cCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHH
Q 016812 344 KDHFIFTIESTGALSPETLFTEAVKILEDKCERVIT 379 (382)
Q Consensus 344 ~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~ 379 (382)
.++.-|.|.|.|.++.-++|.+|+.-|.+=|+.+..
T Consensus 55 e~k~niRIQt~~~~~A~evl~kgl~el~~~c~~v~~ 90 (105)
T KOG3438|consen 55 EDKINIRIQTRDGDPAVEVLKKGLEELMQLCDHVRS 90 (105)
T ss_pred hhhheEEEEecCCCcchHHHHHHHHHHHHHHHHHHH
Confidence 577789999999999999999999999999887754
No 37
>KOG4392 consensus RNA polymerase, subunit L [Transcription]
Probab=38.07 E-value=79 Score=27.49 Aligned_cols=38 Identities=18% Similarity=0.306 Sum_probs=33.7
Q ss_pred cCEEEEEEEecCcCCHHHHHHHHHHHHHHHHHHHHHhh
Q 016812 344 KDHFIFTIESTGALSPETLFTEAVKILEDKCERVITEL 381 (382)
Q Consensus 344 ~d~fiF~IEStGsl~P~~i~~eAikiL~~K~~~~~~~L 381 (382)
.-||++-|.|+-..+|.+++..|++-|...+..+...+
T Consensus 68 ~~~~~LRiqtt~d~~p~~al~~a~~~l~~el~~l~~~f 105 (117)
T KOG4392|consen 68 EHKIILRVQTTEDCSPADALTNAITDLIEELSLLENRF 105 (117)
T ss_pred cccEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999999999999988776554
No 38
>PRK06273 ferredoxin; Provisional
Probab=29.71 E-value=79 Score=28.88 Aligned_cols=90 Identities=16% Similarity=0.282 Sum_probs=46.9
Q ss_pred hHHHHhhcCCCceEEeccCCC-----C--ceeEEEecCcccccccccee-cCcccccceEEEEEcCEEEEEEEecCcCCH
Q 016812 288 DAEKLVKTCPVNVFDIEDIGS-----G--KKRATVAQPRACTLCRECLR-CGEEWEKRVSIRRVKDHFIFTIESTGALSP 359 (382)
Q Consensus 288 ~a~~l~~~~p~gvi~id~~~~-----g--~~~~~V~~~r~~t~~rec~r-~~~~~~~~V~l~~~~d~fiF~IEStGsl~P 359 (382)
.+..+...||.++|.++.... + .....+-++.+|+.|..|.. |.. +.+......-| .-.+|+-=.+..
T Consensus 53 gCg~C~~aCP~~AI~~~~~ep~~~~~~~~~~~~~~Id~~kCi~Cg~C~~aCP~---~AI~~~~~~~~-~~~~~~~~~~~~ 128 (165)
T PRK06273 53 GCGGCANVCPTKAIEMIPVEPVKITEGYVKTKIPKIDYEKCVYCLYCHDFCPV---FALFNEISPIH-PRDVGEDIEVDV 128 (165)
T ss_pred ChhHHHHhcCccceeeecccccchhcccccccceecccccCcCCCCcchhCCH---hheecccccCC-hhhhhhHhhccH
Confidence 366788889999988763210 0 01123557788999999988 532 12211100000 022333223455
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q 016812 360 ETLFTEAVKILEDKCERVITEL 381 (382)
Q Consensus 360 ~~i~~eAikiL~~K~~~~~~~L 381 (382)
++++..=.++=.+|++.+.+-|
T Consensus 129 ~~ll~~~~~~~~~~~~~~~~~l 150 (165)
T PRK06273 129 SKLLEKPVEISEEQLSKISQIL 150 (165)
T ss_pred HHHhhCHHHhhHHHHHHHHHHc
Confidence 5666655565555555554433
No 39
>COG4003 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.15 E-value=6.5 Score=32.47 Aligned_cols=41 Identities=17% Similarity=0.283 Sum_probs=28.0
Q ss_pred ccchhhccCCceEEEEEecCce--EEEEEEccChhhHHHHHHH
Q 016812 66 SLQLDHFCNNFRVEVIRLTKDD--MEFDLIGIDAAIANAFRRI 106 (382)
Q Consensus 66 ~~~~~~f~~~~~I~i~~~~~~~--~~F~l~Gvd~siaNAlRRI 106 (382)
.|+.++|++.|.--..++..-. -+.++.|+.+++-.-|||.
T Consensus 2 e~~~~~fkk~fp~l~~eleg~~l~~~~~~~gy~PtV~D~L~rC 44 (98)
T COG4003 2 EYDKEEFKKKFPALAKELEGIRLEPKIDFSGYNPTVIDFLRRC 44 (98)
T ss_pred cccHHHHHHHhHHHHHHhhcccccccCCcCCCCchHHHHHHHh
Confidence 4888888887754444444433 3667788888887777774
No 40
>KOG3307 consensus Molybdopterin converting factor subunit 2 [Coenzyme transport and metabolism]
Probab=27.97 E-value=21 Score=31.55 Aligned_cols=43 Identities=28% Similarity=0.444 Sum_probs=28.3
Q ss_pred EEEEEEccChhhHHHHHHHHH---hhCCcceEEEEEEeeCcccccccceeeecccCCCccC
Q 016812 88 MEFDLIGIDAAIANAFRRILI---AELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVD 145 (382)
Q Consensus 88 ~~F~l~Gvd~siaNAlRRILl---sEVPT~AIe~V~I~~NTSvi~DEvLAHRLGLIPl~~d 145 (382)
+.+.-+-+++---|-||-|.- ++-| |.++- ++||||++|+-+.
T Consensus 50 ~~L~Yeay~pMA~~~lr~IC~~iR~~wp---vkkIA------------vfHRLG~VpvgEs 95 (150)
T KOG3307|consen 50 SNLSYEAYDPMAYKKLRGICAEIRAEWP---VKKIA------------VFHRLGKVPVGES 95 (150)
T ss_pred eeeehhhhcHHHHHHHHHHHHHHHhhCc---hhhhh------------hhhhccCcccCcc
Confidence 344445677777788888763 3444 55543 4699999998643
Done!