Query psy3879
Match_columns 247
No_of_seqs 237 out of 1801
Neff 8.0
Searched_HMMs 46136
Date Fri Aug 16 19:42:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3879.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3879hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0142 IspA Geranylgeranyl py 100.0 7.1E-42 1.5E-46 304.8 22.7 175 9-185 25-252 (322)
2 PRK10581 geranyltranstransfera 100.0 6.6E-42 1.4E-46 301.8 22.0 185 11-201 29-225 (299)
3 TIGR02748 GerC3_HepT heptapren 100.0 3E-42 6.6E-47 307.0 19.8 186 10-201 27-212 (319)
4 PRK10888 octaprenyl diphosphat 100.0 5.4E-42 1.2E-46 305.5 19.7 186 10-201 28-213 (323)
5 TIGR02749 prenyl_cyano solanes 100.0 1.3E-41 2.9E-46 303.0 19.4 186 10-201 28-216 (322)
6 PLN02890 geranyl diphosphate s 100.0 3.1E-41 6.8E-46 307.7 19.6 186 10-201 106-310 (422)
7 cd00685 Trans_IPPS_HT Trans-Is 100.0 1.1E-40 2.5E-45 289.2 19.4 186 10-201 2-191 (259)
8 PLN02857 octaprenyl-diphosphat 100.0 9.8E-41 2.1E-45 304.5 17.6 186 10-201 119-310 (416)
9 CHL00151 preA prenyl transfera 100.0 1.6E-40 3.4E-45 296.5 18.4 185 11-201 30-217 (323)
10 PF00348 polyprenyl_synt: Poly 100.0 7E-39 1.5E-43 278.2 15.7 180 15-201 2-188 (260)
11 KOG0776|consensus 100.0 3.5E-35 7.5E-40 260.6 16.0 187 10-201 91-283 (384)
12 KOG0777|consensus 100.0 2.4E-32 5.2E-37 225.5 12.1 186 7-201 16-201 (322)
13 cd00867 Trans_IPPS Trans-Isopr 100.0 9.2E-29 2E-33 211.1 17.2 167 29-201 1-168 (236)
14 KOG0711|consensus 99.9 4E-25 8.6E-30 190.4 15.2 223 8-231 34-330 (347)
15 KOG0777|consensus 99.7 4.6E-18 9.9E-23 141.1 5.4 97 151-247 67-163 (322)
16 COG0142 IspA Geranylgeranyl py 99.7 2.1E-17 4.6E-22 147.5 8.6 95 151-247 78-174 (322)
17 TIGR02748 GerC3_HepT heptapren 99.7 4.4E-17 9.6E-22 145.4 9.3 96 151-247 75-170 (319)
18 PLN02890 geranyl diphosphate s 99.7 8.8E-17 1.9E-21 147.3 9.5 96 151-247 173-268 (422)
19 cd00385 Isoprenoid_Biosyn_C1 I 99.7 2.4E-15 5.1E-20 126.0 16.3 147 49-201 13-162 (243)
20 TIGR02749 prenyl_cyano solanes 99.7 1.6E-16 3.5E-21 141.9 9.6 96 151-247 79-174 (322)
21 PRK10888 octaprenyl diphosphat 99.7 1.7E-16 3.7E-21 141.8 9.1 96 151-247 76-171 (323)
22 PLN02857 octaprenyl-diphosphat 99.6 3.6E-16 7.8E-21 143.3 6.4 96 151-247 173-268 (416)
23 CHL00151 preA prenyl transfera 99.6 1.3E-15 2.9E-20 136.1 8.3 96 151-247 80-175 (323)
24 cd00685 Trans_IPPS_HT Trans-Is 99.6 2.6E-15 5.5E-20 130.4 8.6 96 151-247 51-149 (259)
25 PRK10581 geranyltranstransfera 99.6 2.3E-15 4.9E-20 133.2 7.8 95 151-247 76-182 (299)
26 PF00348 polyprenyl_synt: Poly 99.4 2.7E-13 5.8E-18 117.8 6.6 95 151-247 45-146 (260)
27 cd00867 Trans_IPPS Trans-Isopr 99.3 8E-12 1.7E-16 106.5 10.3 96 151-247 30-126 (236)
28 KOG0776|consensus 99.3 3.2E-12 6.9E-17 114.4 7.9 105 142-247 132-241 (384)
29 cd00385 Isoprenoid_Biosyn_C1 I 98.5 3.4E-07 7.3E-12 76.4 8.2 93 154-247 25-120 (243)
30 PF07307 HEPPP_synt_1: Heptapr 97.8 0.00051 1.1E-08 57.7 12.5 106 42-156 29-135 (212)
31 KOG0711|consensus 97.6 0.00011 2.5E-09 64.4 5.3 108 140-247 71-193 (347)
32 PF07307 HEPPP_synt_1: Heptapr 86.9 3 6.5E-05 35.2 7.1 59 181-243 70-128 (212)
33 PF03936 Terpene_synth_C: Terp 72.3 34 0.00074 29.0 9.1 44 113-156 138-181 (270)
34 cd00868 Terpene_cyclase_C1 Ter 71.4 52 0.0011 28.0 10.2 45 112-156 122-166 (284)
35 cd00687 Terpene_cyclase_nonpla 67.6 23 0.00049 30.9 7.1 47 110-156 127-173 (303)
36 cd00868 Terpene_cyclase_C1 Ter 57.1 17 0.00036 31.2 4.3 40 205-244 122-161 (284)
37 cd00684 Terpene_cyclase_plant_ 51.0 73 0.0016 30.7 7.9 42 203-244 354-395 (542)
38 cd00687 Terpene_cyclase_nonpla 47.1 70 0.0015 27.8 6.7 41 203-243 127-167 (303)
39 TIGR01476 chlor_syn_BchG bacte 40.8 1.4E+02 0.0029 26.0 7.5 49 49-97 164-213 (283)
40 PF00494 SQS_PSY: Squalene/phy 40.0 2E+02 0.0042 24.5 8.3 41 116-159 88-128 (267)
41 cd00684 Terpene_cyclase_plant_ 39.1 3.6E+02 0.0078 26.0 16.8 91 110-200 354-490 (542)
42 PF03936 Terpene_synth_C: Terp 39.1 40 0.00087 28.5 3.8 39 206-244 138-176 (270)
43 KOG1345|consensus 37.2 22 0.00047 31.6 1.8 21 48-68 127-147 (378)
44 PLN02878 homogentisate phytylt 36.7 41 0.00088 29.7 3.4 40 157-196 174-214 (280)
45 PLN02279 ent-kaur-16-ene synth 35.0 1.9E+02 0.0041 29.4 8.2 38 205-242 590-627 (784)
46 PRK13591 ubiA prenyltransferas 32.9 31 0.00066 30.9 2.0 39 157-195 197-236 (307)
47 PRK12887 ubiA tocopherol phyty 31.7 58 0.0013 29.0 3.6 41 157-197 200-241 (308)
48 PRK12869 ubiA protoheme IX far 31.2 50 0.0011 28.8 3.1 38 55-94 171-208 (279)
49 TIGR01476 chlor_syn_BchG bacte 28.5 51 0.0011 28.7 2.7 39 157-195 179-218 (283)
50 PRK13105 ubiA prenyltransferas 27.7 79 0.0017 27.8 3.7 39 157-195 178-217 (282)
51 PRK13387 1,4-dihydroxy-2-napht 26.4 58 0.0013 29.1 2.7 40 157-196 207-247 (317)
52 TIGR02235 menA_cyano-plnt 1,4- 26.0 75 0.0016 28.0 3.3 38 159-196 181-219 (285)
53 PLN02922 prenyltransferase 25.4 76 0.0017 28.4 3.3 41 158-198 207-248 (315)
54 PRK12882 ubiA prenyltransferas 24.9 3.3E+02 0.0071 23.5 7.1 72 31-102 142-214 (276)
55 TIGR02056 ChlG chlorophyll syn 24.5 3.6E+02 0.0078 23.8 7.4 52 48-99 185-237 (306)
56 PRK07419 1,4-dihydroxy-2-napht 23.6 75 0.0016 28.3 2.9 40 158-197 193-233 (304)
57 PRK12869 ubiA protoheme IX far 23.0 4.8E+02 0.01 22.6 7.8 58 47-104 37-99 (279)
58 TIGR00751 menA 1,4-dihydroxy-2 22.5 1E+02 0.0022 27.1 3.4 37 159-195 184-221 (284)
59 TIGR03464 HpnC squalene syntha 21.7 4.8E+02 0.01 22.3 7.5 37 119-158 86-122 (266)
60 PRK12872 ubiA prenyltransferas 21.2 1.1E+02 0.0023 26.6 3.3 39 157-195 179-218 (285)
61 PRK11409 antitoxin YefM; Provi 20.1 1.2E+02 0.0027 21.3 2.9 62 61-131 13-78 (83)
No 1
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=100.00 E-value=7.1e-42 Score=304.75 Aligned_cols=175 Identities=29% Similarity=0.420 Sum_probs=159.1
Q ss_pred CcchhHHhHHHHhhcCCCcchHHHHHHHHHHhcCCCh----HHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCchhhh
Q psy3879 9 EQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPE----EKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSI 84 (247)
Q Consensus 9 ~~~~~l~~~~~y~~~~~GK~~R~~l~~~~~~~~~~~~----~~~~~~a~avElih~asLihDDI~D~s~~RRG~p~~h~~ 84 (247)
+.++.+.+++.|.+..||||+||+++++++++++.+. +++..+|++|||||++|||||||||+|++|||+||+|.+
T Consensus 25 ~~~~~l~~a~~~~~~aGGKrlRP~l~l~~~~~~~~~~~~~~~~~~~~aaavEliH~~SLiHDDvmD~s~~RRG~pt~~~~ 104 (322)
T COG0142 25 SDPELLLEAMRYLLLAGGKRLRPLLVLLAAEALGIDLETGGNDALDLAAAIELIHTASLIHDDLMDDDDLRRGKPTVHAK 104 (322)
T ss_pred cccHHHHHHHHHHHhcCCccHhHHHHHHHHHHcCCCcccchhhHHHHHHHHHHHHHHHHHHhhcccCCCccCCCCCchhH
Confidence 6788999999999999999999999999999998443 368999999999999999999999999999999999999
Q ss_pred cchhHHHHHHHHHHHHHHHHHHhcCC--hHHHHHHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhhhh----
Q psy3879 85 YGIASTINAANYVVAIALEKVQSLGH--PEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRI---- 158 (247)
Q Consensus 85 ~G~~~Ai~~gd~l~~~~~~~l~~~~~--~~~~~~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~~~---- 158 (247)
||+..||++||+|++.+|+++++.+. +.+.+.+++.+..+|.||.+|+.+..+. +|+++|++|+++|||.++
T Consensus 105 ~g~~~AIlaGD~L~~~Af~~l~~~~~~~~~~~~~~~~~~~~~~~GQ~lDl~~~~~~--~t~e~y~~~i~~KTa~L~~~a~ 182 (322)
T COG0142 105 FGEATAILAGDALLAAAFELLSKLGSEALEAIKALAEAINGLCGGQALDLAFENKP--VTLEEYLRVIELKTAALFAAAA 182 (322)
T ss_pred hccHHHHHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHHHHHhHHHHHHccCCC--CCHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999977 7899999999999999999999988764 899999999999999998
Q ss_pred -------------------------------ccccc------------chhhhcCCCchhhhhcHHHHHH
Q psy3879 159 -------------------------------DDIED------------NSILRRGIPVAHSIYGIASTIN 185 (247)
Q Consensus 159 -------------------------------dd~~d------------~~~lr~g~~t~~~~~g~~~ai~ 185 (247)
||++| ++|++.|++|+|.+++.+.+..
T Consensus 183 ~~ga~la~~~~~~~~~l~~~g~~lGlaFQi~DDiLD~~~d~~~lGK~~g~Dl~~gK~T~p~l~~l~~~~~ 252 (322)
T COG0142 183 VLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEKANE 252 (322)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHhhHHHHHHHHhhcCCCChHHhCCCcchHHHcCCchHHHHHHHHcCch
Confidence 77776 2577778888888887775444
No 2
>PRK10581 geranyltranstransferase; Provisional
Probab=100.00 E-value=6.6e-42 Score=301.85 Aligned_cols=185 Identities=18% Similarity=0.278 Sum_probs=154.9
Q ss_pred chhHHhHHHHhhcCCCcchHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhhhc--cCCCCCCCCCCchhhhcchh
Q psy3879 11 DEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDI--EDNSILRRGIPVAHSIYGIA 88 (247)
Q Consensus 11 ~~~l~~~~~y~~~~~GK~~R~~l~~~~~~~~~~~~~~~~~~a~avElih~asLihDDI--~D~s~~RRG~p~~h~~~G~~ 88 (247)
++.+.+++.|++..||||+||.|++++++++|.+++.+..+|+++|++|+|||||||| ||+|++|||+||+|++||++
T Consensus 29 ~~~l~~~~~~~~~~gGKrlRp~L~l~~~~~~g~~~~~~~~~A~avEliH~aSLiHDDip~~D~s~~RRG~pt~h~~~G~~ 108 (299)
T PRK10581 29 NTPVVEAMQYGALLGGKRLRPFLVYATGQMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEA 108 (299)
T ss_pred chHHHHHHHHHHhcCcccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHcCcccccCCCccCCCcChHHHhCcc
Confidence 5679999999999999999999999999999999889999999999999999999999 99999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCh--------HHHHHHHHH--HHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhhhh
Q psy3879 89 STINAANYVVAIALEKVQSLGHP--------EATAVYTEQ--LLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRI 158 (247)
Q Consensus 89 ~Ai~~gd~l~~~~~~~l~~~~~~--------~~~~~~~~~--~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~~~ 158 (247)
.||++||+|++.+|+.++..+.+ ++++.++.+ +..++.||.+|+.+... .+++++|++|+.+|||.++
T Consensus 109 ~AIl~GD~L~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~GQ~ld~~~~~~--~~~~~~y~~i~~~KTa~L~ 186 (299)
T PRK10581 109 NAILAGDALQTLAFSILSDAPMPEVSDRDRISMISELASASGIAGMCGGQALDLEAEGK--QVPLDALERIHRHKTGALI 186 (299)
T ss_pred hHHHHHHHHHHHHHHHHHhCCCccCChHHHHHHHHHHHHhcccchhhHhhHHHHhccCC--CCCHHHHHHHHHHhhHHHH
Confidence 99999999999999999876432 234444543 56899999999988754 5799999999999999999
Q ss_pred cccccchhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcC
Q psy3879 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSL 201 (247)
Q Consensus 159 dd~~d~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l 201 (247)
.-++..+.+..|.+.- ....++..++..+|.|||+.||+
T Consensus 187 ~~~~~~gailag~~~~----~~~~~l~~~g~~lG~aFQI~DDi 225 (299)
T PRK10581 187 RAAVRLGALSAGDKGR----RALPVLDRYAESIGLAFQVQDDI 225 (299)
T ss_pred HHHHHHHHHHcCCCcH----HHHHHHHHHHHHHHHHHHHHHHH
Confidence 6666666666665320 12345666677777777777763
No 3
>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=100.00 E-value=3e-42 Score=307.01 Aligned_cols=186 Identities=20% Similarity=0.304 Sum_probs=172.6
Q ss_pred cchhHHhHHHHhhcCCCcchHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCchhhhcchhH
Q psy3879 10 QDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSIYGIAS 89 (247)
Q Consensus 10 ~~~~l~~~~~y~~~~~GK~~R~~l~~~~~~~~~~~~~~~~~~a~avElih~asLihDDI~D~s~~RRG~p~~h~~~G~~~ 89 (247)
.++.+.+++.|++..||||+||.|++++++++|.+.+.+..+|+++|+||+||||||||||+|++|||+||+|.+||++.
T Consensus 27 ~~~~l~~~~~~~~~~gGKriRp~L~ll~~~~~~~~~~~~~~~A~aiEliH~asLiHDDI~D~s~~RRg~pt~~~~~G~~~ 106 (319)
T TIGR02748 27 EHPVLSEASLHLLEAGGKRIRPVFVLLAGKFGDYDLDAIKHVAVALELIHMASLVHDDVIDDADLRRGRPTIKSKWGNRI 106 (319)
T ss_pred CchHHHHHHHHHHhcCCchHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHhccccCCCCCCCCCcCHHHHhChHH
Confidence 35678999999999999999999999999999888889999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhhhhcccccchhhhc
Q psy3879 90 TINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRIDDIEDNSILRR 169 (247)
Q Consensus 90 Ai~~gd~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~~~dd~~d~~~lr~ 169 (247)
||++||||++++++.+++.+.+++++.+++++.+++.||.+|+.+..+. .+++++|++++.+|||.++.-++..+.+..
T Consensus 107 Ail~GD~L~~~a~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~~~~~~~~~-~~~~~~Y~~~i~~KTa~L~~~~~~~ga~~a 185 (319)
T TIGR02748 107 AMYTGDYLFAKSLETMTEIKDPRAHQILSHTIVEVCRGEIEQIKDKYNF-DQNLRTYLRRIKRKTALLIAASCQLGAIAS 185 (319)
T ss_pred HHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHHHHHHHhccCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 9999999999999999998888999999999999999999999886554 579999999999999999998888888888
Q ss_pred CCCchhhhhcHHHHHHHHHHHHHHHHHHHhcC
Q psy3879 170 GIPVAHSIYGIASTINAANYVVAIALEKVQSL 201 (247)
Q Consensus 170 g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l 201 (247)
|.+. ....++..++..+|.|||+.||+
T Consensus 186 g~~~-----~~~~~l~~~g~~lG~aFQI~DDi 212 (319)
T TIGR02748 186 GANE-----AIVKKLYWFGYYVGMSYQITDDI 212 (319)
T ss_pred CCCH-----HHHHHHHHHHHHHHHHHHHHHHH
Confidence 8875 44577899999999999999985
No 4
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=100.00 E-value=5.4e-42 Score=305.53 Aligned_cols=186 Identities=20% Similarity=0.279 Sum_probs=173.0
Q ss_pred cchhHHhHHHHhhcCCCcchHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCchhhhcchhH
Q psy3879 10 QDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSIYGIAS 89 (247)
Q Consensus 10 ~~~~l~~~~~y~~~~~GK~~R~~l~~~~~~~~~~~~~~~~~~a~avElih~asLihDDI~D~s~~RRG~p~~h~~~G~~~ 89 (247)
..+.+.++.+|++..||||+||.|++++++++|++.+.+.++|+++|+||+||||||||||+|++|||+||+|++||++.
T Consensus 28 ~~~~l~~~~~~~~~~~GKrlRp~l~ll~~~~~g~~~~~~~~~A~avEllH~asLiHDDI~D~s~~RRG~pt~~~~~G~~~ 107 (323)
T PRK10888 28 DVQLINQLGYYIISGGGKRIRPMIAVLAARAVGYQGNAHVTIAALIEFIHTATLLHDDVVDESDMRRGKATANAAFGNAA 107 (323)
T ss_pred cchhHHHHHHHHHhCCCchHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHHHHHcccccCCcccCCCCCHHHHhCccH
Confidence 34568999999999999999999999999999998899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhhhhcccccchhhhc
Q psy3879 90 TINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRIDDIEDNSILRR 169 (247)
Q Consensus 90 Ai~~gd~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~~~dd~~d~~~lr~ 169 (247)
||++||||++.+++.+.+.+.+++++.+++++..++.||.+|+.+..+. .+++++|++++.+|||.++.-++..+.+..
T Consensus 108 Ail~GD~L~~~a~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~d~~~~~~~-~~s~~~y~~~i~~KTa~lf~~~~~~ga~la 186 (323)
T PRK10888 108 SVLVGDFIYTRAFQMMTSLGSLKVLEVMSEAVNVIAEGEVLQLMNVNDP-DITEENYMRVIYSKTARLFEAAAQCSGILA 186 (323)
T ss_pred HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHhccCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 9999999999999999998888999999999999999999999876553 589999999999999999998888888888
Q ss_pred CCCchhhhhcHHHHHHHHHHHHHHHHHHHhcC
Q psy3879 170 GIPVAHSIYGIASTINAANYVVAIALEKVQSL 201 (247)
Q Consensus 170 g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l 201 (247)
|.+. ....++..+++.+|.|||+.||+
T Consensus 187 g~~~-----~~~~~l~~~g~~lG~aFQi~DD~ 213 (323)
T PRK10888 187 GCTP-----EQEKGLQDYGRYLGTAFQLIDDL 213 (323)
T ss_pred CCCH-----HHHHHHHHHHHHHHHHHHHHHHh
Confidence 8876 45677889999999999999985
No 5
>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=100.00 E-value=1.3e-41 Score=303.00 Aligned_cols=186 Identities=18% Similarity=0.252 Sum_probs=172.1
Q ss_pred cchhHHhHHHHhhcCCCcchHHHHHHHHHHhcCCC---hHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCchhhhcc
Q psy3879 10 QDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIP---EEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSIYG 86 (247)
Q Consensus 10 ~~~~l~~~~~y~~~~~GK~~R~~l~~~~~~~~~~~---~~~~~~~a~avElih~asLihDDI~D~s~~RRG~p~~h~~~G 86 (247)
.++.+.++++|++..||||+||.|+++++++++.+ .+..+.+|+++|+||+||||||||||+|++|||+||+|++||
T Consensus 28 ~~~~l~~~~~~~~~~gGKrlRp~l~ll~~~~~~~~~~~~~~~~~~A~avEliH~asLiHDDiiD~s~~RRG~pt~h~~~G 107 (322)
T TIGR02749 28 RHPILYAAAEHLFSAGGKRLRPAIVLLVSRATAEQQELTPRHRRLAEITEMIHTASLVHDDVIDESDTRRGIETVHSLFG 107 (322)
T ss_pred CChHHHHHHHHHHHCCCchHHHHHHHHHHHHcCCCccccHHHHHHHHHHHHHHHHHHHHcccccCccccCCCccHHHHhC
Confidence 45678999999999999999999999999998753 477889999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhhhhcccccchh
Q psy3879 87 IASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRIDDIEDNSI 166 (247)
Q Consensus 87 ~~~Ai~~gd~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~~~dd~~d~~~ 166 (247)
++.||++||||++.+++.++..+++++++.+++++.+++.||.+|+.+..+. .+++++|++|+.+|||.++.-+|..+.
T Consensus 108 ~~~Ail~GD~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~~~~~~~~~-~~~~~~y~~~~~~KTa~L~~~~~~~ga 186 (322)
T TIGR02749 108 TRVAVLAGDFLFAQASWYLANLENLEVVKLISKVITDFAEGEIKQGLNQFDS-DLSLEDYLEKSFYKTASLVAASSKAAA 186 (322)
T ss_pred cHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHcccCC-CCCHHHHHHHHHccHHHHHHHHHHHHH
Confidence 9999999999999999999988888999999999999999999998776554 589999999999999999999998888
Q ss_pred hhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcC
Q psy3879 167 LRRGIPVAHSIYGIASTINAANYVVAIALEKVQSL 201 (247)
Q Consensus 167 lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l 201 (247)
+..|.+. ....++..++..+|.|||+.||+
T Consensus 187 ~~ag~~~-----~~~~~l~~~G~~lG~aFQi~DDi 216 (322)
T TIGR02749 187 VLSDVPS-----QVANDLYEYGKHLGLAFQVVDDI 216 (322)
T ss_pred HHcCcCH-----HHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999886 56788999999999999999986
No 6
>PLN02890 geranyl diphosphate synthase
Probab=100.00 E-value=3.1e-41 Score=307.65 Aligned_cols=186 Identities=22% Similarity=0.282 Sum_probs=170.7
Q ss_pred cchhHHhHHHHhhcCC--CcchHHHHHHHHHHhcCCCh-----------------HHHHHHHHHHHHHHHHHHHhhhccC
Q psy3879 10 QDEKLLQPYTYISQVP--GKQIRTKLAYAFNNWLNIPE-----------------EKLLAIGDIIQMLHNSSLLIDDIED 70 (247)
Q Consensus 10 ~~~~l~~~~~y~~~~~--GK~~R~~l~~~~~~~~~~~~-----------------~~~~~~a~avElih~asLihDDI~D 70 (247)
..+.+.+++.|++..| |||+||.|++++++++|.+. ++++.+|+++|+||+||||||||||
T Consensus 106 ~~~~l~~a~~y~~~~G~~GKrlRP~LvLL~a~a~g~~~~~~~~~~~~~~~~~~~~~~~~~~AaavEliH~ASLVHDDIiD 185 (422)
T PLN02890 106 EVPKLASAAEYFFKVGVEGKRFRPTVLLLMATALNVPLPESTEGGVLDIVASELRTRQQNIAEITEMIHVASLLHDDVLD 185 (422)
T ss_pred CChHHHHHHHHHHhCCCCCccHhHHHHHHHHHHcCCCcccccccccchhhccchhhhHHHHHHHHHHHHHHHHHHccccc
Confidence 4567999999999888 99999999999999988641 4578999999999999999999999
Q ss_pred CCCCCCCCCchhhhcchhHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHh
Q psy3879 71 NSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMT 150 (247)
Q Consensus 71 ~s~~RRG~p~~h~~~G~~~Ai~~gd~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii 150 (247)
+|++|||+||+|.+||++.||++||||++.++..+...+++++++.+++++..++.||.+|+.+..+. .+++++|++++
T Consensus 186 ~s~~RRG~pt~~~~~G~~~AIlaGD~Lla~A~~~l~~~~~~~~~~~~s~a~~~l~~Gq~ld~~~~~~~-~~s~~~Yl~~i 264 (422)
T PLN02890 186 DADTRRGVGSLNVVMGNKLSVLAGDFLLSRACVALAALKNTEVVSLLATAVEHLVTGETMQITSSREQ-RRSMDYYMQKT 264 (422)
T ss_pred CCCCcCCCcChhhhcChHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHhccCC-CCCHHHHHHHH
Confidence 99999999999999999999999999999999999988888999999999999999999999887654 68999999999
Q ss_pred HHhhhhhhcccccchhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcC
Q psy3879 151 IRKFDMRIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSL 201 (247)
Q Consensus 151 ~~Kt~~~~dd~~d~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l 201 (247)
.+|||.|+.-+|..+.+..|.+. ....++..++..+|.|||+.||+
T Consensus 265 ~~KTa~Lf~~s~~~gAilaga~~-----~~~~~l~~fG~~lGlAFQI~DDi 310 (422)
T PLN02890 265 YYKTASLISNSCKAVAILAGQTA-----EVAVLAFEYGRNLGLAFQLIDDV 310 (422)
T ss_pred HHhHHHHHHHHHHHHHHHcCcCH-----HHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999888888888876 44567889999999999999985
No 7
>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=100.00 E-value=1.1e-40 Score=289.23 Aligned_cols=186 Identities=30% Similarity=0.402 Sum_probs=171.2
Q ss_pred cchhHHhHHHHhhcCCCcchHHHHHHHHHHhcCCCh-HHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCchhhhcchh
Q psy3879 10 QDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPE-EKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSIYGIA 88 (247)
Q Consensus 10 ~~~~l~~~~~y~~~~~GK~~R~~l~~~~~~~~~~~~-~~~~~~a~avElih~asLihDDI~D~s~~RRG~p~~h~~~G~~ 88 (247)
..+.+.++++|++..+||++||.+++++++++|+++ +.+..+|+++|++|+||||||||||+|+.|||+||+|.+||+.
T Consensus 2 ~~~~l~~~~~~~~~~~GK~~Rp~l~~~~~~~~g~~~~~~~~~la~aiEllh~asLIhDDI~D~s~~RRG~p~~~~~~G~~ 81 (259)
T cd00685 2 EVELLREALRYLLLAGGKRLRPLLVLLAARALGGPELEAALRLAAAIELLHTASLVHDDVMDNSDLRRGKPTVHKVFGNA 81 (259)
T ss_pred CchHHHHHHHHHHHcCCccHhHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHHHHHHhhhccCCcccCCCCcHHHHhCcc
Confidence 356789999999999999999999999999999987 9999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhcCC---hHHHHHHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhhhhcccccch
Q psy3879 89 STINAANYVVAIALEKVQSLGH---PEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRIDDIEDNS 165 (247)
Q Consensus 89 ~Ai~~gd~l~~~~~~~l~~~~~---~~~~~~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~~~dd~~d~~ 165 (247)
.|||+||+|++.+++.+..... +++++.+++.+.+++.||++|+.+..+. .+++++|++|+.+|||.++.-.+-.+
T Consensus 82 ~Ail~gd~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~GQ~~d~~~~~~~-~~~~~~y~~~~~~KT~~l~~~~~~~~ 160 (259)
T cd00685 82 TAILAGDYLLARAFELLARLGNPYYPRALELFSEAILELVEGQLLDLLSEYDT-DVTEEEYLRIIRLKTAALFAAAPLLG 160 (259)
T ss_pred cHHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHHccCCC-CCCHHHHHHHHHHhHHHHHHHHHHHH
Confidence 9999999999999999998866 6899999999999999999999987663 68999999999999999998777777
Q ss_pred hhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcC
Q psy3879 166 ILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSL 201 (247)
Q Consensus 166 ~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l 201 (247)
.+..|.+. .....+...+..+|.+||+.+|+
T Consensus 161 a~l~~~~~-----~~~~~l~~~g~~lG~afQi~DD~ 191 (259)
T cd00685 161 ALLAGADE-----EEAEALKRFGRNLGLAFQIQDDI 191 (259)
T ss_pred HHHcCCCH-----HHHHHHHHHHHHHHHHHHHHHHh
Confidence 77777664 45677999999999999999985
No 8
>PLN02857 octaprenyl-diphosphate synthase
Probab=100.00 E-value=9.8e-41 Score=304.50 Aligned_cols=186 Identities=18% Similarity=0.253 Sum_probs=170.7
Q ss_pred cchhHHhHHHHhhcCCCcchHHHHHHHHHHhcC------CChHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCchhh
Q psy3879 10 QDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLN------IPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHS 83 (247)
Q Consensus 10 ~~~~l~~~~~y~~~~~GK~~R~~l~~~~~~~~~------~~~~~~~~~a~avElih~asLihDDI~D~s~~RRG~p~~h~ 83 (247)
.++.+.++++|++..||||+||.|+++++++++ ...++++.+|+++||||+||||||||||+|++|||+||+|+
T Consensus 119 ~~~~l~~~~~~~~~~gGKriRP~Lvll~a~a~g~~~g~~~~~~~~~~lAaaiEliH~ASLIHDDI~D~s~~RRG~pt~h~ 198 (416)
T PLN02857 119 ENPVLMSAAEQIFGAGGKRMRPALVFLVSRATAELAGLKELTTEHRRLAEITEMIHTASLIHDDVLDESDMRRGKETVHQ 198 (416)
T ss_pred CchHHHHHHHHHHhCCCccHhHHHHHHHHHHhccccCCCcchHHHHHHHHHHHHHHHHHHHHCccccCCcccCCCCCccc
Confidence 455689999999999999999999999999875 23478899999999999999999999999999999999999
Q ss_pred hcchhHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhhhhccccc
Q psy3879 84 IYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRIDDIED 163 (247)
Q Consensus 84 ~~G~~~Ai~~gd~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~~~dd~~d 163 (247)
+||+..|||+||||++++++.++..+++++++.+++.+.+++.||..|+.+..+. ..++++|++++.+|||.|+.-.+.
T Consensus 199 ~~G~~~AIlaGD~L~a~A~~~la~~~~~~~~~~~s~~~~~l~~Gei~q~~~~~~~-~~s~~~Yl~~i~~KTa~L~~~a~~ 277 (416)
T PLN02857 199 LYGTRVAVLAGDFMFAQSSWYLANLDNLEVIKLISQVIKDFASGEIKQASSLFDC-DVTLDEYLLKSYYKTASLIAASTK 277 (416)
T ss_pred cCCcceeeeHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhHHHHHhcccCC-CCCHHHHHHHHHHhHHHHHHHHHH
Confidence 9999999999999999999999988888999999999999999999998876654 579999999999999999999888
Q ss_pred chhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcC
Q psy3879 164 NSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSL 201 (247)
Q Consensus 164 ~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l 201 (247)
.+.+..|.+. ....++..++..+|.|||+.||+
T Consensus 278 ~gallaga~~-----~~~~~l~~fG~~LGiAFQI~DDi 310 (416)
T PLN02857 278 SAAIFSGVDS-----SVKEQMYEYGKNLGLAFQVVDDI 310 (416)
T ss_pred HHHHHcCCCH-----HHHHHHHHHHHHHHHHHHHHHHH
Confidence 8999999886 45678999999999999999985
No 9
>CHL00151 preA prenyl transferase; Reviewed
Probab=100.00 E-value=1.6e-40 Score=296.49 Aligned_cols=185 Identities=17% Similarity=0.205 Sum_probs=169.7
Q ss_pred chhHHhHHHHhhcCCCcchHHHHHHHHHHhcCCC---hHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCchhhhcch
Q psy3879 11 DEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIP---EEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSIYGI 87 (247)
Q Consensus 11 ~~~l~~~~~y~~~~~GK~~R~~l~~~~~~~~~~~---~~~~~~~a~avElih~asLihDDI~D~s~~RRG~p~~h~~~G~ 87 (247)
++.+.++++|++..||||+||.|++++++++|++ .++++.+|+++|++|+||||||||||+|++|||+||+|++||+
T Consensus 30 ~~~l~~~~~~~~~~gGKr~Rp~L~ll~~~~~~~~~~~~~~~~~~A~aiEllH~asLiHDDi~D~s~~RRG~pt~h~~~G~ 109 (323)
T CHL00151 30 HPILYAAAKHLFSAGGKRIRPAIVLLVAKATGGNMEIKTSQQRLAEITEIIHTASLVHDDVIDECSIRRGIPTVHKIFGT 109 (323)
T ss_pred ChhHHHHHHHHHhcCCccHHHHHHHHHHHHcCCCccccHHHHHHHHHHHHHHHHHHHHcccccCccccCCCccHHHHhCC
Confidence 4578999999999999999999999999999874 3567889999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhhhhcccccchhh
Q psy3879 88 ASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRIDDIEDNSIL 167 (247)
Q Consensus 88 ~~Ai~~gd~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~~~dd~~d~~~l 167 (247)
+.||++||||++.++..++..+.+++.+.+++++..++.||..+..+..+. .+++++|++++.+|||.++.-++..+.+
T Consensus 110 ~~Ail~GD~l~~~a~~~l~~~~~~~~~~~~~~~~~~l~~G~~~~~~~~~~~-~~~~~~yl~~i~~KTa~L~~~~~~~ga~ 188 (323)
T CHL00151 110 KIAVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGEIRQGLVQFDT-TLSILNYIEKSFYKTASLIAASCKAAAL 188 (323)
T ss_pred cchhhhHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHhcCCCC-CCCHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 999999999999999999988778889999999999999999998765543 5799999999999999999988888999
Q ss_pred hcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcC
Q psy3879 168 RRGIPVAHSIYGIASTINAANYVVAIALEKVQSL 201 (247)
Q Consensus 168 r~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l 201 (247)
..|.+. ....++..++..+|.|||+.||+
T Consensus 189 lag~~~-----~~~~~l~~~G~~lG~aFQi~DDi 217 (323)
T CHL00151 189 LSDADE-----KDHNDFYLYGKHLGLAFQIIDDV 217 (323)
T ss_pred HcCCCH-----HHHHHHHHHHHHHHHHHHHHHHH
Confidence 989875 45678999999999999999985
No 10
>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=100.00 E-value=7e-39 Score=278.17 Aligned_cols=180 Identities=29% Similarity=0.400 Sum_probs=162.5
Q ss_pred HhHHHHhhcCCCcchHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCchhhhcchhHHHHHH
Q psy3879 15 LQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSIYGIASTINAA 94 (247)
Q Consensus 15 ~~~~~y~~~~~GK~~R~~l~~~~~~~~~~~~~~~~~~a~avElih~asLihDDI~D~s~~RRG~p~~h~~~G~~~Ai~~g 94 (247)
.+++.|++..|||++||.|+++++++++++.+.+..+|+++|+||++|||||||+|+|++|||+||+|.+||++.|||+|
T Consensus 2 ~~~~~~~~~~~GK~~Rp~l~~~~~~~~~~~~~~~~~~a~avEliH~asLIhDDI~D~s~~RRG~pt~~~~~G~~~Ail~g 81 (260)
T PF00348_consen 2 LEPARYYILRGGKRIRPLLVLLAAEALGGDPEKAIPLAAAVELIHAASLIHDDIIDNSDLRRGKPTVHKKFGNAIAILAG 81 (260)
T ss_dssp HHHHHHHHHSSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEETTEECHHHHHHHHHHHHHH
T ss_pred hHHHHHHhhCCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCCCccccccccccchhhhc
Confidence 57788888899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcC--Ch--H---HHHHHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhhhhcccccchhh
Q psy3879 95 NYVVAIALEKVQSLG--HP--E---ATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRIDDIEDNSIL 167 (247)
Q Consensus 95 d~l~~~~~~~l~~~~--~~--~---~~~~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~~~dd~~d~~~l 167 (247)
|+|++.++..++..+ +| . +.+.+...+.....||..|+.+... .+++++|++|+++|||.++.-.+..+.+
T Consensus 82 d~ll~~a~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~~~~q~~d~~~~~~--~~~~~~y~~i~~~KTg~l~~~~~~~ga~ 159 (260)
T PF00348_consen 82 DYLLALAFELLARLGHFDPSERVLRILELFIEALIEGEIGQALDLANEDK--DPTEEEYLEIIRLKTGSLFALACQLGAI 159 (260)
T ss_dssp HHHHHHHHHHHHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS--STSHHHHHHHHHHHTHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHhhcccchHHHHHHHHHHHHhcccceeehhhccccccc--cccHHHHHHHHhhcchHHHHHHHHHHHH
Confidence 999999999999986 22 2 3445555666777789999987755 5899999999999999999999999999
Q ss_pred hcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcC
Q psy3879 168 RRGIPVAHSIYGIASTINAANYVVAIALEKVQSL 201 (247)
Q Consensus 168 r~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l 201 (247)
..|.+. ....++..++..+|.|||+.+|+
T Consensus 160 lag~~~-----~~~~~l~~~g~~lG~afQi~DD~ 188 (260)
T PF00348_consen 160 LAGADE-----EQIEALREFGRHLGIAFQIRDDL 188 (260)
T ss_dssp HTTSGH-----HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hccchh-----HHHHHHHHHHHHHHHHHhhhhhh
Confidence 999885 56788999999999999999986
No 11
>KOG0776|consensus
Probab=100.00 E-value=3.5e-35 Score=260.65 Aligned_cols=187 Identities=20% Similarity=0.279 Sum_probs=171.9
Q ss_pred cchhHHhHHHHhhcCCCcchHHHHHHHHHHhcC-CChHHHHHHHHHHHHHHHHHHHhhhc--cCCCCCCCCCCchhhhcc
Q psy3879 10 QDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLN-IPEEKLLAIGDIIQMLHNSSLLIDDI--EDNSILRRGIPVAHSIYG 86 (247)
Q Consensus 10 ~~~~l~~~~~y~~~~~GK~~R~~l~~~~~~~~~-~~~~~~~~~a~avElih~asLihDDI--~D~s~~RRG~p~~h~~~G 86 (247)
.+..+..+++|.+..+||++||.+|++.|+.++ +....+..+|+++||||++||||||| ||++++|||+|+.|++||
T Consensus 91 ~~~~i~~a~ry~~la~gKr~rP~l~~~~~e~~~~g~~~~q~~~A~i~EMIHtaSLIHDDv~~mD~~d~RRGkpt~h~vfG 170 (384)
T KOG0776|consen 91 EPLLISEAMRYLLLAGGKRVRPLLCLAACELVGSGDESSQRSLAEIVEMIHTASLIHDDVPCMDDADLRRGKPTNHKVFG 170 (384)
T ss_pred ccchhHHHHHHHHHhcccccCchhhhhHHHhccccccHHHHHHHHHHHHHHHHHHHhcCcccccccccccCCCCcchhhc
Confidence 467788899999999999999999999999999 88888999999999999999999999 999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhHhhhhhhhhhcc---CCCCCCHHHHHHHhHHhhhhhhccccc
Q psy3879 87 IASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRD---NYTCPSEEEYRTMTIRKFDMRIDDIED 163 (247)
Q Consensus 87 ~~~Ai~~gd~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~dl~~~~---~~~~~s~~~Y~~ii~~Kt~~~~dd~~d 163 (247)
++.||++||||++.|+..++.+.++.+.+.++.++.+++.|++.+..... ......++.|..+..+|||+|....|-
T Consensus 171 ~k~AvLaGD~LLa~A~~~la~l~n~~v~elm~~aI~dLv~ge~~~~~~~~~~~d~~~~~~e~~e~~~~~KTAsLla~Sc~ 250 (384)
T KOG0776|consen 171 NKMAVLAGDALLALASEHLASLENPVVVELMASAIADLVRGEFTQGLVAGEGLDLDDVGLEYLEFKTLLKTASLLAKSCV 250 (384)
T ss_pred chhhhhhhHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHhhhhcccccccccccCCcchHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999998876653 222347899999999999999999999
Q ss_pred chhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcC
Q psy3879 164 NSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSL 201 (247)
Q Consensus 164 ~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l 201 (247)
.+.+..|... .+......+++.+|++||+.+|.
T Consensus 251 ~~aILgg~s~-----ev~e~~~~yGR~lGL~fQvvDDi 283 (384)
T KOG0776|consen 251 AAAILGGGSE-----EVIEAAFEYGRCLGLAFQVVDDI 283 (384)
T ss_pred HHHHHcCCCH-----HHHHHHHHHHHHHHHHHHHhhcc
Confidence 8888887776 66788999999999999999986
No 12
>KOG0777|consensus
Probab=99.98 E-value=2.4e-32 Score=225.53 Aligned_cols=186 Identities=51% Similarity=0.800 Sum_probs=163.3
Q ss_pred CCCcchhHHhHHHHhhcCCCcchHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCchhhhcc
Q psy3879 7 DPEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSIYG 86 (247)
Q Consensus 7 ~~~~~~~l~~~~~y~~~~~GK~~R~~l~~~~~~~~~~~~~~~~~~a~avElih~asLihDDI~D~s~~RRG~p~~h~~~G 86 (247)
....+..+.+|+.|++..|||.+|..|.+++.+|+..|.++...+..++||+|++||..|||.|+|..|||+|+.|..||
T Consensus 16 q~~~~~ill~Py~yilq~PGKqfR~~L~~afNhwl~~P~dkLaii~~ivemLHNsSLLIDDIEDNs~LRRG~pvaHsIyG 95 (322)
T KOG0777|consen 16 QSQNESILLKPYNYILQKPGKQFRLNLIVAFNHWLNLPKDKLAIISQIVEMLHNSSLLIDDIEDNSPLRRGQPVAHSIYG 95 (322)
T ss_pred HHHHHHHHhchHHHHHhCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhccceeeccccccchhhcCCcchhhhcc
Confidence 34456778999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhhhhcccccchh
Q psy3879 87 IASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRIDDIEDNSI 166 (247)
Q Consensus 87 ~~~Ai~~gd~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~~~dd~~d~~~ 166 (247)
+...||+++|++..+.+.++.+.+|+++++|.+.+.+++.||.+|+.|+....+||+++|+.|+-+|||-+|.-.+..-.
T Consensus 96 vpStINtANY~yFlalekV~qLdhP~a~kifteqLleLHrGQGldIYWRD~~tcPtee~Yk~Mv~~KTGGLF~La~rLMq 175 (322)
T KOG0777|consen 96 VPSTINTANYMYFLALEKVSQLDHPNAIKIFTEQLLELHRGQGLDIYWRDFLTCPTEEMYKNMVMNKTGGLFRLALRLMQ 175 (322)
T ss_pred CcchhhhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHhcCCCcceeeeccCcCCCHHHHHHHHHHhcccHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998865443211
Q ss_pred hhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcC
Q psy3879 167 LRRGIPVAHSIYGIASTINAANYVVAIALEKVQSL 201 (247)
Q Consensus 167 lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l 201 (247)
+- ..++.+ +.-.--++|.-||+.+|.
T Consensus 176 lf-------S~~ked--l~pl~n~LGl~fQIRDDY 201 (322)
T KOG0777|consen 176 LF-------SHHKED--LVPLINLLGLIFQIRDDY 201 (322)
T ss_pred HH-------Hhcchh--HHHHHHHHhHhhhhhhhh
Confidence 11 111211 122234688999999985
No 13
>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=99.96 E-value=9.2e-29 Score=211.12 Aligned_cols=167 Identities=27% Similarity=0.334 Sum_probs=150.1
Q ss_pred hHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCchhhh-cchhHHHHHHHHHHHHHHHHHHh
Q psy3879 29 IRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSI-YGIASTINAANYVVAIALEKVQS 107 (247)
Q Consensus 29 ~R~~l~~~~~~~~~~~~~~~~~~a~avElih~asLihDDI~D~s~~RRG~p~~h~~-~G~~~Ai~~gd~l~~~~~~~l~~ 107 (247)
+||.+++++++++|.+.+++..+++++|+||++++|||||+|++..|||+|++|.. ||...|++.||+++..++..+.+
T Consensus 1 ~r~~~~~~~~~~~~~~~~~~~~~a~ave~l~~~~li~DDI~D~~~~rrg~~~~~~~~~g~~~ai~~gd~l~~~a~~~l~~ 80 (236)
T cd00867 1 SRPLLVLLLARALGGDLEAALRLAAAVELLHAASLVHDDIVDDSDLRRGKPTAHLRRFGNALAILAGDYLLARAFQLLAR 80 (236)
T ss_pred CcHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHcccccCCccCCCCccHhHHhhCHhHHHHHHHHHHHHHHHHHHh
Confidence 58999999999999999999999999999999999999999999999999999999 99999999999999999999998
Q ss_pred cCChHHHHHHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhhhhcccccchhhhcCCCchhhhhcHHHHHHHH
Q psy3879 108 LGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRIDDIEDNSILRRGIPVAHSIYGIASTINAA 187 (247)
Q Consensus 108 ~~~~~~~~~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~~~dd~~d~~~lr~g~~t~~~~~g~~~ai~~~ 187 (247)
...++..+.+.+.+.+++.||..|+.+..+. .+|+++|.+++++|||.++.-.+-......|.+. .....+...
T Consensus 81 ~~~~~~~~~~~~~~~~~~~Gq~~Dl~~~~~~-~~t~~~y~~~~~~Kta~l~~~~~~~~~~~~~~~~-----~~~~~~~~~ 154 (236)
T cd00867 81 LGYPRALELFAEALRELLEGQALDLEFERDT-YETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADD-----EQAEALKDY 154 (236)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHhccCC-CCCHHHHHHHHHhccHHHHHHHHHHHHHHcCcCH-----HHHHHHHHH
Confidence 8777889999999999999999999987652 5899999999999999998776665555555543 334667788
Q ss_pred HHHHHHHHHHHhcC
Q psy3879 188 NYVVAIALEKVQSL 201 (247)
Q Consensus 188 ~~l~~~a~q~~~~l 201 (247)
+..+|.|||+.+++
T Consensus 155 ~~~lG~a~Qi~dd~ 168 (236)
T cd00867 155 GRALGLAFQLTDDL 168 (236)
T ss_pred HHHHHHHHHHHHHh
Confidence 89999999999986
No 14
>KOG0711|consensus
Probab=99.93 E-value=4e-25 Score=190.43 Aligned_cols=223 Identities=18% Similarity=0.107 Sum_probs=180.1
Q ss_pred CCcchhHHhHHHHhhcCCCcchHHHHHHHHHHhcCCC-------hHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCc
Q psy3879 8 PEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIP-------EEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPV 80 (247)
Q Consensus 8 ~~~~~~l~~~~~y~~~~~GK~~R~~l~~~~~~~~~~~-------~~~~~~~a~avElih~asLihDDI~D~s~~RRG~p~ 80 (247)
....+++...+.|.+ .|||..|+..++...+++..+ ...+..++|+||++|+.+||.|||||+|.+|||+||
T Consensus 34 ~da~~~~~~~L~yN~-~GGK~nRgl~vv~s~~~L~~~~~l~~~~~~~a~~lGw~vElLQaffLiaDDIMDnS~tRRGqpC 112 (347)
T KOG0711|consen 34 GDATEWLKEVLDYNV-IGGKLNRGLSVVDSFKALVEPRKLDEEELQLALILGWCVELLQAFFLVADDIMDNSKTRRGQPC 112 (347)
T ss_pred hHHHHHHHHHHhccC-cccccccchhHHHHHHHhcCccCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccCCCcc
Confidence 355678889999996 899999999999999988663 245788999999999999999999999999999999
Q ss_pred hhhhcchh-HHHHHHHHHHHHHHHHHHhc-C----ChHHHHHHHHHHHHhHhhhhhhhhhccC-CCCCCHHHHHHHhHHh
Q psy3879 81 AHSIYGIA-STINAANYVVAIALEKVQSL-G----HPEATAVYTEQLLELHRGQGMEIYWRDN-YTCPSEEEYRTMTIRK 153 (247)
Q Consensus 81 ~h~~~G~~-~Ai~~gd~l~~~~~~~l~~~-~----~~~~~~~~~~~~~~~~~Gq~~dl~~~~~-~~~~s~~~Y~~ii~~K 153 (247)
||.+.|++ .|||.+-+|.+....+|.+. + ..++++.|.+....++.||.++-...+. ...+|++.|..|+.+|
T Consensus 113 Wy~~~gVG~~AINDA~lLea~Iy~lLkk~fr~~~~y~~l~elf~ev~f~T~lGdllt~~~~~~~ls~fsl~~y~~Iv~~K 192 (347)
T KOG0711|consen 113 WYQKPGVGLDAINDAFLLEAAIYKLLKKHFRNIYCYVDLVELFHEVTFQTELGDLLTTPEGNKDLSKFSLEKYVFIVEYK 192 (347)
T ss_pred eeecCCcchhhhhHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHHHHHhhhccccCcccchhHhhhhHHHHHHHhhcc
Confidence 99999995 89999999988887777754 1 2367899999999999997777443321 1357999999999999
Q ss_pred hhhhh-------------------------------------ccccc-----------chhhhcCCCchhhhhcHHHHHH
Q psy3879 154 FDMRI-------------------------------------DDIED-----------NSILRRGIPVAHSIYGIASTIN 185 (247)
Q Consensus 154 t~~~~-------------------------------------dd~~d-----------~~~lr~g~~t~~~~~g~~~ai~ 185 (247)
||.+. ||.+| +.|+..++.+|..+..++.|-.
T Consensus 193 Ta~YsFYLPialAl~~ag~~~~k~~~~~k~v~~~lg~~FQvQDDYLd~fgDp~vtgkiGtDIqDnKCsWlv~~al~~~~~ 272 (347)
T KOG0711|consen 193 TAYYSFYLPVALALLLAGIANLKEHACEKKVLLLLGEYFQVQDDYLDCFGDPEVTGKIGTDIQDNKCSWLVVKALQRASA 272 (347)
T ss_pred ccceeeecHHHHHHHHhhhhhHHHhhhHHHHHHHHHHHHhcchHHHHhcCChhhcCCCCCccccCceeeehHHHHhhcCH
Confidence 98642 67666 2588899999999888777755
Q ss_pred HHHHHHHHHH------------HHHhcCCChHHHHHHHHHHHHHHHHHHhccccccCC
Q psy3879 186 AANYVVAIAL------------EKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNY 231 (247)
Q Consensus 186 ~~~~l~~~a~------------q~~~~l~~~~~~~~~~~~~~~l~~Gq~~~i~~~~~~ 231 (247)
..-..+...| ++..++..+.....+++.......+.+.++.-....
T Consensus 273 eq~~~l~~~yg~~~~~~v~~vk~ly~el~l~~~f~~yE~~~~~~Ik~~I~~~~~~~~~ 330 (347)
T KOG0711|consen 273 EQYKILFENYGKPEAEAVAKVKALYKELHLPALFIEYEEGSYKKIKKLISQVDEDTGV 330 (347)
T ss_pred HHHHHHHHhcCCccHHHHHHHHHHHHHhccHHHHHHhhhhHHHHHHHHHHHccCCCcc
Confidence 5544444433 555667888899999999999999998888766543
No 15
>KOG0777|consensus
Probab=99.72 E-value=4.6e-18 Score=141.06 Aligned_cols=97 Identities=62% Similarity=1.035 Sum_probs=94.4
Q ss_pred HHhhhhhhcccccchhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHhccccccC
Q psy3879 151 IRKFDMRIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDN 230 (247)
Q Consensus 151 ~~Kt~~~~dd~~d~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l~~~~~~~~~~~~~~~l~~Gq~~~i~~~~~ 230 (247)
.|.+++++||+.|.+.+|||.|+.|.+||+...|+.++|++..|.+....++.|+++.+|.+.+..+++||.+||.|++.
T Consensus 67 LHNsSLLIDDIEDNs~LRRG~pvaHsIyGvpStINtANY~yFlalekV~qLdhP~a~kifteqLleLHrGQGldIYWRD~ 146 (322)
T KOG0777|consen 67 LHNSSLLIDDIEDNSPLRRGQPVAHSIYGVPSTINTANYMYFLALEKVSQLDHPNAIKIFTEQLLELHRGQGLDIYWRDF 146 (322)
T ss_pred HhccceeeccccccchhhcCCcchhhhccCcchhhhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHhcCCCcceeeecc
Confidence 56778899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCHHHHHHHHhccC
Q psy3879 231 YTCPSEEEYRTMTIRSE 247 (247)
Q Consensus 231 ~~~~~~~~y~~~~~~KT 247 (247)
+.|||+++|..|+..||
T Consensus 147 ~tcPtee~Yk~Mv~~KT 163 (322)
T KOG0777|consen 147 LTCPTEEMYKNMVMNKT 163 (322)
T ss_pred CcCCCHHHHHHHHHHhc
Confidence 99999999999999998
No 16
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=99.71 E-value=2.1e-17 Score=147.55 Aligned_cols=95 Identities=29% Similarity=0.420 Sum_probs=91.1
Q ss_pred HHhhhhhhcccccchhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcCCC--hHHHHHHHHHHHHHHHHHHhccccc
Q psy3879 151 IRKFDMRIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGH--PEATAVYTEQLLELHRGQGMEIYWR 228 (247)
Q Consensus 151 ~~Kt~~~~dd~~d~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l~~--~~~~~~~~~~~~~l~~Gq~~~i~~~ 228 (247)
-|..+++|||++|.+++|||+||+|.+||...||++||+++..||+++...+. +.+...+++....+|+||.+|+.+.
T Consensus 78 iH~~SLiHDDvmD~s~~RRG~pt~~~~~g~~~AIlaGD~L~~~Af~~l~~~~~~~~~~~~~~~~~~~~~~~GQ~lDl~~~ 157 (322)
T COG0142 78 IHTASLIHDDLMDDDDLRRGKPTVHAKFGEATAILAGDALLAAAFELLSKLGSEALEAIKALAEAINGLCGGQALDLAFE 157 (322)
T ss_pred HHHHHHHHhhcccCCCccCCCCCchhHhccHHHHHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHHHHHhHHHHHHcc
Confidence 57789999999999999999999999999999999999999999999999988 8899999999999999999999999
Q ss_pred cCCCCCCHHHHHHHHhccC
Q psy3879 229 DNYTCPSEEEYRTMTIRSE 247 (247)
Q Consensus 229 ~~~~~~~~~~y~~~~~~KT 247 (247)
.+. +|+++|++|++.||
T Consensus 158 ~~~--~t~e~y~~~i~~KT 174 (322)
T COG0142 158 NKP--VTLEEYLRVIELKT 174 (322)
T ss_pred CCC--CCHHHHHHHHHHHH
Confidence 876 59999999999998
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=99.70 E-value=4.4e-17 Score=145.41 Aligned_cols=96 Identities=25% Similarity=0.395 Sum_probs=91.2
Q ss_pred HHhhhhhhcccccchhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHhccccccC
Q psy3879 151 IRKFDMRIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDN 230 (247)
Q Consensus 151 ~~Kt~~~~dd~~d~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l~~~~~~~~~~~~~~~l~~Gq~~~i~~~~~ 230 (247)
-|..+++|||++|.+++|||+||+|..||...|++.||+++..||+++.+++.+++...+++++..+|+||.+|+.+..+
T Consensus 75 iH~asLiHDDI~D~s~~RRg~pt~~~~~G~~~Ail~GD~L~~~a~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~~~~~~~~ 154 (319)
T TIGR02748 75 IHMASLVHDDVIDDADLRRGRPTIKSKWGNRIAMYTGDYLFAKSLETMTEIKDPRAHQILSHTIVEVCRGEIEQIKDKYN 154 (319)
T ss_pred HHHHHHHhccccCCCCCCCCCcCHHHHhChHHHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 57889999999999999999999999999999999999999999999999988899999999999999999999999877
Q ss_pred CCCCCHHHHHHHHhccC
Q psy3879 231 YTCPSEEEYRTMTIRSE 247 (247)
Q Consensus 231 ~~~~~~~~y~~~~~~KT 247 (247)
.. +++++|++||.+||
T Consensus 155 ~~-~~~~~Y~~~i~~KT 170 (319)
T TIGR02748 155 FD-QNLRTYLRRIKRKT 170 (319)
T ss_pred CC-CCHHHHHHHHHHHH
Confidence 65 49999999999998
No 18
>PLN02890 geranyl diphosphate synthase
Probab=99.69 E-value=8.8e-17 Score=147.35 Aligned_cols=96 Identities=20% Similarity=0.259 Sum_probs=91.5
Q ss_pred HHhhhhhhcccccchhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHhccccccC
Q psy3879 151 IRKFDMRIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDN 230 (247)
Q Consensus 151 ~~Kt~~~~dd~~d~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l~~~~~~~~~~~~~~~l~~Gq~~~i~~~~~ 230 (247)
.|..+++|||++|.+++|||+||+|..||...|++.||+++..||+.+..++.++++..+++++..+++||.+|+.|..+
T Consensus 173 iH~ASLVHDDIiD~s~~RRG~pt~~~~~G~~~AIlaGD~Lla~A~~~l~~~~~~~~~~~~s~a~~~l~~Gq~ld~~~~~~ 252 (422)
T PLN02890 173 IHVASLLHDDVLDDADTRRGVGSLNVVMGNKLSVLAGDFLLSRACVALAALKNTEVVSLLATAVEHLVTGETMQITSSRE 252 (422)
T ss_pred HHHHHHHHcccccCCCCcCCCcChhhhcChHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 57888999999999999999999999999999999999999999999999988999999999999999999999999987
Q ss_pred CCCCCHHHHHHHHhccC
Q psy3879 231 YTCPSEEEYRTMTIRSE 247 (247)
Q Consensus 231 ~~~~~~~~y~~~~~~KT 247 (247)
.. +++++|++|+.+||
T Consensus 253 ~~-~s~~~Yl~~i~~KT 268 (422)
T PLN02890 253 QR-RSMDYYMQKTYYKT 268 (422)
T ss_pred CC-CCHHHHHHHHHHhH
Confidence 66 49999999999998
No 19
>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=99.68 E-value=2.4e-15 Score=126.04 Aligned_cols=147 Identities=28% Similarity=0.390 Sum_probs=125.2
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCCCCCCCCchhhh---cchhHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhH
Q psy3879 49 LAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSI---YGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELH 125 (247)
Q Consensus 49 ~~~a~avElih~asLihDDI~D~s~~RRG~p~~h~~---~G~~~Ai~~gd~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 125 (247)
..++.+++.+|+++++||||+|++..|+|.|++|.. +|...+++.|+.++..++..+.....+.....+.+.+.+++
T Consensus 13 ~~~~~~~~~~~~~~~~~DDi~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 (243)
T cd00385 13 SRLRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAFEELAREGSPEALEILAEALLDLL 92 (243)
T ss_pred HHHHHHHHHHHHHHHHHhhcccCCCCCCCchhhhhhHHhcCchHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 588899999999999999999999999999999998 99999999999999999999998766788899999999999
Q ss_pred hhhhhhhhhccCCCCCCHHHHHHHhHHhhhhhhcccccchhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcC
Q psy3879 126 RGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSL 201 (247)
Q Consensus 126 ~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~~~dd~~d~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l 201 (247)
.||..|+.+..+ ..+|.++|.++++.||+.++-..+.......+.+. .....+......+|.++|+.+|+
T Consensus 93 ~g~~~d~~~~~~-~~~t~~ey~~~~~~~t~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~g~~~ql~nDl 162 (243)
T cd00385 93 EGQLLDLKWRRE-YVPTLEEYLEYCRYKTAGLVGALCLLGAGLSGGEA-----ELLEALRKLGRALGLAFQLTNDL 162 (243)
T ss_pred HHHHHHHHhccC-CCCCHHHHHHHHHHhHHHHHHHHHHHHHHHhCCCH-----HHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999876 46899999999999988776655544433333321 23455667778899999999985
No 20
>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=99.67 E-value=1.6e-16 Score=141.87 Aligned_cols=96 Identities=22% Similarity=0.275 Sum_probs=90.9
Q ss_pred HHhhhhhhcccccchhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHhccccccC
Q psy3879 151 IRKFDMRIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDN 230 (247)
Q Consensus 151 ~~Kt~~~~dd~~d~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l~~~~~~~~~~~~~~~l~~Gq~~~i~~~~~ 230 (247)
.|..+++|||++|.+++|||+||+|.+||...|++.||++++.||+.+..++.+++...+++++..+++||..|+.+..+
T Consensus 79 iH~asLiHDDiiD~s~~RRG~pt~h~~~G~~~Ail~GD~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~~~~~~~~ 158 (322)
T TIGR02749 79 IHTASLVHDDVIDESDTRRGIETVHSLFGTRVAVLAGDFLFAQASWYLANLENLEVVKLISKVITDFAEGEIKQGLNQFD 158 (322)
T ss_pred HHHHHHHHcccccCccccCCCccHHHHhCcHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHcccC
Confidence 57788999999999999999999999999999999999999999999999988899999999999999999999998877
Q ss_pred CCCCCHHHHHHHHhccC
Q psy3879 231 YTCPSEEEYRTMTIRSE 247 (247)
Q Consensus 231 ~~~~~~~~y~~~~~~KT 247 (247)
.. +++++|++|+.+||
T Consensus 159 ~~-~~~~~y~~~~~~KT 174 (322)
T TIGR02749 159 SD-LSLEDYLEKSFYKT 174 (322)
T ss_pred CC-CCHHHHHHHHHccH
Confidence 65 59999999999998
No 21
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=99.67 E-value=1.7e-16 Score=141.79 Aligned_cols=96 Identities=22% Similarity=0.360 Sum_probs=90.2
Q ss_pred HHhhhhhhcccccchhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHhccccccC
Q psy3879 151 IRKFDMRIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDN 230 (247)
Q Consensus 151 ~~Kt~~~~dd~~d~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l~~~~~~~~~~~~~~~l~~Gq~~~i~~~~~ 230 (247)
.|..+++|||++|.+++|||+|++|..||...|++.||+++..||+++..++.++++..+++++..+++||.+|+.+..+
T Consensus 76 lH~asLiHDDI~D~s~~RRG~pt~~~~~G~~~Ail~GD~L~~~a~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~d~~~~~~ 155 (323)
T PRK10888 76 IHTATLLHDDVVDESDMRRGKATANAAFGNAASVLVGDFIYTRAFQMMTSLGSLKVLEVMSEAVNVIAEGEVLQLMNVND 155 (323)
T ss_pred HHHHHHHHcccccCCcccCCCCCHHHHhCccHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 56778999999999999999999999999999999999999999999999988899999999999999999999998766
Q ss_pred CCCCCHHHHHHHHhccC
Q psy3879 231 YTCPSEEEYRTMTIRSE 247 (247)
Q Consensus 231 ~~~~~~~~y~~~~~~KT 247 (247)
.. +++++|++|+.+||
T Consensus 156 ~~-~s~~~y~~~i~~KT 171 (323)
T PRK10888 156 PD-ITEENYMRVIYSKT 171 (323)
T ss_pred CC-CCHHHHHHHHHHHH
Confidence 54 59999999999998
No 22
>PLN02857 octaprenyl-diphosphate synthase
Probab=99.63 E-value=3.6e-16 Score=143.31 Aligned_cols=96 Identities=19% Similarity=0.250 Sum_probs=91.0
Q ss_pred HHhhhhhhcccccchhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHhccccccC
Q psy3879 151 IRKFDMRIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDN 230 (247)
Q Consensus 151 ~~Kt~~~~dd~~d~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l~~~~~~~~~~~~~~~l~~Gq~~~i~~~~~ 230 (247)
.|..+++|||++|.+++|||+||+|.+||...||+.||+++..||+.+.+++.++++..+++.+..+++||+.|+.+..+
T Consensus 173 iH~ASLIHDDI~D~s~~RRG~pt~h~~~G~~~AIlaGD~L~a~A~~~la~~~~~~~~~~~s~~~~~l~~Gei~q~~~~~~ 252 (416)
T PLN02857 173 IHTASLIHDDVLDESDMRRGKETVHQLYGTRVAVLAGDFMFAQSSWYLANLDNLEVIKLISQVIKDFASGEIKQASSLFD 252 (416)
T ss_pred HHHHHHHHCccccCCcccCCCCCccccCCcceeeeHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhHHHHHhcccC
Confidence 57788999999999999999999999999999999999999999999999988999999999999999999999998877
Q ss_pred CCCCCHHHHHHHHhccC
Q psy3879 231 YTCPSEEEYRTMTIRSE 247 (247)
Q Consensus 231 ~~~~~~~~y~~~~~~KT 247 (247)
.. +++++|++|+.+||
T Consensus 253 ~~-~s~~~Yl~~i~~KT 268 (416)
T PLN02857 253 CD-VTLDEYLLKSYYKT 268 (416)
T ss_pred CC-CCHHHHHHHHHHhH
Confidence 65 49999999999998
No 23
>CHL00151 preA prenyl transferase; Reviewed
Probab=99.61 E-value=1.3e-15 Score=136.12 Aligned_cols=96 Identities=21% Similarity=0.294 Sum_probs=89.9
Q ss_pred HHhhhhhhcccccchhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHhccccccC
Q psy3879 151 IRKFDMRIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDN 230 (247)
Q Consensus 151 ~~Kt~~~~dd~~d~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l~~~~~~~~~~~~~~~l~~Gq~~~i~~~~~ 230 (247)
.|..+++|||++|.+++|||+|++|..||...|++.||+++..||+.+..++.+.....+.+++..+++||..|..+..+
T Consensus 80 lH~asLiHDDi~D~s~~RRG~pt~h~~~G~~~Ail~GD~l~~~a~~~l~~~~~~~~~~~~~~~~~~l~~G~~~~~~~~~~ 159 (323)
T CHL00151 80 IHTASLVHDDVIDECSIRRGIPTVHKIFGTKIAVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGEIRQGLVQFD 159 (323)
T ss_pred HHHHHHHHcccccCccccCCCccHHHHhCCcchhhhHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 57789999999999999999999999999999999999999999999998888888999999999999999999988766
Q ss_pred CCCCCHHHHHHHHhccC
Q psy3879 231 YTCPSEEEYRTMTIRSE 247 (247)
Q Consensus 231 ~~~~~~~~y~~~~~~KT 247 (247)
.. +++++|++|+.+||
T Consensus 160 ~~-~~~~~yl~~i~~KT 175 (323)
T CHL00151 160 TT-LSILNYIEKSFYKT 175 (323)
T ss_pred CC-CCHHHHHHHHHhHH
Confidence 55 49999999999998
No 24
>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=99.60 E-value=2.6e-15 Score=130.39 Aligned_cols=96 Identities=34% Similarity=0.535 Sum_probs=89.9
Q ss_pred HHhhhhhhcccccchhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcCCC---hHHHHHHHHHHHHHHHHHHhcccc
Q psy3879 151 IRKFDMRIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGH---PEATAVYTEQLLELHRGQGMEIYW 227 (247)
Q Consensus 151 ~~Kt~~~~dd~~d~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l~~---~~~~~~~~~~~~~l~~Gq~~~i~~ 227 (247)
.|-.+.+|||++|.+..|||+|++|..||...|++.|++++..+|+++...+. ++++..+++.+..+++||.+|+.|
T Consensus 51 lh~asLIhDDI~D~s~~RRG~p~~~~~~G~~~Ail~gd~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~GQ~~d~~~ 130 (259)
T cd00685 51 LHTASLVHDDVMDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLGNPYYPRALELFSEAILELVEGQLLDLLS 130 (259)
T ss_pred HHHHHHHHhhhccCCcccCCCCcHHHHhCcccHHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 57778899999999999999999999999999999999999999999998877 689999999999999999999999
Q ss_pred ccCCCCCCHHHHHHHHhccC
Q psy3879 228 RDNYTCPSEEEYRTMTIRSE 247 (247)
Q Consensus 228 ~~~~~~~~~~~y~~~~~~KT 247 (247)
..+. .+++++|++|+..||
T Consensus 131 ~~~~-~~~~~~y~~~~~~KT 149 (259)
T cd00685 131 EYDT-DVTEEEYLRIIRLKT 149 (259)
T ss_pred cCCC-CCCHHHHHHHHHHhH
Confidence 8863 469999999999998
No 25
>PRK10581 geranyltranstransferase; Provisional
Probab=99.59 E-value=2.3e-15 Score=133.16 Aligned_cols=95 Identities=19% Similarity=0.333 Sum_probs=82.0
Q ss_pred HHhhhhhhccc--ccchhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcCCCh--------HHHHHHHHH--HHHHH
Q psy3879 151 IRKFDMRIDDI--EDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHP--------EATAVYTEQ--LLELH 218 (247)
Q Consensus 151 ~~Kt~~~~dd~--~d~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l~~~--------~~~~~~~~~--~~~l~ 218 (247)
-|..+++|||+ +|.+++|||+||+|.+||...||++||++++.||+++.+.+.+ +++..++++ +..+|
T Consensus 76 iH~aSLiHDDip~~D~s~~RRG~pt~h~~~G~~~AIl~GD~L~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 155 (299)
T PRK10581 76 IHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDAPMPEVSDRDRISMISELASASGIAGMC 155 (299)
T ss_pred HHHHHHHHcCcccccCCCccCCCcChHHHhCcchHHHHHHHHHHHHHHHHHhCCCccCChHHHHHHHHHHHHhcccchhh
Confidence 57889999999 9999999999999999999999999999999999999876432 234444543 46799
Q ss_pred HHHHhccccccCCCCCCHHHHHHHHhccC
Q psy3879 219 RGQGMEIYWRDNYTCPSEEEYRTMTIRSE 247 (247)
Q Consensus 219 ~Gq~~~i~~~~~~~~~~~~~y~~~~~~KT 247 (247)
+||.+|+.|..+ .+++++|++|+.+||
T Consensus 156 ~GQ~ld~~~~~~--~~~~~~y~~i~~~KT 182 (299)
T PRK10581 156 GGQALDLEAEGK--QVPLDALERIHRHKT 182 (299)
T ss_pred HhhHHHHhccCC--CCCHHHHHHHHHHhh
Confidence 999999999865 469999999999998
No 26
>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=99.42 E-value=2.7e-13 Score=117.83 Aligned_cols=95 Identities=37% Similarity=0.549 Sum_probs=80.5
Q ss_pred HHhhhhhhcccccchhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcCC--Ch--H---HHHHHHHHHHHHHHHHHh
Q psy3879 151 IRKFDMRIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLG--HP--E---ATAVYTEQLLELHRGQGM 223 (247)
Q Consensus 151 ~~Kt~~~~dd~~d~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l~--~~--~---~~~~~~~~~~~l~~Gq~~ 223 (247)
-|..+++|||++|.+.+|||+||+|..||...|++.||+++..||+.+.+++ .+ . +...+...+.....||..
T Consensus 45 iH~asLIhDDI~D~s~~RRG~pt~~~~~G~~~Ail~gd~ll~~a~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~~~~q~~ 124 (260)
T PF00348_consen 45 IHAASLIHDDIIDNSDLRRGKPTVHKKFGNAIAILAGDYLLALAFELLARLGHFDPSERVLRILELFIEALIEGEIGQAL 124 (260)
T ss_dssp HHHHHHHHHHHHTTCSEETTEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhhhhhcccccCCCCccccccccccchhhhchHHHHHHHHHHHHhhcccchHHHHHHHHHHHHhcccceeehhh
Confidence 5778999999999999999999999999999999999999999999999886 22 2 334444455666777888
Q ss_pred ccccccCCCCCCHHHHHHHHhccC
Q psy3879 224 EIYWRDNYTCPSEEEYRTMTIRSE 247 (247)
Q Consensus 224 ~i~~~~~~~~~~~~~y~~~~~~KT 247 (247)
|+.+.+. .+++++|++|+..||
T Consensus 125 d~~~~~~--~~~~~~y~~i~~~KT 146 (260)
T PF00348_consen 125 DLANEDK--DPTEEEYLEIIRLKT 146 (260)
T ss_dssp HHHTTTS--STSHHHHHHHHHHHT
T ss_pred ccccccc--cccHHHHHHHHhhcc
Confidence 8888765 459999999999998
No 27
>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=99.33 E-value=8e-12 Score=106.52 Aligned_cols=96 Identities=33% Similarity=0.499 Sum_probs=89.0
Q ss_pred HHhhhhhhcccccchhhhcCCCchhhh-hcHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHhcccccc
Q psy3879 151 IRKFDMRIDDIEDNSILRRGIPVAHSI-YGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRD 229 (247)
Q Consensus 151 ~~Kt~~~~dd~~d~~~lr~g~~t~~~~-~g~~~ai~~~~~l~~~a~q~~~~l~~~~~~~~~~~~~~~l~~Gq~~~i~~~~ 229 (247)
-|-.+.+|||++|.+..|||+|+++.. ||...|++.+++++..+|+.+..++.++....+.+.+..+++||.+|+.+..
T Consensus 30 l~~~~li~DDI~D~~~~rrg~~~~~~~~~g~~~ai~~gd~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~Dl~~~~ 109 (236)
T cd00867 30 LHAASLVHDDIVDDSDLRRGKPTAHLRRFGNALAILAGDYLLARAFQLLARLGYPRALELFAEALRELLEGQALDLEFER 109 (236)
T ss_pred HHHHHHHHcccccCCccCCCCccHhHHhhCHhHHHHHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 566688999999999999999999999 9999999999999999999999888778899999999999999999999987
Q ss_pred CCCCCCHHHHHHHHhccC
Q psy3879 230 NYTCPSEEEYRTMTIRSE 247 (247)
Q Consensus 230 ~~~~~~~~~y~~~~~~KT 247 (247)
+ ..+|+++|++++++||
T Consensus 110 ~-~~~t~~~y~~~~~~Kt 126 (236)
T cd00867 110 D-TYETLDEYLEYCRYKT 126 (236)
T ss_pred C-CCCCHHHHHHHHHhcc
Confidence 6 3469999999999998
No 28
>KOG0776|consensus
Probab=99.33 E-value=3.2e-12 Score=114.44 Aligned_cols=105 Identities=24% Similarity=0.298 Sum_probs=95.2
Q ss_pred CHHHHHHHhHHhhhhhhccc--ccchhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHH
Q psy3879 142 SEEEYRTMTIRKFDMRIDDI--EDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHR 219 (247)
Q Consensus 142 s~~~Y~~ii~~Kt~~~~dd~--~d~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~~~l~~~~~~~~~~~~~~~l~~ 219 (247)
....+.+|| |.++++|||+ +|.+++|||+||.|..||...|+.+||++++.|++.+..+.++.+.+.+++++.++.+
T Consensus 132 ~~A~i~EMI-HtaSLIHDDv~~mD~~d~RRGkpt~h~vfG~k~AvLaGD~LLa~A~~~la~l~n~~v~elm~~aI~dLv~ 210 (384)
T KOG0776|consen 132 SLAEIVEMI-HTASLIHDDVPCMDDADLRRGKPTNHKVFGNKMAVLAGDALLALASEHLASLENPVVVELMASAIADLVR 210 (384)
T ss_pred HHHHHHHHH-HHHHHHhcCcccccccccccCCCCcchhhcchhhhhhhHHHHHHHHHHHHhccCchHHHHHHHHHHHHHH
Confidence 456677776 6789999999 9999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcccccc---CCCCCCHHHHHHHHhccC
Q psy3879 220 GQGMEIYWRD---NYTCPSEEEYRTMTIRSE 247 (247)
Q Consensus 220 Gq~~~i~~~~---~~~~~~~~~y~~~~~~KT 247 (247)
|+..+..... +.+...+++|..+...||
T Consensus 211 ge~~~~~~~~~~~d~~~~~~e~~e~~~~~KT 241 (384)
T KOG0776|consen 211 GEFTQGLVAGEGLDLDDVGLEYLEFKTLLKT 241 (384)
T ss_pred hhhhcccccccccccCCcchHHHHHHHHHHH
Confidence 9999998873 444458999999999987
No 29
>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=98.53 E-value=3.4e-07 Score=76.37 Aligned_cols=93 Identities=35% Similarity=0.535 Sum_probs=84.5
Q ss_pred hhhhhcccccchhhhcCCCchhhh---hcHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHhccccccC
Q psy3879 154 FDMRIDDIEDNSILRRGIPVAHSI---YGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDN 230 (247)
Q Consensus 154 t~~~~dd~~d~~~lr~g~~t~~~~---~g~~~ai~~~~~l~~~a~q~~~~l~~~~~~~~~~~~~~~l~~Gq~~~i~~~~~ 230 (247)
...+|||++|.+..+++.++++.. +|...+++.++..+..+++.+.....+.....+.+.+.+++.||..|+.|..+
T Consensus 25 ~~~~~DDi~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~d~~~~~~ 104 (243)
T cd00385 25 ASLVHDDIVDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAFEELAREGSPEALEILAEALLDLLEGQLLDLKWRRE 104 (243)
T ss_pred HHHHHhhcccCCCCCCCchhhhhhHHhcCchHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 355789999999999999999988 99999999999999999999987766788999999999999999999999987
Q ss_pred CCCCCHHHHHHHHhccC
Q psy3879 231 YTCPSEEEYRTMTIRSE 247 (247)
Q Consensus 231 ~~~~~~~~y~~~~~~KT 247 (247)
..|+.++|+.+.+.||
T Consensus 105 -~~~t~~ey~~~~~~~t 120 (243)
T cd00385 105 -YVPTLEEYLEYCRYKT 120 (243)
T ss_pred -CCCCHHHHHHHHHHhH
Confidence 5579999999999886
No 30
>PF07307 HEPPP_synt_1: Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1; InterPro: IPR009920 This family contains subunit 1 of bacterial heptaprenyl diphosphate synthase (HEPPP synthase) (2.5.1.30 from EC) (approximately 230 residues long). The enzyme consists of two subunits, both of which are required for catalysis of heptaprenyl diphosphate synthesis, the precursor for the side chain of the isoprenoid quinone menaquinone-7 (MQ-7) [, ].
Probab=97.81 E-value=0.00051 Score=57.72 Aligned_cols=106 Identities=11% Similarity=0.088 Sum_probs=78.3
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCchhhhcchhHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHH
Q psy3879 42 NIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQL 121 (247)
Q Consensus 42 ~~~~~~~~~~a~avElih~asLihDDI~D~s~~RRG~p~~h~~~G~~~Ai~~gd~l~~~~~~~l~~~~~~~~~~~~~~~~ 121 (247)
+.+++.....+.++-++|.|...||.|-. +..+++...- .....|++|||.-+.-+.+|+..++..+++.+++++
T Consensus 29 ~l~~~~~~~~~~a~~LVq~aLDtHd~V~~-~~~~~~~~~k----~RQLtVLAGDy~S~~yY~lLA~~~~i~li~~ls~aI 103 (212)
T PF07307_consen 29 ELSEEEAERYALATMLVQIALDTHDEVDN-AGDESEESSK----ERQLTVLAGDYYSGLYYQLLAESGDISLIRALSEAI 103 (212)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhhhhhcc-ccccccHHHH----hhhhhhhhHHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 34578888999999999999999999966 2222222111 114689999999999999999999999999999999
Q ss_pred HHhHhhhhhhhhhccCCCCCCHHHHHHHhHH-hhhh
Q psy3879 122 LELHRGQGMEIYWRDNYTCPSEEEYRTMTIR-KFDM 156 (247)
Q Consensus 122 ~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~-Kt~~ 156 (247)
.++++....=-. .. ..+.++|++.+.. +|+.
T Consensus 104 ~eiNE~K~~ly~-~~---~~~~e~~~~~~~~ies~l 135 (212)
T PF07307_consen 104 KEINELKMSLYQ-KK---KETAEEYLESVVTIESAL 135 (212)
T ss_pred HHHHHHHHHHHH-hh---hCCHHHHHHHHHHHHHHH
Confidence 999988754322 21 2477887765543 4443
No 31
>KOG0711|consensus
Probab=97.57 E-value=0.00011 Score=64.43 Aligned_cols=108 Identities=22% Similarity=0.193 Sum_probs=77.6
Q ss_pred CCCHHHHHHHhHHhh--------hhhhcccccchhhhcCCCchhhhhcH-HHHHHHHHHHHHHHHHHHhc-CC----ChH
Q psy3879 140 CPSEEEYRTMTIRKF--------DMRIDDIEDNSILRRGIPVAHSIYGI-ASTINAANYVVAIALEKVQS-LG----HPE 205 (247)
Q Consensus 140 ~~s~~~Y~~ii~~Kt--------~~~~dd~~d~~~lr~g~~t~~~~~g~-~~ai~~~~~l~~~a~q~~~~-l~----~~~ 205 (247)
..+++++......-- =++.|||+|.+..|||+|.|..+-|+ ..||+-+-.+-+.-+.++.. +. ..+
T Consensus 71 ~l~~~~~~~a~~lGw~vElLQaffLiaDDIMDnS~tRRGqpCWy~~~gVG~~AINDA~lLea~Iy~lLkk~fr~~~~y~~ 150 (347)
T KOG0711|consen 71 KLDEEELQLALILGWCVELLQAFFLVADDIMDNSKTRRGQPCWYQKPGVGLDAINDAFLLEAAIYKLLKKHFRNIYCYVD 150 (347)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccCCCcceeecCCcchhhhhHHHHHHHHHHHHHHHhccCCccHHH
Confidence 356666654432211 23459999999999999999999999 68999886666666677663 22 246
Q ss_pred HHHHHHHHHHHHHHHHHhcccccc-CCCCCCHHHHHHHHhccC
Q psy3879 206 ATAVYTEQLLELHRGQGMEIYWRD-NYTCPSEEEYRTMTIRSE 247 (247)
Q Consensus 206 ~~~~~~~~~~~l~~Gq~~~i~~~~-~~~~~~~~~y~~~~~~KT 247 (247)
+++.|.+..-.++.|+.+.-.-.+ .....|.+.|-.|+..||
T Consensus 151 l~elf~ev~f~T~lGdllt~~~~~~~ls~fsl~~y~~Iv~~KT 193 (347)
T KOG0711|consen 151 LVELFHEVTFQTELGDLLTTPEGNKDLSKFSLEKYVFIVEYKT 193 (347)
T ss_pred HHHHHHHHHHHHhhhccccCcccchhHhhhhHHHHHHHhhccc
Confidence 788898989999999555433222 223358999999999998
No 32
>PF07307 HEPPP_synt_1: Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1; InterPro: IPR009920 This family contains subunit 1 of bacterial heptaprenyl diphosphate synthase (HEPPP synthase) (2.5.1.30 from EC) (approximately 230 residues long). The enzyme consists of two subunits, both of which are required for catalysis of heptaprenyl diphosphate synthesis, the precursor for the side chain of the isoprenoid quinone menaquinone-7 (MQ-7) [, ].
Probab=86.92 E-value=3 Score=35.18 Aligned_cols=59 Identities=15% Similarity=0.151 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHhccccccCCCCCCHHHHHHHH
Q psy3879 181 ASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMT 243 (247)
Q Consensus 181 ~~ai~~~~~l~~~a~q~~~~l~~~~~~~~~~~~~~~l~~Gq~~~i~~~~~~~~~~~~~y~~~~ 243 (247)
+-.+.+||+.-+.-|+++++.|+-..++.+++++.++.+.+..=..... .+.++|++.+
T Consensus 70 QLtVLAGDy~S~~yY~lLA~~~~i~li~~ls~aI~eiNE~K~~ly~~~~----~~~e~~~~~~ 128 (212)
T PF07307_consen 70 QLTVLAGDYYSGLYYQLLAESGDISLIRALSEAIKEINELKMSLYQKKK----ETAEEYLESV 128 (212)
T ss_pred hhhhhhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHhhh----CCHHHHHHHH
Confidence 4569999999999999999999999999999999999998876544433 2788888764
No 33
>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=72.28 E-value=34 Score=28.97 Aligned_cols=44 Identities=23% Similarity=0.259 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhh
Q psy3879 113 ATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDM 156 (247)
Q Consensus 113 ~~~~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~ 156 (247)
..+.|.+.+.+.+.|...+..++.....||.++|+.+-+..+|.
T Consensus 138 ~~~~~~~~~~~~~~~~~~e~~~~~~~~~ps~eeYl~~R~~t~g~ 181 (270)
T PF03936_consen 138 QIKRFRNSWREYLNAYLWEARWRERGRIPSLEEYLEMRRHTSGV 181 (270)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTTS--SHHHHHHHHHHHTSH
T ss_pred HhhHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHhccccccc
Confidence 34458888889999999998888776679999999887777765
No 34
>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=71.38 E-value=52 Score=28.03 Aligned_cols=45 Identities=24% Similarity=0.247 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhh
Q psy3879 112 EATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDM 156 (247)
Q Consensus 112 ~~~~~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~ 156 (247)
.....+.+.+...+.|...+..+......|+.++|+.+-....|.
T Consensus 122 ~~~~r~~~~~~~~~~~~~~e~~~~~~~~~p~~~eYl~~R~~~~g~ 166 (284)
T cd00868 122 ESLPYLKEAWKDLLRAYLVEAKWANEGYVPSFEEYLENRRVSIGY 166 (284)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHhceehhhH
Confidence 556678888889999999998887665679999999887766544
No 35
>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=67.62 E-value=23 Score=30.95 Aligned_cols=47 Identities=17% Similarity=0.003 Sum_probs=37.4
Q ss_pred ChHHHHHHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhh
Q psy3879 110 HPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDM 156 (247)
Q Consensus 110 ~~~~~~~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~ 156 (247)
.+.....|.+.+.+.+.|+..+..++.....||.++|+++-....|.
T Consensus 127 ~~~~~~r~~~~~~~~~~a~~~e~~~~~~~~~psl~eYl~~R~~~~g~ 173 (303)
T cd00687 127 SAEWFNRFAHYTEDYFDAYIWEGKNRLNGHVPDVAEYLEMRRFNIGA 173 (303)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhhhcccc
Confidence 36667788888999999999998887766679999999776666554
No 36
>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=57.14 E-value=17 Score=31.19 Aligned_cols=40 Identities=28% Similarity=0.286 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHHHHHHhccccccCCCCCCHHHHHHHHh
Q psy3879 205 EATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTI 244 (247)
Q Consensus 205 ~~~~~~~~~~~~l~~Gq~~~i~~~~~~~~~~~~~y~~~~~ 244 (247)
.....+.+.+...+.+...+..|+.....|+.++|+.+-.
T Consensus 122 ~~~~r~~~~~~~~~~~~~~e~~~~~~~~~p~~~eYl~~R~ 161 (284)
T cd00868 122 ESLPYLKEAWKDLLRAYLVEAKWANEGYVPSFEEYLENRR 161 (284)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHhce
Confidence 5667788889999999999999998877899999997643
No 37
>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=50.99 E-value=73 Score=30.73 Aligned_cols=42 Identities=19% Similarity=0.232 Sum_probs=36.2
Q ss_pred ChHHHHHHHHHHHHHHHHHHhccccccCCCCCCHHHHHHHHh
Q psy3879 203 HPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTI 244 (247)
Q Consensus 203 ~~~~~~~~~~~~~~l~~Gq~~~i~~~~~~~~~~~~~y~~~~~ 244 (247)
.+....-+.+++..++.+-..+..|+.....||.++|+++..
T Consensus 354 ~~~~~~~~~~~~~~~~~a~l~EA~w~~~g~vPt~eEYl~~~~ 395 (542)
T cd00684 354 GSYVVPYLKEAWKDLVKAYLVEAKWAHEGYVPTFEEYMENAL 395 (542)
T ss_pred CcchHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhhhh
Confidence 345677788999999999999999999888899999998753
No 38
>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=47.13 E-value=70 Score=27.81 Aligned_cols=41 Identities=20% Similarity=0.039 Sum_probs=35.0
Q ss_pred ChHHHHHHHHHHHHHHHHHHhccccccCCCCCCHHHHHHHH
Q psy3879 203 HPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMT 243 (247)
Q Consensus 203 ~~~~~~~~~~~~~~l~~Gq~~~i~~~~~~~~~~~~~y~~~~ 243 (247)
.+....-+.+.+...+.+...+..|+.+...||.++|+++-
T Consensus 127 ~~~~~~r~~~~~~~~~~a~~~e~~~~~~~~~psl~eYl~~R 167 (303)
T cd00687 127 SAEWFNRFAHYTEDYFDAYIWEGKNRLNGHVPDVAEYLEMR 167 (303)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHHHHHh
Confidence 35667778888999999999999998888889999999764
No 39
>TIGR01476 chlor_syn_BchG bacteriochlorophyll/chlorophyll synthetase. This model describes a subfamily of a large family of polyprenyltransferases (pfam01040) that also includes 4-hydroxybenzoate octaprenyltransferase and protoheme IX farnesyltransferase (heme O synthase). Members of this family are found exclusively in photosynthetic organisms, including a single copy in Arabidopsis thaliana.
Probab=40.83 E-value=1.4e+02 Score=25.99 Aligned_cols=49 Identities=10% Similarity=0.148 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHHHhhhccC-CCCCCCCCCchhhhcchhHHHHHHHHH
Q psy3879 49 LAIGDIIQMLHNSSLLIDDIED-NSILRRGIPVAHSIYGIASTINAANYV 97 (247)
Q Consensus 49 ~~~a~avElih~asLihDDI~D-~s~~RRG~p~~h~~~G~~~Ai~~gd~l 97 (247)
.-++..+-+.-.+.+..+|+.| +.|.+.|++|.-..+|.+.+...--.+
T Consensus 164 ~~~~~~~~l~~~~i~~~nd~~D~~~D~~~G~~Tl~v~lG~~~a~~l~~~l 213 (283)
T TIGR01476 164 VVVALIYSLGAHGIMTLNDFKSVEGDRQLGLRSLPVMIGVKRAAIVAVTT 213 (283)
T ss_pred HHHHHHHHHHHHHHHHHHhccchhhHHHcCCcCcceEEcHHHHHHHHHHH
Confidence 3344455566667788999999 667778999999999999887654443
No 40
>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=39.96 E-value=2e+02 Score=24.49 Aligned_cols=41 Identities=17% Similarity=0.084 Sum_probs=29.7
Q ss_pred HHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhhhhc
Q psy3879 116 VYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRID 159 (247)
Q Consensus 116 ~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~~~d 159 (247)
+-.+.+.+++.|...|+.... -.|.+++..-++.-+|.+.-
T Consensus 88 l~~~~l~~li~~~~~dl~~~~---~~t~~~L~~Y~~~vag~vg~ 128 (267)
T PF00494_consen 88 LPREPLLELIDGMEMDLEFTP---YETFADLERYCYYVAGSVGL 128 (267)
T ss_dssp HHHHHHHHHHHHHHHCTT-S-----SSHHHHHHHHHHHTHHHHH
T ss_pred hhHHHHHHHHHHhcccccCCC---CCCHHHHHHHHHHHHHHHHH
Confidence 445667889999999987543 35888888888888887653
No 41
>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=39.14 E-value=3.6e+02 Score=25.96 Aligned_cols=91 Identities=15% Similarity=0.205 Sum_probs=62.0
Q ss_pred ChHHHHHHHHHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhhhh-------------------------------
Q psy3879 110 HPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRI------------------------------- 158 (247)
Q Consensus 110 ~~~~~~~~~~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~~~------------------------------- 158 (247)
.+.....+.+.+.+++.+-..+..|......||.++|+++...-+|.-.
T Consensus 354 ~~~~~~~~~~~~~~~~~a~l~EA~w~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~e~~e~~~~~~~l~~~~ 433 (542)
T cd00684 354 GSYVVPYLKEAWKDLVKAYLVEAKWAHEGYVPTFEEYMENALVSIGLGPLLLTSFLGMGDILTEEAFEWLESRPKLVRAS 433 (542)
T ss_pred CcchHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhhhhHHhhHHHHHHHHHHhcCCCCCHHHHHHHhccHHHHHHH
Confidence 3456677888999999999999999987778999999988776654421
Q ss_pred -------cccccc-hhhhcCC-Cchhhhh------cHHHHHHHHHHHHHHHHHHHhc
Q psy3879 159 -------DDIEDN-SILRRGI-PVAHSIY------GIASTINAANYVVAIALEKVQS 200 (247)
Q Consensus 159 -------dd~~d~-~~lr~g~-~t~~~~~------g~~~ai~~~~~l~~~a~q~~~~ 200 (247)
+|+... ....+|. ++...+| ..+.|+.....++..+++.+..
T Consensus 434 ~~i~rL~NDi~S~~kE~~rGdv~n~V~~ymke~g~s~eeA~~~i~~~ie~~wk~ln~ 490 (542)
T cd00684 434 STIGRLMNDIATYEDEMKRGDVASSIECYMKEYGVSEEEAREEIKKMIEDAWKELNE 490 (542)
T ss_pred HHHHHHhcChhhhHHHHhcCCcccHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 233221 2334554 4444443 3567777777777777766664
No 42
>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=39.11 E-value=40 Score=28.51 Aligned_cols=39 Identities=26% Similarity=0.295 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHHHHhccccccCCCCCCHHHHHHHHh
Q psy3879 206 ATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTI 244 (247)
Q Consensus 206 ~~~~~~~~~~~l~~Gq~~~i~~~~~~~~~~~~~y~~~~~ 244 (247)
....+.+.+...+.|...+..|+.+...||.++|+.+-+
T Consensus 138 ~~~~~~~~~~~~~~~~~~e~~~~~~~~~ps~eeYl~~R~ 176 (270)
T PF03936_consen 138 QIKRFRNSWREYLNAYLWEARWRERGRIPSLEEYLEMRR 176 (270)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTTS--SHHHHHHHHH
T ss_pred HhhHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHhcc
Confidence 445688999999999999999999888899999998743
No 43
>KOG1345|consensus
Probab=37.24 E-value=22 Score=31.63 Aligned_cols=21 Identities=19% Similarity=0.438 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHhhhc
Q psy3879 48 LLAIGDIIQMLHNSSLLIDDI 68 (247)
Q Consensus 48 ~~~~a~avElih~asLihDDI 68 (247)
...++.|+|++|.--|||.||
T Consensus 127 ~~ql~SAi~fMHsknlVHRdl 147 (378)
T KOG1345|consen 127 FAQLLSAIEFMHSKNLVHRDL 147 (378)
T ss_pred HHHHHHHHHHhhccchhhccc
Confidence 457889999999999999998
No 44
>PLN02878 homogentisate phytyltransferase
Probab=36.72 E-value=41 Score=29.67 Aligned_cols=40 Identities=18% Similarity=0.089 Sum_probs=35.6
Q ss_pred hhccccc-chhhhcCCCchhhhhcHHHHHHHHHHHHHHHHH
Q psy3879 157 RIDDIED-NSILRRGIPVAHSIYGIASTINAANYVVAIALE 196 (247)
Q Consensus 157 ~~dd~~d-~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q 196 (247)
++.|+.| ++|.+.|..|.+..+|.+.+....-.++..||-
T Consensus 174 i~KDi~DieGD~~~Gi~Tlpv~lG~~~~~~i~~~ll~~aY~ 214 (280)
T PLN02878 174 LFKDIPDVEGDRIFGIRSFSVRLGQKRVFWLCVNLLEMAYA 214 (280)
T ss_pred HHhhCcCchhHHHCCCceechhhChHHHHHHHHHHHHHHHH
Confidence 5688888 589999999999999999999888888888885
No 45
>PLN02279 ent-kaur-16-ene synthase
Probab=35.03 E-value=1.9e+02 Score=29.45 Aligned_cols=38 Identities=26% Similarity=0.379 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHHhccccccCCCCCCHHHHHHH
Q psy3879 205 EATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTM 242 (247)
Q Consensus 205 ~~~~~~~~~~~~l~~Gq~~~i~~~~~~~~~~~~~y~~~ 242 (247)
.++..+.+++..++.+=..+-.|......||.+||++.
T Consensus 590 ~v~~~l~~aW~~ll~ayl~EAeW~~~g~vPT~eEYL~n 627 (784)
T PLN02279 590 NVTSHIIKIWLDLLKSMLTEAQWSSNKSTPTLDEYMTN 627 (784)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhh
Confidence 56777888899999999999999998888999999975
No 46
>PRK13591 ubiA prenyltransferase; Provisional
Probab=32.89 E-value=31 Score=30.88 Aligned_cols=39 Identities=18% Similarity=0.056 Sum_probs=32.2
Q ss_pred hhccccc-chhhhcCCCchhhhhcHHHHHHHHHHHHHHHH
Q psy3879 157 RIDDIED-NSILRRGIPVAHSIYGIASTINAANYVVAIAL 195 (247)
Q Consensus 157 ~~dd~~d-~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~ 195 (247)
+..|+.| ++|.+.|+.|.+..+|.+.|....-.++..++
T Consensus 197 iindirDiEGDr~~G~kTLPV~lG~~~A~~l~~~l~~~~~ 236 (307)
T PRK13591 197 CVYDFKDVKGDTLAGIKTLPVSLGEQKTRNLLLGIHLFSH 236 (307)
T ss_pred HHHHhhhhHhHHHcCCeeEEEEECHHHHHHHHHHHHHHHH
Confidence 3588888 58999999999999999999877766666555
No 47
>PRK12887 ubiA tocopherol phytyltransferase; Reviewed
Probab=31.68 E-value=58 Score=28.99 Aligned_cols=41 Identities=15% Similarity=0.116 Sum_probs=33.8
Q ss_pred hhccccc-chhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHH
Q psy3879 157 RIDDIED-NSILRRGIPVAHSIYGIASTINAANYVVAIALEK 197 (247)
Q Consensus 157 ~~dd~~d-~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~ 197 (247)
+..|+.| ++|.+.|+.|.+..+|...+....-.++..+|-.
T Consensus 200 l~~di~D~egD~~~Gi~Tlav~lG~~~a~~l~~~ll~~~y~~ 241 (308)
T PRK12887 200 IFKDIPDMEGDRQYQITTFTLRLGKQAVFKLSCWVLTACYLG 241 (308)
T ss_pred HHHhccchhhHHHcCCcchhHHHhHHHHHHHHHHHHHHHHHH
Confidence 3578888 5799999999999999999988777777776643
No 48
>PRK12869 ubiA protoheme IX farnesyltransferase; Reviewed
Probab=31.23 E-value=50 Score=28.80 Aligned_cols=38 Identities=26% Similarity=0.303 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhhhccCCCCCCCCCCchhhhcchhHHHHHH
Q psy3879 55 IQMLHNSSLLIDDIEDNSILRRGIPVAHSIYGIASTINAA 94 (247)
Q Consensus 55 vElih~asLihDDI~D~s~~RRG~p~~h~~~G~~~Ai~~g 94 (247)
...-|.+++..+|+.|+ .|.|.|+.-.++|.+.|...-
T Consensus 171 w~~~~~~~l~~~d~edd--~~~G~~tlpv~~G~~~a~~~~ 208 (279)
T PRK12869 171 WTPGHIWSLALKYREDY--RRAGVPMLPAVVGEKTSVRAI 208 (279)
T ss_pred HHHHHHHHHHHHhHHhH--HHcCCeecceeecHHHHHHHH
Confidence 45567888888999777 788999999999998775443
No 49
>TIGR01476 chlor_syn_BchG bacteriochlorophyll/chlorophyll synthetase. This model describes a subfamily of a large family of polyprenyltransferases (pfam01040) that also includes 4-hydroxybenzoate octaprenyltransferase and protoheme IX farnesyltransferase (heme O synthase). Members of this family are found exclusively in photosynthetic organisms, including a single copy in Arabidopsis thaliana.
Probab=28.51 E-value=51 Score=28.70 Aligned_cols=39 Identities=10% Similarity=0.167 Sum_probs=30.7
Q ss_pred hhccccc-chhhhcCCCchhhhhcHHHHHHHHHHHHHHHH
Q psy3879 157 RIDDIED-NSILRRGIPVAHSIYGIASTINAANYVVAIAL 195 (247)
Q Consensus 157 ~~dd~~d-~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~ 195 (247)
+.+|+.| .+|.++|++|.+..+|...+....-.++..++
T Consensus 179 ~~nd~~D~~~D~~~G~~Tl~v~lG~~~a~~l~~~l~~~~~ 218 (283)
T TIGR01476 179 TLNDFKSVEGDRQLGLRSLPVMIGVKRAAIVAVTTINVFQ 218 (283)
T ss_pred HHHhccchhhHHHcCCcCcceEEcHHHHHHHHHHHHHHHH
Confidence 4578888 68999999999999999988776655544443
No 50
>PRK13105 ubiA prenyltransferase; Reviewed
Probab=27.65 E-value=79 Score=27.83 Aligned_cols=39 Identities=21% Similarity=0.213 Sum_probs=0.0
Q ss_pred hhccccc-chhhhcCCCchhhhhcHHHHHHHHHHHHHHHH
Q psy3879 157 RIDDIED-NSILRRGIPVAHSIYGIASTINAANYVVAIAL 195 (247)
Q Consensus 157 ~~dd~~d-~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~ 195 (247)
++.++.| ++|.+.|+.|.+..+|.+.|......++..++
T Consensus 178 ii~~irDie~Dr~~G~~Tlpv~lG~~~a~~~~~~l~~~a~ 217 (282)
T PRK13105 178 AFGAVQDVVADREAGIASIATVLGARRTVRLAVGLYAAAA 217 (282)
T ss_pred HHHhCcchHhHHHcCCccchHHhcHHHHHHHHHHHHHHHH
No 51
>PRK13387 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Provisional
Probab=26.40 E-value=58 Score=29.10 Aligned_cols=40 Identities=5% Similarity=-0.022 Sum_probs=34.0
Q ss_pred hhccccc-chhhhcCCCchhhhhcHHHHHHHHHHHHHHHHH
Q psy3879 157 RIDDIED-NSILRRGIPVAHSIYGIASTINAANYVVAIALE 196 (247)
Q Consensus 157 ~~dd~~d-~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q 196 (247)
+.+++.| ++|.+.|+.|.+..+|.+.|......++..+|-
T Consensus 207 l~Nn~~D~e~D~~~gk~TL~v~lG~~~a~~l~~~l~~~a~l 247 (317)
T PRK13387 207 LANNLRDLDEDIKNHRYTLVYYIGREKGVVLFAILFYASYL 247 (317)
T ss_pred HhcCCccchhHHHcCCeeeeeeEcHHhHHHHHHHHHHHHHH
Confidence 4478888 689999999999999999999888777777764
No 52
>TIGR02235 menA_cyano-plnt 1,4-dihydroxy-2-naphthoate phytyltransferase. This family of phytyltransferases, found in plants and cyanobacteria, are involved in the biosythesis of phylloquinone (Vitamin K1). Phylloquinone is a critical component of photosystem I. The closely related MenA enzyme from bacteria transfers a prenyl group (which only differs in the saturation of the isoprenyl groups) in the biosynthesis of menaquinone. Activity towards both substrates in certain organisms should be considered a possibility.
Probab=26.01 E-value=75 Score=27.96 Aligned_cols=38 Identities=11% Similarity=0.164 Sum_probs=33.2
Q ss_pred ccccc-chhhhcCCCchhhhhcHHHHHHHHHHHHHHHHH
Q psy3879 159 DDIED-NSILRRGIPVAHSIYGIASTINAANYVVAIALE 196 (247)
Q Consensus 159 dd~~d-~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q 196 (247)
+++.| ++|.+.|+.|....+|.+.|......++..+|-
T Consensus 181 Nn~rD~e~D~~~Gk~TL~v~lG~~~a~~l~~~l~~~~y~ 219 (285)
T TIGR02235 181 SHFHQVEDDLAHGKRSPVVRLGTKLAAKIVPWVISLSYV 219 (285)
T ss_pred cCCccchhHHHcCCcceeheecHHhHHHHHHHHHHHHHH
Confidence 67888 579999999999999999999988888877774
No 53
>PLN02922 prenyltransferase
Probab=25.36 E-value=76 Score=28.37 Aligned_cols=41 Identities=7% Similarity=0.036 Sum_probs=34.6
Q ss_pred hccccc-chhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHHH
Q psy3879 158 IDDIED-NSILRRGIPVAHSIYGIASTINAANYVVAIALEKV 198 (247)
Q Consensus 158 ~dd~~d-~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~~ 198 (247)
.+++.| ++|.+.|+.|++..+|.+.+......++..+|-.+
T Consensus 207 ~Nn~rD~e~D~~~Gk~TL~v~lG~~~a~~l~~~l~~~~y~~~ 248 (315)
T PLN02922 207 CSHFHQIDGDRAVGKMSPLVRLGTEKGSRVVRWAVLLLYSLL 248 (315)
T ss_pred HccCcchhhHHHcCccceeeEEChHHHHHHHHHHHHHHHHHH
Confidence 367888 57999999999999999999998888888777443
No 54
>PRK12882 ubiA prenyltransferase; Reviewed
Probab=24.94 E-value=3.3e+02 Score=23.49 Aligned_cols=72 Identities=14% Similarity=0.139 Sum_probs=0.0
Q ss_pred HHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhhhccC-CCCCCCCCCchhhhcchhHHHHHHHHHHHHHH
Q psy3879 31 TKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIED-NSILRRGIPVAHSIYGIASTINAANYVVAIAL 102 (247)
Q Consensus 31 ~~l~~~~~~~~~~~~~~~~~~a~avElih~asLihDDI~D-~s~~RRG~p~~h~~~G~~~Ai~~gd~l~~~~~ 102 (247)
+..+...+-...........++..+=+.-.+-.+..|+.| +++.+.|.||.-.++|.+.+....-.+....+
T Consensus 142 ~~~~~g~~~~~~~~~~~~~~l~~~~fl~~~~~~~~~~~~D~e~D~~~G~~tlpv~~G~~~t~~~~~~~~~~~~ 214 (276)
T PRK12882 142 STFLFGGAAVGTEGLLALLVLFALAALATLAREIIKDVEDIEGDRAEGARTLPILIGVRKALYVAAAFLLVAV 214 (276)
T ss_pred HHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHcCCccccHHhhHHHHHHHHHHHHHHHH
No 55
>TIGR02056 ChlG chlorophyll synthase, ChlG. This model represents the strictly cyanobacterial and plant-specific chlorophyll synthase ChlG. ChlG is the enzyme (esterase) which attaches the side chain moiety onto chlorophyllide a. Both geranylgeranyl and phytyl pyrophosphates are substrates to varying degrees in enzymes from different sources. Thus, ChlG may act as the final or penultimate step in chlorophyll biosynthesis (along with the geranylgeranyl reductase, ChlP).
Probab=24.47 E-value=3.6e+02 Score=23.80 Aligned_cols=52 Identities=10% Similarity=0.125 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHHHHhhhccC-CCCCCCCCCchhhhcchhHHHHHHHHHHH
Q psy3879 48 LLAIGDIIQMLHNSSLLIDDIED-NSILRRGIPVAHSIYGIASTINAANYVVA 99 (247)
Q Consensus 48 ~~~~a~avElih~asLihDDI~D-~s~~RRG~p~~h~~~G~~~Ai~~gd~l~~ 99 (247)
..-++..+=+.=.+.++.+|+.| +.|.|.|++|.-..+|.+.+......++.
T Consensus 185 ~~l~~~~~~l~~~~i~~~n~~~D~e~D~~~G~~Tlpv~lG~~~a~~~~~~l~~ 237 (306)
T TIGR02056 185 IAVLTLIYSIAGLGIAIVNDFKSVEGDRALGLQSLPVAFGIETAAWICVGAID 237 (306)
T ss_pred HHHHHHHHHHHHHHHHHHHHccChHHHHHcCCcCcchhcChHHHHHHHHHHHH
Confidence 33444444456667778899988 44557799999999999988776664443
No 56
>PRK07419 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Provisional
Probab=23.62 E-value=75 Score=28.29 Aligned_cols=40 Identities=10% Similarity=0.100 Sum_probs=33.9
Q ss_pred hccccc-chhhhcCCCchhhhhcHHHHHHHHHHHHHHHHHH
Q psy3879 158 IDDIED-NSILRRGIPVAHSIYGIASTINAANYVVAIALEK 197 (247)
Q Consensus 158 ~dd~~d-~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~q~ 197 (247)
.+++.| ++|.+.|+.|++..+|.+.|......++..+|-.
T Consensus 193 ~Nn~rD~e~D~~~Gk~TL~v~lG~~~a~~ly~~l~~~ay~~ 233 (304)
T PRK07419 193 CSHFHQVEDDLAAGKRSPIVRLGTKRGAQLLPWIVGLIYAL 233 (304)
T ss_pred HcCCcchhhHHHcCCcceeeeechHhHHHHHHHHHHHHHHH
Confidence 377888 5799999999999999999998888887777743
No 57
>PRK12869 ubiA protoheme IX farnesyltransferase; Reviewed
Probab=23.04 E-value=4.8e+02 Score=22.61 Aligned_cols=58 Identities=10% Similarity=0.050 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhhccCCCC----CC-CCCCchhhhcchhHHHHHHHHHHHHHHHH
Q psy3879 47 KLLAIGDIIQMLHNSSLLIDDIEDNSI----LR-RGIPVAHSIYGIASTINAANYVVAIALEK 104 (247)
Q Consensus 47 ~~~~~a~avElih~asLihDDI~D~s~----~R-RG~p~~h~~~G~~~Ai~~gd~l~~~~~~~ 104 (247)
.......+.=++++++.+..|+.|.+- .| +.+|-.-..-....|...+-.++..++-.
T Consensus 37 ~~~l~~~~~~l~~~a~~~~Nd~~D~~iD~~~~Rt~~RPl~sG~is~~~a~~~~~~~~~~~~~l 99 (279)
T PRK12869 37 PLIPLLIGGTLASGGSAAFNHGIERDIDKVMSRTSKRPTPVGLVNRKEALAVGSALSALGTAL 99 (279)
T ss_pred HHHHHHHHHHHHHHHHHHHhchHhcCCCCCCCCCCCCCcCCCCcCHHHHHHHHHHHHHHHHHH
Confidence 445566677889999999999966432 23 56887777778888877776665555443
No 58
>TIGR00751 menA 1,4-dihydroxy-2-naphthoate octaprenyltransferase. This membrane-associated enzyme converts 1,4-dihydroxy-2-naphthoic acid (DHNA) to demethylmenaquinone, a step in menaquinone biosynthesis.
Probab=22.52 E-value=1e+02 Score=27.14 Aligned_cols=37 Identities=22% Similarity=0.127 Sum_probs=32.3
Q ss_pred ccccc-chhhhcCCCchhhhhcHHHHHHHHHHHHHHHH
Q psy3879 159 DDIED-NSILRRGIPVAHSIYGIASTINAANYVVAIAL 195 (247)
Q Consensus 159 dd~~d-~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~ 195 (247)
+++.| .+|.+.|+.|.+..+|.+.|....-.++..+|
T Consensus 184 Nn~~D~~~D~~~Gk~Tl~v~lG~~~a~~l~~~l~~~ay 221 (284)
T TIGR00751 184 NNLRDIPTDARAGKNTLAVRLGDARTRMYHQGLLAVAG 221 (284)
T ss_pred cCcccchhHHHcCCEeehhhcchHhHHHHHHHHHHHHH
Confidence 67777 47999999999999999999988888877776
No 59
>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=21.67 E-value=4.8e+02 Score=22.34 Aligned_cols=37 Identities=11% Similarity=-0.033 Sum_probs=24.3
Q ss_pred HHHHHhHhhhhhhhhhccCCCCCCHHHHHHHhHHhhhhhh
Q psy3879 119 EQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRI 158 (247)
Q Consensus 119 ~~~~~~~~Gq~~dl~~~~~~~~~s~~~Y~~ii~~Kt~~~~ 158 (247)
+.+.+++.|...|+.... -.|.+++..-+++-.|.+.
T Consensus 86 ~~~~~li~~~~~Dl~~~~---~~t~~eL~~Y~~~vAg~vg 122 (266)
T TIGR03464 86 EPFLDLLDAFRQDVVVTR---YATWAELLDYCRYSANPVG 122 (266)
T ss_pred HHHHHHHHHHHHhccCCC---CCCHHHHHHHHHHhHHHHH
Confidence 356677788888876442 3577777666666666544
No 60
>PRK12872 ubiA prenyltransferase; Reviewed
Probab=21.19 E-value=1.1e+02 Score=26.58 Aligned_cols=39 Identities=18% Similarity=0.194 Sum_probs=0.0
Q ss_pred hhccccc-chhhhcCCCchhhhhcHHHHHHHHHHHHHHHH
Q psy3879 157 RIDDIED-NSILRRGIPVAHSIYGIASTINAANYVVAIAL 195 (247)
Q Consensus 157 ~~dd~~d-~~~lr~g~~t~~~~~g~~~ai~~~~~l~~~a~ 195 (247)
+..|+.| ++|.+.|.+|.+..+|.+.+....-.+...++
T Consensus 179 ~~~d~~D~e~D~~~G~~Tlpv~lG~~~t~~~~~~~~~~~~ 218 (285)
T PRK12872 179 IVFDIKDIEGDRKSGLKTLPIVLGKERTLKFLLILNLLFL 218 (285)
T ss_pred HHHhcccchhHHHcCCcccchhcchHHHHHHHHHHHHHHH
No 61
>PRK11409 antitoxin YefM; Provisional
Probab=20.09 E-value=1.2e+02 Score=21.28 Aligned_cols=62 Identities=15% Similarity=0.093 Sum_probs=35.6
Q ss_pred HHHHhhhccCCCC----CCCCCCchhhhcchhHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHhHhhhhhh
Q psy3879 61 SSLLIDDIEDNSI----LRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGME 131 (247)
Q Consensus 61 asLihDDI~D~s~----~RRG~p~~h~~~G~~~Ai~~gd~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gq~~d 131 (247)
..-+.|++.++.+ +|+|.|.+ |+..--=+..-.+.+.-+.+|...+.+.+++.++-.|+...
T Consensus 13 l~~~l~~v~~~~epv~ITr~g~~~~---------Vl~S~~~yesl~Etl~ll~~p~~~~~l~~~i~~~~~G~~~~ 78 (83)
T PRK11409 13 LSATMMKAVEDHAPILITRQNGEAC---------VLMSLEEYNSLEETAYLLRSPANARRLMDSIDSLKSGKGTE 78 (83)
T ss_pred HHHHHHHHhccCCcEEEEeCCCCCE---------EEEeHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHcCCCcc
Confidence 3446677766554 47777643 22221111111222333357888888889998888887653
Done!