Query 033231
Match_columns 124
No_of_seqs 103 out of 279
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 11:24:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033231.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033231hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00152 DNA-directed RNA poly 100.0 3.1E-40 6.8E-45 248.4 9.2 112 4-115 19-130 (130)
2 KOG3405 RNA polymerase subunit 100.0 8.9E-40 1.9E-44 246.7 7.1 94 21-115 43-136 (136)
3 PRK01099 rpoK DNA-directed RNA 99.9 2.6E-26 5.7E-31 153.5 7.5 61 40-100 2-62 (62)
4 COG1758 RpoZ DNA-directed RNA 99.7 2E-18 4.2E-23 117.6 4.9 67 38-104 7-74 (74)
5 PF01192 RNA_pol_Rpb6: RNA pol 99.7 7.6E-17 1.7E-21 104.1 4.7 55 40-94 3-57 (57)
6 PRK00392 rpoZ DNA-directed RNA 99.3 5.2E-12 1.1E-16 83.7 5.7 49 46-95 15-63 (69)
7 TIGR00690 rpoZ DNA-directed RN 99.2 2.4E-11 5.1E-16 80.0 5.4 45 46-91 14-59 (59)
8 PF05320 Pox_RNA_Pol_19: Poxvi 88.5 1.2 2.5E-05 35.6 5.2 61 36-96 71-135 (167)
9 PF08372 PRT_C: Plant phosphor 43.8 22 0.00048 27.7 2.6 19 46-65 59-77 (156)
10 CHL00191 ycf61 DNA-directed RN 43.0 30 0.00064 24.5 2.8 43 46-89 26-68 (76)
11 PF15277 Sec3-PIP2_bind: Exocy 21.4 1E+02 0.0023 21.5 2.7 23 90-112 20-45 (91)
12 PRK13698 plasmid-partitioning 20.6 1.3E+02 0.0029 26.1 3.6 26 79-106 86-117 (323)
No 1
>PLN00152 DNA-directed RNA polymerase; Provisional
Probab=100.00 E-value=3.1e-40 Score=248.45 Aligned_cols=112 Identities=83% Similarity=1.219 Sum_probs=101.1
Q ss_pred cCccchhhhccCCCCCCCCCCcchhHHHHHhHHhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHH
Q 033231 4 QEGAEEDAENINNDDINGEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMK 83 (124)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~ 83 (124)
+++++++.+++|+++.++......++..++....+|+|++||||||+|||+|+||+|||||||+||++++.++|+.||++
T Consensus 19 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~T~p~lTkyErARIiG~RALQIsmgApvlV~~~g~tdPl~IA~~ 98 (130)
T PLN00152 19 EEGAEEDSESNNNDEVKGSIGENEDKEEQEPVQRPRKTTPYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMK 98 (130)
T ss_pred cccccccccccCcccccccccchhccccccccccccccccchhHHHHHhhHhHHHHHHhcCCceEEccCCCcCHHHHHHH
Confidence 35666666777777767777777777777778889999999999999999999999999999999999878999999999
Q ss_pred HHHcCCccEEEEEecCCCcEEEeecceeeecc
Q 033231 84 ELRERKIPFTIRRYLPDGSYEDWGVDELIVED 115 (124)
Q Consensus 84 EL~eGkIpi~IrR~lpdg~yE~~~l~eL~i~~ 115 (124)
||.+|+|||+|||+||||+||+|+|+||++++
T Consensus 99 El~~~~iP~iVrR~lPdG~yEd~~v~EL~~~~ 130 (130)
T PLN00152 99 ELRERKIPFTIRRYLPDGSYEDWGVDELIVED 130 (130)
T ss_pred HHHcCCCCeEEEEECCCCCEEeeEeeeEeecC
Confidence 99999999999999999999999999999875
No 2
>KOG3405 consensus RNA polymerase subunit K [Transcription]
Probab=100.00 E-value=8.9e-40 Score=246.66 Aligned_cols=94 Identities=76% Similarity=1.178 Sum_probs=86.7
Q ss_pred CCCCcchhHHHHHhHHhhhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEEEEecCC
Q 033231 21 GEPIETEEKEEQEQKEAARKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPD 100 (124)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~r~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lpd 100 (124)
.+.+++.+-. +.++.++|+|.|||||||+|||+|+||+|||||||+||++++.+||+.||++||+++||||+|||||||
T Consensus 43 e~~~e~~~~g-~~v~~s~R~TtpyMTKYErArvLGtRAlQIsm~APvmVeLegETdPL~IAmkEL~qkKIP~iIRRyLPD 121 (136)
T KOG3405|consen 43 EDVVEIEDAG-KAVPKSERKTTPYMTKYERARVLGTRALQISMNAPVMVELEGETDPLEIAMKELKQKKIPFIIRRYLPD 121 (136)
T ss_pred hhhhcccccc-ccccccccccCcchhHHHHHHhhhHHHHHHhcCCCeEEecCCCCCHHHHHHHHHhhccCceEEeeeCCC
Confidence 4555555554 566788999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcEEEeecceeeecc
Q 033231 101 GSYEDWGVDELIVED 115 (124)
Q Consensus 101 g~yE~~~l~eL~i~~ 115 (124)
|+||+|+++||+|++
T Consensus 122 gSyEDW~vdELiv~d 136 (136)
T KOG3405|consen 122 GSYEDWSVDELIVED 136 (136)
T ss_pred CCccccccceeeccC
Confidence 999999999999875
No 3
>PRK01099 rpoK DNA-directed RNA polymerase subunit K; Provisional
Probab=99.93 E-value=2.6e-26 Score=153.53 Aligned_cols=61 Identities=48% Similarity=0.838 Sum_probs=58.3
Q ss_pred cCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEEEEecCC
Q 033231 40 KTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPD 100 (124)
Q Consensus 40 ~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~IrR~lpd 100 (124)
.+++||||||+||++|+||+||++||+|+|+.+.++||+.||++||++|+||++|+|++||
T Consensus 2 ~~~~~ltrfe~a~i~akRArQl~~Ga~~lv~~~~~~kPv~iAl~Ei~~gkI~~~v~r~~p~ 62 (62)
T PRK01099 2 MGPMKLTRFERARIIGARALQISMGAPVLIDIPESTDPLDIAEEEFKRGVLPITVKRPLPN 62 (62)
T ss_pred CCCcccCHHHHHHHHHHHHHHHHcCCCceecCCCCCCHHHHHHHHHHcCCCCeEeecCCCC
Confidence 4789999999999999999999999999999855899999999999999999999999997
No 4
>COG1758 RpoZ DNA-directed RNA polymerase, subunit K/omega [Transcription]
Probab=99.74 E-value=2e-18 Score=117.58 Aligned_cols=67 Identities=33% Similarity=0.422 Sum_probs=60.3
Q ss_pred hhcCCccccHHHHHHHHHHHHHHHhhcCCceecCCCC-CChHHHHHHHHHcCCccEEEEEecCCCcEE
Q 033231 38 ARKTSKYMTKYERARILGTRALQISMNAPVMVELEGE-TDPLEIAMKELRERKIPFTIRRYLPDGSYE 104 (124)
Q Consensus 38 ~r~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~-~dPv~IA~~EL~eGkIpi~IrR~lpdg~yE 104 (124)
+.......|||++|+++|+||+||++||+++++.... .+|+.||++||.+|+||+.+.|..++++.+
T Consensus 7 ~~l~~~~~~ryelv~~aa~RA~Ql~~ga~~~~~~~~~~~kpv~iAl~Ei~~g~i~~~i~~~~~~~~~~ 74 (74)
T COG1758 7 EDLLDKVGNRYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKIPIEILRELLIHSLQ 74 (74)
T ss_pred HHHHhhccCHHHHHHHHHHHHHHHHcCCCCccccccccCChHHHHHHHHHcCCCCcccchhhhccccC
Confidence 4456788899999999999999999999999988753 899999999999999999999999988753
No 5
>PF01192 RNA_pol_Rpb6: RNA polymerase Rpb6 ; InterPro: IPR006110 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. A component of 14 to 18 kDa shared by all three forms of eukaryotic RNA polymerases and which has been sequenced in budding yeast (gene RPB6 or RPO26), in Schizosaccharomyces pombe (Fission yeast) (gene rpb6 or rpo15), in human and in African swine fever virus (ASFV) is evolutionary related to the archaebacterial subunit K (gene rpoK). The archaebacterial protein is colinear with the C-terminal part of the eukaryotic subunit. The structures of the omega subunit and RBP6, and the structures of the omega/beta' and RPB6/RPB1 interfaces, suggest a molecular mechanism for the function of omega and RPB6 in promoting RNAP assembly and/or stability. The conserved regions of omega and RPB6 form a compact structural domain that interacts simultaneously with conserved regions of the largest RNAP subunit and with the C-terminal tail following a conserved region of the largest RNAP subunit. The second half of the conserved region of omega and RPB6 forms an arc that projects away from the remainder of the structural domain and wraps over and around the C-terminal tail of the largest RNAP subunit, clamping it in a crevice, and threading the C-terminal tail of the largest RNAP subunit through the narrow gap between omega and RPB6 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_R 2Y0S_I 3HKZ_U 2PMZ_K 3M3Y_F 3HOX_F 3GTJ_F 4A3K_F 2VUM_F 3S14_F ....
Probab=99.67 E-value=7.6e-17 Score=104.07 Aligned_cols=55 Identities=36% Similarity=0.491 Sum_probs=50.3
Q ss_pred cCCccccHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEE
Q 033231 40 KTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTI 94 (124)
Q Consensus 40 ~T~~~LTKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~I 94 (124)
......|||++++++|+||+||++||+|+++.+...+|+.||++||.+|+|+|.|
T Consensus 3 l~~~~~~rY~Lv~~~akRArql~~g~~~~~~~~~~~k~v~iAl~EI~~gki~~~i 57 (57)
T PF01192_consen 3 LLEKVDNRYELVILAAKRARQLSEGAPPLVEEDNEMKPVSIALEEIAEGKIKIEI 57 (57)
T ss_dssp HHHSSSSHHHHHHHHHHHHHHHHTTSTTSSSSSSSSSSSHHHHHHHHTTSSCEEE
T ss_pred hhhccCCHhHHHHHHHHHHHHHHcCcccccccccCCCcHHHHHHHHHcCCCCCcC
Confidence 3457789999999999999999999999998875669999999999999999986
No 6
>PRK00392 rpoZ DNA-directed RNA polymerase subunit omega; Reviewed
Probab=99.30 E-value=5.2e-12 Score=83.73 Aligned_cols=49 Identities=29% Similarity=0.449 Sum_probs=45.2
Q ss_pred cHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCCccEEEE
Q 033231 46 TKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIR 95 (124)
Q Consensus 46 TKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGkIpi~Ir 95 (124)
+||.++.++++||+||+.|++++++.. ..+|+.||++||.+|+|.|..-
T Consensus 15 ~ry~Lv~~aakRArql~~~~~~~~~~~-~~K~~~~Al~EI~~gki~~~~~ 63 (69)
T PRK00392 15 NRYELVLLAAKRARQLRAGAKPPVDKS-SDKPVVIALREIAEGKVTYEIL 63 (69)
T ss_pred CHHHHHHHHHHHHHHHHcCCCCCCCCc-CCChHHHHHHHHHcCCCceecc
Confidence 899999999999999999999987765 6899999999999999998764
No 7
>TIGR00690 rpoZ DNA-directed RNA polymerase, omega subunit. The trusted cutoff excludes archaeal homologs but captures some organellar sequences.
Probab=99.22 E-value=2.4e-11 Score=80.04 Aligned_cols=45 Identities=22% Similarity=0.408 Sum_probs=39.5
Q ss_pred cHHHHHHHHHHHHHHHhhcC-CceecCCCCCChHHHHHHHHHcCCcc
Q 033231 46 TKYERARILGTRALQISMNA-PVMVELEGETDPLEIAMKELRERKIP 91 (124)
Q Consensus 46 TKYElARIiG~RAlQLs~GA-pplVd~~~~~dPv~IA~~EL~eGkIp 91 (124)
+||.++.++++||+||+.|+ +++++.. +.+|+.||++||.+|+|.
T Consensus 14 srY~Lv~~aakRArqL~~~~~~~~~~~~-~~Kp~~iAl~EIa~gkvs 59 (59)
T TIGR00690 14 SRYDLVLVAARRARQLQLKGTDPIVPEE-NDKPTVIALREIAAGLVS 59 (59)
T ss_pred CHhHHHHHHHHHHHHHHhCCCCCccCcc-cCchHHHHHHHHHcCCCC
Confidence 89999999999999999876 5555554 799999999999999974
No 8
>PF05320 Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymerase 19 kDa subunit; InterPro: IPR007984 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. The poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses the transcription of DNA into RNA. It consists of at least eight subunits, this is the 19 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=88.45 E-value=1.2 Score=35.61 Aligned_cols=61 Identities=16% Similarity=0.322 Sum_probs=49.9
Q ss_pred HhhhcCCccccHHHHHHHHHHHHHHHhhcCCceec-CCC---CCChHHHHHHHHHcCCccEEEEE
Q 033231 36 EAARKTSKYMTKYERARILGTRALQISMNAPVMVE-LEG---ETDPLEIAMKELRERKIPFTIRR 96 (124)
Q Consensus 36 ~~~r~T~~~LTKYElARIiG~RAlQLs~GApplVd-~~~---~~dPv~IA~~EL~eGkIpi~IrR 96 (124)
+-.|+-...++=||+.=|+|.--.-|..|-.|||. ... ..+-+.|-++||.+|.-|++|..
T Consensus 71 ~iK~RYTRRiSLfEiTGIiaESyNLLqRGRlPLv~dlsdeT~k~n~L~vvi~EIeEg~CPIVIeK 135 (167)
T PF05320_consen 71 AIKKRYTRRISLFEITGIIAESYNLLQRGRLPLVSDLSDETLKDNILHVVIKEIEEGTCPIVIEK 135 (167)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHHHccccccccccchHHHHHhHHHHHHHHHhcCCCcEEEee
Confidence 33455557789999999999999999999999995 221 24568899999999999999986
No 9
>PF08372 PRT_C: Plant phosphoribosyltransferase C-terminal; InterPro: IPR013583 This domain is found at the C terminus of phosphoribosyltransferases and phosphoribosyltransferase-like proteins. It contains putative transmembrane regions. It often appears together with calcium-ion dependent C2 domains (IPR000008 from INTERPRO).
Probab=43.79 E-value=22 Score=27.70 Aligned_cols=19 Identities=26% Similarity=0.471 Sum_probs=15.2
Q ss_pred cHHHHHHHHHHHHHHHhhcC
Q 033231 46 TKYERARILGTRALQISMNA 65 (124)
Q Consensus 46 TKYElARIiG~RAlQLs~GA 65 (124)
-||.+.|-++.|+ |-.+|.
T Consensus 59 ~Rydrlr~va~rv-Q~vlgd 77 (156)
T PF08372_consen 59 MRYDRLRSVAGRV-QNVLGD 77 (156)
T ss_pred HHHHHHHHHHHHH-HHHHHH
Confidence 4999999999998 555553
No 10
>CHL00191 ycf61 DNA-directed RNA polymerase subunit omega; Provisional
Probab=42.95 E-value=30 Score=24.55 Aligned_cols=43 Identities=14% Similarity=0.183 Sum_probs=34.0
Q ss_pred cHHHHHHHHHHHHHHHhhcCCceecCCCCCChHHHHHHHHHcCC
Q 033231 46 TKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERK 89 (124)
Q Consensus 46 TKYElARIiG~RAlQLs~GApplVd~~~~~dPv~IA~~EL~eGk 89 (124)
+||-...=+|.||+|--.-..--++-. ..+||--|+-|+..-.
T Consensus 26 NRY~iTvqVAnRAKrrRyed~d~~d~~-~~KPv~RAIiEMsDEl 68 (76)
T CHL00191 26 NRYKITIQVANRAKRRRYEDIDIINDP-SIKPIIRAILEMVDEI 68 (76)
T ss_pred cceeehHHHHHHHHHhhhhcccccccc-cccHHHHHHHHHhccc
Confidence 689999999999999877665444433 7899999999987654
No 11
>PF15277 Sec3-PIP2_bind: Exocyst complex component SEC3 N-terminal PIP2 binding PH; PDB: 3HIE_D 3A58_E.
Probab=21.42 E-value=1e+02 Score=21.46 Aligned_cols=23 Identities=26% Similarity=0.543 Sum_probs=15.5
Q ss_pred ccEEEEEecCCCcEEE---eecceee
Q 033231 90 IPFTIRRYLPDGSYED---WGVDELI 112 (124)
Q Consensus 90 Ipi~IrR~lpdg~yE~---~~l~eL~ 112 (124)
+-|...|..+||+|+. |+|+||-
T Consensus 20 v~l~k~K~~~~g~f~i~ktW~L~eL~ 45 (91)
T PF15277_consen 20 VRLHKVKQNDNGSFQIGKTWDLDELK 45 (91)
T ss_dssp EEEEEEEE-CCS-EEEEEEEEGGG--
T ss_pred EEEEEEEecCCCcEEEeeEEehhhce
Confidence 5566778899998875 9999986
No 12
>PRK13698 plasmid-partitioning protein; Provisional
Probab=20.57 E-value=1.3e+02 Score=26.10 Aligned_cols=26 Identities=27% Similarity=0.220 Sum_probs=20.2
Q ss_pred HHHHHHH-----HcCC-ccEEEEEecCCCcEEEe
Q 033231 79 EIAMKEL-----RERK-IPFTIRRYLPDGSYEDW 106 (124)
Q Consensus 79 ~IA~~EL-----~eGk-Ipi~IrR~lpdg~yE~~ 106 (124)
.-++.|| .+|. .|+++||. +|.||.+
T Consensus 86 e~sL~dL~~SIk~~G~~qPiivR~~--~g~yEII 117 (323)
T PRK13698 86 EDSLDDLIPSFLLTGQQTPAFGRRV--SGVIEIA 117 (323)
T ss_pred HHHHHHHHHHHHHhCCCcCeEEEEe--CCeEEEE
Confidence 3667777 6788 79999987 6889875
Done!