Query 003032
Match_columns 855
No_of_seqs 22 out of 24
Neff 1.7
Searched_HMMs 46136
Date Thu Mar 28 15:41:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003032.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003032hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12657 TFIIIC_delta: Transcr 94.0 0.12 2.7E-06 48.3 6.0 76 157-250 87-167 (173)
2 PF11635 Med16: Mediator compl 93.2 0.62 1.3E-05 53.3 10.8 157 471-677 214-392 (753)
3 smart00320 WD40 WD40 repeats. 66.8 9.5 0.00021 22.7 3.2 29 155-185 12-40 (40)
4 PF08662 eIF2A: Eukaryotic tra 65.8 12 0.00026 35.9 5.2 79 101-186 11-90 (194)
5 PF00400 WD40: WD domain, G-be 57.5 17 0.00037 25.2 3.5 31 153-185 9-39 (39)
6 PF01361 Tautomerase: Tautomer 41.6 40 0.00087 26.5 3.7 56 717-773 3-58 (60)
7 TIGR00013 taut 4-oxalocrotonat 39.0 31 0.00066 27.2 2.7 57 717-774 3-60 (63)
8 PF13454 NAD_binding_9: FAD-NA 36.1 11 0.00024 34.5 -0.2 44 296-348 2-45 (156)
9 cd00491 4Oxalocrotonate_Tautom 35.0 52 0.0011 25.3 3.4 56 717-773 3-58 (58)
10 cd00200 WD40 WD40 domain, foun 31.2 1.2E+02 0.0026 26.1 5.3 50 133-188 159-208 (289)
11 cd00200 WD40 WD40 domain, foun 31.0 1.1E+02 0.0023 26.4 4.9 29 155-185 261-289 (289)
12 COG2072 TrkA Predicted flavopr 25.4 61 0.0013 35.2 3.0 70 296-379 13-93 (443)
13 PF13738 Pyr_redox_3: Pyridine 24.3 16 0.00034 33.1 -1.3 40 296-347 2-41 (203)
14 KOG2212 Alpha-amylase [Carbohy 21.5 30 0.00065 38.9 -0.1 14 199-212 388-401 (504)
15 PF12195 End_beta_barrel: Beta 21.0 60 0.0013 29.9 1.7 29 302-330 26-61 (83)
16 PRK02113 putative hydrolase; P 20.8 41 0.00088 32.6 0.6 64 251-324 9-85 (252)
17 PRK09897 hypothetical protein; 20.7 30 0.00066 38.9 -0.3 41 295-346 5-45 (534)
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=94.01 E-value=0.12 Score=48.26 Aligned_cols=76 Identities=24% Similarity=0.350 Sum_probs=47.5
Q ss_pred ceEEEEecCCCcc----hheeeeeccccEEEeecCCCCCCcccccccccccchhcccceeeeeeeccCCCCeeec-ccCC
Q 003032 157 SVQFIEWSPTSCP----RALLIANFYGRVTIWTQPSHGPANLVRDASCWQREHEWRQDIAVVTKWLSGVSPYRWL-SSKS 231 (855)
Q Consensus 157 svq~ieWSp~~cp----RALLiAnf~GRvtIWtQPsqg~~nlv~da~~w~~ehEWrqd~avvTKWLsg~spyrwl-ssks 231 (855)
.|-.++|||.+|- =.|.+.+-.|||+||..+..- ..||. .+++|+|-|. ++.. ...+
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 6889999998883 246788999999999987641 24565 4566666665 2221 1222
Q ss_pred CCCCCccchhhHhhhccCc
Q 003032 232 TSPLNAKSIFEEKFLSQNS 250 (855)
Q Consensus 232 Ss~~~~kstFeEKflsqq~ 250 (855)
.........|.+.|..++.
T Consensus 149 ~~~~~~~~~~~~~~~~~~i 167 (173)
T PF12657_consen 149 ESSPLDFEEFQRRFRKQRI 167 (173)
T ss_pred cccccccchhhhhhhccce
Confidence 2233334456666776664
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=93.16 E-value=0.62 Score=53.34 Aligned_cols=157 Identities=19% Similarity=0.199 Sum_probs=98.8
Q ss_pred eEEeeccCCCceeeeeccCCCCC--CCCCCCCceeEEEeeeecccCCCCccccccccCCCcccccccccccccccceeec
Q 003032 471 RVQRWESSVQPVVLHQIFGNPTS--SFGGQAPMQTVWVSKVDTSIPTSNFKIHQLAAAGPTCDVWKTTDSGLEKSKIVSF 548 (855)
Q Consensus 471 RVqrWESs~qpVvlHpifgnpts--s~gGqpPmqTvW~skvd~SIp~tdfkn~q~~~~g~~~d~~k~s~~~~dksk~v~F 548 (855)
-|.|||=..++..|||+|..-.| +.++++++.+.|+..-|+.++.. -+.+
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 45578999999998877765432 1222
Q ss_pred CCCCCcccHHHHHhhhhcccCCeEEEEEecCceeEeeCCCCCcccce-----ee-------eccccccc------CccCc
Q 003032 549 DPFDLPSDIRSLARIVYSAHGGEIAIALLRGGVHIFSGPNFAPVDNY-----QI-------SVGSAIAA------PAFSS 610 (855)
Q Consensus 549 dpfdlP~d~r~lAriVySAhGGEiavAfl~GgVHIFSG~nftpVdny-----qI-------nVgs~Ia~------PAFSs 610 (855)
++. -.|+=++++|--|-||++.=.+|.++... .. .+|=+.+. -|||+
T Consensus 266 ~~~---------------~~~~~v~~~~~DGsI~~~dr~t~~~~~~~~~~~~~~~~v~s~~~~Gf~fp~~~~~~~vafSP 330 (753)
T PF11635_consen 266 TSP---------------ELDIVVAFAFSDGSIEFRDRNTMKELNETRTNGEPPNTVTSLFQAGFHFPCIQPPLHVAFSP 330 (753)
T ss_pred Eec---------------ccCcEEEEEEcCCeEEEEecCcchhhcccccccCCccccccccccccccccCCCCceEEECc
Confidence 222 22337899999999999999999766544 11 13434432 26999
Q ss_pred cccccceeeecCCCCceEEEEEeecCCCccccccccchhhHHHHHHHHH--hHhhhhcccccccccccc
Q 003032 611 TSCCSASVWHDTNKDRTILKIIRVLPPAVPSSQVKANSSTWERAIAERF--WWSLLVNVDWWDAVGCTQ 677 (855)
Q Consensus 611 TSCCsASVWHDt~kd~tiLkIirVLPPa~p~~q~ka~ss~weraiaeRF--WwSLlvgVdWWDaVgcTQ 677 (855)
|+|..+-. |...+.. |....+....-..|.-..+++ ++|=+| =.-...+-|||+++-+++
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 99977655 2222211 555555544433333332111 222233 122457899999998776
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=66.83 E-value=9.5 Score=22.72 Aligned_cols=29 Identities=24% Similarity=0.483 Sum_probs=24.6
Q ss_pred CCceEEEEecCCCcchheeeeeccccEEEee
Q 003032 155 RDSVQFIEWSPTSCPRALLIANFYGRVTIWT 185 (855)
Q Consensus 155 ~dsvq~ieWSp~~cpRALLiAnf~GRvtIWt 185 (855)
.+.|..+.|.+.. +-++.+..+|.+.+|.
T Consensus 12 ~~~i~~~~~~~~~--~~~~~~~~d~~~~~~~ 40 (40)
T smart00320 12 TGPVTSVAFSPDG--KYLASASDDGTIKLWD 40 (40)
T ss_pred CCceeEEEECCCC--CEEEEecCCCeEEEcC
Confidence 4579999999977 6788889999999984
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=65.81 E-value=12 Score=35.88 Aligned_cols=79 Identities=15% Similarity=0.279 Sum_probs=52.1
Q ss_pred hhhhccccceeccccccccCCCCCCCCCceeeEEEe-cCCCCcceeEEEeecCCCCCceEEEEecCCCcchheeeeeccc
Q 003032 101 VAWCGKLNAIACASETCARIPSSNANTPFWIPIHIV-IPERPTECAVFNVIADCPRDSVQFIEWSPTSCPRALLIANFYG 179 (855)
Q Consensus 101 vawc~klN~Iaca~eTCarip~S~~np~FWiPIhIv-iPerPtE~avfnV~adsp~dsvq~ieWSp~~cpRALLiAnf~G 179 (855)
+.|..+-+.+++.+.| +..++....--=.=|+.+ +.+.| +..+++..++| |..++|||.+=.-|++..+..+
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 4688899999998885 444443321111234444 44444 44555555544 9999999999777777677788
Q ss_pred cEEEeec
Q 003032 180 RVTIWTQ 186 (855)
Q Consensus 180 RvtIWtQ 186 (855)
+|+||.-
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=57.46 E-value=17 Score=25.22 Aligned_cols=31 Identities=26% Similarity=0.519 Sum_probs=27.1
Q ss_pred CCCCceEEEEecCCCcchheeeeeccccEEEee
Q 003032 153 CPRDSVQFIEWSPTSCPRALLIANFYGRVTIWT 185 (855)
Q Consensus 153 sp~dsvq~ieWSp~~cpRALLiAnf~GRvtIWt 185 (855)
.-.+.|..|.|+|. .+-|+.+-.+|.|.||.
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 78888999999999994
No 6
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=41.65 E-value=40 Score=26.53 Aligned_cols=56 Identities=23% Similarity=0.452 Sum_probs=41.1
Q ss_pred eeeeeccCCchHHHHHHHHhhhHHHHHHHhhcchhhhccCCCCCCCCcccccccccc
Q 003032 717 IKCRLLEGTNAQEVRAMVLDMQARLLLDMLGKGIESALINPSALVPDPWQASGETLS 773 (855)
Q Consensus 717 ikcrlleg~naqevramvldmqarllldmlgkgiesalinpsalv~epwqas~etls 773 (855)
|.|.+.+|.+++.-++++-.+ ..++.+-||+.-|..-|.=.-.-++-|...|+.++
T Consensus 3 I~i~~~~g~~~e~K~~l~~~i-t~~~~~~lg~~~~~i~V~i~E~~~~~w~~gG~~~~ 58 (60)
T PF01361_consen 3 ITIKIPEGRTAEQKRELAEAI-TDAVVEVLGIPPERISVVIEEVPPENWGIGGKSLS 58 (60)
T ss_dssp EEEEEESTS-HHHHHHHHHHH-HHHHHHHHTS-GGGEEEEEEEE-CCCEEETTEETT
T ss_pred EEEEECCCCCHHHHHHHHHHH-HHHHHHHhCcCCCeEEEEEEEEChhheEECCEEcC
Confidence 678888999888877777666 45788999998888777666667788887777654
No 7
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=39.00 E-value=31 Score=27.17 Aligned_cols=57 Identities=19% Similarity=0.397 Sum_probs=47.3
Q ss_pred eeeeec-cCCchHHHHHHHHhhhHHHHHHHhhcchhhhccCCCCCCCCccccccccccC
Q 003032 717 IKCRLL-EGTNAQEVRAMVLDMQARLLLDMLGKGIESALINPSALVPDPWQASGETLSG 774 (855)
Q Consensus 717 ikcrll-eg~naqevramvldmqarllldmlgkgiesalinpsalv~epwqas~etls~ 774 (855)
|...++ +|.++++-+++.-.+. +.|.+.||..-|+..|.=...-++-|-..|.+++.
T Consensus 3 i~i~i~~~grt~eqK~~l~~~it-~~l~~~lg~~~~~v~V~i~e~~~~~w~~gG~~~~~ 60 (63)
T TIGR00013 3 VNIYILKEGRTDEQKRQLIEGVT-EAMAETLGANLESIVVIIDEMPKNNYGIGGELVSD 60 (63)
T ss_pred EEEEECCCCCCHHHHHHHHHHHH-HHHHHHhCCCcccEEEEEEEcCHHHeeECCEEhhH
Confidence 567788 8999999888887775 56789999999988888777888888888888764
No 8
>PF13454 NAD_binding_9: FAD-NAD(P)-binding
Probab=36.08 E-value=11 Score=34.55 Aligned_cols=44 Identities=23% Similarity=0.479 Sum_probs=33.9
Q ss_pred ccCCCcccccccceEEecCCceEEeeecccCCceEEEEEeeCCCCCCcccccc
Q 003032 296 LLGAGPSGIMAADVIITDSGAMHVAGVPIVNPSTVVVWEVTPGPGNGFQAAPK 348 (855)
Q Consensus 296 lLg~GpSGIma~DAIItdsGamhVAGVpivNPSTVVVWEV~pg~gNg~q~tpk 348 (855)
++|+||+|+.+...++... .-..|..|.|+|- ...|-|.-.-++
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 4567888999998 555766555443
No 9
>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=34.97 E-value=52 Score=25.28 Aligned_cols=56 Identities=18% Similarity=0.409 Sum_probs=42.7
Q ss_pred eeeeeccCCchHHHHHHHHhhhHHHHHHHhhcchhhhccCCCCCCCCcccccccccc
Q 003032 717 IKCRLLEGTNAQEVRAMVLDMQARLLLDMLGKGIESALINPSALVPDPWQASGETLS 773 (855)
Q Consensus 717 ikcrlleg~naqevramvldmqarllldmlgkgiesalinpsalv~epwqas~etls 773 (855)
|.+.+++|.+.++-|+++=++ .+.|.+.+|.--|...|+=...-++-|-..|.+|+
T Consensus 3 i~i~~~~grt~eqk~~l~~~i-~~~l~~~~g~~~~~v~V~i~e~~~~~~~~gg~~~~ 58 (58)
T cd00491 3 VQIYILEGRTDEQKRELIERV-TEAVSEILGAPEATIVVIIDEMPKENWGIGGESAS 58 (58)
T ss_pred EEEEEcCCCCHHHHHHHHHHH-HHHHHHHhCcCcccEEEEEEEeCchhceECCEECc
Confidence 678899999876666665444 67788999998888877777777788877777664
No 10
>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=31.19 E-value=1.2e+02 Score=26.09 Aligned_cols=50 Identities=18% Similarity=0.295 Sum_probs=33.5
Q ss_pred EEEecCCCCcceeEEEeecCCCCCceEEEEecCCCcchheeeeeccccEEEeecCC
Q 003032 133 IHIVIPERPTECAVFNVIADCPRDSVQFIEWSPTSCPRALLIANFYGRVTIWTQPS 188 (855)
Q Consensus 133 IhIviPerPtE~avfnV~adsp~dsvq~ieWSp~~cpRALLiAnf~GRvtIWtQPs 188 (855)
|+|+..+.......|. ...+.|..+.|+|.. +-|+++..+|.|.||.-.+
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 3444444344444443 334579999999987 5677777799999997654
No 11
>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=30.99 E-value=1.1e+02 Score=26.38 Aligned_cols=29 Identities=31% Similarity=0.654 Sum_probs=24.3
Q ss_pred CCceEEEEecCCCcchheeeeeccccEEEee
Q 003032 155 RDSVQFIEWSPTSCPRALLIANFYGRVTIWT 185 (855)
Q Consensus 155 ~dsvq~ieWSp~~cpRALLiAnf~GRvtIWt 185 (855)
.+.|..+.|+|. .+.|+.+..+|.+.||.
T Consensus 261 ~~~i~~~~~~~~--~~~l~~~~~d~~i~iw~ 289 (289)
T cd00200 261 TNSVTSLAWSPD--GKRLASGSADGTIRIWD 289 (289)
T ss_pred CCcEEEEEECCC--CCEEEEecCCCeEEecC
Confidence 456999999987 46788899999999994
No 12
>COG2072 TrkA Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]
Probab=25.39 E-value=61 Score=35.20 Aligned_cols=70 Identities=33% Similarity=0.512 Sum_probs=41.4
Q ss_pred ccCCCcccccccceEEecCCceEEeeecccCCceEEEEEeeCCCCCCcc---------ccccccccCCCCCCC--CCCCc
Q 003032 296 LLGAGPSGIMAADVIITDSGAMHVAGVPIVNPSTVVVWEVTPGPGNGFQ---------AAPKTTTSNGVPPSL--SPPKW 364 (855)
Q Consensus 296 lLg~GpSGIma~DAIItdsGamhVAGVpivNPSTVVVWEV~pg~gNg~q---------~tpktS~~~~vpp~l--~pp~W 364 (855)
++|+|+|||.+|=+... +|++= ++|.|-....|..-- .+||--. ++|..- ...+|
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 58999999999854322 33332 666666655554311 1222222 333222 35789
Q ss_pred CCcchhhhhhhHHHH
Q 003032 365 AGFAPLAAYLFSWQE 379 (855)
Q Consensus 365 ~GFaPLaAYLfswq~ 379 (855)
++|+++-.|+-.+.+
T Consensus 79 ~~~~~~~~y~~~~~~ 93 (443)
T COG2072 79 APFAEIKDYIKDYLE 93 (443)
T ss_pred CCcccHHHHHHHHHH
Confidence 999988888777764
No 13
>PF13738 Pyr_redox_3: Pyridine nucleotide-disulphide oxidoreductase; PDB: 3D1C_A 4A9W_B 2YLX_A 2YM2_A 2YLW_A 2YLR_A 2YM1_A 2YLS_A 1W4X_A 2YLT_A ....
Probab=24.26 E-value=16 Score=33.15 Aligned_cols=40 Identities=35% Similarity=0.600 Sum_probs=25.1
Q ss_pred ccCCCcccccccceEEecCCceEEeeecccCCceEEEEEeeCCCCCCccccc
Q 003032 296 LLGAGPSGIMAADVIITDSGAMHVAGVPIVNPSTVVVWEVTPGPGNGFQAAP 347 (855)
Q Consensus 296 lLg~GpSGIma~DAIItdsGamhVAGVpivNPSTVVVWEV~pg~gNg~q~tp 347 (855)
++|+||+||.++-.. .+.|. ..|+|.|=.+.+|......+
T Consensus 2 IIGaG~aGl~~a~~l-~~~g~-----------~~v~v~e~~~~~Gg~w~~~~ 41 (203)
T PF13738_consen 2 IIGAGPAGLAAAAHL-LERGI-----------DPVVVLERNDRPGGVWRRYY 41 (203)
T ss_dssp EE--SHHHHHHHHHH-HHTT--------------EEEEESSSSSTTHHHCH-
T ss_pred EECcCHHHHHHHHHH-HhCCC-----------CcEEEEeCCCCCCCeeEEeC
Confidence 479999999998443 33343 23899998877887776433
No 14
>KOG2212 consensus Alpha-amylase [Carbohydrate transport and metabolism]
Probab=21.50 E-value=30 Score=38.92 Aligned_cols=14 Identities=43% Similarity=0.821 Sum_probs=11.3
Q ss_pred cccccchhccccee
Q 003032 199 SCWQREHEWRQDIA 212 (855)
Q Consensus 199 ~~w~~ehEWrqd~a 212 (855)
+.|-|||.|||--.
T Consensus 388 ~GWvCEHRWrqI~~ 401 (504)
T KOG2212|consen 388 NGWVCEHRWRQIRN 401 (504)
T ss_pred CceeeechHHHHHH
Confidence 46999999998543
No 15
>PF12195 End_beta_barrel: Beta barrel domain of bacteriophage endosialidase; InterPro: IPR024427 This entry represents the beta barrel domain of endosialidases which is nested in a beta propeller domain. This beta barrel domain is approximately 80 amino acids in length and represents one of the two sialic acid binding sites of the enzyme [].; PDB: 1V0E_B 1V0F_E 3JU4_A 3GVL_A 3GVK_B 3GVJ_A.
Probab=21.02 E-value=60 Score=29.87 Aligned_cols=29 Identities=38% Similarity=0.416 Sum_probs=19.1
Q ss_pred ccccccceEEec-------CCceEEeeecccCCceE
Q 003032 302 SGIMAADVIITD-------SGAMHVAGVPIVNPSTV 330 (855)
Q Consensus 302 SGIma~DAIItd-------sGamhVAGVpivNPSTV 330 (855)
=|+++||.|.-+ ||.|-||-|+=-|--||
T Consensus 26 HGl~vGD~VnFsnsa~tGvSG~mTVatVid~ntFTV 61 (83)
T PF12195_consen 26 HGLFVGDFVNFSNSAVTGVSGNMTVATVIDANTFTV 61 (83)
T ss_dssp ----TT-EEEEES-SSTT--EEEEEEEEEETTEEEE
T ss_pred CceeecceEEEeccccccccccEEEEEEecCCcEEE
Confidence 388999999876 68999999987776555
No 16
>PRK02113 putative hydrolase; Provisional
Probab=20.77 E-value=41 Score=32.56 Aligned_cols=64 Identities=28% Similarity=0.459 Sum_probs=37.4
Q ss_pred cccCCCCceeEEeeeeecceeEEeeecCCCCCCCCCCcceecccc---ccCCCcccccc---------cce-EEecCCce
Q 003032 251 QTSDRWPNFLCVCSVFSSGSVQLNWSQWPPSQNGAASKWFPTAKG---LLGAGPSGIMA---------ADV-IITDSGAM 317 (855)
Q Consensus 251 qtsarwpnflcvcsVf~sGsVQlhWsqwPp~qn~t~pkWF~TsKG---lLg~GpSGIma---------~DA-IItdsGam 317 (855)
-++.++|++.|.|.+-.+.. |... ...+--+....| |++||+ |+.. -|+ +||+.-.=
T Consensus 9 g~~~g~P~~~c~c~~C~~~~--------~~~~-R~~~s~li~~~~~~iLiD~G~-g~~~~l~~~~~~~id~I~lTH~H~D 78 (252)
T PRK02113 9 GTSTGVPEIGCTCPVCTSKD--------PRDN-RLRTSALVETEGARILIDCGP-DFREQMLRLPFGKIDAVLITHEHYD 78 (252)
T ss_pred CCCCCeecCCCCCccCCCCC--------CCCc-ceeeEEEEEECCeEEEEECCc-hHHHHHHhcCccccCEEEECCCChh
Confidence 45779999999999998842 4433 333333443333 788887 3221 232 35555555
Q ss_pred EEeeecc
Q 003032 318 HVAGVPI 324 (855)
Q Consensus 318 hVAGVpi 324 (855)
|+.|.|.
T Consensus 79 H~~gl~~ 85 (252)
T PRK02113 79 HVGGLDD 85 (252)
T ss_pred hhCCHHH
Confidence 6666553
No 17
>PRK09897 hypothetical protein; Provisional
Probab=20.68 E-value=30 Score=38.88 Aligned_cols=41 Identities=24% Similarity=0.546 Sum_probs=31.5
Q ss_pred cccCCCcccccccceEEecCCceEEeeecccCCceEEEEEeeCCCCCCcccc
Q 003032 295 GLLGAGPSGIMAADVIITDSGAMHVAGVPIVNPSTVVVWEVTPGPGNGFQAA 346 (855)
Q Consensus 295 GlLg~GpSGIma~DAIItdsGamhVAGVpivNPSTVVVWEV~pg~gNg~q~t 346 (855)
.++|+||+|+|++...+.. ..|-.|.|.|=.+-+|-|.-..
T Consensus 5 AIIGgGp~Gl~~a~~L~~~-----------~~~l~V~lfEp~~~~G~G~ays 45 (534)
T PRK09897 5 AIVGAGPTGIYTFFSLLQQ-----------QTPLSISIFEQADEAGVGMPYS 45 (534)
T ss_pred EEECCcHHHHHHHHHHHhc-----------CCCCcEEEEecCCCCCcceeec
Confidence 4789999999999988762 1367899999877677776443
Done!