Query 020983
Match_columns 319
No_of_seqs 106 out of 1085
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 06:42:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020983.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020983hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd07032 RNAP_I_II_AC40 AC40 su 100.0 1.3E-78 2.7E-83 568.4 25.8 270 11-297 2-289 (291)
2 KOG1522 RNA polymerase II, sub 100.0 2.9E-73 6.3E-78 506.2 19.2 283 6-319 2-285 (285)
3 cd07031 RNAP_II_RPB3 RPB3 subu 100.0 5.4E-72 1.2E-76 520.6 22.1 253 10-297 1-259 (265)
4 KOG1521 RNA polymerase I and I 100.0 2.2E-71 4.7E-76 506.1 21.2 281 5-297 41-334 (338)
5 PRK00783 DNA-directed RNA poly 100.0 4.8E-66 1E-70 481.2 23.0 256 10-297 1-256 (263)
6 cd07030 RNAP_D D subunit of Ar 100.0 1.4E-63 2.9E-68 463.8 23.0 256 10-297 1-256 (259)
7 cd07028 RNAP_RPB3_like RPB3 su 100.0 2.9E-60 6.2E-65 428.2 18.6 203 10-297 1-210 (212)
8 smart00662 RPOLD RNA polymeras 100.0 2.5E-55 5.4E-60 400.2 19.2 223 21-296 1-224 (224)
9 PRK14979 DNA-directed RNA poly 100.0 9.4E-51 2E-55 360.4 18.3 180 10-297 4-183 (195)
10 cd06928 RNAP_alpha_NTD N-termi 100.0 2.2E-38 4.9E-43 286.9 17.3 202 14-296 3-215 (215)
11 PRK05182 DNA-directed RNA poly 100.0 2.2E-37 4.7E-42 294.0 18.7 217 5-299 2-227 (310)
12 COG0202 RpoA DNA-directed RNA 100.0 2.1E-37 4.7E-42 294.1 12.6 259 12-286 7-298 (317)
13 TIGR02027 rpoA DNA-directed RN 100.0 2.4E-34 5.1E-39 271.9 15.0 203 21-299 1-210 (297)
14 CHL00013 rpoA RNA polymerase a 100.0 8.6E-29 1.9E-33 236.1 17.2 207 10-297 10-222 (327)
15 PF01000 RNA_pol_A_bac: RNA po 100.0 1.9E-29 4.2E-34 206.4 8.5 111 53-181 1-112 (112)
16 PF01193 RNA_pol_L: RNA polyme 99.5 9E-14 2E-18 103.3 6.6 31 22-52 1-31 (66)
17 COG0202 RpoA DNA-directed RNA 99.2 1.6E-11 3.5E-16 117.3 7.7 162 68-297 58-221 (317)
18 cd00460 RNAP_RPB11_RPB3 RPB11 99.0 1.1E-09 2.4E-14 85.6 8.8 35 262-296 52-86 (86)
19 PRK01146 DNA-directed RNA poly 95.9 0.013 2.9E-07 45.7 4.4 40 10-50 1-40 (85)
20 cd06927 RNAP_L L subunit of Ar 94.9 0.035 7.6E-07 43.1 3.9 38 12-50 1-38 (83)
21 cd07027 RNAP_RPB11_like RPB11 94.2 0.06 1.3E-06 41.8 3.7 33 12-44 1-33 (83)
22 COG1761 RPB11 DNA-directed RNA 94.0 0.083 1.8E-06 42.4 4.3 36 8-43 3-38 (99)
23 PF13656 RNA_pol_L_2: RNA poly 92.9 0.21 4.5E-06 38.2 4.6 37 261-297 38-74 (77)
24 cd06927 RNAP_L L subunit of Ar 91.8 0.27 5.8E-06 38.1 4.2 35 262-296 47-81 (83)
25 PRK01146 DNA-directed RNA poly 91.6 0.29 6.2E-06 38.2 4.1 34 263-296 50-83 (85)
26 cd07027 RNAP_RPB11_like RPB11 91.4 0.33 7.2E-06 37.6 4.3 35 262-296 47-81 (83)
27 cd07029 RNAP_I_III_AC19 AC19 s 90.8 0.39 8.4E-06 37.4 4.1 37 261-297 46-82 (85)
28 cd06926 RNAP_II_RPB11 RPB11 su 90.0 0.5 1.1E-05 37.4 4.2 36 262-297 55-90 (93)
29 cd06926 RNAP_II_RPB11 RPB11 su 89.3 0.53 1.2E-05 37.2 3.9 37 10-47 7-43 (93)
30 cd07029 RNAP_I_III_AC19 AC19 s 83.7 1.3 2.9E-05 34.4 3.3 28 16-43 5-32 (85)
31 PF13656 RNA_pol_L_2: RNA poly 76.5 1.2 2.5E-05 34.0 0.9 35 20-55 1-35 (77)
32 COG1761 RPB11 DNA-directed RNA 75.4 4.2 9E-05 32.7 3.8 37 261-297 52-88 (99)
33 KOG3438 DNA-directed RNA polym 69.7 4.9 0.00011 32.3 2.9 36 18-59 14-49 (105)
34 KOG3438 DNA-directed RNA polym 62.9 5.7 0.00012 31.9 2.1 37 261-297 53-89 (105)
35 PRK15449 ferredoxin-like prote 50.5 13 0.00028 29.7 2.2 52 191-248 22-73 (95)
36 TIGR02060 aprB adenosine phosp 44.8 26 0.00056 29.4 3.4 47 211-261 20-66 (132)
37 PF12690 BsuPI: Intracellular 36.5 1.9E+02 0.004 22.1 6.7 63 103-169 1-68 (82)
38 COG1146 Ferredoxin [Energy pro 34.7 50 0.0011 23.9 3.2 41 209-249 13-54 (68)
39 KOG4392 RNA polymerase, subuni 34.0 70 0.0015 26.3 4.1 37 261-297 66-102 (117)
40 PRK08348 NADH-plastoquinone ox 33.3 33 0.00071 27.9 2.2 40 209-249 47-86 (120)
41 KOG3307 Molybdopterin converti 32.6 18 0.00038 30.3 0.4 43 24-78 52-94 (150)
42 PF13237 Fer4_10: 4Fe-4S diclu 27.8 50 0.0011 22.3 2.1 39 209-248 12-51 (52)
43 KOG3256 NADH:ubiquinone oxidor 27.4 39 0.00084 29.8 1.7 58 209-273 116-180 (212)
44 PRK10882 hydrogenase 2 protein 25.9 1E+02 0.0022 29.9 4.5 57 179-243 122-179 (328)
45 PF13247 Fer4_11: 4Fe-4S diclu 25.1 1E+02 0.0022 24.5 3.6 39 211-250 16-54 (98)
46 TIGR02936 fdxN_nitrog ferredox 24.6 58 0.0012 24.7 2.1 65 172-249 2-83 (91)
47 TIGR00402 napF ferredoxin-type 23.9 56 0.0012 25.7 2.0 41 209-249 39-79 (101)
48 COG1143 NuoI Formate hydrogenl 23.5 47 0.001 29.3 1.5 41 209-249 60-108 (172)
49 KOG4392 RNA polymerase, subuni 23.1 92 0.002 25.6 3.0 35 10-44 17-53 (117)
50 PRK06273 ferredoxin; Provision 23.1 44 0.00095 29.2 1.2 42 208-249 53-104 (165)
51 PF01514 YscJ_FliF: Secretory 22.6 72 0.0016 28.7 2.6 41 20-60 152-196 (206)
52 PF13187 Fer4_9: 4Fe-4S diclus 21.5 67 0.0015 21.7 1.7 39 210-248 6-50 (55)
53 PRK14993 tetrathionate reducta 21.4 66 0.0014 29.8 2.2 39 194-242 125-163 (244)
54 COG0437 HybA Fe-S-cluster-cont 21.0 64 0.0014 29.3 1.9 53 181-243 81-134 (203)
55 PF11611 DUF4352: Domain of un 20.6 4.2E+02 0.009 20.7 7.1 67 101-173 35-103 (123)
No 1
>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=1.3e-78 Score=568.45 Aligned_cols=270 Identities=38% Similarity=0.556 Sum_probs=240.4
Q ss_pred cEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceeccccceeeeccC
Q 020983 11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDC 90 (319)
Q Consensus 11 ~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~~~~~~~c 90 (319)
+|+|+++++++++|.|.|+++||||||||+|||||||||||.|+|++|||+|+|||||||||||||.++ .+.|+|+.+|
T Consensus 2 ~i~i~~~~~~~~~f~l~~~d~s~ANAlRRimiaEVPt~AId~V~i~~NTSvl~DE~lAHRLGLIPL~~d-~~~~~~~~~~ 80 (291)
T cd07032 2 KIEIISLSDEELEFDLIGVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLIPIKAD-PRLFEYREDS 80 (291)
T ss_pred eEEEEECCCCEEEEEEecCCHHHHHHHHHHHHhcCcceeEEEEEEEECCccchhHHHHHhhcCceeecC-HHHccccccc
Confidence 689999999999999999999999999999999999999999999999999999999999999999996 4579999998
Q ss_pred CCCCCCCCCCCceEEEEEEEEeccCCC--------------ceeeccCeeeCCCceeeccccCCCC--CCCCCCCCCeEE
Q 020983 91 DACDGDGQCEFCSVEFHLRAKCHSDQT--------------LDVTSKDLYSSDHSVVPVDFVDPAG--YDSTDQQRGIII 154 (319)
Q Consensus 91 ~~~~~~~~~~~c~v~~~L~v~~~~~~~--------------~~V~s~Dl~~~~~~~~Pv~~~~~~~--~~~~~~~~~I~I 154 (319)
+ +..|+.|+|+|+|+|+|+.++. ..|||+||+ |.|.+.|.... ..-.+.+++|+|
T Consensus 81 -~---~~~~~~~~v~f~L~v~c~~~~~~~~~~~~~~~~~~~~~VyS~dl~-----~~p~g~q~~~~~~~~v~~v~~dI~I 151 (291)
T cd07032 81 -D---DEPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHKVYSGDLK-----WVPIGSQEKRFADNPIRPVHPDILI 151 (291)
T ss_pred -c---cCCCCCcEEEEEEEEEccCCcccccccccccccccccEEECCCCE-----ecCCCccccccCCCCcEEeCCCcEE
Confidence 3 2479999999999999986542 467777775 77888765321 122577999999
Q ss_pred EEeCCCCEEEEEEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCC--CCceee
Q 020983 155 VKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPN--TGQVYV 232 (319)
Q Consensus 155 ~kL~~gq~I~le~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~--~~~~~~ 232 (319)
+||++||+|+|+|+|+||+||+|||||||++++|||+|.|+|+++. +++++++|+++||.|||.+++. ++++.+
T Consensus 152 ~kL~~gQ~l~le~~a~kG~Gk~HAKwsPv~ta~yr~~P~I~i~~~~----~~~~~~~~~~~cP~~Vf~i~~~~~~~~~~V 227 (291)
T cd07032 152 AKLRPGQEIDLELHCVKGIGKDHAKFSPVATASYRLLPEITLLKPI----TGEDAEKLQKCFPPGVIDIEEVKGKKKAVV 227 (291)
T ss_pred EEECCCCEEEEEEEEEcCcccccceecCceeEEEEecceEEEcCcC----CHHHHHHHHhhCCCccEEecccCCCceEEE
Confidence 9999999999999999999999999999999999999999998764 3577889999999999999752 347889
Q ss_pred cCCccccchHHHHHHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983 233 VDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 233 ~~~~~~~~~~e~~~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
.+++.|++|++|++.++. .+.|++++++|||+|+|||+|+|+|+++|.+|+++|++|++.|.
T Consensus 228 ~~~~~ct~crec~~~~~~---~~~V~v~~~~d~fiF~VES~G~l~p~~i~~~Ai~iL~~K~~~l~ 289 (291)
T cd07032 228 ANPRKDTLSREVLRHEEF---KDKVELGRVRDHFIFSIESTGALPPDVLFLEAIKILKEKCRKLL 289 (291)
T ss_pred cccccCcccHhHhhhhcc---CCceeEEEeCCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999987644 46799999999999999999999999999999999999998874
No 2
>KOG1522 consensus RNA polymerase II, subunit POLR2C/RPB3 [Transcription]
Probab=100.00 E-value=2.9e-73 Score=506.20 Aligned_cols=283 Identities=54% Similarity=0.822 Sum_probs=237.3
Q ss_pred CCCCCcEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceecccccee
Q 020983 6 YQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMR 85 (319)
Q Consensus 6 ~~~~~~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~~~ 85 (319)
|++.|.|+|+++++++++|+|.++++++||||||+|||||||+|||.|.|+-|||||+||||||||||||+.|+++..++
T Consensus 2 y~~~p~v~I~Elt~d~vkF~L~nTdlsvANsLRRV~iaEvPTiAID~VeIe~NssVL~DEFiAHRLGLIPl~S~~~~~l~ 81 (285)
T KOG1522|consen 2 YANQPTVKIRELTDDNVKFVLSNTDLSVANSLRRVMIAEVPTIAIDLVEIEVNSSVLPDEFIAHRLGLIPLISDRIVELQ 81 (285)
T ss_pred CCCCCceEEEecCCCceEEEEecChHHHHHHHHHHHHhcCceeEEEEEEEecccccccHHHHHhhhcceeccchhhhhhh
Confidence 57889999999999999999999999999999999999999999999999999999999999999999999999998999
Q ss_pred eeccCCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCceeeccccCCCCCCCCCCCCCeEEEEeCCCCEEEE
Q 020983 86 FSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRL 165 (319)
Q Consensus 86 ~~~~c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~I~l 165 (319)
|.++|.|+ ++|+.|+|.|.|+++|++++.+.|||+||++.++.+.|+.+.............+|+|+||++||+|++
T Consensus 82 ytrdC~C~---~~C~eCSVef~L~~kc~~d~T~~VtsrDL~s~~~~v~pv~~~~~~~~~~~~e~~gilI~KLRkgQELkL 158 (285)
T KOG1522|consen 82 YTRDCECD---EFCPECSVEFTLDVKCTDDQTRDVTSRDLVSLDPTVTPVDSNRGSEIDDDSESKGILIVKLRKGQELKL 158 (285)
T ss_pred hcccCchh---ccCCcceEEEEEeeeecccceeeeehHhhhccCCcccccccCCCCccccccccCCcEEEEeecCCceee
Confidence 99999995 499999999999999999999999999999999999999872211011134467899999999999999
Q ss_pred EEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchHHHH
Q 020983 166 RAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVI 245 (319)
Q Consensus 166 e~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~ 245 (319)
+|+|+||+||+||||+|+++++|.|+|+..+.+...+.. .....+|. +.....++... ....
T Consensus 159 ra~akKGigKeHAKWsPta~V~FeYDPdn~lrhT~y~~e-~~~~~Ewp---~sk~~e~~~~~-------~e~~------- 220 (285)
T KOG1522|consen 159 RAIAKKGIGKEHAKWSPTAAVAFEYDPDNKLRHTLYWFE-EDDLIEWP---KSKNSELEEDP-------EEGA------- 220 (285)
T ss_pred eeeecccccccccccCCcceEEEEECccHhhhccCCCcc-ccchhhCC---cccccCCCCCc-------cccC-------
Confidence 999999999999999999999999999998877654321 11122332 22333333210 1100
Q ss_pred HHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccccCccc-hhhhhccccccccccCC
Q 020983 246 KKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDT-VEADDQFGELGAHMRGG 319 (319)
Q Consensus 246 ~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~~~~~~-~~~~~~~~~~~~~~~~~ 319 (319)
...-...+++|+|+|||.|+++|.+++.+|+.+|++||..|.++.+. +..+.|+.+.|+|+++.
T Consensus 221 ----------pyd~~~kpd~F~~~VEs~Gal~~~~iVl~gi~iLk~Kl~~l~~~l~~~~q~~~~~~~L~~~~~~~ 285 (285)
T KOG1522|consen 221 ----------PYDPEGKPDKFYFNVESVGALPPSQIVLMGIDILKEKLAALRLALSTEDQNDAQANELGAHERAG 285 (285)
T ss_pred ----------CCCccCCCceEEEEeEecCCCCHHHHHHHHHHHHHHHHHHHHhhhcccchhhhhhhhhhhhhcCC
Confidence 11123467999999999999999999999999999999999966654 44589999999999863
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=5.4e-72 Score=520.62 Aligned_cols=253 Identities=54% Similarity=0.811 Sum_probs=220.5
Q ss_pred CcEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceeccccceeee-c
Q 020983 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFS-R 88 (319)
Q Consensus 10 ~~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~~~~~-~ 88 (319)
|+|+|.++++++++|.|+|+++++||||||+|||||||+||+.|+|++|||+|+||||||||||||+.++++..|.+. +
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 579999999999999999999999999999999999999999999999999999999999999999999987655554 5
Q ss_pred cCCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeC-----CCceeeccccCCCCCCCCCCCCCeEEEEeCCCCEE
Q 020983 89 DCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSS-----DHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQEL 163 (319)
Q Consensus 89 ~c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~-----~~~~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~I 163 (319)
+|.|.+ .|+.|+++|+|+++|++++++.|||+||++. ++...|+...... +..+++|+|+||+|||+|
T Consensus 81 ~~~~~~---~~~~~~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~~~~~~pi~~~~~~----~~~~~~i~I~kL~~gq~i 153 (265)
T cd07031 81 DCDCDE---FCDKCSVELTLDVKCTGDQTREVTSRDLVSSGPKVNDVVPVPIRNDSED----NGEEDGILIVKLRKGQEL 153 (265)
T ss_pred hccccC---CCCCCeEEEEEEEEeccCCCceEEHHHcccccccccccCCccccccccc----ccCCCCeEEEEECCCCEE
Confidence 777643 5889999999999999889999999999875 2233444432211 255789999999999999
Q ss_pred EEEEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchHH
Q 020983 164 RLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDE 243 (319)
Q Consensus 164 ~le~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e 243 (319)
+|+|+|+||+||+|||||||++++|||+|.|+|+++..+.+ . ..+++.|++|++
T Consensus 154 ~le~~a~kG~Gk~HAKwsPv~~~~y~~~p~i~i~~~~~~~~----------~----------------~~~~~~c~~c~~ 207 (265)
T cd07031 154 KLRCIAKKGIGKEHAKWSPTAAVTFEYDPDNALRHTDYWYL----------E----------------DEDKEWPKSENA 207 (265)
T ss_pred EEEEEEECCEeccCCEeccceEEEEEEccceEEccccccch----------h----------------hcccccCchhHH
Confidence 99999999999999999999999999999999986542210 0 126789999999
Q ss_pred HHHHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983 244 VIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 244 ~~~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
|.+.++. .++.|++++++|+|+|+|||+|+|+|+++|.+|+++|++|++.|.
T Consensus 208 c~~~~~~--~~~~v~i~~~~~~fiF~VES~Gsl~p~~Iv~~Al~iL~~K~~~l~ 259 (265)
T cd07031 208 CIEEPPE--KDALFDIDAKPDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQ 259 (265)
T ss_pred Hhhcccc--cCCceEEEeeCCEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 9987753 356899999999999999999999999999999999999999987
No 4
>KOG1521 consensus RNA polymerase I and III, subunit RPA40/RPC40 [Transcription]
Probab=100.00 E-value=2.2e-71 Score=506.11 Aligned_cols=281 Identities=38% Similarity=0.552 Sum_probs=248.8
Q ss_pred CCCCCCcEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceeccccce
Q 020983 5 SYQRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSM 84 (319)
Q Consensus 5 ~~~~~~~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~~ 84 (319)
.|.+..+|.|.+++++.++|.|.|+++++|||+|||||||||||||+.|+|++||||++||+||||||||||..+|. .|
T Consensus 41 ~f~~~~~V~iv~~~~~~leFDligIda~IANAfRRILiaEVPtmAiEkVyi~nNTSViqDEvLaHRlGLvPl~aDPr-lF 119 (338)
T KOG1521|consen 41 NFKDNFKVDIVSLDEETLEFDLIGIDASIANAFRRILIAEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLVPLRADPR-LF 119 (338)
T ss_pred HhhhceEEEEEeccCcceeEEEeeccHHHHHHHHHHHHhhcchhheeeeEEecCccccHHHHHHHhhcCcccccCcc-hh
Confidence 35667899999999999999999999999999999999999999999999999999999999999999999999986 58
Q ss_pred eeeccCCCCCCCCCCCCceEEEEEEEEeccCCCceeeccC---------eeeCCCceeeccccCCCCCC--CCCCCCCeE
Q 020983 85 RFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKD---------LYSSDHSVVPVDFVDPAGYD--STDQQRGII 153 (319)
Q Consensus 85 ~~~~~c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~D---------l~~~~~~~~Pv~~~~~~~~~--~~~~~~~I~ 153 (319)
.|..+-++.+ -...+++|+|+|+|+.+....+.+.| +++.+..|.|.+.|.....+ ..++++||+
T Consensus 120 e~~~e~d~~~----e~~ntlvF~L~VkC~~n~~a~~~~sdpk~Ly~ns~vyS~~~~w~P~g~Q~~~f~e~~i~~~~~DIL 195 (338)
T KOG1521|consen 120 EYRSENDEDD----EKENTLVFKLNVKCTKNPNAKKDSSDPKELYNNSEVYSRDLTWKPKGYQAEIFAENPIRPVHDDIL 195 (338)
T ss_pred hccccCCCcc----CccceEEEEEEeeccCCCCcccCCCChhHhccCcEEecCcceeccccchhhhcccCCccccCcceE
Confidence 8877643321 12279999999999988655666666 67778889999998865332 266799999
Q ss_pred EEEeCCCCEEEEEEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCC--cee
Q 020983 154 IVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTG--QVY 231 (319)
Q Consensus 154 I~kL~~gq~I~le~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~--~~~ 231 (319)
|+||+|||+|+++|+|+||+||+|||||||++++||++|.|.|+.+.. ++++.++.+.||.|||.+++..+ +++
T Consensus 196 iAkLrPGQEI~le~havkGIGkdHAKfSPVaTAsYRLlP~I~l~~ei~----ge~A~~lqkcfs~gVi~iee~~~kk~A~ 271 (338)
T KOG1521|consen 196 IAKLRPGQEIELEAHAVKGIGKDHAKFSPVATASYRLLPTIVLLAEIE----GEDAERLQKCFSPGVIDIEEMGGKKRAY 271 (338)
T ss_pred EEecCCCCEeeeeeeeecccCcccccccCcccceeeccceeEecCccc----chhHHHHHhhCCCCeEeeecCCCceEEE
Confidence 999999999999999999999999999999999999999999987764 57788899999999999987543 688
Q ss_pred ecCCccccchHHHHHHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983 232 VVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 232 ~~~~~~~~~~~e~~~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
+.++++|++|+||.|..+. .+.|.++...|||+|+|||+|+|+|+.++.+|+++|+.|+..++
T Consensus 272 Vad~R~dT~sRe~~R~ee~---~d~V~LgrvrdHfIFsvestgal~p~~lf~eavkvle~Kc~al~ 334 (338)
T KOG1521|consen 272 VADPRKDTCSREVLRHEEL---KDKVQLGRVRDHFIFSVESTGALKPEVLFEEAVKVLEEKCRALR 334 (338)
T ss_pred ecCcccchhhHHHhccHHh---hhheeeccccceEEEEeecccCCCchhhHHHHHHHHHHHHHHHh
Confidence 9999999999999998654 46789999999999999999999999999999999999998765
No 5
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=100.00 E-value=4.8e-66 Score=481.23 Aligned_cols=256 Identities=37% Similarity=0.579 Sum_probs=230.9
Q ss_pred CcEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceeccccceeeecc
Q 020983 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRD 89 (319)
Q Consensus 10 ~~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~~~~~~~ 89 (319)
++|+|++.++++++|.++|+++|+||||||+|||||||+||+.|+|++|||+++||+|||||||||++++ +++|+|+.+
T Consensus 1 ~~~~~~~~~~~~~~f~~~g~~~t~~NalRRvlls~vp~~Ai~~v~i~~n~s~~~de~i~hrl~lip~~~~-~~~~~~~~~ 79 (263)
T PRK00783 1 MEIEILELDDRSARFVVEGVTPAFANAIRRAMIADVPTMAIDDVRFYENTSVLFDEILAHRLGLIPLTTD-LDKYKPPEE 79 (263)
T ss_pred CceEEEEcCCcEEEEEEeCCCHHHHHHHHHHHHHcCCeeeEEEEEEEECCcchhHHHHHHhhcCcccccC-HHHCCCccc
Confidence 4689999999999999999999999999999999999999999999999999999999999999999995 678899888
Q ss_pred CCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCceeeccccCCCCCCCCCCCCCeEEEEeCCCCEEEEEEEE
Q 020983 90 CDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIA 169 (319)
Q Consensus 90 c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~I~le~~a 169 (319)
|.|+ ++.|+.|+++|+|+++ ++.+|||+||...++.+ .+++|+++|+||++||+|+|+++|
T Consensus 80 ~~~~--~~~~~~~~~~~~l~~~----~~~~V~a~dl~~~~~~v-------------~~v~~~~~I~~L~~~~~l~~e~~~ 140 (263)
T PRK00783 80 CTCE--GEGCPDCTVTLSLEVE----GPKTVYSGDLKSSDPDV-------------KPVDPNIPIVKLKEGQKLVLEAYA 140 (263)
T ss_pred cccc--CCCCCCcEEEEEEEec----CCCcEEccccccCCCCc-------------eecCCCcEEEEeCCCCEEEEEEEE
Confidence 8763 3479999999999998 78899999998633333 566788999999999999999999
Q ss_pred EecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchHHHHHHHh
Q 020983 170 RKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAE 249 (319)
Q Consensus 170 ~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~~~~~ 249 (319)
.+|+||+||||+|+++++|++.|.+.+ .+.+ ..+..|.+.||.+++.+++. .+.+.+...|.+|.+|++.++
T Consensus 141 ~~G~G~~HAKw~p~~~~~yr~~p~I~i-~~~C-----~~C~~C~~~CP~~vi~~~~~--~~~v~~~~~C~~C~~Ci~~CP 212 (263)
T PRK00783 141 RLGRGKEHAKWQPGSACGYKYYPRIEV-SEDC-----DECEKCVEACPRGVLELKEG--KLVVTDLLNCSLCKLCERACP 212 (263)
T ss_pred EcCcccccCccCcceEeeecccccccc-cccC-----CchHHHHHhCCccccEecCC--eEEEeChhhCCCchHHHHhCC
Confidence 999999999999999999999999999 5544 35778899999999999763 345567889999999998874
Q ss_pred hcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983 250 AMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 250 ~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
.+++++..++++|+|+|||+|+++|+++|.+|+++|++||+.|.
T Consensus 213 ----~~AI~i~~~~~~~if~vEs~G~l~p~~iv~~A~~~l~~k~~~~~ 256 (263)
T PRK00783 213 ----GKAIRVSDDENKFIFTVESDGSLPVEEILLEALKILKRKADELI 256 (263)
T ss_pred ----CCceEEEEcCCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999999999999999999999999987
No 6
>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=1.4e-63 Score=463.83 Aligned_cols=256 Identities=39% Similarity=0.622 Sum_probs=225.7
Q ss_pred CcEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceeccccceeeecc
Q 020983 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRD 89 (319)
Q Consensus 10 ~~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~~~~~~~ 89 (319)
++|+|++.++++++|.++|+++++||||||+|||||||+||+.|+|++|||+|+||+|||||||||++++++..+ +..+
T Consensus 1 ~~~~~~~~~~~~~~f~~~g~~~s~~NalRRills~vp~~Ai~~V~i~~n~s~~~de~i~hrl~~ip~~~e~~~~~-~~~~ 79 (259)
T cd07030 1 MEIEVLELDDDRARFVLEGVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAHRLGLIPLRTDLDLYK-YRSE 79 (259)
T ss_pred CceEEEecCCCEEEEEEeCCCHHHHHHHHHHHHhcCCeeeEEEEEEEeCCchhhHHHHHHhhcCcccccCHHHhc-cccc
Confidence 468999999999999999999999999999999999999999999999999999999999999999999987532 3336
Q ss_pred CCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCceeeccccCCCCCCCCCCCCCeEEEEeCCCCEEEEEEEE
Q 020983 90 CDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIA 169 (319)
Q Consensus 90 c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~I~le~~a 169 (319)
|.+. ...|+.|++.|+|+++ ++.+|||+||+..++.+ .+++|+++|+||++||+|+|+++|
T Consensus 80 ~~~~--~~~~~~~~~~~~l~~~----~~~~v~s~dl~~~~~~v-------------~~~~~~~~I~~l~~~~~l~~~~~~ 140 (259)
T cd07030 80 CSCG--GAGCPLCTVTLTLSVE----GPGTVYSGDLKSSDPDV-------------KPVYDNIPIVKLGKGQKLVLEAYA 140 (259)
T ss_pred cccc--CCCCCCcEEEEEEEcc----CCceEEccccccCCCCc-------------cccCCCcEEEEeCCCCEEEEEEEE
Confidence 6542 2367889999999998 67899999998744334 566778999999999999999999
Q ss_pred EecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchHHHHHHHh
Q 020983 170 RKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAE 249 (319)
Q Consensus 170 ~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~~~~~ 249 (319)
++|+||+||||+|+++++|++.|.+.+++.. ..+..|.+.||.+++.+++. ...+.+...|.+|.+|.+.++
T Consensus 141 ~kg~g~~hakw~p~~~~~yr~~P~i~i~~~C------~~C~~C~~~CP~~vi~~d~~--~~~v~~~~~C~~C~~C~~~Cp 212 (259)
T cd07030 141 RLGRGKEHAKWQPTTACGYKYYPVIEIDEDC------DGCGKCVEECPRGVLELEEG--KVVVEDLEDCSLCKLCERACD 212 (259)
T ss_pred ecCccCCCCCCCCccEEEEEeecceechhhC------CChHHHHHhCCccceEccCC--eeEEeChhhCcCchHHHHhCC
Confidence 9999999999999999999999999887443 23678999999999998754 344567789999999999874
Q ss_pred hcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983 250 AMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 250 ~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
. +++++..++++|+|+|||+|+++|++||++|+++|++||+.|.
T Consensus 213 ~----~AI~~~~~~~~~if~vEs~Gsl~p~~il~~A~~~l~~k~~~~~ 256 (259)
T cd07030 213 A----GAIRVGWDEDRFIFEVESDGSLPPKEILLEALRILKEKADELI 256 (259)
T ss_pred C----CcEEEEecCCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 2 6899999999999999999999999999999999999999875
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=2.9e-60 Score=428.18 Aligned_cols=203 Identities=48% Similarity=0.764 Sum_probs=179.3
Q ss_pred CcEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceeccccc--eeee
Q 020983 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMS--MRFS 87 (319)
Q Consensus 10 ~~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~--~~~~ 87 (319)
|+|+++++++++++|.|+|+++++||||||+|||||||+||+.|+|++|||+|+||++||||||||++++++.. ++.+
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 46999999999999999999999999999999999999999999999999999999999999999999998643 3344
Q ss_pred ccCCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCC-----CceeeccccCCCCCCCCCCCCCeEEEEeCCCCE
Q 020983 88 RDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSD-----HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQE 162 (319)
Q Consensus 88 ~~c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~-----~~~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~ 162 (319)
+.|.|.. .|..|+++++|+++++++.+.+|||+||...+ +.+ .+++++|+|+||++||+
T Consensus 81 ~~~~~~~---~~~~~~v~~~l~~~g~~~~~~~V~s~DL~~~~~~~~~~~v-------------~pv~~di~I~kL~~gq~ 144 (212)
T cd07028 81 EDCECED---HCDKCSVVLTLQAFAESESTTNVYSKDLVIVSNLMGRNIG-------------HPIIQDILICKLRKGQE 144 (212)
T ss_pred ccccccc---cccceeEEEEEEccCCCCCcceEEHHHcccCCccccCCCe-------------EEeCCCcEEEEECCCCE
Confidence 4444532 57889999999999765556789999998754 223 45667899999999999
Q ss_pred EEEEEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchH
Q 020983 163 LRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDD 242 (319)
Q Consensus 163 I~le~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~ 242 (319)
|+|+|+|++|+||+|||||||++++|+++|
T Consensus 145 i~le~~~~~G~G~~hAk~sPV~~v~y~~~~-------------------------------------------------- 174 (212)
T cd07028 145 IKLTCVAKKGIGKEHAKFGPVAAIEFRYDP-------------------------------------------------- 174 (212)
T ss_pred EEEEEEEECCCcCCCCEeCCceEEEEEEEc--------------------------------------------------
Confidence 999999999999999999999999998643
Q ss_pred HHHHHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983 243 EVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 243 e~~~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
++|+|+|+|||+|+++|++|+.+|+++|++|++.|.
T Consensus 175 -------------------~~d~li~~VeT~Gsi~p~~~l~~A~~iL~~~~~~~~ 210 (212)
T cd07028 175 -------------------VADTYIMNVESVGSLPPDQVVVEAIKTLQKKVASIL 210 (212)
T ss_pred -------------------cCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHh
Confidence 248999999999999999999999999999998874
No 8
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=100.00 E-value=2.5e-55 Score=400.24 Aligned_cols=223 Identities=42% Similarity=0.614 Sum_probs=195.2
Q ss_pred eEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceeccccceeeeccCCCCCCCCCCC
Q 020983 21 YAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCE 100 (319)
Q Consensus 21 ~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~~~~~~~c~~~~~~~~~~ 100 (319)
+++|.++++++++||||||+||++|||+||+.|+|++|+|.++||+++|||||+|+.... ..+.++++|.|. ..|+
T Consensus 1 ~~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~I~~n~~~v~eev~~~rLnL~pl~~~~-~~~~~~~~~~~~---~~~~ 76 (224)
T smart00662 1 RAKFVLEPYGLTLANALRRVLLSSVPGMAVTEVEIEGNTSGVQDEVLAHRLGLKPLASDP-DGDEYQRDCECE---EGCE 76 (224)
T ss_pred CeEEEEEcCCchHHHHHHHHHHHcCccceEEEEEEecCCcchhHHHHHHHhCCeeEEEec-hhcccccccccc---ccCC
Confidence 478999999999999999999999999999999999999999999999999999999964 457788888774 3799
Q ss_pred CceEEEEEEEEeccCCCceeeccCeeeC-CCceeeccccCCCCCCCCCCCCCeEEEEeCCCCEEEEEEEEEecccccccc
Q 020983 101 FCSVEFHLRAKCHSDQTLDVTSKDLYSS-DHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAK 179 (319)
Q Consensus 101 ~c~v~~~L~v~~~~~~~~~V~s~Dl~~~-~~~~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~I~le~~a~kG~Gk~HAK 179 (319)
.|++.++|+++ +|.+|||+||+.. |+.+ .+++|+++|+||++||+|+|+++|++|+||+|||
T Consensus 77 ~~~~~~~L~~~----gp~~V~a~Dl~~~~~~~v-------------~~vnp~~~I~~L~~gq~l~~e~~~~~G~G~~hak 139 (224)
T smart00662 77 KCSVTLTLDVK----GPGEVTAGDLKSDSDPDV-------------EIVNPDIPIAKLREGQELELEARAEKGRGYVHAK 139 (224)
T ss_pred CceEEEEEEEE----cCCcEEHHHcccCCCCCc-------------EEeCCCcEEEEECCCCEEEEEEEEECCcccccCc
Confidence 99999999999 6778999999875 4344 4567789999999999999999999999999999
Q ss_pred cCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchHHHHHHHhhcCCCCcEEE
Q 020983 180 WSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEI 259 (319)
Q Consensus 180 w~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~i~v 259 (319)
|+|+++++|++.|.+.+|... ++..+..+...||++++..+ | |++|.+.
T Consensus 140 ~~p~~~~~~~~~~~i~id~~~----~pv~~v~~~~~~~~~~~~~~-------------~--~~~c~~~------------ 188 (224)
T smart00662 140 WSPVSTVEYRYIPRIPVDASF----SPVDRVAYQVECPRVVQRTD-------------C--CRECDEG------------ 188 (224)
T ss_pred cccccCCCcCcCCEEEECCCC----ChhhheeeeccCCccceecc-------------c--chhhhcc------------
Confidence 999999999999999998653 34556667777877655432 5 8888752
Q ss_pred eeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhccc
Q 020983 260 YAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAV 296 (319)
Q Consensus 260 ~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l 296 (319)
.++|+|+|+|||+|+++|++||.+|+++|++|++.|
T Consensus 189 -~~~d~l~f~IeT~G~i~p~~al~~A~~iL~~k~~~~ 224 (224)
T smart00662 189 -EEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEAF 224 (224)
T ss_pred -CCCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHhhC
Confidence 357999999999999999999999999999999865
No 9
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=100.00 E-value=9.4e-51 Score=360.36 Aligned_cols=180 Identities=38% Similarity=0.508 Sum_probs=159.6
Q ss_pred CcEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceeccccceeeecc
Q 020983 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRD 89 (319)
Q Consensus 10 ~~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~~~~~~~ 89 (319)
+++++....+++++|.++ +++++||||||+|||+|||+||+.|+|++|||+|+||++||||||||+.+..+.
T Consensus 4 ~~~~~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~V~I~~Nts~~~DEivaHe~~lIpLK~~~~~------- 75 (195)
T PRK14979 4 IKEKEKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIENVYFYENSSSMYDEILAHRLGLIPIKGKPVS------- 75 (195)
T ss_pred cceeeeccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEEEEEecCcccccchheeeeeeeeeeeeeecc-------
Confidence 567888888999999999 999999999999999999999999999999999999999999999998875331
Q ss_pred CCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCceeeccccCCCCCCCCCCCCCeEEEEeCCCCEEEEEEEE
Q 020983 90 CDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIA 169 (319)
Q Consensus 90 c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~I~le~~a 169 (319)
..++++|+|+++ +|+.|||+||.+.++ ++++|+++|++|++||+|+|+|+|
T Consensus 76 ----------~~~~~~l~L~~~----gp~~Vta~Di~~~~~---------------~ivnpdi~I~tL~~g~~l~~e~~~ 126 (195)
T PRK14979 76 ----------GDEVITFTLSKE----GPCTVYSSDLKSENG---------------EVAFKNIPIVKLAEGQKLEIECEA 126 (195)
T ss_pred ----------CCCcEEEEEEEe----CCceEEHHHcCCCCC---------------cccCCCcEEEEECCCCEEEEEEEE
Confidence 123779999987 888999999987532 467889999999999999999999
Q ss_pred EecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchHHHHHHHh
Q 020983 170 RKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAE 249 (319)
Q Consensus 170 ~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~~~~~ 249 (319)
++|+||+||||+|+. +.|++
T Consensus 127 ~~G~Gy~hAk~~pvd-a~y~~----------------------------------------------------------- 146 (195)
T PRK14979 127 LVGTGKIHAKWQPCN-AVYKQ----------------------------------------------------------- 146 (195)
T ss_pred ECCCcccccccccee-eEEec-----------------------------------------------------------
Confidence 999999999999953 33321
Q ss_pred hcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983 250 AMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 250 ~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
.++|+|+|+|||+|+++|++|+.+|+++|++||+.|.
T Consensus 147 -----------~~~dkl~leIeTdGsi~P~~al~~Aa~iL~~~l~~~~ 183 (195)
T PRK14979 147 -----------ISNDEVEFKVESFGQMDAEDILRSALEILKNKAEKFL 183 (195)
T ss_pred -----------CCCcEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 2358999999999999999999999999999999997
No 10
>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=2.2e-38 Score=286.94 Aligned_cols=202 Identities=23% Similarity=0.330 Sum_probs=168.7
Q ss_pred EEEecCceEEEEEE----ecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceecccc-------
Q 020983 14 IRELKDDYAKFELR----DTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAM------- 82 (319)
Q Consensus 14 i~~~~~~~~~f~l~----g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~------- 82 (319)
+.+.++.+++|.++ |++.++||||||+||+++||+||+.|+|++| +||||+||++++++.
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 44567789999994 7999999999999999999999999999995 899999999999863
Q ss_pred ceeeeccCCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCceeeccccCCCCCCCCCCCCCeEEEEeCCCCE
Q 020983 83 SMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQE 162 (319)
Q Consensus 83 ~~~~~~~c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~ 162 (319)
++.++.. |..|++.++|+++ ||+.|||+||.+++ .+ ++++|+++|++|++||+
T Consensus 74 ~~~~~~~---------~~~~~~~~~l~~~----gp~~V~a~Di~~~~-~i-------------~ivnp~~~IatL~~~~~ 126 (215)
T cd06928 74 EIVFKSD---------SEDEPQVLRLKVK----GPGVVTAADIELPS-GV-------------EIVNPDQYIATLTEDAS 126 (215)
T ss_pred cEEEEec---------CCCceEEEEEEEe----cCeEEEhHhcCcCC-Cc-------------EEeCCCcEEEEECCCCE
Confidence 3444433 3357899999998 88999999998743 12 56778899999999999
Q ss_pred EEEEEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchH
Q 020983 163 LRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDD 242 (319)
Q Consensus 163 I~le~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~ 242 (319)
|+|+|+|.+|+||.+|+|+.- ..-+.+.+.+|+. +.|+.+++|..
T Consensus 127 l~ie~~i~~G~Gy~~~~~~~~------------------------------~~~~~~~~~iDa~-----f~PV~~vny~v 171 (215)
T cd06928 127 LEMELRIEKGRGYVPAEENKS------------------------------EEKPIGFIPIDAI-----FSPVRKVNYSV 171 (215)
T ss_pred EEEEEEEECcCcceecccccc------------------------------ccCCCceEEeCCC-----cCCeEEEEEEE
Confidence 999999999999999998720 1235688999985 78999999887
Q ss_pred HHHHHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhccc
Q 020983 243 EVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAV 296 (319)
Q Consensus 243 e~~~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l 296 (319)
+-.+ +.-..+.++++|+|||||+++|++|+.+|+++|+++|+.|
T Consensus 172 ~~~~----------~~~~~~~e~L~leI~TnGsi~P~~Al~~A~~il~~~~~~~ 215 (215)
T cd06928 172 ESTR----------VGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHFSPF 215 (215)
T ss_pred EEee----------cCCCCCceeEEEEEEECCCCCHHHHHHHHHHHHHHHhhcC
Confidence 6221 1113678999999999999999999999999999998764
No 11
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=100.00 E-value=2.2e-37 Score=294.02 Aligned_cols=217 Identities=23% Similarity=0.353 Sum_probs=173.5
Q ss_pred CCCCCCcEEEEEec--CceEEEEEE----ecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCccee
Q 020983 5 SYQRFPKVKIRELK--DDYAKFELR----DTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTS 78 (319)
Q Consensus 5 ~~~~~~~iei~~~~--~~~~~f~l~----g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~ 78 (319)
.+.....+++.+.+ +++++|.++ |++.++||||||+||+++||+||+.|+|.+ ++|||++||+++
T Consensus 2 ~~~~~~~i~~~e~~~~~~~~~F~i~Ple~G~g~tlgNaLRRvLLs~ipg~aI~~VkI~g---------v~hEf~~Ipgv~ 72 (310)
T PRK05182 2 EFLKPQKIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKIDG---------VLHEFSTIPGVR 72 (310)
T ss_pred CcccCcEEEEEeccCCCcEEEEEEeccCCCchhHHHHHHHHHHHhcCCeeEEEEEEEcc---------eeeeccccCCcc
Confidence 34555678888876 789999997 999999999999999999999999999966 899999999999
Q ss_pred ccccc--eeeeccCCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCceeeccccCCCCCCCCCCCCCeEEEE
Q 020983 79 ERAMS--MRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVK 156 (319)
Q Consensus 79 ~~~~~--~~~~~~c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~Pv~~~~~~~~~~~~~~~~I~I~k 156 (319)
+++.. ++++. +.... .|. |++.++|+++ ||+.|||+||.++ +.+ ++++|+++||+
T Consensus 73 Edv~eIllNlk~-i~~~~---~~~-~~~~~~l~~~----gp~~VtA~Di~~~-~~v-------------~ivn~d~~Iat 129 (310)
T PRK05182 73 EDVTEIILNLKG-LRLKL---HGD-EPVTLTLSKK----GPGEVTAGDIETD-GDV-------------EIVNPDLVIAT 129 (310)
T ss_pred cchhHhhhhhcc-ceeec---CCC-ceEEEEEEec----CCeEEEHHHcCCC-CCc-------------EEeCCCeEEEE
Confidence 97642 22221 11111 233 7889999998 8899999999862 222 56778899999
Q ss_pred eCCCCEEEEEEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCc
Q 020983 157 LRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAE 236 (319)
Q Consensus 157 L~~gq~I~le~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~ 236 (319)
|++||+|+|+++|.+|+||.+|+-+- . ..+.|.+.+|+. +.|+.
T Consensus 130 L~~~~~l~ie~~~~kG~Gy~~~~~~~---------------------------~----~~~~g~i~iDa~-----f~PV~ 173 (310)
T PRK05182 130 LNEGAKLEMELTVERGRGYVPAEENK---------------------------E----DAPIGRIPVDAI-----FSPVK 173 (310)
T ss_pred ECCCCEEEEEEEEECcCCCccccccc---------------------------c----cCCcccEEecCC-----cCCcc
Confidence 99999999999999999997765330 0 124578888875 78999
Q ss_pred cccchHHHHHHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc-cC
Q 020983 237 AYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR-LS 299 (319)
Q Consensus 237 ~~~~~~e~~~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~-~~ 299 (319)
+++|+.+-.+ +.-..++++++|+|||||+++|.+|+.+|+++|+++|..|. +.
T Consensus 174 ~vny~ve~~~----------~~~~~~~e~L~leI~TnGsi~P~eAl~~A~~iL~~~l~~f~~~~ 227 (310)
T PRK05182 174 KVNYTVENTR----------VGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVDLE 227 (310)
T ss_pred ceEEEecccc----------cCCCCcceEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhCcc
Confidence 9999877321 11235678999999999999999999999999999999987 54
No 12
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=100.00 E-value=2.1e-37 Score=294.12 Aligned_cols=259 Identities=20% Similarity=0.258 Sum_probs=197.8
Q ss_pred EEEEEec----CceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEee--C---cc-cccchhhhhhhcCCcceeccc
Q 020983 12 VKIRELK----DDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEV--N---SS-VLNDEFIAHRLGLIPLTSERA 81 (319)
Q Consensus 12 iei~~~~----~~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~--N---tS-vl~DE~laHRLgLIPi~~~~~ 81 (319)
|++.+++ ...++|..+|+++|+||||||+|||+|||+||+.|+|++ | |+ .++||+++|||||+||....-
T Consensus 7 i~i~~~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~V~I~~v~hef~s~~gv~Edvl~~~LnLk~L~~~~~ 86 (317)
T COG0202 7 VKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEIDGVLHEFDSIEGVQEDVLAHRLNLKPLAVKLD 86 (317)
T ss_pred eEEEEcccccccEEEEEeeeCCcchhHHHHHHHHHHcCccceEEEEEEeccccccccCcCcHHHHHHHHhcCceeeeecc
Confidence 9999988 567788888999999999999999999999999999999 3 43 899999999999999999765
Q ss_pred c----ceeeeccCCCCCCCCCCCCceEEEEEEEEeccCC------------CceeeccCeeeCCCceeeccccCCCCCCC
Q 020983 82 M----SMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQ------------TLDVTSKDLYSSDHSVVPVDFVDPAGYDS 145 (319)
Q Consensus 82 ~----~~~~~~~c~~~~~~~~~~~c~v~~~L~v~~~~~~------------~~~V~s~Dl~~~~~~~~Pv~~~~~~~~~~ 145 (319)
. .|.+...|.|. ..|+.|++.+.|++.|++.. ...|+++|++.... ..+... ..-
T Consensus 87 ~~~~~~~~~~~~g~g~---v~a~d~~~~~~lEv~np~~~ia~~~~~~~l~~~~~V~~G~gyv~~~-----~~~~~~-~~v 157 (317)
T COG0202 87 GDEEVTLELDKEGPGE---VTASDITVPLDLEVVNPDHVIATLTEDAKLEMELRVYSGDGYVPAE-----GNREDD-PPV 157 (317)
T ss_pred cccceEEEEeccCCcc---ccHhhcccceeEEEECCCceeeeccCCcceEEEEEEEcCccEeccc-----cccccC-CCc
Confidence 3 26777665543 47999999999999987544 24689999986311 000000 011
Q ss_pred CCCCCCeEEEEeCCCCEEEEEEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCe-eEEeC
Q 020983 146 TDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTK-VFDID 224 (319)
Q Consensus 146 ~~~~~~I~I~kL~~gq~I~le~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~-v~~id 224 (319)
.....|+++++|+++|.+..++.|.+|+||+||||+|++..+|+++|.+..-.+.+ .+++..+.+.||.. .+..+
T Consensus 158 ~~i~~D~~~spv~kvqy~ve~~r~~~~~~~Dhl~~~~~T~gsi~~~~a~~~aa~il----~e~~~~~~~~~~~~~~~~~e 233 (317)
T COG0202 158 GPIAVDAPFSPVRKVQYIVEEARVGQGTDKDHLKWEPETNGSIRPEEALAIAAKIL----IEHLEVFVELCPKAVEIEEE 233 (317)
T ss_pred eeeeCCCceeeeeeceEEEEeEEEeccCCceeEEEEEeeccEeehHHHHHHHHHHH----HHHHHHHHhhccccceeecc
Confidence 34566899999999999999999999999999999999999999999877655543 36677788888864 33333
Q ss_pred CC----CC--ceeecCCccccchHHHHHHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHH
Q 020983 225 PN----TG--QVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAI 286 (319)
Q Consensus 225 ~~----~~--~~~~~~~~~~~~~~e~~~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~ 286 (319)
.. .. ...+.+...+..|..|.+...- .....+....+.+.|.|++.|..++++++.++.
T Consensus 234 ~~~~~~~~~~~~~I~~l~lsvrs~ncLk~~~i---~~i~~L~~~~e~~l~~v~n~G~ksleEi~~kl~ 298 (317)
T COG0202 234 KPEFPILLVLEAPIDELDLSVRSYNCLKREGI---ETIGELVQRTEEELLKVENLGKKSLEEIKEKLA 298 (317)
T ss_pred cccccccccccccccccccceeeehhhcccCc---hhhHHHHhcCHHHHhcccccccCCHHHHHHHHH
Confidence 21 11 2256778888888999876521 011112345789999999999999999985544
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=100.00 E-value=2.4e-34 Score=271.91 Aligned_cols=203 Identities=23% Similarity=0.320 Sum_probs=161.4
Q ss_pred eEEEEEE----ecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceeccccc--eeeeccCCCCC
Q 020983 21 YAKFELR----DTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMS--MRFSRDCDACD 94 (319)
Q Consensus 21 ~~~f~l~----g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~--~~~~~~c~~~~ 94 (319)
+.+|.+. |++.++||||||+||+++|++||+.|+|++ ++|||++||++.+++.. +|++.-. ...
T Consensus 1 y~~f~i~Ple~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~g---------v~HEf~~I~GV~Edv~eIllNlK~i~-~~~ 70 (297)
T TIGR02027 1 YGKFVLEPLERGFGITLGNALRRVLLSSIPGAAITAVKIDG---------VLHEFSTIEGVKEDVTEIILNLKQLV-VKS 70 (297)
T ss_pred CcEEEEecCCCCchhHHHHHHHHHHHhcCCceEEEEEEEcc---------eecccccCCCccccHHHHHhhhhceE-Eec
Confidence 3678886 899999999999999999999999999998 99999999999998752 2322211 100
Q ss_pred CCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCceeeccccCCCCCCCCCCCCCeEEEEeCCCCEEEEEEEEEeccc
Q 020983 95 GDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIG 174 (319)
Q Consensus 95 ~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~I~le~~a~kG~G 174 (319)
.|+.++ .++|+++ ||++|||+||.+..+ +. ++++|+++||+|.+||.|+|++++.+|+|
T Consensus 71 ---~~~~~~-~~~l~~~----gp~~VtA~Di~~~p~-----~i--------eivnpd~~IatL~~~~~L~iel~i~~G~G 129 (297)
T TIGR02027 71 ---EGDGER-TMTLSKK----GPGVVTAGDIKAPPG-----DV--------EIVNPDLVIATLTEPADLEIELRVERGRG 129 (297)
T ss_pred ---cCCCcE-EEEEEEe----CCEEEEhhhcccCCC-----Cc--------EEeCCCeEEEEECCCCEEEEEEEEEcccc
Confidence 122223 7888888 899999999984222 22 67888999999999999999999999999
Q ss_pred ccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchHHHHHHHhhcCCC
Q 020983 175 KDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKP 254 (319)
Q Consensus 175 k~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~ 254 (319)
|.+|+-+- ...|+.+.+.+|+. ++|+.+++|+.+..+
T Consensus 130 y~~~~~~~------------------------------~~~~~~~~i~iDa~-----FsPV~~Vny~ve~~r-------- 166 (297)
T TIGR02027 130 YVPAEENR------------------------------EEDRPVGVIAVDAI-----FSPVLKVNYEVENTR-------- 166 (297)
T ss_pred cCcccccc------------------------------cccCcccccccccc-----ccCeEEEEEEEeeee--------
Confidence 96655320 13467788888874 889999999987432
Q ss_pred CcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc-cC
Q 020983 255 GLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR-LS 299 (319)
Q Consensus 255 ~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~-~~ 299 (319)
+.-..+.++|+|+|||+|+++|.+|+.+|+++|+++++.|. ++
T Consensus 167 --v~~~~~~d~li~eIeT~Gsi~P~~al~~A~~iL~~~~~~~~~~~ 210 (297)
T TIGR02027 167 --VGQRTDYDKLILEIETNGSITPKDAIAEAAKILIEHLEPFVNLD 210 (297)
T ss_pred --ccCCccccEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhcch
Confidence 11234578999999999999999999999999999999997 54
No 14
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=99.96 E-value=8.6e-29 Score=236.06 Aligned_cols=207 Identities=15% Similarity=0.177 Sum_probs=164.4
Q ss_pred CcEEEEEecCceEEEEEE----ecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceeccccc--
Q 020983 10 PKVKIRELKDDYAKFELR----DTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMS-- 83 (319)
Q Consensus 10 ~~iei~~~~~~~~~f~l~----g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~-- 83 (319)
.+.++.+.++.+++|.++ |++.++||||||+||+++|++||..|+|++ +.|++..||++.+++..
T Consensus 10 ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g---------v~hEfs~i~GV~Edv~eIi 80 (327)
T CHL00013 10 VESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG---------VPHEYSTIPGIRESVLEIL 80 (327)
T ss_pred eeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC---------ccccccCCCCcccCHHHHH
Confidence 566677778899999998 566699999999999999999999999988 77999999999999752
Q ss_pred eeeeccCCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCceeeccccCCCCCCCCCCCCCeEEEEeCCCCEE
Q 020983 84 MRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQEL 163 (319)
Q Consensus 84 ~~~~~~c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~I 163 (319)
+|++...-.. .......+.|+++ ||+.|||+||..+ .+. +++||+.+||+|..|+.|
T Consensus 81 lNLK~I~~k~-----~~~~~~~~~l~~~----Gp~~vtA~Di~~p------~~i--------eivnpd~~Iatl~~~~~l 137 (327)
T CHL00013 81 LNLKEIVLKS-----NLYGPQKASICVQ----GPKYVTAQDIILP------PSV--------EIVDPTQHIATITEPIDL 137 (327)
T ss_pred HhhhcCeEEc-----cCCCcEEEEEEEe----CCeEEEeeeeccC------CCe--------EEeCCCeEEEEeCCCCEE
Confidence 2332221100 0112468888887 8999999999863 233 788899999999999999
Q ss_pred EEEEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchHH
Q 020983 164 RLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDE 243 (319)
Q Consensus 164 ~le~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e 243 (319)
+|++++.+|+||.-|.-+ . . ..|.|++|+. ++|+.+++|..+
T Consensus 138 ~~el~ie~G~GY~~~~~~----------------------------~----~-~~g~i~iDa~-----FsPV~kVny~Ve 179 (327)
T CHL00013 138 EIELKIEKGRGYRLKTPK----------------------------N----F-QDGSFPIDAV-----FMPVRNVNYSIH 179 (327)
T ss_pred EEEEEEECccCceecccc----------------------------c----c-CCCcEEeCCC-----CCCeeEEEEEEE
Confidence 999999999998444321 0 0 2478889875 789999998876
Q ss_pred HHHHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983 244 VIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 244 ~~~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
-.+ +. ....++++|+|||||+++|.+|+.+|+++|.+.|..|.
T Consensus 180 ~~~----------~~-~~~~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~ 222 (327)
T CHL00013 180 SYG----------NG-NEKQEILFLEIWTNGSITPKEALHEASRNLIDLFIPFL 222 (327)
T ss_pred Ecc----------cC-CcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 311 11 12379999999999999999999999999999999887
No 15
>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=99.96 E-value=1.9e-29 Score=206.44 Aligned_cols=111 Identities=37% Similarity=0.501 Sum_probs=91.9
Q ss_pred EEEeeCcccccchhhhhhhcCCcceeccccc-eeeeccCCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCc
Q 020983 53 VEIEVNSSVLNDEFIAHRLGLIPLTSERAMS-MRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHS 131 (319)
Q Consensus 53 V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~-~~~~~~c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~ 131 (319)
|+|++|||+|+||++|||||+||+.++++.. +...++|.. .....|+.|+++++|+++ +++.|||+||+..++.
T Consensus 1 v~i~~n~s~~~dE~v~He~~~Ipgv~Edv~~iilnlk~i~~-~~~~~~~~~~~~~~L~~~----g~~~V~a~di~~~~~~ 75 (112)
T PF01000_consen 1 VYIYENTSVLPDEGVAHEFGLIPGVSEDVLEIILNLKKIVI-DCEEGCDDCSVTFSLKVK----GPGEVTAGDIKLEPSG 75 (112)
T ss_dssp EEEEEETSSS-HHHHHCHHHBSTCBSSCHHHHHHHHHTT-E-SSSSSTTTSEEEEEEEEE----SSSCEEGGGSEESBTT
T ss_pred CEEEECCCeeccceeEeccccCCccccchhhhhhcchhhcc-ccccCCCCceEEEEEEec----CCCccccceeEecCCc
Confidence 7899999999999999999999999998754 334444521 012378999999999999 7778999999985444
Q ss_pred eeeccccCCCCCCCCCCCCCeEEEEeCCCCEEEEEEEEEecccccccccC
Q 020983 132 VVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWS 181 (319)
Q Consensus 132 ~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~I~le~~a~kG~Gk~HAKw~ 181 (319)
+ ++++|+++||+|++||+|+|++++++|+||+|||||
T Consensus 76 i-------------~ivn~d~~I~tl~~~~~l~~e~~i~~G~Gy~~ak~~ 112 (112)
T PF01000_consen 76 I-------------EIVNPDIYIATLSEGQKLEMELYIEKGRGYVHAKWS 112 (112)
T ss_dssp E-------------EESSTTSEEEEEESSTEEEEEEEEEEEESEECCTS-
T ss_pred e-------------EEecCCeEEEEECCCCEEEEEEEEECCCcccccccC
Confidence 4 566778999999999999999999999999999997
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=99.47 E-value=9e-14 Score=103.34 Aligned_cols=31 Identities=45% Similarity=0.782 Sum_probs=30.1
Q ss_pred EEEEEEecCcchhhHHHHHHHhhcCcceEEE
Q 020983 22 AKFELRDTDASMANALRRVMIAEVPTIAIDL 52 (319)
Q Consensus 22 ~~f~l~g~~~s~aNaLRRillseVPt~AId~ 52 (319)
++|.+.|.++++||||||+||++||++||+.
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=99.23 E-value=1.6e-11 Score=117.27 Aligned_cols=162 Identities=18% Similarity=0.219 Sum_probs=120.4
Q ss_pred hhhhcCCcceecccc--ceeeeccCCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCceeeccccCCCCCCC
Q 020983 68 AHRLGLIPLTSERAM--SMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDS 145 (319)
Q Consensus 68 aHRLgLIPi~~~~~~--~~~~~~~c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~Pv~~~~~~~~~~ 145 (319)
.|+|..+|+..+++. .++++........ ... ++|++++. +++.||++|+... ...
T Consensus 58 ~hef~s~~gv~Edvl~~~LnLk~L~~~~~~----~~~-~~~~~~~~----g~g~v~a~d~~~~------~~l-------- 114 (317)
T COG0202 58 LHEFDSIEGVQEDVLAHRLNLKPLAVKLDG----DEE-VTLELDKE----GPGEVTASDITVP------LDL-------- 114 (317)
T ss_pred ccccccCcCcHHHHHHHHhcCceeeeeccc----ccc-eEEEEecc----CCccccHhhcccc------eeE--------
Confidence 699999999988864 2344332211100 001 78888887 8899999999863 222
Q ss_pred CCCCCCeEEEEeCCCCEEEEEEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCC
Q 020983 146 TDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDP 225 (319)
Q Consensus 146 ~~~~~~I~I~kL~~gq~I~le~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~ 225 (319)
++.||+.+||+|+.|.+|.|++++..|+||..|.-+ + ....+.+.+..|.
T Consensus 115 Ev~np~~~ia~~~~~~~l~~~~~V~~G~gyv~~~~~----------------------------~--~~~~~v~~i~~D~ 164 (317)
T COG0202 115 EVVNPDHVIATLTEDAKLEMELRVYSGDGYVPAEGN----------------------------R--EDDPPVGPIAVDA 164 (317)
T ss_pred EEECCCceeeeccCCcceEEEEEEEcCccEeccccc----------------------------c--ccCCCceeeeCCC
Confidence 788999999999999999999999999998322211 0 1224556677775
Q ss_pred CCCceeecCCccccchHHHHHHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983 226 NTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 226 ~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
. +++..++.|-.+.. .+..+.+.||..|.+||+|++.|++++..|.++|.++|+.|.
T Consensus 165 ~-----~spv~kvqy~ve~~----------r~~~~~~~Dhl~~~~~T~gsi~~~~a~~~aa~il~e~~~~~~ 221 (317)
T COG0202 165 P-----FSPVRKVQYIVEEA----------RVGQGTDKDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFV 221 (317)
T ss_pred c-----eeeeeeceEEEEeE----------EEeccCCceeEEEEEeeccEeehHHHHHHHHHHHHHHHHHHH
Confidence 3 67777777765532 244568899999999999999999999999999999999998
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=99.04 E-value=1.1e-09 Score=85.64 Aligned_cols=35 Identities=34% Similarity=0.697 Sum_probs=32.3
Q ss_pred eCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhccc
Q 020983 262 KEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAV 296 (319)
Q Consensus 262 ~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l 296 (319)
+.++|+|+|||+|+++|.+++.+|+++|+++++.|
T Consensus 52 ~~d~~~~~VeT~Gs~~P~~al~~Ai~~L~~~~~~~ 86 (86)
T cd00460 52 DEDKFILRIETVGSIPPEEALRRAVEILRKKLEHL 86 (86)
T ss_pred CCCeEEEEEEECCCCCHHHHHHHHHHHHHHHHhhC
Confidence 35789999999999999999999999999999865
No 19
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=95.86 E-value=0.013 Score=45.66 Aligned_cols=40 Identities=20% Similarity=0.405 Sum_probs=34.4
Q ss_pred CcEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcceE
Q 020983 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAI 50 (319)
Q Consensus 10 ~~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~AI 50 (319)
++++|.+.+++.++|.+.|-|.+++|+||-.|+. -|...+
T Consensus 1 m~ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~-~~~V~f 40 (85)
T PRK01146 1 MEIKVLEKEDNELELEIEGEDHTLMNLLKEELLE-DPGVEA 40 (85)
T ss_pred CeEEEEecCCCEEEEEEeCCCchHHHHHHHHHhc-CCCeeE
Confidence 4689999999999999999999999999999885 454443
No 20
>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=94.92 E-value=0.035 Score=43.10 Aligned_cols=38 Identities=21% Similarity=0.494 Sum_probs=32.0
Q ss_pred EEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcceE
Q 020983 12 VKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAI 50 (319)
Q Consensus 12 iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~AI 50 (319)
++|++.+++.++|.+.|-|.+++|+||-.|+.. |..-+
T Consensus 1 ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~V~f 38 (83)
T cd06927 1 LKVIEKEDNELELEIEGEDHTLLNLLKEELLRD-PGVKV 38 (83)
T ss_pred CeEEEcCCCEEEEEEeCCCchHHHHHHHHHhcC-CCeEE
Confidence 578899999999999999999999999888875 44433
No 21
>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=94.22 E-value=0.06 Score=41.80 Aligned_cols=33 Identities=18% Similarity=0.423 Sum_probs=28.7
Q ss_pred EEEEEecCceEEEEEEecCcchhhHHHHHHHhh
Q 020983 12 VKIRELKDDYAKFELRDTDASMANALRRVMIAE 44 (319)
Q Consensus 12 iei~~~~~~~~~f~l~g~~~s~aNaLRRillse 44 (319)
|+|++.+++.++|.+.|-|.+++|+||-.|+..
T Consensus 1 ~kii~~~~n~~~~~i~~EdHTLgNlLr~~L~~~ 33 (83)
T cd07027 1 LRIISKEKNSVTVEMENEDHTLGNLLREELLKD 33 (83)
T ss_pred CeeEecCCCEEEEEEeCCCchHHHHHHHHHhcC
Confidence 467888999999999999999999999887765
No 22
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=94.02 E-value=0.083 Score=42.38 Aligned_cols=36 Identities=19% Similarity=0.346 Sum_probs=33.3
Q ss_pred CCCcEEEEEecCceEEEEEEecCcchhhHHHHHHHh
Q 020983 8 RFPKVKIRELKDDYAKFELRDTDASMANALRRVMIA 43 (319)
Q Consensus 8 ~~~~iei~~~~~~~~~f~l~g~~~s~aNaLRRills 43 (319)
+.+++++.+.++++++|.++|-|.||+|.||-.|+.
T Consensus 3 ~~~~l~ii~~~~n~~~i~i~gEdHTL~NlL~~~L~~ 38 (99)
T COG1761 3 PEMELRIIKKDDNSLELEIEGEDHTLGNLLREELLK 38 (99)
T ss_pred CceEEEEeccCCCEEEEEEecCCchHHHHHHHHHhC
Confidence 457888999999999999999999999999999987
No 23
>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=92.86 E-value=0.21 Score=38.16 Aligned_cols=37 Identities=16% Similarity=0.309 Sum_probs=32.1
Q ss_pred eeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983 261 AKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 261 ~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
+-.++..|.|.|+|..+|.++|++|++-|.+.++.|.
T Consensus 38 Pl~~~i~l~Iqt~~~~~p~~~l~~a~~~l~~~~~~l~ 74 (77)
T PF13656_consen 38 PLENKINLRIQTKGGITPIEALKKALEDLIKICEELK 74 (77)
T ss_dssp TTSSEEEEEEEESTTS-HHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4478999999999999999999999999999887663
No 24
>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=91.84 E-value=0.27 Score=38.15 Aligned_cols=35 Identities=9% Similarity=0.159 Sum_probs=32.1
Q ss_pred eCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhccc
Q 020983 262 KEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAV 296 (319)
Q Consensus 262 ~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l 296 (319)
-.++..|.|.|+|+.+|.+++.+|++-|.+.++.|
T Consensus 47 l~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~~ 81 (83)
T cd06927 47 LLSNPVLKIKTDGGVDPLEALKEAAKRLIDLCEEF 81 (83)
T ss_pred CCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999999999999998876
No 25
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=91.56 E-value=0.29 Score=38.17 Aligned_cols=34 Identities=12% Similarity=0.202 Sum_probs=31.6
Q ss_pred CCEEEEEEEeCcccCHHHHHHHHHHHHHHHhccc
Q 020983 263 EDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAV 296 (319)
Q Consensus 263 ~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l 296 (319)
.++..|.|.|+|+.+|.+++.+|++-|.+.++.|
T Consensus 50 ~~~~~lrIqt~~~~~p~~al~~a~~~L~~~~~~~ 83 (85)
T PRK01146 50 ISNPVLKIKTDGGIDPLEALKEAAKRIIDLCDEF 83 (85)
T ss_pred CCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999999999998776
No 26
>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=91.38 E-value=0.33 Score=37.61 Aligned_cols=35 Identities=14% Similarity=0.257 Sum_probs=31.9
Q ss_pred eCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhccc
Q 020983 262 KEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAV 296 (319)
Q Consensus 262 ~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l 296 (319)
-.++..|.|.|+|..+|.+++.+|++-|.+.++.|
T Consensus 47 l~~~~~lrI~T~~~~~P~~al~~a~~~l~~~~~~l 81 (83)
T cd07027 47 VIDKIQIRIQTKSGIKPKDALKRAVNKLSKLYEHL 81 (83)
T ss_pred CCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHh
Confidence 35789999999999999999999999999988766
No 27
>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=90.76 E-value=0.39 Score=37.43 Aligned_cols=37 Identities=19% Similarity=0.310 Sum_probs=32.6
Q ss_pred eeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983 261 AKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 261 ~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
.-.++..|.|.|+|+.+|.+++.+|++-|.+.++.|.
T Consensus 46 Pl~~~~~lriqT~~~~~p~~al~~a~~~l~~~~~~~~ 82 (85)
T cd07029 46 PSENKINLRIQTKGGEPAVDVLKKGLEDLEQICDHIL 82 (85)
T ss_pred CCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3356889999999999999999999999999887663
No 28
>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=89.97 E-value=0.5 Score=37.43 Aligned_cols=36 Identities=22% Similarity=0.363 Sum_probs=32.2
Q ss_pred eCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983 262 KEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 262 ~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
-.++..|.|.|+|+.+|.+++++|++-|.+.++.|.
T Consensus 55 l~~~~~l~i~t~~~~~p~~al~~a~~~l~~~~~~~~ 90 (93)
T cd06926 55 LEHKIELRIQTDGSITPKEALKNAITDLISELSLLK 90 (93)
T ss_pred CCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 357889999999999999999999999999887664
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=89.27 E-value=0.53 Score=37.25 Aligned_cols=37 Identities=22% Similarity=0.289 Sum_probs=29.6
Q ss_pred CcEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCc
Q 020983 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPT 47 (319)
Q Consensus 10 ~~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt 47 (319)
..++.....++.++|.+.|=|.+++|+||-.|+. -|.
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 3444444567899999999999999999999887 454
No 30
>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=83.72 E-value=1.3 Score=34.42 Aligned_cols=28 Identities=25% Similarity=0.446 Sum_probs=25.2
Q ss_pred EecCceEEEEEEecCcchhhHHHHHHHh
Q 020983 16 ELKDDYAKFELRDTDASMANALRRVMIA 43 (319)
Q Consensus 16 ~~~~~~~~f~l~g~~~s~aNaLRRills 43 (319)
...++.++|.+.|=|.+++|+||-.|+.
T Consensus 5 ~~~~n~~~~~i~~EdHTLgNlLr~~L~~ 32 (85)
T cd07029 5 GTDESCATFVFYGEDHTLGNSLRYVIMK 32 (85)
T ss_pred cCCCCeEEEEEeCCCcchHHHHHHHHhh
Confidence 3567899999999999999999999887
No 31
>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=76.47 E-value=1.2 Score=34.00 Aligned_cols=35 Identities=17% Similarity=0.385 Sum_probs=25.4
Q ss_pred ceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEE
Q 020983 20 DYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEI 55 (319)
Q Consensus 20 ~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I 55 (319)
+.++|.+.|-|.|++|+||-.|+.. |...+=.-.+
T Consensus 1 n~~~f~i~~EDHTlgNlLr~~L~~~-p~V~fagY~v 35 (77)
T PF13656_consen 1 NEITFTIYGEDHTLGNLLRYELLKD-PDVEFAGYRV 35 (77)
T ss_dssp TEEEEEEES--HHHHHHHHHCCTTS-TTEEEEEEEE
T ss_pred CeEEEEEeCCCccHHHHHHHHHhhC-CCeEEEEecc
Confidence 4689999999999999999988875 6555444433
No 32
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=75.42 E-value=4.2 Score=32.67 Aligned_cols=37 Identities=11% Similarity=0.207 Sum_probs=33.2
Q ss_pred eeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983 261 AKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 261 ~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
...+.+.+.|-|.|...|.+++.+|++-+.+++..|.
T Consensus 52 P~~~~~~i~Ikt~~~~dp~~aL~~A~~~i~~~~~~l~ 88 (99)
T COG1761 52 PLIDNPKIRIKTKGGVDPKEALKRAARKILKDLEELL 88 (99)
T ss_pred CCCCCceEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3467889999999999999999999999999998875
No 33
>KOG3438 consensus DNA-directed RNA polymerase, subunit L [Transcription]
Probab=69.73 E-value=4.9 Score=32.31 Aligned_cols=36 Identities=33% Similarity=0.398 Sum_probs=26.0
Q ss_pred cCceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCc
Q 020983 18 KDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNS 59 (319)
Q Consensus 18 ~~~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~Nt 59 (319)
.....+|.+..-|.+++||||=+|+- =..|.+-+.|
T Consensus 14 d~~~~Tf~~~eEDHTlgNalR~vI~k------~peVefcGYt 49 (105)
T KOG3438|consen 14 DLSSATFQLREEDHTLGNALRYVIMK------NPEVEFCGYT 49 (105)
T ss_pred CCCceEEEEEecCcchhHHHHHHHhc------CCceEEEecc
Confidence 34578888888888888888887765 2456666644
No 34
>KOG3438 consensus DNA-directed RNA polymerase, subunit L [Transcription]
Probab=62.91 E-value=5.7 Score=31.94 Aligned_cols=37 Identities=24% Similarity=0.310 Sum_probs=33.3
Q ss_pred eeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983 261 AKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 261 ~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
..+++..|.|.|.|++++.++|++|++-|++=++.+.
T Consensus 53 Pse~k~niRIQt~~~~~A~evl~kgl~el~~~c~~v~ 89 (105)
T KOG3438|consen 53 PSEDKINIRIQTRDGDPAVEVLKKGLEELMQLCDHVR 89 (105)
T ss_pred CchhhheEEEEecCCCcchHHHHHHHHHHHHHHHHHH
Confidence 5578999999999999999999999999998887765
No 35
>PRK15449 ferredoxin-like protein FixX; Provisional
Probab=50.50 E-value=13 Score=29.65 Aligned_cols=52 Identities=15% Similarity=0.199 Sum_probs=36.1
Q ss_pred ccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchHHHHHHH
Q 020983 191 EPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKA 248 (319)
Q Consensus 191 ~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~~~~ 248 (319)
.|.|.++.+. +....+.+++.||.+.+..+. ++.+. .+..+|.-|..|...+
T Consensus 22 ~~HI~i~~~~----~~~~~k~C~~aCPagA~~~~e-~G~V~-vd~e~CigCg~C~~~C 73 (95)
T PRK15449 22 HPHIVVKADA----DKQALELLVKACPAGLYKKQD-DGSVR-FDYAGCLECGTCRILG 73 (95)
T ss_pred CCcEEEcCCC----CchhhhHHHHHCCHhhcEeCC-CCCEE-EcCCCCCcchhhhhhc
Confidence 3667776543 112345788999999998863 44443 4778999999998766
No 36
>TIGR02060 aprB adenosine phosphosulphate reductase, beta subunit. During dissimilatory sulfate reduction and sulfur oxidation, adenylylsulfate (APS) reductase catalyzes reversibly the two-electron reduction of APS to sulfite and AMP. Found in several bacterial lineages and in Archaeoglobales, APS reductase is a heterodimer composed of an alpha subunit containing a noncovalently bound FAD, and a beta subunit containing two [4Fe-4S] clusters. Described by this model is the beta subunit of APS reductase, sharing common evolutionary origin with other iron-sulfur cluster-binding proteins.
Probab=44.83 E-value=26 Score=29.45 Aligned_cols=47 Identities=13% Similarity=0.267 Sum_probs=32.5
Q ss_pred hhhccCCCeeEEeCCCCCceeecCCccccchHHHHHHHhhcCCCCcEEEee
Q 020983 211 SWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYA 261 (319)
Q Consensus 211 ~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~i~v~~ 261 (319)
.+...||.+.+.++.........+...|..|..|...+.. +++.+..
T Consensus 20 ~Cv~~CP~~ai~~~~~~~~~~~id~~~C~~Cg~Cv~~CP~----~AI~~~~ 66 (132)
T TIGR02060 20 ACVYICPNDLMHLDTEIMKAYNIEPDMCWECYSCVKACPQ----GAIDVRG 66 (132)
T ss_pred cCHhhcCccceEecCCCceeeecCchhCccHHHHHHhCCc----CceEEEC
Confidence 6788999998888754323333567889999999988742 4555543
No 37
>PF12690 BsuPI: Intracellular proteinase inhibitor; InterPro: IPR020481 BsuPI is a intracellular proteinase inhibitor that directly regulates the major intracellular proteinase (ISP-1) activity in vivo. It inhibits ISP-1 in the early stages of sporulation and then may be inactivated by a membrane-bound proteinase [].; PDB: 3ISY_A.
Probab=36.52 E-value=1.9e+02 Score=22.09 Aligned_cols=63 Identities=21% Similarity=0.181 Sum_probs=27.8
Q ss_pred eEEEEEEEEeccCCCceeecc-----CeeeCCCceeeccccCCCCCCCCCCCCCeEEEEeCCCCEEEEEEEE
Q 020983 103 SVEFHLRAKCHSDQTLDVTSK-----DLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIA 169 (319)
Q Consensus 103 ~v~~~L~v~~~~~~~~~V~s~-----Dl~~~~~~~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~I~le~~a 169 (319)
++.+.|.++|+++.+.++.-. |+...|..-..++.-+ .+...-+-+-=.+|.||+.+..+...
T Consensus 1 ~v~~~l~v~N~s~~~v~l~f~sgq~~D~~v~d~~g~~vwrwS----~~~~FtQal~~~~l~pGe~~~~~~~~ 68 (82)
T PF12690_consen 1 QVEFTLTVTNNSDEPVTLQFPSGQRYDFVVKDKEGKEVWRWS----DGKMFTQALQEETLEPGESLTYEETW 68 (82)
T ss_dssp -EEEEEEEEE-SSS-EEEEESSS--EEEEEE-TT--EEEETT----TT-------EEEEE-TT-EEEEEEEE
T ss_pred CEEEEEEEEeCCCCeEEEEeCCCCEEEEEEECCCCCEEEEec----CCchhhheeeEEEECCCCEEEEEEEE
Confidence 467888888887776665533 4444333222232211 11222333444689999999887653
No 38
>COG1146 Ferredoxin [Energy production and conversion]
Probab=34.70 E-value=50 Score=23.86 Aligned_cols=41 Identities=22% Similarity=0.185 Sum_probs=31.6
Q ss_pred hhhhhccCCCeeEEeCCC-CCceeecCCccccchHHHHHHHh
Q 020983 209 KQSWVESSPTKVFDIDPN-TGQVYVVDAEAYTYDDEVIKKAE 249 (319)
Q Consensus 209 ~~~~~~~cp~~v~~id~~-~~~~~~~~~~~~~~~~e~~~~~~ 249 (319)
...+...||.++|..... ++...+.+...|.-|..|+..+.
T Consensus 13 c~~C~~~CP~~~~~~~~~~~~~~~~~~~e~C~~C~~C~~~CP 54 (68)
T COG1146 13 CGICVEVCPAGVFDLGEDEGGKPVVARPEECIDCGLCELACP 54 (68)
T ss_pred CChheeccChhhEEeccccCcceeEeccccCccchhhhhhCC
Confidence 345788999999988653 34556778899999999998764
No 39
>KOG4392 consensus RNA polymerase, subunit L [Transcription]
Probab=33.97 E-value=70 Score=26.30 Aligned_cols=37 Identities=24% Similarity=0.319 Sum_probs=33.7
Q ss_pred eeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020983 261 AKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 261 ~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
.-..+|++.|.|+-..+|.+++..|++-|...+..+.
T Consensus 66 Pl~~~~~LRiqtt~d~~p~~al~~a~~~l~~el~~l~ 102 (117)
T KOG4392|consen 66 PLEHKIILRVQTTEDCSPADALTNAITDLIEELSLLE 102 (117)
T ss_pred cccccEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3467999999999999999999999999999998887
No 40
>PRK08348 NADH-plastoquinone oxidoreductase subunit; Provisional
Probab=33.28 E-value=33 Score=27.86 Aligned_cols=40 Identities=15% Similarity=0.161 Sum_probs=28.6
Q ss_pred hhhhhccCCCeeEEeCCCCCceeecCCccccchHHHHHHHh
Q 020983 209 KQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAE 249 (319)
Q Consensus 209 ~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~~~~~ 249 (319)
+..+...||.+.+..+.....+. .+...|..|..|+..+.
T Consensus 47 C~~C~~~CP~~ai~~~~~~~~~~-i~~~~C~~Cg~Cv~~CP 86 (120)
T PRK08348 47 CRMCVTVCPAGVFVYLPEIRKVA-LWTGRCVFCGQCVDVCP 86 (120)
T ss_pred cccHHHHCCccceEccccccceE-ecCCcCcChhhhHHhCC
Confidence 56788899998887764333332 34568999999998874
No 41
>KOG3307 consensus Molybdopterin converting factor subunit 2 [Coenzyme transport and metabolism]
Probab=32.59 E-value=18 Score=30.31 Aligned_cols=43 Identities=19% Similarity=0.318 Sum_probs=25.7
Q ss_pred EEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCccee
Q 020983 24 FELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTS 78 (319)
Q Consensus 24 f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~ 78 (319)
+.-+-+++---|-||-|.-.-=.+.-|..+- +.||||++|+--
T Consensus 52 L~Yeay~pMA~~~lr~IC~~iR~~wpvkkIA------------vfHRLG~VpvgE 94 (150)
T KOG3307|consen 52 LSYEAYDPMAYKKLRGICAEIRAEWPVKKIA------------VFHRLGKVPVGE 94 (150)
T ss_pred eehhhhcHHHHHHHHHHHHHHHhhCchhhhh------------hhhhccCcccCc
Confidence 3334556666678887764322233344432 569999999754
No 42
>PF13237 Fer4_10: 4Fe-4S dicluster domain; PDB: 2FGO_A.
Probab=27.80 E-value=50 Score=22.26 Aligned_cols=39 Identities=18% Similarity=0.206 Sum_probs=17.6
Q ss_pred hhhhhccCCC-eeEEeCCCCCceeecCCccccchHHHHHHH
Q 020983 209 KQSWVESSPT-KVFDIDPNTGQVYVVDAEAYTYDDEVIKKA 248 (319)
Q Consensus 209 ~~~~~~~cp~-~v~~id~~~~~~~~~~~~~~~~~~e~~~~~ 248 (319)
...+.+.||. ...........+.+ +..+|..|..|+...
T Consensus 12 C~~C~~~CP~~~~~~~~~~~~~~~~-~~~~C~~Cg~C~~~C 51 (52)
T PF13237_consen 12 CGRCVKVCPADNAIAIDDGEKKVEI-DPERCIGCGACVEVC 51 (52)
T ss_dssp --TTGGG-TT-----EEE-SSSEEE--TTT--TTSHHHHH-
T ss_pred CcChHHHccchhHHHhhccCCCeEe-CcccccccChhhhhC
Confidence 4567788997 33333322333333 788899999887643
No 43
>KOG3256 consensus NADH:ubiquinone oxidoreductase, NDUFS8/23 kDa subunit [Energy production and conversion]
Probab=27.38 E-value=39 Score=29.80 Aligned_cols=58 Identities=14% Similarity=0.244 Sum_probs=38.1
Q ss_pred hhhhhccCCCeeEEeCCC-----CCce--eecCCccccchHHHHHHHhhcCCCCcEEEeeeCCEEEEEEEeC
Q 020983 209 KQSWVESSPTKVFDIDPN-----TGQV--YVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVEST 273 (319)
Q Consensus 209 ~~~~~~~cp~~v~~id~~-----~~~~--~~~~~~~~~~~~e~~~~~~~~~~~~~i~v~~~~d~f~f~IET~ 273 (319)
++-|...||...+.+|.. .++. ..-|--+|.||.-|...+. .+.| .....|.|+-||-
T Consensus 116 CklCeavCPaqaitieae~r~dgsrRttrYdIDmtkCIyCG~CqEaCP----vdai---vegpnfEfsTeth 180 (212)
T KOG3256|consen 116 CKLCEAVCPAQAITIEAEERTDGSRRTTRYDIDMTKCIYCGFCQEACP----VDAI---VEGPNFEFSTETH 180 (212)
T ss_pred HHHHHHhCCcccceeeceecCCccccceeecccceeeeeecchhhhCC----ccce---eccCCceeccccH
Confidence 455677899988888742 1111 2335668999999988773 2333 3346788888875
No 44
>PRK10882 hydrogenase 2 protein HybA; Provisional
Probab=25.86 E-value=1e+02 Score=29.94 Aligned_cols=57 Identities=14% Similarity=0.106 Sum_probs=33.3
Q ss_pred ccCccceeecccc-cccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchHH
Q 020983 179 KWSPAATVTFMYE-PEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDE 243 (319)
Q Consensus 179 Kw~Pvs~~~y~~~-p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e 243 (319)
+..|+.+...... ..+.++.+.+ ..+..+...||.+++.++.... .....+|++|.+
T Consensus 122 ~aCP~gAi~k~~~~g~V~id~dkC-----igCg~Cv~aCP~gai~~~~~~~---~~~~~KC~~C~~ 179 (328)
T PRK10882 122 SVCPVSALTKDPKTGIVHYDKDVC-----TGCRYCMVACPFNVPKYDYNNP---FGAIHKCELCNQ 179 (328)
T ss_pred hhCCCCCEEecccCCcccCCHHHc-----CcccHHHHhCCccceecccccc---ccceeecccccc
Confidence 3456554443322 3445565555 2466788889988877653211 224578999987
No 45
>PF13247 Fer4_11: 4Fe-4S dicluster domain; PDB: 2VPY_F 2VPX_B 2VPZ_B 2VPW_F 3IR7_B 1Y5N_B 1R27_D 3EGW_B 1Y5I_B 1Q16_B ....
Probab=25.10 E-value=1e+02 Score=24.46 Aligned_cols=39 Identities=26% Similarity=0.330 Sum_probs=24.3
Q ss_pred hhhccCCCeeEEeCCCCCceeecCCccccchHHHHHHHhh
Q 020983 211 SWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEA 250 (319)
Q Consensus 211 ~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~~~~~~ 250 (319)
.+++.||.+.+..++.++.+ +.+..+|.-|..|...+.+
T Consensus 16 pC~~~CP~~Ai~~~~~~G~V-~id~~~CigC~~C~~aCP~ 54 (98)
T PF13247_consen 16 PCVEACPTGAIYKDPEDGIV-VIDEDKCIGCGYCVEACPY 54 (98)
T ss_dssp HHHHHCTTTSEEEETTTS-E-EE-TTTCCTHHHHHHH-TT
T ss_pred chhhhCCccceEEEcCCCeE-EechhhccCchhhhhhhcc
Confidence 45667888777776644544 4456778778777777643
No 46
>TIGR02936 fdxN_nitrog ferredoxin III, nif-specific. Members of this family are homodimeric ferredoxins from nitrogen fixation regions of many nitrogen-fixing bacteria. As characterized in Rhodobacter capsulatus, these proteins are homodimeric, with two 4Fe-4S clusters bound per monomer. Although nif-specific, this protein family is not usiveral, as other nitrogenase systems may substitute flavodoxins, or different types of ferredoxin.
Probab=24.65 E-value=58 Score=24.70 Aligned_cols=65 Identities=9% Similarity=0.149 Sum_probs=38.5
Q ss_pred cccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCC----------------C-ceeecC
Q 020983 172 GIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNT----------------G-QVYVVD 234 (319)
Q Consensus 172 G~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~----------------~-~~~~~~ 234 (319)
|.-+.-+-|+|-.. +.++.+.+ ..+..+++.||.+++.++..+ . .....+
T Consensus 2 ~~~~~~~~~~~~~~--------~~i~~~~C-----i~C~~Cv~~CP~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ 68 (91)
T TIGR02936 2 GLTRGGSEWTPQFV--------TSIDQEKC-----IGCGRCYKVCGRDVLTLKGINEEGELVASDDDDDEIERKVMVVAN 68 (91)
T ss_pred ccccCCCccCccee--------EEECHhHC-----CCcchHHHHcChhhceeeccccccccccccccccccccceeeecC
Confidence 33444566775432 33444444 235678889999888765210 0 112346
Q ss_pred CccccchHHHHHHHh
Q 020983 235 AEAYTYDDEVIKKAE 249 (319)
Q Consensus 235 ~~~~~~~~e~~~~~~ 249 (319)
...|..|..|...+.
T Consensus 69 ~~~C~~Cg~C~~~CP 83 (91)
T TIGR02936 69 PGNCIGCGACARVCP 83 (91)
T ss_pred CccCcChhhhhhhCC
Confidence 788999999987763
No 47
>TIGR00402 napF ferredoxin-type protein NapF. The gene codes for a ferredoxin-type cytosolic protein, NapF, of the periplasmic nitrate reductase system, as in Escherichia coli. NapF interacts with the catalytic subunit, NapA, and may be an accessory protein for NapA maturation.
Probab=23.95 E-value=56 Score=25.74 Aligned_cols=41 Identities=2% Similarity=0.075 Sum_probs=28.4
Q ss_pred hhhhhccCCCeeEEeCCCCCceeecCCccccchHHHHHHHh
Q 020983 209 KQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAE 249 (319)
Q Consensus 209 ~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~~~~~ 249 (319)
+..+...||.+.+..+..+......+...|++|..|...+.
T Consensus 39 C~~C~~~CP~~~i~~~~~g~~~~~i~~~~C~~Cg~C~~~CP 79 (101)
T TIGR00402 39 CGECASACENNILQLGQQGQPTVEFDNAECDFCGKCAEACP 79 (101)
T ss_pred hhHHHHHcCcccceeccCCceeeEecCccCcCccChhhHCC
Confidence 56688899998887764322222345568999999988764
No 48
>COG1143 NuoI Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]
Probab=23.47 E-value=47 Score=29.28 Aligned_cols=41 Identities=2% Similarity=0.026 Sum_probs=28.8
Q ss_pred hhhhhccCCCeeEEeCCC--C------CceeecCCccccchHHHHHHHh
Q 020983 209 KQSWVESSPTKVFDIDPN--T------GQVYVVDAEAYTYDDEVIKKAE 249 (319)
Q Consensus 209 ~~~~~~~cp~~v~~id~~--~------~~~~~~~~~~~~~~~e~~~~~~ 249 (319)
+.-|.+.||.+.+.+... . .+...-+-.+|.||.-|+..+.
T Consensus 60 C~lCa~iCP~~aI~m~~~~~~~~g~~~~~~~~In~grCIfCg~C~e~CP 108 (172)
T COG1143 60 CGLCANICPANAITMETAERKVDGRKKPKRPDINLGRCIFCGLCVEVCP 108 (172)
T ss_pred hhHHHhhCCcCceEEEEcccCCCCccccccceeccccccccCchhhhCc
Confidence 456778999998877431 1 1223446789999999998874
No 49
>KOG4392 consensus RNA polymerase, subunit L [Transcription]
Probab=23.13 E-value=92 Score=25.61 Aligned_cols=35 Identities=17% Similarity=0.392 Sum_probs=28.7
Q ss_pred CcEEEEE--ecCceEEEEEEecCcchhhHHHHHHHhh
Q 020983 10 PKVKIRE--LKDDYAKFELRDTDASMANALRRVMIAE 44 (319)
Q Consensus 10 ~~iei~~--~~~~~~~f~l~g~~~s~aNaLRRillse 44 (319)
.+|.+.. ..++.+.|+++.-|.++||-||-=|+.+
T Consensus 17 kKvtin~DtKvpNA~~fTiekEDHTLGNii~~qLl~D 53 (117)
T KOG4392|consen 17 KKITINKDTKVPNAALFTIEKEDHTLGNIIKSQLLKD 53 (117)
T ss_pred ceeEEecCCCCCceEEEEEecccchHHHHHHHHHccC
Confidence 3455543 4578999999999999999999988876
No 50
>PRK06273 ferredoxin; Provisional
Probab=23.06 E-value=44 Score=29.16 Aligned_cols=42 Identities=17% Similarity=0.128 Sum_probs=28.7
Q ss_pred hhhhhhccCCCeeEEeCCCC----------CceeecCCccccchHHHHHHHh
Q 020983 208 EKQSWVESSPTKVFDIDPNT----------GQVYVVDAEAYTYDDEVIKKAE 249 (319)
Q Consensus 208 ~~~~~~~~cp~~v~~id~~~----------~~~~~~~~~~~~~~~e~~~~~~ 249 (319)
.+..|...||.+.+..+... ......+..+|.+|..|...+.
T Consensus 53 gCg~C~~aCP~~AI~~~~~ep~~~~~~~~~~~~~~Id~~kCi~Cg~C~~aCP 104 (165)
T PRK06273 53 GCGGCANVCPTKAIEMIPVEPVKITEGYVKTKIPKIDYEKCVYCLYCHDFCP 104 (165)
T ss_pred ChhHHHHhcCccceeeecccccchhcccccccceecccccCcCCCCcchhCC
Confidence 35678889999888765311 0112446688999999998874
No 51
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=22.55 E-value=72 Score=28.71 Aligned_cols=41 Identities=15% Similarity=0.261 Sum_probs=30.1
Q ss_pred ceEEEEEE---ecCcc-hhhHHHHHHHhhcCcceEEEEEEeeCcc
Q 020983 20 DYAKFELR---DTDAS-MANALRRVMIAEVPTIAIDLVEIEVNSS 60 (319)
Q Consensus 20 ~~~~f~l~---g~~~s-~aNaLRRillseVPt~AId~V~I~~NtS 60 (319)
-++...|. |...+ .+.+||+.+-++||+|..+.|.|.++.+
T Consensus 152 ~sASV~l~~~~g~~l~~qv~~I~~LVa~sV~gL~~enVtVvD~~G 196 (206)
T PF01514_consen 152 PSASVVLKLKPGSELSEQVQGIQNLVASSVPGLKPENVTVVDQNG 196 (206)
T ss_dssp EEEEEEEEE-TTS--GGGHHHHHHHHHHHSTT--GGGEEEEEEET
T ss_pred CeEEEEEEECCCCChHHHHHHHHHHHHHhcCCCCcccEEEEeCCC
Confidence 35555554 66666 9999999999999999999999987665
No 52
>PF13187 Fer4_9: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_C 2O01_C 2WSC_C 3LW5_C 2VKR_C 1KQG_B 1KQF_B 3GYX_J.
Probab=21.51 E-value=67 Score=21.74 Aligned_cols=39 Identities=26% Similarity=0.309 Sum_probs=23.6
Q ss_pred hhhhccCCCeeEEeCCCCCceeecC------CccccchHHHHHHH
Q 020983 210 QSWVESSPTKVFDIDPNTGQVYVVD------AEAYTYDDEVIKKA 248 (319)
Q Consensus 210 ~~~~~~cp~~v~~id~~~~~~~~~~------~~~~~~~~e~~~~~ 248 (319)
..+.+.||.+++..+.......... ...|..|..|+...
T Consensus 6 g~C~~~CP~~~~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~C 50 (55)
T PF13187_consen 6 GRCVEACPVGVIEFDEDGGKKVVDKDNERRNAEKCIGCGACVKAC 50 (55)
T ss_dssp THHHHHSTTT-EEEETTTTCEECSECCESTTGGG--TTCHHHHHS
T ss_pred chHHHHCCccCeEccCccccccccccccCCCCCccccHhHHHHHc
Confidence 3466789999998876544332222 23799999998775
No 53
>PRK14993 tetrathionate reductase subunit B; Provisional
Probab=21.44 E-value=66 Score=29.77 Aligned_cols=39 Identities=15% Similarity=0.119 Sum_probs=27.0
Q ss_pred cccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchH
Q 020983 194 IHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDD 242 (319)
Q Consensus 194 i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~ 242 (319)
+.++.+.+ ..+..+...||.+.+.++... ....+|++|.
T Consensus 125 v~id~~~C-----igC~~Cv~aCP~~Ai~~~~~~-----~~~~KC~~C~ 163 (244)
T PRK14993 125 VVVDNKRC-----VGCAYCVQACPYDARFINHET-----QTADKCTFCV 163 (244)
T ss_pred EEEcHHHC-----CCHHHHHHhcCCCCCEEeCCC-----CCcccCcCCc
Confidence 34555554 246678889999988886542 2457899997
No 54
>COG0437 HybA Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]
Probab=20.98 E-value=64 Score=29.25 Aligned_cols=53 Identities=13% Similarity=0.224 Sum_probs=33.3
Q ss_pred Cccceeeccc-ccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchHH
Q 020983 181 SPAATVTFMY-EPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDE 243 (319)
Q Consensus 181 ~Pvs~~~y~~-~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e 243 (319)
-|+++...++ .=.+.+|++.+ -.+..+...||-++..+++.++. ..+|+||.+
T Consensus 81 CPtgA~~k~~~dGiV~vd~d~C-----IGC~yCi~ACPyga~~~~~~~~~-----~~KCt~C~~ 134 (203)
T COG0437 81 CPTGALFKREEDGIVLVDKDLC-----IGCGYCIAACPYGAPQFNPDKGV-----VDKCTFCVD 134 (203)
T ss_pred CCCcceEEecCCCEEEecCCcc-----cCchHHHhhCCCCCceeCcccCc-----ccccCcchh
Confidence 4555555554 44555666655 34667778888877777664332 578888865
No 55
>PF11611 DUF4352: Domain of unknown function (DUF4352); InterPro: IPR021652 This entry is represented by Bacteriophage A118, Gp32. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a group of putative lipoproteins of unknown function.; PDB: 3CFU_A.
Probab=20.64 E-value=4.2e+02 Score=20.66 Aligned_cols=67 Identities=15% Similarity=0.192 Sum_probs=36.4
Q ss_pred CceEEEEEEEEeccCCCceeeccCeeeCCC--ceeeccccCCCCCCCCCCCCCeEEEEeCCCCEEEEEEEEEecc
Q 020983 101 FCSVEFHLRAKCHSDQTLDVTSKDLYSSDH--SVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGI 173 (319)
Q Consensus 101 ~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~--~~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~I~le~~a~kG~ 173 (319)
...+.+.+.++|.++.+..+.+.++...+. ...+..... ........-..|.||+++.-.+....--
T Consensus 35 ~~fv~v~v~v~N~~~~~~~~~~~~f~l~d~~g~~~~~~~~~------~~~~~~~~~~~i~pG~~~~g~l~F~vp~ 103 (123)
T PF11611_consen 35 NKFVVVDVTVKNNGDEPLDFSPSDFKLYDSDGNKYDPDFSA------SSNDNDLFSETIKPGESVTGKLVFEVPK 103 (123)
T ss_dssp SEEEEEEEEEEE-SSS-EEEEGGGEEEE-TT--B--EEE-C------CCTTTB--EEEE-TT-EEEEEEEEEEST
T ss_pred CEEEEEEEEEEECCCCcEEecccceEEEeCCCCEEcccccc------hhccccccccEECCCCEEEEEEEEEECC
Confidence 457899999999988888888888765321 111211100 0011124567899999998887665543
Done!