Query 040856
Match_columns 391
No_of_seqs 167 out of 814
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 12:31:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040856.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040856hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02279 ent-kaur-16-ene synth 100.0 6E-106 1E-110 856.8 35.8 375 1-383 376-781 (784)
2 cd00684 Terpene_cyclase_plant_ 100.0 1E-104 2E-109 830.0 38.5 372 1-377 158-542 (542)
3 PLN02592 ent-copalyl diphospha 100.0 1.5E-81 3.1E-86 667.0 33.3 343 1-379 422-800 (800)
4 PF03936 Terpene_synth_C: Terp 100.0 2.4E-47 5.2E-52 364.2 20.7 248 63-311 1-249 (270)
5 cd00868 Terpene_cyclase_C1 Ter 100.0 7.5E-44 1.6E-48 342.5 28.6 272 77-353 1-284 (284)
6 cd00687 Terpene_cyclase_nonpla 100.0 6.3E-31 1.4E-35 256.1 19.0 228 77-311 10-241 (303)
7 PLN02150 terpene synthase/cycl 99.9 3.5E-27 7.7E-32 191.4 8.1 83 293-380 1-96 (96)
8 cd00385 Isoprenoid_Biosyn_C1 I 99.8 4E-18 8.6E-23 156.9 11.1 186 111-311 2-188 (243)
9 PF06330 TRI5: Trichodiene syn 97.1 0.004 8.7E-08 62.0 10.5 189 110-322 71-265 (376)
10 cd00686 Terpene_cyclase_cis_tr 96.8 0.0085 1.8E-07 58.9 9.9 198 102-322 60-265 (357)
11 cd00867 Trans_IPPS Trans-Isopr 92.5 5 0.00011 37.2 14.6 101 200-306 86-197 (236)
12 PF00494 SQS_PSY: Squalene/phy 59.8 53 0.0012 31.0 8.7 116 122-254 17-136 (267)
13 TIGR03486 cas_csx13_C CRISPR-a 34.5 3E+02 0.0064 24.3 8.3 67 124-194 8-74 (152)
14 cd00683 Trans_IPPS_HH Trans-Is 33.7 4.1E+02 0.0089 25.0 11.3 108 123-252 24-136 (265)
15 TIGR03464 HpnC squalene syntha 28.9 5E+02 0.011 24.5 14.6 106 125-253 20-130 (266)
16 cd00685 Trans_IPPS_HT Trans-Is 27.9 2.2E+02 0.0047 26.9 7.2 88 198-291 107-196 (259)
17 cd01040 globin Globins are hem 25.6 3.7E+02 0.0079 21.8 9.2 77 130-215 60-136 (140)
18 PLN02857 octaprenyl-diphosphat 21.6 9E+02 0.019 24.9 11.5 86 199-290 227-314 (416)
19 PLN02890 geranyl diphosphate s 21.5 4.8E+02 0.01 27.0 8.6 90 198-292 226-316 (422)
20 KOG1914 mRNA cleavage and poly 20.3 2.3E+02 0.005 30.3 5.9 107 69-183 221-336 (656)
No 1
>PLN02279 ent-kaur-16-ene synthase
Probab=100.00 E-value=5.8e-106 Score=856.81 Aligned_cols=375 Identities=27% Similarity=0.429 Sum_probs=354.2
Q ss_pred ChhHHHHHHHHHHHHhhCC-----CCCccHHHHHHHHcCCCcCCCCchHHHHhhHHHhhcccc------------ccHHH
Q 040856 1 MEEAWQFTSKHLKQCLNSN-----KDDEDLNEQARRALELPLHWRMPRLEARWFINVYEKRKD------------KNHAL 63 (391)
Q Consensus 1 L~eA~~ft~~~L~~~~~~~-----~~~~~l~~eV~~aL~~P~~~~l~Rlear~yI~~Y~~~~~------------~n~~l 63 (391)
||||+.||++||++++.++ ..+++|++||+|||++|||++|||||||+||++|++++. +|++|
T Consensus 376 LdeA~~Fs~~~L~~~~~~~~~~~~~~~~~L~~eV~~AL~~P~~~~l~RlEaR~yI~~Y~~~~~~i~Kt~yr~~~~~n~~l 455 (784)
T PLN02279 376 LEKQNSWTSHFLEQGLSNWSKTADRLRKYIKKEVEDALNFPYYANLERLANRRSIENYAVDDTRILKTSYRCSNICNQDF 455 (784)
T ss_pred HHHHHHHHHHHHHHHHhcccccccccCccHHHHHHHHhcCchhcCccHHHHHHHHHHhccccchhccccccccccccHHH
Confidence 7999999999999988531 125889999999999999999999999999999999885 89999
Q ss_pred HHHHhhhhHHHhhhcHHHHHHHHHHHhhcCCCccCcchhhhhhHhhhhhhccccCCCchhHHHHHHHHHHHHHHhhhhhc
Q 040856 64 LELAKLDFNILQATYQEELKDISGWWKDKGLGEKLSFARSRLVTSFFWGMGMVFEPQFAYSRRVLTITLALITVIDDIYD 143 (391)
Q Consensus 64 LelAkldFn~~Q~~hq~El~~l~rW~~~~~l~~~l~faRdr~~e~yf~~~a~~feP~~s~~Rl~~aK~~~l~~~iDD~~D 143 (391)
|||||+|||+||++||+||++++|||+++|| +++||||||++|||||++|++|||++|.+|++|||+++|++++||+||
T Consensus 456 LeLAklDFN~~Qs~hq~EL~~l~rWwke~~L-~~L~faRdr~ve~Yf~aaa~~fEPe~S~aRi~~aK~~~L~tviDD~fD 534 (784)
T PLN02279 456 LKLAVEDFNFCQSIHREELKQLERWIVENRL-DKLKFARQKLAYCYFSAAATLFSPELSDARLSWAKNGVLTTVVDDFFD 534 (784)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCeeHHhcCC-ccCCchhhHHHHHHHHHHHhhcCchhhHHHHHHHHHHHHHHHHHHHhh
Confidence 9999999999999999999999999999999 799999999999999999999999999999999999999999999999
Q ss_pred ccCCHHHHHHHHHHhhhcchhhhhhcCChhHHHHHHHHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHHHHHHHHHHhh
Q 040856 144 IYGTLDELELFTNAVERWDINFAIKQLPDYMKICFFALYNFVSEVAYDILKQQDSDQLLRIKNSWLGLLQAFLVEAKWYH 223 (391)
Q Consensus 144 ~~gt~eel~~~~~ai~rWd~~~~~~~lp~~mk~~~~al~~~~~e~~~~~~~~~~~~~~~~l~~~w~~~~~a~~~EA~W~~ 223 (391)
+|||.|||+.||+||+|||++..++.+|+|||+||.+|+++++|++.++.+.||+++++|++++|++++++|++||+|+.
T Consensus 535 ~yGt~eEL~~ft~aVeRWD~~~~~~~lpeymki~f~aL~~t~nei~~~~~~~qGr~v~~~l~~aW~~ll~ayl~EAeW~~ 614 (784)
T PLN02279 535 VGGSEEELENLIQLVEKWDVNGSPDFCSEQVEIIFSALRSTISEIGDKAFTWQGRNVTSHIIKIWLDLLKSMLTEAQWSS 614 (784)
T ss_pred ccCCHHHHHHHHHHHHHhccccchhhCcHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999998834589999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCChHHHHhhccccchhhHHHHHHHhhcCCCCchHHHhhhccChHHHHHHHHHHHHhcCCCCChhhhhcCCCcchHH
Q 040856 224 NKYAPTLEEYLKNAALSIAGPLITITAYLSATDPIVEKELEYLESNPDVIQWSSRIFRLLDDLGTSSDEIQRGDVSKSIQ 303 (391)
Q Consensus 224 ~~~iPs~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~e~~~~~p~l~~~~~~i~RL~NDi~S~~~E~~~G~~~n~V~ 303 (391)
+||+||+||||+|+.+|+|.+++++.+++++|+.+|+++++| .++|+|+++++.|+||+|||+||++|+++||+ |+|+
T Consensus 615 ~g~vPT~eEYL~na~vS~~l~~i~l~~~~~~G~~l~eev~e~-~~~~~L~~l~s~I~RLlNDI~S~e~E~~rG~~-nsV~ 692 (784)
T PLN02279 615 NKSTPTLDEYMTNAYVSFALGPIVLPALYLVGPKLSEEVVDS-PELHKLYKLMSTCGRLLNDIRGFKRESKEGKL-NAVS 692 (784)
T ss_pred cCCCCCHHHHHhhchhhhhhHHHHHHHHHHhCCCCCHHHHhC-cchhHHHHHHHHHHHHHHhccccHhHHhCCCc-ceeh
Confidence 999999999999999999998888888888999999999999 58999999999999999999999999999998 9999
Q ss_pred HHHhhc--ch------------HHHHHHHHHhhhhhccCCCCCCCcHhHHHHHHHHhhhhhhhcccCCCCCCCchhHHHH
Q 040856 304 CYMHET--NL------------IRQMWKKVMMDVSRASNNKDSPLSQITNEFILNLVRVSHFMYLHGDGHGVQNQETMDE 369 (391)
Q Consensus 304 ~yM~e~--g~------------ie~~wK~ln~e~~~~~~~~~~~vp~~~~~~~~n~~R~~~~~Y~~~D~~t~~~~~~k~~ 369 (391)
|||+|+ |+ |+++||+||++ ++++. +++||++|++++||++|++++||++|||||.+ +||++
T Consensus 693 cYMke~~~gvSeEEAi~~i~~~Ie~~wKeLn~~--~l~~~-~~~vp~~~~~~~ln~aR~~~~~Y~~~Dgyt~~--~~k~~ 767 (784)
T PLN02279 693 LHMIHGNGNSTEEEAIESMKGLIESQRRELLRL--VLQEK-GSNVPRECKDLFWKMSKVLHLFYRKDDGFTSN--DMMSL 767 (784)
T ss_pred hhhccCCCCCCHHHHHHHHHHHHHHHHHHHHHH--HhccC-CCCCCHHHHHHHHHHHHhhhhheeCCCCCChH--HHHHH
Confidence 999997 44 99999999999 99741 22799999999999999999999999999963 69999
Q ss_pred HHhhccccccCCCC
Q 040856 370 AFALLFQPIPLEDN 383 (391)
Q Consensus 370 i~~ll~~pv~~~~~ 383 (391)
|++||++|||+..+
T Consensus 768 i~~ll~ePi~l~~~ 781 (784)
T PLN02279 768 VKSVIYEPVSLQEE 781 (784)
T ss_pred HHHHhccCCcCCcc
Confidence 99999999998654
No 2
>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=1.1e-104 Score=829.96 Aligned_cols=372 Identities=50% Similarity=0.824 Sum_probs=360.6
Q ss_pred ChhHHHHHHHHHHHHhhC-CCCCccHHHHHHHHcCCCcCCCCchHHHHhhHHHhhccccccHHHHHHHhhhhHHHhhhcH
Q 040856 1 MEEAWQFTSKHLKQCLNS-NKDDEDLNEQARRALELPLHWRMPRLEARWFINVYEKRKDKNHALLELAKLDFNILQATYQ 79 (391)
Q Consensus 1 L~eA~~ft~~~L~~~~~~-~~~~~~l~~eV~~aL~~P~~~~l~Rlear~yI~~Y~~~~~~n~~lLelAkldFn~~Q~~hq 79 (391)
||||++||++||++++.+ +..+++|++||+|||++|||+++||||||+||++|++++++|++||||||+|||+||++||
T Consensus 158 LdeA~~ft~~~L~~~~~~~~~~~~~l~~~V~~aL~~P~~~~~~rlear~yi~~Y~~~~~~n~~lLelAkldfn~~Q~~hq 237 (542)
T cd00684 158 LDEALSFTTKHLEEKLESNWIIDPDLSGEIEYALEIPLHASLPRLEARWYIEFYEQEDDHNETLLELAKLDFNILQALHQ 237 (542)
T ss_pred HHHHHHHHHHHHHHHhhccCCCCchHHHHHHHHccCchhcCCchHHHHHHHHHhCCCccccHHHHHHHHHHHHHHhHhHH
Confidence 799999999999999953 2336899999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcCCCccCcchhhhhhHhhhhhhccccCCCchhHHHHHHHHHHHHHHhhhhhcccCCHHHHHHHHHHhh
Q 040856 80 EELKDISGWWKDKGLGEKLSFARSRLVTSFFWGMGMVFEPQFAYSRRVLTITLALITVIDDIYDIYGTLDELELFTNAVE 159 (391)
Q Consensus 80 ~El~~l~rW~~~~~l~~~l~faRdr~~e~yf~~~a~~feP~~s~~Rl~~aK~~~l~~~iDD~~D~~gt~eel~~~~~ai~ 159 (391)
+||++++|||+++||.+++||+|+|+++||||++|++|||++|.+|+++||+++|++++||+||.|||.+|++.||+||+
T Consensus 238 ~El~~~~rWwk~~gL~~~l~~aRdr~ve~yf~~~a~~feP~~s~~Rl~~aK~~~l~~~iDD~fD~~gt~eEl~~ft~ai~ 317 (542)
T cd00684 238 EELKILSRWWKDLDLASKLPFARDRLVECYFWAAGTYFEPQYSLARIALAKTIALITVIDDTYDVYGTLEELELFTEAVE 317 (542)
T ss_pred HHHHHHhHHHHhcCCcccCCcccchhHHHHHHHHhcccCccchHHHHHHHHHHHHHhhhHhhhccCCCHHHHHHHHHHHH
Confidence 99999999999999988889999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcchhhhhhcCChhHHHHHHHHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhccc
Q 040856 160 RWDINFAIKQLPDYMKICFFALYNFVSEVAYDILKQQDSDQLLRIKNSWLGLLQAFLVEAKWYHNKYAPTLEEYLKNAAL 239 (391)
Q Consensus 160 rWd~~~~~~~lp~~mk~~~~al~~~~~e~~~~~~~~~~~~~~~~l~~~w~~~~~a~~~EA~W~~~~~iPs~eEYl~~~~~ 239 (391)
|||++ +++.+|+|||+||.+|++++++++.++.+.+|+++.+|++++|++++++|++||+|+++|++||++||+++|.+
T Consensus 318 rwd~~-~~~~lPe~mk~~~~al~~~~~ei~~~~~~~~~~~~~~~~~~~~~~~~~a~l~EA~w~~~g~vPt~eEYl~~~~~ 396 (542)
T cd00684 318 RWDIS-AIDQLPEYMKIVFKALLNTVNEIEEELLKEGGSYVVPYLKEAWKDLVKAYLVEAKWAHEGYVPTFEEYMENALV 396 (542)
T ss_pred hcccc-chhhccHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhhhhH
Confidence 99999 99999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhHHHHHHHhhcCCCCchHHHhhhccChHHHHHHHHHHHHhcCCCCChhhhhcCCCcchHHHHHhhcch--------
Q 040856 240 SIAGPLITITAYLSATDPIVEKELEYLESNPDVIQWSSRIFRLLDDLGTSSDEIQRGDVSKSIQCYMHETNL-------- 311 (391)
Q Consensus 240 s~g~~~~~~~~~~~~g~~l~~e~~e~~~~~p~l~~~~~~i~RL~NDi~S~~~E~~~G~~~n~V~~yM~e~g~-------- 311 (391)
|+|++++++++++++|+.+|+++++|+..+|+++++++.++||+|||+||++|+++|+++|+|+|||+|+|+
T Consensus 397 S~g~~~~~~~~~~~~g~~l~~e~~e~~~~~~~l~~~~~~i~rL~NDi~S~~kE~~rGdv~n~V~~ymke~g~s~eeA~~~ 476 (542)
T cd00684 397 SIGLGPLLLTSFLGMGDILTEEAFEWLESRPKLVRASSTIGRLMNDIATYEDEMKRGDVASSIECYMKEYGVSEEEAREE 476 (542)
T ss_pred HhhHHHHHHHHHHhcCCCCCHHHHHHHhccHHHHHHHHHHHHHhcChhhhHHHHhcCCcccHHHHHHHhcCCCHHHHHHH
Confidence 999999999999999999999999998877999999999999999999999999999999999999999987
Q ss_pred ----HHHHHHHHHhhhhhccCCCCCCCcHhHHHHHHHHhhhhhhhcccCCCCCCCchhHHHHHHhhcccc
Q 040856 312 ----IRQMWKKVMMDVSRASNNKDSPLSQITNEFILNLVRVSHFMYLHGDGHGVQNQETMDEAFALLFQP 377 (391)
Q Consensus 312 ----ie~~wK~ln~e~~~~~~~~~~~vp~~~~~~~~n~~R~~~~~Y~~~D~~t~~~~~~k~~i~~ll~~p 377 (391)
|+++||+||++ ++++ ++++|++|++.++|++|+++++|+++||||.|++.||++|++||++|
T Consensus 477 i~~~ie~~wk~ln~e--~l~~--~~~~p~~~~~~~~n~~r~~~~~Y~~~D~~t~~~~~~~~~i~~ll~~p 542 (542)
T cd00684 477 IKKMIEDAWKELNEE--FLKP--SSDVPRPIKQRFLNLARVIDVFYKEGDGFTHPEGEIKDHITSLLFEP 542 (542)
T ss_pred HHHHHHHHHHHHHHH--HhcC--CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCccHHHHHHHHHHhcCC
Confidence 99999999999 9986 34799999999999999999999999999998778999999999998
No 3
>PLN02592 ent-copalyl diphosphate synthase
Probab=100.00 E-value=1.5e-81 Score=666.98 Aligned_cols=343 Identities=21% Similarity=0.285 Sum_probs=305.8
Q ss_pred ChhHHHHHHHHHHHHhh-CCC-----CCccHHHHHHHHcCCCcCCCCchHHHHhhHHHhhcccc-------------ccH
Q 040856 1 MEEAWQFTSKHLKQCLN-SNK-----DDEDLNEQARRALELPLHWRMPRLEARWFINVYEKRKD-------------KNH 61 (391)
Q Consensus 1 L~eA~~ft~~~L~~~~~-~~~-----~~~~l~~eV~~aL~~P~~~~l~Rlear~yI~~Y~~~~~-------------~n~ 61 (391)
||||+.||++||++.+. +++ .+++|++||+|||++|||++|||||||+||++|+++++ +|+
T Consensus 422 LdeA~~Fs~~~L~~~~~~~~l~d~~~~~~~L~~eV~~AL~~P~~~~l~RlEaR~yI~~Y~~~~~~~i~Kt~yr~~~~~n~ 501 (800)
T PLN02592 422 LENAKEFSSKFLREKQEANELLDKWIIMKDLPGEVGFALEIPWYASLPRVETRFYIEQYGGEDDVWIGKTLYRMPYVNNN 501 (800)
T ss_pred HHHHHHHHHHHHHHHhhccccccccccCccHHHHHHHhccChhhcCcchHHHHHHHHHhcCCcccchhhhhccccccCCH
Confidence 79999999999999863 222 35789999999999999999999999999999998775 499
Q ss_pred HHHHHHhhhhHHHhhhcHHHHHHHHHHHhhcCCCccCcchhhhhhHhhhhhhccccCCCchhHHHHHHHHHHHHHHhhhh
Q 040856 62 ALLELAKLDFNILQATYQEELKDISGWWKDKGLGEKLSFARSRLVTSFFWGMGMVFEPQFAYSRRVLTITLALITVIDDI 141 (391)
Q Consensus 62 ~lLelAkldFn~~Q~~hq~El~~l~rW~~~~~l~~~l~faRdr~~e~yf~~~a~~feP~~s~~Rl~~aK~~~l~~~iDD~ 141 (391)
+||||||+|||+||++||+||++++|||+++|| .++||||||++|||||++|++|||++|.+|++|||+++|++++||+
T Consensus 502 ~lLeLAklDFn~~Qs~hq~EL~~lsrWwke~~L-~~L~faRdr~ve~Yfwa~~~~feP~~s~~Ri~~aK~~~LitviDD~ 580 (800)
T PLN02592 502 EYLELAKLDYNNCQALHQLEWDNFQKWYEECNL-GEFGVSRSELLLAYFLAAASIFEPERSHERLAWAKTTVLVEAISSY 580 (800)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHhHHHHhcCC-CcCCcchhHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHhhccc
Confidence 999999999999999999999999999999999 6999999999999999999999999999999999999999999999
Q ss_pred hcccCCHHHHHHHHHHhh--------hcchhhhhhcCCh------hHHHHHHHHHHHHHHHHHHHHhhcCcchhHHHHHH
Q 040856 142 YDIYGTLDELELFTNAVE--------RWDINFAIKQLPD------YMKICFFALYNFVSEVAYDILKQQDSDQLLRIKNS 207 (391)
Q Consensus 142 ~D~~gt~eel~~~~~ai~--------rWd~~~~~~~lp~------~mk~~~~al~~~~~e~~~~~~~~~~~~~~~~l~~~ 207 (391)
||+|||.||++.||++|+ |||.+ .++++|+ |||+||.||++++||++.++.+.||+++++|++++
T Consensus 581 fD~yGt~eEl~~ft~~v~~~~~~~~~rWd~~-~~~~lp~~~~~~~~mki~f~aLy~tineia~~a~~~qGr~v~~~L~~~ 659 (800)
T PLN02592 581 FNKETSSKQRRAFLHEFGYGYKINGRRSDHH-FNDRNMRRSGSVKTGEELVGLLLGTLNQLSLDALEAHGRDISHLLRHA 659 (800)
T ss_pred ccCCCCHHHHHHHHHHHHhcccccccccCch-hhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHHH
Confidence 999999999999999996 89999 9999988 99999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhCCCCCChHHHHhhccccchhhHHHHHHHh-hcCCCCchHHHhhhccChHHHHHHHHHHHHhcCC
Q 040856 208 WLGLLQAFLVEAKWYHNKYAPTLEEYLKNAALSIAGPLITITAYL-SATDPIVEKELEYLESNPDVIQWSSRIFRLLDDL 286 (391)
Q Consensus 208 w~~~~~a~~~EA~W~~~~~iPs~eEYl~~~~~s~g~~~~~~~~~~-~~g~~l~~e~~e~~~~~p~l~~~~~~i~RL~NDi 286 (391)
|.++++ +|..+|+ +|+|++.+++++++ .+|..+|++++ ++|++.+++++++||+||+
T Consensus 660 W~~l~~------~w~~~g~------------~s~~~~~ilv~~~~l~~g~~lsee~l----~~~~~~~l~~li~Rl~nDl 717 (800)
T PLN02592 660 WEMWLL------KWLLEGD------------GRQGEAELLVKTINLTAGRSLSEELL----AHPQYEQLAQLTNRICYQL 717 (800)
T ss_pred HHHHHH------HHHhcCc------------eeccchhhHHHHHHHhcCCCCCHHHc----cchhHHHHHHHHHHHHHhh
Confidence 999998 4665554 45577778888888 45999999995 4899999999999999999
Q ss_pred CCChhhhhcCCCcchHHHHHhhc--chHHHHHHHHHhhhhhccCCCCCCCcHhHHHHHHHHhhhhhhhcccCCCCCCCch
Q 040856 287 GTSSDEIQRGDVSKSIQCYMHET--NLIRQMWKKVMMDVSRASNNKDSPLSQITNEFILNLVRVSHFMYLHGDGHGVQNQ 364 (391)
Q Consensus 287 ~S~~~E~~~G~~~n~V~~yM~e~--g~ie~~wK~ln~e~~~~~~~~~~~vp~~~~~~~~n~~R~~~~~Y~~~D~~t~~~~ 364 (391)
+|+++|+..|...+. + .++. ..|+..+++|.+. +++.. ++.||++||++||+|+|+ |+|. ||++| +
T Consensus 718 ~t~~~e~~~~~~~~~-~--a~~~~~~~ie~~~~eL~~l--vl~~~-~~~vp~~cK~~f~~~~k~--fy~~---~~~~~-~ 785 (800)
T PLN02592 718 GHYKKNKVHINTYNP-E--EKSKTTPSIESDMQELVQL--VLQNS-SDDIDPVIKQTFLMVAKS--FYYA---AYCDP-G 785 (800)
T ss_pred hHHhhhcccCCcccH-H--HHHHHHHHHHHHHHHHHHH--HhhcC-CCCCCHHHHHHHHHHHHH--HHHh---hcCCH-H
Confidence 999999975542221 2 1222 3499999999999 99731 336999999999999995 4555 99987 6
Q ss_pred hHHHHHHhhcccccc
Q 040856 365 ETMDEAFALLFQPIP 379 (391)
Q Consensus 365 ~~k~~i~~ll~~pv~ 379 (391)
+|++||.+||+|||+
T Consensus 786 ~~~~~i~~vl~epv~ 800 (800)
T PLN02592 786 TINYHIAKVLFERVA 800 (800)
T ss_pred HHHHHHHHHhCCCCC
Confidence 899999999999985
No 4
>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=2.4e-47 Score=364.16 Aligned_cols=248 Identities=34% Similarity=0.442 Sum_probs=229.7
Q ss_pred HHHHHhhhhHHHhhhcHHHHHHHHHHHhhcCCCccCcchhhhhhHhhhhhhccccCCCchhHHHHHHHHHHHHHHhhhhh
Q 040856 63 LLELAKLDFNILQATYQEELKDISGWWKDKGLGEKLSFARSRLVTSFFWGMGMVFEPQFAYSRRVLTITLALITVIDDIY 142 (391)
Q Consensus 63 lLelAkldFn~~Q~~hq~El~~l~rW~~~~~l~~~l~faRdr~~e~yf~~~a~~feP~~s~~Rl~~aK~~~l~~~iDD~~ 142 (391)
||+|||+|||+||+.||+|++++++||+++|+..+.+.+|+|+..++|+.+|++++|+.+..|+++||+++|+|++||+|
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 79999999999999999999999999999999778887799999999999999999996667779999999999999999
Q ss_pred cccCCHHHHHHHHHHhhhcchhhhhhcCChhHHHHHHHHHHHHHHHHHHHHhhcCc-chhHHHHHHHHHHHHHHHHHHHH
Q 040856 143 DIYGTLDELELFTNAVERWDINFAIKQLPDYMKICFFALYNFVSEVAYDILKQQDS-DQLLRIKNSWLGLLQAFLVEAKW 221 (391)
Q Consensus 143 D~~gt~eel~~~~~ai~rWd~~~~~~~lp~~mk~~~~al~~~~~e~~~~~~~~~~~-~~~~~l~~~w~~~~~a~~~EA~W 221 (391)
|..|+.++++.|+++++||++. ....+|+.+++++.++.++++++...+.+.+++ ++.++|+++|.++++++++|++|
T Consensus 81 D~~~~~~~~~~l~~~~~~~~~~-~~~~~~~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 159 (270)
T PF03936_consen 81 DDGGSAEELEALTDAVERWDPN-SGDPLPDPDKPLFRALADIWNRIAARMSPAQRRRDQIKRFRNSWREYLNAYLWEARW 159 (270)
T ss_dssp HTTSHHHHHHHHHHHHHHTSSG-GGGGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccchHHHHHHHHHHhccccc-ccccccchhHHHHHHHHHHHHHHHHHhhhhhcccHHhhHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999986 888999999999999999999998888887654 48889999999999999999999
Q ss_pred hhCCCCCChHHHHhhccccchhhHHHHHHHhhcCCCCchHHHhhhccChHHHHHHHHHHHHhcCCCCChhhhhcCCCcch
Q 040856 222 YHNKYAPTLEEYLKNAALSIAGPLITITAYLSATDPIVEKELEYLESNPDVIQWSSRIFRLLDDLGTSSDEIQRGDVSKS 301 (391)
Q Consensus 222 ~~~~~iPs~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~e~~~~~p~l~~~~~~i~RL~NDi~S~~~E~~~G~~~n~ 301 (391)
+..|++||++||+..|+.|+|+++++..+.+++|..+++...+++..+|.+.++++.+++|+|||+||+||+++|+.+|.
T Consensus 160 ~~~~~~ps~eeYl~~R~~t~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~NDl~S~~KE~~~g~~~N~ 239 (270)
T PF03936_consen 160 RERGRIPSLEEYLEMRRHTSGVYPCLALIEFALEFALGELPPEVLEHPPMLRRLAADIIRLVNDLYSYKKEIARGDVHNL 239 (270)
T ss_dssp HHTTS--SHHHHHHHHHHHTSHHHHHHHHHHHCSSCHTHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCSH
T ss_pred hccCCCCCHHHHHHhccccccccHHHHHHHHhCCCccccccHHHHHhchHHHHHHHHHHHHhcccchhhcchhhcccccH
Confidence 99999999999999999999999999999888876677666677676788999999999999999999999999999999
Q ss_pred HHHHHhhcch
Q 040856 302 IQCYMHETNL 311 (391)
Q Consensus 302 V~~yM~e~g~ 311 (391)
|.++|+++|+
T Consensus 240 v~~l~~~~~~ 249 (270)
T PF03936_consen 240 VVVLMNEHGL 249 (270)
T ss_dssp HHHHHHHHTH
T ss_pred HHHhhhhcCC
Confidence 9999999987
No 5
>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=7.5e-44 Score=342.46 Aligned_cols=272 Identities=46% Similarity=0.802 Sum_probs=250.2
Q ss_pred hcHHHHHHHHHHHhhcCCCccCcchhhhhhHhhhhhhccccCCCchhHHHHHHHHHHHHHHhhhhhcccCCHHHHHHHHH
Q 040856 77 TYQEELKDISGWWKDKGLGEKLSFARSRLVTSFFWGMGMVFEPQFAYSRRVLTITLALITVIDDIYDIYGTLDELELFTN 156 (391)
Q Consensus 77 ~hq~El~~l~rW~~~~~l~~~l~faRdr~~e~yf~~~a~~feP~~s~~Rl~~aK~~~l~~~iDD~~D~~gt~eel~~~~~ 156 (391)
.||+|++++++||+++||....+++|.+..++|+|+++++|+|+.+..|+++||+++|+|++||+||.+++.+++..+++
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 59999999999999999965555999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhcchhhhhhcCChhHHHHHHHHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhh
Q 040856 157 AVERWDINFAIKQLPDYMKICFFALYNFVSEVAYDILKQQDSDQLLRIKNSWLGLLQAFLVEAKWYHNKYAPTLEEYLKN 236 (391)
Q Consensus 157 ai~rWd~~~~~~~lp~~mk~~~~al~~~~~e~~~~~~~~~~~~~~~~l~~~w~~~~~a~~~EA~W~~~~~iPs~eEYl~~ 236 (391)
+++||+.. ..+.+|+++++++.++.++++++...+.+.+|+....++++.|.+++.++.+||+|+..|++||++||+.+
T Consensus 81 ~~~~~~~~-~~~~~p~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~e~~~~~~~~~p~~~eYl~~ 159 (284)
T cd00868 81 AVERWDIS-AIDELPEYMKPVFKALYDLVNEIEEELAKEGGSESLPYLKEAWKDLLRAYLVEAKWANEGYVPSFEEYLEN 159 (284)
T ss_pred HHHhcChh-hhhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHh
Confidence 99999988 88999999999999999999999999999899999999999999999999999999999999999999999
Q ss_pred ccccchhhHHHHHHHhhcCCCCchHHHhhhccChHHHHHHHHHHHHhcCCCCChhhhhcCCCcchHHHHHhhcch-----
Q 040856 237 AALSIAGPLITITAYLSATDPIVEKELEYLESNPDVIQWSSRIFRLLDDLGTSSDEIQRGDVSKSIQCYMHETNL----- 311 (391)
Q Consensus 237 ~~~s~g~~~~~~~~~~~~g~~l~~e~~e~~~~~p~l~~~~~~i~RL~NDi~S~~~E~~~G~~~n~V~~yM~e~g~----- 311 (391)
|+.|+|+++++..+.+++|..+|++.+.+......+.+.++.+++|+||++||+||+.+|+.+|+|.|+|+++|+
T Consensus 160 R~~~~g~~~~~~l~~~~~g~~l~~~~~~~~~~~~~l~~~~~~~~~l~NDl~S~~kE~~~g~~~N~v~vl~~~~~~~~~eA 239 (284)
T cd00868 160 RRVSIGYPPLLALSFLGMGDILPEEAFEWLPSYPKLVRASSTIGRLLNDIASYEKEIARGEVANSVECYMKEYGVSEEEA 239 (284)
T ss_pred ceehhhHHHHHHHHHHHcCCCCCHHHHHHhhhhHHHHHHHHHHHHHhccchHHHHHHccCCcccHHHHHHhccCCCHHHH
Confidence 999999999999999999999998444555678889999999999999999999999999999999999999986
Q ss_pred -------HHHHHHHHHhhhhhccCCCCCCCcHhHHHHHHHHhhhhhhhc
Q 040856 312 -------IRQMWKKVMMDVSRASNNKDSPLSQITNEFILNLVRVSHFMY 353 (391)
Q Consensus 312 -------ie~~wK~ln~e~~~~~~~~~~~vp~~~~~~~~n~~R~~~~~Y 353 (391)
+++.|+++++. +.+. ++ +.|+.+++.+.+++|..+..|
T Consensus 240 ~~~~~~~~~~~~~~~~~~--~~~~-~~-~~~~~~~~~l~~~~~g~~~w~ 284 (284)
T cd00868 240 LEELRKMIEEAWKELNEE--VLKL-SS-DVPRAVLETLLNLARGIYVWY 284 (284)
T ss_pred HHHHHHHHHHHHHHHHHH--HhcC-CC-CCCHHHHHHHHHHHHhhhhcC
Confidence 67777777777 6543 12 578999999999999876654
No 6
>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=99.97 E-value=6.3e-31 Score=256.11 Aligned_cols=228 Identities=18% Similarity=0.153 Sum_probs=193.8
Q ss_pred hcHHHHHH-HHHHHhhcCCCccCcchhhhhhHhhhhhhccccCCCchhHHH-HHHHHHHHHHHhhhhhccc-CCHHHHHH
Q 040856 77 TYQEELKD-ISGWWKDKGLGEKLSFARSRLVTSFFWGMGMVFEPQFAYSRR-VLTITLALITVIDDIYDIY-GTLDELEL 153 (391)
Q Consensus 77 ~hq~El~~-l~rW~~~~~l~~~l~faRdr~~e~yf~~~a~~feP~~s~~Rl-~~aK~~~l~~~iDD~~D~~-gt~eel~~ 153 (391)
.|-.+++. ...|.++.|+.. -+.+|+++.+++|+.++.++.|+++.+|+ +.++++.|+|++||+||.. +++++++.
T Consensus 10 p~~~~~~~~~~~w~~~~~l~~-~~~~~~~~~~~~~~~~~a~~~P~a~~~~l~l~~~~~~w~f~~DD~~D~~~~~~~~~~~ 88 (303)
T cd00687 10 PYVKEAQDEYLEWVLEEMLIP-SEKAEKRFLSADFGDLAALFYPDADDERLMLAADLMAWLFVFDDLLDRDQKSPEDGEA 88 (303)
T ss_pred cChHHHHHHHHHHHHHcCCCC-cchhHHHHhcCCHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhcccCCccccCHHHHHH
Confidence 45556555 556999998743 34699999999998888888899999999 7889999999999999986 59999999
Q ss_pred HHHHhhhcchhhhhhcCChhHHHHHHHHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHHHHHHHHHHhhCCCCCChHHH
Q 040856 154 FTNAVERWDINFAIKQLPDYMKICFFALYNFVSEVAYDILKQQDSDQLLRIKNSWLGLLQAFLVEAKWYHNKYAPTLEEY 233 (391)
Q Consensus 154 ~~~ai~rWd~~~~~~~lp~~mk~~~~al~~~~~e~~~~~~~~~~~~~~~~l~~~w~~~~~a~~~EA~W~~~~~iPs~eEY 233 (391)
+++.+.++... ....-|....++..++.+++.++... .++....+|++.|.+++.++++|++|+.+|++||++||
T Consensus 89 ~~~~~~~~~~~-~~~~~~~~~~p~~~~~~d~~~r~~~~----~~~~~~~r~~~~~~~~~~a~~~e~~~~~~~~~psl~eY 163 (303)
T cd00687 89 GVTRLLDILRG-DGLDSPDDATPLEFGLADLWRRTLAR----MSAEWFNRFAHYTEDYFDAYIWEGKNRLNGHVPDVAEY 163 (303)
T ss_pred HHHHHHhccCC-CCCCCCCCCCHHHHHHHHHHHHhccC----CCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHH
Confidence 99988885443 22111467888999999888887544 33556789999999999999999999999999999999
Q ss_pred HhhccccchhhHHHHHHHhhcCCCCchHHHhhhccChHHHHHHHHHHHHhcCCCCChhhh-hcCCCcchHHHHHhhcch
Q 040856 234 LKNAALSIAGPLITITAYLSATDPIVEKELEYLESNPDVIQWSSRIFRLLDDLGTSSDEI-QRGDVSKSIQCYMHETNL 311 (391)
Q Consensus 234 l~~~~~s~g~~~~~~~~~~~~g~~l~~e~~e~~~~~p~l~~~~~~i~RL~NDi~S~~~E~-~~G~~~n~V~~yM~e~g~ 311 (391)
+++|+.|+|+.+++..+.+++|..+|+++.+. .....+.++++.+++|+|||+||+||+ +.|+.+|.|.|+|+++|+
T Consensus 164 l~~R~~~~g~~~~~~l~~~~~g~~lp~~~~~~-~~~~~l~~~~~~~~~l~NDl~S~~KE~~~~g~~~N~V~vl~~~~g~ 241 (303)
T cd00687 164 LEMRRFNIGADPCLGLSEFIGGPEVPAAVRLD-PVMRALEALASDAIALVNDIYSYEKEIKANGEVHNLVKVLAEEHGL 241 (303)
T ss_pred HHHhhhcccccccHHHHHHhcCCCCCHHHHhC-hHHHHHHHHHHHHHHHHHHHHhhHHHHHhCCccchHHHHHHHHcCC
Confidence 99999999999999999999999999998544 223459999999999999999999999 889999999999999987
No 7
>PLN02150 terpene synthase/cyclase family protein
Probab=99.94 E-value=3.5e-27 Score=191.39 Aligned_cols=83 Identities=30% Similarity=0.542 Sum_probs=79.2
Q ss_pred hhcCCCcchHHHHHhhcch------------HHHHHHHHHhhhhhccCCCCCCCcHhHHHHHHHHhhhhhhh-cccCCCC
Q 040856 293 IQRGDVSKSIQCYMHETNL------------IRQMWKKVMMDVSRASNNKDSPLSQITNEFILNLVRVSHFM-YLHGDGH 359 (391)
Q Consensus 293 ~~~G~~~n~V~~yM~e~g~------------ie~~wK~ln~e~~~~~~~~~~~vp~~~~~~~~n~~R~~~~~-Y~~~D~~ 359 (391)
|+|||++|+|+|||||||+ |+++||+||+| ++++ + ++|.+++++++|+||+++|+ |++||||
T Consensus 1 ~~rg~vaSsIeCYMke~g~seeeA~~~i~~li~~~WK~iN~e--~l~~--~-~~p~~~~~~~~NlaR~~~~~~Y~~~Dg~ 75 (96)
T PLN02150 1 MRRGEVANGVNCYMKQHGVTKEEAVSELKKMIRDNYKIVMEE--FLTI--K-DVPRPVLVRCLNLARLIDVYCYNEGDGF 75 (96)
T ss_pred CCCCcchHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHH--HcCC--C-CCCHHHHHHHHHHHHHHHhheecCCCCC
Confidence 5789999999999999997 99999999999 9997 7 79999999999999999999 9999999
Q ss_pred CCCchhHHHHHHhhccccccC
Q 040856 360 GVQNQETMDEAFALLFQPIPL 380 (391)
Q Consensus 360 t~~~~~~k~~i~~ll~~pv~~ 380 (391)
|.++..+|++|.+||++|||+
T Consensus 76 t~~~~~~K~~I~sLlv~pi~i 96 (96)
T PLN02150 76 TYPHGKLKDLITSLFFHPLPL 96 (96)
T ss_pred CCCcHHHHHHHHHHhccCCCC
Confidence 988888999999999999985
No 8
>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=99.75 E-value=4e-18 Score=156.93 Aligned_cols=186 Identities=27% Similarity=0.285 Sum_probs=144.6
Q ss_pred hhhccccCCCchhHHHHHHHHHHHHHHhhhhhcccCCHHHHHHHHHHhhhcchhhhhhcCChhHHHHHHHHHHHHHHHHH
Q 040856 111 WGMGMVFEPQFAYSRRVLTITLALITVIDDIYDIYGTLDELELFTNAVERWDINFAIKQLPDYMKICFFALYNFVSEVAY 190 (391)
Q Consensus 111 ~~~a~~feP~~s~~Rl~~aK~~~l~~~iDD~~D~~gt~eel~~~~~ai~rWd~~~~~~~lp~~mk~~~~al~~~~~e~~~ 190 (391)
+.++++++|+++..|..++++..+++++||++|..++..........+.. ...|..+...+..+.+.++++..
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~DDi~D~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~ 74 (243)
T cd00385 2 RPLAVLLEPEASRLRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAVAI-------DGLPEAILAGDLLLADAFEELAR 74 (243)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCchhhhhhHHh-------cCchHHHHHHHHHHHHHHHHHHh
Confidence 45677888999999999999999999999999987776666554433311 23455666777788888887754
Q ss_pred HHHhhcCcchhHHHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhccccchhhHHHHHHHhhcCCCCchHHHhhhccCh
Q 040856 191 DILKQQDSDQLLRIKNSWLGLLQAFLVEAKWYHNKYAPTLEEYLKNAALSIAGPLITITAYLSATDPIVEKELEYLESNP 270 (391)
Q Consensus 191 ~~~~~~~~~~~~~l~~~w~~~~~a~~~EA~W~~~~~iPs~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~e~~~~~p 270 (391)
.. .+....++.+.|.+++.++.+|+.|+.. ++||++||+..+..++|.. +......+++...++ ........
T Consensus 75 ~~----~~~~~~~~~~~~~~~~~g~~~d~~~~~~-~~~t~~ey~~~~~~~t~~~-~~~~~~~~~~~~~~~--~~~~~~~~ 146 (243)
T cd00385 75 EG----SPEALEILAEALLDLLEGQLLDLKWRRE-YVPTLEEYLEYCRYKTAGL-VGALCLLGAGLSGGE--AELLEALR 146 (243)
T ss_pred CC----CHHHHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHHhHHHH-HHHHHHHHHHHhCCC--HHHHHHHH
Confidence 32 2456789999999999999999999977 8999999999999998444 444444445555454 23324456
Q ss_pred HHHHHHHHHHHHhcCCCCChhhhhcC-CCcchHHHHHhhcch
Q 040856 271 DVIQWSSRIFRLLDDLGTSSDEIQRG-DVSKSIQCYMHETNL 311 (391)
Q Consensus 271 ~l~~~~~~i~RL~NDi~S~~~E~~~G-~~~n~V~~yM~e~g~ 311 (391)
.+...++.+.+|.||+.|+.+|.+.| +..|.+.++|+++|+
T Consensus 147 ~~~~~~g~~~ql~nDl~~~~~e~~~~~~~~~l~~~~~~~~~~ 188 (243)
T cd00385 147 KLGRALGLAFQLTNDLLDYEGDAERGEGKCTLPVLYALEYGV 188 (243)
T ss_pred HHHHHHHHHHHHHHHHHhccCCHHHhCCchHHHHHHHHHhCC
Confidence 78888999999999999999999996 678999999999863
No 9
>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=97.08 E-value=0.004 Score=62.04 Aligned_cols=189 Identities=11% Similarity=0.076 Sum_probs=106.0
Q ss_pred hhhhccccCCCchhH-HHHHHHHHHHHHHhhhhhcccCCHHHHHHHHHHhhhcchhhhhhcCChhHHHHHHHHHHHHHHH
Q 040856 110 FWGMGMVFEPQFAYS-RRVLTITLALITVIDDIYDIYGTLDELELFTNAVERWDINFAIKQLPDYMKICFFALYNFVSEV 188 (391)
Q Consensus 110 f~~~a~~feP~~s~~-Rl~~aK~~~l~~~iDD~~D~~gt~eel~~~~~ai~rWd~~~~~~~lp~~mk~~~~al~~~~~e~ 188 (391)
-+++...| |..+.+ ++..+-..++++++||.++.. .+++..|-+-+-. + ... | .++..++.+.+.
T Consensus 71 v~~~~~~y-~~~~~evqv~IaiyT~yvi~iDD~~~~~--~~~l~~F~~~l~~--G--q~Q--~---~p~L~~~~~~L~-- 136 (376)
T PF06330_consen 71 VNMAVYCY-PHLPKEVQVAIAIYTTYVIIIDDSSQEP--SDDLRTFHQRLIL--G--QPQ--K---HPLLDGFASLLR-- 136 (376)
T ss_dssp HHHHHHHS-TTS-HHHHHHHHHHHHHHHHHTT--S-S--HHHHTTHHHHHHH--T-------S---SHHHHHHHHHHH--
T ss_pred hheeEeec-CCCCHHHHHHHHHHHHHHHhcccccccc--cHHHHHHHHHHhc--C--CCC--C---CHHHHHHHHHHH--
Confidence 34433344 777765 568899999999999998654 3666666554433 1 111 1 133344444444
Q ss_pred HHHHHhhcCcchhHHHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhccccchhhHHHHHHHhhcCCCCchHHHhhhcc
Q 040856 189 AYDILKQQDSDQLLRIKNSWLGLLQAFLVEAKWYHNKYAPTLEEYLKNAALSIAGPLITITAYLSATDPIVEKELEYLES 268 (391)
Q Consensus 189 ~~~~~~~~~~~~~~~l~~~w~~~~~a~~~EA~W~~~~~iPs~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~e~~~~ 268 (391)
++.+.-|+.+..-+..+-.+++.+..-|.+.. +-.|.-..|-..-+.=+|.....+...+ .....++. ..
T Consensus 137 --~~~~~fgpf~anmI~~STLdFi~g~~LE~~~f--~~~p~A~~FP~fLR~ktGlsEaYA~FiF--Pk~~fpe~----~~ 206 (376)
T PF06330_consen 137 --EMWRHFGPFCANMIVKSTLDFINGCWLEQKNF--HGSPGAPDFPDFLRRKTGLSEAYAFFIF--PKALFPEV----EY 206 (376)
T ss_dssp --HHHTTS-HHHHHHHHHHHHHHHHHHHHHTTT------TT-TTHHHHHHHHHH-HHHHHHHT----TTTS-TT----TT
T ss_pred --HHHHHcchHHHHHHHHHHHHHHHHHHhhcccC--CCCCCCccccHHHHhccCcchhheeeec--ccccCChH----HH
Confidence 45556688888899999999999999998643 2234333344443444565555433333 12222222 22
Q ss_pred ChHHHHH---HHHHHHHhcCCCCChhhhh-cCCCcchHHHHHhhcch-HHHHHHHHHhh
Q 040856 269 NPDVIQW---SSRIFRLLDDLGTSSDEIQ-RGDVSKSIQCYMHETNL-IRQMWKKVMMD 322 (391)
Q Consensus 269 ~p~l~~~---~~~i~RL~NDi~S~~~E~~-~G~~~n~V~~yM~e~g~-ie~~wK~ln~e 322 (391)
...++.+ .....-++|||.||=||.- .|+..|.|.-+-.-+|+ +.++-+++.+|
T Consensus 207 ~~~y~~AIpdl~~fi~~~NDILSFYKE~l~a~E~~NyI~n~A~~~g~S~~eaL~~l~~e 265 (376)
T PF06330_consen 207 FIQYTPAIPDLMRFINYVNDILSFYKEELVAGETGNYIHNRARVHGVSILEALRELTDE 265 (376)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSSSSHHHHHHHHHT--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhhhhHHHHHHhhcccccccchhhhhhhccCCCHHHHHHHHHHH
Confidence 3333333 3444568999999999976 77889999777766777 55555555444
No 10
>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=96.81 E-value=0.0085 Score=58.93 Aligned_cols=198 Identities=14% Similarity=0.089 Sum_probs=115.7
Q ss_pred hhhhhHhhhhhhccccCCC--chhHHH-HHHHHHHHHHHhhhhhcccCCHHHHHHHHHHhhhcchhhhhhcCChhHHHHH
Q 040856 102 RSRLVTSFFWGMGMVFEPQ--FAYSRR-VLTITLALITVIDDIYDIYGTLDELELFTNAVERWDINFAIKQLPDYMKICF 178 (391)
Q Consensus 102 Rdr~~e~yf~~~a~~feP~--~s~~Rl-~~aK~~~l~~~iDD~~D~~gt~eel~~~~~ai~rWd~~~~~~~lp~~mk~~~ 178 (391)
..|+.-+-=.++++.-.|. .|.+=+ .++-..+.++++||.-|.. .+.++.|.+-+.. + .....| +.
T Consensus 60 p~ri~~~~~T~v~~~~Y~w~~~skev~~~isi~~tY~~~lDD~~~e~--~~~m~~f~~dL~~--G--~~qkhP-----~l 128 (357)
T cd00686 60 PKRLQASLQTIVGMVVYSWAKVSKECMADLSIHYTYTLVLDDSKDDP--YPTMVNYFDDLQA--G--REQAHP-----WW 128 (357)
T ss_pred HHHHHHHHHHhhceEEeeccCCCHHHHHHHHHHHheeeEeccccccc--chHHHHHHHHHhc--C--CCCCCc-----HH
Confidence 3444444335555533366 666655 7777788889999997643 2455555555544 1 122222 22
Q ss_pred HHHHHHHHHHHHHHHhhcCcchhHHHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhccccchhhHHHHHHHhhcCCCC
Q 040856 179 FALYNFVSEVAYDILKQQDSDQLLRIKNSWLGLLQAFLVEAKWYHNKYAPTLEEYLKNAALSIAGPLITITAYLSATDPI 258 (391)
Q Consensus 179 ~al~~~~~e~~~~~~~~~~~~~~~~l~~~w~~~~~a~~~EA~W~~~~~iPs~eEYl~~~~~s~g~~~~~~~~~~~~g~~l 258 (391)
..+.+.+. .....-|+.+..-+..+--+++.+..-|... .+.-|.-..|-...+.=+|...+.+...+
T Consensus 129 ~~v~~~l~----~~lr~fGpF~s~~IikSTLdFv~g~~iEq~n--f~~~p~A~~fP~ylR~ksGl~E~yA~FiF------ 196 (357)
T cd00686 129 ALVNEHFP----NVLRHFGPFCSLNLIRSTLDFFEGCWIEQYN--FGGFPGSHDYPQFLRRMNGLGHCVGASLW------ 196 (357)
T ss_pred HHHHHHHH----HHHHHhhhhhHHHHHHHHHHHHHHHHHhhhc--cCCCCCCcccchHHHhccCCcceeEEEec------
Confidence 22222233 2333456777777788888899999888663 33356656666665666665554432222
Q ss_pred chHHHhhhccChHHHHHHH---HHHHHhcCCCCChhhhhc-CCCcchHHHHHhhcch-HHHHHHHHHhh
Q 040856 259 VEKELEYLESNPDVIQWSS---RIFRLLDDLGTSSDEIQR-GDVSKSIQCYMHETNL-IRQMWKKVMMD 322 (391)
Q Consensus 259 ~~e~~e~~~~~p~l~~~~~---~i~RL~NDi~S~~~E~~~-G~~~n~V~~yM~e~g~-ie~~wK~ln~e 322 (391)
|++.+.....+..+..+.. ...-++|||.||=||--. ++-.|.|.-|-+.+|+ ..++-+++-++
T Consensus 197 Pk~~FpE~~~~~qi~~AIp~~~~~i~~~NDILSFYKEe~~~~E~~n~V~Nya~~~GiS~~eAL~~lt~d 265 (357)
T cd00686 197 PKEQFNERSLFLEITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQD 265 (357)
T ss_pred chhhCchHhhHHHhhHHHHHHHHHHHhhhhhhheehhhcccccccchHHHhhhhcCCCHHHHHHHHHHH
Confidence 4444322222233333333 344589999999998854 4567888888888998 55555555555
No 11
>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=92.53 E-value=5 Score=37.15 Aligned_cols=101 Identities=16% Similarity=0.101 Sum_probs=65.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhccc-cchhhHHHHHHHhhcCCCCchHHHhhhccChHHHHHHHH
Q 040856 200 QLLRIKNSWLGLLQAFLVEAKWYHNKYAPTLEEYLKNAAL-SIAGPLITITAYLSATDPIVEKELEYLESNPDVIQWSSR 278 (391)
Q Consensus 200 ~~~~l~~~w~~~~~a~~~EA~W~~~~~iPs~eEYl~~~~~-s~g~~~~~~~~~~~~g~~l~~e~~e~~~~~p~l~~~~~~ 278 (391)
....+.+...+++.+...+..|... ..||.++|.+.... |.+.....+....+++.. +++..+. ..++-...+.
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 4556778889999999999988754 57999999999887 666543333333323322 2223222 2456667777
Q ss_pred HHHHhcCCCCChhhh----------hcCCCcchHHHHH
Q 040856 279 IFRLLDDLGTSSDEI----------QRGDVSKSIQCYM 306 (391)
Q Consensus 279 i~RL~NDi~S~~~E~----------~~G~~~n~V~~yM 306 (391)
..-+.||+..+.... +.|.. +....++
T Consensus 161 a~Qi~dd~~D~~~d~~~~gk~~~D~~~gr~-tlp~~~~ 197 (236)
T cd00867 161 AFQLTDDLLDVFGDAEELGKVGSDLREGRI-TLPVILA 197 (236)
T ss_pred HHHHHHHhccccCChHHHCccHHHHHcCCc-hHHHHHH
Confidence 778888888876544 45544 6666666
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=59.84 E-value=53 Score=30.99 Aligned_cols=116 Identities=16% Similarity=0.129 Sum_probs=66.1
Q ss_pred hhHHHHHHHHHHHHHHhhhhhcccCCHH----HHHHHHHHhhhcchhhhhhcCChhHHHHHHHHHHHHHHHHHHHHhhcC
Q 040856 122 AYSRRVLTITLALITVIDDIYDIYGTLD----ELELFTNAVERWDINFAIKQLPDYMKICFFALYNFVSEVAYDILKQQD 197 (391)
Q Consensus 122 s~~Rl~~aK~~~l~~~iDD~~D~~gt~e----el~~~~~ai~rWd~~~~~~~lp~~mk~~~~al~~~~~e~~~~~~~~~~ 197 (391)
...|-.+.-+-.+.-.+||+-|...... .++-+-+++...-.+ ..+..+....++..++..+++...
T Consensus 17 ~~~R~~~~alyaf~r~~d~i~D~~~~~~~~~~~L~~w~~~l~~~~~~-~~~~~~~~~~pv~~~l~~~~~~~~-------- 87 (267)
T PF00494_consen 17 KEKRPAVFALYAFCRELDDIVDEPSDPEEARARLQWWRDALNSIFAS-YEDSLPEPSHPVARALADLVRRYG-------- 87 (267)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCTSS-HSCHHHHHHHHHHHHHHHH--TSTHHHSSHHHHHHHHHHHHCCSH--------
T ss_pred HHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHHHHHHHhhh-hhhccCCCcCHHHHHHHHHHHHHh--------
Confidence 3445555557778888999998655322 344455555542211 111223344566666666554331
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhccccchhhHHHHHHHhhc
Q 040856 198 SDQLLRIKNSWLGLLQAFLVEAKWYHNKYAPTLEEYLKNAALSIAGPLITITAYLSA 254 (391)
Q Consensus 198 ~~~~~~l~~~w~~~~~a~~~EA~W~~~~~iPs~eEYl~~~~~s~g~~~~~~~~~~~~ 254 (391)
.-++.+.+++.++.+... ...++|++|+......+.|....++.-.++.
T Consensus 88 -----l~~~~l~~li~~~~~dl~---~~~~~t~~~L~~Y~~~vag~vg~l~~~~~~~ 136 (267)
T PF00494_consen 88 -----LPREPLLELIDGMEMDLE---FTPYETFADLERYCYYVAGSVGLLLLQLLGA 136 (267)
T ss_dssp -----HHHHHHHHHHHHHHHCTT----S--SSHHHHHHHHHHHTHHHHHHHHHHHHS
T ss_pred -----hhHHHHHHHHHHhccccc---CCCCCCHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 233455667766664433 3558899999999988888766665555544
No 13
>TIGR03486 cas_csx13_C CRISPR-associated protein, Cas_csx13 family, C-terminal region. Members of this family are found among cas (CRISPR-Associated) genes close to CRISPR repeats in Leptospira interrogans (a spirochete), Myxococcus xanthus (a delta-proteobacterium), and Lyngbya sp. PCC 8106 (a cyanobacterium). It is found with other cas genes in Anabaena variabilis ATCC 29413. In Lyngbya sp., the protein is split into two tandem genes. This model corresponds to the C-terminal region or upstream gene; the N-terminal region is modelled by TIGR03485. CRISPR/cas systems are associated with prokaryotic acquired resistance to phage and other exogenous DNA.
Probab=34.47 E-value=3e+02 Score=24.31 Aligned_cols=67 Identities=19% Similarity=0.156 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHHhhhhhcccCCHHHHHHHHHHhhhcchhhhhhcCChhHHHHHHHHHHHHHHHHHHHHh
Q 040856 124 SRRVLTITLALITVIDDIYDIYGTLDELELFTNAVERWDINFAIKQLPDYMKICFFALYNFVSEVAYDILK 194 (391)
Q Consensus 124 ~Rl~~aK~~~l~~~iDD~~D~~gt~eel~~~~~ai~rWd~~~~~~~lp~~mk~~~~al~~~~~e~~~~~~~ 194 (391)
.|=+|+.+...++-=||+-.-.--...|..+++..+.||.+ . ++ --++.|..|+-.++..|..+...
T Consensus 8 grpW~a~F~~~~~~~~~f~~~~~er~gL~~M~~~~~~~~~e-~-eq--~fiqa~HeAlr~~~~qI~~~tk~ 74 (152)
T TIGR03486 8 GRPWYANFAKPLKWKIDFKERKRERDELNKMIENSEIWDSE-A-EQ--WFVQSFHEALRRIYAKIASHTKR 74 (152)
T ss_pred CCcHHHHHHHHHHhhHHHHHHHHHHHhHHHHHHHHHhcccH-H-HH--HHHHHHHHHHHHHHHHHHHHhhh
Confidence 34455555555555544433222455677777777778754 2 11 13456667777777777666554
No 14
>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=33.68 E-value=4.1e+02 Score=24.99 Aligned_cols=108 Identities=16% Similarity=0.130 Sum_probs=59.0
Q ss_pred hHHHHHHHHHHHHHHhhhhhcccCCH-----HHHHHHHHHhhhcchhhhhhcCChhHHHHHHHHHHHHHHHHHHHHhhcC
Q 040856 123 YSRRVLTITLALITVIDDIYDIYGTL-----DELELFTNAVERWDINFAIKQLPDYMKICFFALYNFVSEVAYDILKQQD 197 (391)
Q Consensus 123 ~~Rl~~aK~~~l~~~iDD~~D~~gt~-----eel~~~~~ai~rWd~~~~~~~lp~~mk~~~~al~~~~~e~~~~~~~~~~ 197 (391)
..|-.+.-+-.+.-.+||+=|..... ..|+-+-++++.-... .-| -.++..+|..++.+. +
T Consensus 24 ~~R~~~~alYaf~r~~Ddi~D~~~~~~~~~~~~L~~w~~~l~~~~~~----~~~--~~pv~~al~~~~~~~--------~ 89 (265)
T cd00683 24 ELRRAVCALYAFCRAADDIVDDPAAPPDEKLALLDAFRAELDAAYWG----GAP--THPVLRALADLARRY--------G 89 (265)
T ss_pred HHHHHHHHHHHHHHHHHhhhhCCCCCchhHHHHHHHHHHHHHHHHcC----CCC--CChHHHHHHHHHHHc--------C
Confidence 34444444666777799999964422 2334444444331110 011 125666666655422 1
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhccccchhhHHHHHHHh
Q 040856 198 SDQLLRIKNSWLGLLQAFLVEAKWYHNKYAPTLEEYLKNAALSIAGPLITITAYL 252 (391)
Q Consensus 198 ~~~~~~l~~~w~~~~~a~~~EA~W~~~~~iPs~eEYl~~~~~s~g~~~~~~~~~~ 252 (391)
.-++.+.+++.++.+... ....||++|.......+.|.--.++.-.+
T Consensus 90 -----l~~~~~~~li~g~~~Dl~---~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~ 136 (265)
T cd00683 90 -----IPREPFRDLLAGMAMDLD---KRRYETLDELDEYCYYVAGVVGLMLLRVF 136 (265)
T ss_pred -----CCHHHHHHHHHHHHHhCC---CCCCCCHHHHHHHHHHhHHHHHHHHHHHh
Confidence 223456677777765544 45678998888887777775444444444
No 15
>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=28.90 E-value=5e+02 Score=24.54 Aligned_cols=106 Identities=22% Similarity=0.190 Sum_probs=56.8
Q ss_pred HHHHHHHHHHHHHhhhhhccc-CCHHHH----HHHHHHhhhcchhhhhhcCChhHHHHHHHHHHHHHHHHHHHHhhcCcc
Q 040856 125 RRVLTITLALITVIDDIYDIY-GTLDEL----ELFTNAVERWDINFAIKQLPDYMKICFFALYNFVSEVAYDILKQQDSD 199 (391)
Q Consensus 125 Rl~~aK~~~l~~~iDD~~D~~-gt~eel----~~~~~ai~rWd~~~~~~~lp~~mk~~~~al~~~~~e~~~~~~~~~~~~ 199 (391)
|-.+.-+-.+.=.+||+=|.. ++.++- .-+-+.++. ....-| -.++..+|.+++.+. +..
T Consensus 20 R~~~~alYAf~R~~Ddi~D~~~~~~~~~~~~L~~wr~~l~~-----~~~g~~--~~pv~~aL~~~~~~~--------~l~ 84 (266)
T TIGR03464 20 RAPIHAVYAFARTADDIADEGDGSAEERLALLDDFRAELDA-----IYSGEP--AAPVFVALARTVQRH--------GLP 84 (266)
T ss_pred HHHHHHHHHHHHHHHHhccCCCCChHHHHHHHHHHHHHHHH-----HhCCCC--CChHHHHHHHHHHHc--------CCC
Confidence 333333555667899999974 455543 333333322 111112 135667776666543 111
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhccccchhhHHHHHHHhh
Q 040856 200 QLLRIKNSWLGLLQAFLVEAKWYHNKYAPTLEEYLKNAALSIAGPLITITAYLS 253 (391)
Q Consensus 200 ~~~~l~~~w~~~~~a~~~EA~W~~~~~iPs~eEYl~~~~~s~g~~~~~~~~~~~ 253 (391)
++.+.+++.++.... .....+|++|.......+.|+--.+++-.++
T Consensus 85 -----~~~~~~li~~~~~Dl---~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~g 130 (266)
T TIGR03464 85 -----IEPFLDLLDAFRQDV---VVTRYATWAELLDYCRYSANPVGRLVLDLYG 130 (266)
T ss_pred -----hHHHHHHHHHHHHhc---cCCCCCCHHHHHHHHHHhHHHHHHHHHHHcC
Confidence 234455555554332 2455789999998888888865554444443
No 16
>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=27.91 E-value=2.2e+02 Score=26.87 Aligned_cols=88 Identities=22% Similarity=0.121 Sum_probs=56.1
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhccccchhhHHHHHHH--hhcCCCCchHHHhhhccChHHHHH
Q 040856 198 SDQLLRIKNSWLGLLQAFLVEAKWYHNKYAPTLEEYLKNAALSIAGPLITITAY--LSATDPIVEKELEYLESNPDVIQW 275 (391)
Q Consensus 198 ~~~~~~l~~~w~~~~~a~~~EA~W~~~~~iPs~eEYl~~~~~s~g~~~~~~~~~--~~~g~~l~~e~~e~~~~~p~l~~~ 275 (391)
..+...+.+.....+.+-..+..|... ..||.++|++....-+|.....+... ...|. +++..+. .-++-..
T Consensus 107 ~~~~~~~~~~~~~~~~GQ~~d~~~~~~-~~~~~~~y~~~~~~KT~~l~~~~~~~~a~l~~~--~~~~~~~---l~~~g~~ 180 (259)
T cd00685 107 PRALELFSEAILELVEGQLLDLLSEYD-TDVTEEEYLRIIRLKTAALFAAAPLLGALLAGA--DEEEAEA---LKRFGRN 180 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHccCC-CCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCC--CHHHHHH---HHHHHHH
Confidence 345667778888889988888888754 57999999999776666543322211 11222 3333222 2345666
Q ss_pred HHHHHHHhcCCCCChh
Q 040856 276 SSRIFRLLDDLGTSSD 291 (391)
Q Consensus 276 ~~~i~RL~NDi~S~~~ 291 (391)
.+...-+.||+..+..
T Consensus 181 lG~afQi~DD~ld~~~ 196 (259)
T cd00685 181 LGLAFQIQDDILDLFG 196 (259)
T ss_pred HHHHHHHHHHhhcccC
Confidence 6777778888876644
No 17
>cd01040 globin Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen in the bloodstream, (2) microorganismal flavohemoglobins, which are linked to C-terminal FAD-dependend reductase domains, (3) homodimeric bacterial hemoglobins, such as from Vitreoscilla, (4) plant leghemoglobins (symbiotic hemoglobins, involved in nitrogen metabolism in plant rhizomes), (5) plant non-symbiotic hexacoordinate globins and hexacoordinate globins from bacteria and animals, such as neuroglobin, (6) invertebrate hemoglobins, which may occur in tandem-repeat arrangements, and (7) monomeric myoglobins found in animal muscle tissue.
Probab=25.64 E-value=3.7e+02 Score=21.84 Aligned_cols=77 Identities=19% Similarity=0.249 Sum_probs=48.9
Q ss_pred HHHHHHHHhhhhhcccCCHHHHHHHHHHhhhcchhhhhhcCChhHHHHHHHHHHHHHHHHHHHHhhcCcchhHHHHHHHH
Q 040856 130 ITLALITVIDDIYDIYGTLDELELFTNAVERWDINFAIKQLPDYMKICFFALYNFVSEVAYDILKQQDSDQLLRIKNSWL 209 (391)
Q Consensus 130 K~~~l~~~iDD~~D~~gt~eel~~~~~ai~rWd~~~~~~~lp~~mk~~~~al~~~~~e~~~~~~~~~~~~~~~~l~~~w~ 209 (391)
....++..++.+.+.-+..+.+..+...+.+ .+....--|++...+..++..++.+.- |....+-..++|.
T Consensus 60 ~~~~~~~~l~~~v~~l~~~~~l~~~l~~lg~--~H~~~~v~~~~~~~~~~~l~~~l~~~~-------~~~~~~~~~~aW~ 130 (140)
T cd01040 60 HGKRVLNALDEAIKNLDDLEALKALLAKLGR--KHAKRGVDPEHFKLFGEALLEVLAEVL-------GDDFTPEVKAAWD 130 (140)
T ss_pred HHHHHHHHHHHHHHhccChHHHHHHHHHHHH--HHHHhCCCHHHHHHHHHHHHHHHHHHh-------CCcCCHHHHHHHH
Confidence 4456677777777777777777777776654 221222246677777777777766652 2234567788898
Q ss_pred HHHHHH
Q 040856 210 GLLQAF 215 (391)
Q Consensus 210 ~~~~a~ 215 (391)
.++...
T Consensus 131 ~~~~~i 136 (140)
T cd01040 131 KLLDVI 136 (140)
T ss_pred HHHHHH
Confidence 877554
No 18
>PLN02857 octaprenyl-diphosphate synthase
Probab=21.57 E-value=9e+02 Score=24.89 Aligned_cols=86 Identities=16% Similarity=0.098 Sum_probs=53.2
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhccccchhhHHHHH--HHhhcCCCCchHHHhhhccChHHHHHH
Q 040856 199 DQLLRIKNSWLGLLQAFLVEAKWYHNKYAPTLEEYLKNAALSIAGPLITIT--AYLSATDPIVEKELEYLESNPDVIQWS 276 (391)
Q Consensus 199 ~~~~~l~~~w~~~~~a~~~EA~W~~~~~iPs~eEYl~~~~~s~g~~~~~~~--~~~~~g~~l~~e~~e~~~~~p~l~~~~ 276 (391)
.+...+.+...+++.+-+.+..+.. +.-++.++|++....=+|.-+..+. .-...| .+++..+. .-++-+..
T Consensus 227 ~~~~~~s~~~~~l~~Gei~q~~~~~-~~~~s~~~Yl~~i~~KTa~L~~~a~~~gallag--a~~~~~~~---l~~fG~~L 300 (416)
T PLN02857 227 EVIKLISQVIKDFASGEIKQASSLF-DCDVTLDEYLLKSYYKTASLIAASTKSAAIFSG--VDSSVKEQ---MYEYGKNL 300 (416)
T ss_pred HHHHHHHHHHHHHHhhHHHHHhccc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcC--CCHHHHHH---HHHHHHHH
Confidence 4566777888888888777777764 4457999999876555543322211 111122 24444333 24456666
Q ss_pred HHHHHHhcCCCCCh
Q 040856 277 SRIFRLLDDLGTSS 290 (391)
Q Consensus 277 ~~i~RL~NDi~S~~ 290 (391)
.+..-+.||+..+.
T Consensus 301 GiAFQI~DDiLD~~ 314 (416)
T PLN02857 301 GLAFQVVDDILDFT 314 (416)
T ss_pred HHHHHHHHHHHhhc
Confidence 77778889988775
No 19
>PLN02890 geranyl diphosphate synthase
Probab=21.50 E-value=4.8e+02 Score=26.96 Aligned_cols=90 Identities=8% Similarity=0.016 Sum_probs=57.8
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhccccchhhHHHHHHH-hhcCCCCchHHHhhhccChHHHHHH
Q 040856 198 SDQLLRIKNSWLGLLQAFLVEAKWYHNKYAPTLEEYLKNAALSIAGPLITITAY-LSATDPIVEKELEYLESNPDVIQWS 276 (391)
Q Consensus 198 ~~~~~~l~~~w~~~~~a~~~EA~W~~~~~iPs~eEYl~~~~~s~g~~~~~~~~~-~~~g~~l~~e~~e~~~~~p~l~~~~ 276 (391)
..++..+.++...++.+-+.+..|.. ...+|+++|++....-+|.-+..+... ..++. .+++..+.+ -.+-...
T Consensus 226 ~~~~~~~s~a~~~l~~Gq~ld~~~~~-~~~~s~~~Yl~~i~~KTa~Lf~~s~~~gAilag-a~~~~~~~l---~~fG~~l 300 (422)
T PLN02890 226 TEVVSLLATAVEHLVTGETMQITSSR-EQRRSMDYYMQKTYYKTASLISNSCKAVAILAG-QTAEVAVLA---FEYGRNL 300 (422)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcC-cCHHHHHHH---HHHHHHH
Confidence 34567888889999999999998874 456899999987554444332221111 11222 255554442 3566777
Q ss_pred HHHHHHhcCCCCChhh
Q 040856 277 SRIFRLLDDLGTSSDE 292 (391)
Q Consensus 277 ~~i~RL~NDi~S~~~E 292 (391)
++..-+.||+..|.-.
T Consensus 301 GlAFQI~DDiLD~~g~ 316 (422)
T PLN02890 301 GLAFQLIDDVLDFTGT 316 (422)
T ss_pred HHHHHHHHHHHhhcCC
Confidence 7778889999887543
No 20
>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]
Probab=20.33 E-value=2.3e+02 Score=30.32 Aligned_cols=107 Identities=17% Similarity=0.273 Sum_probs=69.2
Q ss_pred hhhHHHhhhcHHHHHHHHHH--Hh----hcCCCccCc--chhhhhhHhhh-hhhccccCCCchhHHHHHHHHHHHHHHhh
Q 040856 69 LDFNILQATYQEELKDISGW--WK----DKGLGEKLS--FARSRLVTSFF-WGMGMVFEPQFAYSRRVLTITLALITVID 139 (391)
Q Consensus 69 ldFn~~Q~~hq~El~~l~rW--~~----~~~l~~~l~--faRdr~~e~yf-~~~a~~feP~~s~~Rl~~aK~~~l~~~iD 139 (391)
-++-+=|..-..|.+++++| |- +.+| ..++ ---.|++..|= ......|.|+ +|=.....+.-+.
T Consensus 221 ~~~~vp~~~T~~e~~qv~~W~n~I~wEksNpL-~t~~~~~~~~Rv~yayeQ~ll~l~~~pe------iWy~~s~yl~~~s 293 (656)
T KOG1914|consen 221 NAPAVPPKGTKDEIQQVELWKNWIKWEKSNPL-RTLDGTMLTRRVMYAYEQCLLYLGYHPE------IWYDYSMYLIEIS 293 (656)
T ss_pred cCCCCCCCCChHHHHHHHHHHHHHHHHhcCCc-ccccccHHHHHHHHHHHHHHHHHhcCHH------HHHHHHHHHHHhh
Confidence 34555566677889999999 43 3334 3232 23467877776 5566677675 5667778888888
Q ss_pred hhhcccCCHHHHHHHHHHhhhcchhhhhhcCChhHHHHHHHHHH
Q 040856 140 DIYDIYGTLDELELFTNAVERWDINFAIKQLPDYMKICFFALYN 183 (391)
Q Consensus 140 D~~D~~gt~eel~~~~~ai~rWd~~~~~~~lp~~mk~~~~al~~ 183 (391)
|+++.+|...+...|++-...-=.. +++.+....+.+|.++.+
T Consensus 294 ~l~~~~~d~~~a~~~t~e~~~~yEr-~I~~l~~~~~~Ly~~~a~ 336 (656)
T KOG1914|consen 294 DLLTEKGDVPDAKSLTDEAASIYER-AIEGLLKENKLLYFALAD 336 (656)
T ss_pred HHHHHhcccccchhhHHHHHHHHHH-HHHHHHHHHHHHHHHHHh
Confidence 8999999888888888765432222 455554455566655543
Done!