Query 000935
Match_columns 1219
No_of_seqs 27 out of 29
Neff 1.7
Searched_HMMs 46136
Date Tue Apr 2 00:54:40 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000935.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000935hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12657 TFIIIC_delta: Transcr 94.4 0.11 2.5E-06 50.5 6.9 77 157-251 87-168 (173)
2 PF11635 Med16: Mediator compl 91.5 1 2.2E-05 53.5 10.3 157 471-677 214-392 (753)
3 smart00320 WD40 WD40 repeats. 66.1 13 0.00028 23.2 3.9 29 155-185 12-40 (40)
4 PF08662 eIF2A: Eukaryotic tra 64.5 14 0.0003 36.9 5.6 79 101-186 11-90 (194)
5 PF00400 WD40: WD domain, G-be 57.5 24 0.00052 25.6 4.4 31 153-185 9-39 (39)
6 cd00200 WD40 WD40 domain, foun 29.9 1.3E+02 0.0029 27.0 5.6 29 155-185 261-289 (289)
7 cd00200 WD40 WD40 domain, foun 29.3 1.5E+02 0.0033 26.7 5.8 50 133-188 159-208 (289)
8 PF13454 NAD_binding_9: FAD-NA 27.0 20 0.00043 34.3 -0.2 44 296-348 2-45 (156)
9 COG2072 TrkA Predicted flavopr 22.2 1.5E+02 0.0032 33.7 5.3 68 296-377 13-91 (443)
10 cd00491 4Oxalocrotonate_Tautom 22.0 1.2E+02 0.0026 24.4 3.5 56 717-773 3-58 (58)
No 1
>PF12657 TFIIIC_delta: Transcription factor IIIC subunit delta N-term; InterPro: IPR024761 This entry represents a domain found towards the N terminus of the 90 kDa subunit of transcription factor IIIC (also known as subunit 9 in yeast []). The whole subunit is involved in RNA polymerase III-mediated transcription. It is possible that this N-terminal domain interacts with TFIIIC subunit 8 [].
Probab=94.43 E-value=0.11 Score=50.46 Aligned_cols=77 Identities=23% Similarity=0.352 Sum_probs=48.7
Q ss_pred ceEEEeecCCCCc----ceEEEEeccceEEEEecCCCCCCcccccccccchhhhccccceeeeecccCCCCcccc-ccCC
Q 000935 157 SVQFIEWSPTSCP----RALLIANFYGRVTIWTQPSHGPANLVRDASCWQREHEWRQDIAVVTKWLSGVSPYRWL-SSKS 231 (1219)
Q Consensus 157 ~vq~ieWSp~~cp----RALLiAnf~GRvtIWtQPsqg~~nlv~da~~wq~ehEWrqd~avvtkwlsg~spyrwl-ssks 231 (1219)
.|-.++|||.+|- =.|.+.+-.|||+||..+..- ..||. .+++|+|-|. ++.. ...+
T Consensus 87 ~vv~~aWSP~Gl~~~~rClLavLTs~~~l~l~~~~~~~-------------~~~W~-~v~dvs~~l~----~~~~~~~~~ 148 (173)
T PF12657_consen 87 QVVSAAWSPSGLGPNGRCLLAVLTSNGRLSLYGPPGNP-------------QGEWN-RVADVSEALY----SYFYNWEPS 148 (173)
T ss_pred cEEEEEECCCCCCCCCceEEEEEcCCCeEEEEecCCCc-------------cccEe-eeeehhHHHH----HhhhccCCC
Confidence 6789999998882 257788999999999887621 34666 4566777665 2221 1222
Q ss_pred CCCCCcchhhHHhhhccCcc
Q 000935 232 TSPLNAKSIFEEKFLSQNSQ 251 (1219)
Q Consensus 232 ss~~n~kstFeEKflsqq~q 251 (1219)
.........|.+.|..++.+
T Consensus 149 ~~~~~~~~~~~~~~~~~~i~ 168 (173)
T PF12657_consen 149 ESSPLDFEEFQRRFRKQRIR 168 (173)
T ss_pred cccccccchhhhhhhccceE
Confidence 23333344567777777643
No 2
>PF11635 Med16: Mediator complex subunit 16; InterPro: IPR021665 Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression []. Several members including the human protein, Q9Y2X0 from SWISSPROT, have one or more WD40 domains on them, PF00400 from PFAM.
Probab=91.47 E-value=1 Score=53.48 Aligned_cols=157 Identities=19% Similarity=0.208 Sum_probs=99.3
Q ss_pred eEEeeccCCCceeeeeccCCCCC--CCCCCCCceeEEEeeeecccCCCCccccccccCCCcccccccccccccccceecc
Q 000935 471 RVQRWESSVQPVVLHQIFGNPTS--SFGGQAPMQTVWVSKVDTSIPTSNFKIHQLAAAGPTCDVWKTTDSGLEKSKIVSF 548 (1219)
Q Consensus 471 RvqrWESs~qpvvlhpifgnpts--s~gGqpPmqTvW~skvd~SIpptdfkn~q~~~~~~~~d~~~~s~~~~dksk~v~F 548 (1219)
-|.|||=..++..|||+|..-.| +.++++++.+.|+..-|+.++.. -+.+
T Consensus 214 iI~RweL~~~~~~lh~~F~ql~s~~~~~~~~~~~~~l~~~~~i~~~~~----------------------------V~si 265 (753)
T PF11635_consen 214 IIERWELREEQQPLHPAFQQLGSKKNSSSEPPPTYRLRRLDDITLNKR----------------------------VVSI 265 (753)
T ss_pred EEEEEEEEccCcccchhhhhcCCCCcCCCCCCCceeEEEecccccCCe----------------------------EEEE
Confidence 38999988888999999988763 34578999999998877765432 1122
Q ss_pred CCCCCccchhhHhheeeccCCceEEeeeeeCceeeeeCCCCCcccce-----eE-------eccccccC------CccCc
Q 000935 549 DPFDLPSDIRSLARIVYSAHGGEIAIALLRGGVHIFSGPNFAPVDNY-----QI-------SVGSAIAA------PAFSS 610 (1219)
Q Consensus 549 dpfdlP~dvr~LAriVySAhGGEiavAflrGgVHIFSGpnf~pVdny-----qI-------nVgsaIa~------PAFSs 610 (1219)
++ .--|+=++++|--|-||++.=.+|.++... .. .+|=..+. -|||+
T Consensus 266 ~~---------------~~~~~~v~~~~~DGsI~~~dr~t~~~~~~~~~~~~~~~~v~s~~~~Gf~fp~~~~~~~vafSP 330 (753)
T PF11635_consen 266 TS---------------PELDIVVAFAFSDGSIEFRDRNTMKELNETRTNGEPPNTVTSLFQAGFHFPCIQPPLHVAFSP 330 (753)
T ss_pred Ee---------------cccCcEEEEEEcCCeEEEEecCcchhhcccccccCCccccccccccccccccCCCCceEEECc
Confidence 22 223447899999999999999999766544 11 13434432 26999
Q ss_pred cccccceeeeccCCCceEEEEEeecCCCccccccccchhhHHHHHHHHH--hhhhhccccccccccccc
Q 000935 611 TSCCSASVWHDTNKDRTILKIIRVLPPAVPSSQVKANSSTWERAIAERF--WWSLLVNVDWWDAVGCTQ 677 (1219)
Q Consensus 611 TSCCsASVWHDt~kd~~iLkIirVLPPa~p~~q~ka~ss~weraiaeRf--wwSLlvgVdWWDaVgcTQ 677 (1219)
|+|..+-. |...+.. |...++....-..|.-..+++ ++|=+| =.-...+-|||+++-+++
T Consensus 331 t~c~~v~~--~~~~~~~--~~~~~~~~~~~~~~~~~~~a~---~~al~~~~a~~~~~~~DDl~~l~~~~ 392 (753)
T PF11635_consen 331 TMCSLVQI--DEDGKTK--KLLYMMRDSGSSPQDLYITAA---ALALRFSLACCSQTSSDDLLILIKTE 392 (753)
T ss_pred ccceEEEE--ecCCCce--eeEEeecCCCCCccccchhHH---HHHHHHHHHHHHhcCcchHHHhhhhh
Confidence 99987665 2222211 555555544444333332211 122233 223457999999998776
No 3
>smart00320 WD40 WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
Probab=66.07 E-value=13 Score=23.19 Aligned_cols=29 Identities=24% Similarity=0.483 Sum_probs=24.9
Q ss_pred CCceEEEeecCCCCcceEEEEeccceEEEEe
Q 000935 155 RDSVQFIEWSPTSCPRALLIANFYGRVTIWT 185 (1219)
Q Consensus 155 ~d~vq~ieWSp~~cpRALLiAnf~GRvtIWt 185 (1219)
.+.|..+.|.+.. +-++.+..+|.|.+|.
T Consensus 12 ~~~i~~~~~~~~~--~~~~~~~~d~~~~~~~ 40 (40)
T smart00320 12 TGPVTSVAFSPDG--KYLASASDDGTIKLWD 40 (40)
T ss_pred CCceeEEEECCCC--CEEEEecCCCeEEEcC
Confidence 4579999999987 7788889999999984
No 4
>PF08662 eIF2A: Eukaryotic translation initiation factor eIF2A; InterPro: IPR013979 This entry contains beta propellor domains found in eukaryotic translation initiation factors and TolB domain-containing proteins.
Probab=64.54 E-value=14 Score=36.90 Aligned_cols=79 Identities=15% Similarity=0.279 Sum_probs=52.8
Q ss_pred hhhhccccceeccccccccCCCCCCCCCceeeEEEe-cCCCCcceeEEEeecCCCCCceEEEeecCCCCcceEEEEeccc
Q 000935 101 VAWCGKLNAIACASETCARIPSSNANTPFWIPIHIV-IPERPTECAVFNVIADCPRDSVQFIEWSPTSCPRALLIANFYG 179 (1219)
Q Consensus 101 vawc~klN~iaca~eTCarip~S~~np~FWiPihIv-iPerPtE~avfnv~adsp~d~vq~ieWSp~~cpRALLiAnf~G 179 (1219)
+.|..+-+.+++.+.| +..++....--=.=|+++ +.+.| +..+++..++| |..++|||.+=.-|++..+..+
T Consensus 11 ~~W~~~G~~l~~~~~~--~~~~~~ks~~~~~~l~~~~~~~~~--~~~i~l~~~~~---I~~~~WsP~g~~favi~g~~~~ 83 (194)
T PF08662_consen 11 LHWQPSGDYLLVKVQT--RVDKSGKSYYGEFELFYLNEKNIP--VESIELKKEGP---IHDVAWSPNGNEFAVIYGSMPA 83 (194)
T ss_pred EEecccCCEEEEEEEE--eeccCcceEEeeEEEEEEecCCCc--cceeeccCCCc---eEEEEECcCCCEEEEEEccCCc
Confidence 4688999999998885 444443321111334444 44444 45556655554 9999999998777777667778
Q ss_pred eEEEEec
Q 000935 180 RVTIWTQ 186 (1219)
Q Consensus 180 RvtIWtQ 186 (1219)
+|+||.-
T Consensus 84 ~v~lyd~ 90 (194)
T PF08662_consen 84 KVTLYDV 90 (194)
T ss_pred ccEEEcC
Confidence 9999975
No 5
>PF00400 WD40: WD domain, G-beta repeat; InterPro: IPR019781 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events.; PDB: 2ZKQ_a 3CFV_B 3CFS_B 1PEV_A 1NR0_A 1VYH_T 3RFH_A 3O2Z_T 3FRX_C 3U5G_g ....
Probab=57.54 E-value=24 Score=25.65 Aligned_cols=31 Identities=26% Similarity=0.519 Sum_probs=27.5
Q ss_pred CCCCceEEEeecCCCCcceEEEEeccceEEEEe
Q 000935 153 CPRDSVQFIEWSPTSCPRALLIANFYGRVTIWT 185 (1219)
Q Consensus 153 sp~d~vq~ieWSp~~cpRALLiAnf~GRvtIWt 185 (1219)
.-.+.|..|.|+|. .+-|+.+-.+|.|.||.
T Consensus 9 ~h~~~i~~i~~~~~--~~~~~s~~~D~~i~vwd 39 (39)
T PF00400_consen 9 GHSSSINSIAWSPD--GNFLASGSSDGTIRVWD 39 (39)
T ss_dssp SSSSSEEEEEEETT--SSEEEEEETTSEEEEEE
T ss_pred CCCCcEEEEEEecc--cccceeeCCCCEEEEEC
Confidence 45678999999999 78899999999999994
No 6
>cd00200 WD40 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and botto
Probab=29.90 E-value=1.3e+02 Score=27.03 Aligned_cols=29 Identities=31% Similarity=0.654 Sum_probs=24.5
Q ss_pred CCceEEEeecCCCCcceEEEEeccceEEEEe
Q 000935 155 RDSVQFIEWSPTSCPRALLIANFYGRVTIWT 185 (1219)
Q Consensus 155 ~d~vq~ieWSp~~cpRALLiAnf~GRvtIWt 185 (1219)
.+.|..+.|+|. .+.|+.+..+|.|.||.
T Consensus 261 ~~~i~~~~~~~~--~~~l~~~~~d~~i~iw~ 289 (289)
T cd00200 261 TNSVTSLAWSPD--GKRLASGSADGTIRIWD 289 (289)
T ss_pred CCcEEEEEECCC--CCEEEEecCCCeEEecC
Confidence 456899999987 46888999999999994
No 7
>cd00200 WD40 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and botto
Probab=29.29 E-value=1.5e+02 Score=26.68 Aligned_cols=50 Identities=18% Similarity=0.295 Sum_probs=34.0
Q ss_pred EEEecCCCCcceeEEEeecCCCCCceEEEeecCCCCcceEEEEeccceEEEEecCC
Q 000935 133 IHIVIPERPTECAVFNVIADCPRDSVQFIEWSPTSCPRALLIANFYGRVTIWTQPS 188 (1219)
Q Consensus 133 ihIviPerPtE~avfnv~adsp~d~vq~ieWSp~~cpRALLiAnf~GRvtIWtQPs 188 (1219)
|+|+..+.......|. ...+.|..+.|+|.. +-|+++..+|.|.||.-.+
T Consensus 159 i~i~d~~~~~~~~~~~----~~~~~i~~~~~~~~~--~~l~~~~~~~~i~i~d~~~ 208 (289)
T cd00200 159 IKLWDLRTGKCVATLT----GHTGEVNSVAFSPDG--EKLLSSSSDGTIKLWDLST 208 (289)
T ss_pred EEEEEccccccceeEe----cCccccceEEECCCc--CEEEEecCCCcEEEEECCC
Confidence 4444444444444444 334579999999987 6677787899999997654
No 8
>PF13454 NAD_binding_9: FAD-NAD(P)-binding
Probab=27.01 E-value=20 Score=34.34 Aligned_cols=44 Identities=23% Similarity=0.479 Sum_probs=34.1
Q ss_pred cccCCcccccccceEEccCCceEEeeecccCCceEEEEEecCCCCCCcccccc
Q 000935 296 LLGAGPSGIMAADVIITDSGAMHVAGVPIVNPSTVVVWEVTPGPGNGFQAAPK 348 (1219)
Q Consensus 296 lLg~GpSGIma~DAIItdsGamhVAGVpivNPSTVVVWEV~pg~gNg~q~tpk 348 (1219)
++|+||+|+.+...++... .-..|..|.|+|- -..|-|.-.-++
T Consensus 2 IIG~G~~G~~~l~~L~~~~--------~~~~~~~I~vfd~-~~~G~G~~~~~~ 45 (156)
T PF13454_consen 2 IIGGGPSGLAVLERLLRQA--------DPKPPLEITVFDP-SPFGAGGAYRPD 45 (156)
T ss_pred EECcCHHHHHHHHHHHHhc--------CCCCCCEEEEEcC-CCccccccCCCC
Confidence 5799999999999988765 5567888999998 555767555443
No 9
>COG2072 TrkA Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]
Probab=22.16 E-value=1.5e+02 Score=33.68 Aligned_cols=68 Identities=32% Similarity=0.517 Sum_probs=39.0
Q ss_pred cccCCcccccccceEEccCCceEEeeecccCCceEEEEEecCCCCCCcc---------ccccccccCCCCCCC--CCCCC
Q 000935 296 LLGAGPSGIMAADVIITDSGAMHVAGVPIVNPSTVVVWEVTPGPGNGFQ---------AAPKTTTSNGVPPSL--SPPKW 364 (1219)
Q Consensus 296 lLg~GpSGIma~DAIItdsGamhVAGVpivNPSTVVVWEV~pg~gNg~q---------~tpk~s~~~~vpp~l--~pp~W 364 (1219)
++|+|+|||.+|=+... +|++- ++|.|-....|-.-- .+||--. +.|..- ...+|
T Consensus 13 IIGaG~sGlaaa~~L~~-------~g~~~-----~~i~Ek~~~~Gg~W~~~ry~~l~~~~p~~~~--~~~~~p~~~~~~~ 78 (443)
T COG2072 13 IIGAGQSGLAAAYALKQ-------AGVPD-----FVIFEKRDDVGGTWRYNRYPGLRLDSPKWLL--GFPFLPFRWDEAF 78 (443)
T ss_pred EECCCHHHHHHHHHHHH-------cCCCc-----EEEEEccCCcCCcchhccCCceEECCchhee--ccCCCccCCcccC
Confidence 68999999999865332 33332 666666655554311 1222222 333222 35789
Q ss_pred CCcchhhhhhhhH
Q 000935 365 AGFAPLAAYLFSW 377 (1219)
Q Consensus 365 ~GFaPLaAYLfsw 377 (1219)
++|+++-.|+-.+
T Consensus 79 ~~~~~~~~y~~~~ 91 (443)
T COG2072 79 APFAEIKDYIKDY 91 (443)
T ss_pred CCcccHHHHHHHH
Confidence 9999877776555
No 10
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=22.04 E-value=1.2e+02 Score=24.36 Aligned_cols=56 Identities=18% Similarity=0.415 Sum_probs=40.8
Q ss_pred eeeeeccCcchHHHHHHHHHhHHHHHHHHhhcchhhhccCCCCCCCCcccccccccc
Q 000935 717 IKCRLLEGTNAQEVRAMVLDMQARLLLDMLGKGIESALINPSALVPDPWQASGETLS 773 (1219)
Q Consensus 717 IkCrlLeG~nAqeVRamVLDMQaRllLDMLGkGIEsALinpsalvpepWqas~etls 773 (1219)
|.+.+++|.+.++-|+++ .-=.+.|.+.+|+--|...|+=...-++-|-..|.+||
T Consensus 3 i~i~~~~grt~eqk~~l~-~~i~~~l~~~~g~~~~~v~V~i~e~~~~~~~~gg~~~~ 58 (58)
T cd00491 3 VQIYILEGRTDEQKRELI-ERVTEAVSEILGAPEATIVVIIDEMPKENWGIGGESAS 58 (58)
T ss_pred EEEEEcCCCCHHHHHHHH-HHHHHHHHHHhCcCcccEEEEEEEeCchhceECCEECc
Confidence 578899999866666555 44467788899988888777766666777776666554
Done!