Query 040042
Match_columns 363
No_of_seqs 144 out of 729
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 04:31:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040042.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040042hhsearch_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-106 3E-111 840.6 32.9 335 27-363 1-363 (542)
2 PLN02279 ent-kaur-16-ene synth 100.0 9E-101 2E-105 820.3 28.7 316 45-363 245-597 (784)
3 PLN02592 ent-copalyl diphospha 100.0 4.7E-98 1E-102 797.5 29.5 316 45-363 285-658 (800)
4 PF01397 Terpene_synth: Terpen 100.0 2.9E-49 6.3E-54 360.2 16.6 147 42-191 22-183 (183)
5 PF03936 Terpene_synth_C: Terp 99.9 6.6E-23 1.4E-27 192.2 9.0 136 221-356 1-136 (270)
6 cd00868 Terpene_cyclase_C1 Ter 99.8 4.3E-19 9.4E-24 167.6 11.7 125 235-359 1-125 (284)
7 cd00687 Terpene_cyclase_nonpla 98.1 2.3E-06 5E-11 82.5 4.6 107 242-349 18-126 (303)
8 cd00385 Isoprenoid_Biosyn_C1 I 96.4 0.0023 5E-08 57.0 3.0 74 269-348 2-75 (243)
9 PF14165 YtzH: YtzH-like prote 51.7 33 0.00072 28.2 4.8 39 300-340 19-57 (87)
10 cd07604 BAR_ASAPs The Bin/Amph 27.4 1.2E+02 0.0026 28.7 5.2 91 42-143 12-105 (215)
11 PRK09177 xanthine-guanine phos 24.9 18 0.00039 32.2 -0.8 23 293-315 87-109 (156)
12 COG2976 Uncharacterized protei 23.7 55 0.0012 31.0 2.1 35 236-279 7-41 (207)
13 COG5123 TOA2 Transcription ini 22.8 44 0.00096 28.3 1.2 42 140-191 1-42 (113)
14 PF00156 Pribosyltran: Phospho 21.8 22 0.00047 29.2 -0.9 21 293-313 91-111 (125)
15 PF12626 PolyA_pol_arg_C: Poly 21.1 1.1E+02 0.0024 26.5 3.4 28 225-252 65-92 (124)
16 COG4738 Predicted transcriptio 20.6 1.9E+02 0.004 25.2 4.5 53 71-128 14-73 (124)
17 smart00027 EH Eps15 homology d 20.3 4.4E+02 0.0095 20.8 7.3 59 65-128 24-84 (96)
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-106 Score=840.57 Aligned_cols=335 Identities=47% Similarity=0.746 Sum_probs=315.2
Q ss_pred CCCCCCCC----C-ccccc-----hH-HHHHHHHHHHHHHHHHHhhc-ccCCccchhhHHHHHHhhCCccchHHHHHHHH
Q 040042 27 PRSCHFTP----F-QVQCL-----GK-SYAKRIEELKADVRAMLDKA-VVMDPLHQFELRDALQRLGVSYHFGDEIKKLR 94 (363)
Q Consensus 27 r~~a~~~p----~-f~~~~-----~~-~~~~~~~~Lk~~Vk~~l~~~-~~~d~~~~L~lID~LqRLGI~~hFe~EI~~~L 94 (363)
|++++|+| + ++++. +. .+.+++++||++||+|+... .|.|++++|++||+||||||+|||++||+++|
T Consensus 1 r~~~~~~~~~w~~~~~~s~~~~~~~~~~~~~~~~~lk~~v~~~~~~~~~~~~~~~~l~liD~lqrLGi~~hF~~EI~~~L 80 (542)
T cd00684 1 RPSANFPPSLWGDDHFLSLSSDYSEEDELEEEIEELKEEVRKMLEDSEYPVDLFERLWLIDRLQRLGISYHFEDEIKEIL 80 (542)
T ss_pred CCCCCCCCCcCCCcceeecCCCcchhHHHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHcCchhhhHHHHHHHH
Confidence 78899999 3 55542 22 67899999999999999763 12899999999999999999999999999999
Q ss_pred HHHHhhCccc---CCCChhHHHHHHHhhhhcCCccccccccccccc-----------cchHHHHHHHHhhcCCCCCchHH
Q 040042 95 NAIYRNNNLQ---KQESLYDVALEFRLLRQHGYDTATTASIQLKFF-----------DDWKGILSMYEAAYLLVEGENIF 160 (363)
Q Consensus 95 ~~iy~~~~~~---~~~DL~~~AL~FRLLR~hGy~VSs~~DvF~~F~-----------~dv~glLsLYeAS~l~~~gE~iL 160 (363)
+++|++|... ...||++|||+|||||||||+||| |||++|+ +||+||||||||||+++|||+||
T Consensus 81 ~~i~~~~~~~~~~~~~dl~~~al~FRlLR~~Gy~vs~--dvf~~F~~~~g~f~~~~~~d~~g~l~Ly~As~l~~~gE~iL 158 (542)
T cd00684 81 DYIYRYWTERGESNEDDLYTTALGFRLLRQHGYNVSS--DVFKKFKDEDGKFKESLTQDVKGMLSLYEASHLSFPGEDIL 158 (542)
T ss_pred HHHHHhhcccccccCCCHHHHHHHHHHHHHcCCCcCH--HHHhhhcCCCCCcCchhhhhhHHHHHHHHHhhcCCCCcHHH
Confidence 9999987521 247999999999999999999999 9999999 59999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcC--CCchHHHHHHHhccCcccccchhhHHHHHHHHhcCCCCCcHHHHHHHHhhhHHHHHhhHH
Q 040042 161 YEIRNFTTTYLKEYIKHN--KDPYILTLVNHALELPLHWRMQRMETRWFIDAYESGPDINHVLLELAKLDFNMVQAKHQE 238 (363)
Q Consensus 161 deA~~Ft~~~L~~~~~~~--~~~~L~~~V~~aL~~P~~~~l~Rlear~yI~~Y~~~~~~n~~lLelAKlDFn~~Q~~hq~ 238 (363)
|||++||++||++.++++ ++++|+++|+|||++|||+++||+|||+||++|++++++|++||||||+|||+||++||+
T Consensus 159 deA~~ft~~~L~~~~~~~~~~~~~l~~~V~~aL~~P~~~~~~rlear~yi~~Y~~~~~~n~~lLelAkldfn~~Q~~hq~ 238 (542)
T cd00684 159 DEALSFTTKHLEEKLESNWIIDPDLSGEIEYALEIPLHASLPRLEARWYIEFYEQEDDHNETLLELAKLDFNILQALHQE 238 (542)
T ss_pred HHHHHHHHHHHHHHhhccCCCCchHHHHHHHHccCchhcCCchHHHHHHHHHhCCCccccHHHHHHHHHHHHHHhHhHHH
Confidence 999999999999999643 788999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhccCCCCccccchhhHHHHHHhhcccCCCchhhhHhHHhHHHHHhhhhhhhcccCCHHHHHHHHHHhhh
Q 040042 239 DLESVSEWWEYVGFGNKLNFARDRLMENFLWTVGVTSEPQFGYFRRMSTKVSALITSIDDAYDVYGTLDELKLFTNSVER 318 (363)
Q Consensus 239 EL~~lsrWw~~~~l~~~L~faRdr~ve~yfwa~~~~fEP~~s~~Ri~~aK~~~litviDD~yD~yGtleEl~~ft~aveR 318 (363)
||++++|||+++||.++|||+|+|++|||||++|++|||++|.+|+++||++++++++||+||+|||+|||+.||+||+|
T Consensus 239 El~~~~rWwk~~gL~~~l~~aRdr~ve~yf~~~a~~feP~~s~~Rl~~aK~~~l~~~iDD~fD~~gt~eEl~~ft~ai~r 318 (542)
T cd00684 239 ELKILSRWWKDLDLASKLPFARDRLVECYFWAAGTYFEPQYSLARIALAKTIALITVIDDTYDVYGTLEELELFTEAVER 318 (542)
T ss_pred HHHHHhHHHHhcCCcccCCcccchhHHHHHHHHhcccCccchHHHHHHHHHHHHHhhhHhhhccCCCHHHHHHHHHHHHh
Confidence 99999999999999988899999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCCChHHHHHHHHHHHHHHHHHHHHHhccCCccchhccC
Q 040042 319 WDVSAMDQHPYYLKFCFLALHNFIMKLLLTLSKKKKLTSFVILKK 363 (363)
Q Consensus 319 WD~~~~~~Lpeymk~~f~aL~~~~~ei~~~~~~~~g~~~~~~lk~ 363 (363)
||+++++++|+|||+||.+|+++++|+++++.+.+|+++++|+++
T Consensus 319 wd~~~~~~lPe~mk~~~~al~~~~~ei~~~~~~~~~~~~~~~~~~ 363 (542)
T cd00684 319 WDISAIDQLPEYMKIVFKALLNTVNEIEEELLKEGGSYVVPYLKE 363 (542)
T ss_pred ccccchhhccHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHH
Confidence 999999999999999999999999999999999999998888763
No 2
>PLN02279 ent-kaur-16-ene synthase
Probab=100.00 E-value=8.5e-101 Score=820.34 Aligned_cols=316 Identities=26% Similarity=0.386 Sum_probs=295.1
Q ss_pred HHHHHHHHHHHHHHHhhcc---cCCccchhhHHHHHHhhCCccchHHHHHHHHHHHHhhCcc---cCCCChhHHHHHHHh
Q 040042 45 AKRIEELKADVRAMLDKAV---VMDPLHQFELRDALQRLGVSYHFGDEIKKLRNAIYRNNNL---QKQESLYDVALEFRL 118 (363)
Q Consensus 45 ~~~~~~Lk~~Vk~~l~~~~---~~d~~~~L~lID~LqRLGI~~hFe~EI~~~L~~iy~~~~~---~~~~DL~~~AL~FRL 118 (363)
.++...|...|++.-.+.| |.+.++++|+||+||||||+|||++||+++|+++|++|.. ....|+++|||+|||
T Consensus 245 ~~~~~yL~~~~~~~~g~vP~~yp~~~fe~l~lvd~L~rlGi~~hF~~EI~~~L~~~~~~~~~~~~~~~~Dl~~tAl~FRL 324 (784)
T PLN02279 245 AGCLRYLRSLLQKFGNAVPTVYPLDQYARLSMVDTLERLGIDRHFRKEIKSVLDETYRYWLQGEEEIFLDLATCALAFRI 324 (784)
T ss_pred hHHHHHHHHHHHhcCCCCCCCCcccHHHHhHHHHHHHHhCCccccHHHHHHHHHHHHHhhcccccCCCCCHHHHHHHHHH
Confidence 4666777777766543332 6799999999999999999999999999999999997652 134799999999999
Q ss_pred hhhcCCccccccccccccc------------cchHHHHHHHHhhcCCCCCchHHHHHHHHHHHHHHHHHhc------CCC
Q 040042 119 LRQHGYDTATTASIQLKFF------------DDWKGILSMYEAAYLLVEGENIFYEIRNFTTTYLKEYIKH------NKD 180 (363)
Q Consensus 119 LR~hGy~VSs~~DvF~~F~------------~dv~glLsLYeAS~l~~~gE~iLdeA~~Ft~~~L~~~~~~------~~~ 180 (363)
||||||+||| |||++|+ +||+||||||||||+++|||+|||||+.||++||++.+++ .++
T Consensus 325 LR~hGy~VS~--dvf~~F~~~~F~~~l~~~~~dv~gmL~LY~AS~l~~~gE~iLdeA~~Fs~~~L~~~~~~~~~~~~~~~ 402 (784)
T PLN02279 325 LRLNGYDVSS--DPLKQFAEDHFSDSLGGYLKDTGAVLELFRASQISYPDESLLEKQNSWTSHFLEQGLSNWSKTADRLR 402 (784)
T ss_pred HHHcCCCCCh--hHHhhcCCCcccchhcccchhhHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHHhcccccccccC
Confidence 9999999999 9999997 6999999999999999999999999999999999998853 257
Q ss_pred chHHHHHHHhccCcccccchhhHHHHHHHHhcCCCC------------CcHHHHHHHHhhhHHHHHhhHHHHHHHHHHHH
Q 040042 181 PYILTLVNHALELPLHWRMQRMETRWFIDAYESGPD------------INHVLLELAKLDFNMVQAKHQEDLESVSEWWE 248 (363)
Q Consensus 181 ~~L~~~V~~aL~~P~~~~l~Rlear~yI~~Y~~~~~------------~n~~lLelAKlDFn~~Q~~hq~EL~~lsrWw~ 248 (363)
++|+++|+|||++|||+++||||||+||++|++++. +|++||||||+|||+||++||+||++|+|||+
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 889999999999999999999999999999998885 89999999999999999999999999999999
Q ss_pred HhccCCCCccccchhhHHHHHHhhcccCCCchhhhHhHHhHHHHHhhhhhhhcccCCHHHHHHHHHHhhhcccc-cccCC
Q 040042 249 YVGFGNKLNFARDRLMENFLWTVGVTSEPQFGYFRRMSTKVSALITSIDDAYDVYGTLDELKLFTNSVERWDVS-AMDQH 327 (363)
Q Consensus 249 ~~~l~~~L~faRdr~ve~yfwa~~~~fEP~~s~~Ri~~aK~~~litviDD~yD~yGtleEl~~ft~aveRWD~~-~~~~L 327 (363)
++|| .+|||||||++|||||++|++||||||.+|++|||+++|+|++||+||+|||+|||++||+||+|||++ ++++|
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 67999
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHhccCCccchhccC
Q 040042 328 PYYLKFCFLALHNFIMKLLLTLSKKKKLTSFVILKK 363 (363)
Q Consensus 328 peymk~~f~aL~~~~~ei~~~~~~~~g~~~~~~lk~ 363 (363)
|+|||+||.+|++++||++.++.+.||+++++|+++
T Consensus 562 peymki~f~aL~~t~nei~~~~~~~qGr~v~~~l~~ 597 (784)
T PLN02279 562 SEQVEIIFSALRSTISEIGDKAFTWQGRNVTSHIIK 597 (784)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHH
Confidence 999999999999999999999999999999999874
No 3
>PLN02592 ent-copalyl diphosphate synthase
Probab=100.00 E-value=4.7e-98 Score=797.54 Aligned_cols=316 Identities=25% Similarity=0.346 Sum_probs=294.0
Q ss_pred HHHHHHHHHHHHHHHhhcc---cCCccchhhHHHHHHhhCCccchHHHHHHHHHHHHhhCccc--------CCCChhHHH
Q 040042 45 AKRIEELKADVRAMLDKAV---VMDPLHQFELRDALQRLGVSYHFGDEIKKLRNAIYRNNNLQ--------KQESLYDVA 113 (363)
Q Consensus 45 ~~~~~~Lk~~Vk~~l~~~~---~~d~~~~L~lID~LqRLGI~~hFe~EI~~~L~~iy~~~~~~--------~~~DL~~~A 113 (363)
.++.+.|...|++.-.+.| |.+++++|++||+||||||+|||++||+++|+++|++|.+. ...|+++||
T Consensus 285 ~~cl~YL~~~~~k~~GgVP~vyP~d~fE~LwlVDtLqRLGIs~hF~~EI~~iLd~iy~~w~~~g~~~a~~~~~~Dld~TA 364 (800)
T PLN02592 285 ENCLEYLNKAVQRFNGGVPNVYPVDLFEHIWAVDRLQRLGISRYFEPEIKECIDYVHRYWTENGICWARNSHVHDIDDTA 364 (800)
T ss_pred hHHHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHcCCccccHHHHHHHHHHHHHHHhhcCcccccCCCcCCHHHHH
Confidence 4667778777777543333 68999999999999999999999999999999999965421 136999999
Q ss_pred HHHHhhhhcCCccccccccccccc-------------cchHHHHHHHHhhcCCCCCchHHHHHHHHHHHHHHHHHh-c--
Q 040042 114 LEFRLLRQHGYDTATTASIQLKFF-------------DDWKGILSMYEAAYLLVEGENIFYEIRNFTTTYLKEYIK-H-- 177 (363)
Q Consensus 114 L~FRLLR~hGy~VSs~~DvF~~F~-------------~dv~glLsLYeAS~l~~~gE~iLdeA~~Ft~~~L~~~~~-~-- 177 (363)
|+|||||||||+||| |||++|+ +|++|||+||||||+++|||.|||+|+.||+++|++.+. +
T Consensus 365 LaFRLLRqhGy~VS~--DvF~~F~~~g~F~~~~ge~~~Dv~glL~LYeAS~l~~~gE~iLdeA~~Fs~~~L~~~~~~~~l 442 (800)
T PLN02592 365 MGFRLLRLHGHQVSA--DVFKHFEKGGEFFCFAGQSTQAVTGMFNLYRASQVLFPGEKILENAKEFSSKFLREKQEANEL 442 (800)
T ss_pred HHHHHHHHcCCCCCh--HHHHhhcCCCCccccccccccchHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHHHHhhcccc
Confidence 999999999999999 9999997 799999999999999999999999999999999999863 1
Q ss_pred ----CCCchHHHHHHHhccCcccccchhhHHHHHHHHhcCCCCC-------------cHHHHHHHHhhhHHHHHhhHHHH
Q 040042 178 ----NKDPYILTLVNHALELPLHWRMQRMETRWFIDAYESGPDI-------------NHVLLELAKLDFNMVQAKHQEDL 240 (363)
Q Consensus 178 ----~~~~~L~~~V~~aL~~P~~~~l~Rlear~yI~~Y~~~~~~-------------n~~lLelAKlDFn~~Q~~hq~EL 240 (363)
.++++|+++|+|||++|||+++||+|||+||++|+++++. |++||||||+|||+||++||+||
T Consensus 443 ~d~~~~~~~L~~eV~~AL~~P~~~~l~RlEaR~yI~~Y~~~~~~~i~Kt~yr~~~~~n~~lLeLAklDFn~~Qs~hq~EL 522 (800)
T PLN02592 443 LDKWIIMKDLPGEVGFALEIPWYASLPRVETRFYIEQYGGEDDVWIGKTLYRMPYVNNNEYLELAKLDYNNCQALHQLEW 522 (800)
T ss_pred ccccccCccHHHHHHHhccChhhcCcchHHHHHHHHHhcCCcccchhhhhccccccCCHHHHHHHHHHHHHHHHHhHHHH
Confidence 1467899999999999999999999999999999987764 99999999999999999999999
Q ss_pred HHHHHHHHHhccCCCCccccchhhHHHHHHhhcccCCCchhhhHhHHhHHHHHhhhhhhhcccCCHHHHHHHHHHhh---
Q 040042 241 ESVSEWWEYVGFGNKLNFARDRLMENFLWTVGVTSEPQFGYFRRMSTKVSALITSIDDAYDVYGTLDELKLFTNSVE--- 317 (363)
Q Consensus 241 ~~lsrWw~~~~l~~~L~faRdr~ve~yfwa~~~~fEP~~s~~Ri~~aK~~~litviDD~yD~yGtleEl~~ft~ave--- 317 (363)
++++|||+++|| .+|||||||++|||||++|++||||||.+|++|||+++|+|+|||+||+|||+|||++||++|+
T Consensus 523 ~~lsrWwke~~L-~~L~faRdr~ve~Yfwa~~~~feP~~s~~Ri~~aK~~~LitviDD~fD~yGt~eEl~~ft~~v~~~~ 601 (800)
T PLN02592 523 DNFQKWYEECNL-GEFGVSRSELLLAYFLAAASIFEPERSHERLAWAKTTVLVEAISSYFNKETSSKQRRAFLHEFGYGY 601 (800)
T ss_pred HHHhHHHHhcCC-CcCCcchhHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHhhcccccCCCCHHHHHHHHHHHHhcc
Confidence 999999999999 5999999999999999999999999999999999999999999999999999999999999997
Q ss_pred -----hcccccccCCCh------HHHHHHHHHHHHHHHHHHHHHhccCCccchhccC
Q 040042 318 -----RWDVSAMDQHPY------YLKFCFLALHNFIMKLLLTLSKKKKLTSFVILKK 363 (363)
Q Consensus 318 -----RWD~~~~~~Lpe------ymk~~f~aL~~~~~ei~~~~~~~~g~~~~~~lk~ 363 (363)
|||.+++++||+ |||+||.|||||+||++.++.++||+++++||++
T Consensus 602 ~~~~~rWd~~~~~~lp~~~~~~~~mki~f~aLy~tineia~~a~~~qGr~v~~~L~~ 658 (800)
T PLN02592 602 KINGRRSDHHFNDRNMRRSGSVKTGEELVGLLLGTLNQLSLDALEAHGRDISHLLRH 658 (800)
T ss_pred cccccccCchhhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHH
Confidence 999999999988 9999999999999999999999999999999974
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=2.9e-49 Score=360.19 Aligned_cols=147 Identities=48% Similarity=0.746 Sum_probs=127.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccCCccchhhHHHHHHhhCCccchHHHHHHHHHHHHhhCccc--CCCChhHHHHHHHhh
Q 040042 42 KSYAKRIEELKADVRAMLDKAVVMDPLHQFELRDALQRLGVSYHFGDEIKKLRNAIYRNNNLQ--KQESLYDVALEFRLL 119 (363)
Q Consensus 42 ~~~~~~~~~Lk~~Vk~~l~~~~~~d~~~~L~lID~LqRLGI~~hFe~EI~~~L~~iy~~~~~~--~~~DL~~~AL~FRLL 119 (363)
+.+.+++++||++||+|+..+. .|++++|+|||+||||||+|||++||+++|+++|+.+... ...||++|||+||||
T Consensus 22 ~~~~~~~~~Lk~~v~~~l~~~~-~d~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~~~~~~dL~~~AL~FRLL 100 (183)
T PF01397_consen 22 EKCKERAEELKEEVRNMLPASY-PDPLEKLELIDTLQRLGISYHFEDEIKEILDSIYRSWDEDNEEIDDLYTTALRFRLL 100 (183)
T ss_dssp HHHHHHHHHHHHHHHHHHHSSS-SHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHHTTTTTSHTSSCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhhcC-CCHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHhhhccccccccCchhHHHHHHHHH
Confidence 6788999999999999998874 3899999999999999999999999999999999987632 235999999999999
Q ss_pred hhcCCccccccccccccc-----------cchHHHHHHHHhhcCCCCCchHHHHHHHHHHHHHHHHHhcCC--CchHHHH
Q 040042 120 RQHGYDTATTASIQLKFF-----------DDWKGILSMYEAAYLLVEGENIFYEIRNFTTTYLKEYIKHNK--DPYILTL 186 (363)
Q Consensus 120 R~hGy~VSs~~DvF~~F~-----------~dv~glLsLYeAS~l~~~gE~iLdeA~~Ft~~~L~~~~~~~~--~~~L~~~ 186 (363)
|||||+||| |||++|+ +||+||||||||||+++|||+|||||+.||++||++++++.- +++|+++
T Consensus 101 RqhGy~VS~--DvF~~F~d~~g~F~~~l~~Dv~glLsLYeAS~l~~~gE~iLdeA~~Ft~~~L~~~~~~~~~~~~~L~~~ 178 (183)
T PF01397_consen 101 RQHGYYVSS--DVFNKFKDEKGNFKESLSNDVKGLLSLYEASHLRFHGEDILDEARAFTTKHLKSLLSNLSIPDPHLAKE 178 (183)
T ss_dssp HHTT----G--GGGGGGBETTSSBSGGGGGHHHHHHHHHHHHTT--TT-HHHHHHHHHHHHHHHHHHTTTCTTSCHHHHH
T ss_pred HHcCCcccH--HHHhCcccCCCccchhhhHhHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHhccCCCCcHHHHHH
Confidence 999999999 9999999 899999999999999999999999999999999999985322 2359999
Q ss_pred HHHhc
Q 040042 187 VNHAL 191 (363)
Q Consensus 187 V~~aL 191 (363)
|+|||
T Consensus 179 V~~AL 183 (183)
T PF01397_consen 179 VKHAL 183 (183)
T ss_dssp HHHHH
T ss_pred HHHhC
Confidence 99997
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=99.88 E-value=6.6e-23 Score=192.23 Aligned_cols=136 Identities=29% Similarity=0.368 Sum_probs=129.7
Q ss_pred HHHHHHhhhHHHHHhhHHHHHHHHHHHHHhccCCCCccccchhhHHHHHHhhcccCCCchhhhHhHHhHHHHHhhhhhhh
Q 040042 221 LLELAKLDFNMVQAKHQEDLESVSEWWEYVGFGNKLNFARDRLMENFLWTVGVTSEPQFGYFRRMSTKVSALITSIDDAY 300 (363)
Q Consensus 221 lLelAKlDFn~~Q~~hq~EL~~lsrWw~~~~l~~~L~faRdr~ve~yfwa~~~~fEP~~s~~Ri~~aK~~~litviDD~y 300 (363)
+|+|||+|||+||++||+|++++.+||+++|+..+.+.+|+|++.++||.+++++.|..+..|+++||.++++.++||+|
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 68999999999999999999999999999999778888999999999999999999998888999999999999999999
Q ss_pred cccCCHHHHHHHHHHhhhcccccccCCChHHHHHHHHHHHHHHHHHHHHHhccCCc
Q 040042 301 DVYGTLDELKLFTNSVERWDVSAMDQHPYYLKFCFLALHNFIMKLLLTLSKKKKLT 356 (363)
Q Consensus 301 D~yGtleEl~~ft~aveRWD~~~~~~Lpeymk~~f~aL~~~~~ei~~~~~~~~g~~ 356 (363)
|..|+.++++.|+++++|||+...+.+|++++.++.++.++++++...+.+.++..
T Consensus 81 D~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~d~~~r~~~~~~~~~~~~ 136 (270)
T PF03936_consen 81 DDGGSAEELEALTDAVERWDPNSGDPLPDPDKPLFRALADIWNRIAARMSPAQRRR 136 (270)
T ss_dssp HTTSHHHHHHHHHHHHHHTSSGGGGGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccchHHHHHHHHHHhcccccccccccchhHHHHHHHHHHHHHHHHHhhhhhccc
Confidence 99999999999999999999988889999999999999999999999998876543
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=99.79 E-value=4.3e-19 Score=167.60 Aligned_cols=125 Identities=46% Similarity=0.795 Sum_probs=117.7
Q ss_pred hhHHHHHHHHHHHHHhccCCCCccccchhhHHHHHHhhcccCCCchhhhHhHHhHHHHHhhhhhhhcccCCHHHHHHHHH
Q 040042 235 KHQEDLESVSEWWEYVGFGNKLNFARDRLMENFLWTVGVTSEPQFGYFRRMSTKVSALITSIDDAYDVYGTLDELKLFTN 314 (363)
Q Consensus 235 ~hq~EL~~lsrWw~~~~l~~~L~faRdr~ve~yfwa~~~~fEP~~s~~Ri~~aK~~~litviDD~yD~yGtleEl~~ft~ 314 (363)
.||+|++++++||+++|+....+++|.+..++|+|+++++|+|+.+..|+++||.++++.++||.||.+|+.+|+..+++
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 49999999999999999976666999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhcccccccCCChHHHHHHHHHHHHHHHHHHHHHhccCCccch
Q 040042 315 SVERWDVSAMDQHPYYLKFCFLALHNFIMKLLLTLSKKKKLTSFV 359 (363)
Q Consensus 315 aveRWD~~~~~~Lpeymk~~f~aL~~~~~ei~~~~~~~~g~~~~~ 359 (363)
+++||+...++.+|++++.++.+++++.++++..+.+.+|+....
T Consensus 81 ~~~~~~~~~~~~~p~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~ 125 (284)
T cd00868 81 AVERWDISAIDELPEYMKPVFKALYDLVNEIEEELAKEGGSESLP 125 (284)
T ss_pred HHHhcChhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCchHHH
Confidence 999999999999999999999999999999999999877755433
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=98.13 E-value=2.3e-06 Score=82.50 Aligned_cols=107 Identities=13% Similarity=-0.008 Sum_probs=84.9
Q ss_pred HHHHHHHHhccCCCCccccchhhHHHHHHhhcccCCCchhhhHhHH-hHHHHHhhhhhhhccc-CCHHHHHHHHHHhhhc
Q 040042 242 SVSEWWEYVGFGNKLNFARDRLMENFLWTVGVTSEPQFGYFRRMST-KVSALITSIDDAYDVY-GTLDELKLFTNSVERW 319 (363)
Q Consensus 242 ~lsrWw~~~~l~~~L~faRdr~ve~yfwa~~~~fEP~~s~~Ri~~a-K~~~litviDD~yD~y-GtleEl~~ft~aveRW 319 (363)
+...|.++.|+ -.-+.+|++.++++|+.++.++.|+.+..|+.++ +.++++.++||.||.. ++.+++..+++.+.+|
T Consensus 18 ~~~~w~~~~~l-~~~~~~~~~~~~~~~~~~~a~~~P~a~~~~l~l~~~~~~w~f~~DD~~D~~~~~~~~~~~~~~~~~~~ 96 (303)
T cd00687 18 EYLEWVLEEML-IPSEKAEKRFLSADFGDLAALFYPDADDERLMLAADLMAWLFVFDDLLDRDQKSPEDGEAGVTRLLDI 96 (303)
T ss_pred HHHHHHHHcCC-CCcchhHHHHhcCCHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhcccCCccccCHHHHHHHHHHHHhc
Confidence 36679888866 2445899999999999999999999999999555 9999999999999997 5999999999988887
Q ss_pred ccccccCCChHHHHHHHHHHHHHHHHHHHH
Q 040042 320 DVSAMDQHPYYLKFCFLALHNFIMKLLLTL 349 (363)
Q Consensus 320 D~~~~~~Lpeymk~~f~aL~~~~~ei~~~~ 349 (363)
.......-|+....+..++.++.+.+...+
T Consensus 97 ~~~~~~~~~~~~~p~~~~~~d~~~r~~~~~ 126 (303)
T cd00687 97 LRGDGLDSPDDATPLEFGLADLWRRTLARM 126 (303)
T ss_pred cCCCCCCCCCCCCHHHHHHHHHHHHhccCC
Confidence 664322114666777777777777665544
No 8
>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1. Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoter
Probab=96.41 E-value=0.0023 Score=57.03 Aligned_cols=74 Identities=26% Similarity=0.165 Sum_probs=56.6
Q ss_pred HHhhcccCCCchhhhHhHHhHHHHHhhhhhhhcccCCHHHHHHHHHHhhhcccccccCCChHHHHHHHHHHHHHHHHHHH
Q 040042 269 WTVGVTSEPQFGYFRRMSTKVSALITSIDDAYDVYGTLDELKLFTNSVERWDVSAMDQHPYYLKFCFLALHNFIMKLLLT 348 (363)
Q Consensus 269 wa~~~~fEP~~s~~Ri~~aK~~~litviDD~yD~yGtleEl~~ft~aveRWD~~~~~~Lpeymk~~f~aL~~~~~ei~~~ 348 (363)
|+++++++|+++..|..+++..++..++||++|..++..+.......+ .....|.++...+..+...++++...
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~DDi~D~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (243)
T cd00385 2 RPLAVLLEPEASRLRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAV------AIDGLPEAILAGDLLLADAFEELARE 75 (243)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCchhhhhhH------HhcCchHHHHHHHHHHHHHHHHHHhC
Confidence 567889999999999999999999999999999998877766554443 23445666666666666666666543
No 9
>PF14165 YtzH: YtzH-like protein
Probab=51.72 E-value=33 Score=28.20 Aligned_cols=39 Identities=18% Similarity=0.148 Sum_probs=30.5
Q ss_pred hcccCCHHHHHHHHHHhhhcccccccCCChHHHHHHHHHHH
Q 040042 300 YDVYGTLDELKLFTNSVERWDVSAMDQHPYYLKFCFLALHN 340 (363)
Q Consensus 300 yD~yGtleEl~~ft~aveRWD~~~~~~Lpeymk~~f~aL~~ 340 (363)
-|.+||..|++.+...|+. +-+-+.++..+|-+..-+|+
T Consensus 19 ~DccgTvsEcEQieRLvks--Lm~n~~i~~~ik~~L~~Iy~ 57 (87)
T PF14165_consen 19 LDCCGTVSECEQIERLVKS--LMANPNIDADIKQTLEEIYS 57 (87)
T ss_pred hhccCcHHHHHHHHHHHHH--HHcCCCcCHHHHHHHHHHHH
Confidence 4789999999998888876 55556778888877776664
No 10
>cd07604 BAR_ASAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ASAPs (ArfGAP with SH3 domain, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) with similarity to ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins) in that they contain an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and ankyrin (ANK) repeats. However, ASAPs contain an additional C-terminal SH3 domain. ASAPs function in regulating cell growth, migration, and invasion. Vertebrates contain at least three members, ASAP1, ASAP2, and ASAP3. ASAP1 and ASAP2 shows GTPase activating protein (GAP) activity towards Arf1 and Arf5. They do not show GAP activity towards Arf6, but is able to mediate
Probab=27.43 E-value=1.2e+02 Score=28.66 Aligned_cols=91 Identities=16% Similarity=0.162 Sum_probs=55.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccCCccchhhHHHHHHhhCCccc--hHHHHHHHHHHHHhhCcccCCCChhHHHHHHHhh
Q 040042 42 KSYAKRIEELKADVRAMLDKAVVMDPLHQFELRDALQRLGVSYH--FGDEIKKLRNAIYRNNNLQKQESLYDVALEFRLL 119 (363)
Q Consensus 42 ~~~~~~~~~Lk~~Vk~~l~~~~~~d~~~~L~lID~LqRLGI~~h--Fe~EI~~~L~~iy~~~~~~~~~DL~~~AL~FRLL 119 (363)
+....++++++.-+|.|..+.. .=.-....+++.|+.||=..- -+.+|..+|.+.-.. +..++=.+-.|
T Consensus 12 ~~~~~~l~Kl~K~~k~~~~~g~-~~~~~~~~F~~aL~~~g~~~~~~~~~~i~~~l~kF~~~--------l~El~~~~~~L 82 (215)
T cd07604 12 EGDRVGLQKLKKAVKAIHNSGL-AHVENELQFAEALEKLGSKALSREEEDLGAAFLKFSVF--------TKELAALFKNL 82 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHhHH-HHHHHHHHHHHHHHHHhccccCcccHHHHHHHHHHHHH--------HHHHHHHHHHH
Confidence 3456778888888888886531 123457889999999993221 233577777543221 33445556667
Q ss_pred hhcCCccccccccccccc-cchHHH
Q 040042 120 RQHGYDTATTASIQLKFF-DDWKGI 143 (363)
Q Consensus 120 R~hGy~VSs~~DvF~~F~-~dv~gl 143 (363)
++|=-++-. ..+.+|. .|+++.
T Consensus 83 ~~~~~~~i~--~pL~~f~k~dL~~~ 105 (215)
T cd07604 83 MQNLNNIIM--FPLDSLLKGDLKGS 105 (215)
T ss_pred HHHHHHHHH--HHHHHHHHHHhHHH
Confidence 776555555 5677776 445443
No 11
>PRK09177 xanthine-guanine phosphoribosyltransferase; Validated
Probab=24.86 E-value=18 Score=32.22 Aligned_cols=23 Identities=22% Similarity=0.260 Sum_probs=18.9
Q ss_pred HhhhhhhhcccCCHHHHHHHHHH
Q 040042 293 ITSIDDAYDVYGTLDELKLFTNS 315 (363)
Q Consensus 293 itviDD~yD~yGtleEl~~ft~a 315 (363)
+.++||+.|.++|+.++..+...
T Consensus 87 VLIVDDIiDTG~Tl~~v~~~l~~ 109 (156)
T PRK09177 87 FLVVDDLVDTGGTARAVREMYPK 109 (156)
T ss_pred EEEEeeeeCCHHHHHHHHHHHhh
Confidence 45699999999999998876543
No 12
>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.75 E-value=55 Score=31.01 Aligned_cols=35 Identities=23% Similarity=0.541 Sum_probs=23.7
Q ss_pred hHHHHHHHHHHHHHhccCCCCccccchhhHHHHHHhhcccCCCc
Q 040042 236 HQEDLESVSEWWEYVGFGNKLNFARDRLMENFLWTVGVTSEPQF 279 (363)
Q Consensus 236 hq~EL~~lsrWw~~~~l~~~L~faRdr~ve~yfwa~~~~fEP~~ 279 (363)
-|+|+..|.+||+++|-. ++-...-++|.+|.=+|
T Consensus 7 E~qql~~ik~wwkeNGk~---------li~gviLg~~~lfGW~y 41 (207)
T COG2976 7 EQQQLEAIKDWWKENGKA---------LIVGVILGLGGLFGWRY 41 (207)
T ss_pred HHHHHHHHHHHHHHCCch---------hHHHHHHHHHHHHHHHH
Confidence 378999999999999952 23334455555665544
No 13
>COG5123 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=22.81 E-value=44 Score=28.29 Aligned_cols=42 Identities=14% Similarity=0.135 Sum_probs=27.8
Q ss_pred hHHHHHHHHhhcCCCCCchHHHHHHHHHHHHHHHHHhcCCCchHHHHHHHhc
Q 040042 140 WKGILSMYEAAYLLVEGENIFYEIRNFTTTYLKEYIKHNKDPYILTLVNHAL 191 (363)
Q Consensus 140 v~glLsLYeAS~l~~~gE~iLdeA~~Ft~~~L~~~~~~~~~~~L~~~V~~aL 191 (363)
+.|+.+|||-|-++--=|++||+-++ .+.++|+|+..|-...
T Consensus 1 v~~yYElYRrs~ig~~L~dalD~lis----------~g~isp~lam~vLetF 42 (113)
T COG5123 1 VPGYYELYRRSMIGKVLEDALDELIS----------AGVISPNLAMHVLETF 42 (113)
T ss_pred CccHHHHHHHHHHHHHHHHHHHHHHh----------cCCcCHHHHHHHHHHh
Confidence 35899999999887655677776442 1355666766654443
No 14
>PF00156 Pribosyltran: Phosphoribosyl transferase domain; InterPro: IPR000836 The name PRT comes from phosphoribosyltransferase (PRTase) enzymes, which carry out phosphoryl transfer reactions on 5-phosphoribosyl-alpha1-pyrophosphate PRPP, an activated form of ribose-5-phosphate. Members of Phosphoribosyltransferase (PRT) are catalytic and are regulatory proteins involved in nucleotide synthesis and salvage []. This includes a range of diverse phosphoribosyl transferase enzymes including adenine phosphoribosyltransferase (2.4.2.7 from EC); hypoxanthine-guanine-xanthine phosphoribosyltransferase; hypoxanthine phosphoribosyltransferase (2.4.2.8 from EC); ribose-phosphate pyrophosphokinase (2.7.6.1 from EC); amidophosphoribosyltransferase (2.4.2.14 from EC); orotate phosphoribosyltransferase (2.4.2.10 from EC);uracil phosphoribosyltransferase (2.4.2.9 from EC); and xanthine-guanine phosphoribosyltransferase (2.4.2.22 from EC). Not all PRT proteins are enzymes. For example, in some bacteria PRT proteins regulate the expression of purine and pyrimidine synthetic genes. Members of PRT are defined by the protein fold and by a short 13-residue sequence motif, The motif consists of four hydrophobic amino acids, two acidic amino acids and seven amino acids of variable character, usually including glycine and threonine. The motif has been predicted to be a PRPP-binding site in advance of structural information [, ]. Apart of this motif, different PRT proteins have a low level of sequence identity, less than 15%. The PRT sequence motif is only found in PRTases from the nucleotide synthesis and salvage pathways. Other PRTases, from the tryptophan, histidine and nicotinamide synthetic and salvage pathways, lack the PRT sequence motif and appear to be unrelated to each other and unrelated to the PRT family.; GO: 0009116 nucleoside metabolic process; PDB: 2JBH_A 1Y0B_D 2FXV_B 1GPH_1 1AO0_D 1ORO_B 1VCH_C 2WNS_A 2PRZ_B 2PS1_A ....
Probab=21.78 E-value=22 Score=29.16 Aligned_cols=21 Identities=33% Similarity=0.389 Sum_probs=16.6
Q ss_pred HhhhhhhhcccCCHHHHHHHH
Q 040042 293 ITSIDDAYDVYGTLDELKLFT 313 (363)
Q Consensus 293 itviDD~yD~yGtleEl~~ft 313 (363)
+.++||++|.++|+.++..+.
T Consensus 91 vliVDDvi~tG~Tl~~~~~~L 111 (125)
T PF00156_consen 91 VLIVDDVIDTGGTLKEAIELL 111 (125)
T ss_dssp EEEEEEEESSSHHHHHHHHHH
T ss_pred EEEEeeeEcccHHHHHHHHHH
Confidence 356999999999998875543
No 15
>PF12626 PolyA_pol_arg_C: Polymerase A arginine-rich C-terminus; PDB: 3AQN_A 3AQK_A 3AQM_B 3AQL_B.
Probab=21.06 E-value=1.1e+02 Score=26.47 Aligned_cols=28 Identities=32% Similarity=0.674 Sum_probs=23.8
Q ss_pred HHhhhHHHHHhhHHHHHHHHHHHHHhcc
Q 040042 225 AKLDFNMVQAKHQEDLESVSEWWEYVGF 252 (363)
Q Consensus 225 AKlDFn~~Q~~hq~EL~~lsrWw~~~~l 252 (363)
|-.||=.|.+.--+++.++..||.+.--
T Consensus 65 AAyDFL~LR~~~ge~~~~l~~WW~~fq~ 92 (124)
T PF12626_consen 65 AAYDFLLLRAEAGEELSELAEWWTEFQE 92 (124)
T ss_dssp HHHHHHHHHHHH-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHhCCCcHHHHHHHHHHHh
Confidence 6789999888889999999999999754
No 16
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=20.62 E-value=1.9e+02 Score=25.24 Aligned_cols=53 Identities=17% Similarity=0.303 Sum_probs=32.8
Q ss_pred hhHHHHHHhhCCccchHHHHHHHHHHHHhhCccc-------CCCChhHHHHHHHhhhhcCCcccc
Q 040042 71 FELRDALQRLGVSYHFGDEIKKLRNAIYRNNNLQ-------KQESLYDVALEFRLLRQHGYDTAT 128 (363)
Q Consensus 71 L~lID~LqRLGI~~hFe~EI~~~L~~iy~~~~~~-------~~~DL~~~AL~FRLLR~hGy~VSs 128 (363)
-.+|+.|++|||++.- -.+|-.+-.+.+-. ..--=-.+|++-|.||.+| +|--
T Consensus 14 ~~~ie~L~~lgi~R~v----A~tlv~L~~~~E~sS~~IE~~sgLRQPEVSiAMr~Lre~g-WV~~ 73 (124)
T COG4738 14 YEIIELLRILGIPRNV----ATTLVCLAKGDEASSREIERVSGLRQPEVSIAMRYLRENG-WVDE 73 (124)
T ss_pred HHHHHHHHHcCCCchH----HHHHHHHhcCcchhhhhhHHhhcCCCchhHHHHHHHHHcc-ccch
Confidence 4689999999999874 23333333322100 0111235899999999999 4543
No 17
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=20.32 E-value=4.4e+02 Score=20.82 Aligned_cols=59 Identities=14% Similarity=0.193 Sum_probs=35.1
Q ss_pred CCccchhhHHHHHHhhCCccchHHHHHHHHHHHHhhCcccCCCChhH--HHHHHHhhhhcCCcccc
Q 040042 65 MDPLHQFELRDALQRLGVSYHFGDEIKKLRNAIYRNNNLQKQESLYD--VALEFRLLRQHGYDTAT 128 (363)
Q Consensus 65 ~d~~~~L~lID~LqRLGI~~hFe~EI~~~L~~iy~~~~~~~~~DL~~--~AL~FRLLR~hGy~VSs 128 (363)
+..+..-.+...+.++|++ ++|+++++..+-...+ ..-|... .++..---.+.|+.+++
T Consensus 24 ~G~Is~~el~~~l~~~~~~---~~ev~~i~~~~d~~~~--g~I~~~eF~~~~~~~~~~~~g~~~~~ 84 (96)
T smart00027 24 DGTVTGAQAKPILLKSGLP---QTLLAKIWNLADIDND--GELDKDEFALAMHLIYRKLNGYPIPA 84 (96)
T ss_pred CCeEeHHHHHHHHHHcCCC---HHHHHHHHHHhcCCCC--CCcCHHHHHHHHHHHHHHHcCCCCCc
Confidence 3456666778888888875 4677777654321111 1124433 34444445567999988
Done!