Query 047640
Match_columns 111
No_of_seqs 127 out of 1102
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 13:11:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047640.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047640hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10581 geranyltranstransfera 99.9 4.1E-25 9E-30 168.0 12.1 107 1-108 113-224 (299)
2 COG0142 IspA Geranylgeranyl py 99.9 6.8E-25 1.5E-29 168.2 11.8 100 1-109 113-216 (322)
3 TIGR02748 GerC3_HepT heptapren 99.9 2.3E-23 5E-28 159.5 11.5 97 1-108 110-211 (319)
4 PLN02890 geranyl diphosphate s 99.9 2.6E-23 5.7E-28 164.2 11.5 97 1-108 208-309 (422)
5 PRK10888 octaprenyl diphosphat 99.9 3.6E-23 7.8E-28 158.8 11.7 97 1-108 111-212 (323)
6 TIGR02749 prenyl_cyano solanes 99.9 4.2E-23 9E-28 158.3 11.6 97 1-108 114-215 (322)
7 KOG0776 Geranylgeranyl pyropho 99.9 8.3E-23 1.8E-27 158.6 9.8 105 1-108 177-282 (384)
8 PLN02857 octaprenyl-diphosphat 99.9 2.6E-22 5.6E-27 158.4 11.7 97 1-108 208-309 (416)
9 CHL00151 preA prenyl transfera 99.9 1E-21 2.3E-26 150.6 12.0 97 1-108 115-216 (323)
10 cd00685 Trans_IPPS_HT Trans-Is 99.9 5E-21 1.1E-25 142.4 11.8 100 1-108 86-190 (259)
11 PF00348 polyprenyl_synt: Poly 99.8 2.8E-20 6.1E-25 138.5 11.2 103 1-108 80-187 (260)
12 cd00867 Trans_IPPS Trans-Isopr 99.7 3.1E-17 6.7E-22 119.3 11.3 97 1-108 66-167 (236)
13 cd00385 Isoprenoid_Biosyn_C1 I 98.9 4.9E-08 1.1E-12 68.7 11.9 96 2-108 61-161 (243)
14 KOG0777 Geranylgeranyl pyropho 98.7 4.5E-08 9.7E-13 72.8 7.1 92 2-108 103-200 (322)
15 KOG0711 Polyprenyl synthetase 97.6 0.00023 4.9E-09 55.1 6.7 68 41-108 160-236 (347)
16 PLN02632 phytoene synthase 91.3 1.1 2.5E-05 34.7 7.1 64 41-107 143-211 (334)
17 PF00494 SQS_PSY: Squalene/phy 88.2 2 4.3E-05 31.6 6.1 61 41-106 94-157 (267)
18 cd00683 Trans_IPPS_HH Trans-Is 87.3 2.1 4.5E-05 31.7 5.7 60 41-106 96-158 (265)
19 PF07307 HEPPP_synt_1: Heptapr 84.4 11 0.00024 27.7 8.1 64 1-75 75-140 (212)
20 TIGR03465 HpnD squalene syntha 82.0 13 0.00028 27.6 8.0 59 41-106 88-149 (266)
21 TIGR03464 HpnC squalene syntha 76.5 23 0.0005 26.3 7.8 60 41-106 89-150 (266)
22 PF06783 UPF0239: Uncharacteri 73.0 3.8 8.1E-05 26.0 2.4 19 88-106 16-35 (85)
23 TIGR01559 squal_synth farnesyl 71.3 33 0.00071 26.9 7.7 65 41-106 111-180 (336)
24 PF10655 DUF2482: Hypothetical 44.2 35 0.00076 22.1 3.1 24 55-78 8-31 (100)
25 PF07077 DUF1345: Protein of u 21.5 47 0.001 23.6 0.9 26 85-110 129-154 (180)
26 PF13062 DUF3924: Protein of u 21.4 83 0.0018 18.2 1.8 26 58-83 17-42 (62)
27 PF13072 DUF3936: Protein of u 20.3 64 0.0014 17.3 1.1 27 81-107 11-38 (38)
No 1
>PRK10581 geranyltranstransferase; Provisional
Probab=99.93 E-value=4.1e-25 Score=168.01 Aligned_cols=107 Identities=15% Similarity=0.200 Sum_probs=93.5
Q ss_pred ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640 1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA 77 (111)
Q Consensus 1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~ 77 (111)
+||+|+++||+++++... ..+.+...+++++.++++.|..+||.||++|+.+. .++++|++|+++|||+||++|+.
T Consensus 113 ~GD~L~~~a~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~GQ~ld~~~~~~~~~~~~y~~i~~~KTa~L~~~~~~ 191 (299)
T PRK10581 113 AGDALQTLAFSILSDAPM-PEVSDRDRISMISELASASGIAGMCGGQALDLEAEGKQVPLDALERIHRHKTGALIRAAVR 191 (299)
T ss_pred HHHHHHHHHHHHHHhCCC-ccCChHHHHHHHHHHHHhcccchhhHhhHHHHhccCCCCCHHHHHHHHHHhhHHHHHHHHH
Confidence 599999999999987642 12344567788888998878899999999999873 78899999999999999999999
Q ss_pred HHHHhCCCCH-HHHHHHH-HhHHhhHhhhhhcC
Q 047640 78 CGAILGGGSV-EEIEKKF-RGLIIKITKMMIRN 108 (111)
Q Consensus 78 ~Gai~~g~~~-e~~~~l~-~G~~~GiafQi~D~ 108 (111)
+|++++|+++ +.++.++ ||+++|+||||+||
T Consensus 192 ~gailag~~~~~~~~~l~~~g~~lG~aFQI~DD 224 (299)
T PRK10581 192 LGALSAGDKGRRALPVLDRYAESIGLAFQVQDD 224 (299)
T ss_pred HHHHHcCCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999864 5789999 99999999999998
No 2
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=99.92 E-value=6.8e-25 Score=168.22 Aligned_cols=100 Identities=23% Similarity=0.295 Sum_probs=91.5
Q ss_pred ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHHH
Q 047640 1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGAA 77 (111)
Q Consensus 1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~~ 77 (111)
+||+|+++||+++++.++ + ..++++.++.++ .+||+||++|+.++ +|+++|.+|+++|||+||++|+.
T Consensus 113 aGD~L~~~Af~~l~~~~~-----~--~~~~~~~~~~~~--~~~~~GQ~lDl~~~~~~~t~e~y~~~i~~KTa~L~~~a~~ 183 (322)
T COG0142 113 AGDALLAAAFELLSKLGS-----E--ALEAIKALAEAI--NGLCGGQALDLAFENKPVTLEEYLRVIELKTAALFAAAAV 183 (322)
T ss_pred HHHHHHHHHHHHHHhCCc-----h--hHHHHHHHHHHH--HHHHHhHHHHHHccCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 599999999999999853 1 456777788887 99999999999885 78999999999999999999999
Q ss_pred HHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcCC
Q 047640 78 CGAILGGGSVEEIEKKF-RGLIIKITKMMIRNS 109 (111)
Q Consensus 78 ~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~~ 109 (111)
+||++++++++..+.++ ||+++|+||||+||-
T Consensus 184 ~ga~la~~~~~~~~~l~~~g~~lGlaFQi~DDi 216 (322)
T COG0142 184 LGAILAGADEELLEALEDYGRNLGLAFQIQDDI 216 (322)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHhhHHHHHHHHh
Confidence 99999999999999999 999999999999984
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=99.90 E-value=2.3e-23 Score=159.50 Aligned_cols=97 Identities=15% Similarity=0.256 Sum_probs=87.2
Q ss_pred ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640 1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA 76 (111)
Q Consensus 1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~ 76 (111)
+||+|+++||+++++.++ .++++.+++++ ..|+.||++|+... .+++.|.+|+++|||+||++||
T Consensus 110 ~GD~L~~~a~~~l~~~~~---------~~~~~~~~~~~--~~~~~Gq~~~~~~~~~~~~~~~~Y~~~i~~KTa~L~~~~~ 178 (319)
T TIGR02748 110 TGDYLFAKSLETMTEIKD---------PRAHQILSHTI--VEVCRGEIEQIKDKYNFDQNLRTYLRRIKRKTALLIAASC 178 (319)
T ss_pred HHHHHHHHHHHHHHhCCc---------HHHHHHHHHHH--HHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 599999999999987631 24566778888 89999999999763 6789999999999999999999
Q ss_pred HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640 77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN 108 (111)
Q Consensus 77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~ 108 (111)
.+|++++|++++.++.++ ||.++|++|||+||
T Consensus 179 ~~ga~~ag~~~~~~~~l~~~g~~lG~aFQI~DD 211 (319)
T TIGR02748 179 QLGAIASGANEAIVKKLYWFGYYVGMSYQITDD 211 (319)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999 99999999999998
No 4
>PLN02890 geranyl diphosphate synthase
Probab=99.90 E-value=2.6e-23 Score=164.21 Aligned_cols=97 Identities=20% Similarity=0.224 Sum_probs=88.1
Q ss_pred ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640 1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA 76 (111)
Q Consensus 1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~ 76 (111)
+||+|+++|++.+++..+ .++++.+++++ ..|++||++|+.+. .++++|.+|+.+|||+||++||
T Consensus 208 aGD~Lla~A~~~l~~~~~---------~~~~~~~s~a~--~~l~~Gq~ld~~~~~~~~~s~~~Yl~~i~~KTa~Lf~~s~ 276 (422)
T PLN02890 208 AGDFLLSRACVALAALKN---------TEVVSLLATAV--EHLVTGETMQITSSREQRRSMDYYMQKTYYKTASLISNSC 276 (422)
T ss_pred HHHHHHHHHHHHHHcCCc---------HHHHHHHHHHH--HHHHHHHHHHHHhccCCCCCHHHHHHHHHHhHHHHHHHHH
Confidence 599999999999987631 35667788888 99999999999763 7899999999999999999999
Q ss_pred HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640 77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN 108 (111)
Q Consensus 77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~ 108 (111)
.+||+++|++++.++.++ ||+++|+||||+||
T Consensus 277 ~~gAilaga~~~~~~~l~~fG~~lGlAFQI~DD 309 (422)
T PLN02890 277 KAVAILAGQTAEVAVLAFEYGRNLGLAFQLIDD 309 (422)
T ss_pred HHHHHHcCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999 99999999999998
No 5
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=99.90 E-value=3.6e-23 Score=158.78 Aligned_cols=97 Identities=21% Similarity=0.263 Sum_probs=87.2
Q ss_pred ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640 1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA 76 (111)
Q Consensus 1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~ 76 (111)
+||+|+++||+++++.+ . .+++..+++++ ..|++||++|+... .++++|.+|+.+|||+||++||
T Consensus 111 ~GD~L~~~a~~~l~~~~------~---~~~~~~~~~~~--~~~~~Gq~~d~~~~~~~~~s~~~y~~~i~~KTa~lf~~~~ 179 (323)
T PRK10888 111 VGDFIYTRAFQMMTSLG------S---LKVLEVMSEAV--NVIAEGEVLQLMNVNDPDITEENYMRVIYSKTARLFEAAA 179 (323)
T ss_pred HHHHHHHHHHHHHHhCC------C---HHHHHHHHHHH--HHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 59999999999998763 1 24566678888 89999999999752 7889999999999999999999
Q ss_pred HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640 77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN 108 (111)
Q Consensus 77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~ 108 (111)
++|++++|.++++++.++ ||+++|+||||+||
T Consensus 180 ~~ga~lag~~~~~~~~l~~~g~~lG~aFQi~DD 212 (323)
T PRK10888 180 QCSGILAGCTPEQEKGLQDYGRYLGTAFQLIDD 212 (323)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999 99999999999998
No 6
>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=99.90 E-value=4.2e-23 Score=158.34 Aligned_cols=97 Identities=14% Similarity=0.169 Sum_probs=86.9
Q ss_pred ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640 1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA 76 (111)
Q Consensus 1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~ 76 (111)
+||+|+++|++++++.++ .++++.+++++ ..|+.||++|+... .++++|.+|+.+|||+||++||
T Consensus 114 ~GD~l~~~a~~~l~~~~~---------~~~~~~~~~~~--~~~~~Gq~~~~~~~~~~~~~~~~y~~~~~~KTa~L~~~~~ 182 (322)
T TIGR02749 114 AGDFLFAQASWYLANLEN---------LEVVKLISKVI--TDFAEGEIKQGLNQFDSDLSLEDYLEKSFYKTASLVAASS 182 (322)
T ss_pred HHHHHHHHHHHHHHhcCC---------HHHHHHHHHHH--HHHHHHHHHHHHcccCCCCCHHHHHHHHHccHHHHHHHHH
Confidence 599999999999987632 24566678887 88999999998652 7899999999999999999999
Q ss_pred HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640 77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN 108 (111)
Q Consensus 77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~ 108 (111)
.+|++++|+++++++.++ ||.++|+||||+||
T Consensus 183 ~~ga~~ag~~~~~~~~l~~~G~~lG~aFQi~DD 215 (322)
T TIGR02749 183 KAAAVLSDVPSQVANDLYEYGKHLGLAFQVVDD 215 (322)
T ss_pred HHHHHHcCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999 99999999999998
No 7
>KOG0776 consensus Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism]
Probab=99.89 E-value=8.3e-23 Score=158.63 Aligned_cols=105 Identities=27% Similarity=0.295 Sum_probs=93.2
Q ss_pred ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhcccCCHHHHHHHHHhhhHHHHHHHHHHHH
Q 047640 1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQYVEMTYETYKKNEGGLHTCGAACGA 80 (111)
Q Consensus 1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~~~~~~~~~i~~~KTa~L~~~~~~~Ga 80 (111)
+||||+++|++.+++..+ ...++.+.++|..+++..+.+++..||.+|... ..+++|+.++.+|||+|+++||++|+
T Consensus 177 aGD~LLa~A~~~la~l~n--~~v~elm~~aI~dLv~ge~~~~~~~~~~~d~~~-~~~e~~e~~~~~KTAsLla~Sc~~~a 253 (384)
T KOG0776|consen 177 AGDALLALASEHLASLEN--PVVVELMASAIADLVRGEFTQGLVAGEGLDLDD-VGLEYLEFKTLLKTASLLAKSCVAAA 253 (384)
T ss_pred hhHHHHHHHHHHHHhccC--chHHHHHHHHHHHHHHhhhhcccccccccccCC-cchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 699999999999999875 244567788888888888888888887666643 57899999999999999999999999
Q ss_pred HhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640 81 ILGGGSVEEIEKKF-RGLIIKITKMMIRN 108 (111)
Q Consensus 81 i~~g~~~e~~~~l~-~G~~~GiafQi~D~ 108 (111)
|++|.++++++.++ ||+++|++||++||
T Consensus 254 ILgg~s~ev~e~~~~yGR~lGL~fQvvDD 282 (384)
T KOG0776|consen 254 ILGGGSEEVIEAAFEYGRCLGLAFQVVDD 282 (384)
T ss_pred HHcCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 99999999999999 99999999999998
No 8
>PLN02857 octaprenyl-diphosphate synthase
Probab=99.88 E-value=2.6e-22 Score=158.42 Aligned_cols=97 Identities=14% Similarity=0.190 Sum_probs=86.5
Q ss_pred ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhcc----cCCHHHHHHHHHhhhHHHHHHHH
Q 047640 1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQC----SQYVEMTYETYKKNEGGLHTCGA 76 (111)
Q Consensus 1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~----~~~~~~~~~i~~~KTa~L~~~~~ 76 (111)
+||+|+++||+.+++.+ . .++++.+++++ ..++.||+.|+.. +.++++|.+|+++|||+||++||
T Consensus 208 aGD~L~a~A~~~la~~~------~---~~~~~~~s~~~--~~l~~Gei~q~~~~~~~~~s~~~Yl~~i~~KTa~L~~~a~ 276 (416)
T PLN02857 208 AGDFMFAQSSWYLANLD------N---LEVIKLISQVI--KDFASGEIKQASSLFDCDVTLDEYLLKSYYKTASLIAAST 276 (416)
T ss_pred HHHHHHHHHHHHHHcCC------c---HHHHHHHHHHH--HHHHhhHHHHHhcccCCCCCHHHHHHHHHHhHHHHHHHHH
Confidence 69999999999998763 1 24556677777 8899999999875 27899999999999999999999
Q ss_pred HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640 77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN 108 (111)
Q Consensus 77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~ 108 (111)
.+||+++|+++++++.++ ||+++|++|||+||
T Consensus 277 ~~gallaga~~~~~~~l~~fG~~LGiAFQI~DD 309 (416)
T PLN02857 277 KSAAIFSGVDSSVKEQMYEYGKNLGLAFQVVDD 309 (416)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999 99999999999998
No 9
>CHL00151 preA prenyl transferase; Reviewed
Probab=99.87 E-value=1e-21 Score=150.58 Aligned_cols=97 Identities=14% Similarity=0.177 Sum_probs=85.4
Q ss_pred ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhcc----cCCHHHHHHHHHhhhHHHHHHHH
Q 047640 1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQC----SQYVEMTYETYKKNEGGLHTCGA 76 (111)
Q Consensus 1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~----~~~~~~~~~i~~~KTa~L~~~~~ 76 (111)
+||+|+++||+++++..+ .++++.+++++ ..++.||..|... ..++++|.+|+.+|||+||++||
T Consensus 115 ~GD~l~~~a~~~l~~~~~---------~~~~~~~~~~~--~~l~~G~~~~~~~~~~~~~~~~~yl~~i~~KTa~L~~~~~ 183 (323)
T CHL00151 115 AGDFLFAQSSWYLANLNN---------LEVVKLISKVI--TDFAEGEIRQGLVQFDTTLSILNYIEKSFYKTASLIAASC 183 (323)
T ss_pred hHHHHHHHHHHHHHhCCC---------hHHHHHHHHHH--HHHHHHHHHHHhcCCCCCCCHHHHHHHHHhHHHHHHHHHH
Confidence 699999999999987631 13445567777 8899999999765 26788999999999999999999
Q ss_pred HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640 77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN 108 (111)
Q Consensus 77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~ 108 (111)
.+||+++|.++++++.++ ||.++|+||||+||
T Consensus 184 ~~ga~lag~~~~~~~~l~~~G~~lG~aFQi~DD 216 (323)
T CHL00151 184 KAAALLSDADEKDHNDFYLYGKHLGLAFQIIDD 216 (323)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999 99999999999998
No 10
>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=99.86 E-value=5e-21 Score=142.38 Aligned_cols=100 Identities=24% Similarity=0.255 Sum_probs=90.6
Q ss_pred ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640 1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA 76 (111)
Q Consensus 1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~ 76 (111)
+||+|++++++++++..+ + ...++++.+++.+ ..++.||++|+.+. .+++.|.+|+.+|||+||..++
T Consensus 86 ~gd~l~~~a~~~l~~~~~-----~-~~~~~~~~~~~~~--~~~~~GQ~~d~~~~~~~~~~~~~y~~~~~~KT~~l~~~~~ 157 (259)
T cd00685 86 AGDYLLARAFELLARLGN-----P-YYPRALELFSEAI--LELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAP 157 (259)
T ss_pred HHHHHHHHHHHHHHhCCC-----c-cHHHHHHHHHHHH--HHHHHHHHHHHHccCCCCCCHHHHHHHHHHhHHHHHHHHH
Confidence 599999999999998742 1 3567788888888 99999999999873 6789999999999999999999
Q ss_pred HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640 77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN 108 (111)
Q Consensus 77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~ 108 (111)
++|++++++++++++.++ ||.++|++|||.||
T Consensus 158 ~~~a~l~~~~~~~~~~l~~~g~~lG~afQi~DD 190 (259)
T cd00685 158 LLGALLAGADEEEAEALKRFGRNLGLAFQIQDD 190 (259)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999 99999999999998
No 11
>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=99.84 E-value=2.8e-20 Score=138.48 Aligned_cols=103 Identities=26% Similarity=0.285 Sum_probs=85.1
Q ss_pred ChhhHHHHHHHHHHcCCCCCCCCh-HHHHHHHHHHHHhhchhHHHHhhHHHhccc---CCHHHHHHHHHhhhHHHHHHHH
Q 047640 1 MADAMLPFGLELLASSDNPAGNNS-GRILRVMVEMTRAMGSQGVVEGQYNELQCS---QYVEMTYETYKKNEGGLHTCGA 76 (111)
Q Consensus 1 aGD~Ll~~A~~~l~~~~~~~~~~~-~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~---~~~~~~~~i~~~KTa~L~~~~~ 76 (111)
+||+|+++|++++++.. ..++ .....++..+...+ .....||..|+... .++++|.+|+++|||+||++||
T Consensus 80 ~gd~ll~~a~~~l~~~~---~~~~~~~~~~i~~~~~~~~--~~~~~~q~~d~~~~~~~~~~~~y~~i~~~KTg~l~~~~~ 154 (260)
T PF00348_consen 80 AGDYLLALAFELLARLG---HFDPSERVLRILELFIEAL--IEGEIGQALDLANEDKDPTEEEYLEIIRLKTGSLFALAC 154 (260)
T ss_dssp HHHHHHHHHHHHHHHHC---HSHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHTTTSSTSHHHHHHHHHHHTHHHHHHHH
T ss_pred hchHHHHHHHHHHHHhh---cccchHHHHHHHHHHHHhc--ccceeehhhccccccccccHHHHHHHHhhcchHHHHHHH
Confidence 59999999999999874 1123 34555555555444 33344599999774 7899999999999999999999
Q ss_pred HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640 77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN 108 (111)
Q Consensus 77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~ 108 (111)
.+|++++|.+++..+.++ ||+++|++|||.||
T Consensus 155 ~~ga~lag~~~~~~~~l~~~g~~lG~afQi~DD 187 (260)
T PF00348_consen 155 QLGAILAGADEEQIEALREFGRHLGIAFQIRDD 187 (260)
T ss_dssp HHHHHHTTSGHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHhccchhHHHHHHHHHHHHHHHHHhhhhh
Confidence 999999999999999999 99999999999997
No 12
>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=99.74 E-value=3.1e-17 Score=119.34 Aligned_cols=97 Identities=22% Similarity=0.247 Sum_probs=85.8
Q ss_pred ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHH
Q 047640 1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGA 76 (111)
Q Consensus 1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~ 76 (111)
+||++++.+|+.+++.. ..+.++.+++.+ ..|+.||.+|+... .++++|.+++++|||++++.++
T Consensus 66 ~gd~l~~~a~~~l~~~~---------~~~~~~~~~~~~--~~~~~Gq~~Dl~~~~~~~~t~~~y~~~~~~Kta~l~~~~~ 134 (236)
T cd00867 66 AGDYLLARAFQLLARLG---------YPRALELFAEAL--RELLEGQALDLEFERDTYETLDEYLEYCRYKTAGLVGLLC 134 (236)
T ss_pred HHHHHHHHHHHHHHhCC---------hHHHHHHHHHHH--HHHHHHHHHHHHhccCCCCCHHHHHHHHHhccHHHHHHHH
Confidence 48999999999998762 234455567777 99999999999863 6789999999999999999999
Q ss_pred HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640 77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN 108 (111)
Q Consensus 77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~ 108 (111)
..++++++.+++..+.+. ||.++|++|||.||
T Consensus 135 ~~~~~~~~~~~~~~~~~~~~~~~lG~a~Qi~dd 167 (236)
T cd00867 135 LLGAGLSGADDEQAEALKDYGRALGLAFQLTDD 167 (236)
T ss_pred HHHHHHcCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999 99999999999997
No 13
>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=98.90 E-value=4.9e-08 Score=68.74 Aligned_cols=96 Identities=23% Similarity=0.267 Sum_probs=80.2
Q ss_pred hhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHHH
Q 047640 2 ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGAA 77 (111)
Q Consensus 2 GD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~~ 77 (111)
||.++..+++.+.... + ......+.+.+ ..++.||..|+.+. .+.++|.++.+.|||.++..++.
T Consensus 61 ~~~~~~~~~~~~~~~~-----~----~~~~~~~~~~~--~~~~~g~~~d~~~~~~~~~t~~ey~~~~~~~t~~~~~~~~~ 129 (243)
T cd00385 61 GDLLLADAFEELAREG-----S----PEALEILAEAL--LDLLEGQLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCL 129 (243)
T ss_pred HHHHHHHHHHHHHhCC-----C----HHHHHHHHHHH--HHHHHHHHHHHHhccCCCCCHHHHHHHHHHhHHHHHHHHHH
Confidence 6778888888887653 1 24445566777 89999999999873 77899999999999999999999
Q ss_pred HHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640 78 CGAILGGGSVEEIEKKF-RGLIIKITKMMIRN 108 (111)
Q Consensus 78 ~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~ 108 (111)
.++.....+.+....+. ++.++|+++|+.||
T Consensus 130 ~~~~~~~~~~~~~~~~~~~~~~~g~~~ql~nD 161 (243)
T cd00385 130 LGAGLSGGEAELLEALRKLGRALGLAFQLTND 161 (243)
T ss_pred HHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99998887777778888 99999999999987
No 14
>KOG0777 consensus Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism]
Probab=98.73 E-value=4.5e-08 Score=72.78 Aligned_cols=92 Identities=14% Similarity=0.105 Sum_probs=74.7
Q ss_pred hhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc-----CCHHHHHHHHHhhhHHHHHHHH
Q 047640 2 ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS-----QYVEMTYETYKKNEGGLHTCGA 76 (111)
Q Consensus 2 GD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~-----~~~~~~~~i~~~KTa~L~~~~~ 76 (111)
.+|++-+|++.+++... | .++..+.+.. ..+..||-+|+.|. .+++.|..|..+|||-||..+.
T Consensus 103 ANY~yFlalekV~qLdh-----P----~a~kifteqL--leLHrGQGldIYWRD~~tcPtee~Yk~Mv~~KTGGLF~La~ 171 (322)
T KOG0777|consen 103 ANYMYFLALEKVSQLDH-----P----NAIKIFTEQL--LELHRGQGLDIYWRDFLTCPTEEMYKNMVMNKTGGLFRLAL 171 (322)
T ss_pred hHHHHHHHHHHHHhcCC-----c----hHHHHHHHHH--HHHhcCCCcceeeeccCcCCCHHHHHHHHHHhcccHHHHHH
Confidence 57889999999998753 2 4556677777 88999999999984 6789999999999999999999
Q ss_pred HHHHHhCCCCHHHHHHHH-HhHHhhHhhhhhcC
Q 047640 77 ACGAILGGGSVEEIEKKF-RGLIIKITKMMIRN 108 (111)
Q Consensus 77 ~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~D~ 108 (111)
++--.++.-.+ .+. +=--+|+.|||+||
T Consensus 172 rLMqlfS~~ke----dl~pl~n~LGl~fQIRDD 200 (322)
T KOG0777|consen 172 RLMQLFSHHKE----DLVPLINLLGLIFQIRDD 200 (322)
T ss_pred HHHHHHHhcch----hHHHHHHHHhHhhhhhhh
Confidence 98877774333 344 66678899999987
No 15
>KOG0711 consensus Polyprenyl synthetase [Coenzyme transport and metabolism]
Probab=97.60 E-value=0.00023 Score=55.06 Aligned_cols=68 Identities=10% Similarity=-0.101 Sum_probs=55.8
Q ss_pred hHHHHhhHHHhcc------cCCHHHHHHHHHhhhHHH-HHHHHHHHHHhCCCC-HHHHHHHH-HhHHhhHhhhhhcC
Q 047640 41 QGVVEGQYNELQC------SQYVEMTYETYKKNEGGL-HTCGAACGAILGGGS-VEEIEKKF-RGLIIKITKMMIRN 108 (111)
Q Consensus 41 ~~m~~GQ~lDl~~------~~~~~~~~~i~~~KTa~L-~~~~~~~Gai~~g~~-~e~~~~l~-~G~~~GiafQi~D~ 108 (111)
...+.||.++-.. +.|++.|..|...|||.+ |-.|..++-+++|.+ .+...... +-..+|..||+.||
T Consensus 160 f~T~lGdllt~~~~~~~ls~fsl~~y~~Iv~~KTa~YsFYLPialAl~~ag~~~~k~~~~~k~v~~~lg~~FQvQDD 236 (347)
T KOG0711|consen 160 FQTELGDLLTTPEGNKDLSKFSLEKYVFIVEYKTAYYSFYLPVALALLLAGIANLKEHACEKKVLLLLGEYFQVQDD 236 (347)
T ss_pred HHHhhhccccCcccchhHhhhhHHHHHHHhhccccceeeecHHHHHHHHhhhhhHHHhhhHHHHHHHHHHHHhcchH
Confidence 5567777766543 167899999999999999 999999999999854 55556666 99999999999997
No 16
>PLN02632 phytoene synthase
Probab=91.25 E-value=1.1 Score=34.73 Aligned_cols=64 Identities=16% Similarity=0.206 Sum_probs=43.1
Q ss_pred hHHHHhhHHHhccc--CCHHHHHHHHHhhhHHHHHHHHHHHHHhCCCC--HHHHHHHH-HhHHhhHhhhhhc
Q 047640 41 QGVVEGQYNELQCS--QYVEMTYETYKKNEGGLHTCGAACGAILGGGS--VEEIEKKF-RGLIIKITKMMIR 107 (111)
Q Consensus 41 ~~m~~GQ~lDl~~~--~~~~~~~~i~~~KTa~L~~~~~~~Gai~~g~~--~e~~~~l~-~G~~~GiafQi~D 107 (111)
..|+.|...|+... .|.++++...+.--|.+...++.+ ++..+ +...+.+. .+.++|+|+|+.+
T Consensus 143 ~~li~g~~~Dl~~~~~~t~~eL~~Ycy~vAgtVG~l~l~v---lg~~~~~~~~~~~~~~~A~~lG~AlQltN 211 (334)
T PLN02632 143 RDMIEGMRMDLVKSRYENFDELYLYCYYVAGTVGLMSVPV---MGIAPESKASTESVYNAALALGIANQLTN 211 (334)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHHHhhHHHHHHHHHH---hCCCCccccchHHHHHHHHHHHHHHHHHH
Confidence 77899999999764 578888887766556666555544 33222 22234455 8888899988763
No 17
>PF00494 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR002060 Squalene synthase 2.5.1.21 from EC (farnesyl-diphosphate farnesyltransferase) (SQS) and Phytoene synthase 2.5.1.32 from EC (PSY) share a number of functional similarities. These similarities are also reflected at the level of their primary structure [, , ]. In particular three well conserved regions are shared by SQS and PSY; they could be involved in substrate binding and/or the catalytic mechanism. SQS catalyzes the conversion of two molecules of farnesyl diphosphate (FPP) into squalene. It is the first committed step in the cholesterol biosynthetic pathway. The reaction carried out by SQS is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of FPP to form presqualene diphosphate; this intermediate is then rearranged in a NADP-dependent reduction, to form squalene: 2 FPP -> presqualene diphosphate + NADP -> squalene SQS is found in eukaryotes. In yeast it is encoded by the ERG9 gene, in mammals by the FDFT1 gene. SQS seems to be membrane-bound. PSY catalyzes the conversion of two molecules of geranylgeranyl diphosphate (GGPP) into phytoene. It is the second step in the biosynthesis of carotenoids from isopentenyl diphosphate. The reaction carried out by PSY is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of GGPP to form prephytoene diphosphate; this intermediate is then rearranged to form phytoene. 2 GGPP -> prephytoene diphosphate -> phytoene PSY is found in all organisms that synthesize carotenoids: plants and photosynthetic bacteria as well as some non- photosynthetic bacteria and fungi. In bacteria PSY is encoded by the gene crtB. In plants PSY is localized in the chloroplast.; GO: 0016740 transferase activity, 0009058 biosynthetic process; PDB: 3NRI_A 3NPR_A 2ZCR_A 2ZCP_B 4F6V_A 4EA0_A 3ACW_A 4F6X_A 3VJE_B 3ACX_A ....
Probab=88.20 E-value=2 Score=31.62 Aligned_cols=61 Identities=7% Similarity=-0.088 Sum_probs=41.0
Q ss_pred hHHHHhhHHHhccc--CCHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhh
Q 047640 41 QGVVEGQYNELQCS--QYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKF-RGLIIKITKMMI 106 (111)
Q Consensus 41 ~~m~~GQ~lDl~~~--~~~~~~~~i~~~KTa~L~~~~~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~ 106 (111)
..|+.|...|+... .|.+++....+.-.|++....+.+-..- .+. .... ...++|.++|+.
T Consensus 94 ~~li~~~~~dl~~~~~~t~~~L~~Y~~~vag~vg~l~~~~~~~~--~~~---~~~~~~a~~lG~alql~ 157 (267)
T PF00494_consen 94 LELIDGMEMDLEFTPYETFADLERYCYYVAGSVGLLLLQLLGAH--DPD---EAARDAARALGRALQLT 157 (267)
T ss_dssp HHHHHHHHHCTT-S--SSHHHHHHHHHHHTHHHHHHHHHHHHSS--TSH---HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhcccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccc--cch---hhHHHHHHHHHHHHHHH
Confidence 78999999999864 6889998888888888887777665442 222 2233 555555555554
No 18
>cd00683 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases, head-to-head. These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes
Probab=87.26 E-value=2.1 Score=31.75 Aligned_cols=60 Identities=13% Similarity=0.109 Sum_probs=39.1
Q ss_pred hHHHHhhHHHhccc--CCHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhh
Q 047640 41 QGVVEGQYNELQCS--QYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKF-RGLIIKITKMMI 106 (111)
Q Consensus 41 ~~m~~GQ~lDl~~~--~~~~~~~~i~~~KTa~L~~~~~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~ 106 (111)
..|+.|...|+... .|.+++......--|++...++.+ ++.... +... ++.++|+|+|+.
T Consensus 96 ~~li~g~~~Dl~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i---~~~~~~---~~~~~~A~~lG~Alqlt 158 (265)
T cd00683 96 RDLLAGMAMDLDKRRYETLDELDEYCYYVAGVVGLMLLRV---FGASSD---EAALERARALGLALQLT 158 (265)
T ss_pred HHHHHHHHHhCCCCCCCCHHHHHHHHHHhHHHHHHHHHHH---hCCCCC---hHHHHHHHHHHHHHHHH
Confidence 78999999999874 677888887766556665555543 332111 2234 677777777765
No 19
>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=84.41 E-value=11 Score=27.75 Aligned_cols=64 Identities=14% Similarity=0.137 Sum_probs=41.8
Q ss_pred ChhhHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHhhchhHHHHhhHHHhccc-CCHH-HHHHHHHhhhHHHHHHH
Q 047640 1 MADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS-QYVE-MTYETYKKNEGGLHTCG 75 (111)
Q Consensus 1 aGD~Ll~~A~~~l~~~~~~~~~~~~~~~~~i~~~~~~~G~~~m~~GQ~lDl~~~-~~~~-~~~~i~~~KTa~L~~~~ 75 (111)
|||+.-++-+.+|++.++ +.+++.+|.++ ..+.+..+.=-... .+.+ .+..+..-+|+.+...+
T Consensus 75 AGDy~S~~yY~lLA~~~~---------i~li~~ls~aI--~eiNE~K~~ly~~~~~~~e~~~~~~~~ies~l~~~~~ 140 (212)
T PF07307_consen 75 AGDYYSGLYYQLLAESGD---------ISLIRALSEAI--KEINELKMSLYQKKKETAEEYLESVVTIESALFQSFA 140 (212)
T ss_pred hHHHHHHHHHHHHHhCCC---------HHHHHHHHHHH--HHHHHHHHHHHHhhhCCHHHHHHHHHHHHHHHHHHHH
Confidence 799999999999999863 47777888887 77777765433222 3444 34444444555444433
No 20
>TIGR03465 HpnD squalene synthase HpnD. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated.
Probab=82.05 E-value=13 Score=27.56 Aligned_cols=59 Identities=10% Similarity=0.078 Sum_probs=39.8
Q ss_pred hHHHHhhHHHhccc--CCHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhh
Q 047640 41 QGVVEGQYNELQCS--QYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKF-RGLIIKITKMMI 106 (111)
Q Consensus 41 ~~m~~GQ~lDl~~~--~~~~~~~~i~~~KTa~L~~~~~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~ 106 (111)
..|++|...|+... .|.+++....+.--|.+...++.+ ++..++. .. .+.++|+|+|+.
T Consensus 88 ~~li~g~~~Dl~~~~~~t~~dL~~Y~~~vAg~vg~l~~~l---lg~~~~~----~~~~a~~lG~Alqlt 149 (266)
T TIGR03465 88 LEVIDGMEMDLEQTRYPDFAELDLYCDRVAGAVGRLSARI---FGATDAR----TLEYAHHLGRALQLT 149 (266)
T ss_pred HHHHHHHHHHcCCCCCCCHHHHHHHHHHhHHHHHHHHHHH---hCCCChh----HHHHHHHHHHHHHHH
Confidence 78999999999864 678888887766666666666654 3433322 23 666667776664
No 21
>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=76.51 E-value=23 Score=26.32 Aligned_cols=60 Identities=7% Similarity=-0.019 Sum_probs=39.9
Q ss_pred hHHHHhhHHHhccc--CCHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHhHHhhHhhhhh
Q 047640 41 QGVVEGQYNELQCS--QYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKFRGLIIKITKMMI 106 (111)
Q Consensus 41 ~~m~~GQ~lDl~~~--~~~~~~~~i~~~KTa~L~~~~~~~Gai~~g~~~e~~~~l~~G~~~GiafQi~ 106 (111)
..|++|...|+... .|.++++.....--|++...++.+ ++..+++. ..++.++|+|+|+.
T Consensus 89 ~~li~~~~~Dl~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i---~g~~~~~~---~~~A~~lG~AlQlt 150 (266)
T TIGR03464 89 LDLLDAFRQDVVVTRYATWAELLDYCRYSANPVGRLVLDL---YGASDPEN---VALSDAICTALQLI 150 (266)
T ss_pred HHHHHHHHHhccCCCCCCHHHHHHHHHHhHHHHHHHHHHH---cCCCChhH---HHHHHHHHHHHHHH
Confidence 67899999998764 688888888766666666666543 33333332 12666777777765
No 22
>PF06783 UPF0239: Uncharacterised protein family (UPF0239); InterPro: IPR009621 This is a group of transmembrane proteins of unknown function.; GO: 0016021 integral to membrane
Probab=73.02 E-value=3.8 Score=25.98 Aligned_cols=19 Identities=21% Similarity=0.251 Sum_probs=14.8
Q ss_pred HHHHHHH-HhHHhhHhhhhh
Q 047640 88 EEIEKKF-RGLIIKITKMMI 106 (111)
Q Consensus 88 e~~~~l~-~G~~~GiafQi~ 106 (111)
.-.+.+- ||..+|=.||++
T Consensus 16 t~~e~llRYGLf~GAIFQli 35 (85)
T PF06783_consen 16 TFFENLLRYGLFVGAIFQLI 35 (85)
T ss_pred hHHHHHHHHHHHHHHHHHHH
Confidence 3445555 999999999986
No 23
>TIGR01559 squal_synth farnesyl-diphosphate farnesyltransferase. This model describes farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes. This family is related to phytoene synthases. Tentatively identified archaeal homologs (excluded from this model) lack the C-terminal predicted transmembrane region universally conserved among members of this family.
Probab=71.30 E-value=33 Score=26.86 Aligned_cols=65 Identities=8% Similarity=-0.148 Sum_probs=36.1
Q ss_pred hHHHHhhHHHhccc----CCHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHHHH-HhHHhhHhhhhh
Q 047640 41 QGVVEGQYNELQCS----QYVEMTYETYKKNEGGLHTCGAACGAILGGGSVEEIEKKF-RGLIIKITKMMI 106 (111)
Q Consensus 41 ~~m~~GQ~lDl~~~----~~~~~~~~i~~~KTa~L~~~~~~~Gai~~g~~~e~~~~l~-~G~~~GiafQi~ 106 (111)
..|+.|...|+... .|.++|......=-|..-...+.+=+. .|..++...... ++..+|+++|+.
T Consensus 111 ~~M~~GMa~dl~~~~~~~~T~~dL~~YCy~VAG~VG~mlt~l~~~-~~~~~~~~~~~~~~A~~lG~aLQlT 180 (336)
T TIGR01559 111 RRMGNGMADFIDKEVTNEQTVGDYDKYCHYVAGLVGIGLSRLFVA-SGFEDPSLGESEALSNSMGLFLQKT 180 (336)
T ss_pred HHHHHHHHHHHhcCcCCCCCHHHHHHHHhccccHHHHHHHHHHhh-cCCCCcchhhhHHHHHHHHHHHHHH
Confidence 56779998888764 567777776644444433334443222 222222222234 777778887763
No 24
>PF10655 DUF2482: Hypothetical protein of unknown function (DUF2482); InterPro: IPR018917 This entry is represented by Bacteriophage 80, Orf10. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. All the members of this very small, very short family are derived from bacteriophages, of the SA bacteriophages 11, Mu50B, system, and from the Staphylococcal_phi-Mu50B-like_prophages subsystem. All members are hypothetical proteins.
Probab=44.17 E-value=35 Score=22.05 Aligned_cols=24 Identities=13% Similarity=0.054 Sum_probs=20.0
Q ss_pred CCHHHHHHHHHhhhHHHHHHHHHH
Q 047640 55 QYVEMTYETYKKNEGGLHTCGAAC 78 (111)
Q Consensus 55 ~~~~~~~~i~~~KTa~L~~~~~~~ 78 (111)
++.+++..+...||+.|++.+-++
T Consensus 8 MTqeelr~llseK~~ELydL~~eI 31 (100)
T PF10655_consen 8 MTQEELRDLLSEKNGELYDLANEI 31 (100)
T ss_pred hhHHHHHHHHHHhhHHHHHHHHHh
Confidence 667888888889999999988765
No 25
>PF07077 DUF1345: Protein of unknown function (DUF1345); InterPro: IPR009781 This family consists of several hypothetical bacterial proteins of around 230 residues in length. The function of this family is unknown.
Probab=21.48 E-value=47 Score=23.61 Aligned_cols=26 Identities=8% Similarity=-0.083 Sum_probs=19.9
Q ss_pred CCHHHHHHHHHhHHhhHhhhhhcCCC
Q 047640 85 GSVEEIEKKFRGLIIKITKMMIRNSF 110 (111)
Q Consensus 85 ~~~e~~~~l~~G~~~GiafQi~D~~~ 110 (111)
.+|.-.+-++|.-.+|++||.-|.+.
T Consensus 129 ~~P~y~DFlYfsftiG~t~q~SDv~v 154 (180)
T PF07077_consen 129 WEPDYWDFLYFSFTIGMTFQTSDVNV 154 (180)
T ss_pred CCCCchhhhHHHHHHHhhccccCCCc
Confidence 34555566669999999999998753
No 26
>PF13062 DUF3924: Protein of unknown function (DUF3924)
Probab=21.39 E-value=83 Score=18.18 Aligned_cols=26 Identities=12% Similarity=0.330 Sum_probs=19.0
Q ss_pred HHHHHHHHhhhHHHHHHHHHHHHHhC
Q 047640 58 EMTYETYKKNEGGLHTCGAACGAILG 83 (111)
Q Consensus 58 ~~~~~i~~~KTa~L~~~~~~~Gai~~ 83 (111)
+-+.+.+.+|||+-++-+...-.+++
T Consensus 17 ~llkqayqkktgatisestlvq~lis 42 (62)
T PF13062_consen 17 DLLKQAYQKKTGATISESTLVQSLIS 42 (62)
T ss_pred HHHHHHHHhhcCCccchhHHHHHHHH
Confidence 34667788999998888776655554
No 27
>PF13072 DUF3936: Protein of unknown function (DUF3936)
Probab=20.28 E-value=64 Score=17.32 Aligned_cols=27 Identities=30% Similarity=0.113 Sum_probs=19.2
Q ss_pred HhCCCCHHHHHHHH-HhHHhhHhhhhhc
Q 047640 81 ILGGGSVEEIEKKF-RGLIIKITKMMIR 107 (111)
Q Consensus 81 i~~g~~~e~~~~l~-~G~~~GiafQi~D 107 (111)
++.|..-|....|+ |+..++....++|
T Consensus 11 ~lvGKAWeIr~~Lkey~k~~~~v~ewi~ 38 (38)
T PF13072_consen 11 ILVGKAWEIRAKLKEYGKQFGYVKEWIS 38 (38)
T ss_pred EEEehHHHHHHHHHHHHHhhhhHHHhcC
Confidence 34455556777888 9999888877654
Done!