Query 016607
Match_columns 386
No_of_seqs 280 out of 1462
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 08:22:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016607.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016607hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01559 squal_synth farnesyl 100.0 7.9E-88 1.7E-92 661.9 35.5 329 36-367 1-336 (336)
2 KOG1459 Squalene synthetase [L 100.0 7.3E-83 1.6E-87 608.3 18.8 369 6-380 2-381 (413)
3 COG1562 ERG9 Phytoene/squalene 100.0 6.1E-54 1.3E-58 413.8 27.3 279 32-328 5-285 (288)
4 PLN02632 phytoene synthase 100.0 3.1E-53 6.8E-58 418.5 29.8 275 33-325 45-324 (334)
5 TIGR03465 HpnD squalene syntha 100.0 5.6E-53 1.2E-57 405.1 27.7 260 45-325 2-263 (266)
6 cd00683 Trans_IPPS_HH Trans-Is 100.0 4E-53 8.7E-58 405.7 26.5 261 38-317 1-264 (265)
7 TIGR03464 HpnC squalene syntha 100.0 1E-52 2.2E-57 403.3 28.1 261 45-325 2-264 (266)
8 PF00494 SQS_PSY: Squalene/phy 100.0 3.2E-50 7E-55 385.3 18.9 261 44-317 1-267 (267)
9 KOG4411 Phytoene/squalene synt 99.9 2.4E-25 5.2E-30 202.2 22.9 252 34-309 9-269 (292)
10 cd00867 Trans_IPPS Trans-Isopr 99.8 1.3E-18 2.7E-23 163.4 13.5 169 50-233 1-197 (236)
11 cd00385 Isoprenoid_Biosyn_C1 I 99.7 1.3E-16 2.9E-21 146.3 14.3 217 50-278 1-228 (243)
12 KOG1459 Squalene synthetase [L 98.8 6.4E-08 1.4E-12 94.3 11.8 205 42-272 134-346 (413)
13 cd00685 Trans_IPPS_HT Trans-Is 95.3 1.5 3.3E-05 41.8 17.3 192 62-280 44-243 (259)
14 TIGR02749 prenyl_cyano solanes 94.2 3.3 7.2E-05 41.1 17.1 93 135-230 133-243 (322)
15 PRK10888 octaprenyl diphosphat 94.0 7.2 0.00016 38.7 19.3 93 135-230 130-240 (323)
16 PLN02890 geranyl diphosphate s 93.5 5.2 0.00011 41.2 17.3 143 135-280 227-398 (422)
17 TIGR02748 GerC3_HepT heptapren 93.4 5.1 0.00011 39.6 16.7 93 135-230 129-239 (319)
18 CHL00151 preA prenyl transfera 91.5 11 0.00024 37.3 16.4 83 195-280 201-305 (323)
19 PF00348 polyprenyl_synt: Poly 90.3 7.2 0.00016 37.2 13.4 147 62-217 38-194 (260)
20 PLN02857 octaprenyl-diphosphat 90.1 4.9 0.00011 41.3 12.6 93 135-230 227-337 (416)
21 PRK10581 geranyltranstransfera 88.5 12 0.00025 36.8 13.5 121 146-280 153-280 (299)
22 PF06330 TRI5: Trichodiene syn 88.2 11 0.00023 38.2 13.1 171 54-242 77-257 (376)
23 PF03936 Terpene_synth_C: Terp 78.3 59 0.0013 30.4 15.8 173 60-241 60-252 (270)
24 cd00684 Terpene_cyclase_plant_ 74.7 1.2E+02 0.0027 32.2 21.2 235 8-271 234-492 (542)
25 cd00868 Terpene_cyclase_C1 Ter 70.4 96 0.0021 29.1 16.5 192 61-271 47-258 (284)
26 cd00687 Terpene_cyclase_nonpla 62.7 1.5E+02 0.0032 28.5 19.7 206 53-274 46-268 (303)
27 COG0142 IspA Geranylgeranyl py 48.6 2.8E+02 0.0061 27.4 18.2 140 136-278 135-302 (322)
28 cd00686 Terpene_cyclase_cis_tr 45.2 69 0.0015 32.2 6.8 59 58-130 81-143 (357)
29 TIGR01439 lp_hng_hel_AbrB loop 22.1 52 0.0011 21.7 1.2 20 223-242 6-25 (43)
30 PF08281 Sigma70_r4_2: Sigma-7 20.1 1.6E+02 0.0035 20.3 3.5 38 51-88 4-41 (54)
No 1
>TIGR01559 squal_synth farnesyl-diphosphate farnesyltransferase. This model describes farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes. This family is related to phytoene synthases. Tentatively identified archaeal homologs (excluded from this model) lack the C-terminal predicted transmembrane region universally conserved among members of this family.
Probab=100.00 E-value=7.9e-88 Score=661.86 Aligned_cols=329 Identities=60% Similarity=1.017 Sum_probs=312.5
Q ss_pred hHHHHHHHHhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccC-CCc
Q 016607 36 HWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCG-TKE 114 (386)
Q Consensus 36 ~~~~C~~~l~~~srsF~~a~~~Lp~~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G-~~~ 114 (386)
++++|+++++++|||||+++++||+++|++|+++|+|||++|||+|+++++.+.|++.|++|++.+.+.+|.|..+ .+.
T Consensus 1 ~~~~C~~~l~~~SrSF~~ai~~Lp~~lR~aV~~~Yl~cR~~DdIeDd~~~~~~~kl~~l~~~~~~l~~~~~~~~~~~~~~ 80 (336)
T TIGR01559 1 SLGFCYELLNLTSRSFAAVIQELPPELRNAVCIFYLVLRALDTVEDDMTISVDKKIPLLRDFHEKIYDPDWRFTESDNEK 80 (336)
T ss_pred ChHHHHHHHhhcCccHHHHHHHcCHHHHHHHHHHHHHHHhccccccCCCCCHHHHHHHHHHHHHHHhccCcccCCCCChh
Confidence 3689999999999999999999999999999999999999999999999988899999999999999988988622 566
Q ss_pred chHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhhhhHHHhhhhh-cC--CCHHHHHHHHHhhhhHHHHHHHHHhcccCCCC
Q 016607 115 YKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICK-EV--ESIDDYDEYCYYVAGLVGLGLSKLFYASGTED 191 (386)
Q Consensus 115 ~~~l~~~~~~v~~~~~~l~~~~~~lI~~i~~~m~~Gm~~dl~~-~~--~t~~dl~~Yc~~VAG~VG~ll~~l~~~~~~~~ 191 (386)
++.++++|+.+..+|..++++++++|.+|+++|++||++|+.. .+ +|++||+.|||||||+||+|+++||+.+|..+
T Consensus 81 ~~~L~~~~~~v~~~~~~l~~~~~~~I~~~~~~M~~GMa~dl~~~~~~~~T~~dL~~YCy~VAG~VG~mlt~l~~~~~~~~ 160 (336)
T TIGR01559 81 DRQVLDDFPVVSLEFLKLKPKYQEVIADITRRMGNGMADFIDKEVTNEQTVGDYDKYCHYVAGLVGIGLSRLFVASGFED 160 (336)
T ss_pred hHHHHHhchHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHhcCcCCCCCHHHHHHHHhccccHHHHHHHHHHhhcCCCC
Confidence 7889999999999999999999999999999999999999974 46 99999999999999999999999998754333
Q ss_pred C---ChhHHHHHHHHHHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHH
Q 016607 192 L---APDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVE 268 (386)
Q Consensus 192 ~---~~~~~A~~lG~aLQltNIlRD~~ED~~e~~~GR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~l~ 268 (386)
. ...++|++||+|||+||||||++||++ +||+|||+|+|++||++.+|+..+++++++.+|+++|+.+|+.|+.
T Consensus 161 ~~~~~~~~~A~~lG~aLQlTNIlRDv~ED~~---~GR~YlP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~ 237 (336)
T TIGR01559 161 PSLGESEALSNSMGLFLQKTNIIRDYLEDIN---EGRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELVTNALHHAT 237 (336)
T ss_pred cchhhhHHHHHHHHHHHHHHHHHHHHHhHHh---CCCCCCCHHHHHHcCCCHHHhcCccccHHHHHHHHHHHHHHHHHHH
Confidence 2 235899999999999999999999998 8999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcchhcccchhhhhHHHHHHHHHHHhcCCCCCcCccccChHHHHHHHHHhcChhHHHHHHHHHHHHhcccCCC
Q 016607 269 DCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYDFSNILKPKINK 348 (386)
Q Consensus 269 ~a~~yl~~l~~~~~~~f~aiP~~~AiatL~~~~~~~~vf~~~vki~k~~~~~l~~~~~~~~~v~~~~~~~~~~i~~~~~~ 348 (386)
+|+.|++.|+++++|+||+||++||++||++|++|++||+++|||||++++.+|++|+|+++|+.+|++|+++|++|++|
T Consensus 238 ~al~yl~~l~~~~~~~fcaip~~mAi~TL~~~~~n~~~~~~~VKi~r~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~ 317 (336)
T TIGR01559 238 DCLTYLSRLRDQSIFNFCAIPQVMAIATLALCYNNPQVFQGNVKIRKGTTVKLILDSTNMPAVYDIFYRYARKIYHKIDP 317 (336)
T ss_pred HHHHHHHhCCCcchhHHHHHHHHHHHHHHHHHhcChhhcCCCceecHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCChHHHHHHHHHHHHHh
Q 016607 349 NDPNATKTLSRVEAIQKAC 367 (386)
Q Consensus 349 ~dp~~~~~~~~~~~i~~~~ 367 (386)
+||||.++++.|++|+++|
T Consensus 318 ~dp~~~~~~~~~~~~~~~~ 336 (336)
T TIGR01559 318 NDPNFSKTLIIISKIEQQC 336 (336)
T ss_pred CCCCHHHHHHHHHHHHHhC
Confidence 9999999999999999997
No 2
>KOG1459 consensus Squalene synthetase [Lipid transport and metabolism]
Probab=100.00 E-value=7.3e-83 Score=608.28 Aligned_cols=369 Identities=57% Similarity=0.901 Sum_probs=347.6
Q ss_pred hhhcChhhHHHHHHHHHhcccccC---CCCCchhHHHHHHHHhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccC
Q 016607 6 AVLRHPDDLYPLLKLKMASRQAEK---QIPPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDD 82 (386)
Q Consensus 6 ~~~~hp~e~~~~~~~~~~~~~~~~---~~~~~~~~~~C~~~l~~~srsF~~a~~~Lp~~lR~av~alYaf~R~lD~I~D~ 82 (386)
.++.||+|+++++++| ..+..+ +.|+ +.+..|++++..+||||+++++.|++++|++||+||+++|++||++||
T Consensus 2 ~~l~~p~e~~~l~~~k--~~~l~~~~eq~~~-~~~~~Cy~~l~~tsrsfa~Vi~~l~~elRNav~ifylVlraLdtvedd 78 (413)
T KOG1459|consen 2 ALLWHPEESYNLLKMK--KLPLVRVLEQSPL-PLLSPCYNLLNLTSRSFAAVIQELSSELRNAVCIFYLVLRALDTVEDD 78 (413)
T ss_pred ccccChhhhcCchhhc--cCCcchhhhcCCc-hHHHHHHHHHHhhcchHHHHHHhhCHHHhhhhheeeeehhhhccCCCC
Confidence 4689999999999997 333322 3333 799999999999999999999999999999999999999999999999
Q ss_pred CCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhhhhHHHhhhhhcCCCH
Q 016607 83 TSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESI 162 (386)
Q Consensus 83 ~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~~~~v~~~~~~l~~~~~~lI~~i~~~m~~Gm~~dl~~~~~t~ 162 (386)
|++|.+.|++.|+.|+..++..+|.|.+|.++++.++.+|+.+..+|.++.+.|+++|++||++||.||+.++..+++|+
T Consensus 79 ~sI~~d~kvpil~~fhk~i~~~~w~f~~s~~k~r~~l~qf~~v~~ef~~L~e~Yqeviaeitk~mg~Gma~~~~~~v~ti 158 (413)
T KOG1459|consen 79 MSIPLDKKVPILRVFHKQIYLVDWQFRESSPKDRQLLPQFVVVSGEFLNLGEGYQEVIAEITKRMGLGMALFIPEEVETI 158 (413)
T ss_pred CcccccccccHHHHHHHHHhhcCceecCCChhhhhhccccccchHHHHHhhHHHHHHHHHHHHHHhchHHHhhHHHHhHH
Confidence 99999999999999999999999999988889999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhhhHHHHHHHHHhcccCCCC--CChhHHHHHHHHHHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCCh
Q 016607 163 DDYDEYCYYVAGLVGLGLSKLFYASGTED--LAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKL 240 (386)
Q Consensus 163 ~dl~~Yc~~VAG~VG~ll~~l~~~~~~~~--~~~~~~A~~lG~aLQltNIlRD~~ED~~e~~~GR~ylP~e~l~~~g~~~ 240 (386)
.|++.|||||||+||.+++++|.+++.++ ....+++++||++||+||||||+.||.. .||.|||+|+|++|..+.
T Consensus 159 ~d~d~yChyvagLVg~glsrlf~~s~le~~~~~~e~l~ns~glfLqktnIirdy~ed~~---d~r~Fwp~eIwg~y~d~L 235 (413)
T KOG1459|consen 159 WDYDVYCHYVAGLVGIGLSRLFTASKLEDLLARLEQLSNSMGLFLQKTNIIRDYLEDPV---DGRPFWPREIWGKYMDKL 235 (413)
T ss_pred HHHHHHHHHHHHhhCCchHhhhhHHHHhhhhhhHHHHhcccchHHHHhHHHHHHHhccc---cCCccChHHHHHHHHHHH
Confidence 99999999999999999999999876655 2334899999999999999999999999 799999999999999999
Q ss_pred hhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhcccchhhhhHHHHHHHHHHHhcCCCCCcCccccChHHHHH
Q 016607 241 EDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 320 (386)
Q Consensus 241 ~dl~~~~~~~~~~~~l~~lv~~A~~~l~~a~~yl~~l~~~~~~~f~aiP~~~AiatL~~~~~~~~vf~~~vki~k~~~~~ 320 (386)
+|+..+++++.+.+|+++|+++|+.|.++++.|++.++.+++|+||||||+|||+||++||+|.+||+|+||||||.++.
T Consensus 236 ~d~~~~en~dl~l~Cln~m~tnaL~hv~d~l~yls~l~~qsvfnfcaipqimai~Tlal~~nn~dvfrG~VklrkGl~~~ 315 (413)
T KOG1459|consen 236 KDFRYPENDDLALQCLNEMVTNALMHVPDVLTYLSKLRTQSVFNFCAIPQIMAIATLALCYNNEDVFRGNVKLRKGLAVE 315 (413)
T ss_pred HhhhCccchhHHHHHHHHHHHHHhhccHHHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHhcCHhHhccceeecCCchHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcChhHHHHHHHHHHHHhcccCCCCCCC-----hHHHHHHHHHHHHHhhhcCCcccc-cccc
Q 016607 321 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPN-----ATKTLSRVEAIQKACMDSGVLNKR-FVKV 380 (386)
Q Consensus 321 l~~~~~~~~~v~~~~~~~~~~i~~~~~~~dp~-----~~~~~~~~~~i~~~~~~~~~~~~~-~~~~ 380 (386)
+|+++.|+.+|+.+|..|.+.|+.|.+++||| ..++.+..++|.+.|.+.+++.+| ++|+
T Consensus 316 ~I~~~k~~~~v~~~f~~y~~~i~~k~d~~dpnflklsask~~qv~esl~~~~~~~~il~n~~~~f~ 381 (413)
T KOG1459|consen 316 LILASKTMDKVRNIFYMYLRDIRMKFDEADPNFLKLSASKTEQVWESLLLYRRPDEILANRYNNFT 381 (413)
T ss_pred HHHhcccHHHHHHHHHHHHHHHHhhCCccCCCchhhhhhhHHHHHHHHHHhhcccccccccccccc
Confidence 99999999999999999999999999999999 666677788888889999999999 6666
No 3
>COG1562 ERG9 Phytoene/squalene synthetase [Lipid metabolism]
Probab=100.00 E-value=6.1e-54 Score=413.77 Aligned_cols=279 Identities=24% Similarity=0.309 Sum_probs=248.7
Q ss_pred CCchhHHHHHHHHhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccC
Q 016607 32 PPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCG 111 (386)
Q Consensus 32 ~~~~~~~~C~~~l~~~srsF~~a~~~Lp~~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G 111 (386)
+...++++|.++++.+|+|||+++++||+++|++|+++|+|||++|||+|+++.| +.....+.+|+..+... ++ |
T Consensus 5 ~~~~~~~~c~~i~~~~srtf~la~~~lp~~~R~av~alYa~~R~~Ddv~D~~~~~-~~~~e~~~~~~~~~~~~---~~-~ 79 (288)
T COG1562 5 EIMEALDYCLDILRETSRTFYLAILLLPPEKREAVWALYAFCREADDVVDGVSDP-DLPAEILLAWRRELDGD---FS-G 79 (288)
T ss_pred chhHHHHHHHHHHHHhCcchHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhcccch-hhHHHHHHHHHHHHhcc---cc-C
Confidence 3467889999999999999999999999999999999999999999999999876 33344555555555441 23 4
Q ss_pred C-CcchHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhhhhHHHhhhh-hcCCCHHHHHHHHHhhhhHHHHHHHHHhcccCC
Q 016607 112 T-KEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGT 189 (386)
Q Consensus 112 ~-~~~~~l~~~~~~v~~~~~~l~~~~~~lI~~i~~~m~~Gm~~dl~-~~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~~~~ 189 (386)
. .+++|++.+|.+++++|..+.+.+.++|+ ||++|+. .++.+++||+.|||+|||+||.|+++|++..+
T Consensus 80 ~~~~~~pv~~al~~~~~~~~~~~~~~~~~~d--------a~~~Dl~~~~y~~~~eL~~Yc~~vAg~vG~l~~~Il~~~~- 150 (288)
T COG1562 80 QPASDHPVLAALVEVARRFGLPREAFPALID--------AMRMDLDRTRYLDFEELEEYCYGVAGAVGLLLARILGPDK- 150 (288)
T ss_pred CCcccCHHHHHHHHHHHHcCCCHHHHHHHHH--------HHHHHhhhccccCHHHHHHHHHHhHHHHHHHHHHHhCccc-
Confidence 4 36789999999999999888888888886 9999997 78999999999999999999999999999642
Q ss_pred CCCChhHHHHHHHHHHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHH
Q 016607 190 EDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVED 269 (386)
Q Consensus 190 ~~~~~~~~A~~lG~aLQltNIlRD~~ED~~e~~~GR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~l~~ 269 (386)
+....+.|..+|.|+|+||||||++||.. +||+|||+|+|++||++.+|+..+.+.++++.||+.++.+|+.|+.+
T Consensus 151 -~~~~~~~a~~lG~A~QlvNilRdv~eD~~---~GrvylP~e~l~~~g~~~~d~~~~~~~~~~~~~~~~~~~~ar~~~~~ 226 (288)
T COG1562 151 -DAATRAYARGLGLALQLVNILRDVGEDRR---RGRVYLPAEELARFGVSEADLLAGRVDDAFRELMRFEADRARDHLAE 226 (288)
T ss_pred -chhhHHHHHHHHHHHHHHHHHHHhHHHHh---CCcccCCHHHHHHhCCCHHHHHcccchhHHHHHHHHHHHHHHHHHHH
Confidence 22334678889999999999999999999 99999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcchhcccchhhhhHHHHHHHHHHHhcCCCCCcCccccChHHHHHHHHHhcCh
Q 016607 270 CLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNM 328 (386)
Q Consensus 270 a~~yl~~l~~~~~~~f~aiP~~~AiatL~~~~~~~~vf~~~vki~k~~~~~l~~~~~~~ 328 (386)
|..++..+|.++.+.+|++|+.++..+.+...++.+||++++.+++++++|+++++...
T Consensus 227 a~~~~~~lp~~~~~~~~~~~~~~~~~~~~i~a~~~~vl~~~~~l~~~~~~~~~~~~~~~ 285 (288)
T COG1562 227 ARRGLPALPGRAQLAVLAAALLYAYLLDAIEADPADVLSQRAVLPKLRKLWLLLKAWLR 285 (288)
T ss_pred HHHhhhhCCccccchhhHHHHHHHHHHHHHHccchhhhccCcccCcchHHHHHHHHHHh
Confidence 99999999999988999999999998988888899999999999999999999887543
No 4
>PLN02632 phytoene synthase
Probab=100.00 E-value=3.1e-53 Score=418.50 Aligned_cols=275 Identities=20% Similarity=0.241 Sum_probs=243.1
Q ss_pred CchhHHHHHHHHhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCC
Q 016607 33 PEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGT 112 (386)
Q Consensus 33 ~~~~~~~C~~~l~~~srsF~~a~~~Lp~~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~ 112 (386)
.++++.+|.++++++|+|||+++++||++.|++++++|+|||++|||+|+.+.+. ....+|+||++.+.. .|. |.
T Consensus 45 l~~a~~~c~~i~r~~s~sFyla~~lLP~~~R~ai~alYAf~R~~DdI~D~~~~~~-~~~~~L~~w~~~l~~---~~~-g~ 119 (334)
T PLN02632 45 LEEAYDRCGEVCAEYAKTFYLGTLLMTPERRKAIWAIYVWCRRTDELVDGPNASH-ITPAALDRWEARLED---LFD-GR 119 (334)
T ss_pred chHHHHHHHHHHhhcCchHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCCCCCh-hhHHHHHHHHHHHHH---HhC-CC
Confidence 5788999999999999999999999999999999999999999999999877654 345689999999987 465 65
Q ss_pred CcchHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhhhhHHHhhhh-hcCCCHHHHHHHHHhhhhHHHHHHHHHhcccCCCC
Q 016607 113 KEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTED 191 (386)
Q Consensus 113 ~~~~~l~~~~~~v~~~~~~l~~~~~~lI~~i~~~m~~Gm~~dl~-~~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~~~~~~ 191 (386)
+ .+|+..++.+++.+|..+..++.++|+ ||++|+. .+++|++||+.|||+|||+||+|++++++......
T Consensus 120 ~-~~pv~~aL~~~~~~~~L~~~~~~~li~--------g~~~Dl~~~~~~t~~eL~~Ycy~vAgtVG~l~l~vlg~~~~~~ 190 (334)
T PLN02632 120 P-YDMLDAALADTVSKFPLDIQPFRDMIE--------GMRMDLVKSRYENFDELYLYCYYVAGTVGLMSVPVMGIAPESK 190 (334)
T ss_pred C-CChHHHHHHHHHHHCCCChHHHHHHHH--------HHHHHhccCCCCCHHHHHHHHHHhhHHHHHHHHHHhCCCCccc
Confidence 5 578999999999999887778888886 9999997 68999999999999999999999999998632111
Q ss_pred ---CChhHHHHHHHHHHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHH
Q 016607 192 ---LAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVE 268 (386)
Q Consensus 192 ---~~~~~~A~~lG~aLQltNIlRD~~ED~~e~~~GR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~l~ 268 (386)
....+.|.+||.|||+|||+||++||++ +||+|||.|+|.+||++.+|++.+..+++++.++.+++.+|+.||.
T Consensus 191 ~~~~~~~~~A~~lG~AlQltNILRDv~eD~~---~GRvYLP~e~L~~~Gv~~edl~~~~~~~~~~~l~~~~~~~Ar~~~~ 267 (334)
T PLN02632 191 ASTESVYNAALALGIANQLTNILRDVGEDAR---RGRVYLPQDELAQFGLTDEDIFAGKVTDKWRAFMKFQIKRARMYFA 267 (334)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHHh---CCceeCCHHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHH
Confidence 1235789999999999999999999998 9999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcchhcccchhhhhHHHHHHHHHHH-hcCCCCCcCccccChHHHHHHHHHh
Q 016607 269 DCLKYMSALRDHAIFRFCAIPQIMAIGTLALC-YNNIEVFRGVVKMRRGLTAKVIDRT 325 (386)
Q Consensus 269 ~a~~yl~~l~~~~~~~f~aiP~~~AiatL~~~-~~~~~vf~~~vki~k~~~~~l~~~~ 325 (386)
+|+.++..+|..+ ...+.++..+..+.|..+ .+|++||++++.++++++.|++.++
T Consensus 268 ~a~~~l~~lp~~~-r~~v~~a~~~y~~iL~~i~~~~~~v~~~R~~l~~~~Kl~~~~~~ 324 (334)
T PLN02632 268 EAEEGVSELDPAS-RWPVWASLLLYRQILDAIEANDYDNFTKRAYVGKWKKLLALPLA 324 (334)
T ss_pred HHHHhHhhCCHHh-HHHHHHHHHHHHHHHHHHHHcCCCcCCCCCccCHHHHHHHHHHH
Confidence 9999999999875 224556666677777766 4899999999999999999998765
No 5
>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=100.00 E-value=5.6e-53 Score=405.09 Aligned_cols=260 Identities=21% Similarity=0.231 Sum_probs=235.9
Q ss_pred hhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHHhHHH
Q 016607 45 HKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHH 124 (386)
Q Consensus 45 ~~~srsF~~a~~~Lp~~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~~~~ 124 (386)
+++|+|||+++++||++.|++++++|+|||++|||+|+.. ++..+..+|+||++.+.. .+. |.+ .+|++.++..
T Consensus 2 ~~~s~sF~~a~~~lp~~~R~~~~alYaf~r~~d~i~D~~~-~~~~~~~~L~~w~~~l~~---~~~-g~~-~~pv~~al~~ 75 (266)
T TIGR03465 2 AASGSSFYYGMRLLPPERRRAMTALYAFCREVDDIVDEDS-DPEVAQAKLAWWRAEIDR---LYA-GAP-SHPVARALAD 75 (266)
T ss_pred CCCcCcHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CchHHHHHHHHHHHHHHH---HhC-CCC-CChHHHHHHH
Confidence 5799999999999999999999999999999999999854 456788999999999987 354 654 6889999999
Q ss_pred HHHHHhhcCHHHHHHHHHHHHhhhhHHHhhhh-hcCCCHHHHHHHHHhhhhHHHHHHHHHhcccCCCCCChhHHHHHHHH
Q 016607 125 VSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGL 203 (386)
Q Consensus 125 v~~~~~~l~~~~~~lI~~i~~~m~~Gm~~dl~-~~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~~~~~~~~~~~~A~~lG~ 203 (386)
++..+....+.+.++|+ ||++|+. ++++|++||+.|||+|||+||+|++++++.. +....+.|+++|.
T Consensus 76 ~~~~~~l~~~~~~~li~--------g~~~Dl~~~~~~t~~dL~~Y~~~vAg~vg~l~~~llg~~---~~~~~~~a~~lG~ 144 (266)
T TIGR03465 76 PARRFDLPQEDFLEVID--------GMEMDLEQTRYPDFAELDLYCDRVAGAVGRLSARIFGAT---DARTLEYAHHLGR 144 (266)
T ss_pred HHHHcCCCHHHHHHHHH--------HHHHHcCCCCCCCHHHHHHHHHHhHHHHHHHHHHHhCCC---ChhHHHHHHHHHH
Confidence 99999877777788776 9999997 7899999999999999999999999999742 2335689999999
Q ss_pred HHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhccc
Q 016607 204 FLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIF 283 (386)
Q Consensus 204 aLQltNIlRD~~ED~~e~~~GR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~l~~a~~yl~~l~~~~~~ 283 (386)
|+|+||||||++||+. +||+|||.|+|.+||++.+||..++++++++.++.+++..|+.||.++..++..+|... +
T Consensus 145 AlqltnilRdv~eD~~---~gR~ylP~~~l~~~gv~~~~l~~~~~~~~~~~~~~~l~~~A~~~l~~a~~~~~~~p~~~-~ 220 (266)
T TIGR03465 145 ALQLTNILRDVGEDAR---RGRIYLPAEELQRFGVPAADILEGRYSPALAALCRFQAERARAHYAEADALLPACDRRA-Q 220 (266)
T ss_pred HHHHHHHHHHhHHHHh---CCCeecCHHHHHHcCCCHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhCCHhh-h
Confidence 9999999999999999 99999999999999999999999999999999999999999999999999999999765 3
Q ss_pred chhhhhHHHHHHHHHHHh-cCCCCCcCccccChHHHHHHHHHh
Q 016607 284 RFCAIPQIMAIGTLALCY-NNIEVFRGVVKMRRGLTAKVIDRT 325 (386)
Q Consensus 284 ~f~aiP~~~AiatL~~~~-~~~~vf~~~vki~k~~~~~l~~~~ 325 (386)
.++.++..++.++|..+. ++++||++++++++.++.|+++++
T Consensus 221 ~~~~~~~~~~~~iL~~i~~~~~~~~~~r~~~~~~~k~~~~~~~ 263 (266)
T TIGR03465 221 RAARAMAAIYRALLDEIEADGFQVLRQRVSLTPLRKLWIALRT 263 (266)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCcCCHHHHHHHHHHH
Confidence 567888899999998874 789999999999999999999876
No 6
>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=100.00 E-value=4e-53 Score=405.66 Aligned_cols=261 Identities=34% Similarity=0.508 Sum_probs=234.3
Q ss_pred HHHHHHHhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchH
Q 016607 38 AFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKV 117 (386)
Q Consensus 38 ~~C~~~l~~~srsF~~a~~~Lp~~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~ 117 (386)
.+|.++++++|+|||+++++||++.|++++++|+|||++|||+|+++.+...+..+|+||++.+.. .+. |....+|
T Consensus 1 ~~c~~~~~~~~~sf~~a~~~lp~~~R~~~~alYaf~r~~Ddi~D~~~~~~~~~~~~L~~w~~~l~~---~~~-~~~~~~p 76 (265)
T cd00683 1 AYCRAILRKGSRSFYLASRLLPPELRRAVCALYAFCRAADDIVDDPAAPPDEKLALLDAFRAELDA---AYW-GGAPTHP 76 (265)
T ss_pred CHHHHHHHHhCCcHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhCCCCCchhHHHHHHHHHHHHHH---HHc-CCCCCCh
Confidence 379999999999999999999999999999999999999999999887756788999999999987 355 5566789
Q ss_pred HHHhHHHHHHHHhhcCHHHHHHHHHHHHhhhhHHHhhhh-hcCCCHHHHHHHHHhhhhHHHHHHHHHhcccCCCCCChhH
Q 016607 118 LMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDS 196 (386)
Q Consensus 118 l~~~~~~v~~~~~~l~~~~~~lI~~i~~~m~~Gm~~dl~-~~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~~~~~~~~~~~ 196 (386)
++.+|..++..+..+...+.++|+ ||++|+. .+++|++||+.|||+|||+||+|++++++.. ......+
T Consensus 77 v~~al~~~~~~~~l~~~~~~~li~--------g~~~Dl~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~~~~--~~~~~~~ 146 (265)
T cd00683 77 VLRALADLARRYGIPREPFRDLLA--------GMAMDLDKRRYETLDELDEYCYYVAGVVGLMLLRVFGAS--SDEAALE 146 (265)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHH--------HHHHhCCCCCCCCHHHHHHHHHHhHHHHHHHHHHHhCCC--CChHHHH
Confidence 999999999998877778888886 9999997 6899999999999999999999999999852 2233568
Q ss_pred HHHHHHHHHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 016607 197 LSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSA 276 (386)
Q Consensus 197 ~A~~lG~aLQltNIlRD~~ED~~e~~~GR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~l~~a~~yl~~ 276 (386)
.|.++|.|+|+||||||++||++ +||+|||.|+|.+||++.+|+..+..+++++.++.+++..|+.|+..|..++..
T Consensus 147 ~A~~lG~AlqltnilRdv~eD~~---~gR~YlP~d~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~ 223 (265)
T cd00683 147 RARALGLALQLTNILRDVGEDAR---RGRIYLPREELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAA 223 (265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHc---cCCCcCCHHHHHHcCCCHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHh
Confidence 99999999999999999999998 999999999999999999999999999999999999999999999999999999
Q ss_pred cchhcccchhhhhHHHHHHH-HHHH-hcCCCCCcCccccChHH
Q 016607 277 LRDHAIFRFCAIPQIMAIGT-LALC-YNNIEVFRGVVKMRRGL 317 (386)
Q Consensus 277 l~~~~~~~f~aiP~~~Aiat-L~~~-~~~~~vf~~~vki~k~~ 317 (386)
+|... ++|++|.+.+..+ +..+ .+++++|++++.+++.+
T Consensus 224 lp~~~--~~~~~~~~~~y~~il~~i~~~~~~~~~~r~~~~~~~ 264 (265)
T cd00683 224 LPRRS--RFCVRAAAMLYRTILDEIEARGYDVLSVRVRVPKAR 264 (265)
T ss_pred CCHhh--HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Confidence 99765 7888888777444 4444 47899999999888764
No 7
>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=100.00 E-value=1e-52 Score=403.33 Aligned_cols=261 Identities=17% Similarity=0.162 Sum_probs=234.5
Q ss_pred hhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHHhHHH
Q 016607 45 HKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHH 124 (386)
Q Consensus 45 ~~~srsF~~a~~~Lp~~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~~~~ 124 (386)
+++++|||+++++||++.|++++++|+|||++|||+|+.+.+++++..+|+||++.+.. .+. |++ .+|++.++..
T Consensus 2 ~~~~~sf~~a~~~lp~~~R~~~~alYAf~R~~Ddi~D~~~~~~~~~~~~L~~wr~~l~~---~~~-g~~-~~pv~~aL~~ 76 (266)
T TIGR03464 2 VAHYENFPVASLLLPARLRAPIHAVYAFARTADDIADEGDGSAEERLALLDDFRAELDA---IYS-GEP-AAPVFVALAR 76 (266)
T ss_pred CCccCcHHHHHHhCCHHHHHHHHHHHHHHHHHHHhccCCCCChHHHHHHHHHHHHHHHH---HhC-CCC-CChHHHHHHH
Confidence 57899999999999999999999999999999999999766677888999999999986 355 655 6889999999
Q ss_pred HHHHHhhcCHHHHHHHHHHHHhhhhHHHhhhh-hcCCCHHHHHHHHHhhhhHHHHHHHHHhcccCCCCCChhHHHHHHHH
Q 016607 125 VSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGL 203 (386)
Q Consensus 125 v~~~~~~l~~~~~~lI~~i~~~m~~Gm~~dl~-~~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~~~~~~~~~~~~A~~lG~ 203 (386)
++.++....+.+.++|+ ||.+|+. .++.|++||+.|||+|||+||+|++++++... ....+.|.++|.
T Consensus 77 ~~~~~~l~~~~~~~li~--------~~~~Dl~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~g~~~---~~~~~~A~~lG~ 145 (266)
T TIGR03464 77 TVQRHGLPIEPFLDLLD--------AFRQDVVVTRYATWAELLDYCRYSANPVGRLVLDLYGASD---PENVALSDAICT 145 (266)
T ss_pred HHHHcCCChHHHHHHHH--------HHHHhccCCCCCCHHHHHHHHHHhHHHHHHHHHHHcCCCC---hhHHHHHHHHHH
Confidence 99999888788888886 9999997 68999999999999999999999999998632 234578999999
Q ss_pred HHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhccc
Q 016607 204 FLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIF 283 (386)
Q Consensus 204 aLQltNIlRD~~ED~~e~~~GR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~l~~a~~yl~~l~~~~~~ 283 (386)
|||+|||+||++||++ +||+|||.|+|.+||++++|+.+++.+++++.++.+++.+|+.||.+++.++..+|..+ .
T Consensus 146 AlQltniLRDl~eD~~---~gR~YLP~~~l~~~Gv~~edl~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~~-~ 221 (266)
T TIGR03464 146 ALQLINFWQDVGVDYR---KGRVYLPRDDLARFGVSEEDLAAGRATPALRELMAFEVSRTRALLDRGAPLAARVDGRL-G 221 (266)
T ss_pred HHHHHHHHHhhHHHHh---cCCccCCHHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCCHhh-h
Confidence 9999999999999999 99999999999999999999999999999999999999999999999999999998764 3
Q ss_pred chhhhhHHHHHHHHHHH-hcCCCCCcCccccChHHHHHHHHHh
Q 016607 284 RFCAIPQIMAIGTLALC-YNNIEVFRGVVKMRRGLTAKVIDRT 325 (386)
Q Consensus 284 ~f~aiP~~~AiatL~~~-~~~~~vf~~~vki~k~~~~~l~~~~ 325 (386)
.++..+..++.++|..+ .++++||++++.+++.++.|+++++
T Consensus 222 ~~~~~~~~~y~~iL~~l~~~~~~~~~~r~~~~~~~kl~~~~~a 264 (266)
T TIGR03464 222 LELALIVRGGLRILEKIERQGYDVLRERPKLGKFDWAGLLLRA 264 (266)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCCCCCCcCCHHHHHHHHHHH
Confidence 34456666777778777 4789999999999999999999876
No 8
>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=100.00 E-value=3.2e-50 Score=385.29 Aligned_cols=261 Identities=26% Similarity=0.309 Sum_probs=213.7
Q ss_pred HhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccc-cCCCcchHHHHhH
Q 016607 44 LHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFS-CGTKEYKVLMDQF 122 (386)
Q Consensus 44 l~~~srsF~~a~~~Lp~~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~-~G~~~~~~l~~~~ 122 (386)
|+++|+|||+++++||++.|++++++|+|||++|||+|+++.+ ..+..+|+||++.+....+... .+.+..+|++.+|
T Consensus 1 lr~~~~sf~~a~~~lP~~~R~~~~alyaf~r~~d~i~D~~~~~-~~~~~~L~~w~~~l~~~~~~~~~~~~~~~~pv~~~l 79 (267)
T PF00494_consen 1 LRKHSRSFYLASLLLPKEKRPAVFALYAFCRELDDIVDEPSDP-EEARARLQWWRDALNSIFASYEDSLPEPSHPVARAL 79 (267)
T ss_dssp -HHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHCTSS--HSCHHHHHHHHHHHHHHHH-TSTHHHSSHHHHHHHH
T ss_pred CCCCCccHHHHHHHCCHHHHHHHHHHHHHHHHHhhccccchhh-HHHHHHHHHHHHHHHHHhhhhhhccCCCcCHHHHHH
Confidence 6899999999999999999999999999999999999999854 5667799999999987311111 1245678999999
Q ss_pred HHHHHHHhhcCHHHHHHHHHHHHhhhhHHHhhhh-hcCCCHHHHHHHHHhhhhHHHHHHHHHhcccCCCCCChhHHHHHH
Q 016607 123 HHVSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSM 201 (386)
Q Consensus 123 ~~v~~~~~~l~~~~~~lI~~i~~~m~~Gm~~dl~-~~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~~~~~~~~~~~~A~~l 201 (386)
..+++.+..+...+.++|+ ||++|+. ++++|++||+.||++|||+||+|++++++... ++....+.|+++
T Consensus 80 ~~~~~~~~l~~~~l~~li~--------~~~~dl~~~~~~t~~~L~~Y~~~vag~vg~l~~~~~~~~~-~~~~~~~~a~~l 150 (267)
T PF00494_consen 80 ADLVRRYGLPREPLLELID--------GMEMDLEFTPYETFADLERYCYYVAGSVGLLLLQLLGAHD-PDEAARDAARAL 150 (267)
T ss_dssp HHHHCCSHHHHHHHHHHHH--------HHHHCTT-S--SSHHHHHHHHHHHTHHHHHHHHHHHHSST-SHHHHHHHHHHH
T ss_pred HHHHHHHhhhHHHHHHHHH--------HhcccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcccc-chhhHHHHHHHH
Confidence 9999988877777777776 9999997 78999999999999999999999999998631 112356899999
Q ss_pred HHHHHHHHHHhchHhh-hhcCCCCCccccHHHHHhccCChhhhhccc-CCHHHHHHHHHHHHHHHHHHHHHHHHHHhcch
Q 016607 202 GLFLQKTNIIRDYLED-INEIPKCRMFWPREIWSKYVNKLEDLKYEE-NSDKAVQCLNDMVTNALMHVEDCLKYMSALRD 279 (386)
Q Consensus 202 G~aLQltNIlRD~~ED-~~e~~~GR~ylP~e~l~~~g~~~~dl~~~~-~~~~~~~~l~~lv~~A~~~l~~a~~yl~~l~~ 279 (386)
|.|+|+||||||++|| +. +||+|||.|+|.+||++++|+..+. .+++++.++.+++..|+.|+.+++.++..+|+
T Consensus 151 G~alql~nilRd~~~D~~~---~gR~ylP~d~l~~~gv~~~dl~~~~~~~~~~~~~~~~~~~~A~~~l~~a~~~~~~l~~ 227 (267)
T PF00494_consen 151 GRALQLTNILRDIPEDALR---RGRIYLPLDDLRRFGVTPEDLLAGRPRSERLRALIRELAARARAHLDEARAGLSALPP 227 (267)
T ss_dssp HHHHHHHHHHHTHHHH-HH---TT---S-HHHHHHTTSSHHHHHHHG-GGHHHHHHHHHHHHHHHHHHHHHHHGGGGS--
T ss_pred HHHHHHHHHHHHhHHHHHh---cccccCCchhHHHcCCCHHHHHhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 9999999999999999 78 8999999999999999999998876 78889999999999999999999999999966
Q ss_pred hcccchhhhhHHHHHHHHHHHh-cCCC-CCcCccccChHH
Q 016607 280 HAIFRFCAIPQIMAIGTLALCY-NNIE-VFRGVVKMRRGL 317 (386)
Q Consensus 280 ~~~~~f~aiP~~~AiatL~~~~-~~~~-vf~~~vki~k~~ 317 (386)
.....+|.+|..++.++|..+. ++++ ||+++++++|++
T Consensus 228 ~~~~~~~~~~~~~~~~~l~~l~~~~~~~v~~~r~~~~~~r 267 (267)
T PF00494_consen 228 PRARPAVAAAAALYRAILDKLERNGYDPVFQRRVKVSKWR 267 (267)
T ss_dssp TTHHHHHHHHHHHHHHHHHHHHHTTT--GSSS-----HH-
T ss_pred HhhhHHHHHHHHHHHHHHHHHHcCCCcccCCCCCcCCCCC
Confidence 6556788999999999998885 7888 889999999974
No 9
>KOG4411 consensus Phytoene/squalene synthetase [Lipid transport and metabolism]
Probab=99.94 E-value=2.4e-25 Score=202.22 Aligned_cols=252 Identities=15% Similarity=0.158 Sum_probs=202.3
Q ss_pred chhHHHHHHHHhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccC--
Q 016607 34 EPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCG-- 111 (386)
Q Consensus 34 ~~~~~~C~~~l~~~srsF~~a~~~Lp~~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G-- 111 (386)
..++. |.+.++..+..-|++...||.++|.+++++.||+.++..|.=|....+.+..++|+||++.++. +|...
T Consensus 9 ~~A~s-c~~~vr~ydy~~ylc~l~lp~e~r~aafaLrAfNVE~ar~~~d~~~~p~ia~mRL~fW~daIdk---~y~~~p~ 84 (292)
T KOG4411|consen 9 RSALS-CVQQVRNYDYHHYLCLLELPTEMRKAAFALRAFNVELARIKVDTRKGPAIAMMRLQFWKDAIDK---IYGISPL 84 (292)
T ss_pred hhHHH-HHHHHHhhhHHHHHHHHhCcHHHHHHHHHHHHhhHHHHHHhhccccCcHHHHHHHHHHHHHHHH---HcCCCCC
Confidence 34555 9999999999999999999999999999999999999997666655667888999999999987 56411
Q ss_pred CCcchHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhhhhHHHhhhh-hcCCCHHHHHHHHHhhhhHHHHHHHHHhcccCCC
Q 016607 112 TKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTE 190 (386)
Q Consensus 112 ~~~~~~l~~~~~~v~~~~~~l~~~~~~lI~~i~~~m~~Gm~~dl~-~~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~~~~~ 190 (386)
..+++|++.++-..+.....-++.+..++ ++...+.. +.++++.||++|...+ +|-+++-.+.+.|..
T Consensus 85 ~v~~qPva~aL~~~~~~~~~nk~~L~rlV--------~aR~r~~~d~~fesI~eLeeY~e~T---issLL~l~l~agg~~ 153 (292)
T KOG4411|consen 85 PVPRQPVAIALCSFAAGHNANKDMLLRLV--------EARQRTIGDRQFESINELEEYGEST---ISSLLCLQLDAGGKV 153 (292)
T ss_pred CCCCcHHHHHHHHHHhccccCHHHHHHHH--------HHhhcCCcccchHHHHHHHHHHHhH---HHHHHHHHHHhcCcc
Confidence 22578899888888877644433344444 48777764 6799999999998885 555555555554455
Q ss_pred CCChhHHHHHHHHHHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhh-hcccCCHHHHHHHHHHHHHHHHHHHH
Q 016607 191 DLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDL-KYEENSDKAVQCLNDMVTNALMHVED 269 (386)
Q Consensus 191 ~~~~~~~A~~lG~aLQltNIlRD~~ED~~e~~~GR~ylP~e~l~~~g~~~~dl-~~~~~~~~~~~~l~~lv~~A~~~l~~ 269 (386)
.+.+++.|.|+|.|.+++|.||.++.... +|-.|+|.|++..||++..|+ .+....++...|+.+++..|..|+.+
T Consensus 154 ~~~AdhaAshlGkA~gia~llrs~p~~~~---r~~~~iPadv~~lhGvtq~~il~~k~~~~g~~~~~fd~as~an~hL~~ 230 (292)
T KOG4411|consen 154 LPMADHAASHLGKAYGIANLLRSTPPLLA---RGIVLIPADVMSLHGVTQLDILYKKKKLDGMVGMTFDLASEANRHLID 230 (292)
T ss_pred ccchHHHHHHHhHHHHHHHHHHhccHHHh---CCCccccHHHHHHcCCCHHHHHhhccchhhhhhHHHHHHHHHHHHHHH
Confidence 56678999999999999999999999999 999999999999999999665 45667889999999999999999999
Q ss_pred HHHHHHhcchhcccchhhhhHHHHHHH----HHHH-hcCCCCCcC
Q 016607 270 CLKYMSALRDHAIFRFCAIPQIMAIGT----LALC-YNNIEVFRG 309 (386)
Q Consensus 270 a~~yl~~l~~~~~~~f~aiP~~~Aiat----L~~~-~~~~~vf~~ 309 (386)
|+..+..+|.+. .|..++..+ |+.+ .+||++|++
T Consensus 231 AR~l~~kVP~~v------rp~ll~tv~td~~l~~l~k~nfdi~~p 269 (292)
T KOG4411|consen 231 ARSLIEKVPKAV------RPALLATVTTDYILKTLEKNNFDIYSP 269 (292)
T ss_pred HHhHhhhCCHHH------HHHHHHhhhHHHHHHHHHHccccccCH
Confidence 999999999874 333333333 3333 489999986
No 10
>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=99.78 E-value=1.3e-18 Score=163.37 Aligned_cols=169 Identities=24% Similarity=0.247 Sum_probs=126.3
Q ss_pred cHHHHHHhcCh----------hhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHH-HHHHHcccccccccCCCcchHH
Q 016607 50 SFALVIQQLGT----------DLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIA-FHRHVYDREWHFSCGTKEYKVL 118 (386)
Q Consensus 50 sF~~a~~~Lp~----------~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~-~~~~l~~~~~~~~~G~~~~~~l 118 (386)
+|++.+.++|+ +++.++.++|++++..|||.|+...+. .+.....+ |...... ...+.++
T Consensus 1 ~r~~~~~~~~~~~~~~~~~~~~~a~ave~l~~~~li~DDI~D~~~~rr-g~~~~~~~~~g~~~ai--------~~gd~l~ 71 (236)
T cd00867 1 SRPLLVLLLARALGGDLEAALRLAAAVELLHAASLVHDDIVDDSDLRR-GKPTAHLRRFGNALAI--------LAGDYLL 71 (236)
T ss_pred CcHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHcccccCCccCC-CCccHhHHhhCHhHHH--------HHHHHHH
Confidence 57888899999 999999999999999999999976543 23334444 5443321 1234566
Q ss_pred HHhHHHHHHHHhhcCHHHHHHHHHHHHhhhhHHHhhhh-hc--CCCHHHHHHHHHh-hhhHHHHHHHHHhcccCCCC---
Q 016607 119 MDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KE--VESIDDYDEYCYY-VAGLVGLGLSKLFYASGTED--- 191 (386)
Q Consensus 119 ~~~~~~v~~~~~~l~~~~~~lI~~i~~~m~~Gm~~dl~-~~--~~t~~dl~~Yc~~-VAG~VG~ll~~l~~~~~~~~--- 191 (386)
...|..+.... .....+++.+.+..|..|+..|+. .. +.|+++|..||++ |||+||.++..+....+.+.
T Consensus 72 ~~a~~~l~~~~---~~~~~~~~~~~~~~~~~Gq~~Dl~~~~~~~~t~~~y~~~~~~Kta~l~~~~~~~~~~~~~~~~~~~ 148 (236)
T cd00867 72 ARAFQLLARLG---YPRALELFAEALRELLEGQALDLEFERDTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQA 148 (236)
T ss_pred HHHHHHHHhCC---hHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHhccHHHHHHHHHHHHHHcCcCHHHH
Confidence 66666665411 222344555666677789999997 33 8999999999999 99999998888876543221
Q ss_pred CChhHHHHHHHHHHHHHHHHhchHhhh----------hcCCCCCccccHHHH
Q 016607 192 LAPDSLSNSMGLFLQKTNIIRDYLEDI----------NEIPKCRMFWPREIW 233 (386)
Q Consensus 192 ~~~~~~A~~lG~aLQltNIlRD~~ED~----------~e~~~GR~ylP~e~l 233 (386)
.....++.++|+|+|++|++||+.+|. . .||+|||.+.+
T Consensus 149 ~~~~~~~~~lG~a~Qi~dd~~D~~~d~~~~gk~~~D~~---~gr~tlp~~~~ 197 (236)
T cd00867 149 EALKDYGRALGLAFQLTDDLLDVFGDAEELGKVGSDLR---EGRITLPVILA 197 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccCChHHHCccHHHHH---cCCchHHHHHH
Confidence 223488999999999999999999988 7 79999999876
No 11
>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=99.71 E-value=1.3e-16 Score=146.34 Aligned_cols=217 Identities=22% Similarity=0.158 Sum_probs=160.7
Q ss_pred cHHHHHHhcCh--hhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHHhHHHHHH
Q 016607 50 SFALVIQQLGT--DLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVST 127 (386)
Q Consensus 50 sF~~a~~~Lp~--~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~~~~v~~ 127 (386)
+|++++.++|+ +.|.++..+|++++.+|||.|+...+. .+.....+| + ..+. ... ....+.++...+..+..
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~DDi~D~~~~~~-~~~~~~~~~-~-~~~~--~~~-~~~~~~~~~~~~~~~~~ 74 (243)
T cd00385 1 FRPLAVLLEPEASRLRAAVEKLHAASLVHDDIVDDSGTRR-GLPTAHLAV-A-IDGL--PEA-ILAGDLLLADAFEELAR 74 (243)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCC-CchhhhhhH-H-hcCc--hHH-HHHHHHHHHHHHHHHHh
Confidence 57889999999 999999999999999999999887543 232344444 1 1110 000 12223444444444443
Q ss_pred HHhhcCHHHHHHHHHHHHhhhhHHHhhhhh-c--CCCHHHHHHHHHhh-hhHHHHHHHHHhcccCCC---CCChhHHHHH
Q 016607 128 AFLELGKGYQDAIEDITKRMGAGMAKFICK-E--VESIDDYDEYCYYV-AGLVGLGLSKLFYASGTE---DLAPDSLSNS 200 (386)
Q Consensus 128 ~~~~l~~~~~~lI~~i~~~m~~Gm~~dl~~-~--~~t~~dl~~Yc~~V-AG~VG~ll~~l~~~~~~~---~~~~~~~A~~ 200 (386)
.. .....+.+.+.+..+..|+..|+.. . +.|++||..||+++ ++++|.++....+..+.+ ......++.+
T Consensus 75 ~~---~~~~~~~~~~~~~~~~~g~~~d~~~~~~~~~t~~ey~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 151 (243)
T cd00385 75 EG---SPEALEILAEALLDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCLLGAGLSGGEAELLEALRKLGRA 151 (243)
T ss_pred CC---CHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 31 1334455556667777899999974 3 89999999999999 999998888777653221 1223478999
Q ss_pred HHHHHHHHHHHhchHhhhhcCCC--CCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 016607 201 MGLFLQKTNIIRDYLEDINEIPK--CRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALR 278 (386)
Q Consensus 201 lG~aLQltNIlRD~~ED~~e~~~--GR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~l~~a~~yl~~l~ 278 (386)
+|.++|++|.++|+..|.+ . ||+++|...+.++|.+.+++..+..++...++++.+...+...+.+.......++
T Consensus 152 ~g~~~ql~nDl~~~~~e~~---~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~ 228 (243)
T cd00385 152 LGLAFQLTNDLLDYEGDAE---RGEGKCTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKLAEEALKELNELILSLP 228 (243)
T ss_pred HHHHHHHHHHHHhccCCHH---HhCCchHHHHHHHHHhCChhhHHHHHHHCChHHHHHHHHHHHHHHHHHHHhcCCCCcH
Confidence 9999999999999999998 5 8999999999999999998888888888888888888888888887776655554
No 12
>KOG1459 consensus Squalene synthetase [Lipid transport and metabolism]
Probab=98.77 E-value=6.4e-08 Score=94.31 Aligned_cols=205 Identities=10% Similarity=-0.010 Sum_probs=142.4
Q ss_pred HHHhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHHh
Q 016607 42 SMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQ 121 (386)
Q Consensus 42 ~~l~~~srsF~~a~~~Lp~~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~ 121 (386)
++....-+.|+......-++.+.+++.+|-+||.+|.++|..-. .-.-...|+.|....++ .++ |.+ +.-.
T Consensus 134 eviaeitk~mg~Gma~~~~~~v~ti~d~d~yChyvagLVg~gls-rlf~~s~le~~~~~~e~---l~n-s~g----lfLq 204 (413)
T KOG1459|consen 134 EVIAEITKRMGLGMALFIPEEVETIWDYDVYCHYVAGLVGIGLS-RLFTASKLEDLLARLEQ---LSN-SMG----LFLQ 204 (413)
T ss_pred HHHHHHHHHHhchHHHhhHHHHhHHHHHHHHHHHHHHhhCCchH-hhhhHHHHhhhhhhHHH---Hhc-ccc----hHHH
Confidence 45555556788888888788899999999999999999997532 11222344444444333 222 222 2111
Q ss_pred HHHHHHHHhhcC---HHHH-HHHHHHHHhhhhHHHhh-hh-hcCCCHHHHHHHHHhhhhHHHHHHHHHhcc--cCCCCCC
Q 016607 122 FHHVSTAFLELG---KGYQ-DAIEDITKRMGAGMAKF-IC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYA--SGTEDLA 193 (386)
Q Consensus 122 ~~~v~~~~~~l~---~~~~-~lI~~i~~~m~~Gm~~d-l~-~~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~--~~~~~~~ 193 (386)
=..+++.|..-+ .+|. +.| -||-.| +. -.++..+|+-.||+++++++|.+-....-. ++..+..
T Consensus 205 ktnIirdy~ed~~d~r~Fwp~eI--------wg~y~d~L~d~~~~en~dl~l~Cln~m~tnaL~hv~d~l~yls~l~~qs 276 (413)
T KOG1459|consen 205 KTNIIRDYLEDPVDGRPFWPREI--------WGKYMDKLKDFRYPENDDLALQCLNEMVTNALMHVPDVLTYLSKLRTQS 276 (413)
T ss_pred HhHHHHHHHhccccCCccChHHH--------HHHHHHHHHhhhCccchhHHHHHHHHHHHHHhhccHHHHHHHhhcccHH
Confidence 122333333222 2332 334 499888 54 479999999999999999999886544321 2222333
Q ss_pred hhHHHHHHHHHHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHH
Q 016607 194 PDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLK 272 (386)
Q Consensus 194 ~~~~A~~lG~aLQltNIlRD~~ED~~e~~~GR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~l~~a~~ 272 (386)
.-..+--.|++-|.||++++..||.- +|++++|+ |.+.+++.++.+.++++.++-....++...++++..
T Consensus 277 vfnfcaipqimai~Tlal~~nn~dvf---rG~Vklrk------Gl~~~~I~~~k~~~~v~~~f~~y~~~i~~k~d~~dp 346 (413)
T KOG1459|consen 277 VFNFCAIPQIMAIATLALCYNNEDVF---RGNVKLRK------GLAVELILASKTMDKVRNIFYMYLRDIRMKFDEADP 346 (413)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCHhHh---ccceeecC------CchHHHHHhcccHHHHHHHHHHHHHHHHhhCCccCC
Confidence 34677789999999999999999999 99999998 888899999999999999888887777776665554
No 13
>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=95.28 E-value=1.5 Score=41.77 Aligned_cols=192 Identities=16% Similarity=0.095 Sum_probs=102.7
Q ss_pred hhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHHhHHHHHHHHhh-cCHHHHHHH
Q 016607 62 LRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLE-LGKGYQDAI 140 (386)
Q Consensus 62 lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~~~~v~~~~~~-l~~~~~~lI 140 (386)
+--++-.+.......|||.|+.+.... + +. |+...... .. -...+-.+...+..+. .... ......+.+
T Consensus 44 la~aiEllh~asLIhDDI~D~s~~RRG-~-p~---~~~~~G~~---~A-il~gd~l~~~a~~~l~-~~~~~~~~~~~~~~ 113 (259)
T cd00685 44 LAAAIELLHTASLVHDDVMDNSDLRRG-K-PT---VHKVFGNA---TA-ILAGDYLLARAFELLA-RLGNPYYPRALELF 113 (259)
T ss_pred HHHHHHHHHHHHHHHhhhccCCcccCC-C-Cc---HHHHhCcc---cH-HHHHHHHHHHHHHHHH-hCCCccHHHHHHHH
Confidence 346677888889999999998653211 1 11 22211110 00 0000111111122221 1110 012334445
Q ss_pred HHHHHhhhhHHHhhhhh---cCCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCC-CC--CChhHHHHHHHHHHHHHHHHhc
Q 016607 141 EDITKRMGAGMAKFICK---EVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGT-ED--LAPDSLSNSMGLFLQKTNIIRD 213 (386)
Q Consensus 141 ~~i~~~m~~Gm~~dl~~---~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~-~~~-~~--~~~~~~A~~lG~aLQltNIlRD 213 (386)
.+....|..|-..|+.. ...|++++..-+.+-.|....+++.+.+. .+. +. .....++.++|.++|+.|=+.|
T Consensus 114 ~~~~~~~~~GQ~~d~~~~~~~~~~~~~y~~~~~~KT~~l~~~~~~~~a~l~~~~~~~~~~l~~~g~~lG~afQi~DD~ld 193 (259)
T cd00685 114 SEAILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEALKRFGRNLGLAFQIQDDILD 193 (259)
T ss_pred HHHHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 55666778888888863 26789999888877777766666554432 111 11 1234789999999999998877
Q ss_pred hHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcchh
Q 016607 214 YLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH 280 (386)
Q Consensus 214 ~~ED~~e~~~GR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~l~~a~~yl~~l~~~ 280 (386)
+.-|..+ .|+- ..+|+.++..+=.+.-++ -..+..+..++...++.++..
T Consensus 194 ~~~~~~~--~gK~------------~~~Di~~gk~T~~~~~~l---~~~~~~~~~~a~~~l~~~~~~ 243 (259)
T cd00685 194 LFGDPET--LGKP------------VGSDLREGKCTLPVLLAL---RELAREYEEKALEALKALPES 243 (259)
T ss_pred ccCChHH--HCCC------------cchHHHcCCchHHHHHHH---HHHHHHHHHHHHHHHHcCCCc
Confidence 7544321 1221 113444444332222222 456677777788888888755
No 14
>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=94.22 E-value=3.3 Score=41.05 Aligned_cols=93 Identities=20% Similarity=0.169 Sum_probs=56.9
Q ss_pred HHHHHHHHHHHhhhhHHHhhhhh---cCCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC---CChhHHHHHHHHHHHH
Q 016607 135 GYQDAIEDITKRMGAGMAKFICK---EVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED---LAPDSLSNSMGLFLQK 207 (386)
Q Consensus 135 ~~~~lI~~i~~~m~~Gm~~dl~~---~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~-~~~~~---~~~~~~A~~lG~aLQl 207 (386)
...+.+.+....|+.|...|+.. .-.|.++|..-..+=.|......+.+-.. +|.+. .....++.++|+|+|+
T Consensus 133 ~~~~~~~~~~~~~~~Gq~~~~~~~~~~~~~~~~y~~~~~~KTa~L~~~~~~~ga~~ag~~~~~~~~l~~~G~~lG~aFQi 212 (322)
T TIGR02749 133 EVVKLISKVITDFAEGEIKQGLNQFDSDLSLEDYLEKSFYKTASLVAASSKAAAVLSDVPSQVANDLYEYGKHLGLAFQV 212 (322)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcccCCCCCHHHHHHHHHccHHHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHHHHH
Confidence 34455666666777887777642 23577777665554444443333333221 22211 1234788899999999
Q ss_pred HHHHhch-----------HhhhhcCCCCCccccH
Q 016607 208 TNIIRDY-----------LEDINEIPKCRMFWPR 230 (386)
Q Consensus 208 tNIlRD~-----------~ED~~e~~~GR~ylP~ 230 (386)
.+=+.|+ +.|+. .|.+=+|.
T Consensus 213 ~DDild~~~~~~~~GK~~g~Dl~---~Gk~Tlp~ 243 (322)
T TIGR02749 213 VDDILDFTGSTEQLGKPAGSDLM---KGNLTAPV 243 (322)
T ss_pred HHHhccCCCChHhhCCChhHHHh---CCCchHHH
Confidence 9888885 57777 58877885
No 15
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=93.95 E-value=7.2 Score=38.68 Aligned_cols=93 Identities=12% Similarity=0.116 Sum_probs=62.8
Q ss_pred HHHHHHHHHHHhhhhHHHhhhh---hcCCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC---CChhHHHHHHHHHHHH
Q 016607 135 GYQDAIEDITKRMGAGMAKFIC---KEVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED---LAPDSLSNSMGLFLQK 207 (386)
Q Consensus 135 ~~~~lI~~i~~~m~~Gm~~dl~---~~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~-~~~~~---~~~~~~A~~lG~aLQl 207 (386)
.+.+++.+.+..|..|-..|+. ..-.|.++|..-+.+=.|....+.+.+-.. +|.+. .....++.++|+|+|+
T Consensus 130 ~~~~~~~~~~~~~~~Gq~~d~~~~~~~~~s~~~y~~~i~~KTa~lf~~~~~~ga~lag~~~~~~~~l~~~g~~lG~aFQi 209 (323)
T PRK10888 130 KVLEVMSEAVNVIAEGEVLQLMNVNDPDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRYLGTAFQL 209 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3445566666777788877774 234688888877777666666666554332 22211 1123788999999999
Q ss_pred HHHHhch-----------HhhhhcCCCCCccccH
Q 016607 208 TNIIRDY-----------LEDINEIPKCRMFWPR 230 (386)
Q Consensus 208 tNIlRD~-----------~ED~~e~~~GR~ylP~ 230 (386)
.+=+-|+ +.|+. .|.+=||.
T Consensus 210 ~DD~ld~~~~~~~~GK~~g~Dl~---~gk~Tlp~ 240 (323)
T PRK10888 210 IDDLLDYSADGETLGKNVGDDLN---EGKPTLPL 240 (323)
T ss_pred HHHhhcccCChHhhCCCchhhhh---cCCchHHH
Confidence 9988887 57777 68888885
No 16
>PLN02890 geranyl diphosphate synthase
Probab=93.46 E-value=5.2 Score=41.25 Aligned_cols=143 Identities=14% Similarity=0.117 Sum_probs=80.9
Q ss_pred HHHHHHHHHHHhhhhHHHhhhhh---cCCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC---CChhHHHHHHHHHHHH
Q 016607 135 GYQDAIEDITKRMGAGMAKFICK---EVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED---LAPDSLSNSMGLFLQK 207 (386)
Q Consensus 135 ~~~~lI~~i~~~m~~Gm~~dl~~---~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~-~~~~~---~~~~~~A~~lG~aLQl 207 (386)
...+++.+.+..|..|-..|+.. .-.|+++|..-.++=.|......+.+-.. +|... .....++.++|+|+|+
T Consensus 227 ~~~~~~s~a~~~l~~Gq~ld~~~~~~~~~s~~~Yl~~i~~KTa~Lf~~s~~~gAilaga~~~~~~~l~~fG~~lGlAFQI 306 (422)
T PLN02890 227 EVVSLLATAVEHLVTGETMQITSSREQRRSMDYYMQKTYYKTASLISNSCKAVAILAGQTAEVAVLAFEYGRNLGLAFQL 306 (422)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHHHHH
Confidence 34455666667777888888753 24578888776665555555545443221 22211 1124788999999999
Q ss_pred HHHHhchH-----------hhhhcCCCCCccccHHHHHhccCChhhhh-cccCCH-HHHH---------HHHHHHHHHHH
Q 016607 208 TNIIRDYL-----------EDINEIPKCRMFWPREIWSKYVNKLEDLK-YEENSD-KAVQ---------CLNDMVTNALM 265 (386)
Q Consensus 208 tNIlRD~~-----------ED~~e~~~GR~ylP~e~l~~~g~~~~dl~-~~~~~~-~~~~---------~l~~lv~~A~~ 265 (386)
.+=+-|+- .|+. .|.+=+|-=..-+.......+. .+..++ .+.. .+..-...|..
T Consensus 307 ~DDiLD~~g~~~~~GK~~g~DL~---eGk~TlPvl~al~~~~~l~~~l~~~~~~~~~v~~~~~~i~~~gaie~a~~la~~ 383 (422)
T PLN02890 307 IDDVLDFTGTSASLGKGSLSDIR---HGVITAPILFAMEEFPQLREVVDRGFDNPANVDIALEYLGKSRGIQRTRELARE 383 (422)
T ss_pred HHHHHhhcCChhhhCCCchhhHh---cCCccHHHHHHHhcCHHHHHHHhcccCCHHHHHHHHHHHHHcCHHHHHHHHHHH
Confidence 99888874 6677 5777777632211110111111 111111 1111 13334445777
Q ss_pred HHHHHHHHHHhcchh
Q 016607 266 HVEDCLKYMSALRDH 280 (386)
Q Consensus 266 ~l~~a~~yl~~l~~~ 280 (386)
|..+|...+..+|+.
T Consensus 384 ~~~~A~~~L~~lp~s 398 (422)
T PLN02890 384 HANLAAAAIESLPET 398 (422)
T ss_pred HHHHHHHHHHhCCCC
Confidence 788888888877754
No 17
>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=93.42 E-value=5.1 Score=39.64 Aligned_cols=93 Identities=15% Similarity=0.096 Sum_probs=60.2
Q ss_pred HHHHHHHHHHHhhhhHHHhhhhh---cCCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCCC---ChhHHHHHHHHHHHH
Q 016607 135 GYQDAIEDITKRMGAGMAKFICK---EVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTEDL---APDSLSNSMGLFLQK 207 (386)
Q Consensus 135 ~~~~lI~~i~~~m~~Gm~~dl~~---~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~-~~~~~~---~~~~~A~~lG~aLQl 207 (386)
...+.+.+.+..|..|-..|+.. .-.|.++|..-.+.=.|......+.+-.. +|.... ....++.++|+|+|+
T Consensus 129 ~~~~~~~~~~~~~~~Gq~~~~~~~~~~~~~~~~Y~~~i~~KTa~L~~~~~~~ga~~ag~~~~~~~~l~~~g~~lG~aFQI 208 (319)
T TIGR02748 129 RAHQILSHTIVEVCRGEIEQIKDKYNFDQNLRTYLRRIKRKTALLIAASCQLGAIASGANEAIVKKLYWFGYYVGMSYQI 208 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 34455566677777887777752 24578887776666666655544443221 121111 123688999999999
Q ss_pred HHHHhchH-----------hhhhcCCCCCccccH
Q 016607 208 TNIIRDYL-----------EDINEIPKCRMFWPR 230 (386)
Q Consensus 208 tNIlRD~~-----------ED~~e~~~GR~ylP~ 230 (386)
.|=+.|+- .|+. .|..=+|-
T Consensus 209 ~DDilD~~~~~~~~GK~~~~Dl~---~gk~Tlp~ 239 (319)
T TIGR02748 209 TDDILDFVGTEEELGKPAGGDLL---QGNVTLPV 239 (319)
T ss_pred HHHHHHccCCHHhhCCChhhHHh---CCCchHHH
Confidence 99998874 6777 58887886
No 18
>CHL00151 preA prenyl transferase; Reviewed
Probab=91.53 E-value=11 Score=37.29 Aligned_cols=83 Identities=18% Similarity=0.150 Sum_probs=47.9
Q ss_pred hHHHHHHHHHHHHHHHHhch-----------HhhhhcCCCCCccccHHHHHhccCChhhhh-cccC-CHHHHHH------
Q 016607 195 DSLSNSMGLFLQKTNIIRDY-----------LEDINEIPKCRMFWPREIWSKYVNKLEDLK-YEEN-SDKAVQC------ 255 (386)
Q Consensus 195 ~~~A~~lG~aLQltNIlRD~-----------~ED~~e~~~GR~ylP~e~l~~~g~~~~dl~-~~~~-~~~~~~~------ 255 (386)
..++.++|.|+|+.+=+-|+ +.|+. .|.+=||.=..-+.......+. .... .+...++
T Consensus 201 ~~~G~~lG~aFQi~DDilD~~~~~~~~GK~~g~Dl~---eGk~Tlp~l~al~~~~~~~~~l~~~~~~~~~~~~~~~~l~~ 277 (323)
T CHL00151 201 YLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLK---NGNLTAPVLFALTQNSKLAKLIEREFCETKDISQALQIIKE 277 (323)
T ss_pred HHHHHHHHHHHHHHHHHhhcccChhhhCCCchhhHh---cCchHHHHHHHHhcChHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence 47889999999999888885 56787 6888888521111110011111 1111 1112222
Q ss_pred ---HHHHHHHHHHHHHHHHHHHHhcchh
Q 016607 256 ---LNDMVTNALMHVEDCLKYMSALRDH 280 (386)
Q Consensus 256 ---l~~lv~~A~~~l~~a~~yl~~l~~~ 280 (386)
+.+....+..|..+|...+..+|..
T Consensus 278 ~g~~~~a~~~a~~~~~~A~~~L~~lp~~ 305 (323)
T CHL00151 278 TNGIEKAKDLALEHMQAAIQCLKFLPPS 305 (323)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 3444455777888888888777654
No 19
>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=90.33 E-value=7.2 Score=37.18 Aligned_cols=147 Identities=15% Similarity=0.080 Sum_probs=78.2
Q ss_pred hhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHHhHHHHHHHHhhcC-HHHHHHH
Q 016607 62 LRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELG-KGYQDAI 140 (386)
Q Consensus 62 lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~~~~v~~~~~~l~-~~~~~lI 140 (386)
...+|-.+.+..-..|||.|+...- .-+-..-..|-.... . ...+-.+..++..+...-...+ .....++
T Consensus 38 ~a~avEliH~asLIhDDI~D~s~~R-RG~pt~~~~~G~~~A----i----l~gd~ll~~a~~~l~~~~~~~~~~~~~~i~ 108 (260)
T PF00348_consen 38 LAAAVELIHAASLIHDDIIDNSDLR-RGKPTVHKKFGNAIA----I----LAGDYLLALAFELLARLGHFDPSERVLRIL 108 (260)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTCSEE-TTEECHHHHHHHHHH----H----HHHHHHHHHHHHHHHHHCHSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhhhhcccccC-CCCccccccccccch----h----hhchHHHHHHHHHHHHhhcccchHHHHHHH
Confidence 3446677888888999999986431 000000001111000 0 0011122223333322210111 2334455
Q ss_pred HHHHHhhhhHHHh---hhhhc--CCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC---CChhHHHHHHHHHHHHHHHH
Q 016607 141 EDITKRMGAGMAK---FICKE--VESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED---LAPDSLSNSMGLFLQKTNII 211 (386)
Q Consensus 141 ~~i~~~m~~Gm~~---dl~~~--~~t~~dl~~Yc~~VAG~VG~ll~~l~~~-~~~~~---~~~~~~A~~lG~aLQltNIl 211 (386)
+.+...++.|+.. |+... ..|+++|..-+++=.|+...+.+++-.. ++.+. .....++.++|+|+|+.|=+
T Consensus 109 ~~~~~~~~~~~~~q~~d~~~~~~~~~~~~y~~i~~~KTg~l~~~~~~~ga~lag~~~~~~~~l~~~g~~lG~afQi~DD~ 188 (260)
T PF00348_consen 109 ELFIEALIEGEIGQALDLANEDKDPTEEEYLEIIRLKTGSLFALACQLGAILAGADEEQIEALREFGRHLGIAFQIRDDL 188 (260)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTTSSTSHHHHHHHHHHHTHHHHHHHHHHHHHHTTSGHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHhcccceeehhhccccccccccHHHHHHHHhhcchHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHhhhhhh
Confidence 5555555555444 44333 7799999998888888877776666543 22211 12237899999999999987
Q ss_pred hchHhh
Q 016607 212 RDYLED 217 (386)
Q Consensus 212 RD~~ED 217 (386)
.|+.-|
T Consensus 189 ~d~~~~ 194 (260)
T PF00348_consen 189 LDLFGD 194 (260)
T ss_dssp HHHHSH
T ss_pred hhccCc
Confidence 777644
No 20
>PLN02857 octaprenyl-diphosphate synthase
Probab=90.06 E-value=4.9 Score=41.35 Aligned_cols=93 Identities=20% Similarity=0.211 Sum_probs=59.1
Q ss_pred HHHHHHHHHHHhhhhHHHhhhh---hcCCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC---CChhHHHHHHHHHHHH
Q 016607 135 GYQDAIEDITKRMGAGMAKFIC---KEVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED---LAPDSLSNSMGLFLQK 207 (386)
Q Consensus 135 ~~~~lI~~i~~~m~~Gm~~dl~---~~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~-~~~~~---~~~~~~A~~lG~aLQl 207 (386)
...+++.+.+..|..|...++. ..-.|.++|..-.++=.|......+.+-.. +|.+. .....++.++|+|+|+
T Consensus 227 ~~~~~~s~~~~~l~~Gei~q~~~~~~~~~s~~~Yl~~i~~KTa~L~~~a~~~gallaga~~~~~~~l~~fG~~LGiAFQI 306 (416)
T PLN02857 227 EVIKLISQVIKDFASGEIKQASSLFDCDVTLDEYLLKSYYKTASLIAASTKSAAIFSGVDSSVKEQMYEYGKNLGLAFQV 306 (416)
T ss_pred HHHHHHHHHHHHHHhhHHHHHhcccCCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4456666667777788765553 224577887776665555554444443221 22211 1234788999999999
Q ss_pred HHHHhch-----------HhhhhcCCCCCccccH
Q 016607 208 TNIIRDY-----------LEDINEIPKCRMFWPR 230 (386)
Q Consensus 208 tNIlRD~-----------~ED~~e~~~GR~ylP~ 230 (386)
.+=+.|+ +.|+. .|..=+|.
T Consensus 307 ~DDiLD~~~~~~~~GK~~g~DL~---eGK~TlPl 337 (416)
T PLN02857 307 VDDILDFTQSTEQLGKPAGSDLA---KGNLTAPV 337 (416)
T ss_pred HHHHHhhcCCHHHhCCCcchhhh---cCCccHHH
Confidence 9888885 46787 58887885
No 21
>PRK10581 geranyltranstransferase; Provisional
Probab=88.53 E-value=12 Score=36.84 Aligned_cols=121 Identities=18% Similarity=0.140 Sum_probs=71.7
Q ss_pred hhhhHHHhhhh--hcCCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC----CChhHHHHHHHHHHHHHHHHhchHhhh
Q 016607 146 RMGAGMAKFIC--KEVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED----LAPDSLSNSMGLFLQKTNIIRDYLEDI 218 (386)
Q Consensus 146 ~m~~Gm~~dl~--~~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~-~~~~~----~~~~~~A~~lG~aLQltNIlRD~~ED~ 218 (386)
.|..|-..|+. ....|.++|..-+++=.|......+.+-.. +|... .....++.++|+|+|+.+=+.|+--|.
T Consensus 153 ~l~~GQ~ld~~~~~~~~~~~~y~~i~~~KTa~L~~~~~~~gailag~~~~~~~~~l~~~g~~lG~aFQI~DDilD~~g~~ 232 (299)
T PRK10581 153 GMCGGQALDLEAEGKQVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDT 232 (299)
T ss_pred hhhHhhHHHHhccCCCCCHHHHHHHHHHhhHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHccccCCh
Confidence 46678777775 234678888876665555554444433221 22211 112378999999999998887764333
Q ss_pred hcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcchh
Q 016607 219 NEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH 280 (386)
Q Consensus 219 ~e~~~GR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~l~~a~~yl~~l~~~ 280 (386)
+ .++|-. -.|+..+..+-.....+...-..+..++.+|...+..++..
T Consensus 233 ~------------~~GK~~--g~Dl~~gk~T~p~l~~~e~a~~~a~~~~~~A~~~l~~l~~~ 280 (299)
T PRK10581 233 A------------TLGKRQ--GADQQLGKSTYPALLGLEQARKKARDLIDDARQSLDQLAAQ 280 (299)
T ss_pred H------------HHCCCc--chhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCC
Confidence 2 122210 13444444444444445566667888888888888888753
No 22
>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=88.21 E-value=11 Score=38.21 Aligned_cols=171 Identities=12% Similarity=0.073 Sum_probs=86.4
Q ss_pred HHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHHhHHHHHHHHhhcC
Q 016607 54 VIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELG 133 (386)
Q Consensus 54 a~~~Lp~~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~~~~v~~~~~~l~ 133 (386)
+-..+|.+.+-.|.+++.+.-.+||+.++.. ..+..|++.+.. |++..+|++..|...+..+...=
T Consensus 77 ~y~~~~~evqv~IaiyT~yvi~iDD~~~~~~-------~~l~~F~~~l~~-------Gq~Q~~p~L~~~~~~L~~~~~~f 142 (376)
T PF06330_consen 77 CYPHLPKEVQVAIAIYTTYVIIIDDSSQEPS-------DDLRTFHQRLIL-------GQPQKHPLLDGFASLLREMWRHF 142 (376)
T ss_dssp HSTTS-HHHHHHHHHHHHHHHHHTT--S-SH-------HHHTTHHHHHHH-------T---SSHHHHHHHHHHHHHHTTS
T ss_pred ecCCCCHHHHHHHHHHHHHHHhccccccccc-------HHHHHHHHHHhc-------CCCCCCHHHHHHHHHHHHHHHHc
Confidence 3357899999999999999999999987652 355667777754 66667899999999988876655
Q ss_pred HHH-HHHHHHHHHhhhhH--HHhhhhhcC---CCHHHHHHHHHhhhhHHHHHHHHHhcccCCCC-CChhHHHHHHHHHHH
Q 016607 134 KGY-QDAIEDITKRMGAG--MAKFICKEV---ESIDDYDEYCYYVAGLVGLGLSKLFYASGTED-LAPDSLSNSMGLFLQ 206 (386)
Q Consensus 134 ~~~-~~lI~~i~~~m~~G--m~~dl~~~~---~t~~dl~~Yc~~VAG~VG~ll~~l~~~~~~~~-~~~~~~A~~lG~aLQ 206 (386)
.++ .++|-.-+-+..+| .+..-.+.. ..+.++.+=.-+++...+.+ +|-.+..++ ....++...+.....
T Consensus 143 gpf~anmI~~STLdFi~g~~LE~~~f~~~p~A~~FP~fLR~ktGlsEaYA~F---iFPk~~fpe~~~~~~y~~AIpdl~~ 219 (376)
T PF06330_consen 143 GPFCANMIVKSTLDFINGCWLEQKNFHGSPGAPDFPDFLRRKTGLSEAYAFF---IFPKALFPEVEYFIQYTPAIPDLMR 219 (376)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHTTT----TT-TTHHHHHHHHHH-HHHHHHH---T--TTTS-TTTTHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHhhcccCCCCCCCccccHHHHhccCcchhheee---ecccccCChHHHHHHHHHHHHHHHH
Confidence 555 33333222222222 222111112 24555555555544444433 343221111 112244445666677
Q ss_pred HHHHHhchHhhhhcCC--CCC-ccccHHHHHhccCChhh
Q 016607 207 KTNIIRDYLEDINEIP--KCR-MFWPREIWSKYVNKLED 242 (386)
Q Consensus 207 ltNIlRD~~ED~~e~~--~GR-~ylP~e~l~~~g~~~~d 242 (386)
.+|++-|+.-=..|+- ..+ .|+ ...-.-+|++..+
T Consensus 220 fi~~~NDILSFYKE~l~a~E~~NyI-~n~A~~~g~S~~e 257 (376)
T PF06330_consen 220 FINYVNDILSFYKEELVAGETGNYI-HNRARVHGVSILE 257 (376)
T ss_dssp HHHHHHHHHHHHHHHTTSSSSSSHH-HHHHHHHT--HHH
T ss_pred HHHhhhhHHHHHHhhcccccccchh-hhhhhccCCCHHH
Confidence 7777777752222100 223 455 3344456665544
No 23
>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=78.31 E-value=59 Score=30.35 Aligned_cols=173 Identities=14% Similarity=0.020 Sum_probs=89.6
Q ss_pred hhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccc-cccccCCCcchHHHHhHHHHHHHHhhcCH-H-H
Q 016607 60 TDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDRE-WHFSCGTKEYKVLMDQFHHVSTAFLELGK-G-Y 136 (386)
Q Consensus 60 ~~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~-~~~~~G~~~~~~l~~~~~~v~~~~~~l~~-~-~ 136 (386)
++.+..++-+..+.-.+||+-|+.+. ... ++.+.+.+..-. .....+.....++..++..+..+...... . .
T Consensus 60 ~~~l~~~a~~~~w~f~~DD~~D~~~~--~~~---~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~d~~~r~~~~~~~~~~ 134 (270)
T PF03936_consen 60 SDELLAAADWMAWLFIFDDFFDDGGS--AEE---LEALTDAVERWDPNSGDPLPDPDKPLFRALADIWNRIAARMSPAQR 134 (270)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTSH--HHH---HHHHHHHHHHTSSGGGGGSTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhhchheeeeeeccccccc--hHH---HHHHHHHHhcccccccccccchhHHHHHHHHHHHHHHHHHhhhhhc
Confidence 46677888999999999999997643 222 444444444100 01111233445677777777766543222 2 2
Q ss_pred HH-HHHHHH---HhhhhHHHhhhh----hcCCCHHHHHHHHHhhhhHHHHHHHHHhcccC--CCCC-----ChhHHHHHH
Q 016607 137 QD-AIEDIT---KRMGAGMAKFIC----KEVESIDDYDEYCYYVAGLVGLGLSKLFYASG--TEDL-----APDSLSNSM 201 (386)
Q Consensus 137 ~~-lI~~i~---~~m~~Gm~~dl~----~~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~~~--~~~~-----~~~~~A~~l 201 (386)
.. .+..+. .+..+|...... ..++|++||..+=..+.|.--.+.+-.++... .+.. ....+....
T Consensus 135 ~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~ps~eeYl~~R~~t~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~ 214 (270)
T PF03936_consen 135 RRDQIKRFRNSWREYLNAYLWEARWRERGRIPSLEEYLEMRRHTSGVYPCLALIEFALEFALGELPPEVLEHPPMLRRLA 214 (270)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS--SHHHHHHHHHHHTSHHHHHHHHHHHCSSCHTHHHHHHHHTTHHHHHHH
T ss_pred ccHHhhHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHhccccccccHHHHHHHHhCCCccccccHHHHHhchHHHHHH
Confidence 22 111111 122223322222 24888888888777777765444444332210 0000 001255566
Q ss_pred HHHHHHHHHHhchHhhhhcCCCCCc--cccHHHHHhccCChh
Q 016607 202 GLFLQKTNIIRDYLEDINEIPKCRM--FWPREIWSKYVNKLE 241 (386)
Q Consensus 202 G~aLQltNIlRD~~ED~~e~~~GR~--ylP~e~l~~~g~~~~ 241 (386)
+...-++|=|-.+..+.. .|.. .++- ++..+|++.+
T Consensus 215 ~~~~~l~NDl~S~~KE~~---~g~~~N~v~~-l~~~~~~s~e 252 (270)
T PF03936_consen 215 ADIIRLVNDLYSYKKEIA---RGDVHNLVVV-LMNEHGLSLE 252 (270)
T ss_dssp HHHHHHHHHHHHHHHHHH---TTSCCSHHHH-HHHHHTHHHH
T ss_pred HHHHHHhcccchhhcchh---hcccccHHHH-hhhhcCCCHH
Confidence 777777788888877777 5654 4443 4555565444
No 24
>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=74.65 E-value=1.2e+02 Score=32.20 Aligned_cols=235 Identities=15% Similarity=0.122 Sum_probs=115.7
Q ss_pred hcChhhHHHHHHHHHhcccccCCCC-CchhHHHHHHHHhhcCCcHHHHHHhcC--hhhhhHHHHHHHHHHhhhhhccCCC
Q 016607 8 LRHPDDLYPLLKLKMASRQAEKQIP-PEPHWAFCYSMLHKVSRSFALVIQQLG--TDLRNAVCIFYLVLRALDTVEDDTS 84 (386)
Q Consensus 8 ~~hp~e~~~~~~~~~~~~~~~~~~~-~~~~~~~C~~~l~~~srsF~~a~~~Lp--~~lR~av~alYaf~R~lD~I~D~~~ 84 (386)
..|=.||..+.+|.--..- ...++ .++-+..|+ -..+++.+-| ...|-.++-+-.+.-.+||+=|.-.
T Consensus 234 ~~hq~El~~~~rWwk~~gL-~~~l~~aRdr~ve~y--------f~~~a~~feP~~s~~Rl~~aK~~~l~~~iDD~fD~~g 304 (542)
T cd00684 234 ALHQEELKILSRWWKDLDL-ASKLPFARDRLVECY--------FWAAGTYFEPQYSLARIALAKTIALITVIDDTYDVYG 304 (542)
T ss_pred HhHHHHHHHHhHHHHhcCC-cccCCcccchhHHHH--------HHHHhcccCccchHHHHHHHHHHHHHhhhHhhhccCC
Confidence 3688999999887543221 11111 122222332 1233344444 2445556667777778899988543
Q ss_pred CChhhhHHHHHHHHHHHcccccccc--cCCC-cchHHHHhHHHHHHHHhh----c-CHHHHHHHHHHHHhhhhHHHhhhh
Q 016607 85 IPTDVKVPILIAFHRHVYDREWHFS--CGTK-EYKVLMDQFHHVSTAFLE----L-GKGYQDAIEDITKRMGAGMAKFIC 156 (386)
Q Consensus 85 ~~~~~k~~~L~~~~~~l~~~~~~~~--~G~~-~~~~l~~~~~~v~~~~~~----l-~~~~~~lI~~i~~~m~~Gm~~dl~ 156 (386)
. ...|+.|-+.+.. |.-. .+-| ..+++..++..+..++.. - ......-+.+..++...|+.....
T Consensus 305 t-----~eEl~~ft~ai~r--wd~~~~~~lPe~mk~~~~al~~~~~ei~~~~~~~~~~~~~~~~~~~~~~~~~a~l~EA~ 377 (542)
T cd00684 305 T-----LEELELFTEAVER--WDISAIDQLPEYMKIVFKALLNTVNEIEEELLKEGGSYVVPYLKEAWKDLVKAYLVEAK 377 (542)
T ss_pred C-----HHHHHHHHHHHHh--ccccchhhccHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHH
Confidence 2 2356666666653 3211 1212 123455556655443221 1 001112222233333445555543
Q ss_pred ----hcCCCHHHHHHHHHhhhhHHHHHHHHHhcccCCCC-CCh-------hHHHHHHHHHHHHHHHHhchHhhhhcCCCC
Q 016607 157 ----KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTED-LAP-------DSLSNSMGLFLQKTNIIRDYLEDINEIPKC 224 (386)
Q Consensus 157 ----~~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~~~~~~-~~~-------~~~A~~lG~aLQltNIlRD~~ED~~e~~~G 224 (386)
..++|++|+......++|.--.+++-.++. |... ... ..+-...+...-+.|=|-.+..... +|
T Consensus 378 w~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~-g~~l~~e~~e~~~~~~~l~~~~~~i~rL~NDi~S~~kE~~---rG 453 (542)
T cd00684 378 WAHEGYVPTFEEYMENALVSIGLGPLLLTSFLGM-GDILTEEAFEWLESRPKLVRASSTIGRLMNDIATYEDEMK---RG 453 (542)
T ss_pred HHhcCCCCCHHHHHhhhhHHhhHHHHHHHHHHhc-CCCCCHHHHHHHhccHHHHHHHHHHHHHhcChhhhHHHHh---cC
Confidence 348899999888777665544444444432 2111 001 1222333444444454444544444 55
Q ss_pred Cc-cccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHH
Q 016607 225 RM-FWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCL 271 (386)
Q Consensus 225 R~-ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~l~~a~ 271 (386)
.+ =.-.=.+.++|++. +.+.+.+..++..+...+.+..
T Consensus 454 dv~n~V~~ymke~g~s~---------eeA~~~i~~~ie~~wk~ln~e~ 492 (542)
T cd00684 454 DVASSIECYMKEYGVSE---------EEAREEIKKMIEDAWKELNEEF 492 (542)
T ss_pred CcccHHHHHHHhcCCCH---------HHHHHHHHHHHHHHHHHHHHHH
Confidence 53 11122445566553 4467778888888888776654
No 25
>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=70.44 E-value=96 Score=29.14 Aligned_cols=192 Identities=16% Similarity=0.078 Sum_probs=97.4
Q ss_pred hhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHccccccc--ccCCC-cchHHHHhHHHHHHHHhhcCH---
Q 016607 61 DLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHF--SCGTK-EYKVLMDQFHHVSTAFLELGK--- 134 (386)
Q Consensus 61 ~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~--~~G~~-~~~~l~~~~~~v~~~~~~l~~--- 134 (386)
+.+..++-+.+++-.+||.-|+.... + .+..+.+.+.. |.. ..+.+ ...|+...+.++..+......
T Consensus 47 ~~l~~~a~~~~~~f~~DD~~D~~~~~-~----~~~~~~~~~~~--~~~~~~~~~p~~~~~~~~~l~d~~~r~~~~~~~~~ 119 (284)
T cd00868 47 EARIALAKTIALLTVIDDTYDDYGTL-E----ELELFTEAVER--WDISAIDELPEYMKPVFKALYDLVNEIEEELAKEG 119 (284)
T ss_pred HHHHHHHHHHHHHHHHHhccccCCCH-H----HHHHHHHHHHh--cChhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 57888889999999999999985432 1 12223333321 110 11222 245677777777665543322
Q ss_pred --HHHHHHHHHHHhhhhHHHhhhh----hcCCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC------CChhHHHHHH
Q 016607 135 --GYQDAIEDITKRMGAGMAKFIC----KEVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED------LAPDSLSNSM 201 (386)
Q Consensus 135 --~~~~lI~~i~~~m~~Gm~~dl~----~~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~-~~~~~------~~~~~~A~~l 201 (386)
.....+.+-+..+..|+..... ..++|++||..+-...+|.--.+.+--++. ...+. .....+....
T Consensus 120 ~~~~~~r~~~~~~~~~~~~~~e~~~~~~~~~p~~~eYl~~R~~~~g~~~~~~l~~~~~g~~l~~~~~~~~~~~~~l~~~~ 199 (284)
T cd00868 120 GSESLPYLKEAWKDLLRAYLVEAKWANEGYVPSFEEYLENRRVSIGYPPLLALSFLGMGDILPEEAFEWLPSYPKLVRAS 199 (284)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHhceehhhHHHHHHHHHHHcCCCCCHHHHHHhhhhHHHHHHH
Confidence 2222222233334445555443 237788887776666655432222222221 11110 1112455556
Q ss_pred HHHHHHHHHHhchHhhhhcCCCCCc-cccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHH
Q 016607 202 GLFLQKTNIIRDYLEDINEIPKCRM-FWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCL 271 (386)
Q Consensus 202 G~aLQltNIlRD~~ED~~e~~~GR~-ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~l~~a~ 271 (386)
+...-++|=+-.+..+.. .|.. =+..=++.++|++.+ .+...+.+++......+.+..
T Consensus 200 ~~~~~l~NDl~S~~kE~~---~g~~~N~v~vl~~~~~~~~~---------eA~~~~~~~~~~~~~~~~~~~ 258 (284)
T cd00868 200 STIGRLLNDIASYEKEIA---RGEVANSVECYMKEYGVSEE---------EALEELRKMIEEAWKELNEEV 258 (284)
T ss_pred HHHHHHhccchHHHHHHc---cCCcccHHHHHHhccCCCHH---------HHHHHHHHHHHHHHHHHHHHH
Confidence 666666666666666665 5654 222324555565443 345555666666655555443
No 26
>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=62.69 E-value=1.5e+02 Score=28.47 Aligned_cols=206 Identities=13% Similarity=0.027 Sum_probs=107.2
Q ss_pred HHHHhcC---hhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHHhHHHHHHHH
Q 016607 53 LVIQQLG---TDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAF 129 (386)
Q Consensus 53 ~a~~~Lp---~~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~~~~v~~~~ 129 (386)
++..+.| ++.-..++-+..+.-..||.-|+.....+........+-+.+.+.. ..+.....|+...+.++..++
T Consensus 46 ~~a~~~P~a~~~~l~l~~~~~~w~f~~DD~~D~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~p~~~~~~d~~~r~ 122 (303)
T cd00687 46 LAALFYPDADDERLMLAADLMAWLFVFDDLLDRDQKSPEDGEAGVTRLLDILRGDG---LDSPDDATPLEFGLADLWRRT 122 (303)
T ss_pred HHhhcCCCCCHHHHHHHHHHHHHHHHhcccCCccccCHHHHHHHHHHHHhccCCCC---CCCCCCCCHHHHHHHHHHHHh
Confidence 4455554 4455556677888899999999863222222222222222222210 001123456777778877766
Q ss_pred hhcC-HHH-HHHHHHHHHhhhhHHHhhhh----hcCCCHHHHHHHHHhhhhHHH-HHHHHHhcccCCCC-----CChhHH
Q 016607 130 LELG-KGY-QDAIEDITKRMGAGMAKFIC----KEVESIDDYDEYCYYVAGLVG-LGLSKLFYASGTED-----LAPDSL 197 (386)
Q Consensus 130 ~~l~-~~~-~~lI~~i~~~m~~Gm~~dl~----~~~~t~~dl~~Yc~~VAG~VG-~ll~~l~~~~~~~~-----~~~~~~ 197 (386)
.... +.. ..+++ -+..+..|+..-.. ..++|++||..+=....|.-. ..++.+........ +....+
T Consensus 123 ~~~~~~~~~~r~~~-~~~~~~~a~~~e~~~~~~~~~psl~eYl~~R~~~~g~~~~~~l~~~~~g~~lp~~~~~~~~~~~l 201 (303)
T cd00687 123 LARMSAEWFNRFAH-YTEDYFDAYIWEGKNRLNGHVPDVAEYLEMRRFNIGADPCLGLSEFIGGPEVPAAVRLDPVMRAL 201 (303)
T ss_pred ccCCCHHHHHHHHH-HHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhhhcccccccHHHHHHhcCCCCCHHHHhChHHHHH
Confidence 5432 222 22332 22233334443332 236777777766665544322 23333332111111 112246
Q ss_pred HHHHHHHHHHHHHHhchHhhh-hcCCCCCcc-ccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016607 198 SNSMGLFLQKTNIIRDYLEDI-NEIPKCRMF-WPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYM 274 (386)
Q Consensus 198 A~~lG~aLQltNIlRD~~ED~-~e~~~GR~y-lP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~l~~a~~yl 274 (386)
-...+..+-++|=|=.+..+. + .|... +-.=++.++|++.+ ++.+.+.+++......+.+...-+
T Consensus 202 ~~~~~~~~~l~NDl~S~~KE~~~---~g~~~N~V~vl~~~~g~s~~---------eA~~~~~~~~~~~~~~f~~~~~~l 268 (303)
T cd00687 202 EALASDAIALVNDIYSYEKEIKA---NGEVHNLVKVLAEEHGLSLE---------EAISVVRDMHNERITQFEELEASL 268 (303)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHh---CCccchHHHHHHHHcCCCHH---------HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 667777788888888888888 5 67632 11224455676554 355666777777777777666544
No 27
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=48.57 E-value=2.8e+02 Score=27.38 Aligned_cols=140 Identities=16% Similarity=0.129 Sum_probs=73.9
Q ss_pred HHHHHHHHHHhhhhHHHhhhhh--cCCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCC-C--CChhHHHHHHHHHHHHHH
Q 016607 136 YQDAIEDITKRMGAGMAKFICK--EVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTE-D--LAPDSLSNSMGLFLQKTN 209 (386)
Q Consensus 136 ~~~lI~~i~~~m~~Gm~~dl~~--~~~t~~dl~~Yc~~VAG~VG~ll~~l~~~-~~~~-~--~~~~~~A~~lG~aLQltN 209 (386)
....+.+-+..|..|-..|+.. ...|.++|..=-+.=-|..-...+.+-+. ++.. . .....++..+|+|+|+.+
T Consensus 135 ~~~~~~~~~~~~~~GQ~lDl~~~~~~~t~e~y~~~i~~KTa~L~~~a~~~ga~la~~~~~~~~~l~~~g~~lGlaFQi~D 214 (322)
T COG0142 135 AIKALAEAINGLCGGQALDLAFENKPVTLEEYLRVIELKTAALFAAAAVLGAILAGADEELLEALEDYGRNLGLAFQIQD 214 (322)
T ss_pred HHHHHHHHHHHHHHhHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhHHHHHHH
Confidence 3445566677888899999863 23677777654444333333333333222 2211 1 123478999999999988
Q ss_pred HHhchHh-----------hhhcCCCCCccccHHHHHhccCChhh-hh----cccCCHHHHHHH------HHHHHHHHHHH
Q 016607 210 IIRDYLE-----------DINEIPKCRMFWPREIWSKYVNKLED-LK----YEENSDKAVQCL------NDMVTNALMHV 267 (386)
Q Consensus 210 IlRD~~E-----------D~~e~~~GR~ylP~e~l~~~g~~~~d-l~----~~~~~~~~~~~l------~~lv~~A~~~l 267 (386)
=+=|+-- |+. .|..=||.-..-+.+...+. +. .+..-+++...+ ..-...+..+.
T Consensus 215 DiLD~~~d~~~lGK~~g~Dl~---~gK~T~p~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~a~~~~ 291 (322)
T COG0142 215 DILDITGDEEELGKPVGSDLK---EGKPTLPVLLALEKANEDQKLLRILLEGGGEVEEALELLRKSGAIEYAKNLAKTYV 291 (322)
T ss_pred HhhcCCCChHHhCCCcchHHH---cCCchHHHHHHHHcCchhhHHHHHHhhcchHHHHHHHHHHHcchHHHHHHHHHHHH
Confidence 7777664 444 35666666433333221110 00 000001111111 12223467777
Q ss_pred HHHHHHHHhcc
Q 016607 268 EDCLKYMSALR 278 (386)
Q Consensus 268 ~~a~~yl~~l~ 278 (386)
.+|...++.+|
T Consensus 292 ~~a~~~L~~l~ 302 (322)
T COG0142 292 EKAKEALEKLP 302 (322)
T ss_pred HHHHHHHHhCC
Confidence 88888887777
No 28
>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=45.24 E-value=69 Score=32.20 Aligned_cols=59 Identities=19% Similarity=0.340 Sum_probs=44.1
Q ss_pred cChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHH----HHhHHHHHHHHh
Q 016607 58 LGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVL----MDQFHHVSTAFL 130 (386)
Q Consensus 58 Lp~~lR~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l----~~~~~~v~~~~~ 130 (386)
.++++..++.+.|...-.+||+.|++. +-|+.|.+.|.. |++..+|+ ...|+.+.+.|+
T Consensus 81 ~skev~~~isi~~tY~~~lDD~~~e~~-------~~m~~f~~dL~~-------G~~qkhP~l~~v~~~l~~~lr~fG 143 (357)
T cd00686 81 VSKECMADLSIHYTYTLVLDDSKDDPY-------PTMVNYFDDLQA-------GREQAHPWWALVNEHFPNVLRHFG 143 (357)
T ss_pred CCHHHHHHHHHHHheeeEecccccccc-------hHHHHHHHHHhc-------CCCCCCcHHHHHHHHHHHHHHHhh
Confidence 688999999999999999999999865 245667776754 77767774 445555666554
No 29
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=22.09 E-value=52 Score=21.70 Aligned_cols=20 Identities=35% Similarity=0.355 Sum_probs=16.8
Q ss_pred CCCccccHHHHHhccCChhh
Q 016607 223 KCRMFWPREIWSKYVNKLED 242 (386)
Q Consensus 223 ~GR~ylP~e~l~~~g~~~~d 242 (386)
.||+.+|.++..+.+....|
T Consensus 6 kgri~iP~~~r~~l~~~~gd 25 (43)
T TIGR01439 6 KGQIVIPKEIREKLGLKEGD 25 (43)
T ss_pred CCeEEecHHHHHHcCcCCCC
Confidence 59999999999998876544
No 30
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=20.07 E-value=1.6e+02 Score=20.32 Aligned_cols=38 Identities=13% Similarity=0.158 Sum_probs=28.0
Q ss_pred HHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChh
Q 016607 51 FALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTD 88 (386)
Q Consensus 51 F~~a~~~Lp~~lR~av~alYaf~R~lD~I~D~~~~~~~ 88 (386)
+.-++..||++.|..+...|....-.++|++....+..
T Consensus 4 l~~~l~~L~~~~r~i~~l~~~~g~s~~eIa~~l~~s~~ 41 (54)
T PF08281_consen 4 LQQALAQLPERQREIFLLRYFQGMSYAEIAEILGISES 41 (54)
T ss_dssp HHHHHHCS-HHHHHHHHHHHTS---HHHHHHHCTS-HH
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCcCHHHHHHHHCcCHH
Confidence 34577889999999999999999999999998877643
Done!