Query 031227
Match_columns 163
No_of_seqs 174 out of 1065
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 11:05:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031227.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031227hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03030 cationic peroxidase; 100.0 6.4E-32 1.4E-36 234.2 11.4 131 12-147 102-313 (324)
2 cd00693 secretory_peroxidase H 100.0 3.7E-30 7.9E-35 221.0 11.8 127 12-147 82-288 (298)
3 PLN02608 L-ascorbate peroxidas 100.0 9.8E-30 2.1E-34 217.8 10.0 129 9-147 76-249 (289)
4 cd00691 ascorbate_peroxidase A 100.0 9.5E-30 2.1E-34 214.2 9.7 127 9-145 75-253 (253)
5 PLN02879 L-ascorbate peroxidas 100.0 2.9E-29 6.3E-34 211.3 11.6 126 9-144 79-249 (251)
6 PLN02364 L-ascorbate peroxidas 100.0 1.9E-29 4.2E-34 212.1 10.1 126 9-144 78-249 (250)
7 cd00692 ligninase Ligninase an 99.9 4E-28 8.6E-33 211.0 9.4 124 10-144 91-277 (328)
8 cd00314 plant_peroxidase_like 99.9 8.3E-23 1.8E-27 170.4 7.6 122 9-139 64-255 (255)
9 PF00141 peroxidase: Peroxidas 99.8 1.3E-22 2.8E-27 168.4 -0.3 101 13-117 63-230 (230)
10 TIGR00198 cat_per_HPI catalase 99.8 3.5E-20 7.6E-25 173.9 10.7 135 10-153 127-413 (716)
11 cd00649 catalase_peroxidase_1 99.8 1.1E-19 2.3E-24 161.8 11.1 138 10-155 117-408 (409)
12 PRK15061 catalase/hydroperoxid 99.7 3.3E-16 7.2E-21 147.0 10.5 56 95-155 364-421 (726)
13 cd08200 catalase_peroxidase_2 99.5 1.5E-14 3.3E-19 124.5 6.5 98 38-141 123-296 (297)
14 cd08201 plant_peroxidase_like_ 99.4 6.8E-14 1.5E-18 118.9 3.4 62 22-88 97-166 (264)
15 PRK15061 catalase/hydroperoxid 99.3 6.7E-12 1.5E-16 118.3 6.3 97 39-141 549-721 (726)
16 TIGR00198 cat_per_HPI catalase 99.2 2.8E-11 6.1E-16 114.3 6.0 100 40-142 538-710 (716)
17 COG0376 KatG Catalase (peroxid 98.4 8.5E-07 1.8E-11 82.2 8.5 138 7-153 140-430 (730)
18 COG0376 KatG Catalase (peroxid 89.6 0.53 1.2E-05 44.6 4.7 98 40-140 554-724 (730)
19 PF11895 DUF3415: Domain of un 85.6 0.67 1.4E-05 33.3 2.2 22 125-146 2-23 (80)
20 PF02954 HTH_8: Bacterial regu 39.2 11 0.00024 23.0 0.2 26 8-33 6-31 (42)
21 PHA00435 capsid assembly prote 26.4 1E+02 0.0023 27.1 4.1 64 68-136 128-194 (306)
22 PF04225 OapA: Opacity-associa 25.6 26 0.00056 24.8 0.2 22 67-88 11-32 (85)
23 PF10518 TAT_signal: TAT (twin 22.2 61 0.0013 18.1 1.3 12 7-18 3-14 (26)
24 PF09533 DUF2380: Predicted li 20.2 2.2E+02 0.0049 23.5 4.7 23 66-88 107-129 (188)
No 1
>PLN03030 cationic peroxidase; Provisional
Probab=99.97 E-value=6.4e-32 Score=234.23 Aligned_cols=131 Identities=20% Similarity=0.336 Sum_probs=107.4
Q ss_pred HHHHHhh-CCCCcccceeeec--------cCCcccccccccCCCCCCCCCCCC--CCCCCCcccCHHHHHHHHHhCCCCh
Q 031227 12 WHQPSAN-VEGMKRKGAYCTL--------HMAQMWGLFEKQFGRTDAQEPDPE--GRVPQWEKATVQEMKDKFSAIGLGP 80 (163)
Q Consensus 12 ~~~~~~~-c~g~vsca~~la~--------g~~~~w~v~~v~~GRrDg~~s~~~--~~LP~~p~~~~~~L~~~F~~kGL~~ 80 (163)
||+++|+ |||+||||++++. ..||.|+| ++|||||++|.++ ++||+ |+.++++|++.|+++||+.
T Consensus 102 iK~~~e~~CPg~VSCADilalAarDaV~~~gGP~~~v---~~GRrDg~~s~~~~~~~LP~-p~~~~~~l~~~F~~~Gl~~ 177 (324)
T PLN03030 102 AKTQLEAACPGVVSCADILALAARDSVVLTNGLTWPV---PTGRRDGRVSLASDASNLPG-FTDSIDVQKQKFAAKGLNT 177 (324)
T ss_pred HHHHHHhhCCCcccHHHHHHHHhhccccccCCCceee---eccccCCCCCCcccccCCcC-CCCCHHHHHHHHHHcCCCH
Confidence 6777775 9999999965542 12445766 9999999987533 57999 9999999999999999999
Q ss_pred hcceeeec-----------CC-------------C-------------------------------C---C---------
Q 031227 81 RQLAVMSA-----------FL-------------G-------------------------------P---D--------- 93 (163)
Q Consensus 81 ~DlVaLsG-----------F~-------------~-------------------------------p---D--------- 93 (163)
+|||+||| |. + | |
T Consensus 178 ~DlVaLsGAHTiG~ahC~~f~~Rlynf~~~~~~~Dp~~d~~~~~~L~~~Cp~~~~~~~~~~lD~~Tp~~FDn~Yy~nll~ 257 (324)
T PLN03030 178 QDLVTLVGGHTIGTTACQFFRYRLYNFTTTGNGADPSIDASFVPQLQALCPQNGDGSRRIALDTGSSNRFDASFFSNLKN 257 (324)
T ss_pred HHheeeeeccccceeeeeccccccccccCCCCCCCCchhHHHHHHHhccCCCCCCCCccccCCCCCCcccccHHHHHHHh
Confidence 99999999 20 0 0 1
Q ss_pred --C-chhHHHhccCCCcHHHHHHHhhcCCCCChHHHHHHHHHHHHHHhcCCCCCCCC
Q 031227 94 --Q-AATEALLATDKDVSPWVQKYQRSRETVSQTDYEVDLITTFTKLSSLGQQINYE 147 (163)
Q Consensus 94 --~-L~SDq~L~~D~~t~~~V~~yA~~~~~~~~~~Ff~dFa~AmvKMg~lgv~~~~~ 147 (163)
| |+|||+|+.|++|+.+|+.||.|+. ..++.|+++|++||+|||+|||..+.+
T Consensus 258 ~rGlL~SDq~L~~d~~T~~~V~~~A~~~~-~~~~~F~~~Fa~AmvKMg~i~VlTG~~ 313 (324)
T PLN03030 258 GRGILESDQKLWTDASTRTFVQRFLGVRG-LAGLNFNVEFGRSMVKMSNIGVKTGTN 313 (324)
T ss_pred cCCCcCCchHhhcCccHHHHHHHHhcccc-cchhhhHHHHHHHHHHHccCCCCCCCC
Confidence 3 8999999999999999999998750 012599999999999999999988654
No 2
>cd00693 secretory_peroxidase Horseradish peroxidase and related secretory plant peroxidases. Secretory peroxidases belong to class III of the plant heme-dependent peroxidase superfamily. All members of the superfamily share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Class III peroxidases are found in the extracellular space or in the vacuole in plants where they have been implicated in hydrogen peroxide detoxification, auxin catabolism and lignin biosynthesis, and stress response. Class III peroxidases contain four conserved disulphide bridges and two conserved calcium binding sites.
Probab=99.97 E-value=3.7e-30 Score=221.05 Aligned_cols=127 Identities=18% Similarity=0.326 Sum_probs=107.0
Q ss_pred HHHHHhh-CCCCcccceeeec--------cCCcccccccccCCCCCCCCCCCC--CCCCCCcccCHHHHHHHHHhCCCCh
Q 031227 12 WHQPSAN-VEGMKRKGAYCTL--------HMAQMWGLFEKQFGRTDAQEPDPE--GRVPQWEKATVQEMKDKFSAIGLGP 80 (163)
Q Consensus 12 ~~~~~~~-c~g~vsca~~la~--------g~~~~w~v~~v~~GRrDg~~s~~~--~~LP~~p~~~~~~L~~~F~~kGL~~ 80 (163)
||+++|+ ||++||||++++. ..||.|+| ++||+|+++|.+. ++||+ |+.++++|++.|+++||++
T Consensus 82 iK~~~e~~cp~~VScADiialAar~av~~~GGP~~~v---~~GR~D~~~s~~~~~~~lP~-p~~~~~~l~~~F~~~G~~~ 157 (298)
T cd00693 82 IKAALEAACPGVVSCADILALAARDAVVLAGGPSYEV---PLGRRDGRVSSANDVGNLPS-PFFSVSQLISLFASKGLTV 157 (298)
T ss_pred HHHHHHhhCCCcccHHHHHHHhhhhceeccCCCcccc---cCCCcCCcccCcccccCCCC-cccCHHHHHHHHHHcCCCH
Confidence 4556655 9999999966542 12344666 9999999977644 68999 9999999999999999999
Q ss_pred hcceeeec------------------CC------------------------------------CC---C----------
Q 031227 81 RQLAVMSA------------------FL------------------------------------GP---D---------- 93 (163)
Q Consensus 81 ~DlVaLsG------------------F~------------------------------------~p---D---------- 93 (163)
+|||+|+| |. +| |
T Consensus 158 ~d~VaL~GaHTiG~~hc~~f~~Rl~~f~g~~~~dp~~~~~~~~~L~~~Cp~~~~~~~~~~lD~~Tp~~FDn~Yy~~l~~~ 237 (298)
T cd00693 158 TDLVALSGAHTIGRAHCSSFSDRLYNFSGTGDPDPTLDPAYAAQLRKKCPAGGDDDTLVPLDPGTPNTFDNSYYKNLLAG 237 (298)
T ss_pred HHheeecccceeeeeecccccccccCCCCCCCCCCCccHHHHHHhcCCCCCCCCCCccccCCCCCCCccccHHHHHHHhc
Confidence 99999999 10 01 1
Q ss_pred -C-chhHHHhccCCCcHHHHHHHhhcCCCCChHHHHHHHHHHHHHHhcCCCCCCCC
Q 031227 94 -Q-AATEALLATDKDVSPWVQKYQRSRETVSQTDYEVDLITTFTKLSSLGQQINYE 147 (163)
Q Consensus 94 -~-L~SDq~L~~D~~t~~~V~~yA~~~~~~~~~~Ff~dFa~AmvKMg~lgv~~~~~ 147 (163)
+ |+|||+|+.|++|+.+|+.||.|+ +.|+++|++||+|||+|||+...+
T Consensus 238 ~glL~SD~~L~~d~~t~~~V~~~A~d~-----~~F~~~Fa~Am~Kl~~l~v~tg~~ 288 (298)
T cd00693 238 RGLLTSDQALLSDPRTRAIVNRYAANQ-----DAFFRDFAAAMVKMGNIGVLTGSQ 288 (298)
T ss_pred ccCccCCHHhccCccHHHHHHHHhhCH-----HHHHHHHHHHHHHHhhcCCccCCC
Confidence 3 899999999999999999999999 999999999999999999988654
No 3
>PLN02608 L-ascorbate peroxidase
Probab=99.96 E-value=9.8e-30 Score=217.75 Aligned_cols=129 Identities=24% Similarity=0.372 Sum_probs=111.2
Q ss_pred HhhHHHHHhhCCCCcccceeeec--------cCCcccccccccCCCCCCCCCCCCCCCCCCcccCHHHHHHHHHhCCCCh
Q 031227 9 QHFWHQPSANVEGMKRKGAYCTL--------HMAQMWGLFEKQFGRTDAQEPDPEGRVPQWEKATVQEMKDKFSAIGLGP 80 (163)
Q Consensus 9 ~~~~~~~~~~c~g~vsca~~la~--------g~~~~w~v~~v~~GRrDg~~s~~~~~LP~~p~~~~~~L~~~F~~kGL~~ 80 (163)
..+++.++++++ +||||++++. ..||.|+| ++||+|+++++++++||+ |+.++++|++.|+++|||+
T Consensus 76 ~~vid~iK~~~~-~VScADilalAardAV~~~GGP~~~v---~~GR~D~~~s~~~~~LP~-p~~~~~~l~~~F~~~Gl~~ 150 (289)
T PLN02608 76 IDLCEPVKAKHP-KITYADLYQLAGVVAVEVTGGPTIDF---VPGRKDSNACPEEGRLPD-AKKGAKHLRDVFYRMGLSD 150 (289)
T ss_pred HHHHHHHHHHcC-CcCHHHHHHHHHHHHHHhcCCCccCC---CCCCCCCCcCCccCCCcC-CCCCHHHHHHHHHHcCCCH
Confidence 357888888894 9999966652 12344666 999999999988889999 9999999999999999999
Q ss_pred hcceeeec-------------CCC-----C---C-------------C---chhHHHhccCCCcHHHHHHHhhcCCCCCh
Q 031227 81 RQLAVMSA-------------FLG-----P---D-------------Q---AATEALLATDKDVSPWVQKYQRSRETVSQ 123 (163)
Q Consensus 81 ~DlVaLsG-------------F~~-----p---D-------------~---L~SDq~L~~D~~t~~~V~~yA~~~~~~~~ 123 (163)
+|||+|+| |.+ | | + |+|||+|+.|++|+.+|+.||.|+
T Consensus 151 ~D~VaLsGAHTiG~ahc~r~g~~g~~~~Tp~~FDN~Yy~~ll~~~~~gll~L~SD~~L~~d~~T~~~V~~fA~~~----- 225 (289)
T PLN02608 151 KDIVALSGGHTLGRAHPERSGFDGPWTKEPLKFDNSYFVELLKGESEGLLKLPTDKALLEDPEFRPYVELYAKDE----- 225 (289)
T ss_pred HHHhhhccccccccccccCCCCCCCCCCCCCccChHHHHHHHcCCcCCccccccCHhhhcChhHHHHHHHHhhCH-----
Confidence 99999999 111 1 1 2 699999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCCC
Q 031227 124 TDYEVDLITTFTKLSSLGQQINYE 147 (163)
Q Consensus 124 ~~Ff~dFa~AmvKMg~lgv~~~~~ 147 (163)
+.|+++|++||+|||+|||+.+..
T Consensus 226 ~~F~~~Fa~Am~Km~~lgvltg~~ 249 (289)
T PLN02608 226 DAFFRDYAESHKKLSELGFTPPSS 249 (289)
T ss_pred HHHHHHHHHHHHHHHcCCCCCCCC
Confidence 999999999999999999988764
No 4
>cd00691 ascorbate_peroxidase Ascorbate peroxidases and cytochrome C peroxidases. Ascorbate peroxidases are a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Along with related catalase-peroxidases, ascorbate peroxidases belong to class I of the plant superfamily. Ascorbate peroxidases are found in the chloroplasts and/or cytosol of algae and plants, where they have been shown to control the concentration of lethal hydrogen peroxide molecules. The yeast cytochrome c peroxidase is a divergent member of the family; it forms a complex with cytochrome c to catalyze the reduction of hydrogen peroxide to water.
Probab=99.96 E-value=9.5e-30 Score=214.17 Aligned_cols=127 Identities=22% Similarity=0.382 Sum_probs=109.3
Q ss_pred HhhHHHHHhhCCCCcccceeeec--------cCCcccccccccCCCCCCCCCC---CCCCCCCCcccCHHHHHHHHHhCC
Q 031227 9 QHFWHQPSANVEGMKRKGAYCTL--------HMAQMWGLFEKQFGRTDAQEPD---PEGRVPQWEKATVQEMKDKFSAIG 77 (163)
Q Consensus 9 ~~~~~~~~~~c~g~vsca~~la~--------g~~~~w~v~~v~~GRrDg~~s~---~~~~LP~~p~~~~~~L~~~F~~kG 77 (163)
-..|++++++|+ +||||++++. ..||.|+| ++||+|+++|. ++++||. |+.++++|++.|+++|
T Consensus 75 ~~~i~~iK~~~~-~VScADilalAar~Av~~~GGP~~~v---~~GR~D~~~s~~~~~~~~lP~-p~~~~~~l~~~F~~~G 149 (253)
T cd00691 75 RKLLEPIKKKYP-DISYADLWQLAGVVAIEEMGGPKIPF---RPGRVDASDPEECPPEGRLPD-ASKGADHLRDVFYRMG 149 (253)
T ss_pred HHHHHHHHHHcC-CCCHHHHHHHHHHHHHHHcCCCccCc---ccCCCCCCcccccCcccCCCC-CCCCHHHHHHHHHhcC
Confidence 357889999996 8999966653 23444666 99999999987 5678999 9999999999999999
Q ss_pred CChhcceeeec---C----------C-----CC---------------C--------CchhHHHhccCCCcHHHHHHHhh
Q 031227 78 LGPRQLAVMSA---F----------L-----GP---------------D--------QAATEALLATDKDVSPWVQKYQR 116 (163)
Q Consensus 78 L~~~DlVaLsG---F----------~-----~p---------------D--------~L~SDq~L~~D~~t~~~V~~yA~ 116 (163)
|+++|||+||| + . +| . .|+||++|+.|++|+.+|+.||.
T Consensus 150 ls~~d~VaLsGaHTiG~a~c~~~~~~g~~~~tp~~FDn~Yy~~ll~~~g~~~~~~~~~L~sD~~L~~d~~t~~~v~~~a~ 229 (253)
T cd00691 150 FNDQEIVALSGAHTLGRCHKERSGYDGPWTKNPLKFDNSYFKELLEEDWKLPTPGLLMLPTDKALLEDPKFRPYVELYAK 229 (253)
T ss_pred CCHHHHHHhcccceeecccccCCCCCCCCCCCCCcccHHHHHHHhcCCCccCcCcceechhhHHHHcCccHHHHHHHHhh
Confidence 99999999999 1 1 11 1 37999999999999999999999
Q ss_pred cCCCCChHHHHHHHHHHHHHHhcCCCCCC
Q 031227 117 SRETVSQTDYEVDLITTFTKLSSLGQQIN 145 (163)
Q Consensus 117 ~~~~~~~~~Ff~dFa~AmvKMg~lgv~~~ 145 (163)
|+ +.|+++|++||+|||+|||.|.
T Consensus 230 ~~-----~~F~~~Fa~Am~Km~~l~v~~~ 253 (253)
T cd00691 230 DQ-----DAFFKDYAEAHKKLSELGVPFP 253 (253)
T ss_pred CH-----HHHHHHHHHHHHHHHhcCCCCC
Confidence 99 9999999999999999999874
No 5
>PLN02879 L-ascorbate peroxidase
Probab=99.96 E-value=2.9e-29 Score=211.26 Aligned_cols=126 Identities=26% Similarity=0.398 Sum_probs=107.7
Q ss_pred HhhHHHHHhhCCCCcccceeeec--------cCCcccccccccCCCCCCCCCCCCCCCCCCcccCHHHHHHHHHhCCCCh
Q 031227 9 QHFWHQPSANVEGMKRKGAYCTL--------HMAQMWGLFEKQFGRTDAQEPDPEGRVPQWEKATVQEMKDKFSAIGLGP 80 (163)
Q Consensus 9 ~~~~~~~~~~c~g~vsca~~la~--------g~~~~w~v~~v~~GRrDg~~s~~~~~LP~~p~~~~~~L~~~F~~kGL~~ 80 (163)
..+++.+.++. ++||||++++. -.||.|++ ++||+|+++++++++||+ |+.++++|++.|+++|||+
T Consensus 79 ~~~i~~iK~~~-~~VScADilalAa~~AV~~~GGP~~~~---~~GR~D~~~~~~~~~lP~-p~~~~~~l~~~F~~~Gl~~ 153 (251)
T PLN02879 79 VRLLDPIKELF-PILSYADFYQLAGVVAVEITGGPEIPF---HPGRLDKVEPPPEGRLPQ-ATKGVDHLRDVFGRMGLND 153 (251)
T ss_pred HHHHHHHHHHc-CCcCHHHHHHHHHHHHHHhcCCCccCC---CCCCCCCCCCCcccCCCC-CCCCHHHHHHHHHHcCCCH
Confidence 35677777777 68999965542 12334665 999999999998899999 9999999999999999999
Q ss_pred hcceeeec---C----------C-----CC---C-------------C---chhHHHhccCCCcHHHHHHHhhcCCCCCh
Q 031227 81 RQLAVMSA---F----------L-----GP---D-------------Q---AATEALLATDKDVSPWVQKYQRSRETVSQ 123 (163)
Q Consensus 81 ~DlVaLsG---F----------~-----~p---D-------------~---L~SDq~L~~D~~t~~~V~~yA~~~~~~~~ 123 (163)
+|||+||| + . +| | + |+||++|+.|++|+.+|+.||.|+
T Consensus 154 ~dlVALsGaHTiG~ah~~r~g~~g~~d~tp~~FDN~Yy~~ll~~~~~gll~L~SD~aL~~D~~t~~~V~~~A~d~----- 228 (251)
T PLN02879 154 KDIVALSGGHTLGRCHKERSGFEGAWTPNPLIFDNSYFKEILSGEKEGLLQLPTDKALLDDPLFLPFVEKYAADE----- 228 (251)
T ss_pred HHHeeeeccccccccccccccCCCCCCCCccceeHHHHHHHHcCCcCCCccchhhHHHhcCCcHHHHHHHHhhCH-----
Confidence 99999999 1 1 12 1 2 689999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCC
Q 031227 124 TDYEVDLITTFTKLSSLGQQI 144 (163)
Q Consensus 124 ~~Ff~dFa~AmvKMg~lgv~~ 144 (163)
+.||++|++||+|||+||+.+
T Consensus 229 ~~F~~~Fa~Am~KL~~lg~~~ 249 (251)
T PLN02879 229 DAFFEDYTEAHLKLSELGFAD 249 (251)
T ss_pred HHHHHHHHHHHHHHHccCCCC
Confidence 999999999999999999875
No 6
>PLN02364 L-ascorbate peroxidase 1
Probab=99.96 E-value=1.9e-29 Score=212.14 Aligned_cols=126 Identities=23% Similarity=0.381 Sum_probs=107.2
Q ss_pred HhhHHHHHhhCCCCcccceeeec--------cCCcccccccccCCCCCCCCCCCCCCCCCCcccCHHHHHHHHHh-CCCC
Q 031227 9 QHFWHQPSANVEGMKRKGAYCTL--------HMAQMWGLFEKQFGRTDAQEPDPEGRVPQWEKATVQEMKDKFSA-IGLG 79 (163)
Q Consensus 9 ~~~~~~~~~~c~g~vsca~~la~--------g~~~~w~v~~v~~GRrDg~~s~~~~~LP~~p~~~~~~L~~~F~~-kGL~ 79 (163)
-.+|+.+.+++ ++||||++++. -.||.|+| ++||+|+++|+++++||. |+.++++|++.|++ +|||
T Consensus 78 ~~~i~~ik~~~-~~VScADilalAardAV~~~GGP~~~v---~~GR~D~~~s~~~~~lP~-p~~~~~~l~~~F~~~~Gl~ 152 (250)
T PLN02364 78 LRLLDPIREQF-PTISFADFHQLAGVVAVEVTGGPDIPF---HPGREDKPQPPPEGRLPD-ATKGCDHLRDVFAKQMGLS 152 (250)
T ss_pred HHHHHHHHHHc-CCcCHHHHHHHHHHHHHHhcCCCeeCC---CCCCCCcccccccCCCCC-CCcCHHHHHHHHHHhcCCC
Confidence 35788888888 69999966542 12334655 999999999999889999 99999999999997 5999
Q ss_pred hhcceeeec---C----------C-----CC---C-------------C---chhHHHhccCCCcHHHHHHHhhcCCCCC
Q 031227 80 PRQLAVMSA---F----------L-----GP---D-------------Q---AATEALLATDKDVSPWVQKYQRSRETVS 122 (163)
Q Consensus 80 ~~DlVaLsG---F----------~-----~p---D-------------~---L~SDq~L~~D~~t~~~V~~yA~~~~~~~ 122 (163)
++|||+||| + . +| | + |+|||+|+.|++|+.+|+.||.|+
T Consensus 153 ~~d~VaLsGaHTiG~~hc~r~~~~g~~~~tp~~fDn~Yy~~ll~~~~~gll~l~sD~~L~~d~~T~~~v~~~a~~~---- 228 (250)
T PLN02364 153 DKDIVALSGAHTLGRCHKDRSGFEGAWTSNPLIFDNSYFKELLSGEKEGLLQLVSDKALLDDPVFRPLVEKYAADE---- 228 (250)
T ss_pred HHHheeeecceeeccccCCCCCCCCCCCCCCCccchHHHHHHhcCCcCCCccccchHHHccCchHHHHHHHHhhCH----
Confidence 999999999 1 1 11 1 2 469999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHhcCCCCC
Q 031227 123 QTDYEVDLITTFTKLSSLGQQI 144 (163)
Q Consensus 123 ~~~Ff~dFa~AmvKMg~lgv~~ 144 (163)
+.|+++|++||+|||+||+..
T Consensus 229 -~~F~~~Fa~Am~Km~~lg~~~ 249 (250)
T PLN02364 229 -DAFFADYAEAHMKLSELGFAD 249 (250)
T ss_pred -HHHHHHHHHHHHHHHccCCCC
Confidence 999999999999999999864
No 7
>cd00692 ligninase Ligninase and other manganese-dependent fungal peroxidases. Ligninases and related extracellular fungal peroxidases belong to class II of the plant heme-dependent peroxidase superfamily. All members of the superfamily share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Class II peroxidases are fungal glycoproteins that have been implicated in the oxidative breakdown of lignin, the main cell wall component of woody plants. They contain four conserved disulphide bridges and two conserved calcium binding sites.
Probab=99.95 E-value=4e-28 Score=210.96 Aligned_cols=124 Identities=23% Similarity=0.353 Sum_probs=104.9
Q ss_pred hhHHHHHhhCCCCcccceeeec---------cCCcccccccccCCCCCCCCCCCCCCCCCCcccCHHHHHHHHHhCCCCh
Q 031227 10 HFWHQPSANVEGMKRKGAYCTL---------HMAQMWGLFEKQFGRTDAQEPDPEGRVPQWEKATVQEMKDKFSAIGLGP 80 (163)
Q Consensus 10 ~~~~~~~~~c~g~vsca~~la~---------g~~~~w~v~~v~~GRrDg~~s~~~~~LP~~p~~~~~~L~~~F~~kGL~~ 80 (163)
..+|..+|+.+ ||||++++. ..||.|++ ++||+|++++.++++||. |+.++++|++.|+++|||+
T Consensus 91 d~lk~~~e~~c--VScADiialAa~~AV~~~~GGP~i~v---~~GR~D~~~s~~~g~LP~-p~~sv~~l~~~F~~~Gf~~ 164 (328)
T cd00692 91 EALRPFHQKHN--VSMADFIQFAGAVAVSNCPGAPRLEF---YAGRKDATQPAPDGLVPE-PFDSVDKILARFADAGFSP 164 (328)
T ss_pred HHHHHHHHhcC--cCHHHHHHHHHHHHHHhcCCCCcccc---cCCCCCCCCCCcccCCCC-CCCCHHHHHHHHHHcCCCH
Confidence 45677777743 999965542 12334655 999999999999999999 9999999999999999999
Q ss_pred hcceeeec---CC----------------CC---C--------------------------------CchhHHHhccCCC
Q 031227 81 RQLAVMSA---FL----------------GP---D--------------------------------QAATEALLATDKD 106 (163)
Q Consensus 81 ~DlVaLsG---F~----------------~p---D--------------------------------~L~SDq~L~~D~~ 106 (163)
+|||+||| ++ +| | .|+||++|+.|++
T Consensus 165 ~E~VaLsGAHTiG~a~~~Dps~~g~p~D~TP~~FDn~Yf~~ll~~~~~~~g~~~~~~e~~~~~~g~~~L~SD~~L~~D~~ 244 (328)
T cd00692 165 DELVALLAAHSVAAQDFVDPSIAGTPFDSTPGVFDTQFFIETLLKGTAFPGSGGNQGEVESPLPGEFRLQSDFLLARDPR 244 (328)
T ss_pred HHHhhhcccccccccCCCCCCCCCCCCCCCcchhcHHHHHHHHHcCCCCCCccccccccccCccccccccchHHHhcCCc
Confidence 99999999 10 01 0 1799999999999
Q ss_pred cHHHHHHHhhcCCCCChHHHHHHHHHHHHHHhcCCCCC
Q 031227 107 VSPWVQKYQRSRETVSQTDYEVDLITTFTKLSSLGQQI 144 (163)
Q Consensus 107 t~~~V~~yA~~~~~~~~~~Ff~dFa~AmvKMg~lgv~~ 144 (163)
|+.+|+.||+|| +.|+++|++||+|||+|||+-
T Consensus 245 T~~~v~~fa~dq-----~~f~~~Fa~Am~KLs~lgv~~ 277 (328)
T cd00692 245 TACEWQSFVNNQ-----AKMNAAFAAAMLKLSLLGQDN 277 (328)
T ss_pred HHHHHHHHhcCH-----HHHHHHHHHHHHHHHcCCCCc
Confidence 999999999999 999999999999999999964
No 8
>cd00314 plant_peroxidase_like Heme-dependent peroxidases similar to plant peroxidases. Along with animal peroxidases, these enzymes belong to a group of peroxidases containing a heme prosthetic group (ferriprotoporphyrin IX), which catalyzes a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. The plant peroxidase-like superfamily is found in all three kingdoms of life and carries out a variety of biosynthetic and degradative functions. Several sub-families can be identified. Class I includes intracellular peroxidases present in fungi, plants, archaea and bacteria, called catalase-peroxidases, that can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen peroxide. Catalase-peroxidases are typically comprised of two homologous domains that probably arose via a single gene duplication event. Class II includes ligninase and other extracellular fungal peroxidases, while class III is comprised
Probab=99.88 E-value=8.3e-23 Score=170.37 Aligned_cols=122 Identities=25% Similarity=0.452 Sum_probs=99.6
Q ss_pred HhhHHHHHhhC--CCCcccceeeec--------c--CCcccccccccCCCCCCC-----CCCCCCCCCCCcccCHHHHHH
Q 031227 9 QHFWHQPSANV--EGMKRKGAYCTL--------H--MAQMWGLFEKQFGRTDAQ-----EPDPEGRVPQWEKATVQEMKD 71 (163)
Q Consensus 9 ~~~~~~~~~~c--~g~vsca~~la~--------g--~~~~w~v~~v~~GRrDg~-----~s~~~~~LP~~p~~~~~~L~~ 71 (163)
..+++.+.++. +++||||++++. . .++ .|+|++||+|++ .+.|.+++|. |+.+++++++
T Consensus 64 ~~~l~~ik~~~~~~~~vS~ADlialAa~~Av~~~~~ggp---~~~~~~GR~D~~~~~~~~p~P~~~~p~-~~~~~~~~~~ 139 (255)
T cd00314 64 LRALEPIKSAYDGGNPVSRADLIALAGAVAVESTFGGGP---LIPFRFGRLDATEPDLGVPDPEGLLPN-ETSSATELRD 139 (255)
T ss_pred HHHHHHHHHHcCCCCcccHHHHHHHHHHHHHHHhccCCC---eeeeCCCCCCCchhhccCCCCCCCCCC-ccchHHHHHH
Confidence 34566666665 489999966642 2 333 345599999999 4566788999 9999999999
Q ss_pred HHHhCCCChhcceeee-c---C-C-----------------CC--------------C-----------------CchhH
Q 031227 72 KFSAIGLGPRQLAVMS-A---F-L-----------------GP--------------D-----------------QAATE 98 (163)
Q Consensus 72 ~F~~kGL~~~DlVaLs-G---F-~-----------------~p--------------D-----------------~L~SD 98 (163)
.|.++||+++|||||+ | + + +| . .|+||
T Consensus 140 ~F~~~Gl~~~e~VAL~~GaHti~G~~~~~~~~~~~~~~~~~tp~~fDN~yy~~l~~~~~~~~~~~~~~~~~~~~~~l~sD 219 (255)
T cd00314 140 KFKRMGLSPSELVALSAGAHTLGGKNHGDLLNYEGSGLWTSTPFTFDNAYFKNLLDMNWEWRVGSPDPDGVKGPGLLPSD 219 (255)
T ss_pred HHHHcCCCHHHHHhhccCCeeccCcccCCCCCcccCCCCCCCCCccchHHHHHHhcCCcccccCCccCCCcccCCCchhh
Confidence 9999999999999999 4 2 1 01 1 37999
Q ss_pred HHhccCCCcHHHHHHHhhcCCCCChHHHHHHHHHHHHHHhc
Q 031227 99 ALLATDKDVSPWVQKYQRSRETVSQTDYEVDLITTFTKLSS 139 (163)
Q Consensus 99 q~L~~D~~t~~~V~~yA~~~~~~~~~~Ff~dFa~AmvKMg~ 139 (163)
++|+.|++|+.+|+.||.|+ +.|+++|++||+||++
T Consensus 220 ~~L~~d~~t~~~v~~ya~~~-----~~f~~~Fa~a~~Km~~ 255 (255)
T cd00314 220 YALLSDSETRALVERYASDQ-----EKFFEDFAKAWIKMVN 255 (255)
T ss_pred HHHhcCHhHHHHHHHHHhCH-----HHHHHHHHHHHHHHcC
Confidence 99999999999999999999 9999999999999985
No 9
>PF00141 peroxidase: Peroxidase; InterPro: IPR002016 Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. Most haem peroxidases follow the reaction scheme: Fe3+ + H2O2 --> [Fe4+=O]R' (Compound I) + H2O [Fe4+=O]R' + substrate --> [Fe4+=O]R (Compound II) + oxidised substrate [Fe4+=O]R + substrate --> Fe3+ + H2O + oxidised substrate In this mechanism, the enzyme reacts with one equivalent of H2O2 to give [Fe4+=O]R' (compound I). This is a two-electron oxidation/reduction reaction where H2O2 is reduced to water and the enzyme is oxidised. One oxidising equivalent resides on iron, giving the oxyferryl [] intermediate, while in many peroxidases the porphyrin (R) is oxidised to the porphyrin pi-cation radical (R'). Compound I then oxidises an organic substrate to give a substrate radical []. Haem peroxidases include two superfamilies: one found in bacteria, fungi, plants and the second found in animals. The first one can be viewed as consisting of 3 major classes []. Class I, the intracellular peroxidases, includes: yeast cytochrome c peroxidase (CCP), a soluble protein found in the mitochondrial electron transport chain, where it probably protects against toxic peroxides; ascorbate peroxidase (AP), the main enzyme responsible for hydrogen peroxide removal in chloroplasts and cytosol of higher plants; and bacterial catalase- peroxidases, exhibiting both peroxidase and catalase activities. It is thought that catalase-peroxidase provides protection to cells under oxidative stress []. Class II consists of secretory fungal peroxidases: ligninases, or lignin peroxidases (LiPs), and manganese-dependent peroxidases (MnPs). These are monomeric glycoproteins involved in the degradation of lignin. In MnP, Mn2+ serves as the reducing substrate []. Class II proteins contain four conserved disulphide bridges and two conserved calcium-binding sites. Class III consists of the secretory plant peroxidases, which have multiple tissue-specific functions: e.g., removal of hydrogen peroxide from chloroplasts and cytosol; oxidation of toxic compounds; biosynthesis of the cell wall; defence responses towards wounding; indole-3-acetic acid (IAA) catabolism; ethylene biosynthesis; and so on. Class III proteins are also monomeric glycoproteins, containing four conserved disulphide bridges and two calcium ions, although the placement of the disulphides differs from class II enzymes. The crystal structures of a number of these proteins show that they share the same architecture - two all-alpha domains between which the haem group is embedded. ; GO: 0004601 peroxidase activity, 0020037 heme binding, 0006979 response to oxidative stress, 0055114 oxidation-reduction process; PDB: 1QPA_B 2DV2_A 2B2R_B 1MWV_B 2FXJ_A 2FXG_A 2B2O_B 1X7U_B 2B2Q_A 2FXH_A ....
Probab=99.84 E-value=1.3e-22 Score=168.37 Aligned_cols=101 Identities=21% Similarity=0.390 Sum_probs=78.2
Q ss_pred HHHHhh-CCCCcccceeeec--------cCCcccccccccCCCCCCCCCCCCC--CCCCCcccCHHHHHHHHHhCCCChh
Q 031227 13 HQPSAN-VEGMKRKGAYCTL--------HMAQMWGLFEKQFGRTDAQEPDPEG--RVPQWEKATVQEMKDKFSAIGLGPR 81 (163)
Q Consensus 13 ~~~~~~-c~g~vsca~~la~--------g~~~~w~v~~v~~GRrDg~~s~~~~--~LP~~p~~~~~~L~~~F~~kGL~~~ 81 (163)
|+.+++ ||++||||++++. ..||.|+| ++||+|+++|++.+ +||+ |+.++++|++.|+++|||++
T Consensus 63 k~~~~~~cp~~VS~ADiialAa~~av~~~GGP~~~v---~~GR~D~~~s~~~~~~~lP~-p~~~~~~l~~~F~~~Gls~~ 138 (230)
T PF00141_consen 63 KAKLEAACPGVVSCADIIALAARDAVELCGGPRIPV---PLGRRDGTVSSPSGASNLPS-PTDSVDQLLAFFARKGLSAE 138 (230)
T ss_dssp HHHHCHHSTTTS-HHHHHHHHHHHHHHHTTGGHSHB---EB-EBB-SSGGHHHHHHSST-TTSHHHHHHHHHHHTT--HH
T ss_pred HhhhcccccCCCCHHHHHHHHhhhcccccccccccc---cccccccccccccccccccc-cccccchhhhhhhccccchh
Confidence 444544 9999999966653 12334555 99999999998764 5999 99999999999999999999
Q ss_pred cceeeec-----------CC------------------------------CC---C------------CchhHHHhccCC
Q 031227 82 QLAVMSA-----------FL------------------------------GP---D------------QAATEALLATDK 105 (163)
Q Consensus 82 DlVaLsG-----------F~------------------------------~p---D------------~L~SDq~L~~D~ 105 (163)
|||+||| |. +| | .|+||++|+.|+
T Consensus 139 e~VaLsGaHTiG~~~c~~f~rl~~~~dp~~d~~~~~~~C~~~~~~~~~~dtp~~fDN~Yy~~ll~~~gll~SD~~L~~d~ 218 (230)
T PF00141_consen 139 EMVALSGAHTIGRAHCSSFSRLYFPPDPTMDPGYAGQNCNSGGDNGVPLDTPTVFDNSYYKNLLNGRGLLPSDQALLNDP 218 (230)
T ss_dssp HHHHHHGGGGSTEESGGCTGGTSCSSGTTSTHHHHHHSSSTSGCTCEESSSTTS-SSHHHHHHHHTEEEEHHHHHHHHST
T ss_pred hhcceecccccccceeccccccccccccccccccceeccCCCccccccccCCCcchhHHHHHHhcCCCcCHHHHHHhcCH
Confidence 9999999 21 13 2 389999999999
Q ss_pred CcHHHHHHHhhc
Q 031227 106 DVSPWVQKYQRS 117 (163)
Q Consensus 106 ~t~~~V~~yA~~ 117 (163)
+|+.+|+.||+|
T Consensus 219 ~t~~~V~~yA~d 230 (230)
T PF00141_consen 219 ETRPIVERYAQD 230 (230)
T ss_dssp THHHHHHHHHHT
T ss_pred HHHHHHHHHhcC
Confidence 999999999975
No 10
>TIGR00198 cat_per_HPI catalase/peroxidase HPI. Note that the translation PID:g296476 from accession X71420 from Rhodobacter capsulatus B10 contains extensive frameshift differences from the rest of the orthologous family.
Probab=99.82 E-value=3.5e-20 Score=173.86 Aligned_cols=135 Identities=19% Similarity=0.296 Sum_probs=104.9
Q ss_pred hhHHHHHhhCCCCcccceeeec--------cCCcccccccccCCCCCCCCCC----------------------------
Q 031227 10 HFWHQPSANVEGMKRKGAYCTL--------HMAQMWGLFEKQFGRTDAQEPD---------------------------- 53 (163)
Q Consensus 10 ~~~~~~~~~c~g~vsca~~la~--------g~~~~w~v~~v~~GRrDg~~s~---------------------------- 53 (163)
.+...+.++||++||||++++. -.+ |.|+|.+||+|+..+.
T Consensus 127 ~lL~pIk~kyp~~VS~ADLivLAG~vAVE~~Gg---p~i~f~~GR~D~~~~~~d~~~g~e~~~l~~~~~~~~~l~~p~a~ 203 (716)
T TIGR00198 127 RLLWPIKKKYGNKLSWADLIILAGTVAYESMGL---KVFGFAGGREDIWEPDKDIYWGAEKEWLTSSREDRESLENPLAA 203 (716)
T ss_pred HHHHHHHHHCCCceeHHHHHHHHHHHHHHHhCC---CccCCCCCCCCCCCcccccccccccchhhccccccccccccchh
Confidence 4667788889999999955542 112 2355599999994221
Q ss_pred ---------CCC--CCCCCcccCHHHHHHHHHhCCCChhcceeee-c---CC----------------------------
Q 031227 54 ---------PEG--RVPQWEKATVQEMKDKFSAIGLGPRQLAVMS-A---FL---------------------------- 90 (163)
Q Consensus 54 ---------~~~--~LP~~p~~~~~~L~~~F~~kGL~~~DlVaLs-G---F~---------------------------- 90 (163)
+++ .||+ |..++++|++.|+++|||.+|||||+ | |+
T Consensus 204 ~~~Gliyvnpeg~~~lPd-P~~sa~~Lrd~F~rmGLnd~EmVALiaGaHTiGkaHc~s~~~rlg~dP~~~~~~~~gLg~~ 282 (716)
T TIGR00198 204 TEMGLIYVNPEGPDGHPD-PLCTAQDIRTTFARMGMNDEETVALIAGGHTVGKCHGAGPAELIGPDPEGAPIEEQGLGWH 282 (716)
T ss_pred hhccccccCcccccCCCC-CCCCHHHHHHHHHHcCCChHHHeeeecCceeccccCCCcccccCCCCCCcCHHHHHHhccc
Confidence 222 6999 99999999999999999999999996 4 00
Q ss_pred -----------------C-------------------------------------------CC-----------CchhHH
Q 031227 91 -----------------G-------------------------------------------PD-----------QAATEA 99 (163)
Q Consensus 91 -----------------~-------------------------------------------pD-----------~L~SDq 99 (163)
+ || +|+||+
T Consensus 283 c~~~~g~g~dt~~sglDG~wT~TP~~FDN~YF~nLl~~~w~~~~s~~g~~q~~~~~~~~~~p~~~~~~~~~~~~mL~SDl 362 (716)
T TIGR00198 283 NQYGKGVGRDTMTSGLEVAWTTTPTQWDNGYFYMLFNYEWELKKSPAGAWQWEAVDAPEIIPDVEDPNKKHNPIMLDADL 362 (716)
T ss_pred CCCCCCCCCCcccccCCCCCCCCCCccchHHHHHHhcCCceeeecCCCCceeeecccccccccccccccccccCccchhH
Confidence 0 00 279999
Q ss_pred HhccCCCcHHHHHHHhhcCCCCChHHHHHHHHHHHHHHh--cCCCCCCCCCccCCc
Q 031227 100 LLATDKDVSPWVQKYQRSRETVSQTDYEVDLITTFTKLS--SLGQQINYEAYTYPA 153 (163)
Q Consensus 100 ~L~~D~~t~~~V~~yA~~~~~~~~~~Ff~dFa~AmvKMg--~lgv~~~~~~y~~~~ 153 (163)
+|..|++++.+|+.||.|+ +.|+++|++||+||+ .+|++-.+....-|+
T Consensus 363 aL~~Dp~~r~iVe~yA~d~-----~~F~~dFA~Aw~KL~~~d~gp~~~y~g~~vp~ 413 (716)
T TIGR00198 363 ALRFDPEFRKISRRFLREP-----DYFAEAFAKAWFKLTHRDMGPKSRYIGPDVPQ 413 (716)
T ss_pred HhccCccHHHHHHHHhcCH-----HHHHHHHHHHHHHHcccccCchhhhcCCCCCc
Confidence 9999999999999999999 999999999999999 477655555544443
No 11
>cd00649 catalase_peroxidase_1 N-terminal catalytic domain of catalase-peroxidases. This is a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Catalase-peroxidases can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen peroxide. These enzymes are found in many archaeal and bacterial organisms, where they neutralize potentially lethal hydrogen peroxide molecules generated during photosynthesis or stationary phase. Along with related intracellular fungal and plant peroxidases, catalase-peroxidases belong to class I of the plant peroxidase superfamily. Unlike the eukaryotic enzymes, they are typically comprised of two homologous domains that probably arose via a single gene duplication event. The heme binding motif is present only in the N-terminal domain; the function of the C
Probab=99.81 E-value=1.1e-19 Score=161.77 Aligned_cols=138 Identities=18% Similarity=0.314 Sum_probs=109.7
Q ss_pred hhHHHHHhhCCCCcccceeee--c-----cCCcccccccccCCCCCCCCCC-----------------------------
Q 031227 10 HFWHQPSANVEGMKRKGAYCT--L-----HMAQMWGLFEKQFGRTDAQEPD----------------------------- 53 (163)
Q Consensus 10 ~~~~~~~~~c~g~vsca~~la--~-----g~~~~w~v~~v~~GRrDg~~s~----------------------------- 53 (163)
.+...+.++.+.-||+|+.++ | ..| -+.|++..||.|...+.
T Consensus 117 ~~L~pik~k~~~~iS~ADL~~LaG~~AiE~~G--gp~ipf~~GR~Da~~~~~~v~wg~~~~~~~~~~~~~~~~l~~pl~a 194 (409)
T cd00649 117 RLLWPIKQKYGNKISWADLMILAGNVALESMG--FKTFGFAGGREDVWEPDEDVYWGPEKEWLADKRYSGDRDLENPLAA 194 (409)
T ss_pred HHHHHHHHHcCCCccHHHHHHHHHHHHHHHcC--CCcccccCCCCccCCCccccccCcchhcccccccccchhhccchhh
Confidence 466677777887799994433 2 011 14567799999986432
Q ss_pred ---------CCC--CCCCCcccCHHHHHHHHHhCCCChhcceeee-c-----------C---------------------
Q 031227 54 ---------PEG--RVPQWEKATVQEMKDKFSAIGLGPRQLAVMS-A-----------F--------------------- 89 (163)
Q Consensus 54 ---------~~~--~LP~~p~~~~~~L~~~F~~kGL~~~DlVaLs-G-----------F--------------------- 89 (163)
+++ .||+ |+.++++|++.|++||||.+|||||+ | |
T Consensus 195 ~~mgliyv~Pegp~gLPd-P~~sa~~LR~~F~RmGlnd~E~VAL~sGAHTiGkaHc~~~~~rlg~dP~~~~~~~~gLgw~ 273 (409)
T cd00649 195 VQMGLIYVNPEGPDGNPD-PLAAAKDIRETFARMAMNDEETVALIAGGHTFGKTHGAGPASHVGPEPEAAPIEQQGLGWK 273 (409)
T ss_pred hhccccccCCCCCCCCCC-CccCHHHHHHHHHHcCCCHHHHeeeccCCcceeecCcccccccCCCCCCcCHHHHHhhccc
Confidence 333 6999 99999999999999999999999994 6 1
Q ss_pred ----------------C-------------------C--------------------------CC----------C-chh
Q 031227 90 ----------------L-------------------G--------------------------PD----------Q-AAT 97 (163)
Q Consensus 90 ----------------~-------------------~--------------------------pD----------~-L~S 97 (163)
. . || + |+|
T Consensus 274 ~~Cp~g~g~~t~~sglDG~Wt~tP~~FDN~YF~nLl~~eW~~~~~p~g~~Q~~~~~~~~~~~~~d~~~~~~~~~~gmL~S 353 (409)
T cd00649 274 NSYGTGKGKDTITSGLEGAWTPTPTKWDNNYLKNLFGYEWELTKSPAGAWQWVPKNAAGENTVPDAHDPSKKHAPMMLTT 353 (409)
T ss_pred ccCCCCCCCCCccccCCCCCCCCcchhhHHHHHHHHhccceeccCCCCcccccccCccccccCCCccccccccCcccchh
Confidence 0 0 00 2 799
Q ss_pred HHHhccCCCcHHHHHHHhhcCCCCChHHHHHHHHHHHHHH--hcCCCCCCCCCccCCccc
Q 031227 98 EALLATDKDVSPWVQKYQRSRETVSQTDYEVDLITTFTKL--SSLGQQINYEAYTYPAQK 155 (163)
Q Consensus 98 Dq~L~~D~~t~~~V~~yA~~~~~~~~~~Ff~dFa~AmvKM--g~lgv~~~~~~y~~~~~~ 155 (163)
|++|+.|++|+.+|+.||+|+ +.||++|++||+|| +.+|++..+....-|+..
T Consensus 354 D~aL~~Dp~tr~iV~~yA~d~-----~~Ff~dFA~A~~KL~hrdmgp~~~~~g~~~p~~~ 408 (409)
T cd00649 354 DLALRFDPEYEKISRRFLENP-----DEFADAFAKAWFKLTHRDMGPKSRYLGPEVPEED 408 (409)
T ss_pred hHhhhcCccHHHHHHHHhcCH-----HHHHHHHHHHHHHHccccCCchhhhcCCCCCcCc
Confidence 999999999999999999999 99999999999999 689998888877777653
No 12
>PRK15061 catalase/hydroperoxidase HPI(I); Provisional
Probab=99.66 E-value=3.3e-16 Score=146.99 Aligned_cols=56 Identities=14% Similarity=0.298 Sum_probs=49.1
Q ss_pred chhHHHhccCCCcHHHHHHHhhcCCCCChHHHHHHHHHHHHHHhc--CCCCCCCCCccCCccc
Q 031227 95 AATEALLATDKDVSPWVQKYQRSRETVSQTDYEVDLITTFTKLSS--LGQQINYEAYTYPAQK 155 (163)
Q Consensus 95 L~SDq~L~~D~~t~~~V~~yA~~~~~~~~~~Ff~dFa~AmvKMg~--lgv~~~~~~y~~~~~~ 155 (163)
|+||++|..||+++.+|++||.|+ +.|+++|++||+||.. +|++-.+.....|+..
T Consensus 364 LtSD~AL~~DP~~r~iV~~fA~d~-----~~F~~~FA~A~~KL~hrdmgp~~ry~g~~vp~e~ 421 (726)
T PRK15061 364 LTTDLALRFDPEYEKISRRFLENP-----EEFADAFARAWFKLTHRDMGPKSRYLGPEVPKED 421 (726)
T ss_pred ccccHHhhcCCcHHHHHHHHhcCH-----HHHHHHHHHHHHHHcccCCCchhhhcCCCCCccc
Confidence 799999999999999999999999 9999999999999955 7877777776666544
No 13
>cd08200 catalase_peroxidase_2 C-terminal non-catalytic domain of catalase-peroxidases. This is a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Catalase-peroxidases can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen peroxide. These enzymes are found in many archaeal and bacterial organisms where they neutralize potentially lethal hydrogen peroxide molecules generated during photosynthesis or stationary phase. Along with related intracellular fungal and plant peroxidases, catalase-peroxidases belong to plant peroxidase superfamily. Unlike the eukaryotic enzymes, they are typically comprised of two homologous domains that probably arose via a single gene duplication event. The heme binding motif is present only in the N-terminal domain; the function of the C-terminal do
Probab=99.52 E-value=1.5e-14 Score=124.48 Aligned_cols=98 Identities=18% Similarity=0.335 Sum_probs=78.1
Q ss_pred ccccccCCCCCCCCCCCC-----CCCCCCcc------------cCHHHHHHHHHhCCCChhcceeeec------------
Q 031227 38 GLFEKQFGRTDAQEPDPE-----GRVPQWEK------------ATVQEMKDKFSAIGLGPRQLAVMSA------------ 88 (163)
Q Consensus 38 ~v~~v~~GRrDg~~s~~~-----~~LP~~p~------------~~~~~L~~~F~~kGL~~~DlVaLsG------------ 88 (163)
+.|++..||.|.+.+... ..+|. +. ...++|++.|.++|||+.|||||+|
T Consensus 123 p~Ipf~pGR~Da~~~~td~~sf~~l~P~-adg~rny~~~~~~~~~~~~Lrd~f~rlglsd~EmvaL~Gg~r~lG~~~~~s 201 (297)
T cd08200 123 IKVPFTPGRTDATQEQTDVESFEVLEPK-ADGFRNYLKKGYRVPPEEMLVDKAQLLTLTAPEMTVLVGGLRVLGANYGGS 201 (297)
T ss_pred ceeccCCCCCCcccCCCCcccccccCCC-CcccccccccCCCCCHHHHHHHHHHhCCCChHHHhheecchhhcccCCCCC
Confidence 356779999999865321 23453 21 2457899999999999999999999
Q ss_pred ----CC-C--------------------C-----------C---------CchhHHHhccCCCcHHHHHHHhhc--CCCC
Q 031227 89 ----FL-G--------------------P-----------D---------QAATEALLATDKDVSPWVQKYQRS--RETV 121 (163)
Q Consensus 89 ----F~-~--------------------p-----------D---------~L~SDq~L~~D~~t~~~V~~yA~~--~~~~ 121 (163)
|. . | | .+++|.+|.+|+..|.+|+.||.| +
T Consensus 202 ~~G~wT~~p~~f~N~fF~nLLd~~~~W~~~~~~~~~~~~~dr~~g~~~~~~t~~Dl~l~sd~~~R~~ve~YA~dd~~--- 278 (297)
T cd08200 202 KHGVFTDRPGVLTNDFFVNLLDMSTEWKPADEDDGLFEGRDRKTGEVKWTATRVDLVFGSNSELRAVAEVYASDDAQ--- 278 (297)
T ss_pred CCCCCcCCCCccccHHHHHHhcccceeeecCCCCCceeeccCCCCceeeccChhhhhhccCHHHHHHHHHHhcccch---
Confidence 00 0 0 1 268999999999999999999998 7
Q ss_pred ChHHHHHHHHHHHHHHhcCC
Q 031227 122 SQTDYEVDLITTFTKLSSLG 141 (163)
Q Consensus 122 ~~~~Ff~dFa~AmvKMg~lg 141 (163)
+.||+||++|+.||.++.
T Consensus 279 --~~F~~DF~~A~~Klmeld 296 (297)
T cd08200 279 --EKFVKDFVAAWTKVMNLD 296 (297)
T ss_pred --hHHHHHHHHHHHHHHhcC
Confidence 999999999999999874
No 14
>cd08201 plant_peroxidase_like_1 Uncharacterized family of plant peroxidase-like proteins. This is a subgroup of heme-dependent peroxidases similar to plant peroxidases. Along with animal peroxidases, these enzymes belong to a group of peroxidases containing a heme prosthetic group (ferriprotoporphyrin IX) which catalyzes a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. The plant peroxidase-like superfamily is found in all three kingdoms of life and carries out a variety of biosynthetic and degradative functions.
Probab=99.43 E-value=6.8e-14 Score=118.92 Aligned_cols=62 Identities=18% Similarity=0.325 Sum_probs=53.1
Q ss_pred Ccccceeeec--------cCCcccccccccCCCCCCCCCCCCCCCCCCcccCHHHHHHHHHhCCCChhcceeeec
Q 031227 22 MKRKGAYCTL--------HMAQMWGLFEKQFGRTDAQEPDPEGRVPQWEKATVQEMKDKFSAIGLGPRQLAVMSA 88 (163)
Q Consensus 22 ~vsca~~la~--------g~~~~w~v~~v~~GRrDg~~s~~~~~LP~~p~~~~~~L~~~F~~kGL~~~DlVaLsG 88 (163)
.||||++++. -+||.|++ ++||+|++++.+.+ ||. |+.++++|++.|+++||+++|||+|||
T Consensus 97 ~VScADiialAa~~AV~~~GGP~i~v---~~GR~Da~~s~~~g-lP~-P~~~v~~l~~~Fa~~Gfs~~DmVaLsg 166 (264)
T cd08201 97 RSSMADLIAMGVVTSVASCGGPVVPF---RAGRIDATEAGQAG-VPE-PQTDLGTTTESFRRQGFSTSEMIALVA 166 (264)
T ss_pred ccCHHHHHHHHHHHHHHHcCCCeecc---cccCCCcccccccc-CCC-CccCHHHHHHHHHHcCCChHHHheeec
Confidence 6999966642 23344555 99999999998886 999 999999999999999999999999994
No 15
>PRK15061 catalase/hydroperoxidase HPI(I); Provisional
Probab=99.26 E-value=6.7e-12 Score=118.30 Aligned_cols=97 Identities=19% Similarity=0.360 Sum_probs=78.1
Q ss_pred cccccCCCCCCCCCCCC-----CCCCCCcc------------cCHHHHHHHHHhCCCChhcceeeec-------------
Q 031227 39 LFEKQFGRTDAQEPDPE-----GRVPQWEK------------ATVQEMKDKFSAIGLGPRQLAVMSA------------- 88 (163)
Q Consensus 39 v~~v~~GRrDg~~s~~~-----~~LP~~p~------------~~~~~L~~~F~~kGL~~~DlVaLsG------------- 88 (163)
.|++..||.|.+....+ .++|. .. ...+.|+++|.++|||+.|||||+|
T Consensus 549 ~VPf~pGR~Da~~~~td~esf~~l~P~-Adgfrny~~~~~~~~~e~~L~d~a~~lglt~~EmvaL~Gg~r~Lg~~~~~S~ 627 (726)
T PRK15061 549 TVPFTPGRTDATQEQTDVESFAVLEPK-ADGFRNYLKKGYSVSPEELLVDKAQLLTLTAPEMTVLVGGLRVLGANYGGSK 627 (726)
T ss_pred ccCcCCCCCCcccCCCCcccccccCCC-CccccccccccCCCCHHHHHHHHHHhCCCChHHHhheecchhhcccCCCCCC
Confidence 35669999999865322 24565 32 2348999999999999999999999
Q ss_pred ---CC-C--------------------C-----------C---------CchhHHHhccCCCcHHHHHHHhhc--CCCCC
Q 031227 89 ---FL-G--------------------P-----------D---------QAATEALLATDKDVSPWVQKYQRS--RETVS 122 (163)
Q Consensus 89 ---F~-~--------------------p-----------D---------~L~SDq~L~~D~~t~~~V~~yA~~--~~~~~ 122 (163)
|. . + | ++++|.+|.+|+..|.+|+.||.| +
T Consensus 628 ~G~~T~~p~~fsNdfFvnLLdm~~~W~~~~~~~~~ye~~Dr~tg~~~~~~t~~Dlvfgsds~lRa~aEvYA~dd~~---- 703 (726)
T PRK15061 628 HGVFTDRPGVLTNDFFVNLLDMGTEWKPTDEDEEVYEGRDRKTGEVKWTATRVDLVFGSNSQLRALAEVYASDDAK---- 703 (726)
T ss_pred CCCCcCCCCccccHHHHHHhcCCceeeecCCCCCceeeccCCCcceeeccChhheecccCHHHHHHHHHHhcccch----
Confidence 10 0 0 1 258899999999999999999998 7
Q ss_pred hHHHHHHHHHHHHHHhcCC
Q 031227 123 QTDYEVDLITTFTKLSSLG 141 (163)
Q Consensus 123 ~~~Ff~dFa~AmvKMg~lg 141 (163)
+.|++||++|+.|+.+++
T Consensus 704 -~kF~~DF~~Aw~Kvmeld 721 (726)
T PRK15061 704 -EKFVRDFVAAWTKVMNLD 721 (726)
T ss_pred -hHHHHHHHHHHHHHHhCC
Confidence 999999999999999987
No 16
>TIGR00198 cat_per_HPI catalase/peroxidase HPI. Note that the translation PID:g296476 from accession X71420 from Rhodobacter capsulatus B10 contains extensive frameshift differences from the rest of the orthologous family.
Probab=99.17 E-value=2.8e-11 Score=114.30 Aligned_cols=100 Identities=17% Similarity=0.272 Sum_probs=77.0
Q ss_pred ccccCCCCCCCCCC--CCCCCCCC--------------cccCHHHHHHHHHhCCCChhcceeeec-C---C--------C
Q 031227 40 FEKQFGRTDAQEPD--PEGRVPQW--------------EKATVQEMKDKFSAIGLGPRQLAVMSA-F---L--------G 91 (163)
Q Consensus 40 ~~v~~GRrDg~~s~--~~~~LP~~--------------p~~~~~~L~~~F~~kGL~~~DlVaLsG-F---~--------~ 91 (163)
|++..||.|.+... ++..+|.- .....+.|+++|.++|||+.|||||+| . + +
T Consensus 538 Vpf~pGR~Da~~~~td~~~~~~l~p~adgfRn~~~~~~~~~~~~~l~d~a~~lglt~~EmvaL~Gg~r~lG~~~~~s~~G 617 (716)
T TIGR00198 538 VPFLPGRVDATQAMTDAESFTPLEPIADGFRNYLKRDYAVTPEELLLDKAQLLTLTAPEMTVLIGGMRVLGANHGGSKHG 617 (716)
T ss_pred cCcCCCCCccccCCCCccccccCCCCCcccchhccccccCCHHHHHHHHHHhCCCChHHHHheecchhhccccCCCCCCC
Confidence 46699999998653 22222210 223457799999999999999999999 1 0 0
Q ss_pred -------------------------C-----------C---------CchhHHHhccCCCcHHHHHHHhhcCCCCChHHH
Q 031227 92 -------------------------P-----------D---------QAATEALLATDKDVSPWVQKYQRSRETVSQTDY 126 (163)
Q Consensus 92 -------------------------p-----------D---------~L~SDq~L~~D~~t~~~V~~yA~~~~~~~~~~F 126 (163)
+ | +.++|.+|.+|+..|.+|+.||.|+ .++.|
T Consensus 618 ~~T~~p~~f~NdfF~~LLd~~~~w~~~~~~~~~~~~~dr~tg~~~~~~t~~Dl~~~sd~~lra~aE~YA~dd---~~~~F 694 (716)
T TIGR00198 618 VFTDRVGVLSNDFFVNLLDMAYEWRAADNNRYLFEGGDRQTGEVKWTATRVDLVFGSNSILRAVAEVYAQDD---AREKF 694 (716)
T ss_pred CCcCCCCccccHHHHHHhcCCceeeecCCCCceeeeecCCCCceeeccChhheeeccCHHHHHHHHHHhccc---ccchH
Confidence 0 1 1378999999999999999999986 23799
Q ss_pred HHHHHHHHHHHhcCCC
Q 031227 127 EVDLITTFTKLSSLGQ 142 (163)
Q Consensus 127 f~dFa~AmvKMg~lgv 142 (163)
++||++|+.|+.+++-
T Consensus 695 ~~DF~~Aw~Klm~ldr 710 (716)
T TIGR00198 695 VKDFVAAWTKVMNLDR 710 (716)
T ss_pred HHHHHHHHHHHHhCCC
Confidence 9999999999999874
No 17
>COG0376 KatG Catalase (peroxidase I) [Inorganic ion transport and metabolism]
Probab=98.43 E-value=8.5e-07 Score=82.15 Aligned_cols=138 Identities=19% Similarity=0.334 Sum_probs=102.7
Q ss_pred hHHhhHHHHHhhCCCCcccceee--ecc-----CCcccccccccCCCCCCCCCCC-------------------------
Q 031227 7 LRQHFWHQPSANVEGMKRKGAYC--TLH-----MAQMWGLFEKQFGRTDAQEPDP------------------------- 54 (163)
Q Consensus 7 ~~~~~~~~~~~~c~g~vsca~~l--a~g-----~~~~w~v~~v~~GRrDg~~s~~------------------------- 54 (163)
+||-.| -+..+-|.-+|-|+.+ +|. +| .+.|.+..||.|-..+..
T Consensus 140 arRLLW-PIKkKYG~kiSWaDL~iLaGnvAlEsMG--fktfGFa~GR~D~wepd~dvyWG~e~~wl~d~Ry~~~~~Le~P 216 (730)
T COG0376 140 ARRLLW-PIKKKYGRKISWADLIILAGNVALESMG--FKTFGFAGGREDVWEPDEDVYWGSEKTWLGDERYSGDRDLENP 216 (730)
T ss_pred HHHHhh-hHhHhhcccccHhHhhhhhchhhhhhcC--CccccccCCCCcCCCCccccccCccccccccccccccccccCc
Confidence 344333 4556688889988443 331 11 456677889988543322
Q ss_pred -------------C--CCCCCCcccCHHHHHHHHHhCCCChhcceeeec----CC-------------------------
Q 031227 55 -------------E--GRVPQWEKATVQEMKDKFSAIGLGPRQLAVMSA----FL------------------------- 90 (163)
Q Consensus 55 -------------~--~~LP~~p~~~~~~L~~~F~~kGL~~~DlVaLsG----F~------------------------- 90 (163)
+ +..|+ |-.+..+++..|+++++|.+|.|||.+ |+
T Consensus 217 laavqMGLIYVNPEGpng~PD-pl~aA~dIRetFaRMaMNDeETVALiaGGHtfGKtHGag~a~~vg~ePe~a~ie~qGl 295 (730)
T COG0376 217 LAAVQMGLIYVNPEGPNGNPD-PLAAARDIRETFARMAMNDEETVALIAGGHTFGKTHGAGPASNVGPEPEAAPIEQQGL 295 (730)
T ss_pred hhhheeeeEEeCCCCCCCCCC-hhhhHHHHHHHHHHhcCCcHhhhhhhhcccccccccCCCchhhcCCCccccchhhhcc
Confidence 3 35888 999999999999999999999999996 21
Q ss_pred -----------------------------------------------C-----------------CC-----------Cc
Q 031227 91 -----------------------------------------------G-----------------PD-----------QA 95 (163)
Q Consensus 91 -----------------------------------------------~-----------------pD-----------~L 95 (163)
+ || +|
T Consensus 296 GW~~~~g~G~G~dtitsGlE~~Wt~tPT~w~n~ff~~Lf~yEWeltksPAGa~Qw~~k~~~~~~~pd~~dp~~~~~p~Ml 375 (730)
T COG0376 296 GWANTYGSGKGPDTITSGLEGAWTTTPTQWSNEFFENLFNYEWELTKSPAGAWQWDAKSAAAETIPDAHDPSKKHGPMML 375 (730)
T ss_pred ccccccCCCcCcccccccccccCCCCcchhhhHHHHHHhccceeeecCCCccccccccCccccCCCCCCCcccccCceee
Confidence 0 01 48
Q ss_pred hhHHHhccCCCcHHHHHHHhhcCCCCChHHHHHHHHHHHHHHhc--CCCCCCCCCccCCc
Q 031227 96 ATEALLATDKDVSPWVQKYQRSRETVSQTDYEVDLITTFTKLSS--LGQQINYEAYTYPA 153 (163)
Q Consensus 96 ~SDq~L~~D~~t~~~V~~yA~~~~~~~~~~Ff~dFa~AmvKMg~--lgv~~~~~~y~~~~ 153 (163)
++|.+|-.||..+.+.++|..|+ +.|...|+.|.-||.. +|.+-.+....-|+
T Consensus 376 ttDlaLr~DP~Y~kIs~rf~e~p-----d~F~~~FArAWfKLtHRDMGP~~rylGp~VP~ 430 (730)
T COG0376 376 TTDLALRFDPEYEKISRRFLEDP-----DEFADAFARAWFKLTHRDMGPKARYLGPEVPK 430 (730)
T ss_pred ccchhhhcChHHHHHHHHHHhCH-----HHHHHHHHHHHHHHhhccCCchhhccCCCCch
Confidence 99999999999999999999999 9999999999999987 55555555554443
No 18
>COG0376 KatG Catalase (peroxidase I) [Inorganic ion transport and metabolism]
Probab=89.65 E-value=0.53 Score=44.60 Aligned_cols=98 Identities=19% Similarity=0.391 Sum_probs=66.2
Q ss_pred ccccCCCCCCCCCC------------CCC--C-C-CCCcccCHHHHHHHHHhCCCChhcceeeec---------------
Q 031227 40 FEKQFGRTDAQEPD------------PEG--R-V-PQWEKATVQEMKDKFSAIGLGPRQLAVMSA--------------- 88 (163)
Q Consensus 40 ~~v~~GRrDg~~s~------------~~~--~-L-P~~p~~~~~~L~~~F~~kGL~~~DlVaLsG--------------- 88 (163)
+|+..||.|.+..- +++ + + ..+....-.-|+++-.-.+|+.-||.+|.|
T Consensus 554 VPF~pGR~DA~qeqtDv~sf~~LeP~aDGfRNy~~~~~~~~pe~~LvDkAqlL~LtapemtVLiGGlRvLg~n~g~s~~G 633 (730)
T COG0376 554 VPFAPGRTDASQEQTDVESFAVLEPIADGFRNYVKKDYVLTPEELLVDKAQLLTLTAPEMTVLIGGLRVLGANYGGSKHG 633 (730)
T ss_pred eccCCCCcccchhhcchhhhhcccccchhhhhhccCCCcCCHHHHHHHHHHHhccCCccceEEEcceEeeccCCCCCccc
Confidence 36789999986431 111 0 1 111223345678888889999999999998
Q ss_pred -CC-C--------------------C-----------C---------CchhHHHhccCCCcHHHHHHHhhcCCCCChHHH
Q 031227 89 -FL-G--------------------P-----------D---------QAATEALLATDKDVSPWVQKYQRSRETVSQTDY 126 (163)
Q Consensus 89 -F~-~--------------------p-----------D---------~L~SDq~L~~D~~t~~~V~~yA~~~~~~~~~~F 126 (163)
|. . | | +-..|..+-+++..|.+.+-||.+. .++.|
T Consensus 634 VfT~~pg~LtndFFvnLlDM~~~W~~~~~~~~~feg~DrktG~~kwt~trvDLvfGsns~LRA~aEVYa~dd---a~ekF 710 (730)
T COG0376 634 VFTDRPGVLTNDFFVNLLDMGTEWKPTDDARGLFEGRDRKTGEVKWTATRVDLVFGSNSELRALAEVYASDD---AKEKF 710 (730)
T ss_pred eeccCcccccchhhhhhhhccceeeeccccccceeccccccCceEeeeeEEeEEecCcHHHHHHHHHHhccc---hHHHH
Confidence 11 0 0 1 1235555555667788999999865 35999
Q ss_pred HHHHHHHHHHHhcC
Q 031227 127 EVDLITTFTKLSSL 140 (163)
Q Consensus 127 f~dFa~AmvKMg~l 140 (163)
..||++|..|.-++
T Consensus 711 v~DFvaaw~kVMn~ 724 (730)
T COG0376 711 VKDFVAAWTKVMNL 724 (730)
T ss_pred HHHHHHHHHHHhcc
Confidence 99999999998665
No 19
>PF11895 DUF3415: Domain of unknown function (DUF3415); InterPro: IPR024589 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. Fungal ligninases are extracellular haem enzymes involved in the degradation of lignin. They include lignin peroxidases (LiPs), manganese-dependent peroxidases (MnPs) and versatile peroxidases, which combine the substrate-specificity characteristics of the other two []. In MnP, Mn2+ serves as the reducing substrate []. It is commonly thought that the plant polymer lignin is the second most abundant organic compound on Earth, exceeded only by cellulose. Higher plants synthesise vast quantities of insoluble macromolecules, including lignins. Lignin is an amorphous three-dimensional aromatic biopolymer composed of oxyphenylpropane units. Biodegradation of lignins is slow - it is probable that their decomposition is the rate-limiting step in the biospheric carbon-oxygen cycle, which is mediated almost entirely by the catabolic activities of microorganisms. The white-rot fungi are able extensively to decompose all the important structural components of wood, including both cellulose and lignin. Under the proper environmental conditions, white-rot fungi completely degrade all structural components of lignin, with ultimate formation of CO2 and H2O. The first step in lignin degradation is depolymerisation, catalysed by the LiPs (ligninases). LiPs are secreted, along with hydrogen peroxide (H2O2), by white-rot fungi under conditions of nutrient limitation. The enzymes are not only important in lignin biodegradation, but are also potentially valuable in chemical waste disposal because of their ability to degrade environmental pollutants []. To date, 3D structures have been determined for LiP [] and MnP [] from Phanerochaete chrysosporium (White-rot fungus), and for the fungal peroxidase from Arthromyces ramosus []. All these proteins share the same architecture and consist of 2 all-alpha domains, between which is embedded the haem group. The helical topography of LiPs is nearly identical to that of yeast cytochrome c peroxidase (CCP) [], despite the former having 4 disulphide bonds, which are absent in CCP (MnP has an additional disulphide bond at the C terminus). This uncharacterised C-terminal domain is found in fungal ligninases. It is about 80 amino acids in length and associated with Pfam:PF00141.; PDB: 1B85_B 1B82_A 1B80_A 1YYG_A 1YZP_A 1MNP_A 1MN1_A 1YZR_A 1MN2_A 3M8M_A ....
Probab=85.59 E-value=0.67 Score=33.29 Aligned_cols=22 Identities=18% Similarity=0.300 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHhcCCCCCCC
Q 031227 125 DYEVDLITTFTKLSSLGQQINY 146 (163)
Q Consensus 125 ~Ff~dFa~AmvKMg~lgv~~~~ 146 (163)
...+.|..||.||+.||.+.+.
T Consensus 2 ~m~~~F~~am~KlavLG~d~~~ 23 (80)
T PF11895_consen 2 KMQSAFKAAMAKLAVLGHDRSD 23 (80)
T ss_dssp HHHHHHHHHHHHHCTTTS-GGG
T ss_pred hHHHHHHHHHHHHHHhcCChhh
Confidence 3568899999999999987543
No 20
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=39.17 E-value=11 Score=22.98 Aligned_cols=26 Identities=15% Similarity=0.006 Sum_probs=19.2
Q ss_pred HHhhHHHHHhhCCCCcccceeeeccC
Q 031227 8 RQHFWHQPSANVEGMKRKGAYCTLHM 33 (163)
Q Consensus 8 ~~~~~~~~~~~c~g~vsca~~la~g~ 33 (163)
=+++|.++++.|+|.++-|.-..|.+
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~Lgis 31 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLLGIS 31 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHHTS-
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHCCC
Confidence 36889999999999998876655543
No 21
>PHA00435 capsid assembly protein
Probab=26.36 E-value=1e+02 Score=27.11 Aligned_cols=64 Identities=16% Similarity=0.220 Sum_probs=40.9
Q ss_pred HHHHHHHhCCCChhcceeeec-CCCCCCc--hhHHHhccCCCcHHHHHHHhhcCCCCChHHHHHHHHHHHHH
Q 031227 68 EMKDKFSAIGLGPRQLAVMSA-FLGPDQA--ATEALLATDKDVSPWVQKYQRSRETVSQTDYEVDLITTFTK 136 (163)
Q Consensus 68 ~L~~~F~~kGL~~~DlVaLsG-F~~pD~L--~SDq~L~~D~~t~~~V~~yA~~~~~~~~~~Ff~dFa~AmvK 136 (163)
.|+..-..+||+...+..+.- |...++| .|=..|..=.-+|.+|+.|-+.| ++..+.|+.+++-
T Consensus 128 ~mv~~Ave~Glsae~i~~i~aEY~~~g~LSeeSY~~La~AGysR~fVDsYI~GQ-----EAL~eQyV~sv~~ 194 (306)
T PHA00435 128 AMVEQAVERGLSAETITRIQAEYEEEGGLSEESYAELAAAGYSKAFVDSYIRGQ-----EALVEQYVESVVE 194 (306)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHhcCCcCHHHHHHHHHcCCcHHHHHHHHHHH-----HHHHHHHHHHHHH
Confidence 344444455555554333322 2111235 57777887778999999999988 8888888887764
No 22
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=25.64 E-value=26 Score=24.83 Aligned_cols=22 Identities=18% Similarity=0.311 Sum_probs=15.5
Q ss_pred HHHHHHHHhCCCChhcceeeec
Q 031227 67 QEMKDKFSAIGLGPRQLAVMSA 88 (163)
Q Consensus 67 ~~L~~~F~~kGL~~~DlVaLsG 88 (163)
+.|-..|.+.||+..||-.++-
T Consensus 11 DtLs~iF~~~gls~~dl~~v~~ 32 (85)
T PF04225_consen 11 DTLSTIFRRAGLSASDLYAVLE 32 (85)
T ss_dssp --HHHHHHHTT--HHHHHHHHH
T ss_pred CcHHHHHHHcCCCHHHHHHHHh
Confidence 5688899999999999877765
No 23
>PF10518 TAT_signal: TAT (twin-arginine translocation) pathway signal sequence; InterPro: IPR019546 The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []. Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state []. It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases []. In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength []. The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].
Probab=22.22 E-value=61 Score=18.07 Aligned_cols=12 Identities=25% Similarity=0.357 Sum_probs=9.2
Q ss_pred hHHhhHHHHHhh
Q 031227 7 LRQHFWHQPSAN 18 (163)
Q Consensus 7 ~~~~~~~~~~~~ 18 (163)
-||+|+|.....
T Consensus 3 sRR~fLk~~~a~ 14 (26)
T PF10518_consen 3 SRRQFLKGGAAA 14 (26)
T ss_pred cHHHHHHHHHHH
Confidence 499999976554
No 24
>PF09533 DUF2380: Predicted lipoprotein of unknown function (DUF2380); InterPro: IPR011755 This family consists of at least 9 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. One appears truncated toward the N terminus; the others are predicted lipoproteins. The function is unknown.
Probab=20.24 E-value=2.2e+02 Score=23.48 Aligned_cols=23 Identities=13% Similarity=0.283 Sum_probs=19.9
Q ss_pred HHHHHHHHHhCCCChhcceeeec
Q 031227 66 VQEMKDKFSAIGLGPRQLAVMSA 88 (163)
Q Consensus 66 ~~~L~~~F~~kGL~~~DlVaLsG 88 (163)
..+|...|.++|++..|-+.+..
T Consensus 107 a~~la~wF~~~Gi~IHd~ti~Ip 129 (188)
T PF09533_consen 107 AEELAEWFERRGIDIHDYTIPIP 129 (188)
T ss_pred cHHHHHHHHHcCCChhheeEecC
Confidence 46899999999999999887755
Done!