Query 035568
Match_columns 518
No_of_seqs 212 out of 892
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 04:08:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035568.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035568hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00684 Terpene_cyclase_plant_ 100.0 3E-147 7E-152 1205.6 50.3 501 8-515 29-542 (542)
2 PLN02279 ent-kaur-16-ene synth 100.0 9E-138 2E-142 1153.4 44.7 479 27-518 267-778 (784)
3 PLN02592 ent-copalyl diphospha 100.0 4E-110 9E-115 927.3 41.4 442 27-517 307-800 (800)
4 PF01397 Terpene_synth: Terpen 100.0 7.1E-53 1.5E-57 398.3 13.4 152 6-159 22-183 (183)
5 PF03936 Terpene_synth_C: Terp 100.0 9.2E-49 2E-53 391.5 21.3 269 190-463 1-270 (270)
6 cd00868 Terpene_cyclase_C1 Ter 100.0 1.6E-46 3.5E-51 378.0 29.8 282 204-491 1-284 (284)
7 cd00687 Terpene_cyclase_nonpla 100.0 3E-34 6.5E-39 292.8 20.1 246 210-467 17-266 (303)
8 PLN02150 terpene synthase/cycl 100.0 3.9E-30 8.4E-35 219.0 10.6 95 419-518 1-96 (96)
9 cd00385 Isoprenoid_Biosyn_C1 I 99.9 5.2E-21 1.1E-25 184.3 13.0 229 238-485 2-243 (243)
10 PF06330 TRI5: Trichodiene syn 97.8 0.00036 7.8E-09 72.8 14.6 202 237-466 71-277 (376)
11 cd00686 Terpene_cyclase_cis_tr 97.5 0.0031 6.8E-08 65.0 15.5 191 248-465 81-276 (357)
12 PF00494 SQS_PSY: Squalene/phy 88.6 14 0.00031 36.8 14.7 184 249-464 17-217 (267)
13 TIGR02749 prenyl_cyano solanes 83.2 54 0.0012 34.1 16.1 88 325-416 133-220 (322)
14 PLN02890 geranyl diphosphate s 78.5 56 0.0012 35.5 14.6 89 325-417 227-315 (422)
15 cd00867 Trans_IPPS Trans-Isopr 77.9 13 0.00027 36.2 8.9 127 326-464 86-214 (236)
16 PLN02857 octaprenyl-diphosphat 77.6 67 0.0015 34.8 14.9 89 325-417 227-315 (416)
17 cd00683 Trans_IPPS_HH Trans-Is 75.0 94 0.002 31.0 18.0 199 250-486 24-238 (265)
18 TIGR03465 HpnD squalene syntha 70.9 1.2E+02 0.0026 30.4 17.3 193 250-481 18-224 (266)
19 COG0142 IspA Geranylgeranyl py 62.8 1.7E+02 0.0036 30.5 13.6 106 325-435 134-249 (322)
20 TIGR02748 GerC3_HepT heptapren 62.7 2E+02 0.0042 29.9 15.5 85 326-416 130-216 (319)
21 cd00685 Trans_IPPS_HT Trans-Is 61.2 74 0.0016 31.7 10.4 89 325-417 108-196 (259)
22 KOG1719 Dual specificity phosp 59.2 8.1 0.00018 36.0 2.7 30 420-453 119-148 (183)
23 TIGR03464 HpnC squalene syntha 57.1 2.2E+02 0.0047 28.6 19.0 120 235-380 7-131 (266)
24 CHL00151 preA prenyl transfera 50.8 3.1E+02 0.0066 28.5 16.2 86 326-417 135-222 (323)
25 KOG3951 Uncharacterized conser 48.0 30 0.00064 34.7 4.7 56 103-160 264-320 (321)
26 PRK10888 octaprenyl diphosphat 46.3 3.6E+02 0.0078 28.0 16.0 89 325-417 130-218 (323)
27 PF03861 ANTAR: ANTAR domain; 30.0 61 0.0013 24.5 3.0 29 423-456 14-42 (56)
28 PF03701 UPF0181: Uncharacteri 28.2 1E+02 0.0022 23.3 3.7 45 409-460 2-46 (51)
29 COG3707 AmiR Response regulato 27.1 53 0.0012 31.7 2.7 44 407-455 129-173 (194)
30 smart00400 ZnF_CHCC zinc finge 25.8 79 0.0017 23.7 3.0 25 422-451 30-54 (55)
31 PF03000 NPH3: NPH3 family; I 23.8 92 0.002 31.5 3.9 44 396-455 205-248 (258)
32 PF11848 DUF3368: Domain of un 22.7 59 0.0013 23.9 1.7 20 83-102 25-44 (48)
33 COG3140 Uncharacterized protei 21.5 85 0.0018 24.1 2.3 49 409-464 2-50 (60)
34 KOG3109 Haloacid dehalogenase- 21.4 1.1E+02 0.0025 30.3 3.8 47 40-104 46-92 (244)
35 smart00463 SMR Small MutS-rela 21.3 1.1E+02 0.0023 24.6 3.2 23 439-463 8-30 (80)
36 PRK05114 hypothetical protein; 20.8 1.5E+02 0.0032 23.1 3.5 45 409-460 2-46 (59)
37 PF00348 polyprenyl_synt: Poly 20.4 8.2E+02 0.018 24.2 10.0 65 351-418 130-194 (260)
No 1
>cd00684 Terpene_cyclase_plant_C1 Plant Terpene Cyclases, Class 1. This CD includes a diverse group of monomeric plant terpene cyclases (Tspa-Tspf) that convert the acyclic isoprenoid diphosphates, geranyl diphosphate (GPP), farnesyl diphosphate (FPP), or geranylgeranyl diphosphate (GGPP) into cyclic monoterpenes, diterpenes, or sesquiterpenes, respectively; a few form acyclic species. Terpnoid cyclases are soluble enzymes localized to the cytosol (sesquiterpene synthases) or plastids (mono- and diterpene synthases). All monoterpene and diterpene synthases have restrict substrate specificity, however, some sesquiterpene synthases can accept both FPP and GPP. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl diphosphates, via bridging Mg2+ ions (K+ preferred by gymnosperm cyclases), inducing conformational changes such that an N-terminal regi
Probab=100.00 E-value=3.1e-147 Score=1205.62 Aligned_cols=501 Identities=57% Similarity=0.951 Sum_probs=485.6
Q ss_pred hHHHHHHHHHHHHHHhhcc--CcChhhhhHHHHHHHHhCCccccHHHHHHHHHHHHHhcccCcCCCCCCChhHHHHHHHH
Q 035568 8 QSQEIEELKEEVRRELLGS--GVDSLSRLKLIDAILRLGVGYQFERELEEALQNLYDAFSNNFYNIEDNDLYHVALRFRI 85 (518)
Q Consensus 8 ~~~~~~~lk~~v~~~l~~~--~~~~~~~l~liD~lqrLGi~~hF~~EI~~~L~~~~~~~~~~~~~~~~~dl~~~al~FRl 85 (518)
+.+++++||++||+||... +.|++++|+|||+||||||+|||++||+++|+++|++|.++| .....||++|||+|||
T Consensus 29 ~~~~~~~lk~~v~~~~~~~~~~~~~~~~l~liD~lqrLGi~~hF~~EI~~~L~~i~~~~~~~~-~~~~~dl~~~al~FRl 107 (542)
T cd00684 29 LEEEIEELKEEVRKMLEDSEYPVDLFERLWLIDRLQRLGISYHFEDEIKEILDYIYRYWTERG-ESNEDDLYTTALGFRL 107 (542)
T ss_pred HHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHcCchhhhHHHHHHHHHHHHHhhcccc-cccCCCHHHHHHHHHH
Confidence 5789999999999999865 789999999999999999999999999999999999986543 1235799999999999
Q ss_pred hhhcCceechhhhhcccccccccccccccchhhhhhHhhhcccCCCCchHHHHHHHHHHhhcc----------cCcHHHH
Q 035568 86 LRQRGYKVSCDIFNKFKDGKGNFKESLKTDVSGMLSLYEAAHLVVHGEDILNEAIAFTTAHLQ----------SSMAPQV 155 (518)
Q Consensus 86 LR~hGy~vS~dvf~~F~d~~g~F~~~~~~dv~~lL~LyeAs~l~~~gE~iLdea~~ft~~~L~----------~~l~~~V 155 (518)
||||||+||||||++|+|++|+|++++.+||+||||||||||+++|||+|||||++||++||+ ++|+++|
T Consensus 108 LR~~Gy~vs~dvf~~F~~~~g~f~~~~~~d~~g~l~Ly~As~l~~~gE~iLdeA~~ft~~~L~~~~~~~~~~~~~l~~~V 187 (542)
T cd00684 108 LRQHGYNVSSDVFKKFKDEDGKFKESLTQDVKGMLSLYEASHLSFPGEDILDEALSFTTKHLEEKLESNWIIDPDLSGEI 187 (542)
T ss_pred HHHcCCCcCHHHHhhhcCCCCCcCchhhhhhHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHhhccCCCCchHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999 5799999
Q ss_pred HHHccCCccCCchhhHHhhhhhhhhccCCcccHHHHHHHhhhhHHHHHhhHHHHHHHHHHHHHhCCCCCCchhhhhhhHh
Q 035568 156 IHALRQPLYKGLPRIEARFFISLYQEHEPLHNKALLKLAKLDFNQVQSLYKIELSEISRWWKDLDFARKLPFARDRVVEC 235 (518)
Q Consensus 156 ~~aL~~P~~~~~~r~e~r~yI~~y~~~~~~~n~~ll~lAkldFn~~Q~~hq~El~~l~rWwk~~~l~~~l~faRdR~ve~ 235 (518)
++||++|||+++||||||+||++|++ ++++|++||||||+|||+||++||+||+++++||+++||.++|||+|+|+++|
T Consensus 188 ~~aL~~P~~~~~~rlear~yi~~Y~~-~~~~n~~lLelAkldfn~~Q~~hq~El~~~~rWwk~~gL~~~l~~aRdr~ve~ 266 (542)
T cd00684 188 EYALEIPLHASLPRLEARWYIEFYEQ-EDDHNETLLELAKLDFNILQALHQEELKILSRWWKDLDLASKLPFARDRLVEC 266 (542)
T ss_pred HHHccCchhcCCchHHHHHHHHHhCC-CccccHHHHHHHHHHHHHHhHhHHHHHHHHhHHHHhcCCcccCCcccchhHHH
Confidence 99999999999999999999999999 99999999999999999999999999999999999999988889999999999
Q ss_pred HHHHhccccCcchhHHHHHHHHHhhhhhhhhcccccCCCHHHHHHHHHHhhhcCccccccCChhHHHHHHHHHHHHHHHH
Q 035568 236 YFWIVGVYFEPQYSLARKLLTKVISMTSIIDDIYDVYGIPEELDLFTAAIDRWDVSCIDQLPEYMQTFYVALLDLYKEIE 315 (518)
Q Consensus 236 yf~~~a~~feP~~s~~Rl~laK~~~l~~i~DD~fD~~gt~eEl~~~t~ai~rWd~~~~~~lpe~mk~~f~al~~~~~ei~ 315 (518)
|||++|++|+|++|.+|+++||+++|+|++||+||.|||++|++.||+||+|||.++++.+|+|||+||.++++++++++
T Consensus 267 yf~~~a~~feP~~s~~Rl~~aK~~~l~~~iDD~fD~~gt~eEl~~ft~ai~rwd~~~~~~lPe~mk~~~~al~~~~~ei~ 346 (542)
T cd00684 267 YFWAAGTYFEPQYSLARIALAKTIALITVIDDTYDVYGTLEELELFTEAVERWDISAIDQLPEYMKIVFKALLNTVNEIE 346 (542)
T ss_pred HHHHHhcccCccchHHHHHHHHHHHHHhhhHhhhccCCCHHHHHHHHHHHHhccccchhhccHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcCCcchHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCc
Q 035568 316 EELATKGWSYRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGK 395 (518)
Q Consensus 316 ~~~~~~~~~~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~ 395 (518)
.++.++|+.+++.+++++|++++++|++||+|+++||+||++|||++|.+|+|+++++++++++||+.+|+++++|+..+
T Consensus 347 ~~~~~~~~~~~~~~~~~~~~~~~~a~l~EA~w~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~e~~e~~~~~ 426 (542)
T cd00684 347 EELLKEGGSYVVPYLKEAWKDLVKAYLVEAKWAHEGYVPTFEEYMENALVSIGLGPLLLTSFLGMGDILTEEAFEWLESR 426 (542)
T ss_pred HHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhhhhHHhhHHHHHHHHHHhcCCCCCHHHHHHHhcc
Confidence 99998888889999999999999999999999999999999999999999999999999999999999999999997677
Q ss_pred hHHHHHHhhhhhhccCccchhhhhhcCCCchHHHHHHhhcccCCcccCHHHHHHHHHHHHHHHHHHHHhhccCC-CCCCH
Q 035568 396 PKIIRASTIIGRLMDDIKSHKFEQERGHAASAIECYMKEKEREGVSVTEQEVHEELYKKVGDAWKDINEECLMP-TEVPR 474 (518)
Q Consensus 396 ~~i~~~~~~i~RL~NDI~S~~kE~~~G~~~n~V~cym~e~~~~g~~vS~eeA~~~i~~~i~~~~k~ln~~~l~~-~~~p~ 474 (518)
|+|+++++.++||+|||+|+++|+++|+++|+|.|||+|+ | +|+|+|+++++++|+++||++|++++++ +++|+
T Consensus 427 ~~l~~~~~~i~rL~NDi~S~~kE~~rGdv~n~V~~ymke~---g--~s~eeA~~~i~~~ie~~wk~ln~e~l~~~~~~p~ 501 (542)
T cd00684 427 PKLVRASSTIGRLMNDIATYEDEMKRGDVASSIECYMKEY---G--VSEEEAREEIKKMIEDAWKELNEEFLKPSSDVPR 501 (542)
T ss_pred HHHHHHHHHHHHHhcChhhhHHHHhcCCcccHHHHHHHhc---C--CCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCH
Confidence 9999999999999999999999999999999999999999 9 9999999999999999999999999987 78999
Q ss_pred HHHHHHHHHHhhhhhhcccCCCCCCCChhHHHHHHHhcccc
Q 035568 475 PLLMRVLNLSRVIDVIYKEGDGYTHVGQVMKDNIASVLIHP 515 (518)
Q Consensus 475 ~~~~~~~n~aR~~~~~Y~~~Dg~t~~~~~~k~~i~~ll~~p 515 (518)
+|+++++|++|+++++|+++||||.|++.||++|++||++|
T Consensus 502 ~~~~~~~n~~r~~~~~Y~~~D~~t~~~~~~~~~i~~ll~~p 542 (542)
T cd00684 502 PIKQRFLNLARVIDVFYKEGDGFTHPEGEIKDHITSLLFEP 542 (542)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCCCccHHHHHHHHHHhcCC
Confidence 99999999999999999999999999878999999999998
No 2
>PLN02279 ent-kaur-16-ene synthase
Probab=100.00 E-value=9.5e-138 Score=1153.37 Aligned_cols=479 Identities=28% Similarity=0.450 Sum_probs=453.5
Q ss_pred CcChhhhhHHHHHHHHhCCccccHHHHHHHHHHHHHhcccCcCCCCCCChhHHHHHHHHhhhcCceechhhhhccccccc
Q 035568 27 GVDSLSRLKLIDAILRLGVGYQFERELEEALQNLYDAFSNNFYNIEDNDLYHVALRFRILRQRGYKVSCDIFNKFKDGKG 106 (518)
Q Consensus 27 ~~~~~~~l~liD~lqrLGi~~hF~~EI~~~L~~~~~~~~~~~~~~~~~dl~~~al~FRlLR~hGy~vS~dvf~~F~d~~g 106 (518)
|.+.++++|+||+||||||+|||++||+++|+++|++|...+ .....|+++|||+|||||||||+||||||++|+|+ +
T Consensus 267 p~~~fe~l~lvd~L~rlGi~~hF~~EI~~~L~~~~~~~~~~~-~~~~~Dl~~tAl~FRLLR~hGy~VS~dvf~~F~~~-~ 344 (784)
T PLN02279 267 PLDQYARLSMVDTLERLGIDRHFRKEIKSVLDETYRYWLQGE-EEIFLDLATCALAFRILRLNGYDVSSDPLKQFAED-H 344 (784)
T ss_pred cccHHHHhHHHHHHHHhCCccccHHHHHHHHHHHHHhhcccc-cCCCCCHHHHHHHHHHHHHcCCCCChhHHhhcCCC-c
Confidence 688999999999999999999999999999999999986421 11246999999999999999999999999999965 4
Q ss_pred cccccc---ccchhhhhhHhhhcccCCCCchHHHHHHHHHHhhcc--------------cCcHHHHHHHccCCccCCchh
Q 035568 107 NFKESL---KTDVSGMLSLYEAAHLVVHGEDILNEAIAFTTAHLQ--------------SSMAPQVIHALRQPLYKGLPR 169 (518)
Q Consensus 107 ~F~~~~---~~dv~~lL~LyeAs~l~~~gE~iLdea~~ft~~~L~--------------~~l~~~V~~aL~~P~~~~~~r 169 (518)
|++++ .+||+||||||||||+++|||+|||||+.||++||+ ++|+++|+|||++|||+++||
T Consensus 345 -F~~~l~~~~~dv~gmL~LY~AS~l~~~gE~iLdeA~~Fs~~~L~~~~~~~~~~~~~~~~~L~~eV~~AL~~P~~~~l~R 423 (784)
T PLN02279 345 -FSDSLGGYLKDTGAVLELFRASQISYPDESLLEKQNSWTSHFLEQGLSNWSKTADRLRKYIKKEVEDALNFPYYANLER 423 (784)
T ss_pred -ccchhcccchhhHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHHhcccccccccCccHHHHHHHHhcCchhcCccH
Confidence 99998 599999999999999999999999999999999998 248999999999999999999
Q ss_pred hHHhhhhhhhhccCCc------------ccHHHHHHHhhhhHHHHHhhHHHHHHHHHHHHHhCCCCCCchhhhhhhHhHH
Q 035568 170 IEARFFISLYQEHEPL------------HNKALLKLAKLDFNQVQSLYKIELSEISRWWKDLDFARKLPFARDRVVECYF 237 (518)
Q Consensus 170 ~e~r~yI~~y~~~~~~------------~n~~ll~lAkldFn~~Q~~hq~El~~l~rWwk~~~l~~~l~faRdR~ve~yf 237 (518)
||||+||++|++ ++. +|++||||||+|||+||++||+||++++|||+++|| .++||||||++||||
T Consensus 424 lEaR~yI~~Y~~-~~~~i~Kt~yr~~~~~n~~lLeLAklDFN~~Qs~hq~EL~~l~rWwke~~L-~~L~faRdr~ve~Yf 501 (784)
T PLN02279 424 LANRRSIENYAV-DDTRILKTSYRCSNICNQDFLKLAVEDFNFCQSIHREELKQLERWIVENRL-DKLKFARQKLAYCYF 501 (784)
T ss_pred HHHHHHHHHhcc-ccchhccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhCeeHHhcCC-ccCCchhhHHHHHHH
Confidence 999999999998 875 899999999999999999999999999999999999 699999999999999
Q ss_pred HHhccccCcchhHHHHHHHHHhhhhhhhhcccccCCCHHHHHHHHHHhhhcCcc-ccccCChhHHHHHHHHHHHHHHHHH
Q 035568 238 WIVGVYFEPQYSLARKLLTKVISMTSIIDDIYDVYGIPEELDLFTAAIDRWDVS-CIDQLPEYMQTFYVALLDLYKEIEE 316 (518)
Q Consensus 238 ~~~a~~feP~~s~~Rl~laK~~~l~~i~DD~fD~~gt~eEl~~~t~ai~rWd~~-~~~~lpe~mk~~f~al~~~~~ei~~ 316 (518)
|++|++|||+||.+|++|||.+++++++||+||+|||+|||++||+||+|||.+ .++.+|+|||+||.+|+++++|++.
T Consensus 502 ~aaa~~fEPe~S~aRi~~aK~~~L~tviDD~fD~yGt~eEL~~ft~aVeRWD~~~~~~~lpeymki~f~aL~~t~nei~~ 581 (784)
T PLN02279 502 SAAATLFSPELSDARLSWAKNGVLTTVVDDFFDVGGSEEELENLIQLVEKWDVNGSPDFCSEQVEIIFSALRSTISEIGD 581 (784)
T ss_pred HHHHhhcCchhhHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHhccccchhhCcHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999998 6689999999999999999999997
Q ss_pred HHH-hcCCcchHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCc
Q 035568 317 ELA-TKGWSYRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGK 395 (518)
Q Consensus 317 ~~~-~~~~~~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~ 395 (518)
++. ++|+ ++++|++++|++++++|++||+|+.+||+||++|||+|+.+|+|+++++..+++++|+.+|+++++| +++
T Consensus 582 ~~~~~qGr-~v~~~l~~aW~~ll~ayl~EAeW~~~g~vPT~eEYL~na~vS~~l~~i~l~~~~~~G~~l~eev~e~-~~~ 659 (784)
T PLN02279 582 KAFTWQGR-NVTSHIIKIWLDLLKSMLTEAQWSSNKSTPTLDEYMTNAYVSFALGPIVLPALYLVGPKLSEEVVDS-PEL 659 (784)
T ss_pred HHHHHcCc-hHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhhchhhhhhHHHHHHHHHHhCCCCCHHHHhC-cch
Confidence 754 5666 7899999999999999999999999999999999999999999999999999999999999999999 799
Q ss_pred hHHHHHHhhhhhhccCccchhhhhhcCCCchHHHHHHhhcccCCcccCHHHHHHHHHHHHHHHHHHHHhhccCC--CCCC
Q 035568 396 PKIIRASTIIGRLMDDIKSHKFEQERGHAASAIECYMKEKEREGVSVTEQEVHEELYKKVGDAWKDINEECLMP--TEVP 473 (518)
Q Consensus 396 ~~i~~~~~~i~RL~NDI~S~~kE~~~G~~~n~V~cym~e~~~~g~~vS~eeA~~~i~~~i~~~~k~ln~~~l~~--~~~p 473 (518)
|+|+++++.|+||+|||+||++|+++|++ |+|+|||+|++ +| +|+|||+++++++|+++||+||++++++ +++|
T Consensus 660 ~~L~~l~s~I~RLlNDI~S~e~E~~rG~~-nsV~cYMke~~-~g--vSeEEAi~~i~~~Ie~~wKeLn~~~l~~~~~~vp 735 (784)
T PLN02279 660 HKLYKLMSTCGRLLNDIRGFKRESKEGKL-NAVSLHMIHGN-GN--STEEEAIESMKGLIESQRRELLRLVLQEKGSNVP 735 (784)
T ss_pred hHHHHHHHHHHHHHHhccccHhHHhCCCc-ceehhhhccCC-CC--CCHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCC
Confidence 99999999999999999999999999998 99999999972 05 9999999999999999999999999963 5799
Q ss_pred HHHHHHHHHHHhhhhhhcccCCCCCCCChhHHHHHHHhcccccCC
Q 035568 474 RPLLMRVLNLSRVIDVIYKEGDGYTHVGQVMKDNIASVLIHPVAI 518 (518)
Q Consensus 474 ~~~~~~~~n~aR~~~~~Y~~~Dg~t~~~~~~k~~i~~ll~~pi~~ 518 (518)
++|++++||++|++++||+++||||.+ .||++|++||++|||+
T Consensus 736 ~~~~~~~ln~aR~~~~~Y~~~Dgyt~~--~~k~~i~~ll~ePi~l 778 (784)
T PLN02279 736 RECKDLFWKMSKVLHLFYRKDDGFTSN--DMMSLVKSVIYEPVSL 778 (784)
T ss_pred HHHHHHHHHHHHhhhhheeCCCCCChH--HHHHHHHHHhccCCcC
Confidence 999999999999999999999999974 5999999999999985
No 3
>PLN02592 ent-copalyl diphosphate synthase
Probab=100.00 E-value=4e-110 Score=927.29 Aligned_cols=442 Identities=23% Similarity=0.368 Sum_probs=400.4
Q ss_pred CcChhhhhHHHHHHHHhCCccccHHHHHHHHHHHHHhcccCcCCC----CCCChhHHHHHHHHhhhcCceechhhhhccc
Q 035568 27 GVDSLSRLKLIDAILRLGVGYQFERELEEALQNLYDAFSNNFYNI----EDNDLYHVALRFRILRQRGYKVSCDIFNKFK 102 (518)
Q Consensus 27 ~~~~~~~l~liD~lqrLGi~~hF~~EI~~~L~~~~~~~~~~~~~~----~~~dl~~~al~FRlLR~hGy~vS~dvf~~F~ 102 (518)
|.+++++|++||+||||||+|||++||+++|+++|++|.++|+.. ...|+++|||+|||||||||+||||||++|+
T Consensus 307 P~d~fE~LwlVDtLqRLGIs~hF~~EI~~iLd~iy~~w~~~g~~~a~~~~~~Dld~TALaFRLLRqhGy~VS~DvF~~F~ 386 (800)
T PLN02592 307 PVDLFEHIWAVDRLQRLGISRYFEPEIKECIDYVHRYWTENGICWARNSHVHDIDDTAMGFRLLRLHGHQVSADVFKHFE 386 (800)
T ss_pred CCcHHHHHHHHHHHHHcCCccccHHHHHHHHHHHHHHHhhcCcccccCCCcCCHHHHHHHHHHHHHcCCCCChHHHHhhc
Confidence 689999999999999999999999999999999999997655422 1369999999999999999999999999998
Q ss_pred cccccccccc---ccchhhhhhHhhhcccCCCCchHHHHHHHHHHhhcc---------------cCcHHHHHHHccCCcc
Q 035568 103 DGKGNFKESL---KTDVSGMLSLYEAAHLVVHGEDILNEAIAFTTAHLQ---------------SSMAPQVIHALRQPLY 164 (518)
Q Consensus 103 d~~g~F~~~~---~~dv~~lL~LyeAs~l~~~gE~iLdea~~ft~~~L~---------------~~l~~~V~~aL~~P~~ 164 (518)
+ +|+|++.+ .+|++||||||||||+++|||+|||+|+.||++||+ ++|+++|+|||++|||
T Consensus 387 ~-~g~F~~~~ge~~~Dv~glL~LYeAS~l~~~gE~iLdeA~~Fs~~~L~~~~~~~~l~d~~~~~~~L~~eV~~AL~~P~~ 465 (800)
T PLN02592 387 K-GGEFFCFAGQSTQAVTGMFNLYRASQVLFPGEKILENAKEFSSKFLREKQEANELLDKWIIMKDLPGEVGFALEIPWY 465 (800)
T ss_pred C-CCCccccccccccchHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHHHHhhccccccccccCccHHHHHHHhccChhh
Confidence 6 89998765 799999999999999999999999999999999998 2588999999999999
Q ss_pred CCchhhHHhhhhhhhhccCCcc-------------cHHHHHHHhhhhHHHHHhhHHHHHHHHHHHHHhCCCCCCchhhhh
Q 035568 165 KGLPRIEARFFISLYQEHEPLH-------------NKALLKLAKLDFNQVQSLYKIELSEISRWWKDLDFARKLPFARDR 231 (518)
Q Consensus 165 ~~~~r~e~r~yI~~y~~~~~~~-------------n~~ll~lAkldFn~~Q~~hq~El~~l~rWwk~~~l~~~l~faRdR 231 (518)
+++||+|||+||++|++ ++++ |+.||||||+|||+||++||+||++++||||++|| .+|||||||
T Consensus 466 ~~l~RlEaR~yI~~Y~~-~~~~~i~Kt~yr~~~~~n~~lLeLAklDFn~~Qs~hq~EL~~lsrWwke~~L-~~L~faRdr 543 (800)
T PLN02592 466 ASLPRVETRFYIEQYGG-EDDVWIGKTLYRMPYVNNNEYLELAKLDYNNCQALHQLEWDNFQKWYEECNL-GEFGVSRSE 543 (800)
T ss_pred cCcchHHHHHHHHHhcC-CcccchhhhhccccccCCHHHHHHHHHHHHHHHHHhHHHHHHHhHHHHhcCC-CcCCcchhH
Confidence 99999999999999997 6654 99999999999999999999999999999999999 599999999
Q ss_pred hhHhHHHHhccccCcchhHHHHHHHHHhhhhhhhhcccccCCCHHHHHHHHHHhh--------hcCccccccCCh-----
Q 035568 232 VVECYFWIVGVYFEPQYSLARKLLTKVISMTSIIDDIYDVYGIPEELDLFTAAID--------RWDVSCIDQLPE----- 298 (518)
Q Consensus 232 ~ve~yf~~~a~~feP~~s~~Rl~laK~~~l~~i~DD~fD~~gt~eEl~~~t~ai~--------rWd~~~~~~lpe----- 298 (518)
++|||||++|++|||+||.+|++|||.+++++++||+||+|||+||+++||++|+ |||.+.+++||+
T Consensus 544 ~ve~Yfwa~~~~feP~~s~~Ri~~aK~~~LitviDD~fD~yGt~eEl~~ft~~v~~~~~~~~~rWd~~~~~~lp~~~~~~ 623 (800)
T PLN02592 544 LLLAYFLAAASIFEPERSHERLAWAKTTVLVEAISSYFNKETSSKQRRAFLHEFGYGYKINGRRSDHHFNDRNMRRSGSV 623 (800)
T ss_pred HHHHHHHHHHhhcCccchHHHHHHHHHHHHHHhhcccccCCCCHHHHHHHHHHHHhcccccccccCchhhhcccccccch
Confidence 9999999999999999999999999999999999999999999999999999996 999999999988
Q ss_pred -hHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHH
Q 035568 299 -YMQTFYVALLDLYKEIEEELATKGWSYRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASF 377 (518)
Q Consensus 299 -~mk~~f~al~~~~~ei~~~~~~~~~~~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~ 377 (518)
|||+||.||++++|+++.++.+.+|.++.+|++++|.++|+ +|..+|+ +|+|...+++.++
T Consensus 624 ~~mki~f~aLy~tineia~~a~~~qGr~v~~~L~~~W~~l~~------~w~~~g~------------~s~~~~~ilv~~~ 685 (800)
T PLN02592 624 KTGEELVGLLLGTLNQLSLDALEAHGRDISHLLRHAWEMWLL------KWLLEGD------------GRQGEAELLVKTI 685 (800)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHH------HHHhcCc------------eeccchhhHHHHH
Confidence 99999999999999998777665555789999999999999 4555554 4456666666777
Q ss_pred H-hcCCCCchHHHhhccCchHHHHHHhhhhhhccCccchhhhhhcCCCchHHHHHHhhcccCCcccCHHHHHHHHHHHHH
Q 035568 378 L-GMDSVVTKEAFDWVSGKPKIIRASTIIGRLMDDIKSHKFEQERGHAASAIECYMKEKEREGVSVTEQEVHEELYKKVG 456 (518)
Q Consensus 378 ~-~~g~~l~~ev~e~~~~~~~i~~~~~~i~RL~NDI~S~~kE~~~G~~~n~V~cym~e~~~~g~~vS~eeA~~~i~~~i~ 456 (518)
+ .+|+.+|+++++ +|++.++++.+.||+||++|+++|+. ++ | ++|+ +|.+++.+.|+
T Consensus 686 ~l~~g~~lsee~l~----~~~~~~l~~li~Rl~nDl~t~~~e~~--------------~~--~-~~~~-~a~~~~~~~ie 743 (800)
T PLN02592 686 NLTAGRSLSEELLA----HPQYEQLAQLTNRICYQLGHYKKNKV--------------HI--N-TYNP-EEKSKTTPSIE 743 (800)
T ss_pred HHhcCCCCCHHHcc----chhHHHHHHHHHHHHHhhhHHhhhcc--------------cC--C-cccH-HHHHHHHHHHH
Confidence 7 559999999887 48888999999999999999999873 32 3 2566 89999999999
Q ss_pred HHHHHHHhhccC--CCCCCHHHHHHHHHHHhhhhhhcccCCCCCCCChhHHHHHHHhcccccC
Q 035568 457 DAWKDINEECLM--PTEVPRPLLMRVLNLSRVIDVIYKEGDGYTHVGQVMKDNIASVLIHPVA 517 (518)
Q Consensus 457 ~~~k~ln~~~l~--~~~~p~~~~~~~~n~aR~~~~~Y~~~Dg~t~~~~~~k~~i~~ll~~pi~ 517 (518)
.+++++.+.+++ ++.+|++|++.|||++| +||.. ||+.| ++|+.+|.++|++||+
T Consensus 744 ~~~~eL~~lvl~~~~~~vp~~cK~~f~~~~k---~fy~~--~~~~~-~~~~~~i~~vl~epv~ 800 (800)
T PLN02592 744 SDMQELVQLVLQNSSDDIDPVIKQTFLMVAK---SFYYA--AYCDP-GTINYHIAKVLFERVA 800 (800)
T ss_pred HHHHHHHHHHhhcCCCCCCHHHHHHHHHHHH---HHHHh--hcCCH-HHHHHHHHHHhCCCCC
Confidence 999999999996 35699999999999999 45655 99998 4699999999999985
No 4
>PF01397 Terpene_synth: Terpene synthase, N-terminal domain; InterPro: IPR001906 Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C10) synthases, sesquiterpene (C15) synthases and the diterpene (C20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf []. Tpsa includes vetispiridiene synthase Q39979 from SWISSPROT, 5-epi- aristolochene synthase, Q40577 from SWISSPROT and (+)-delta-cadinene synthase P93665 from SWISSPROT . Tpsb includes (-)-limonene synthase, Q40322 from SWISSPROT. Tpsc includes copalyl diphosphate synthase (kaurene synthase A), O04408 from SWISSPROT. Tpsd includes taxadiene synthase, Q41594 from SWISSPROT, pinene synthase, O24475 from SWISSPROT and myrcene synthase, O24474 from SWISSPROT. Tpse includes ent-kaurene synthase B Q39548 from SWISSPROT. Tpsf includes linalool synthase Q9ZPN5 from SWISSPROT. In the fungus Phaeosphaeria sp. (strain L487) the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein [].; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 2ONH_A 2ONG_B 3P5R_A 3P5P_A 3N0F_A 3N0G_B 3PYB_A 3PYA_A 3G4F_A 3G4D_B ....
Probab=100.00 E-value=7.1e-53 Score=398.27 Aligned_cols=152 Identities=57% Similarity=0.872 Sum_probs=133.7
Q ss_pred cchHHHHHHHHHHHHHHhhccCcChhhhhHHHHHHHHhCCccccHHHHHHHHHHHHHhcccCcCCCCCCChhHHHHHHHH
Q 035568 6 GGQSQEIEELKEEVRRELLGSGVDSLSRLKLIDAILRLGVGYQFERELEEALQNLYDAFSNNFYNIEDNDLYHVALRFRI 85 (518)
Q Consensus 6 ~~~~~~~~~lk~~v~~~l~~~~~~~~~~l~liD~lqrLGi~~hF~~EI~~~L~~~~~~~~~~~~~~~~~dl~~~al~FRl 85 (518)
+.+.+++++||++||.||.....|++++|+|||+||||||+|||++||+++|+++|+.|...+. ...||++|||+|||
T Consensus 22 ~~~~~~~~~Lk~~v~~~l~~~~~d~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~~~--~~~dL~~~AL~FRL 99 (183)
T PF01397_consen 22 EKCKERAEELKEEVRNMLPASYPDPLEKLELIDTLQRLGISYHFEDEIKEILDSIYRSWDEDNE--EIDDLYTTALRFRL 99 (183)
T ss_dssp HHHHHHHHHHHHHHHHHHHSSSSHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHHTTTTTSH--TSSCHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHhhhcccccc--ccCchhHHHHHHHH
Confidence 4568999999999999998754589999999999999999999999999999999999865321 22499999999999
Q ss_pred hhhcCceechhhhhcccccccccccccccchhhhhhHhhhcccCCCCchHHHHHHHHHHhhcc--------c--CcHHHH
Q 035568 86 LRQRGYKVSCDIFNKFKDGKGNFKESLKTDVSGMLSLYEAAHLVVHGEDILNEAIAFTTAHLQ--------S--SMAPQV 155 (518)
Q Consensus 86 LR~hGy~vS~dvf~~F~d~~g~F~~~~~~dv~~lL~LyeAs~l~~~gE~iLdea~~ft~~~L~--------~--~l~~~V 155 (518)
||||||+||||||++|+|++|+|++++.+||+||||||||||+++|||+|||||+.||++||+ + +|+++|
T Consensus 100 LRqhGy~VS~DvF~~F~d~~g~F~~~l~~Dv~glLsLYeAS~l~~~gE~iLdeA~~Ft~~~L~~~~~~~~~~~~~L~~~V 179 (183)
T PF01397_consen 100 LRQHGYYVSSDVFNKFKDEKGNFKESLSNDVKGLLSLYEASHLRFHGEDILDEARAFTTKHLKSLLSNLSIPDPHLAKEV 179 (183)
T ss_dssp HHHTT----GGGGGGGBETTSSBSGGGGGHHHHHHHHHHHHTT--TT-HHHHHHHHHHHHHHHHHHTTTCTTSCHHHHHH
T ss_pred HHHcCCcccHHHHhCcccCCCccchhhhHhHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999 2 399999
Q ss_pred HHHc
Q 035568 156 IHAL 159 (518)
Q Consensus 156 ~~aL 159 (518)
+|||
T Consensus 180 ~~AL 183 (183)
T PF01397_consen 180 KHAL 183 (183)
T ss_dssp HHHH
T ss_pred HHhC
Confidence 9997
No 5
>PF03936 Terpene_synth_C: Terpene synthase family, metal binding domain; InterPro: IPR005630 Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C10) synthases, sesquiterpene (C15) synthases and the diterpene (C20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf []. Tpsa includes vetispiridiene synthase Q39979 from SWISSPROT, 5-epi- aristolochene synthase, Q40577 from SWISSPROT and (+)-delta-cadinene synthase P93665 from SWISSPROT . Tpsb includes (-)-limonene synthase, Q40322 from SWISSPROT. Tpsc includes copalyl diphosphate synthase (kaurene synthase A), O04408 from SWISSPROT. Tpsd includes taxadiene synthase, Q41594 from SWISSPROT, pinene synthase, O24475 from SWISSPROT and myrcene synthase, O24474 from SWISSPROT. Tpse includes ent-kaurene synthase B Q39548 from SWISSPROT. Tpsf includes linalool synthase Q9ZPN5 from SWISSPROT. In the fungus Phaeosphaeria sp. (strain L487) the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein [].; GO: 0000287 magnesium ion binding, 0016829 lyase activity; PDB: 3PYB_A 3PYA_A 3G4F_A 3G4D_B 3CKE_A 2OA6_D 2E4O_B 3BNY_B 3BNX_A 3LG5_A ....
Probab=100.00 E-value=9.2e-49 Score=391.49 Aligned_cols=269 Identities=26% Similarity=0.413 Sum_probs=247.6
Q ss_pred HHHHHhhhhHHHHHhhHHHHHHHHHHHHHhCCCCCCchhhhhhhHhHHHHhccccCcchhHHHHHHHHHhhhhhhhhccc
Q 035568 190 LLKLAKLDFNQVQSLYKIELSEISRWWKDLDFARKLPFARDRVVECYFWIVGVYFEPQYSLARKLLTKVISMTSIIDDIY 269 (518)
Q Consensus 190 ll~lAkldFn~~Q~~hq~El~~l~rWwk~~~l~~~l~faRdR~ve~yf~~~a~~feP~~s~~Rl~laK~~~l~~i~DD~f 269 (518)
+|+|||+|||.||++||+|++++++||+++||..+.+.+|+|++.++|+.++.++.|..+..|+++||+++|+|++||+|
T Consensus 1 ~~~la~~~~~~~~~~~~~e~~~~~~W~~~~~l~~~~~~~~~~~~~~~~~~~aa~~~P~~~~~l~~~a~~~~w~f~~DD~~ 80 (270)
T PF03936_consen 1 YLELAKRDFPHCQALHQQELEEIDRWVKEFGLFDEDKAARQRFRQAYFGLLAARFYPDSSDELLAAADWMAWLFIFDDFF 80 (270)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTHHHHHTTSHHHHHHHHHHHHHHHHSGCGHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcccchhhcHhhHHHHHHHHHHHHHHHHHcCCccccccchhhhhHhHHhhhhheeCCCcHHHHHHHHhhchheeeeeecc
Confidence 68999999999999999999999999999999767787899999999999999999997777889999999999999999
Q ss_pred ccCCCHHHHHHHHHHhhhcCccccccCChhHHHHHHHHHHHHHHHHHHHHhc-CCcchHHHHHHHHHHHHHHHHHHHhHh
Q 035568 270 DVYGIPEELDLFTAAIDRWDVSCIDQLPEYMQTFYVALLDLYKEIEEELATK-GWSYRVHYAKEEMKILVHGYHDESKWF 348 (518)
Q Consensus 270 D~~gt~eEl~~~t~ai~rWd~~~~~~lpe~mk~~f~al~~~~~ei~~~~~~~-~~~~~~~~~k~~~~~~~~a~l~EA~W~ 348 (518)
|.+|+.++++.|+++++||++...+.+|+.+++++.++.++++++...+.+. ++....+++++.|.++++++++|++|+
T Consensus 81 D~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 160 (270)
T PF03936_consen 81 DDGGSAEELEALTDAVERWDPNSGDPLPDPDKPLFRALADIWNRIAARMSPAQRRRDQIKRFRNSWREYLNAYLWEARWR 160 (270)
T ss_dssp HTTSHHHHHHHHHHHHHHTSSGGGGGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccchHHHHHHHHHHhcccccccccccchhHHHHHHHHHHHHHHHHHhhhhhcccHHhhHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999888888899999999999999999998777664 222357789999999999999999999
Q ss_pred cCCCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCchHHHHHHhhhhhhccCccchhhhhhcCCCchHH
Q 035568 349 HNNYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGKPKIIRASTIIGRLMDDIKSHKFEQERGHAASAI 428 (518)
Q Consensus 349 ~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~i~~~~~~i~RL~NDI~S~~kE~~~G~~~n~V 428 (518)
..|++||++||+++|+.|+|+++++.++.+++|..+++...+++.+.+.+.++++.+++|+|||.||+||+++|+.+|.|
T Consensus 161 ~~~~~ps~eeYl~~R~~t~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~NDl~S~~KE~~~g~~~N~v 240 (270)
T PF03936_consen 161 ERGRIPSLEEYLEMRRHTSGVYPCLALIEFALEFALGELPPEVLEHPPMLRRLAADIIRLVNDLYSYKKEIARGDVHNLV 240 (270)
T ss_dssp HTTS--SHHHHHHHHHHHTSHHHHHHHHHHHCSSCHTHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCSHH
T ss_pred ccCCCCCHHHHHHhccccccccHHHHHHHHhCCCccccccHHHHHhchHHHHHHHHHHHHhcccchhhcchhhcccccHH
Confidence 99999999999999999999999999999999877776666665566779999999999999999999999999999999
Q ss_pred HHHHhhcccCCcccCHHHHHHHHHHHHHHHHHHHH
Q 035568 429 ECYMKEKEREGVSVTEQEVHEELYKKVGDAWKDIN 463 (518)
Q Consensus 429 ~cym~e~~~~g~~vS~eeA~~~i~~~i~~~~k~ln 463 (518)
.|+|+++ | +|.|+|++++.+|+++++++||
T Consensus 241 ~~l~~~~---~--~s~e~A~~~v~~~~~~~~~efn 270 (270)
T PF03936_consen 241 VVLMNEH---G--LSLEEAVDEVAEMINECIREFN 270 (270)
T ss_dssp HHHHHHH---T--HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHhhhhc---C--CCHHHHHHHHHHHHHHHHHhcC
Confidence 9999999 9 9999999999999999999998
No 6
>cd00868 Terpene_cyclase_C1 Terpene cyclases, Class 1. Terpene cyclases, Class 1 (C1) of the class 1 family of isoprenoid biosynthesis enzymes, which share the 'isoprenoid synthase fold' and convert linear, all-trans, isoprenoids, geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate into numerous cyclic forms of monoterpenes, diterpenes, and sesquiterpenes. Also included in this CD are the cis-trans terpene cyclases such as trichodiene synthase. The class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational ch
Probab=100.00 E-value=1.6e-46 Score=377.96 Aligned_cols=282 Identities=52% Similarity=0.883 Sum_probs=265.4
Q ss_pred hhHHHHHHHHHHHHHhCCCCCCchhhhhhhHhHHHHhccccCcchhHHHHHHHHHhhhhhhhhcccccCCCHHHHHHHHH
Q 035568 204 LYKIELSEISRWWKDLDFARKLPFARDRVVECYFWIVGVYFEPQYSLARKLLTKVISMTSIIDDIYDVYGIPEELDLFTA 283 (518)
Q Consensus 204 ~hq~El~~l~rWwk~~~l~~~l~faRdR~ve~yf~~~a~~feP~~s~~Rl~laK~~~l~~i~DD~fD~~gt~eEl~~~t~ 283 (518)
.||+|++++++||+++||....+++|.+...+|+|+++++++|+.+..|+++||+++|+|++||+||.+|+.+++..+++
T Consensus 1 ~~~~e~~~~~~W~~~~~l~~~~~~~r~~~~~~~~~~a~~~p~~~~~~~l~~~a~~~~~~f~~DD~~D~~~~~~~~~~~~~ 80 (284)
T cd00868 1 LHQEELKELSRWWKELGLQEKLPFARDRLVECYFWAAGSYFEPQYSEARIALAKTIALLTVIDDTYDDYGTLEELELFTE 80 (284)
T ss_pred CCHHHHHHHHHHHHHhCCcccCCchhhHhHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHHHhccccCCCHHHHHHHHH
Confidence 49999999999999999976666999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhcCccccccCChhHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhh
Q 035568 284 AIDRWDVSCIDQLPEYMQTFYVALLDLYKEIEEELATKGWSYRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVS 363 (518)
Q Consensus 284 ai~rWd~~~~~~lpe~mk~~f~al~~~~~ei~~~~~~~~~~~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~ 363 (518)
+++||+....+.+|+++++++.++.++++++...+.++++.....++++.|.+++.++.+|++|+..|++||++||+.+|
T Consensus 81 ~~~~~~~~~~~~~p~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~e~~~~~~~~~p~~~eYl~~R 160 (284)
T cd00868 81 AVERWDISAIDELPEYMKPVFKALYDLVNEIEEELAKEGGSESLPYLKEAWKDLLRAYLVEAKWANEGYVPSFEEYLENR 160 (284)
T ss_pred HHHhcChhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHhc
Confidence 99999988888999999999999999999999888876666779999999999999999999999999999999999999
Q ss_pred hcccchhHHHHHHHHhcCCCCch-HHHhhccCchHHHHHHhhhhhhccCccchhhhhhcCCCchHHHHHHhhcccCCccc
Q 035568 364 LVTSGYSMLTAASFLGMDSVVTK-EAFDWVSGKPKIIRASTIIGRLMDDIKSHKFEQERGHAASAIECYMKEKEREGVSV 442 (518)
Q Consensus 364 ~~S~g~~~~~~~~~~~~g~~l~~-ev~e~~~~~~~i~~~~~~i~RL~NDI~S~~kE~~~G~~~n~V~cym~e~~~~g~~v 442 (518)
+.|+|++++++++++++|..+|+ ++.+. +..+++++.++.+++|+||++||+||+.+|+.+|+|.|||+++ | +
T Consensus 161 ~~~~g~~~~~~l~~~~~g~~l~~~~~~~~-~~~~~l~~~~~~~~~l~NDl~S~~kE~~~g~~~N~v~vl~~~~---~--~ 234 (284)
T cd00868 161 RVSIGYPPLLALSFLGMGDILPEEAFEWL-PSYPKLVRASSTIGRLLNDIASYEKEIARGEVANSVECYMKEY---G--V 234 (284)
T ss_pred eehhhHHHHHHHHHHHcCCCCCHHHHHHh-hhhHHHHHHHHHHHHHhccchHHHHHHccCCcccHHHHHHhcc---C--C
Confidence 99999999999999999999998 55555 8999999999999999999999999999999999999999999 9 9
Q ss_pred CHHHHHHHHHHHHHHHHHHHHhhccCC-CCCCHHHHHHHHHHHhhhhhhc
Q 035568 443 TEQEVHEELYKKVGDAWKDINEECLMP-TEVPRPLLMRVLNLSRVIDVIY 491 (518)
Q Consensus 443 S~eeA~~~i~~~i~~~~k~ln~~~l~~-~~~p~~~~~~~~n~aR~~~~~Y 491 (518)
|.++|++++.++++++|++|++..... ++.|+.+++.+.|.+|.....|
T Consensus 235 ~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~g~~~w~ 284 (284)
T cd00868 235 SEEEALEELRKMIEEAWKELNEEVLKLSSDVPRAVLETLLNLARGIYVWY 284 (284)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhhhhcC
Confidence 999999999999999999999999863 3678999999999999876654
No 7
>cd00687 Terpene_cyclase_nonplant_C1 Non-plant Terpene Cyclases, Class 1. This CD includes terpenoid cyclases such as pentalenene synthase and aristolochene synthase which, using an all-trans pathway, catalyze the ionization of farnesyl diphosphate, followed by the formation of a macrocyclic intermediate by bond formation between C1 with either C10 (aristolochene synthase) or C11 (pentalenene synthase), resulting in production of tricyclic hydrocarbon pentalenene or bicyclic hydrocarbon aristolochene. As with other enzymes with the 'terpenoid synthase fold', they have two conserved metal binding motifs, proposed to coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP to the enzymes. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function in the monomeric form and are found in
Probab=100.00 E-value=3e-34 Score=292.84 Aligned_cols=246 Identities=16% Similarity=0.117 Sum_probs=217.5
Q ss_pred HHHHHHHHHhCCCCCCchhhhhhhHhHHHHhccccCcchhHHHH-HHHHHhhhhhhhhcccccC-CCHHHHHHHHHHhhh
Q 035568 210 SEISRWWKDLDFARKLPFARDRVVECYFWIVGVYFEPQYSLARK-LLTKVISMTSIIDDIYDVY-GIPEELDLFTAAIDR 287 (518)
Q Consensus 210 ~~l~rWwk~~~l~~~l~faRdR~ve~yf~~~a~~feP~~s~~Rl-~laK~~~l~~i~DD~fD~~-gt~eEl~~~t~ai~r 287 (518)
++...|.++.|+. .-+.+|++...++|+.++.++.|+++..|+ +.++++.|+|++||+||.. +++++++.+++.+.+
T Consensus 17 ~~~~~w~~~~~l~-~~~~~~~~~~~~~~~~~~a~~~P~a~~~~l~l~~~~~~w~f~~DD~~D~~~~~~~~~~~~~~~~~~ 95 (303)
T cd00687 17 DEYLEWVLEEMLI-PSEKAEKRFLSADFGDLAALFYPDADDERLMLAADLMAWLFVFDDLLDRDQKSPEDGEAGVTRLLD 95 (303)
T ss_pred HHHHHHHHHcCCC-CcchhHHHHhcCCHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhcccCCccccCHHHHHHHHHHHHh
Confidence 3467899999774 334699999998888877778899999999 7779999999999999987 499999999988888
Q ss_pred cCcc-ccccCChhHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcc
Q 035568 288 WDVS-CIDQLPEYMQTFYVALLDLYKEIEEELATKGWSYRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVT 366 (518)
Q Consensus 288 Wd~~-~~~~lpe~mk~~f~al~~~~~ei~~~~~~~~~~~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S 366 (518)
+... ..+. |....++..++.+++.++...+.. ....++++.|.+++.++++|++|+.+|++||++||+++|+.|
T Consensus 96 ~~~~~~~~~-~~~~~p~~~~~~d~~~r~~~~~~~----~~~~r~~~~~~~~~~a~~~e~~~~~~~~~psl~eYl~~R~~~ 170 (303)
T cd00687 96 ILRGDGLDS-PDDATPLEFGLADLWRRTLARMSA----EWFNRFAHYTEDYFDAYIWEGKNRLNGHVPDVAEYLEMRRFN 170 (303)
T ss_pred ccCCCCCCC-CCCCCHHHHHHHHHHHHhccCCCH----HHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhhhc
Confidence 7443 2222 567788999999999998654322 347889999999999999999999999999999999999999
Q ss_pred cchhHHHHHHHHhcCCCCchHHHhhccCchHHHHHHhhhhhhccCccchhhhh-hcCCCchHHHHHHhhcccCCcccCHH
Q 035568 367 SGYSMLTAASFLGMDSVVTKEAFDWVSGKPKIIRASTIIGRLMDDIKSHKFEQ-ERGHAASAIECYMKEKEREGVSVTEQ 445 (518)
Q Consensus 367 ~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~i~~~~~~i~RL~NDI~S~~kE~-~~G~~~n~V~cym~e~~~~g~~vS~e 445 (518)
+|+.+++.++++++|..+|+++.++ +.+.++.++++.+++|+|||+||+||+ +.|+.+|+|.|+|+++ | +|.|
T Consensus 171 ~g~~~~~~l~~~~~g~~lp~~~~~~-~~~~~l~~~~~~~~~l~NDl~S~~KE~~~~g~~~N~V~vl~~~~---g--~s~~ 244 (303)
T cd00687 171 IGADPCLGLSEFIGGPEVPAAVRLD-PVMRALEALASDAIALVNDIYSYEKEIKANGEVHNLVKVLAEEH---G--LSLE 244 (303)
T ss_pred ccccccHHHHHHhcCCCCCHHHHhC-hHHHHHHHHHHHHHHHHHHHHhhHHHHHhCCccchHHHHHHHHc---C--CCHH
Confidence 9999999999999999999999998 778899999999999999999999999 8999999999999999 9 9999
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc
Q 035568 446 EVHEELYKKVGDAWKDINEECL 467 (518)
Q Consensus 446 eA~~~i~~~i~~~~k~ln~~~l 467 (518)
+|++++.++++++++++.+..-
T Consensus 245 eA~~~~~~~~~~~~~~f~~~~~ 266 (303)
T cd00687 245 EAISVVRDMHNERITQFEELEA 266 (303)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999877543
No 8
>PLN02150 terpene synthase/cyclase family protein
Probab=99.96 E-value=3.9e-30 Score=219.01 Aligned_cols=95 Identities=46% Similarity=0.797 Sum_probs=92.1
Q ss_pred hhcCCCchHHHHHHhhcccCCcccCHHHHHHHHHHHHHHHHHHHHhhccCCCCCCHHHHHHHHHHHhhhhhh-cccCCCC
Q 035568 419 QERGHAASAIECYMKEKEREGVSVTEQEVHEELYKKVGDAWKDINEECLMPTEVPRPLLMRVLNLSRVIDVI-YKEGDGY 497 (518)
Q Consensus 419 ~~~G~~~n~V~cym~e~~~~g~~vS~eeA~~~i~~~i~~~~k~ln~~~l~~~~~p~~~~~~~~n~aR~~~~~-Y~~~Dg~ 497 (518)
++|||++|+|+|||+|| | +|+|||++++++||+++||++|+++++++++|.+++++++|+||+++|+ |++||||
T Consensus 1 ~~rg~vaSsIeCYMke~---g--~seeeA~~~i~~li~~~WK~iN~e~l~~~~~p~~~~~~~~NlaR~~~~~~Y~~~Dg~ 75 (96)
T PLN02150 1 MRRGEVANGVNCYMKQH---G--VTKEEAVSELKKMIRDNYKIVMEEFLTIKDVPRPVLVRCLNLARLIDVYCYNEGDGF 75 (96)
T ss_pred CCCCcchHHHHHHhccC---C--CCHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHhheecCCCCC
Confidence 47899999999999999 9 9999999999999999999999999999999999999999999999999 9999999
Q ss_pred CCCChhHHHHHHHhcccccCC
Q 035568 498 THVGQVMKDNIASVLIHPVAI 518 (518)
Q Consensus 498 t~~~~~~k~~i~~ll~~pi~~ 518 (518)
|.+++.+|++|++||++|||+
T Consensus 76 t~~~~~~K~~I~sLlv~pi~i 96 (96)
T PLN02150 76 TYPHGKLKDLITSLFFHPLPL 96 (96)
T ss_pred CCCcHHHHHHHHHHhccCCCC
Confidence 988888999999999999986
No 9
>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1. Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoter
Probab=99.85 E-value=5.2e-21 Score=184.28 Aligned_cols=229 Identities=30% Similarity=0.360 Sum_probs=184.7
Q ss_pred HHhccccCcchhHHHHHHHHHhhhhhhhhcccccCCCHHHHHHHHHHhhhcCccccccCChhHHHHHHHHHHHHHHHHHH
Q 035568 238 WIVGVYFEPQYSLARKLLTKVISMTSIIDDIYDVYGIPEELDLFTAAIDRWDVSCIDQLPEYMQTFYVALLDLYKEIEEE 317 (518)
Q Consensus 238 ~~~a~~feP~~s~~Rl~laK~~~l~~i~DD~fD~~gt~eEl~~~t~ai~rWd~~~~~~lpe~mk~~f~al~~~~~ei~~~ 317 (518)
++++.++.|+.+..|..++++..|++++||++|..++..........+ .....|..+...+..+.+.+.++...
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~DDi~D~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (243)
T cd00385 2 RPLAVLLEPEASRLRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAV------AIDGLPEAILAGDLLLADAFEELARE 75 (243)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCchhhhhhH------HhcCchHHHHHHHHHHHHHHHHHHhC
Confidence 456677889989999999999999999999999988776655554332 12345677778888888888888643
Q ss_pred HHhcCCcchHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCchH
Q 035568 318 LATKGWSYRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGKPK 397 (518)
Q Consensus 318 ~~~~~~~~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~ 397 (518)
.. .....++.+.|.+++.|+.+|+.|... +.||++||+.++..++ +.++..+...+++...|+ ..+.+...+
T Consensus 76 ~~----~~~~~~~~~~~~~~~~g~~~d~~~~~~-~~~t~~ey~~~~~~~t-~~~~~~~~~~~~~~~~~~--~~~~~~~~~ 147 (243)
T cd00385 76 GS----PEALEILAEALLDLLEGQLLDLKWRRE-YVPTLEEYLEYCRYKT-AGLVGALCLLGAGLSGGE--AELLEALRK 147 (243)
T ss_pred CC----HHHHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHHhH-HHHHHHHHHHHHHHhCCC--HHHHHHHHH
Confidence 22 245888999999999999999999877 8899999999999998 455555566666666665 333366788
Q ss_pred HHHHHhhhhhhccCccchhhhhhcC-CCchHHHHHHhhcccCCccc------------CHHHHHHHHHHHHHHHHHHHHh
Q 035568 398 IIRASTIIGRLMDDIKSHKFEQERG-HAASAIECYMKEKEREGVSV------------TEQEVHEELYKKVGDAWKDINE 464 (518)
Q Consensus 398 i~~~~~~i~RL~NDI~S~~kE~~~G-~~~n~V~cym~e~~~~g~~v------------S~eeA~~~i~~~i~~~~k~ln~ 464 (518)
+...++.+.+|.||+.|+.+|.++| +..|++.++|+++ | + +.++|.+++.++++++++++++
T Consensus 148 ~~~~~g~~~ql~nDl~~~~~e~~~~~~~~~l~~~~~~~~---~--~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~ 222 (243)
T cd00385 148 LGRALGLAFQLTNDLLDYEGDAERGEGKCTLPVLYALEY---G--VPAEDLLLVEKSGSLEEALEELAKLAEEALKELNE 222 (243)
T ss_pred HHHHHHHHHHHHHHHHhccCCHHHhCCchHHHHHHHHHh---C--ChhhHHHHHHHCChHHHHHHHHHHHHHHHHHHHhc
Confidence 8999999999999999999999986 6789999999999 8 7 8899999999999999999998
Q ss_pred hccCCCCCCHHHHHHHHHHHh
Q 035568 465 ECLMPTEVPRPLLMRVLNLSR 485 (518)
Q Consensus 465 ~~l~~~~~p~~~~~~~~n~aR 485 (518)
........+..+++.+.+++|
T Consensus 223 ~~~~~~~~~~~~~~~~~~~~~ 243 (243)
T cd00385 223 LILSLPDVPRALLALALNLYR 243 (243)
T ss_pred CCCCcHHHHHHHHHHHHHHhC
Confidence 776532356677777777653
No 10
>PF06330 TRI5: Trichodiene synthase (TRI5); InterPro: IPR024652 This family consists of several fungal trichodiene synthase proteins (EC:4.2.3.6). TRI5 encodes the enzyme trichodiene synthase, which has been shown to catalyse the first step in the trichothecene pathways of Fusarium and Trichothecium species [, ].; GO: 0045482 trichodiene synthase activity, 0016106 sesquiterpenoid biosynthetic process; PDB: 1YYT_A 2PS5_A 2AEL_A 1YYS_A 1YJ4_A 2Q9Y_A 2PS4_A 2AEK_B 1KIY_B 2PS7_A ....
Probab=97.83 E-value=0.00036 Score=72.79 Aligned_cols=202 Identities=15% Similarity=0.096 Sum_probs=117.3
Q ss_pred HHHhccccCcchh-HHHHHHHHHhhhhhhhhcccccCCCHHHHHHHHHHhhhcCccccccCChhHHHHHHHHHHHHHHHH
Q 035568 237 FWIVGVYFEPQYS-LARKLLTKVISMTSIIDDIYDVYGIPEELDLFTAAIDRWDVSCIDQLPEYMQTFYVALLDLYKEIE 315 (518)
Q Consensus 237 f~~~a~~feP~~s-~~Rl~laK~~~l~~i~DD~fD~~gt~eEl~~~t~ai~rWd~~~~~~lpe~mk~~f~al~~~~~ei~ 315 (518)
-+++...| |..+ +.++.+|=+.++++++||.++.. .+++..|-+-+-. +.+- |. ++..++.+.+.++-
T Consensus 71 v~~~~~~y-~~~~~evqv~IaiyT~yvi~iDD~~~~~--~~~l~~F~~~l~~--Gq~Q---~~---p~L~~~~~~L~~~~ 139 (376)
T PF06330_consen 71 VNMAVYCY-PHLPKEVQVAIAIYTTYVIIIDDSSQEP--SDDLRTFHQRLIL--GQPQ---KH---PLLDGFASLLREMW 139 (376)
T ss_dssp HHHHHHHS-TTS-HHHHHHHHHHHHHHHHHTT--S-S--HHHHTTHHHHHHH--T------SS---HHHHHHHHHHHHHH
T ss_pred hheeEeec-CCCCHHHHHHHHHHHHHHHhcccccccc--cHHHHHHHHHHhc--CCCC---CC---HHHHHHHHHHHHHH
Confidence 33433344 4433 56778899999999999998765 3566666544332 1111 11 34444455444443
Q ss_pred HHHHhcCCcchHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCc
Q 035568 316 EELATKGWSYRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGK 395 (518)
Q Consensus 316 ~~~~~~~~~~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~ 395 (518)
+.=++.+-+-+.++--+++.+..-|++.. +-.|.-..|-..-+.=+|+..+.+...+ -....|+. ..+
T Consensus 140 ----~~fgpf~anmI~~STLdFi~g~~LE~~~f--~~~p~A~~FP~fLR~ktGlsEaYA~FiF-Pk~~fpe~-----~~~ 207 (376)
T PF06330_consen 140 ----RHFGPFCANMIVKSTLDFINGCWLEQKNF--HGSPGAPDFPDFLRRKTGLSEAYAFFIF-PKALFPEV-----EYF 207 (376)
T ss_dssp ----TTS-HHHHHHHHHHHHHHHHHHHHHTTT------TT-TTHHHHHHHHHH-HHHHHHHT---TTTS-TT-----TTH
T ss_pred ----HHcchHHHHHHHHHHHHHHHHHHhhcccC--CCCCCCccccHHHHhccCcchhheeeec-ccccCChH-----HHH
Confidence 22123456677888999999999998753 2235444455555555666666554333 22222322 223
Q ss_pred hH---HHHHHhhhhhhccCccchhhhhh-cCCCchHHHHHHhhcccCCcccCHHHHHHHHHHHHHHHHHHHHhhc
Q 035568 396 PK---IIRASTIIGRLMDDIKSHKFEQE-RGHAASAIECYMKEKEREGVSVTEQEVHEELYKKVGDAWKDINEEC 466 (518)
Q Consensus 396 ~~---i~~~~~~i~RL~NDI~S~~kE~~-~G~~~n~V~cym~e~~~~g~~vS~eeA~~~i~~~i~~~~k~ln~~~ 466 (518)
.. ++--.+..+-++|||.||=||.- .|+-.|.|.-+..-+ | +|.-+|...+.+-.-++-+++.+..
T Consensus 208 ~~y~~AIpdl~~fi~~~NDILSFYKE~l~a~E~~NyI~n~A~~~---g--~S~~eaL~~l~~eti~a~~rv~~vL 277 (376)
T PF06330_consen 208 IQYTPAIPDLMRFINYVNDILSFYKEELVAGETGNYIHNRARVH---G--VSILEALRELTDETIEAVERVRRVL 277 (376)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSSSSHHHHHHHHH---T----HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhhhhHHHHHHhhcccccccchhhhhhhcc---C--CCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34 34444555569999999999976 788999998888878 9 9999999998666666666655543
No 11
>cd00686 Terpene_cyclase_cis_trans_C1 Cis, Trans, Terpene Cyclases, Class 1. This CD includes the terpenoid cyclase, trichodiene synthase, which catalyzes the cyclization of farnesyl diphosphate (FPP) to trichodiene using a cis-trans pathway, and is the first committed step in the biosynthesis of trichothecene toxins and antibiotics. As with other enzymes with the 'terpenoid synthase fold', this enzyme has two conserved metal binding motifs that coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function as homodimers and are found in several genera of fungi.
Probab=97.50 E-value=0.0031 Score=64.96 Aligned_cols=191 Identities=15% Similarity=0.070 Sum_probs=114.7
Q ss_pred hhHHHH-HHHHHhhhhhhhhcccccCCCHHHHHHHHHHhhhcCccccccCChhHHHHHHHHHHHHHHHHHHHHhcCCcch
Q 035568 248 YSLARK-LLTKVISMTSIIDDIYDVYGIPEELDLFTAAIDRWDVSCIDQLPEYMQTFYVALLDLYKEIEEELATKGWSYR 326 (518)
Q Consensus 248 ~s~~Rl-~laK~~~l~~i~DD~fD~~gt~eEl~~~t~ai~rWd~~~~~~lpe~mk~~f~al~~~~~ei~~~~~~~~~~~~ 326 (518)
.|..=+ .++-..+.++++||.-|... +.++.|.+-+.. +.+- ..| +...+.+.+..+-+.. |++.
T Consensus 81 ~skev~~~isi~~tY~~~lDD~~~e~~--~~m~~f~~dL~~--G~~q-khP-----~l~~v~~~l~~~lr~f----GpF~ 146 (357)
T cd00686 81 VSKECMADLSIHYTYTLVLDDSKDDPY--PTMVNYFDDLQA--GREQ-AHP-----WWALVNEHFPNVLRHF----GPFC 146 (357)
T ss_pred CCHHHHHHHHHHHheeeEecccccccc--hHHHHHHHHHhc--CCCC-CCc-----HHHHHHHHHHHHHHHh----hhhh
Confidence 444433 66777788999999976543 345555544432 1111 112 2222222233222111 2344
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCchHHHHHHh---
Q 035568 327 VHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGKPKIIRAST--- 403 (518)
Q Consensus 327 ~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~i~~~~~--- 403 (518)
-.-+.++--+++.+.+-|... .+..|.-.+|-...+.=+|.+-+.+.+. -|++.|.-..-+..+..+..
T Consensus 147 s~~IikSTLdFv~g~~iEq~n--f~~~p~A~~fP~ylR~ksGl~E~yA~Fi------FPk~~FpE~~~~~qi~~AIp~~~ 218 (357)
T cd00686 147 SLNLIRSTLDFFEGCWIEQYN--FGGFPGSHDYPQFLRRMNGLGHCVGASL------WPKEQFNERSLFLEITSAIAQME 218 (357)
T ss_pred HHHHHHHHHHHHHHHHHhhhc--cCCCCCCcccchHHHhccCCcceeEEEe------cchhhCchHhhHHHhhHHHHHHH
Confidence 555678888999999999764 3446766777777677666665544322 24443332222333333444
Q ss_pred hhhhhccCccchhhhhhc-CCCchHHHHHHhhcccCCcccCHHHHHHHHHHHHHHHHHHHHhh
Q 035568 404 IIGRLMDDIKSHKFEQER-GHAASAIECYMKEKEREGVSVTEQEVHEELYKKVGDAWKDINEE 465 (518)
Q Consensus 404 ~i~RL~NDI~S~~kE~~~-G~~~n~V~cym~e~~~~g~~vS~eeA~~~i~~~i~~~~k~ln~~ 465 (518)
...-++|||.||=||.-. ++-.|.|.-|.+-| | +|..+|++.+.+-.-.+-+++..-
T Consensus 219 ~~i~~~NDILSFYKEe~~~~E~~n~V~Nya~~~---G--iS~~eAL~~lt~dTv~~s~rv~~V 276 (357)
T cd00686 219 NWMVWVNDLMSFYKEFDDERDQISLVKNYVVSD---E--ISLHEALEKLTQDTLHSSKQMVAV 276 (357)
T ss_pred HHHHhhhhhhheehhhcccccccchHHHhhhhc---C--CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 445589999999998743 55678888888889 9 999999998766666666666543
No 12
>PF00494 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR002060 Squalene synthase 2.5.1.21 from EC (farnesyl-diphosphate farnesyltransferase) (SQS) and Phytoene synthase 2.5.1.32 from EC (PSY) share a number of functional similarities. These similarities are also reflected at the level of their primary structure [, , ]. In particular three well conserved regions are shared by SQS and PSY; they could be involved in substrate binding and/or the catalytic mechanism. SQS catalyzes the conversion of two molecules of farnesyl diphosphate (FPP) into squalene. It is the first committed step in the cholesterol biosynthetic pathway. The reaction carried out by SQS is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of FPP to form presqualene diphosphate; this intermediate is then rearranged in a NADP-dependent reduction, to form squalene: 2 FPP -> presqualene diphosphate + NADP -> squalene SQS is found in eukaryotes. In yeast it is encoded by the ERG9 gene, in mammals by the FDFT1 gene. SQS seems to be membrane-bound. PSY catalyzes the conversion of two molecules of geranylgeranyl diphosphate (GGPP) into phytoene. It is the second step in the biosynthesis of carotenoids from isopentenyl diphosphate. The reaction carried out by PSY is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of GGPP to form prephytoene diphosphate; this intermediate is then rearranged to form phytoene. 2 GGPP -> prephytoene diphosphate -> phytoene PSY is found in all organisms that synthesize carotenoids: plants and photosynthetic bacteria as well as some non- photosynthetic bacteria and fungi. In bacteria PSY is encoded by the gene crtB. In plants PSY is localized in the chloroplast.; GO: 0016740 transferase activity, 0009058 biosynthetic process; PDB: 3NRI_A 3NPR_A 2ZCR_A 2ZCP_B 4F6V_A 4EA0_A 3ACW_A 4F6X_A 3VJE_B 3ACX_A ....
Probab=88.65 E-value=14 Score=36.82 Aligned_cols=184 Identities=22% Similarity=0.223 Sum_probs=97.5
Q ss_pred hHHHHHHHHHhhhhhhhhcccccCCCHHH----HHHHHHHhhhcCccccccCChhHHHHHHHHHHHHHHHHHHHHhcCCc
Q 035568 249 SLARKLLTKVISMTSIIDDIYDVYGIPEE----LDLFTAAIDRWDVSCIDQLPEYMQTFYVALLDLYKEIEEELATKGWS 324 (518)
Q Consensus 249 s~~Rl~laK~~~l~~i~DD~fD~~gt~eE----l~~~t~ai~rWd~~~~~~lpe~mk~~f~al~~~~~ei~~~~~~~~~~ 324 (518)
...|-.+.-+-.+.-.+||+-|......+ |+-+-+++...-.+..+..+....++..++..+.....
T Consensus 17 ~~~R~~~~alyaf~r~~d~i~D~~~~~~~~~~~L~~w~~~l~~~~~~~~~~~~~~~~pv~~~l~~~~~~~~--------- 87 (267)
T PF00494_consen 17 KEKRPAVFALYAFCRELDDIVDEPSDPEEARARLQWWRDALNSIFASYEDSLPEPSHPVARALADLVRRYG--------- 87 (267)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCTSS-HSCHHHHHHHHHHHHHHHH-TSTHHHSSHHHHHHHHHHHHCCSH---------
T ss_pred HHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHHHHHHHhhhhhhccCCCcCHHHHHHHHHHHHHh---------
Confidence 45555566777888899999997774332 33344444433211111233344456555554443321
Q ss_pred chHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCchHHHHHHhh
Q 035568 325 YRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGKPKIIRASTI 404 (518)
Q Consensus 325 ~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~i~~~~~~ 404 (518)
.-++.+.+++.|+..... ....+|++|+......+.|....+++..++..... .++.+. ....+.
T Consensus 88 ----l~~~~l~~li~~~~~dl~---~~~~~t~~~L~~Y~~~vag~vg~l~~~~~~~~~~~-~~~~~~-------a~~lG~ 152 (267)
T PF00494_consen 88 ----LPREPLLELIDGMEMDLE---FTPYETFADLERYCYYVAGSVGLLLLQLLGAHDPD-EAARDA-------ARALGR 152 (267)
T ss_dssp ----HHHHHHHHHHHHHHHCTT----S--SSHHHHHHHHHHHTHHHHHHHHHHHHSSTSH-HHHHHH-------HHHHHH
T ss_pred ----hhHHHHHHHHHHhccccc---CCCCCCHHHHHHHHHHHHHHHHHHHHHHhccccch-hhHHHH-------HHHHHH
Confidence 234556777777754433 34578999999999888888777776666553211 123332 233333
Q ss_pred hhhhccCccchhhh-hhcCC--CchHHHHHHhhcccCCcccCHHHHHHH----------HHHHHHHHHHHHHh
Q 035568 405 IGRLMDDIKSHKFE-QERGH--AASAIECYMKEKEREGVSVTEQEVHEE----------LYKKVGDAWKDINE 464 (518)
Q Consensus 405 i~RL~NDI~S~~kE-~~~G~--~~n~V~cym~e~~~~g~~vS~eeA~~~----------i~~~i~~~~k~ln~ 464 (518)
..-+.|=+...... ..+|. ++.- .|.+| | +|.++-... +..+++.+...+.+
T Consensus 153 alql~nilRd~~~D~~~~gR~ylP~d---~l~~~---g--v~~~dl~~~~~~~~~~~~~~~~~~~~A~~~l~~ 217 (267)
T PF00494_consen 153 ALQLTNILRDIPEDALRRGRIYLPLD---DLRRF---G--VTPEDLLAGRPRSERLRALIRELAARARAHLDE 217 (267)
T ss_dssp HHHHHHHHHTHHHH-HHTT---S-HH---HHHHT---T--SSHHHHHHHG-GGHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhHHHHHhcccccCCch---hHHHc---C--CCHHHHHhcccCCHHHHHHHHHHHHHHHHHHHH
Confidence 33333433344445 44554 4433 36778 8 887765432 34555555544444
No 13
>TIGR02749 prenyl_cyano solanesyl diphosphate synthase. Members of this family all are from cyanobacteria or plastid-containing eukaryotes. A member from Arabidopsis (where both plastoquinone and ubiquinone contain the C(45) prenyl moiety) was characterized by heterologous expression as a solanesyl diphosphate synthase.
Probab=83.18 E-value=54 Score=34.12 Aligned_cols=88 Identities=11% Similarity=0.046 Sum_probs=56.6
Q ss_pred chHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCchHHHHHHhh
Q 035568 325 YRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGKPKIIRASTI 404 (518)
Q Consensus 325 ~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~i~~~~~~ 404 (518)
.....+.+...+++.|-+.+..|... ..+|.++|+..-..-+|..+..++..-++--..+++..+. ..++-...+.
T Consensus 133 ~~~~~~~~~~~~~~~Gq~~~~~~~~~-~~~~~~~y~~~~~~KTa~L~~~~~~~ga~~ag~~~~~~~~---l~~~G~~lG~ 208 (322)
T TIGR02749 133 EVVKLISKVITDFAEGEIKQGLNQFD-SDLSLEDYLEKSFYKTASLVAASSKAAAVLSDVPSQVAND---LYEYGKHLGL 208 (322)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcccC-CCCCHHHHHHHHHccHHHHHHHHHHHHHHHcCcCHHHHHH---HHHHHHHHHH
Confidence 35667778888899998888776543 3479999999766555555433321111111234544443 3556677888
Q ss_pred hhhhccCccchh
Q 035568 405 IGRLMDDIKSHK 416 (518)
Q Consensus 405 i~RL~NDI~S~~ 416 (518)
..-+.||+..+.
T Consensus 209 aFQi~DDild~~ 220 (322)
T TIGR02749 209 AFQVVDDILDFT 220 (322)
T ss_pred HHHHHHHhccCC
Confidence 888899998865
No 14
>PLN02890 geranyl diphosphate synthase
Probab=78.48 E-value=56 Score=35.48 Aligned_cols=89 Identities=15% Similarity=0.053 Sum_probs=59.5
Q ss_pred chHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCchHHHHHHhh
Q 035568 325 YRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGKPKIIRASTI 404 (518)
Q Consensus 325 ~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~i~~~~~~ 404 (518)
..+..+.++...++.|-+.+..|.. ...+|+++|+.....-+|..+..++..-++--..+++..+.+ .++-+..+.
T Consensus 227 ~~~~~~s~a~~~l~~Gq~ld~~~~~-~~~~s~~~Yl~~i~~KTa~Lf~~s~~~gAilaga~~~~~~~l---~~fG~~lGl 302 (422)
T PLN02890 227 EVVSLLATAVEHLVTGETMQITSSR-EQRRSMDYYMQKTYYKTASLISNSCKAVAILAGQTAEVAVLA---FEYGRNLGL 302 (422)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCcCHHHHHHH---HHHHHHHHH
Confidence 4567788889999999999998864 345899999987665555554333222111112355555543 456677788
Q ss_pred hhhhccCccchhh
Q 035568 405 IGRLMDDIKSHKF 417 (518)
Q Consensus 405 i~RL~NDI~S~~k 417 (518)
..-+.||+..+.-
T Consensus 303 AFQI~DDiLD~~g 315 (422)
T PLN02890 303 AFQLIDDVLDFTG 315 (422)
T ss_pred HHHHHHHHHhhcC
Confidence 8888899988754
No 15
>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates
Probab=77.92 E-value=13 Score=36.24 Aligned_cols=127 Identities=17% Similarity=0.190 Sum_probs=76.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhc-ccchhHHHHHHHHhcCCCCchHHHhhccCchHHHHHHhh
Q 035568 326 RVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLV-TSGYSMLTAASFLGMDSVVTKEAFDWVSGKPKIIRASTI 404 (518)
Q Consensus 326 ~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~-S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~i~~~~~~ 404 (518)
....+.+....++.|...+..|... ..||.++|++.... |.+..-..+......+.. +++..+. ..++-+..+.
T Consensus 86 ~~~~~~~~~~~~~~Gq~~Dl~~~~~-~~~t~~~y~~~~~~Kta~l~~~~~~~~~~~~~~-~~~~~~~---~~~~~~~lG~ 160 (236)
T cd00867 86 ALELFAEALRELLEGQALDLEFERD-TYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGA-DDEQAEA---LKDYGRALGL 160 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHhccHHHHHHHHHHHHHHcCc-CHHHHHH---HHHHHHHHHH
Confidence 3556778889999999999988654 57999999999887 655543333322222222 2222222 3566778888
Q ss_pred hhhhccCccchhhhh-hcCCCchHHHHHHhhcccCCcccCHHHHHHHHHHHHHHHHHHHHh
Q 035568 405 IGRLMDDIKSHKFEQ-ERGHAASAIECYMKEKEREGVSVTEQEVHEELYKKVGDAWKDINE 464 (518)
Q Consensus 405 i~RL~NDI~S~~kE~-~~G~~~n~V~cym~e~~~~g~~vS~eeA~~~i~~~i~~~~k~ln~ 464 (518)
..-+.||+..+.... ..|+..+=+ ++. ..+.....+.+.+.+.++++++.+..
T Consensus 161 a~Qi~dd~~D~~~d~~~~gk~~~D~----~~g---r~tlp~~~~~~~~~~~~~~~~~~~~~ 214 (236)
T cd00867 161 AFQLTDDLLDVFGDAEELGKVGSDL----REG---RITLPVILARERAAEYAEEAYAALEA 214 (236)
T ss_pred HHHHHHHhccccCChHHHCccHHHH----HcC---CchHHHHHHHHHHHHHHHHHHHHHHh
Confidence 888999999876543 223321111 011 10133445566667777777766654
No 16
>PLN02857 octaprenyl-diphosphate synthase
Probab=77.62 E-value=67 Score=34.79 Aligned_cols=89 Identities=12% Similarity=0.075 Sum_probs=56.7
Q ss_pred chHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCchHHHHHHhh
Q 035568 325 YRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGKPKIIRASTI 404 (518)
Q Consensus 325 ~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~i~~~~~~ 404 (518)
.....+.+...+++.|-+.+..+.. +.-+|.++|+.....-+|..+..++..-++--..+++..+. ..++-+..+.
T Consensus 227 ~~~~~~s~~~~~l~~Gei~q~~~~~-~~~~s~~~Yl~~i~~KTa~L~~~a~~~gallaga~~~~~~~---l~~fG~~LGi 302 (416)
T PLN02857 227 EVIKLISQVIKDFASGEIKQASSLF-DCDVTLDEYLLKSYYKTASLIAASTKSAAIFSGVDSSVKEQ---MYEYGKNLGL 302 (416)
T ss_pred HHHHHHHHHHHHHHhhHHHHHhccc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHH---HHHHHHHHHH
Confidence 3466677788888888887877764 34579999999866655555433321111111235554443 2556677788
Q ss_pred hhhhccCccchhh
Q 035568 405 IGRLMDDIKSHKF 417 (518)
Q Consensus 405 i~RL~NDI~S~~k 417 (518)
..-+.||+..+..
T Consensus 303 AFQI~DDiLD~~~ 315 (416)
T PLN02857 303 AFQVVDDILDFTQ 315 (416)
T ss_pred HHHHHHHHHhhcC
Confidence 8888899988753
No 17
>cd00683 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases, head-to-head. These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes
Probab=75.02 E-value=94 Score=31.01 Aligned_cols=199 Identities=19% Similarity=0.214 Sum_probs=98.9
Q ss_pred HHHHHHHHHhhhhhhhhcccccCCCH-H----HHHHHHHHhhhcCccccccCChhHHHHHHHHHHHHHHHHHHHHhcCCc
Q 035568 250 LARKLLTKVISMTSIIDDIYDVYGIP-E----ELDLFTAAIDRWDVSCIDQLPEYMQTFYVALLDLYKEIEEELATKGWS 324 (518)
Q Consensus 250 ~~Rl~laK~~~l~~i~DD~fD~~gt~-e----El~~~t~ai~rWd~~~~~~lpe~mk~~f~al~~~~~ei~~~~~~~~~~ 324 (518)
..|-.+.-+-.+.-.+||+-|..... . .|+-+.++++.-... ..|. .++..++..+..+. +.
T Consensus 24 ~~R~~~~alYaf~r~~Ddi~D~~~~~~~~~~~~L~~w~~~l~~~~~~---~~~~--~pv~~al~~~~~~~--------~l 90 (265)
T cd00683 24 ELRRAVCALYAFCRAADDIVDDPAAPPDEKLALLDAFRAELDAAYWG---GAPT--HPVLRALADLARRY--------GI 90 (265)
T ss_pred HHHHHHHHHHHHHHHHHhhhhCCCCCchhHHHHHHHHHHHHHHHHcC---CCCC--ChHHHHHHHHHHHc--------CC
Confidence 44555556667777899999976533 2 233333333322110 1121 25566666655421 11
Q ss_pred chHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCchHHHHHHhh
Q 035568 325 YRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGKPKIIRASTI 404 (518)
Q Consensus 325 ~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~i~~~~~~ 404 (518)
-++.+.+++.|+..... ....||++|.......+.|.--.+++..++.+ -+++......+.- .+.-
T Consensus 91 -----~~~~~~~li~g~~~Dl~---~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~~~~--~~~~~~~~A~~lG----~Alq 156 (265)
T cd00683 91 -----PREPFRDLLAGMAMDLD---KRRYETLDELDEYCYYVAGVVGLMLLRVFGAS--SDEAALERARALG----LALQ 156 (265)
T ss_pred -----CHHHHHHHHHHHHHhCC---CCCCCCHHHHHHHHHHhHHHHHHHHHHHhCCC--CChHHHHHHHHHH----HHHH
Confidence 13556777888765555 35678998888887777766655555444431 1222222211111 1222
Q ss_pred hhhhccCccchhhhhhcCC--CchHHHHHHhhcccCCcccCHHHH---------HHHHHHHHHHHHHHHHhhccCCCCCC
Q 035568 405 IGRLMDDIKSHKFEQERGH--AASAIECYMKEKEREGVSVTEQEV---------HEELYKKVGDAWKDINEECLMPTEVP 473 (518)
Q Consensus 405 i~RL~NDI~S~~kE~~~G~--~~n~V~cym~e~~~~g~~vS~eeA---------~~~i~~~i~~~~k~ln~~~l~~~~~p 473 (518)
++.++-|+. ...++|- ++.-+ |.++ | +|.++- ..-+..+++.+.+-+....-....+|
T Consensus 157 ltnilRdv~---eD~~~gR~YlP~d~---l~~~---g--v~~~~l~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp 225 (265)
T cd00683 157 LTNILRDVG---EDARRGRIYLPREE---LARF---G--VTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAALP 225 (265)
T ss_pred HHHHHHHHH---HHHccCCCcCCHHH---HHHc---C--CCHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCC
Confidence 233333444 3334554 33333 6777 7 776552 23345555555555444332223477
Q ss_pred HHHHHHHHHHHhh
Q 035568 474 RPLLMRVLNLSRV 486 (518)
Q Consensus 474 ~~~~~~~~n~aR~ 486 (518)
....-.++-++.+
T Consensus 226 ~~~~~~~~~~~~~ 238 (265)
T cd00683 226 RRSRFCVRAAAML 238 (265)
T ss_pred HhhHHHHHHHHHH
Confidence 6554444444433
No 18
>TIGR03465 HpnD squalene synthase HpnD. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated.
Probab=70.91 E-value=1.2e+02 Score=30.39 Aligned_cols=193 Identities=15% Similarity=0.172 Sum_probs=95.5
Q ss_pred HHHHHHHHHhhhhhhhhcccccCCCHHHHHHHHHHhhhcCc--c-ccccCChhHHHHHHHHHHHHHHHHHHHHhcCCcch
Q 035568 250 LARKLLTKVISMTSIIDDIYDVYGIPEELDLFTAAIDRWDV--S-CIDQLPEYMQTFYVALLDLYKEIEEELATKGWSYR 326 (518)
Q Consensus 250 ~~Rl~laK~~~l~~i~DD~fD~~gt~eEl~~~t~ai~rWd~--~-~~~~lpe~mk~~f~al~~~~~ei~~~~~~~~~~~~ 326 (518)
..|-.+.-+-.+.-.+||+-|..++.++-+. .++.|.. . ....-|. .++..++..++... +.
T Consensus 18 ~~R~~~~alYaf~r~~d~i~D~~~~~~~~~~---~L~~w~~~l~~~~~g~~~--~pv~~al~~~~~~~--------~l-- 82 (266)
T TIGR03465 18 ERRRAMTALYAFCREVDDIVDEDSDPEVAQA---KLAWWRAEIDRLYAGAPS--HPVARALADPARRF--------DL-- 82 (266)
T ss_pred HHHHHHHHHHHHHHHHHhhhcCCCCchHHHH---HHHHHHHHHHHHhCCCCC--ChHHHHHHHHHHHc--------CC--
Confidence 4455555667777789999998555433221 1233321 1 0111121 34555655544332 11
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCchHHHHHHhhhh
Q 035568 327 VHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGKPKIIRASTIIG 406 (518)
Q Consensus 327 ~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~i~~~~~~i~ 406 (518)
-++.+.+++.++-+... ....+|++|+......+.|.-..+++..++.. ++........ +-.+.-++
T Consensus 83 ---~~~~~~~li~g~~~Dl~---~~~~~t~~dL~~Y~~~vAg~vg~l~~~llg~~---~~~~~~~a~~----lG~Alqlt 149 (266)
T TIGR03465 83 ---PQEDFLEVIDGMEMDLE---QTRYPDFAELDLYCDRVAGAVGRLSARIFGAT---DARTLEYAHH----LGRALQLT 149 (266)
T ss_pred ---CHHHHHHHHHHHHHHcC---CCCCCCHHHHHHHHHHhHHHHHHHHHHHhCCC---ChhHHHHHHH----HHHHHHHH
Confidence 13446777777754443 34578999988888777766665555444321 2222222111 12222233
Q ss_pred hhccCccchhhhhhcCCC--chHHHHHHhhcccCCcccCHH---------HHHHHHHHHHHHHHHHHHhhccCCCCCCHH
Q 035568 407 RLMDDIKSHKFEQERGHA--ASAIECYMKEKEREGVSVTEQ---------EVHEELYKKVGDAWKDINEECLMPTEVPRP 475 (518)
Q Consensus 407 RL~NDI~S~~kE~~~G~~--~n~V~cym~e~~~~g~~vS~e---------eA~~~i~~~i~~~~k~ln~~~l~~~~~p~~ 475 (518)
-++-|+. ...++|.+ +-- .|.++ | +|.+ ...+-+..+++.+..-+.+..---..+|..
T Consensus 150 nilRdv~---eD~~~gR~ylP~~---~l~~~---g--v~~~~l~~~~~~~~~~~~~~~l~~~A~~~l~~a~~~~~~~p~~ 218 (266)
T TIGR03465 150 NILRDVG---EDARRGRIYLPAE---ELQRF---G--VPAADILEGRYSPALAALCRFQAERARAHYAEADALLPACDRR 218 (266)
T ss_pred HHHHHhH---HHHhCCCeecCHH---HHHHc---C--CCHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhCCHh
Confidence 3334543 33456653 222 35677 7 7766 334445566666665554433222347754
Q ss_pred HHHHHH
Q 035568 476 LLMRVL 481 (518)
Q Consensus 476 ~~~~~~ 481 (518)
....++
T Consensus 219 ~~~~~~ 224 (266)
T TIGR03465 219 AQRAAR 224 (266)
T ss_pred hhHHHH
Confidence 443333
No 19
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=62.78 E-value=1.7e+02 Score=30.45 Aligned_cols=106 Identities=19% Similarity=0.145 Sum_probs=70.1
Q ss_pred chHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCchHHHHHHhh
Q 035568 325 YRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGKPKIIRASTI 404 (518)
Q Consensus 325 ~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~i~~~~~~ 404 (518)
.....+.+....++.|-..+-.|.... +|.++|+.+-.-=+|.....+...-++--..+++..+.+ ...-+....
T Consensus 134 ~~~~~~~~~~~~~~~GQ~lDl~~~~~~--~t~e~y~~~i~~KTa~L~~~a~~~ga~la~~~~~~~~~l---~~~g~~lGl 208 (322)
T COG0142 134 EAIKALAEAINGLCGGQALDLAFENKP--VTLEEYLRVIELKTAALFAAAAVLGAILAGADEELLEAL---EDYGRNLGL 208 (322)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHccCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHH---HHHHHHhhH
Confidence 346677888899999999888886655 999999999666555555433322222112234555543 556678888
Q ss_pred hhhhccCccchhhhh-hcCCC---------chHHHHHHhhc
Q 035568 405 IGRLMDDIKSHKFEQ-ERGHA---------ASAIECYMKEK 435 (518)
Q Consensus 405 i~RL~NDI~S~~kE~-~~G~~---------~n~V~cym~e~ 435 (518)
..-+.|||..+.-+. .-|+. .+...++.-++
T Consensus 209 aFQi~DDiLD~~~d~~~lGK~~g~Dl~~gK~T~p~l~~l~~ 249 (322)
T COG0142 209 AFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEK 249 (322)
T ss_pred HHHHHHHhhcCCCChHHhCCCcchHHHcCCchHHHHHHHHc
Confidence 888999998887642 23332 36666777775
No 20
>TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II. Members of this family are component II of the heterodimeric heptaprenyl diphosphate synthase. The trusted cutoff was set such that all members identified are encoded near to a recognizable gene for component I (in Pfam family pfam07307). This enzyme acts in menaquinone-7 isoprenoid side chain biosynthesis.
Probab=62.70 E-value=2e+02 Score=29.87 Aligned_cols=85 Identities=9% Similarity=0.038 Sum_probs=55.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHH--HhcCCCCchHHHhhccCchHHHHHHh
Q 035568 326 RVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASF--LGMDSVVTKEAFDWVSGKPKIIRAST 403 (518)
Q Consensus 326 ~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~--~~~g~~l~~ev~e~~~~~~~i~~~~~ 403 (518)
....+.++...++.|-..+..|.. +.-+|.++|++.-..-+|..+..++.. ...| .+++..+. ..++-+..+
T Consensus 130 ~~~~~~~~~~~~~~Gq~~~~~~~~-~~~~~~~~Y~~~i~~KTa~L~~~~~~~ga~~ag--~~~~~~~~---l~~~g~~lG 203 (319)
T TIGR02748 130 AHQILSHTIVEVCRGEIEQIKDKY-NFDQNLRTYLRRIKRKTALLIAASCQLGAIASG--ANEAIVKK---LYWFGYYVG 203 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHcC--CCHHHHHH---HHHHHHHHH
Confidence 456677888889999888888753 345799999988766666554333211 1112 23443333 245566778
Q ss_pred hhhhhccCccchh
Q 035568 404 IIGRLMDDIKSHK 416 (518)
Q Consensus 404 ~i~RL~NDI~S~~ 416 (518)
...-+.||+..+.
T Consensus 204 ~aFQI~DDilD~~ 216 (319)
T TIGR02748 204 MSYQITDDILDFV 216 (319)
T ss_pred HHHHHHHHHHHcc
Confidence 8888889987764
No 21
>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases, head-to-tail. These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4) condensation reactions. This CD includes all-trans (E)-isoprenyl diphosphate synthases which synthesize various chain length (C10, C15, C20, C25, C30, C35, C40, C45, and C50) linear isoprenyl diphosphates from precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They catalyze the successive 1'-4 condensation of the 5-carbon IPP to allylic substrates geranyl-, farnesyl-, or geranylgeranyl-diphosphate. Isoprenoid chain elongation reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DDXX(XX
Probab=61.24 E-value=74 Score=31.69 Aligned_cols=89 Identities=17% Similarity=0.037 Sum_probs=59.6
Q ss_pred chHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCchHHHHHHhh
Q 035568 325 YRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGKPKIIRASTI 404 (518)
Q Consensus 325 ~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~i~~~~~~ 404 (518)
.....+.+.....+.|-..+..|... ..||.++|++...--+|.....+....++--..+++..+- ..++-...+.
T Consensus 108 ~~~~~~~~~~~~~~~GQ~~d~~~~~~-~~~~~~~y~~~~~~KT~~l~~~~~~~~a~l~~~~~~~~~~---l~~~g~~lG~ 183 (259)
T cd00685 108 RALELFSEAILELVEGQLLDLLSEYD-TDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEA---LKRFGRNLGL 183 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCC-CCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHH---HHHHHHHHHH
Confidence 35666778888999999989988654 5799999999987777666543332222111123333332 3566777888
Q ss_pred hhhhccCccchhh
Q 035568 405 IGRLMDDIKSHKF 417 (518)
Q Consensus 405 i~RL~NDI~S~~k 417 (518)
..-+.||+..+..
T Consensus 184 afQi~DD~ld~~~ 196 (259)
T cd00685 184 AFQIQDDILDLFG 196 (259)
T ss_pred HHHHHHHhhcccC
Confidence 8888999887754
No 22
>KOG1719 consensus Dual specificity phosphatase [Defense mechanisms]
Probab=59.19 E-value=8.1 Score=36.02 Aligned_cols=30 Identities=23% Similarity=0.474 Sum_probs=26.5
Q ss_pred hcCCCchHHHHHHhhcccCCcccCHHHHHHHHHH
Q 035568 420 ERGHAASAIECYMKEKEREGVSVTEQEVHEELYK 453 (518)
Q Consensus 420 ~~G~~~n~V~cym~e~~~~g~~vS~eeA~~~i~~ 453 (518)
.||.-+..|.||+-+|. + .|.++|.+++++
T Consensus 119 GRtRSaTvV~cYLmq~~--~--wtpe~A~~~vr~ 148 (183)
T KOG1719|consen 119 GRTRSATVVACYLMQHK--N--WTPEAAVEHVRK 148 (183)
T ss_pred CCccchhhhhhhhhhhc--C--CCHHHHHHHHHh
Confidence 46777899999999985 7 999999999988
No 23
>TIGR03464 HpnC squalene synthase HpnC. This family of genes are members of a superfamily (pfam00494) of phytoene and squalene synthases which catalyze the head-t0-head condensation of polyisoprene pyrophosphates. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnD gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated.
Probab=57.11 E-value=2.2e+02 Score=28.58 Aligned_cols=120 Identities=20% Similarity=0.172 Sum_probs=64.7
Q ss_pred hHHHHhccccCcchhHHHHHHHHHhhhhhhhhcccccC-CCHHH----HHHHHHHhhhcCccccccCChhHHHHHHHHHH
Q 035568 235 CYFWIVGVYFEPQYSLARKLLTKVISMTSIIDDIYDVY-GIPEE----LDLFTAAIDRWDVSCIDQLPEYMQTFYVALLD 309 (518)
Q Consensus 235 ~yf~~~a~~feP~~s~~Rl~laK~~~l~~i~DD~fD~~-gt~eE----l~~~t~ai~rWd~~~~~~lpe~mk~~f~al~~ 309 (518)
+|+|+.-.. | ...|..+.-+-.+.=.+||+-|.. ++.++ |+.+-+.++. ....-|. .++..++.+
T Consensus 7 sf~~a~~~l--p--~~~R~~~~alYAf~R~~Ddi~D~~~~~~~~~~~~L~~wr~~l~~----~~~g~~~--~pv~~aL~~ 76 (266)
T TIGR03464 7 NFPVASLLL--P--ARLRAPIHAVYAFARTADDIADEGDGSAEERLALLDDFRAELDA----IYSGEPA--APVFVALAR 76 (266)
T ss_pred cHHHHHHhC--C--HHHHHHHHHHHHHHHHHHHhccCCCCChHHHHHHHHHHHHHHHH----HhCCCCC--ChHHHHHHH
Confidence 455554333 4 234444455666678899999975 44443 2222222221 1111121 245666666
Q ss_pred HHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHHHhc
Q 035568 310 LYKEIEEELATKGWSYRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASFLGM 380 (518)
Q Consensus 310 ~~~ei~~~~~~~~~~~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~ 380 (518)
++.+. +.. ++.+.+++.++.... .....+|++|.......+.|+--.+++..++.
T Consensus 77 ~~~~~--------~l~-----~~~~~~li~~~~~Dl---~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~g~ 131 (266)
T TIGR03464 77 TVQRH--------GLP-----IEPFLDLLDAFRQDV---VVTRYATWAELLDYCRYSANPVGRLVLDLYGA 131 (266)
T ss_pred HHHHc--------CCC-----hHHHHHHHHHHHHhc---cCCCCCCHHHHHHHHHHhHHHHHHHHHHHcCC
Confidence 55532 111 234556666664332 23456899999998888877776666655543
No 24
>CHL00151 preA prenyl transferase; Reviewed
Probab=50.84 E-value=3.1e+02 Score=28.48 Aligned_cols=86 Identities=9% Similarity=0.026 Sum_probs=54.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHH--HHhcCCCCchHHHhhccCchHHHHHHh
Q 035568 326 RVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAAS--FLGMDSVVTKEAFDWVSGKPKIIRAST 403 (518)
Q Consensus 326 ~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~--~~~~g~~l~~ev~e~~~~~~~i~~~~~ 403 (518)
....+.+....++.|-+.+..|.. ..-+|.++|+.....=+|..+..++. -...| .+++..+. ..++-+..+
T Consensus 135 ~~~~~~~~~~~l~~G~~~~~~~~~-~~~~~~~~yl~~i~~KTa~L~~~~~~~ga~lag--~~~~~~~~---l~~~G~~lG 208 (323)
T CHL00151 135 VVKLISKVITDFAEGEIRQGLVQF-DTTLSILNYIEKSFYKTASLIAASCKAAALLSD--ADEKDHND---FYLYGKHLG 208 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCC-CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHcC--CCHHHHHH---HHHHHHHHH
Confidence 456677888888888877776643 33578999999754444444433222 22223 34444433 356667788
Q ss_pred hhhhhccCccchhh
Q 035568 404 IIGRLMDDIKSHKF 417 (518)
Q Consensus 404 ~i~RL~NDI~S~~k 417 (518)
...-+.||+..+.-
T Consensus 209 ~aFQi~DDilD~~~ 222 (323)
T CHL00151 209 LAFQIIDDVLDITS 222 (323)
T ss_pred HHHHHHHHHhhccc
Confidence 88888999988753
No 25
>KOG3951 consensus Uncharacterized conserved protein [Function unknown]
Probab=47.98 E-value=30 Score=34.74 Aligned_cols=56 Identities=27% Similarity=0.394 Sum_probs=43.6
Q ss_pred ccccccccccccchhhhhhHhhhcccCCCCchHHHHHHHHHHhhcc-cCcHHHHHHHcc
Q 035568 103 DGKGNFKESLKTDVSGMLSLYEAAHLVVHGEDILNEAIAFTTAHLQ-SSMAPQVIHALR 160 (518)
Q Consensus 103 d~~g~F~~~~~~dv~~lL~LyeAs~l~~~gE~iLdea~~ft~~~L~-~~l~~~V~~aL~ 160 (518)
+.+|-|.....-|+||-..|-++-- .... +-|=.|+.||++||. .+-+++|++-|+
T Consensus 264 hp~GAFv~~s~iDmkgcvrllk~q~-p~~~-e~LLnaLRfTTKHlNdesTpK~ir~ll~ 320 (321)
T KOG3951|consen 264 HPNGAFVSNSSIDMKGCVRLLKLQP-PEQS-ECLLNALRFTTKHLNDESTPKSIRHLLE 320 (321)
T ss_pred cccccccccCcCcHHHHHHHHHcCC-chhh-HHHHHHHHHHHhhcCCCCChHHHHHHhc
Confidence 5678888888899999999988743 2222 356679999999998 577888888774
No 26
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=46.31 E-value=3.6e+02 Score=28.01 Aligned_cols=89 Identities=19% Similarity=0.073 Sum_probs=56.4
Q ss_pred chHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCchHHHHHHhh
Q 035568 325 YRVHYAKEEMKILVHGYHDESKWFHNNYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGKPKIIRASTI 404 (518)
Q Consensus 325 ~~~~~~k~~~~~~~~a~l~EA~W~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~i~~~~~~ 404 (518)
.....+.++...++.|-..+..|.. +.-+|.++|+.....-+|..+..++..-++--..+++..+. ...+-+..+.
T Consensus 130 ~~~~~~~~~~~~~~~Gq~~d~~~~~-~~~~s~~~y~~~i~~KTa~lf~~~~~~ga~lag~~~~~~~~---l~~~g~~lG~ 205 (323)
T PRK10888 130 KVLEVMSEAVNVIAEGEVLQLMNVN-DPDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKG---LQDYGRYLGT 205 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHH---HHHHHHHHHH
Confidence 3466677888889999888887754 33589999999877666655433322111101134443333 3456677777
Q ss_pred hhhhccCccchhh
Q 035568 405 IGRLMDDIKSHKF 417 (518)
Q Consensus 405 i~RL~NDI~S~~k 417 (518)
..-+.||+..+..
T Consensus 206 aFQi~DD~ld~~~ 218 (323)
T PRK10888 206 AFQLIDDLLDYSA 218 (323)
T ss_pred HHHHHHHhhcccC
Confidence 7888899987753
No 27
>PF03861 ANTAR: ANTAR domain; InterPro: IPR005561 ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins []. This domain has been detected in various response regulators of two-component systems, which are structured around two proteins, a histidine kinase and a response regulator. This domain is also found in one-component sensory regulators from a variety of bacteria. Most response regulators interact with DNA, however ANTAR-containing regulators interact with RNA. The majority of the domain consists of a coiled-coil.; PDB: 4AKK_A 1SD5_A 1S8N_A 1QO0_E.
Probab=30.01 E-value=61 Score=24.49 Aligned_cols=29 Identities=21% Similarity=0.169 Sum_probs=22.0
Q ss_pred CCchHHHHHHhhcccCCcccCHHHHHHHHHHHHH
Q 035568 423 HAASAIECYMKEKEREGVSVTEQEVHEELYKKVG 456 (518)
Q Consensus 423 ~~~n~V~cym~e~~~~g~~vS~eeA~~~i~~~i~ 456 (518)
-+.-++.+.|..+ | +|+++|.+.+++.--
T Consensus 14 ~I~~AkgiLm~~~---g--~~e~~A~~~Lr~~Am 42 (56)
T PF03861_consen 14 VIEQAKGILMARY---G--LSEDEAYRLLRRQAM 42 (56)
T ss_dssp HHHHHHHHHHHHH---T----HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHh---C--cCHHHHHHHHHHHHH
Confidence 3556788899999 9 999999999987544
No 28
>PF03701 UPF0181: Uncharacterised protein family (UPF0181); InterPro: IPR005371 This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH P76260 from SWISSPROT.
Probab=28.25 E-value=1e+02 Score=23.29 Aligned_cols=45 Identities=16% Similarity=0.307 Sum_probs=31.9
Q ss_pred ccCccchhhhhhcCCCchHHHHHHhhcccCCcccCHHHHHHHHHHHHHHHHH
Q 035568 409 MDDIKSHKFEQERGHAASAIECYMKEKEREGVSVTEQEVHEELYKKVGDAWK 460 (518)
Q Consensus 409 ~NDI~S~~kE~~~G~~~n~V~cym~e~~~~g~~vS~eeA~~~i~~~i~~~~k 460 (518)
.||+-+...|+..--+ -=|.-+|.+ | +|.-||+..|..-|.+..+
T Consensus 2 ~~~lp~LtHeeQQ~Av-E~Iq~LMaq----G--mSsgEAI~~VA~~iRe~~~ 46 (51)
T PF03701_consen 2 FNDLPSLTHEEQQQAV-ERIQELMAQ----G--MSSGEAIAIVAQEIREEHQ 46 (51)
T ss_pred CCCCCCCCHHHHHHHH-HHHHHHHHh----c--ccHHHHHHHHHHHHHHHHH
Confidence 3677777776654333 335668877 8 9999999999887776543
No 29
>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]
Probab=27.13 E-value=53 Score=31.71 Aligned_cols=44 Identities=23% Similarity=0.236 Sum_probs=29.5
Q ss_pred hhccCccchhhhhhc-CCCchHHHHHHhhcccCCcccCHHHHHHHHHHHH
Q 035568 407 RLMDDIKSHKFEQER-GHAASAIECYMKEKEREGVSVTEQEVHEELYKKV 455 (518)
Q Consensus 407 RL~NDI~S~~kE~~~-G~~~n~V~cym~e~~~~g~~vS~eeA~~~i~~~i 455 (518)
.|--++..+|+..+. -.+.-+=.++|++| | +|++||..+++++-
T Consensus 129 ~L~~el~~~k~~L~~rK~ierAKglLM~~~---g--~sE~EAy~~lR~~A 173 (194)
T COG3707 129 ALRRELAKLKDRLEERKVIERAKGLLMKRR---G--LSEEEAYKLLRRTA 173 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh---C--CCHHHHHHHHHHHH
Confidence 344455555654432 22334445699999 9 99999999999864
No 30
>smart00400 ZnF_CHCC zinc finger.
Probab=25.83 E-value=79 Score=23.70 Aligned_cols=25 Identities=24% Similarity=0.287 Sum_probs=20.5
Q ss_pred CCCchHHHHHHhhcccCCcccCHHHHHHHH
Q 035568 422 GHAASAIECYMKEKEREGVSVTEQEVHEEL 451 (518)
Q Consensus 422 G~~~n~V~cym~e~~~~g~~vS~eeA~~~i 451 (518)
|.-.++|.++|+-+ | +|-.||++.+
T Consensus 30 g~gGd~i~fv~~~~---~--~sf~eA~~~L 54 (55)
T smart00400 30 GAGGNVISFLMKYD---K--LSFVEAVKKL 54 (55)
T ss_pred CCCCCHHHHHHHHH---C--cCHHHHHHHh
Confidence 34457899999998 8 9999999865
No 31
>PF03000 NPH3: NPH3 family; InterPro: IPR004249 The RPT2 protein is a signal transducer of the phototropic response in Arabidopsis thaliana. The RPT2 gene is light inducible; encodes a novel protein with putative phosphorylation sites, a nuclear localization signal, a BTB/POZ domain (IPR000210 from INTERPRO), and a coiled-coil domain. RPT2 belongs to a large gene family that includes the recently isolated NPH3 gene []. The NPH3 protein is a NPH1 photoreceptor-interacting protein that is essential for phototropism. Phototropism of A. thaliana seedlings in response to a blue light source is initiated by nonphototropic hypocotyl 1 (NPH1), a light-activated serine-threonine protein kinase []. NPH3 is a member of a large protein family, apparently specific to higher plants, and may function as an adapter or scaffold protein to bring together the enzymatic components of a NPH1-activated phosphorelay []. Many of the proteins in this group also contain the BTB/POZ domain (IPR000210 from INTERPRO) at the N-terminal.; GO: 0004871 signal transducer activity, 0009416 response to light stimulus
Probab=23.84 E-value=92 Score=31.51 Aligned_cols=44 Identities=25% Similarity=0.345 Sum_probs=29.1
Q ss_pred hHHHHHHhhhhhhccCccchhhhhhcCCCchHHHHHHhhcccCCcccCHHHHHHHHHHHH
Q 035568 396 PKIIRASTIIGRLMDDIKSHKFEQERGHAASAIECYMKEKEREGVSVTEQEVHEELYKKV 455 (518)
Q Consensus 396 ~~i~~~~~~i~RL~NDI~S~~kE~~~G~~~n~V~cym~e~~~~g~~vS~eeA~~~i~~~i 455 (518)
..+..+.-...|-..| .+--+|..|+|.|| + +|++| ...+.+++
T Consensus 205 ~~Lae~lP~~aR~~hD-----------~LYrAID~YLk~Hp--~--ls~~E-r~~lC~~l 248 (258)
T PF03000_consen 205 VALAEALPDSARPSHD-----------GLYRAIDIYLKAHP--G--LSEEE-RKRLCRLL 248 (258)
T ss_pred HHHHHHCCHhhhhccc-----------hHHHHHHHHHHHcc--c--CCHHH-HHHHHhhC
Confidence 3445555555565555 23478999999999 9 99999 44444433
No 32
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=22.70 E-value=59 Score=23.89 Aligned_cols=20 Identities=20% Similarity=0.481 Sum_probs=15.0
Q ss_pred HHHhhhcCceechhhhhccc
Q 035568 83 FRILRQRGYKVSCDIFNKFK 102 (518)
Q Consensus 83 FRlLR~hGy~vS~dvf~~F~ 102 (518)
+.-|+++|+++|+++++.+.
T Consensus 25 l~~l~~~g~~is~~l~~~~L 44 (48)
T PF11848_consen 25 LDRLQQAGFRISPKLIEEIL 44 (48)
T ss_pred HHHHHHcCcccCHHHHHHHH
Confidence 44457889999999887764
No 33
>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.48 E-value=85 Score=24.07 Aligned_cols=49 Identities=20% Similarity=0.264 Sum_probs=33.6
Q ss_pred ccCccchhhhhhcCCCchHHHHHHhhcccCCcccCHHHHHHHHHHHHHHHHHHHHh
Q 035568 409 MDDIKSHKFEQERGHAASAIECYMKEKEREGVSVTEQEVHEELYKKVGDAWKDINE 464 (518)
Q Consensus 409 ~NDI~S~~kE~~~G~~~n~V~cym~e~~~~g~~vS~eeA~~~i~~~i~~~~k~ln~ 464 (518)
.+++.|+-.|+.+--+ --|.=+|.| | +|--||+..|.+-+.+.-+.-|+
T Consensus 2 ~~~lp~LtHeqQQ~AV-E~Iq~lMae----G--mSsGEAIa~VA~elRe~hk~~~~ 50 (60)
T COG3140 2 FAGLPSLTHEQQQKAV-ERIQELMAE----G--MSSGEAIALVAQELRENHKGENR 50 (60)
T ss_pred CCccccccHHHHHHHH-HHHHHHHHc----c--ccchhHHHHHHHHHHHHhccccc
Confidence 3566666677665444 235568887 7 99999999988877765554443
No 34
>KOG3109 consensus Haloacid dehalogenase-like hydrolase [General function prediction only]
Probab=21.36 E-value=1.1e+02 Score=30.26 Aligned_cols=47 Identities=32% Similarity=0.634 Sum_probs=34.0
Q ss_pred HHHhCCccccHHHHHHHHHHHHHhcccCcCCCCCCChhHHHHHHHHhhhcCceechhhhhccccc
Q 035568 40 ILRLGVGYQFERELEEALQNLYDAFSNNFYNIEDNDLYHVALRFRILRQRGYKVSCDIFNKFKDG 104 (518)
Q Consensus 40 lqrLGi~~hF~~EI~~~L~~~~~~~~~~~~~~~~~dl~~~al~FRlLR~hGy~vS~dvf~~F~d~ 104 (518)
.+.|||+ ++|....-...|+++ ++.-+=|+.+||..+.|.|..|-++
T Consensus 46 ~eklgi~---~e~a~~L~~~~yk~Y---------------G~t~aGL~~~~~~~d~deY~~~V~~ 92 (244)
T KOG3109|consen 46 VEKLGIS---EEEAEELRESLYKEY---------------GLTMAGLKAVGYIFDADEYHRFVHG 92 (244)
T ss_pred HHHhCCC---hhhhHHHHHHHHHHH---------------hHHHHHHHHhcccCCHHHHHHHhhc
Confidence 4667776 345555444455544 6677889999999999999999744
No 35
>smart00463 SMR Small MutS-related domain.
Probab=21.33 E-value=1.1e+02 Score=24.56 Aligned_cols=23 Identities=26% Similarity=0.141 Sum_probs=20.6
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHH
Q 035568 439 GVSVTEQEVHEELYKKVGDAWKDIN 463 (518)
Q Consensus 439 g~~vS~eeA~~~i~~~i~~~~k~ln 463 (518)
| +|.++|+..+...++++++.-.
T Consensus 8 G--~~~~eA~~~l~~~l~~~~~~~~ 30 (80)
T smart00463 8 G--LTVEEALTALDKFLNNARLKGL 30 (80)
T ss_pred C--CCHHHHHHHHHHHHHHHHHcCC
Confidence 8 9999999999999999987644
No 36
>PRK05114 hypothetical protein; Provisional
Probab=20.85 E-value=1.5e+02 Score=23.05 Aligned_cols=45 Identities=16% Similarity=0.224 Sum_probs=31.0
Q ss_pred ccCccchhhhhhcCCCchHHHHHHhhcccCCcccCHHHHHHHHHHHHHHHHH
Q 035568 409 MDDIKSHKFEQERGHAASAIECYMKEKEREGVSVTEQEVHEELYKKVGDAWK 460 (518)
Q Consensus 409 ~NDI~S~~kE~~~G~~~n~V~cym~e~~~~g~~vS~eeA~~~i~~~i~~~~k 460 (518)
.||+-++..|+.+--+ -=|.-+|.+ | +|--||+.-|..-|.+..+
T Consensus 2 ~~~lp~LtHeeQQ~AV-ErIq~LMaq----G--mSsgEAI~~VA~eiRe~~~ 46 (59)
T PRK05114 2 FAGLPSLTHEQQQKAV-ERIQELMAQ----G--MSSGEAIALVAEELRANHQ 46 (59)
T ss_pred CCCcccCCHHHHHHHH-HHHHHHHHc----c--ccHHHHHHHHHHHHHHHHh
Confidence 4566666665544333 335678887 8 9999999999888876553
No 37
>PF00348 polyprenyl_synt: Polyprenyl synthetase; InterPro: IPR000092 A variety of isoprenoid compounds are synthesized by various organisms. For example in eukaryotes the isoprenoid biosynthetic pathway is responsible for the synthesis of a variety of end products including cholesterol, dolichol, ubiquinone or coenzyme Q. In bacteria this pathway leads to the synthesis of isopentenyl tRNA, isoprenoid quinones, and sugar carrier lipids. Among the enzymes that participate in that pathway, are a number of polyprenyl synthetase enzymes which catalyze a 1'4-condensation between 5 carbon isoprene units. It has been shown [, , , , ] that all the above enzymes share some regions of sequence similarity. Two of these regions are rich in aspartic-acid residues and could be involved in the catalytic mechanism and/or the binding of the substrates.; GO: 0008299 isoprenoid biosynthetic process; PDB: 3AQC_B 3AQB_D 3Q1O_C 3LLW_B 3EFQ_A 3EGT_A 3DYG_A 2P1C_A 2OGD_A 2EWG_B ....
Probab=20.43 E-value=8.2e+02 Score=24.19 Aligned_cols=65 Identities=18% Similarity=0.150 Sum_probs=42.0
Q ss_pred CCCCChHHHHhhhhcccchhHHHHHHHHhcCCCCchHHHhhccCchHHHHHHhhhhhhccCccchhhh
Q 035568 351 NYVPTMEEYMRVSLVTSGYSMLTAASFLGMDSVVTKEAFDWVSGKPKIIRASTIIGRLMDDIKSHKFE 418 (518)
Q Consensus 351 g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~i~~~~~~i~RL~NDI~S~~kE 418 (518)
+..+|.++|++.-.--+|..+..++..-++=-..+++..+. ..++-...+...-+.||+..+...
T Consensus 130 ~~~~~~~~y~~i~~~KTg~l~~~~~~~ga~lag~~~~~~~~---l~~~g~~lG~afQi~DD~~d~~~~ 194 (260)
T PF00348_consen 130 DKDPTEEEYLEIIRLKTGSLFALACQLGAILAGADEEQIEA---LREFGRHLGIAFQIRDDLLDLFGD 194 (260)
T ss_dssp TSSTSHHHHHHHHHHHTHHHHHHHHHHHHHHTTSGHHHHHH---HHHHHHHHHHHHHHHHHHHHHHSH
T ss_pred cccccHHHHHHHHhhcchHHHHHHHHHHHHhccchhHHHHH---HHHHHHHHHHHHhhhhhhhhccCc
Confidence 34789999999977777666443332222111234444443 366778888888899999888753
Done!