Query psy746
Match_columns 178
No_of_seqs 116 out of 848
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 18:52:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy746.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/746hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2408|consensus 100.0 5.4E-52 1.2E-56 388.1 10.9 171 2-178 484-661 (719)
2 PF03098 An_peroxidase: Animal 100.0 1E-48 2.2E-53 357.1 6.3 163 8-178 332-500 (530)
3 PLN02283 alpha-dioxygenase 100.0 1.2E-42 2.6E-47 321.6 12.6 164 9-178 409-578 (633)
4 KOG1712|consensus 71.5 0.83 1.8E-05 36.5 -1.1 58 100-161 26-90 (183)
5 PRK14460 ribosomal RNA large s 47.3 35 0.00075 30.2 4.7 53 68-121 6-60 (354)
6 PRK14469 ribosomal RNA large s 46.6 22 0.00047 31.1 3.3 54 67-122 5-60 (343)
7 KOG0358|consensus 41.7 16 0.00034 33.3 1.6 38 110-148 198-235 (534)
8 KOG0941|consensus 41.3 16 0.00035 35.9 1.7 42 78-122 591-643 (850)
9 PRK14455 ribosomal RNA large s 36.3 36 0.00079 30.1 3.1 41 81-122 27-69 (356)
10 TIGR00048 radical SAM enzyme, 35.7 36 0.00079 30.0 3.0 41 80-121 22-64 (355)
11 PRK14453 chloramphenicol/florf 35.5 45 0.00097 29.5 3.5 40 81-121 16-57 (347)
12 PRK14459 ribosomal RNA large s 35.5 43 0.00094 30.0 3.4 42 79-121 36-79 (373)
13 PRK14465 ribosomal RNA large s 35.3 38 0.00083 29.9 3.0 41 81-122 21-63 (342)
14 PRK14467 ribosomal RNA large s 34.8 37 0.00079 30.0 2.8 42 80-122 17-60 (348)
15 PRK14461 ribosomal RNA large s 34.3 43 0.00094 30.0 3.2 42 80-122 23-66 (371)
16 PRK14456 ribosomal RNA large s 33.5 39 0.00085 30.1 2.8 53 67-121 21-75 (368)
17 PRK14463 ribosomal RNA large s 32.7 32 0.00069 30.4 2.1 41 80-121 20-62 (349)
18 PRK14454 ribosomal RNA large s 31.2 51 0.0011 29.0 3.2 41 80-121 17-59 (342)
19 COG4190 Predicted transcriptio 30.5 43 0.00092 26.0 2.2 41 82-122 19-75 (144)
20 PHA02681 ORF089 virion membran 30.1 1E+02 0.0022 22.0 3.9 41 86-126 20-70 (92)
21 PRK14466 ribosomal RNA large s 29.9 38 0.00083 30.0 2.1 53 67-121 8-62 (345)
22 PRK11194 ribosomal RNA large s 29.4 52 0.0011 29.4 2.9 41 80-121 21-63 (372)
23 PRK14457 ribosomal RNA large s 28.6 68 0.0015 28.3 3.5 40 80-120 17-58 (345)
24 PF12836 HHH_3: Helix-hairpin- 28.2 62 0.0013 21.1 2.5 29 88-118 31-61 (65)
25 PRK14470 ribosomal RNA large s 28.1 65 0.0014 28.3 3.3 41 79-121 13-55 (336)
26 PF12080 GldM_C: GldM C-termin 26.9 43 0.00094 26.7 1.8 27 143-169 148-174 (181)
27 smart00119 HECTc Domain Homolo 25.9 64 0.0014 28.1 2.8 30 88-120 97-126 (336)
28 TIGR00165 S18 ribosomal protei 25.2 53 0.0012 22.4 1.7 19 70-88 50-68 (70)
29 PRK14468 ribosomal RNA large s 24.7 86 0.0019 27.5 3.4 38 83-121 13-52 (343)
30 COG1555 ComEA DNA uptake prote 23.3 81 0.0018 24.4 2.7 31 88-120 114-146 (149)
31 PF03705 CheR_N: CheR methyltr 21.0 87 0.0019 19.4 2.1 19 76-94 33-51 (57)
32 COG3965 Predicted Co/Zn/Cd cat 20.8 1.2E+02 0.0026 26.3 3.4 44 48-96 217-260 (314)
33 PRK00391 rpsR 30S ribosomal pr 20.1 80 0.0017 22.1 1.8 19 70-88 59-77 (79)
No 1
>KOG2408|consensus
Probab=100.00 E-value=5.4e-52 Score=388.10 Aligned_cols=171 Identities=40% Similarity=0.635 Sum_probs=159.8
Q ss_pred CCCCCC-Cc---ccchhhhccChhhhh--hhHHHHHHHHhhccccCc-CCCccchhhhhhhhcCCCCCCCCCCCchHHHH
Q psy746 2 IAKSGK-AA---QIDMVTWMHRPSIVQ--GYLDHLLEGQQTQFIQPF-EDWWEDFNINNKLKTNHPPFQYDPHGDDLTAI 74 (178)
Q Consensus 2 ~~~~~~-~~---~~~L~d~~~~p~~l~--~~~d~llrGl~~q~~~~~-d~~~~~~~l~~~lf~~~~~~~~~~~g~DL~al 74 (178)
.+++++ .+ .+++++.|++|..+. +|+|+++|||.++++++. |..+ +.+|++++|.... ....+||+||
T Consensus 484 l~~~~~~~~~~~~l~~~~~~~~~~~i~~~ggid~llrGl~~~~~~~~~d~~~-~~~i~~~lf~~~~----~~~~~DL~ai 558 (719)
T KOG2408|consen 484 LDENFQPIGEVVNLPLHDAFFNPWLILNEGGIDPLLRGLTTQPAKMPDDQLL-NGEITERLFVKTD----EDGELDLAAL 558 (719)
T ss_pred hcccCcccccccCchhhhhhcchhhhhhccChhHHHHHHHhchhhcccchhc-CHHHHHHHhhhcC----cccccchhhh
Confidence 355666 33 688899999999887 999999999999999999 8999 9999999998877 4233999999
Q ss_pred HHHHHHhcCCccHHHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhccCCCcccccccccCCCCCCCCCCChHHHHHHHH
Q psy746 75 GIQRQRDYGMPGYNEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGYKHVDDIDLFVGGYLENPLHDSLFGPTFTYVIAD 154 (178)
Q Consensus 75 nIqRgRDhGlp~Yn~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY~~vddVDL~vG~l~E~~~~gs~~Gpt~~cii~~ 154 (178)
|||||||||||+||+||++|||+++.+|+||+.+|.++++++|+++|++|||||||||+++|++++|+++|||++|||++
T Consensus 559 nIQRgRDhGlp~Yn~yR~~cgL~~~~s~edL~~~i~~~~~~kl~~lY~~~ddiDL~vG~~~E~~~~g~~vGPTl~cii~~ 638 (719)
T KOG2408|consen 559 NIQRGRDHGLPPYNEYRKFCGLSPATSFEDLSDEIEPEIINKLRTLYGTPDDIDLYVGLLLEKPLPGGLVGPTLACIIAE 638 (719)
T ss_pred hhhccccCCCCCHHHHHHHcCCCCCCCHHHhhhhhhHHHHHHHHHhcCCchhhcccccccccccCCCceecccHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcCCcceeecCCCCCCCCC
Q psy746 155 QFYRWKFGDRFWFSVLGKPWSFTE 178 (178)
Q Consensus 155 qF~rl~~gDRf~ye~~~~p~~Ft~ 178 (178)
||.|+|+|||||||| .+|+.||+
T Consensus 639 Qf~r~r~gDRf~yen-~~~~~Ft~ 661 (719)
T KOG2408|consen 639 QFLRLRDGDRFWYEN-FNPGVFTP 661 (719)
T ss_pred HHHHHhccCceeecC-CCCCccCH
Confidence 999999999999999 88999985
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=100.00 E-value=1e-48 Score=357.11 Aligned_cols=163 Identities=40% Similarity=0.683 Sum_probs=142.5
Q ss_pred CcccchhhhccChh-hhh--hhHHHHHHHHhhccccCcC--CCccchhhhhhhhcCCCCCCCCCCCchHHHHHHHHHHhc
Q psy746 8 AAQIDMVTWMHRPS-IVQ--GYLDHLLEGQQTQFIQPFE--DWWEDFNINNKLKTNHPPFQYDPHGDDLTAIGIQRQRDY 82 (178)
Q Consensus 8 ~~~~~L~d~~~~p~-~l~--~~~d~llrGl~~q~~~~~d--~~~~~~~l~~~lf~~~~~~~~~~~g~DL~alnIqRgRDh 82 (178)
.+.++|.+.|++|. .+. ++++.+++|+++|+++++| .++ +++|++++|+..+ .+..+||+|+||||||||
T Consensus 332 ~~~~~L~d~f~~~~~~~~~~~gid~ll~G~~~~~a~~~d~~~~~-~~~l~~~lf~~~~----~~~~~DL~a~nIqRGRdh 406 (530)
T PF03098_consen 332 EPSLPLSDAFFNPSNRLLEEGGIDPLLRGLASQPAQKVDNPRFL-VDDLRNHLFGPRN----VPGSLDLAALNIQRGRDH 406 (530)
T ss_dssp TSEEEGGGGBT-HH-HHHTTTCSHHHHHHHHHSEEEHHBTTBHS-HHHHHTSEESTTS----SSEEEHHHHHHHHHHHHT
T ss_pred cccccccccccCcchhhhhccchHHHHhHHhhCccccccHHHHh-hhHhhcccccccC----CcchhHHHHHHHHHHHHh
Confidence 56789999999999 444 8999999999999999999 999 9999999997665 334469999999999999
Q ss_pred CCccHHHHHHHhCCCCCCCcccccCCC-CHHHHHHHHHhccCCCcccccccccCCCCCCCCCCChHHHHHHHHHHHHhhc
Q psy746 83 GMPGYNEFRKYAGLKPVKSFEELSDVI-GPENIHLLKLGYKHVDDIDLFVGGYLENPLHDSLFGPTFTYVIADQFYRWKF 161 (178)
Q Consensus 83 Glp~Yn~~R~~cgl~~~~~f~dl~~~~-~~~~~~~L~~lY~~vddVDL~vG~l~E~~~~gs~~Gpt~~cii~~qF~rl~~ 161 (178)
|||+||+||++|||+++++|+||++.+ +++++++|+++|++|+|||||||+++|++++|+.+|||++|||++||.|+|+
T Consensus 407 GLp~yn~~R~~cgl~~~~sf~dl~~~~~~~~i~~~L~~~Y~~vddvDL~vG~laE~~~~G~~lGpt~~~Ii~~qf~~l~~ 486 (530)
T PF03098_consen 407 GLPSYNDYREFCGLPPATSFEDLTDEISDEEIAAALRALYGHVDDVDLWVGGLAEKPVPGGLLGPTFSCIIAEQFSRLRR 486 (530)
T ss_dssp TB-BHHHHHHHTT----SSHHHHHHHHTSHHHHHHHHHHHSSGGGSBHHHHHHHS-BSTTSSSBHHHHHHHHHHHHHHHH
T ss_pred CCchHHHHHHHhccCCCCCHHHhhhhhhHHHHHHHHHHhccchhcccccceeeeeccccCCCCCHHHHhHHHHHHHHHHh
Confidence 999999999999999999999996644 5777799999999999999999999999999999999999999999999999
Q ss_pred CCcceeecCCCCCCCCC
Q psy746 162 GDRFWFSVLGKPWSFTE 178 (178)
Q Consensus 162 gDRf~ye~~~~p~~Ft~ 178 (178)
||||||||+ ++||+
T Consensus 487 gDRf~yen~---~~ft~ 500 (530)
T PF03098_consen 487 GDRFWYENP---GSFTP 500 (530)
T ss_dssp TSTTGTTSC---TTCTH
T ss_pred cCcccccCc---CcCCH
Confidence 999999944 68984
No 3
>PLN02283 alpha-dioxygenase
Probab=100.00 E-value=1.2e-42 Score=321.61 Aligned_cols=164 Identities=24% Similarity=0.339 Sum_probs=139.1
Q ss_pred cccchhhhcc--Chhhhh-hhHHHHHHHHhhccccCcCCCccchh-hhhhhhcCC-CCCCCCCCCchHHHHHHHHHHhcC
Q psy746 9 AQIDMVTWMH--RPSIVQ-GYLDHLLEGQQTQFIQPFEDWWEDFN-INNKLKTNH-PPFQYDPHGDDLTAIGIQRQRDYG 83 (178)
Q Consensus 9 ~~~~L~d~~~--~p~~l~-~~~d~llrGl~~q~~~~~d~~~~~~~-l~~~lf~~~-~~~~~~~~g~DL~alnIqRgRDhG 83 (178)
..+++.+.++ .+..+. .|++.+++|+..|++++++... .+. +++.+.... +.. .+.++||+|+|||||||||
T Consensus 409 ~~~~l~d~~~~~~~~~l~~~Gl~~ll~~l~~q~aga~~l~n-~p~~l~~l~~~~~~g~~--~~~g~DLaal~IqRgRDhG 485 (633)
T PLN02283 409 EEIPMPELIGLKGEKKLSKIGFEKLMVSMGHQACGALELWN-YPSWMRDLVPQDIDGED--RPDHVDMAALEIYRDRERG 485 (633)
T ss_pred ccccHHHHHhhcccccccccCHHHHHHHHhhcchhcccccc-CcHHHHhhhhccccCCc--ccccccHHHHHHHhhhhcC
Confidence 4577777765 333444 8999999999999999998876 544 444332210 100 2379999999999999999
Q ss_pred CccHHHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhcc-CCCcccccccccCCCCCCCCCCChHHHHHHHHHHHHhhcC
Q psy746 84 MPGYNEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGYK-HVDDIDLFVGGYLENPLHDSLFGPTFTYVIADQFYRWKFG 162 (178)
Q Consensus 84 lp~Yn~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY~-~vddVDL~vG~l~E~~~~gs~~Gpt~~cii~~qF~rl~~g 162 (178)
||+||+||++|||+++++|+||++ +++++++|+++|+ +|||||||||+++|++++|+.+|||+.||+..||.|+++|
T Consensus 486 lp~YNefR~~~gL~~~~sFedlt~--d~e~~~~L~~lY~~~vddVDL~VG~laE~~v~G~~vG~T~~~i~~~~a~r~~~g 563 (633)
T PLN02283 486 VARYNEFRRNLLMIPISKWEDLTD--DEEAIEVLREVYGDDVEKLDLLVGLMAEKKIKGFAISETAFFIFLLMASRRLEA 563 (633)
T ss_pred CccHHHHHHHcCCCCCCCHHHcCC--CHHHHHHHHHHhCCCHHHHHhhhhheecccCCCCCcCHHHHHHHHHHHHHHhcC
Confidence 999999999999999999999998 8999999999998 8999999999999999999999999999998888888899
Q ss_pred CcceeecCCCCCCCCC
Q psy746 163 DRFWFSVLGKPWSFTE 178 (178)
Q Consensus 163 DRf~ye~~~~p~~Ft~ 178 (178)
|||||||.+ |++||+
T Consensus 564 DRF~~en~n-p~~fT~ 578 (633)
T PLN02283 564 DRFFTSNFN-EKTYTK 578 (633)
T ss_pred CCCeEecCC-cCcCCH
Confidence 999999864 789984
No 4
>KOG1712|consensus
Probab=71.45 E-value=0.83 Score=36.55 Aligned_cols=58 Identities=22% Similarity=0.430 Sum_probs=40.7
Q ss_pred CCcccccCCC-CHH----HHHHHHHhccC-C-CcccccccccCCCCCCCCCCChHHHHHHHHHHHHhhc
Q psy746 100 KSFEELSDVI-GPE----NIHLLKLGYKH-V-DDIDLFVGGYLENPLHDSLFGPTFTYVIADQFYRWKF 161 (178)
Q Consensus 100 ~~f~dl~~~~-~~~----~~~~L~~lY~~-v-ddVDL~vG~l~E~~~~gs~~Gpt~~cii~~qF~rl~~ 161 (178)
--|+|++..+ +|. ++..+...|++ . ..||+.+|.=+ -|-++||+.+--++--|.-+|+
T Consensus 26 I~F~Di~pll~dP~af~~lidlf~~h~~~~~~~~Id~iaGlEa----RGFLFGP~iAlalG~~fVPiRK 90 (183)
T KOG1712|consen 26 IMFQDITPLLLDPKAFKKLIDLFVDHYRETFEMKIDVIAGLEA----RGFLFGPSIALALGAGFVPIRK 90 (183)
T ss_pred eehhhhhhhhcCHHHHHHHHHHHHHHHHHHhcCcceEEEeeee----cceecCcHHHHHhCCCeeeccc
Confidence 4588887765 665 45555566664 3 45999988644 4899999999777766765554
No 5
>PRK14460 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=47.25 E-value=35 Score=30.19 Aligned_cols=53 Identities=9% Similarity=0.157 Sum_probs=36.5
Q ss_pred CchHHHHHHHHHHhcCCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhc
Q psy746 68 GDDLTAIGIQRQRDYGMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGY 121 (178)
Q Consensus 68 g~DL~alnIqRgRDhGlp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY 121 (178)
++++..+-=.-.+++|.|+| .+..++.=-+.+.+|++|++ ++.++.++|++.|
T Consensus 6 ~~~~~~l~~~~~~~~g~~~~r~~qi~~~~~~~~~~~~~~m~~-l~~~~r~~l~~~~ 60 (354)
T PRK14460 6 NLTYPELEAFITAELGEPRFRARQIWQWLWQKGARDFDSMTN-VSKALRARLAEKA 60 (354)
T ss_pred cCCHHHHHHHHHHhcCCCchHHHHHHHHHHHcCCCCHHHhcc-ccHHHHHHHhcce
Confidence 44444442222237899988 34445555567899999998 5899999999876
No 6
>PRK14469 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=46.65 E-value=22 Score=31.14 Aligned_cols=54 Identities=15% Similarity=0.292 Sum_probs=37.7
Q ss_pred CCchHHHHHHHHHHhcCCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhcc
Q psy746 67 HGDDLTAIGIQRQRDYGMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGYK 122 (178)
Q Consensus 67 ~g~DL~alnIqRgRDhGlp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY~ 122 (178)
.++++..+- ..-.++|+|.| .+..++.=-+.+.+|++|++ ++.++.++|++.|.
T Consensus 5 ~~~~~~~~~-~~~~~~g~~~~r~~qi~~~~~~~~~~~~~~~~~-~~~~~r~~l~~~~~ 60 (343)
T PRK14469 5 LDLSYEELV-SEITELGLEKYRADQILDWIYKKKVFNFDEMTN-LSKDHRALLSEHFS 60 (343)
T ss_pred ccCCHHHHH-HHHHHcCCCchHHHHHHHHHHhcCCCCHHHhcc-ccHHHHHHHhhccc
Confidence 345555442 23447899988 34444544567899999998 59999999998873
No 7
>KOG0358|consensus
Probab=41.71 E-value=16 Score=33.28 Aligned_cols=38 Identities=32% Similarity=0.340 Sum_probs=32.7
Q ss_pred CHHHHHHHHHhccCCCcccccccccCCCCCCCCCCChHH
Q psy746 110 GPENIHLLKLGYKHVDDIDLFVGGYLENPLHDSLFGPTF 148 (178)
Q Consensus 110 ~~~~~~~L~~lY~~vddVDL~vG~l~E~~~~gs~~Gpt~ 148 (178)
+-+.++..+++=+++||.+++-|.+++....++. |||=
T Consensus 198 dlkdIkivkklGgtvdDte~i~glvl~~~~~~~~-gptr 235 (534)
T KOG0358|consen 198 DLKDIKIVKKLGGTVDDTELIKGLVLTQKASKSA-GPTR 235 (534)
T ss_pred chhhhhhHHhhCCccchhhhhcceEEeeecccCC-Ccch
Confidence 3456788888889999999999999999998877 8884
No 8
>KOG0941|consensus
Probab=41.32 E-value=16 Score=35.93 Aligned_cols=42 Identities=26% Similarity=0.305 Sum_probs=34.0
Q ss_pred HHHhcCCccHH-----------HHHHHhCCCCCCCcccccCCCCHHHHHHHHHhcc
Q psy746 78 RQRDYGMPGYN-----------EFRKYAGLKPVKSFEELSDVIGPENIHLLKLGYK 122 (178)
Q Consensus 78 RgRDhGlp~Yn-----------~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY~ 122 (178)
=|+-.||+-|| -|++.|+.++ +|+||.+ ++|++.+.|+++-.
T Consensus 591 iGil~GLAIyN~~ildlpFPlAlykkLl~~~~--sl~DL~e-lsP~~~~sL~~lL~ 643 (850)
T KOG0941|consen 591 IGILCGLAIYNNTILDLPFPLALYKKLLDKPP--SLEDLKE-LSPSLGKSLKELLD 643 (850)
T ss_pred hhHHHHHHHhccceecCCCcHHHHHHHhcCCC--CHHHHHh-hChHhhhhHHHHHh
Confidence 46777888886 4899999887 9999987 48999998887753
No 9
>PRK14455 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=36.31 E-value=36 Score=30.07 Aligned_cols=41 Identities=20% Similarity=0.332 Sum_probs=32.4
Q ss_pred hcCCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhcc
Q psy746 81 DYGMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGYK 122 (178)
Q Consensus 81 DhGlp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY~ 122 (178)
++|.|+| .+..++.--+.+.+|++|++ ++.++.++|++.|.
T Consensus 27 ~~g~~~~r~~qi~~~~~~~~~~~~~~m~~-l~~~~r~~l~~~~~ 69 (356)
T PRK14455 27 EQGEKKFRATQIWDWLYRKRVQSFEEMTN-LSKDLREKLNDNFV 69 (356)
T ss_pred HcCCCchHHHHHHHHHHHcCCCCHHHhcc-cCHHHHHHHhcccc
Confidence 6899988 44555555577899999998 58999999998873
No 10
>TIGR00048 radical SAM enzyme, Cfr family. A Staphylococcus sciuri plasmid-borne member of this family, Cfr, has been identified as essential to transferrable resistance to chloramphenicol and florfenicol by an unknown mechanism. A 14-15 residue cluster with four perfectly conserved Cys residues suggests this protein may be an enzyme with an iron-sulfur cluster. The Cys cluster is part of the radical SAM domain, suggested to provide a general mechanism by which the Fe-S center cleaves S-adenosylmethionine to initiate radical-based catalysis. Members of this family lack apparent transmembrane domains.
Probab=35.71 E-value=36 Score=30.04 Aligned_cols=41 Identities=17% Similarity=0.334 Sum_probs=32.1
Q ss_pred HhcCCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhc
Q psy746 80 RDYGMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGY 121 (178)
Q Consensus 80 RDhGlp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY 121 (178)
.++|.|+| .+..++.--+.+.+|++|++ ++.++.++|++.|
T Consensus 22 ~~~g~~~~r~~qi~~~~~~~~~~~~~~m~~-l~~~~r~~l~~~~ 64 (355)
T TIGR00048 22 KDLGEKPFRAKQIYKWLYHKGKDSFDDMTN-LSKDLREKLNRVF 64 (355)
T ss_pred HHcCCCchhHHHHHHHHHHcCCCCHHHccc-cCHHHHHHHhhcE
Confidence 46899988 44455555567899999987 6999999999887
No 11
>PRK14453 chloramphenicol/florfenicol resistance protein; Provisional
Probab=35.50 E-value=45 Score=29.45 Aligned_cols=40 Identities=15% Similarity=0.248 Sum_probs=31.6
Q ss_pred hcCCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhc
Q psy746 81 DYGMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGY 121 (178)
Q Consensus 81 DhGlp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY 121 (178)
++|.|+| .+..++.=-+.+.+|++|++ ++.++.++|++.|
T Consensus 16 ~~g~~~~r~~qi~~~~~~~~~~~~~~m~~-l~~~~r~~l~~~~ 57 (347)
T PRK14453 16 NLKLPDYRYEQITKAIFKQRIDNFEDMHI-LPKALRESLINEF 57 (347)
T ss_pred HcCCCcHHHHHHHHHHHhcCCCCHHHhcc-CCHHHHHHHHHHH
Confidence 6899988 34444545567899999998 5999999999987
No 12
>PRK14459 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=35.48 E-value=43 Score=29.96 Aligned_cols=42 Identities=10% Similarity=0.168 Sum_probs=32.8
Q ss_pred HHhcCCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhc
Q psy746 79 QRDYGMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGY 121 (178)
Q Consensus 79 gRDhGlp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY 121 (178)
-.++|.|.| .+..++.=-+.+.+|++|++ ++.++.++|++.|
T Consensus 36 ~~~~g~~~~ra~Qi~~wiy~~~~~~~~~mt~-l~k~~r~~L~~~~ 79 (373)
T PRK14459 36 VAELGLPAFRAKQLARHYFGRLTADPAQMTD-LPAAAREELAEAL 79 (373)
T ss_pred HHHcCCCcHHHHHHHHHHHhcCCCCHHHhcc-cCHHHHHHHHhhc
Confidence 346899988 44555555577899999998 5899999999887
No 13
>PRK14465 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=35.26 E-value=38 Score=29.89 Aligned_cols=41 Identities=7% Similarity=0.103 Sum_probs=32.6
Q ss_pred hcCCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhcc
Q psy746 81 DYGMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGYK 122 (178)
Q Consensus 81 DhGlp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY~ 122 (178)
++|.|+| .+..++.--+.+.+|++|++ ++.++.++|++.|.
T Consensus 21 ~~g~~~fra~Qi~~wiy~~~~~~~~~mt~-l~~~~r~~L~~~~~ 63 (342)
T PRK14465 21 SLGEKKFRAKQIYHGLYVNRYETWDQFTT-FSKEVKEKLEELCS 63 (342)
T ss_pred HcCCCchHHHHHHHHHHHcCCCCHHHhcc-ccHHHHHHHhcccc
Confidence 5899988 45556655667899999998 58999999998763
No 14
>PRK14467 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=34.81 E-value=37 Score=30.04 Aligned_cols=42 Identities=29% Similarity=0.540 Sum_probs=32.1
Q ss_pred HhcCCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhcc
Q psy746 80 RDYGMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGYK 122 (178)
Q Consensus 80 RDhGlp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY~ 122 (178)
.++|.|+| .+..++.--+.+.+|++|++ ++.++.++|++.|.
T Consensus 17 ~~~g~~~~r~~qi~~~~~~~~~~~~~~m~~-l~~~~r~~l~~~~~ 60 (348)
T PRK14467 17 VELGWEKYRAKQIAKWVYKKKVTDFDEMTD-LSKEDRQLLKENFE 60 (348)
T ss_pred HHcCCCchHHHHHHHHHHhcCCCCHHHhcc-ccHHHHHHHhcCcc
Confidence 36899988 44445555567899999998 58999999988863
No 15
>PRK14461 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=34.28 E-value=43 Score=30.03 Aligned_cols=42 Identities=12% Similarity=0.180 Sum_probs=33.0
Q ss_pred HhcCCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhcc
Q psy746 80 RDYGMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGYK 122 (178)
Q Consensus 80 RDhGlp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY~ 122 (178)
.++|.|.| .+..++.=.+.+.+|++|++ ++.++.++|++.|.
T Consensus 23 ~~~g~~~fRa~Qi~~wiy~~~~~~~~~mtn-lpk~lR~~L~~~~~ 66 (371)
T PRK14461 23 TAWGQPAFRARQLYRHLYVNLADSVLAMTD-LPLALRERLTAELP 66 (371)
T ss_pred HHcCCCchHHHHHHHHHHHcCCCCHHHccc-cCHHHHHHHhhccc
Confidence 46899988 45555555567899999998 58999999998773
No 16
>PRK14456 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=33.48 E-value=39 Score=30.10 Aligned_cols=53 Identities=13% Similarity=0.197 Sum_probs=36.9
Q ss_pred CCchHHHHHHHHHHhcCCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhc
Q psy746 67 HGDDLTAIGIQRQRDYGMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGY 121 (178)
Q Consensus 67 ~g~DL~alnIqRgRDhGlp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY 121 (178)
.++++..+- +--.++|.|.| .+..++.--+.+.+|++|++ ++.++.++|++.|
T Consensus 21 ~~~~~~el~-~~~~~~g~~~~r~~qi~~w~y~~~~~~~~~m~~-l~~~~r~~l~~~~ 75 (368)
T PRK14456 21 RNLRRQELT-ELLARLGEPAWRAAQLHQWLFSHRALSFEEMTT-LSKPLRRKLAESF 75 (368)
T ss_pred ccCCHHHHH-HHHHHcCCCchHHHHHHHHHHHcCCCCHHHhcc-ccHHHHHHHhcce
Confidence 344444431 12336899988 45555555567899999998 5899999999877
No 17
>PRK14463 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=32.68 E-value=32 Score=30.35 Aligned_cols=41 Identities=15% Similarity=0.220 Sum_probs=31.0
Q ss_pred HhcCCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhc
Q psy746 80 RDYGMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGY 121 (178)
Q Consensus 80 RDhGlp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY 121 (178)
.++|.|.| .+..++.=-+.+.+|++|++ +++++.++|++.+
T Consensus 20 ~~~g~~~~r~~qi~~~~~~~~~~~~~~m~~-l~~~~r~~l~~~~ 62 (349)
T PRK14463 20 AGQGKERFRAKQIFKWLYQRDARSFAEMTN-LSKDLRAELEETA 62 (349)
T ss_pred HHcCCCchHHHHHHHHHHHhCCCCHHHhcc-cCHHHHHhhcCCe
Confidence 46899988 34444544456799999998 5899999998875
No 18
>PRK14454 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=31.21 E-value=51 Score=28.97 Aligned_cols=41 Identities=20% Similarity=0.334 Sum_probs=31.4
Q ss_pred HhcCCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhc
Q psy746 80 RDYGMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGY 121 (178)
Q Consensus 80 RDhGlp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY 121 (178)
.++|.|+| .+..++.=-+.+.+|++|++ ++.++.++|++.|
T Consensus 17 ~~~g~~~~r~~qi~~~~~~~~~~~~~~m~~-l~~~~r~~l~~~~ 59 (342)
T PRK14454 17 KENGEKKFRAKQIFDWIYKKGVTDFDEMTN-IPKNLREKLKENF 59 (342)
T ss_pred HHcCCCchHHHHHHHHHHHcCCCCHHHhcc-ccHHHHHHHHhce
Confidence 46899988 34444444567899999998 5899999999876
No 19
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=30.50 E-value=43 Score=26.00 Aligned_cols=41 Identities=24% Similarity=0.390 Sum_probs=30.9
Q ss_pred cCCccHHHHHHHhCC--------------C--CCCCcccccCCCCHHHHHHHHHhcc
Q psy746 82 YGMPGYNEFRKYAGL--------------K--PVKSFEELSDVIGPENIHLLKLGYK 122 (178)
Q Consensus 82 hGlp~Yn~~R~~cgl--------------~--~~~~f~dl~~~~~~~~~~~L~~lY~ 122 (178)
-||.+|-+|++.|-- | -..|++||...++|...+.|+.+-+
T Consensus 19 V~l~~~ddi~kR~~~~ir~~~~g~~~~~~Ptl~F~Sye~la~vLsp~nleLl~~Ia~ 75 (144)
T COG4190 19 VTLAPSDDIHKRITVSIRAAEEGDAMDATPTLWFTSYEDLARVLSPRNLELLELIAQ 75 (144)
T ss_pred EEeccHHHHHHHHHHHHhhhhcCCCccCCceeccccHHHHHHHhChhHHHHHHHHHh
Confidence 489999999999811 0 1567788888888888888877665
No 20
>PHA02681 ORF089 virion membrane protein; Provisional
Probab=30.13 E-value=1e+02 Score=21.97 Aligned_cols=41 Identities=12% Similarity=0.138 Sum_probs=26.7
Q ss_pred cHHHHHHHhC-CCCCCCcccc--------cCCCCHHHHHHHHHhcc-CCCc
Q psy746 86 GYNEFRKYAG-LKPVKSFEEL--------SDVIGPENIHLLKLGYK-HVDD 126 (178)
Q Consensus 86 ~Yn~~R~~cg-l~~~~~f~dl--------~~~~~~~~~~~L~~lY~-~vdd 126 (178)
-|..||++|- .+..+.+.|. .+.|.|+-++.|-++.. +|++
T Consensus 20 iya~YRR~~i~~p~~~r~~D~L~~~ds~F~D~lTpDQVrAlHRlvTsSpe~ 70 (92)
T PHA02681 20 VIMMYRRSCVSAPAVPRNKDLLPPGASSFEDKMTDDQVRAFHALVTSSPED 70 (92)
T ss_pred HHHHHHhccCCCCCCCcccccCCCCCchhhccCCHHHHHHHHHHHhCCCCC
Confidence 4788999983 3443344432 23456888899988886 5765
No 21
>PRK14466 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=29.90 E-value=38 Score=30.01 Aligned_cols=53 Identities=23% Similarity=0.372 Sum_probs=36.1
Q ss_pred CCchHHHHHHHHHHhcCCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhc
Q psy746 67 HGDDLTAIGIQRQRDYGMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGY 121 (178)
Q Consensus 67 ~g~DL~alnIqRgRDhGlp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY 121 (178)
.++++..+- .--.++|.|+| .+..++.--+.+.+|++|++ ++.++.++|++.|
T Consensus 8 ~~l~~~el~-~~~~~~g~~~fra~Qi~~wi~~~~~~~~~~mt~-l~~~~r~~L~~~~ 62 (345)
T PRK14466 8 LGMTLEELQ-SVAKRLGMPAFAAKQIASWLYDKKVTSIDEMTN-ISLAHREKLAEEY 62 (345)
T ss_pred ccCCHHHHH-HHHHHcCCCchHHHHHHHHHHhcCCCCHHHHhh-hhHHHHHhhcCCe
Confidence 344444432 22347899988 44445555567899999998 5889999998876
No 22
>PRK11194 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=29.43 E-value=52 Score=29.39 Aligned_cols=41 Identities=17% Similarity=0.191 Sum_probs=31.3
Q ss_pred HhcCCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhc
Q psy746 80 RDYGMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGY 121 (178)
Q Consensus 80 RDhGlp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY 121 (178)
.++|.|+| .+..++.--+.+.+|++|++ ++.++.+.|++-|
T Consensus 21 ~~~g~~~~ra~qi~~w~y~~~~~~~~~mt~-l~~~~r~~L~~~~ 63 (372)
T PRK11194 21 AELGEKPFRADQVMKWIYHYGCDDFDEMTN-INKVLREKLKEVA 63 (372)
T ss_pred HHcCCCchHHHHHHHHHHhcCCCCHHHhcc-ccHHHHHHHhccc
Confidence 36889988 34444555577899999997 5899999998876
No 23
>PRK14457 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=28.65 E-value=68 Score=28.30 Aligned_cols=40 Identities=23% Similarity=0.271 Sum_probs=31.7
Q ss_pred HhcCCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHh
Q psy746 80 RDYGMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLG 120 (178)
Q Consensus 80 RDhGlp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~l 120 (178)
.++|.|.| .+..++.--+.+.+|++|++ ++.++.++|++.
T Consensus 17 ~~~g~~~~r~~qi~~w~~~~~~~~~~~m~~-l~~~~r~~l~~~ 58 (345)
T PRK14457 17 VAQGQPAFRGRQLHDWLYNKGVRSLDEISV-LPKAWRESLKDD 58 (345)
T ss_pred HHcCCCchHHHHHHHHHHhcCCCCHHHcCc-cCHHHHHHHhhc
Confidence 46899988 45556655577899999998 599999999993
No 24
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=28.16 E-value=62 Score=21.10 Aligned_cols=29 Identities=48% Similarity=0.838 Sum_probs=19.5
Q ss_pred HHHHHHhCCCCCCCcccccCC--CCHHHHHHHH
Q psy746 88 NEFRKYAGLKPVKSFEELSDV--IGPENIHLLK 118 (178)
Q Consensus 88 n~~R~~cgl~~~~~f~dl~~~--~~~~~~~~L~ 118 (178)
.+||+.-| ++.+++||... |+++.+++|+
T Consensus 31 v~~R~~~G--~f~s~~dL~~v~gi~~~~~~~l~ 61 (65)
T PF12836_consen 31 VEYREKNG--PFKSLEDLKEVPGIGPKTYEKLK 61 (65)
T ss_dssp HHHHHHH---S-SSGGGGGGSTT--HHHHHHHC
T ss_pred HHHHHhCc--CCCCHHHHhhCCCCCHHHHHHHH
Confidence 46787776 88999999764 6888888775
No 25
>PRK14470 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=28.14 E-value=65 Score=28.31 Aligned_cols=41 Identities=5% Similarity=-0.051 Sum_probs=30.2
Q ss_pred HHhcCCccHH--HHHHHhCCCCCCCcccccCCCCHHHHHHHHHhc
Q psy746 79 QRDYGMPGYN--EFRKYAGLKPVKSFEELSDVIGPENIHLLKLGY 121 (178)
Q Consensus 79 gRDhGlp~Yn--~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY 121 (178)
-.++|.|+|- +..++.--+.+. |++|++ ++.++.++|++.|
T Consensus 13 ~~~~g~~~~r~~qi~~~~~~~~~~-~~~m~~-l~~~~r~~l~~~~ 55 (336)
T PRK14470 13 ARPAGISLEDARRITGAVIGRGAP-LRSARN-VRRSVLDEVDALA 55 (336)
T ss_pred HHHcCCCcHHHHHHHHHHHhCCCC-HHHhcc-CCHHHHHHHhccc
Confidence 3479999884 333444445566 999998 5999999999876
No 26
>PF12080 GldM_C: GldM C-terminal domain; InterPro: IPR022719 This domain is found in bacteria at the C terminus of the GldM protein. This domain is typically between 169 to 182 amino acids in length and has two completely conserved residues (Y and N) that may be functionally important. GldM, is named for the member from Bacteriodetes Flavobacterium johnsoniae, which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes [].
Probab=26.91 E-value=43 Score=26.75 Aligned_cols=27 Identities=26% Similarity=0.354 Sum_probs=21.5
Q ss_pred CCChHHHHHHHHHHHHhhcCCcceeec
Q psy746 143 LFGPTFTYVIADQFYRWKFGDRFWFSV 169 (178)
Q Consensus 143 ~~Gpt~~cii~~qF~rl~~gDRf~ye~ 169 (178)
.-|..|..-+...+.++++||||+..+
T Consensus 148 ~~G~~~s~~~~~~l~~~~~Gd~i~I~~ 174 (181)
T PF12080_consen 148 VNGNKFSARAKSALRKAKRGDRIYISD 174 (181)
T ss_pred cccccccHHHHHHHHhcCCCCEEEEEE
Confidence 445666667778899999999998765
No 27
>smart00119 HECTc Domain Homologous to E6-AP Carboxyl Terminus with. E3 ubiquitin-protein ligases. Can bind to E2 enzymes.
Probab=25.88 E-value=64 Score=28.08 Aligned_cols=30 Identities=23% Similarity=0.328 Sum_probs=23.9
Q ss_pred HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHh
Q psy746 88 NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLG 120 (178)
Q Consensus 88 n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~l 120 (178)
.-|+..+|.+. +++||.. +|+++.+.|+.+
T Consensus 97 ~f~k~L~~~~~--tl~Dl~~-~D~~~~~sl~~l 126 (336)
T smart00119 97 PFYKKLLGKPV--TLHDLES-LDPELYKSLKWL 126 (336)
T ss_pred HHHHHHhCCCC--CHHHHHH-hCHHHHHHHHHH
Confidence 35777788765 8999976 599999988887
No 28
>TIGR00165 S18 ribosomal protein S18. This ribosomal small subunit protein is found in all eubacteria so far, as well as in chloroplasts. YER050C from Saccharomyces cerevisiae and a related protein from Caenorhabditis elegans appear to be homologous and may represent mitochondrial forms. The trusted cutoff is set high enough that these two candidate S18 proteins are not categorized automatically.
Probab=25.16 E-value=53 Score=22.42 Aligned_cols=19 Identities=26% Similarity=0.240 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHhcCCccHH
Q psy746 70 DLTAIGIQRQRDYGMPGYN 88 (178)
Q Consensus 70 DL~alnIqRgRDhGlp~Yn 88 (178)
-.++..|.|+|..||=||.
T Consensus 50 r~l~~aIKrAR~~~LlP~~ 68 (70)
T TIGR00165 50 RRLARAIKRARYLALLPYV 68 (70)
T ss_pred HHHHHHHHHHHHHhcCCcc
Confidence 4588899999999999884
No 29
>PRK14468 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=24.71 E-value=86 Score=27.54 Aligned_cols=38 Identities=13% Similarity=0.273 Sum_probs=29.1
Q ss_pred CCccH--HHHHHHhCCCCCCCcccccCCCCHHHHHHHHHhc
Q psy746 83 GMPGY--NEFRKYAGLKPVKSFEELSDVIGPENIHLLKLGY 121 (178)
Q Consensus 83 Glp~Y--n~~R~~cgl~~~~~f~dl~~~~~~~~~~~L~~lY 121 (178)
|.|.| .+..++.=-+.+.+|++|++ ++.++.++|++-|
T Consensus 13 ~~~~~r~~qi~~~~~~~~~~~~~~m~~-l~~~~r~~l~~~~ 52 (343)
T PRK14468 13 PGEGYRRAQLAEWLYAQGARTFDAMTN-LPKALRAELAREY 52 (343)
T ss_pred CCCchHHHHHHHHHHhcCCCCHHHhcc-ccHHHHHHHhhcc
Confidence 78877 34444544567899999998 5899999999876
No 30
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=23.28 E-value=81 Score=24.43 Aligned_cols=31 Identities=35% Similarity=0.598 Sum_probs=26.1
Q ss_pred HHHHHHhCCCCCCCcccccC--CCCHHHHHHHHHh
Q psy746 88 NEFRKYAGLKPVKSFEELSD--VIGPENIHLLKLG 120 (178)
Q Consensus 88 n~~R~~cgl~~~~~f~dl~~--~~~~~~~~~L~~l 120 (178)
.+||+.-| +.++++||.. .|.++++++++..
T Consensus 114 i~yRe~~G--~f~sv~dL~~v~GiG~~~~ekl~~~ 146 (149)
T COG1555 114 IDYREENG--PFKSVDDLAKVKGIGPKTLEKLKDY 146 (149)
T ss_pred HHHHHHcC--CCCcHHHHHhccCCCHHHHHHHHhh
Confidence 68999999 8999999975 4789999998753
No 31
>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=21.03 E-value=87 Score=19.37 Aligned_cols=19 Identities=26% Similarity=0.665 Sum_probs=13.1
Q ss_pred HHHHHhcCCccHHHHHHHh
Q psy746 76 IQRQRDYGMPGYNEFRKYA 94 (178)
Q Consensus 76 IqRgRDhGlp~Yn~~R~~c 94 (178)
-.|-|.+|+++|.+|....
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 3678899999999998765
No 32
>COG3965 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]
Probab=20.83 E-value=1.2e+02 Score=26.34 Aligned_cols=44 Identities=14% Similarity=0.246 Sum_probs=33.0
Q ss_pred chhhhhhhhcCCCCCCCCCCCchHHHHHHHHHHhcCCccHHHHHHHhCC
Q psy746 48 DFNINNKLKTNHPPFQYDPHGDDLTAIGIQRQRDYGMPGYNEFRKYAGL 96 (178)
Q Consensus 48 ~~~l~~~lf~~~~~~~~~~~g~DL~alnIqRgRDhGlp~Yn~~R~~cgl 96 (178)
...+++.|...|++ ..--+.+..-+--++||.|+|..|-...|.
T Consensus 217 k~al~eiLlmtP~e-----l~q~ies~~~~~v~k~~f~~~~~yvArVGr 260 (314)
T COG3965 217 KSALREILLMTPNE-----LQQSIESHAHEIVEKYGFPSYHVYVARVGR 260 (314)
T ss_pred HHHHHHHHhcCcHH-----HHHHHHHHHHHHHHHhcCchHHHHHHHhcc
Confidence 66778888776652 333456667777899999999999888875
No 33
>PRK00391 rpsR 30S ribosomal protein S18; Reviewed
Probab=20.07 E-value=80 Score=22.07 Aligned_cols=19 Identities=26% Similarity=0.252 Sum_probs=16.6
Q ss_pred hHHHHHHHHHHhcCCccHH
Q psy746 70 DLTAIGIQRQRDYGMPGYN 88 (178)
Q Consensus 70 DL~alnIqRgRDhGlp~Yn 88 (178)
-.++..|.|+|..||=||.
T Consensus 59 r~l~~aIkrAR~~~LlPf~ 77 (79)
T PRK00391 59 RQLATAIKRARFLALLPYV 77 (79)
T ss_pred HHHHHHHHHHHHhhCCCcc
Confidence 4588899999999999885
Done!