Query psy12830
Match_columns 94
No_of_seqs 108 out of 173
Neff 3.5
Searched_HMMs 46136
Date Fri Aug 16 20:55:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12830.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12830hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1522|consensus 99.9 1.4E-27 3.1E-32 188.8 3.7 72 2-78 1-79 (285)
2 cd07032 RNAP_I_II_AC40 AC40 su 99.8 1.9E-21 4.1E-26 153.7 3.7 62 8-74 2-70 (291)
3 cd07031 RNAP_II_RPB3 RPB3 subu 99.8 9.3E-20 2E-24 141.0 5.0 65 7-76 1-72 (265)
4 cd07028 RNAP_RPB3_like RPB3 su 99.8 8.9E-19 1.9E-23 132.5 5.3 63 7-74 1-70 (212)
5 PRK00783 DNA-directed RNA poly 99.7 1.2E-17 2.6E-22 126.9 3.2 62 7-73 1-69 (263)
6 cd07030 RNAP_D D subunit of Ar 99.7 1.2E-17 2.7E-22 126.6 3.2 64 7-75 1-71 (259)
7 PRK14979 DNA-directed RNA poly 99.5 7.2E-15 1.6E-19 111.0 4.4 62 6-73 3-71 (195)
8 KOG1521|consensus 99.5 3.5E-15 7.5E-20 120.9 1.6 65 4-73 43-114 (338)
9 smart00662 RPOLD RNA polymeras 99.1 1.4E-11 3E-16 92.9 1.2 50 18-67 1-59 (224)
10 COG0202 RpoA DNA-directed RNA 99.0 1.5E-10 3.3E-15 92.5 3.7 79 9-87 7-111 (317)
11 cd06928 RNAP_alpha_NTD N-termi 98.1 2.4E-06 5.2E-11 64.6 3.1 48 10-64 2-60 (215)
12 PRK05182 DNA-directed RNA poly 98.1 5.7E-06 1.2E-10 65.9 4.6 52 5-63 5-69 (310)
13 PF01193 RNA_pol_L: RNA polyme 97.2 9.5E-05 2.1E-09 46.2 0.3 24 19-42 1-31 (66)
14 cd00460 RNAP_RPB11_RPB3 RPB11 96.2 0.0024 5.2E-08 42.0 1.4 29 9-37 1-29 (86)
15 PF01000 RNA_pol_A_bac: RNA po 96.2 0.0011 2.4E-08 44.7 -0.4 23 43-65 1-25 (112)
16 CHL00013 rpoA RNA polymerase a 95.0 0.027 5.9E-07 45.7 3.5 41 7-47 10-61 (327)
17 PRK01146 DNA-directed RNA poly 93.8 0.062 1.3E-06 35.9 2.7 39 7-45 1-40 (85)
18 TIGR02027 rpoA DNA-directed RN 88.5 0.2 4.4E-06 39.8 1.0 28 20-47 3-41 (297)
19 cd06927 RNAP_L L subunit of Ar 84.5 0.78 1.7E-05 30.5 2.0 37 9-45 1-38 (83)
20 cd07027 RNAP_RPB11_like RPB11 83.2 0.9 2E-05 30.2 1.9 37 9-45 1-38 (83)
21 COG1761 RPB11 DNA-directed RNA 78.2 2.4 5.1E-05 29.6 2.7 41 5-45 3-44 (99)
22 KOG3438|consensus 56.4 6 0.00013 28.3 1.1 39 15-53 14-53 (105)
23 PF07865 DUF1652: Protein of u 47.4 25 0.00055 23.0 2.9 34 4-37 24-57 (69)
24 cd06926 RNAP_II_RPB11 RPB11 su 35.1 49 0.0011 22.2 2.9 39 7-45 7-46 (93)
25 PF00629 MAM: MAM domain; Int 32.9 90 0.0019 20.2 3.8 36 8-47 120-155 (160)
26 cd07029 RNAP_I_III_AC19 AC19 s 29.9 29 0.00062 23.1 1.0 33 13-45 5-38 (85)
27 KOG2485|consensus 23.9 29 0.00064 29.1 0.3 33 29-75 32-64 (335)
28 PF11175 DUF2961: Protein of u 21.9 94 0.002 24.4 2.7 20 1-20 56-75 (237)
No 1
>KOG1522|consensus
Probab=99.94 E-value=1.4e-27 Score=188.79 Aligned_cols=72 Identities=28% Similarity=0.401 Sum_probs=69.9
Q ss_pred CCCCCCeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceecccc
Q psy12830 2 PYANQPSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQT 74 (94)
Q Consensus 2 py~~qP~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~t 74 (94)
||++||.|+|+||++++|||+|+|||+|+||||||+ +|||||+|+.|||||+| ||++||+|+|||.|.
T Consensus 1 ~y~~~p~v~I~Elt~d~vkF~L~nTdlsvANsLRRV~iaEvPTiAID~VeIe~NssVL~D-----EFiAHRLGLIPl~S~ 75 (285)
T KOG1522|consen 1 PYANQPTVKIRELTDDNVKFVLSNTDLSVANSLRRVMIAEVPTIAIDLVEIEVNSSVLPD-----EFIAHRLGLIPLISD 75 (285)
T ss_pred CCCCCCceEEEecCCCceEEEEecChHHHHHHHHHHHHhcCceeEEEEEEEecccccccH-----HHHHhhhcceeccch
Confidence 799999999999999999999999999999999999 99999999999999999 999999999999998
Q ss_pred ccee
Q psy12830 75 GFRK 78 (94)
Q Consensus 75 ~~~~ 78 (94)
.+-+
T Consensus 76 ~~~~ 79 (285)
T KOG1522|consen 76 RIVE 79 (285)
T ss_pred hhhh
Confidence 8755
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=99.83 E-value=1.9e-21 Score=153.68 Aligned_cols=62 Identities=13% Similarity=0.109 Sum_probs=57.6
Q ss_pred eEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceecccc
Q psy12830 8 SVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQT 74 (94)
Q Consensus 8 ~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~t 74 (94)
+|+|.+++++.++|.|+|+|+||||||||+ ||||.|.|++|||||+| |||+||+|+|||.+.
T Consensus 2 ~i~i~~~~~~~~~f~l~~~d~s~ANAlRRimiaEVPt~AId~V~i~~NTSvl~D-----E~lAHRLGLIPL~~d 70 (291)
T cd07032 2 KIEIISLSDEELEFDLIGVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQD-----EVLAHRLGLIPIKAD 70 (291)
T ss_pred eEEEEECCCCEEEEEEecCCHHHHHHHHHHHHhcCcceeEEEEEEEECCccchh-----HHHHHhhcCceeecC
Confidence 689999999999999999999999999999 99999999999999999 778888888887764
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=99.79 E-value=9.3e-20 Score=141.03 Aligned_cols=65 Identities=25% Similarity=0.346 Sum_probs=60.5
Q ss_pred CeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceecccccc
Q psy12830 7 PSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTGF 76 (94)
Q Consensus 7 P~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~t~~ 76 (94)
|+|+|.++++++++|+|+|+|.++||||||+ +|||.|.|++|||||+| |||+||+++||+-+..+
T Consensus 1 p~i~i~~~~~~~~~F~l~~~~~s~aNALRRillsevPt~AI~~V~I~~NtSvl~D-----E~iaHRlglIPl~~e~~ 72 (265)
T cd07031 1 PRVEITELTDDKVKFILENTDLSVANSLRRVMIAEVPTLAIDLVEIEENTSVLHD-----EFIAHRLGLIPLTSDDV 72 (265)
T ss_pred CcEEEEEcCCCEEEEEEEcCcHHHHHHHHHHHHHcCccceEEEEEEecCCccccc-----ceeeeecccCCCccCcH
Confidence 6899999999999999999999999999999 99999999999999999 88888888888877654
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=99.75 E-value=8.9e-19 Score=132.50 Aligned_cols=63 Identities=14% Similarity=0.186 Sum_probs=57.3
Q ss_pred CeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceecccc
Q psy12830 7 PSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQT 74 (94)
Q Consensus 7 P~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~t 74 (94)
|+|+|.++++++++|.|+|+++++||||||+ +|||.|.|++|||+++| |+++||.+.||+-+.
T Consensus 1 ~~i~i~~~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~~AI~~V~I~~NtS~~~D-----E~iaHrlglIP~~~e 70 (212)
T cd07028 1 PQVKIREADKDNVDFILSGVDLAMANALRRVMIAEVPTMAVDSVEVETNTSVLAD-----EILAHRLGLIPLQSM 70 (212)
T ss_pred CcEEEEEcCCCEEEEEEEccChhHHHHHHHHHHHcCcceEEEEEEEEcCCCcccc-----eeeeeeeeecccccC
Confidence 6899999999999999999999999999999 99999999999999999 666666667776654
No 5
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=99.69 E-value=1.2e-17 Score=126.94 Aligned_cols=62 Identities=13% Similarity=0.086 Sum_probs=54.3
Q ss_pred CeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceeccc
Q psy12830 7 PSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQ 73 (94)
Q Consensus 7 P~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~ 73 (94)
|+|+|.+.+++.++|.++|.+.++||||||+ +|||.|.|++|||+++|| |++||+++||+-+
T Consensus 1 ~~~~~~~~~~~~~~f~~~g~~~t~~NalRRvlls~vp~~Ai~~v~i~~n~s~~~de-----~i~hrl~lip~~~ 69 (263)
T PRK00783 1 MEIEILELDDRSARFVVEGVTPAFANAIRRAMIADVPTMAIDDVRFYENTSVLFDE-----ILAHRLGLIPLTT 69 (263)
T ss_pred CceEEEEcCCcEEEEEEeCCCHHHHHHHHHHHHHcCCeeeEEEEEEEECCcchhHH-----HHHHhhcCccccc
Confidence 6799999999999999999999999999999 999999999999999995 4555555555544
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=99.69 E-value=1.2e-17 Score=126.62 Aligned_cols=64 Identities=9% Similarity=0.058 Sum_probs=55.9
Q ss_pred CeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceeccccc
Q psy12830 7 PSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTG 75 (94)
Q Consensus 7 P~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~t~ 75 (94)
|+|+|.+++++.++|+++|.+.++||||||+ +|||.|.|++|||+++| ||++||.+.||+-+..
T Consensus 1 ~~~~~~~~~~~~~~f~~~g~~~s~~NalRRills~vp~~Ai~~V~i~~n~s~~~d-----e~i~hrl~~ip~~~e~ 71 (259)
T cd07030 1 MEIEVLELDDDRARFVLEGVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFD-----EMLAHRLGLIPLRTDL 71 (259)
T ss_pred CceEEEecCCCEEEEEEeCCCHHHHHHHHHHHHhcCCeeeEEEEEEEeCCchhhH-----HHHHHhhcCcccccCH
Confidence 6899999999999999999999999999999 99999999999999999 5555555555554443
No 7
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=99.53 E-value=7.2e-15 Score=111.02 Aligned_cols=62 Identities=10% Similarity=-0.046 Sum_probs=53.3
Q ss_pred CCeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceeccc
Q psy12830 6 QPSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQ 73 (94)
Q Consensus 6 qP~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~ 73 (94)
.+++++..-++++++|.|+ ++++++|||||+ +||+.|.|+.|||+++| |+++|+.+.|||-+
T Consensus 3 ~~~~~~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~V~I~~Nts~~~D-----EivaHe~~lIpLK~ 71 (195)
T PRK14979 3 TIKEKEKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIENVYFYENSSSMYD-----EILAHRLGLIPIKG 71 (195)
T ss_pred ccceeeeccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEEEEEecCcccccc-----hheeeeeeeeeeee
Confidence 3678999999999999999 999999999999 99999999999999999 55555555555444
No 8
>KOG1521|consensus
Probab=99.51 E-value=3.5e-15 Score=120.90 Aligned_cols=65 Identities=14% Similarity=0.078 Sum_probs=59.6
Q ss_pred CCCCeEEEeecCCceEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeeeeccceeccc
Q psy12830 4 ANQPSVHITDLTDENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQ 73 (94)
Q Consensus 4 ~~qP~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~ 73 (94)
..+-+|.|.+++++.+.|.+.|+|.|+|||+||+ ||||.|.|..||||..| |+||||+|+|||.-
T Consensus 43 ~~~~~V~iv~~~~~~leFDligIda~IANAfRRILiaEVPtmAiEkVyi~nNTSViqD-----EvLaHRlGLvPl~a 114 (338)
T KOG1521|consen 43 KDNFKVDIVSLDEETLEFDLIGIDASIANAFRRILIAEVPTMAIEKVYIYNNTSVIQD-----EVLAHRLGLVPLRA 114 (338)
T ss_pred hhceEEEEEeccCcceeEEEeeccHHHHHHHHHHHHhhcchhheeeeEEecCccccHH-----HHHHHhhcCccccc
Confidence 3457899999999999999999999999999999 99999999999999999 78888888888753
No 9
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=99.13 E-value=1.4e-11 Score=92.92 Aligned_cols=50 Identities=8% Similarity=-0.038 Sum_probs=42.8
Q ss_pred eEEEEEccCCchhhhcceee-------EEeeeEEEeecccccCCcc--cceeeeeeecc
Q psy12830 18 NVKFQVEDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPS--FLFAFLCIYEN 67 (94)
Q Consensus 18 ~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~--~~~~fl~~~~~ 67 (94)
+++|+|++.++++||||||+ +|||.|.|+.|+|.+.|++ |||++.+++.+
T Consensus 1 ~~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~I~~n~~~v~eev~~~rLnL~pl~~~ 59 (224)
T smart00662 1 RAKFVLEPYGLTLANALRRVLLSSVPGMAVTEVEIEGNTSGVQDEVLAHRLGLKPLASD 59 (224)
T ss_pred CeEEEEEcCCchHHHHHHHHHHHcCccceEEEEEEecCCcchhHHHHHHHhCCeeEEEe
Confidence 37999999999999999999 9999999999999999955 55555555543
No 10
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=99.04 E-value=1.5e-10 Score=92.52 Aligned_cols=79 Identities=9% Similarity=-0.024 Sum_probs=63.7
Q ss_pred EEEeecC----CceEEEEEccCCchhhhcceee-------EEeeeEEEee------cccccCCcc--cceeeeeeeccce
Q psy12830 9 VHITDLT----DENVKFQVEDTELSKRTNGNWK-------ENMEWKGLSA------QLLLCSRPS--FLFAFLCIYENRL 69 (94)
Q Consensus 9 V~I~eLt----d~~vkFiL~ntDlS~ANaLRRi-------lAID~V~I~~------NTSVL~d~~--~~~~fl~~~~~~~ 69 (94)
|+|.+++ +..+.|.++|.+.++||||||+ +||+.|+|.. +.+.+.|++ |||++.++..+.-
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 9999999 8899999999999999999999 9999999999 334999988 8888888777655
Q ss_pred -------ecccccceeeecCCCCCC
Q psy12830 70 -------ALSQTGFRKTFCSPNQSP 87 (94)
Q Consensus 70 -------~l~~t~~~~~~~~~~~~~ 87 (94)
-++..|--..+|+-.+.+
T Consensus 87 ~~~~~~~~~~~~g~g~v~a~d~~~~ 111 (317)
T COG0202 87 GDEEVTLELDKEGPGEVTASDITVP 111 (317)
T ss_pred cccceEEEEeccCCccccHhhcccc
Confidence 344445455556555555
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=98.09 E-value=2.4e-06 Score=64.57 Aligned_cols=48 Identities=4% Similarity=-0.017 Sum_probs=40.9
Q ss_pred EEeecCCceEEEEE----ccCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeeee
Q psy12830 10 HITDLTDENVKFQV----EDTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLCI 64 (94)
Q Consensus 10 ~I~eLtd~~vkFiL----~ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~~ 64 (94)
++.+.++.+.+|.+ .|..+++||||||+ +||+.|+|+.| .|+|+.+|.
T Consensus 2 ~~~~~~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~I~~~-------~He~~~Ipg 60 (215)
T cd06928 2 KVENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGV-------LHEFSTIPG 60 (215)
T ss_pred eeccCCCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEEEccc-------ccccccCCC
Confidence 35567889999999 67999999999999 99999999988 467777664
No 12
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=98.05 E-value=5.7e-06 Score=65.91 Aligned_cols=52 Identities=10% Similarity=0.054 Sum_probs=42.4
Q ss_pred CCCeEEEeecC--CceEEEEEc----cCCchhhhcceee-------EEeeeEEEeecccccCCcccceeeee
Q psy12830 5 NQPSVHITDLT--DENVKFQVE----DTELSKRTNGNWK-------ENMEWKGLSAQLLLCSRPSFLFAFLC 63 (94)
Q Consensus 5 ~qP~V~I~eLt--d~~vkFiL~----ntDlS~ANaLRRi-------lAID~V~I~~NTSVL~d~~~~~~fl~ 63 (94)
+-..+++.+.+ +.+.+|+++ |...++||||||+ +||+.|.|+. ..|+|+.+|
T Consensus 5 ~~~~i~~~e~~~~~~~~~F~i~Ple~G~g~tlgNaLRRvLLs~ipg~aI~~VkI~g-------v~hEf~~Ip 69 (310)
T PRK05182 5 KPQKIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKIDG-------VLHEFSTIP 69 (310)
T ss_pred cCcEEEEEeccCCCcEEEEEEeccCCCchhHHHHHHHHHHHhcCCeeEEEEEEEcc-------eeeeccccC
Confidence 33468899986 899999997 9999999999999 9999999931 226666655
No 13
>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=97.20 E-value=9.5e-05 Score=46.24 Aligned_cols=24 Identities=4% Similarity=0.048 Sum_probs=22.4
Q ss_pred EEEEEccCCchhhhcceee-------EEeee
Q psy12830 19 VKFQVEDTELSKRTNGNWK-------ENMEW 42 (94)
Q Consensus 19 vkFiL~ntDlS~ANaLRRi-------lAID~ 42 (94)
++|.++|.|.+++|+|||+ +||+.
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 5899999999999999999 88887
No 14
>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=96.20 E-value=0.0024 Score=42.05 Aligned_cols=29 Identities=17% Similarity=0.196 Sum_probs=27.8
Q ss_pred EEEeecCCceEEEEEccCCchhhhcceee
Q psy12830 9 VHITDLTDENVKFQVEDTELSKRTNGNWK 37 (94)
Q Consensus 9 V~I~eLtd~~vkFiL~ntDlS~ANaLRRi 37 (94)
|+|.+.+++.++|+++|-|-.++|+||+.
T Consensus 1 ~ki~~~~~~~~~~~~~~edhTl~n~L~~~ 29 (86)
T cd00460 1 VKILEKEKNYVDFVLENEDHTLGNSLRRI 29 (86)
T ss_pred CceecCCCCEEEEEEeCCCchHHHHHHHH
Confidence 57889999999999999999999999999
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=96.16 E-value=0.0011 Score=44.71 Aligned_cols=23 Identities=4% Similarity=-0.092 Sum_probs=16.7
Q ss_pred EEEeecccccCCcc--cceeeeeee
Q psy12830 43 KGLSAQLLLCSRPS--FLFAFLCIY 65 (94)
Q Consensus 43 V~I~~NTSVL~d~~--~~~~fl~~~ 65 (94)
|.|.+||||++||+ |||+.+|..
T Consensus 1 v~i~~n~s~~~dE~v~He~~~Ipgv 25 (112)
T PF01000_consen 1 VYIYENTSVLPDEGVAHEFGLIPGV 25 (112)
T ss_dssp EEEEEETSSS-HHHHHCHHHBSTCB
T ss_pred CEEEECCCeeccceeEeccccCCcc
Confidence 78999999999965 555555554
No 16
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=94.99 E-value=0.027 Score=45.69 Aligned_cols=41 Identities=2% Similarity=-0.128 Sum_probs=37.5
Q ss_pred CeEEEeecCCceEEEEEccCCc----hhhhcceee-------EEeeeEEEee
Q psy12830 7 PSVHITDLTDENVKFQVEDTEL----SKRTNGNWK-------ENMEWKGLSA 47 (94)
Q Consensus 7 P~V~I~eLtd~~vkFiL~ntDl----S~ANaLRRi-------lAID~V~I~~ 47 (94)
.+.++.+.++.+.+|.++.... .++|||||+ .||..|.|+.
T Consensus 10 ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g 61 (327)
T CHL00013 10 VESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG 61 (327)
T ss_pred eeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC
Confidence 5678889999999999999998 999999999 9999999965
No 17
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=93.80 E-value=0.062 Score=35.91 Aligned_cols=39 Identities=5% Similarity=0.002 Sum_probs=34.3
Q ss_pred CeEEEeecCCceEEEEEccCCchhhhcceee-EEeeeEEE
Q psy12830 7 PSVHITDLTDENVKFQVEDTELSKRTNGNWK-ENMEWKGL 45 (94)
Q Consensus 7 P~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-lAID~V~I 45 (94)
|+|+|.+.+++.+.|.+.|=|=.+.|+||-. +.-+.|.+
T Consensus 1 m~ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~f 40 (85)
T PRK01146 1 MEIKVLEKEDNELELEIEGEDHTLMNLLKEELLEDPGVEA 40 (85)
T ss_pred CeEEEEecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeE
Confidence 6899999999999999999999999999988 55555544
No 18
>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=88.53 E-value=0.2 Score=39.82 Aligned_cols=28 Identities=11% Similarity=0.058 Sum_probs=23.1
Q ss_pred EEEEc----cCCchhhhcceee-------EEeeeEEEee
Q psy12830 20 KFQVE----DTELSKRTNGNWK-------ENMEWKGLSA 47 (94)
Q Consensus 20 kFiL~----ntDlS~ANaLRRi-------lAID~V~I~~ 47 (94)
+|+++ |...+++|||||+ .||..|.|+.
T Consensus 3 ~f~i~Ple~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~g 41 (297)
T TIGR02027 3 KFVLEPLERGFGITLGNALRRVLLSSIPGAAITAVKIDG 41 (297)
T ss_pred EEEEecCCCCchhHHHHHHHHHHHhcCCceEEEEEEEcc
Confidence 45553 6678999999999 9999999974
No 19
>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=84.47 E-value=0.78 Score=30.48 Aligned_cols=37 Identities=5% Similarity=0.030 Sum_probs=31.0
Q ss_pred EEEeecCCceEEEEEccCCchhhhcceee-EEeeeEEE
Q psy12830 9 VHITDLTDENVKFQVEDTELSKRTNGNWK-ENMEWKGL 45 (94)
Q Consensus 9 V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-lAID~V~I 45 (94)
|+|.+.+++.++|++.|=|=.+.|+||-. +.-+.|.+
T Consensus 1 ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~f 38 (83)
T cd06927 1 LKVIEKEDNELELEIEGEDHTLLNLLKEELLRDPGVKV 38 (83)
T ss_pred CeEEEcCCCEEEEEEeCCCchHHHHHHHHHhcCCCeEE
Confidence 57899999999999999999999999987 44444443
No 20
>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=83.18 E-value=0.9 Score=30.17 Aligned_cols=37 Identities=8% Similarity=0.038 Sum_probs=31.1
Q ss_pred EEEeecCCceEEEEEccCCchhhhcceee-EEeeeEEE
Q psy12830 9 VHITDLTDENVKFQVEDTELSKRTNGNWK-ENMEWKGL 45 (94)
Q Consensus 9 V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-lAID~V~I 45 (94)
|+|.+.+++.++|+++|=|=.+.|+||-. +.-+.|.+
T Consensus 1 ~kii~~~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~f 38 (83)
T cd07027 1 LRIISKEKNSVTVEMENEDHTLGNLLREELLKDDQVDF 38 (83)
T ss_pred CeeEecCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeE
Confidence 57889999999999999999999999987 44444443
No 21
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=78.24 E-value=2.4 Score=29.57 Aligned_cols=41 Identities=10% Similarity=0.044 Sum_probs=35.1
Q ss_pred CCCeEEEeecCCceEEEEEccCCchhhhcceee-EEeeeEEE
Q psy12830 5 NQPSVHITDLTDENVKFQVEDTELSKRTNGNWK-ENMEWKGL 45 (94)
Q Consensus 5 ~qP~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-lAID~V~I 45 (94)
..|+++|.+.+++.+.|+++|=|=.++|.||.. +--|.|.+
T Consensus 3 ~~~~l~ii~~~~n~~~i~i~gEdHTL~NlL~~~L~~d~~V~~ 44 (99)
T COG1761 3 PEMELRIIKKDDNSLELEIEGEDHTLGNLLREELLKDEDVEF 44 (99)
T ss_pred CceEEEEeccCCCEEEEEEecCCchHHHHHHHHHhCCCCeeE
Confidence 468899999999999999999999999999998 55555543
No 22
>KOG3438|consensus
Probab=56.42 E-value=6 Score=28.29 Aligned_cols=39 Identities=5% Similarity=-0.014 Sum_probs=30.1
Q ss_pred CCceEEEEEccCCchhhhcceee-EEeeeEEEeecccccC
Q psy12830 15 TDENVKFQVEDTELSKRTNGNWK-ENMEWKGLSAQLLLCS 53 (94)
Q Consensus 15 td~~vkFiL~ntDlS~ANaLRRi-lAID~V~I~~NTSVL~ 53 (94)
+...+.|++..=|=.++||||++ +--+.|++--=|-.=|
T Consensus 14 d~~~~Tf~~~eEDHTlgNalR~vI~k~peVefcGYtIPHP 53 (105)
T KOG3438|consen 14 DLSSATFQLREEDHTLGNALRYVIMKNPEVEFCGYTIPHP 53 (105)
T ss_pred CCCceEEEEEecCcchhHHHHHHHhcCCceEEEeccCCCC
Confidence 56789999999999999999999 5566676655544333
No 23
>PF07865 DUF1652: Protein of unknown function (DUF1652); InterPro: IPR012448 The proteins in this entry have not been characterised.
Probab=47.36 E-value=25 Score=22.96 Aligned_cols=34 Identities=15% Similarity=0.097 Sum_probs=29.5
Q ss_pred CCCCeEEEeecCCceEEEEEccCCchhhhcceee
Q psy12830 4 ANQPSVHITDLTDENVKFQVEDTELSKRTNGNWK 37 (94)
Q Consensus 4 ~~qP~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi 37 (94)
...|.|+|.+-....+.|.+.|.+++--++-|=+
T Consensus 24 ~~smtvrl~d~~sg~~~l~vtGI~~~~l~s~rdI 57 (69)
T PF07865_consen 24 DGSMTVRLFDPASGRVELTVTGISTSALNSSRDI 57 (69)
T ss_pred CCcEEEEEecCCCCcEEEEEcCcCHHHcCCHHHH
Confidence 4579999999999999999999999888876643
No 24
>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=35.13 E-value=49 Score=22.22 Aligned_cols=39 Identities=3% Similarity=-0.127 Sum_probs=30.0
Q ss_pred CeEEEeecCCceEEEEEccCCchhhhcceee-EEeeeEEE
Q psy12830 7 PSVHITDLTDENVKFQVEDTELSKRTNGNWK-ENMEWKGL 45 (94)
Q Consensus 7 P~V~I~eLtd~~vkFiL~ntDlS~ANaLRRi-lAID~V~I 45 (94)
..++.-+..++.+.|++.+=|=.+.|+||-. +.-..|.+
T Consensus 7 v~~~~d~k~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~f 46 (93)
T cd06926 7 ITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLF 46 (93)
T ss_pred eEEeecCCCCcEEEEEEeCCCchHHHHHHHHHhcCCCeeE
Confidence 4455556677889999999999999999988 55555544
No 25
>PF00629 MAM: MAM domain; InterPro: IPR000998 MAM is an acronym derived from meprin, A-5 protein, and receptor protein-tyrosine phosphatase mu. The MAM domain consists of approximately 170 amino acids. It occurs in several cell surface proteins, including Meprins, and is thought to function as an interaction or adhesion domain []. The domain has been shown to play a role in homodimerization of protein-tyrosine phosphatase mu [] and appears to help determine the specificity of these interactions. It has been reported that certain cysteine mutations in the MAM domain of murine meprin A result in the formation of monomeric meprin, which has altered stability and activity []. This indicates that these domain-domain interactions are critical for structure and function of the enzyme. It has also been shown that the MAM domain of meprins is necessary for correct folding and transport through the secretory pathway []. ; GO: 0016020 membrane; PDB: 2C9A_A 2V5Y_A.
Probab=32.90 E-value=90 Score=20.18 Aligned_cols=36 Identities=14% Similarity=0.065 Sum_probs=16.5
Q ss_pred eEEEeecCCceEEEEEccCCchhhhcceeeEEeeeEEEee
Q psy12830 8 SVHITDLTDENVKFQVEDTELSKRTNGNWKENMEWKGLSA 47 (94)
Q Consensus 8 ~V~I~eLtd~~vkFiL~ntDlS~ANaLRRilAID~V~I~~ 47 (94)
+|.|... ....+++++.+.-. +.+=.+|||+|.|..
T Consensus 120 ~v~l~~~-~~~~~i~f~~~~~~---~~~~~iaiDdi~~~~ 155 (160)
T PF00629_consen 120 QVNLPPI-SSPFQIIFEAIRGS---SYRGDIAIDDISLSP 155 (160)
T ss_dssp EEEE----TS-EEEEEEEEE-----SS--EEEEEEEEEES
T ss_pred EEEcccc-cccceEEEEEEEcC---CCceEEEEEEEEEeC
Confidence 3445443 55556666543222 222228999998863
No 26
>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=29.94 E-value=29 Score=23.05 Aligned_cols=33 Identities=3% Similarity=-0.066 Sum_probs=26.9
Q ss_pred ecCCceEEEEEccCCchhhhcceee-EEeeeEEE
Q psy12830 13 DLTDENVKFQVEDTELSKRTNGNWK-ENMEWKGL 45 (94)
Q Consensus 13 eLtd~~vkFiL~ntDlS~ANaLRRi-lAID~V~I 45 (94)
...++.++|.+.|=|=.+.|+||-. +.-+.|.+
T Consensus 5 ~~~~n~~~~~i~~EdHTLgNlLr~~L~~~p~V~f 38 (85)
T cd07029 5 GTDESCATFVFYGEDHTLGNSLRYVIMKNPEVEF 38 (85)
T ss_pred cCCCCeEEEEEeCCCcchHHHHHHHHhhCCCceE
Confidence 4578899999999999999999998 55555544
No 27
>KOG2485|consensus
Probab=23.87 E-value=29 Score=29.07 Aligned_cols=33 Identities=12% Similarity=0.047 Sum_probs=27.1
Q ss_pred hhhhcceeeEEeeeEEEeecccccCCcccceeeeeeeccceeccccc
Q psy12830 29 SKRTNGNWKENMEWKGLSAQLLLCSRPSFLFAFLCIYENRLALSQTG 75 (94)
Q Consensus 29 S~ANaLRRilAID~V~I~~NTSVL~d~~~~~~fl~~~~~~~~l~~t~ 75 (94)
.||-|+|++ +|...+.| =++-++-.|||||+-+
T Consensus 32 Hmakalr~i---------~~~l~~~D-----~iiEvrDaRiPLssrn 64 (335)
T KOG2485|consen 32 HMAKALRAI---------QNRLPLVD-----CIIEVRDARIPLSSRN 64 (335)
T ss_pred HHHHHHHHH---------Hhhccccc-----EEEEeeccccCCcccc
Confidence 467777775 67778888 8889999999999876
No 28
>PF11175 DUF2961: Protein of unknown function (DUF2961); InterPro: IPR021345 This family of proteins has no known function.
Probab=21.94 E-value=94 Score=24.40 Aligned_cols=20 Identities=25% Similarity=0.581 Sum_probs=18.4
Q ss_pred CCCCCCCeEEEeecCCceEE
Q psy12830 1 MPYANQPSVHITDLTDENVK 20 (94)
Q Consensus 1 mpy~~qP~V~I~eLtd~~vk 20 (94)
|||+++-+|++....+..+.
T Consensus 56 MPF~k~arItl~N~~~~~~~ 75 (237)
T PF11175_consen 56 MPFRKSARITLENESDEPVS 75 (237)
T ss_pred cccCCCeEEEEEeCCCCcee
Confidence 99999999999999998874
Done!