Query 027501
Match_columns 222
No_of_seqs 90 out of 106
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 10:52:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027501.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027501hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4309 Transcription mediator 100.0 1.3E-58 2.9E-63 384.5 17.3 208 1-221 1-217 (217)
2 PF08612 Med20: TATA-binding r 100.0 6.1E-53 1.3E-57 365.9 15.6 199 1-208 1-225 (225)
3 KOG1383 Glutamate decarboxylas 99.3 1.3E-14 2.8E-19 136.7 -9.6 208 1-210 83-297 (491)
4 TIGR00318 cyaB adenylyl cyclas 90.4 8.7 0.00019 31.9 12.3 131 22-165 13-157 (174)
5 PF10765 DUF2591: Protein of u 65.2 4.1 8.9E-05 31.2 1.7 20 142-161 49-68 (109)
6 TIGR02174 CXXU_selWTH selT/sel 55.0 13 0.00029 26.5 2.8 26 141-166 1-27 (72)
7 PF14302 DUF4377: Domain of un 47.8 27 0.00058 25.7 3.4 55 72-143 17-76 (80)
8 PF10262 Rdx: Rdx family; Int 46.2 29 0.00063 24.8 3.4 27 140-166 2-29 (76)
9 PF00181 Ribosomal_L2: Ribosom 39.5 26 0.00057 25.4 2.3 18 134-151 31-48 (77)
10 cd04713 BAH_plant_3 BAH, or Br 39.2 46 0.001 27.0 3.9 37 107-146 12-48 (146)
11 PF06528 Phage_P2_GpE: Phage P 32.6 27 0.00058 22.7 1.2 32 3-34 4-36 (39)
12 PF15043 CNRIP1: CB1 cannabino 29.4 1E+02 0.0022 26.0 4.5 59 67-146 12-73 (161)
13 PF14427 Pput2613-deam: Pput_2 28.9 54 0.0012 26.1 2.6 23 139-164 69-91 (118)
14 PTZ00180 60S ribosomal protein 26.3 36 0.00078 30.8 1.4 33 114-154 27-59 (260)
15 KOG0438 Mitochondrial/chloropl 24.3 42 0.00092 31.0 1.4 36 113-151 79-116 (312)
16 COG0621 MiaB 2-methylthioadeni 22.9 1.5E+02 0.0032 28.7 4.9 52 155-214 238-293 (437)
17 cd07890 CYTH-like_AC_IV-like A 22.4 4.2E+02 0.009 21.3 13.4 133 22-165 11-154 (169)
18 COG2065 PyrR Pyrimidine operon 21.2 98 0.0021 26.5 2.9 103 19-131 43-154 (179)
19 PF09637 Med18: Med18 protein; 20.9 5.7E+02 0.012 22.4 8.3 77 89-166 139-234 (250)
No 1
>KOG4309 consensus Transcription mediator-related factor [Transcription]
Probab=100.00 E-value=1.3e-58 Score=384.53 Aligned_cols=208 Identities=23% Similarity=0.325 Sum_probs=186.8
Q ss_pred CCceEEEEecCCCCCCchhhHHHHHHHHHHhcCcEEEeeEEEEEEEcccccccccccCCCCceEEEEecCCCCceEEEEE
Q 027501 1 MTIKRVLHWQPNVGTSVNSQILNEVSQCVESINGVKEGRWKATLTFYKPMLRDQSLASEFPRDFLGIMVPECPNKYFFVI 80 (222)
Q Consensus 1 M~v~~v~~w~~~~~~t~~~q~~~~L~k~le~lga~k~Grw~vd~~~Yr~~~~~~~~~~~~~r~~~~l~~se~P~~~f~v~ 80 (222)
|||++|-..+-+.+-+ .+|+++.|+|+||+|||.+.|+|.|||++|+++++.... ..-|.+|++|+||+|.+.|.|+
T Consensus 1 mgvt~~~~mpv~egks-~~qt~~~l~r~Le~lGa~~~GtF~VDcetF~~~~~~~~g--~~g~~~~VmHnSeyP~STFSI~ 77 (217)
T KOG4309|consen 1 MGVTCVSQMPVAEGKS-VQQTVELLTRKLEMLGAEKQGTFCVDCETFHTAASTLGG--QTGKLMYVMHNSEYPLSTFSIF 77 (217)
T ss_pred CCceeecccCcccccc-HHHHHHHHHHHHHHhCccccCeEEEeccccCCCCCCCCC--CcCceEEEEecCCCCcceeEEe
Confidence 8999888877666666 599999999999999999999999999999998653211 1359999999999999999999
Q ss_pred ecCc---eeeecCchHHHHHHHhhh-hhcceeEEEe--eeeEeeeceEEEEEEeeeCCCCcceeEEEEEEEeccccHHHH
Q 027501 81 RTQR---IVLEADSTIQTIMEKLQS-YKMRVALNFE--GFQYQLGDFQLRVGKVVPTHSENLRGIVMEVEYLPISSIEKS 154 (222)
Q Consensus 81 ~~~~---~~l~aD~~~~~il~kl~s-y~~r~~~~iE--G~~y~~GDF~VrvG~v~~~~~~~~rGilvEVEY~Pc~~~~~~ 154 (222)
++++ .+++||++||.||.||++ |+++++.||| |.+|++|||.||+|+| +|++++|||+|||||.||.++.+|
T Consensus 78 ~ngTfKks~~VaD~~FDLlm~Kl~~~f~s~ka~KIE~rG~ry~Y~Df~IkvGtv--Tmg~tvKGi~vEIEY~pcvI~~~C 155 (217)
T KOG4309|consen 78 ENGTFKKSCLVADTNFDLLMVKLKGFFQSAKASKIETRGTRYQYCDFLIKVGTV--TMGPTVKGISVEIEYGPCVIASDC 155 (217)
T ss_pred cCCCcceeEEEecCCcceeehhhccceeeccccceeeccceeeecceEEEEcce--EeccccceEEEEEeeCCEEEhHHH
Confidence 9986 499999999999999999 8999999999 9999999999999999 799999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhccCCCCCCccCCCccccccCCCCCCChhhHHHHHHHHHHHHHHhhc---cccccc
Q 027501 155 RQIMEEFLEIWQEALSKRTLPGHFMPMEPNFIEYGLSDHYSSQHTAVQYATVMAQLIASVQ---SVQSMR 221 (222)
Q Consensus 155 ~~ll~EF~~~~~~~~~~~~~p~~~~~~~p~~~~~~~~~~Ys~~dT~~QY~~~f~~~~~~~~---~~~~~~ 221 (222)
|+||.||++++++.+ .+++|..|-+ .++|+.|+|+|||+||+++|.|+||-+| +|||+|
T Consensus 156 w~M~~Eflqsflg~~-~p~aP~~fg~-------t~h~~~y~p~DTm~QYLe~fTk~RKkt~qqv~vag~~ 217 (217)
T KOG4309|consen 156 WSMLLEFLQSFLGSH-TPGAPAVFGN-------TRHDAVYGPADTMVQYLELFTKIRKKTQQQVPVAGIR 217 (217)
T ss_pred HHHHHHHHHHHhccc-CCCchHhhcC-------ccCccccCcHHHHHHHHHHHHHHHHhhhhhccccccC
Confidence 999999999998765 3666766643 5999999999999999999999996554 999987
No 2
>PF08612 Med20: TATA-binding related factor (TRF) of subunit 20 of Mediator complex; InterPro: IPR013921 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. Proteins in this entry are subunit Med20 of the Mediator complex, and is found in the non-essential part of the head []. and related to the TATA-binding protein (TBP). TBP is a highly conserved RNA polymerase II general transcription factor that binds to the core promoter and initiates assembly of the pre-initiation complex. Human TRF has been shown to associate with an RNA polymerase II-SRB complex []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2HZS_C 3RJ1_M 2HZM_G.
Probab=100.00 E-value=6.1e-53 Score=365.88 Aligned_cols=199 Identities=32% Similarity=0.516 Sum_probs=148.3
Q ss_pred CCceEEEEecCCCCCCchhhHHHHHHHHHHhcCcEEEeeEEEEEEEcccccccc--cccCCCCceEEEEecCCCCceEEE
Q 027501 1 MTIKRVLHWQPNVGTSVNSQILNEVSQCVESINGVKEGRWKATLTFYKPMLRDQ--SLASEFPRDFLGIMVPECPNKYFF 78 (222)
Q Consensus 1 M~v~~v~~w~~~~~~t~~~q~~~~L~k~le~lga~k~Grw~vd~~~Yr~~~~~~--~~~~~~~r~~~~l~~se~P~~~f~ 78 (222)
|||+||++|+|+|+++..+|++++++++|+++||++.|+|++||++||+++... +++...+|.||+||+||+|+++|+
T Consensus 1 M~vt~v~~~~~~p~~~~~~qti~~~~~~l~~~~~~~~g~w~v~~k~yr~~~~~~p~~~~~~~~r~~~~L~~S~~p~~~f~ 80 (225)
T PF08612_consen 1 MGVTVVFFQKATPEAKTASQTITELHDRLENLGATKQGRWSVECKTYRDTPSSLPASQPPSQPRYMYVLSLSEYPNSTFI 80 (225)
T ss_dssp --EEEEEESS--TT------HHHHHHHHCTTTEEEEE--EEEEEEEEEE-SSS------SSS-SEEEEEEEESSSEEEEE
T ss_pred CcEEEEEEECCCcccchhHHHHHHHHHHHHhcCCEEeeeEEEEEEEecCCCCCCCcccccccccEEEEEecccCCCcEEE
Confidence 999999999999999889999999999999999999999999999999987632 233457899999999999999999
Q ss_pred EEecCce-----------------eeecCchHHHHHHHhhh-hhcceeEEEeeee-EeeeceEEEEEEeeeCCCCcceeE
Q 027501 79 VIRTQRI-----------------VLEADSTIQTIMEKLQS-YKMRVALNFEGFQ-YQLGDFQLRVGKVVPTHSENLRGI 139 (222)
Q Consensus 79 v~~~~~~-----------------~l~aD~~~~~il~kl~s-y~~r~~~~iEG~~-y~~GDF~VrvG~v~~~~~~~~rGi 139 (222)
++++++. ++++|+.|+.||.||++ |+.|+++++||.. |++|||+||+|+|+ +++++|||
T Consensus 81 i~~~~~~~~~~~~~~~~~~~~~~~~~~~D~~~~~i~~KL~~~w~~Rq~~kie~~~~YelgDf~VRvg~v~--~~~~~rGi 158 (225)
T PF08612_consen 81 IINNGPAKTTTNSQTNSHLMNGCPTLVADSFFDLIMSKLQSLWTQRQTIKIEGGGTYELGDFTVRVGNVF--QGQSFRGI 158 (225)
T ss_dssp EETTEEEEEES-GGGHHHHHTTSS-S-B--HHHHHHHHSTTTEEEEEEEEEESEEEEEETTEEEEEEEEE--ETTEEEEE
T ss_pred EEcCCCcccccccCCccceeccccccccChHHHHHHHHHHhhhhhcEEEEEeeeeEEEECCEEEEEEEEE--ECCCCcEE
Confidence 9977641 88999999999999999 8999999999555 99999999999996 66799999
Q ss_pred EEEEEE---eccccHHHHHHHHHHHHHHHHhhhccCCCCCCc-cCCCccccccCCCCCCChh-hHHHHHHHHHH
Q 027501 140 VMEVEY---LPISSIEKSRQIMEEFLEIWQEALSKRTLPGHF-MPMEPNFIEYGLSDHYSSQ-HTAVQYATVMA 208 (222)
Q Consensus 140 lvEVEY---~Pc~~~~~~~~ll~EF~~~~~~~~~~~~~p~~~-~~~~p~~~~~~~~~~Ys~~-dT~~QY~~~f~ 208 (222)
+||||| .||++++.||+||+||++.+.. |+.- ....|++...++++.|++. |||+||+++|+
T Consensus 159 lvEVEy~~~~p~~~~~~~~~li~efl~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~dta~QY~e~~~ 225 (225)
T PF08612_consen 159 LVEVEYRGSDPCVSFEQCWELIREFLQSFGI-------PDAKESIFVPNLGPEKLDDLYTPGSDTAYQYMEIFN 225 (225)
T ss_dssp EEEEEE---SSSTTHHHHHHHHHHHHHHTTS--------S-EEE-----SSSS---HH----HHHHHHHHHHH-
T ss_pred EEEEEEccCCccccHHHHHHHHHHHHHHhCC-------CCCcccccCcccccccccccccchhhHHHHHHHHhC
Confidence 999999 9999999999999999999732 1111 1124777778999999998 99999999996
No 3
>KOG1383 consensus Glutamate decarboxylase/sphingosine phosphate lyase [Amino acid transport and metabolism]
Probab=99.30 E-value=1.3e-14 Score=136.65 Aligned_cols=208 Identities=16% Similarity=0.125 Sum_probs=172.3
Q ss_pred CCceEEEEecCCCCCCchhhHHHHHHHHHHhcCcEEEeeEEEEEEEcccccccccccCCCCceEEEEecC-CCCceEEEE
Q 027501 1 MTIKRVLHWQPNVGTSVNSQILNEVSQCVESINGVKEGRWKATLTFYKPMLRDQSLASEFPRDFLGIMVP-ECPNKYFFV 79 (222)
Q Consensus 1 M~v~~v~~w~~~~~~t~~~q~~~~L~k~le~lga~k~Grw~vd~~~Yr~~~~~~~~~~~~~r~~~~l~~s-e~P~~~f~v 79 (222)
|.++|+.||.+++..+...++++.+....+.+.+++.+.|.--+.-|.+...++ ...+++.+-+.+.+ ..|.+.+..
T Consensus 83 ~~vS~~v~~~~~~~~~l~~~~~~k~N~l~~d~fp~~~~~e~~~Vnm~~~L~~~~--~~~~g~~t~G~Ses~l~~~k~~~~ 160 (491)
T KOG1383|consen 83 GLASGVVYWGEPELDKLIMEAYNKFNPLHPDEFPVVRKLEAECVNMIANLFNAP--SDSCGCGTVGGSESGLAAKKSYRN 160 (491)
T ss_pred CeeeEEEecCCcchhhHHHHHHhhcCccCccccchhHHHHHHHHHHHHHHhcCC--ccccCccccccchHHHHHHHHHHH
Confidence 568999999988888887777777666667788888888876555555554443 22578888888877 777776654
Q ss_pred EecC--ceeeecCchHHHHHHHhhhhhcceeEEEeeeeEeeeceEEEEEEeeeCCCCcceeEEEEEEEeccccHHHHHHH
Q 027501 80 IRTQ--RIVLEADSTIQTIMEKLQSYKMRVALNFEGFQYQLGDFQLRVGKVVPTHSENLRGIVMEVEYLPISSIEKSRQI 157 (222)
Q Consensus 80 ~~~~--~~~l~aD~~~~~il~kl~sy~~r~~~~iEG~~y~~GDF~VrvG~v~~~~~~~~rGilvEVEY~Pc~~~~~~~~l 157 (222)
.+.. +.....+..-..+++.+..|...-.+++++..|..|||.+++|.++....++.+|++.+++|.|-..+++...|
T Consensus 161 ~r~~~k~I~~p~iv~~~~v~~a~eK~a~yf~v~l~~V~~~~~~~~~D~~k~~~~i~eNti~lv~~~~~~p~G~~e~ve~l 240 (491)
T KOG1383|consen 161 RRKAQKGIDKPNIVTPQNVHAAFEKAARYFEVELREVPLDEGDYRVDPGKVVRMIDENTIMLVGSLPNFPTGEIEDVEKL 240 (491)
T ss_pred HHHhccCCCCccccchHHHHHHHHHHHhhEEEEEEeeeccccceEecHHHHHHHhccceEEEEEEcCCCCccchhhHHHH
Confidence 5554 45677889999999999999999999999999999999999999998889999999999999999999999999
Q ss_pred HHHHHHHHHhhhccCCCCCCccC--CCccccccCCCCCCChhhHHHH--HHHHHHHH
Q 027501 158 MEEFLEIWQEALSKRTLPGHFMP--MEPNFIEYGLSDHYSSQHTAVQ--YATVMAQL 210 (222)
Q Consensus 158 l~EF~~~~~~~~~~~~~p~~~~~--~~p~~~~~~~~~~Ys~~dT~~Q--Y~~~f~~~ 210 (222)
+++|++.|...+++++.+|.|+. ...++.+++....|.+.+++.- |--..+.+
T Consensus 241 ~~l~~e~w~ipiHvDa~~GgFi~p~~~~~~~~fdFr~p~V~Sisa~~HKYGl~~~G~ 297 (491)
T KOG1383|consen 241 ADLLLEIWDIPIHVDACLGGFINPAGYLNEEEFDFRVPGVTSISADGHKYGLAPAGS 297 (491)
T ss_pred HHHHHHHhCCceeecccCccccccccccCccccccCCCCceeEeeccceeeeeecCc
Confidence 99999999988999999999997 5667777888888999998876 65444433
No 4
>TIGR00318 cyaB adenylyl cyclase CyaB, putative. The protein CyaB from Aeromonas hydrophila is a second adenylyl cyclase from that species, as demonstrated by complementation in E. coli and by assay of the enzymatic properties of purified recombinant protein. It has no detectable homology to any other protein of known function, and has several unusual properties, including an optimal temperature of 65 degrees and an optimal pH of 9.5. A cluster of uncharaterized archaeal homologs may be orthologous and serve (under certain circumstances) to produce the regulatory metabolite cyclic AMP (cAMP).
Probab=90.42 E-value=8.7 Score=31.90 Aligned_cols=131 Identities=14% Similarity=0.104 Sum_probs=73.8
Q ss_pred HHHHHHHHHhcCcEEEeeEEEEEEEcccccccccccCCCCceEEEEecCCCCceEEEEEecCc-----------eeeecC
Q 027501 22 LNEVSQCVESINGVKEGRWKATLTFYKPMLRDQSLASEFPRDFLGIMVPECPNKYFFVIRTQR-----------IVLEAD 90 (222)
Q Consensus 22 ~~~L~k~le~lga~k~Grw~vd~~~Yr~~~~~~~~~~~~~r~~~~l~~se~P~~~f~v~~~~~-----------~~l~aD 90 (222)
.+.+.++|+++|+...+ ....-..|..++...-.. ......+.... ..+++-...+. -+-++|
T Consensus 13 ~~~~~~~L~~~g~~~~~-~~~q~D~Yfd~p~~~l~~---~~~~LRiR~~~--~~~~lT~Kgp~~~~~~~~~~E~e~~v~d 86 (174)
T TIGR00318 13 KEKVVEKLKNKGFKFIK-KEFQHDIYFSNPCRDFAS---TDEALRIRKLT--GEKFVTYKGPKIDNESKTRKEIEFKIED 86 (174)
T ss_pred HHHHHHHHHhcCccccc-ccceEEEeecCCCcchhh---CCcEEEEEEcC--CcEEEEEeCCccCCcceEEEEEEEEECC
Confidence 56788899999987666 555567777765421000 11111222110 11222222221 122233
Q ss_pred -chHHHHHHHhhhhhcceeEEEeeeeEeeeceEEEEEEeeeCCCCcceeEEEEEEEecc--ccHHHHHHHHHHHHHHH
Q 027501 91 -STIQTIMEKLQSYKMRVALNFEGFQYQLGDFQLRVGKVVPTHSENLRGIVMEVEYLPI--SSIEKSRQIMEEFLEIW 165 (222)
Q Consensus 91 -~~~~~il~kl~sy~~r~~~~iEG~~y~~GDF~VrvG~v~~~~~~~~rGilvEVEY~Pc--~~~~~~~~ll~EF~~~~ 165 (222)
..+..||..|. |...-.++=.-..|.+|++.|.+-.|- .+ |-.+|||...= ...+.+.+-+.++++.+
T Consensus 87 ~~~~~~iL~~LG-~~~~~~v~K~R~~~~l~~~~i~lD~v~-----~l-G~FvEIE~~~~~~~~~~~~~~~i~~~~~~L 157 (174)
T TIGR00318 87 IENALQILKKLG-FKKVYEVIKKRRIYQTNELNVSIDDVE-----GL-GFFLEIEKIINNINDKDLALEEIFEIINQL 157 (174)
T ss_pred HHHHHHHHHHCC-CeEEEEEEEEEEEEEECCEEEEEEccC-----CC-ccEEEEEEecCCccchHHHHHHHHHHHHHc
Confidence 55666777554 543222222255589999999998772 34 89999999743 56677777777777763
No 5
>PF10765 DUF2591: Protein of unknown function (DUF2591); InterPro: IPR019701 This entry is represented by Bacteriophage P22, NinX. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=65.22 E-value=4.1 Score=31.25 Aligned_cols=20 Identities=15% Similarity=0.165 Sum_probs=18.4
Q ss_pred EEEEeccccHHHHHHHHHHH
Q 027501 142 EVEYLPISSIEKSRQIMEEF 161 (222)
Q Consensus 142 EVEY~Pc~~~~~~~~ll~EF 161 (222)
-..|.||..+++||++|.+-
T Consensus 49 ~~~f~Pc~nwada~PII~~~ 68 (109)
T PF10765_consen 49 IGRFDPCNNWADAGPIIERN 68 (109)
T ss_pred ccccCCCCCHHHhhHHHHHc
Confidence 47899999999999999995
No 6
>TIGR02174 CXXU_selWTH selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam.
Probab=54.96 E-value=13 Score=26.53 Aligned_cols=26 Identities=23% Similarity=0.397 Sum_probs=22.0
Q ss_pred EEEEEe-ccccHHHHHHHHHHHHHHHH
Q 027501 141 MEVEYL-PISSIEKSRQIMEEFLEIWQ 166 (222)
Q Consensus 141 vEVEY~-Pc~~~~~~~~ll~EF~~~~~ 166 (222)
|+|||+ +|-....+..+-+|.++.+.
T Consensus 1 V~IeyC~~C~y~~Ra~~l~q~L~~~Fp 27 (72)
T TIGR02174 1 VEIEYCGSCGYKPRAAWLKQELLEEFP 27 (72)
T ss_pred CEEEECCCCCChHHHHHHHHHHHHHCC
Confidence 689999 89988888888888888763
No 7
>PF14302 DUF4377: Domain of unknown function (DUF4377)
Probab=47.79 E-value=27 Score=25.67 Aligned_cols=55 Identities=22% Similarity=0.445 Sum_probs=37.3
Q ss_pred CCceEEEEEecCceeeecCchHHHHHHHhhhhhcceeEEEeeeeEeee-ceEEEEEEeee----CCCCcceeEEEEE
Q 027501 72 CPNKYFFVIRTQRIVLEADSTIQTIMEKLQSYKMRVALNFEGFQYQLG-DFQLRVGKVVP----THSENLRGIVMEV 143 (222)
Q Consensus 72 ~P~~~f~v~~~~~~~l~aD~~~~~il~kl~sy~~r~~~~iEG~~y~~G-DF~VrvG~v~~----~~~~~~rGilvEV 143 (222)
.|.+|+.+.+.+. . .|. ---..|||..||-| .+.|||-.... .-+.+.+-.|++|
T Consensus 17 ~~~~Cl~Vk~~~~------~----------~W~-~fy~~IeGF~yE~Gy~Y~L~Vk~~~~~nppaD~ss~~Y~L~~v 76 (80)
T PF14302_consen 17 APMECLQVKEEDN------D----------DWE-LFYGSIEGFEYEPGYEYVLRVKRTPVANPPADASSYRYVLIKV 76 (80)
T ss_pred CccEEEEEEEcCC------C----------CcE-ECcCcccCcCcCCCcEEEEEEEEEECCCCCCCCCceeEEEEEE
Confidence 5777887665432 1 343 12246899999999 99999998742 1246778888877
No 8
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=46.23 E-value=29 Score=24.80 Aligned_cols=27 Identities=15% Similarity=0.358 Sum_probs=21.8
Q ss_pred EEEEEEe-ccccHHHHHHHHHHHHHHHH
Q 027501 140 VMEVEYL-PISSIEKSRQIMEEFLEIWQ 166 (222)
Q Consensus 140 lvEVEY~-Pc~~~~~~~~ll~EF~~~~~ 166 (222)
-|+|||+ +|..-..+..+-++..+.+.
T Consensus 2 ~V~IeYC~~C~~~~~a~~l~~~l~~~fp 29 (76)
T PF10262_consen 2 KVTIEYCTSCGYRPRALELAQELLQTFP 29 (76)
T ss_dssp EEEEEEETTTTCHHHHHHHHHHHHHHST
T ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHCC
Confidence 3899998 88888888888888877753
No 9
>PF00181 Ribosomal_L2: Ribosomal Proteins L2, RNA binding domain; InterPro: IPR022666 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YIT_A 1Q7Y_C 1YJN_A 3CPW_A 3I56_A 1VQ9_A 1M1K_C 3CC7_A 1YIJ_A 1K9M_C ....
Probab=39.46 E-value=26 Score=25.44 Aligned_cols=18 Identities=44% Similarity=0.818 Sum_probs=15.0
Q ss_pred CcceeEEEEEEEeccccH
Q 027501 134 ENLRGIVMEVEYLPISSI 151 (222)
Q Consensus 134 ~~~rGilvEVEY~Pc~~~ 151 (222)
...+|++++|||.|+-++
T Consensus 31 ~~~~g~V~~i~~DP~Rsa 48 (77)
T PF00181_consen 31 GNIKGIVIDIEYDPNRSA 48 (77)
T ss_dssp TSEEEEEEEEEEETTTSS
T ss_pred CCCcEEEEEEEecCCcCc
Confidence 357899999999999654
No 10
>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=39.21 E-value=46 Score=27.03 Aligned_cols=37 Identities=19% Similarity=0.266 Sum_probs=24.7
Q ss_pred eeEEEeeeeEeeeceEEEEEEeeeCCCCcceeEEEEEEEe
Q 027501 107 VALNFEGFQYQLGDFQLRVGKVVPTHSENLRGIVMEVEYL 146 (222)
Q Consensus 107 ~~~~iEG~~y~~GDF~VrvG~v~~~~~~~~rGilvEVEY~ 146 (222)
.+++++|..|.+||++.=-+.- ....+=|+|.|+.-.
T Consensus 12 ~s~~~dg~~y~vgD~Vlv~~~~---~~~pyI~~I~~i~~~ 48 (146)
T cd04713 12 TSFEKDGNKYRLEDCVLLVPED---DQKPYIAIIKDIYKQ 48 (146)
T ss_pred eeEEECCEEEECCCEEEEeCCC---CCCCEEEEEEEEEEc
Confidence 4588889999999998733211 133456777777643
No 11
>PF06528 Phage_P2_GpE: Phage P2 GpE; InterPro: IPR009493 This entry is represented by Burkholderia phage phiE202, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins which are closely related to the GpE tail protein from Phage P2.
Probab=32.64 E-value=27 Score=22.66 Aligned_cols=32 Identities=16% Similarity=0.349 Sum_probs=21.0
Q ss_pred ceEEEEecCCCCCCc-hhhHHHHHHHHHHhcCc
Q 027501 3 IKRVLHWQPNVGTSV-NSQILNEVSQCVESING 34 (222)
Q Consensus 3 v~~v~~w~~~~~~t~-~~q~~~~L~k~le~lga 34 (222)
|-+++||+|++-..+ ..-..+=..|+++..|+
T Consensus 4 iA~~FhW~Pse~~~m~l~El~~Wre~A~~R~~a 36 (39)
T PF06528_consen 4 IAWVFHWPPSEMDAMSLDELMDWRERARRRSGA 36 (39)
T ss_pred eeeecCCCHHHHhcCCHHHHHHHHHHHHHHhcc
Confidence 567999999987765 33355555566665554
No 12
>PF15043 CNRIP1: CB1 cannabinoid receptor-interacting protein 1
Probab=29.44 E-value=1e+02 Score=25.95 Aligned_cols=59 Identities=20% Similarity=0.375 Sum_probs=41.9
Q ss_pred EecCCCCce--EEEEEecCceeeecCchHHHHHHHhhhhhcceeEEEe-eeeEeeeceEEEEEEeeeCCCCcceeEEEEE
Q 027501 67 IMVPECPNK--YFFVIRTQRIVLEADSTIQTIMEKLQSYKMRVALNFE-GFQYQLGDFQLRVGKVVPTHSENLRGIVMEV 143 (222)
Q Consensus 67 l~~se~P~~--~f~v~~~~~~~l~aD~~~~~il~kl~sy~~r~~~~iE-G~~y~~GDF~VrvG~v~~~~~~~~rGilvEV 143 (222)
|++-.+|+. +|+=.|+.| |....++|+- |..|.+ |=.+|-+++. ..-++-|..+++
T Consensus 12 lslk~~pn~~PVffKvDG~R------------------F~q~RTiKl~tdskYkv-~V~~kP~~~~--~~~~igg~~~~l 70 (161)
T PF15043_consen 12 LSLKIQPNDGPVFFKVDGQR------------------FGQNRTIKLLTDSKYKV-DVTIKPPTVE--TSLSIGGVSLPL 70 (161)
T ss_pred EEEEeCCCCCcEEEEecccc------------------cCCceEEEEecCCEEEE-EEEEcCCcce--eeeEecceeece
Confidence 444455555 676555554 5445778888 999998 8888888886 355888999988
Q ss_pred EEe
Q 027501 144 EYL 146 (222)
Q Consensus 144 EY~ 146 (222)
|=.
T Consensus 71 ~~k 73 (161)
T PF15043_consen 71 EEK 73 (161)
T ss_pred eec
Confidence 864
No 13
>PF14427 Pput2613-deam: Pput_2613-like deaminase
Probab=28.91 E-value=54 Score=26.15 Aligned_cols=23 Identities=17% Similarity=0.332 Sum_probs=19.3
Q ss_pred EEEEEEEeccccHHHHHHHHHHHHHH
Q 027501 139 IVMEVEYLPISSIEKSRQIMEEFLEI 164 (222)
Q Consensus 139 ilvEVEY~Pc~~~~~~~~ll~EF~~~ 164 (222)
++||=+|.||. .|+..|+-|-+.
T Consensus 69 m~I~G~ypPC~---~CkG~Mr~~s~~ 91 (118)
T PF14427_consen 69 MLIDGQYPPCN---SCKGKMRRASEK 91 (118)
T ss_pred EEEeeecCCCc---hhHHHHHHhhhc
Confidence 35667899998 899999999885
No 14
>PTZ00180 60S ribosomal protein L8; Provisional
Probab=26.34 E-value=36 Score=30.75 Aligned_cols=33 Identities=21% Similarity=0.302 Sum_probs=23.7
Q ss_pred eeEeeeceEEEEEEeeeCCCCcceeEEEEEEEeccccHHHH
Q 027501 114 FQYQLGDFQLRVGKVVPTHSENLRGIVMEVEYLPISSIEKS 154 (222)
Q Consensus 114 ~~y~~GDF~VrvG~v~~~~~~~~rGilvEVEY~Pc~~~~~~ 154 (222)
.+|.+-||.=+. ....|++++|||.|+-+...|
T Consensus 27 ~~yR~iDf~r~~--------~~~~g~V~~IeyDPnRsA~IA 59 (260)
T PTZ00180 27 AKLRILDYAERH--------GYIRGVVKDIEHDPGRGAPLA 59 (260)
T ss_pred cccccccccccc--------CCcCEEEEEEEECCCCCceEE
Confidence 458888885322 234599999999999776555
No 15
>KOG0438 consensus Mitochondrial/chloroplast ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=24.34 E-value=42 Score=31.02 Aligned_cols=36 Identities=28% Similarity=0.425 Sum_probs=24.3
Q ss_pred eee--EeeeceEEEEEEeeeCCCCcceeEEEEEEEeccccH
Q 027501 113 GFQ--YQLGDFQLRVGKVVPTHSENLRGIVMEVEYLPISSI 151 (222)
Q Consensus 113 G~~--y~~GDF~VrvG~v~~~~~~~~rGilvEVEY~Pc~~~ 151 (222)
|++ |.+=||.=. +... +++++---++||||.||-+.
T Consensus 79 GhKq~yr~idF~R~-~p~~--~~~~~~e~v~~i~yDP~Rs~ 116 (312)
T KOG0438|consen 79 GHKQRYRMIDFARP-RPIE--QGTTTEERVIEIEYDPGRSA 116 (312)
T ss_pred ceeeeeeEeeeccC-CCcc--ccccccceEEEEEECCCccc
Confidence 444 777799744 4442 44446667999999999544
No 16
>COG0621 MiaB 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]
Probab=22.92 E-value=1.5e+02 Score=28.74 Aligned_cols=52 Identities=15% Similarity=0.250 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhhhccCCCCCCccCCCc----cccccCCCCCCChhhHHHHHHHHHHHHHHhh
Q 027501 155 RQIMEEFLEIWQEALSKRTLPGHFMPMEP----NFIEYGLSDHYSSQHTAVQYATVMAQLIASV 214 (222)
Q Consensus 155 ~~ll~EF~~~~~~~~~~~~~p~~~~~~~p----~~~~~~~~~~Ys~~dT~~QY~~~f~~~~~~~ 214 (222)
.++.+++++.+.+. +-+-+ |.|++= +-.-..+...| |.-+|+++.+++|++.
T Consensus 238 ~~~~d~lI~~~~~~---~kv~~-~lHlPvQsGsd~ILk~M~R~y----t~e~~~~~i~k~R~~~ 293 (437)
T COG0621 238 LEFTDDLIEAIAET---PKVCP-HLHLPVQSGSDRILKRMKRGY----TVEEYLEIIEKLRAAR 293 (437)
T ss_pred hhcCHHHHHHHhcC---Ccccc-cccCccccCCHHHHHHhCCCc----CHHHHHHHHHHHHHhC
Confidence 56777777776542 11222 222211 11113555556 8999999999999765
No 17
>cd07890 CYTH-like_AC_IV-like Adenylyl cyclase (AC) class IV-like, a subgroup of the CYTH-like superfamily. This subgroup contains class IV ACs and similar proteins. AC catalyzes the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. cAMP is a key signaling molecule which conveys a variety of signals in different cell types. In prokaryotes, cAMP is a catabolite derepression signal which triggers the expression of metabolic pathways including the lactose operon. Six non-homologous classes of ACs have been identified (I-VI). Class IV ACs are found in this group. In bacteria, the gene encoding Class IV AC has been designated cyaB and the protein as AC2. AC-IV occurs in addition to AC-I in bacterial pathogens such as Yersinia pestis (plague disease). The role of AC-IV is unknown but it has been speculated that it may be a factor in pathogenesis, perhaps providing cAMP for a secondary internal signaling function, or for secretion and uptake into host cells, where it may disrupt normal cel
Probab=22.44 E-value=4.2e+02 Score=21.35 Aligned_cols=133 Identities=18% Similarity=0.195 Sum_probs=70.0
Q ss_pred HHHHHHHHHhcCcEEEeeEEEEEEEcccccccc------ccc--CCC--CceEEEEecCCCCceEEEEEecCceeeecC-
Q 027501 22 LNEVSQCVESINGVKEGRWKATLTFYKPMLRDQ------SLA--SEF--PRDFLGIMVPECPNKYFFVIRTQRIVLEAD- 90 (222)
Q Consensus 22 ~~~L~k~le~lga~k~Grw~vd~~~Yr~~~~~~------~~~--~~~--~r~~~~l~~se~P~~~f~v~~~~~~~l~aD- 90 (222)
.+.+.++|..+|+... ........|..++... ... ... .+.+..+.-...-. .+- .+.+-.+-++|
T Consensus 11 ~~~~~~~l~~l~~~~~-~~~~q~d~Yfd~p~~~l~~~~~~LRiR~~~~~~~~~lT~K~~~~~~-~~~-~~~E~e~~v~~~ 87 (169)
T cd07890 11 LEALRERLAALGGAEG-GREFQEDIYFDHPDRDLAATDEALRLRRMGDSGKTLLTYKGPKLDG-GPK-VREEIETEVADP 87 (169)
T ss_pred HHHHHHHHHhcccccc-cceeEeEEEEcCCchhHHhCCCcEEEEEeCCCCcEEEEEECCCCCC-Ccc-ceEEEEEecCCH
Confidence 5677888888887776 4555667777765311 100 000 12222222111000 000 00000111122
Q ss_pred chHHHHHHHhhhhhcceeEEEeeeeEeeeceEEEEEEeeeCCCCcceeEEEEEEEeccccHHHHHHHHHHHHHHH
Q 027501 91 STIQTIMEKLQSYKMRVALNFEGFQYQLGDFQLRVGKVVPTHSENLRGIVMEVEYLPISSIEKSRQIMEEFLEIW 165 (222)
Q Consensus 91 ~~~~~il~kl~sy~~r~~~~iEG~~y~~GDF~VrvG~v~~~~~~~~rGilvEVEY~Pc~~~~~~~~ll~EF~~~~ 165 (222)
..+..||.+|. |...-.++-+=..|.+|++.|-+=.+- . -|-.+|||-..-. ++.+.+-|.++++.+
T Consensus 88 ~~~~~iL~~lg-~~~~~~~~K~R~~~~~~~~~v~lD~~~-----~-lG~f~EiE~~~~~-~~~~~~~l~~~~~~l 154 (169)
T cd07890 88 EAMKEILERLG-FGPVGRVKKEREIYLLGQTRVHLDRVE-----G-LGDFVEIEVVLED-IEEAEEGLGEAAELL 154 (169)
T ss_pred HHHHHHHHHcC-CceeEEEEEEEEEEEECCEEEEEEccC-----C-CCceEEEEEEeCC-cHHHHHHHHHHHHHc
Confidence 34455555553 443333333345588999888877772 1 3889999998555 688888888888764
No 18
>COG2065 PyrR Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=21.17 E-value=98 Score=26.45 Aligned_cols=103 Identities=18% Similarity=0.347 Sum_probs=62.5
Q ss_pred hhHHHHHHHHHHhcCcEEEeeEEEEEEEccccccccc--ccCCCCceEEEEecCCCCceEEEEEecCceeeecCchHHHH
Q 027501 19 SQILNEVSQCVESINGVKEGRWKATLTFYKPMLRDQS--LASEFPRDFLGIMVPECPNKYFFVIRTQRIVLEADSTIQTI 96 (222)
Q Consensus 19 ~q~~~~L~k~le~lga~k~Grw~vd~~~Yr~~~~~~~--~~~~~~r~~~~l~~se~P~~~f~v~~~~~~~l~aD~~~~~i 96 (222)
--+.+.|.++|+.+-+.+...-.+|.++||.-..... ++...+-.+.+ +=-++..+++++ ||=+.+++..-
T Consensus 43 v~lA~rl~~~i~~~Eg~~vp~g~lDIt~yRDDl~~~~~~~p~~~~t~~~~----di~~k~VILVDD---VLytGRTIRAA 115 (179)
T COG2065 43 VPLAERLAERIEELEGIEVPVGELDITLYRDDLTQKGPLRPQAKTTILPF----DITGKRVILVDD---VLYTGRTIRAA 115 (179)
T ss_pred HHHHHHHHHHHHHHhCCCCCeeeEEeEEeechhhhcCccCCcccCccCcc----cccCCEEEEEee---ecccCccHHHH
Confidence 3468899999999999999999999999999654211 11001111111 111234444442 77777888888
Q ss_pred HHHhhhh-hc---ceeEEEe-eee-Eeee-ceEEEEEEeeeC
Q 027501 97 MEKLQSY-KM---RVALNFE-GFQ-YQLG-DFQLRVGKVVPT 131 (222)
Q Consensus 97 l~kl~sy-~~---r~~~~iE-G~~-y~~G-DF~VrvG~v~~~ 131 (222)
|.-|-.| +. ..++-++ |++ .-+- ||+ |+-+++
T Consensus 116 ldal~d~GRPa~I~LavLVDRGHRELPIRaDyV---GKniPT 154 (179)
T COG2065 116 LDALVDYGRPAKIQLAVLVDRGHRELPIRADYV---GKNIPT 154 (179)
T ss_pred HHHHHhcCCcceEEEEEEEcCCCccCCcccccc---cCcCCC
Confidence 8877774 32 3345555 887 3343 774 544433
No 19
>PF09637 Med18: Med18 protein; InterPro: IPR019095 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. Med18 is one subunit of the Mediator complex and a component of the head module that is involved in stimulating basal RNA polymerase II (PolII) transcription. Med18 consists of an eight-stranded beta-barrel with a central pore and three flanking helices. It complexes with Med8 and Med20 proteins by forming a heterodimer of two-fold symmetry with Med20 and binding the C-terminal alpha-helix region of Med8 across the top of its barrel. This complex creates a multipartite TBP-binding site that can be modulated by transcriptional activators []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2HZM_F 2HZS_H 3RJ1_E 3C0T_A.
Probab=20.94 E-value=5.7e+02 Score=22.39 Aligned_cols=77 Identities=14% Similarity=0.283 Sum_probs=53.4
Q ss_pred cCchHHHHHHHhhhhhcceeEEEeeeeEeeeceEEEEEEeee--CCCC------------cceeEEEEEEEe--ccccHH
Q 027501 89 ADSTIQTIMEKLQSYKMRVALNFEGFQYQLGDFQLRVGKVVP--THSE------------NLRGIVMEVEYL--PISSIE 152 (222)
Q Consensus 89 aD~~~~~il~kl~sy~~r~~~~iEG~~y~~GDF~VrvG~v~~--~~~~------------~~rGilvEVEY~--Pc~~~~ 152 (222)
...++-.+|..|. |........||.+|..||=.|-+-++.. ..++ ...+.+||+--. ....++
T Consensus 139 ~~~~~~~fl~~lG-y~~~~Eyv~~G~~F~~g~i~I~l~ri~~~~~~~~~~~~~~~l~~~d~s~~~lv~a~v~v~~~~d~~ 217 (250)
T PF09637_consen 139 TSGSLLSFLNELG-YRFDYEYVVEGYRFFKGDIVIELFRIFKVPPPGQYPPPFDKLKPLDPSGSWLVEASVNVPDGTDPE 217 (250)
T ss_dssp SSSSHHHHHHHTT-EEEEEEEEEEEEEEEECCEEEEEEEEEEEETTCCE---SS-EEECTTTTEEEEEEEEEESTTTSHH
T ss_pred CCCCHHHHHHHcC-CceEEEEEEEEEEEEECCEEEEEEEEEecCCCCCCCCCcccCCccCCCCCEEEEEEEEccCCCCHH
Confidence 6788888998887 9999999999999999998888888763 2222 256888888665 223333
Q ss_pred ---HHHHHHHHHHHHHH
Q 027501 153 ---KSRQIMEEFLEIWQ 166 (222)
Q Consensus 153 ---~~~~ll~EF~~~~~ 166 (222)
.+..-|..|-+.+.
T Consensus 218 ~i~~~~~~L~~~~~~Lk 234 (250)
T PF09637_consen 218 RINKASKELLKFQEQLK 234 (250)
T ss_dssp HHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 33344444555443
Done!