Query 008620
Match_columns 559
No_of_seqs 247 out of 921
Neff 6.7
Searched_HMMs 46136
Date Thu Mar 28 14:27:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008620.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008620hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00684 Terpene_cyclase_plant_ 100.0 1E-152 3E-157 1261.8 51.5 532 22-556 1-542 (542)
2 PLN02279 ent-kaur-16-ene synth 100.0 7E-138 1E-142 1167.0 46.1 498 53-559 247-778 (784)
3 PLN02592 ent-copalyl diphospha 100.0 4E-110 8E-115 937.3 42.0 464 52-558 286-800 (800)
4 PF01397 Terpene_synth: Terpen 100.0 1.7E-55 3.6E-60 420.7 12.1 173 32-207 1-183 (183)
5 PF03936 Terpene_synth_C: Terp 100.0 1E-48 2.2E-53 395.7 21.8 269 237-505 1-270 (270)
6 cd00868 Terpene_cyclase_C1 Ter 100.0 3.6E-46 7.9E-51 379.7 30.2 282 251-533 1-284 (284)
7 cd00687 Terpene_cyclase_nonpla 100.0 1.6E-34 3.4E-39 298.3 21.7 244 259-508 19-265 (303)
8 PLN02150 terpene synthase/cycl 100.0 2.2E-30 4.8E-35 222.9 10.2 94 466-559 1-96 (96)
9 cd00385 Isoprenoid_Biosyn_C1 I 99.8 7.2E-21 1.6E-25 185.4 12.6 229 285-527 2-243 (243)
10 PF06330 TRI5: Trichodiene syn 97.8 0.00016 3.6E-09 76.1 11.7 194 292-507 78-276 (376)
11 cd00686 Terpene_cyclase_cis_tr 97.7 0.00068 1.5E-08 70.5 14.6 195 293-510 79-278 (357)
12 PF00494 SQS_PSY: Squalene/phy 91.0 7.3 0.00016 39.4 14.9 164 296-490 17-191 (267)
13 cd00867 Trans_IPPS Trans-Isopr 89.5 6.3 0.00014 38.9 12.7 118 373-506 86-214 (236)
14 TIGR03465 HpnD squalene syntha 88.1 33 0.00071 34.9 17.4 205 282-522 7-223 (266)
15 cd00683 Trans_IPPS_HH Trans-Is 85.9 31 0.00067 34.9 15.5 198 297-527 24-237 (265)
16 TIGR03464 HpnC squalene syntha 84.7 49 0.0011 33.7 17.8 120 282-426 7-130 (266)
17 PLN02890 geranyl diphosphate s 80.1 55 0.0012 36.0 15.3 91 371-465 226-316 (422)
18 TIGR02749 prenyl_cyano solanes 79.9 80 0.0017 33.2 16.1 88 372-463 133-220 (322)
19 PLN02857 octaprenyl-diphosphat 78.1 70 0.0015 35.1 15.3 89 372-464 227-315 (416)
20 cd00685 Trans_IPPS_HT Trans-Is 73.5 42 0.00091 33.9 11.6 121 372-506 108-239 (259)
21 COG0142 IspA Geranylgeranyl py 68.3 1.2E+02 0.0026 32.0 13.9 107 372-483 134-250 (322)
22 PF10776 DUF2600: Protein of u 64.4 1.8E+02 0.004 30.8 14.0 103 419-538 194-296 (330)
23 CHL00151 preA prenyl transfera 64.1 1.7E+02 0.0038 30.7 14.2 87 372-464 134-222 (323)
24 TIGR02748 GerC3_HepT heptapren 60.4 2.2E+02 0.0048 29.8 15.9 87 372-464 129-217 (319)
25 KOG1719 Dual specificity phosp 60.1 7.3 0.00016 36.7 2.6 31 466-496 118-149 (183)
26 PLN02632 phytoene synthase 54.3 2.9E+02 0.0063 29.2 17.7 190 298-519 74-281 (334)
27 PRK10888 octaprenyl diphosphat 50.4 3.3E+02 0.0071 28.7 16.4 88 372-464 130-218 (323)
28 PF03861 ANTAR: ANTAR domain; 48.7 18 0.00039 27.8 2.7 28 471-498 15-42 (56)
29 COG3707 AmiR Response regulato 47.5 16 0.00035 35.6 2.8 46 453-498 128-174 (194)
30 PF13798 PCYCGC: Protein of un 33.6 45 0.00098 31.5 3.4 34 477-517 125-158 (158)
31 PRK10581 geranyltranstransfera 28.0 5.8E+02 0.013 26.5 10.9 113 382-506 152-276 (299)
32 PF00348 polyprenyl_synt: Poly 28.0 5.8E+02 0.013 25.6 10.8 64 398-464 130-193 (260)
33 KOG3730 Acyl-CoA:dihydroxyacte 27.9 4.2E+02 0.0091 29.6 9.8 76 470-557 76-152 (685)
34 smart00400 ZnF_CHCC zinc finge 27.8 66 0.0014 24.4 2.9 25 469-493 30-54 (55)
35 smart00463 SMR Small MutS-rela 26.5 77 0.0017 25.8 3.3 22 482-503 7-28 (80)
36 PF05772 NinB: NinB protein; 26.1 28 0.00061 31.7 0.6 58 353-414 42-100 (127)
37 TIGR03486 cas_csx13_C CRISPR-a 24.8 3.1E+02 0.0068 25.8 7.2 13 394-406 112-124 (152)
38 PF01713 Smr: Smr domain; Int 22.8 96 0.0021 25.4 3.2 23 482-504 4-26 (83)
39 PF12368 DUF3650: Protein of u 22.4 69 0.0015 21.5 1.7 18 477-494 9-26 (28)
40 COG1308 EGD2 Transcription fac 21.6 90 0.0019 28.3 2.9 21 475-495 88-108 (122)
No 1
>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=1.4e-152 Score=1261.76 Aligned_cols=532 Identities=54% Similarity=0.918 Sum_probs=506.3
Q ss_pred CCCCCCCCCCCCc-CCccccCCCchhhHHHHHHHH-HHHHHHHHhhh---ccCcccchhHHHHHHHhCcccccHHHHHHH
Q 008620 22 RGSANFPPSIWGD-HFFQYTCDSQETDDQNVKHLE-LKKEIRRMLKA---VNKTSHTLELIDAIQRLGVSYHFESEIDEI 96 (559)
Q Consensus 22 r~~~~~~ps~W~~-~fl~~~~~~~~~~~~~~~~~~-lk~~v~~~~~~---~~~~~~~l~lID~lqrLGi~~hFe~EI~~~ 96 (559)
||+++||||+||| +|++++++... ...+.++++ ||++||+|+.. +.|++++|++||+||||||+|||++||+++
T Consensus 1 r~~~~~~~~~w~~~~~~s~~~~~~~-~~~~~~~~~~lk~~v~~~~~~~~~~~~~~~~l~liD~lqrLGi~~hF~~EI~~~ 79 (542)
T cd00684 1 RPSANFPPSLWGDDHFLSLSSDYSE-EDELEEEIEELKEEVRKMLEDSEYPVDLFERLWLIDRLQRLGISYHFEDEIKEI 79 (542)
T ss_pred CCCCCCCCCcCCCcceeecCCCcch-hHHHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHcCchhhhHHHHHHH
Confidence 7899999999999 66665544322 226789999 99999999976 679999999999999999999999999999
Q ss_pred HHHhHhcCCCCCCCCCCCCChhHHHHHHHHhhhcCccccccccccccccccccccccccChHHHHhHhhhcccCCCCccH
Q 008620 97 LGKMHKTYRDCDLCDNENDELYYISLQFRLFRQNGYRISADVFNTFEGSDGKFKASLAKDVRGMLSLYEATHLRVHGENI 176 (559)
Q Consensus 97 L~~i~~~~~~~~~~~~~~~dl~~~al~FRlLR~~Gy~vS~dvf~~F~d~~g~F~~~l~~d~~glL~LYeAs~l~~~gE~i 176 (559)
|++||++ ...... ....||++|||+|||||||||+||||||++|+|++|+|++++.+||+|||||||||||++|||+|
T Consensus 80 L~~i~~~-~~~~~~-~~~~dl~~~al~FRlLR~~Gy~vs~dvf~~F~~~~g~f~~~~~~d~~g~l~Ly~As~l~~~gE~i 157 (542)
T cd00684 80 LDYIYRY-WTERGE-SNEDDLYTTALGFRLLRQHGYNVSSDVFKKFKDEDGKFKESLTQDVKGMLSLYEASHLSFPGEDI 157 (542)
T ss_pred HHHHHHh-hccccc-ccCCCHHHHHHHHHHHHHcCCCcCHHHHhhhcCCCCCcCchhhhhhHHHHHHHHHhhcCCCCcHH
Confidence 9999986 100000 02479999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhh---cCCcHHHHHHHHccCcccccchhhHHhhhhhcccCCCcCcHHHHHHHhhhhHHHhHhhH
Q 008620 177 LDEALAFTTSHLESVAKQ---VCSPLAEQVKHALVQPIHKGLERLEARHYIPIYQGESSHNEALLTFAKLDFNGLQKLHQ 253 (559)
Q Consensus 177 Ldea~~ft~~~L~~~~~~---~~~~l~~~V~~aL~~P~~~~~~rlear~yI~~y~~~~~~n~~lLelAkldFn~~Q~~hq 253 (559)
||||++||++||++.++. ++++|+++|++||++|||+++||||||+||++|++++++|++||||||+|||+||++||
T Consensus 158 LdeA~~ft~~~L~~~~~~~~~~~~~l~~~V~~aL~~P~~~~~~rlear~yi~~Y~~~~~~n~~lLelAkldfn~~Q~~hq 237 (542)
T cd00684 158 LDEALSFTTKHLEEKLESNWIIDPDLSGEIEYALEIPLHASLPRLEARWYIEFYEQEDDHNETLLELAKLDFNILQALHQ 237 (542)
T ss_pred HHHHHHHHHHHHHHHhhccCCCCchHHHHHHHHccCchhcCCchHHHHHHHHHhCCCccccHHHHHHHHHHHHHHhHhHH
Confidence 999999999999999986 78899999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhCCCCCChhhHhhHHHHHHhhhccccCCCcchhHHHHHHHHHHhhhhhccccccCCHHHHHHHHHHHh
Q 008620 254 KELGDISRWWKELDFAHKLPFVRDRIAEVYFWAVGVHFEPQYSFARKLFTKVIYMTSIIDDIYDVYGKIEELDLFTSAIE 333 (559)
Q Consensus 254 ~El~~lsrWwk~~~l~~~l~faRdr~ve~yf~~~~~~feP~~s~~Rl~~aK~~~l~~iiDD~yD~~gt~eEl~~ft~ai~ 333 (559)
+||++++|||+++||.+++||+|+|+++||||++|++|+|++|.+|+++||+++|+|++||+||.|||.+|++.||+||+
T Consensus 238 ~El~~~~rWwk~~gL~~~l~~aRdr~ve~yf~~~a~~feP~~s~~Rl~~aK~~~l~~~iDD~fD~~gt~eEl~~ft~ai~ 317 (542)
T cd00684 238 EELKILSRWWKDLDLASKLPFARDRLVECYFWAAGTYFEPQYSLARIALAKTIALITVIDDTYDVYGTLEELELFTEAVE 317 (542)
T ss_pred HHHHHHhHHHHhcCCcccCCcccchhHHHHHHHHhcccCccchHHHHHHHHHHHHHhhhHhhhccCCCHHHHHHHHHHHH
Confidence 99999999999999988889999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhchhhhccCChhHHHHHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhh
Q 008620 334 RWDINAIDQLPEYMKLCYRALINVYSEVEKDLASQAKLYRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALIS 413 (559)
Q Consensus 334 rWd~~~~~~lpeymk~~~~al~~~~~ei~~~~~~~~~~~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S 413 (559)
|||+++++.+|+|||+||.+|++++++++.++.+++++++++|++++|+++++||++||+|+++||+||++|||++|++|
T Consensus 318 rwd~~~~~~lPe~mk~~~~al~~~~~ei~~~~~~~~~~~~~~~~~~~~~~~~~a~l~EA~w~~~g~vPt~eEYl~~~~~S 397 (542)
T cd00684 318 RWDISAIDQLPEYMKIVFKALLNTVNEIEEELLKEGGSYVVPYLKEAWKDLVKAYLVEAKWAHEGYVPTFEEYMENALVS 397 (542)
T ss_pred hccccchhhccHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhhhhHH
Confidence 99999999999999999999999999999998888888999999999999999999999999999999999999999999
Q ss_pred cchhhHHHHHHHhcCCCCChhHHhhhcCchHHHHHHhHHhHhccCccchhhhhccCCCcchhHHHHhhcCCCHHHHHHHH
Q 008620 414 SGHPNLSAISFVGMGDIVTKESFEWLFSNPRSIRASCAVGRLMNDMASHKFEQSRGHVASSVECYINQYGATEEEAYSEF 493 (559)
Q Consensus 414 ~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~l~~~~~~i~RL~NDI~S~~kE~~~G~~~n~V~cyM~e~g~S~eeA~~~i 493 (559)
+|++++++++++++|..+|+++++|+..+|+|+++++.++||+|||+||++|+++|+++|+|.|||+|+|+|+|+|++++
T Consensus 398 ~g~~~~~~~~~~~~g~~l~~e~~e~~~~~~~l~~~~~~i~rL~NDi~S~~kE~~rGdv~n~V~~ymke~g~s~eeA~~~i 477 (542)
T cd00684 398 IGLGPLLLTSFLGMGDILTEEAFEWLESRPKLVRASSTIGRLMNDIATYEDEMKRGDVASSIECYMKEYGVSEEEAREEI 477 (542)
T ss_pred hhHHHHHHHHHHhcCCCCCHHHHHHHhccHHHHHHHHHHHHHhcChhhhHHHHhcCCcccHHHHHHHhcCCCHHHHHHHH
Confidence 99999999999999999999999997777999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhcCC-CCCCHHHHHHHHHHhhhhccccccCCCCCCChh-HHHHHHhhhccc
Q 008620 494 RKQVSNAWKDINEECLRP-TVVPVPLLIRILNLTRAADVIYKYKDGYTDSEE-LKDFIVSLLINP 556 (559)
Q Consensus 494 ~~~i~~~wk~ln~e~l~~-~~~p~~~~~~~ln~aR~~~~~Y~~~Dg~t~~~~-~k~~i~~ll~~p 556 (559)
+++|+++||++|++++++ +++|++|+++++|++|+++++|+++||||.|+. ||++|++||++|
T Consensus 478 ~~~ie~~wk~ln~e~l~~~~~~p~~~~~~~~n~~r~~~~~Y~~~D~~t~~~~~~~~~i~~ll~~p 542 (542)
T cd00684 478 KKMIEDAWKELNEEFLKPSSDVPRPIKQRFLNLARVIDVFYKEGDGFTHPEGEIKDHITSLLFEP 542 (542)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCccHHHHHHHHHHhcCC
Confidence 999999999999999997 789999999999999999999999999999966 999999999998
No 2
>PLN02279 ent-kaur-16-ene synthase
Probab=100.00 E-value=6.7e-138 Score=1166.96 Aligned_cols=498 Identities=27% Similarity=0.425 Sum_probs=467.8
Q ss_pred HHH-HHHHHHHHhhh-----ccCcccchhHHHHHHHhCcccccHHHHHHHHHHhHhcCCCCCCCCCCCCChhHHHHHHHH
Q 008620 53 HLE-LKKEIRRMLKA-----VNKTSHTLELIDAIQRLGVSYHFESEIDEILGKMHKTYRDCDLCDNENDELYYISLQFRL 126 (559)
Q Consensus 53 ~~~-lk~~v~~~~~~-----~~~~~~~l~lID~lqrLGi~~hFe~EI~~~L~~i~~~~~~~~~~~~~~~dl~~~al~FRl 126 (559)
-.. |...|+++.++ +.++++++|+||+||||||+|||++||+++|+++|++ .... ..+...|+++|||+|||
T Consensus 247 ~~~yL~~~~~~~~g~vP~~yp~~~fe~l~lvd~L~rlGi~~hF~~EI~~~L~~~~~~-~~~~-~~~~~~Dl~~tAl~FRL 324 (784)
T PLN02279 247 CLRYLRSLLQKFGNAVPTVYPLDQYARLSMVDTLERLGIDRHFRKEIKSVLDETYRY-WLQG-EEEIFLDLATCALAFRI 324 (784)
T ss_pred HHHHHHHHHHhcCCCCCCCCcccHHHHhHHHHHHHHhCCccccHHHHHHHHHHHHHh-hccc-ccCCCCCHHHHHHHHHH
Confidence 345 88888887764 3789999999999999999999999999999999985 1000 00123799999999999
Q ss_pred hhhcCcccccccccccccccccccccc---ccChHHHHhHhhhcccCCCCccHHHHHHHHHHHHHHHHHhh-------cC
Q 008620 127 FRQNGYRISADVFNTFEGSDGKFKASL---AKDVRGMLSLYEATHLRVHGENILDEALAFTTSHLESVAKQ-------VC 196 (559)
Q Consensus 127 LR~~Gy~vS~dvf~~F~d~~g~F~~~l---~~d~~glL~LYeAs~l~~~gE~iLdea~~ft~~~L~~~~~~-------~~ 196 (559)
||||||+||||||++|+|+ + |++++ .+||+||||||||||+++|||+|||||++||++||++.++. ++
T Consensus 325 LR~hGy~VS~dvf~~F~~~-~-F~~~l~~~~~dv~gmL~LY~AS~l~~~gE~iLdeA~~Fs~~~L~~~~~~~~~~~~~~~ 402 (784)
T PLN02279 325 LRLNGYDVSSDPLKQFAED-H-FSDSLGGYLKDTGAVLELFRASQISYPDESLLEKQNSWTSHFLEQGLSNWSKTADRLR 402 (784)
T ss_pred HHHcCCCCChhHHhhcCCC-c-ccchhcccchhhHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHHhcccccccccC
Confidence 9999999999999999965 4 99998 59999999999999999999999999999999999998874 46
Q ss_pred CcHHHHHHHHccCcccccchhhHHhhhhhcccCCCc------------CcHHHHHHHhhhhHHHhHhhHHHHHHHHHHHH
Q 008620 197 SPLAEQVKHALVQPIHKGLERLEARHYIPIYQGESS------------HNEALLTFAKLDFNGLQKLHQKELGDISRWWK 264 (559)
Q Consensus 197 ~~l~~~V~~aL~~P~~~~~~rlear~yI~~y~~~~~------------~n~~lLelAkldFn~~Q~~hq~El~~lsrWwk 264 (559)
++|++||+|||++|||+++||||||+||++|++++. +|++||||||+|||+||++||+||++++|||+
T Consensus 403 ~~L~~eV~~AL~~P~~~~l~RlEaR~yI~~Y~~~~~~i~Kt~yr~~~~~n~~lLeLAklDFN~~Qs~hq~EL~~l~rWwk 482 (784)
T PLN02279 403 KYIKKEVEDALNFPYYANLERLANRRSIENYAVDDTRILKTSYRCSNICNQDFLKLAVEDFNFCQSIHREELKQLERWIV 482 (784)
T ss_pred ccHHHHHHHHhcCchhcCccHHHHHHHHHHhccccchhccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhCeeHH
Confidence 789999999999999999999999999999998875 89999999999999999999999999999999
Q ss_pred HhCCCCCChhhHhhHHHHHHhhhccccCCCcchhHHHHHHHHHHhhhhhccccccCCHHHHHHHHHHHhhhchh-hhccC
Q 008620 265 ELDFAHKLPFVRDRIAEVYFWAVGVHFEPQYSFARKLFTKVIYMTSIIDDIYDVYGKIEELDLFTSAIERWDIN-AIDQL 343 (559)
Q Consensus 265 ~~~l~~~l~faRdr~ve~yf~~~~~~feP~~s~~Rl~~aK~~~l~~iiDD~yD~~gt~eEl~~ft~ai~rWd~~-~~~~l 343 (559)
++|| .++||||||++|||||++|++|||++|.+|++|||.+++++++||+||+|||.|||++||+||+|||.+ .++.+
T Consensus 483 e~~L-~~L~faRdr~ve~Yf~aaa~~fEPe~S~aRi~~aK~~~L~tviDD~fD~yGt~eEL~~ft~aVeRWD~~~~~~~l 561 (784)
T PLN02279 483 ENRL-DKLKFARQKLAYCYFSAAATLFSPELSDARLSWAKNGVLTTVVDDFFDVGGSEEELENLIQLVEKWDVNGSPDFC 561 (784)
T ss_pred hcCC-ccCCchhhHHHHHHHHHHHhhcCchhhHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHhccccchhhC
Confidence 9999 699999999999999999999999999999999999999999999999999999999999999999998 66899
Q ss_pred ChhHHHHHHHHHHHHHHHHHH-HHhhcccchHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHH
Q 008620 344 PEYMKLCYRALINVYSEVEKD-LASQAKLYRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAI 422 (559)
Q Consensus 344 peymk~~~~al~~~~~ei~~~-~~~~~~~~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~ 422 (559)
|+|||+||.+|+++++|++.+ +.++|+ ++++|++++|++++++|++||+|+++||+||+||||+|+.+|+|+++++..
T Consensus 562 peymki~f~aL~~t~nei~~~~~~~qGr-~v~~~l~~aW~~ll~ayl~EAeW~~~g~vPT~eEYL~na~vS~~l~~i~l~ 640 (784)
T PLN02279 562 SEQVEIIFSALRSTISEIGDKAFTWQGR-NVTSHIIKIWLDLLKSMLTEAQWSSNKSTPTLDEYMTNAYVSFALGPIVLP 640 (784)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHcCc-hHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhhchhhhhhHHHHHH
Confidence 999999999999999999987 556776 999999999999999999999999999999999999999999999999899
Q ss_pred HHHhcCCCCChhHHhhhcCchHHHHHHhHHhHhccCccchhhhhccCCCcchhHHHHhhc--CCCHHHHHHHHHHHHHHH
Q 008620 423 SFVGMGDIVTKESFEWLFSNPRSIRASCAVGRLMNDMASHKFEQSRGHVASSVECYINQY--GATEEEAYSEFRKQVSNA 500 (559)
Q Consensus 423 ~~~~~g~~l~~ev~e~~~~~~~l~~~~~~i~RL~NDI~S~~kE~~~G~~~n~V~cyM~e~--g~S~eeA~~~i~~~i~~~ 500 (559)
+++++|..+|+++++| +++|+|+++++.|+||+|||+||++|+++|++ |+|+|||+|+ |+|+|||+++++++|+++
T Consensus 641 ~~~~~G~~l~eev~e~-~~~~~L~~l~s~I~RLlNDI~S~e~E~~rG~~-nsV~cYMke~~~gvSeEEAi~~i~~~Ie~~ 718 (784)
T PLN02279 641 ALYLVGPKLSEEVVDS-PELHKLYKLMSTCGRLLNDIRGFKRESKEGKL-NAVSLHMIHGNGNSTEEEAIESMKGLIESQ 718 (784)
T ss_pred HHHHhCCCCCHHHHhC-cchhHHHHHHHHHHHHHHhccccHhHHhCCCc-ceehhhhccCCCCCCHHHHHHHHHHHHHHH
Confidence 9999999999999999 79999999999999999999999999999998 9999999986 899999999999999999
Q ss_pred HHHHHHhhcCC--CCCCHHHHHHHHHHhhhhccccccCCCCCCChhHHHHHHhhhccccCC
Q 008620 501 WKDINEECLRP--TVVPVPLLIRILNLTRAADVIYKYKDGYTDSEELKDFIVSLLINPVPI 559 (559)
Q Consensus 501 wk~ln~e~l~~--~~~p~~~~~~~ln~aR~~~~~Y~~~Dg~t~~~~~k~~i~~ll~~pi~~ 559 (559)
||+||++++++ +++|++|++++||++|++++||+++||||.+ .||++|++||++||++
T Consensus 719 wKeLn~~~l~~~~~~vp~~~~~~~ln~aR~~~~~Y~~~Dgyt~~-~~k~~i~~ll~ePi~l 778 (784)
T PLN02279 719 RRELLRLVLQEKGSNVPRECKDLFWKMSKVLHLFYRKDDGFTSN-DMMSLVKSVIYEPVSL 778 (784)
T ss_pred HHHHHHHHhccCCCCCCHHHHHHHHHHHHhhhhheeCCCCCChH-HHHHHHHHHhccCCcC
Confidence 99999999964 5799999999999999999999999999975 7999999999999985
No 3
>PLN02592 ent-copalyl diphosphate synthase
Probab=100.00 E-value=3.9e-110 Score=937.29 Aligned_cols=464 Identities=24% Similarity=0.354 Sum_probs=413.7
Q ss_pred HHHH-HHHHHHHHhhh-----ccCcccchhHHHHHHHhCcccccHHHHHHHHHHhHhc-CCCCCCCCCC--CCChhHHHH
Q 008620 52 KHLE-LKKEIRRMLKA-----VNKTSHTLELIDAIQRLGVSYHFESEIDEILGKMHKT-YRDCDLCDNE--NDELYYISL 122 (559)
Q Consensus 52 ~~~~-lk~~v~~~~~~-----~~~~~~~l~lID~lqrLGi~~hFe~EI~~~L~~i~~~-~~~~~~~~~~--~~dl~~~al 122 (559)
+-.+ |...|++..++ +.+++++||+||+||||||+|||++||+++|+++|+. ...+..+.+. ..|+++|||
T Consensus 286 ~cl~YL~~~~~k~~GgVP~vyP~d~fE~LwlVDtLqRLGIs~hF~~EI~~iLd~iy~~w~~~g~~~a~~~~~~Dld~TAL 365 (800)
T PLN02592 286 NCLEYLNKAVQRFNGGVPNVYPVDLFEHIWAVDRLQRLGISRYFEPEIKECIDYVHRYWTENGICWARNSHVHDIDDTAM 365 (800)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHcCCccccHHHHHHHHHHHHHHHhhcCcccccCCCcCCHHHHHH
Confidence 3445 88889887654 3789999999999999999999999999999999984 1111111001 369999999
Q ss_pred HHHHhhhcCcccccccccccccccccccccc---ccChHHHHhHhhhcccCCCCccHHHHHHHHHHHHHHHHHh--h---
Q 008620 123 QFRLFRQNGYRISADVFNTFEGSDGKFKASL---AKDVRGMLSLYEATHLRVHGENILDEALAFTTSHLESVAK--Q--- 194 (559)
Q Consensus 123 ~FRlLR~~Gy~vS~dvf~~F~d~~g~F~~~l---~~d~~glL~LYeAs~l~~~gE~iLdea~~ft~~~L~~~~~--~--- 194 (559)
+|||||||||+||||||++|++ +|+|++++ .+|++|||+|||||||++|||.|||+|+.||++||++.+. +
T Consensus 366 aFRLLRqhGy~VS~DvF~~F~~-~g~F~~~~ge~~~Dv~glL~LYeAS~l~~~gE~iLdeA~~Fs~~~L~~~~~~~~l~d 444 (800)
T PLN02592 366 GFRLLRLHGHQVSADVFKHFEK-GGEFFCFAGQSTQAVTGMFNLYRASQVLFPGEKILENAKEFSSKFLREKQEANELLD 444 (800)
T ss_pred HHHHHHHcCCCCChHHHHhhcC-CCCccccccccccchHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHHHHhhcccccc
Confidence 9999999999999999999986 89999776 7999999999999999999999999999999999999863 1
Q ss_pred ---cCCcHHHHHHHHccCcccccchhhHHhhhhhcccCCCcC-------------cHHHHHHHhhhhHHHhHhhHHHHHH
Q 008620 195 ---VCSPLAEQVKHALVQPIHKGLERLEARHYIPIYQGESSH-------------NEALLTFAKLDFNGLQKLHQKELGD 258 (559)
Q Consensus 195 ---~~~~l~~~V~~aL~~P~~~~~~rlear~yI~~y~~~~~~-------------n~~lLelAkldFn~~Q~~hq~El~~ 258 (559)
++++|+++|+|||++|||+++||||||+||++|++++++ |+.||||||+|||+||++||+||++
T Consensus 445 ~~~~~~~L~~eV~~AL~~P~~~~l~RlEaR~yI~~Y~~~~~~~i~Kt~yr~~~~~n~~lLeLAklDFn~~Qs~hq~EL~~ 524 (800)
T PLN02592 445 KWIIMKDLPGEVGFALEIPWYASLPRVETRFYIEQYGGEDDVWIGKTLYRMPYVNNNEYLELAKLDYNNCQALHQLEWDN 524 (800)
T ss_pred ccccCccHHHHHHHhccChhhcCcchHHHHHHHHHhcCCcccchhhhhccccccCCHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 367899999999999999999999999999999987764 9999999999999999999999999
Q ss_pred HHHHHHHhCCCCCChhhHhhHHHHHHhhhccccCCCcchhHHHHHHHHHHhhhhhccccccCCHHHHHHHHHHHh-----
Q 008620 259 ISRWWKELDFAHKLPFVRDRIAEVYFWAVGVHFEPQYSFARKLFTKVIYMTSIIDDIYDVYGKIEELDLFTSAIE----- 333 (559)
Q Consensus 259 lsrWwk~~~l~~~l~faRdr~ve~yf~~~~~~feP~~s~~Rl~~aK~~~l~~iiDD~yD~~gt~eEl~~ft~ai~----- 333 (559)
++|||+++||. ++||||||++|||||++|++|||+||.+|+++||++++++++||+||+|||+||+++||++|+
T Consensus 525 lsrWwke~~L~-~L~faRdr~ve~Yfwa~~~~feP~~s~~Ri~~aK~~~LitviDD~fD~yGt~eEl~~ft~~v~~~~~~ 603 (800)
T PLN02592 525 FQKWYEECNLG-EFGVSRSELLLAYFLAAASIFEPERSHERLAWAKTTVLVEAISSYFNKETSSKQRRAFLHEFGYGYKI 603 (800)
T ss_pred HhHHHHhcCCC-cCCcchhHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHhhcccccCCCCHHHHHHHHHHHHhcccc
Confidence 99999999995 999999999999999999999999999999999999999999999999999999999999996
Q ss_pred ---hhchhhhccCCh------hHHHHHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHH
Q 008620 334 ---RWDINAIDQLPE------YMKLCYRALINVYSEVEKDLASQAKLYRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVD 404 (559)
Q Consensus 334 ---rWd~~~~~~lpe------ymk~~~~al~~~~~ei~~~~~~~~~~~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~e 404 (559)
|||.+.+++||+ |||+||.||++++|+++.++.+.+|.++++|++++|.++|+ +|..+|+
T Consensus 604 ~~~rWd~~~~~~lp~~~~~~~~mki~f~aLy~tineia~~a~~~qGr~v~~~L~~~W~~l~~------~w~~~g~----- 672 (800)
T PLN02592 604 NGRRSDHHFNDRNMRRSGSVKTGEELVGLLLGTLNQLSLDALEAHGRDISHLLRHAWEMWLL------KWLLEGD----- 672 (800)
T ss_pred cccccCchhhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHH------HHHhcCc-----
Confidence 899999999988 99999999999999999875554445999999999999998 6666665
Q ss_pred HHHHhhhhhcchhhHHHHHHH-hcCCCCChhHHhhhcCchHHHHHHhHHhHhccCccchhhhhccCCCcchhHHHHhhcC
Q 008620 405 EYMTVALISSGHPNLSAISFV-GMGDIVTKESFEWLFSNPRSIRASCAVGRLMNDMASHKFEQSRGHVASSVECYINQYG 483 (559)
Q Consensus 405 EYl~~~~~S~g~~~~~~~~~~-~~g~~l~~ev~e~~~~~~~l~~~~~~i~RL~NDI~S~~kE~~~G~~~n~V~cyM~e~g 483 (559)
+|+|++.+++++++ .+|..+|+|+++ +|++.++++.+.||+||++|+++|... .|
T Consensus 673 -------~s~~~~~ilv~~~~l~~g~~lsee~l~----~~~~~~l~~li~Rl~nDl~t~~~e~~~-------------~~ 728 (800)
T PLN02592 673 -------GRQGEAELLVKTINLTAGRSLSEELLA----HPQYEQLAQLTNRICYQLGHYKKNKVH-------------IN 728 (800)
T ss_pred -------eeccchhhHHHHHHHhcCCCCCHHHcc----chhHHHHHHHHHHHHHhhhHHhhhccc-------------CC
Confidence 44566667777777 569999999987 588999999999999999999998841 23
Q ss_pred -CCHHHHHHHHHHHHHHHHHHHHHhhcC-C-CCCCHHHHHHHHHHhhhhccccccCCCCCCChhHHHHHHhhhccccC
Q 008620 484 -ATEEEAYSEFRKQVSNAWKDINEECLR-P-TVVPVPLLIRILNLTRAADVIYKYKDGYTDSEELKDFIVSLLINPVP 558 (559)
Q Consensus 484 -~S~eeA~~~i~~~i~~~wk~ln~e~l~-~-~~~p~~~~~~~ln~aR~~~~~Y~~~Dg~t~~~~~k~~i~~ll~~pi~ 558 (559)
+++ +|.+++.+.|+.+++++.+.+++ . +.+|++|+++|||++|+ ||.. ||+.|++|++||+.+|++||+
T Consensus 729 ~~~~-~a~~~~~~~ie~~~~eL~~lvl~~~~~~vp~~cK~~f~~~~k~---fy~~--~~~~~~~~~~~i~~vl~epv~ 800 (800)
T PLN02592 729 TYNP-EEKSKTTPSIESDMQELVQLVLQNSSDDIDPVIKQTFLMVAKS---FYYA--AYCDPGTINYHIAKVLFERVA 800 (800)
T ss_pred cccH-HHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHH---HHHh--hcCCHHHHHHHHHHHhCCCCC
Confidence 455 89999999999999999999996 3 56999999999999994 4654 999998899999999999985
No 4
>PF01397 Terpene_synth: Terpene synthase, N-terminal domain; InterPro: IPR001906 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: 0016829 lyase activity, 0008152 metabolic process; PDB: 2ONH_A 2ONG_B 3P5R_A 3P5P_A 3N0F_A 3N0G_B 3PYB_A 3PYA_A 3G4F_A 3G4D_B ....
Probab=100.00 E-value=1.7e-55 Score=420.65 Aligned_cols=173 Identities=54% Similarity=0.855 Sum_probs=144.7
Q ss_pred CCcCCccc-----cCCCchhhHHHHHHHH-HHHHHHHHhhhc-cCcccchhHHHHHHHhCcccccHHHHHHHHHHhHhcC
Q 008620 32 WGDHFFQY-----TCDSQETDDQNVKHLE-LKKEIRRMLKAV-NKTSHTLELIDAIQRLGVSYHFESEIDEILGKMHKTY 104 (559)
Q Consensus 32 W~~~fl~~-----~~~~~~~~~~~~~~~~-lk~~v~~~~~~~-~~~~~~l~lID~lqrLGi~~hFe~EI~~~L~~i~~~~ 104 (559)
|||+||++ +++.+...+.+.++++ ||++||+|+... .|++++|+|||+||||||+|||++||+++|++||+.
T Consensus 1 W~d~fl~s~s~~~~~~~~~~~~~~~~~~~~Lk~~v~~~l~~~~~d~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~- 79 (183)
T PF01397_consen 1 WGDDFLQSLSPSYTACMQSEDEKCKERAEELKEEVRNMLPASYPDPLEKLELIDTLQRLGISYHFEDEIKEILDSIYRS- 79 (183)
T ss_dssp TTHHHHHHTBHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHSSSSHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHHT-
T ss_pred CCCceecCCCCcchhccchhHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHhhh-
Confidence 99999953 2111223467899999 999999999876 479999999999999999999999999999999986
Q ss_pred CCCCCCCCCCCChhHHHHHHHHhhhcCccccccccccccccccccccccccChHHHHhHhhhcccCCCCccHHHHHHHHH
Q 008620 105 RDCDLCDNENDELYYISLQFRLFRQNGYRISADVFNTFEGSDGKFKASLAKDVRGMLSLYEATHLRVHGENILDEALAFT 184 (559)
Q Consensus 105 ~~~~~~~~~~~dl~~~al~FRlLR~~Gy~vS~dvf~~F~d~~g~F~~~l~~d~~glL~LYeAs~l~~~gE~iLdea~~ft 184 (559)
...... ...||++|||+|||||||||+||||||++|+|++|+|++++.+||+|||||||||||++|||+|||||+.||
T Consensus 80 ~~~~~~--~~~dL~~~AL~FRLLRqhGy~VS~DvF~~F~d~~g~F~~~l~~Dv~glLsLYeAS~l~~~gE~iLdeA~~Ft 157 (183)
T PF01397_consen 80 WDEDNE--EIDDLYTTALRFRLLRQHGYYVSSDVFNKFKDEKGNFKESLSNDVKGLLSLYEASHLRFHGEDILDEARAFT 157 (183)
T ss_dssp TTTTSH--TSSCHHHHHHHHHHHHHTT----GGGGGGGBETTSSBSGGGGGHHHHHHHHHHHHTT--TT-HHHHHHHHHH
T ss_pred cccccc--ccCchhHHHHHHHHHHHcCCcccHHHHhCcccCCCccchhhhHhHHHHHHHHHHHHccCCChHHHHHHHHHH
Confidence 100000 124999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcCC---cHHHHHHHHc
Q 008620 185 TSHLESVAKQVCS---PLAEQVKHAL 207 (559)
Q Consensus 185 ~~~L~~~~~~~~~---~l~~~V~~aL 207 (559)
++||++.+++..+ +|+++|+|||
T Consensus 158 ~~~L~~~~~~~~~~~~~L~~~V~~AL 183 (183)
T PF01397_consen 158 TKHLKSLLSNLSIPDPHLAKEVKHAL 183 (183)
T ss_dssp HHHHHHHHTTTCTTSCHHHHHHHHHH
T ss_pred HHHHHHHhccCCCCcHHHHHHHHHhC
Confidence 9999999986543 4999999997
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=1e-48 Score=395.70 Aligned_cols=269 Identities=29% Similarity=0.427 Sum_probs=247.4
Q ss_pred HHHHHhhhhHHHhHhhHHHHHHHHHHHHHhCCCCCChhhHhhHHHHHHhhhccccCCCcchhHHHHHHHHHHhhhhhccc
Q 008620 237 LLTFAKLDFNGLQKLHQKELGDISRWWKELDFAHKLPFVRDRIAEVYFWAVGVHFEPQYSFARKLFTKVIYMTSIIDDIY 316 (559)
Q Consensus 237 lLelAkldFn~~Q~~hq~El~~lsrWwk~~~l~~~l~faRdr~ve~yf~~~~~~feP~~s~~Rl~~aK~~~l~~iiDD~y 316 (559)
+|+|||+|||.||++||+|++++++||+++|+..+.+.+|+|++.++|+.++++++|+.+..|+++||+++|+|++||+|
T Consensus 1 ~~~la~~~~~~~~~~~~~e~~~~~~W~~~~~l~~~~~~~~~~~~~~~~~~~aa~~~P~~~~~l~~~a~~~~w~f~~DD~~ 80 (270)
T PF03936_consen 1 YLELAKRDFPHCQALHQQELEEIDRWVKEFGLFDEDKAARQRFRQAYFGLLAARFYPDSSDELLAAADWMAWLFIFDDFF 80 (270)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTHHHHHTTSHHHHHHHHHHHHHHHHSGCGHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcccchhhcHhhHHHHHHHHHHHHHHHHHcCCccccccchhhhhHhHHhhhhheeCCCcHHHHHHHHhhchheeeeeecc
Confidence 68999999999999999999999999999999667777799999999999999999997777779999999999999999
Q ss_pred cccCCHHHHHHHHHHHhhhchhhhccCChhHHHHHHHHHHHHHHHHHHHHhh-cccchHHHHHHHHHHHHHHHHHHHHHh
Q 008620 317 DVYGKIEELDLFTSAIERWDINAIDQLPEYMKLCYRALINVYSEVEKDLASQ-AKLYRLHYAKEAMKNQVKHYFFEAKWY 395 (559)
Q Consensus 317 D~~gt~eEl~~ft~ai~rWd~~~~~~lpeymk~~~~al~~~~~ei~~~~~~~-~~~~~~~~~~~~w~~~~~a~l~EAkW~ 395 (559)
|.+|+.++++.|++++.||++.....+|+..++++.++.++++++...+.+. ++..+.++|+++|.+|++++++|++|+
T Consensus 81 D~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 160 (270)
T PF03936_consen 81 DDGGSAEELEALTDAVERWDPNSGDPLPDPDKPLFRALADIWNRIAARMSPAQRRRDQIKRFRNSWREYLNAYLWEARWR 160 (270)
T ss_dssp HTTSHHHHHHHHHHHHHHTSSGGGGGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccchHHHHHHHHHHhcccccccccccchhHHHHHHHHHHHHHHHHHhhhhhcccHHhhHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999988888899999999999999999998776554 332367789999999999999999999
Q ss_pred hcCCCCCHHHHHHhhhhhcchhhHHHHHHHhcCCCCChhHHhhhcCchHHHHHHhHHhHhccCccchhhhhccCCCcchh
Q 008620 396 HQNYIPTVDEYMTVALISSGHPNLSAISFVGMGDIVTKESFEWLFSNPRSIRASCAVGRLMNDMASHKFEQSRGHVASSV 475 (559)
Q Consensus 396 ~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~l~~~~~~i~RL~NDI~S~~kE~~~G~~~n~V 475 (559)
..|++||++||+++|+.|+|+++++.++.+++|..++++..+++...+.+.++++.+++|+|||+||+||+++|+.+|+|
T Consensus 161 ~~~~~ps~eeYl~~R~~t~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~NDl~S~~KE~~~g~~~N~v 240 (270)
T PF03936_consen 161 ERGRIPSLEEYLEMRRHTSGVYPCLALIEFALEFALGELPPEVLEHPPMLRRLAADIIRLVNDLYSYKKEIARGDVHNLV 240 (270)
T ss_dssp HTTS--SHHHHHHHHHHHTSHHHHHHHHHHHCSSCHTHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCSHH
T ss_pred ccCCCCCHHHHHHhccccccccHHHHHHHHhCCCccccccHHHHHhchHHHHHHHHHHHHhcccchhhcchhhcccccHH
Confidence 99999999999999999999999999999999776676666665666779999999999999999999999999999999
Q ss_pred HHHHhhcCCCHHHHHHHHHHHHHHHHHHHH
Q 008620 476 ECYINQYGATEEEAYSEFRKQVSNAWKDIN 505 (559)
Q Consensus 476 ~cyM~e~g~S~eeA~~~i~~~i~~~wk~ln 505 (559)
.|+|+++|+|.|+|++++.+|+++++++||
T Consensus 241 ~~l~~~~~~s~e~A~~~v~~~~~~~~~efn 270 (270)
T PF03936_consen 241 VVLMNEHGLSLEEAVDEVAEMINECIREFN 270 (270)
T ss_dssp HHHHHHHTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHhhhhcCCCHHHHHHHHHHHHHHHHHhcC
Confidence 999999999999999999999999999998
No 6
>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=3.6e-46 Score=379.70 Aligned_cols=282 Identities=51% Similarity=0.888 Sum_probs=265.4
Q ss_pred hhHHHHHHHHHHHHHhCCCCCChhhHhhHHHHHHhhhccccCCCcchhHHHHHHHHHHhhhhhccccccCCHHHHHHHHH
Q 008620 251 LHQKELGDISRWWKELDFAHKLPFVRDRIAEVYFWAVGVHFEPQYSFARKLFTKVIYMTSIIDDIYDVYGKIEELDLFTS 330 (559)
Q Consensus 251 ~hq~El~~lsrWwk~~~l~~~l~faRdr~ve~yf~~~~~~feP~~s~~Rl~~aK~~~l~~iiDD~yD~~gt~eEl~~ft~ 330 (559)
.||+|++++++||+++||....+++|.+...+|+|+++++|+|+.+..|+++||+++|+|++||+||.+|+.+++..+++
T Consensus 1 ~~~~e~~~~~~W~~~~~l~~~~~~~r~~~~~~~~~~a~~~p~~~~~~~l~~~a~~~~~~f~~DD~~D~~~~~~~~~~~~~ 80 (284)
T cd00868 1 LHQEELKELSRWWKELGLQEKLPFARDRLVECYFWAAGSYFEPQYSEARIALAKTIALLTVIDDTYDDYGTLEELELFTE 80 (284)
T ss_pred CCHHHHHHHHHHHHHhCCcccCCchhhHhHHHHHHHHHhhcCccchHHHHHHHHHHHHHHHHHhccccCCCHHHHHHHHH
Confidence 49999999999999999975555999999999999999999999899999999999999999999999999999999999
Q ss_pred HHhhhchhhhccCChhHHHHHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhh
Q 008620 331 AIERWDINAIDQLPEYMKLCYRALINVYSEVEKDLASQAKLYRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVA 410 (559)
Q Consensus 331 ai~rWd~~~~~~lpeymk~~~~al~~~~~ei~~~~~~~~~~~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~ 410 (559)
+++||+....+.+|+++++++.+++++++++...+.+++++....++++.|.++++++.+||+|+..|++||++||+.+|
T Consensus 81 ~~~~~~~~~~~~~p~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~e~~~~~~~~~p~~~eYl~~R 160 (284)
T cd00868 81 AVERWDISAIDELPEYMKPVFKALYDLVNEIEEELAKEGGSESLPYLKEAWKDLLRAYLVEAKWANEGYVPSFEEYLENR 160 (284)
T ss_pred HHHhcChhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHhc
Confidence 99999998888999999999999999999999887776677889999999999999999999999999999999999999
Q ss_pred hhhcchhhHHHHHHHhcCCCCCh-hHHhhhcCchHHHHHHhHHhHhccCccchhhhhccCCCcchhHHHHhhcCCCHHHH
Q 008620 411 LISSGHPNLSAISFVGMGDIVTK-ESFEWLFSNPRSIRASCAVGRLMNDMASHKFEQSRGHVASSVECYINQYGATEEEA 489 (559)
Q Consensus 411 ~~S~g~~~~~~~~~~~~g~~l~~-ev~e~~~~~~~l~~~~~~i~RL~NDI~S~~kE~~~G~~~n~V~cyM~e~g~S~eeA 489 (559)
+.|+|++++++++++++|..+|+ ++.+ .+..+++++.++.+++|+||++||+||+.+|+.+|+|.|||+++|+|.++|
T Consensus 161 ~~~~g~~~~~~l~~~~~g~~l~~~~~~~-~~~~~~l~~~~~~~~~l~NDl~S~~kE~~~g~~~N~v~vl~~~~~~~~~eA 239 (284)
T cd00868 161 RVSIGYPPLLALSFLGMGDILPEEAFEW-LPSYPKLVRASSTIGRLLNDIASYEKEIARGEVANSVECYMKEYGVSEEEA 239 (284)
T ss_pred eehhhHHHHHHHHHHHcCCCCCHHHHHH-hhhhHHHHHHHHHHHHHhccchHHHHHHccCCcccHHHHHHhccCCCHHHH
Confidence 99999999999999999999999 4555 499999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhcCC-CCCCHHHHHHHHHHhhhhcccc
Q 008620 490 YSEFRKQVSNAWKDINEECLRP-TVVPVPLLIRILNLTRAADVIY 533 (559)
Q Consensus 490 ~~~i~~~i~~~wk~ln~e~l~~-~~~p~~~~~~~ln~aR~~~~~Y 533 (559)
++++.++++++|+++++.+.+. ++.|+.+++.+.|.+|.....|
T Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~g~~~w~ 284 (284)
T cd00868 240 LEELRKMIEEAWKELNEEVLKLSSDVPRAVLETLLNLARGIYVWY 284 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhhhhcC
Confidence 9999999999999999998863 4678999999999999876654
No 7
>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=1.6e-34 Score=298.27 Aligned_cols=244 Identities=16% Similarity=0.085 Sum_probs=216.4
Q ss_pred HHHHHHHhCCCCCChhhHhhHHHHHHhhhccccCCCcchhHH-HHHHHHHHhhhhhcccccc-CCHHHHHHHHHHHhhhc
Q 008620 259 ISRWWKELDFAHKLPFVRDRIAEVYFWAVGVHFEPQYSFARK-LFTKVIYMTSIIDDIYDVY-GKIEELDLFTSAIERWD 336 (559)
Q Consensus 259 lsrWwk~~~l~~~l~faRdr~ve~yf~~~~~~feP~~s~~Rl-~~aK~~~l~~iiDD~yD~~-gt~eEl~~ft~ai~rWd 336 (559)
...|.++.|+. .-+.+|+++..++|+.+++++.|+++..|+ +.|+++.|+|++||+||.. ++++++..+++.+.++.
T Consensus 19 ~~~w~~~~~l~-~~~~~~~~~~~~~~~~~~a~~~P~a~~~~l~l~~~~~~w~f~~DD~~D~~~~~~~~~~~~~~~~~~~~ 97 (303)
T cd00687 19 YLEWVLEEMLI-PSEKAEKRFLSADFGDLAALFYPDADDERLMLAADLMAWLFVFDDLLDRDQKSPEDGEAGVTRLLDIL 97 (303)
T ss_pred HHHHHHHcCCC-CcchhHHHHhcCCHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhcccCCccccCHHHHHHHHHHHHhcc
Confidence 45799999774 334699999999999888888999999999 7779999999999999987 49999999999888854
Q ss_pred hhhhccCChhHHHHHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcch
Q 008620 337 INAIDQLPEYMKLCYRALINVYSEVEKDLASQAKLYRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGH 416 (559)
Q Consensus 337 ~~~~~~lpeymk~~~~al~~~~~ei~~~~~~~~~~~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~ 416 (559)
......-|....++..++.+++.++.... ++....++++.|.+|+.|+++|++|+.+|++||++||+++|+.|+|+
T Consensus 98 ~~~~~~~~~~~~p~~~~~~d~~~r~~~~~----~~~~~~r~~~~~~~~~~a~~~e~~~~~~~~~psl~eYl~~R~~~~g~ 173 (303)
T cd00687 98 RGDGLDSPDDATPLEFGLADLWRRTLARM----SAEWFNRFAHYTEDYFDAYIWEGKNRLNGHVPDVAEYLEMRRFNIGA 173 (303)
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhccCC----CHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhhhcccc
Confidence 43221114677888999999998886542 23456799999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHhcCCCCChhHHhhhcCchHHHHHHhHHhHhccCccchhhhh-ccCCCcchhHHHHhhcCCCHHHHHHHHHH
Q 008620 417 PNLSAISFVGMGDIVTKESFEWLFSNPRSIRASCAVGRLMNDMASHKFEQ-SRGHVASSVECYINQYGATEEEAYSEFRK 495 (559)
Q Consensus 417 ~~~~~~~~~~~g~~l~~ev~e~~~~~~~l~~~~~~i~RL~NDI~S~~kE~-~~G~~~n~V~cyM~e~g~S~eeA~~~i~~ 495 (559)
.+++.++++++|..+|+++.++ +.+.+++++++.+++|+|||+||+||+ +.|+.+|+|.|+|+++|+|.|+|++++.+
T Consensus 174 ~~~~~l~~~~~g~~lp~~~~~~-~~~~~l~~~~~~~~~l~NDl~S~~KE~~~~g~~~N~V~vl~~~~g~s~~eA~~~~~~ 252 (303)
T cd00687 174 DPCLGLSEFIGGPEVPAAVRLD-PVMRALEALASDAIALVNDIYSYEKEIKANGEVHNLVKVLAEEHGLSLEEAISVVRD 252 (303)
T ss_pred cccHHHHHHhcCCCCCHHHHhC-hHHHHHHHHHHHHHHHHHHHHhhHHHHHhCCccchHHHHHHHHcCCCHHHHHHHHHH
Confidence 9999999999999999999987 778889999999999999999999999 89999999999999999999999999999
Q ss_pred HHHHHHHHHHHhh
Q 008620 496 QVSNAWKDINEEC 508 (559)
Q Consensus 496 ~i~~~wk~ln~e~ 508 (559)
+++++++++.+..
T Consensus 253 ~~~~~~~~f~~~~ 265 (303)
T cd00687 253 MHNERITQFEELE 265 (303)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999987654
No 8
>PLN02150 terpene synthase/cyclase family protein
Probab=99.97 E-value=2.2e-30 Score=222.87 Aligned_cols=94 Identities=46% Similarity=0.749 Sum_probs=91.0
Q ss_pred hccCCCcchhHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhhhhccc-cccCCCCCCChh
Q 008620 466 QSRGHVASSVECYINQYGATEEEAYSEFRKQVSNAWKDINEECLRPTVVPVPLLIRILNLTRAADVI-YKYKDGYTDSEE 544 (559)
Q Consensus 466 ~~~G~~~n~V~cyM~e~g~S~eeA~~~i~~~i~~~wk~ln~e~l~~~~~p~~~~~~~ln~aR~~~~~-Y~~~Dg~t~~~~ 544 (559)
++|||++|+|+|||+|||+|+|||++++++||+++||++|+++++++++|.+++++++|+||+++|+ |++|||||.++.
T Consensus 1 ~~rg~vaSsIeCYMke~g~seeeA~~~i~~li~~~WK~iN~e~l~~~~~p~~~~~~~~NlaR~~~~~~Y~~~Dg~t~~~~ 80 (96)
T PLN02150 1 MRRGEVANGVNCYMKQHGVTKEEAVSELKKMIRDNYKIVMEEFLTIKDVPRPVLVRCLNLARLIDVYCYNEGDGFTYPHG 80 (96)
T ss_pred CCCCcchHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHhheecCCCCCCCCcH
Confidence 5789999999999999999999999999999999999999999999999999999999999999999 999999998866
Q ss_pred -HHHHHHhhhccccCC
Q 008620 545 -LKDFIVSLLINPVPI 559 (559)
Q Consensus 545 -~k~~i~~ll~~pi~~ 559 (559)
+|++|++||++|||+
T Consensus 81 ~~K~~I~sLlv~pi~i 96 (96)
T PLN02150 81 KLKDLITSLFFHPLPL 96 (96)
T ss_pred HHHHHHHHHhccCCCC
Confidence 999999999999986
No 9
>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=99.84 E-value=7.2e-21 Score=185.42 Aligned_cols=229 Identities=28% Similarity=0.327 Sum_probs=183.2
Q ss_pred hhhccccCCCcchhHHHHHHHHHHhhhhhccccccCCHHHHHHHHHHHhhhchhhhccCChhHHHHHHHHHHHHHHHHHH
Q 008620 285 WAVGVHFEPQYSFARKLFTKVIYMTSIIDDIYDVYGKIEELDLFTSAIERWDINAIDQLPEYMKLCYRALINVYSEVEKD 364 (559)
Q Consensus 285 ~~~~~~feP~~s~~Rl~~aK~~~l~~iiDD~yD~~gt~eEl~~ft~ai~rWd~~~~~~lpeymk~~~~al~~~~~ei~~~ 364 (559)
+.++.++.|+++..|..++++.+|++++||++|..++..+.......+ .....|..+...+..+.+.+.++...
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~DDi~D~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (243)
T cd00385 2 RPLAVLLEPEASRLRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAV------AIDGLPEAILAGDLLLADAFEELARE 75 (243)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCchhhhhhH------HhcCchHHHHHHHHHHHHHHHHHHhC
Confidence 456667889888999999999999999999999887665554443322 12345667777788888888877643
Q ss_pred HHhhcccchHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHHHhcCCCCChhHHhhhcCchH
Q 008620 365 LASQAKLYRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISFVGMGDIVTKESFEWLFSNPR 444 (559)
Q Consensus 365 ~~~~~~~~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~ 444 (559)
. .+....++.+.|.+++.++..|+.|+.. +.||++||+.++..++ +.++......+++...++ ..+.+...+
T Consensus 76 ~----~~~~~~~~~~~~~~~~~g~~~d~~~~~~-~~~t~~ey~~~~~~~t-~~~~~~~~~~~~~~~~~~--~~~~~~~~~ 147 (243)
T cd00385 76 G----SPEALEILAEALLDLLEGQLLDLKWRRE-YVPTLEEYLEYCRYKT-AGLVGALCLLGAGLSGGE--AELLEALRK 147 (243)
T ss_pred C----CHHHHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHHhH-HHHHHHHHHHHHHHhCCC--HHHHHHHHH
Confidence 1 1356789999999999999999999877 8899999999999998 455556666666666665 333366788
Q ss_pred HHHHHhHHhHhccCccchhhhhccC-CCcchhHHHHhhcCC------------CHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 008620 445 SIRASCAVGRLMNDMASHKFEQSRG-HVASSVECYINQYGA------------TEEEAYSEFRKQVSNAWKDINEECLRP 511 (559)
Q Consensus 445 l~~~~~~i~RL~NDI~S~~kE~~~G-~~~n~V~cyM~e~g~------------S~eeA~~~i~~~i~~~wk~ln~e~l~~ 511 (559)
+....+.+.+|.||+.|+.+|.+.| +..|++.++|+++|+ +.++|.+++.++++++|+++++.....
T Consensus 148 ~~~~~g~~~ql~nDl~~~~~e~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ 227 (243)
T cd00385 148 LGRALGLAFQLTNDLLDYEGDAERGEGKCTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKLAEEALKELNELILSL 227 (243)
T ss_pred HHHHHHHHHHHHHHHHhccCCHHHhCCchHHHHHHHHHhCChhhHHHHHHHCChHHHHHHHHHHHHHHHHHHHhcCCCCc
Confidence 8999999999999999999999986 678999999999998 889999999999999999999876542
Q ss_pred CCCCHHHHHHHHHHhh
Q 008620 512 TVVPVPLLIRILNLTR 527 (559)
Q Consensus 512 ~~~p~~~~~~~ln~aR 527 (559)
+..+..+++.++++.|
T Consensus 228 ~~~~~~~~~~~~~~~~ 243 (243)
T cd00385 228 PDVPRALLALALNLYR 243 (243)
T ss_pred HHHHHHHHHHHHHHhC
Confidence 2356677777777653
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=97.80 E-value=0.00016 Score=76.08 Aligned_cols=194 Identities=14% Similarity=0.097 Sum_probs=113.1
Q ss_pred CCCcch-hHHHHHHHHHHhhhhhccccccCCHHHHHHHHHHHhhhchhhhccCChhHHHHHHHHHHHHHHHHHHHHhhcc
Q 008620 292 EPQYSF-ARKLFTKVIYMTSIIDDIYDVYGKIEELDLFTSAIERWDINAIDQLPEYMKLCYRALINVYSEVEKDLASQAK 370 (559)
Q Consensus 292 eP~~s~-~Rl~~aK~~~l~~iiDD~yD~~gt~eEl~~ft~ai~rWd~~~~~~lpeymk~~~~al~~~~~ei~~~~~~~~~ 370 (559)
.|..+. .++.++-+.++++++||.++.. .+++..|-+-+-. ... + |. ++...+.+.+.++. +.=+
T Consensus 78 y~~~~~evqv~IaiyT~yvi~iDD~~~~~--~~~l~~F~~~l~~--Gq~--Q-~~---p~L~~~~~~L~~~~----~~fg 143 (376)
T PF06330_consen 78 YPHLPKEVQVAIAIYTTYVIIIDDSSQEP--SDDLRTFHQRLIL--GQP--Q-KH---PLLDGFASLLREMW----RHFG 143 (376)
T ss_dssp STTS-HHHHHHHHHHHHHHHHHTT--S-S--HHHHTTHHHHHHH--T------SS---HHHHHHHHHHHHHH----TTS-
T ss_pred cCCCCHHHHHHHHHHHHHHHhcccccccc--cHHHHHHHHHHhc--CCC--C-CC---HHHHHHHHHHHHHH----HHcc
Confidence 365554 4558888999999999998765 4666666544432 111 1 11 33344444444332 2223
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHHHhcCCCCChhHHhhhcCchH---HHH
Q 008620 371 LYRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISFVGMGDIVTKESFEWLFSNPR---SIR 447 (559)
Q Consensus 371 ~~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~---l~~ 447 (559)
+.+-.-+.++--+++.+...|++.. +-.|.-..|-..-|.=+|+..+.+...+ |++.+.-...+.. .+-
T Consensus 144 pf~anmI~~STLdFi~g~~LE~~~f--~~~p~A~~FP~fLR~ktGlsEaYA~FiF------Pk~~fpe~~~~~~y~~AIp 215 (376)
T PF06330_consen 144 PFCANMIVKSTLDFINGCWLEQKNF--HGSPGAPDFPDFLRRKTGLSEAYAFFIF------PKALFPEVEYFIQYTPAIP 215 (376)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTTT------TT-TTHHHHHHHHHH-HHHHHHHT--------TTTS-TTTTHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHhhcccC--CCCCCCccccHHHHhccCcchhheeeec------ccccCChHHHHHHHHHHHH
Confidence 3566677888899999999998642 3346555566666666677766654333 2222211122233 333
Q ss_pred HHhHHhHhccCccchhhhhc-cCCCcchhHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHh
Q 008620 448 ASCAVGRLMNDMASHKFEQS-RGHVASSVECYINQYGATEEEAYSEFRKQVSNAWKDINEE 507 (559)
Q Consensus 448 ~~~~i~RL~NDI~S~~kE~~-~G~~~n~V~cyM~e~g~S~eeA~~~i~~~i~~~wk~ln~e 507 (559)
-....+-++|||.||=||.- .|+..|.|.-+..-+|+|.-+|.+.+.+-.-.+-+++.+.
T Consensus 216 dl~~fi~~~NDILSFYKE~l~a~E~~NyI~n~A~~~g~S~~eaL~~l~~eti~a~~rv~~v 276 (376)
T PF06330_consen 216 DLMRFINYVNDILSFYKEELVAGETGNYIHNRARVHGVSILEALRELTDETIEAVERVRRV 276 (376)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTSSSSSSHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhhhhHHHHHHhhcccccccchhhhhhhccCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 44445669999999999977 7888999988887789999999998866665565555443
No 11
>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=97.73 E-value=0.00068 Score=70.48 Aligned_cols=195 Identities=13% Similarity=0.043 Sum_probs=119.1
Q ss_pred CCcchhHH-HHHHHHHHhhhhhccccccCCHHHHHHHHHHHhhhchhhhccCChhHHHHHHHHHHHHHHHHHHHHhhccc
Q 008620 293 PQYSFARK-LFTKVIYMTSIIDDIYDVYGKIEELDLFTSAIERWDINAIDQLPEYMKLCYRALINVYSEVEKDLASQAKL 371 (559)
Q Consensus 293 P~~s~~Rl-~~aK~~~l~~iiDD~yD~~gt~eEl~~ft~ai~rWd~~~~~~lpeymk~~~~al~~~~~ei~~~~~~~~~~ 371 (559)
+..|..=+ .++-..+.++++||.-|.. .+.++.|.+-+.. ..+ ..-| +...+.+.+..+... =|+
T Consensus 79 ~~~skev~~~isi~~tY~~~lDD~~~e~--~~~m~~f~~dL~~--G~~-qkhP-----~l~~v~~~l~~~lr~----fGp 144 (357)
T cd00686 79 AKVSKECMADLSIHYTYTLVLDDSKDDP--YPTMVNYFDDLQA--GRE-QAHP-----WWALVNEHFPNVLRH----FGP 144 (357)
T ss_pred cCCCHHHHHHHHHHHheeeEeccccccc--chHHHHHHHHHhc--CCC-CCCc-----HHHHHHHHHHHHHHH----hhh
Confidence 33565544 6677778899999997654 3345556554432 111 1112 222222222222211 123
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHHHhcCCCCChhHHhhhcCchHHHHHHh-
Q 008620 372 YRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISFVGMGDIVTKESFEWLFSNPRSIRASC- 450 (559)
Q Consensus 372 ~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~l~~~~~- 450 (559)
++-.-+.++--+++.+.+.|... -+.-|.-.+|-...|.=+|.+-+.+...+ |++.|.-..-+..+.-+..
T Consensus 145 F~s~~IikSTLdFv~g~~iEq~n--f~~~p~A~~fP~ylR~ksGl~E~yA~FiF------Pk~~FpE~~~~~qi~~AIp~ 216 (357)
T cd00686 145 FCSLNLIRSTLDFFEGCWIEQYN--FGGFPGSHDYPQFLRRMNGLGHCVGASLW------PKEQFNERSLFLEITSAIAQ 216 (357)
T ss_pred hhHHHHHHHHHHHHHHHHHhhhc--cCCCCCCcccchHHHhccCCcceeEEEec------chhhCchHhhHHHhhHHHHH
Confidence 55556778888999999999763 34467777787777777777766553332 4444322122233333333
Q ss_pred --HHhHhccCccchhhhhcc-CCCcchhHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHhhcC
Q 008620 451 --AVGRLMNDMASHKFEQSR-GHVASSVECYINQYGATEEEAYSEFRKQVSNAWKDINEECLR 510 (559)
Q Consensus 451 --~i~RL~NDI~S~~kE~~~-G~~~n~V~cyM~e~g~S~eeA~~~i~~~i~~~wk~ln~e~l~ 510 (559)
..+-++|||.||=||.-. ++-.|.|.-|.+.+|+|..+|.+.+.+-.-.+-+++.+ .|.
T Consensus 217 ~~~~i~~~NDILSFYKEe~~~~E~~n~V~Nya~~~GiS~~eAL~~lt~dTv~~s~rv~~-VLs 278 (357)
T cd00686 217 MENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVA-VFS 278 (357)
T ss_pred HHHHHHhhhhhhheehhhcccccccchHHHhhhhcCCCHHHHHHHHHHHHHHHHHHHHH-Hhc
Confidence 345589999999999854 45678888888889999999999886666666666544 344
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=90.97 E-value=7.3 Score=39.36 Aligned_cols=164 Identities=18% Similarity=0.219 Sum_probs=88.2
Q ss_pred chhHHHHHHHHHHhhhhhccccccCCHHH----HHHHHHHHhhhchhhhccCChhHHHHHHHHHHHHHHHHHHHHhhccc
Q 008620 296 SFARKLFTKVIYMTSIIDDIYDVYGKIEE----LDLFTSAIERWDINAIDQLPEYMKLCYRALINVYSEVEKDLASQAKL 371 (559)
Q Consensus 296 s~~Rl~~aK~~~l~~iiDD~yD~~gt~eE----l~~ft~ai~rWd~~~~~~lpeymk~~~~al~~~~~ei~~~~~~~~~~ 371 (559)
...|-.+.-+-.+.-.+||+-|......+ ++-+-+++...-....+..+....++..++..+.....
T Consensus 17 ~~~R~~~~alyaf~r~~d~i~D~~~~~~~~~~~L~~w~~~l~~~~~~~~~~~~~~~~pv~~~l~~~~~~~~--------- 87 (267)
T PF00494_consen 17 KEKRPAVFALYAFCRELDDIVDEPSDPEEARARLQWWRDALNSIFASYEDSLPEPSHPVARALADLVRRYG--------- 87 (267)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCTSS-HSCHHHHHHHHHHHHHHHH-TSTHHHSSHHHHHHHHHHHHCCSH---------
T ss_pred HHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHHHHHHHhhhhhhccCCCcCHHHHHHHHHHHHHh---------
Confidence 45566556677888899999997664332 33344444432111111223344566666665533211
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHHHhcCCCCCh-hHHhhhcCchHHHHHHh
Q 008620 372 YRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISFVGMGDIVTK-ESFEWLFSNPRSIRASC 450 (559)
Q Consensus 372 ~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~-ev~e~~~~~~~l~~~~~ 450 (559)
--.+.+.+++.++.+. .....++|++|+......+.|....+++..++... ++ ++.+. ....+
T Consensus 88 ----l~~~~l~~li~~~~~d---l~~~~~~t~~~L~~Y~~~vag~vg~l~~~~~~~~~--~~~~~~~~-------a~~lG 151 (267)
T PF00494_consen 88 ----LPREPLLELIDGMEMD---LEFTPYETFADLERYCYYVAGSVGLLLLQLLGAHD--PDEAARDA-------ARALG 151 (267)
T ss_dssp ----HHHHHHHHHHHHHHHC---TT-S--SSHHHHHHHHHHHTHHHHHHHHHHHHSST--SHHHHHHH-------HHHHH
T ss_pred ----hhHHHHHHHHHHhccc---ccCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcccc--chhhHHHH-------HHHHH
Confidence 2345567777777633 33355789999999999998887777666665431 22 33333 22223
Q ss_pred H---HhHhccCccchhhh-hccCCC--cchhHHHHhhcCCCHHHHH
Q 008620 451 A---VGRLMNDMASHKFE-QSRGHV--ASSVECYINQYGATEEEAY 490 (559)
Q Consensus 451 ~---i~RL~NDI~S~~kE-~~~G~~--~n~V~cyM~e~g~S~eeA~ 490 (559)
. ++.++-|+ ... ..+|.+ +. =.|.++|+|.++-.
T Consensus 152 ~alql~nilRd~---~~D~~~~gR~ylP~---d~l~~~gv~~~dl~ 191 (267)
T PF00494_consen 152 RALQLTNILRDI---PEDALRRGRIYLPL---DDLRRFGVTPEDLL 191 (267)
T ss_dssp HHHHHHHHHHTH---HHH-HHTT---S-H---HHHHHTTSSHHHHH
T ss_pred HHHHHHHHHHHh---HHHHHhcccccCCc---hhHHHcCCCHHHHH
Confidence 3 33333454 344 345543 32 25678899887654
No 13
>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates
Probab=89.46 E-value=6.3 Score=38.86 Aligned_cols=118 Identities=15% Similarity=0.148 Sum_probs=76.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhh-hcchhhHHHHHHHhcCCCCChhHHhhhcCchHHHHHHhH
Q 008620 373 RLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALI-SSGHPNLSAISFVGMGDIVTKESFEWLFSNPRSIRASCA 451 (559)
Q Consensus 373 ~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~-S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~l~~~~~~ 451 (559)
....+.+....++.+...+..|... ..||.++|++.... |+++....+......+. -+++..+. ..++-+..+.
T Consensus 86 ~~~~~~~~~~~~~~Gq~~Dl~~~~~-~~~t~~~y~~~~~~Kta~l~~~~~~~~~~~~~-~~~~~~~~---~~~~~~~lG~ 160 (236)
T cd00867 86 ALELFAEALRELLEGQALDLEFERD-TYETLDEYLEYCRYKTAGLVGLLCLLGAGLSG-ADDEQAEA---LKDYGRALGL 160 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHhccHHHHHHHHHHHHHHcC-cCHHHHHH---HHHHHHHHHH
Confidence 4556778889999999999988654 57899999999998 66654443332222222 23333332 3566778888
Q ss_pred HhHhccCccchhhhh----------ccCCCcchhHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHH
Q 008620 452 VGRLMNDMASHKFEQ----------SRGHVASSVECYINQYGATEEEAYSEFRKQVSNAWKDINE 506 (559)
Q Consensus 452 i~RL~NDI~S~~kE~----------~~G~~~n~V~cyM~e~g~S~eeA~~~i~~~i~~~wk~ln~ 506 (559)
..-+.||+..+.... ++|.. +...+++ .+.+.+.++++++.+..
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 888999998876544 44544 4444444 55566666666665544
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=88.06 E-value=33 Score=34.89 Aligned_cols=205 Identities=14% Similarity=0.142 Sum_probs=100.1
Q ss_pred HHHhhhccccCCCcchhHHHHHHHHHHhhhhhccccccCCHHHHHHHHHHHhhhchh---hhccCChhHHHHHHHHHHHH
Q 008620 282 VYFWAVGVHFEPQYSFARKLFTKVIYMTSIIDDIYDVYGKIEELDLFTSAIERWDIN---AIDQLPEYMKLCYRALINVY 358 (559)
Q Consensus 282 ~yf~~~~~~feP~~s~~Rl~~aK~~~l~~iiDD~yD~~gt~eEl~~ft~ai~rWd~~---~~~~lpeymk~~~~al~~~~ 358 (559)
+|+++.-..+ ...|-.+.-+-.+.-.+||+-|..++.++-+.- ++.|... ....-|. .++..++..++
T Consensus 7 sF~~a~~~lp----~~~R~~~~alYaf~r~~d~i~D~~~~~~~~~~~---L~~w~~~l~~~~~g~~~--~pv~~al~~~~ 77 (266)
T TIGR03465 7 SFYYGMRLLP----PERRRAMTALYAFCREVDDIVDEDSDPEVAQAK---LAWWRAEIDRLYAGAPS--HPVARALADPA 77 (266)
T ss_pred cHHHHHHHCC----HHHHHHHHHHHHHHHHHHhhhcCCCCchHHHHH---HHHHHHHHHHHhCCCCC--ChHHHHHHHHH
Confidence 3444444333 344555555677777899999975544332221 3333221 1111121 24555555543
Q ss_pred HHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHHHhcCCCCChhHHhh
Q 008620 359 SEVEKDLASQAKLYRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISFVGMGDIVTKESFEW 438 (559)
Q Consensus 359 ~ei~~~~~~~~~~~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~ 438 (559)
... +. -++.+.+++.++.+.. ....++|++|+......+.|.-..+++-.+ |.. ++.....
T Consensus 78 ~~~--------~l-----~~~~~~~li~g~~~Dl---~~~~~~t~~dL~~Y~~~vAg~vg~l~~~ll--g~~-~~~~~~~ 138 (266)
T TIGR03465 78 RRF--------DL-----PQEDFLEVIDGMEMDL---EQTRYPDFAELDLYCDRVAGAVGRLSARIF--GAT-DARTLEY 138 (266)
T ss_pred HHc--------CC-----CHHHHHHHHHHHHHHc---CCCCCCCHHHHHHHHHHhHHHHHHHHHHHh--CCC-ChhHHHH
Confidence 321 10 1344667777766433 334578999988888877776666555444 321 2222222
Q ss_pred hcCchHHHHHHhHHhHhccCccchhhhhccCCCcchhHHHHhhcCCCHH---------HHHHHHHHHHHHHHHHHHHhhc
Q 008620 439 LFSNPRSIRASCAVGRLMNDMASHKFEQSRGHVASSVECYINQYGATEE---------EAYSEFRKQVSNAWKDINEECL 509 (559)
Q Consensus 439 ~~~~~~l~~~~~~i~RL~NDI~S~~kE~~~G~~~n~V~cyM~e~g~S~e---------eA~~~i~~~i~~~wk~ln~e~l 509 (559)
... + -.+.-++.++-|+. ....+|.+- +=.=.|.++|+|.+ ...+-+..+++.+..-+.+..-
T Consensus 139 a~~---l-G~AlqltnilRdv~---eD~~~gR~y-lP~~~l~~~gv~~~~l~~~~~~~~~~~~~~~l~~~A~~~l~~a~~ 210 (266)
T TIGR03465 139 AHH---L-GRALQLTNILRDVG---EDARRGRIY-LPAEELQRFGVPAADILEGRYSPALAALCRFQAERARAHYAEADA 210 (266)
T ss_pred HHH---H-HHHHHHHHHHHHhH---HHHhCCCee-cCHHHHHHcCCCHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 111 1 11222344445553 334466531 00123577888866 3344556666666655444321
Q ss_pred CCCCCCHHHHHHH
Q 008620 510 RPTVVPVPLLIRI 522 (559)
Q Consensus 510 ~~~~~p~~~~~~~ 522 (559)
-...+|......+
T Consensus 211 ~~~~~p~~~~~~~ 223 (266)
T TIGR03465 211 LLPACDRRAQRAA 223 (266)
T ss_pred hhhhCCHhhhHHH
Confidence 1245775444333
No 15
>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=85.86 E-value=31 Score=34.93 Aligned_cols=198 Identities=15% Similarity=0.208 Sum_probs=97.3
Q ss_pred hhHHHHHHHHHHhhhhhccccccCCH-H----HHHHHHHHHhhhchhhhccCChhHHHHHHHHHHHHHHHHHHHHhhccc
Q 008620 297 FARKLFTKVIYMTSIIDDIYDVYGKI-E----ELDLFTSAIERWDINAIDQLPEYMKLCYRALINVYSEVEKDLASQAKL 371 (559)
Q Consensus 297 ~~Rl~~aK~~~l~~iiDD~yD~~gt~-e----El~~ft~ai~rWd~~~~~~lpeymk~~~~al~~~~~ei~~~~~~~~~~ 371 (559)
..|..+.-+-.+.-.+||+-|..... . .|+-+-+++..-.. ...|. .++..++..+..+. +
T Consensus 24 ~~R~~~~alYaf~r~~Ddi~D~~~~~~~~~~~~L~~w~~~l~~~~~---~~~~~--~pv~~al~~~~~~~--------~- 89 (265)
T cd00683 24 ELRRAVCALYAFCRAADDIVDDPAAPPDEKLALLDAFRAELDAAYW---GGAPT--HPVLRALADLARRY--------G- 89 (265)
T ss_pred HHHHHHHHHHHHHHHHHhhhhCCCCCchhHHHHHHHHHHHHHHHHc---CCCCC--ChHHHHHHHHHHHc--------C-
Confidence 44554455667777899999975532 2 23333333322100 01121 25566666654311 1
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHHHhcCCCCChhHHhhhcCchHHHHHHhH
Q 008620 372 YRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISFVGMGDIVTKESFEWLFSNPRSIRASCA 451 (559)
Q Consensus 372 ~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~l~~~~~~ 451 (559)
--++.+.+++.++..... ....||++|.......+.|+-..+++-.++.+ -+++........-.-++
T Consensus 90 ----l~~~~~~~li~g~~~Dl~---~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~~~~--~~~~~~~~A~~lG~Alq---- 156 (265)
T cd00683 90 ----IPREPFRDLLAGMAMDLD---KRRYETLDELDEYCYYVAGVVGLMLLRVFGAS--SDEAALERARALGLALQ---- 156 (265)
T ss_pred ----CCHHHHHHHHHHHHHhCC---CCCCCCHHHHHHHHHHhHHHHHHHHHHHhCCC--CChHHHHHHHHHHHHHH----
Confidence 113556777777774444 45678998888888877776655554444321 12222222111111222
Q ss_pred HhHhccCccchhhhhccCCC--cchhHHHHhhcCCCHHHH---------HHHHHHHHHHHHHHHHHhhcCCCCCCHHHHH
Q 008620 452 VGRLMNDMASHKFEQSRGHV--ASSVECYINQYGATEEEA---------YSEFRKQVSNAWKDINEECLRPTVVPVPLLI 520 (559)
Q Consensus 452 i~RL~NDI~S~~kE~~~G~~--~n~V~cyM~e~g~S~eeA---------~~~i~~~i~~~wk~ln~e~l~~~~~p~~~~~ 520 (559)
++.++-|+.- ..++|-+ +.- .|.++|+|.++- ..-+..+++.+.+-+....-....+|....-
T Consensus 157 ltnilRdv~e---D~~~gR~YlP~d---~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~~~~ 230 (265)
T cd00683 157 LTNILRDVGE---DARRGRIYLPRE---ELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAALPRRSRF 230 (265)
T ss_pred HHHHHHHHHH---HHccCCCcCCHH---HHHHcCCCHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCCHhhHH
Confidence 3344445542 2345542 322 367788877552 2344555555555444332222447755444
Q ss_pred HHHHHhh
Q 008620 521 RILNLTR 527 (559)
Q Consensus 521 ~~ln~aR 527 (559)
.++-++.
T Consensus 231 ~~~~~~~ 237 (265)
T cd00683 231 CVRAAAM 237 (265)
T ss_pred HHHHHHH
Confidence 4444433
No 16
>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=84.70 E-value=49 Score=33.66 Aligned_cols=120 Identities=16% Similarity=0.088 Sum_probs=64.0
Q ss_pred HHHhhhccccCCCcchhHHHHHHHHHHhhhhhcccccc-CCHHHHHHHHHHHhhhchh---hhccCChhHHHHHHHHHHH
Q 008620 282 VYFWAVGVHFEPQYSFARKLFTKVIYMTSIIDDIYDVY-GKIEELDLFTSAIERWDIN---AIDQLPEYMKLCYRALINV 357 (559)
Q Consensus 282 ~yf~~~~~~feP~~s~~Rl~~aK~~~l~~iiDD~yD~~-gt~eEl~~ft~ai~rWd~~---~~~~lpeymk~~~~al~~~ 357 (559)
+|+|+.-..+ ...|..+.-+-.|.=.+||+-|.. ++.++-.. .++.|... ....-|. .++..++..+
T Consensus 7 sf~~a~~~lp----~~~R~~~~alYAf~R~~Ddi~D~~~~~~~~~~~---~L~~wr~~l~~~~~g~~~--~pv~~aL~~~ 77 (266)
T TIGR03464 7 NFPVASLLLP----ARLRAPIHAVYAFARTADDIADEGDGSAEERLA---LLDDFRAELDAIYSGEPA--APVFVALART 77 (266)
T ss_pred cHHHHHHhCC----HHHHHHHHHHHHHHHHHHHhccCCCCChHHHHH---HHHHHHHHHHHHhCCCCC--ChHHHHHHHH
Confidence 4555554443 234554445666778899999975 45443211 12233221 1111121 2456666665
Q ss_pred HHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHHHh
Q 008620 358 YSEVEKDLASQAKLYRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISFVG 426 (559)
Q Consensus 358 ~~ei~~~~~~~~~~~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~ 426 (559)
+.+. +. . ++.+.+++.++... ......+|++|.......+.|+-..+++..++
T Consensus 78 ~~~~--------~l-~----~~~~~~li~~~~~D---l~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~g 130 (266)
T TIGR03464 78 VQRH--------GL-P----IEPFLDLLDAFRQD---VVVTRYATWAELLDYCRYSANPVGRLVLDLYG 130 (266)
T ss_pred HHHc--------CC-C----hHHHHHHHHHHHHh---ccCCCCCCHHHHHHHHHHhHHHHHHHHHHHcC
Confidence 5432 11 1 23445566665422 23445679999998888888877666655554
No 17
>PLN02890 geranyl diphosphate synthase
Probab=80.13 E-value=55 Score=35.96 Aligned_cols=91 Identities=12% Similarity=-0.043 Sum_probs=61.3
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHHHhcCCCCChhHHhhhcCchHHHHHHh
Q 008620 371 LYRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISFVGMGDIVTKESFEWLFSNPRSIRASC 450 (559)
Q Consensus 371 ~~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~l~~~~~ 450 (559)
..++..+.++...++.+-+.+..|.. ...+|+++|+.....-+|..+..++..-++--..+++..+.+ ..+-+..+
T Consensus 226 ~~~~~~~s~a~~~l~~Gq~ld~~~~~-~~~~s~~~Yl~~i~~KTa~Lf~~s~~~gAilaga~~~~~~~l---~~fG~~lG 301 (422)
T PLN02890 226 TEVVSLLATAVEHLVTGETMQITSSR-EQRRSMDYYMQKTYYKTASLISNSCKAVAILAGQTAEVAVLA---FEYGRNLG 301 (422)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCcCHHHHHHH---HHHHHHHH
Confidence 35677888899999999999998864 346899999987666555554333222111112456665543 46667778
Q ss_pred HHhHhccCccchhhh
Q 008620 451 AVGRLMNDMASHKFE 465 (559)
Q Consensus 451 ~i~RL~NDI~S~~kE 465 (559)
+..-+.||+..|.-.
T Consensus 302 lAFQI~DDiLD~~g~ 316 (422)
T PLN02890 302 LAFQLIDDVLDFTGT 316 (422)
T ss_pred HHHHHHHHHHhhcCC
Confidence 888889999877543
No 18
>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=79.88 E-value=80 Score=33.23 Aligned_cols=88 Identities=3% Similarity=-0.064 Sum_probs=57.3
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHHHhcCCCCChhHHhhhcCchHHHHHHhH
Q 008620 372 YRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISFVGMGDIVTKESFEWLFSNPRSIRASCA 451 (559)
Q Consensus 372 ~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~l~~~~~~ 451 (559)
.....+.+....++.+-+.+..|... ..+|.++|++.-..=+|..+..++..-++--..+++..+. ..++-+..+.
T Consensus 133 ~~~~~~~~~~~~~~~Gq~~~~~~~~~-~~~~~~~y~~~~~~KTa~L~~~~~~~ga~~ag~~~~~~~~---l~~~G~~lG~ 208 (322)
T TIGR02749 133 EVVKLISKVITDFAEGEIKQGLNQFD-SDLSLEDYLEKSFYKTASLVAASSKAAAVLSDVPSQVAND---LYEYGKHLGL 208 (322)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcccC-CCCCHHHHHHHHHccHHHHHHHHHHHHHHHcCcCHHHHHH---HHHHHHHHHH
Confidence 45667778888889888888776533 3479999999766655555433221111111345555544 3566778888
Q ss_pred HhHhccCccchh
Q 008620 452 VGRLMNDMASHK 463 (559)
Q Consensus 452 i~RL~NDI~S~~ 463 (559)
..-+.||+..+.
T Consensus 209 aFQi~DDild~~ 220 (322)
T TIGR02749 209 AFQVVDDILDFT 220 (322)
T ss_pred HHHHHHHhccCC
Confidence 889999998765
No 19
>PLN02857 octaprenyl-diphosphate synthase
Probab=78.11 E-value=70 Score=35.09 Aligned_cols=89 Identities=10% Similarity=-0.009 Sum_probs=57.8
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHHHhcCCCCChhHHhhhcCchHHHHHHhH
Q 008620 372 YRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISFVGMGDIVTKESFEWLFSNPRSIRASCA 451 (559)
Q Consensus 372 ~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~l~~~~~~ 451 (559)
.....+.+...+++.+-+.+..+.. +.-+|.++|++....=+|..+..++..-++=-..+++..+. ..++-+..++
T Consensus 227 ~~~~~~s~~~~~l~~Gei~q~~~~~-~~~~s~~~Yl~~i~~KTa~L~~~a~~~gallaga~~~~~~~---l~~fG~~LGi 302 (416)
T PLN02857 227 EVIKLISQVIKDFASGEIKQASSLF-DCDVTLDEYLLKSYYKTASLIAASTKSAAIFSGVDSSVKEQ---MYEYGKNLGL 302 (416)
T ss_pred HHHHHHHHHHHHHHhhHHHHHhccc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHH---HHHHHHHHHH
Confidence 4566777788888888877877764 44579999999877666555433321111111345555544 3566677788
Q ss_pred HhHhccCccchhh
Q 008620 452 VGRLMNDMASHKF 464 (559)
Q Consensus 452 i~RL~NDI~S~~k 464 (559)
..-+.||+..+..
T Consensus 303 AFQI~DDiLD~~~ 315 (416)
T PLN02857 303 AFQVVDDILDFTQ 315 (416)
T ss_pred HHHHHHHHHhhcC
Confidence 8888899988753
No 20
>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=73.54 E-value=42 Score=33.90 Aligned_cols=121 Identities=13% Similarity=-0.005 Sum_probs=76.0
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHHHhcCCCCChhHHhhhcCchHHHHHHhH
Q 008620 372 YRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISFVGMGDIVTKESFEWLFSNPRSIRASCA 451 (559)
Q Consensus 372 ~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~l~~~~~~ 451 (559)
.....+.+.....+.+-..+..|... ..||.++|++....-+|.....+....++--..+++..+. ..++-+..+.
T Consensus 108 ~~~~~~~~~~~~~~~GQ~~d~~~~~~-~~~~~~~y~~~~~~KT~~l~~~~~~~~a~l~~~~~~~~~~---l~~~g~~lG~ 183 (259)
T cd00685 108 RALELFSEAILELVEGQLLDLLSEYD-TDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEA---LKRFGRNLGL 183 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCC-CCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHH---HHHHHHHHHH
Confidence 45667778888889998889888654 5799999999988777766544332222111123444332 3567777888
Q ss_pred HhHhccCccchhhhh-----------ccCCCcchhHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHH
Q 008620 452 VGRLMNDMASHKFEQ-----------SRGHVASSVECYINQYGATEEEAYSEFRKQVSNAWKDINE 506 (559)
Q Consensus 452 i~RL~NDI~S~~kE~-----------~~G~~~n~V~cyM~e~g~S~eeA~~~i~~~i~~~wk~ln~ 506 (559)
..-+.||+..+.... ..|.. |...+|.. .+.+...++++++.+..
T Consensus 184 afQi~DD~ld~~~~~~~~gK~~~~Di~~gk~-T~~~~~~l---------~~~~~~~~~~a~~~l~~ 239 (259)
T cd00685 184 AFQIQDDILDLFGDPETLGKPVGSDLREGKC-TLPVLLAL---------RELAREYEEKALEALKA 239 (259)
T ss_pred HHHHHHHhhcccCChHHHCCCcchHHHcCCc-hHHHHHHH---------HHHHHHHHHHHHHHHHc
Confidence 888899987664432 12332 44444443 45566667777766544
No 21
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=68.30 E-value=1.2e+02 Score=31.96 Aligned_cols=107 Identities=12% Similarity=0.044 Sum_probs=71.8
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHHHhcCCCCChhHHhhhcCchHHHHHHhH
Q 008620 372 YRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISFVGMGDIVTKESFEWLFSNPRSIRASCA 451 (559)
Q Consensus 372 ~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~l~~~~~~ 451 (559)
.....+.+....++.+-..+-.+.... +|.|+|+.+-..=+|.....+...-++--..+++..+.+ ...-+..++
T Consensus 134 ~~~~~~~~~~~~~~~GQ~lDl~~~~~~--~t~e~y~~~i~~KTa~L~~~a~~~ga~la~~~~~~~~~l---~~~g~~lGl 208 (322)
T COG0142 134 EAIKALAEAINGLCGGQALDLAFENKP--VTLEEYLRVIELKTAALFAAAAVLGAILAGADEELLEAL---EDYGRNLGL 208 (322)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHccCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHH---HHHHHHhhH
Confidence 456678888999999999888886655 999999999877666665443322221112235665554 566778888
Q ss_pred HhHhccCccchhhhh-ccCCC---------cchhHHHHhhcC
Q 008620 452 VGRLMNDMASHKFEQ-SRGHV---------ASSVECYINQYG 483 (559)
Q Consensus 452 i~RL~NDI~S~~kE~-~~G~~---------~n~V~cyM~e~g 483 (559)
..-+.||+..+.-+. .-|+. .++..++.-+.+
T Consensus 209 aFQi~DDiLD~~~d~~~lGK~~g~Dl~~gK~T~p~l~~l~~~ 250 (322)
T COG0142 209 AFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEKA 250 (322)
T ss_pred HHHHHHHhhcCCCChHHhCCCcchHHHcCCchHHHHHHHHcC
Confidence 899999998877642 23332 366666666554
No 22
>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=64.42 E-value=1.8e+02 Score=30.83 Aligned_cols=103 Identities=17% Similarity=0.188 Sum_probs=62.2
Q ss_pred HHHHHHHhcCCCCChhHHhhhcCchHHHHHHhHHhHhccCccchhhhhccCCCcchhHHHHhhcCCCHHHHHHHHHHHHH
Q 008620 419 LSAISFVGMGDIVTKESFEWLFSNPRSIRASCAVGRLMNDMASHKFEQSRGHVASSVECYINQYGATEEEAYSEFRKQVS 498 (559)
Q Consensus 419 ~~~~~~~~~g~~l~~ev~e~~~~~~~l~~~~~~i~RL~NDI~S~~kE~~~G~~~n~V~cyM~e~g~S~eeA~~~i~~~i~ 498 (559)
++++.-++..+.++++..+.+.. .-.=..+-+-.|++=....+.....|+. |.|..|- +.+++.+.+.-.++
T Consensus 194 IF~L~a~A~~p~~t~~~a~~i~~--aYFPwI~gLHILLDy~IDq~EDr~~GdL-NFv~YY~-----~~~~~~~Rl~~f~~ 265 (330)
T PF10776_consen 194 IFALFAYAADPDLTPEDAEKIKD--AYFPWICGLHILLDYFIDQEEDREGGDL-NFVFYYP-----DEEEMEERLKYFVE 265 (330)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHH--cccHHHHHHHHHHHHHhhhHhHhcCCCc-eeeeeCC-----CHHHHHHHHHHHHH
Confidence 33444455677788887776422 1122334455566656665656666665 9997543 78999999999999
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHHHHhhhhccccccCCC
Q 008620 499 NAWKDINEECLRPTVVPVPLLIRILNLTRAADVIYKYKDG 538 (559)
Q Consensus 499 ~~wk~ln~e~l~~~~~p~~~~~~~ln~aR~~~~~Y~~~Dg 538 (559)
++-+...+ +|.+--.+.++=+ +--||-.++.
T Consensus 266 ~A~~~~~~-------Lp~~~fHr~iv~G--Lla~YLSD~K 296 (330)
T PF10776_consen 266 KALEQASR-------LPYPKFHRMIVRG--LLAMYLSDPK 296 (330)
T ss_pred HHHHHHHh-------CCCchHHHHHHHH--HHHHHhCCHh
Confidence 88876554 5554444433333 3345754443
No 23
>CHL00151 preA prenyl transferase; Reviewed
Probab=64.07 E-value=1.7e+02 Score=30.69 Aligned_cols=87 Identities=2% Similarity=-0.087 Sum_probs=55.1
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHH--HhcCCCCChhHHhhhcCchHHHHHH
Q 008620 372 YRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISF--VGMGDIVTKESFEWLFSNPRSIRAS 449 (559)
Q Consensus 372 ~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~--~~~g~~l~~ev~e~~~~~~~l~~~~ 449 (559)
.....+.+....++.+-+.+..|.. ..-+|.++|+.....=+|.....++.. ...| .+++..+. ..++-+..
T Consensus 134 ~~~~~~~~~~~~l~~G~~~~~~~~~-~~~~~~~~yl~~i~~KTa~L~~~~~~~ga~lag--~~~~~~~~---l~~~G~~l 207 (323)
T CHL00151 134 EVVKLISKVITDFAEGEIRQGLVQF-DTTLSILNYIEKSFYKTASLIAASCKAAALLSD--ADEKDHND---FYLYGKHL 207 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCC-CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHcC--CCHHHHHH---HHHHHHHH
Confidence 3456677888888888777776643 334799999997555444444322211 2123 34554443 35667788
Q ss_pred hHHhHhccCccchhh
Q 008620 450 CAVGRLMNDMASHKF 464 (559)
Q Consensus 450 ~~i~RL~NDI~S~~k 464 (559)
+...-+.||+..+.-
T Consensus 208 G~aFQi~DDilD~~~ 222 (323)
T CHL00151 208 GLAFQIIDDVLDITS 222 (323)
T ss_pred HHHHHHHHHHhhccc
Confidence 888889999987753
No 24
>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=60.38 E-value=2.2e+02 Score=29.80 Aligned_cols=87 Identities=6% Similarity=-0.120 Sum_probs=56.7
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHHHhc--CCCCChhHHhhhcCchHHHHHH
Q 008620 372 YRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISFVGM--GDIVTKESFEWLFSNPRSIRAS 449 (559)
Q Consensus 372 ~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~--g~~l~~ev~e~~~~~~~l~~~~ 449 (559)
..+..+.++....+.+-..+..|.. +.-+|.++|++.-..-+|..+..++ ..|. + ..+++..+. ..++-+..
T Consensus 129 ~~~~~~~~~~~~~~~Gq~~~~~~~~-~~~~~~~~Y~~~i~~KTa~L~~~~~-~~ga~~a-g~~~~~~~~---l~~~g~~l 202 (319)
T TIGR02748 129 RAHQILSHTIVEVCRGEIEQIKDKY-NFDQNLRTYLRRIKRKTALLIAASC-QLGAIAS-GANEAIVKK---LYWFGYYV 202 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHc-CCCHHHHHH---HHHHHHHH
Confidence 4556777888889999888888753 3457999999887776665543322 2221 1 234444443 25566777
Q ss_pred hHHhHhccCccchhh
Q 008620 450 CAVGRLMNDMASHKF 464 (559)
Q Consensus 450 ~~i~RL~NDI~S~~k 464 (559)
+...-+.||+..+..
T Consensus 203 G~aFQI~DDilD~~~ 217 (319)
T TIGR02748 203 GMSYQITDDILDFVG 217 (319)
T ss_pred HHHHHHHHHHHHccC
Confidence 888888999977643
No 25
>KOG1719 consensus Dual specificity phosphatase [Defense mechanisms]
Probab=60.07 E-value=7.3 Score=36.70 Aligned_cols=31 Identities=35% Similarity=0.437 Sum_probs=26.4
Q ss_pred hccCCCcchhHHHHhhc-CCCHHHHHHHHHHH
Q 008620 466 QSRGHVASSVECYINQY-GATEEEAYSEFRKQ 496 (559)
Q Consensus 466 ~~~G~~~n~V~cyM~e~-g~S~eeA~~~i~~~ 496 (559)
..||..+..|.||+-++ +.|.++|.++++++
T Consensus 118 AGRtRSaTvV~cYLmq~~~wtpe~A~~~vr~i 149 (183)
T KOG1719|consen 118 AGRTRSATVVACYLMQHKNWTPEAAVEHVRKI 149 (183)
T ss_pred CCCccchhhhhhhhhhhcCCCHHHHHHHHHhc
Confidence 35677889999998885 99999999999873
No 26
>PLN02632 phytoene synthase
Probab=54.27 E-value=2.9e+02 Score=29.22 Aligned_cols=190 Identities=15% Similarity=0.184 Sum_probs=91.9
Q ss_pred hHHHHHHHHHHhhhhhccccccCCHH----HHHHHHHHHhhhchhhhccCChhHHHHHHHHHHHHHHHHHHHHhhcccch
Q 008620 298 ARKLFTKVIYMTSIIDDIYDVYGKIE----ELDLFTSAIERWDINAIDQLPEYMKLCYRALINVYSEVEKDLASQAKLYR 373 (559)
Q Consensus 298 ~Rl~~aK~~~l~~iiDD~yD~~gt~e----El~~ft~ai~rWd~~~~~~lpeymk~~~~al~~~~~ei~~~~~~~~~~~~ 373 (559)
.|..+.-+-.|.-.+||+=|...... .|+..-+.+.. ....-|. .++..++.+++.+.. -
T Consensus 74 ~R~ai~alYAf~R~~DdI~D~~~~~~~~~~~L~~w~~~l~~----~~~g~~~--~pv~~aL~~~~~~~~---------L- 137 (334)
T PLN02632 74 RRKAIWAIYVWCRRTDELVDGPNASHITPAALDRWEARLED----LFDGRPY--DMLDAALADTVSKFP---------L- 137 (334)
T ss_pred HHHHHHHHHHHHHHHhHHhcCCCCChhhHHHHHHHHHHHHH----HhCCCCC--ChHHHHHHHHHHHCC---------C-
Confidence 44444446677778999999654322 22222222222 1111122 145666666544321 1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHHHhcCCCCC---hhHHhhhcCchHHHHHHh
Q 008620 374 LHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISFVGMGDIVT---KESFEWLFSNPRSIRASC 450 (559)
Q Consensus 374 ~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~---~ev~e~~~~~~~l~~~~~ 450 (559)
-++.+.+++.++..... ....+|++|+......+.|+--.+++..++.....+ +++..... .+ -.+-
T Consensus 138 ---~~~~~~~li~g~~~Dl~---~~~~~t~~eL~~Ycy~vAgtVG~l~l~vlg~~~~~~~~~~~~~~~A~---~l-G~Al 207 (334)
T PLN02632 138 ---DIQPFRDMIEGMRMDLV---KSRYENFDELYLYCYYVAGTVGLMSVPVMGIAPESKASTESVYNAAL---AL-GIAN 207 (334)
T ss_pred ---ChHHHHHHHHHHHHHhc---cCCCCCHHHHHHHHHHhhHHHHHHHHHHhCCCCccccchHHHHHHHH---HH-HHHH
Confidence 13345667777664332 345779998888887777766655555444322111 11222111 11 1112
Q ss_pred HHhHhccCccchhhhhccCCC--cchhHHHHhhcCCCHHHH---------HHHHHHHHHHHHHHHHHhhcCCCCCCHHHH
Q 008620 451 AVGRLMNDMASHKFEQSRGHV--ASSVECYINQYGATEEEA---------YSEFRKQVSNAWKDINEECLRPTVVPVPLL 519 (559)
Q Consensus 451 ~i~RL~NDI~S~~kE~~~G~~--~n~V~cyM~e~g~S~eeA---------~~~i~~~i~~~wk~ln~e~l~~~~~p~~~~ 519 (559)
-++.++-|+. ....+|-+ +- =.|.++|+|.++- ..-+..++..+..-+.+..---..+|..+.
T Consensus 208 QltNILRDv~---eD~~~GRvYLP~---e~L~~~Gv~~edl~~~~~~~~~~~l~~~~~~~Ar~~~~~a~~~l~~lp~~~r 281 (334)
T PLN02632 208 QLTNILRDVG---EDARRGRVYLPQ---DELAQFGLTDEDIFAGKVTDKWRAFMKFQIKRARMYFAEAEEGVSELDPASR 281 (334)
T ss_pred HHHHHHHHHH---HHHhCCceeCCH---HHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhHhhCCHHhH
Confidence 2444445654 33456653 21 1367889988772 233445555554443332211234776544
No 27
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=50.40 E-value=3.3e+02 Score=28.68 Aligned_cols=88 Identities=15% Similarity=-0.053 Sum_probs=58.1
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHHHHHhc-CCCCChhHHhhhcCchHHHHHHh
Q 008620 372 YRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAISFVGM-GDIVTKESFEWLFSNPRSIRASC 450 (559)
Q Consensus 372 ~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~-g~~l~~ev~e~~~~~~~l~~~~~ 450 (559)
..+..+.++....+.+-..+..|.. +.-+|.++|+.....-+|..+..++ ..|. --..+++..+. ...+-+..+
T Consensus 130 ~~~~~~~~~~~~~~~Gq~~d~~~~~-~~~~s~~~y~~~i~~KTa~lf~~~~-~~ga~lag~~~~~~~~---l~~~g~~lG 204 (323)
T PRK10888 130 KVLEVMSEAVNVIAEGEVLQLMNVN-DPDITEENYMRVIYSKTARLFEAAA-QCSGILAGCTPEQEKG---LQDYGRYLG 204 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHcCCCHHHHHH---HHHHHHHHH
Confidence 4566778888888998888887754 3357999999988776666543332 2221 01234544443 356667778
Q ss_pred HHhHhccCccchhh
Q 008620 451 AVGRLMNDMASHKF 464 (559)
Q Consensus 451 ~i~RL~NDI~S~~k 464 (559)
...-+.||+..+..
T Consensus 205 ~aFQi~DD~ld~~~ 218 (323)
T PRK10888 205 TAFQLIDDLLDYSA 218 (323)
T ss_pred HHHHHHHHhhcccC
Confidence 88888999987753
No 28
>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=48.65 E-value=18 Score=27.80 Aligned_cols=28 Identities=29% Similarity=0.561 Sum_probs=21.2
Q ss_pred CcchhHHHHhhcCCCHHHHHHHHHHHHH
Q 008620 471 VASSVECYINQYGATEEEAYSEFRKQVS 498 (559)
Q Consensus 471 ~~n~V~cyM~e~g~S~eeA~~~i~~~i~ 498 (559)
+.-++.+.|..+|+|+++|.+.+++.-.
T Consensus 15 I~~AkgiLm~~~g~~e~~A~~~Lr~~Am 42 (56)
T PF03861_consen 15 IEQAKGILMARYGLSEDEAYRLLRRQAM 42 (56)
T ss_dssp HHHHHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 4456778999999999999999987544
No 29
>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]
Probab=47.51 E-value=16 Score=35.62 Aligned_cols=46 Identities=22% Similarity=0.281 Sum_probs=30.0
Q ss_pred hHhccCccchhhhhccC-CCcchhHHHHhhcCCCHHHHHHHHHHHHH
Q 008620 453 GRLMNDMASHKFEQSRG-HVASSVECYINQYGATEEEAYSEFRKQVS 498 (559)
Q Consensus 453 ~RL~NDI~S~~kE~~~G-~~~n~V~cyM~e~g~S~eeA~~~i~~~i~ 498 (559)
-.|--++..+|+..+.- .+.-+=.+.|+++|+|++||+.+++++-=
T Consensus 128 ~~L~~el~~~k~~L~~rK~ierAKglLM~~~g~sE~EAy~~lR~~AM 174 (194)
T COG3707 128 RALRRELAKLKDRLEERKVIERAKGLLMKRRGLSEEEAYKLLRRTAM 174 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34444555555544322 22334457999999999999999988643
No 30
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=33.63 E-value=45 Score=31.48 Aligned_cols=34 Identities=26% Similarity=0.553 Sum_probs=25.5
Q ss_pred HHHhhcCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHH
Q 008620 477 CYINQYGATEEEAYSEFRKQVSNAWKDINEECLRPTVVPVP 517 (559)
Q Consensus 477 cyM~e~g~S~eeA~~~i~~~i~~~wk~ln~e~l~~~~~p~~ 517 (559)
.-|++.|.|..+ |++.|++.||+ .+.+|++-|+|
T Consensus 125 ~~~~~~Gks~~e----IR~~ID~kYk~---g~~~pTpTp~P 158 (158)
T PF13798_consen 125 VQMYQEGKSPKE----IRQYIDEKYKE---GYAKPTPTPMP 158 (158)
T ss_pred HHHHHcCCCHHH----HHHHHHHHHHh---CCCCCCCCCCC
Confidence 356777888655 89999999984 57787776654
No 31
>PRK10581 geranyltranstransferase; Provisional
Probab=28.03 E-value=5.8e+02 Score=26.51 Aligned_cols=113 Identities=11% Similarity=0.063 Sum_probs=67.5
Q ss_pred HHHHHHHHHHHHHhhcCCCCCHHHHHHhhhhhcchhhHHHH--HHHhcCCCCChhHHhhhcCchHHHHHHhHHhHhccCc
Q 008620 382 KNQVKHYFFEAKWYHQNYIPTVDEYMTVALISSGHPNLSAI--SFVGMGDIVTKESFEWLFSNPRSIRASCAVGRLMNDM 459 (559)
Q Consensus 382 ~~~~~a~l~EAkW~~~g~vPs~eEYl~~~~~S~g~~~~~~~--~~~~~g~~l~~ev~e~~~~~~~l~~~~~~i~RL~NDI 459 (559)
..++.+-..+..|.. ..+|.++|++.-..=+|.....++ .-+..|. -+++..+. ..++-+..+...-+.||+
T Consensus 152 ~~l~~GQ~ld~~~~~--~~~~~~~y~~i~~~KTa~L~~~~~~~gailag~-~~~~~~~~---l~~~g~~lG~aFQI~DDi 225 (299)
T PRK10581 152 AGMCGGQALDLEAEG--KQVPLDALERIHRHKTGALIRAAVRLGALSAGD-KGRRALPV---LDRYAESIGLAFQVQDDI 225 (299)
T ss_pred chhhHhhHHHHhccC--CCCCHHHHHHHHHHhhHHHHHHHHHHHHHHcCC-CcHHHHHH---HHHHHHHHHHHHHHHHHH
Confidence 356677777777753 468999999876654444433222 1112232 12334443 356677788888889999
Q ss_pred cchhhh-hccCC-----C----cchhHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHH
Q 008620 460 ASHKFE-QSRGH-----V----ASSVECYINQYGATEEEAYSEFRKQVSNAWKDINE 506 (559)
Q Consensus 460 ~S~~kE-~~~G~-----~----~n~V~cyM~e~g~S~eeA~~~i~~~i~~~wk~ln~ 506 (559)
..+... ..-|. . .+++.++ ..+.|.+.+++.++++.+.+..
T Consensus 226 lD~~g~~~~~GK~~g~Dl~~gk~T~p~l~------~~e~a~~~a~~~~~~A~~~l~~ 276 (299)
T PRK10581 226 LDVVGDTATLGKRQGADQQLGKSTYPALL------GLEQARKKARDLIDDARQSLDQ 276 (299)
T ss_pred ccccCChHHHCCCcchhhhcCCCCHHHHH------HHHHHHHHHHHHHHHHHHHHHh
Confidence 887432 22222 1 2444343 2578888888888888876654
No 32
>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=27.97 E-value=5.8e+02 Score=25.60 Aligned_cols=64 Identities=16% Similarity=0.044 Sum_probs=42.3
Q ss_pred CCCCCHHHHHHhhhhhcchhhHHHHHHHhcCCCCChhHHhhhcCchHHHHHHhHHhHhccCccchhh
Q 008620 398 NYIPTVDEYMTVALISSGHPNLSAISFVGMGDIVTKESFEWLFSNPRSIRASCAVGRLMNDMASHKF 464 (559)
Q Consensus 398 g~vPs~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~ev~e~~~~~~~l~~~~~~i~RL~NDI~S~~k 464 (559)
+..+|.++|+++-..-+|..+..++..-++=-..+++..+. ..++-+..+...-+.||+..+..
T Consensus 130 ~~~~~~~~y~~i~~~KTg~l~~~~~~~ga~lag~~~~~~~~---l~~~g~~lG~afQi~DD~~d~~~ 193 (260)
T PF00348_consen 130 DKDPTEEEYLEIIRLKTGSLFALACQLGAILAGADEEQIEA---LREFGRHLGIAFQIRDDLLDLFG 193 (260)
T ss_dssp TSSTSHHHHHHHHHHHTHHHHHHHHHHHHHHTTSGHHHHHH---HHHHHHHHHHHHHHHHHHHHHHS
T ss_pred cccccHHHHHHHHhhcchHHHHHHHHHHHHhccchhHHHHH---HHHHHHHHHHHHhhhhhhhhccC
Confidence 34789999999988877776543322222111234555544 36777888888899999877765
No 33
>KOG3730 consensus Acyl-CoA:dihydroxyactetone-phosphate acyltransferase DHAPAT [Lipid transport and metabolism]
Probab=27.95 E-value=4.2e+02 Score=29.64 Aligned_cols=76 Identities=20% Similarity=0.249 Sum_probs=51.2
Q ss_pred CCcchhHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhhhhccccccCCCCCCChh-HHHH
Q 008620 470 HVASSVECYINQYGATEEEAYSEFRKQVSNAWKDINEECLRPTVVPVPLLIRILNLTRAADVIYKYKDGYTDSEE-LKDF 548 (559)
Q Consensus 470 ~~~n~V~cyM~e~g~S~eeA~~~i~~~i~~~wk~ln~e~l~~~~~p~~~~~~~ln~aR~~~~~Y~~~Dg~t~~~~-~k~~ 548 (559)
.+.+.|.-|-+|.|+|.+.-.+++++++++.--++|-. .++-..+-+++++.-+| ||+...+. |.+.
T Consensus 76 ~~~sVi~~~~kes~~s~d~~r~ea~eIlDEmsh~~nl~---------~IR~cg~ai~ki~k~i~---dg~yVNe~~~~~v 143 (685)
T KOG3730|consen 76 KLRSVIEHYAKESGTSLDQMRREAREILDEMSHDRNLA---------IIRWCGIAITKIGKRIC---DGFYVNEASMANV 143 (685)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhcchH---------HHHHHHHHHHHHHHHHh---cceeECHHHHHHH
Confidence 35688899999999999998888888888655555432 23445566677766555 78776554 6655
Q ss_pred HHhhhcccc
Q 008620 549 IVSLLINPV 557 (559)
Q Consensus 549 i~~ll~~pi 557 (559)
=+..=-+||
T Consensus 144 r~~~~k~pV 152 (685)
T KOG3730|consen 144 RKDMGKCPV 152 (685)
T ss_pred HHHhccCCE
Confidence 554444443
No 34
>smart00400 ZnF_CHCC zinc finger.
Probab=27.83 E-value=66 Score=24.42 Aligned_cols=25 Identities=12% Similarity=0.080 Sum_probs=20.7
Q ss_pred CCCcchhHHHHhhcCCCHHHHHHHH
Q 008620 469 GHVASSVECYINQYGATEEEAYSEF 493 (559)
Q Consensus 469 G~~~n~V~cyM~e~g~S~eeA~~~i 493 (559)
|.-.+.|..+|+-.|+|-.||++.+
T Consensus 30 g~gGd~i~fv~~~~~~sf~eA~~~L 54 (55)
T smart00400 30 GAGGNVISFLMKYDKLSFVEAVKKL 54 (55)
T ss_pred CCCCCHHHHHHHHHCcCHHHHHHHh
Confidence 4445789999998999999998875
No 35
>smart00463 SMR Small MutS-related domain.
Probab=26.50 E-value=77 Score=25.77 Aligned_cols=22 Identities=36% Similarity=0.348 Sum_probs=20.4
Q ss_pred cCCCHHHHHHHHHHHHHHHHHH
Q 008620 482 YGATEEEAYSEFRKQVSNAWKD 503 (559)
Q Consensus 482 ~g~S~eeA~~~i~~~i~~~wk~ 503 (559)
||++.++|+..+...++++++.
T Consensus 7 HG~~~~eA~~~l~~~l~~~~~~ 28 (80)
T smart00463 7 HGLTVEEALTALDKFLNNARLK 28 (80)
T ss_pred CCCCHHHHHHHHHHHHHHHHHc
Confidence 7999999999999999988875
No 36
>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=26.11 E-value=28 Score=31.75 Aligned_cols=58 Identities=16% Similarity=0.260 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHH-HHHHhhhhhc
Q 008620 353 ALINVYSEVEKDLASQAKLYRLHYAKEAMKNQVKHYFFEAKWYHQNYIPTVD-EYMTVALISS 414 (559)
Q Consensus 353 al~~~~~ei~~~~~~~~~~~~~~~~~~~w~~~~~a~l~EAkW~~~g~vPs~e-EYl~~~~~S~ 414 (559)
.++-.+.+|++.+.+.|+ .+-.+.|++++.+.+.-++.....-+|.++ |+...+..|+
T Consensus 42 ~lwa~l~dIs~qv~~~G~----k~~~e~WK~~~~~~~~~~~~~~~~~~~gl~Gg~v~~g~sTs 100 (127)
T PF05772_consen 42 KLWAMLGDISRQVEWNGR----KLDPEDWKELFTAAFLIATGEEQRVVPGLDGGFVVLGESTS 100 (127)
T ss_dssp HHHHHHHHHHHH--BTTB-------HHHHHHHHHHHH-----S--EEEE-TTSSEEEE---TT
T ss_pred HHHHHHHHHHHHhHhcCc----cCCHHHHHHHHHHHHhhhccchhhhccCCCCCeEEEeeech
Confidence 345567788888888776 356889999999988666665555667765 5554444444
No 37
>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=24.80 E-value=3.1e+02 Score=25.80 Aligned_cols=13 Identities=31% Similarity=0.723 Sum_probs=9.4
Q ss_pred HhhcCCCCCHHHH
Q 008620 394 WYHQNYIPTVDEY 406 (559)
Q Consensus 394 W~~~g~vPs~eEY 406 (559)
|...|..||++|+
T Consensus 112 ~srAg~~~~Lqe~ 124 (152)
T TIGR03486 112 WARAGRIPSLQEH 124 (152)
T ss_pred HHHccCCcchHHH
Confidence 4567788888776
No 38
>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=22.77 E-value=96 Score=25.37 Aligned_cols=23 Identities=26% Similarity=0.218 Sum_probs=19.6
Q ss_pred cCCCHHHHHHHHHHHHHHHHHHH
Q 008620 482 YGATEEEAYSEFRKQVSNAWKDI 504 (559)
Q Consensus 482 ~g~S~eeA~~~i~~~i~~~wk~l 504 (559)
||++.+||+..+...++++++.-
T Consensus 4 HG~~~~eA~~~l~~~l~~~~~~~ 26 (83)
T PF01713_consen 4 HGLTVEEALRALEEFLDEARQRG 26 (83)
T ss_dssp TTS-HHHHHHHHHHHHHHHHHTT
T ss_pred CCCcHHHHHHHHHHHHHHHHHcC
Confidence 79999999999999999988653
No 39
>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=22.44 E-value=69 Score=21.47 Aligned_cols=18 Identities=28% Similarity=0.493 Sum_probs=14.0
Q ss_pred HHHhhcCCCHHHHHHHHH
Q 008620 477 CYINQYGATEEEAYSEFR 494 (559)
Q Consensus 477 cyM~e~g~S~eeA~~~i~ 494 (559)
-|.++||+|.||..+.+.
T Consensus 9 rYV~eh~ls~ee~~~RL~ 26 (28)
T PF12368_consen 9 RYVKEHGLSEEEVAERLA 26 (28)
T ss_pred hhHHhcCCCHHHHHHHHH
Confidence 588999999998655543
No 40
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=21.59 E-value=90 Score=28.26 Aligned_cols=21 Identities=24% Similarity=0.426 Sum_probs=18.1
Q ss_pred hHHHHhhcCCCHHHHHHHHHH
Q 008620 475 VECYINQYGATEEEAYSEFRK 495 (559)
Q Consensus 475 V~cyM~e~g~S~eeA~~~i~~ 495 (559)
|.+.|.|.|+|.++|++.+..
T Consensus 88 IkLV~eQa~VsreeA~kAL~e 108 (122)
T COG1308 88 IKLVMEQAGVSREEAIKALEE 108 (122)
T ss_pred HHHHHHHhCCCHHHHHHHHHH
Confidence 678999999999999987743
Done!