Query 044462
Match_columns 299
No_of_seqs 167 out of 844
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 03:28:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044462.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044462hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02279 ent-kaur-16-ene synth 100.0 2.5E-78 5.4E-83 600.0 28.0 293 1-299 480-777 (784)
2 cd00684 Terpene_cyclase_plant_ 100.0 8.8E-77 1.9E-81 577.8 28.8 295 1-297 246-542 (542)
3 PLN02592 ent-copalyl diphospha 100.0 5.9E-54 1.3E-58 424.3 22.6 256 1-299 528-800 (800)
4 cd00868 Terpene_cyclase_C1 Ter 100.0 1.1E-47 2.3E-52 346.2 26.2 271 1-274 12-284 (284)
5 PF03936 Terpene_synth_C: Terp 100.0 1.9E-44 4.1E-49 322.8 12.4 244 1-245 26-270 (270)
6 cd00687 Terpene_cyclase_nonpla 100.0 7.7E-38 1.7E-42 285.1 17.6 243 1-250 22-267 (303)
7 PLN02150 terpene synthase/cycl 100.0 3.9E-31 8.5E-36 198.9 9.8 93 206-299 1-95 (96)
8 cd00385 Isoprenoid_Biosyn_C1 I 99.9 6.2E-23 1.4E-27 178.2 12.0 229 24-268 2-243 (243)
9 cd00686 Terpene_cyclase_cis_tr 98.4 7.9E-06 1.7E-10 74.0 12.7 212 32-270 79-295 (357)
10 PF06330 TRI5: Trichodiene syn 98.3 1.1E-05 2.4E-10 74.2 12.5 223 32-282 79-307 (376)
11 cd00867 Trans_IPPS Trans-Isopr 94.1 1.9 4.1E-05 37.4 13.4 118 113-246 86-214 (236)
12 PF00494 SQS_PSY: Squalene/phy 94.0 1.1 2.4E-05 39.8 12.1 178 20-230 6-191 (267)
13 TIGR02749 prenyl_cyano solanes 89.9 16 0.00034 33.7 15.0 87 113-203 134-220 (322)
14 TIGR03465 HpnD squalene syntha 89.4 15 0.00032 32.7 16.6 197 37-267 19-227 (266)
15 PLN02857 octaprenyl-diphosphat 88.9 15 0.00032 35.2 14.0 88 113-204 228-315 (416)
16 cd00685 Trans_IPPS_HT Trans-Is 87.3 14 0.0003 32.7 12.1 88 113-204 109-196 (259)
17 COG0142 IspA Geranylgeranyl py 86.7 26 0.00056 32.3 14.3 108 113-225 135-252 (322)
18 TIGR03464 HpnC squalene syntha 86.0 24 0.00053 31.3 16.1 118 21-164 7-128 (266)
19 PLN02890 geranyl diphosphate s 85.0 28 0.00061 33.4 13.5 89 113-205 228-316 (422)
20 cd00683 Trans_IPPS_HH Trans-Is 83.6 31 0.00068 30.5 16.6 198 36-268 24-237 (265)
21 TIGR02748 GerC3_HepT heptapren 83.5 36 0.00079 31.2 14.7 85 113-203 130-216 (319)
22 PLN02632 phytoene synthase 75.4 69 0.0015 29.6 14.8 106 37-165 74-183 (334)
23 KOG1719 Dual specificity phosp 71.8 3.4 7.3E-05 33.8 2.4 29 207-235 119-148 (183)
24 COG3707 AmiR Response regulato 68.8 4.3 9.4E-05 34.4 2.6 26 213-238 149-174 (194)
25 PF03861 ANTAR: ANTAR domain; 67.7 5 0.00011 26.7 2.3 27 212-238 16-42 (56)
26 PF12368 DUF3650: Protein of u 67.2 4.4 9.5E-05 23.0 1.6 18 217-234 9-26 (28)
27 PRK10888 octaprenyl diphosphat 65.1 1.1E+02 0.0025 28.0 16.6 87 113-204 131-218 (323)
28 PRK10581 geranyltranstransfera 63.4 1.1E+02 0.0023 27.9 10.8 111 123-246 153-276 (299)
29 smart00400 ZnF_CHCC zinc finge 54.0 15 0.00033 24.1 2.7 25 209-233 30-54 (55)
30 smart00463 SMR Small MutS-rela 47.7 25 0.00053 24.9 3.2 54 222-275 7-67 (80)
31 CHL00151 preA prenyl transfera 46.3 2.4E+02 0.0051 25.9 15.8 87 113-204 135-222 (323)
32 PF01713 Smr: Smr domain; Int 45.9 26 0.00056 25.0 3.1 46 222-267 4-53 (83)
33 PF00348 polyprenyl_synt: Poly 42.3 2.4E+02 0.0052 24.8 10.2 66 136-204 128-193 (260)
34 PF10776 DUF2600: Protein of u 42.2 2.9E+02 0.0062 25.6 15.1 77 162-246 197-273 (330)
35 COG1308 EGD2 Transcription fac 41.3 27 0.00059 27.2 2.7 20 215-234 88-107 (122)
36 TIGR03486 cas_csx13_C CRISPR-a 37.4 1.2E+02 0.0026 24.7 5.9 69 35-106 6-74 (152)
37 COG1093 SUI2 Translation initi 35.7 66 0.0014 28.6 4.5 63 202-268 97-169 (269)
38 PHA01082 putative transcriptio 34.5 86 0.0019 24.5 4.4 44 221-270 28-72 (133)
39 PF01807 zf-CHC2: CHC2 zinc fi 32.1 34 0.00073 25.5 1.9 28 211-238 63-90 (97)
40 PF13189 Cytidylate_kin2: Cyti 31.7 14 0.00031 30.7 -0.2 35 215-250 128-162 (179)
41 PRK06369 nac nascent polypepti 29.1 52 0.0011 25.5 2.5 25 211-235 76-100 (115)
42 PTZ00393 protein tyrosine phos 27.5 46 0.00099 29.3 2.2 27 209-235 182-208 (241)
43 PF03000 NPH3: NPH3 family; I 27.4 64 0.0014 28.8 3.1 41 185-237 207-248 (258)
44 KOG3730 Acyl-CoA:dihydroxyacte 27.3 2.1E+02 0.0045 28.0 6.5 60 211-283 77-136 (685)
45 TIGR00264 alpha-NAC-related pr 26.8 62 0.0013 25.1 2.5 23 212-234 79-101 (116)
46 KOG0776 Geranylgeranyl pyropho 26.6 5.6E+02 0.012 24.3 9.9 96 108-208 193-292 (384)
47 COG5095 TAF6 Transcription ini 23.5 3E+02 0.0065 25.4 6.5 118 149-275 221-349 (450)
48 PF03701 UPF0181: Uncharacteri 22.0 1.4E+02 0.003 19.5 3.0 24 218-242 23-46 (51)
49 KOG1720 Protein tyrosine phosp 21.9 73 0.0016 27.5 2.3 28 208-235 158-186 (225)
50 PRK12793 flaF flagellar biosyn 21.9 3.5E+02 0.0076 20.9 5.9 41 226-268 42-83 (115)
51 COG1562 ERG9 Phytoene/squalene 21.6 5.4E+02 0.012 23.3 8.0 112 36-164 34-145 (288)
52 PF00156 Pribosyltran: Phospho 20.8 32 0.00069 26.1 -0.1 20 49-68 92-111 (125)
53 KOG2077 JNK/SAPK-associated pr 20.8 1.5E+02 0.0033 29.5 4.4 96 166-270 298-405 (832)
54 COG2236 Predicted phosphoribos 20.4 45 0.00098 28.3 0.7 22 49-70 91-112 (192)
55 PF10397 ADSL_C: Adenylosuccin 20.2 1.3E+02 0.0029 21.3 3.2 30 214-243 8-37 (81)
56 PF05772 NinB: NinB protein; 20.2 36 0.00077 26.9 0.1 57 93-154 43-100 (127)
57 PRK09177 xanthine-guanine phos 20.2 38 0.00082 27.6 0.2 22 49-70 88-109 (156)
No 1
>PLN02279 ent-kaur-16-ene synthase
Probab=100.00 E-value=2.5e-78 Score=599.96 Aligned_cols=293 Identities=26% Similarity=0.415 Sum_probs=283.4
Q ss_pred CCccCCCCCCCchhhhHHHHHHHhhhccccCCCccchhHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHhhcCcc-cc
Q 044462 1 WWKKTGLGEKLNFARDRVVENFFWTVGDIFEPQFGYCRRMSAMVNCLLTSIDDVYDVYGTLDELELFTDAVERWDAT-AT 79 (299)
Q Consensus 1 W~~~~~l~~~l~~~r~r~~e~y~~~~a~~~eP~~s~~Rl~~ak~~~l~~~~DD~~D~~~t~ee~~~~~~ai~rwd~~-~~ 79 (299)
||+++|| .++||+|+|+++||||++|++|||++|.+|++|||.+++++++||+||.|||.||++.|++||+|||.+ ..
T Consensus 480 Wwke~~L-~~L~faRdr~ve~Yf~aaa~~fEPe~S~aRi~~aK~~~L~tviDD~fD~yGt~eEL~~ft~aVeRWD~~~~~ 558 (784)
T PLN02279 480 WIVENRL-DKLKFARQKLAYCYFSAAATLFSPELSDARLSWAKNGVLTTVVDDFFDVGGSEEELENLIQLVEKWDVNGSP 558 (784)
T ss_pred eHHhcCC-ccCCchhhHHHHHHHHHHHhhcCchhhHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHhccccch
Confidence 9999999 799999999999999999999999999999999999999999999999999999999999999999988 56
Q ss_pred ccCchhHHHHHHHHHhhHHHHHHHHHhcCCccchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHH
Q 044462 80 EQLPYYMKLCFHALYNSVNEMGFIALRDQEVGMIIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVM 159 (299)
Q Consensus 80 ~~lp~~~~~~~~~l~~~~~ei~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~ 159 (299)
+.+|+|||++|.+++++++|++.++.+.||++ +.+|++++|++++++|++||+|+.+|++||+||||+++.+|+|..++
T Consensus 559 ~~lpeymki~f~aL~~t~nei~~~~~~~qGr~-v~~~l~~aW~~ll~ayl~EAeW~~~g~vPT~eEYL~na~vS~~l~~i 637 (784)
T PLN02279 559 DFCSEQVEIIFSALRSTISEIGDKAFTWQGRN-VTSHIIKIWLDLLKSMLTEAQWSSNKSTPTLDEYMTNAYVSFALGPI 637 (784)
T ss_pred hhCcHHHHHHHHHHHHHHHHHHHHHHHHcCch-HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhhchhhhhhHHH
Confidence 89999999999999999999999988889999 99999999999999999999999999999999999999999999988
Q ss_pred HHHHHHhhcCCCchHHHhhccCchHHHHHHhhHhhhccCCCCChhhhhcCCCCchHHHHhhcC--CCCHHHHHHHHHHHH
Q 044462 160 LLHAYAFTANPITKEALEFLQDSPDIIRISSMIVRLEDDLGTSSDELKRGDVPKSIQCYMHET--RVSEDEAREHIRDLI 237 (299)
Q Consensus 160 ~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~V~~ym~e~--g~s~eeA~~~i~~~i 237 (299)
+..+.+++|..+|+++++|. .+|+++++++.++||+|||+||++|+++|++ |+|.|||+|+ |+|+|||+++++++|
T Consensus 638 ~l~~~~~~G~~l~eev~e~~-~~~~L~~l~s~I~RLlNDI~S~e~E~~rG~~-nsV~cYMke~~~gvSeEEAi~~i~~~I 715 (784)
T PLN02279 638 VLPALYLVGPKLSEEVVDSP-ELHKLYKLMSTCGRLLNDIRGFKRESKEGKL-NAVSLHMIHGNGNSTEEEAIESMKGLI 715 (784)
T ss_pred HHHHHHHhCCCCCHHHHhCc-chhHHHHHHHHHHHHHHhccccHhHHhCCCc-ceehhhhccCCCCCCHHHHHHHHHHHH
Confidence 88888889999999999995 8999999999999999999999999999998 9999999987 899999999999999
Q ss_pred HHHHHHHhhhhhCC--CCCCcHHHHHHHHHHhhhhhhhcccCCCCCCchhHHHHHHhcccccCC
Q 044462 238 AETWMKMNSARFGN--PPYLPDVFIGMAMNLVRMSQCMYLYGDGHGVQENTKDRVLSLFIDPIP 299 (299)
Q Consensus 238 ~~~~k~l~~~~l~~--~~~~p~~~~~~~~n~~r~~~~~Y~~~d~~~~~~~~~~~i~~~~~~p~~ 299 (299)
+++||+||++++++ +. +|++|+++|+|++|+++++|+++||||.+ .||++|++||++||+
T Consensus 716 e~~wKeLn~~~l~~~~~~-vp~~~~~~~ln~aR~~~~~Y~~~Dgyt~~-~~k~~i~~ll~ePi~ 777 (784)
T PLN02279 716 ESQRRELLRLVLQEKGSN-VPRECKDLFWKMSKVLHLFYRKDDGFTSN-DMMSLVKSVIYEPVS 777 (784)
T ss_pred HHHHHHHHHHHhccCCCC-CCHHHHHHHHHHHHhhhhheeCCCCCChH-HHHHHHHHHhccCCc
Confidence 99999999999974 46 99999999999999999999999999976 799999999999986
No 2
>cd00684 Terpene_cyclase_plant_C1 Plant Terpene Cyclases, Class 1. This CD includes a diverse group of monomeric plant terpene cyclases (Tspa-Tspf) that convert the acyclic isoprenoid diphosphates, geranyl diphosphate (GPP), farnesyl diphosphate (FPP), or geranylgeranyl diphosphate (GGPP) into cyclic monoterpenes, diterpenes, or sesquiterpenes, respectively; a few form acyclic species. Terpnoid cyclases are soluble enzymes localized to the cytosol (sesquiterpene synthases) or plastids (mono- and diterpene synthases). All monoterpene and diterpene synthases have restrict substrate specificity, however, some sesquiterpene synthases can accept both FPP and GPP. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl diphosphates, via bridging Mg2+ ions (K+ preferred by gymnosperm cyclases), inducing conformational changes such that an N-terminal regi
Probab=100.00 E-value=8.8e-77 Score=577.84 Aligned_cols=295 Identities=47% Similarity=0.830 Sum_probs=289.0
Q ss_pred CCccCCCCCCCchhhhHHHHHHHhhhccccCCCccchhHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHhhcCccccc
Q 044462 1 WWKKTGLGEKLNFARDRVVENFFWTVGDIFEPQFGYCRRMSAMVNCLLTSIDDVYDVYGTLDELELFTDAVERWDATATE 80 (299)
Q Consensus 1 W~~~~~l~~~l~~~r~r~~e~y~~~~a~~~eP~~s~~Rl~~ak~~~l~~~~DD~~D~~~t~ee~~~~~~ai~rwd~~~~~ 80 (299)
||+++||.+++||+|+|+++||||++|++|||++|.+|+++||+++|+|++||+||.+||.+|++.|+++++|||.++++
T Consensus 246 Wwk~~gL~~~l~~aRdr~ve~yf~~~a~~feP~~s~~Rl~~aK~~~l~~~iDD~fD~~gt~eEl~~ft~ai~rwd~~~~~ 325 (542)
T cd00684 246 WWKDLDLASKLPFARDRLVECYFWAAGTYFEPQYSLARIALAKTIALITVIDDTYDVYGTLEELELFTEAVERWDISAID 325 (542)
T ss_pred HHHhcCCcccCCcccchhHHHHHHHHhcccCccchHHHHHHHHHHHHHhhhHhhhccCCCHHHHHHHHHHHHhccccchh
Confidence 99999998888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCchhHHHHHHHHHhhHHHHHHHHHhcCCccchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHH
Q 044462 81 QLPYYMKLCFHALYNSVNEMGFIALRDQEVGMIIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVML 160 (299)
Q Consensus 81 ~lp~~~~~~~~~l~~~~~ei~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~ 160 (299)
++|++||++|.++++++++++.++.+.+++. +..+++++|++++++|++||+|+++|++||++||+++|.+|+|+++++
T Consensus 326 ~lPe~mk~~~~al~~~~~ei~~~~~~~~~~~-~~~~~~~~~~~~~~a~l~EA~w~~~g~vPt~eEYl~~~~~S~g~~~~~ 404 (542)
T cd00684 326 QLPEYMKIVFKALLNTVNEIEEELLKEGGSY-VVPYLKEAWKDLVKAYLVEAKWAHEGYVPTFEEYMENALVSIGLGPLL 404 (542)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHHHhcCcc-hHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhhhhHHhhHHHHH
Confidence 9999999999999999999999999999988 999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcCCCchHHHhhccCchHHHHHHhhHhhhccCCCCChhhhhcCCCCchHHHHhhcCCCCHHHHHHHHHHHHHHH
Q 044462 161 LHAYAFTANPITKEALEFLQDSPDIIRISSMIVRLEDDLGTSSDELKRGDVPKSIQCYMHETRVSEDEAREHIRDLIAET 240 (299)
Q Consensus 161 ~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~ 240 (299)
.++++++|+.+|+++++|+..+|+++++++.++||+|||.||++|+++|+++|+|.|||+|+|+|+|+|+++++++++++
T Consensus 405 ~~~~~~~g~~l~~e~~e~~~~~~~l~~~~~~i~rL~NDi~S~~kE~~rGdv~n~V~~ymke~g~s~eeA~~~i~~~ie~~ 484 (542)
T cd00684 405 LTSFLGMGDILTEEAFEWLESRPKLVRASSTIGRLMNDIATYEDEMKRGDVASSIECYMKEYGVSEEEAREEIKKMIEDA 484 (542)
T ss_pred HHHHHhcCCCCCHHHHHHHhccHHHHHHHHHHHHHhcChhhhHHHHhcCCcccHHHHHHHhcCCCHHHHHHHHHHHHHHH
Confidence 99999999999999999987669999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhhhCC-CCCCcHHHHHHHHHHhhhhhhhcccCCCCCCc-hhHHHHHHhccccc
Q 044462 241 WMKMNSARFGN-PPYLPDVFIGMAMNLVRMSQCMYLYGDGHGVQ-ENTKDRVLSLFIDP 297 (299)
Q Consensus 241 ~k~l~~~~l~~-~~~~p~~~~~~~~n~~r~~~~~Y~~~d~~~~~-~~~~~~i~~~~~~p 297 (299)
||++|++++++ +. +|++|+++++|++|+++++|+++||||.| +.+|+||++||++|
T Consensus 485 wk~ln~e~l~~~~~-~p~~~~~~~~n~~r~~~~~Y~~~D~~t~~~~~~~~~i~~ll~~p 542 (542)
T cd00684 485 WKELNEEFLKPSSD-VPRPIKQRFLNLARVIDVFYKEGDGFTHPEGEIKDHITSLLFEP 542 (542)
T ss_pred HHHHHHHHhcCCCC-CCHHHHHHHHHHHHHHHHHhcCCCCCCCccHHHHHHHHHHhcCC
Confidence 99999999987 67 99999999999999999999999999998 67999999999998
No 3
>PLN02592 ent-copalyl diphosphate synthase
Probab=100.00 E-value=5.9e-54 Score=424.34 Aligned_cols=256 Identities=15% Similarity=0.222 Sum_probs=232.4
Q ss_pred CCccCCCCCCCchhhhHHHHHHHhhhccccCCCccchhHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHh--------
Q 044462 1 WWKKTGLGEKLNFARDRVVENFFWTVGDIFEPQFGYCRRMSAMVNCLLTSIDDVYDVYGTLDELELFTDAVE-------- 72 (299)
Q Consensus 1 W~~~~~l~~~l~~~r~r~~e~y~~~~a~~~eP~~s~~Rl~~ak~~~l~~~~DD~~D~~~t~ee~~~~~~ai~-------- 72 (299)
||+++|| .+|||+|+|++|||||++|++|||++|.+|++|||.+++++++||+||.|||.||++.||++++
T Consensus 528 Wwke~~L-~~L~faRdr~ve~Yfwa~~~~feP~~s~~Ri~~aK~~~LitviDD~fD~yGt~eEl~~ft~~v~~~~~~~~~ 606 (800)
T PLN02592 528 WYEECNL-GEFGVSRSELLLAYFLAAASIFEPERSHERLAWAKTTVLVEAISSYFNKETSSKQRRAFLHEFGYGYKINGR 606 (800)
T ss_pred HHHhcCC-CcCCcchhHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHhhcccccCCCCHHHHHHHHHHHHhccccccc
Confidence 9999999 6999999999999999999999999999999999999999999999999999999999999996
Q ss_pred hcCccccccCch------hHHHHHHHHHhhHHHHHHHHHhcCCccchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHH
Q 044462 73 RWDATATEQLPY------YMKLCFHALYNSVNEMGFIALRDQEVGMIIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEY 146 (299)
Q Consensus 73 rwd~~~~~~lp~------~~~~~~~~l~~~~~ei~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEY 146 (299)
|||.+..+++|+ +||+||.++++++|+++.++.+.||++ +.+|++++|.+|++ +|..+|+
T Consensus 607 rWd~~~~~~lp~~~~~~~~mki~f~aLy~tineia~~a~~~qGr~-v~~~L~~~W~~l~~------~w~~~g~------- 672 (800)
T PLN02592 607 RSDHHFNDRNMRRSGSVKTGEELVGLLLGTLNQLSLDALEAHGRD-ISHLLRHAWEMWLL------KWLLEGD------- 672 (800)
T ss_pred ccCchhhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHhCcc-HHHHHHHHHHHHHH------HHHhcCc-------
Confidence 899988888877 999999999999999999999999999 99999999999999 6777765
Q ss_pred HHhhhhhcchhHHHHHHHH-hhcCCCchHHHhhccCchHHHHHHhhHhhhccCCCCChhhhhcCCCCchHHHHhhcCCCC
Q 044462 147 MENAWISVTAPVMLLHAYA-FTANPITKEALEFLQDSPDIIRISSMIVRLEDDLGTSSDELKRGDVPKSIQCYMHETRVS 225 (299)
Q Consensus 147 l~~~~~s~g~~~~~~~~~~-~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~V~~ym~e~g~s 225 (299)
.|+|.+.+++.+++ .+|..+|+++++ +|++.++.+.+.||+||++++++|+..|. +.+
T Consensus 673 -----~s~~~~~ilv~~~~l~~g~~lsee~l~----~~~~~~l~~li~Rl~nDl~t~~~e~~~~~------------~~~ 731 (800)
T PLN02592 673 -----GRQGEAELLVKTINLTAGRSLSEELLA----HPQYEQLAQLTNRICYQLGHYKKNKVHIN------------TYN 731 (800)
T ss_pred -----eeccchhhHHHHHHHhcCCCCCHHHcc----chhHHHHHHHHHHHHHhhhHHhhhcccCC------------ccc
Confidence 34566666666666 569999999865 68899999999999999999999885221 234
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhCC--CCCCcHHHHHHHHHHhhhhhhhcccCCCCCCchhHHHHHHhcccccCC
Q 044462 226 EDEAREHIRDLIAETWMKMNSARFGN--PPYLPDVFIGMAMNLVRMSQCMYLYGDGHGVQENTKDRVLSLFIDPIP 299 (299)
Q Consensus 226 ~eeA~~~i~~~i~~~~k~l~~~~l~~--~~~~p~~~~~~~~n~~r~~~~~Y~~~d~~~~~~~~~~~i~~~~~~p~~ 299 (299)
+ +|.+++.+.|+.++|+|.+++++. +. +|++||++||+++|++ +|. ||++|++|++||++|+||||+
T Consensus 732 ~-~a~~~~~~~ie~~~~eL~~lvl~~~~~~-vp~~cK~~f~~~~k~f--y~~---~~~~~~~~~~~i~~vl~epv~ 800 (800)
T PLN02592 732 P-EEKSKTTPSIESDMQELVQLVLQNSSDD-IDPVIKQTFLMVAKSF--YYA---AYCDPGTINYHIAKVLFERVA 800 (800)
T ss_pred H-HHHHHHHHHHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHHHHHHH--HHh---hcCCHHHHHHHHHHHhCCCCC
Confidence 5 899999999999999999999973 45 9999999999999966 677 999999999999999999985
No 4
>cd00868 Terpene_cyclase_C1 Terpene cyclases, Class 1. Terpene cyclases, Class 1 (C1) of the class 1 family of isoprenoid biosynthesis enzymes, which share the 'isoprenoid synthase fold' and convert linear, all-trans, isoprenoids, geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate into numerous cyclic forms of monoterpenes, diterpenes, and sesquiterpenes. Also included in this CD are the cis-trans terpene cyclases such as trichodiene synthase. The class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational ch
Probab=100.00 E-value=1.1e-47 Score=346.18 Aligned_cols=271 Identities=44% Similarity=0.775 Sum_probs=254.7
Q ss_pred CCccCCCCCCCchhhhHHHHHHHhhhccccCCCccchhHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHhhcCccccc
Q 044462 1 WWKKTGLGEKLNFARDRVVENFFWTVGDIFEPQFGYCRRMSAMVNCLLTSIDDVYDVYGTLDELELFTDAVERWDATATE 80 (299)
Q Consensus 1 W~~~~~l~~~l~~~r~r~~e~y~~~~a~~~eP~~s~~Rl~~ak~~~l~~~~DD~~D~~~t~ee~~~~~~ai~rwd~~~~~ 80 (299)
||+++||....+++|.+...+|+|+++.+++|+.+..|+++||+++|+|++||+||.+++.+++..+++.++||+....+
T Consensus 12 W~~~~~l~~~~~~~r~~~~~~~~~~a~~~p~~~~~~~l~~~a~~~~~~f~~DD~~D~~~~~~~~~~~~~~~~~~~~~~~~ 91 (284)
T cd00868 12 WWKELGLQEKLPFARDRLVECYFWAAGSYFEPQYSEARIALAKTIALLTVIDDTYDDYGTLEELELFTEAVERWDISAID 91 (284)
T ss_pred HHHHhCCcccCCchhhHhHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHHHhccccCCCHHHHHHHHHHHHhcChhhhh
Confidence 89999997665589999999999999999999889999999999999999999999999999999999999999988888
Q ss_pred cCchhHHHHHHHHHhhHHHHHHHHHhcCCccchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHH
Q 044462 81 QLPYYMKLCFHALYNSVNEMGFIALRDQEVGMIIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVML 160 (299)
Q Consensus 81 ~lp~~~~~~~~~l~~~~~ei~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~ 160 (299)
.+|+++++++.++.++++++...+.+.+|+. ...++++.|.+|+.++.+|++|+..|++||++||+.+|+.|+|+++++
T Consensus 92 ~~p~~~~~~~~~l~d~~~r~~~~~~~~~~~~-~~~r~~~~~~~~~~~~~~e~~~~~~~~~p~~~eYl~~R~~~~g~~~~~ 170 (284)
T cd00868 92 ELPEYMKPVFKALYDLVNEIEEELAKEGGSE-SLPYLKEAWKDLLRAYLVEAKWANEGYVPSFEEYLENRRVSIGYPPLL 170 (284)
T ss_pred hCCHHHHHHHHHHHHHHHHHHHHHHHhcCch-HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHhceehhhHHHHH
Confidence 8999999999999999999998888888878 899999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcCCCch-HHHhhccCchHHHHHHhhHhhhccCCCCChhhhhcCCCCchHHHHhhcCCCCHHHHHHHHHHHHHH
Q 044462 161 LHAYAFTANPITK-EALEFLQDSPDIIRISSMIVRLEDDLGTSSDELKRGDVPKSIQCYMHETRVSEDEAREHIRDLIAE 239 (299)
Q Consensus 161 ~~~~~~~g~~l~~-e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~ 239 (299)
.++++++|..+|+ ++.+. +...++++.++.+++|+||++||+||+..|+.+|+|.|||+++|+|.++|++++.+++++
T Consensus 171 ~l~~~~~g~~l~~~~~~~~-~~~~~l~~~~~~~~~l~NDl~S~~kE~~~g~~~N~v~vl~~~~~~~~~eA~~~~~~~~~~ 249 (284)
T cd00868 171 ALSFLGMGDILPEEAFEWL-PSYPKLVRASSTIGRLLNDIASYEKEIARGEVANSVECYMKEYGVSEEEALEELRKMIEE 249 (284)
T ss_pred HHHHHHcCCCCCHHHHHHh-hhhHHHHHHHHHHHHHhccchHHHHHHccCCcccHHHHHHhccCCCHHHHHHHHHHHHHH
Confidence 9999999999998 56665 578999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhhCC-CCCCcHHHHHHHHHHhhhhhhhc
Q 044462 240 TWMKMNSARFGN-PPYLPDVFIGMAMNLVRMSQCMY 274 (299)
Q Consensus 240 ~~k~l~~~~l~~-~~~~p~~~~~~~~n~~r~~~~~Y 274 (299)
++++|++++.+. ++ .+..+++.+.+.+|.....|
T Consensus 250 ~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~g~~~w~ 284 (284)
T cd00868 250 AWKELNEEVLKLSSD-VPRAVLETLLNLARGIYVWY 284 (284)
T ss_pred HHHHHHHHHhcCCCC-CCHHHHHHHHHHHHhhhhcC
Confidence 999999999975 35 78999999999999886544
No 5
>PF03936 Terpene_synth_C: Terpene synthase family, metal binding domain; InterPro: IPR005630 Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C10) synthases, sesquiterpene (C15) synthases and the diterpene (C20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf []. Tpsa includes vetispiridiene synthase Q39979 from SWISSPROT, 5-epi- aristolochene synthase, Q40577 from SWISSPROT and (+)-delta-cadinene synthase P93665 from SWISSPROT . Tpsb includes (-)-limonene synthase, Q40322 from SWISSPROT. Tpsc includes copalyl diphosphate synthase (kaurene synthase A), O04408 from SWISSPROT. Tpsd includes taxadiene synthase, Q41594 from SWISSPROT, pinene synthase, O24475 from SWISSPROT and myrcene synthase, O24474 from SWISSPROT. Tpse includes ent-kaurene synthase B Q39548 from SWISSPROT. Tpsf includes linalool synthase Q9ZPN5 from SWISSPROT. In the fungus Phaeosphaeria sp. (strain L487) the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein [].; GO: 0000287 magnesium ion binding, 0016829 lyase activity; PDB: 3PYB_A 3PYA_A 3G4F_A 3G4D_B 3CKE_A 2OA6_D 2E4O_B 3BNY_B 3BNX_A 3LG5_A ....
Probab=100.00 E-value=1.9e-44 Score=322.76 Aligned_cols=244 Identities=30% Similarity=0.401 Sum_probs=220.0
Q ss_pred CCccCCCCCCCchhhhHHHHHHHhhhccccCCCccchhHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHhhcCccccc
Q 044462 1 WWKKTGLGEKLNFARDRVVENFFWTVGDIFEPQFGYCRRMSAMVNCLLTSIDDVYDVYGTLDELELFTDAVERWDATATE 80 (299)
Q Consensus 1 W~~~~~l~~~l~~~r~r~~e~y~~~~a~~~eP~~s~~Rl~~ak~~~l~~~~DD~~D~~~t~ee~~~~~~ai~rwd~~~~~ 80 (299)
||+++||..+.+.+|+|++.++|+.++++++|+.+..|+++||+++|+|++||+||.+++.++++.+++++++|++....
T Consensus 26 W~~~~~l~~~~~~~~~~~~~~~~~~~aa~~~P~~~~~l~~~a~~~~w~f~~DD~~D~~~~~~~~~~l~~~~~~~~~~~~~ 105 (270)
T PF03936_consen 26 WVKEFGLFDEDKAARQRFRQAYFGLLAARFYPDSSDELLAAADWMAWLFIFDDFFDDGGSAEELEALTDAVERWDPNSGD 105 (270)
T ss_dssp HHHHCTHHHHHTTSHHHHHHHHHHHHHHHHSGCGHHHHHHHHHHHHHHHHHHHHHHTTSHHHHHHHHHHHHHHTSSGGGG
T ss_pred HHHHcCCccccccchhhhhHhHHhhhhheeCCCcHHHHHHHHhhchheeeeeeccccccchHHHHHHHHHHhcccccccc
Confidence 89999997677767999999999999999999966777799999999999999999999888899999999999887778
Q ss_pred cCchhHHHHHHHHHhhHHHHHHHHHhcC-CccchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHH
Q 044462 81 QLPYYMKLCFHALYNSVNEMGFIALRDQ-EVGMIIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVM 159 (299)
Q Consensus 81 ~lp~~~~~~~~~l~~~~~ei~~~~~~~~-~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~ 159 (299)
.+|...++++.++.++++++...+.+.+ .+. +.++|+++|.+|+.++.+|++|+..|++||++||++.|+.|+|++++
T Consensus 106 ~~~~~~~~~~~~l~d~~~r~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~e~~~~~~~~~ps~eeYl~~R~~t~g~~~~ 184 (270)
T PF03936_consen 106 PLPDPDKPLFRALADIWNRIAARMSPAQRRRD-QIKRFRNSWREYLNAYLWEARWRERGRIPSLEEYLEMRRHTSGVYPC 184 (270)
T ss_dssp GSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTTS--SHHHHHHHHHHHTSHHHH
T ss_pred cccchhHHHHHHHHHHHHHHHHHhhhhhcccH-HhhHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHhccccccccHH
Confidence 8899999999999999999987777654 344 67889999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCCCchHHHhhccCchHHHHHHhhHhhhccCCCCChhhhhcCCCCchHHHHhhcCCCCHHHHHHHHHHHHHH
Q 044462 160 LLHAYAFTANPITKEALEFLQDSPDIIRISSMIVRLEDDLGTSSDELKRGDVPKSIQCYMHETRVSEDEAREHIRDLIAE 239 (299)
Q Consensus 160 ~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~ 239 (299)
+.++.+++|..+++...+++...+.+.++++.+++|+|||.||+||+++|+.+|.|.++|+++|+|.|+|++++.+|+++
T Consensus 185 ~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~NDl~S~~KE~~~g~~~N~v~~l~~~~~~s~e~A~~~v~~~~~~ 264 (270)
T PF03936_consen 185 LALIEFALEFALGELPPEVLEHPPMLRRLAADIIRLVNDLYSYKKEIARGDVHNLVVVLMNEHGLSLEEAVDEVAEMINE 264 (270)
T ss_dssp HHHHHHHCSSCHTHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCSHHHHHHHHHTHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhCCCccccccHHHHHhchHHHHHHHHHHHHhcccchhhcchhhcccccHHHHhhhhcCCCHHHHHHHHHHHHHH
Confidence 99998888766665544444445679999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHh
Q 044462 240 TWMKMN 245 (299)
Q Consensus 240 ~~k~l~ 245 (299)
++++||
T Consensus 265 ~~~efn 270 (270)
T PF03936_consen 265 CIREFN 270 (270)
T ss_dssp HHHHHH
T ss_pred HHHhcC
Confidence 999987
No 6
>cd00687 Terpene_cyclase_nonplant_C1 Non-plant Terpene Cyclases, Class 1. This CD includes terpenoid cyclases such as pentalenene synthase and aristolochene synthase which, using an all-trans pathway, catalyze the ionization of farnesyl diphosphate, followed by the formation of a macrocyclic intermediate by bond formation between C1 with either C10 (aristolochene synthase) or C11 (pentalenene synthase), resulting in production of tricyclic hydrocarbon pentalenene or bicyclic hydrocarbon aristolochene. As with other enzymes with the 'terpenoid synthase fold', they have two conserved metal binding motifs, proposed to coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP to the enzymes. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function in the monomeric form and are found in
Probab=100.00 E-value=7.7e-38 Score=285.11 Aligned_cols=243 Identities=16% Similarity=0.111 Sum_probs=210.6
Q ss_pred CCccCCCCCCCchhhhHHHHHHHhhhccccCCCccchhH-HHHHHHHHHhhcccccccC-CCHHHHHHHHHHHhhcCccc
Q 044462 1 WWKKTGLGEKLNFARDRVVENFFWTVGDIFEPQFGYCRR-MSAMVNCLLTSIDDVYDVY-GTLDELELFTDAVERWDATA 78 (299)
Q Consensus 1 W~~~~~l~~~l~~~r~r~~e~y~~~~a~~~eP~~s~~Rl-~~ak~~~l~~~~DD~~D~~-~t~ee~~~~~~ai~rwd~~~ 78 (299)
|.++.|+... +.+|+++..++|+..+.++.|+++.+|+ ..++++.|+|++||+||.. +++++.+.+++.+.++....
T Consensus 22 w~~~~~l~~~-~~~~~~~~~~~~~~~~a~~~P~a~~~~l~l~~~~~~w~f~~DD~~D~~~~~~~~~~~~~~~~~~~~~~~ 100 (303)
T cd00687 22 WVLEEMLIPS-EKAEKRFLSADFGDLAALFYPDADDERLMLAADLMAWLFVFDDLLDRDQKSPEDGEAGVTRLLDILRGD 100 (303)
T ss_pred HHHHcCCCCc-chhHHHHhcCCHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhcccCCccccCHHHHHHHHHHHHhccCCC
Confidence 5556666433 4589999998888888888899999999 6679999999999999986 58999999998888754432
Q ss_pred cccCchhHHHHHHHHHhhHHHHHHHHHhcCCccchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhH
Q 044462 79 TEQLPYYMKLCFHALYNSVNEMGFIALRDQEVGMIIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPV 158 (299)
Q Consensus 79 ~~~lp~~~~~~~~~l~~~~~ei~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~ 158 (299)
...-|....++..++.+++.++.... +.. ..+++++.|.+|+.++++|++|+..|++||++||+++|+.|+|+.+
T Consensus 101 ~~~~~~~~~p~~~~~~d~~~r~~~~~----~~~-~~~r~~~~~~~~~~a~~~e~~~~~~~~~psl~eYl~~R~~~~g~~~ 175 (303)
T cd00687 101 GLDSPDDATPLEFGLADLWRRTLARM----SAE-WFNRFAHYTEDYFDAYIWEGKNRLNGHVPDVAEYLEMRRFNIGADP 175 (303)
T ss_pred CCCCCCCCCHHHHHHHHHHHHhccCC----CHH-HHHHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhhhcccccc
Confidence 11114566788889999998886542 234 6888999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCCCchHHHhhccCchHHHHHHhhHhhhccCCCCChhhh-hcCCCCchHHHHhhcCCCCHHHHHHHHHHHH
Q 044462 159 MLLHAYAFTANPITKEALEFLQDSPDIIRISSMIVRLEDDLGTSSDEL-KRGDVPKSIQCYMHETRVSEDEAREHIRDLI 237 (299)
Q Consensus 159 ~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~-~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i 237 (299)
++.++++++|..+|+++.++ +...++.++++.+++|+|||+||+||+ +.|+.+|+|.|+|+++|+|.|+|++++.+++
T Consensus 176 ~~~l~~~~~g~~lp~~~~~~-~~~~~l~~~~~~~~~l~NDl~S~~KE~~~~g~~~N~V~vl~~~~g~s~~eA~~~~~~~~ 254 (303)
T cd00687 176 CLGLSEFIGGPEVPAAVRLD-PVMRALEALASDAIALVNDIYSYEKEIKANGEVHNLVKVLAEEHGLSLEEAISVVRDMH 254 (303)
T ss_pred cHHHHHHhcCCCCCHHHHhC-hHHHHHHHHHHHHHHHHHHHHhhHHHHHhCCccchHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 99999999999999999887 357889999999999999999999999 8999999999999999999999999999999
Q ss_pred HHHHHHHhhhhhC
Q 044462 238 AETWMKMNSARFG 250 (299)
Q Consensus 238 ~~~~k~l~~~~l~ 250 (299)
++.++++.+..-+
T Consensus 255 ~~~~~~f~~~~~~ 267 (303)
T cd00687 255 NERITQFEELEAS 267 (303)
T ss_pred HHHHHHHHHHHHh
Confidence 9999998876554
No 7
>PLN02150 terpene synthase/cyclase family protein
Probab=99.97 E-value=3.9e-31 Score=198.93 Aligned_cols=93 Identities=27% Similarity=0.554 Sum_probs=89.7
Q ss_pred hhcCCCCchHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHhhhhhCCCCCCcHHHHHHHHHHhhhhhhh-cccCCCCCCc-
Q 044462 206 LKRGDVPKSIQCYMHETRVSEDEAREHIRDLIAETWMKMNSARFGNPPYLPDVFIGMAMNLVRMSQCM-YLYGDGHGVQ- 283 (299)
Q Consensus 206 ~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~~~l~~~~~~p~~~~~~~~n~~r~~~~~-Y~~~d~~~~~- 283 (299)
|++||++|+|+|||||||+|+|||+++++++|+++||++|+++|+++. +|.++++.++|+||+++++ |+++||||.+
T Consensus 1 ~~rg~vaSsIeCYMke~g~seeeA~~~i~~li~~~WK~iN~e~l~~~~-~p~~~~~~~~NlaR~~~~~~Y~~~Dg~t~~~ 79 (96)
T PLN02150 1 MRRGEVANGVNCYMKQHGVTKEEAVSELKKMIRDNYKIVMEEFLTIKD-VPRPVLVRCLNLARLIDVYCYNEGDGFTYPH 79 (96)
T ss_pred CCCCcchHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHHHcCCCC-CCHHHHHHHHHHHHHHHhheecCCCCCCCCc
Confidence 478999999999999999999999999999999999999999999888 9999999999999999999 9999999977
Q ss_pred hhHHHHHHhcccccCC
Q 044462 284 ENTKDRVLSLFIDPIP 299 (299)
Q Consensus 284 ~~~~~~i~~~~~~p~~ 299 (299)
..+|++|.+||++||+
T Consensus 80 ~~~K~~I~sLlv~pi~ 95 (96)
T PLN02150 80 GKLKDLITSLFFHPLP 95 (96)
T ss_pred HHHHHHHHHHhccCCC
Confidence 6899999999999986
No 8
>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1. Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoter
Probab=99.89 E-value=6.2e-23 Score=178.17 Aligned_cols=229 Identities=24% Similarity=0.264 Sum_probs=181.2
Q ss_pred hhhccccCCCccchhHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHhhcCccccccCchhHHHHHHHHHhhHHHHHHH
Q 044462 24 WTVGDIFEPQFGYCRRMSAMVNCLLTSIDDVYDVYGTLDELELFTDAVERWDATATEQLPYYMKLCFHALYNSVNEMGFI 103 (299)
Q Consensus 24 ~~~a~~~eP~~s~~Rl~~ak~~~l~~~~DD~~D~~~t~ee~~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~~~~ei~~~ 103 (299)
++++.+++|+.+..|..++++..|++++||++|...+..........+. ....|..+......+...+.++...
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~DDi~D~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (243)
T cd00385 2 RPLAVLLEPEASRLRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAVA------IDGLPEAILAGDLLLADAFEELARE 75 (243)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCchhhhhhHH------hcCchHHHHHHHHHHHHHHHHHHhC
Confidence 4566678888889999999999999999999998776555444333221 1234556666777777778877543
Q ss_pred HHhcCCccchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHHHhhcCCCchHHHhhccCch
Q 044462 104 ALRDQEVGMIIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAYAFTANPITKEALEFLQDSP 183 (299)
Q Consensus 104 ~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~ 183 (299)
.. .. +.+++.+.|.+++.|+.+|+.|+.. ..||++||+..+..++ +.++......+++...|+ . ...+...
T Consensus 76 ~~----~~-~~~~~~~~~~~~~~g~~~d~~~~~~-~~~t~~ey~~~~~~~t-~~~~~~~~~~~~~~~~~~-~-~~~~~~~ 146 (243)
T cd00385 76 GS----PE-ALEILAEALLDLLEGQLLDLKWRRE-YVPTLEEYLEYCRYKT-AGLVGALCLLGAGLSGGE-A-ELLEALR 146 (243)
T ss_pred CC----HH-HHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHHhH-HHHHHHHHHHHHHHhCCC-H-HHHHHHH
Confidence 21 34 6888999999999999999999887 8899999999999998 455556666666666665 2 2223467
Q ss_pred HHHHHHhhHhhhccCCCCChhhhhcC-CCCchHHHHhhcCCC------------CHHHHHHHHHHHHHHHHHHHhhhhhC
Q 044462 184 DIIRISSMIVRLEDDLGTSSDELKRG-DVPKSIQCYMHETRV------------SEDEAREHIRDLIAETWMKMNSARFG 250 (299)
Q Consensus 184 ~l~~~~~~i~rL~NDi~S~~~E~~~g-~~~n~V~~ym~e~g~------------s~eeA~~~i~~~i~~~~k~l~~~~l~ 250 (299)
++...++.+..|.||+.|+.+|.+.| +..|++.++|+++|+ +.++|.+.+.++++++++++.+....
T Consensus 147 ~~~~~~g~~~ql~nDl~~~~~e~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ 226 (243)
T cd00385 147 KLGRALGLAFQLTNDLLDYEGDAERGEGKCTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKLAEEALKELNELILS 226 (243)
T ss_pred HHHHHHHHHHHHHHHHHhccCCHHHhCCchHHHHHHHHHhCChhhHHHHHHHCChHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 88899999999999999999999986 678999999999998 88999999999999999999998776
Q ss_pred CCCCCcHHHHHHHHHHhh
Q 044462 251 NPPYLPDVFIGMAMNLVR 268 (299)
Q Consensus 251 ~~~~~p~~~~~~~~n~~r 268 (299)
.+. .+..+++.+.+++|
T Consensus 227 ~~~-~~~~~~~~~~~~~~ 243 (243)
T cd00385 227 LPD-VPRALLALALNLYR 243 (243)
T ss_pred cHH-HHHHHHHHHHHHhC
Confidence 434 67788888877754
No 9
>cd00686 Terpene_cyclase_cis_trans_C1 Cis, Trans, Terpene Cyclases, Class 1. This CD includes the terpenoid cyclase, trichodiene synthase, which catalyzes the cyclization of farnesyl diphosphate (FPP) to trichodiene using a cis-trans pathway, and is the first committed step in the biosynthesis of trichothecene toxins and antibiotics. As with other enzymes with the 'terpenoid synthase fold', this enzyme has two conserved metal binding motifs that coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function as homodimers and are found in several genera of fungi.
Probab=98.35 E-value=7.9e-06 Score=74.05 Aligned_cols=212 Identities=12% Similarity=-0.006 Sum_probs=123.6
Q ss_pred CCccchhH-HHHHHHHHHhhcccccccCCCHHHHHHHHHHHhhcCccccccCchhHHHHHHHHHhhHHHHHHHHHhcCCc
Q 044462 32 PQFGYCRR-MSAMVNCLLTSIDDVYDVYGTLDELELFTDAVERWDATATEQLPYYMKLCFHALYNSVNEMGFIALRDQEV 110 (299)
Q Consensus 32 P~~s~~Rl-~~ak~~~l~~~~DD~~D~~~t~ee~~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~~~~ei~~~~~~~~~~ 110 (299)
+..|.+=+ .++-..+.++++||.-|... +.++.|.+.+.. +.+ ... ++...+.+.+..+- .--|+
T Consensus 79 ~~~skev~~~isi~~tY~~~lDD~~~e~~--~~m~~f~~dL~~--G~~-qkh-----P~l~~v~~~l~~~l----r~fGp 144 (357)
T cd00686 79 AKVSKECMADLSIHYTYTLVLDDSKDDPY--PTMVNYFDDLQA--GRE-QAH-----PWWALVNEHFPNVL----RHFGP 144 (357)
T ss_pred cCCCHHHHHHHHHHHheeeEecccccccc--hHHHHHHHHHhc--CCC-CCC-----cHHHHHHHHHHHHH----HHhhh
Confidence 33666655 66788888999999977654 366777666553 111 111 23333333333322 22344
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHHHhhcCCCchHHHhhccCchH---HHH
Q 044462 111 GMIIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAYAFTANPITKEALEFLQDSPD---IIR 187 (299)
Q Consensus 111 ~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~---l~~ 187 (299)
. ...-+.++--+++.+..-|... .+..|.-.+|-...+.-+|.+-..+...+ |++.+.--..+.. .+-
T Consensus 145 F-~s~~IikSTLdFv~g~~iEq~n--f~~~p~A~~fP~ylR~ksGl~E~yA~FiF------Pk~~FpE~~~~~qi~~AIp 215 (357)
T cd00686 145 F-CSLNLIRSTLDFFEGCWIEQYN--FGGFPGSHDYPQFLRRMNGLGHCVGASLW------PKEQFNERSLFLEITSAIA 215 (357)
T ss_pred h-hHHHHHHHHHHHHHHHHHhhhc--cCCCCCCcccchHHHhccCCcceeEEEec------chhhCchHhhHHHhhHHHH
Confidence 4 5666678888999999988763 33355444444444555665444333222 3332211111222 222
Q ss_pred HHhhHhhhccCCCCChhhhhc-CCCCchHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHhhhhhCCCCCCcHHHHHHHHHH
Q 044462 188 ISSMIVRLEDDLGTSSDELKR-GDVPKSIQCYMHETRVSEDEAREHIRDLIAETWMKMNSARFGNPPYLPDVFIGMAMNL 266 (299)
Q Consensus 188 ~~~~i~rL~NDi~S~~~E~~~-g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~~~l~~~~~~p~~~~~~~~n~ 266 (299)
.....+.++|||.||=||... ++..|.|.-|.+.+|+|..+|.+.+..-.-.+-+++.+ +|++++ ...+.++-++
T Consensus 216 ~~~~~i~~~NDILSFYKEe~~~~E~~n~V~Nya~~~GiS~~eAL~~lt~dTv~~s~rv~~-VLse~d---p~l~~av~~F 291 (357)
T cd00686 216 QMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVA-VFSDKD---PQVMDTIECF 291 (357)
T ss_pred HHHHHHHhhhhhhheehhhcccccccchHHHhhhhcCCCHHHHHHHHHHHHHHHHHHHHH-HhcCCC---hHHHHHHHHH
Confidence 333455689999999999854 56689999999999999999999877666556555544 354332 2334444444
Q ss_pred hhhh
Q 044462 267 VRMS 270 (299)
Q Consensus 267 ~r~~ 270 (299)
++..
T Consensus 292 i~GY 295 (357)
T cd00686 292 MHGY 295 (357)
T ss_pred HHHH
Confidence 4433
No 10
>PF06330 TRI5: Trichodiene synthase (TRI5); InterPro: IPR024652 This family consists of several fungal trichodiene synthase proteins (EC:4.2.3.6). TRI5 encodes the enzyme trichodiene synthase, which has been shown to catalyse the first step in the trichothecene pathways of Fusarium and Trichothecium species [, ].; GO: 0045482 trichodiene synthase activity, 0016106 sesquiterpenoid biosynthetic process; PDB: 1YYT_A 2PS5_A 2AEL_A 1YYS_A 1YJ4_A 2Q9Y_A 2PS4_A 2AEK_B 1KIY_B 2PS7_A ....
Probab=98.29 E-value=1.1e-05 Score=74.17 Aligned_cols=223 Identities=13% Similarity=0.073 Sum_probs=126.0
Q ss_pred CCccch-hHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHhhcCccccccCchhHHHHHHHHHhhHHHHHHHHHhcCCc
Q 044462 32 PQFGYC-RRMSAMVNCLLTSIDDVYDVYGTLDELELFTDAVERWDATATEQLPYYMKLCFHALYNSVNEMGFIALRDQEV 110 (299)
Q Consensus 32 P~~s~~-Rl~~ak~~~l~~~~DD~~D~~~t~ee~~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~~~~ei~~~~~~~~~~ 110 (299)
|..+.+ ++..+-+.++++++||.++.. .+++..|-+.+-. +.. .. .++...+.+.+.++ .+.-|+
T Consensus 79 ~~~~~evqv~IaiyT~yvi~iDD~~~~~--~~~l~~F~~~l~~--Gq~-Q~-----~p~L~~~~~~L~~~----~~~fgp 144 (376)
T PF06330_consen 79 PHLPKEVQVAIAIYTTYVIIIDDSSQEP--SDDLRTFHQRLIL--GQP-QK-----HPLLDGFASLLREM----WRHFGP 144 (376)
T ss_dssp TTS-HHHHHHHHHHHHHHHHHTT--S-S--HHHHTTHHHHHHH--T----S-----SHHHHHHHHHHHHH----HTTS-H
T ss_pred CCCCHHHHHHHHHHHHHHHhcccccccc--cHHHHHHHHHHhc--CCC-CC-----CHHHHHHHHHHHHH----HHHcch
Confidence 665554 458899999999999998765 3666666655543 111 11 13344444444433 333455
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHhcCC-CCCCHHHHHHhhhhhcchhHHHHHHHHhhcCCCchHHHhhccCchHH---H
Q 044462 111 GMIIPYLKKAWADQCKSYLVEAKWYNSG-YIPTLQEYMENAWISVTAPVMLLHAYAFTANPITKEALEFLQDSPDI---I 186 (299)
Q Consensus 111 ~~~~~~l~~~w~~~~~~~~~Ea~w~~~~-~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l---~ 186 (299)
. +.+-+.++--+++.+..-|++..+.. ..|.+-+|++ .-+|.....+...+ -...-|+. ..+..+ +
T Consensus 145 f-~anmI~~STLdFi~g~~LE~~~f~~~p~A~~FP~fLR---~ktGlsEaYA~FiF-Pk~~fpe~-----~~~~~y~~AI 214 (376)
T PF06330_consen 145 F-CANMIVKSTLDFINGCWLEQKNFHGSPGAPDFPDFLR---RKTGLSEAYAFFIF-PKALFPEV-----EYFIQYTPAI 214 (376)
T ss_dssp H-HHHHHHHHHHHHHHHHHHHTTT----TT-TTHHHHHH---HHHH-HHHHHHHT---TTTS-TT-----TTHHHHHHHH
T ss_pred H-HHHHHHHHHHHHHHHHHhhcccCCCCCCCccccHHHH---hccCcchhheeeec-ccccCChH-----HHHHHHHHHH
Confidence 5 77788899999999999988642211 1346777764 34555555444333 12222332 123333 3
Q ss_pred HHHhhHhhhccCCCCChhhhh-cCCCCchHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHhhhhhCCCCCCcHHHHHHHHH
Q 044462 187 RISSMIVRLEDDLGTSSDELK-RGDVPKSIQCYMHETRVSEDEAREHIRDLIAETWMKMNSARFGNPPYLPDVFIGMAMN 265 (299)
Q Consensus 187 ~~~~~i~rL~NDi~S~~~E~~-~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~~~l~~~~~~p~~~~~~~~n 265 (299)
--....+-++|||.||=||.. .|+..|.|.-+-.-+|+|.-+|...+.+..-++.+++.+. |.+.+ | ..++.+-+
T Consensus 215 pdl~~fi~~~NDILSFYKE~l~a~E~~NyI~n~A~~~g~S~~eaL~~l~~eti~a~~rv~~v-L~~~d--p-~ll~a~~~ 290 (376)
T PF06330_consen 215 PDLMRFINYVNDILSFYKEELVAGETGNYIHNRARVHGVSILEALRELTDETIEAVERVRRV-LSDKD--P-ELLAAWDS 290 (376)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTSSSSSSHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHHH-HTTS---H-HHHHHHHH
T ss_pred HHHHHHHHhhhhHHHHHHhhcccccccchhhhhhhccCCCHHHHHHHHHHHHHHHHHHHHHH-hccCC--h-HHHHHHHH
Confidence 344455668999999999987 8888999988888889999999998766555555555443 33222 2 34445555
Q ss_pred HhhhhhhhcccCCCCCC
Q 044462 266 LVRMSQCMYLYGDGHGV 282 (299)
Q Consensus 266 ~~r~~~~~Y~~~d~~~~ 282 (299)
+++..-.++.....|..
T Consensus 291 Fi~GYi~~H~~~~RYRL 307 (376)
T PF06330_consen 291 FIQGYIAFHTSNPRYRL 307 (376)
T ss_dssp HHHHHHHHHHHSGGGTT
T ss_pred HHHHHHHhhcCCCccCH
Confidence 55544333333334433
No 11
>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates
Probab=94.06 E-value=1.9 Score=37.38 Aligned_cols=118 Identities=17% Similarity=0.183 Sum_probs=74.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhh-hcchhHHHHHHHHhhcCCCchHHHhhccCchHHHHHHhh
Q 044462 113 IIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWI-SVTAPVMLLHAYAFTANPITKEALEFLQDSPDIIRISSM 191 (299)
Q Consensus 113 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~-s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~ 191 (299)
..+.+.+.....+.|...+..|... ..||.++|.+.-.. |.+.....+..-...+.. +++..+ ...++-+..++
T Consensus 86 ~~~~~~~~~~~~~~Gq~~Dl~~~~~-~~~t~~~y~~~~~~Kta~l~~~~~~~~~~~~~~-~~~~~~---~~~~~~~~lG~ 160 (236)
T cd00867 86 ALELFAEALRELLEGQALDLEFERD-TYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGA-DDEQAE---ALKDYGRALGL 160 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHhccHHHHHHHHHHHHHHcCc-CHHHHH---HHHHHHHHHHH
Confidence 4556678889999999999888654 57899999999887 555433322222222222 222222 24567788889
Q ss_pred HhhhccCCCCChhhh----------hcCCCCchHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHhh
Q 044462 192 IVRLEDDLGTSSDEL----------KRGDVPKSIQCYMHETRVSEDEAREHIRDLIAETWMKMNS 246 (299)
Q Consensus 192 i~rL~NDi~S~~~E~----------~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~ 246 (299)
...+.||+..+.... .+|.. +...+++ .+.+.+..++..+.+.+
T Consensus 161 a~Qi~dd~~D~~~d~~~~gk~~~D~~~gr~-tlp~~~~----------~~~~~~~~~~~~~~~~~ 214 (236)
T cd00867 161 AFQLTDDLLDVFGDAEELGKVGSDLREGRI-TLPVILA----------RERAAEYAEEAYAALEA 214 (236)
T ss_pred HHHHHHHhccccCChHHHCccHHHHHcCCc-hHHHHHH----------HHHHHHHHHHHHHHHHh
Confidence 999999999887654 44543 4554444 44455555555555443
No 12
>PF00494 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR002060 Squalene synthase 2.5.1.21 from EC (farnesyl-diphosphate farnesyltransferase) (SQS) and Phytoene synthase 2.5.1.32 from EC (PSY) share a number of functional similarities. These similarities are also reflected at the level of their primary structure [, , ]. In particular three well conserved regions are shared by SQS and PSY; they could be involved in substrate binding and/or the catalytic mechanism. SQS catalyzes the conversion of two molecules of farnesyl diphosphate (FPP) into squalene. It is the first committed step in the cholesterol biosynthetic pathway. The reaction carried out by SQS is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of FPP to form presqualene diphosphate; this intermediate is then rearranged in a NADP-dependent reduction, to form squalene: 2 FPP -> presqualene diphosphate + NADP -> squalene SQS is found in eukaryotes. In yeast it is encoded by the ERG9 gene, in mammals by the FDFT1 gene. SQS seems to be membrane-bound. PSY catalyzes the conversion of two molecules of geranylgeranyl diphosphate (GGPP) into phytoene. It is the second step in the biosynthesis of carotenoids from isopentenyl diphosphate. The reaction carried out by PSY is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of GGPP to form prephytoene diphosphate; this intermediate is then rearranged to form phytoene. 2 GGPP -> prephytoene diphosphate -> phytoene PSY is found in all organisms that synthesize carotenoids: plants and photosynthetic bacteria as well as some non- photosynthetic bacteria and fungi. In bacteria PSY is encoded by the gene crtB. In plants PSY is localized in the chloroplast.; GO: 0016740 transferase activity, 0009058 biosynthetic process; PDB: 3NRI_A 3NPR_A 2ZCR_A 2ZCP_B 4F6V_A 4EA0_A 3ACW_A 4F6X_A 3VJE_B 3ACX_A ....
Probab=94.01 E-value=1.1 Score=39.76 Aligned_cols=178 Identities=17% Similarity=0.187 Sum_probs=88.9
Q ss_pred HHHHhhhccccCCCccchhHHHHHHHHHHhhcccccccCCCHHH----HHHHHHHHhhcCccccccCchhHHHHHHHHHh
Q 044462 20 ENFFWTVGDIFEPQFGYCRRMSAMVNCLLTSIDDVYDVYGTLDE----LELFTDAVERWDATATEQLPYYMKLCFHALYN 95 (299)
Q Consensus 20 e~y~~~~a~~~eP~~s~~Rl~~ak~~~l~~~~DD~~D~~~t~ee----~~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~ 95 (299)
.+++++.-. . | ...|-.+.-+-.|.-.+||+-|......+ ++-+-++++..-.+..+..+....++..++..
T Consensus 6 ~sf~~a~~~-l-P--~~~R~~~~alyaf~r~~d~i~D~~~~~~~~~~~L~~w~~~l~~~~~~~~~~~~~~~~pv~~~l~~ 81 (267)
T PF00494_consen 6 RSFYLASLL-L-P--KEKRPAVFALYAFCRELDDIVDEPSDPEEARARLQWWRDALNSIFASYEDSLPEPSHPVARALAD 81 (267)
T ss_dssp HHHHHHHTT-S----HHHHHHHHHHHHHHHHHHHHHHCTSS-HSCHHHHHHHHHHHHHHHH-TSTHHHSSHHHHHHHHHH
T ss_pred ccHHHHHHH-C-C--HHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHHHHHHHhhhhhhccCCCcCHHHHHHHH
Confidence 344444433 3 5 34555556777888889999997664333 33333333331111111122233455555543
Q ss_pred hHHHHHHHHHhcCCccchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHHHhhcCCCch-H
Q 044462 96 SVNEMGFIALRDQEVGMIIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAYAFTANPITK-E 174 (299)
Q Consensus 96 ~~~ei~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~-e 174 (299)
+..... .-.+.+.+++.++.+... ....+|++|+......+.|....+.+-.++. .-++ +
T Consensus 82 ~~~~~~--------------l~~~~l~~li~~~~~dl~---~~~~~t~~~L~~Y~~~vag~vg~l~~~~~~~--~~~~~~ 142 (267)
T PF00494_consen 82 LVRRYG--------------LPREPLLELIDGMEMDLE---FTPYETFADLERYCYYVAGSVGLLLLQLLGA--HDPDEA 142 (267)
T ss_dssp HHCCSH--------------HHHHHHHHHHHHHHHCTT----S--SSHHHHHHHHHHHTHHHHHHHHHHHHS--STSHHH
T ss_pred HHHHHh--------------hhHHHHHHHHHHhccccc---CCCCCCHHHHHHHHHHHHHHHHHHHHHHhcc--ccchhh
Confidence 332211 124556777777654332 3457899999988888888655555444432 2222 2
Q ss_pred HHhhccCchHHHHHHhhHhhhccCCCCChhh-hhcCCC--CchHHHHhhcCCCCHHHHH
Q 044462 175 ALEFLQDSPDIIRISSMIVRLEDDLGTSSDE-LKRGDV--PKSIQCYMHETRVSEDEAR 230 (299)
Q Consensus 175 ~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E-~~~g~~--~n~V~~ym~e~g~s~eeA~ 230 (299)
.. +.....+...-+.|=+...... ..+|.+ +.- .|+++|+|.++-.
T Consensus 143 ~~-------~~a~~lG~alql~nilRd~~~D~~~~gR~ylP~d---~l~~~gv~~~dl~ 191 (267)
T PF00494_consen 143 AR-------DAARALGRALQLTNILRDIPEDALRRGRIYLPLD---DLRRFGVTPEDLL 191 (267)
T ss_dssp HH-------HHHHHHHHHHHHHHHHHTHHHH-HHTT---S-HH---HHHHTTSSHHHHH
T ss_pred HH-------HHHHHHHHHHHHHHHHHHhHHHHHhcccccCCch---hHHHcCCCHHHHH
Confidence 22 2233444444444444445566 566653 222 4678899888654
No 13
>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=89.89 E-value=16 Score=33.65 Aligned_cols=87 Identities=10% Similarity=0.090 Sum_probs=55.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHHHhhcCCCchHHHhhccCchHHHHHHhhH
Q 044462 113 IIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAYAFTANPITKEALEFLQDSPDIIRISSMI 192 (299)
Q Consensus 113 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i 192 (299)
+...+.+.....+.|.+.+..+... ..+|.++|++.-..-+|..+..++..-++--..+++..+. ..++-+..++.
T Consensus 134 ~~~~~~~~~~~~~~Gq~~~~~~~~~-~~~~~~~y~~~~~~KTa~L~~~~~~~ga~~ag~~~~~~~~---l~~~G~~lG~a 209 (322)
T TIGR02749 134 VVKLISKVITDFAEGEIKQGLNQFD-SDLSLEDYLEKSFYKTASLVAASSKAAAVLSDVPSQVAND---LYEYGKHLGLA 209 (322)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcccC-CCCCHHHHHHHHHccHHHHHHHHHHHHHHHcCcCHHHHHH---HHHHHHHHHHH
Confidence 5667778888888888877766433 3479999998766555544332221111111234444333 45677788899
Q ss_pred hhhccCCCCCh
Q 044462 193 VRLEDDLGTSS 203 (299)
Q Consensus 193 ~rL~NDi~S~~ 203 (299)
.-+.||+..+.
T Consensus 210 FQi~DDild~~ 220 (322)
T TIGR02749 210 FQVVDDILDFT 220 (322)
T ss_pred HHHHHHhccCC
Confidence 99999999876
No 14
>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=89.43 E-value=15 Score=32.68 Aligned_cols=197 Identities=12% Similarity=0.070 Sum_probs=91.4
Q ss_pred hhHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHhhcCccc---cccCchhHHHHHHHHHhhHHHHHHHHHhcCCccch
Q 044462 37 CRRMSAMVNCLLTSIDDVYDVYGTLDELELFTDAVERWDATA---TEQLPYYMKLCFHALYNSVNEMGFIALRDQEVGMI 113 (299)
Q Consensus 37 ~Rl~~ak~~~l~~~~DD~~D~~~t~ee~~~~~~ai~rwd~~~---~~~lp~~~~~~~~~l~~~~~ei~~~~~~~~~~~~~ 113 (299)
.|-.+.-+-.+.-.+||+-|...++++.+.- ++.|.... ...-| -.++..++..++.+ .+-.
T Consensus 19 ~R~~~~alYaf~r~~d~i~D~~~~~~~~~~~---L~~w~~~l~~~~~g~~--~~pv~~al~~~~~~--------~~l~-- 83 (266)
T TIGR03465 19 RRRAMTALYAFCREVDDIVDEDSDPEVAQAK---LAWWRAEIDRLYAGAP--SHPVARALADPARR--------FDLP-- 83 (266)
T ss_pred HHHHHHHHHHHHHHHHhhhcCCCCchHHHHH---HHHHHHHHHHHhCCCC--CChHHHHHHHHHHH--------cCCC--
Confidence 4444456667777799999975444333222 23333210 01112 12455555444332 1222
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHHHhhcCCCchHHHhhccCchHHHHHHhhHh
Q 044462 114 IPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAYAFTANPITKEALEFLQDSPDIIRISSMIV 193 (299)
Q Consensus 114 ~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~ 193 (299)
++.+.+++.++.+... ....+|++|+......+.|+-..+.+-.+ |.. +++.. ......+...
T Consensus 84 ----~~~~~~li~g~~~Dl~---~~~~~t~~dL~~Y~~~vAg~vg~l~~~ll--g~~-~~~~~-------~~a~~lG~Al 146 (266)
T TIGR03465 84 ----QEDFLEVIDGMEMDLE---QTRYPDFAELDLYCDRVAGAVGRLSARIF--GAT-DARTL-------EYAHHLGRAL 146 (266)
T ss_pred ----HHHHHHHHHHHHHHcC---CCCCCCHHHHHHHHHHhHHHHHHHHHHHh--CCC-ChhHH-------HHHHHHHHHH
Confidence 4556777777654333 34567998888777777665444333332 321 12211 1222233333
Q ss_pred hhccCCCCChhhhhcCCCCchHHHHhhcCCCCHHH---------HHHHHHHHHHHHHHHHhhhhhCCCCCCcHHHHHHHH
Q 044462 194 RLEDDLGTSSDELKRGDVPKSIQCYMHETRVSEDE---------AREHIRDLIAETWMKMNSARFGNPPYLPDVFIGMAM 264 (299)
Q Consensus 194 rL~NDi~S~~~E~~~g~~~n~V~~ym~e~g~s~ee---------A~~~i~~~i~~~~k~l~~~~l~~~~~~p~~~~~~~~ 264 (299)
-|.|=+........+|.+- .=.=.|.++|+|.++ ..+-+..+++.+...+.+..-.... +|......++
T Consensus 147 qltnilRdv~eD~~~gR~y-lP~~~l~~~gv~~~~l~~~~~~~~~~~~~~~l~~~A~~~l~~a~~~~~~-~p~~~~~~~~ 224 (266)
T TIGR03465 147 QLTNILRDVGEDARRGRIY-LPAEELQRFGVPAADILEGRYSPALAALCRFQAERARAHYAEADALLPA-CDRRAQRAAR 224 (266)
T ss_pred HHHHHHHHhHHHHhCCCee-cCHHHHHHcCCCHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhh-CCHhhhHHHH
Confidence 3333333333445566531 111135678888763 2333445555444443333222234 7765554444
Q ss_pred HHh
Q 044462 265 NLV 267 (299)
Q Consensus 265 n~~ 267 (299)
-.+
T Consensus 225 ~~~ 227 (266)
T TIGR03465 225 AMA 227 (266)
T ss_pred HHH
Confidence 333
No 15
>PLN02857 octaprenyl-diphosphate synthase
Probab=88.95 E-value=15 Score=35.23 Aligned_cols=88 Identities=13% Similarity=0.090 Sum_probs=56.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHHHhhcCCCchHHHhhccCchHHHHHHhhH
Q 044462 113 IIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAYAFTANPITKEALEFLQDSPDIIRISSMI 192 (299)
Q Consensus 113 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i 192 (299)
+...+.++..+...+.+.+..+.. +..+|.++|++.-..-+|..+..++..-++--..+++..+. ..++-+..++.
T Consensus 228 ~~~~~s~~~~~l~~Gei~q~~~~~-~~~~s~~~Yl~~i~~KTa~L~~~a~~~gallaga~~~~~~~---l~~fG~~LGiA 303 (416)
T PLN02857 228 VIKLISQVIKDFASGEIKQASSLF-DCDVTLDEYLLKSYYKTASLIAASTKSAAIFSGVDSSVKEQ---MYEYGKNLGLA 303 (416)
T ss_pred HHHHHHHHHHHHHhhHHHHHhccc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHH---HHHHHHHHHHH
Confidence 566777778888888777777654 34579999998876666654332221111111234444333 45677788888
Q ss_pred hhhccCCCCChh
Q 044462 193 VRLEDDLGTSSD 204 (299)
Q Consensus 193 ~rL~NDi~S~~~ 204 (299)
.-+.+|+..+..
T Consensus 304 FQI~DDiLD~~~ 315 (416)
T PLN02857 304 FQVVDDILDFTQ 315 (416)
T ss_pred HHHHHHHHhhcC
Confidence 899999998763
No 16
>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases, head-to-tail. These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4) condensation reactions. This CD includes all-trans (E)-isoprenyl diphosphate synthases which synthesize various chain length (C10, C15, C20, C25, C30, C35, C40, C45, and C50) linear isoprenyl diphosphates from precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They catalyze the successive 1'-4 condensation of the 5-carbon IPP to allylic substrates geranyl-, farnesyl-, or geranylgeranyl-diphosphate. Isoprenoid chain elongation reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DDXX(XX
Probab=87.28 E-value=14 Score=32.73 Aligned_cols=88 Identities=13% Similarity=0.032 Sum_probs=59.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHHHhhcCCCchHHHhhccCchHHHHHHhhH
Q 044462 113 IIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAYAFTANPITKEALEFLQDSPDIIRISSMI 192 (299)
Q Consensus 113 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i 192 (299)
+...+.+.....+.|...+..|... ..||.++|++.-..-+|.....+....++--..+++..+. ..++-+..+..
T Consensus 109 ~~~~~~~~~~~~~~GQ~~d~~~~~~-~~~~~~~y~~~~~~KT~~l~~~~~~~~a~l~~~~~~~~~~---l~~~g~~lG~a 184 (259)
T cd00685 109 ALELFSEAILELVEGQLLDLLSEYD-TDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEA---LKRFGRNLGLA 184 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCC-CCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHH---HHHHHHHHHHH
Confidence 6677788888899999888888654 5799999999987777765443332222111123333322 45677788888
Q ss_pred hhhccCCCCChh
Q 044462 193 VRLEDDLGTSSD 204 (299)
Q Consensus 193 ~rL~NDi~S~~~ 204 (299)
.-+.||+..+..
T Consensus 185 fQi~DD~ld~~~ 196 (259)
T cd00685 185 FQIQDDILDLFG 196 (259)
T ss_pred HHHHHHhhcccC
Confidence 888999887754
No 17
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=86.71 E-value=26 Score=32.27 Aligned_cols=108 Identities=19% Similarity=0.155 Sum_probs=70.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHHHhhcCCCchHHHhhccCchHHHHHHhhH
Q 044462 113 IIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAYAFTANPITKEALEFLQDSPDIIRISSMI 192 (299)
Q Consensus 113 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i 192 (299)
....+.+.....+.+...+-.+.... +|.++|++.-..-+|.....+...-++--..+++..+. ...+-+..++.
T Consensus 135 ~~~~~~~~~~~~~~GQ~lDl~~~~~~--~t~e~y~~~i~~KTa~L~~~a~~~ga~la~~~~~~~~~---l~~~g~~lGla 209 (322)
T COG0142 135 AIKALAEAINGLCGGQALDLAFENKP--VTLEEYLRVIELKTAALFAAAAVLGAILAGADEELLEA---LEDYGRNLGLA 209 (322)
T ss_pred HHHHHHHHHHHHHHhHHHHHHccCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHH---HHHHHHHhhHH
Confidence 56677888889999988888876655 99999999876666654443332222111222454444 35677888899
Q ss_pred hhhccCCCCChhhh-hcCCC---------CchHHHHhhcCCCC
Q 044462 193 VRLEDDLGTSSDEL-KRGDV---------PKSIQCYMHETRVS 225 (299)
Q Consensus 193 ~rL~NDi~S~~~E~-~~g~~---------~n~V~~ym~e~g~s 225 (299)
.-+.+|+..+.-+. ..|+. .+...++.-+++..
T Consensus 210 FQi~DDiLD~~~d~~~lGK~~g~Dl~~gK~T~p~l~~l~~~~~ 252 (322)
T COG0142 210 FQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEKANE 252 (322)
T ss_pred HHHHHHhhcCCCChHHhCCCcchHHHcCCchHHHHHHHHcCch
Confidence 99999999888542 22322 46677776666433
No 18
>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=85.99 E-value=24 Score=31.33 Aligned_cols=118 Identities=18% Similarity=0.152 Sum_probs=59.0
Q ss_pred HHHhhhccccCCCccchhHHHHHHHHHHhhcccccccC-CCHHHHHHHHHHHhhcCcc---ccccCchhHHHHHHHHHhh
Q 044462 21 NFFWTVGDIFEPQFGYCRRMSAMVNCLLTSIDDVYDVY-GTLDELELFTDAVERWDAT---ATEQLPYYMKLCFHALYNS 96 (299)
Q Consensus 21 ~y~~~~a~~~eP~~s~~Rl~~ak~~~l~~~~DD~~D~~-~t~ee~~~~~~ai~rwd~~---~~~~lp~~~~~~~~~l~~~ 96 (299)
+|+++.-.. |. ..|-.+.-+-.|.=..||+-|+. .++++...- ++.|... ....-| -.++..++.++
T Consensus 7 sf~~a~~~l--p~--~~R~~~~alYAf~R~~Ddi~D~~~~~~~~~~~~---L~~wr~~l~~~~~g~~--~~pv~~aL~~~ 77 (266)
T TIGR03464 7 NFPVASLLL--PA--RLRAPIHAVYAFARTADDIADEGDGSAEERLAL---LDDFRAELDAIYSGEP--AAPVFVALART 77 (266)
T ss_pred cHHHHHHhC--CH--HHHHHHHHHHHHHHHHHHhccCCCCChHHHHHH---HHHHHHHHHHHhCCCC--CChHHHHHHHH
Confidence 345444433 33 33444445556667899999975 444433221 2233321 011112 12455666555
Q ss_pred HHHHHHHHHhcCCccchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHH
Q 044462 97 VNEMGFIALRDQEVGMIIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAY 164 (299)
Q Consensus 97 ~~ei~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~ 164 (299)
+.+. +-. ++.+.+++.++... ......+|++|.......+.|+--.+.+-.
T Consensus 78 ~~~~--------~l~------~~~~~~li~~~~~D---l~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i 128 (266)
T TIGR03464 78 VQRH--------GLP------IEPFLDLLDAFRQD---VVVTRYATWAELLDYCRYSANPVGRLVLDL 128 (266)
T ss_pred HHHc--------CCC------hHHHHHHHHHHHHh---ccCCCCCCHHHHHHHHHHhHHHHHHHHHHH
Confidence 4432 322 34455666665432 223456798888888777777544444433
No 19
>PLN02890 geranyl diphosphate synthase
Probab=84.98 E-value=28 Score=33.36 Aligned_cols=89 Identities=11% Similarity=0.054 Sum_probs=59.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHHHhhcCCCchHHHhhccCchHHHHHHhhH
Q 044462 113 IIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAYAFTANPITKEALEFLQDSPDIIRISSMI 192 (299)
Q Consensus 113 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i 192 (299)
+...+.++....+.|-+.+..|... ..+|.++|++.-..-+|..+..++-.-++--..+++..+. ..++-+..++.
T Consensus 228 ~~~~~s~a~~~l~~Gq~ld~~~~~~-~~~s~~~Yl~~i~~KTa~Lf~~s~~~gAilaga~~~~~~~---l~~fG~~lGlA 303 (422)
T PLN02890 228 VVSLLATAVEHLVTGETMQITSSRE-QRRSMDYYMQKTYYKTASLISNSCKAVAILAGQTAEVAVL---AFEYGRNLGLA 303 (422)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCcCHHHHHH---HHHHHHHHHHH
Confidence 6777888899999999999888643 4589999998766555554333222111111234554443 34667888889
Q ss_pred hhhccCCCCChhh
Q 044462 193 VRLEDDLGTSSDE 205 (299)
Q Consensus 193 ~rL~NDi~S~~~E 205 (299)
.-+.||+..|.-.
T Consensus 304 FQI~DDiLD~~g~ 316 (422)
T PLN02890 304 FQLIDDVLDFTGT 316 (422)
T ss_pred HHHHHHHHhhcCC
Confidence 9999999988643
No 20
>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=83.55 E-value=31 Score=30.51 Aligned_cols=198 Identities=17% Similarity=0.184 Sum_probs=91.5
Q ss_pred chhHHHHHHHHHHhhcccccccCCCH-H----HHHHHHHHHhhcCccccccCchhHHHHHHHHHhhHHHHHHHHHhcCCc
Q 044462 36 YCRRMSAMVNCLLTSIDDVYDVYGTL-D----ELELFTDAVERWDATATEQLPYYMKLCFHALYNSVNEMGFIALRDQEV 110 (299)
Q Consensus 36 ~~Rl~~ak~~~l~~~~DD~~D~~~t~-e----e~~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~~~~ei~~~~~~~~~~ 110 (299)
..|-.+.-+-.|.-.+||+-|+.... . .++.+.+.++.-.. ...|. .++..++..+..+ .+-
T Consensus 24 ~~R~~~~alYaf~r~~Ddi~D~~~~~~~~~~~~L~~w~~~l~~~~~---~~~~~--~pv~~al~~~~~~--------~~l 90 (265)
T cd00683 24 ELRRAVCALYAFCRAADDIVDDPAAPPDEKLALLDAFRAELDAAYW---GGAPT--HPVLRALADLARR--------YGI 90 (265)
T ss_pred HHHHHHHHHHHHHHHHHhhhhCCCCCchhHHHHHHHHHHHHHHHHc---CCCCC--ChHHHHHHHHHHH--------cCC
Confidence 34444445666777789999975432 2 22223333322110 01111 2455566444431 232
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHHHhhcCCCchHHHhhccCchHHHHHHh
Q 044462 111 GMIIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAYAFTANPITKEALEFLQDSPDIIRISS 190 (299)
Q Consensus 111 ~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~ 190 (299)
. ++.+.+++.++..... ....||++|.......+.|+--.+++-.+ |..-+++.. +.....+
T Consensus 91 ~------~~~~~~li~g~~~Dl~---~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~--~~~~~~~~~-------~~A~~lG 152 (265)
T cd00683 91 P------REPFRDLLAGMAMDLD---KRRYETLDELDEYCYYVAGVVGLMLLRVF--GASSDEAAL-------ERARALG 152 (265)
T ss_pred C------HHHHHHHHHHHHHhCC---CCCCCCHHHHHHHHHHhHHHHHHHHHHHh--CCCCChHHH-------HHHHHHH
Confidence 3 4567777777765444 45677988777776666664433333333 321122222 1222222
Q ss_pred hHhhhccCCCCChhhhhcCCC--CchHHHHhhcCCCCHHHHH---------HHHHHHHHHHHHHHhhhhhCCCCCCcHHH
Q 044462 191 MIVRLEDDLGTSSDELKRGDV--PKSIQCYMHETRVSEDEAR---------EHIRDLIAETWMKMNSARFGNPPYLPDVF 259 (299)
Q Consensus 191 ~i~rL~NDi~S~~~E~~~g~~--~n~V~~ym~e~g~s~eeA~---------~~i~~~i~~~~k~l~~~~l~~~~~~p~~~ 259 (299)
....|.|=+........+|.+ +.- .|.++|+|.++-. .-+..+++.+.+.+....-.... +|...
T Consensus 153 ~AlqltnilRdv~eD~~~gR~YlP~d---~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~-lp~~~ 228 (265)
T cd00683 153 LALQLTNILRDVGEDARRGRIYLPRE---ELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAA-LPRRS 228 (265)
T ss_pred HHHHHHHHHHHHHHHHccCCCcCCHH---HHHHcCCCHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHh-CCHhh
Confidence 222222222222233445542 222 2677888876532 22444444444433333222234 77655
Q ss_pred HHHHHHHhh
Q 044462 260 IGMAMNLVR 268 (299)
Q Consensus 260 ~~~~~n~~r 268 (299)
+-.++-++.
T Consensus 229 ~~~~~~~~~ 237 (265)
T cd00683 229 RFCVRAAAM 237 (265)
T ss_pred HHHHHHHHH
Confidence 555544444
No 21
>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=83.48 E-value=36 Score=31.21 Aligned_cols=85 Identities=9% Similarity=0.012 Sum_probs=55.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHHHh--hcCCCchHHHhhccCchHHHHHHh
Q 044462 113 IIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAYAF--TANPITKEALEFLQDSPDIIRISS 190 (299)
Q Consensus 113 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~--~g~~l~~e~~~~~~~~~~l~~~~~ 190 (299)
+...+.++....+.|-..+..|.. +..+|.++|++.-..-+|..+..+ ...+ ++ ..+++..+. ..++-+..+
T Consensus 130 ~~~~~~~~~~~~~~Gq~~~~~~~~-~~~~~~~~Y~~~i~~KTa~L~~~~-~~~ga~~a-g~~~~~~~~---l~~~g~~lG 203 (319)
T TIGR02748 130 AHQILSHTIVEVCRGEIEQIKDKY-NFDQNLRTYLRRIKRKTALLIAAS-CQLGAIAS-GANEAIVKK---LYWFGYYVG 203 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHc-CCCHHHHHH---HHHHHHHHH
Confidence 566778888889999888887743 345799999988766666543322 2222 11 223333332 355667888
Q ss_pred hHhhhccCCCCCh
Q 044462 191 MIVRLEDDLGTSS 203 (299)
Q Consensus 191 ~i~rL~NDi~S~~ 203 (299)
+..-+.||+..+.
T Consensus 204 ~aFQI~DDilD~~ 216 (319)
T TIGR02748 204 MSYQITDDILDFV 216 (319)
T ss_pred HHHHHHHHHHHcc
Confidence 8888999998775
No 22
>PLN02632 phytoene synthase
Probab=75.43 E-value=69 Score=29.65 Aligned_cols=106 Identities=11% Similarity=0.134 Sum_probs=54.0
Q ss_pred hhHHHHHHHHHHhhcccccccCCCH----HHHHHHHHHHhhcCccccccCchhHHHHHHHHHhhHHHHHHHHHhcCCccc
Q 044462 37 CRRMSAMVNCLLTSIDDVYDVYGTL----DELELFTDAVERWDATATEQLPYYMKLCFHALYNSVNEMGFIALRDQEVGM 112 (299)
Q Consensus 37 ~Rl~~ak~~~l~~~~DD~~D~~~t~----ee~~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~~~~ei~~~~~~~~~~~~ 112 (299)
.|-.+.-+-.|.-.+||+-|+.... ..++...+.++. ....-|. .++..++.++..+. +-.
T Consensus 74 ~R~ai~alYAf~R~~DdI~D~~~~~~~~~~~L~~w~~~l~~----~~~g~~~--~pv~~aL~~~~~~~--------~L~- 138 (334)
T PLN02632 74 RRKAIWAIYVWCRRTDELVDGPNASHITPAALDRWEARLED----LFDGRPY--DMLDAALADTVSKF--------PLD- 138 (334)
T ss_pred HHHHHHHHHHHHHHHhHHhcCCCCChhhHHHHHHHHHHHHH----HhCCCCC--ChHHHHHHHHHHHC--------CCC-
Confidence 3444456667777899999964432 223333332222 0111121 24455555544432 212
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHHH
Q 044462 113 IIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAYA 165 (299)
Q Consensus 113 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~ 165 (299)
++.+.+++.++..... ....+|++|+......+.|+--.+++..+
T Consensus 139 -----~~~~~~li~g~~~Dl~---~~~~~t~~eL~~Ycy~vAgtVG~l~l~vl 183 (334)
T PLN02632 139 -----IQPFRDMIEGMRMDLV---KSRYENFDELYLYCYYVAGTVGLMSVPVM 183 (334)
T ss_pred -----hHHHHHHHHHHHHHhc---cCCCCCHHHHHHHHHHhhHHHHHHHHHHh
Confidence 3445677777654332 34567888888877766665444343333
No 23
>KOG1719 consensus Dual specificity phosphatase [Defense mechanisms]
Probab=71.81 E-value=3.4 Score=33.80 Aligned_cols=29 Identities=24% Similarity=0.523 Sum_probs=25.0
Q ss_pred hcCCCCchHHHHhhcC-CCCHHHHHHHHHH
Q 044462 207 KRGDVPKSIQCYMHET-RVSEDEAREHIRD 235 (299)
Q Consensus 207 ~~g~~~n~V~~ym~e~-g~s~eeA~~~i~~ 235 (299)
.+|..+..|.||+-++ +.|.++|.+++++
T Consensus 119 GRtRSaTvV~cYLmq~~~wtpe~A~~~vr~ 148 (183)
T KOG1719|consen 119 GRTRSATVVACYLMQHKNWTPEAAVEHVRK 148 (183)
T ss_pred CCccchhhhhhhhhhhcCCCHHHHHHHHHh
Confidence 4566678999998888 9999999999887
No 24
>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]
Probab=68.78 E-value=4.3 Score=34.35 Aligned_cols=26 Identities=23% Similarity=0.277 Sum_probs=21.5
Q ss_pred chHHHHhhcCCCCHHHHHHHHHHHHH
Q 044462 213 KSIQCYMHETRVSEDEAREHIRDLIA 238 (299)
Q Consensus 213 n~V~~ym~e~g~s~eeA~~~i~~~i~ 238 (299)
-+=.++|+++|+|++||.++++++--
T Consensus 149 rAKglLM~~~g~sE~EAy~~lR~~AM 174 (194)
T COG3707 149 RAKGLLMKRRGLSEEEAYKLLRRTAM 174 (194)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34457999999999999999988543
No 25
>PF03861 ANTAR: ANTAR domain; InterPro: IPR005561 ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins []. This domain has been detected in various response regulators of two-component systems, which are structured around two proteins, a histidine kinase and a response regulator. This domain is also found in one-component sensory regulators from a variety of bacteria. Most response regulators interact with DNA, however ANTAR-containing regulators interact with RNA. The majority of the domain consists of a coiled-coil.; PDB: 4AKK_A 1SD5_A 1S8N_A 1QO0_E.
Probab=67.75 E-value=5 Score=26.66 Aligned_cols=27 Identities=26% Similarity=0.224 Sum_probs=20.3
Q ss_pred CchHHHHhhcCCCCHHHHHHHHHHHHH
Q 044462 212 PKSIQCYMHETRVSEDEAREHIRDLIA 238 (299)
Q Consensus 212 ~n~V~~ym~e~g~s~eeA~~~i~~~i~ 238 (299)
.-++.++|..+|+|+++|.+.++..-.
T Consensus 16 ~~AkgiLm~~~g~~e~~A~~~Lr~~Am 42 (56)
T PF03861_consen 16 EQAKGILMARYGLSEDEAYRLLRRQAM 42 (56)
T ss_dssp HHHHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 456778999999999999998877544
No 26
>PF12368 DUF3650: Protein of unknown function (DUF3650) ; InterPro: IPR022111 This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with PF00581 from PFAM. There is a single completely conserved residue N that may be functionally important.
Probab=67.17 E-value=4.4 Score=23.01 Aligned_cols=18 Identities=33% Similarity=0.554 Sum_probs=14.1
Q ss_pred HHhhcCCCCHHHHHHHHH
Q 044462 217 CYMHETRVSEDEAREHIR 234 (299)
Q Consensus 217 ~ym~e~g~s~eeA~~~i~ 234 (299)
-|.++||+|.||-.+.+.
T Consensus 9 rYV~eh~ls~ee~~~RL~ 26 (28)
T PF12368_consen 9 RYVKEHGLSEEEVAERLA 26 (28)
T ss_pred hhHHhcCCCHHHHHHHHH
Confidence 488999999998665543
No 27
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=65.06 E-value=1.1e+02 Score=28.02 Aligned_cols=87 Identities=16% Similarity=0.008 Sum_probs=56.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHHHhh-cCCCchHHHhhccCchHHHHHHhh
Q 044462 113 IIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAYAFT-ANPITKEALEFLQDSPDIIRISSM 191 (299)
Q Consensus 113 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~-g~~l~~e~~~~~~~~~~l~~~~~~ 191 (299)
+...+.++....+.|-..+..+... .-+|.++|++.-..-+|.....++ ..+. --..+++..+. ..++-+..++
T Consensus 131 ~~~~~~~~~~~~~~Gq~~d~~~~~~-~~~s~~~y~~~i~~KTa~lf~~~~-~~ga~lag~~~~~~~~---l~~~g~~lG~ 205 (323)
T PRK10888 131 VLEVMSEAVNVIAEGEVLQLMNVND-PDITEENYMRVIYSKTARLFEAAA-QCSGILAGCTPEQEKG---LQDYGRYLGT 205 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHcCCCHHHHHH---HHHHHHHHHH
Confidence 5667788888888888888776433 357999999887666665433222 2221 01223443332 4567788888
Q ss_pred HhhhccCCCCChh
Q 044462 192 IVRLEDDLGTSSD 204 (299)
Q Consensus 192 i~rL~NDi~S~~~ 204 (299)
..-+.||+..+..
T Consensus 206 aFQi~DD~ld~~~ 218 (323)
T PRK10888 206 AFQLIDDLLDYSA 218 (323)
T ss_pred HHHHHHHhhcccC
Confidence 8999999998853
No 28
>PRK10581 geranyltranstransferase; Provisional
Probab=63.42 E-value=1.1e+02 Score=27.94 Aligned_cols=111 Identities=13% Similarity=0.110 Sum_probs=66.4
Q ss_pred HHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHH--HHHhhcCCCchHHHhhccCchHHHHHHhhHhhhccCCC
Q 044462 123 DQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLH--AYAFTANPITKEALEFLQDSPDIIRISSMIVRLEDDLG 200 (299)
Q Consensus 123 ~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~--~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~ 200 (299)
..+.|...+..|.. ..+|.++|++.-..-+|.....++ .-+..|. -+++..+. ..++-+..++..-+.+|+.
T Consensus 153 ~l~~GQ~ld~~~~~--~~~~~~~y~~i~~~KTa~L~~~~~~~gailag~-~~~~~~~~---l~~~g~~lG~aFQI~DDil 226 (299)
T PRK10581 153 GMCGGQALDLEAEG--KQVPLDALERIHRHKTGALIRAAVRLGALSAGD-KGRRALPV---LDRYAESIGLAFQVQDDIL 226 (299)
T ss_pred hhhHhhHHHHhccC--CCCCHHHHHHHHHHhhHHHHHHHHHHHHHHcCC-CcHHHHHH---HHHHHHHHHHHHHHHHHHc
Confidence 46677776777643 468999999876555554432222 1111222 12233333 4567788889999999999
Q ss_pred CChhh-----------hhcCCCCchHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHhh
Q 044462 201 TSSDE-----------LKRGDVPKSIQCYMHETRVSEDEAREHIRDLIAETWMKMNS 246 (299)
Q Consensus 201 S~~~E-----------~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~ 246 (299)
.+.-. ...|. .+.+.++ ..|+|.+.+++.++++.+.+..
T Consensus 227 D~~g~~~~~GK~~g~Dl~~gk-~T~p~l~------~~e~a~~~a~~~~~~A~~~l~~ 276 (299)
T PRK10581 227 DVVGDTATLGKRQGADQQLGK-STYPALL------GLEQARKKARDLIDDARQSLDQ 276 (299)
T ss_pred cccCChHHHCCCcchhhhcCC-CCHHHHH------HHHHHHHHHHHHHHHHHHHHHh
Confidence 98432 12232 2454444 2467777788888877766655
No 29
>smart00400 ZnF_CHCC zinc finger.
Probab=53.97 E-value=15 Score=24.14 Aligned_cols=25 Identities=24% Similarity=0.206 Sum_probs=20.7
Q ss_pred CCCCchHHHHhhcCCCCHHHHHHHH
Q 044462 209 GDVPKSIQCYMHETRVSEDEAREHI 233 (299)
Q Consensus 209 g~~~n~V~~ym~e~g~s~eeA~~~i 233 (299)
|.-.|.|..+|+-.|+|-.||++.+
T Consensus 30 g~gGd~i~fv~~~~~~sf~eA~~~L 54 (55)
T smart00400 30 GAGGNVISFLMKYDKLSFVEAVKKL 54 (55)
T ss_pred CCCCCHHHHHHHHHCcCHHHHHHHh
Confidence 3345899999999999999998865
No 30
>smart00463 SMR Small MutS-related domain.
Probab=47.70 E-value=25 Score=24.89 Aligned_cols=54 Identities=9% Similarity=0.031 Sum_probs=33.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHh-hhhhC---CC-CCC--cHHHHHHHHHHhhhhhhhcc
Q 044462 222 TRVSEDEAREHIRDLIAETWMKMN-SARFG---NP-PYL--PDVFIGMAMNLVRMSQCMYL 275 (299)
Q Consensus 222 ~g~s~eeA~~~i~~~i~~~~k~l~-~~~l~---~~-~~~--p~~~~~~~~n~~r~~~~~Y~ 275 (299)
||++.++|...+...++++++.-. +.+.= .+ ... -+.+++.+....+...+-|.
T Consensus 7 HG~~~~eA~~~l~~~l~~~~~~~~~~~~~II~G~G~~s~~g~~~i~~~l~~~l~~~~~~~~ 67 (80)
T smart00463 7 HGLTVEEALTALDKFLNNARLKGLEQKLVIITGKGKHSLGGKSGVKPALKEHLRVESFRFA 67 (80)
T ss_pred CCCCHHHHHHHHHHHHHHHHHcCCCceEEEEEcccCCCccchhhHHHHHHhchhhcccccC
Confidence 799999999999999999988765 33321 11 112 34555555555555544443
No 31
>CHL00151 preA prenyl transferase; Reviewed
Probab=46.33 E-value=2.4e+02 Score=25.89 Aligned_cols=87 Identities=8% Similarity=0.030 Sum_probs=53.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHHHh-hcCCCchHHHhhccCchHHHHHHhh
Q 044462 113 IIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAYAF-TANPITKEALEFLQDSPDIIRISSM 191 (299)
Q Consensus 113 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~-~g~~l~~e~~~~~~~~~~l~~~~~~ 191 (299)
+...+.+.....+.+-..+..+.. ..-+|.++|+..-..-+|...-.++..-+ ++ ..+++..+. ..++-+..++
T Consensus 135 ~~~~~~~~~~~l~~G~~~~~~~~~-~~~~~~~~yl~~i~~KTa~L~~~~~~~ga~la-g~~~~~~~~---l~~~G~~lG~ 209 (323)
T CHL00151 135 VVKLISKVITDFAEGEIRQGLVQF-DTTLSILNYIEKSFYKTASLIAASCKAAALLS-DADEKDHND---FYLYGKHLGL 209 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCC-CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHc-CCCHHHHHH---HHHHHHHHHH
Confidence 456677777888888777666543 33479999998755445543322221111 11 123443333 3567778889
Q ss_pred HhhhccCCCCChh
Q 044462 192 IVRLEDDLGTSSD 204 (299)
Q Consensus 192 i~rL~NDi~S~~~ 204 (299)
..-+.||+..+.-
T Consensus 210 aFQi~DDilD~~~ 222 (323)
T CHL00151 210 AFQIIDDVLDITS 222 (323)
T ss_pred HHHHHHHHhhccc
Confidence 9999999988753
No 32
>PF01713 Smr: Smr domain; InterPro: IPR002625 This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 (P23909 from SWISSPROT) protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2, P94545 from SWISSPROT [].; PDB: 3QD7_X 2D9I_A 3FAU_A 2VKC_A 2ZQE_A.
Probab=45.87 E-value=26 Score=24.96 Aligned_cols=46 Identities=9% Similarity=-0.008 Sum_probs=30.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhhC---CC-CCCcHHHHHHHHHHh
Q 044462 222 TRVSEDEAREHIRDLIAETWMKMNSARFG---NP-PYLPDVFIGMAMNLV 267 (299)
Q Consensus 222 ~g~s~eeA~~~i~~~i~~~~k~l~~~~l~---~~-~~~p~~~~~~~~n~~ 267 (299)
||++.+||...+.+.++++++.-.+.+.- .+ ..-.-.+++.+....
T Consensus 4 HG~~~~eA~~~l~~~l~~~~~~~~~~~~II~G~G~hS~~g~Lk~~V~~~L 53 (83)
T PF01713_consen 4 HGLTVEEALRALEEFLDEARQRGIRELRIITGKGNHSKGGVLKRAVRRWL 53 (83)
T ss_dssp TTS-HHHHHHHHHHHHHHHHHTTHSEEEEE--STCTCCTSHHHHHHHHHH
T ss_pred CCCcHHHHHHHHHHHHHHHHHcCCCEEEEEeccCCCCCCCcHHHHHHHHH
Confidence 79999999999999999998776665551 11 001223666666666
No 33
>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=42.33 E-value=2.4e+02 Score=24.79 Aligned_cols=66 Identities=20% Similarity=0.160 Sum_probs=40.7
Q ss_pred cCCCCCCHHHHHHhhhhhcchhHHHHHHHHhhcCCCchHHHhhccCchHHHHHHhhHhhhccCCCCChh
Q 044462 136 NSGYIPTLQEYMENAWISVTAPVMLLHAYAFTANPITKEALEFLQDSPDIIRISSMIVRLEDDLGTSSD 204 (299)
Q Consensus 136 ~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~ 204 (299)
..+..+|.++|++.-..-+|....+++..-++=-..+++..+. ..++-+..++..-+.||+..+..
T Consensus 128 ~~~~~~~~~~y~~i~~~KTg~l~~~~~~~ga~lag~~~~~~~~---l~~~g~~lG~afQi~DD~~d~~~ 193 (260)
T PF00348_consen 128 NEDKDPTEEEYLEIIRLKTGSLFALACQLGAILAGADEEQIEA---LREFGRHLGIAFQIRDDLLDLFG 193 (260)
T ss_dssp TTTSSTSHHHHHHHHHHHTHHHHHHHHHHHHHHTTSGHHHHHH---HHHHHHHHHHHHHHHHHHHHHHS
T ss_pred cccccccHHHHHHHHhhcchHHHHHHHHHHHHhccchhHHHHH---HHHHHHHHHHHHhhhhhhhhccC
Confidence 3344789999999987777755333222221111223444333 46677888888888888887764
No 34
>PF10776 DUF2600: Protein of unknown function (DUF2600); InterPro: IPR019712 This is a bacterial family of proteins. Some members in the family are annotated as YtpB, however no function is currently known.
Probab=42.18 E-value=2.9e+02 Score=25.65 Aligned_cols=77 Identities=14% Similarity=0.137 Sum_probs=46.4
Q ss_pred HHHHhhcCCCchHHHhhccCchHHHHHHhhHhhhccCCCCChhhhhcCCCCchHHHHhhcCCCCHHHHHHHHHHHHHHHH
Q 044462 162 HAYAFTANPITKEALEFLQDSPDIIRISSMIVRLEDDLGTSSDELKRGDVPKSIQCYMHETRVSEDEAREHIRDLIAETW 241 (299)
Q Consensus 162 ~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~ 241 (299)
+.-++..+.++++..+.+ .....=.++-+..|++=....+.+...|+. |.|..|- +.+++.+.+.-.++++-
T Consensus 197 L~a~A~~p~~t~~~a~~i--~~aYFPwI~gLHILLDy~IDq~EDr~~GdL-NFv~YY~-----~~~~~~~Rl~~f~~~A~ 268 (330)
T PF10776_consen 197 LFAYAADPDLTPEDAEKI--KDAYFPWICGLHILLDYFIDQEEDREGGDL-NFVFYYP-----DEEEMEERLKYFVEKAL 268 (330)
T ss_pred HHHHHcCCCCCHHHHHHH--HHcccHHHHHHHHHHHHHhhhHhHhcCCCc-eeeeeCC-----CHHHHHHHHHHHHHHHH
Confidence 333445666777665554 222222333344455555555555566665 9997664 78888888888888877
Q ss_pred HHHhh
Q 044462 242 MKMNS 246 (299)
Q Consensus 242 k~l~~ 246 (299)
+...+
T Consensus 269 ~~~~~ 273 (330)
T PF10776_consen 269 EQASR 273 (330)
T ss_pred HHHHh
Confidence 66554
No 35
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=41.25 E-value=27 Score=27.24 Aligned_cols=20 Identities=30% Similarity=0.414 Sum_probs=17.5
Q ss_pred HHHHhhcCCCCHHHHHHHHH
Q 044462 215 IQCYMHETRVSEDEAREHIR 234 (299)
Q Consensus 215 V~~ym~e~g~s~eeA~~~i~ 234 (299)
|.+.|.|.|+|.++|++.+.
T Consensus 88 IkLV~eQa~VsreeA~kAL~ 107 (122)
T COG1308 88 IKLVMEQAGVSREEAIKALE 107 (122)
T ss_pred HHHHHHHhCCCHHHHHHHHH
Confidence 78899999999999988654
No 36
>TIGR03486 cas_csx13_C CRISPR-associated protein, Cas_csx13 family, C-terminal region. Members of this family are found among cas (CRISPR-Associated) genes close to CRISPR repeats in Leptospira interrogans (a spirochete), Myxococcus xanthus (a delta-proteobacterium), and Lyngbya sp. PCC 8106 (a cyanobacterium). It is found with other cas genes in Anabaena variabilis ATCC 29413. In Lyngbya sp., the protein is split into two tandem genes. This model corresponds to the C-terminal region or upstream gene; the N-terminal region is modelled by TIGR03485. CRISPR/cas systems are associated with prokaryotic acquired resistance to phage and other exogenous DNA.
Probab=37.43 E-value=1.2e+02 Score=24.71 Aligned_cols=69 Identities=20% Similarity=0.185 Sum_probs=34.1
Q ss_pred cchhHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHhhcCccccccCchhHHHHHHHHHhhHHHHHHHHHh
Q 044462 35 GYCRRMSAMVNCLLTSIDDVYDVYGTLDELELFTDAVERWDATATEQLPYYMKLCFHALYNSVNEMGFIALR 106 (299)
Q Consensus 35 s~~Rl~~ak~~~l~~~~DD~~D~~~t~ee~~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~~~~ei~~~~~~ 106 (299)
...|=+|+.+..++.-=||+-.-.-....+..+++..+.|+.+.-. --++.|..++-.++..|..+...
T Consensus 6 a~grpW~a~F~~~~~~~~~f~~~~~er~gL~~M~~~~~~~~~e~eq---~fiqa~HeAlr~~~~qI~~~tk~ 74 (152)
T TIGR03486 6 AQGRPWYANFAKPLKWKIDFKERKRERDELNKMIENSEIWDSEAEQ---WFVQSFHEALRRIYAKIASHTKR 74 (152)
T ss_pred hcCCcHHHHHHHHHHhhHHHHHHHHHHHhHHHHHHHHHhcccHHHH---HHHHHHHHHHHHHHHHHHHHhhh
Confidence 4455566666666665554433222234555666666657643200 01234445555556666554433
No 37
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=35.68 E-value=66 Score=28.64 Aligned_cols=63 Identities=16% Similarity=0.142 Sum_probs=46.8
Q ss_pred ChhhhhcCCCCchHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHhhhhh----------CCCCCCcHHHHHHHHHHhh
Q 044462 202 SSDELKRGDVPKSIQCYMHETRVSEDEAREHIRDLIAETWMKMNSARF----------GNPPYLPDVFIGMAMNLVR 268 (299)
Q Consensus 202 ~~~E~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~~~l----------~~~~~~p~~~~~~~~n~~r 268 (299)
|++||+ .++...+.+...|.+.++|..++.--+++.+-.+-..|= .+.+ +|...+..+.++||
T Consensus 97 wk~~qk---a~klle~aaekl~~~~ee~~~~vg~~L~e~fG~~y~aFE~aa~~g~~~l~~~~-~~~~~~~~l~e~a~ 169 (269)
T COG1093 97 WKKEQK---ADKLLELAAEKLGKDLEEAYEEVGWKLEEEFGSLYDAFEAAAKEGGEVLDDEG-VPEEWKEVLKEIAR 169 (269)
T ss_pred HHHHHH---HHHHHHHHHHHhCCCHHHHHHHHhHHHHHHhCCHHHHHHHHHhcCCcccccCC-CCHHHHHHHHHHHH
Confidence 455554 347788888889999999999998888877765544332 2234 88889999999987
No 38
>PHA01082 putative transcription regulator
Probab=34.54 E-value=86 Score=24.51 Aligned_cols=44 Identities=14% Similarity=0.134 Sum_probs=27.2
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHHhhhhhCCCCCCcHHHHHHH-HHHhhhh
Q 044462 221 ETRVSEDEAREHIRDLIAETWMKMNSARFGNPPYLPDVFIGMA-MNLVRMS 270 (299)
Q Consensus 221 e~g~s~eeA~~~i~~~i~~~~k~l~~~~l~~~~~~p~~~~~~~-~n~~r~~ 270 (299)
|-|+|+|||.+-+-+-+. ..|+..+ -.. +|..|++.. ++-.|-.
T Consensus 28 eCgLsveeaa~LCfKsVr-tVk~WD~----G~~-IPPeCkRLMr~~~gREL 72 (133)
T PHA01082 28 ECGLSVEEAAKLCFKTVS-EVKQWDA----GEK-IPPICKRLMRWHSRREL 72 (133)
T ss_pred ccCccHHHHHHHHHHhHH-HHhhccC----CCc-CChHHHHHHHHhccccc
Confidence 459999999876555332 3333332 234 999999876 4444433
No 39
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=32.07 E-value=34 Score=25.46 Aligned_cols=28 Identities=18% Similarity=0.068 Sum_probs=20.8
Q ss_pred CCchHHHHhhcCCCCHHHHHHHHHHHHH
Q 044462 211 VPKSIQCYMHETRVSEDEAREHIRDLIA 238 (299)
Q Consensus 211 ~~n~V~~ym~e~g~s~eeA~~~i~~~i~ 238 (299)
-.|+|..+|+-.|+|-.||++.+.++..
T Consensus 63 ~Gd~i~~v~~~~~~~f~eAv~~l~~~~~ 90 (97)
T PF01807_consen 63 GGDVIDFVMKYEGCSFKEAVKWLAEEFG 90 (97)
T ss_dssp EE-HHHHHHHHHT--HHHHHHHHHHHHT
T ss_pred CCcHHhHHHHHhCCCHHHHHHHHHHHhC
Confidence 3488999999889999999998887654
No 40
>PF13189 Cytidylate_kin2: Cytidylate kinase-like family; PDB: 3FDI_A.
Probab=31.72 E-value=14 Score=30.66 Aligned_cols=35 Identities=20% Similarity=0.227 Sum_probs=25.1
Q ss_pred HHHHhhcCCCCHHHHHHHHHHHHHHHHHHHhhhhhC
Q 044462 215 IQCYMHETRVSEDEAREHIRDLIAETWMKMNSARFG 250 (299)
Q Consensus 215 V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~~~l~ 250 (299)
|.-.|+++|+|.++|.+.+.+ .+...+.+.+.+..
T Consensus 128 v~ri~~~~~~s~~~A~~~i~~-~D~~R~~~~~~~~~ 162 (179)
T PF13189_consen 128 VERIMEREGISEEEAEKLIKK-EDKRRRAYYKYYTG 162 (179)
T ss_dssp HHHHHHHHT--HHHHHHHHHH-HHHHHHHHHHHH-S
T ss_pred HHHHHHHcCCCHHHHHHHHHH-HHHHHHHHHHHHhC
Confidence 344577789999999988877 78888888888875
No 41
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=29.13 E-value=52 Score=25.50 Aligned_cols=25 Identities=32% Similarity=0.458 Sum_probs=20.3
Q ss_pred CCchHHHHhhcCCCCHHHHHHHHHH
Q 044462 211 VPKSIQCYMHETRVSEDEAREHIRD 235 (299)
Q Consensus 211 ~~n~V~~ym~e~g~s~eeA~~~i~~ 235 (299)
...-|.+.|.|.|+|.++|++.+.+
T Consensus 76 ~~edI~lv~~q~gvs~~~A~~AL~~ 100 (115)
T PRK06369 76 PEEDIELVAEQTGVSEEEARKALEE 100 (115)
T ss_pred CHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 3466899999999999999886553
No 42
>PTZ00393 protein tyrosine phosphatase; Provisional
Probab=27.47 E-value=46 Score=29.35 Aligned_cols=27 Identities=26% Similarity=0.252 Sum_probs=22.8
Q ss_pred CCCCchHHHHhhcCCCCHHHHHHHHHH
Q 044462 209 GDVPKSIQCYMHETRVSEDEAREHIRD 235 (299)
Q Consensus 209 g~~~n~V~~ym~e~g~s~eeA~~~i~~ 235 (299)
|..+.++.+||-++|++.++|++.+++
T Consensus 182 GRTGtl~AayLI~~GmspeeAI~~VR~ 208 (241)
T PTZ00393 182 GRAPVLASIVLIEFGMDPIDAIVFIRD 208 (241)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 444578889999999999999998876
No 43
>PF03000 NPH3: NPH3 family; InterPro: IPR004249 The RPT2 protein is a signal transducer of the phototropic response in Arabidopsis thaliana. The RPT2 gene is light inducible; encodes a novel protein with putative phosphorylation sites, a nuclear localization signal, a BTB/POZ domain (IPR000210 from INTERPRO), and a coiled-coil domain. RPT2 belongs to a large gene family that includes the recently isolated NPH3 gene []. The NPH3 protein is a NPH1 photoreceptor-interacting protein that is essential for phototropism. Phototropism of A. thaliana seedlings in response to a blue light source is initiated by nonphototropic hypocotyl 1 (NPH1), a light-activated serine-threonine protein kinase []. NPH3 is a member of a large protein family, apparently specific to higher plants, and may function as an adapter or scaffold protein to bring together the enzymatic components of a NPH1-activated phosphorelay []. Many of the proteins in this group also contain the BTB/POZ domain (IPR000210 from INTERPRO) at the N-terminal.; GO: 0004871 signal transducer activity, 0009416 response to light stimulus
Probab=27.39 E-value=64 Score=28.79 Aligned_cols=41 Identities=20% Similarity=0.338 Sum_probs=26.8
Q ss_pred HHHHHhhHhhhccCCCCChhhhhcCCCCchHHHHhhcC-CCCHHHHHHHHHHHH
Q 044462 185 IIRISSMIVRLEDDLGTSSDELKRGDVPKSIQCYMHET-RVSEDEAREHIRDLI 237 (299)
Q Consensus 185 l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~V~~ym~e~-g~s~eeA~~~i~~~i 237 (299)
+.++.-...|-++| .+--+|.+|+|.| ++|++|- +.+-+.+
T Consensus 207 Lae~lP~~aR~~hD-----------~LYrAID~YLk~Hp~ls~~Er-~~lC~~l 248 (258)
T PF03000_consen 207 LAEALPDSARPSHD-----------GLYRAIDIYLKAHPGLSEEER-KRLCRLL 248 (258)
T ss_pred HHHHCCHhhhhccc-----------hHHHHHHHHHHHcccCCHHHH-HHHHhhC
Confidence 34444455555554 3457999999999 9999984 3344433
No 44
>KOG3730 consensus Acyl-CoA:dihydroxyactetone-phosphate acyltransferase DHAPAT [Lipid transport and metabolism]
Probab=27.35 E-value=2.1e+02 Score=28.01 Aligned_cols=60 Identities=18% Similarity=0.274 Sum_probs=40.0
Q ss_pred CCchHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHhhhhhCCCCCCcHHHHHHHHHHhhhhhhhcccCCCCCCc
Q 044462 211 VPKSIQCYMHETRVSEDEAREHIRDLIAETWMKMNSARFGNPPYLPDVFIGMAMNLVRMSQCMYLYGDGHGVQ 283 (299)
Q Consensus 211 ~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~~~l~~~~~~p~~~~~~~~n~~r~~~~~Y~~~d~~~~~ 283 (299)
+++.|.=|-++.|.|.+.-.+++.+++++--.++|- -.++-.-+.+++++.=+|. |++..
T Consensus 77 ~~sVi~~~~kes~~s~d~~r~ea~eIlDEmsh~~nl----------~~IR~cg~ai~ki~k~i~d---g~yVN 136 (685)
T KOG3730|consen 77 LRSVIEHYAKESGTSLDQMRREAREILDEMSHDRNL----------AIIRWCGIAITKIGKRICD---GFYVN 136 (685)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhcch----------HHHHHHHHHHHHHHHHHhc---ceeEC
Confidence 457888899999999988777777766643333222 1334445777787766676 88776
No 45
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=26.82 E-value=62 Score=25.12 Aligned_cols=23 Identities=30% Similarity=0.479 Sum_probs=19.2
Q ss_pred CchHHHHhhcCCCCHHHHHHHHH
Q 044462 212 PKSIQCYMHETRVSEDEAREHIR 234 (299)
Q Consensus 212 ~n~V~~ym~e~g~s~eeA~~~i~ 234 (299)
..-|.+.|.+.|+|.++|++.+.
T Consensus 79 ~eDI~lV~eq~gvs~e~A~~AL~ 101 (116)
T TIGR00264 79 EDDIELVMKQCNVSKEEARRALE 101 (116)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHH
Confidence 35688999999999999988655
No 46
>KOG0776 consensus Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism]
Probab=26.63 E-value=5.6e+02 Score=24.31 Aligned_cols=96 Identities=11% Similarity=0.042 Sum_probs=64.9
Q ss_pred CCccchHHHHHHHHHHHHHHHHHHHHHhcCCCCC---CHHHHHHhhhhhcchhHHHHHHHHh-hcCCCchHHHhhccCch
Q 044462 108 QEVGMIIPYLKKAWADQCKSYLVEAKWYNSGYIP---TLQEYMENAWISVTAPVMLLHAYAF-TANPITKEALEFLQDSP 183 (299)
Q Consensus 108 ~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~P---s~eEYl~~~~~s~g~~~~~~~~~~~-~g~~l~~e~~~~~~~~~ 183 (299)
++.. +...+..+.++++++...|.....+|.-+ .+++|...-...+|.-+-.++-.-+ +| ..++++.+.+ -
T Consensus 193 ~n~~-v~elm~~aI~dLv~ge~~~~~~~~~~~d~~~~~~e~~e~~~~~KTAsLla~Sc~~~aILg-g~s~ev~e~~---~ 267 (384)
T KOG0776|consen 193 ENPV-VVELMASAIADLVRGEFTQGLVAGEGLDLDDVGLEYLEFKTLLKTASLLAKSCVAAAILG-GGSEEVIEAA---F 267 (384)
T ss_pred cCch-HHHHHHHHHHHHHHhhhhcccccccccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCHHHHHHH---H
Confidence 3445 78889999999999988877655433333 5788877766666643322221111 33 3456666653 5
Q ss_pred HHHHHHhhHhhhccCCCCChhhhhc
Q 044462 184 DIIRISSMIVRLEDDLGTSSDELKR 208 (299)
Q Consensus 184 ~l~~~~~~i~rL~NDi~S~~~E~~~ 208 (299)
++-+..++..-+++||..+.+....
T Consensus 268 ~yGR~lGL~fQvvDDildftkss~e 292 (384)
T KOG0776|consen 268 EYGRCLGLAFQVVDDILDFTKSSEE 292 (384)
T ss_pred HHHHHHHHHHHHhhcccCcccchhh
Confidence 6778899999999999999987654
No 47
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=23.53 E-value=3e+02 Score=25.41 Aligned_cols=118 Identities=15% Similarity=0.187 Sum_probs=65.7
Q ss_pred hhhhhcchhHHHHHHHHhhcCCCchHHHhhccCchHHHHHHhhHhhhccCCCCChhhhhcCCCCchHHHHhhcC-CCCHH
Q 044462 149 NAWISVTAPVMLLHAYAFTANPITKEALEFLQDSPDIIRISSMIVRLEDDLGTSSDELKRGDVPKSIQCYMHET-RVSED 227 (299)
Q Consensus 149 ~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~V~~ym~e~-g~s~e 227 (299)
.-+..+|.+.++.-...+..+.+++. +....++......+..|+..-.-|-.---+.-++|.++|..... |-+..
T Consensus 221 sLr~dsGlhQLvPYFi~f~~eqit~N----l~nl~~LtTv~~m~~sLL~N~~iFvdPY~hqlmPSilTcliakklg~~p~ 296 (450)
T COG5095 221 SLRNDSGLHQLVPYFIHFFNEQITKN----LKNLEKLTTVVMMYSSLLKNKYIFVDPYLHQLMPSILTCLIAKKLGNVPD 296 (450)
T ss_pred HhccCccHHHHHHHHHHHHHHHHHHh----hhhHHHHHHHHHHHHHHhcCCceeecHHHHHHHHHHHHHHHHHHhcCCCc
Confidence 33456787776655544444544443 44456677777777777754433332223334578899988755 54333
Q ss_pred H-HHHHHHHHHHHHHHHHhhhhhCC---------CCCCcHHHHHHHHHHhhhhhhhcc
Q 044462 228 E-AREHIRDLIAETWMKMNSARFGN---------PPYLPDVFIGMAMNLVRMSQCMYL 275 (299)
Q Consensus 228 e-A~~~i~~~i~~~~k~l~~~~l~~---------~~~~p~~~~~~~~n~~r~~~~~Y~ 275 (299)
+ ---.+++... .+..-+++. .. +-+...++|++..|+....|.
T Consensus 297 dhe~~alRd~AA----~ll~yV~~~F~~~YktLkPR-vtrTllKafLD~~k~~sT~YG 349 (450)
T COG5095 297 DHEHYALRDVAA----DLLKYVFSNFSSSYKTLKPR-VTRTLLKAFLDREKTESTQYG 349 (450)
T ss_pred chhHHHHHHHHH----HHHHHHHhhhhHhhhhhchH-HHHHHHHHHHhcccccchhhh
Confidence 2 0111222222 333334321 12 445778889999998887775
No 48
>PF03701 UPF0181: Uncharacterised protein family (UPF0181); InterPro: IPR005371 This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH P76260 from SWISSPROT.
Probab=22.04 E-value=1.4e+02 Score=19.53 Aligned_cols=24 Identities=25% Similarity=0.203 Sum_probs=17.9
Q ss_pred HhhcCCCCHHHHHHHHHHHHHHHHH
Q 044462 218 YMHETRVSEDEAREHIRDLIAETWM 242 (299)
Q Consensus 218 ym~e~g~s~eeA~~~i~~~i~~~~k 242 (299)
+| ..|+|--||+..+...|.+..+
T Consensus 23 LM-aqGmSsgEAI~~VA~~iRe~~~ 46 (51)
T PF03701_consen 23 LM-AQGMSSGEAIAIVAQEIREEHQ 46 (51)
T ss_pred HH-HhcccHHHHHHHHHHHHHHHHH
Confidence 44 3688999999988887776543
No 49
>KOG1720 consensus Protein tyrosine phosphatase CDC14 [Defense mechanisms]
Probab=21.91 E-value=73 Score=27.51 Aligned_cols=28 Identities=29% Similarity=0.424 Sum_probs=22.0
Q ss_pred cCCCCchHHHHhh-cCCCCHHHHHHHHHH
Q 044462 208 RGDVPKSIQCYMH-ETRVSEDEAREHIRD 235 (299)
Q Consensus 208 ~g~~~n~V~~ym~-e~g~s~eeA~~~i~~ 235 (299)
.|.....|.|||- ++|+|..||++.++.
T Consensus 158 lGRTG~liAc~lmy~~g~ta~eaI~~lR~ 186 (225)
T KOG1720|consen 158 LGRTGTLIACYLMYEYGMTAGEAIAWLRI 186 (225)
T ss_pred CCchhHHHHHHHHHHhCCCHHHHHHHHHh
Confidence 4556688999865 569999999998875
No 50
>PRK12793 flaF flagellar biosynthesis regulatory protein FlaF; Reviewed
Probab=21.88 E-value=3.5e+02 Score=20.90 Aligned_cols=41 Identities=15% Similarity=0.108 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhCC-CCCCcHHHHHHHHHHhh
Q 044462 226 EDEAREHIRDLIAETWMKMNSARFGN-PPYLPDVFIGMAMNLVR 268 (299)
Q Consensus 226 ~eeA~~~i~~~i~~~~k~l~~~~l~~-~~~~p~~~~~~~~n~~r 268 (299)
..++++.+.. -..-|..|...+..+ ++ +|..++.-.++++-
T Consensus 42 ~~~~~eAL~~-NrrLWt~~~~Dl~~p~N~-LP~eLRa~lisL~~ 83 (115)
T PRK12793 42 SREAIEALYF-TRRLWTVLIEDLGSPENA-LPEELRADLISIGL 83 (115)
T ss_pred hHHHHHHHHH-HHHHHHHHHHHhCCCCCC-CCHHHHHHHHHHHH
Confidence 3444444443 667888999999987 45 99999999988873
No 51
>COG1562 ERG9 Phytoene/squalene synthetase [Lipid metabolism]
Probab=21.59 E-value=5.4e+02 Score=23.28 Aligned_cols=112 Identities=16% Similarity=0.006 Sum_probs=57.4
Q ss_pred chhHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHhhcCccccccCchhHHHHHHHHHhhHHHHHHHHHhcCCccchHH
Q 044462 36 YCRRMSAMVNCLLTSIDDVYDVYGTLDELELFTDAVERWDATATEQLPYYMKLCFHALYNSVNEMGFIALRDQEVGMIIP 115 (299)
Q Consensus 36 ~~Rl~~ak~~~l~~~~DD~~D~~~t~ee~~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~~~~ei~~~~~~~~~~~~~~~ 115 (299)
..|-..+-+-.+.=.+||+-|..+.++....+.+..++=-....+.-|..-.++..++..+..+ .+-.
T Consensus 34 ~~R~av~alYa~~R~~Ddv~D~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~pv~~al~~~~~~--------~~~~---- 101 (288)
T COG1562 34 EKREAVWALYAFCREADDVVDGVSDPDLPAEILLAWRRELDGDFSGQPASDHPVLAALVEVARR--------FGLP---- 101 (288)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHhccccCCCcccCHHHHHHHHHHHH--------cCCC----
Confidence 4555566788888899999998876655555555555411111011111112444455433333 2322
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhhhhhcchhHHHHHHH
Q 044462 116 YLKKAWADQCKSYLVEAKWYNSGYIPTLQEYMENAWISVTAPVMLLHAY 164 (299)
Q Consensus 116 ~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~ 164 (299)
++.+.+++.|+........-.....+++|.. .+.|+--.+.+..
T Consensus 102 --~~~~~~~~da~~~Dl~~~~y~~~~eL~~Yc~---~vAg~vG~l~~~I 145 (288)
T COG1562 102 --REAFPALIDAMRMDLDRTRYLDFEELEEYCY---GVAGAVGLLLARI 145 (288)
T ss_pred --HHHHHHHHHHHHHHhhhccccCHHHHHHHHH---HhHHHHHHHHHHH
Confidence 4556667777666555444333345666654 4444433333333
No 52
>PF00156 Pribosyltran: Phosphoribosyl transferase domain; InterPro: IPR000836 The name PRT comes from phosphoribosyltransferase (PRTase) enzymes, which carry out phosphoryl transfer reactions on 5-phosphoribosyl-alpha1-pyrophosphate PRPP, an activated form of ribose-5-phosphate. Members of Phosphoribosyltransferase (PRT) are catalytic and are regulatory proteins involved in nucleotide synthesis and salvage []. This includes a range of diverse phosphoribosyl transferase enzymes including adenine phosphoribosyltransferase (2.4.2.7 from EC); hypoxanthine-guanine-xanthine phosphoribosyltransferase; hypoxanthine phosphoribosyltransferase (2.4.2.8 from EC); ribose-phosphate pyrophosphokinase (2.7.6.1 from EC); amidophosphoribosyltransferase (2.4.2.14 from EC); orotate phosphoribosyltransferase (2.4.2.10 from EC);uracil phosphoribosyltransferase (2.4.2.9 from EC); and xanthine-guanine phosphoribosyltransferase (2.4.2.22 from EC). Not all PRT proteins are enzymes. For example, in some bacteria PRT proteins regulate the expression of purine and pyrimidine synthetic genes. Members of PRT are defined by the protein fold and by a short 13-residue sequence motif, The motif consists of four hydrophobic amino acids, two acidic amino acids and seven amino acids of variable character, usually including glycine and threonine. The motif has been predicted to be a PRPP-binding site in advance of structural information [, ]. Apart of this motif, different PRT proteins have a low level of sequence identity, less than 15%. The PRT sequence motif is only found in PRTases from the nucleotide synthesis and salvage pathways. Other PRTases, from the tryptophan, histidine and nicotinamide synthetic and salvage pathways, lack the PRT sequence motif and appear to be unrelated to each other and unrelated to the PRT family.; GO: 0009116 nucleoside metabolic process; PDB: 2JBH_A 1Y0B_D 2FXV_B 1GPH_1 1AO0_D 1ORO_B 1VCH_C 2WNS_A 2PRZ_B 2PS1_A ....
Probab=20.84 E-value=32 Score=26.13 Aligned_cols=20 Identities=40% Similarity=0.401 Sum_probs=15.7
Q ss_pred hhcccccccCCCHHHHHHHH
Q 044462 49 TSIDDVYDVYGTLDELELFT 68 (299)
Q Consensus 49 ~~~DD~~D~~~t~ee~~~~~ 68 (299)
.++||.+|+++|..++....
T Consensus 92 liVDDvi~tG~Tl~~~~~~L 111 (125)
T PF00156_consen 92 LIVDDVIDTGGTLKEAIELL 111 (125)
T ss_dssp EEEEEEESSSHHHHHHHHHH
T ss_pred EEEeeeEcccHHHHHHHHHH
Confidence 37999999999877765544
No 53
>KOG2077 consensus JNK/SAPK-associated protein-1 [Signal transduction mechanisms]
Probab=20.82 E-value=1.5e+02 Score=29.50 Aligned_cols=96 Identities=10% Similarity=0.147 Sum_probs=49.0
Q ss_pred hhcCCCchHHHhhccCchHHHHHHhhHhhhccCC------CCChhhhhcCCCCch--HHHHhhcCCCCHHHHHHHHHHHH
Q 044462 166 FTANPITKEALEFLQDSPDIIRISSMIVRLEDDL------GTSSDELKRGDVPKS--IQCYMHETRVSEDEAREHIRDLI 237 (299)
Q Consensus 166 ~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi------~S~~~E~~~g~~~n~--V~~ym~e~g~s~eeA~~~i~~~i 237 (299)
+||.. |-+-+..+..++..-+.....-||+ .+.+++.-+|..-.. +..=|.+.---.||-++.++...
T Consensus 298 GMGrE----VeNLilENsqLLetKNALNiVKNDLIakVDeL~~E~~vLrgElea~kqak~Klee~i~elEEElk~~k~ea 373 (832)
T KOG2077|consen 298 GMGRE----VENLILENSQLLETKNALNIVKNDLIAKVDELTCEKDVLRGELEAVKQAKLKLEEKIRELEEELKKAKAEA 373 (832)
T ss_pred cchHH----HHHHHHhhHHHHhhhhHHHHHHHHHHHHHHhhccHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56654 3333445677777666666666776 355566666654211 11111111111222233333333
Q ss_pred HHHHHHHhhhhh--CCCCCCcHHHHHHH--HHHhhhh
Q 044462 238 AETWMKMNSARF--GNPPYLPDVFIGMA--MNLVRMS 270 (299)
Q Consensus 238 ~~~~k~l~~~~l--~~~~~~p~~~~~~~--~n~~r~~ 270 (299)
.++.++ .. .+++ +|..-+++| ..++|++
T Consensus 374 ~~ar~~----~~~~e~dd-iPmAqRkRFTRvEMaRVL 405 (832)
T KOG2077|consen 374 EDARQK----AKDDEDDD-IPMAQRKRFTRVEMARVL 405 (832)
T ss_pred HHHHHh----hccccccc-ccHHHHhhhHHHHHHHHH
Confidence 333222 22 2256 999999988 6788877
No 54
>COG2236 Predicted phosphoribosyltransferases [General function prediction only]
Probab=20.37 E-value=45 Score=28.34 Aligned_cols=22 Identities=23% Similarity=0.090 Sum_probs=17.9
Q ss_pred hhcccccccCCCHHHHHHHHHH
Q 044462 49 TSIDDVYDVYGTLDELELFTDA 70 (299)
Q Consensus 49 ~~~DD~~D~~~t~ee~~~~~~a 70 (299)
.++||+.|++.|++.+..+.+.
T Consensus 91 LIVDDI~DTG~Tl~~a~~~l~~ 112 (192)
T COG2236 91 LIVDDIVDTGETLELALEELKK 112 (192)
T ss_pred EEEecccCchHhHHHHHHHHHh
Confidence 3799999999998887766654
No 55
>PF10397 ADSL_C: Adenylosuccinate lyase C-terminus; InterPro: IPR019468 Adenylosuccinate lyase catalyses two steps in the synthesis of purine nucleotides: the conversion of succinylaminoimidazole-carboxamide ribotide into aminoimidazole-carboxamide ribotide (the fifth step of de novo IMP biosynthesis); the formation of adenosine monophosphate (AMP) from adenylosuccinate (the final step in the synthesis of AMP from IMP) []. This entry represents the C-terminal, seven alpha-helical, domain of adenylosuccinate lyase [].; PDB: 1YIS_A 1C3U_B 1C3C_A 3C8T_A 2PFM_B 1RE5_D 1Q5N_A 2VD6_D 2J91_B 2X75_A.
Probab=20.21 E-value=1.3e+02 Score=21.26 Aligned_cols=30 Identities=20% Similarity=0.407 Sum_probs=24.0
Q ss_pred hHHHHhhcCCCCHHHHHHHHHHHHHHHHHH
Q 044462 214 SIQCYMHETRVSEDEAREHIRDLIAETWMK 243 (299)
Q Consensus 214 ~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ 243 (299)
.|...+-+.|++.|+|-+.+++...++|+.
T Consensus 8 ~v~~~L~~~G~gR~~Ah~lv~~~a~~a~~~ 37 (81)
T PF10397_consen 8 RVMLALAEKGLGRQEAHELVQEAAMEAWEN 37 (81)
T ss_dssp HHHHHHHHTTH-HHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHHHHHHH
Confidence 355666678999999999999999999864
No 56
>PF05772 NinB: NinB protein; InterPro: IPR008711 The ninR region of Bacteriophage lambda contains two recombination genes, orf (ninB) and rap (ninG), that have roles when the RecF and RecBCD recombination pathways of Escherichia coli, respectively, operate on phage lambda []. Genetic recombination in phage lambda relies on DNA end processing by Exo to expose 3'-tailed strands for annealing and exchange by beta protein. Phage lambda encodes an additional recombinase, NinB (Orf), which participates in the early stages of recombination by supplying a function equivalent to the E. coli RecFOR complex. These host enzymes assist loading of the RecA strand exchange protein onto ssDNA coated with ssDNA-binding protein. NinB has two structural domains with unusual folds, and exists as an intertwined dimer [].; PDB: 1PC6_B.
Probab=20.20 E-value=36 Score=26.91 Aligned_cols=57 Identities=9% Similarity=0.101 Sum_probs=27.2
Q ss_pred HHhhHHHHHHHHHhcCCccchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHH-HHHHhhhhhc
Q 044462 93 LYNSVNEMGFIALRDQEVGMIIPYLKKAWADQCKSYLVEAKWYNSGYIPTLQ-EYMENAWISV 154 (299)
Q Consensus 93 l~~~~~ei~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Ps~e-EYl~~~~~s~ 154 (299)
++..+.+|+..+ .++|+. +-.+.|++++.+.+.-++.....-+|.++ |+...|..|+
T Consensus 43 lwa~l~dIs~qv-~~~G~k----~~~e~WK~~~~~~~~~~~~~~~~~~~gl~Gg~v~~g~sTs 100 (127)
T PF05772_consen 43 LWAMLGDISRQV-EWNGRK----LDPEDWKELFTAAFLIATGEEQRVVPGLDGGFVVLGESTS 100 (127)
T ss_dssp HHHHHHHHHHH---BTTB-------HHHHHHHHHHHH-----S--EEEE-TTSSEEEE---TT
T ss_pred HHHHHHHHHHHh-HhcCcc----CCHHHHHHHHHHHHhhhccchhhhccCCCCCeEEEeeech
Confidence 445678887764 345533 34788999999888666655555566665 4444443333
No 57
>PRK09177 xanthine-guanine phosphoribosyltransferase; Validated
Probab=20.16 E-value=38 Score=27.62 Aligned_cols=22 Identities=23% Similarity=0.262 Sum_probs=17.7
Q ss_pred hhcccccccCCCHHHHHHHHHH
Q 044462 49 TSIDDVYDVYGTLDELELFTDA 70 (299)
Q Consensus 49 ~~~DD~~D~~~t~ee~~~~~~a 70 (299)
.++||++|+++|+.++......
T Consensus 88 LIVDDIiDTG~Tl~~v~~~l~~ 109 (156)
T PRK09177 88 LVVDDLVDTGGTARAVREMYPK 109 (156)
T ss_pred EEEeeeeCCHHHHHHHHHHHhh
Confidence 4789999999999887766543
Done!