Query psy12829
Match_columns 181
No_of_seqs 128 out of 1038
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 20:53:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12829.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12829hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1522|consensus 100.0 1.5E-62 3.2E-67 404.2 13.5 178 2-181 1-178 (285)
2 cd07032 RNAP_I_II_AC40 AC40 su 100.0 4.4E-59 9.6E-64 398.5 15.7 167 7-181 1-182 (291)
3 cd07031 RNAP_II_RPB3 RPB3 subu 100.0 9.7E-57 2.1E-61 380.7 16.0 169 7-181 1-175 (265)
4 cd07028 RNAP_RPB3_like RPB3 su 100.0 2.3E-54 5E-59 355.7 15.5 165 7-180 1-166 (212)
5 KOG1521|consensus 100.0 8.3E-55 1.8E-59 366.5 12.4 176 3-181 42-227 (338)
6 PRK00783 DNA-directed RNA poly 100.0 8.1E-53 1.8E-57 355.8 14.1 155 7-181 1-156 (263)
7 cd07030 RNAP_D D subunit of Ar 100.0 6.3E-50 1.4E-54 337.5 14.3 154 7-180 1-155 (259)
8 PRK14979 DNA-directed RNA poly 100.0 3.1E-45 6.8E-50 297.5 14.2 139 6-180 3-141 (195)
9 smart00662 RPOLD RNA polymeras 100.0 1.4E-45 3.1E-50 305.7 11.9 143 18-180 1-144 (224)
10 PRK05182 DNA-directed RNA poly 100.0 1.7E-33 3.6E-38 243.4 15.6 140 1-175 1-152 (310)
11 cd06928 RNAP_alpha_NTD N-termi 100.0 1.8E-33 3.8E-38 232.2 14.6 132 11-176 3-144 (215)
12 COG0202 RpoA DNA-directed RNA 100.0 1.1E-33 2.5E-38 244.8 12.8 165 9-180 7-196 (317)
13 PF01000 RNA_pol_A_bac: RNA po 100.0 4.2E-34 9.2E-39 213.4 5.9 110 50-177 1-112 (112)
14 TIGR02027 rpoA DNA-directed RN 100.0 6.1E-30 1.3E-34 220.1 13.5 124 18-175 1-134 (297)
15 CHL00013 rpoA RNA polymerase a 99.9 5.3E-27 1.2E-31 204.0 14.3 133 7-174 10-152 (327)
16 PF01193 RNA_pol_L: RNA polyme 99.0 3E-10 6.5E-15 77.2 3.0 31 19-49 1-31 (66)
17 COG0202 RpoA DNA-directed RNA 98.5 2.2E-07 4.8E-12 81.1 6.1 90 58-174 52-147 (317)
18 cd00460 RNAP_RPB11_RPB3 RPB11 97.7 6.2E-05 1.3E-09 53.7 5.2 32 9-40 1-32 (86)
19 PRK01146 DNA-directed RNA poly 97.0 0.0011 2.5E-08 47.3 4.6 43 7-50 1-43 (85)
20 cd06927 RNAP_L L subunit of Ar 96.6 0.0033 7.1E-08 44.7 4.1 41 9-50 1-41 (83)
21 cd07027 RNAP_RPB11_like RPB11 96.4 0.0048 1E-07 43.9 4.0 36 9-45 1-36 (83)
22 COG1761 RPB11 DNA-directed RNA 96.0 0.014 3E-07 42.9 4.6 36 5-40 3-38 (99)
23 cd06926 RNAP_II_RPB11 RPB11 su 95.4 0.026 5.7E-07 40.9 4.2 42 5-47 5-46 (93)
24 cd07029 RNAP_I_III_AC19 AC19 s 93.7 0.084 1.8E-06 37.6 3.4 31 13-44 5-35 (85)
25 PF13656 RNA_pol_L_2: RNA poly 93.1 0.1 2.2E-06 36.5 3.0 35 17-52 1-35 (77)
26 KOG3438|consensus 86.5 0.8 1.7E-05 33.8 3.0 35 15-55 14-48 (105)
27 KOG4392|consensus 68.0 7.1 0.00015 29.4 3.3 33 9-41 21-53 (117)
28 cd04932 ACT_AKiii-LysC-EC_1 AC 50.8 60 0.0013 22.0 5.4 41 6-46 29-69 (75)
29 TIGR01444 fkbM_fam methyltrans 41.1 28 0.00061 25.5 2.8 33 16-48 109-141 (143)
30 PF01883 DUF59: Domain of unkn 36.0 1.1E+02 0.0025 20.0 4.9 41 9-52 26-72 (72)
31 PF01514 YscJ_FliF: Secretory 33.3 47 0.001 27.1 3.1 41 18-58 153-197 (206)
32 TIGR01608 citD citrate lyase a 31.3 75 0.0016 23.1 3.5 38 16-53 26-64 (92)
33 KOG3307|consensus 28.2 21 0.00045 27.5 0.2 43 23-77 54-96 (150)
34 PF10633 NPCBM_assoc: NPCBM-as 28.0 1.9E+02 0.0041 19.3 5.1 59 97-170 5-63 (78)
35 PF06857 ACP: Malonate decarbo 27.1 1.2E+02 0.0026 21.6 3.9 56 9-75 18-74 (87)
36 PF11604 CusF_Ec: Copper bindi 26.2 52 0.0011 22.1 1.8 30 143-172 33-62 (70)
37 PF06031 SERTA: SERTA motif; 23.1 44 0.00095 20.3 0.9 9 29-37 25-33 (38)
38 PF12988 DUF3872: Domain of un 22.4 70 0.0015 24.9 2.1 26 152-177 43-68 (137)
39 PF11175 DUF2961: Protein of u 21.7 1E+02 0.0022 26.0 3.2 19 1-19 56-74 (237)
40 PF01629 DUF22: Domain of unkn 21.3 46 0.00099 24.9 0.9 32 40-71 52-83 (112)
No 1
>KOG1522|consensus
Probab=100.00 E-value=1.5e-62 Score=404.24 Aligned_cols=178 Identities=67% Similarity=1.084 Sum_probs=166.1
Q ss_pred CCCCCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccce
Q psy12829 2 PYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDR 81 (181)
Q Consensus 2 ~~~~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~ 81 (181)
||+++|.|+|.+++++.++|+|++.+.++||||||||||||||+||++|+|+-|||||+||||||||||||+.+++.+ .
T Consensus 1 ~y~~~p~v~I~Elt~d~vkF~L~nTdlsvANsLRRV~iaEvPTiAID~VeIe~NssVL~DEFiAHRLGLIPl~S~~~~-~ 79 (285)
T KOG1522|consen 1 PYANQPTVKIRELTDDNVKFVLSNTDLSVANSLRRVMIAEVPTIAIDLVEIEVNSSVLPDEFIAHRLGLIPLISDRIV-E 79 (285)
T ss_pred CCCCCCceEEEecCCCceEEEEecChHHHHHHHHHHHHhcCceeEEEEEEEecccccccHHHHHhhhcceeccchhhh-h
Confidence 799999999999999999999999999999999999999999999999999999999999999999999999999865 4
Q ss_pred EEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEE
Q psy12829 82 ILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRL 161 (181)
Q Consensus 82 ~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~ 161 (181)
++|..+|.|+++|++|+|.|+|+++|+.++...||+.||++.++.+.|+.+ .+......+.-..+|+|+||++||+|++
T Consensus 80 l~ytrdC~C~~~C~eCSVef~L~~kc~~d~T~~VtsrDL~s~~~~v~pv~~-~~~~~~~~~~e~~gilI~KLRkgQELkL 158 (285)
T KOG1522|consen 80 LQYTRDCECDEFCPECSVEFTLDVKCTDDQTRDVTSRDLVSLDPTVTPVDS-NRGSEIDDDSESKGILIVKLRKGQELKL 158 (285)
T ss_pred hhhcccCchhccCCcceEEEEEeeeecccceeeeehHhhhccCCccccccc-CCCCccccccccCCcEEEEeecCCceee
Confidence 999999999999999999999999999999999999999998999999987 2333333334468999999999999999
Q ss_pred EEEEEeccccccceeccCCC
Q psy12829 162 RAYAKKGFGKEHAKWNPTAG 181 (181)
Q Consensus 162 e~~~~kG~G~~HAKw~pv~~ 181 (181)
+|+|+||+||+||||+|+++
T Consensus 159 ra~akKGigKeHAKWsPta~ 178 (285)
T KOG1522|consen 159 RAIAKKGIGKEHAKWSPTAA 178 (285)
T ss_pred eeeecccccccccccCCcce
Confidence 99999999999999999985
No 2
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun
Probab=100.00 E-value=4.4e-59 Score=398.53 Aligned_cols=167 Identities=39% Similarity=0.611 Sum_probs=151.9
Q ss_pred CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEEee
Q psy12829 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSR 86 (181)
Q Consensus 7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~~ 86 (181)
.+|++.++++++++|+|+|+++|+||||||+|||||||||||.|+|++|||+|+||+|||||||||+.++. +.+.|+.
T Consensus 1 ~~i~i~~~~~~~~~f~l~~~d~s~ANAlRRimiaEVPt~AId~V~i~~NTSvl~DE~lAHRLGLIPL~~d~--~~~~~~~ 78 (291)
T cd07032 1 FKIEIISLSDEELEFDLIGVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLIPIKADP--RLFEYRE 78 (291)
T ss_pred CeEEEEECCCCEEEEEEecCCHHHHHHHHHHHHhcCcceeEEEEEEEECCccchhHHHHHhhcCceeecCH--HHccccc
Confidence 36899999999999999999999999999999999999999999999999999999999999999999973 6789999
Q ss_pred cCCCcCCCCCceEEEEEEEEecCCCc--------------eeEEeccceeCCCeeeeccccCcCC-CCCCccCCCCeEEE
Q psy12829 87 DCTCVDFCSECSVEFTLDVKCVDDQT--------------RHVTTADLKSTDARVVPVTSRNRDA-DMNEYGETDDILIV 151 (181)
Q Consensus 87 ~~~~~~~~~~~~v~~~L~v~~~~~~~--------------~~V~s~di~~~~~~~~p~~~~~~~~-~~~~~~~~~di~I~ 151 (181)
+| |+++|+.|++.|+|+++|+.++. ..|||+||+ |.|.+.|.+.+ +.+..++++||+|+
T Consensus 79 ~~-~~~~~~~~~v~f~L~v~c~~~~~~~~~~~~~~~~~~~~~VyS~dl~-----~~p~g~q~~~~~~~~v~~v~~dI~I~ 152 (291)
T cd07032 79 DS-DDEPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHKVYSGDLK-----WVPIGSQEKRFADNPIRPVHPDILIA 152 (291)
T ss_pred cc-ccCCCCCcEEEEEEEEEccCCcccccccccccccccccEEECCCCE-----ecCCCccccccCCCCcEEeCCCcEEE
Confidence 98 77899999999999999987642 578888887 78988876543 44566889999999
Q ss_pred EeCCCCEEEEEEEEEeccccccceeccCCC
Q psy12829 152 KLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181 (181)
Q Consensus 152 kL~~gq~i~~e~~~~kG~G~~HAKw~pv~~ 181 (181)
||++||+|+|+|+|+||+||+||||||||+
T Consensus 153 kL~~gQ~l~le~~a~kG~Gk~HAKwsPv~t 182 (291)
T cd07032 153 KLRPGQEIDLELHCVKGIGKDHAKFSPVAT 182 (291)
T ss_pred EECCCCEEEEEEEEEcCcccccceecCcee
Confidence 999999999999999999999999999974
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=9.7e-57 Score=380.75 Aligned_cols=169 Identities=66% Similarity=1.051 Sum_probs=146.2
Q ss_pred CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEEe-
Q psy12829 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYS- 85 (181)
Q Consensus 7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~- 85 (181)
|+|++.+.++++++|.++|+++|+||||||+|||||||+||+.|+|++|||+|+||||||||||||++++++ ..+.+.
T Consensus 1 p~i~i~~~~~~~~~F~l~~~~~s~aNALRRillsevPt~AI~~V~I~~NtSvl~DE~iaHRlglIPl~~e~~-~~~~~~~ 79 (265)
T cd07031 1 PRVEITELTDDKVKFILENTDLSVANSLRRVMIAEVPTLAIDLVEIEENTSVLHDEFIAHRLGLIPLTSDDV-DEFLYYS 79 (265)
T ss_pred CcEEEEEcCCCEEEEEEEcCcHHHHHHHHHHHHHcCccceEEEEEEecCCcccccceeeeecccCCCccCcH-HHHhhhh
Confidence 579999999999999999999999999999999999999999999999999999999999999999999985 334444
Q ss_pred ecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCC-----CeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEE
Q psy12829 86 RDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTD-----ARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELR 160 (181)
Q Consensus 86 ~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~-----~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~ 160 (181)
++|.|.+.|+.|++.|+|+++|++++++.|||+||++.. ....|+... ......++||+|+||++||+|+
T Consensus 80 ~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~~~~~~pi~~~-----~~~~~~~~~i~I~kL~~gq~i~ 154 (265)
T cd07031 80 RDCDCDEFCDKCSVELTLDVKCTGDQTREVTSRDLVSSGPKVNDVVPVPIRND-----SEDNGEEDGILIVKLRKGQELK 154 (265)
T ss_pred hhccccCCCCCCeEEEEEEEEeccCCCceEEHHHcccccccccccCCcccccc-----cccccCCCCeEEEEECCCCEEE
Confidence 578888889999999999999999999999999998742 111222210 0011346999999999999999
Q ss_pred EEEEEEeccccccceeccCCC
Q psy12829 161 LRAYAKKGFGKEHAKWNPTAG 181 (181)
Q Consensus 161 ~e~~~~kG~G~~HAKw~pv~~ 181 (181)
|+|+|+||+||+|||||||++
T Consensus 155 le~~a~kG~Gk~HAKwsPv~~ 175 (265)
T cd07031 155 LRCIAKKGIGKEHAKWSPTAA 175 (265)
T ss_pred EEEEEECCEeccCCEeccceE
Confidence 999999999999999999974
No 4
>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=2.3e-54 Score=355.68 Aligned_cols=165 Identities=45% Similarity=0.698 Sum_probs=141.3
Q ss_pred CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceE-EEe
Q psy12829 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRI-LYS 85 (181)
Q Consensus 7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~-~~~ 85 (181)
|.|++.+.++++++|.|+|+++|+||||||+|||||||+||+.|+|++|||+|+||++|||||||||++++++..+ +.+
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 5689999999999999999999999999999999999999999999999999999999999999999999865432 234
Q ss_pred ecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEE
Q psy12829 86 RDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYA 165 (181)
Q Consensus 86 ~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~ 165 (181)
..|.|...|..|++.++|+++++.+.+..|||+||++.+ .+.. .+...+++|||+|+||++||+|+|+|+|
T Consensus 81 ~~~~~~~~~~~~~v~~~l~~~g~~~~~~~V~s~DL~~~~-----~~~~----~~~v~pv~~di~I~kL~~gq~i~le~~~ 151 (212)
T cd07028 81 EDCECEDHCDKCSVVLTLQAFAESESTTNVYSKDLVIVS-----NLMG----RNIGHPIIQDILICKLRKGQEIKLTCVA 151 (212)
T ss_pred ccccccccccceeEEEEEEccCCCCCcceEEHHHcccCC-----cccc----CCCeEEeCCCcEEEEECCCCEEEEEEEE
Confidence 445577788889999999998555445689999998743 1100 0112367899999999999999999999
Q ss_pred EeccccccceeccCC
Q psy12829 166 KKGFGKEHAKWNPTA 180 (181)
Q Consensus 166 ~kG~G~~HAKw~pv~ 180 (181)
++|+||+|||||||+
T Consensus 152 ~~G~G~~hAk~sPV~ 166 (212)
T cd07028 152 KKGIGKEHAKFGPVA 166 (212)
T ss_pred ECCCcCCCCEeCCce
Confidence 999999999999996
No 5
>KOG1521|consensus
Probab=100.00 E-value=8.3e-55 Score=366.51 Aligned_cols=176 Identities=37% Similarity=0.553 Sum_probs=153.9
Q ss_pred CCCCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceE
Q psy12829 3 YANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRI 82 (181)
Q Consensus 3 ~~~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~ 82 (181)
|.++++|.+.+++++.++|++.|++.+||||+||+||||||||||+.|+|++||||++||+|||||||||+..++ +.|
T Consensus 42 f~~~~~V~iv~~~~~~leFDligIda~IANAfRRILiaEVPtmAiEkVyi~nNTSViqDEvLaHRlGLvPl~aDP--rlF 119 (338)
T KOG1521|consen 42 FKDNFKVDIVSLDEETLEFDLIGIDASIANAFRRILIAEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLVPLRADP--RLF 119 (338)
T ss_pred hhhceEEEEEeccCcceeEEEeeccHHHHHHHHHHHHhhcchhheeeeEEecCccccHHHHHHHhhcCcccccCc--chh
Confidence 677899999999999999999999999999999999999999999999999999999999999999999999998 567
Q ss_pred EEeecCCCcCCCCCceEEEEEEEEecCCCceeEEecc---------ceeCCCeeeeccccCcCCCC-CCccCCCCeEEEE
Q psy12829 83 LYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTAD---------LKSTDARVVPVTSRNRDADM-NEYGETDDILIVK 152 (181)
Q Consensus 83 ~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~d---------i~~~~~~~~p~~~~~~~~~~-~~~~~~~di~I~k 152 (181)
.|..+..|++. ..++++|+|+|+|+.+....+.+.| +++.+..|.|.+.|...+.+ ++.++++||+|+|
T Consensus 120 e~~~e~d~~~e-~~ntlvF~L~VkC~~n~~a~~~~sdpk~Ly~ns~vyS~~~~w~P~g~Q~~~f~e~~i~~~~~DILiAk 198 (338)
T KOG1521|consen 120 EYRSENDEDDE-KENTLVFKLNVKCTKNPNAKKDSSDPKELYNNSEVYSRDLTWKPKGYQAEIFAENPIRPVHDDILIAK 198 (338)
T ss_pred hccccCCCccC-ccceEEEEEEeeccCCCCcccCCCChhHhccCcEEecCcceeccccchhhhcccCCccccCcceEEEe
Confidence 78776544432 2289999999999998444444444 55566669999999877655 4556799999999
Q ss_pred eCCCCEEEEEEEEEeccccccceeccCCC
Q psy12829 153 LRKGQELRLRAYAKKGFGKEHAKWNPTAG 181 (181)
Q Consensus 153 L~~gq~i~~e~~~~kG~G~~HAKw~pv~~ 181 (181)
|+|||+|+++++|+||+|++|||||||+.
T Consensus 199 LrPGQEI~le~havkGIGkdHAKfSPVaT 227 (338)
T KOG1521|consen 199 LRPGQEIELEAHAVKGIGKDHAKFSPVAT 227 (338)
T ss_pred cCCCCEeeeeeeeecccCcccccccCccc
Confidence 99999999999999999999999999974
No 6
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=100.00 E-value=8.1e-53 Score=355.83 Aligned_cols=155 Identities=45% Similarity=0.761 Sum_probs=142.7
Q ss_pred CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEEee
Q psy12829 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSR 86 (181)
Q Consensus 7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~~ 86 (181)
++|++.+.++++++|.+.|+++|+||||||+|||||||+||+.|+|++|||+++||+|+|||||||++++ +++++|+.
T Consensus 1 ~~~~~~~~~~~~~~f~~~g~~~t~~NalRRvlls~vp~~Ai~~v~i~~n~s~~~de~i~hrl~lip~~~~--~~~~~~~~ 78 (263)
T PRK00783 1 MEIEILELDDRSARFVVEGVTPAFANAIRRAMIADVPTMAIDDVRFYENTSVLFDEILAHRLGLIPLTTD--LDKYKPPE 78 (263)
T ss_pred CceEEEEcCCcEEEEEEeCCCHHHHHHHHHHHHHcCCeeeEEEEEEEECCcchhHHHHHHhhcCcccccC--HHHCCCcc
Confidence 4689999999999999999999999999999999999999999999999999999999999999999996 58899998
Q ss_pred cCCCc-CCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEE
Q psy12829 87 DCTCV-DFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYA 165 (181)
Q Consensus 87 ~~~~~-~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~ 165 (181)
+|.|+ +.|++|++.|+|+++ ||+.|||+||+..+..++ ++|||++|+||++||+|+|++++
T Consensus 79 ~~~~~~~~~~~~~~~~~l~~~----~~~~V~a~dl~~~~~~v~--------------~v~~~~~I~~L~~~~~l~~e~~~ 140 (263)
T PRK00783 79 ECTCEGEGCPDCTVTLSLEVE----GPKTVYSGDLKSSDPDVK--------------PVDPNIPIVKLKEGQKLVLEAYA 140 (263)
T ss_pred cccccCCCCCCcEEEEEEEec----CCCcEEccccccCCCCce--------------ecCCCcEEEEeCCCCEEEEEEEE
Confidence 88764 679999999999998 899999999986333333 67899999999999999999999
Q ss_pred EeccccccceeccCCC
Q psy12829 166 KKGFGKEHAKWNPTAG 181 (181)
Q Consensus 166 ~kG~G~~HAKw~pv~~ 181 (181)
.+|+||+||||+|+++
T Consensus 141 ~~G~G~~HAKw~p~~~ 156 (263)
T PRK00783 141 RLGRGKEHAKWQPGSA 156 (263)
T ss_pred EcCcccccCccCcceE
Confidence 9999999999999863
No 7
>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=6.3e-50 Score=337.52 Aligned_cols=154 Identities=44% Similarity=0.709 Sum_probs=138.1
Q ss_pred CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEEee
Q psy12829 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSR 86 (181)
Q Consensus 7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~~ 86 (181)
++|++.+.++++++|.++|++.|+||||||+|||||||+||+.|+|++|||+|+||+++|||||||++++++...+ ..
T Consensus 1 ~~~~~~~~~~~~~~f~~~g~~~s~~NalRRills~vp~~Ai~~V~i~~n~s~~~de~i~hrl~~ip~~~e~~~~~~--~~ 78 (259)
T cd07030 1 MEIEVLELDDDRARFVLEGVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAHRLGLIPLRTDLDLYKY--RS 78 (259)
T ss_pred CceEEEecCCCEEEEEEeCCCHHHHHHHHHHHHhcCCeeeEEEEEEEeCCchhhHHHHHHhhcCcccccCHHHhcc--cc
Confidence 5789999999999999999999999999999999999999999999999999999999999999999999864332 22
Q ss_pred cCCC-cCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEE
Q psy12829 87 DCTC-VDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYA 165 (181)
Q Consensus 87 ~~~~-~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~ 165 (181)
+|.| ...|+.|++.|+|+++ +++.|||+||++.+..++ ++||+++|+||++||+|+|++++
T Consensus 79 ~~~~~~~~~~~~~~~~~l~~~----~~~~v~s~dl~~~~~~v~--------------~~~~~~~I~~l~~~~~l~~~~~~ 140 (259)
T cd07030 79 ECSCGGAGCPLCTVTLTLSVE----GPGTVYSGDLKSSDPDVK--------------PVYDNIPIVKLGKGQKLVLEAYA 140 (259)
T ss_pred cccccCCCCCCcEEEEEEEcc----CCceEEccccccCCCCcc--------------ccCCCcEEEEeCCCCEEEEEEEE
Confidence 5654 3568889999999998 889999999986443343 67899999999999999999999
Q ss_pred EeccccccceeccCC
Q psy12829 166 KKGFGKEHAKWNPTA 180 (181)
Q Consensus 166 ~kG~G~~HAKw~pv~ 180 (181)
.||+|++||||+|++
T Consensus 141 ~kg~g~~hakw~p~~ 155 (259)
T cd07030 141 RLGRGKEHAKWQPTT 155 (259)
T ss_pred ecCccCCCCCCCCcc
Confidence 999999999999985
No 8
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=100.00 E-value=3.1e-45 Score=297.48 Aligned_cols=139 Identities=36% Similarity=0.527 Sum_probs=123.4
Q ss_pred CCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEEe
Q psy12829 6 QPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYS 85 (181)
Q Consensus 6 ~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~ 85 (181)
.+++++....+++++|.++ +++|+||||||+|||++||+||+.|+|++|||+++||+++||||+||++... ++
T Consensus 3 ~~~~~~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~V~I~~Nts~~~DEivaHe~~lIpLK~~~------~~ 75 (195)
T PRK14979 3 TIKEKEKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIENVYFYENSSSMYDEILAHRLGLIPIKGKP------VS 75 (195)
T ss_pred ccceeeeccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEEEEEecCcccccchheeeeeeeeeeeeee------cc
Confidence 3567777778899999999 9999999999999999999999999999999999999999999999977653 11
Q ss_pred ecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEE
Q psy12829 86 RDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYA 165 (181)
Q Consensus 86 ~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~ 165 (181)
. ++++.++|+++ ||+.|||+||++.+. + ++|||++||||++||+|+|+|+|
T Consensus 76 ~---------~~~~~l~L~~~----gp~~Vta~Di~~~~~--~--------------ivnpdi~I~tL~~g~~l~~e~~~ 126 (195)
T PRK14979 76 G---------DEVITFTLSKE----GPCTVYSSDLKSENG--E--------------VAFKNIPIVKLAEGQKLEIECEA 126 (195)
T ss_pred C---------CCcEEEEEEEe----CCceEEHHHcCCCCC--c--------------ccCCCcEEEEECCCCEEEEEEEE
Confidence 1 24678999987 999999999986332 1 67899999999999999999999
Q ss_pred EeccccccceeccCC
Q psy12829 166 KKGFGKEHAKWNPTA 180 (181)
Q Consensus 166 ~kG~G~~HAKw~pv~ 180 (181)
.+|+||+||||+|+.
T Consensus 127 ~~G~Gy~hAk~~pvd 141 (195)
T PRK14979 127 LVGTGKIHAKWQPCN 141 (195)
T ss_pred ECCCcccccccccee
Confidence 999999999999974
No 9
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=100.00 E-value=1.4e-45 Score=305.69 Aligned_cols=143 Identities=49% Similarity=0.751 Sum_probs=131.7
Q ss_pred eEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEEeecCCCcCCCCCc
Q psy12829 18 NVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSEC 97 (181)
Q Consensus 18 ~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~~~~~~~~~~~~~ 97 (181)
+++|.++++++|+||||||+||||+||+||+.|+|++|+|.+.||+++|||||+|+.... +.+.++.+|.|+..|+.|
T Consensus 1 ~~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~I~~n~~~v~eev~~~rLnL~pl~~~~--~~~~~~~~~~~~~~~~~~ 78 (224)
T smart00662 1 RAKFVLEPYGLTLANALRRVLLSSVPGMAVTEVEIEGNTSGVQDEVLAHRLGLKPLASDP--DGDEYQRDCECEEGCEKC 78 (224)
T ss_pred CeEEEEEcCCchHHHHHHHHHHHcCccceEEEEEEecCCcchhHHHHHHHhCCeeEEEec--hhccccccccccccCCCc
Confidence 479999999999999999999999999999999999999999999999999999999864 456677889999999999
Q ss_pred eEEEEEEEEecCCCceeEEeccceeC-CCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEEEecccccccee
Q psy12829 98 SVEFTLDVKCVDDQTRHVTTADLKST-DARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKW 176 (181)
Q Consensus 98 ~v~~~L~v~~~~~~~~~V~s~di~~~-~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~~kG~G~~HAKw 176 (181)
++.++|+++ ||+.|||+||++. +..++ ++|||++|+||++||+|+|+++|.+|+||+||||
T Consensus 79 ~~~~~L~~~----gp~~V~a~Dl~~~~~~~v~--------------~vnp~~~I~~L~~gq~l~~e~~~~~G~G~~hak~ 140 (224)
T smart00662 79 SVTLTLDVK----GPGEVTAGDLKSDSDPDVE--------------IVNPDIPIAKLREGQELELEARAEKGRGYVHAKW 140 (224)
T ss_pred eEEEEEEEE----cCCcEEHHHcccCCCCCcE--------------EeCCCcEEEEECCCCEEEEEEEEECCcccccCcc
Confidence 999999998 8889999999875 33344 6689999999999999999999999999999999
Q ss_pred ccCC
Q psy12829 177 NPTA 180 (181)
Q Consensus 177 ~pv~ 180 (181)
+|++
T Consensus 141 ~p~~ 144 (224)
T smart00662 141 SPVS 144 (224)
T ss_pred cccc
Confidence 9986
No 10
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=100.00 E-value=1.7e-33 Score=243.38 Aligned_cols=140 Identities=22% Similarity=0.366 Sum_probs=121.8
Q ss_pred CCCCCCCcEEEEEec--CCeEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccc
Q psy12829 1 MPYANQPSVHITDLT--DENVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLT 74 (181)
Q Consensus 1 ~~~~~~~~i~i~~~~--~~~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~ 74 (181)
+.|.....+++.+.+ +++++|.++ |++.|+||||||+|||++||+||+.|+|++ ++|||++||++
T Consensus 1 ~~~~~~~~i~~~e~~~~~~~~~F~i~Ple~G~g~tlgNaLRRvLLs~ipg~aI~~VkI~g---------v~hEf~~Ipgv 71 (310)
T PRK05182 1 TEFLKPQKIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKIDG---------VLHEFSTIPGV 71 (310)
T ss_pred CCcccCcEEEEEeccCCCcEEEEEEeccCCCchhHHHHHHHHHHHhcCCeeEEEEEEEcc---------eeeeccccCCc
Confidence 457777788888876 789999998 999999999999999999999999999966 89999999999
Q ss_pred cccc------cceEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCe
Q psy12829 75 SDEV------VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDI 148 (181)
Q Consensus 75 ~~~~------~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di 148 (181)
.||+ ++++.++.+| . |++.++|+++ ||+.|||+||.+.. .++ ++|||+
T Consensus 72 ~Edv~eIllNlk~i~~~~~~------~-~~~~~~l~~~----gp~~VtA~Di~~~~-~v~--------------ivn~d~ 125 (310)
T PRK05182 72 REDVTEIILNLKGLRLKLHG------D-EPVTLTLSKK----GPGEVTAGDIETDG-DVE--------------IVNPDL 125 (310)
T ss_pred ccchhHhhhhhccceeecCC------C-ceEEEEEEec----CCeEEEHHHcCCCC-CcE--------------EeCCCe
Confidence 9986 4666666554 2 7789999987 99999999998622 233 678999
Q ss_pred EEEEeCCCCEEEEEEEEEeccccccce
Q psy12829 149 LIVKLRKGQELRLRAYAKKGFGKEHAK 175 (181)
Q Consensus 149 ~I~kL~~gq~i~~e~~~~kG~G~~HAK 175 (181)
+||||++||+|+|+++|.+|+||++|+
T Consensus 126 ~IatL~~~~~l~ie~~~~kG~Gy~~~~ 152 (310)
T PRK05182 126 VIATLNEGAKLEMELTVERGRGYVPAE 152 (310)
T ss_pred EEEEECCCCEEEEEEEEECcCCCcccc
Confidence 999999999999999999999998776
No 11
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=100.00 E-value=1.8e-33 Score=232.22 Aligned_cols=132 Identities=25% Similarity=0.350 Sum_probs=117.5
Q ss_pred EEEecCCeEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccc------cc
Q psy12829 11 ITDLTDENVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV------VD 80 (181)
Q Consensus 11 i~~~~~~~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~------~~ 80 (181)
+.+.++.+++|.++ |++.|+||||||+||||+||+||+.|+|++| +|||++||++.|++ +|
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 45567889999995 8999999999999999999999999999995 79999999999996 47
Q ss_pred eEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEE
Q psy12829 81 RILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELR 160 (181)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~ 160 (181)
++.++.+|. .|++.++|+++ ||+.|||+||.+.+. ++ ++||+++||||.+||+|+
T Consensus 74 ~~~~~~~~~------~~~~~~~l~~~----gp~~V~a~Di~~~~~-i~--------------ivnp~~~IatL~~~~~l~ 128 (215)
T cd06928 74 EIVFKSDSE------DEPQVLRLKVK----GPGVVTAADIELPSG-VE--------------IVNPDQYIATLTEDASLE 128 (215)
T ss_pred cEEEEecCC------CceEEEEEEEe----cCeEEEhHhcCcCCC-cE--------------EeCCCcEEEEECCCCEEE
Confidence 888876652 57889999998 999999999987432 33 678999999999999999
Q ss_pred EEEEEEecccccccee
Q psy12829 161 LRAYAKKGFGKEHAKW 176 (181)
Q Consensus 161 ~e~~~~kG~G~~HAKw 176 (181)
|+|++.+|+||.+|+|
T Consensus 129 ie~~i~~G~Gy~~~~~ 144 (215)
T cd06928 129 MELRIEKGRGYVPAEE 144 (215)
T ss_pred EEEEEECcCcceeccc
Confidence 9999999999999998
No 12
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=100.00 E-value=1.1e-33 Score=244.82 Aligned_cols=165 Identities=22% Similarity=0.272 Sum_probs=134.8
Q ss_pred EEEEEec----CCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEee--C---c-cccccceeeeeccCCccccccc
Q psy12829 9 VHITDLT----DENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEA--N---S-TVLSDEFIASRIGLIPLTSDEV 78 (181)
Q Consensus 9 i~i~~~~----~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~--N---t-Svl~DE~laHRlglIP~~~~~~ 78 (181)
|++.+.+ ...++|...|+++|+||||||+|||||||+||+.|+|++ | | +.++||+++|||||+|+....-
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 8898888 456666667999999999999999999999999999999 3 3 3899999999999999998753
Q ss_pred c---ceEEEeecCCCcCCCCCceEEEEEEEEecCCC------------ceeEEeccceeCCCeeeeccccCcCCCCCCcc
Q psy12829 79 V---DRILYSRDCTCVDFCSECSVEFTLDVKCVDDQ------------TRHVTTADLKSTDARVVPVTSRNRDADMNEYG 143 (181)
Q Consensus 79 ~---~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~------------~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~ 143 (181)
. +.+.+...|.|...|.+|++.+.|++.|+... ...|+++|+++.. .+.+ ..+++..+
T Consensus 87 ~~~~~~~~~~~~g~g~v~a~d~~~~~~lEv~np~~~ia~~~~~~~l~~~~~V~~G~gyv~~-----~~~~--~~~~~v~~ 159 (317)
T COG0202 87 GDEEVTLELDKEGPGEVTASDITVPLDLEVVNPDHVIATLTEDAKLEMELRVYSGDGYVPA-----EGNR--EDDPPVGP 159 (317)
T ss_pred cccceEEEEeccCCccccHhhcccceeEEEECCCceeeeccCCcceEEEEEEEcCccEecc-----cccc--ccCCCcee
Confidence 2 24777777777788999999999999976544 3467888888621 1111 11122235
Q ss_pred CCCCeEEEEeCCCCEEEEEEEEEeccccccceeccCC
Q psy12829 144 ETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180 (181)
Q Consensus 144 ~~~di~I~kL~~gq~i~~e~~~~kG~G~~HAKw~pv~ 180 (181)
+.+|+++++|+++|.+..++++.+|+||+||||+|++
T Consensus 160 i~~D~~~spv~kvqy~ve~~r~~~~~~~Dhl~~~~~T 196 (317)
T COG0202 160 IAVDAPFSPVRKVQYIVEEARVGQGTDKDHLKWEPET 196 (317)
T ss_pred eeCCCceeeeeeceEEEEeEEEeccCCceeEEEEEee
Confidence 6799999999999999999999999999999999976
No 13
>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=100.00 E-value=4.2e-34 Score=213.41 Aligned_cols=110 Identities=39% Similarity=0.634 Sum_probs=93.8
Q ss_pred EEEeeCccccccceeeeeccCCccccccccceEEEeecC--CCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCee
Q psy12829 50 VQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDC--TCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARV 127 (181)
Q Consensus 50 V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~~~~--~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~ 127 (181)
|+|++|||+++||+++||||+||++.|++++-+..-++| .+...|+.|++.++|+++ |++.|||+||+..+..+
T Consensus 1 v~i~~n~s~~~dE~v~He~~~Ipgv~Edv~~iilnlk~i~~~~~~~~~~~~~~~~L~~~----g~~~V~a~di~~~~~~i 76 (112)
T PF01000_consen 1 VYIYENTSVLPDEGVAHEFGLIPGVSEDVLEIILNLKKIVIDCEEGCDDCSVTFSLKVK----GPGEVTAGDIKLEPSGI 76 (112)
T ss_dssp EEEEEETSSS-HHHHHCHHHBSTCBSSCHHHHHHHHHTT-ESSSSSTTTSEEEEEEEEE----SSSCEEGGGSEESBTTE
T ss_pred CEEEECCCeeccceeEeccccCCccccchhhhhhcchhhccccccCCCCceEEEEEEec----CCCccccceeEecCCce
Confidence 789999999999999999999999999975422233344 355788999999999999 88899999999754445
Q ss_pred eeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEEEeccccccceec
Q psy12829 128 VPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 177 (181)
Q Consensus 128 ~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~~kG~G~~HAKw~ 177 (181)
+ ++|||++||||++||+|+|++++.+|+||+|||||
T Consensus 77 ~--------------ivn~d~~I~tl~~~~~l~~e~~i~~G~Gy~~ak~~ 112 (112)
T PF01000_consen 77 E--------------IVNPDIYIATLSEGQKLEMELYIEKGRGYVHAKWS 112 (112)
T ss_dssp E--------------ESSTTSEEEEEESSTEEEEEEEEEEEESEECCTS-
T ss_pred E--------------EecCCeEEEEECCCCEEEEEEEEECCCcccccccC
Confidence 5 67899999999999999999999999999999997
No 14
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=99.97 E-value=6.1e-30 Score=220.12 Aligned_cols=124 Identities=23% Similarity=0.345 Sum_probs=107.1
Q ss_pred eEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccc------cceEEEeec
Q psy12829 18 NVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV------VDRILYSRD 87 (181)
Q Consensus 18 ~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~------~~~~~~~~~ 87 (181)
+++|.++ |++.|+||||||+|||++||+||+.|+|++ ++|||++||++.||+ +|++.++.+
T Consensus 1 y~~f~i~Ple~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~g---------v~HEf~~I~GV~Edv~eIllNlK~i~~~~~ 71 (297)
T TIGR02027 1 YGKFVLEPLERGFGITLGNALRRVLLSSIPGAAITAVKIDG---------VLHEFSTIEGVKEDVTEIILNLKQLVVKSE 71 (297)
T ss_pred CcEEEEecCCCCchhHHHHHHHHHHHhcCCceEEEEEEEcc---------eecccccCCCccccHHHHHhhhhceEEecc
Confidence 4689998 999999999999999999999999999998 999999999999997 478888765
Q ss_pred CCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEEEe
Q psy12829 88 CTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKK 167 (181)
Q Consensus 88 ~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~~k 167 (181)
|. .+ ..++|+++ ||+.|||+||.+.+..++ ++|||++||||.+||+|+|++++.+
T Consensus 72 ~~------~~-~~~~l~~~----gp~~VtA~Di~~~p~~ie--------------ivnpd~~IatL~~~~~L~iel~i~~ 126 (297)
T TIGR02027 72 GD------GE-RTMTLSKK----GPGVVTAGDIKAPPGDVE--------------IVNPDLVIATLTEPADLEIELRVER 126 (297)
T ss_pred CC------Cc-EEEEEEEe----CCEEEEhhhcccCCCCcE--------------EeCCCeEEEEECCCCEEEEEEEEEc
Confidence 42 22 37888887 999999999984232233 7789999999999999999999999
Q ss_pred ccccccce
Q psy12829 168 GFGKEHAK 175 (181)
Q Consensus 168 G~G~~HAK 175 (181)
|+||.+|+
T Consensus 127 G~Gy~~~~ 134 (297)
T TIGR02027 127 GRGYVPAE 134 (297)
T ss_pred ccccCccc
Confidence 99997664
No 15
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=99.95 E-value=5.3e-27 Score=203.96 Aligned_cols=133 Identities=16% Similarity=0.183 Sum_probs=115.1
Q ss_pred CcEEEEEecCCeEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccc----
Q psy12829 7 PSVHITDLTDENVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV---- 78 (181)
Q Consensus 7 ~~i~i~~~~~~~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~---- 78 (181)
...++.+.++.+++|.++ |++.|+||||||+|||++||+||+.|+|++ +.|+|..||++.||+
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 556667788899999999 788899999999999999999999999988 779999999999998
Q ss_pred --cceEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCC
Q psy12829 79 --VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKG 156 (181)
Q Consensus 79 --~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~g 156 (181)
+|++.++.++ .....+.|+++ ||+.|||+||... ..++ ++|||.+||+|..|
T Consensus 81 lNLK~I~~k~~~-------~~~~~~~l~~~----Gp~~vtA~Di~~p-~~ie--------------ivnpd~~Iatl~~~ 134 (327)
T CHL00013 81 LNLKEIVLKSNL-------YGPQKASICVQ----GPKYVTAQDIILP-PSVE--------------IVDPTQHIATITEP 134 (327)
T ss_pred HhhhcCeEEccC-------CCcEEEEEEEe----CCeEEEeeeeccC-CCeE--------------EeCCCeEEEEeCCC
Confidence 5788887543 13568888887 9999999999863 2233 78999999999999
Q ss_pred CEEEEEEEEEeccccccc
Q psy12829 157 QELRLRAYAKKGFGKEHA 174 (181)
Q Consensus 157 q~i~~e~~~~kG~G~~HA 174 (181)
+.|+|++++.+|+||..|
T Consensus 135 ~~l~~el~ie~G~GY~~~ 152 (327)
T CHL00013 135 IDLEIELKIEKGRGYRLK 152 (327)
T ss_pred CEEEEEEEEECccCceec
Confidence 999999999999999544
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=98.99 E-value=3e-10 Score=77.25 Aligned_cols=31 Identities=32% Similarity=0.682 Sum_probs=30.0
Q ss_pred EEEEEEecCchhhHHHHHHHHhhCCcceEEE
Q psy12829 19 VKFQVEDTELSVANSLRRVFIAETPTMAIDW 49 (181)
Q Consensus 19 ~~F~l~g~~~siaNaLRRvLlsevPt~AI~~ 49 (181)
++|.++|.++|+||||||+||+++|++||+.
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 5899999999999999999999999999998
No 17
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=98.49 E-value=2.2e-07 Score=81.08 Aligned_cols=90 Identities=21% Similarity=0.193 Sum_probs=70.1
Q ss_pred ccccceeeeeccCCccccccc------cceEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeecc
Q psy12829 58 VLSDEFIASRIGLIPLTSDEV------VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVT 131 (181)
Q Consensus 58 vl~DE~laHRlglIP~~~~~~------~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~ 131 (181)
|--+++ .|+|..+|++.||+ ++.+.++.+-. .. ++++++.. |++.+|++|+.... .++
T Consensus 52 V~I~~v-~hef~s~~gv~Edvl~~~LnLk~L~~~~~~~------~~-~~~~~~~~----g~g~v~a~d~~~~~-~lE--- 115 (317)
T COG0202 52 VEIDGV-LHEFDSIEGVQEDVLAHRLNLKPLAVKLDGD------EE-VTLELDKE----GPGEVTASDITVPL-DLE--- 115 (317)
T ss_pred EEEecc-ccccccCcCcHHHHHHHHhcCceeeeecccc------cc-eEEEEecc----CCccccHhhcccce-eEE---
Confidence 433444 59999999999997 35555554310 01 68888887 99999999998622 233
Q ss_pred ccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEEEeccccccc
Q psy12829 132 SRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHA 174 (181)
Q Consensus 132 ~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~~kG~G~~HA 174 (181)
++|||.+||+|+.+.+|+|++++..|+||..|
T Consensus 116 -----------v~np~~~ia~~~~~~~l~~~~~V~~G~gyv~~ 147 (317)
T COG0202 116 -----------VVNPDHVIATLTEDAKLEMELRVYSGDGYVPA 147 (317)
T ss_pred -----------EECCCceeeeccCCcceEEEEEEEcCccEecc
Confidence 78999999999999999999999999999964
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=97.75 E-value=6.2e-05 Score=53.70 Aligned_cols=32 Identities=31% Similarity=0.580 Sum_probs=30.2
Q ss_pred EEEEEecCCeEEEEEEecCchhhHHHHHHHHh
Q psy12829 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIA 40 (181)
Q Consensus 9 i~i~~~~~~~~~F~l~g~~~siaNaLRRvLls 40 (181)
|++.+.+++.++|.++|-|+|+||+||+.|+.
T Consensus 1 ~ki~~~~~~~~~~~~~~edhTl~n~L~~~l~~ 32 (86)
T cd00460 1 VKILEKEKNYVDFVLENEDHTLGNSLRRILLK 32 (86)
T ss_pred CceecCCCCEEEEEEeCCCchHHHHHHHHHhC
Confidence 46788999999999999999999999999999
No 19
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=97.04 E-value=0.0011 Score=47.29 Aligned_cols=43 Identities=12% Similarity=0.322 Sum_probs=36.1
Q ss_pred CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEE
Q psy12829 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWV 50 (181)
Q Consensus 7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V 50 (181)
+++++.+.+++.++|.++|=|+|+||+||-.|+. -|...+-..
T Consensus 1 m~ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~-~~~V~fAgY 43 (85)
T PRK01146 1 MEIKVLEKEDNELELEIEGEDHTLMNLLKEELLE-DPGVEAASY 43 (85)
T ss_pred CeEEEEecCCCEEEEEEeCCCchHHHHHHHHHhc-CCCeeEEEe
Confidence 4789999999999999999999999999999985 555544333
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=96.60 E-value=0.0033 Score=44.71 Aligned_cols=41 Identities=12% Similarity=0.392 Sum_probs=34.3
Q ss_pred EEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEE
Q psy12829 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWV 50 (181)
Q Consensus 9 i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V 50 (181)
+++.+.+++.++|.+.|=|+|+||+||-.|+.. |..-+-..
T Consensus 1 ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~V~fAgY 41 (83)
T cd06927 1 LKVIEKEDNELELEIEGEDHTLLNLLKEELLRD-PGVKVASY 41 (83)
T ss_pred CeEEEcCCCEEEEEEeCCCchHHHHHHHHHhcC-CCeEEEEe
Confidence 478899999999999999999999999999876 55444333
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=96.41 E-value=0.0048 Score=43.89 Aligned_cols=36 Identities=17% Similarity=0.376 Sum_probs=31.2
Q ss_pred EEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcc
Q psy12829 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTM 45 (181)
Q Consensus 9 i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~ 45 (181)
+++.+.+++.++|.++|=|+|+||+||-.|+.. |..
T Consensus 1 ~kii~~~~n~~~~~i~~EdHTLgNlLr~~L~~~-~~V 36 (83)
T cd07027 1 LRIISKEKNSVTVEMENEDHTLGNLLREELLKD-DQV 36 (83)
T ss_pred CeeEecCCCEEEEEEeCCCchHHHHHHHHHhcC-CCe
Confidence 467889999999999999999999999988765 443
No 22
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=95.95 E-value=0.014 Score=42.92 Aligned_cols=36 Identities=17% Similarity=0.377 Sum_probs=33.3
Q ss_pred CCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHh
Q psy12829 5 NQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIA 40 (181)
Q Consensus 5 ~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLls 40 (181)
..+++++.+.+++.++|.++|-|+|++|.||-.|+.
T Consensus 3 ~~~~l~ii~~~~n~~~i~i~gEdHTL~NlL~~~L~~ 38 (99)
T COG1761 3 PEMELRIIKKDDNSLELEIEGEDHTLGNLLREELLK 38 (99)
T ss_pred CceEEEEeccCCCEEEEEEecCCchHHHHHHHHHhC
Confidence 457888899999999999999999999999999987
No 23
>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=95.40 E-value=0.026 Score=40.88 Aligned_cols=42 Identities=12% Similarity=0.263 Sum_probs=32.6
Q ss_pred CCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceE
Q psy12829 5 NQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAI 47 (181)
Q Consensus 5 ~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI 47 (181)
.+..++..+..++.++|.+.|=|+|+||+||-.|+. -|..-+
T Consensus 5 ~kv~~~~d~k~~n~~~~~i~~EdHTLgNlLr~~L~~-~~~V~f 46 (93)
T cd06926 5 KKITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLK-DPNVLF 46 (93)
T ss_pred cceEEeecCCCCcEEEEEEeCCCchHHHHHHHHHhc-CCCeeE
Confidence 344455555678899999999999999999999987 555433
No 24
>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=93.68 E-value=0.084 Score=37.62 Aligned_cols=31 Identities=23% Similarity=0.378 Sum_probs=26.5
Q ss_pred EecCCeEEEEEEecCchhhHHHHHHHHhhCCc
Q psy12829 13 DLTDENVKFQVEDTELSVANSLRRVFIAETPT 44 (181)
Q Consensus 13 ~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt 44 (181)
...++.++|.++|=|+|+||+||-.|+. -|.
T Consensus 5 ~~~~n~~~~~i~~EdHTLgNlLr~~L~~-~p~ 35 (85)
T cd07029 5 GTDESCATFVFYGEDHTLGNSLRYVIMK-NPE 35 (85)
T ss_pred cCCCCeEEEEEeCCCcchHHHHHHHHhh-CCC
Confidence 3567899999999999999999999887 344
No 25
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=93.11 E-value=0.1 Score=36.47 Aligned_cols=35 Identities=14% Similarity=0.372 Sum_probs=26.1
Q ss_pred CeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEE
Q psy12829 17 ENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQL 52 (181)
Q Consensus 17 ~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I 52 (181)
+.+.|.+.|=|+|+||+||-.|+.. |...+-..++
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 4689999999999999999998875 6655554444
No 26
>KOG3438|consensus
Probab=86.45 E-value=0.8 Score=33.83 Aligned_cols=35 Identities=20% Similarity=0.288 Sum_probs=27.4
Q ss_pred cCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeC
Q psy12829 15 TDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEAN 55 (181)
Q Consensus 15 ~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~N 55 (181)
......|.+..=|+|||||||=+|+- =..|.+-+.
T Consensus 14 d~~~~Tf~~~eEDHTlgNalR~vI~k------~peVefcGY 48 (105)
T KOG3438|consen 14 DLSSATFQLREEDHTLGNALRYVIMK------NPEVEFCGY 48 (105)
T ss_pred CCCceEEEEEecCcchhHHHHHHHhc------CCceEEEec
Confidence 44578999999999999999998876 235655554
No 27
>KOG4392|consensus
Probab=68.04 E-value=7.1 Score=29.40 Aligned_cols=33 Identities=9% Similarity=0.301 Sum_probs=27.7
Q ss_pred EEEEEecCCeEEEEEEecCchhhHHHHHHHHhh
Q psy12829 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAE 41 (181)
Q Consensus 9 i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlse 41 (181)
|+-.....+.+.|+++.=|+|+||-||--||..
T Consensus 21 in~DtKvpNA~~fTiekEDHTLGNii~~qLl~D 53 (117)
T KOG4392|consen 21 INKDTKVPNAALFTIEKEDHTLGNIIKSQLLKD 53 (117)
T ss_pred EecCCCCCceEEEEEecccchHHHHHHHHHccC
Confidence 333446788999999999999999999998876
No 28
>cd04932 ACT_AKiii-LysC-EC_1 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The E. coli AKIII (LysC) binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=50.81 E-value=60 Score=22.01 Aligned_cols=41 Identities=15% Similarity=0.270 Sum_probs=30.4
Q ss_pred CCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcce
Q psy12829 6 QPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMA 46 (181)
Q Consensus 6 ~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~A 46 (181)
+.++.+...++..+.|.+..-+.+--|+|++.|++++-.++
T Consensus 29 ~I~VDmI~~s~~~iSftv~~~d~~~~~~~~~~l~~~l~~~~ 69 (75)
T cd04932 29 NISVDLITTSEISVALTLDNTGSTSDQLLTQALLKELSQIC 69 (75)
T ss_pred CCcEEEEeecCCEEEEEEeccccchhHHHHHHHHHHHHhcc
Confidence 34556665577889999987665444788889999988865
No 29
>TIGR01444 fkbM_fam methyltransferase, FkbM family. Members of this family are characterized by two well-conserved short regions separated by a variable in both sequence and length. The first of the two regions is found in a large number of proteins outside this subfamily, a number of which have been characterized as methyltransferases. One member of the present family, FkbM, was shown to be required for a specific methylation in the biosynthesis of the immunosuppressant FK506 in Streptomyces strain MA6548.
Probab=41.09 E-value=28 Score=25.54 Aligned_cols=33 Identities=21% Similarity=0.443 Sum_probs=29.4
Q ss_pred CCeEEEEEEecCchhhHHHHHHHHhhCCcceEE
Q psy12829 16 DENVKFQVEDTELSVANSLRRVFIAETPTMAID 48 (181)
Q Consensus 16 ~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~ 48 (181)
.+.+|.++||....+-.++++.|...+|.+.++
T Consensus 109 i~~lKiDiEG~E~~vL~g~~~~l~~~~~~i~~E 141 (143)
T TIGR01444 109 VDLLKIDVEGAELEVLRGAKETLLRKRPGIVLE 141 (143)
T ss_pred CCEEEEeCCCchHHHHhChHHHHHHhCCeEEEE
Confidence 357899999999999999999998999988876
No 30
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=35.97 E-value=1.1e+02 Score=19.97 Aligned_cols=41 Identities=15% Similarity=0.268 Sum_probs=24.7
Q ss_pred EEEEEecCCeEEEEEE-e-cCch----hhHHHHHHHHhhCCcceEEEEEE
Q psy12829 9 VHITDLTDENVKFQVE-D-TELS----VANSLRRVFIAETPTMAIDWVQL 52 (181)
Q Consensus 9 i~i~~~~~~~~~F~l~-g-~~~s----iaNaLRRvLlsevPt~AI~~V~I 52 (181)
|+-....++.+.|.++ + -+.+ +...+|..|. ++|+ +..|+|
T Consensus 26 V~~i~i~~~~V~v~l~l~~~~~~~~~~l~~~i~~~l~-~l~g--v~~V~V 72 (72)
T PF01883_consen 26 VRDISIEGGKVSVSLELPTPACPAAEPLREEIREALK-ALPG--VKSVKV 72 (72)
T ss_dssp EEEEEECTCEEEEEE--SSTTHTTHHHHHHHHHHHHH-TSTT---SEEEE
T ss_pred eeEEEEECCEEEEEEEECCCCchHHHHHHHHHHHHHH-hCCC--CceEeC
Confidence 4445667788888887 2 3445 4445555555 8888 666654
No 31
>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=33.32 E-value=47 Score=27.13 Aligned_cols=41 Identities=12% Similarity=0.225 Sum_probs=29.3
Q ss_pred eEEEEEE---ecCch-hhHHHHHHHHhhCCcceEEEEEEeeCccc
Q psy12829 18 NVKFQVE---DTELS-VANSLRRVFIAETPTMAIDWVQLEANSTV 58 (181)
Q Consensus 18 ~~~F~l~---g~~~s-iaNaLRRvLlsevPt~AI~~V~I~~NtSv 58 (181)
+....|. |...+ ...++|+.+-++||++.-+.|.|-.+.+-
T Consensus 153 sASV~l~~~~g~~l~~qv~~I~~LVa~sV~gL~~enVtVvD~~G~ 197 (206)
T PF01514_consen 153 SASVVLKLKPGSELSEQVQGIQNLVASSVPGLKPENVTVVDQNGN 197 (206)
T ss_dssp EEEEEEEE-TTS--GGGHHHHHHHHHHHSTT--GGGEEEEEEET-
T ss_pred eEEEEEEECCCCChHHHHHHHHHHHHHhcCCCCcccEEEEeCCCc
Confidence 4555555 77777 99999999999999999999998765543
No 32
>TIGR01608 citD citrate lyase acyl carrier protein. This is a model of the acyl carrier protein (aka gamma subunit) of the holoenzyme citrate lyase (EC 4.1.3.6) composed of alpha (EC 2.8.3.10), beta (EC 4.1.3.34), and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The acyl carrier protein covalently binds the coenzyme of citrate lyase. The seed contains an experimentally characterized member from Leuconostoc mesenteroides. The model covers a wide range of Gram positive bacteria. For Gram negative bacteria, it appears that only gamma proteobacteria hit this model. The model is quite robust with queries scoring either quite well or quite poorly against the model. There are currently no hits in-between the noise cutoff and trusted cutoff.
Probab=31.31 E-value=75 Score=23.06 Aligned_cols=38 Identities=3% Similarity=0.156 Sum_probs=32.0
Q ss_pred CCeEEEEEE-ecCchhhHHHHHHHHhhCCcceEEEEEEe
Q psy12829 16 DENVKFQVE-DTELSVANSLRRVFIAETPTMAIDWVQLE 53 (181)
Q Consensus 16 ~~~~~F~l~-g~~~siaNaLRRvLlsevPt~AI~~V~I~ 53 (181)
+..++++|+ -+---||+.+|.++..-+-.+.|+.++|.
T Consensus 26 ~~gi~iel~S~V~kQfG~~Ir~~v~etL~~lgV~~~~v~ 64 (92)
T TIGR01608 26 QVGIEIDLVSDVKKQFGDDIESTVKETLKLLGVENAVVK 64 (92)
T ss_pred CCcEEEEEEEHHHHHHhHHHHHHHHHHHHHcCCceEEEE
Confidence 445788887 55567999999999999999999998885
No 33
>KOG3307|consensus
Probab=28.17 E-value=21 Score=27.53 Aligned_cols=43 Identities=14% Similarity=0.248 Sum_probs=25.4
Q ss_pred EEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCcccccc
Q psy12829 23 VEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDE 77 (181)
Q Consensus 23 l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~ 77 (181)
-+-+++---|-||.+.-.-=.+.-|..+- +.||||.+|+--..
T Consensus 54 Yeay~pMA~~~lr~IC~~iR~~wpvkkIA------------vfHRLG~VpvgEsS 96 (150)
T KOG3307|consen 54 YEAYDPMAYKKLRGICAEIRAEWPVKKIA------------VFHRLGKVPVGESS 96 (150)
T ss_pred hhhhcHHHHHHHHHHHHHHHhhCchhhhh------------hhhhccCcccCcce
Confidence 33555666678887763222222244443 46999999975443
No 34
>PF10633 NPCBM_assoc: NPCBM-associated, NEW3 domain of alpha-galactosidase; InterPro: IPR018905 This domain has been named NEW3, but its function is not known. It is found on proteins which are bacterial galactosidases [].; PDB: 1EUT_A 2BZD_A 1WCQ_C 2BER_A 1W8O_A 1EUU_A 1W8N_A.
Probab=27.96 E-value=1.9e+02 Score=19.26 Aligned_cols=59 Identities=14% Similarity=0.072 Sum_probs=26.5
Q ss_pred ceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEEEeccc
Q psy12829 97 CSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFG 170 (181)
Q Consensus 97 ~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~~kG~G 170 (181)
.++.++|.++|....+..--+-.+.. ...|. .. ...--+..|.+|+...+.+.+.-.-+
T Consensus 5 ~~~~~~~tv~N~g~~~~~~v~~~l~~-P~GW~-~~-------------~~~~~~~~l~pG~s~~~~~~V~vp~~ 63 (78)
T PF10633_consen 5 ETVTVTLTVTNTGTAPLTNVSLSLSL-PEGWT-VS-------------ASPASVPSLPPGESVTVTFTVTVPAD 63 (78)
T ss_dssp EEEEEEEEEE--SSS-BSS-EEEEE---TTSE-----------------EEEEE--B-TTSEEEEEEEEEE-TT
T ss_pred CEEEEEEEEEECCCCceeeEEEEEeC-CCCcc-cc-------------CCccccccCCCCCEEEEEEEEECCCC
Confidence 56788888887654432111111222 12344 11 12233348999999888887776543
No 35
>PF06857 ACP: Malonate decarboxylase delta subunit (MdcD); InterPro: IPR023439 This family consists of the acyl carrier protein found in malonate decarboxylase and citrate lyase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl groups are transferred to the prosthetic group for catalysis.
Probab=27.14 E-value=1.2e+02 Score=21.58 Aligned_cols=56 Identities=13% Similarity=0.230 Sum_probs=41.5
Q ss_pred EEEEEecCCeEEEEEEec-CchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCcccc
Q psy12829 9 VHITDLTDENVKFQVEDT-ELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTS 75 (181)
Q Consensus 9 i~i~~~~~~~~~F~l~g~-~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~ 75 (181)
|.+.-.++..+++.|+.- -.-||+.+|+++..-+-.+.|..++|.- +-.|-.|.+.
T Consensus 18 V~v~p~~~~gi~i~l~S~v~~~fg~~i~~vi~~~l~~~~i~~~~v~i-----------~D~GAld~vi 74 (87)
T PF06857_consen 18 VTVEPAESGGIEIELESSVVKQFGDQIRAVIRETLEELGIEDAKVEI-----------NDKGALDCVI 74 (87)
T ss_pred EEEEeCCCCcEEEEEEchHHhhhHHHHHHHHHHHHHhcCCCceEEEE-----------EeCCCCHHHH
Confidence 333334457888988855 6779999999999999999999888843 5666666554
No 36
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=26.18 E-value=52 Score=22.15 Aligned_cols=30 Identities=13% Similarity=0.129 Sum_probs=20.4
Q ss_pred cCCCCeEEEEeCCCCEEEEEEEEEeccccc
Q psy12829 143 GETDDILIVKLRKGQELRLRAYAKKGFGKE 172 (181)
Q Consensus 143 ~~~~di~I~kL~~gq~i~~e~~~~kG~G~~ 172 (181)
.+.++..+..|++||++++++....+-.|.
T Consensus 33 ~v~~~~~l~~l~~Gd~V~F~~~~~~~~~~~ 62 (70)
T PF11604_consen 33 PVADPVDLAGLKPGDKVRFTFERTDDGSYV 62 (70)
T ss_dssp E--TTSEESS-STT-EEEEEEEEETTCEEE
T ss_pred EcCChhhhhcCCCCCEEEEEEEECCCCcEE
Confidence 456788899999999999998876654343
No 37
>PF06031 SERTA: SERTA motif; InterPro: IPR009263 This entry represents a novel motif designated as SERTA (for SEI-1, RBT1, and TARA), corresponding to the largest conserved region among TRIP-Br proteins []. The function of this motif is uncertain, but the CDK4-interacting segment of p34SEI-1 (amino acid residues 44-161) includes most of the SERTA motif [].
Probab=23.06 E-value=44 Score=20.31 Aligned_cols=9 Identities=44% Similarity=0.833 Sum_probs=7.5
Q ss_pred hhhHHHHHH
Q psy12829 29 SVANSLRRV 37 (181)
Q Consensus 29 siaNaLRRv 37 (181)
-+.|+|||+
T Consensus 25 LI~Ntlr~i 33 (38)
T PF06031_consen 25 LINNTLRRI 33 (38)
T ss_pred hhhhhHHHH
Confidence 389999996
No 38
>PF12988 DUF3872: Domain of unknown function, B. Theta Gene description (DUF3872); InterPro: IPR024355 This entry represents proteins of unknown function found primarily in Bacteroides species. The Bacteroides thetaiotaomicron gene coding for this protein is located in a conjugate transposon and appears to be upregulated in the presence of host or other bacterial species compared to growth in pure culture [, ].; PDB: 2L3B_A 2L7Q_A.
Probab=22.39 E-value=70 Score=24.86 Aligned_cols=26 Identities=19% Similarity=0.423 Sum_probs=16.8
Q ss_pred EeCCCCEEEEEEEEEeccccccceec
Q psy12829 152 KLRKGQELRLRAYAKKGFGKEHAKWN 177 (181)
Q Consensus 152 kL~~gq~i~~e~~~~kG~G~~HAKw~ 177 (181)
++.+||..+++|.+++.=-|.-|+|.
T Consensus 43 ~I~~GeTvEIR~~l~reG~y~~t~Y~ 68 (137)
T PF12988_consen 43 KIKKGETVEIRCELKREGNYADTRYT 68 (137)
T ss_dssp S--TTEEEEEEEEEEESS--SS---E
T ss_pred ccCCCCEEEEEEEEecCceecccEEE
Confidence 57899999999999998777777763
No 39
>PF11175 DUF2961: Protein of unknown function (DUF2961); InterPro: IPR021345 This family of proteins has no known function.
Probab=21.73 E-value=1e+02 Score=25.96 Aligned_cols=19 Identities=26% Similarity=0.609 Sum_probs=17.0
Q ss_pred CCCCCCCcEEEEEecCCeE
Q psy12829 1 MPYANQPSVHITDLTDENV 19 (181)
Q Consensus 1 ~~~~~~~~i~i~~~~~~~~ 19 (181)
|||++..+|++++.++..+
T Consensus 56 MPF~k~arItl~N~~~~~~ 74 (237)
T PF11175_consen 56 MPFRKSARITLENESDEPV 74 (237)
T ss_pred cccCCCeEEEEEeCCCCce
Confidence 9999999999999887755
No 40
>PF01629 DUF22: Domain of unknown function DUF22; InterPro: IPR002572 This region is found in 1 to 3 copies in archaeal proteins whose function is unknown. It only appears in multiple copies in proteins from Archaeoglobus fulgidus.
Probab=21.30 E-value=46 Score=24.93 Aligned_cols=32 Identities=16% Similarity=0.398 Sum_probs=28.0
Q ss_pred hhCCcceEEEEEEeeCccccccceeeeeccCC
Q psy12829 40 AETPTMAIDWVQLEANSTVLSDEFIASRIGLI 71 (181)
Q Consensus 40 sevPt~AI~~V~I~~NtSvl~DE~laHRlglI 71 (181)
.++--+.|..|.|..||=+++--+..|.+|.+
T Consensus 52 Ge~~~IkIk~I~iP~~tIv~p~~~~rha~G~v 83 (112)
T PF01629_consen 52 GEVKIIKIKKIEIPPNTIVMPCAYMRHALGSV 83 (112)
T ss_pred CCEEEEEEEEEecCCCCEEEEchHhhccCccE
Confidence 45667788999999999999999999999984
Done!