Query 030872
Match_columns 170
No_of_seqs 53 out of 55
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 05:51:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030872.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030872hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2351 RNA polymerase II, fou 99.9 1.2E-26 2.6E-31 183.5 4.7 77 90-168 2-78 (134)
2 smart00657 RPOL4c DNA-directed 99.5 9.3E-15 2E-19 110.7 5.8 62 104-168 1-62 (118)
3 COG5250 RPB4 RNA polymerase II 99.1 1.5E-10 3.4E-15 92.2 4.7 75 91-168 4-82 (138)
4 PF03874 RNA_pol_Rpb4: RNA pol 98.8 8.5E-09 1.8E-13 76.2 4.5 57 112-168 1-64 (117)
5 PRK14981 DNA-directed RNA poly 98.7 1.4E-08 2.9E-13 77.3 4.2 48 110-166 9-56 (112)
6 COG1460 Uncharacterized protei 94.3 0.09 2E-06 41.5 4.8 48 111-168 11-58 (114)
7 PRK13740 conjugal transfer pro 31.2 1.1E+02 0.0024 22.6 4.3 53 110-168 14-66 (70)
8 PF08855 DUF1825: Domain of un 25.6 90 0.0019 24.6 3.3 35 112-147 61-96 (108)
9 PF10018 Med4: Vitamin-D-recep 23.9 75 0.0016 25.8 2.6 25 136-160 75-99 (188)
10 KOG3208 SNARE protein GS28 [In 22.5 1.1E+02 0.0023 27.2 3.5 52 114-167 56-116 (231)
No 1
>KOG2351 consensus RNA polymerase II, fourth largest subunit [Transcription]
Probab=99.93 E-value=1.2e-26 Score=183.54 Aligned_cols=77 Identities=30% Similarity=0.324 Sum_probs=73.3
Q ss_pred cccccCCccccccCcccccchhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872 90 SVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168 (170)
Q Consensus 90 sa~~eEdAaELkf~~EF~~NAkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~ 168 (170)
.+..||||++|+||+||+ +++|||+|||.+||||+.+|.++ |+|+.+++++||.|||+|+.|||||||+++|++||.
T Consensus 2 ~g~~EEdAa~lk~g~EFe-~~~~L~~sEa~lllE~~~~q~~r-s~d~~~~~s~Vf~kTl~Y~~~FsRfKn~etv~avr~ 78 (134)
T KOG2351|consen 2 RGEEEEDAAELKLGKEFE-TADALMLSEARLLLEHRLEQRRR-SEDDESEMSDVFKKTLQYLDRFSRFKNRETVRAVRT 78 (134)
T ss_pred cchhhccHHhccccHHHH-HHHHHHHHHHHHHHHHHHHHHhh-cccccchHHHHHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence 467899999999999998 69999999999999999999874 999999999999999999999999999999999995
No 2
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=99.54 E-value=9.3e-15 Score=110.71 Aligned_cols=62 Identities=24% Similarity=0.380 Sum_probs=55.0
Q ss_pred cccccchhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872 104 QELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168 (170)
Q Consensus 104 ~EF~~NAkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~ 168 (170)
++|. ||+||+||||++||+++++.-. +.++...++.||.|||+|+++|++|+|+++|+++|+
T Consensus 1 ~~f~-~a~~L~n~Ev~~ll~~k~~~~~--~~~~~~~l~~v~~~tl~Yl~~~~~~~~~e~i~~~~~ 62 (118)
T smart00657 1 PEFK-NATCLTNSEVQLLLELKRQSKE--SEEEQQPLSTVMKKTLKYLSKFARFKNREIVRAVRT 62 (118)
T ss_pred CCcc-chhHhHHHHHHHHHHHHHHhhc--cccccchHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence 4787 8999999999999998765332 777788899999999999999999999999999985
No 3
>COG5250 RPB4 RNA polymerase II, fourth largest subunit [Transcription]
Probab=99.06 E-value=1.5e-10 Score=92.23 Aligned_cols=75 Identities=21% Similarity=0.282 Sum_probs=63.3
Q ss_pred ccccCCccccccCcccccchhhhhhHHHHHHHHHHHHHHHhhhcC--CCCcchHH--HHHHHHHHHhcCCCCCHHHHHhh
Q 030872 91 VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSAD--PTIKIPVS--FDKGLLYAKTHSHFTNPQAVKGL 166 (170)
Q Consensus 91 a~~eEdAaELkf~~EF~~NAkcLmnsEVa~ILE~rkeq~~~lSeD--p~~eiseV--F~KTL~YakrFSrfkN~eSVr~V 166 (170)
+.-||||+.|++++||+ |.+.||.||+..|+|...++-. .+. -+..+.+| |.+|++|-..|+||++.+++..+
T Consensus 4 ~~~ee~aa~lklg~efe-~ed~l~lsEAr~lie~~l~~rr--retn~~e~~s~dvk~~k~T~~Yl~~F~Rfkd~e~~~a~ 80 (138)
T COG5250 4 AIFEEDAAQLKLGPEFE-NEDMLMLSEARYLIEGQLERRR--RETNGAEFRSNDVKVFKSTLGYLDDFCRFKDKEVAEAL 80 (138)
T ss_pred hHhhhhHHHhhcCcccc-chHHHHHHHHHHHHHHHHHHHH--HhcccccccchhHHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence 56789999999999998 8999999999999998877543 222 24556666 99999999999999999999888
Q ss_pred hc
Q 030872 167 FQ 168 (170)
Q Consensus 167 R~ 168 (170)
|.
T Consensus 81 ~~ 82 (138)
T COG5250 81 RT 82 (138)
T ss_pred HH
Confidence 74
No 4
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=98.77 E-value=8.5e-09 Score=76.19 Aligned_cols=57 Identities=32% Similarity=0.376 Sum_probs=46.6
Q ss_pred hhhhHHHHHHHHHHH-HHHHh------hhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872 112 CLMDCEAAHILEGIQ-EQMAL------LSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168 (170)
Q Consensus 112 cLmnsEVa~ILE~rk-eq~~~------lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~ 168 (170)
||.|+||..||+++. ++... ..+++...++.++.+|++|+++|++++|+++++++++
T Consensus 1 ~Lsn~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Yl~~~~~~~~~e~~~~l~~ 64 (117)
T PF03874_consen 1 LLSNYEVLQILEKRREEQKNKSKKKQKNKEDPPENLNTIQYKTLEYLEKFSKFQNPESIKELRE 64 (117)
T ss_dssp EE-HHHHHHHHHHHHHHHHCHCHHHHHHHHHCSSCHCHHHHHHHHHHHHH-SSSSHHHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHHHHHccccCCCHHHHHHHHH
Confidence 799999999999554 44332 2467889999999999999999999999999999885
No 5
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=98.71 E-value=1.4e-08 Score=77.34 Aligned_cols=48 Identities=21% Similarity=0.272 Sum_probs=40.0
Q ss_pred hhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhh
Q 030872 110 AKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGL 166 (170)
Q Consensus 110 AkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~V 166 (170)
.+||.++||+.||+++.+. .+++.+|.|||+|+++|++|++.++...|
T Consensus 9 e~~lt~sEa~~iL~~~~~~---------~els~~~~ktl~y~~kFsk~~~e~a~elv 56 (112)
T PRK14981 9 EEYITIAEAKEILSEIEEE---------RELSYELRRTLDYLNRFSKLDPEDAEELV 56 (112)
T ss_pred cccccHHHHHHHHHHHHhc---------cchhHHHHHHHHHHHHHhCCCHHHHHHHH
Confidence 6899999999999998763 18999999999999999999644444443
No 6
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=94.26 E-value=0.09 Score=41.48 Aligned_cols=48 Identities=21% Similarity=0.360 Sum_probs=40.1
Q ss_pred hhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872 111 KCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168 (170)
Q Consensus 111 kcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~ 168 (170)
+-+-.+||+.||..+ +.+.+++-.+..||.|+++|++.- |+.++++.+
T Consensus 11 ~yiti~Eak~il~~~---------~~~~eL~y~~~~al~y~~kFakld-pe~a~e~ve 58 (114)
T COG1460 11 KYITISEAKKILSKV---------EREEELTYEQREALEYAEKFAKLD-PEKARELVE 58 (114)
T ss_pred cCccHHHHHHHHHHh---------cccccchHHHHHHHHHHHHHhcCC-HHHHHHHHH
Confidence 456689999999998 224789999999999999999987 998887753
No 7
>PRK13740 conjugal transfer protein TraY; Provisional
Probab=31.15 E-value=1.1e+02 Score=22.60 Aligned_cols=53 Identities=15% Similarity=0.042 Sum_probs=42.7
Q ss_pred hhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872 110 AKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168 (170)
Q Consensus 110 AkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~ 168 (170)
..+.|+-|...+|..-++. | -..+-.|+.-+--+.-.||.-|-|+|-++++.+
T Consensus 14 V~~~Ld~etn~lL~~A~~R----S--GRSK~~EA~lRL~DHL~rFpDfy~sei~~e~~~ 66 (70)
T PRK13740 14 VSLKLDEDTNNKLIEAKER----S--GRSKTNEVQIRLRDHLKRFPDFYNSEIFREVAE 66 (70)
T ss_pred EEEEeCHHHHHHHHHHHHH----c--CCcccHHHHHHHHHHHHhCccccchHHhhHhhh
Confidence 3456788888888877663 2 246788999999999999999999999998864
No 8
>PF08855 DUF1825: Domain of unknown function (DUF1825); InterPro: IPR014954 These roteins are uncharacterised and are principally found in cyanobacteria.
Probab=25.58 E-value=90 Score=24.56 Aligned_cols=35 Identities=29% Similarity=0.334 Sum_probs=28.2
Q ss_pred hhh-hHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHH
Q 030872 112 CLM-DCEAAHILEGIQEQMALLSADPTIKIPVSFDKG 147 (170)
Q Consensus 112 cLm-nsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KT 147 (170)
||. +-|+++.++.++.|+.++.-.| ..|++.|+.-
T Consensus 61 ~LSdD~~Ak~m~~qi~~~~~~fG~~~-~~l~~~fd~m 96 (108)
T PF08855_consen 61 ELSDDPEAKDMKEQINAQLNQFGYTP-QDLSQMFDQM 96 (108)
T ss_pred HhccCHHHHHHHHHHHHHHHHcCCCc-chHHHHHHHH
Confidence 455 5789999999999998888877 7788888753
No 9
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=23.86 E-value=75 Score=25.81 Aligned_cols=25 Identities=36% Similarity=0.507 Sum_probs=20.0
Q ss_pred CCCcchHHHHHHHHHHHhcCCCCCH
Q 030872 136 PTIKIPVSFDKGLLYAKTHSHFTNP 160 (170)
Q Consensus 136 p~~eiseVF~KTL~YakrFSrfkN~ 160 (170)
....-+.-++-=|.||.|.|+|+.+
T Consensus 75 ~~~~~~v~~~eLL~YA~rISk~t~~ 99 (188)
T PF10018_consen 75 KAEKRPVDYEELLSYAHRISKFTSA 99 (188)
T ss_pred ccccCCCCHHHHHHHHHHHHHhcCC
Confidence 3444556688899999999999987
No 10
>KOG3208 consensus SNARE protein GS28 [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.52 E-value=1.1e+02 Score=27.16 Aligned_cols=52 Identities=10% Similarity=0.118 Sum_probs=32.5
Q ss_pred hhHHHHHHHHHHHHHHHhhhc-CCCCcchHHHHHH--------HHHHHhcCCCCCHHHHHhhh
Q 030872 114 MDCEAAHILEGIQEQMALLSA-DPTIKIPVSFDKG--------LLYAKTHSHFTNPQAVKGLF 167 (170)
Q Consensus 114 mnsEVa~ILE~rkeq~~~lSe-Dp~~eiseVF~KT--------L~YakrFSrfkN~eSVr~VR 167 (170)
|..|+..|||.+.+=++.+++ +..-..+..-+-| .+|.+.|.+-+.- |.++|
T Consensus 56 ~~~eie~LLeql~~vndsm~~~~~s~a~~aa~~htL~RHrEILqdy~qef~rir~n--~~a~~ 116 (231)
T KOG3208|consen 56 LENEIEGLLEQLQDVNDSMNDCASSPANSAAVMHTLQRHREILQDYTQEFRRIRSN--IDAKR 116 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHhhccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHH
Confidence 457899999999866666555 2233344444444 4699999876432 44444
Done!