Query psy2586
Match_columns 125
No_of_seqs 114 out of 982
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 19:57:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2586.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2586hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd08155 catalase_clade_2 Clade 100.0 3.6E-41 7.8E-46 290.8 6.7 110 12-122 207-328 (443)
2 cd00328 catalase Catalase heme 100.0 4.5E-41 9.8E-46 289.4 6.8 110 12-122 200-320 (433)
3 cd08156 catalase_clade_3 Clade 100.0 9.3E-41 2E-45 287.2 6.7 110 12-122 200-320 (429)
4 PLN02609 catalase 100.0 1.4E-40 3.1E-45 290.0 6.5 110 12-122 257-377 (492)
5 cd08154 catalase_clade_1 Clade 100.0 6.1E-40 1.3E-44 284.8 6.9 110 12-122 242-362 (469)
6 COG0753 KatE Catalase [Inorgan 100.0 4.2E-39 9.1E-44 279.3 6.5 101 16-122 276-376 (496)
7 KOG0047|consensus 100.0 8.3E-39 1.8E-43 275.4 4.5 102 16-122 284-385 (505)
8 PRK11249 katE hydroperoxidase 100.0 3.5E-38 7.5E-43 285.5 6.8 110 12-122 321-442 (752)
9 cd08157 catalase_fungal Fungal 100.0 3E-37 6.5E-42 266.4 6.1 111 12-122 216-338 (451)
10 PF00199 Catalase: Catalase; 100.0 5E-35 1.1E-39 246.4 1.8 110 12-122 240-360 (384)
11 cd08153 srpA_like Catalase-lik 99.9 8.7E-25 1.9E-29 178.1 5.6 88 12-100 204-295 (295)
12 cd08150 catalase_like Catalase 99.9 1.1E-22 2.3E-27 164.7 4.7 86 12-100 190-283 (283)
13 cd08151 AOS Allene oxide synth 99.8 5.8E-22 1.3E-26 164.3 4.0 87 12-100 227-328 (328)
14 cd08152 y4iL_like Catalase-lik 99.8 2.8E-21 6E-26 158.4 3.3 89 12-101 207-305 (305)
15 TIGR03784 marine_sortase sorta 56.6 14 0.00031 28.6 3.3 46 32-79 38-87 (174)
16 PF12518 DUF3721: Protein of u 37.0 14 0.00031 22.0 0.4 11 1-11 14-24 (34)
17 PF03568 Peptidase_C50: Peptid 32.7 15 0.00033 31.3 0.1 27 1-27 341-367 (383)
18 PF02122 Peptidase_S39: Peptid 22.9 18 0.0004 28.9 -1.0 24 1-24 95-118 (203)
19 PF13605 DUF4141: Domain of un 20.0 14 0.00031 24.2 -1.8 21 66-86 23-43 (55)
No 1
>cd08155 catalase_clade_2 Clade 2 of the heme-binding enzyme catalase. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes, which is involved in the protection of cells from the toxic effects of peroxides. It catalyzes the conversion of hydrogen peroxide to water and molecular oxygen. Catalases also utilize hydrogen peroxide to oxidize various substrates such as alcohol or phenols. Clade 2 catalases are mostly found in bacteria and fungi; they have a large subunit size of 75 to 84 kDa, and bind a heme d group buried deep inside the structure. They appear to form tetramers. In eukaryotic cells, catalases are located in peroxisomes.
Probab=100.00 E-value=3.6e-41 Score=290.79 Aligned_cols=110 Identities=45% Similarity=0.777 Sum_probs=105.6
Q ss_pred cccccCc-ceeecC----CCCCC------CCCCccccCCCCcCcEEeEEEEEccCCCCchhhhhhhhcCCCccCCCcCCC
Q psy2586 12 SRKQQGT-DTFGYN----DKALP------LETGNKVWPHREFPLIEVGQLVLDKNPSNYFAEVEQIAFSPSHLVPGIEPS 80 (125)
Q Consensus 12 ~r~~~gp-~~f~~~----~~gD~------i~DpTk~WP~d~r~~v~lG~LtLnrn~~n~~~e~eqi~FdP~~lv~GIe~S 80 (125)
.|+++|+ .+|++. .+||. ++|+||+||+++||+|++|+||||+|++|+|++|||++|+|++||+||++|
T Consensus 207 ~~I~~G~~p~w~l~vQv~~~~d~~~~~f~~~D~Tk~WP~~~~p~i~~G~l~Ln~np~n~f~e~eq~aF~P~~lvpGI~~S 286 (443)
T cd08155 207 EAIESGDYPEWELGVQLIDEEDEFKFDFDILDPTKLIPEELVPVQRVGKMVLNRNPDNFFAETEQVAFCPANVVPGIDFS 286 (443)
T ss_pred HHHhcCCCceEEEEEEEcCHHHHhcCCCCCCcCCCcCCccccceEEeEEEEEecCCcchhhhhhhhcccCcCCCCCccCC
Confidence 4788999 999988 68998 999999999998999999999999999999999999999999999999999
Q ss_pred CCcccccccccchhhhhhcc-CCCCcccCCCCCCCccccccee
Q psy2586 81 PDKMLQGRLFSYPDTHRHRL-GPNYLQLPVNCPFATKVANYQR 122 (125)
Q Consensus 81 dDPlLq~R~~aYadS~~~Rl-g~n~~~lpvn~p~~~~~~~~~r 122 (125)
+|||||+|+|||+|||+||+ |+||+|||||||+++ |+||+|
T Consensus 287 ~DpmLq~R~faY~ds~r~RlgG~N~~qlPvN~P~~~-v~n~~r 328 (443)
T cd08155 287 NDPLLQGRLFSYLDTQLSRLGGPNFHELPINRPVCP-VHNNQR 328 (443)
T ss_pred CCcccccccccchHhhhccCCCCChhhCccccccCC-cCCCCc
Confidence 99999999999999999999 799999999999987 999987
No 2
>cd00328 catalase Catalase heme-binding enzyme. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes, which is involved in the protection of cells from the toxic effects of peroxides. It catalyzes the conversion of hydrogen peroxide to water and molecular oxygen. Catalases also utilize hydrogen peroxide to oxidize various substrates such as alcohol or phenols. Most catalases exist as tetramers of 65KD subunits containing a protoheme IX group buried deep inside the structure. In eukaryotic cells, catalases are located in peroxisomes.
Probab=100.00 E-value=4.5e-41 Score=289.36 Aligned_cols=110 Identities=53% Similarity=0.838 Sum_probs=106.1
Q ss_pred cccccCcc-eeecC----CCCCC------CCCCccccCCCCcCcEEeEEEEEccCCCCchhhhhhhhcCCCccCCCcCCC
Q psy2586 12 SRKQQGTD-TFGYN----DKALP------LETGNKVWPHREFPLIEVGQLVLDKNPSNYFAEVEQIAFSPSHLVPGIEPS 80 (125)
Q Consensus 12 ~r~~~gp~-~f~~~----~~gD~------i~DpTk~WP~d~r~~v~lG~LtLnrn~~n~~~e~eqi~FdP~~lv~GIe~S 80 (125)
.|+++|+. +|++. .+||. ++|+||+||+++||++++|+||||+|++|+|++|||++|+|++||+||++|
T Consensus 200 ~~i~~G~~P~w~l~vQv~~~~d~~~~~f~~~D~Tk~WP~~~~p~i~vG~l~Ln~n~~n~f~e~eq~aF~P~~lvpGI~~S 279 (433)
T cd00328 200 EAIEAGDYPSWELYIQVMTFNDAEKFPFNPLDPTKVWPEELVPLIVVGKLVLNRNPLNFFAEVEQAAFDPGHIVPGVEFS 279 (433)
T ss_pred HHHhCCCCceEEEEEEEcCHHHHhcCCCCCCcCCcccCCcCcccEEeEEEEeecCCcchhhhhhhhccCCcCCCCCccCC
Confidence 57899999 99988 68998 899999999999999999999999999999999999999999999999999
Q ss_pred CCcccccccccchhhhhhccCCCCcccCCCCCCCccccccee
Q psy2586 81 PDKMLQGRLFSYPDTHRHRLGPNYLQLPVNCPFATKVANYQR 122 (125)
Q Consensus 81 dDPlLq~R~~aYadS~~~Rlg~n~~~lpvn~p~~~~~~~~~r 122 (125)
+|||||+|+|||+|||++|+|+||+|||||||+|+ ++||||
T Consensus 280 ~DplLq~R~faY~ds~~~R~g~N~~qlpvN~p~~~-~~n~~r 320 (433)
T cd00328 280 EDPLLQGRLFSYADTQLYRLGPNFQQLPVNRPYAP-VHNNQR 320 (433)
T ss_pred CCcccccccccchhhhhcCCCCCHhhCcccCCCCC-cCCCCc
Confidence 99999999999999999999999999999999987 999987
No 3
>cd08156 catalase_clade_3 Clade 3 of the heme-binding enzyme catalase. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes, which is involved in the protection of cells from the toxic effects of peroxides. It catalyzes the conversion of hydrogen peroxide to water and molecular oxygen. Catalases also utilize hydrogen peroxide to oxidize various substrates such as alcohol or phenols. Clade 3 catalases are the most abundant subfamily and are found in all three kingdoms of life; they have a relatively small subunit size of 43 to 75 kDa, and bind a protoheme IX (heme b) group buried deep inside the structure. Clade 3 catalases also bind NADPH as a second redox-active cofactor. They form tetramers, and in eukaryotic cells, catalases are located in peroxisomes.
Probab=100.00 E-value=9.3e-41 Score=287.23 Aligned_cols=110 Identities=60% Similarity=0.959 Sum_probs=104.7
Q ss_pred cccccCcc-eeecC----CCCCCCC------CCccccCCCCcCcEEeEEEEEccCCCCchhhhhhhhcCCCccCCCcCCC
Q psy2586 12 SRKQQGTD-TFGYN----DKALPLE------TGNKVWPHREFPLIEVGQLVLDKNPSNYFAEVEQIAFSPSHLVPGIEPS 80 (125)
Q Consensus 12 ~r~~~gp~-~f~~~----~~gD~i~------DpTk~WP~d~r~~v~lG~LtLnrn~~n~~~e~eqi~FdP~~lv~GIe~S 80 (125)
.|+++|+. +|++. .++|.++ |+||+||+++||++++|+||||+|++|+|++|||++|+|++||+||++|
T Consensus 200 ~~I~~G~~P~w~l~vQv~~~~d~~~~~f~~~D~Tk~Wp~~~~p~i~vG~l~Ln~n~~n~f~e~eq~aF~P~~lvpGI~~S 279 (429)
T cd08156 200 EAIERGDFPSWTLYVQVMPEEDAEKYRFNPFDLTKVWPHKDYPLIEVGKLELNRNPENYFAEVEQAAFSPSNLVPGIGFS 279 (429)
T ss_pred HHHhcCCCceEEEEEEEechhHhhcCCCCCCcCCccCCccCcceEEeEEEEEecCCcchhhhhheecccCcCCCCCccCC
Confidence 47889998 99887 6788777 9999999999999999999999999999999999999999999999999
Q ss_pred CCcccccccccchhhhhhccCCCCcccCCCCCCCccccccee
Q psy2586 81 PDKMLQGRLFSYPDTHRHRLGPNYLQLPVNCPFATKVANYQR 122 (125)
Q Consensus 81 dDPlLq~R~~aYadS~~~Rlg~n~~~lpvn~p~~~~~~~~~r 122 (125)
+|||||+|+|||+|||++|+|+||+|||||||+|+ ++||||
T Consensus 280 ~Dp~Lq~R~faY~dt~~~Rlg~N~~qlPvN~p~~~-~~n~~r 320 (429)
T cd08156 280 PDKMLQGRLFSYADAHRYRLGVNYHQLPVNRPKCP-VNNYQR 320 (429)
T ss_pred CCccccccccccHhhhhcCCCCCHhhCCCCCCCCC-CCCcCc
Confidence 99999999999999999999999999999999987 899987
No 4
>PLN02609 catalase
Probab=100.00 E-value=1.4e-40 Score=289.97 Aligned_cols=110 Identities=47% Similarity=0.754 Sum_probs=105.4
Q ss_pred cccccCcc-eeecC----CCCCCCC------CCccccCCCCcCcEEeEEEEEccCCCCchhhhhhhhcCCCccCCCcCCC
Q psy2586 12 SRKQQGTD-TFGYN----DKALPLE------TGNKVWPHREFPLIEVGQLVLDKNPSNYFAEVEQIAFSPSHLVPGIEPS 80 (125)
Q Consensus 12 ~r~~~gp~-~f~~~----~~gD~i~------DpTk~WP~d~r~~v~lG~LtLnrn~~n~~~e~eqi~FdP~~lv~GIe~S 80 (125)
.|+++|+. +|++. .+||.++ |+||+||+++||++++|+||||+|++|+|++|||++|+|++||+||++|
T Consensus 257 ~~I~~G~~P~w~l~vQv~~~~d~~~~~f~~~D~Tk~WP~~~~p~i~vG~l~Ln~np~n~f~e~eq~aF~P~~lvpGI~~S 336 (492)
T PLN02609 257 DSIAAGNYPEWKLFIQTMDPEDEDKFDFDPLDVTKTWPEDILPLQPVGRLVLNRNIDNFFAENEQLAFCPAIVVPGIYYS 336 (492)
T ss_pred HHHhcCCCceeEEEEEEcCHHHHhcCCCCCCcCCceeCcccceeeEeEEEEEecCCcchhhhhhhhccccccCCCCccCC
Confidence 47789999 99987 6888888 9999999999999999999999999999999999999999999999999
Q ss_pred CCcccccccccchhhhhhccCCCCcccCCCCCCCccccccee
Q psy2586 81 PDKMLQGRLFSYPDTHRHRLGPNYLQLPVNCPFATKVANYQR 122 (125)
Q Consensus 81 dDPlLq~R~~aYadS~~~Rlg~n~~~lpvn~p~~~~~~~~~r 122 (125)
+|||||+|+|||+|||++|+|+||+|||||||+|+ ++||||
T Consensus 337 ~DpmLq~R~faY~ds~~~Rlg~N~~qlPvN~p~~~-~~n~~r 377 (492)
T PLN02609 337 DDKLLQTRIFAYADTQRHRLGPNYLQLPVNAPKCA-HHNNHH 377 (492)
T ss_pred CCcccccccccchhHhhccCCCChhhCcccCCCCC-cCCCCc
Confidence 99999999999999999999999999999999987 999987
No 5
>cd08154 catalase_clade_1 Clade 1 of the heme-binding enzyme catalase. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes, which is involved in the protection of cells from the toxic effects of peroxides. It catalyzes the conversion of hydrogen peroxide to water and molecular oxygen. Catalases also utilize hydrogen peroxide to oxidize various substrates such as alcohol or phenols. Clade 1 catalases are found in bacteria, algae, and plants; they have a relatively small subunit size of 55 to 69 kDa, and bind a protoheme IX (heme b) group buried deep inside the structure. They appear to form tetramers. In eukaryotic cells, catalases are located in peroxisomes.
Probab=100.00 E-value=6.1e-40 Score=284.77 Aligned_cols=110 Identities=58% Similarity=0.944 Sum_probs=104.4
Q ss_pred cccccC-cceeecC----CCCCCC------CCCccccCCCCcCcEEeEEEEEccCCCCchhhhhhhhcCCCccCCCcCCC
Q psy2586 12 SRKQQG-TDTFGYN----DKALPL------ETGNKVWPHREFPLIEVGQLVLDKNPSNYFAEVEQIAFSPSHLVPGIEPS 80 (125)
Q Consensus 12 ~r~~~g-p~~f~~~----~~gD~i------~DpTk~WP~d~r~~v~lG~LtLnrn~~n~~~e~eqi~FdP~~lv~GIe~S 80 (125)
.|+++| +.+|++. .+||.+ +|+||+||++.+|++++|+||||+|++|+|++|||++|+|++||+||++|
T Consensus 242 ~~I~~G~~p~w~l~vQv~~~~D~~~~~f~~~D~Tk~WP~~~~p~i~vG~l~Ln~np~n~f~e~eq~aF~P~~lvpGI~~S 321 (469)
T cd08154 242 DAIAAGNYPEWELYVQIMDPKDLDKLDFDPLDDTKIWPEDQFPLKPVGKMTLNKNPDNFFAEVEQVAFSPGNLVPGIEPS 321 (469)
T ss_pred HHHhcCCCceEEEEEEEcCHHHhhcCCCCCCcCCcccCCcccceEEeEEEEEecCCcchhhhhhhhhccccCCCCCcCCC
Confidence 367778 9999988 688888 79999999996799999999999999999999999999999999999999
Q ss_pred CCcccccccccchhhhhhccCCCCcccCCCCCCCccccccee
Q psy2586 81 PDKMLQGRLFSYPDTHRHRLGPNYLQLPVNCPFATKVANYQR 122 (125)
Q Consensus 81 dDPlLq~R~~aYadS~~~Rlg~n~~~lpvn~p~~~~~~~~~r 122 (125)
+|||||+|+|||+|||++|+|+||+|||||||+|+ |+||||
T Consensus 322 ~DpmLq~R~faY~ds~r~Rlg~N~~qlPvN~p~~~-~~~~~r 362 (469)
T cd08154 322 DDKMLQGRLFSYSDTQRYRLGPNYLQLPINAPKAA-VHNNQR 362 (469)
T ss_pred CCcccccccccchhHhhccCCCChhhCCCCCCCCC-CCCCCc
Confidence 99999999999999999999999999999999987 899987
No 6
>COG0753 KatE Catalase [Inorganic ion transport and metabolism]
Probab=100.00 E-value=4.2e-39 Score=279.28 Aligned_cols=101 Identities=57% Similarity=1.023 Sum_probs=96.8
Q ss_pred cCcceeecCCCCCCCCCCccccCCCCcCcEEeEEEEEccCCCCchhhhhhhhcCCCccCCCcCCCCCcccccccccchhh
Q psy2586 16 QGTDTFGYNDKALPLETGNKVWPHREFPLIEVGQLVLDKNPSNYFAEVEQIAFSPSHLVPGIEPSPDKMLQGRLFSYPDT 95 (125)
Q Consensus 16 ~gp~~f~~~~~gD~i~DpTk~WP~d~r~~v~lG~LtLnrn~~n~~~e~eqi~FdP~~lv~GIe~SdDPlLq~R~~aYadS 95 (125)
....+|+|+ ++|+||+||++++|++++|+|+||||++|+|+||||++|.|++|||||++|+|||||+|.|+|+|+
T Consensus 276 ~da~k~~f~-----~~D~TKvWp~~~~P~~~VG~m~LnrNpdN~FaE~EQaAF~p~nlVPGi~fS~D~lLQgRlFsY~Dt 350 (496)
T COG0753 276 EDAEKFDFD-----PLDLTKLWPEEDYPLIEVGTMVLNRNPDNFFAEVEQAAFAPGNLVPGIDFSPDPLLQGRLFSYGDT 350 (496)
T ss_pred hHhhcCCCC-----CCccccccccccCCceEeeEEEEccCccchhhhhhhhccccccCCCCCCCCCChhhhhccccchhh
Confidence 445677777 899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhccCCCCcccCCCCCCCccccccee
Q psy2586 96 HRHRLGPNYLQLPVNCPFATKVANYQR 122 (125)
Q Consensus 96 ~~~Rlg~n~~~lpvn~p~~~~~~~~~r 122 (125)
|++|+|+||.|||||||+|+ |+||||
T Consensus 351 qryRlG~N~~qlPvN~P~~p-~~~~qr 376 (496)
T COG0753 351 QRYRLGPNYHQIPVNRPKCP-VHNNQR 376 (496)
T ss_pred hHhhcCCCcccccCCCCCCc-cccccc
Confidence 99999999999999999998 999998
No 7
>KOG0047|consensus
Probab=100.00 E-value=8.3e-39 Score=275.37 Aligned_cols=102 Identities=70% Similarity=1.300 Sum_probs=97.5
Q ss_pred cCcceeecCCCCCCCCCCccccCCCCcCcEEeEEEEEccCCCCchhhhhhhhcCCCccCCCcCCCCCcccccccccchhh
Q psy2586 16 QGTDTFGYNDKALPLETGNKVWPHREFPLIEVGQLVLDKNPSNYFAEVEQIAFSPSHLVPGIEPSPDKMLQGRLFSYPDT 95 (125)
Q Consensus 16 ~gp~~f~~~~~gD~i~DpTk~WP~d~r~~v~lG~LtLnrn~~n~~~e~eqi~FdP~~lv~GIe~SdDPlLq~R~~aYadS 95 (125)
+...+|+|+ ++|.||+||++++|++++|+||||+|++|+|+|+||+||+|+++|||||+|+|+|||+|.|+|+||
T Consensus 284 ~qa~K~~fn-----pfDvTKvWP~~~~PL~~VGk~vLn~Np~NyFaevEQ~AF~Pa~~VPGIe~S~Dk~LQ~RlFSY~Dt 358 (505)
T KOG0047|consen 284 EQAEKFRFN-----PFDVTKVWPHKDYPLIPVGKMVLNRNPDNYFAEVEQAAFSPAHIVPGIEPSPDKMLQGRLFSYPDT 358 (505)
T ss_pred hHhhcCCCC-----ccceeccccCcCccccccceEEecCCchHHHHHHHHhccCccccCCCcccCCchhheeeeeccCcc
Confidence 446789999 799999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhccCCCCcccCCCCCCCccccccee
Q psy2586 96 HRHRLGPNYLQLPVNCPFATKVANYQR 122 (125)
Q Consensus 96 ~~~Rlg~n~~~lpvn~p~~~~~~~~~r 122 (125)
+++|||+||+|||||||+...++||||
T Consensus 359 hRHRLGpNy~QlPVNcPy~~~~~n~qr 385 (505)
T KOG0047|consen 359 HRHRLGPNYLQLPVNCPYRVRAHNFQR 385 (505)
T ss_pred cccccCCCeeecccCCCcccccccccc
Confidence 999999999999999999555889988
No 8
>PRK11249 katE hydroperoxidase II; Provisional
Probab=100.00 E-value=3.5e-38 Score=285.51 Aligned_cols=110 Identities=43% Similarity=0.776 Sum_probs=104.3
Q ss_pred cccccCcc-eeecC----CCCCC------CCCCccccCCCCcCcEEeEEEEEccCCCCchhhhhhhhcCCCccCCCcCCC
Q psy2586 12 SRKQQGTD-TFGYN----DKALP------LETGNKVWPHREFPLIEVGQLVLDKNPSNYFAEVEQIAFSPSHLVPGIEPS 80 (125)
Q Consensus 12 ~r~~~gp~-~f~~~----~~gD~------i~DpTk~WP~d~r~~v~lG~LtLnrn~~n~~~e~eqi~FdP~~lv~GIe~S 80 (125)
.+.++|+. +|+|. .++|. ++|+||.||++++|++++|+|||++|++|+|+||||++|+|++||+||++|
T Consensus 321 eaIe~G~~P~WeL~VQl~~~~d~~~~~f~i~D~TK~WPe~~~P~~~VGkLtLnrn~~n~fae~eqvaF~P~~lvpGI~~S 400 (752)
T PRK11249 321 EAIEAGDYPEYELGVQLIPEEDEFKFDFDLLDPTKLIPEELVPVQRVGKMVLNRNPDNFFAETEQVAFHPGHIVPGIDFT 400 (752)
T ss_pred HHHHcCCCceEEEEEEEcChHHhccCCCCCCcCCccCCcccCcceEeEEEEecCCCCcchhhhheeeccCcCCCCCccCC
Confidence 46788888 88887 57777 999999999999999999999999999999999999999999999999999
Q ss_pred CCcccccccccchhhhhhccC-CCCcccCCCCCCCccccccee
Q psy2586 81 PDKMLQGRLFSYPDTHRHRLG-PNYLQLPVNCPFATKVANYQR 122 (125)
Q Consensus 81 dDPlLq~R~~aYadS~~~Rlg-~n~~~lpvn~p~~~~~~~~~r 122 (125)
+|||||+|+|||+|||++|+| +||+|||||||+|+ |+||||
T Consensus 401 ~DplLq~R~fsY~dtq~~Rlgg~N~~qlpvN~p~~~-~~n~~r 442 (752)
T PRK11249 401 NDPLLQGRLFSYTDTQISRLGGPNFHEIPINRPTCP-YHNFQR 442 (752)
T ss_pred CCcccccccccchHHhhccCCCCchhhcccccccCC-cCCCCc
Confidence 999999999999999999997 99999999999998 999997
No 9
>cd08157 catalase_fungal Fungal catalases similar to yeast catalases A and T. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes, which is involved in the protection of cells from the toxic effects of peroxides. It catalyzes the conversion of hydrogen peroxide to water and molecular oxygen. Catalases also utilize hydrogen peroxide to oxidize various substrates such as alcohol or phenols. This family of fungal catalases has a relatively small subunit size, and binds a protoheme IX (heme b) group buried deep inside the structure. Fungal catalases also bind NADPH as a second redox-active cofactor. They form tetramers; in eukaryotic cells, catalases are typically located in peroxisomes. Saccharomyces cerevisiae catalase T is found in the cytoplasm, though.
Probab=100.00 E-value=3e-37 Score=266.42 Aligned_cols=111 Identities=57% Similarity=0.975 Sum_probs=103.0
Q ss_pred cccccCcc-eeecC----CCCCC------CCCCccccCCCCcCcEEeEEEEEccCCCCchhhhhhhhcCCCccCCCcCCC
Q psy2586 12 SRKQQGTD-TFGYN----DKALP------LETGNKVWPHREFPLIEVGQLVLDKNPSNYFAEVEQIAFSPSHLVPGIEPS 80 (125)
Q Consensus 12 ~r~~~gp~-~f~~~----~~gD~------i~DpTk~WP~d~r~~v~lG~LtLnrn~~n~~~e~eqi~FdP~~lv~GIe~S 80 (125)
.|+++|+. +|+|. .++|. ++|+||+||++++|++++|+|+|+++++|+|++|||++|+|+++++||++|
T Consensus 216 ~~i~~g~~p~w~l~vQl~~~~d~~~~~f~i~D~Tk~WPe~~~P~~~vG~l~Ln~~~~~~~~e~eq~aF~P~~~vpGi~ps 295 (451)
T cd08157 216 EAIERGDYPSWTVYVQVMTPEQAEKLRFNIFDLTKVWPHKDFPLRPVGKLTLNENPKNYFAEIEQAAFSPSHMVPGIEPS 295 (451)
T ss_pred HHHhcCCCceEEEEEEEeCHHHHhhCCCCCCcCCcccCcccCccEEeEEEEecCCChhHHhHhhhhcccccccCCCccCC
Confidence 57889998 99988 57776 999999999999999999999999999999999999999999999999999
Q ss_pred CCcccccccccchhhhhhccCCCCcccCCCCCC-Cccccccee
Q psy2586 81 PDKMLQGRLFSYPDTHRHRLGPNYLQLPVNCPF-ATKVANYQR 122 (125)
Q Consensus 81 dDPlLq~R~~aYadS~~~Rlg~n~~~lpvn~p~-~~~~~~~~r 122 (125)
+|||||+|++||++|+++|+|+||+|||||||+ |+..+||||
T Consensus 296 ~DpiLq~R~~aY~ds~~~R~g~N~~qlPvN~p~~~~~~~~~~r 338 (451)
T cd08157 296 ADPVLQARLFSYPDAHRHRLGPNYQQLPVNRPKTSPVYNPYQR 338 (451)
T ss_pred CCchhcccccchHHHHHhccCCChhhCCCCCCCcCCCCCCcCc
Confidence 999999999999999999999999999999999 774444476
No 10
>PF00199 Catalase: Catalase; InterPro: IPR011614 Catalases (1.11.1.6 from EC) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects []. Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (IPR000763 from INTERPRO) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (IPR007760 from INTERPRO) that are found in bacteria []. Based on a phylogenetic analysis, catalases can be classified into clade 1, 2 and 3. Clade 1 contains small subunit catalases from plants and a subset of bacteria; clade 2 contains large subunit catalases from fungi and a second subset of bacteria; and clade 3 contains small subunit catalases from bacteria, fungi, protists, animals, and plants [, ]. This entry represent the core-forming domain of mono-functional, haem-containing catalases. It does not cover the region that carries an immune-responsive amphipathic octa-peptide that is found in the C-terminal of some catalases (IPR010582 from INTERPRO).; GO: 0004096 catalase activity, 0020037 heme binding, 0006979 response to oxidative stress, 0055114 oxidation-reduction process; PDB: 7CAT_A 3NWL_D 4BLC_D 1TH3_D 1TH4_A 1TGU_B 1TH2_D 3RGS_D 3RE8_D 3RGP_C ....
Probab=100.00 E-value=5e-35 Score=246.45 Aligned_cols=110 Identities=49% Similarity=0.837 Sum_probs=87.8
Q ss_pred cccc-cCcceeecC----CCCCCCC------CCccccCCCCcCcEEeEEEEEccCCCCchhhhhhhhcCCCccCCCcCCC
Q psy2586 12 SRKQ-QGTDTFGYN----DKALPLE------TGNKVWPHREFPLIEVGQLVLDKNPSNYFAEVEQIAFSPSHLVPGIEPS 80 (125)
Q Consensus 12 ~r~~-~gp~~f~~~----~~gD~i~------DpTk~WP~d~r~~v~lG~LtLnrn~~n~~~e~eqi~FdP~~lv~GIe~S 80 (125)
.|++ +++++|+|. .++|.+. |+||+||++.+|.++||+|+|++++++++++||+++|+|+++++||++|
T Consensus 240 ~rL~~~~~~~~~l~vQl~~~~d~~~~~~~i~D~T~~Wpe~~~P~~~vg~L~l~~~~~~~~~~~e~l~F~P~~~~~Gi~~s 319 (384)
T PF00199_consen 240 ERLAAGGPVRWDLQVQLATPEDPMPFRFNIEDATKEWPEDRSPLIPVGTLTLNRNPPDFFAECEQLAFNPWHLPPGIEPS 319 (384)
T ss_dssp HHHHTTS-EEEEEEEEEEEGGGCTTSSSHTT-TTS--TTTTSEEEEEEEEEEEEE-SSHHHHTTT----TT--BTTEEE-
T ss_pred HHHhcCCceeEEEEEEecCcccccccCCCcccCCccCCCcCceeeeeeeEeecccccchhhhhhhhhccccccccceecC
Confidence 4677 899999998 4666655 9999999998999999999999999999999999999999999999999
Q ss_pred CCcccccccccchhhhhhccCCCCcccCCCCCCCccccccee
Q psy2586 81 PDKMLQGRLFSYPDTHRHRLGPNYLQLPVNCPFATKVANYQR 122 (125)
Q Consensus 81 dDPlLq~R~~aYadS~~~Rlg~n~~~lpvn~p~~~~~~~~~r 122 (125)
+|||||+|++||++|+++|+|+||+|||||+|+++ ++|++|
T Consensus 320 ~Dpil~aR~~aY~~s~~~R~~~n~~~lp~n~p~~~-~~~~~~ 360 (384)
T PF00199_consen 320 DDPILQARSFAYADSQRRRLGANYQQLPVNEPKCP-VHNNQR 360 (384)
T ss_dssp S-HHHHHHHHHHHHHHHHHTSTTGGGSGGGS-SSS--BSST-
T ss_pred CCcchhcchhhhhhhhhccCCcccccCCCCCCCCC-cCCCCC
Confidence 99999999999999999999999999999999998 888886
No 11
>cd08153 srpA_like Catalase-like heme-binding proteins similar to the uncharacterized srpA. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes involved in the protection of cells from the toxic effects of peroxides. It catalyses the conversion of hydrogen peroxide to water and molecular oxygen. Several other related protein families share the catalase fold and bind to heme, but do not necessarily have catalase activity. This family contains uncharacterized proteins similar to the Synechococcus elongatus PCC 7942 periplasmic protein srpA, of mostly bacterial origin. The plasmid-encoded srpA is regulated by sulfate, but does not seem to function in its uptake or metabolism.
Probab=99.91 E-value=8.7e-25 Score=178.07 Aligned_cols=88 Identities=27% Similarity=0.428 Sum_probs=83.4
Q ss_pred cccccCcceeecC----CCCCCCCCCccccCCCCcCcEEeEEEEEccCCCCchhhhhhhhcCCCccCCCcCCCCCccccc
Q psy2586 12 SRKQQGTDTFGYN----DKALPLETGNKVWPHREFPLIEVGQLVLDKNPSNYFAEVEQIAFSPSHLVPGIEPSPDKMLQG 87 (125)
Q Consensus 12 ~r~~~gp~~f~~~----~~gD~i~DpTk~WP~d~r~~v~lG~LtLnrn~~n~~~e~eqi~FdP~~lv~GIe~SdDPlLq~ 87 (125)
.|+++||.+|+|. +++|+++|+|+.||++ +|.+++|+|+|+++..+.+++|++++|+|+++++||++|+||||++
T Consensus 204 ~~l~~g~~~f~l~vQl~~~~d~i~D~t~~Wpe~-~p~~~vg~l~l~~~~~~~~~~~e~l~F~P~~~~~gi~~~~Dpi~~~ 282 (295)
T cd08153 204 QRLAQGPVRWDLVLQLAEPGDPTDDPTKPWPAD-RKEVDAGTLTITKVAPDQGGACRDINFDPLVLPDGIEPSDDPLLAA 282 (295)
T ss_pred HHHHhCCceEEEEEEEcCCCCcCCCCCccCCCC-CceeEEEEEEECCCCccchhhhhheeeCCccCCCCCCCCCChHHhh
Confidence 4889999999998 6899999999999999 9999999999999977777999999999999999999999999999
Q ss_pred ccccchhhhhhcc
Q psy2586 88 RLFSYPDTHRHRL 100 (125)
Q Consensus 88 R~~aYadS~~~Rl 100 (125)
|.++|++|+++|.
T Consensus 283 R~~aY~~s~~~R~ 295 (295)
T cd08153 283 RSAAYAVSFSRRQ 295 (295)
T ss_pred hhhHHHHHHhhcC
Confidence 9999999999994
No 12
>cd08150 catalase_like Catalase-like heme-binding proteins and protein domains. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes involved in the protection of cells from the toxic effects of peroxides. It catalyses the conversion of hydrogen peroxide to water and molecular oxygen. Several other related protein families share the catalase fold and bind to heme, but do not necessarily have catalase activity.
Probab=99.86 E-value=1.1e-22 Score=164.73 Aligned_cols=86 Identities=22% Similarity=0.397 Sum_probs=81.4
Q ss_pred cccccCcceeecC----CCCC--CCCCCccccCCCCcCcEEeEEEEEccCCCCchhhhhhhhcCCCccCCCcCCCCC--c
Q psy2586 12 SRKQQGTDTFGYN----DKAL--PLETGNKVWPHREFPLIEVGQLVLDKNPSNYFAEVEQIAFSPSHLVPGIEPSPD--K 83 (125)
Q Consensus 12 ~r~~~gp~~f~~~----~~gD--~i~DpTk~WP~d~r~~v~lG~LtLnrn~~n~~~e~eqi~FdP~~lv~GIe~SdD--P 83 (125)
.|+++||++|+|. +++| +++|+||.||++ +|.+++|||+|+++..+ ++|++++|+|.++++||++|+| |
T Consensus 190 ~rl~~~~~~~~l~vQl~~~~d~~~i~D~t~~Wpe~-~p~~~vg~l~i~~~~~~--~~~~~~~f~p~~~~~gi~~~~d~g~ 266 (283)
T cd08150 190 ERLQRGPVVYDFRIQLNDDTDATTIDNPTILWPTE-HPVEAVAKITIPPPTFT--AAQEAFAFNPFTPWHGLLETNDLGP 266 (283)
T ss_pred HHHHhCCceEEEEEEEccccccCCCCCCCcCCCCC-CCceEEEEEEECCCCCc--HHHHHHhcCCCCCCCccCCCCCchH
Confidence 6889999999998 6899 999999999999 99999999999996655 8999999999999999999999 9
Q ss_pred ccccccccchhhhhhcc
Q psy2586 84 MLQGRLFSYPDTHRHRL 100 (125)
Q Consensus 84 lLq~R~~aYadS~~~Rl 100 (125)
||++|+++|++|+++|.
T Consensus 267 i~~~R~~~Y~~S~~~R~ 283 (283)
T cd08150 267 ILEVRRRVYTSSQGLRH 283 (283)
T ss_pred HHHHHHHHHHHHHHhhC
Confidence 99999999999999984
No 13
>cd08151 AOS Allene oxide synthase. Allene oxide synthase converts a fatty acid hydroperoxide to an allene oxide, which is an unstable epoxide. In corals, the enzyme is part of a eiconaosid synthesis pathway that is initiated by a lipoxygenase, which generates the fatty acid hydroperoxides in the first step. The structure of allene oxide synthase closely resembles that of catalase, but allene oxide synthase does not have catalase activity.
Probab=99.84 E-value=5.8e-22 Score=164.31 Aligned_cols=87 Identities=18% Similarity=0.240 Sum_probs=81.3
Q ss_pred cccccCcceeecC----CCCC----CCCCCccccCCCCcCcEEeEEEEEccCCCCchhhhhhhhcCCCccCC--CcCCCC
Q psy2586 12 SRKQQGTDTFGYN----DKAL----PLETGNKVWPHREFPLIEVGQLVLDKNPSNYFAEVEQIAFSPSHLVP--GIEPSP 81 (125)
Q Consensus 12 ~r~~~gp~~f~~~----~~gD----~i~DpTk~WP~d~r~~v~lG~LtLnrn~~n~~~e~eqi~FdP~~lv~--GIe~Sd 81 (125)
.|+++|+++|+|- +++| +++|+||+||++++|.+++|+|+|+++++ +++||+++|+|+++++ ||++|+
T Consensus 227 ~rl~~g~~~~~l~iQl~~~~d~~~~~i~D~T~~Wpe~~~P~i~vg~l~l~~~~~--~~~~e~l~F~P~~~~~~~gi~~~~ 304 (328)
T cd08151 227 QRLQSPGVRYRLQIQLREVSDDATAVALDCCRPWDEDEHPWLDLAVVRLGAPLP--NDELEKLAFNPGNTPESLGLPLAY 304 (328)
T ss_pred HHHHhCCceEEEEEEEechhhcCCCCCCCCCccCCcccCceEEEEEEEECCCCC--hhhhHhhcccccccCCCCCccCCC
Confidence 5789999999998 6788 99999999998789999999999999977 4699999999999999 999999
Q ss_pred Cc-----ccccccccchhhhhhcc
Q psy2586 82 DK-----MLQGRLFSYPDTHRHRL 100 (125)
Q Consensus 82 DP-----lLq~R~~aYadS~~~Rl 100 (125)
|| |+++|+.+|+.|+++|.
T Consensus 305 ~~~d~gsi~~~R~~vY~~s~~~R~ 328 (328)
T cd08151 305 CADDYASLGHLRSLVYEISQRLRK 328 (328)
T ss_pred ChHHhhhHHHHHHHHHHHHHhhcC
Confidence 99 99999999999999983
No 14
>cd08152 y4iL_like Catalase-like heme-binding proteins similar to the uncharacterized y4iL. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes involved in the protection of cells from the toxic effects of peroxides. It catalyses the conversion of hydrogen peroxide to water and molecular oxygen. Several other related protein families share the catalase fold and bind to heme, but do not necessarily have catalase activity. This family contains uncharacterized proteins similar to Rhizobium sp. NGR234 y4iL, of mostly bacterial origin.
Probab=99.82 E-value=2.8e-21 Score=158.36 Aligned_cols=89 Identities=17% Similarity=0.293 Sum_probs=82.6
Q ss_pred cccccCcceeecC----CCCC--CCCCCccccCCCCcCcEEeEEEEEccCCC----CchhhhhhhhcCCCccCCCcCCCC
Q psy2586 12 SRKQQGTDTFGYN----DKAL--PLETGNKVWPHREFPLIEVGQLVLDKNPS----NYFAEVEQIAFSPSHLVPGIEPSP 81 (125)
Q Consensus 12 ~r~~~gp~~f~~~----~~gD--~i~DpTk~WP~d~r~~v~lG~LtLnrn~~----n~~~e~eqi~FdP~~lv~GIe~Sd 81 (125)
.|+++||++|+|. +++| +|+|+|+.||++++|.+++|||+|++... +..+.|++++|||.++++||++|
T Consensus 207 ~~l~~g~~~f~l~vQl~~~~d~~pi~D~tv~W~e~~~p~i~vg~l~i~~~~~~~~~~~~~~~~~l~F~P~~~~~g~~p~- 285 (305)
T cd08152 207 DFLAENDAEFEFRIQLCTDLEKMPIEDASVEWPEALSPFVPVATITIPPQDFDSPARQRAFDDNLSFNPWHGLAEHRPL- 285 (305)
T ss_pred HHHHhCCceEEEEEEecCchhhCCCCcCCccCCCccCCCeEEEEEEECCCCccCHHHHhhhhhccccCccccccccCcC-
Confidence 3889999999998 6788 99999999999889999999999999876 56778999999999999999999
Q ss_pred CcccccccccchhhhhhccC
Q psy2586 82 DKMLQGRLFSYPDTHRHRLG 101 (125)
Q Consensus 82 DPlLq~R~~aYadS~~~Rlg 101 (125)
|+|+++|..+|+.|+++|..
T Consensus 286 g~i~r~R~~vY~~S~~~R~~ 305 (305)
T cd08152 286 GSINRARKAVYEASSAFRHE 305 (305)
T ss_pred hHHHHHHHHHHHHHHHHhcC
Confidence 89999999999999999963
No 15
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=56.55 E-value=14 Score=28.56 Aligned_cols=46 Identities=24% Similarity=0.434 Sum_probs=32.8
Q ss_pred CCccccCCCCcCcEEeEEEEEccCCCCc----hhhhhhhhcCCCccCCCcCC
Q psy2586 32 TGNKVWPHREFPLIEVGQLVLDKNPSNY----FAEVEQIAFSPSHLVPGIEP 79 (125)
Q Consensus 32 DpTk~WP~d~r~~v~lG~LtLnrn~~n~----~~e~eqi~FdP~~lv~GIe~ 79 (125)
.+.|+||-. ...++|+|+|-+.-.+. ....+.++|-|+++...-.+
T Consensus 38 ~~~kpw~wa--dt~pva~L~IP~lg~~~~V~~G~s~~~L~~G~G~~~~t~~P 87 (174)
T TIGR03784 38 KEHKPWPWA--DTYPVAKLSAPRLGASLYVLAGASGRNLAFGPGHMLATAQP 87 (174)
T ss_pred CCCCCCccc--cCceeEEEEEccCCCceeEEecCCHHHHhheeEEecCCCCC
Confidence 578999987 46789999998754432 23456788988887665544
No 16
>PF12518 DUF3721: Protein of unknown function; InterPro: IPR022196 This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length. There is a conserved WMPC sequence motif. There are two completely conserved residues (A and C) that may be functionally important.
Probab=37.01 E-value=14 Score=22.01 Aligned_cols=11 Identities=36% Similarity=1.038 Sum_probs=8.8
Q ss_pred CCCCCCcccCC
Q psy2586 1 MGCSSAHPINN 11 (125)
Q Consensus 1 ~~~~~~~~~~~ 11 (125)
+||+++|..+.
T Consensus 14 ~GC~G~H~mg~ 24 (34)
T PF12518_consen 14 LGCKGAHKMGD 24 (34)
T ss_pred cCCcchhhccC
Confidence 69999998753
No 17
>PF03568 Peptidase_C50: Peptidase family C50; InterPro: IPR005314 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C50 (separase family, clan CD). The active site residues for members of this family and family C14 occur in the same order in the sequence: H,C. The separases are caspase-like proteases, which plays a central role in the chromosome segregation. In yeast they cleave the rad21 subunit of the cohesin complex at the onset of anaphase. During most of the cell cycle, separase is inactivated by the securin/cut2 protein, which probably covers its active site. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0005634 nucleus
Probab=32.71 E-value=15 Score=31.30 Aligned_cols=27 Identities=22% Similarity=0.278 Sum_probs=16.5
Q ss_pred CCCCCCcccCCcccccCcceeecCCCC
Q psy2586 1 MGCSSAHPINNSRKQQGTDTFGYNDKA 27 (125)
Q Consensus 1 ~~~~~~~~~~~~r~~~gp~~f~~~~~g 27 (125)
|||||++...+-..+---.-+.|...|
T Consensus 341 ~GCsS~~l~~~g~~~~~g~~~~yl~ag 367 (383)
T PF03568_consen 341 MGCSSGRLKEQGEFEPYGTPLSYLLAG 367 (383)
T ss_pred ecCCcccccccCCCCCCCcHHHHHhcC
Confidence 899999987765544333344444344
No 18
>PF02122 Peptidase_S39: Peptidase S39; InterPro: IPR000382 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. ORF2 of Potato leafroll virus (PLrV) encodes a polyprotein which is translated following a -1 frameshift. The polyprotein has a putative linear arrangement of membrane achor-VPg-peptidase-polmerase domains. The serine peptidase domain which is found in this group of sequences belongs to MEROPS peptidase family S39 (clan PA(S)). It is likely that the peptidase domain is involved in the cleavage of the polyprotein []. The nucleotide sequence for the RNA of PLrV has been determined [, ]. The sequence contains six large open reading frames (ORFs). The 5' coding region encodes two polypeptides of 28K and 70K, which overlap in different reading frames; it is suggested that the third ORF in the 5' block is translated by frameshift readthrough near the end of the 70K protein, yielding a 118K polypeptide []. Segments of the predicted amino acid sequences of these ORFs resemble those of known viral RNA polymerases, ATP-binding proteins and viral genome-linked proteins. The nucleotide sequence of the genomic RNA of Beet western yellows virus (BWYV) has been determined []. The sequence contains six long ORFs. A cluster of three of these ORFs, including the coat protein cistron, display extensive amino acid sequence similarity to corresponding ORFs of a second luteovirus: Barley yellow dwarf virus [].; GO: 0004252 serine-type endopeptidase activity, 0022415 viral reproductive process, 0016021 integral to membrane; PDB: 1ZYO_A.
Probab=22.86 E-value=18 Score=28.90 Aligned_cols=24 Identities=25% Similarity=0.261 Sum_probs=12.1
Q ss_pred CCCCCCcccCCcccccCcceeecC
Q psy2586 1 MGCSSAHPINNSRKQQGTDTFGYN 24 (125)
Q Consensus 1 ~~~~~~~~~~~~r~~~gp~~f~~~ 24 (125)
|||..+|-..++++++|+++|--.
T Consensus 95 Lg~k~~~~~~~~~~~~g~~~~y~~ 118 (203)
T PF02122_consen 95 LGVKAAQLSQNSQLAKGPVSFYGF 118 (203)
T ss_dssp HT-----B----SEEEEESSTTSE
T ss_pred hCcccccccchhhhCCCCeeeeee
Confidence 699999999999999999986544
No 19
>PF13605 DUF4141: Domain of unknown function (DUF4141)
Probab=20.04 E-value=14 Score=24.15 Aligned_cols=21 Identities=19% Similarity=0.406 Sum_probs=15.5
Q ss_pred hhcCCCccCCCcCCCCCcccc
Q psy2586 66 IAFSPSHLVPGIEPSPDKMLQ 86 (125)
Q Consensus 66 i~FdP~~lv~GIe~SdDPlLq 86 (125)
+.|||+++..||--+..-|.|
T Consensus 23 vV~DP~NlAQ~Iinaa~eivq 43 (55)
T PF13605_consen 23 VVTDPGNLAQNIINAAKEIVQ 43 (55)
T ss_pred EEeCchHHHHHHHHHHHHHHH
Confidence 689999999998655544443
Done!