Query 016722
Match_columns 384
No_of_seqs 251 out of 1463
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 09:24:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016722.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016722hhsearch_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 1.8E-87 3.9E-92 658.8 35.3 329 36-367 1-336 (336)
2 KOG1459 Squalene synthetase [L 100.0 5.5E-83 1.2E-87 608.6 19.1 371 6-384 2-382 (413)
3 COG1562 ERG9 Phytoene/squalene 100.0 4E-54 8.6E-59 414.7 26.8 278 32-327 5-284 (288)
4 PLN02632 phytoene synthase 100.0 2E-53 4.3E-58 419.5 29.5 275 33-325 45-324 (334)
5 TIGR03465 HpnD squalene syntha 100.0 3.3E-53 7.1E-58 406.3 27.4 260 45-325 2-263 (266)
6 cd00683 Trans_IPPS_HH Trans-Is 100.0 2.6E-53 5.7E-58 406.6 26.3 260 39-317 2-264 (265)
7 TIGR03464 HpnC squalene syntha 100.0 5.5E-53 1.2E-57 404.8 27.8 261 45-325 2-264 (266)
8 PF00494 SQS_PSY: Squalene/phy 100.0 2.2E-50 4.7E-55 386.1 18.7 261 44-317 1-267 (267)
9 KOG4411 Phytoene/squalene synt 99.9 5.8E-25 1.3E-29 199.5 22.7 255 34-309 9-269 (292)
10 cd00867 Trans_IPPS Trans-Isopr 99.8 7.7E-19 1.7E-23 164.7 13.4 169 50-233 1-197 (236)
11 cd00385 Isoprenoid_Biosyn_C1 I 99.7 9.8E-17 2.1E-21 147.1 14.2 217 50-278 1-228 (243)
12 KOG1459 Squalene synthetase [L 98.7 7.2E-08 1.6E-12 93.9 11.3 205 42-272 134-346 (413)
13 cd00685 Trans_IPPS_HT Trans-Is 95.5 1.4 3E-05 42.0 17.8 128 136-280 109-243 (259)
14 PRK10888 octaprenyl diphosphat 94.9 3.5 7.6E-05 40.9 19.0 93 135-230 130-240 (323)
15 TIGR02749 prenyl_cyano solanes 94.9 1.9 4.1E-05 42.7 17.0 93 135-230 133-243 (322)
16 TIGR02748 GerC3_HepT heptapren 94.0 3.5 7.5E-05 40.8 16.6 93 135-230 129-239 (319)
17 CHL00151 preA prenyl transfera 92.4 7.6 0.00016 38.4 16.4 139 139-280 138-305 (323)
18 PRK10581 geranyltranstransfera 92.4 2.9 6.3E-05 41.0 13.2 121 146-280 153-280 (299)
19 PLN02857 octaprenyl-diphosphat 92.1 2.1 4.6E-05 44.0 12.3 93 135-230 227-337 (416)
20 PLN02890 geranyl diphosphate s 92.1 2.3 4.9E-05 43.9 12.4 143 135-280 227-398 (422)
21 PF00348 polyprenyl_synt: Poly 90.4 5.6 0.00012 37.9 12.7 82 136-217 104-194 (260)
22 PF06330 TRI5: Trichodiene syn 87.3 12 0.00027 37.8 12.9 146 53-215 76-228 (376)
23 PF03936 Terpene_synth_C: Terp 80.1 52 0.0011 30.7 15.0 173 60-241 60-252 (270)
24 COG0142 IspA Geranylgeranyl py 77.1 64 0.0014 31.9 13.6 82 136-217 135-222 (322)
25 cd00684 Terpene_cyclase_plant_ 75.0 1.2E+02 0.0026 32.2 20.7 234 9-271 235-492 (542)
26 cd00868 Terpene_cyclase_C1 Ter 74.9 75 0.0016 29.9 16.5 193 60-271 46-258 (284)
27 cd00687 Terpene_cyclase_nonpla 72.1 95 0.0021 29.8 19.5 206 53-274 46-268 (303)
28 cd00686 Terpene_cyclase_cis_tr 56.5 1.5E+02 0.0032 29.9 11.1 59 58-130 81-143 (357)
29 COG3455 Type VI protein secret 29.0 66 0.0014 31.1 3.7 87 37-142 68-157 (262)
30 PF08281 Sigma70_r4_2: Sigma-7 23.6 1.2E+02 0.0025 21.1 3.4 38 51-88 4-41 (54)
31 TIGR01439 lp_hng_hel_AbrB loop 21.4 55 0.0012 21.5 1.2 20 223-242 6-25 (43)
32 PRK02899 adaptor protein; Prov 21.4 1.1E+02 0.0025 28.0 3.7 41 224-266 11-51 (197)
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=1.8e-87 Score=658.75 Aligned_cols=329 Identities=60% Similarity=1.017 Sum_probs=312.5
Q ss_pred hHHHHHHHHhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccC-CCc
Q 016722 36 HWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCG-TKE 114 (384)
Q Consensus 36 ~~~~C~~~l~~~srSF~~a~~~Lp~~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G-~~~ 114 (384)
++++|+++++.+|||||+++++||+++|++|+++|+|||++|||+|+++++.+.|++.|++|++.+.+.+|.|..+ .+.
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 4689999999999999999999999999999999999999999999999988899999999999999988988722 566
Q ss_pred chHHHhhHHHHHHHHHhcCHHHHHHHHHHHHhhhhHHHhhhhh-hc--CCHHHHHHHHHhhhhHHHHHHHHHhcccCCCC
Q 016722 115 YKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICK-EV--ESIDDYDEYCYYVAGLVGLGLSKLFYASGTED 191 (384)
Q Consensus 115 ~~~l~~~~~~v~~~~~~l~~~~~~lI~~i~~~m~~gm~~dl~~-~~--~t~~dl~~Yc~~VAG~VG~~l~~l~~~~~~~~ 191 (384)
++.++++|+.++.+|..++++++++|.+|+++|++||++|+.. .+ +|++||+.|||||||+||+|+++||+.+|..+
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 7789999999999999999999999999999999999999974 56 99999999999999999999999998755433
Q ss_pred C---ChhHHHHHHHHHHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHH
Q 016722 192 L---APDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVE 268 (384)
Q Consensus 192 ~---~~~~~A~~lG~alQltNIlRDv~eD~~~~~~gR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~ 268 (384)
. ...++|++||+|||+||||||++||++ +||+|||+|+|++||++.+|+..+++++++.+|+++|+.+|+.|+.
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 HHHHHHHhcchhhccchhhhhHHHHHHHHHHHhcCCCCccCccccChHHHHHHHHHhcChhHHHHHHHHHHHHhcccCCC
Q 016722 269 DCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYDFSNILKPKINK 348 (384)
Q Consensus 269 ~a~~y~~~L~~~~~~~f~aiP~~~AiatL~~~~~~~~vf~~~vki~k~~~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~ 348 (384)
+|+.|++.|+++++|+||+||++||++||+.|++|++||+++|||||++++.+|++++|+++|+.+|++|+++|++|++|
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 016722 349 NDPNATKTLSRVEAIQKAC 367 (384)
Q Consensus 349 ~dp~~~~~~~~~~~i~~~~ 367 (384)
+||||.+|.+.|++|+|+|
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=5.5e-83 Score=608.61 Aligned_cols=371 Identities=57% Similarity=0.913 Sum_probs=348.7
Q ss_pred hhhcChhhHHHHHHHHHhcccc---cCCCCCchhHHHHHHHHhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccC
Q 016722 6 AVLRHPDDLYPLLKLKMASRQA---EKQIPPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDD 82 (384)
Q Consensus 6 ~~~~hp~e~~~~~~~~~~~~~~---~~~~~~~~~~~~C~~~l~~~srSF~~a~~~Lp~~~R~av~alYaf~R~lD~I~D~ 82 (384)
.++.||+|++++++|| ..+. -.+.++ +.+..|++++..+||||+.+++.|+.++|+++|+||+++|++||++||
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 3332 223334 799999999999999999999999999999999999999999999999
Q ss_pred CCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHhhHHHHHHHHHhcCHHHHHHHHHHHHhhhhHHHhhhhhhcCCH
Q 016722 83 TSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFICKEVESI 162 (384)
Q Consensus 83 ~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~~~~v~~~~~~l~~~~~~lI~~i~~~m~~gm~~dl~~~~~t~ 162 (384)
|++|.+.|.+.|..|+..++..+|.|.+|.++++.++.+|+.+..+|.++.+.||++|.+||++||.||+.++..+++|+
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 016722 163 DDYDEYCYYVAGLVGLGLSKLFYASGTED--LAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKL 240 (384)
Q Consensus 163 ~dl~~Yc~~VAG~VG~~l~~l~~~~~~~~--~~~~~~A~~lG~alQltNIlRDv~eD~~~~~~gR~ylP~e~l~~~g~~~ 240 (384)
.|++.|||||||+||.+++++|.+++.++ ....+++++||++||+||||||+.||.. .||.|||+|+|++|..+.
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 99999999999999999999999877665 2334899999999999999999999999 799999999999999999
Q ss_pred hhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhccchhhhhHHHHHHHHHHHhcCCCCccCccccChHHHHH
Q 016722 241 EDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 320 (384)
Q Consensus 241 ~dl~~~~~~~~~~~~l~~lv~~A~~~~~~a~~y~~~L~~~~~~~f~aiP~~~AiatL~~~~~~~~vf~~~vki~k~~~~~ 320 (384)
+|+..++|.+.+.+|+++|+++|+.|.++++.|++.+..+++|+|||+||+||++||++||+|.+||+|+||||||....
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-----hHHHHHHHHHHHHHhhhcccccccccccccCC
Q 016722 321 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPN-----ATKTLSRVEAIQKACMDSGVLNKRFKILHYSK 384 (384)
Q Consensus 321 l~~~~~~~~~v~~~~~~~~~~~~~~~~~~dp~-----~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~ 384 (384)
+|+++.|+.+|+.+|++|.+.|+.|.+++||| ..++.+..++|.+.|.+.+++.++. .||+|
T Consensus 316 ~I~~~k~~~~v~~~f~~y~~~i~~k~d~~dpnflklsask~~qv~esl~~~~~~~~il~n~~--~~f~k 382 (413)
T KOG1459|consen 316 LILASKTMDKVRNIFYMYLRDIRMKFDEADPNFLKLSASKTEQVWESLLLYRRPDEILANRY--NNFTK 382 (413)
T ss_pred HHHhcccHHHHHHHHHHHHHHHHhhCCccCCCchhhhhhhHHHHHHHHHHhhcccccccccc--ccccc
Confidence 99999999999999999999999999999999 6677788888888999999998883 56654
No 3
>COG1562 ERG9 Phytoene/squalene synthetase [Lipid metabolism]
Probab=100.00 E-value=4e-54 Score=414.69 Aligned_cols=278 Identities=24% Similarity=0.312 Sum_probs=247.7
Q ss_pred CCchhHHHHHHHHhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccC
Q 016722 32 PPEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCG 111 (384)
Q Consensus 32 ~~~~~~~~C~~~l~~~srSF~~a~~~Lp~~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G 111 (384)
+...++.+|.++++.+|+|||+++++||+++|++|+++|+|||++|||+|+++.| +.....+.+|+..+... +. |
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 3567889999999999999999999999999999999999999999999999876 33344555555555431 23 4
Q ss_pred C-CcchHHHhhHHHHHHHHHhcCHHHHHHHHHHHHhhhhHHHhhhh-hhcCCHHHHHHHHHhhhhHHHHHHHHHhcccCC
Q 016722 112 T-KEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGT 189 (384)
Q Consensus 112 ~-~~~~~l~~~~~~v~~~~~~l~~~~~~lI~~i~~~m~~gm~~dl~-~~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~~~~ 189 (384)
. .+++|++.+|.+++++|..+.+.+.++|+ ||++|+. .++.|++||+.|||+|||+||.|+++|++..+
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 36789999999999999887777877776 9999997 78999999999999999999999999999643
Q ss_pred CCCChhHHHHHHHHHHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHH
Q 016722 190 EDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVED 269 (384)
Q Consensus 190 ~~~~~~~~A~~lG~alQltNIlRDv~eD~~~~~~gR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~~ 269 (384)
+......|..+|.|+|+||||||++||.. +||+|||+|+|.+||++.+|+.++.+.++++.|++.++.+|+.|+.+
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 23344678889999999999999999999 99999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcchhhccchhhhhHHHHHHHHHHHhcCCCCccCccccChHHHHHHHHHhcC
Q 016722 270 CLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNN 327 (384)
Q Consensus 270 a~~y~~~L~~~~~~~f~aiP~~~AiatL~~~~~~~~vf~~~vki~k~~~~~l~~~~~~ 327 (384)
+..++..+|.++.+.+|++|++++..+.+...++.+||++++.+++++++|+++++..
T Consensus 227 a~~~~~~lp~~~~~~~~~~~~~~~~~~~~i~a~~~~vl~~~~~l~~~~~~~~~~~~~~ 284 (288)
T COG1562 227 ARRGLPALPGRAQLAVLAAALLYAYLLDAIEADPADVLSQRAVLPKLRKLWLLLKAWL 284 (288)
T ss_pred HHHhhhhCCccccchhhHHHHHHHHHHHHHHccchhhhccCcccCcchHHHHHHHHHH
Confidence 9999999999998899999999999888888888999999999999999999988744
No 4
>PLN02632 phytoene synthase
Probab=100.00 E-value=2e-53 Score=419.53 Aligned_cols=275 Identities=20% Similarity=0.241 Sum_probs=243.3
Q ss_pred CchhHHHHHHHHhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCC
Q 016722 33 PEPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGT 112 (384)
Q Consensus 33 ~~~~~~~C~~~l~~~srSF~~a~~~Lp~~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~ 112 (384)
.++++.+|.++++.+|+|||+++++||++.|++++++|+|||++|||+|+.+.+. .+..+|+||++.+.. .|. |+
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 5789999999999999999999999999999999999999999999999877553 445689999999987 466 65
Q ss_pred CcchHHHhhHHHHHHHHHhcCHHHHHHHHHHHHhhhhHHHhhhh-hhcCCHHHHHHHHHhhhhHHHHHHHHHhcccCCCC
Q 016722 113 KEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTED 191 (384)
Q Consensus 113 ~~~~~l~~~~~~v~~~~~~l~~~~~~lI~~i~~~m~~gm~~dl~-~~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~~~~~~ 191 (384)
+ .+|+..++.+++..|..+...+.++|+ ||.+|+. .+++|++||+.|||+|||+||+|+++++|..+...
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 568899999999999877777888887 9999997 68999999999999999999999999998632111
Q ss_pred ---CChhHHHHHHHHHHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHH
Q 016722 192 ---LAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVE 268 (384)
Q Consensus 192 ---~~~~~~A~~lG~alQltNIlRDv~eD~~~~~~gR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~ 268 (384)
....+.|.++|.|||+||||||++||++ +||+|||.|+|.+||++.+|+..+.++++++.++.+++.+|+.||.
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 HHHHHHHhcchhhccchhhhhHHHHHHHHHHH-hcCCCCccCccccChHHHHHHHHHh
Q 016722 269 DCLKYMSALRDHAIFRFCAIPQIMAIGTLALC-YNNIEVFRGVVKMRRGLTAKVIDRT 325 (384)
Q Consensus 269 ~a~~y~~~L~~~~~~~f~aiP~~~AiatL~~~-~~~~~vf~~~vki~k~~~~~l~~~~ 325 (384)
+++.++..+|..+ ...+.++..+..+.|..+ .+|++||++++.+++++|+|++.++
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 9999999999876 224566666777777776 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=3.3e-53 Score=406.34 Aligned_cols=260 Identities=21% Similarity=0.231 Sum_probs=236.0
Q ss_pred hhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHhhHHH
Q 016722 45 HKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHH 124 (384)
Q Consensus 45 ~~~srSF~~a~~~Lp~~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~~~~ 124 (384)
+++|+|||+++++||+++|++++++|+|||++|||+|+.. ++..+..+|+||++.+.+ .+. |.+ .+|++.++..
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 556788999999999987 354 654 6789999999
Q ss_pred HHHHHHhcCHHHHHHHHHHHHhhhhHHHhhhh-hhcCCHHHHHHHHHhhhhHHHHHHHHHhcccCCCCCChhHHHHHHHH
Q 016722 125 VSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGL 203 (384)
Q Consensus 125 v~~~~~~l~~~~~~lI~~i~~~m~~gm~~dl~-~~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~~~~~~~~~~~~A~~lG~ 203 (384)
++..+..+.+.+.++|+ ||++|+. ++++|++||+.|||+|||+||+|++++++.. +....+.|+++|.
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 99999877777777776 9999997 7899999999999999999999999999852 2335689999999
Q ss_pred HHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhcc
Q 016722 204 FLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIF 283 (384)
Q Consensus 204 alQltNIlRDv~eD~~~~~~gR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~~a~~y~~~L~~~~~~ 283 (384)
|+|+||||||++||+. +||+|||.|+|.+||++.+||..++++++++.++.+++..|+.||.++..++..+|... .
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 016722 284 RFCAIPQIMAIGTLALCY-NNIEVFRGVVKMRRGLTAKVIDRT 325 (384)
Q Consensus 284 ~f~aiP~~~AiatL~~~~-~~~~vf~~~vki~k~~~~~l~~~~ 325 (384)
.++.++..++.++|..+. +|++||++++++++.++.|+++++
T Consensus 221 ~~~~~~~~~~~~iL~~i~~~~~~~~~~r~~~~~~~k~~~~~~~ 263 (266)
T TIGR03465 221 RAARAMAAIYRALLDEIEADGFQVLRQRVSLTPLRKLWIALRT 263 (266)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCcCCHHHHHHHHHHH
Confidence 567888899999998884 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=2.6e-53 Score=406.56 Aligned_cols=260 Identities=33% Similarity=0.501 Sum_probs=233.8
Q ss_pred HHHHHHhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHH
Q 016722 39 FCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVL 118 (384)
Q Consensus 39 ~C~~~l~~~srSF~~a~~~Lp~~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l 118 (384)
+|.++++++|+|||+++++||++.|++++++|+|||++|||+|+++.+...+..+|+||++.+.. .+. |....+|+
T Consensus 2 ~c~~~~~~~~~sf~~a~~~lp~~~R~~~~alYaf~r~~Ddi~D~~~~~~~~~~~~L~~w~~~l~~---~~~-~~~~~~pv 77 (265)
T cd00683 2 YCRAILRKGSRSFYLASRLLPPELRRAVCALYAFCRAADDIVDDPAAPPDEKLALLDAFRAELDA---AYW-GGAPTHPV 77 (265)
T ss_pred HHHHHHHHhCCcHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhCCCCCchhHHHHHHHHHHHHHH---HHc-CCCCCChH
Confidence 79999999999999999999999999999999999999999999887757788999999999987 355 55667889
Q ss_pred HhhHHHHHHHHHhcCHHHHHHHHHHHHhhhhHHHhhhh-hhcCCHHHHHHHHHhhhhHHHHHHHHHhcccCCCCCChhHH
Q 016722 119 MDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSL 197 (384)
Q Consensus 119 ~~~~~~v~~~~~~l~~~~~~lI~~i~~~m~~gm~~dl~-~~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~~~~~~~~~~~~ 197 (384)
+.+|..++..+..+...+.++|+ ||.+|+. .+++|++||+.|||+|||+||+|++++++.+ ......+.
T Consensus 78 ~~al~~~~~~~~l~~~~~~~li~--------g~~~Dl~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~~~~--~~~~~~~~ 147 (265)
T cd00683 78 LRALADLARRYGIPREPFRDLLA--------GMAMDLDKRRYETLDELDEYCYYVAGVVGLMLLRVFGAS--SDEAALER 147 (265)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHH--------HHHHhCCCCCCCCHHHHHHHHHHhHHHHHHHHHHHhCCC--CChHHHHH
Confidence 99999999998877777888887 9999997 6899999999999999999999999999852 22335689
Q ss_pred HHHHHHHHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 016722 198 SNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSAL 277 (384)
Q Consensus 198 A~~lG~alQltNIlRDv~eD~~~~~~gR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~~a~~y~~~L 277 (384)
|.++|.|+|+||||||++||++ +||+|||.|+|.+||++.+|+..+..+++++.++.+++..|+.|+..+..++..+
T Consensus 148 A~~lG~AlqltnilRdv~eD~~---~gR~YlP~d~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~l 224 (265)
T cd00683 148 ARALGLALQLTNILRDVGEDAR---RGRIYLPREELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAAL 224 (265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHc---cCCCcCCHHHHHHcCCCHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhC
Confidence 9999999999999999999998 9999999999999999999999999999999999999999999999999999999
Q ss_pred chhhccchhhhhHHHH-HHHHHHH-hcCCCCccCccccChHH
Q 016722 278 RDHAIFRFCAIPQIMA-IGTLALC-YNNIEVFRGVVKMRRGL 317 (384)
Q Consensus 278 ~~~~~~~f~aiP~~~A-iatL~~~-~~~~~vf~~~vki~k~~ 317 (384)
|... ++|++|.+++ ...+..+ .+++++|++++.+++.+
T Consensus 225 p~~~--~~~~~~~~~~y~~il~~i~~~~~~~~~~r~~~~~~~ 264 (265)
T cd00683 225 PRRS--RFCVRAAAMLYRTILDEIEARGYDVLSVRVRVPKAR 264 (265)
T ss_pred CHhh--HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Confidence 9765 7888888776 4444455 47899999999888765
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=5.5e-53 Score=404.84 Aligned_cols=261 Identities=17% Similarity=0.162 Sum_probs=234.6
Q ss_pred hhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHhhHHH
Q 016722 45 HKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHH 124 (384)
Q Consensus 45 ~~~srSF~~a~~~Lp~~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~~~~ 124 (384)
+++++|||+++++||++.|++++++|+|||++|||+|+.+.+++++..+|+||++.+.+ .+. |++ .+|++.++..
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 6789999999
Q ss_pred HHHHHHhcCHHHHHHHHHHHHhhhhHHHhhhh-hhcCCHHHHHHHHHhhhhHHHHHHHHHhcccCCCCCChhHHHHHHHH
Q 016722 125 VSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSMGL 203 (384)
Q Consensus 125 v~~~~~~l~~~~~~lI~~i~~~m~~gm~~dl~-~~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~~~~~~~~~~~~A~~lG~ 203 (384)
++.++..+.+.+.++|+ ||.+|+. .++.|++||+.|||+|||+||+|+++++|... ....+.|.++|.
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 99999887778888887 9999997 68999999999999999999999999998632 234578999999
Q ss_pred HHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhcc
Q 016722 204 FLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIF 283 (384)
Q Consensus 204 alQltNIlRDv~eD~~~~~~gR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~~a~~y~~~L~~~~~~ 283 (384)
|||+|||+||++||++ +||+|||.|+|.+||++.+|+.++..+++++.++.+++.+|+.||.+++.++..+|... .
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 016722 284 RFCAIPQIMAIGTLALC-YNNIEVFRGVVKMRRGLTAKVIDRT 325 (384)
Q Consensus 284 ~f~aiP~~~AiatL~~~-~~~~~vf~~~vki~k~~~~~l~~~~ 325 (384)
.++..+..+..++|..+ .++++||++++.+++.++.|+++++
T Consensus 222 ~~~~~~~~~y~~iL~~l~~~~~~~~~~r~~~~~~~kl~~~~~a 264 (266)
T TIGR03464 222 LELALIVRGGLRILEKIERQGYDVLRERPKLGKFDWAGLLLRA 264 (266)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCCCCCCcCCHHHHHHHHHHH
Confidence 34466666777788777 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=2.2e-50 Score=386.14 Aligned_cols=261 Identities=26% Similarity=0.309 Sum_probs=213.6
Q ss_pred HhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccc-cCCCcchHHHhhH
Q 016722 44 LHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFS-CGTKEYKVLMDQF 122 (384)
Q Consensus 44 l~~~srSF~~a~~~Lp~~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~-~G~~~~~~l~~~~ 122 (384)
|+++|+|||+++++||++.|++++++|+|||++|||+|+.+.+ ..+..+|+||++.+.+..+... .+.+..+|++.+|
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 5677799999999987321111 1235668999999
Q ss_pred HHHHHHHHhcCHHHHHHHHHHHHhhhhHHHhhhh-hhcCCHHHHHHHHHhhhhHHHHHHHHHhcccCCCCCChhHHHHHH
Q 016722 123 HHVSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTEDLAPDSLSNSM 201 (384)
Q Consensus 123 ~~v~~~~~~l~~~~~~lI~~i~~~m~~gm~~dl~-~~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~~~~~~~~~~~~A~~l 201 (384)
..+++.+..++..+.++|+ ||.+|+. ++++|++||+.||++|||+||.|++++++..+ ++....+.|.++
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 9999988876677777776 9999997 78999999999999999999999999998631 112356899999
Q ss_pred HHHHHHHHHHhchHhh-hhcCCCCCccccHHHHHhccCChhhhhccc-CCHHHHHHHHHHHHHHHHHHHHHHHHHHhcch
Q 016722 202 GLFLQKTNIIRDYLED-INEIPKCRMFWPREIWSKYVNKLEDLKYEE-NSDKAVQCLNDMVTNALMHVEDCLKYMSALRD 279 (384)
Q Consensus 202 G~alQltNIlRDv~eD-~~~~~~gR~ylP~e~l~~~g~~~~dl~~~~-~~~~~~~~l~~lv~~A~~~~~~a~~y~~~L~~ 279 (384)
|.|+|+||||||++|| +. +||+|||.|+|.+||++++|+..+. .+++++.++.+++..|..|+.+++.++..+|+
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 hhccchhhhhHHHHHHHHHHHh-cCCC-CccCccccChHH
Q 016722 280 HAIFRFCAIPQIMAIGTLALCY-NNIE-VFRGVVKMRRGL 317 (384)
Q Consensus 280 ~~~~~f~aiP~~~AiatL~~~~-~~~~-vf~~~vki~k~~ 317 (384)
.....+|.+|..++.++|..+. +|++ ||+++++++|++
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 6556788999999999999885 7888 899999999975
No 9
>KOG4411 consensus Phytoene/squalene synthetase [Lipid transport and metabolism]
Probab=99.94 E-value=5.8e-25 Score=199.54 Aligned_cols=255 Identities=14% Similarity=0.134 Sum_probs=203.2
Q ss_pred chhHHHHHHHHhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCC-
Q 016722 34 EPHWAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGT- 112 (384)
Q Consensus 34 ~~~~~~C~~~l~~~srSF~~a~~~Lp~~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~- 112 (384)
..++. |.+.++..+...|++...||.++|.++.++-||+.++..|.-|....+.+..++|+||++.|+. .|. -.
T Consensus 9 ~~A~s-c~~~vr~ydy~~ylc~l~lp~e~r~aafaLrAfNVE~ar~~~d~~~~p~ia~mRL~fW~daIdk---~y~-~~p 83 (292)
T KOG4411|consen 9 RSALS-CVQQVRNYDYHHYLCLLELPTEMRKAAFALRAFNVELARIKVDTRKGPAIAMMRLQFWKDAIDK---IYG-ISP 83 (292)
T ss_pred hhHHH-HHHHHHhhhHHHHHHHHhCcHHHHHHHHHHHHhhHHHHHHhhccccCcHHHHHHHHHHHHHHHH---HcC-CCC
Confidence 34555 9999999999999999999999999999999999999997666666677889999999999987 464 12
Q ss_pred --CcchHHHhhHHHHHHHHHhcCHHHHHHHHHHHHhhhhHHHhhhh-hhcCCHHHHHHHHHhhhhHHHHHHHHHhcccCC
Q 016722 113 --KEYKVLMDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGT 189 (384)
Q Consensus 113 --~~~~~l~~~~~~v~~~~~~l~~~~~~lI~~i~~~m~~gm~~dl~-~~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~~~~ 189 (384)
.++.|++.++-.++...+.-...+..++ ++...+.. +.++++.||++|... |+|-+++-.+.+.|.
T Consensus 84 ~~v~~qPva~aL~~~~~~~~~nk~~L~rlV--------~aR~r~~~d~~fesI~eLeeY~e~---TissLL~l~l~agg~ 152 (292)
T KOG4411|consen 84 LPVPRQPVAIALCSFAAGHNANKDMLLRLV--------EARQRTIGDRQFESINELEEYGES---TISSLLCLQLDAGGK 152 (292)
T ss_pred CCCCCcHHHHHHHHHHhccccCHHHHHHHH--------HHhhcCCcccchHHHHHHHHHHHh---HHHHHHHHHHHhcCc
Confidence 2567888889888887644333334444 48888774 679999999999988 555555555555455
Q ss_pred CCCChhHHHHHHHHHHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhh-hcccCCHHHHHHHHHHHHHHHHHHH
Q 016722 190 EDLAPDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDL-KYEENSDKAVQCLNDMVTNALMHVE 268 (384)
Q Consensus 190 ~~~~~~~~A~~lG~alQltNIlRDv~eD~~~~~~gR~ylP~e~l~~~g~~~~dl-~~~~~~~~~~~~l~~lv~~A~~~~~ 268 (384)
..+.+++.|.|+|.|.+++|.||.++.... +|-.|+|.|++..||++..|+ .+....++...|+.+++..|..|+.
T Consensus 153 ~~~~AdhaAshlGkA~gia~llrs~p~~~~---r~~~~iPadv~~lhGvtq~~il~~k~~~~g~~~~~fd~as~an~hL~ 229 (292)
T KOG4411|consen 153 VLPMADHAASHLGKAYGIANLLRSTPPLLA---RGIVLIPADVMSLHGVTQLDILYKKKKLDGMVGMTFDLASEANRHLI 229 (292)
T ss_pred cccchHHHHHHHhHHHHHHHHHHhccHHHh---CCCccccHHHHHHcCCCHHHHHhhccchhhhhhHHHHHHHHHHHHHH
Confidence 566678999999999999999999999999 999999999999999999665 4566788999999999999999999
Q ss_pred HHHHHHHhcchhhccchhhhhHHHHHHHHHHH-hcCCCCccC
Q 016722 269 DCLKYMSALRDHAIFRFCAIPQIMAIGTLALC-YNNIEVFRG 309 (384)
Q Consensus 269 ~a~~y~~~L~~~~~~~f~aiP~~~AiatL~~~-~~~~~vf~~ 309 (384)
+|+..+..+|.+. +...+..+-.-..|+.+ .+||++|++
T Consensus 230 ~AR~l~~kVP~~v--rp~ll~tv~td~~l~~l~k~nfdi~~p 269 (292)
T KOG4411|consen 230 DARSLIEKVPKAV--RPALLATVTTDYILKTLEKNNFDIYSP 269 (292)
T ss_pred HHHhHhhhCCHHH--HHHHHHhhhHHHHHHHHHHccccccCH
Confidence 9999999999874 22222222222233333 389999986
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=99.79 E-value=7.7e-19 Score=164.66 Aligned_cols=169 Identities=24% Similarity=0.247 Sum_probs=126.6
Q ss_pred cHHHHHHhcCh----------hhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHH-HHHHHcccccccccCCCcchHH
Q 016722 50 SFALVIQQLGT----------DLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIA-FHRHVYDREWHFSCGTKEYKVL 118 (384)
Q Consensus 50 SF~~a~~~Lp~----------~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~-~~~~l~~~~~~~~~G~~~~~~l 118 (384)
+|++++.++|+ +++.++.++|++++..|||.|+.+.+. .+.....+ |...+.. ...+.++
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 57888999999 999999999999999999999976542 23344555 5444321 1234556
Q ss_pred HhhHHHHHHHHHhcCHHHHHHHHHHHHhhhhHHHhhhh-hh--cCCHHHHHHHHHh-hhhHHHHHHHHHhcccCCCC---
Q 016722 119 MDQFHHVSTAFLELGKGYQDAIEDITKRMGAGMAKFIC-KE--VESIDDYDEYCYY-VAGLVGLGLSKLFYASGTED--- 191 (384)
Q Consensus 119 ~~~~~~v~~~~~~l~~~~~~lI~~i~~~m~~gm~~dl~-~~--~~t~~dl~~Yc~~-VAG~VG~~l~~l~~~~~~~~--- 191 (384)
...|..+.... .....+++.+....|..|+..|+. .. +.|+++|..||++ ||++||.++..+...++.+.
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 66666655411 222344555666677789999997 33 8999999999999 99999998888876543221
Q ss_pred CChhHHHHHHHHHHHHHHHHhchHhhh----------hcCCCCCccccHHHH
Q 016722 192 LAPDSLSNSMGLFLQKTNIIRDYLEDI----------NEIPKCRMFWPREIW 233 (384)
Q Consensus 192 ~~~~~~A~~lG~alQltNIlRDv~eD~----------~~~~~gR~ylP~e~l 233 (384)
.....++.++|+|+|++|++||+.+|. . .||+|||...+
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=99.72 E-value=9.8e-17 Score=147.08 Aligned_cols=217 Identities=22% Similarity=0.158 Sum_probs=160.8
Q ss_pred cHHHHHHhcCh--hhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHhhHHHHHH
Q 016722 50 SFALVIQQLGT--DLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVST 127 (384)
Q Consensus 50 SF~~a~~~Lp~--~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~~~~v~~ 127 (384)
+|++++.++|+ +.|.++..+|++++.+|||.|+...+. .+.....+| . ..+. ... ....+.++...+..+..
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 999999999999999999999886543 233344444 1 1110 000 11223344444444433
Q ss_pred HHHhcCHHHHHHHHHHHHhhhhHHHhhhhh-h--cCCHHHHHHHHHhh-hhHHHHHHHHHhcccCCC---CCChhHHHHH
Q 016722 128 AFLELGKGYQDAIEDITKRMGAGMAKFICK-E--VESIDDYDEYCYYV-AGLVGLGLSKLFYASGTE---DLAPDSLSNS 200 (384)
Q Consensus 128 ~~~~l~~~~~~lI~~i~~~m~~gm~~dl~~-~--~~t~~dl~~Yc~~V-AG~VG~~l~~l~~~~~~~---~~~~~~~A~~ 200 (384)
.. +....+.+.+.+..+..|+..|+.. . +.|++||..||+++ ++++|.++....+..+.+ ......++.+
T Consensus 75 ~~---~~~~~~~~~~~~~~~~~g~~~d~~~~~~~~~t~~ey~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 151 (243)
T cd00385 75 EG---SPEALEILAEALLDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCLLGAGLSGGEAELLEALRKLGRA 151 (243)
T ss_pred CC---CHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 21 1234455556667777899999974 3 89999999999999 999998887777653221 1223478999
Q ss_pred HHHHHHHHHHHhchHhhhhcCCC--CCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 016722 201 MGLFLQKTNIIRDYLEDINEIPK--CRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALR 278 (384)
Q Consensus 201 lG~alQltNIlRDv~eD~~~~~~--gR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~~a~~y~~~L~ 278 (384)
+|.++|++|.++|+..|.. . ||+++|...+.++|++.+++..+..++...++++.+...+...+.+.......++
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 8999999999999999999888888888888888888888888887776665554
No 12
>KOG1459 consensus Squalene synthetase [Lipid transport and metabolism]
Probab=98.75 E-value=7.2e-08 Score=93.89 Aligned_cols=205 Identities=10% Similarity=-0.010 Sum_probs=142.2
Q ss_pred HHHhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHhh
Q 016722 42 SMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQ 121 (384)
Q Consensus 42 ~~l~~~srSF~~a~~~Lp~~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~ 121 (384)
++....-+.|+......-++.+.+++.+|-+||.+|-+++..-. .-.-...|+.|....++ .+. |.+ +.-.
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 45555666788888777777799999999999999999997531 11222344444444433 122 222 2111
Q ss_pred HHHHHHHHHhcC---HHHH-HHHHHHHHhhhhHHHhh-hh-hhcCCHHHHHHHHHhhhhHHHHHHHHHhcc--cCCCCCC
Q 016722 122 FHHVSTAFLELG---KGYQ-DAIEDITKRMGAGMAKF-IC-KEVESIDDYDEYCYYVAGLVGLGLSKLFYA--SGTEDLA 193 (384)
Q Consensus 122 ~~~v~~~~~~l~---~~~~-~lI~~i~~~m~~gm~~d-l~-~~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~--~~~~~~~ 193 (384)
=..+++.|..-+ .+|. +.| -||-+| +. -.++..+|+-.||+++++++|.+-....-. ++..+..
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 333 398888 54 479999999999999999999875444311 2223333
Q ss_pred hhHHHHHHHHHHHHHHHHhchHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHH
Q 016722 194 PDSLSNSMGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLK 272 (384)
Q Consensus 194 ~~~~A~~lG~alQltNIlRDv~eD~~~~~~gR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~~a~~ 272 (384)
.-..+--.|++-|.||++++..||.- +|++++|+ |.+.+++.++++.++++.++.....++...++++.+
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 888999999999999999888887777776665554
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=95.49 E-value=1.4 Score=41.98 Aligned_cols=128 Identities=15% Similarity=0.075 Sum_probs=79.2
Q ss_pred HHHHHHHHHHhhhhHHHhhhhh---hcCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC---CChhHHHHHHHHHHHHH
Q 016722 136 YQDAIEDITKRMGAGMAKFICK---EVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED---LAPDSLSNSMGLFLQKT 208 (384)
Q Consensus 136 ~~~lI~~i~~~m~~gm~~dl~~---~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~-~~~~~---~~~~~~A~~lG~alQlt 208 (384)
..+.+.+....|..|...|+.. ...|++++..-+.+-.|....+++.+.+. ++.+. .....++.++|+++|+.
T Consensus 109 ~~~~~~~~~~~~~~GQ~~d~~~~~~~~~~~~~y~~~~~~KT~~l~~~~~~~~a~l~~~~~~~~~~l~~~g~~lG~afQi~ 188 (259)
T cd00685 109 ALELFSEAILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEALKRFGRNLGLAFQIQ 188 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555666778898888863 26789999988877777766666554432 11111 12347899999999999
Q ss_pred HHHhchHhhhhcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcchh
Q 016722 209 NIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH 280 (384)
Q Consensus 209 NIlRDv~eD~~~~~~gR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~~a~~y~~~L~~~ 280 (384)
|=+.|+.-|..+ .|+- ..+|+.+++.+=.+.-++ -..+..+..++...++.++..
T Consensus 189 DD~ld~~~~~~~--~gK~------------~~~Di~~gk~T~~~~~~l---~~~~~~~~~~a~~~l~~~~~~ 243 (259)
T cd00685 189 DDILDLFGDPET--LGKP------------VGSDLREGKCTLPVLLAL---RELAREYEEKALEALKALPES 243 (259)
T ss_pred HHhhcccCChHH--HCCC------------cchHHHcCCchHHHHHHH---HHHHHHHHHHHHHHHHcCCCc
Confidence 987777544321 1221 124555555443333222 456677777788888888755
No 14
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=94.88 E-value=3.5 Score=40.88 Aligned_cols=93 Identities=12% Similarity=0.116 Sum_probs=63.8
Q ss_pred HHHHHHHHHHHhhhhHHHhhhh---hhcCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC---CChhHHHHHHHHHHHH
Q 016722 135 GYQDAIEDITKRMGAGMAKFIC---KEVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED---LAPDSLSNSMGLFLQK 207 (384)
Q Consensus 135 ~~~~lI~~i~~~m~~gm~~dl~---~~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~-~~~~~---~~~~~~A~~lG~alQl 207 (384)
.+.+++.+....|..|-..|+. +.-.|.++|..-+.+=.|....+.+.+-+. +|.+. .....++.++|+|+|+
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 3445566666777788888874 234688888887777777776666654332 22221 1123789999999999
Q ss_pred HHHHhch-----------HhhhhcCCCCCccccH
Q 016722 208 TNIIRDY-----------LEDINEIPKCRMFWPR 230 (384)
Q Consensus 208 tNIlRDv-----------~eD~~~~~~gR~ylP~ 230 (384)
.+=+-|+ +.|+. .|.+=||.
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 15
>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=94.86 E-value=1.9 Score=42.74 Aligned_cols=93 Identities=20% Similarity=0.169 Sum_probs=58.1
Q ss_pred HHHHHHHHHHHhhhhHHHhhhhh---hcCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC---CChhHHHHHHHHHHHH
Q 016722 135 GYQDAIEDITKRMGAGMAKFICK---EVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED---LAPDSLSNSMGLFLQK 207 (384)
Q Consensus 135 ~~~~lI~~i~~~m~~gm~~dl~~---~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~-~~~~~---~~~~~~A~~lG~alQl 207 (384)
...+.+.+....|..|...|+.. .-.|.++|..-..+=.|.....++.+-.. +|.++ .....++.++|+|+|+
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 24577887765555444444434433221 22221 1234788999999999
Q ss_pred HHHHhch-----------HhhhhcCCCCCccccH
Q 016722 208 TNIIRDY-----------LEDINEIPKCRMFWPR 230 (384)
Q Consensus 208 tNIlRDv-----------~eD~~~~~~gR~ylP~ 230 (384)
.+=+.|+ +.|+. .|.+=||-
T Consensus 213 ~DDild~~~~~~~~GK~~g~Dl~---~Gk~Tlp~ 243 (322)
T TIGR02749 213 VDDILDFTGSTEQLGKPAGSDLM---KGNLTAPV 243 (322)
T ss_pred HHHhccCCCChHhhCCChhHHHh---CCCchHHH
Confidence 9888884 57777 58888885
No 16
>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=93.96 E-value=3.5 Score=40.77 Aligned_cols=93 Identities=15% Similarity=0.093 Sum_probs=61.4
Q ss_pred HHHHHHHHHHHhhhhHHHhhhhh---hcCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC---CChhHHHHHHHHHHHH
Q 016722 135 GYQDAIEDITKRMGAGMAKFICK---EVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED---LAPDSLSNSMGLFLQK 207 (384)
Q Consensus 135 ~~~~lI~~i~~~m~~gm~~dl~~---~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~-~~~~~---~~~~~~A~~lG~alQl 207 (384)
...+.+.+.+..|..|-..|+.. .-.|.++|..-++.=.|......+.+-.. +|..+ .....++.++|+|+|+
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 34455666677788898777752 24578887777766666665554444221 22221 1123788999999999
Q ss_pred HHHHhchH-----------hhhhcCCCCCccccH
Q 016722 208 TNIIRDYL-----------EDINEIPKCRMFWPR 230 (384)
Q Consensus 208 tNIlRDv~-----------eD~~~~~~gR~ylP~ 230 (384)
.|=+.|+- .|+. .|..=||-
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 68888886
No 17
>CHL00151 preA prenyl transferase; Reviewed
Probab=92.42 E-value=7.6 Score=38.43 Aligned_cols=139 Identities=17% Similarity=0.125 Sum_probs=69.2
Q ss_pred HHHHHHHhhhhHHHhhhh---hhcCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC---CChhHHHHHHHHHHHHHHHH
Q 016722 139 AIEDITKRMGAGMAKFIC---KEVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED---LAPDSLSNSMGLFLQKTNII 211 (384)
Q Consensus 139 lI~~i~~~m~~gm~~dl~---~~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~-~~~~~---~~~~~~A~~lG~alQltNIl 211 (384)
.+.+....+..|...+.. +.-.|.+++..=+++=.|......+.+-.. +|... .....++.++|+|+|+.+=+
T Consensus 138 ~~~~~~~~l~~G~~~~~~~~~~~~~~~~~yl~~i~~KTa~L~~~~~~~ga~lag~~~~~~~~l~~~G~~lG~aFQi~DDi 217 (323)
T CHL00151 138 LISKVITDFAEGEIRQGLVQFDTTLSILNYIEKSFYKTASLIAASCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDV 217 (323)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444445456544432 223456665553333333333333333211 22211 12347889999999999888
Q ss_pred hch-----------HhhhhcCCCCCccccHHHHHhccCChhhhh-cccCC-HHHHHH---------HHHHHHHHHHHHHH
Q 016722 212 RDY-----------LEDINEIPKCRMFWPREIWSKYVNKLEDLK-YEENS-DKAVQC---------LNDMVTNALMHVED 269 (384)
Q Consensus 212 RDv-----------~eD~~~~~~gR~ylP~e~l~~~g~~~~dl~-~~~~~-~~~~~~---------l~~lv~~A~~~~~~ 269 (384)
.|+ +.|+. .|..=||-=..-+.......+. ....+ +...++ +.+....+..|..+
T Consensus 218 lD~~~~~~~~GK~~g~Dl~---eGk~Tlp~l~al~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~g~~~~a~~~a~~~~~~ 294 (323)
T CHL00151 218 LDITSSTESLGKPIGSDLK---NGNLTAPVLFALTQNSKLAKLIEREFCETKDISQALQIIKETNGIEKAKDLALEHMQA 294 (323)
T ss_pred hhcccChhhhCCCchhhHh---cCchHHHHHHHHhcChHHHHHHHHhcCCHHHHHHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 885 56787 6888888521111100011111 11111 112112 33444557777788
Q ss_pred HHHHHHhcchh
Q 016722 270 CLKYMSALRDH 280 (384)
Q Consensus 270 a~~y~~~L~~~ 280 (384)
|...+..+|..
T Consensus 295 A~~~L~~lp~~ 305 (323)
T CHL00151 295 AIQCLKFLPPS 305 (323)
T ss_pred HHHHHHhCCCC
Confidence 88888887754
No 18
>PRK10581 geranyltranstransferase; Provisional
Probab=92.37 E-value=2.9 Score=40.98 Aligned_cols=121 Identities=18% Similarity=0.140 Sum_probs=74.3
Q ss_pred hhhhHHHhhhh--hhcCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC----CChhHHHHHHHHHHHHHHHHhchHhhh
Q 016722 146 RMGAGMAKFIC--KEVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED----LAPDSLSNSMGLFLQKTNIIRDYLEDI 218 (384)
Q Consensus 146 ~m~~gm~~dl~--~~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~-~~~~~----~~~~~~A~~lG~alQltNIlRDv~eD~ 218 (384)
.|..|-..|+. ....|.++|..-+++=.|......+.+-+. +|..+ .....++.++|+|+|+.+=+.|+--|.
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 235678888877765555554444433221 22211 112378999999999998888774443
Q ss_pred hcCCCCCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcchh
Q 016722 219 NEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH 280 (384)
Q Consensus 219 ~~~~~gR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~~a~~y~~~L~~~ 280 (384)
. .++|-. -.|+.+++.+-.....+......+..++.+|...+..+|+.
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 222211 14555555555555555566677888888888888888754
No 19
>PLN02857 octaprenyl-diphosphate synthase
Probab=92.13 E-value=2.1 Score=44.00 Aligned_cols=93 Identities=20% Similarity=0.211 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHhhhhHHHhhhh---hhcCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC---CChhHHHHHHHHHHHH
Q 016722 135 GYQDAIEDITKRMGAGMAKFIC---KEVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED---LAPDSLSNSMGLFLQK 207 (384)
Q Consensus 135 ~~~~lI~~i~~~m~~gm~~dl~---~~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~-~~~~~---~~~~~~A~~lG~alQl 207 (384)
...+++.+.+..|..|...++. +.-.|.++|..-.++=.|......+.+-.. +|.+. .....++.++|+|+|+
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 4455666667777778766553 234578888776666555555544443321 22221 1234789999999999
Q ss_pred HHHHhch-----------HhhhhcCCCCCccccH
Q 016722 208 TNIIRDY-----------LEDINEIPKCRMFWPR 230 (384)
Q Consensus 208 tNIlRDv-----------~eD~~~~~~gR~ylP~ 230 (384)
.+=+.|+ +.|+. .|..=||.
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 58888885
No 20
>PLN02890 geranyl diphosphate synthase
Probab=92.09 E-value=2.3 Score=43.85 Aligned_cols=143 Identities=14% Similarity=0.140 Sum_probs=82.0
Q ss_pred HHHHHHHHHHHhhhhHHHhhhhh---hcCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC---CChhHHHHHHHHHHHH
Q 016722 135 GYQDAIEDITKRMGAGMAKFICK---EVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED---LAPDSLSNSMGLFLQK 207 (384)
Q Consensus 135 ~~~~lI~~i~~~m~~gm~~dl~~---~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~-~~~~~---~~~~~~A~~lG~alQl 207 (384)
...+++.+.+..|..|-..|+.. .-.|+++|..-.++=.|.....++.+-+. +|... .....++.++|+|+|+
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 34455666677788898888753 34688888876666556555555543221 22221 1124789999999999
Q ss_pred HHHHhchH-----------hhhhcCCCCCccccHHHHHhccCChhhhh-cccCCH-HH---HHH------HHHHHHHHHH
Q 016722 208 TNIIRDYL-----------EDINEIPKCRMFWPREIWSKYVNKLEDLK-YEENSD-KA---VQC------LNDMVTNALM 265 (384)
Q Consensus 208 tNIlRDv~-----------eD~~~~~~gR~ylP~e~l~~~g~~~~dl~-~~~~~~-~~---~~~------l~~lv~~A~~ 265 (384)
.+=+-|+- .|+. .|.+=||-=..-+..-....+. .+..++ .+ .+. +..-...|..
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 5888788622111110111111 111111 11 111 2333445677
Q ss_pred HHHHHHHHHHhcchh
Q 016722 266 HVEDCLKYMSALRDH 280 (384)
Q Consensus 266 ~~~~a~~y~~~L~~~ 280 (384)
|..+|...+..+|+.
T Consensus 384 ~~~~A~~~L~~lp~s 398 (422)
T PLN02890 384 HANLAAAAIESLPET 398 (422)
T ss_pred HHHHHHHHHHhCCCC
Confidence 778888888777755
No 21
>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=90.43 E-value=5.6 Score=37.92 Aligned_cols=82 Identities=16% Similarity=0.141 Sum_probs=53.4
Q ss_pred HHHHHHHHHHhhhhHHHh---hhhhh--cCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC---CChhHHHHHHHHHHH
Q 016722 136 YQDAIEDITKRMGAGMAK---FICKE--VESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED---LAPDSLSNSMGLFLQ 206 (384)
Q Consensus 136 ~~~lI~~i~~~m~~gm~~---dl~~~--~~t~~dl~~Yc~~VAG~VG~~l~~l~~~-~~~~~---~~~~~~A~~lG~alQ 206 (384)
...+++.+...++.|+.. |+... ..|+++|..-+.+=.|+...+.+++-.. +|... .....++.++|+|+|
T Consensus 104 ~~~i~~~~~~~~~~~~~~q~~d~~~~~~~~~~~~y~~i~~~KTg~l~~~~~~~ga~lag~~~~~~~~l~~~g~~lG~afQ 183 (260)
T PF00348_consen 104 VLRILELFIEALIEGEIGQALDLANEDKDPTEEEYLEIIRLKTGSLFALACQLGAILAGADEEQIEALREFGRHLGIAFQ 183 (260)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTTTSSTSHHHHHHHHHHHTHHHHHHHHHHHHHHTTSGHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcccceeehhhccccccccccHHHHHHHHhhcchHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHh
Confidence 344555555445445443 44333 7799999998888888877777666543 22221 123378999999999
Q ss_pred HHHHHhchHhh
Q 016722 207 KTNIIRDYLED 217 (384)
Q Consensus 207 ltNIlRDv~eD 217 (384)
+.|=+.|+.-|
T Consensus 184 i~DD~~d~~~~ 194 (260)
T PF00348_consen 184 IRDDLLDLFGD 194 (260)
T ss_dssp HHHHHHHHHSH
T ss_pred hhhhhhhccCc
Confidence 99977777644
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=87.28 E-value=12 Score=37.76 Aligned_cols=146 Identities=14% Similarity=0.123 Sum_probs=77.0
Q ss_pred HHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHhhHHHHHHHHHhc
Q 016722 53 LVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAFLEL 132 (384)
Q Consensus 53 ~a~~~Lp~~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~~~~v~~~~~~l 132 (384)
.+-..+|.+.+-.|.+++++.-.+||+.++.. .-+..|++.+-. |++..+|++..|...+..+...
T Consensus 76 ~~y~~~~~evqv~IaiyT~yvi~iDD~~~~~~-------~~l~~F~~~l~~-------Gq~Q~~p~L~~~~~~L~~~~~~ 141 (376)
T PF06330_consen 76 YCYPHLPKEVQVAIAIYTTYVIIIDDSSQEPS-------DDLRTFHQRLIL-------GQPQKHPLLDGFASLLREMWRH 141 (376)
T ss_dssp HHSTTS-HHHHHHHHHHHHHHHHHTT--S-SH-------HHHTTHHHHHHH-------T---SSHHHHHHHHHHHHHHTT
T ss_pred eecCCCCHHHHHHHHHHHHHHHhccccccccc-------HHHHHHHHHHhc-------CCCCCCHHHHHHHHHHHHHHHH
Confidence 33467899999999999999999999977642 255667776654 6666678999999988877655
Q ss_pred CHHH-HHHHHHHHHhhhhHH--Hhhhhhhc---CCHHHHHHHHHhhhhHHHHHHHHHhcccCCCC-CChhHHHHHHHHHH
Q 016722 133 GKGY-QDAIEDITKRMGAGM--AKFICKEV---ESIDDYDEYCYYVAGLVGLGLSKLFYASGTED-LAPDSLSNSMGLFL 205 (384)
Q Consensus 133 ~~~~-~~lI~~i~~~m~~gm--~~dl~~~~---~t~~dl~~Yc~~VAG~VG~~l~~l~~~~~~~~-~~~~~~A~~lG~al 205 (384)
=.++ -++|-.-+-+..+|. +..-.+.. ..+.++.+=..+++.+.+.+ +|-.+..++ .....+...+.-..
T Consensus 142 fgpf~anmI~~STLdFi~g~~LE~~~f~~~p~A~~FP~fLR~ktGlsEaYA~F---iFPk~~fpe~~~~~~y~~AIpdl~ 218 (376)
T PF06330_consen 142 FGPFCANMIVKSTLDFINGCWLEQKNFHGSPGAPDFPDFLRRKTGLSEAYAFF---IFPKALFPEVEYFIQYTPAIPDLM 218 (376)
T ss_dssp S-HHHHHHHHHHHHHHHHHHHHHTTT----TT-TTHHHHHHHHHH-HHHHHHH---T--TTTS-TTTTHHHHHHHHHHHH
T ss_pred cchHHHHHHHHHHHHHHHHHHhhcccCCCCCCCccccHHHHhccCcchhheee---ecccccCChHHHHHHHHHHHHHHH
Confidence 4554 233332222222232 22111112 24555555555555444433 343221111 11224444566666
Q ss_pred HHHHHHhchH
Q 016722 206 QKTNIIRDYL 215 (384)
Q Consensus 206 QltNIlRDv~ 215 (384)
..+|++-||.
T Consensus 219 ~fi~~~NDIL 228 (376)
T PF06330_consen 219 RFINYVNDIL 228 (376)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHhhhhHH
Confidence 6777777765
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=80.06 E-value=52 Score=30.71 Aligned_cols=173 Identities=14% Similarity=0.022 Sum_probs=87.9
Q ss_pred hhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccc-cccccCCCcchHHHhhHHHHHHHHHhcCH-H-H
Q 016722 60 TDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDRE-WHFSCGTKEYKVLMDQFHHVSTAFLELGK-G-Y 136 (384)
Q Consensus 60 ~~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~-~~~~~G~~~~~~l~~~~~~v~~~~~~l~~-~-~ 136 (384)
++.+..++-+..+.-.+||+-|+.+. ... ++.+.+.+..-. .....+....+++..++..+..+....-. . .
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 56677888999999999999997642 222 444544444100 01111233445676777777666543221 1 2
Q ss_pred HH-HHHHHH---HhhhhHHHhhhh----hhcCCHHHHHHHHHhhhhHHHHHHHHHhccc--CCCCC-----ChhHHHHHH
Q 016722 137 QD-AIEDIT---KRMGAGMAKFIC----KEVESIDDYDEYCYYVAGLVGLGLSKLFYAS--GTEDL-----APDSLSNSM 201 (384)
Q Consensus 137 ~~-lI~~i~---~~m~~gm~~dl~----~~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~~--~~~~~-----~~~~~A~~l 201 (384)
+. .+..+. .+...|...... ..++|++||..+=..++|.--.+..-.++-. ..+.+ ....+....
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 122223332222 2388888888887777776444444333221 00100 001245556
Q ss_pred HHHHHHHHHHhchHhhhhcCCCCCc--cccHHHHHhccCChh
Q 016722 202 GLFLQKTNIIRDYLEDINEIPKCRM--FWPREIWSKYVNKLE 241 (384)
Q Consensus 202 G~alQltNIlRDv~eD~~~~~~gR~--ylP~e~l~~~g~~~~ 241 (384)
+...-++|=|-.+..+.. .|.. .++- ++..+|++.+
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 677777777777777776 4554 4433 4444465443
No 24
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=77.13 E-value=64 Score=31.92 Aligned_cols=82 Identities=16% Similarity=0.150 Sum_probs=51.0
Q ss_pred HHHHHHHHHHhhhhHHHhhhhh--hcCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCC-C--CChhHHHHHHHHHHHHHH
Q 016722 136 YQDAIEDITKRMGAGMAKFICK--EVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTE-D--LAPDSLSNSMGLFLQKTN 209 (384)
Q Consensus 136 ~~~lI~~i~~~m~~gm~~dl~~--~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~-~~~~-~--~~~~~~A~~lG~alQltN 209 (384)
....+.+-+..|..|-..|+.. ...|.++|..=-+.=.|..-...+.+-+. ++.. . .....++..+|+|+|+.+
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 3445566777888899999862 33677777665554444444444433322 2211 1 223478999999999998
Q ss_pred HHhchHhh
Q 016722 210 IIRDYLED 217 (384)
Q Consensus 210 IlRDv~eD 217 (384)
=+=|+--|
T Consensus 215 DiLD~~~d 222 (322)
T COG0142 215 DILDITGD 222 (322)
T ss_pred HhhcCCCC
Confidence 77776644
No 25
>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=74.96 E-value=1.2e+02 Score=32.24 Aligned_cols=234 Identities=16% Similarity=0.128 Sum_probs=113.7
Q ss_pred cChhhHHHHHHHHHhcccccCCCC-CchhHHHHHHHHhhcCCcHHHHHHhcC--hhhhhHHHHHHHHHHhhhhhccCCCC
Q 016722 9 RHPDDLYPLLKLKMASRQAEKQIP-PEPHWAFCYSMLHKVSRSFALVIQQLG--TDLRNAVCIFYLVLRALDTVEDDTSI 85 (384)
Q Consensus 9 ~hp~e~~~~~~~~~~~~~~~~~~~-~~~~~~~C~~~l~~~srSF~~a~~~Lp--~~~R~av~alYaf~R~lD~I~D~~~~ 85 (384)
.|=.||..+.+|.--..-.. .++ .++-+..|+ -..+++.+-| ...|-.++-+-.+.-.+||+=|.-..
T Consensus 235 ~hq~El~~~~rWwk~~gL~~-~l~~aRdr~ve~y--------f~~~a~~feP~~s~~Rl~~aK~~~l~~~iDD~fD~~gt 305 (542)
T cd00684 235 LHQEELKILSRWWKDLDLAS-KLPFARDRLVECY--------FWAAGTYFEPQYSLARIALAKTIALITVIDDTYDVYGT 305 (542)
T ss_pred hHHHHHHHHhHHHHhcCCcc-cCCcccchhHHHH--------HHHHhcccCccchHHHHHHHHHHHHHhhhHhhhccCCC
Confidence 58899999988754322111 111 122233332 1223344444 23455566677777788999885431
Q ss_pred ChhhhHHHHHHHHHHHcccccccc--cCCC-cchHHHhhHHHHHHHHHh----c-CHHHHHHHHHHHHhhhhHHHhhhh-
Q 016722 86 PTDVKVPILIAFHRHVYDREWHFS--CGTK-EYKVLMDQFHHVSTAFLE----L-GKGYQDAIEDITKRMGAGMAKFIC- 156 (384)
Q Consensus 86 ~~~~k~~~L~~~~~~l~~~~~~~~--~G~~-~~~~l~~~~~~v~~~~~~----l-~~~~~~lI~~i~~~m~~gm~~dl~- 156 (384)
...|+.|-+.+.. |.-. .+-| ..+++..++..+..++.. - +.....-+.+..++...|+.....
T Consensus 306 -----~eEl~~ft~ai~r--wd~~~~~~lPe~mk~~~~al~~~~~ei~~~~~~~~~~~~~~~~~~~~~~~~~a~l~EA~w 378 (542)
T cd00684 306 -----LEELELFTEAVER--WDISAIDQLPEYMKIVFKALLNTVNEIEEELLKEGGSYVVPYLKEAWKDLVKAYLVEAKW 378 (542)
T ss_pred -----HHHHHHHHHHHHh--ccccchhhccHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHH
Confidence 2356666666653 3211 0111 123455555554443221 0 001112222333333446555553
Q ss_pred ---hhcCCHHHHHHHHHhhhhHHHHHHHHHhcccCCCC-CCh-------hHHHHHHHHHHHHHHHHhchHhhhhcCCCCC
Q 016722 157 ---KEVESIDDYDEYCYYVAGLVGLGLSKLFYASGTED-LAP-------DSLSNSMGLFLQKTNIIRDYLEDINEIPKCR 225 (384)
Q Consensus 157 ---~~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~~~~~~-~~~-------~~~A~~lG~alQltNIlRDv~eD~~~~~~gR 225 (384)
..++|++|+......++|.--.+.+-.++. |... ... ..+-...+...-+.|=|-.+..... +|-
T Consensus 379 ~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~-g~~l~~e~~e~~~~~~~l~~~~~~i~rL~NDi~S~~kE~~---rGd 454 (542)
T cd00684 379 AHEGYVPTFEEYMENALVSIGLGPLLLTSFLGM-GDILTEEAFEWLESRPKLVRASSTIGRLMNDIATYEDEMK---RGD 454 (542)
T ss_pred HhcCCCCCHHHHHhhhhHHhhHHHHHHHHHHhc-CCCCCHHHHHHHhccHHHHHHHHHHHHHhcChhhhHHHHh---cCC
Confidence 348899999888777665444444434432 2111 001 1222233333444444444444444 454
Q ss_pred c-cccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHH
Q 016722 226 M-FWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCL 271 (384)
Q Consensus 226 ~-ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~~a~ 271 (384)
+ =.-.=.+..+|++. +.+.+.+..++.++...+.+..
T Consensus 455 v~n~V~~ymke~g~s~---------eeA~~~i~~~ie~~wk~ln~e~ 492 (542)
T cd00684 455 VASSIECYMKEYGVSE---------EEAREEIKKMIEDAWKELNEEF 492 (542)
T ss_pred cccHHHHHHHhcCCCH---------HHHHHHHHHHHHHHHHHHHHHH
Confidence 2 11222345556543 4567778888888888776554
No 26
>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=74.92 E-value=75 Score=29.85 Aligned_cols=193 Identities=16% Similarity=0.080 Sum_probs=98.0
Q ss_pred hhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHccccccc--ccCCC-cchHHHhhHHHHHHHHHhcCH--
Q 016722 60 TDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHF--SCGTK-EYKVLMDQFHHVSTAFLELGK-- 134 (384)
Q Consensus 60 ~~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~--~~G~~-~~~~l~~~~~~v~~~~~~l~~-- 134 (384)
.+.+..++-+.+++-.+||.-|+.... + .+..+.+.+.. |.. ..+.+ ...|+...+.++..+......
T Consensus 46 ~~~l~~~a~~~~~~f~~DD~~D~~~~~-~----~~~~~~~~~~~--~~~~~~~~~p~~~~~~~~~l~d~~~r~~~~~~~~ 118 (284)
T cd00868 46 SEARIALAKTIALLTVIDDTYDDYGTL-E----ELELFTEAVER--WDISAIDELPEYMKPVFKALYDLVNEIEEELAKE 118 (284)
T ss_pred hHHHHHHHHHHHHHHHHHhccccCCCH-H----HHHHHHHHHHh--cChhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 357888899999999999999985432 1 12223333321 110 10222 245677777777665543221
Q ss_pred ---HHHHHHHHHHHhhhhHHHhhhh----hhcCCHHHHHHHHHhhhhHHHHHHHHHhcc-cCCCC------CChhHHHHH
Q 016722 135 ---GYQDAIEDITKRMGAGMAKFIC----KEVESIDDYDEYCYYVAGLVGLGLSKLFYA-SGTED------LAPDSLSNS 200 (384)
Q Consensus 135 ---~~~~lI~~i~~~m~~gm~~dl~----~~~~t~~dl~~Yc~~VAG~VG~~l~~l~~~-~~~~~------~~~~~~A~~ 200 (384)
.....+.+-+..+..|+..... ..++|++||..+-...+|.--.+.+--++. ...+. .....+...
T Consensus 119 ~~~~~~~r~~~~~~~~~~~~~~e~~~~~~~~~p~~~eYl~~R~~~~g~~~~~~l~~~~~g~~l~~~~~~~~~~~~~l~~~ 198 (284)
T cd00868 119 GGSESLPYLKEAWKDLLRAYLVEAKWANEGYVPSFEEYLENRRVSIGYPPLLALSFLGMGDILPEEAFEWLPSYPKLVRA 198 (284)
T ss_pred cCchHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHhceehhhHHHHHHHHHHHcCCCCCHHHHHHhhhhHHHHHH
Confidence 2222222233334445555543 237888888777777665433222222221 11110 112245555
Q ss_pred HHHHHHHHHHHhchHhhhhcCCCCCc-cccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHH
Q 016722 201 MGLFLQKTNIIRDYLEDINEIPKCRM-FWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCL 271 (384)
Q Consensus 201 lG~alQltNIlRDv~eD~~~~~~gR~-ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~~a~ 271 (384)
.+...-++|=+-.+..+.. .|.. =+..=++..+|++.+ .+.+-+.+++......+.+..
T Consensus 199 ~~~~~~l~NDl~S~~kE~~---~g~~~N~v~vl~~~~~~~~~---------eA~~~~~~~~~~~~~~~~~~~ 258 (284)
T cd00868 199 SSTIGRLLNDIASYEKEIA---RGEVANSVECYMKEYGVSEE---------EALEELRKMIEEAWKELNEEV 258 (284)
T ss_pred HHHHHHHhccchHHHHHHc---cCCcccHHHHHHhccCCCHH---------HHHHHHHHHHHHHHHHHHHHH
Confidence 5666666666666666665 5654 333334455555443 345556666666655555433
No 27
>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=72.06 E-value=95 Score=29.77 Aligned_cols=206 Identities=13% Similarity=0.027 Sum_probs=107.1
Q ss_pred HHHHhcC---hhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHhhHHHHHHHH
Q 016722 53 LVIQQLG---TDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMDQFHHVSTAF 129 (384)
Q Consensus 53 ~a~~~Lp---~~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~~~~~v~~~~ 129 (384)
++..+.| ++.-..++-+..+.-..||.-|+....++........+-+.+.+.. ..+.....|+...+.++..++
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 4444544 4555556677888899999999863222222222222222222210 001123456777777777766
Q ss_pred HhcC-HHH-HHHHHHHHHhhhhHHHhhhh----hhcCCHHHHHHHHHhhhhHHH-HHHHHHhcccCCCC-----CChhHH
Q 016722 130 LELG-KGY-QDAIEDITKRMGAGMAKFIC----KEVESIDDYDEYCYYVAGLVG-LGLSKLFYASGTED-----LAPDSL 197 (384)
Q Consensus 130 ~~l~-~~~-~~lI~~i~~~m~~gm~~dl~----~~~~t~~dl~~Yc~~VAG~VG-~~l~~l~~~~~~~~-----~~~~~~ 197 (384)
.... +.. ..+++ -+..+..|+..-.. ..++|++||..+=....|.-. ..++.+........ +....+
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 246788877777666644322 23333332111111 112246
Q ss_pred HHHHHHHHHHHHHHhchHhhh-hcCCCCCcc-ccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016722 198 SNSMGLFLQKTNIIRDYLEDI-NEIPKCRMF-WPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYM 274 (384)
Q Consensus 198 A~~lG~alQltNIlRDv~eD~-~~~~~gR~y-lP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~~a~~y~ 274 (384)
-...+..+-++|=|=.+..+. + .|... +-.=++..+|++.+ ++.+.+..++......+.+...-+
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 667777778888888888887 5 56632 22224455666544 355667777777777777666544
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=56.46 E-value=1.5e+02 Score=29.86 Aligned_cols=59 Identities=19% Similarity=0.330 Sum_probs=43.4
Q ss_pred cChhhhhHHHHHHHHHHhhhhhccCCCCChhhhHHHHHHHHHHHcccccccccCCCcchHHHh----hHHHHHHHHH
Q 016722 58 LGTDLRNAVCIFYLVLRALDTVEDDTSIPTDVKVPILIAFHRHVYDREWHFSCGTKEYKVLMD----QFHHVSTAFL 130 (384)
Q Consensus 58 Lp~~~R~av~alYaf~R~lD~I~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~G~~~~~~l~~----~~~~v~~~~~ 130 (384)
.+++...++.+.|...-.+||+.|++. +-|+.|.+.|.. |++..+|++. .|..+.+.|+
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 689999999999999999999999864 256667777754 7776677543 4555555553
No 29
>COG3455 Type VI protein secretion system component VasF [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.97 E-value=66 Score=31.07 Aligned_cols=87 Identities=18% Similarity=0.272 Sum_probs=51.7
Q ss_pred HHHHHHHHhhcCCcHHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChhh---hHHHHHHHHHHHcccccccccCCC
Q 016722 37 WAFCYSMLHKVSRSFALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTDV---KVPILIAFHRHVYDREWHFSCGTK 113 (384)
Q Consensus 37 ~~~C~~~l~~~srSF~~a~~~Lp~~~R~av~alYaf~R~lD~I~D~~~~~~~~---k~~~L~~~~~~l~~~~~~~~~G~~ 113 (384)
...|..-+ +.|--......-+.-+...+=|+||-.+|+++=....+... |.+++-.|+.+.. |.+
T Consensus 68 r~~~v~~i----~~fe~~l~~ag~~~e~v~~arY~lCa~lDE~vl~~~W~~~~~W~~~sLlv~fhne~~--------gGe 135 (262)
T COG3455 68 RQRLVAEI----EAFEQALQQAGYSPEDVMAARYALCALLDETVLGTPWGNRSAWARQSLLVHFHNEAW--------GGE 135 (262)
T ss_pred HHHHHHHH----HHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHcCCCCCCccccccCCeeeeeecccc--------chh
Confidence 44444444 34556666666666778889999999999999877665432 1222222222211 222
Q ss_pred cchHHHhhHHHHHHHHHhcCHHHHHHHHH
Q 016722 114 EYKVLMDQFHHVSTAFLELGKGYQDAIED 142 (384)
Q Consensus 114 ~~~~l~~~~~~v~~~~~~l~~~~~~lI~~ 142 (384)
.|-..++++..-|..++++++-
T Consensus 136 -------k~f~~L~~l~~~P~~~~dlLe~ 157 (262)
T COG3455 136 -------KVFELLERLLREPARYRDLLEL 157 (262)
T ss_pred -------hHHHHHHHHHhCchhhHHHHHH
Confidence 2455556665667777887763
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=23.60 E-value=1.2e+02 Score=21.07 Aligned_cols=38 Identities=13% Similarity=0.158 Sum_probs=28.3
Q ss_pred HHHHHHhcChhhhhHHHHHHHHHHhhhhhccCCCCChh
Q 016722 51 FALVIQQLGTDLRNAVCIFYLVLRALDTVEDDTSIPTD 88 (384)
Q Consensus 51 F~~a~~~Lp~~~R~av~alYaf~R~lD~I~D~~~~~~~ 88 (384)
+.-++..||++.|..+...|......++|++....+..
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 34577889999999999999999999999999887643
No 31
>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=21.41 E-value=55 Score=21.54 Aligned_cols=20 Identities=35% Similarity=0.355 Sum_probs=16.9
Q ss_pred CCCccccHHHHHhccCChhh
Q 016722 223 KCRMFWPREIWSKYVNKLED 242 (384)
Q Consensus 223 ~gR~ylP~e~l~~~g~~~~d 242 (384)
.||+.+|.++..+.+....|
T Consensus 6 kgri~iP~~~r~~l~~~~gd 25 (43)
T TIGR01439 6 KGQIVIPKEIREKLGLKEGD 25 (43)
T ss_pred CCeEEecHHHHHHcCcCCCC
Confidence 59999999999998876544
No 32
>PRK02899 adaptor protein; Provisional
Probab=21.39 E-value=1.1e+02 Score=28.04 Aligned_cols=41 Identities=24% Similarity=0.190 Sum_probs=35.6
Q ss_pred CCccccHHHHHhccCChhhhhcccCCHHHHHHHHHHHHHHHHH
Q 016722 224 CRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMH 266 (384)
Q Consensus 224 gR~ylP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~ 266 (384)
=||++-.+.|...|++.+||.. +++++.++..+|...|...
T Consensus 11 Irv~it~~DL~eRgi~~~dL~~--n~~k~e~lF~~mm~Ea~~e 51 (197)
T PRK02899 11 IKIFLTFDDLSERGLTKEDLWR--DAPKVHQLFRDMMQEANKE 51 (197)
T ss_pred EEEEEeHHHHHHcCCCHHHHhc--CcHHHHHHHHHHHHHhhhc
Confidence 3799999999999999999965 5799999999998888553
Done!