Query psy8807
Match_columns 136
No_of_seqs 126 out of 717
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 19:45:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8807.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8807hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2408|consensus 100.0 2.6E-32 5.7E-37 248.7 7.5 123 12-134 507-696 (719)
2 PF03098 An_peroxidase: Animal 100.0 1.9E-31 4E-36 234.6 5.3 113 18-130 352-530 (530)
3 PLN02283 alpha-dioxygenase 99.9 4.3E-22 9.4E-27 179.9 6.3 105 18-122 428-601 (633)
4 PHA02681 ORF089 virion membran 41.6 31 0.00067 24.6 2.8 39 70-108 20-62 (92)
5 TIGR01669 phage_XkdX phage unc 35.6 86 0.0019 19.3 3.8 39 69-108 4-42 (45)
6 KOG3801|consensus 34.0 6.5 0.00014 28.3 -1.6 42 68-110 23-70 (94)
7 PF09133 SANTA: SANTA (SANT As 27.1 50 0.0011 23.2 2.0 32 57-91 58-90 (93)
8 PF14253 AbiH: Bacteriophage a 26.2 44 0.00095 26.4 1.7 19 52-79 7-26 (270)
9 KOG4021|consensus 25.4 19 0.00042 29.5 -0.5 17 55-71 155-171 (239)
10 PF03527 RHS: RHS protein; In 25.3 35 0.00076 20.7 0.8 17 3-19 4-20 (41)
11 PRK13495 chemoreceptor glutami 22.8 96 0.0021 23.9 3.0 47 16-65 63-112 (159)
12 PF03705 CheR_N: CheR methyltr 21.6 62 0.0014 19.6 1.4 19 60-78 33-51 (57)
13 COG1048 AcnA Aconitase A [Ener 20.1 15 0.00032 35.7 -2.5 75 2-80 200-278 (861)
No 1
>KOG2408|consensus
Probab=99.97 E-value=2.6e-32 Score=248.68 Aligned_cols=123 Identities=37% Similarity=0.582 Sum_probs=108.7
Q ss_pred hhhhhhhhHHHHHHHHHHhhhhhc----CcHHHHhhcccCCCCCC-cchHHHHHHhhhccCCCcHHHHHHHhCCCCCCCh
Q psy8807 12 SCLTSVIHWELVYSTCYRRAALLA----DDMVITDFLFRNGKPFG-RDLRAIDVQRGRDHGLASYNDYRAFCGLPRAYKF 86 (136)
Q Consensus 12 ~~~~~~~g~~~~~~g~~~~~~~~~----~~~~l~~~LF~~~~~~G-~DL~AinIQRGRDHGlp~Yn~~R~~Cgl~~~~sF 86 (136)
.+...-+||+++++|+..+.++.. .+.+++++||...+..+ +||+|||||||||||||+||+||++|||+++.+|
T Consensus 507 ~~i~~~ggid~llrGl~~~~~~~~~d~~~~~~i~~~lf~~~~~~~~~DL~ainIQRgRDhGlp~Yn~yR~~cgL~~~~s~ 586 (719)
T KOG2408|consen 507 WLILNEGGIDPLLRGLTTQPAKMPDDQLLNGEITERLFVKTDEDGELDLAALNIQRGRDHGLPPYNEYRKFCGLSPATSF 586 (719)
T ss_pred hhhhhccChhHHHHHHHhchhhcccchhcCHHHHHHHhhhcCcccccchhhhhhhccccCCCCCHHHHHHHcCCCCCCCH
Confidence 344455899999999999999998 57999999999877666 9999999999999999999999999999999999
Q ss_pred hhHhhccCcCc-------------c------------------------------------------------CHHHHHH
Q psy8807 87 EDFLDVISPDL-------------L------------------------------------------------LEDQLAE 105 (136)
Q Consensus 87 ~dL~~~~~~~~-------------i------------------------------------------------t~~QL~e 105 (136)
+||..++.++. | |++||+|
T Consensus 587 edL~~~i~~~~~~kl~~lY~~~ddiDL~vG~~~E~~~~g~~vGPTl~cii~~Qf~r~r~gDRf~yen~~~~~Ft~~QL~e 666 (719)
T KOG2408|consen 587 EDLSDEIEPEIINKLRTLYGTPDDIDLYVGLLLEKPLPGGLVGPTLACIIAEQFLRLRDGDRFWYENFNPGVFTPEQLEE 666 (719)
T ss_pred HHhhhhhhHHHHHHHHHhcCCchhhcccccccccccCCCceecccHHHHHHHHHHHHhccCceeecCCCCCccCHHHHHH
Confidence 99998887321 1 9999999
Q ss_pred HHhccccchhhccCcccccccc-ccccCCC
Q psy8807 106 IKKASLARLLCDNSDEIHTMQP-AAFLKIS 134 (136)
Q Consensus 106 Irk~tla~iiC~n~d~i~~iQ~-~~F~~~~ 134 (136)
|||+|||+|||+|++++..++. ++|..++
T Consensus 667 i~k~sLariiC~N~~~~~~~~~~~~f~~~~ 696 (719)
T KOG2408|consen 667 IRKVSLARIICDNGTKITKVSRFDVFDFPD 696 (719)
T ss_pred HHHhhchheeecCCcccccccccCCccccc
Confidence 9999999999999667888777 9998765
No 2
>PF03098 An_peroxidase: Animal haem peroxidase; InterPro: IPR002007 Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. Peroxidases are found in bacteria, fungi, plants and animals. On the basis of sequence similarity, a number of animal haem peroxidases can be categorised as members of a superfamily: myeloperoxidase (MPO); eosinophil peroxidase (EPO); lactoperoxidase (LPO); thyroid peroxidase (TPO); prostaglandin H synthase (PGHS); and peroxidasin [, , ]. MPO plays a major role in the oxygen-dependent microbicidal system of neutrophils. EPO from eosinophilic granulocytes participates in immunological reactions, and potentiates tumor necrosis factor (TNF) production and hydrogen peroxide release by human monocyte-derived macrophages [, ]. In the main, MPO (and possibly EPO) utilises Cl-ions and H2O2 to form hypochlorous acid (HOCl), which can effectively kill bacteria or parasites. In secreted fluids, LPO catalyses the oxidation of thiocyanate ions (SCN-) by H2O2, producing the weak oxidising agent hypothiocyanite (OSCN-), which has bacteriostatic activity []. TPO uses I- ions and H2O2 to generate iodine, and plays a central role in the biosynthesis of thyroid hormones T(3) and T(4). To date, the 3D structures of MPO and PGHS have been reported. MPO is a homodimer: each monomer consists of a light (A or B) and a heavy (C or D) chain resulting from post-translational excision of 6 residues from the common precursor. Monomers are linked by a single inter-chain disulphide. Each monomer includes a bound calcium ion []. PGHS exists as a symmetric dimer, each monomer of which consists of 3 domains: an N-terminal epidermal growth factor (EGF) like module; a membrane-binding domain; and a large C-terminal catalytic domain containing the cyclooxygenase and the peroxidase active sites. The catalytic domain shows striking structural similarity to MPO. The cyclooxygenase active site, which catalyses the formation of prostaglandin G2 (PGG2) from arachidonic acid, resides at the apex of a long hydrophobic channel, extending from the membrane-binding domain to the centre of the molecule. The peroxidase active site, which catalyses the reduction of PGG2 to PGH2, is located on the other side of the molecule, at the haem binding site []. Both MPO and the catalytic domain of PGHS are mainly alpha-helical, 19 helices being identified as topologically and spatially equivalent; PGHS contains 5 additional N-terminal helices that have no equivalent in MPO. In both proteins, three Asn residues in each monomer are glycosylated.; GO: 0004601 peroxidase activity, 0020037 heme binding, 0006979 response to oxidative stress, 0055114 oxidation-reduction process; PDB: 1FE2_A 1PGG_B 1PGF_A 3N8W_B 1IGZ_A 3KK6_B 3N8Z_A 1Q4G_A 1PTH_A 1EQH_A ....
Probab=99.97 E-value=1.9e-31 Score=234.64 Aligned_cols=113 Identities=45% Similarity=0.725 Sum_probs=94.7
Q ss_pred hhHHHHHHHHHHhhhhhcC-----cHHHHhhcccCCCCCC-cchHHHHHHhhhccCCCcHHHHHHHhCCCCCCChhhHhh
Q psy8807 18 IHWELVYSTCYRRAALLAD-----DMVITDFLFRNGKPFG-RDLRAIDVQRGRDHGLASYNDYRAFCGLPRAYKFEDFLD 91 (136)
Q Consensus 18 ~g~~~~~~g~~~~~~~~~~-----~~~l~~~LF~~~~~~G-~DL~AinIQRGRDHGlp~Yn~~R~~Cgl~~~~sF~dL~~ 91 (136)
+|++.+++|+.++.++.++ +++|+++||++.+..+ +||+|+|||||||||||+||+||++|||+++++|+||..
T Consensus 352 ~gid~ll~G~~~~~a~~~d~~~~~~~~l~~~lf~~~~~~~~~DL~a~nIqRGRdhGLp~yn~~R~~cgl~~~~sf~dl~~ 431 (530)
T PF03098_consen 352 GGIDPLLRGLASQPAQKVDNPRFLVDDLRNHLFGPRNVPGSLDLAALNIQRGRDHGLPSYNDYREFCGLPPATSFEDLTD 431 (530)
T ss_dssp TCSHHHHHHHHHSEEEHHBTTBHSHHHHHTSEESTTSSSEEEHHHHHHHHHHHHTTB-BHHHHHHHTT----SSHHHHHH
T ss_pred cchHHHHhHHhhCccccccHHHHhhhHhhcccccccCCcchhHHHHHHHHHHHHhCCchHHHHHHHhccCCCCCHHHhhh
Confidence 6899999999999888766 3899999998766555 599999999999999999999999999999999999976
Q ss_pred ccCcCcc------------------------------------------------------------CHHHHHHHHhccc
Q psy8807 92 VISPDLL------------------------------------------------------------LEDQLAEIKKASL 111 (136)
Q Consensus 92 ~~~~~~i------------------------------------------------------------t~~QL~eIrk~tl 111 (136)
.++++.+ |++||+||||+||
T Consensus 432 ~~~~~~i~~~L~~~Y~~vddvDL~vG~laE~~~~G~~lGpt~~~Ii~~qf~~l~~gDRf~yen~~~ft~~ql~~i~~~tl 511 (530)
T PF03098_consen 432 EISDEEIAAALRALYGHVDDVDLWVGGLAEKPVPGGLLGPTFSCIIAEQFSRLRRGDRFWYENPGSFTPEQLEEIRKTTL 511 (530)
T ss_dssp HHTSHHHHHHHHHHHSSGGGSBHHHHHHHS-BSTTSSSBHHHHHHHHHHHHHHHHTSTTGTTSCTTCTHHHHHHHTTT-H
T ss_pred hhhHHHHHHHHHHhccchhcccccceeeeeccccCCCCCHHHHhHHHHHHHHHHhcCcccccCcCcCCHHHHHHHHHCCH
Confidence 5554321 9999999999999
Q ss_pred cchhhccCccccccccccc
Q psy8807 112 ARLLCDNSDEIHTMQPAAF 130 (136)
Q Consensus 112 a~iiC~n~d~i~~iQ~~~F 130 (136)
|+|||+|+++++.||++||
T Consensus 512 a~iic~n~~~~~~iq~~~F 530 (530)
T PF03098_consen 512 ARIICDNTDDITRIQPNAF 530 (530)
T ss_dssp HHHHHHHSTS-SEEESSTT
T ss_pred HHHHHhcCCccccCCCCCC
Confidence 9999999988999999999
No 3
>PLN02283 alpha-dioxygenase
Probab=99.85 E-value=4.3e-22 Score=179.92 Aligned_cols=105 Identities=22% Similarity=0.278 Sum_probs=83.7
Q ss_pred hhHHHHHHHHHHhhhhhcC---cH-HHHh----hcccCCCCCCcchHHHHHHhhhccCCCcHHHHHHHhCCCCCCChhhH
Q psy8807 18 IHWELVYSTCYRRAALLAD---DM-VITD----FLFRNGKPFGRDLRAIDVQRGRDHGLASYNDYRAFCGLPRAYKFEDF 89 (136)
Q Consensus 18 ~g~~~~~~g~~~~~~~~~~---~~-~l~~----~LF~~~~~~G~DL~AinIQRGRDHGlp~Yn~~R~~Cgl~~~~sF~dL 89 (136)
.|++.+++|+..+.+...+ .+ -+++ .++++..+.|+||+|+|||||||||||+||+||++|||+++++|+||
T Consensus 428 ~Gl~~ll~~l~~q~aga~~l~n~p~~l~~l~~~~~~g~~~~~g~DLaal~IqRgRDhGlp~YNefR~~~gL~~~~sFedl 507 (633)
T PLN02283 428 IGFEKLMVSMGHQACGALELWNYPSWMRDLVPQDIDGEDRPDHVDMAALEIYRDRERGVARYNEFRRNLLMIPISKWEDL 507 (633)
T ss_pred cCHHHHHHHHhhcchhccccccCcHHHHhhhhccccCCcccccccHHHHHHHhhhhcCCccHHHHHHHcCCCCCCCHHHc
Confidence 6899999999777665532 12 2333 34555566899999999999999999999999999999999999998
Q ss_pred hhc----------cC--cCcc------------------------------------------------CHHHHHHHHhc
Q psy8807 90 LDV----------IS--PDLL------------------------------------------------LEDQLAEIKKA 109 (136)
Q Consensus 90 ~~~----------~~--~~~i------------------------------------------------t~~QL~eIrk~ 109 (136)
.+. .. .++| |++|+++|+++
T Consensus 508 t~d~e~~~~L~~lY~~~vddVDL~VG~laE~~v~G~~vG~T~~~i~~~~a~r~~~gDRF~~en~np~~fT~~gl~~I~~t 587 (633)
T PLN02283 508 TDDEEAIEVLREVYGDDVEKLDLLVGLMAEKKIKGFAISETAFFIFLLMASRRLEADRFFTSNFNEKTYTKKGLEWVNTT 587 (633)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHhhhhheecccCCCCCcCHHHHHHHHHHHHHHhcCCCCeEecCCcCcCCHHHHHHHHcc
Confidence 631 11 1222 99999999997
Q ss_pred -cccchhhccCccc
Q psy8807 110 -SLARLLCDNSDEI 122 (136)
Q Consensus 110 -tla~iiC~n~d~i 122 (136)
||++|||+|...+
T Consensus 588 ~tl~dvl~r~~p~~ 601 (633)
T PLN02283 588 ESLKDVIDRHYPEM 601 (633)
T ss_pred CcHHHHHHHhCcch
Confidence 9999999998755
No 4
>PHA02681 ORF089 virion membrane protein; Provisional
Probab=41.61 E-value=31 Score=24.60 Aligned_cols=39 Identities=23% Similarity=0.289 Sum_probs=25.4
Q ss_pred cHHHHHHHhCC-CCCCChhhHhh---ccCcCccCHHHHHHHHh
Q psy8807 70 SYNDYRAFCGL-PRAYKFEDFLD---VISPDLLLEDQLAEIKK 108 (136)
Q Consensus 70 ~Yn~~R~~Cgl-~~~~sF~dL~~---~~~~~~it~~QL~eIrk 108 (136)
-|-.||++|-- +....+.|... .+.++.+|++|+..+.+
T Consensus 20 iya~YRR~~i~~p~~~r~~D~L~~~ds~F~D~lTpDQVrAlHR 62 (92)
T PHA02681 20 VIMMYRRSCVSAPAVPRNKDLLPPGASSFEDKMTDDQVRAFHA 62 (92)
T ss_pred HHHHHHhccCCCCCCCcccccCCCCCchhhccCCHHHHHHHHH
Confidence 47889999843 45456655432 23345569999998753
No 5
>TIGR01669 phage_XkdX phage uncharacterized protein, XkdX family. This model represents a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes.
Probab=35.58 E-value=86 Score=19.31 Aligned_cols=39 Identities=21% Similarity=0.304 Sum_probs=22.7
Q ss_pred CcHHHHHHHhCCCCCCChhhHhhccCcCccCHHHHHHHHh
Q psy8807 69 ASYNDYRAFCGLPRAYKFEDFLDVISPDLLLEDQLAEIKK 108 (136)
Q Consensus 69 p~Yn~~R~~Cgl~~~~sF~dL~~~~~~~~it~~QL~eIrk 108 (136)
|+|-....+....- -+=+++...+.-.-||++|.+||=.
T Consensus 4 ~~~e~iK~~Y~~g~-~t~e~v~~~V~~~~IT~eey~eITG 42 (45)
T TIGR01669 4 ASFEKVKTYYLWGY-YSNEDVNKFVEKKLITREQYKVITG 42 (45)
T ss_pred CCHHHHHHHHHcCC-CCHHHHHHHhhcCccCHHHHHHHhC
Confidence 44555555554432 2334455555556679999999853
No 6
>KOG3801|consensus
Probab=34.04 E-value=6.5 Score=28.32 Aligned_cols=42 Identities=29% Similarity=0.435 Sum_probs=24.8
Q ss_pred CCcHHHHHHHhCCCCCCChhhHhhccCcCcc------CHHHHHHHHhcc
Q psy8807 68 LASYNDYRAFCGLPRAYKFEDFLDVISPDLL------LEDQLAEIKKAS 110 (136)
Q Consensus 68 lp~Yn~~R~~Cgl~~~~sF~dL~~~~~~~~i------t~~QL~eIrk~t 110 (136)
+|.|| ||++.-.+.-.+|-.....-+|..+ .+.||.-|++.+
T Consensus 23 fp~YN-yReY~~RrtRD~Fr~Nkn~~Dp~e~~~l~~eakk~LevikRQ~ 70 (94)
T KOG3801|consen 23 FPQYN-YREYFQRRTRDTFRANKNVCDPAEIKKLYKEAKKQLEVIKRQS 70 (94)
T ss_pred CCccc-HHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 67776 6666644444555544444444333 677888888764
No 7
>PF09133 SANTA: SANTA (SANT Associated); InterPro: IPR015216 The SANTA domain (SANT associated) is approximately 90 amino acids in length and is conserved in eukaryotes. It is sometimes found in association with the SANT domain (IPR001005 from INTERPRO, also known as the Myb-like DNA-binding domain) implying a putative function in regulating chromatin remodelling. Sequence analysis has showed that the SANTA domain is likely to form four central beta-sheets with three flanking alpha-helices. Many conserved hydrophobic residues are present which implies a possible role in protein-protein interactions.
Probab=27.08 E-value=50 Score=23.15 Aligned_cols=32 Identities=28% Similarity=0.644 Sum_probs=23.1
Q ss_pred HHHHHhhhccCCCcHHHHHHH-hCCCCCCChhhHhh
Q psy8807 57 AIDVQRGRDHGLASYNDYRAF-CGLPRAYKFEDFLD 91 (136)
Q Consensus 57 AinIQRGRDHGlp~Yn~~R~~-Cgl~~~~sF~dL~~ 91 (136)
.+|+.+.++.|+|.+. .++| .|.| .+|+++..
T Consensus 58 ~in~~~~~~nGfp~~v-~~~F~~GFP--~~W~~~~~ 90 (93)
T PF09133_consen 58 PINRSRMRENGFPSEV-IKKFMNGFP--ENWEEYIN 90 (93)
T ss_pred ccCHHhHHHcCCCHHH-HHHHhcCCC--HHHHHHHH
Confidence 3688999999999775 4444 3555 78888653
No 8
>PF14253 AbiH: Bacteriophage abortive infection AbiH
Probab=26.21 E-value=44 Score=26.40 Aligned_cols=19 Identities=47% Similarity=0.861 Sum_probs=15.2
Q ss_pred CcchHHHHHHhhhccCCC-cHHHHHHHhC
Q psy8807 52 GRDLRAIDVQRGRDHGLA-SYNDYRAFCG 79 (136)
Q Consensus 52 G~DL~AinIQRGRDHGlp-~Yn~~R~~Cg 79 (136)
|+||+ |||| +|.+|++++.
T Consensus 7 GFDl~---------~gL~TsY~dF~~~~~ 26 (270)
T PF14253_consen 7 GFDLA---------HGLKTSYSDFYEYLK 26 (270)
T ss_pred chhhc---------CCCCCCHHHHHHHHH
Confidence 77876 7998 5899988875
No 9
>KOG4021|consensus
Probab=25.42 E-value=19 Score=29.49 Aligned_cols=17 Identities=35% Similarity=0.597 Sum_probs=13.7
Q ss_pred hHHHHHHhhhccCCCcH
Q psy8807 55 LRAIDVQRGRDHGLASY 71 (136)
Q Consensus 55 L~AinIQRGRDHGlp~Y 71 (136)
+.-.-||.+||||.=.|
T Consensus 155 rL~~a~qkArdhG~lty 171 (239)
T KOG4021|consen 155 RLRAALQKARDHGTLTY 171 (239)
T ss_pred HHHHHHHHhhhcCeEEe
Confidence 34557999999998777
No 10
>PF03527 RHS: RHS protein; InterPro: IPR001826 RHS elements are proteins of non-essential function believed to play an important role in the natural ecology of the cell. The protein sequences comprise highly conserved 141 kDa domain containing multiple tandem 22-residue repeats, followed by divergent C-terminal domains [, ]. The 22 residue repeats contain a YD dipeptide which is the most strongly conserved motif of the repeat.
Probab=25.27 E-value=35 Score=20.75 Aligned_cols=17 Identities=29% Similarity=0.059 Sum_probs=14.0
Q ss_pred ccCCCcchhhhhhhhhh
Q psy8807 3 THTDTNHMQSCLTSVIH 19 (136)
Q Consensus 3 ~~~~~~~~~~~~~~~~g 19 (136)
-|+|.+|.|..++.-.|
T Consensus 4 yH~D~~GtP~~ltd~~G 20 (41)
T PF03527_consen 4 YHTDHLGTPQELTDEDG 20 (41)
T ss_pred EecCCCCCcHHHHHhcC
Confidence 49999999998887655
No 11
>PRK13495 chemoreceptor glutamine deamidase CheD; Provisional
Probab=22.75 E-value=96 Score=23.94 Aligned_cols=47 Identities=11% Similarity=0.083 Sum_probs=34.4
Q ss_pred hhhhHHHHHHHHHHhhhhhcCcHHHHhhcccCCCCC---CcchHHHHHHhhhc
Q psy8807 16 SVIHWELVYSTCYRRAALLADDMVITDFLFRNGKPF---GRDLRAIDVQRGRD 65 (136)
Q Consensus 16 ~~~g~~~~~~g~~~~~~~~~~~~~l~~~LF~~~~~~---G~DL~AinIQRGRD 65 (136)
+-.+++.|++.|....+.. ..+.-++|++...+ .+++-.-||+.+|+
T Consensus 63 ~d~ai~~Li~~m~~~Ga~~---~~l~aKifGGA~m~~~~~~~IG~rNi~~a~~ 112 (159)
T PRK13495 63 ADTAIKTLVEELKKMGAKV---ERLEAKIAGGASMFESSGMNIGARNVEAVKK 112 (159)
T ss_pred HHHHHHHHHHHHHHcCCCH---HHEEEEEEeCCccCCCCCCChHHHHHHHHHH
Confidence 3467999998888776644 67788899864322 37888889988873
No 12
>PF03705 CheR_N: CheR methyltransferase, all-alpha domain; InterPro: IPR022641 CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the N-terminal domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF01739 from PFAM. Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region [].; PDB: 1AF7_A 1BC5_A.
Probab=21.57 E-value=62 Score=19.64 Aligned_cols=19 Identities=32% Similarity=0.569 Sum_probs=12.6
Q ss_pred HHhhhccCCCcHHHHHHHh
Q psy8807 60 VQRGRDHGLASYNDYRAFC 78 (136)
Q Consensus 60 IQRGRDHGlp~Yn~~R~~C 78 (136)
-.|-|.+|+++|.+|....
T Consensus 33 ~~rm~~~~~~~~~~y~~~L 51 (57)
T PF03705_consen 33 ARRMRALGLPSFAEYYELL 51 (57)
T ss_dssp HHHHHHHT---HHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHH
Confidence 3578899999999998764
No 13
>COG1048 AcnA Aconitase A [Energy production and conversion]
Probab=20.10 E-value=15 Score=35.67 Aligned_cols=75 Identities=19% Similarity=0.066 Sum_probs=56.6
Q ss_pred CccC-CCcchhhhhhhhhhHHHHHHHHHHhhhhhcC---cHHHHhhcccCCCCCCcchHHHHHHhhhccCCCcHHHHHHH
Q psy8807 2 DTHT-DTNHMQSCLTSVIHWELVYSTCYRRAALLAD---DMVITDFLFRNGKPFGRDLRAIDVQRGRDHGLASYNDYRAF 77 (136)
Q Consensus 2 ~~~~-~~~~~~~~~~~~~g~~~~~~g~~~~~~~~~~---~~~l~~~LF~~~~~~G~DL~AinIQRGRDHGlp~Yn~~R~~ 77 (136)
|.|| --||+-+.--+++|+|+.--.+..+..+.+. --.|+.+| +....+.||+---.+.=|.+|+-+ +|.+|
T Consensus 200 DSHTtminGLGvLgwGVGGiEAeaaMlG~p~~~~iP~VvGVkLtGkl--~~gvTatDlvL~vt~~Lr~~gvVg--kfVEF 275 (861)
T COG1048 200 DSHTTMIGGLGVLGWGVGGIEAEAAMLGQPWYMLIPEVVGVKLTGKL--PEGVTATDLVLTVTGMLRKKGVVG--KFVEF 275 (861)
T ss_pred cCCCCCcCcceEEEeccchHHHHHHHcCCceEeeCCcEEEEEEeccC--CCCCCHHHHHHHHHHHHHhcCccc--eEEEE
Confidence 7888 6689999999999999988555555555541 12334343 345678999999999999999987 88888
Q ss_pred hCC
Q psy8807 78 CGL 80 (136)
Q Consensus 78 Cgl 80 (136)
+|=
T Consensus 276 fG~ 278 (861)
T COG1048 276 FGP 278 (861)
T ss_pred ECC
Confidence 874
Done!