Query 043754
Match_columns 320
No_of_seqs 195 out of 850
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 08:02:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043754.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043754hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02279 ent-kaur-16-ene synth 100.0 1.1E-88 2.4E-93 684.9 30.6 316 1-320 460-780 (784)
2 cd00684 Terpene_cyclase_plant_ 100.0 1.6E-86 3.5E-91 656.7 33.8 315 1-315 226-542 (542)
3 PLN02592 ent-copalyl diphospha 100.0 3.7E-64 7.9E-69 504.9 26.2 276 1-317 508-800 (800)
4 cd00868 Terpene_cyclase_C1 Ter 100.0 9.3E-50 2E-54 365.4 30.3 282 10-292 1-284 (284)
5 PF03936 Terpene_synth_C: Terp 100.0 1.9E-50 4.2E-55 367.3 19.8 264 1-264 6-270 (270)
6 cd00687 Terpene_cyclase_nonpla 100.0 4.7E-37 1E-41 284.4 20.2 252 11-269 11-267 (303)
7 PLN02150 terpene synthase/cycl 100.0 8.2E-32 1.8E-36 205.8 10.6 94 225-318 1-96 (96)
8 cd00385 Isoprenoid_Biosyn_C1 I 99.9 2.5E-22 5.4E-27 177.1 12.8 229 44-286 2-243 (243)
9 PF06330 TRI5: Trichodiene syn 98.1 0.00015 3.3E-09 67.9 16.3 193 52-266 79-276 (376)
10 cd00686 Terpene_cyclase_cis_tr 98.1 7.5E-05 1.6E-09 68.9 13.6 211 37-270 62-279 (357)
11 PF00494 SQS_PSY: Squalene/phy 95.9 1.2 2.5E-05 40.3 18.1 178 40-249 6-191 (267)
12 cd00867 Trans_IPPS Trans-Isopr 93.0 2.4 5.3E-05 37.3 12.6 117 133-265 87-214 (236)
13 cd00685 Trans_IPPS_HT Trans-Is 91.6 7 0.00015 35.2 13.9 89 131-223 108-196 (259)
14 TIGR03465 HpnD squalene syntha 90.4 13 0.00029 33.5 20.4 210 40-285 6-227 (266)
15 cd00683 Trans_IPPS_HH Trans-Is 88.2 19 0.00042 32.4 17.9 209 41-286 13-237 (265)
16 TIGR03464 HpnC squalene syntha 85.6 27 0.00059 31.5 20.1 121 40-185 6-130 (266)
17 TIGR02749 prenyl_cyano solanes 83.4 39 0.00085 31.6 16.2 87 132-222 134-220 (322)
18 COG0142 IspA Geranylgeranyl py 82.9 41 0.0009 31.4 14.0 108 132-244 135-252 (322)
19 PLN02890 geranyl diphosphate s 81.1 57 0.0012 31.8 14.8 90 131-224 227-316 (422)
20 KOG1719 Dual specificity phosp 74.9 2.7 5.8E-05 34.9 2.6 29 226-254 119-148 (183)
21 PLN02632 phytoene synthase 74.7 76 0.0016 29.8 18.9 108 56-185 73-184 (334)
22 PLN02857 octaprenyl-diphosphat 74.1 90 0.002 30.4 15.2 88 132-223 228-315 (416)
23 TIGR02748 GerC3_HepT heptapren 66.2 1.1E+02 0.0025 28.4 16.1 86 132-222 130-216 (319)
24 COG3707 AmiR Response regulato 64.7 6.3 0.00014 33.9 2.8 47 211-257 127-174 (194)
25 PF03861 ANTAR: ANTAR domain; 64.3 7.8 0.00017 26.1 2.7 28 230-257 15-42 (56)
26 PF12368 DUF3650: Protein of u 60.0 7.8 0.00017 22.4 1.7 18 236-253 9-26 (28)
27 PRK10888 octaprenyl diphosphat 56.5 1.7E+02 0.0037 27.3 16.7 87 132-223 131-218 (323)
28 PRK10581 geranyltranstransfera 54.8 1.5E+02 0.0033 27.3 10.5 111 142-265 153-276 (299)
29 smart00400 ZnF_CHCC zinc finge 44.1 29 0.00062 23.2 2.9 25 228-252 30-54 (55)
30 CHL00151 preA prenyl transfera 43.2 2.8E+02 0.006 25.8 16.0 86 132-223 135-222 (323)
31 COG1093 SUI2 Translation initi 39.1 62 0.0013 29.3 4.9 67 218-287 94-170 (269)
32 smart00463 SMR Small MutS-rela 38.5 43 0.00093 24.0 3.3 24 241-264 7-30 (80)
33 PHA01082 putative transcriptio 35.9 67 0.0014 25.5 4.1 43 240-287 28-71 (133)
34 COG1308 EGD2 Transcription fac 35.1 43 0.00094 26.6 3.0 20 234-253 88-107 (122)
35 PF01713 Smr: Smr domain; Int 34.4 53 0.0011 23.7 3.3 27 241-267 4-30 (83)
36 PF10776 DUF2600: Protein of u 34.4 4E+02 0.0087 25.1 17.4 100 181-297 197-296 (330)
37 PF00348 polyprenyl_synt: Poly 34.3 3.4E+02 0.0073 24.2 10.7 66 156-224 129-194 (260)
38 COG1562 ERG9 Phytoene/squalene 31.6 4.1E+02 0.009 24.4 9.6 114 56-185 34-147 (288)
39 PF03701 UPF0181: Uncharacteri 31.5 1.1E+02 0.0023 20.4 3.8 44 216-261 3-46 (51)
40 PF06603 UpxZ: UpxZ family of 30.8 1E+02 0.0022 23.8 4.2 70 202-280 25-98 (106)
41 TIGR03486 cas_csx13_C CRISPR-a 30.6 3.1E+02 0.0068 22.7 8.6 14 153-166 112-125 (152)
42 PTZ00393 protein tyrosine phos 30.4 50 0.0011 29.5 3.0 27 228-254 182-208 (241)
43 PF11050 Viral_env_E26: Virus 30.3 48 0.001 28.1 2.6 24 1-24 57-80 (206)
44 KOG3730 Acyl-CoA:dihydroxyacte 30.1 3.5E+02 0.0075 26.9 8.6 68 230-309 77-145 (685)
45 PF13189 Cytidylate_kin2: Cyti 29.9 17 0.00038 30.6 -0.0 35 234-269 128-162 (179)
46 KOG2077 JNK/SAPK-associated pr 29.9 1.2E+02 0.0025 30.7 5.5 98 185-288 298-405 (832)
47 PRK06369 nac nascent polypepti 26.4 70 0.0015 25.2 2.8 27 228-254 74-100 (115)
48 PF01807 zf-CHC2: CHC2 zinc fi 26.4 70 0.0015 24.1 2.8 30 228-257 61-90 (97)
49 PF10281 Ish1: Putative stress 25.9 78 0.0017 19.3 2.5 25 16-40 7-32 (38)
50 PF05772 NinB: NinB protein; 25.7 31 0.00068 27.7 0.8 53 113-169 43-96 (127)
51 TIGR00264 alpha-NAC-related pr 25.1 78 0.0017 25.0 2.8 23 231-253 79-101 (116)
52 COG5095 TAF6 Transcription ini 22.2 2.7E+02 0.0059 26.1 6.1 123 167-293 220-349 (450)
53 COG1191 FliA DNA-directed RNA 21.7 5.9E+02 0.013 22.9 11.4 67 11-98 7-73 (247)
54 KOG4098 Molecular chaperone Pr 21.6 3.1E+02 0.0067 22.2 5.6 63 46-119 8-74 (140)
55 PHA03253 UL35; Provisional 20.8 4.2E+02 0.0091 26.7 7.4 21 4-24 247-267 (609)
56 COG2443 Sss1 Preprotein transl 20.5 3.2E+02 0.0068 19.2 6.0 22 157-178 25-46 (65)
57 COG2976 Uncharacterized protei 20.1 80 0.0017 27.5 2.2 17 11-27 7-23 (207)
58 PRK05114 hypothetical protein; 20.1 1.9E+02 0.0041 19.8 3.5 44 216-261 3-46 (59)
No 1
>PLN02279 ent-kaur-16-ene synthase
Probab=100.00 E-value=1.1e-88 Score=684.85 Aligned_cols=316 Identities=24% Similarity=0.392 Sum_probs=302.8
Q ss_pred CcchHHhHHHHHHHHHHHHHHhhhcCCCCCchhhhhhhhhhHHHHhccccCCCchhHHHHHHHHHHHHHHHHhhhhccCC
Q 043754 1 MLDFNILQKQHQEELRDIVRWWKNFDVPNKLPFIRDRVVEGYFWILGVYFEPKFLLARKILTKVISMASIIDDIYDAYGT 80 (320)
Q Consensus 1 kldfn~~Q~~hq~El~~l~~W~~~~~l~~~l~~~R~r~~~~y~~~~a~~feP~~s~~Rl~~ak~~~l~~~iDD~~D~~~t 80 (320)
|+|||+||++||+||++++|||+++|| +++||+|+|+++||||++|++|||++|.+|++|||.++|++++||+||.|||
T Consensus 460 klDFN~~Qs~hq~EL~~l~rWwke~~L-~~L~faRdr~ve~Yf~aaa~~fEPe~S~aRi~~aK~~~L~tviDD~fD~yGt 538 (784)
T PLN02279 460 VEDFNFCQSIHREELKQLERWIVENRL-DKLKFARQKLAYCYFSAAATLFSPELSDARLSWAKNGVLTTVVDDFFDVGGS 538 (784)
T ss_pred HHHHHHHHHHHHHHHHHhCeeHHhcCC-ccCCchhhHHHHHHHHHHHhhcCchhhHHHHHHHHHHHHHHHHHHHhhccCC
Confidence 789999999999999999999999999 7999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcchh-hcccCchhHHHHHHHHHHHHHHHHHHHHhcCCcccHhhHHHHHHHHHHHHHHHHHHhhCCCC
Q 043754 81 IEELELFATAIERWDLS-AIDLLPEYIKLCYCALLDAYSEFEKDLASKGILYGLPFAKESMKILVRSYIIEARWCDQQYV 159 (320)
Q Consensus 81 ~~el~~~~~ai~rwd~~-~~~~lp~~~~~~~~~l~~~~~e~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~ 159 (320)
.||++.||+||+|||.+ .++.+|+|||+||.++++++++++.++.+.+|.++.++++++|++++++|++||+|+++|++
T Consensus 539 ~eEL~~ft~aVeRWD~~~~~~~lpeymki~f~aL~~t~nei~~~~~~~qGr~v~~~l~~aW~~ll~ayl~EAeW~~~g~v 618 (784)
T PLN02279 539 EEELENLIQLVEKWDVNGSPDFCSEQVEIIFSALRSTISEIGDKAFTWQGRNVTSHIIKIWLDLLKSMLTEAQWSSNKST 618 (784)
T ss_pred HHHHHHHHHHHHHhccccchhhCcHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 99999999999999998 56899999999999999999999988654444488999999999999999999999999999
Q ss_pred CChHHHHhhhhhhhhhhHHHHHHHhcCCCCCCHHHHhhccCchHHHHHHHhHHHHhcCccchHHhhhcCCcchhHHHHHh
Q 043754 160 PTMEEYMRVALLSCGYLLLSTSSFLGMEDIVTKEAFEWVSGNPKIVQASSIICRLMDDIVSHKFEQQRGHVASAVECYMK 239 (320)
Q Consensus 160 Pt~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~V~~ym~ 239 (320)
||+||||+|+.+|+|+.+++..+.+++|..+|+++++| +++|+|+++++.++||+|||+||++|+++|++ |+|+|||+
T Consensus 619 PT~eEYL~na~vS~~l~~i~l~~~~~~G~~l~eev~e~-~~~~~L~~l~s~I~RLlNDI~S~e~E~~rG~~-nsV~cYMk 696 (784)
T PLN02279 619 PTLDEYMTNAYVSFALGPIVLPALYLVGPKLSEEVVDS-PELHKLYKLMSTCGRLLNDIRGFKRESKEGKL-NAVSLHMI 696 (784)
T ss_pred CCHHHHHhhchhhhhhHHHHHHHHHHhCCCCCHHHHhC-cchhHHHHHHHHHHHHHHhccccHhHHhCCCc-ceehhhhc
Confidence 99999999999999999998888999999999999999 79999999999999999999999999999998 99999999
Q ss_pred hC--CCCHHHHHHHHHHHHHHHHHHHHHhhcCC--CCCCHHHHHHHHHHHhhhhhhcccCCCCCCchhHHHHHHHhhhcc
Q 043754 240 QH--GVSEEEAVKVFREKVGNAWKDINEELMRP--PVVPMPLLERVLNLARLMDVLYQNNDSYTNPHLMKDHVAALLKDP 315 (320)
Q Consensus 240 e~--g~s~eeA~~~i~~~i~~~~k~l~~~~~~~--~~~p~~~~~~~~n~~r~~~~~Y~~~D~~~~~~~~~~~i~~~l~~p 315 (320)
|+ |+|+|||+++++++|+++||+||++++++ +.+|++|+++|+|++|++++||+++||||.+ .||++|++||++|
T Consensus 697 e~~~gvSeEEAi~~i~~~Ie~~wKeLn~~~l~~~~~~vp~~~~~~~ln~aR~~~~~Y~~~Dgyt~~-~~k~~i~~ll~eP 775 (784)
T PLN02279 697 HGNGNSTEEEAIESMKGLIESQRRELLRLVLQEKGSNVPRECKDLFWKMSKVLHLFYRKDDGFTSN-DMMSLVKSVIYEP 775 (784)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHhhhhheeCCCCCChH-HHHHHHHHHhccC
Confidence 86 89999999999999999999999999973 5799999999999999999999999999975 7999999999999
Q ss_pred ccCCC
Q 043754 316 VFFED 320 (320)
Q Consensus 316 ~~~~~ 320 (320)
||+.+
T Consensus 776 i~l~~ 780 (784)
T PLN02279 776 VSLQE 780 (784)
T ss_pred CcCCc
Confidence 99753
No 2
>cd00684 Terpene_cyclase_plant_C1 Plant Terpene Cyclases, Class 1. This CD includes a diverse group of monomeric plant terpene cyclases (Tspa-Tspf) that convert the acyclic isoprenoid diphosphates, geranyl diphosphate (GPP), farnesyl diphosphate (FPP), or geranylgeranyl diphosphate (GGPP) into cyclic monoterpenes, diterpenes, or sesquiterpenes, respectively; a few form acyclic species. Terpnoid cyclases are soluble enzymes localized to the cytosol (sesquiterpene synthases) or plastids (mono- and diterpene synthases). All monoterpene and diterpene synthases have restrict substrate specificity, however, some sesquiterpene synthases can accept both FPP and GPP. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl diphosphates, via bridging Mg2+ ions (K+ preferred by gymnosperm cyclases), inducing conformational changes such that an N-terminal regi
Probab=100.00 E-value=1.6e-86 Score=656.71 Aligned_cols=315 Identities=54% Similarity=0.965 Sum_probs=308.4
Q ss_pred CcchHHhHHHHHHHHHHHHHHhhhcCCCCCchhhhhhhhhhHHHHhccccCCCchhHHHHHHHHHHHHHHHHhhhhccCC
Q 043754 1 MLDFNILQKQHQEELRDIVRWWKNFDVPNKLPFIRDRVVEGYFWILGVYFEPKFLLARKILTKVISMASIIDDIYDAYGT 80 (320)
Q Consensus 1 kldfn~~Q~~hq~El~~l~~W~~~~~l~~~l~~~R~r~~~~y~~~~a~~feP~~s~~Rl~~ak~~~l~~~iDD~~D~~~t 80 (320)
|+|||+||++||+||+++++||+++||.+++||+|+|+++||||++|++|||++|.+|+++||+++|++++||+||.|||
T Consensus 226 kldfn~~Q~~hq~El~~~~rWwk~~gL~~~l~~aRdr~ve~yf~~~a~~feP~~s~~Rl~~aK~~~l~~~iDD~fD~~gt 305 (542)
T cd00684 226 KLDFNILQALHQEELKILSRWWKDLDLASKLPFARDRLVECYFWAAGTYFEPQYSLARIALAKTIALITVIDDTYDVYGT 305 (542)
T ss_pred HHHHHHHhHhHHHHHHHHhHHHHhcCCcccCCcccchhHHHHHHHHhcccCccchHHHHHHHHHHHHHhhhHhhhccCCC
Confidence 79999999999999999999999999987779999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcchhhcccCchhHHHHHHHHHHHHHHHHHHHHhcCCcccHhhHHHHHHHHHHHHHHHHHHhhCCCCC
Q 043754 81 IEELELFATAIERWDLSAIDLLPEYIKLCYCALLDAYSEFEKDLASKGILYGLPFAKESMKILVRSYIIEARWCDQQYVP 160 (320)
Q Consensus 81 ~~el~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~~~~e~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~P 160 (320)
.+|++.||++++|||.++++.+|+|||++|.++++++++++.++.++++.++..+++++|++++++|++||+|+++|++|
T Consensus 306 ~eEl~~ft~ai~rwd~~~~~~lPe~mk~~~~al~~~~~ei~~~~~~~~~~~~~~~~~~~~~~~~~a~l~EA~w~~~g~vP 385 (542)
T cd00684 306 LEELELFTEAVERWDISAIDQLPEYMKIVFKALLNTVNEIEEELLKEGGSYVVPYLKEAWKDLVKAYLVEAKWAHEGYVP 385 (542)
T ss_pred HHHHHHHHHHHHhccccchhhccHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 99999999999999999999999999999999999999999999888888899999999999999999999999999999
Q ss_pred ChHHHHhhhhhhhhhhHHHHHHHhcCCCCCCHHHHhhccCchHHHHHHHhHHHHhcCccchHHhhhcCCcchhHHHHHhh
Q 043754 161 TMEEYMRVALLSCGYLLLSTSSFLGMEDIVTKEAFEWVSGNPKIVQASSIICRLMDDIVSHKFEQQRGHVASAVECYMKQ 240 (320)
Q Consensus 161 t~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~V~~ym~e 240 (320)
|++||+++|.+|+|++++++++++++|..+|+++++|+..+|++++.++.++||+|||.||++|+++|+++|+|.|||+|
T Consensus 386 t~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~e~~e~~~~~~~l~~~~~~i~rL~NDi~S~~kE~~rGdv~n~V~~ymke 465 (542)
T cd00684 386 TFEEYMENALVSIGLGPLLLTSFLGMGDILTEEAFEWLESRPKLVRASSTIGRLMNDIATYEDEMKRGDVASSIECYMKE 465 (542)
T ss_pred CHHHHHhhhhHHhhHHHHHHHHHHhcCCCCCHHHHHHHhccHHHHHHHHHHHHHhcChhhhHHHHhcCCcccHHHHHHHh
Confidence 99999999999999999999999999999999999997777999999999999999999999999999999999999999
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHhhcCC-CCCCHHHHHHHHHHHhhhhhhcccCCCCCCc-hhHHHHHHHhhhcc
Q 043754 241 HGVSEEEAVKVFREKVGNAWKDINEELMRP-PVVPMPLLERVLNLARLMDVLYQNNDSYTNP-HLMKDHVAALLKDP 315 (320)
Q Consensus 241 ~g~s~eeA~~~i~~~i~~~~k~l~~~~~~~-~~~p~~~~~~~~n~~r~~~~~Y~~~D~~~~~-~~~~~~i~~~l~~p 315 (320)
+|+|+|+|+++++++|+++||++|++++++ +++|++|+++++|++|+++++|+++||||.| +.||+||++|||+|
T Consensus 466 ~g~s~eeA~~~i~~~ie~~wk~ln~e~l~~~~~~p~~~~~~~~n~~r~~~~~Y~~~D~~t~~~~~~~~~i~~ll~~p 542 (542)
T cd00684 466 YGVSEEEAREEIKKMIEDAWKELNEEFLKPSSDVPRPIKQRFLNLARVIDVFYKEGDGFTHPEGEIKDHITSLLFEP 542 (542)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCccHHHHHHHHHHhcCC
Confidence 999999999999999999999999999997 7899999999999999999999999999999 78999999999998
No 3
>PLN02592 ent-copalyl diphosphate synthase
Probab=100.00 E-value=3.7e-64 Score=504.89 Aligned_cols=276 Identities=15% Similarity=0.187 Sum_probs=249.9
Q ss_pred CcchHHhHHHHHHHHHHHHHHhhhcCCCCCchhhhhhhhhhHHHHhccccCCCchhHHHHHHHHHHHHHHHHhhhhccCC
Q 043754 1 MLDFNILQKQHQEELRDIVRWWKNFDVPNKLPFIRDRVVEGYFWILGVYFEPKFLLARKILTKVISMASIIDDIYDAYGT 80 (320)
Q Consensus 1 kldfn~~Q~~hq~El~~l~~W~~~~~l~~~l~~~R~r~~~~y~~~~a~~feP~~s~~Rl~~ak~~~l~~~iDD~~D~~~t 80 (320)
|+|||+||++||+||++++|||+++|| .++||+|+|+++||||++|++|||++|.+|++|||.++|++++||+||.|||
T Consensus 508 klDFn~~Qs~hq~EL~~lsrWwke~~L-~~L~faRdr~ve~Yfwa~~~~feP~~s~~Ri~~aK~~~LitviDD~fD~yGt 586 (800)
T PLN02592 508 KLDYNNCQALHQLEWDNFQKWYEECNL-GEFGVSRSELLLAYFLAAASIFEPERSHERLAWAKTTVLVEAISSYFNKETS 586 (800)
T ss_pred HHHHHHHHHHhHHHHHHHhHHHHhcCC-CcCCcchhHHHHHHHHHHHhhcCccchHHHHHHHHHHHHHHhhcccccCCCC
Confidence 789999999999999999999999999 6999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHH--------hcchhhcccCch------hHHHHHHHHHHHHHHHHHHHHhcCCcccHhhHHHHHHHHHHH
Q 043754 81 IEELELFATAIE--------RWDLSAIDLLPE------YIKLCYCALLDAYSEFEKDLASKGILYGLPFAKESMKILVRS 146 (320)
Q Consensus 81 ~~el~~~~~ai~--------rwd~~~~~~lp~------~~~~~~~~l~~~~~e~~~~~~~~~~~~~~~~l~~~w~~~~~~ 146 (320)
+||++.||++|+ |||.++.++||+ |||+||.++++++|+++.++.+.+|.++.++++++|.+|++
T Consensus 587 ~eEl~~ft~~v~~~~~~~~~rWd~~~~~~lp~~~~~~~~mki~f~aLy~tineia~~a~~~qGr~v~~~L~~~W~~l~~- 665 (800)
T PLN02592 587 SKQRRAFLHEFGYGYKINGRRSDHHFNDRNMRRSGSVKTGEELVGLLLGTLNQLSLDALEAHGRDISHLLRHAWEMWLL- 665 (800)
T ss_pred HHHHHHHHHHHHhcccccccccCchhhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHH-
Confidence 999999999997 899999999987 99999999999999999988887777899999999999999
Q ss_pred HHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHh-cCCCCCCHHHHhhccCchHHHHHHHhHHHHhcCccchHHhh
Q 043754 147 YIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFL-GMEDIVTKEAFEWVSGNPKIVQASSIICRLMDDIVSHKFEQ 225 (320)
Q Consensus 147 ~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~-~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~ 225 (320)
+|..+|+ .|+|...+++.+++ .+|..+|+++++ +|++.++++++.||+||++|+++|+
T Consensus 666 -----~w~~~g~------------~s~~~~~ilv~~~~l~~g~~lsee~l~----~~~~~~l~~li~Rl~nDl~t~~~e~ 724 (800)
T PLN02592 666 -----KWLLEGD------------GRQGEAELLVKTINLTAGRSLSEELLA----HPQYEQLAQLTNRICYQLGHYKKNK 724 (800)
T ss_pred -----HHHhcCc------------eeccchhhHHHHHHHhcCCCCCHHHcc----chhHHHHHHHHHHHHHhhhHHhhhc
Confidence 4666665 34466666666666 559999999865 6999999999999999999999988
Q ss_pred hcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhhcC-C-CCCCHHHHHHHHHHHhhhhhhcccCCCCCCchh
Q 043754 226 QRGHVASAVECYMKQHGVSEEEAVKVFREKVGNAWKDINEELMR-P-PVVPMPLLERVLNLARLMDVLYQNNDSYTNPHL 303 (320)
Q Consensus 226 ~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~~~~~-~-~~~p~~~~~~~~n~~r~~~~~Y~~~D~~~~~~~ 303 (320)
..| .++++ +|.+++.+.|+.++++|.++|++ . +.+|++||++||+++|++ ||. |||+|++
T Consensus 725 ~~~------------~~~~~-~a~~~~~~~ie~~~~eL~~lvl~~~~~~vp~~cK~~f~~~~k~f--y~~---~~~~~~~ 786 (800)
T PLN02592 725 VHI------------NTYNP-EEKSKTTPSIESDMQELVQLVLQNSSDDIDPVIKQTFLMVAKSF--YYA---AYCDPGT 786 (800)
T ss_pred ccC------------CcccH-HHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHH--HHh---hcCCHHH
Confidence 521 12455 89999999999999999999997 3 569999999999999966 677 9999999
Q ss_pred HHHHHHHhhhcccc
Q 043754 304 MKDHVAALLKDPVF 317 (320)
Q Consensus 304 ~~~~i~~~l~~p~~ 317 (320)
|++||++||||||+
T Consensus 787 ~~~~i~~vl~epv~ 800 (800)
T PLN02592 787 INYHIAKVLFERVA 800 (800)
T ss_pred HHHHHHHHhCCCCC
Confidence 99999999999985
No 4
>cd00868 Terpene_cyclase_C1 Terpene cyclases, Class 1. Terpene cyclases, Class 1 (C1) of the class 1 family of isoprenoid biosynthesis enzymes, which share the 'isoprenoid synthase fold' and convert linear, all-trans, isoprenoids, geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate into numerous cyclic forms of monoterpenes, diterpenes, and sesquiterpenes. Also included in this CD are the cis-trans terpene cyclases such as trichodiene synthase. The class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational ch
Probab=100.00 E-value=9.3e-50 Score=365.36 Aligned_cols=282 Identities=51% Similarity=0.865 Sum_probs=264.1
Q ss_pred HHHHHHHHHHHHhhhcCCCCCchhhhhhhhhhHHHHhccccCCCchhHHHHHHHHHHHHHHHHhhhhccCCHHHHHHHHH
Q 043754 10 QHQEELRDIVRWWKNFDVPNKLPFIRDRVVEGYFWILGVYFEPKFLLARKILTKVISMASIIDDIYDAYGTIEELELFAT 89 (320)
Q Consensus 10 ~hq~El~~l~~W~~~~~l~~~l~~~R~r~~~~y~~~~a~~feP~~s~~Rl~~ak~~~l~~~iDD~~D~~~t~~el~~~~~ 89 (320)
.||+|++++++|++++||....+++|.+...+|+|+++++|+|+.+..|+++||++.|+|++||+||.+++.+++..+++
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 49999999999999999965544999999999999999999999899999999999999999999999999999999999
Q ss_pred HHHhcchhhcccCchhHHHHHHHHHHHHHHHHHHHHhcCCcccHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhh
Q 043754 90 AIERWDLSAIDLLPEYIKLCYCALLDAYSEFEKDLASKGILYGLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVA 169 (320)
Q Consensus 90 ai~rwd~~~~~~lp~~~~~~~~~l~~~~~e~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~ 169 (320)
.++||+....+.+|+++++++.++.++++++...+.++++.....++++.|..|+.++.+|++|+.+|++||++||+.+|
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 99999988888899999999999999999999888776676779999999999999999999999999999999999999
Q ss_pred hhhhhhhHHHHHHHhcCCCCCCH-HHHhhccCchHHHHHHHhHHHHhcCccchHHhhhcCCcchhHHHHHhhCCCCHHHH
Q 043754 170 LLSCGYLLLSTSSFLGMEDIVTK-EAFEWVSGNPKIVQASSIICRLMDDIVSHKFEQQRGHVASAVECYMKQHGVSEEEA 248 (320)
Q Consensus 170 ~~s~g~~~~~~~~~~~~g~~l~~-e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~V~~ym~e~g~s~eeA 248 (320)
+.|+|+.+++.++++++|..+|+ ++.+. +..+++++.++.+++|+||+.||+||+..|+.+|+|.|||+++|+|.++|
T Consensus 161 ~~~~g~~~~~~l~~~~~g~~l~~~~~~~~-~~~~~l~~~~~~~~~l~NDl~S~~kE~~~g~~~N~v~vl~~~~~~~~~eA 239 (284)
T cd00868 161 RVSIGYPPLLALSFLGMGDILPEEAFEWL-PSYPKLVRASSTIGRLLNDIASYEKEIARGEVANSVECYMKEYGVSEEEA 239 (284)
T ss_pred eehhhHHHHHHHHHHHcCCCCCHHHHHHh-hhhHHHHHHHHHHHHHhccchHHHHHHccCCcccHHHHHHhccCCCHHHH
Confidence 99999999999999999999999 55554 88999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhcCC-CCCCHHHHHHHHHHHhhhhhhc
Q 043754 249 VKVFREKVGNAWKDINEELMRP-PVVPMPLLERVLNLARLMDVLY 292 (320)
Q Consensus 249 ~~~i~~~i~~~~k~l~~~~~~~-~~~p~~~~~~~~n~~r~~~~~Y 292 (320)
++++.+++++++++|++.+.+. ++.+..+++.+.+++|.....|
T Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~g~~~w~ 284 (284)
T cd00868 240 LEELRKMIEEAWKELNEEVLKLSSDVPRAVLETLLNLARGIYVWY 284 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhhhhcC
Confidence 9999999999999999999974 4678999999999999885544
No 5
>PF03936 Terpene_synth_C: Terpene synthase family, metal binding domain; InterPro: IPR005630 Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C10) synthases, sesquiterpene (C15) synthases and the diterpene (C20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf []. Tpsa includes vetispiridiene synthase Q39979 from SWISSPROT, 5-epi- aristolochene synthase, Q40577 from SWISSPROT and (+)-delta-cadinene synthase P93665 from SWISSPROT . Tpsb includes (-)-limonene synthase, Q40322 from SWISSPROT. Tpsc includes copalyl diphosphate synthase (kaurene synthase A), O04408 from SWISSPROT. Tpsd includes taxadiene synthase, Q41594 from SWISSPROT, pinene synthase, O24475 from SWISSPROT and myrcene synthase, O24474 from SWISSPROT. Tpse includes ent-kaurene synthase B Q39548 from SWISSPROT. Tpsf includes linalool synthase Q9ZPN5 from SWISSPROT. In the fungus Phaeosphaeria sp. (strain L487) the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein [].; GO: 0000287 magnesium ion binding, 0016829 lyase activity; PDB: 3PYB_A 3PYA_A 3G4F_A 3G4D_B 3CKE_A 2OA6_D 2E4O_B 3BNY_B 3BNX_A 3LG5_A ....
Probab=100.00 E-value=1.9e-50 Score=367.31 Aligned_cols=264 Identities=28% Similarity=0.400 Sum_probs=239.8
Q ss_pred CcchHHhHHHHHHHHHHHHHHhhhcCCCCCchhhhhhhhhhHHHHhccccCCCchhHHHHHHHHHHHHHHHHhhhhccCC
Q 043754 1 MLDFNILQKQHQEELRDIVRWWKNFDVPNKLPFIRDRVVEGYFWILGVYFEPKFLLARKILTKVISMASIIDDIYDAYGT 80 (320)
Q Consensus 1 kldfn~~Q~~hq~El~~l~~W~~~~~l~~~l~~~R~r~~~~y~~~~a~~feP~~s~~Rl~~ak~~~l~~~iDD~~D~~~t 80 (320)
|+|||+||+.||+|++++++|++++|+..+.+.+|+|+..++|+.+|+++.|+.+..|+++||++.|+|++||+||..++
T Consensus 6 ~~~~~~~~~~~~~e~~~~~~W~~~~~l~~~~~~~~~~~~~~~~~~~aa~~~P~~~~~l~~~a~~~~w~f~~DD~~D~~~~ 85 (270)
T PF03936_consen 6 KRDFPHCQALHQQELEEIDRWVKEFGLFDEDKAARQRFRQAYFGLLAARFYPDSSDELLAAADWMAWLFIFDDFFDDGGS 85 (270)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHCTHHHHHTTSHHHHHHHHHHHHHHHHSGCGHHHHHHHHHHHHHHHHHHHHHHTTSH
T ss_pred hhhcHhhHHHHHHHHHHHHHHHHHcCCccccccchhhhhHhHHhhhhheeCCCcHHHHHHHHhhchheeeeeeccccccc
Confidence 57999999999999999999999999966777789999999999999999999777778999999999999999999999
Q ss_pred HHHHHHHHHHHHhcchhhcccCchhHHHHHHHHHHHHHHHHHHHHhc-CCcccHhhHHHHHHHHHHHHHHHHHHhhCCCC
Q 043754 81 IEELELFATAIERWDLSAIDLLPEYIKLCYCALLDAYSEFEKDLASK-GILYGLPFAKESMKILVRSYIIEARWCDQQYV 159 (320)
Q Consensus 81 ~~el~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~~~~e~~~~~~~~-~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~ 159 (320)
.++++.+++++++|++.....+|+..++++.++.++++++...+.+. ++.+...+|+++|.+|+.++++|++|+..|++
T Consensus 86 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~ 165 (270)
T PF03936_consen 86 AEELEALTDAVERWDPNSGDPLPDPDKPLFRALADIWNRIAARMSPAQRRRDQIKRFRNSWREYLNAYLWEARWRERGRI 165 (270)
T ss_dssp HHHHHHHHHHHHHTSSGGGGGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-
T ss_pred hHHHHHHHHHHhcccccccccccchhHHHHHHHHHHHHHHHHHhhhhhcccHHhhHHHHHHHHHHHHHHHHHHHhccCCC
Confidence 99999999999999887778899999999999999999998777663 22235677999999999999999999999999
Q ss_pred CChHHHHhhhhhhhhhhHHHHHHHhcCCCCCCHHHHhhccCchHHHHHHHhHHHHhcCccchHHhhhcCCcchhHHHHHh
Q 043754 160 PTMEEYMRVALLSCGYLLLSTSSFLGMEDIVTKEAFEWVSGNPKIVQASSIICRLMDDIVSHKFEQQRGHVASAVECYMK 239 (320)
Q Consensus 160 Pt~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~V~~ym~ 239 (320)
||++||++.|+.|+|+.+++.++.+++|..+++...+++..++.+.++++.+++|+|||.||+||+++|+.+|.|.++|+
T Consensus 166 ps~eeYl~~R~~t~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~NDl~S~~KE~~~g~~~N~v~~l~~ 245 (270)
T PF03936_consen 166 PSLEEYLEMRRHTSGVYPCLALIEFALEFALGELPPEVLEHPPMLRRLAADIIRLVNDLYSYKKEIARGDVHNLVVVLMN 245 (270)
T ss_dssp -SHHHHHHHHHHHTSHHHHHHHHHHHCSSCHTHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCSHHHHHHH
T ss_pred CCHHHHHHhccccccccHHHHHHHHhCCCccccccHHHHHhchHHHHHHHHHHHHhcccchhhcchhhcccccHHHHhhh
Confidence 99999999999999999999999888876666555555555677999999999999999999999999999999999999
Q ss_pred hCCCCHHHHHHHHHHHHHHHHHHHH
Q 043754 240 QHGVSEEEAVKVFREKVGNAWKDIN 264 (320)
Q Consensus 240 e~g~s~eeA~~~i~~~i~~~~k~l~ 264 (320)
++|+|.|+|++++.+++++++++||
T Consensus 246 ~~~~s~e~A~~~v~~~~~~~~~efn 270 (270)
T PF03936_consen 246 EHGLSLEEAVDEVAEMINECIREFN 270 (270)
T ss_dssp HHTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hcCCCHHHHHHHHHHHHHHHHHhcC
Confidence 9999999999999999999999997
No 6
>cd00687 Terpene_cyclase_nonplant_C1 Non-plant Terpene Cyclases, Class 1. This CD includes terpenoid cyclases such as pentalenene synthase and aristolochene synthase which, using an all-trans pathway, catalyze the ionization of farnesyl diphosphate, followed by the formation of a macrocyclic intermediate by bond formation between C1 with either C10 (aristolochene synthase) or C11 (pentalenene synthase), resulting in production of tricyclic hydrocarbon pentalenene or bicyclic hydrocarbon aristolochene. As with other enzymes with the 'terpenoid synthase fold', they have two conserved metal binding motifs, proposed to coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP to the enzymes. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function in the monomeric form and are found in
Probab=100.00 E-value=4.7e-37 Score=284.43 Aligned_cols=252 Identities=19% Similarity=0.114 Sum_probs=219.1
Q ss_pred HHHHHHH-HHHHhhhcCCCCCchhhhhhhhhhHHHHhccccCCCchhHHH-HHHHHHHHHHHHHhhhhcc-CCHHHHHHH
Q 043754 11 HQEELRD-IVRWWKNFDVPNKLPFIRDRVVEGYFWILGVYFEPKFLLARK-ILTKVISMASIIDDIYDAY-GTIEELELF 87 (320)
Q Consensus 11 hq~El~~-l~~W~~~~~l~~~l~~~R~r~~~~y~~~~a~~feP~~s~~Rl-~~ak~~~l~~~iDD~~D~~-~t~~el~~~ 87 (320)
|-.+++. ...|.++.|+. .-+.+|+++..++|+.++.++.|+++.+|+ +.++++.|+|++||.||.. +++++.+.+
T Consensus 11 ~~~~~~~~~~~w~~~~~l~-~~~~~~~~~~~~~~~~~~a~~~P~a~~~~l~l~~~~~~w~f~~DD~~D~~~~~~~~~~~~ 89 (303)
T cd00687 11 YVKEAQDEYLEWVLEEMLI-PSEKAEKRFLSADFGDLAALFYPDADDERLMLAADLMAWLFVFDDLLDRDQKSPEDGEAG 89 (303)
T ss_pred ChHHHHHHHHHHHHHcCCC-CcchhHHHHhcCCHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhcccCCccccCHHHHHHH
Confidence 5556555 66699999774 334789999998888888888899999998 6679999999999999987 589999999
Q ss_pred HHHHHhcchh-hcccCchhHHHHHHHHHHHHHHHHHHHHhcCCcccHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHH
Q 043754 88 ATAIERWDLS-AIDLLPEYIKLCYCALLDAYSEFEKDLASKGILYGLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYM 166 (320)
Q Consensus 88 ~~ai~rwd~~-~~~~lp~~~~~~~~~l~~~~~e~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl 166 (320)
++.+.++... ..+. |....++..++.+++.++..... ....+++++.|.+|+.++++|++|+.+|++||++||+
T Consensus 90 ~~~~~~~~~~~~~~~-~~~~~p~~~~~~d~~~r~~~~~~----~~~~~r~~~~~~~~~~a~~~e~~~~~~~~~psl~eYl 164 (303)
T cd00687 90 VTRLLDILRGDGLDS-PDDATPLEFGLADLWRRTLARMS----AEWFNRFAHYTEDYFDAYIWEGKNRLNGHVPDVAEYL 164 (303)
T ss_pred HHHHHhccCCCCCCC-CCCCCHHHHHHHHHHHHhccCCC----HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHHH
Confidence 9988875433 2221 45667888999999988865432 2447899999999999999999999999999999999
Q ss_pred hhhhhhhhhhHHHHHHHhcCCCCCCHHHHhhccCchHHHHHHHhHHHHhcCccchHHhh-hcCCcchhHHHHHhhCCCCH
Q 043754 167 RVALLSCGYLLLSTSSFLGMEDIVTKEAFEWVSGNPKIVQASSIICRLMDDIVSHKFEQ-QRGHVASAVECYMKQHGVSE 245 (320)
Q Consensus 167 ~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~-~~g~~~n~V~~ym~e~g~s~ 245 (320)
++|+.|+|+.+++.++++++|..+|+++.++ +...++.++++.+++|+|||.||+||+ +.|+.+|+|.|+|+++|+|.
T Consensus 165 ~~R~~~~g~~~~~~l~~~~~g~~lp~~~~~~-~~~~~l~~~~~~~~~l~NDl~S~~KE~~~~g~~~N~V~vl~~~~g~s~ 243 (303)
T cd00687 165 EMRRFNIGADPCLGLSEFIGGPEVPAAVRLD-PVMRALEALASDAIALVNDIYSYEKEIKANGEVHNLVKVLAEEHGLSL 243 (303)
T ss_pred HHhhhcccccccHHHHHHhcCCCCCHHHHhC-hHHHHHHHHHHHHHHHHHHHHhhHHHHHhCCccchHHHHHHHHcCCCH
Confidence 9999999999999999999999999999887 667889999999999999999999999 89999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcC
Q 043754 246 EEAVKVFREKVGNAWKDINEELMR 269 (320)
Q Consensus 246 eeA~~~i~~~i~~~~k~l~~~~~~ 269 (320)
|+|++++.+++++.++++.+..-+
T Consensus 244 ~eA~~~~~~~~~~~~~~f~~~~~~ 267 (303)
T cd00687 244 EEAISVVRDMHNERITQFEELEAS 267 (303)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999988776543
No 7
>PLN02150 terpene synthase/cyclase family protein
Probab=99.97 E-value=8.2e-32 Score=205.82 Aligned_cols=94 Identities=44% Similarity=0.745 Sum_probs=91.0
Q ss_pred hhcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhhhhh-cccCCCCCCc-h
Q 043754 225 QQRGHVASAVECYMKQHGVSEEEAVKVFREKVGNAWKDINEELMRPPVVPMPLLERVLNLARLMDVL-YQNNDSYTNP-H 302 (320)
Q Consensus 225 ~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~~~~~~~~~p~~~~~~~~n~~r~~~~~-Y~~~D~~~~~-~ 302 (320)
++|||++|+|+|||||||+|+|||+++++++|+++||++|+++++++++|.++++.++|+||+++++ |++|||||.+ +
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 4789999999999999999999999999999999999999999999899999999999999999999 9999999987 7
Q ss_pred hHHHHHHHhhhccccC
Q 043754 303 LMKDHVAALLKDPVFF 318 (320)
Q Consensus 303 ~~~~~i~~~l~~p~~~ 318 (320)
.+|++|++||++|||+
T Consensus 81 ~~K~~I~sLlv~pi~i 96 (96)
T PLN02150 81 KLKDLITSLFFHPLPL 96 (96)
T ss_pred HHHHHHHHHhccCCCC
Confidence 8999999999999986
No 8
>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1. Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoter
Probab=99.88 E-value=2.5e-22 Score=177.10 Aligned_cols=229 Identities=29% Similarity=0.358 Sum_probs=180.0
Q ss_pred HHhccccCCCchhHHHHHHHHHHHHHHHHhhhhccCCHHHHHHHHHHHHhcchhhcccCchhHHHHHHHHHHHHHHHHHH
Q 043754 44 WILGVYFEPKFLLARKILTKVISMASIIDDIYDAYGTIEELELFATAIERWDLSAIDLLPEYIKLCYCALLDAYSEFEKD 123 (320)
Q Consensus 44 ~~~a~~feP~~s~~Rl~~ak~~~l~~~iDD~~D~~~t~~el~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~~~~e~~~~ 123 (320)
+++++++.|+.+..|..++++..|++++||++|..++..+.......+ .....|..+......+...++++...
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~DDi~D~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (243)
T cd00385 2 RPLAVLLEPEASRLRAAVEKLHAASLVHDDIVDDSGTRRGLPTAHLAV------AIDGLPEAILAGDLLLADAFEELARE 75 (243)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCchhhhhhH------HhcCchHHHHHHHHHHHHHHHHHHhC
Confidence 356667889888999999999999999999999887655544443322 12334566667777788888777543
Q ss_pred HHhcCCcccHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhcCCCCCCHHHHhhccCchH
Q 043754 124 LASKGILYGLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLGMEDIVTKEAFEWVSGNPK 203 (320)
Q Consensus 124 ~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~ 203 (320)
. ......++.+.|.+++.|+..|+.|+.. +.||++||+.++..++ +.++...+..+++...|+ ....+...+
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 2 1345889999999999999999999887 8899999999999998 455555666666666655 222255678
Q ss_pred HHHHHHhHHHHhcCccchHHhhhcC-CcchhHHHHHhhCCC------------CHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 043754 204 IVQASSIICRLMDDIVSHKFEQQRG-HVASAVECYMKQHGV------------SEEEAVKVFREKVGNAWKDINEELMRP 270 (320)
Q Consensus 204 l~~~~~~i~rL~NDi~S~~~E~~~g-~~~n~V~~ym~e~g~------------s~eeA~~~i~~~i~~~~k~l~~~~~~~ 270 (320)
+....+.+.+|.||+.|+.+|.+.| +..|++.++|+++|+ +.++|.+++..+++++++++++.....
T Consensus 148 ~~~~~g~~~ql~nDl~~~~~e~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ 227 (243)
T cd00385 148 LGRALGLAFQLTNDLLDYEGDAERGEGKCTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKLAEEALKELNELILSL 227 (243)
T ss_pred HHHHHHHHHHHHHHHHhccCCHHHhCCchHHHHHHHHHhCChhhHHHHHHHCChHHHHHHHHHHHHHHHHHHHhcCCCCc
Confidence 8889999999999999999999986 678999999999998 889999999999999999999877753
Q ss_pred CCCCHHHHHHHHHHHh
Q 043754 271 PVVPMPLLERVLNLAR 286 (320)
Q Consensus 271 ~~~p~~~~~~~~n~~r 286 (320)
...+..+++.+.++.|
T Consensus 228 ~~~~~~~~~~~~~~~~ 243 (243)
T cd00385 228 PDVPRALLALALNLYR 243 (243)
T ss_pred HHHHHHHHHHHHHHhC
Confidence 3456677777777653
No 9
>PF06330 TRI5: Trichodiene synthase (TRI5); InterPro: IPR024652 This family consists of several fungal trichodiene synthase proteins (EC:4.2.3.6). TRI5 encodes the enzyme trichodiene synthase, which has been shown to catalyse the first step in the trichothecene pathways of Fusarium and Trichothecium species [, ].; GO: 0045482 trichodiene synthase activity, 0016106 sesquiterpenoid biosynthetic process; PDB: 1YYT_A 2PS5_A 2AEL_A 1YYS_A 1YJ4_A 2Q9Y_A 2PS4_A 2AEK_B 1KIY_B 2PS7_A ....
Probab=98.13 E-value=0.00015 Score=67.90 Aligned_cols=193 Identities=13% Similarity=0.073 Sum_probs=111.7
Q ss_pred CCch-hHHHHHHHHHHHHHHHHhhhhccCCHHHHHHHHHHHHhcchhhcccCchhHHHHHHHHHHHHHHHHHHHHhcCCc
Q 043754 52 PKFL-LARKILTKVISMASIIDDIYDAYGTIEELELFATAIERWDLSAIDLLPEYIKLCYCALLDAYSEFEKDLASKGIL 130 (320)
Q Consensus 52 P~~s-~~Rl~~ak~~~l~~~iDD~~D~~~t~~el~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~~~~e~~~~~~~~~~~ 130 (320)
|..+ +.++.++=...+++++||.++.. .+++..|-+.+-. +. .. + .++...+.+.+.++ ...-++
T Consensus 79 ~~~~~evqv~IaiyT~yvi~iDD~~~~~--~~~l~~F~~~l~~--Gq-~Q--~---~p~L~~~~~~L~~~----~~~fgp 144 (376)
T PF06330_consen 79 PHLPKEVQVAIAIYTTYVIIIDDSSQEP--SDDLRTFHQRLIL--GQ-PQ--K---HPLLDGFASLLREM----WRHFGP 144 (376)
T ss_dssp TTS-HHHHHHHHHHHHHHHHHTT--S-S--HHHHTTHHHHHHH--T------S---SHHHHHHHHHHHHH----HTTS-H
T ss_pred CCCCHHHHHHHHHHHHHHHhcccccccc--cHHHHHHHHHHhc--CC-CC--C---CHHHHHHHHHHHHH----HHHcch
Confidence 4444 56678899999999999997655 3566666655432 11 11 1 13334444444333 332344
Q ss_pred ccHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhcCCCCCCHHHHhhccCchHHHHH---
Q 043754 131 YGLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLGMEDIVTKEAFEWVSGNPKIVQA--- 207 (320)
Q Consensus 131 ~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~--- 207 (320)
.+.+-+.++--+++.+..-|.+.. +-.|.-..|-..-+.=+|...+.+...+- ....|+. ..+..++.+
T Consensus 145 f~anmI~~STLdFi~g~~LE~~~f--~~~p~A~~FP~fLR~ktGlsEaYA~FiFP-k~~fpe~-----~~~~~y~~AIpd 216 (376)
T PF06330_consen 145 FCANMIVKSTLDFINGCWLEQKNF--HGSPGAPDFPDFLRRKTGLSEAYAFFIFP-KALFPEV-----EYFIQYTPAIPD 216 (376)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTT------TT-TTHHHHHHHHHH-HHHHHHHT---TTTS-TT-----TTHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhhcccC--CCCCCCccccHHHHhccCcchhheeeecc-cccCChH-----HHHHHHHHHHHH
Confidence 566777888889999998887642 22343333444445556766666653331 2233332 223443333
Q ss_pred HHhHHHHhcCccchHHhhh-cCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHh
Q 043754 208 SSIICRLMDDIVSHKFEQQ-RGHVASAVECYMKQHGVSEEEAVKVFREKVGNAWKDINEE 266 (320)
Q Consensus 208 ~~~i~rL~NDi~S~~~E~~-~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~~ 266 (320)
....+-++|||.||=||.- .|+..|.|.-+-.-+|+|.-+|...+.+..-.+.+++.+.
T Consensus 217 l~~fi~~~NDILSFYKE~l~a~E~~NyI~n~A~~~g~S~~eaL~~l~~eti~a~~rv~~v 276 (376)
T PF06330_consen 217 LMRFINYVNDILSFYKEELVAGETGNYIHNRARVHGVSILEALRELTDETIEAVERVRRV 276 (376)
T ss_dssp HHHHHHHHHHHHHHHHHHTTSSSSSSHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhhhhHHHHHHhhcccccccchhhhhhhccCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445568999999999977 7888999987877789999999998766666665555443
No 10
>cd00686 Terpene_cyclase_cis_trans_C1 Cis, Trans, Terpene Cyclases, Class 1. This CD includes the terpenoid cyclase, trichodiene synthase, which catalyzes the cyclization of farnesyl diphosphate (FPP) to trichodiene using a cis-trans pathway, and is the first committed step in the biosynthesis of trichothecene toxins and antibiotics. As with other enzymes with the 'terpenoid synthase fold', this enzyme has two conserved metal binding motifs that coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function as homodimers and are found in several genera of fungi.
Probab=98.11 E-value=7.5e-05 Score=68.86 Aligned_cols=211 Identities=14% Similarity=0.043 Sum_probs=123.1
Q ss_pred hhhhhHHHHhccccCCC--chhHHH-HHHHHHHHHHHHHhhhhccCCHHHHHHHHHHHHhcchhhcccCchhHHHHHHHH
Q 043754 37 RVVEGYFWILGVYFEPK--FLLARK-ILTKVISMASIIDDIYDAYGTIEELELFATAIERWDLSAIDLLPEYIKLCYCAL 113 (320)
Q Consensus 37 r~~~~y~~~~a~~feP~--~s~~Rl-~~ak~~~l~~~iDD~~D~~~t~~el~~~~~ai~rwd~~~~~~lp~~~~~~~~~l 113 (320)
|+..+-=.++++.-.|. .|.+=+ .++-....++++||.-|... ++++.|.+.+.. +. ... .++...+
T Consensus 62 ri~~~~~T~v~~~~Y~w~~~skev~~~isi~~tY~~~lDD~~~e~~--~~m~~f~~dL~~--G~-~qk-----hP~l~~v 131 (357)
T cd00686 62 RLQASLQTIVGMVVYSWAKVSKECMADLSIHYTYTLVLDDSKDDPY--PTMVNYFDDLQA--GR-EQA-----HPWWALV 131 (357)
T ss_pred HHHHHHHHhhceEEeeccCCCHHHHHHHHHHHheeeEecccccccc--hHHHHHHHHHhc--CC-CCC-----CcHHHHH
Confidence 33333333444422244 554443 66777778889999876543 356666655442 11 111 1223333
Q ss_pred HHHHHHHHHHHHhcCCcccHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhcCCCCCCHH
Q 043754 114 LDAYSEFEKDLASKGILYGLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLGMEDIVTKE 193 (320)
Q Consensus 114 ~~~~~e~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e 193 (320)
.+.+..+.+ .-|+.+..-+.++--+++.+..-|.. +.+..|.-.+|-...+.=+|.+-+.+... .|++
T Consensus 132 ~~~l~~~lr----~fGpF~s~~IikSTLdFv~g~~iEq~--nf~~~p~A~~fP~ylR~ksGl~E~yA~Fi------FPk~ 199 (357)
T cd00686 132 NEHFPNVLR----HFGPFCSLNLIRSTLDFFEGCWIEQY--NFGGFPGSHDYPQFLRRMNGLGHCVGASL------WPKE 199 (357)
T ss_pred HHHHHHHHH----HhhhhhHHHHHHHHHHHHHHHHHhhh--ccCCCCCCcccchHHHhccCCcceeEEEe------cchh
Confidence 333332222 12445566677888889999988866 33446766666666677677666655422 2433
Q ss_pred HHhhccCchHHHHHH---HhHHHHhcCccchHHhhhc-CCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhhcC
Q 043754 194 AFEWVSGNPKIVQAS---SIICRLMDDIVSHKFEQQR-GHVASAVECYMKQHGVSEEEAVKVFREKVGNAWKDINEELMR 269 (320)
Q Consensus 194 ~~~~~~~~~~l~~~~---~~i~rL~NDi~S~~~E~~~-g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~~~~~ 269 (320)
.+.-...+..+..+. ...+-++|||.||=||... ++..|.|.-|.+.+|+|..+|.+.+..-.-.+-+++.+ +|.
T Consensus 200 ~FpE~~~~~qi~~AIp~~~~~i~~~NDILSFYKEe~~~~E~~n~V~Nya~~~GiS~~eAL~~lt~dTv~~s~rv~~-VLs 278 (357)
T cd00686 200 QFNERSLFLEITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVA-VFS 278 (357)
T ss_pred hCchHhhHHHhhHHHHHHHHHHHhhhhhhheehhhcccccccchHHHhhhhcCCCHHHHHHHHHHHHHHHHHHHHH-Hhc
Confidence 322111223322233 3345688999999999854 55678888888889999999999877666666666554 454
Q ss_pred C
Q 043754 270 P 270 (320)
Q Consensus 270 ~ 270 (320)
+
T Consensus 279 e 279 (357)
T cd00686 279 D 279 (357)
T ss_pred C
Confidence 3
No 11
>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=95.91 E-value=1.2 Score=40.28 Aligned_cols=178 Identities=19% Similarity=0.219 Sum_probs=93.1
Q ss_pred hhHHHHhccccCCCchhHHHHHHHHHHHHHHHHhhhhccCCHHH----HHHHHHHHHhcchhhcccCchhHHHHHHHHHH
Q 043754 40 EGYFWILGVYFEPKFLLARKILTKVISMASIIDDIYDAYGTIEE----LELFATAIERWDLSAIDLLPEYIKLCYCALLD 115 (320)
Q Consensus 40 ~~y~~~~a~~feP~~s~~Rl~~ak~~~l~~~iDD~~D~~~t~~e----l~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~ 115 (320)
.+++++.- .. | ...|-.+.-+-.+.-.+||+-|......+ ++-+-++++..-.+..+..+....++..++..
T Consensus 6 ~sf~~a~~-~l-P--~~~R~~~~alyaf~r~~d~i~D~~~~~~~~~~~L~~w~~~l~~~~~~~~~~~~~~~~pv~~~l~~ 81 (267)
T PF00494_consen 6 RSFYLASL-LL-P--KEKRPAVFALYAFCRELDDIVDEPSDPEEARARLQWWRDALNSIFASYEDSLPEPSHPVARALAD 81 (267)
T ss_dssp HHHHHHHT-TS----HHHHHHHHHHHHHHHHHHHHHHCTSS-HSCHHHHHHHHHHHHHHHH-TSTHHHSSHHHHHHHHHH
T ss_pred ccHHHHHH-HC-C--HHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHHHHHHHhhhhhhccCCCcCHHHHHHHH
Confidence 34444443 33 5 45666666777888889999997764333 33344444432111111233344566666655
Q ss_pred HHHHHHHHHHhcCCcccHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhcCCCCCCH-HH
Q 043754 116 AYSEFEKDLASKGILYGLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLGMEDIVTK-EA 194 (320)
Q Consensus 116 ~~~e~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~-e~ 194 (320)
+.... ..-++.+.+++.++.+.. ....++|++|+......+.|....+.+-.++.. -++ +.
T Consensus 82 ~~~~~-------------~l~~~~l~~li~~~~~dl---~~~~~~t~~~L~~Y~~~vag~vg~l~~~~~~~~--~~~~~~ 143 (267)
T PF00494_consen 82 LVRRY-------------GLPREPLLELIDGMEMDL---EFTPYETFADLERYCYYVAGSVGLLLLQLLGAH--DPDEAA 143 (267)
T ss_dssp HHCCS-------------HHHHHHHHHHHHHHHHCT---T-S--SSHHHHHHHHHHHTHHHHHHHHHHHHSS--TSHHHH
T ss_pred HHHHH-------------hhhHHHHHHHHHHhcccc---cCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccc--cchhhH
Confidence 55222 133455667777765332 234578999999998888888777666555542 122 22
Q ss_pred HhhccCchHHHHHHHhHHHHhcCccchHHh-hhcCCc--chhHHHHHhhCCCCHHHHH
Q 043754 195 FEWVSGNPKIVQASSIICRLMDDIVSHKFE-QQRGHV--ASAVECYMKQHGVSEEEAV 249 (320)
Q Consensus 195 ~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E-~~~g~~--~n~V~~ym~e~g~s~eeA~ 249 (320)
.+ .....+...-+.|=+...... ..+|.+ +. =.|.++|++.++-.
T Consensus 144 ~~-------~a~~lG~alql~nilRd~~~D~~~~gR~ylP~---d~l~~~gv~~~dl~ 191 (267)
T PF00494_consen 144 RD-------AARALGRALQLTNILRDIPEDALRRGRIYLPL---DDLRRFGVTPEDLL 191 (267)
T ss_dssp HH-------HHHHHHHHHHHHHHHHTHHHH-HHTT---S-H---HHHHHTTSSHHHHH
T ss_pred HH-------HHHHHHHHHHHHHHHHHhHHHHHhcccccCCc---hhHHHcCCCHHHHH
Confidence 22 223333333333333344455 455543 32 24678899887653
No 12
>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates
Probab=93.05 E-value=2.4 Score=37.27 Aligned_cols=117 Identities=15% Similarity=0.199 Sum_probs=73.4
Q ss_pred HhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhh-hhhhhHHHHHHHhcCCCCCCHHHHhhccCchHHHHHHHhH
Q 043754 133 LPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALL-SCGYLLLSTSSFLGMEDIVTKEAFEWVSGNPKIVQASSII 211 (320)
Q Consensus 133 ~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~-s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i 211 (320)
...+.+.....+.|...+..|... ..||.++|++.-.. |.+.....+......+. -+++..+ ...++.+..+..
T Consensus 87 ~~~~~~~~~~~~~Gq~~Dl~~~~~-~~~t~~~y~~~~~~Kta~l~~~~~~~~~~~~~-~~~~~~~---~~~~~~~~lG~a 161 (236)
T cd00867 87 LELFAEALRELLEGQALDLEFERD-TYETLDEYLEYCRYKTAGLVGLLCLLGAGLSG-ADDEQAE---ALKDYGRALGLA 161 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHhccHHHHHHHHHHHHHHcC-cCHHHHH---HHHHHHHHHHHH
Confidence 556678888999999999888654 57999999999988 55554333322222222 2222222 235667778888
Q ss_pred HHHhcCccchHHhh----------hcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHH
Q 043754 212 CRLMDDIVSHKFEQ----------QRGHVASAVECYMKQHGVSEEEAVKVFREKVGNAWKDINE 265 (320)
Q Consensus 212 ~rL~NDi~S~~~E~----------~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~ 265 (320)
..+.||+..+.... ..|.. +...+++ .+.+.+.++...+.+..
T Consensus 162 ~Qi~dd~~D~~~d~~~~gk~~~D~~~gr~-tlp~~~~----------~~~~~~~~~~~~~~~~~ 214 (236)
T cd00867 162 FQLTDDLLDVFGDAEELGKVGSDLREGRI-TLPVILA----------RERAAEYAEEAYAALEA 214 (236)
T ss_pred HHHHHHhccccCChHHHCccHHHHHcCCc-hHHHHHH----------HHHHHHHHHHHHHHHHh
Confidence 88899998876654 44544 4444444 44455556666655443
No 13
>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=91.60 E-value=7 Score=35.17 Aligned_cols=89 Identities=18% Similarity=0.140 Sum_probs=58.5
Q ss_pred ccHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhcCCCCCCHHHHhhccCchHHHHHHHh
Q 043754 131 YGLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLGMEDIVTKEAFEWVSGNPKIVQASSI 210 (320)
Q Consensus 131 ~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~ 210 (320)
.+...+.+.....+.|-..+..|... ..||.++|++....-+|.....+...-++--..+++..+ ...++-+..+.
T Consensus 108 ~~~~~~~~~~~~~~~GQ~~d~~~~~~-~~~~~~~y~~~~~~KT~~l~~~~~~~~a~l~~~~~~~~~---~l~~~g~~lG~ 183 (259)
T cd00685 108 RALELFSEAILELVEGQLLDLLSEYD-TDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAE---ALKRFGRNLGL 183 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCC-CCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHH---HHHHHHHHHHH
Confidence 34566777788888888888888654 579999999998887777654433222110112344332 23566777788
Q ss_pred HHHHhcCccchHH
Q 043754 211 ICRLMDDIVSHKF 223 (320)
Q Consensus 211 i~rL~NDi~S~~~ 223 (320)
..-+.||+..+..
T Consensus 184 afQi~DD~ld~~~ 196 (259)
T cd00685 184 AFQIQDDILDLFG 196 (259)
T ss_pred HHHHHHHhhcccC
Confidence 8888888877644
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=90.42 E-value=13 Score=33.54 Aligned_cols=210 Identities=15% Similarity=0.161 Sum_probs=101.7
Q ss_pred hhHHHHhccccCCCchhHHHHHHHHHHHHHHHHhhhhccCCHHHHHHHHHHHHhcchh---hcccCchhHHHHHHHHHHH
Q 043754 40 EGYFWILGVYFEPKFLLARKILTKVISMASIIDDIYDAYGTIEELELFATAIERWDLS---AIDLLPEYIKLCYCALLDA 116 (320)
Q Consensus 40 ~~y~~~~a~~feP~~s~~Rl~~ak~~~l~~~iDD~~D~~~t~~el~~~~~ai~rwd~~---~~~~lp~~~~~~~~~l~~~ 116 (320)
.+|+++.-.. | ...|-.+.-+-.+.-.+||+-|..++.++.+.- ++.|... ....-| ..++..++..+
T Consensus 6 ~sF~~a~~~l--p--~~~R~~~~alYaf~r~~d~i~D~~~~~~~~~~~---L~~w~~~l~~~~~g~~--~~pv~~al~~~ 76 (266)
T TIGR03465 6 SSFYYGMRLL--P--PERRRAMTALYAFCREVDDIVDEDSDPEVAQAK---LAWWRAEIDRLYAGAP--SHPVARALADP 76 (266)
T ss_pred CcHHHHHHHC--C--HHHHHHHHHHHHHHHHHHhhhcCCCCchHHHHH---HHHHHHHHHHHhCCCC--CChHHHHHHHH
Confidence 3555555433 4 345665566677777799999975444332222 2333221 111112 23555666555
Q ss_pred HHHHHHHHHhcCCcccHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhcCCCCCCHHHHh
Q 043754 117 YSEFEKDLASKGILYGLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLGMEDIVTKEAFE 196 (320)
Q Consensus 117 ~~e~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~ 196 (320)
+.+. +. =++.+.+++.++.+.. .....+|++|+......+.|+-..+++..+ |.. ++....
T Consensus 77 ~~~~--------~l-----~~~~~~~li~g~~~Dl---~~~~~~t~~dL~~Y~~~vAg~vg~l~~~ll--g~~-~~~~~~ 137 (266)
T TIGR03465 77 ARRF--------DL-----PQEDFLEVIDGMEMDL---EQTRYPDFAELDLYCDRVAGAVGRLSARIF--GAT-DARTLE 137 (266)
T ss_pred HHHc--------CC-----CHHHHHHHHHHHHHHc---CCCCCCCHHHHHHHHHHhHHHHHHHHHHHh--CCC-ChhHHH
Confidence 4332 11 1345666777764332 234567999888888777776666555444 321 122211
Q ss_pred hccCchHHHHHHHhHHHHhcCccchHHhhhcCCcchhHHHHHhhCCCCHHH---------HHHHHHHHHHHHHHHHHHhh
Q 043754 197 WVSGNPKIVQASSIICRLMDDIVSHKFEQQRGHVASAVECYMKQHGVSEEE---------AVKVFREKVGNAWKDINEEL 267 (320)
Q Consensus 197 ~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~V~~ym~e~g~s~ee---------A~~~i~~~i~~~~k~l~~~~ 267 (320)
.....+...-|.|=+........+|.+ -.=.=.|.++|+|.++ ..+-+..+++.+...+.+..
T Consensus 138 -------~a~~lG~AlqltnilRdv~eD~~~gR~-ylP~~~l~~~gv~~~~l~~~~~~~~~~~~~~~l~~~A~~~l~~a~ 209 (266)
T TIGR03465 138 -------YAHHLGRALQLTNILRDVGEDARRGRI-YLPAEELQRFGVPAADILEGRYSPALAALCRFQAERARAHYAEAD 209 (266)
T ss_pred -------HHHHHHHHHHHHHHHHHhHHHHhCCCe-ecCHHHHHHcCCCHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 122222222222222222334456654 1111235678888763 33445555555554444433
Q ss_pred cCCCCCCHHHHHHHHHHH
Q 043754 268 MRPPVVPMPLLERVLNLA 285 (320)
Q Consensus 268 ~~~~~~p~~~~~~~~n~~ 285 (320)
-.-..+|......++-.+
T Consensus 210 ~~~~~~p~~~~~~~~~~~ 227 (266)
T TIGR03465 210 ALLPACDRRAQRAARAMA 227 (266)
T ss_pred HhhhhCCHhhhHHHHHHH
Confidence 223467765554444333
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=88.19 E-value=19 Score=32.38 Aligned_cols=209 Identities=17% Similarity=0.219 Sum_probs=100.8
Q ss_pred hHHHHhccccCCCchhHHHHHHHHHHHHHHHHhhhhccCCH-HH----HHHHHHHHHhcchhhcccCchhHHHHHHHHHH
Q 043754 41 GYFWILGVYFEPKFLLARKILTKVISMASIIDDIYDAYGTI-EE----LELFATAIERWDLSAIDLLPEYIKLCYCALLD 115 (320)
Q Consensus 41 ~y~~~~a~~feP~~s~~Rl~~ak~~~l~~~iDD~~D~~~t~-~e----l~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~ 115 (320)
+++++.-. . | ...|-.+.-+-.+.-.+||+-|..... .+ ++-+-++++.-.. ...| -.++..++..
T Consensus 13 sf~~a~~~-l-p--~~~R~~~~alYaf~r~~Ddi~D~~~~~~~~~~~~L~~w~~~l~~~~~---~~~~--~~pv~~al~~ 83 (265)
T cd00683 13 SFYLASRL-L-P--PELRRAVCALYAFCRAADDIVDDPAAPPDEKLALLDAFRAELDAAYW---GGAP--THPVLRALAD 83 (265)
T ss_pred cHHHHHHh-C-C--HHHHHHHHHHHHHHHHHHhhhhCCCCCchhHHHHHHHHHHHHHHHHc---CCCC--CChHHHHHHH
Confidence 45555443 3 4 345655556666777799999976432 22 2222222222100 0111 1356666665
Q ss_pred HHHHHHHHHHhcCCcccHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhcCCCCCCHHHH
Q 043754 116 AYSEFEKDLASKGILYGLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLGMEDIVTKEAF 195 (320)
Q Consensus 116 ~~~e~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~ 195 (320)
+..+. + .-++.+.+++.++..... ....||++|.......+.|+--.+++..++.+ -+++..
T Consensus 84 ~~~~~--------~-----l~~~~~~~li~g~~~Dl~---~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~~~~--~~~~~~ 145 (265)
T cd00683 84 LARRY--------G-----IPREPFRDLLAGMAMDLD---KRRYETLDELDEYCYYVAGVVGLMLLRVFGAS--SDEAAL 145 (265)
T ss_pred HHHHc--------C-----CCHHHHHHHHHHHHHhCC---CCCCCCHHHHHHHHHHhHHHHHHHHHHHhCCC--CChHHH
Confidence 55321 1 124566777777764443 35678998877777777766555555444321 122221
Q ss_pred hhccCchHHHHHHHhHHHHhcCccchHHhhhcCCc--chhHHHHHhhCCCCHHHH---------HHHHHHHHHHHHHHHH
Q 043754 196 EWVSGNPKIVQASSIICRLMDDIVSHKFEQQRGHV--ASAVECYMKQHGVSEEEA---------VKVFREKVGNAWKDIN 264 (320)
Q Consensus 196 ~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~g~~--~n~V~~ym~e~g~s~eeA---------~~~i~~~i~~~~k~l~ 264 (320)
+.....+...-|.|=+........+|.+ +.- .|.++|+|.++- ..-+..+++.+.+.+.
T Consensus 146 -------~~A~~lG~AlqltnilRdv~eD~~~gR~YlP~d---~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~A~~~~~ 215 (265)
T cd00683 146 -------ERARALGLALQLTNILRDVGEDARRGRIYLPRE---ELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYR 215 (265)
T ss_pred -------HHHHHHHHHHHHHHHHHHHHHHHccCCCcCCHH---HHHHcCCCHHHHcCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 1222222222222222222333455543 322 367788887652 2234445555444444
Q ss_pred HhhcCCCCCCHHHHHHHHHHHh
Q 043754 265 EELMRPPVVPMPLLERVLNLAR 286 (320)
Q Consensus 265 ~~~~~~~~~p~~~~~~~~n~~r 286 (320)
...-....+|...+-.++-++.
T Consensus 216 ~a~~~~~~lp~~~~~~~~~~~~ 237 (265)
T cd00683 216 EALAGLAALPRRSRFCVRAAAM 237 (265)
T ss_pred HHHHhHHhCCHhhHHHHHHHHH
Confidence 3332234577655544444443
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=85.64 E-value=27 Score=31.53 Aligned_cols=121 Identities=18% Similarity=0.134 Sum_probs=64.6
Q ss_pred hhHHHHhccccCCCchhHHHHHHHHHHHHHHHHhhhhcc-CCHHHHHHHHHHHHhcchh---hcccCchhHHHHHHHHHH
Q 043754 40 EGYFWILGVYFEPKFLLARKILTKVISMASIIDDIYDAY-GTIEELELFATAIERWDLS---AIDLLPEYIKLCYCALLD 115 (320)
Q Consensus 40 ~~y~~~~a~~feP~~s~~Rl~~ak~~~l~~~iDD~~D~~-~t~~el~~~~~ai~rwd~~---~~~~lp~~~~~~~~~l~~ 115 (320)
++|+++.-.. | ...|-.+.-+-.+.=.+||+-|.. .+.++...- ++.|... ....-| -.++..++..
T Consensus 6 ~sf~~a~~~l--p--~~~R~~~~alYAf~R~~Ddi~D~~~~~~~~~~~~---L~~wr~~l~~~~~g~~--~~pv~~aL~~ 76 (266)
T TIGR03464 6 ENFPVASLLL--P--ARLRAPIHAVYAFARTADDIADEGDGSAEERLAL---LDDFRAELDAIYSGEP--AAPVFVALAR 76 (266)
T ss_pred CcHHHHHHhC--C--HHHHHHHHHHHHHHHHHHHhccCCCCChHHHHHH---HHHHHHHHHHHhCCCC--CChHHHHHHH
Confidence 4565555433 4 345555555666667899999975 444432221 2233211 111112 1356666666
Q ss_pred HHHHHHHHHHhcCCcccHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhc
Q 043754 116 AYSEFEKDLASKGILYGLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLG 185 (320)
Q Consensus 116 ~~~e~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~ 185 (320)
++.+. +.. ++.+.+++.++.... .....+|++|...+...+.|+--.+++..++
T Consensus 77 ~~~~~--------~l~-----~~~~~~li~~~~~Dl---~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~g 130 (266)
T TIGR03464 77 TVQRH--------GLP-----IEPFLDLLDAFRQDV---VVTRYATWAELLDYCRYSANPVGRLVLDLYG 130 (266)
T ss_pred HHHHc--------CCC-----hHHHHHHHHHHHHhc---cCCCCCCHHHHHHHHHHhHHHHHHHHHHHcC
Confidence 55432 211 344555666653221 2345679998888888877777666655554
No 17
>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=83.40 E-value=39 Score=31.55 Aligned_cols=87 Identities=10% Similarity=0.069 Sum_probs=55.1
Q ss_pred cHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhcCCCCCCHHHHhhccCchHHHHHHHhH
Q 043754 132 GLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLGMEDIVTKEAFEWVSGNPKIVQASSII 211 (320)
Q Consensus 132 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i 211 (320)
....+.+.....+.+-+.+..+... ..+|.++|++.-..-+|..+..++..-++--..+++..+. ..++-+..++.
T Consensus 134 ~~~~~~~~~~~~~~Gq~~~~~~~~~-~~~~~~~y~~~~~~KTa~L~~~~~~~ga~~ag~~~~~~~~---l~~~G~~lG~a 209 (322)
T TIGR02749 134 VVKLISKVITDFAEGEIKQGLNQFD-SDLSLEDYLEKSFYKTASLVAASSKAAAVLSDVPSQVAND---LYEYGKHLGLA 209 (322)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcccC-CCCCHHHHHHHHHccHHHHHHHHHHHHHHHcCcCHHHHHH---HHHHHHHHHHH
Confidence 4556677777888887777766433 3479999998776666655433221111111234544433 36677788888
Q ss_pred HHHhcCccchH
Q 043754 212 CRLMDDIVSHK 222 (320)
Q Consensus 212 ~rL~NDi~S~~ 222 (320)
.-+.||+..+.
T Consensus 210 FQi~DDild~~ 220 (322)
T TIGR02749 210 FQVVDDILDFT 220 (322)
T ss_pred HHHHHHhccCC
Confidence 89999998765
No 18
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=82.87 E-value=41 Score=31.41 Aligned_cols=108 Identities=15% Similarity=0.163 Sum_probs=70.5
Q ss_pred cHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhcCCCCCCHHHHhhccCchHHHHHHHhH
Q 043754 132 GLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLGMEDIVTKEAFEWVSGNPKIVQASSII 211 (320)
Q Consensus 132 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i 211 (320)
....+.+.....+.+-..+-.+.... +|.++|++.-..=+|.....+...-++--..+++..+. ...+-+..++.
T Consensus 135 ~~~~~~~~~~~~~~GQ~lDl~~~~~~--~t~e~y~~~i~~KTa~L~~~a~~~ga~la~~~~~~~~~---l~~~g~~lGla 209 (322)
T COG0142 135 AIKALAEAINGLCGGQALDLAFENKP--VTLEEYLRVIELKTAALFAAAAVLGAILAGADEELLEA---LEDYGRNLGLA 209 (322)
T ss_pred HHHHHHHHHHHHHHhHHHHHHccCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHH---HHHHHHHhhHH
Confidence 46667788888888888777776555 99999999888777766654432222111123455444 36677888888
Q ss_pred HHHhcCccchHHhhh-cCCc---------chhHHHHHhhCCCC
Q 043754 212 CRLMDDIVSHKFEQQ-RGHV---------ASAVECYMKQHGVS 244 (320)
Q Consensus 212 ~rL~NDi~S~~~E~~-~g~~---------~n~V~~ym~e~g~s 244 (320)
.-+.+|+..+.-+.+ -|+. .+...++.-+.+..
T Consensus 210 FQi~DDiLD~~~d~~~lGK~~g~Dl~~gK~T~p~l~~l~~~~~ 252 (322)
T COG0142 210 FQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEKANE 252 (322)
T ss_pred HHHHHHhhcCCCChHHhCCCcchHHHcCCchHHHHHHHHcCch
Confidence 999999988876422 2332 36666666665433
No 19
>PLN02890 geranyl diphosphate synthase
Probab=81.11 E-value=57 Score=31.82 Aligned_cols=90 Identities=12% Similarity=0.108 Sum_probs=59.8
Q ss_pred ccHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhcCCCCCCHHHHhhccCchHHHHHHHh
Q 043754 131 YGLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLGMEDIVTKEAFEWVSGNPKIVQASSI 210 (320)
Q Consensus 131 ~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~ 210 (320)
.+...+.++....+.|-+.+..|... ..+|.++|++.-..-+|..+..++..-++--..+++..+. ..++-+..++
T Consensus 227 ~~~~~~s~a~~~l~~Gq~ld~~~~~~-~~~s~~~Yl~~i~~KTa~Lf~~s~~~gAilaga~~~~~~~---l~~fG~~lGl 302 (422)
T PLN02890 227 EVVSLLATAVEHLVTGETMQITSSRE-QRRSMDYYMQKTYYKTASLISNSCKAVAILAGQTAEVAVL---AFEYGRNLGL 302 (422)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCcCHHHHHH---HHHHHHHHHH
Confidence 34667788888999999888888643 4589999998776666655443321111101235555443 3566777888
Q ss_pred HHHHhcCccchHHh
Q 043754 211 ICRLMDDIVSHKFE 224 (320)
Q Consensus 211 i~rL~NDi~S~~~E 224 (320)
..-+.||+..|.-.
T Consensus 303 AFQI~DDiLD~~g~ 316 (422)
T PLN02890 303 AFQLIDDVLDFTGT 316 (422)
T ss_pred HHHHHHHHHhhcCC
Confidence 88889999887543
No 20
>KOG1719 consensus Dual specificity phosphatase [Defense mechanisms]
Probab=74.95 E-value=2.7 Score=34.89 Aligned_cols=29 Identities=38% Similarity=0.603 Sum_probs=25.3
Q ss_pred hcCCcchhHHHHHhhC-CCCHHHHHHHHHH
Q 043754 226 QRGHVASAVECYMKQH-GVSEEEAVKVFRE 254 (320)
Q Consensus 226 ~~g~~~n~V~~ym~e~-g~s~eeA~~~i~~ 254 (320)
.||..+..|.||+.++ +.|.++|.+++++
T Consensus 119 GRtRSaTvV~cYLmq~~~wtpe~A~~~vr~ 148 (183)
T KOG1719|consen 119 GRTRSATVVACYLMQHKNWTPEAAVEHVRK 148 (183)
T ss_pred CCccchhhhhhhhhhhcCCCHHHHHHHHHh
Confidence 4677789999999887 9999999999887
No 21
>PLN02632 phytoene synthase
Probab=74.72 E-value=76 Score=29.82 Aligned_cols=108 Identities=17% Similarity=0.228 Sum_probs=58.1
Q ss_pred hHHHHHHHHHHHHHHHHhhhhccCCHH----HHHHHHHHHHhcchhhcccCchhHHHHHHHHHHHHHHHHHHHHhcCCcc
Q 043754 56 LARKILTKVISMASIIDDIYDAYGTIE----ELELFATAIERWDLSAIDLLPEYIKLCYCALLDAYSEFEKDLASKGILY 131 (320)
Q Consensus 56 ~~Rl~~ak~~~l~~~iDD~~D~~~t~~----el~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~~~~e~~~~~~~~~~~~ 131 (320)
..|..+.-+-.|.-.+||+-|...... .++..-+.+++ ....-|. .++..++.++..+. +-
T Consensus 73 ~~R~ai~alYAf~R~~DdI~D~~~~~~~~~~~L~~w~~~l~~----~~~g~~~--~pv~~aL~~~~~~~--------~L- 137 (334)
T PLN02632 73 ERRKAIWAIYVWCRRTDELVDGPNASHITPAALDRWEARLED----LFDGRPY--DMLDAALADTVSKF--------PL- 137 (334)
T ss_pred HHHHHHHHHHHHHHHHhHHhcCCCCChhhHHHHHHHHHHHHH----HhCCCCC--ChHHHHHHHHHHHC--------CC-
Confidence 355555566677778999999654221 22222222222 1111121 24556666655432 11
Q ss_pred cHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhc
Q 043754 132 GLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLG 185 (320)
Q Consensus 132 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~ 185 (320)
-++.+.+++.++..... ....+|++|+..+...+.|+--.+++..++
T Consensus 138 ----~~~~~~~li~g~~~Dl~---~~~~~t~~eL~~Ycy~vAgtVG~l~l~vlg 184 (334)
T PLN02632 138 ----DIQPFRDMIEGMRMDLV---KSRYENFDELYLYCYYVAGTVGLMSVPVMG 184 (334)
T ss_pred ----ChHHHHHHHHHHHHHhc---cCCCCCHHHHHHHHHHhhHHHHHHHHHHhC
Confidence 13445677777654332 345679888888877777766655554444
No 22
>PLN02857 octaprenyl-diphosphate synthase
Probab=74.08 E-value=90 Score=30.38 Aligned_cols=88 Identities=14% Similarity=0.097 Sum_probs=55.8
Q ss_pred cHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhcCCCCCCHHHHhhccCchHHHHHHHhH
Q 043754 132 GLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLGMEDIVTKEAFEWVSGNPKIVQASSII 211 (320)
Q Consensus 132 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i 211 (320)
+...+.+...+.+.+-+.+..+.. ..-+|.++|+..-..-+|..+..++..-+.--..+++..+. ..++-+..++.
T Consensus 228 ~~~~~s~~~~~l~~Gei~q~~~~~-~~~~s~~~Yl~~i~~KTa~L~~~a~~~gallaga~~~~~~~---l~~fG~~LGiA 303 (416)
T PLN02857 228 VIKLISQVIKDFASGEIKQASSLF-DCDVTLDEYLLKSYYKTASLIAASTKSAAIFSGVDSSVKEQ---MYEYGKNLGLA 303 (416)
T ss_pred HHHHHHHHHHHHHhhHHHHHhccc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHH---HHHHHHHHHHH
Confidence 455667777777888777777654 34579999999877766665443321111111234554443 36667777888
Q ss_pred HHHhcCccchHH
Q 043754 212 CRLMDDIVSHKF 223 (320)
Q Consensus 212 ~rL~NDi~S~~~ 223 (320)
.-+.+|+..+..
T Consensus 304 FQI~DDiLD~~~ 315 (416)
T PLN02857 304 FQVVDDILDFTQ 315 (416)
T ss_pred HHHHHHHHhhcC
Confidence 888899988753
No 23
>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=66.22 E-value=1.1e+02 Score=28.39 Aligned_cols=86 Identities=12% Similarity=0.081 Sum_probs=55.1
Q ss_pred cHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhcCC-CCCCHHHHhhccCchHHHHHHHh
Q 043754 132 GLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLGME-DIVTKEAFEWVSGNPKIVQASSI 210 (320)
Q Consensus 132 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~~g-~~l~~e~~~~~~~~~~l~~~~~~ 210 (320)
....+.++....+.|-..+..|.. +..+|.++|++.-..-+|..+..++ ..+.- -..+++..+. ..++-+..++
T Consensus 130 ~~~~~~~~~~~~~~Gq~~~~~~~~-~~~~~~~~Y~~~i~~KTa~L~~~~~-~~ga~~ag~~~~~~~~---l~~~g~~lG~ 204 (319)
T TIGR02748 130 AHQILSHTIVEVCRGEIEQIKDKY-NFDQNLRTYLRRIKRKTALLIAASC-QLGAIASGANEAIVKK---LYWFGYYVGM 204 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHcCCCHHHHHH---HHHHHHHHHH
Confidence 456677778888888887877743 3457999999887777776544332 22110 0123443332 3556677788
Q ss_pred HHHHhcCccchH
Q 043754 211 ICRLMDDIVSHK 222 (320)
Q Consensus 211 i~rL~NDi~S~~ 222 (320)
..-+.||+..+.
T Consensus 205 aFQI~DDilD~~ 216 (319)
T TIGR02748 205 SYQITDDILDFV 216 (319)
T ss_pred HHHHHHHHHHcc
Confidence 888889987764
No 24
>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]
Probab=64.72 E-value=6.3 Score=33.91 Aligned_cols=47 Identities=28% Similarity=0.282 Sum_probs=30.7
Q ss_pred HHHHhcCccchHHhhhcC-CcchhHHHHHhhCCCCHHHHHHHHHHHHH
Q 043754 211 ICRLMDDIVSHKFEQQRG-HVASAVECYMKQHGVSEEEAVKVFREKVG 257 (320)
Q Consensus 211 i~rL~NDi~S~~~E~~~g-~~~n~V~~ym~e~g~s~eeA~~~i~~~i~ 257 (320)
.-.|--++..+++..+.- .+.-+=.++|+++|+|++||.++++++-=
T Consensus 127 ~~~L~~el~~~k~~L~~rK~ierAKglLM~~~g~sE~EAy~~lR~~AM 174 (194)
T COG3707 127 RRALRRELAKLKDRLEERKVIERAKGLLMKRRGLSEEEAYKLLRRTAM 174 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 444555566666654322 22333347999999999999999888543
No 25
>PF03861 ANTAR: ANTAR domain; InterPro: IPR005561 ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins []. This domain has been detected in various response regulators of two-component systems, which are structured around two proteins, a histidine kinase and a response regulator. This domain is also found in one-component sensory regulators from a variety of bacteria. Most response regulators interact with DNA, however ANTAR-containing regulators interact with RNA. The majority of the domain consists of a coiled-coil.; PDB: 4AKK_A 1SD5_A 1S8N_A 1QO0_E.
Probab=64.27 E-value=7.8 Score=26.12 Aligned_cols=28 Identities=29% Similarity=0.439 Sum_probs=20.7
Q ss_pred cchhHHHHHhhCCCCHHHHHHHHHHHHH
Q 043754 230 VASAVECYMKQHGVSEEEAVKVFREKVG 257 (320)
Q Consensus 230 ~~n~V~~ym~e~g~s~eeA~~~i~~~i~ 257 (320)
+.-++.+.|..+|+|+++|.+.++..-.
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 3456778999999999999998877544
No 26
>PF12368 DUF3650: Protein of unknown function (DUF3650) ; InterPro: IPR022111 This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with PF00581 from PFAM. There is a single completely conserved residue N that may be functionally important.
Probab=59.99 E-value=7.8 Score=22.38 Aligned_cols=18 Identities=44% Similarity=0.746 Sum_probs=14.2
Q ss_pred HHHhhCCCCHHHHHHHHH
Q 043754 236 CYMKQHGVSEEEAVKVFR 253 (320)
Q Consensus 236 ~ym~e~g~s~eeA~~~i~ 253 (320)
-|.++||+|.||-.+.+.
T Consensus 9 rYV~eh~ls~ee~~~RL~ 26 (28)
T PF12368_consen 9 RYVKEHGLSEEEVAERLA 26 (28)
T ss_pred hhHHhcCCCHHHHHHHHH
Confidence 488999999999666543
No 27
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=56.50 E-value=1.7e+02 Score=27.28 Aligned_cols=87 Identities=16% Similarity=0.093 Sum_probs=56.3
Q ss_pred cHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhcC-CCCCCHHHHhhccCchHHHHHHHh
Q 043754 132 GLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLGM-EDIVTKEAFEWVSGNPKIVQASSI 210 (320)
Q Consensus 132 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~~-g~~l~~e~~~~~~~~~~l~~~~~~ 210 (320)
....+.++....+.|-..+..|... .-+|.++|+.....-+|..+..++ ..+. --..+++..+. ..++-+..++
T Consensus 131 ~~~~~~~~~~~~~~Gq~~d~~~~~~-~~~s~~~y~~~i~~KTa~lf~~~~-~~ga~lag~~~~~~~~---l~~~g~~lG~ 205 (323)
T PRK10888 131 VLEVMSEAVNVIAEGEVLQLMNVND-PDITEENYMRVIYSKTARLFEAAA-QCSGILAGCTPEQEKG---LQDYGRYLGT 205 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHcCCCHHHHHH---HHHHHHHHHH
Confidence 4556677778888888888776543 358999999988777766643332 2221 01134443332 3567777888
Q ss_pred HHHHhcCccchHH
Q 043754 211 ICRLMDDIVSHKF 223 (320)
Q Consensus 211 i~rL~NDi~S~~~ 223 (320)
..-+.||+..+..
T Consensus 206 aFQi~DD~ld~~~ 218 (323)
T PRK10888 206 AFQLIDDLLDYSA 218 (323)
T ss_pred HHHHHHHhhcccC
Confidence 8888999988753
No 28
>PRK10581 geranyltranstransferase; Provisional
Probab=54.80 E-value=1.5e+02 Score=27.28 Aligned_cols=111 Identities=14% Similarity=0.137 Sum_probs=66.2
Q ss_pred HHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHH--HHhcCCCCCCHHHHhhccCchHHHHHHHhHHHHhcCcc
Q 043754 142 ILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTS--SFLGMEDIVTKEAFEWVSGNPKIVQASSIICRLMDDIV 219 (320)
Q Consensus 142 ~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~--~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~ 219 (320)
..+.|-..+..|.. ..+|.++|++.-..-+|.....+. .-+..|.. +++..+. ..++-+..++..-+.+|+.
T Consensus 153 ~l~~GQ~ld~~~~~--~~~~~~~y~~i~~~KTa~L~~~~~~~gailag~~-~~~~~~~---l~~~g~~lG~aFQI~DDil 226 (299)
T PRK10581 153 GMCGGQALDLEAEG--KQVPLDALERIHRHKTGALIRAAVRLGALSAGDK-GRRALPV---LDRYAESIGLAFQVQDDIL 226 (299)
T ss_pred hhhHhhHHHHhccC--CCCCHHHHHHHHHHhhHHHHHHHHHHHHHHcCCC-cHHHHHH---HHHHHHHHHHHHHHHHHHc
Confidence 45666666666643 468999999877655555543222 11222321 2233332 3667788888888999999
Q ss_pred chHHh-h----------hcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHH
Q 043754 220 SHKFE-Q----------QRGHVASAVECYMKQHGVSEEEAVKVFREKVGNAWKDINE 265 (320)
Q Consensus 220 S~~~E-~----------~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~ 265 (320)
.+... . ..|.. +.+.++- .+.|.+.+++.++.+.+.+..
T Consensus 227 D~~g~~~~~GK~~g~Dl~~gk~-T~p~l~~------~e~a~~~a~~~~~~A~~~l~~ 276 (299)
T PRK10581 227 DVVGDTATLGKRQGADQQLGKS-TYPALLG------LEQARKKARDLIDDARQSLDQ 276 (299)
T ss_pred cccCChHHHCCCcchhhhcCCC-CHHHHHH------HHHHHHHHHHHHHHHHHHHHh
Confidence 87432 1 22322 4443332 467888888888888777664
No 29
>smart00400 ZnF_CHCC zinc finger.
Probab=44.06 E-value=29 Score=23.16 Aligned_cols=25 Identities=32% Similarity=0.304 Sum_probs=20.5
Q ss_pred CCcchhHHHHHhhCCCCHHHHHHHH
Q 043754 228 GHVASAVECYMKQHGVSEEEAVKVF 252 (320)
Q Consensus 228 g~~~n~V~~ym~e~g~s~eeA~~~i 252 (320)
|.-.++|..+|+-.|+|-.||++.+
T Consensus 30 g~gGd~i~fv~~~~~~sf~eA~~~L 54 (55)
T smart00400 30 GAGGNVISFLMKYDKLSFVEAVKKL 54 (55)
T ss_pred CCCCCHHHHHHHHHCcCHHHHHHHh
Confidence 4445889999998899999998865
No 30
>CHL00151 preA prenyl transferase; Reviewed
Probab=43.24 E-value=2.8e+02 Score=25.83 Aligned_cols=86 Identities=7% Similarity=0.041 Sum_probs=53.0
Q ss_pred cHhhHHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHH--HHhcCCCCCCHHHHhhccCchHHHHHHH
Q 043754 132 GLPFAKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTS--SFLGMEDIVTKEAFEWVSGNPKIVQASS 209 (320)
Q Consensus 132 ~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~--~~~~~g~~l~~e~~~~~~~~~~l~~~~~ 209 (320)
....+.+....++.+-+.+..+.. ..-+|.++|+..-..-+|..+..++ .-+..| .+++..+. ..++-+..+
T Consensus 135 ~~~~~~~~~~~l~~G~~~~~~~~~-~~~~~~~~yl~~i~~KTa~L~~~~~~~ga~lag--~~~~~~~~---l~~~G~~lG 208 (323)
T CHL00151 135 VVKLISKVITDFAEGEIRQGLVQF-DTTLSILNYIEKSFYKTASLIAASCKAAALLSD--ADEKDHND---FYLYGKHLG 208 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCC-CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHcC--CCHHHHHH---HHHHHHHHH
Confidence 355667777778887776666533 3347999999975555554443322 112123 34443333 356677788
Q ss_pred hHHHHhcCccchHH
Q 043754 210 IICRLMDDIVSHKF 223 (320)
Q Consensus 210 ~i~rL~NDi~S~~~ 223 (320)
+..-+.||+..+.-
T Consensus 209 ~aFQi~DDilD~~~ 222 (323)
T CHL00151 209 LAFQIIDDVLDITS 222 (323)
T ss_pred HHHHHHHHHhhccc
Confidence 88888999988753
No 31
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=39.14 E-value=62 Score=29.27 Aligned_cols=67 Identities=22% Similarity=0.212 Sum_probs=48.8
Q ss_pred ccchHHhhhcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHh----------hcCCCCCCHHHHHHHHHHHhh
Q 043754 218 IVSHKFEQQRGHVASAVECYMKQHGVSEEEAVKVFREKVGNAWKDINEE----------LMRPPVVPMPLLERVLNLARL 287 (320)
Q Consensus 218 i~S~~~E~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~~----------~~~~~~~p~~~~~~~~n~~r~ 287 (320)
+..|++||+ .++.+...+...|.+.++|.+.+.--+++.+-++-.. +|...++|...+..+.++||-
T Consensus 94 ~~~wk~~qk---a~klle~aaekl~~~~ee~~~~vg~~L~e~fG~~y~aFE~aa~~g~~~l~~~~~~~~~~~~l~e~a~e 170 (269)
T COG1093 94 IQEWKKEQK---ADKLLELAAEKLGKDLEEAYEEVGWKLEEEFGSLYDAFEAAAKEGGEVLDDEGVPEEWKEVLKEIARE 170 (269)
T ss_pred HHHHHHHHH---HHHHHHHHHHHhCCCHHHHHHHHhHHHHHHhCCHHHHHHHHHhcCCcccccCCCCHHHHHHHHHHHHh
Confidence 345666665 3577888888889999999999887777665443322 233357888999999999984
No 32
>smart00463 SMR Small MutS-related domain.
Probab=38.52 E-value=43 Score=24.00 Aligned_cols=24 Identities=29% Similarity=0.320 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q 043754 241 HGVSEEEAVKVFREKVGNAWKDIN 264 (320)
Q Consensus 241 ~g~s~eeA~~~i~~~i~~~~k~l~ 264 (320)
||++.++|+..+...++++++.-.
T Consensus 7 HG~~~~eA~~~l~~~l~~~~~~~~ 30 (80)
T smart00463 7 HGLTVEEALTALDKFLNNARLKGL 30 (80)
T ss_pred CCCCHHHHHHHHHHHHHHHHHcCC
Confidence 799999999999999998887643
No 33
>PHA01082 putative transcription regulator
Probab=35.93 E-value=67 Score=25.48 Aligned_cols=43 Identities=23% Similarity=0.156 Sum_probs=26.8
Q ss_pred hCCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHH-HHHHhh
Q 043754 240 QHGVSEEEAVKVFREKVGNAWKDINEELMRPPVVPMPLLERV-LNLARL 287 (320)
Q Consensus 240 e~g~s~eeA~~~i~~~i~~~~k~l~~~~~~~~~~p~~~~~~~-~n~~r~ 287 (320)
|-|+|.|||.+-+-+-+. ..|+ +=+...+|+.|+++. ++-.|-
T Consensus 28 eCgLsveeaa~LCfKsVr-tVk~----WD~G~~IPPeCkRLMr~~~gRE 71 (133)
T PHA01082 28 ECGLSVEEAAKLCFKTVS-EVKQ----WDAGEKIPPICKRLMRWHSRRE 71 (133)
T ss_pred ccCccHHHHHHHHHHhHH-HHhh----ccCCCcCChHHHHHHHHhcccc
Confidence 459999998765444332 2222 223678999999876 444443
No 34
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=35.07 E-value=43 Score=26.57 Aligned_cols=20 Identities=45% Similarity=0.669 Sum_probs=17.0
Q ss_pred HHHHHhhCCCCHHHHHHHHH
Q 043754 234 VECYMKQHGVSEEEAVKVFR 253 (320)
Q Consensus 234 V~~ym~e~g~s~eeA~~~i~ 253 (320)
|.+.|.|.|+|.++|++.+.
T Consensus 88 IkLV~eQa~VsreeA~kAL~ 107 (122)
T COG1308 88 IKLVMEQAGVSREEAIKALE 107 (122)
T ss_pred HHHHHHHhCCCHHHHHHHHH
Confidence 67889999999999988654
No 35
>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=34.37 E-value=53 Score=23.71 Aligned_cols=27 Identities=33% Similarity=0.450 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 043754 241 HGVSEEEAVKVFREKVGNAWKDINEEL 267 (320)
Q Consensus 241 ~g~s~eeA~~~i~~~i~~~~k~l~~~~ 267 (320)
||++.++|...+...++.+++.-.+.+
T Consensus 4 HG~~~~eA~~~l~~~l~~~~~~~~~~~ 30 (83)
T PF01713_consen 4 HGLTVEEALRALEEFLDEARQRGIREL 30 (83)
T ss_dssp TTS-HHHHHHHHHHHHHHHHHTTHSEE
T ss_pred CCCcHHHHHHHHHHHHHHHHHcCCCEE
Confidence 799999999999999999886655444
No 36
>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=34.37 E-value=4e+02 Score=25.08 Aligned_cols=100 Identities=17% Similarity=0.180 Sum_probs=57.5
Q ss_pred HHHhcCCCCCCHHHHhhccCchHHHHHHHhHHHHhcCccchHHhhhcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHH
Q 043754 181 SSFLGMEDIVTKEAFEWVSGNPKIVQASSIICRLMDDIVSHKFEQQRGHVASAVECYMKQHGVSEEEAVKVFREKVGNAW 260 (320)
Q Consensus 181 ~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~ 260 (320)
+.-++....++++..+.+. ....-.++-+-.|++=....+.+...|+. |.|..| -+.+++.+.+.-.++++-
T Consensus 197 L~a~A~~p~~t~~~a~~i~--~aYFPwI~gLHILLDy~IDq~EDr~~GdL-NFv~YY-----~~~~~~~~Rl~~f~~~A~ 268 (330)
T PF10776_consen 197 LFAYAADPDLTPEDAEKIK--DAYFPWICGLHILLDYFIDQEEDREGGDL-NFVFYY-----PDEEEMEERLKYFVEKAL 268 (330)
T ss_pred HHHHHcCCCCCHHHHHHHH--HcccHHHHHHHHHHHHHhhhHhHhcCCCc-eeeeeC-----CCHHHHHHHHHHHHHHHH
Confidence 3334445667777666542 22222333344455555555666667776 888644 367888999999999888
Q ss_pred HHHHHhhcCCCCCCHHHHHHHHHHHhhhhhhcccCCC
Q 043754 261 KDINEELMRPPVVPMPLLERVLNLARLMDVLYQNNDS 297 (320)
Q Consensus 261 k~l~~~~~~~~~~p~~~~~~~~n~~r~~~~~Y~~~D~ 297 (320)
+...+ +|.+-- +--+.|.+--+|-.++.
T Consensus 269 ~~~~~-------Lp~~~f--Hr~iv~GLla~YLSD~K 296 (330)
T PF10776_consen 269 EQASR-------LPYPKF--HRMIVRGLLAMYLSDPK 296 (330)
T ss_pred HHHHh-------CCCchH--HHHHHHHHHHHHhCCHh
Confidence 77664 665322 22233333336864443
No 37
>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=34.35 E-value=3.4e+02 Score=24.20 Aligned_cols=66 Identities=20% Similarity=0.206 Sum_probs=42.4
Q ss_pred CCCCCChHHHHhhhhhhhhhhHHHHHHHhcCCCCCCHHHHhhccCchHHHHHHHhHHHHhcCccchHHh
Q 043754 156 QQYVPTMEEYMRVALLSCGYLLLSTSSFLGMEDIVTKEAFEWVSGNPKIVQASSIICRLMDDIVSHKFE 224 (320)
Q Consensus 156 ~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E 224 (320)
.+..+|.++|++.-..-+|..+..++..-++=-..+++..+. ..++-+..++..-+.||+..+...
T Consensus 129 ~~~~~~~~~y~~i~~~KTg~l~~~~~~~ga~lag~~~~~~~~---l~~~g~~lG~afQi~DD~~d~~~~ 194 (260)
T PF00348_consen 129 EDKDPTEEEYLEIIRLKTGSLFALACQLGAILAGADEEQIEA---LREFGRHLGIAFQIRDDLLDLFGD 194 (260)
T ss_dssp TTSSTSHHHHHHHHHHHTHHHHHHHHHHHHHHTTSGHHHHHH---HHHHHHHHHHHHHHHHHHHHHHSH
T ss_pred ccccccHHHHHHHHhhcchHHHHHHHHHHHHhccchhHHHHH---HHHHHHHHHHHHhhhhhhhhccCc
Confidence 344889999999988887776544332221101123444333 467778888888899998887754
No 38
>COG1562 ERG9 Phytoene/squalene synthetase [Lipid metabolism]
Probab=31.58 E-value=4.1e+02 Score=24.39 Aligned_cols=114 Identities=16% Similarity=0.128 Sum_probs=59.9
Q ss_pred hHHHHHHHHHHHHHHHHhhhhccCCHHHHHHHHHHHHhcchhhcccCchhHHHHHHHHHHHHHHHHHHHHhcCCcccHhh
Q 043754 56 LARKILTKVISMASIIDDIYDAYGTIEELELFATAIERWDLSAIDLLPEYIKLCYCALLDAYSEFEKDLASKGILYGLPF 135 (320)
Q Consensus 56 ~~Rl~~ak~~~l~~~iDD~~D~~~t~~el~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~~~~e~~~~~~~~~~~~~~~~ 135 (320)
..|-..+-+-.+.=.+||+-|..+.++....+.+.+++=-....+.-|..-.++-.++-.+..+ ...
T Consensus 34 ~~R~av~alYa~~R~~Ddv~D~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~pv~~al~~~~~~-------------~~~ 100 (288)
T COG1562 34 EKREAVWALYAFCREADDVVDGVSDPDLPAEILLAWRRELDGDFSGQPASDHPVLAALVEVARR-------------FGL 100 (288)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHhccccCCCcccCHHHHHHHHHHHH-------------cCC
Confidence 4666666788888899999998876655555655555410111011111123455555444433 112
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCChHHHHhhhhhhhhhhHHHHHHHhc
Q 043754 136 AKESMKILVRSYIIEARWCDQQYVPTMEEYMRVALLSCGYLLLSTSSFLG 185 (320)
Q Consensus 136 l~~~w~~~~~~~~~Ea~w~~~~~~Pt~eEYl~~~~~s~g~~~~~~~~~~~ 185 (320)
-++...+++.++........-.....+++|. ..+.|+--.+++..++
T Consensus 101 ~~~~~~~~~da~~~Dl~~~~y~~~~eL~~Yc---~~vAg~vG~l~~~Il~ 147 (288)
T COG1562 101 PREAFPALIDAMRMDLDRTRYLDFEELEEYC---YGVAGAVGLLLARILG 147 (288)
T ss_pred CHHHHHHHHHHHHHHhhhccccCHHHHHHHH---HHhHHHHHHHHHHHhC
Confidence 2455666777766555543323333455554 4455544444444443
No 39
>PF03701 UPF0181: Uncharacterised protein family (UPF0181); InterPro: IPR005371 This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH P76260 from SWISSPROT.
Probab=31.47 E-value=1.1e+02 Score=20.39 Aligned_cols=44 Identities=23% Similarity=0.408 Sum_probs=27.4
Q ss_pred cCccchHHhhhcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHH
Q 043754 216 DDIVSHKFEQQRGHVASAVECYMKQHGVSEEEAVKVFREKVGNAWK 261 (320)
Q Consensus 216 NDi~S~~~E~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k 261 (320)
||+-+...|+...-+ -=|.-+| ..|+|.-||+..+...|.+..+
T Consensus 3 ~~lp~LtHeeQQ~Av-E~Iq~LM-aqGmSsgEAI~~VA~~iRe~~~ 46 (51)
T PF03701_consen 3 NDLPSLTHEEQQQAV-ERIQELM-AQGMSSGEAIAIVAQEIREEHQ 46 (51)
T ss_pred CCCCCCCHHHHHHHH-HHHHHHH-HhcccHHHHHHHHHHHHHHHHH
Confidence 566666655543222 1233455 4689999999988887776543
No 40
>PF06603 UpxZ: UpxZ family of transcription anti-terminator antagonists; InterPro: IPR010570 This family consists of several hypothetical proteins of unknown function and seems to be specific to Bacteroides species.
Probab=30.75 E-value=1e+02 Score=23.80 Aligned_cols=70 Identities=14% Similarity=0.226 Sum_probs=41.3
Q ss_pred hHHHHHHHhHHHHhcCccchHHhhhcCCcchh-HHHHHhhCCCCH---HHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHH
Q 043754 202 PKIVQASSIICRLMDDIVSHKFEQQRGHVASA-VECYMKQHGVSE---EEAVKVFREKVGNAWKDINEELMRPPVVPMPL 277 (320)
Q Consensus 202 ~~l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~-V~~ym~e~g~s~---eeA~~~i~~~i~~~~k~l~~~~~~~~~~p~~~ 277 (320)
.++.++-..+.+.+||+.+.+-+....+ +|. +.+.| -+++|. -+.-++++..++.+|.-+.+ +|.+.
T Consensus 25 D~~~rLN~ev~~~~~~Ly~~~G~t~Eee-A~lCLaLLm-GYnat~yd~geke~~~Q~vL~Rs~~vL~~-------Lp~Sl 95 (106)
T PF06603_consen 25 DDFSRLNKEVYEQSNDLYSQHGSTPEEE-ANLCLALLM-GYNATIYDNGEKEEKKQEVLDRSWEVLDK-------LPASL 95 (106)
T ss_pred HHHHHHhHHHHHHHHHHHhccCCCHHHH-HHHHHHHHH-hccchhhhCccHHHHHHHHHHHHHHHHHh-------CCcHH
Confidence 4567788888899999988643222111 243 22333 233321 12334678899999977764 77766
Q ss_pred HHH
Q 043754 278 LER 280 (320)
Q Consensus 278 ~~~ 280 (320)
++.
T Consensus 96 LK~ 98 (106)
T PF06603_consen 96 LKV 98 (106)
T ss_pred HHH
Confidence 554
No 41
>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=30.64 E-value=3.1e+02 Score=22.69 Aligned_cols=14 Identities=21% Similarity=0.679 Sum_probs=10.5
Q ss_pred HhhCCCCCChHHHH
Q 043754 153 WCDQQYVPTMEEYM 166 (320)
Q Consensus 153 w~~~~~~Pt~eEYl 166 (320)
|...|..||++|+-
T Consensus 112 ~srAg~~~~Lqe~~ 125 (152)
T TIGR03486 112 WARAGRIPSLQEHW 125 (152)
T ss_pred HHHccCCcchHHHH
Confidence 56778888888763
No 42
>PTZ00393 protein tyrosine phosphatase; Provisional
Probab=30.41 E-value=50 Score=29.54 Aligned_cols=27 Identities=15% Similarity=0.326 Sum_probs=23.3
Q ss_pred CCcchhHHHHHhhCCCCHHHHHHHHHH
Q 043754 228 GHVASAVECYMKQHGVSEEEAVKVFRE 254 (320)
Q Consensus 228 g~~~n~V~~ym~e~g~s~eeA~~~i~~ 254 (320)
|-.+.++.+||-++|++.++|++.++.
T Consensus 182 GRTGtl~AayLI~~GmspeeAI~~VR~ 208 (241)
T PTZ00393 182 GRAPVLASIVLIEFGMDPIDAIVFIRD 208 (241)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 555688889999999999999998876
No 43
>PF11050 Viral_env_E26: Virus envelope protein E26; InterPro: IPR021286 DA26 (E26) is a multifunctional protein. One form of E26 associates with viral DNA or DNA binding proteins, while a second form associates with intracellular membranes [].
Probab=30.31 E-value=48 Score=28.12 Aligned_cols=24 Identities=25% Similarity=0.530 Sum_probs=21.4
Q ss_pred CcchHHhHHHHHHHHHHHHHHhhh
Q 043754 1 MLDFNILQKQHQEELRDIVRWWKN 24 (320)
Q Consensus 1 kldfn~~Q~~hq~El~~l~~W~~~ 24 (320)
.||||-+|.+|++-++++++-.+.
T Consensus 57 rlnF~KlsqlqkKrvRnmQ~LlRK 80 (206)
T PF11050_consen 57 RLNFNKLSQLQKKRVRNMQRLLRK 80 (206)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHh
Confidence 489999999999999999997655
No 44
>KOG3730 consensus Acyl-CoA:dihydroxyactetone-phosphate acyltransferase DHAPAT [Lipid transport and metabolism]
Probab=30.07 E-value=3.5e+02 Score=26.93 Aligned_cols=68 Identities=16% Similarity=0.163 Sum_probs=46.2
Q ss_pred cchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhhhhhcccCCCCCCc-hhHHHHH
Q 043754 230 VASAVECYMKQHGVSEEEAVKVFREKVGNAWKDINEELMRPPVVPMPLLERVLNLARLMDVLYQNNDSYTNP-HLMKDHV 308 (320)
Q Consensus 230 ~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~~~~~~~~~p~~~~~~~~n~~r~~~~~Y~~~D~~~~~-~~~~~~i 308 (320)
+.+.|.-|-+|.|.|.+.-.+++++++++.-.++|-. .++-.-+.+++++.=+|. |++.. ..|.+.=
T Consensus 77 ~~sVi~~~~kes~~s~d~~r~ea~eIlDEmsh~~nl~---------~IR~cg~ai~ki~k~i~d---g~yVNe~~~~~vr 144 (685)
T KOG3730|consen 77 LRSVIEHYAKESGTSLDQMRREAREILDEMSHDRNLA---------IIRWCGIAITKIGKRICD---GFYVNEASMANVR 144 (685)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhcchH---------HHHHHHHHHHHHHHHHhc---ceeECHHHHHHHH
Confidence 4588888999999999888888887777554444421 233445778888877776 88876 4454433
Q ss_pred H
Q 043754 309 A 309 (320)
Q Consensus 309 ~ 309 (320)
+
T Consensus 145 ~ 145 (685)
T KOG3730|consen 145 K 145 (685)
T ss_pred H
Confidence 3
No 45
>PF13189 Cytidylate_kin2: Cytidylate kinase-like family; PDB: 3FDI_A.
Probab=29.92 E-value=17 Score=30.65 Aligned_cols=35 Identities=29% Similarity=0.369 Sum_probs=23.7
Q ss_pred HHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhhcC
Q 043754 234 VECYMKQHGVSEEEAVKVFREKVGNAWKDINEELMR 269 (320)
Q Consensus 234 V~~ym~e~g~s~eeA~~~i~~~i~~~~k~l~~~~~~ 269 (320)
|.-.|+.+|+|+++|.+.+.+ .+...+.+-+.+..
T Consensus 128 v~ri~~~~~~s~~~A~~~i~~-~D~~R~~~~~~~~~ 162 (179)
T PF13189_consen 128 VERIMEREGISEEEAEKLIKK-EDKRRRAYYKYYTG 162 (179)
T ss_dssp HHHHHHHHT--HHHHHHHHHH-HHHHHHHHHHHH-S
T ss_pred HHHHHHHcCCCHHHHHHHHHH-HHHHHHHHHHHHhC
Confidence 344677789999999998877 67777777776664
No 46
>KOG2077 consensus JNK/SAPK-associated protein-1 [Signal transduction mechanisms]
Probab=29.90 E-value=1.2e+02 Score=30.73 Aligned_cols=98 Identities=15% Similarity=0.261 Sum_probs=53.4
Q ss_pred cCCCCCCHHHHhhccCchHHHHHHHhHHHHhcCcc------chHHhhhcCCcchh--HHHHHhhCCCCHHHHHHHHHHHH
Q 043754 185 GMEDIVTKEAFEWVSGNPKIVQASSIICRLMDDIV------SHKFEQQRGHVASA--VECYMKQHGVSEEEAVKVFREKV 256 (320)
Q Consensus 185 ~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~------S~~~E~~~g~~~n~--V~~ym~e~g~s~eeA~~~i~~~i 256 (320)
|||.. |-+-+..+..|+..-+.++..-||+. +.+++.-+|..-.. +..=|.+.---.||-++.++...
T Consensus 298 GMGrE----VeNLilENsqLLetKNALNiVKNDLIakVDeL~~E~~vLrgElea~kqak~Klee~i~elEEElk~~k~ea 373 (832)
T KOG2077|consen 298 GMGRE----VENLILENSQLLETKNALNIVKNDLIAKVDELTCEKDVLRGELEAVKQAKLKLEEKIRELEEELKKAKAEA 373 (832)
T ss_pred cchHH----HHHHHHhhHHHHhhhhHHHHHHHHHHHHHHhhccHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55543 44444556788877777777788875 44555556654221 11122222112233344444444
Q ss_pred HHHHHHHHHhhcCCCCCCHHHHHHH--HHHHhhh
Q 043754 257 GNAWKDINEELMRPPVVPMPLLERV--LNLARLM 288 (320)
Q Consensus 257 ~~~~k~l~~~~~~~~~~p~~~~~~~--~n~~r~~ 288 (320)
.++.++- .+-..+.+|..-+++| ..|+|++
T Consensus 374 ~~ar~~~--~~~e~ddiPmAqRkRFTRvEMaRVL 405 (832)
T KOG2077|consen 374 EDARQKA--KDDEDDDIPMAQRKRFTRVEMARVL 405 (832)
T ss_pred HHHHHhh--cccccccccHHHHhhhHHHHHHHHH
Confidence 4443321 1112478999999988 6788887
No 47
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=26.39 E-value=70 Score=25.22 Aligned_cols=27 Identities=41% Similarity=0.431 Sum_probs=20.8
Q ss_pred CCcchhHHHHHhhCCCCHHHHHHHHHH
Q 043754 228 GHVASAVECYMKQHGVSEEEAVKVFRE 254 (320)
Q Consensus 228 g~~~n~V~~ym~e~g~s~eeA~~~i~~ 254 (320)
|-...-|...|.+.|+|.++|++.+.+
T Consensus 74 ~i~~edI~lv~~q~gvs~~~A~~AL~~ 100 (115)
T PRK06369 74 EIPEEDIELVAEQTGVSEEEARKALEE 100 (115)
T ss_pred CCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 333466889999999999999886543
No 48
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=26.36 E-value=70 Score=24.13 Aligned_cols=30 Identities=37% Similarity=0.491 Sum_probs=20.4
Q ss_pred CCcchhHHHHHhhCCCCHHHHHHHHHHHHH
Q 043754 228 GHVASAVECYMKQHGVSEEEAVKVFREKVG 257 (320)
Q Consensus 228 g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~ 257 (320)
|...|+|..+|+-.|+|-.||++.+.++..
T Consensus 61 g~~Gd~i~~v~~~~~~~f~eAv~~l~~~~~ 90 (97)
T PF01807_consen 61 GKGGDVIDFVMKYEGCSFKEAVKWLAEEFG 90 (97)
T ss_dssp --EE-HHHHHHHHHT--HHHHHHHHHHHHT
T ss_pred CCCCcHHhHHHHHhCCCHHHHHHHHHHHhC
Confidence 444588999998889999999998877543
No 49
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=25.91 E-value=78 Score=19.32 Aligned_cols=25 Identities=24% Similarity=0.546 Sum_probs=18.2
Q ss_pred HHHHHHhhhcCCCCCchh-hhhhhhh
Q 043754 16 RDIVRWWKNFDVPNKLPF-IRDRVVE 40 (320)
Q Consensus 16 ~~l~~W~~~~~l~~~l~~-~R~r~~~ 40 (320)
.+|..|.++.|+...-+. .|+.++.
T Consensus 7 ~~L~~wL~~~gi~~~~~~~~rd~Ll~ 32 (38)
T PF10281_consen 7 SDLKSWLKSHGIPVPKSAKTRDELLK 32 (38)
T ss_pred HHHHHHHHHcCCCCCCCCCCHHHHHH
Confidence 468889999999544444 7887764
No 50
>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=25.66 E-value=31 Score=27.67 Aligned_cols=53 Identities=17% Similarity=0.281 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHhcCCcccHhhHHHHHHHHHHHHHHHHHHhhCCCCCChH-HHHhhh
Q 043754 113 LLDAYSEFEKDLASKGILYGLPFAKESMKILVRSYIIEARWCDQQYVPTME-EYMRVA 169 (320)
Q Consensus 113 l~~~~~e~~~~~~~~~~~~~~~~l~~~w~~~~~~~~~Ea~w~~~~~~Pt~e-EYl~~~ 169 (320)
++..+.+|++.+...| ..+-.+.|++++.+.+.-++.....-+|.++ ++...|
T Consensus 43 lwa~l~dIs~qv~~~G----~k~~~e~WK~~~~~~~~~~~~~~~~~~~gl~Gg~v~~g 96 (127)
T PF05772_consen 43 LWAMLGDISRQVEWNG----RKLDPEDWKELFTAAFLIATGEEQRVVPGLDGGFVVLG 96 (127)
T ss_dssp HHHHHHHHHHH--BTT----B---HHHHHHHHHHHH-----S--EEEE-TTSSEEEE-
T ss_pred HHHHHHHHHHHhHhcC----ccCCHHHHHHHHHHHHhhhccchhhhccCCCCCeEEEe
Confidence 4446778877655544 3566899999999987655555544566655 443333
No 51
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=25.05 E-value=78 Score=24.95 Aligned_cols=23 Identities=39% Similarity=0.482 Sum_probs=19.0
Q ss_pred chhHHHHHhhCCCCHHHHHHHHH
Q 043754 231 ASAVECYMKQHGVSEEEAVKVFR 253 (320)
Q Consensus 231 ~n~V~~ym~e~g~s~eeA~~~i~ 253 (320)
..-|...|.+.|+|.++|++.+.
T Consensus 79 ~eDI~lV~eq~gvs~e~A~~AL~ 101 (116)
T TIGR00264 79 EDDIELVMKQCNVSKEEARRALE 101 (116)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHH
Confidence 35578899999999999988654
No 52
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=22.21 E-value=2.7e+02 Score=26.07 Aligned_cols=123 Identities=11% Similarity=0.125 Sum_probs=67.5
Q ss_pred hhhhhhhhhhHHHHHHHhcCCCCCCHHHHhhccCchHHHHHHHhHHHHhcCccchHHhhhcCCcchhHHHHHhhC-CCCH
Q 043754 167 RVALLSCGYLLLSTSSFLGMEDIVTKEAFEWVSGNPKIVQASSIICRLMDDIVSHKFEQQRGHVASAVECYMKQH-GVSE 245 (320)
Q Consensus 167 ~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~g~~~n~V~~ym~e~-g~s~ 245 (320)
+.=+..+|.+.++.....+ +.+.+-..+.+...+......+..|+..-.-|-.---..-++|.++|..... |.+.
T Consensus 220 ~sLr~dsGlhQLvPYFi~f----~~eqit~Nl~nl~~LtTv~~m~~sLL~N~~iFvdPY~hqlmPSilTcliakklg~~p 295 (450)
T COG5095 220 ESLRNDSGLHQLVPYFIHF----FNEQITKNLKNLEKLTTVVMMYSSLLKNKYIFVDPYLHQLMPSILTCLIAKKLGNVP 295 (450)
T ss_pred HHhccCccHHHHHHHHHHH----HHHHHHHhhhhHHHHHHHHHHHHHHhcCCceeecHHHHHHHHHHHHHHHHHHhcCCC
Confidence 3335567888777654443 3344444456667777777777787766544444444445678899988755 5443
Q ss_pred HH----HHHHH-HHHHHHHHHHHHHhhcCC-CCCCHHHHHHHHHHHhhhhhhcc
Q 043754 246 EE----AVKVF-REKVGNAWKDINEELMRP-PVVPMPLLERVLNLARLMDVLYQ 293 (320)
Q Consensus 246 ee----A~~~i-~~~i~~~~k~l~~~~~~~-~~~p~~~~~~~~n~~r~~~~~Y~ 293 (320)
.. |.+.+ ..++.--.+.|-+.+-.- -.+-+...+.|++..|.....|.
T Consensus 296 ~dhe~~alRd~AA~ll~yV~~~F~~~YktLkPRvtrTllKafLD~~k~~sT~YG 349 (450)
T COG5095 296 DDHEHYALRDVAADLLKYVFSNFSSSYKTLKPRVTRTLLKAFLDREKTESTQYG 349 (450)
T ss_pred cchhHHHHHHHHHHHHHHHHhhhhHhhhhhchHHHHHHHHHHHhcccccchhhh
Confidence 32 22221 122222222222222210 12445677888888888877664
No 53
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=21.70 E-value=5.9e+02 Score=22.86 Aligned_cols=67 Identities=27% Similarity=0.357 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHhhhcCCCCCchhhhhhhhhhHHHHhccccCCCchhHHHHHHHHHHHHHHHHhhhhccCCHHHHHHHHHH
Q 043754 11 HQEELRDIVRWWKNFDVPNKLPFIRDRVVEGYFWILGVYFEPKFLLARKILTKVISMASIIDDIYDAYGTIEELELFATA 90 (320)
Q Consensus 11 hq~El~~l~~W~~~~~l~~~l~~~R~r~~~~y~~~~a~~feP~~s~~Rl~~ak~~~l~~~iDD~~D~~~t~~el~~~~~a 90 (320)
-+.|+....+|+.+ |- .-+| ++++.|.-.+.. -++-+..+.-. -+||.+-.+ +..|++|
T Consensus 7 ~~~e~~~~~~~~~~-g~----~~~~-~Li~~ylpLV~~-------ia~k~~~r~~~---~~dDLiqiG-----~iGLi~A 65 (247)
T COG1191 7 SKEEEEKLLEYYAE-GD----EEAR-RLIERYLPLVKS-------IARKFENRGPS---EYDDLIQIG-----MIGLIKA 65 (247)
T ss_pred chHHHHHHHHHHHh-cC----HHHH-HHHHHHHHHHHH-------HHHHHHhcCCC---chhHHHHHH-----HHHHHHH
Confidence 35677788888887 32 2567 888888755541 12211111111 467777443 3458899
Q ss_pred HHhcchhh
Q 043754 91 IERWDLSA 98 (320)
Q Consensus 91 i~rwd~~~ 98 (320)
++|.|++-
T Consensus 66 ieryd~~k 73 (247)
T COG1191 66 IERYDPSK 73 (247)
T ss_pred HHHcCccc
Confidence 99999864
No 54
>KOG4098 consensus Molecular chaperone Prefoldin, subunit 2 [Posttranslational modification, protein turnover, chaperones]
Probab=21.61 E-value=3.1e+02 Score=22.16 Aligned_cols=63 Identities=17% Similarity=0.251 Sum_probs=39.7
Q ss_pred hccccCCCchhHHHHHHHHHHHHHHHHhhhhc----cCCHHHHHHHHHHHHhcchhhcccCchhHHHHHHHHHHHHHH
Q 043754 46 LGVYFEPKFLLARKILTKVISMASIIDDIYDA----YGTIEELELFATAIERWDLSAIDLLPEYIKLCYCALLDAYSE 119 (320)
Q Consensus 46 ~a~~feP~~s~~Rl~~ak~~~l~~~iDD~~D~----~~t~~el~~~~~ai~rwd~~~~~~lp~~~~~~~~~l~~~~~e 119 (320)
+++.++| +.++.+.+++..+=.-.-+++-. .-..+|-...++.++.-|++ +.||+.+-+++-|
T Consensus 8 ~~~~~~~--~~q~~v~a~yn~~r~el~~ia~ki~~LE~d~~EH~lVi~tlk~~dp~---------RKCfRmIgGvLVE 74 (140)
T KOG4098|consen 8 SGTAKEP--SSQQAVVAKYNALRSELQQIASKITDLEMDLREHKLVIETLKDLDPT---------RKCFRMIGGVLVE 74 (140)
T ss_pred cccccCc--hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcChh---------hHHHHHhccchhh
Confidence 3445555 67888888888887777766642 22444555666666654443 5788888775444
No 55
>PHA03253 UL35; Provisional
Probab=20.84 E-value=4.2e+02 Score=26.73 Aligned_cols=21 Identities=19% Similarity=0.319 Sum_probs=19.0
Q ss_pred hHHhHHHHHHHHHHHHHHhhh
Q 043754 4 FNILQKQHQEELRDIVRWWKN 24 (320)
Q Consensus 4 fn~~Q~~hq~El~~l~~W~~~ 24 (320)
.+.+|..|++||+.+..|...
T Consensus 247 l~nMI~~~~reLr~LR~wI~~ 267 (609)
T PHA03253 247 TWNMIYNCKKEIRRLFTWIKY 267 (609)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999874
No 56
>COG2443 Sss1 Preprotein translocase subunit Sss1 [Intracellular trafficking and secretion]
Probab=20.53 E-value=3.2e+02 Score=19.23 Aligned_cols=22 Identities=32% Similarity=0.415 Sum_probs=16.2
Q ss_pred CCCCChHHHHhhhhhhhhhhHH
Q 043754 157 QYVPTMEEYMRVALLSCGYLLL 178 (320)
Q Consensus 157 ~~~Pt~eEYl~~~~~s~g~~~~ 178 (320)
-..||-|||...+.++...-.+
T Consensus 25 arKP~~eEy~~~aKi~~~Gi~l 46 (65)
T COG2443 25 ARKPDWEEYSKIAKITGLGILL 46 (65)
T ss_pred HhCCCHHHHHHHHHHHHHHHHH
Confidence 3479999999988876644443
No 57
>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.11 E-value=80 Score=27.48 Aligned_cols=17 Identities=35% Similarity=0.792 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHhhhcCC
Q 043754 11 HQEELRDIVRWWKNFDV 27 (320)
Q Consensus 11 hq~El~~l~~W~~~~~l 27 (320)
-++|+..+.+||++.|-
T Consensus 7 E~qql~~ik~wwkeNGk 23 (207)
T COG2976 7 EQQQLEAIKDWWKENGK 23 (207)
T ss_pred HHHHHHHHHHHHHHCCc
Confidence 47899999999999996
No 58
>PRK05114 hypothetical protein; Provisional
Probab=20.09 E-value=1.9e+02 Score=19.79 Aligned_cols=44 Identities=25% Similarity=0.345 Sum_probs=26.2
Q ss_pred cCccchHHhhhcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHH
Q 043754 216 DDIVSHKFEQQRGHVASAVECYMKQHGVSEEEAVKVFREKVGNAWK 261 (320)
Q Consensus 216 NDi~S~~~E~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k 261 (320)
||+-++..|+..--+ -=|.-+| ..|+|--||+.-+...|.+..+
T Consensus 3 ~~lp~LtHeeQQ~AV-ErIq~LM-aqGmSsgEAI~~VA~eiRe~~~ 46 (59)
T PRK05114 3 AGLPSLTHEQQQKAV-ERIQELM-AQGMSSGEAIALVAEELRANHQ 46 (59)
T ss_pred CCcccCCHHHHHHHH-HHHHHHH-HccccHHHHHHHHHHHHHHHHh
Confidence 455444444433212 2233455 3689999999988888876553
Done!