Query 040645
Match_columns 233
No_of_seqs 157 out of 791
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 10:25:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040645.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040645hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00684 Terpene_cyclase_plant_ 100.0 7.8E-61 1.7E-65 453.1 24.7 227 2-230 314-542 (542)
2 PLN02279 ent-kaur-16-ene synth 100.0 6.5E-61 1.4E-65 464.5 23.4 226 2-233 547-778 (784)
3 cd00868 Terpene_cyclase_C1 Ter 100.0 2.1E-35 4.5E-40 257.0 21.7 204 2-206 80-284 (284)
4 PLN02150 terpene synthase/cycl 100.0 2.8E-35 6E-40 218.4 10.5 94 139-233 1-96 (96)
5 PF03936 Terpene_synth_C: Terp 100.0 1.2E-31 2.6E-36 231.7 15.2 176 2-178 94-270 (270)
6 PLN02592 ent-copalyl diphospha 100.0 8.8E-30 1.9E-34 247.0 18.7 185 5-232 606-800 (800)
7 cd00687 Terpene_cyclase_nonpla 99.9 3.8E-27 8.3E-32 207.9 13.8 161 16-182 105-266 (303)
8 cd00385 Isoprenoid_Biosyn_C1 I 99.8 1.7E-17 3.6E-22 138.2 13.8 179 13-200 52-243 (243)
9 cd00686 Terpene_cyclase_cis_tr 97.6 0.0015 3.2E-08 58.6 12.7 164 12-185 103-280 (357)
10 PF06330 TRI5: Trichodiene syn 97.1 0.011 2.4E-07 53.7 12.5 132 44-181 145-277 (376)
11 cd00867 Trans_IPPS Trans-Isopr 95.9 0.31 6.8E-06 41.0 13.5 118 45-179 86-214 (236)
12 cd00685 Trans_IPPS_HT Trans-Is 94.2 2.1 4.6E-05 36.9 13.8 121 44-179 108-239 (259)
13 TIGR02749 prenyl_cyano solanes 93.3 5 0.00011 36.0 15.0 88 44-136 133-220 (322)
14 PLN02890 geranyl diphosphate s 92.3 6 0.00013 37.0 14.3 91 42-137 225-315 (422)
15 PLN02857 octaprenyl-diphosphat 92.3 4.1 8.8E-05 38.0 13.2 88 44-136 227-314 (416)
16 TIGR02748 GerC3_HepT heptapren 91.1 9.9 0.00021 34.0 14.1 104 44-154 129-244 (319)
17 COG0142 IspA Geranylgeranyl py 89.3 16 0.00034 32.8 15.3 109 44-158 134-252 (322)
18 PF00494 SQS_PSY: Squalene/phy 88.7 11 0.00023 32.4 12.1 121 68-198 105-237 (267)
19 TIGR03465 HpnD squalene syntha 88.6 15 0.00033 31.7 13.4 121 69-201 100-229 (266)
20 CHL00151 preA prenyl transfera 84.6 29 0.00063 31.0 14.8 89 44-137 134-222 (323)
21 cd00683 Trans_IPPS_HH Trans-Is 82.8 30 0.00065 29.7 12.9 134 52-201 94-238 (265)
22 PRK10888 octaprenyl diphosphat 80.4 43 0.00093 30.0 17.1 91 41-136 127-217 (323)
23 KOG1719 Dual specificity phosp 77.9 1.9 4.1E-05 34.8 2.4 53 113-169 90-149 (183)
24 PRK10581 geranyltranstransfera 77.3 34 0.00075 30.3 10.6 113 54-179 152-276 (299)
25 COG3707 AmiR Response regulato 75.1 2.8 6E-05 34.9 2.8 49 125-173 127-176 (194)
26 PF03861 ANTAR: ANTAR domain; 73.9 2.9 6.3E-05 27.4 2.2 30 144-173 15-44 (56)
27 PF00348 polyprenyl_synt: Poly 73.8 57 0.0012 28.0 12.3 64 70-137 130-193 (260)
28 PF13060 DUF3921: Protein of u 73.6 21 0.00046 22.9 6.0 45 18-64 5-49 (58)
29 TIGR03464 HpnC squalene syntha 72.3 64 0.0014 27.8 12.9 121 69-201 101-230 (266)
30 PF12368 DUF3650: Protein of u 69.6 3.5 7.7E-05 23.4 1.5 18 150-167 9-26 (28)
31 PLN02632 phytoene synthase 66.2 1E+02 0.0022 27.8 13.6 138 53-199 142-288 (334)
32 smart00463 SMR Small MutS-rela 59.2 13 0.00029 25.7 3.3 23 155-177 7-29 (80)
33 PF03701 UPF0181: Uncharacteri 58.7 16 0.00034 23.7 3.1 45 129-175 2-46 (51)
34 PF01713 Smr: Smr domain; Int 57.6 12 0.00027 26.1 2.9 24 155-178 4-27 (83)
35 smart00400 ZnF_CHCC zinc finge 57.5 11 0.00024 24.4 2.5 25 142-166 30-54 (55)
36 PRK14562 haloacid dehalogenase 55.5 85 0.0019 26.2 8.1 30 47-77 77-106 (204)
37 PF10776 DUF2600: Protein of u 52.5 1.8E+02 0.0039 26.3 10.6 123 68-209 172-294 (330)
38 COG3140 Uncharacterized protei 52.2 9.8 0.00021 25.1 1.5 48 130-179 3-50 (60)
39 COG1308 EGD2 Transcription fac 51.5 15 0.00032 28.3 2.6 23 146-168 86-108 (122)
40 PF05772 NinB: NinB protein; 48.4 7.3 0.00016 30.3 0.5 56 27-86 44-100 (127)
41 COG2443 Sss1 Preprotein transl 48.3 51 0.0011 22.6 4.5 23 70-92 25-47 (65)
42 PF13798 PCYCGC: Protein of un 46.4 22 0.00047 28.7 2.9 25 163-190 134-158 (158)
43 COG4860 Uncharacterized protei 46.1 32 0.00069 27.4 3.7 51 18-76 25-80 (170)
44 PRK05114 hypothetical protein; 44.0 33 0.00072 22.9 3.0 45 129-175 2-46 (59)
45 PF10397 ADSL_C: Adenylosuccin 42.9 33 0.00071 24.0 3.2 29 147-175 8-36 (81)
46 PF02061 Lambda_CIII: Lambda P 42.5 80 0.0017 19.6 4.3 26 156-181 12-39 (45)
47 COG1093 SUI2 Translation initi 41.1 47 0.001 29.0 4.4 65 134-201 96-170 (269)
48 KOG3284 Vacuolar sorting prote 40.2 1.3E+02 0.0028 25.2 6.5 65 14-86 22-91 (213)
49 PF06603 UpxZ: UpxZ family of 38.7 72 0.0016 23.9 4.5 71 116-194 25-98 (106)
50 PF01807 zf-CHC2: CHC2 zinc fi 38.7 26 0.00056 25.6 2.2 30 142-171 61-90 (97)
51 PRK06369 nac nascent polypepti 36.3 33 0.00071 26.2 2.4 27 142-168 74-100 (115)
52 PF13189 Cytidylate_kin2: Cyti 34.9 13 0.00028 30.1 0.1 37 146-183 126-162 (179)
53 TIGR00264 alpha-NAC-related pr 34.3 37 0.00081 25.9 2.4 24 145-168 79-102 (116)
54 PTZ00393 protein tyrosine phos 34.0 35 0.00076 29.5 2.5 39 144-182 184-226 (241)
55 cd00737 endolysin_autolysin En 32.0 2.3E+02 0.0049 21.5 7.4 52 156-215 42-93 (133)
56 KOG0776 Geranylgeranyl pyropho 32.0 3.2E+02 0.0069 25.3 8.4 100 37-141 189-292 (384)
57 COG0864 NikR Predicted transcr 31.9 1.2E+02 0.0027 23.7 5.1 43 14-70 10-52 (136)
58 PF05402 PqqD: Coenzyme PQQ sy 31.0 95 0.0021 20.4 3.9 31 144-174 32-62 (68)
59 KOG4713 Cyclin-dependent kinas 29.4 97 0.0021 25.4 4.1 48 20-67 134-186 (189)
60 PRK12793 flaF flagellar biosyn 28.2 2.7E+02 0.0058 21.2 6.3 42 158-200 41-83 (115)
61 PF02970 TBCA: Tubulin binding 25.5 2.5E+02 0.0054 20.2 5.5 59 120-181 4-68 (90)
62 PHA02896 A-type inclusion like 25.2 1.2E+02 0.0026 29.2 4.6 45 154-201 3-47 (616)
63 KOG2099 Glycogen phosphorylase 23.8 30 0.00064 33.8 0.4 34 2-35 383-417 (843)
64 PRK08470 adenylosuccinate lyas 23.7 3.5E+02 0.0076 25.4 7.5 73 104-177 303-386 (442)
65 TIGR03001 Sig-70_gmx1 RNA poly 23.4 1.9E+02 0.0042 24.6 5.3 70 10-80 157-229 (244)
66 PF12469 DUF3692: CRISPR-assoc 21.8 91 0.002 23.5 2.6 41 140-181 77-117 (117)
67 KOG2077 JNK/SAPK-associated pr 21.4 2.2E+02 0.0047 28.0 5.5 92 107-202 302-405 (832)
68 TIGR03486 cas_csx13_C CRISPR-a 21.0 4E+02 0.0086 21.4 6.1 13 66-78 112-124 (152)
69 PF12550 GCR1_C: Transcription 20.6 1E+02 0.0023 21.5 2.6 25 144-168 55-79 (81)
70 COG5442 FlaF Flagellar biosynt 20.5 3.7E+02 0.0081 20.2 5.5 71 128-199 9-82 (115)
71 TIGR03515 GldC gliding motilit 20.3 3.8E+02 0.0083 20.1 6.4 41 14-60 59-100 (108)
No 1
>cd00684 Terpene_cyclase_plant_C1 Plant Terpene Cyclases, Class 1. This CD includes a diverse group of monomeric plant terpene cyclases (Tspa-Tspf) that convert the acyclic isoprenoid diphosphates, geranyl diphosphate (GPP), farnesyl diphosphate (FPP), or geranylgeranyl diphosphate (GGPP) into cyclic monoterpenes, diterpenes, or sesquiterpenes, respectively; a few form acyclic species. Terpnoid cyclases are soluble enzymes localized to the cytosol (sesquiterpene synthases) or plastids (mono- and diterpene synthases). All monoterpene and diterpene synthases have restrict substrate specificity, however, some sesquiterpene synthases can accept both FPP and GPP. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl diphosphates, via bridging Mg2+ ions (K+ preferred by gymnosperm cyclases), inducing conformational changes such that an N-terminal regi
Probab=100.00 E-value=7.8e-61 Score=453.06 Aligned_cols=227 Identities=45% Similarity=0.776 Sum_probs=221.9
Q ss_pred ccccccCCCCcCCCChhHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhh
Q 040645 2 VLTKKWDIGLIDTLPEYMKFIFKALLDIYREAEEELAKERRSYGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSV 81 (233)
Q Consensus 2 ~ai~RWD~~~~~~lpe~mk~~f~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~ 81 (233)
+||+|||.+++++||+|||+||.+++++++|++.++.+++++++..|++++|+++++||++||+|+++||+||++|||++
T Consensus 314 ~ai~rwd~~~~~~lPe~mk~~~~al~~~~~ei~~~~~~~~~~~~~~~~~~~~~~~~~a~l~EA~w~~~g~vPt~eEYl~~ 393 (542)
T cd00684 314 EAVERWDISAIDQLPEYMKIVFKALLNTVNEIEEELLKEGGSYVVPYLKEAWKDLVKAYLVEAKWAHEGYVPTFEEYMEN 393 (542)
T ss_pred HHHHhccccchhhccHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhh
Confidence 68999999999999999999999999999999999999998899999999999999999999999999999999999999
Q ss_pred hhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHHHHHHHhhCccchhhhhhcCCccchhHHHhhcCCCCHHH
Q 040645 82 ALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQTIVRFMDDIAGYKFEQKRGHIPSAVECYKNQHGVSEEE 161 (233)
Q Consensus 82 ~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~G~~~n~V~~yM~e~g~s~ee 161 (233)
|.+|+|++++++++++++|+. +|+++++|+...|+|+++++.++||+|||+||++|+++|+++|+|.|||+|+|+|+|+
T Consensus 394 ~~~S~g~~~~~~~~~~~~g~~-l~~e~~e~~~~~~~l~~~~~~i~rL~NDi~S~~kE~~rGdv~n~V~~ymke~g~s~ee 472 (542)
T cd00684 394 ALVSIGLGPLLLTSFLGMGDI-LTEEAFEWLESRPKLVRASSTIGRLMNDIATYEDEMKRGDVASSIECYMKEYGVSEEE 472 (542)
T ss_pred hhHHhhHHHHHHHHHHhcCCC-CCHHHHHHHhccHHHHHHHHHHHHHhcChhhhHHHHhcCCcccHHHHHHHhcCCCHHH
Confidence 999999999999999999999 9999999987779999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCC-CCCCHHHHHHHHHHhhhhhhhcccCCCCCCCchh-HHHHHHHHcccc
Q 040645 162 AVKELLLEVADSWKDINEELLNP-TTASLPTLQRVLYFARSGHFIYDDGHDRYTHSLM-MKRQVALLLTEP 230 (233)
Q Consensus 162 A~~~i~~~i~~~~k~ln~e~l~~-~~~p~~~~~~~~n~~R~~~~~Y~~~~D~~t~~~~-~k~~i~~l~~~p 230 (233)
|+++++++++++||++|++++++ +++|++|+++++|++|+++++|+++ ||||.|+. +|++|++||++|
T Consensus 473 A~~~i~~~ie~~wk~ln~e~l~~~~~~p~~~~~~~~n~~r~~~~~Y~~~-D~~t~~~~~~~~~i~~ll~~p 542 (542)
T cd00684 473 AREEIKKMIEDAWKELNEEFLKPSSDVPRPIKQRFLNLARVIDVFYKEG-DGFTHPEGEIKDHITSLLFEP 542 (542)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCC-CCCCCccHHHHHHHHHHhcCC
Confidence 99999999999999999999998 7899999999999999999999999 99999966 999999999998
No 2
>PLN02279 ent-kaur-16-ene synthase
Probab=100.00 E-value=6.5e-61 Score=464.48 Aligned_cols=226 Identities=23% Similarity=0.334 Sum_probs=215.5
Q ss_pred ccccccCCC-CcCCCChhHHHHHHHHHHHHHHHHHH-HHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHH
Q 040645 2 VLTKKWDIG-LIDTLPEYMKFIFKALLDIYREAEEE-LAKERRSYGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYK 79 (233)
Q Consensus 2 ~ai~RWD~~-~~~~lpe~mk~~f~~l~~~~~e~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl 79 (233)
+||||||++ ++++||||||+||.+|++++||++.+ +.+||+ ++++|++++|++++++|++||+|+.+||+||++|||
T Consensus 547 ~aVeRWD~~~~~~~lpeymki~f~aL~~t~nei~~~~~~~qGr-~v~~~l~~aW~~ll~ayl~EAeW~~~g~vPT~eEYL 625 (784)
T PLN02279 547 QLVEKWDVNGSPDFCSEQVEIIFSALRSTISEIGDKAFTWQGR-NVTSHIIKIWLDLLKSMLTEAQWSSNKSTPTLDEYM 625 (784)
T ss_pred HHHHHhccccchhhCcHHHHHHHHHHHHHHHHHHHHHHHHcCc-hHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHH
Confidence 689999998 66999999999999999999999977 556776 999999999999999999999999999999999999
Q ss_pred hhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHHHHHHHhhCccchhhhhhcCCccchhHHHhhcC--CC
Q 040645 80 SVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQTIVRFMDDIAGYKFEQKRGHIPSAVECYKNQH--GV 157 (233)
Q Consensus 80 ~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~G~~~n~V~~yM~e~--g~ 157 (233)
+|+.+|+|+++++..+++++|.. +|+++++| .++|+|+++++.++||+|||+||++|+++||+ |+|+|||+|+ |+
T Consensus 626 ~na~vS~~l~~i~l~~~~~~G~~-l~eev~e~-~~~~~L~~l~s~I~RLlNDI~S~e~E~~rG~~-nsV~cYMke~~~gv 702 (784)
T PLN02279 626 TNAYVSFALGPIVLPALYLVGPK-LSEEVVDS-PELHKLYKLMSTCGRLLNDIRGFKRESKEGKL-NAVSLHMIHGNGNS 702 (784)
T ss_pred hhchhhhhhHHHHHHHHHHhCCC-CCHHHHhC-cchhHHHHHHHHHHHHHHhccccHhHHhCCCc-ceehhhhccCCCCC
Confidence 99999999999999999999999 99999999 59999999999999999999999999999998 9999999987 89
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhhcCC--CCCCHHHHHHHHHHhhhhhhhcccCCCCCCCchhHHHHHHHHcccccCC
Q 040645 158 SEEEAVKELLLEVADSWKDINEELLNP--TTASLPTLQRVLYFARSGHFIYDDGHDRYTHSLMMKRQVALLLTEPLAI 233 (233)
Q Consensus 158 s~eeA~~~i~~~i~~~~k~ln~e~l~~--~~~p~~~~~~~~n~~R~~~~~Y~~~~D~~t~~~~~k~~i~~l~~~pi~~ 233 (233)
|+|||+++++++|+++||+||++++++ +++|++|++++||++|++++||+++ ||||.+ .||++|++||++||++
T Consensus 703 SeEEAi~~i~~~Ie~~wKeLn~~~l~~~~~~vp~~~~~~~ln~aR~~~~~Y~~~-Dgyt~~-~~k~~i~~ll~ePi~l 778 (784)
T PLN02279 703 TEEEAIESMKGLIESQRRELLRLVLQEKGSNVPRECKDLFWKMSKVLHLFYRKD-DGFTSN-DMMSLVKSVIYEPVSL 778 (784)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHhhhhheeCC-CCCChH-HHHHHHHHHhccCCcC
Confidence 999999999999999999999999974 5799999999999999999999999 999975 7999999999999985
No 3
>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=2.1e-35 Score=257.02 Aligned_cols=204 Identities=43% Similarity=0.726 Sum_probs=190.0
Q ss_pred ccccccCCCCcCCCChhHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhh
Q 040645 2 VLTKKWDIGLIDTLPEYMKFIFKALLDIYREAEEELAKERRSYGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSV 81 (233)
Q Consensus 2 ~ai~RWD~~~~~~lpe~mk~~f~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~ 81 (233)
++++||+....+.+|++++.++.+++++.++++....++++.....++++.|.+++.++.+|++|+.+|++||++||+.+
T Consensus 80 ~~~~~~~~~~~~~~p~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~e~~~~~~~~~p~~~eYl~~ 159 (284)
T cd00868 80 EAVERWDISAIDELPEYMKPVFKALYDLVNEIEEELAKEGGSESLPYLKEAWKDLLRAYLVEAKWANEGYVPSFEEYLEN 159 (284)
T ss_pred HHHHhcChhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHh
Confidence 35779999989999999999999999999999988777777688999999999999999999999999999999999999
Q ss_pred hhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHHHHHHHhhCccchhhhhhcCCccchhHHHhhcCCCCHHH
Q 040645 82 ALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQTIVRFMDDIAGYKFEQKRGHIPSAVECYKNQHGVSEEE 161 (233)
Q Consensus 82 ~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~G~~~n~V~~yM~e~g~s~ee 161 (233)
|+.|+|+.+++.++++++|.. +|++.+.+.+..+++.+.++.+++|+||++||+||+.+|+.+|+|.|||+++|+|.++
T Consensus 160 R~~~~g~~~~~~l~~~~~g~~-l~~~~~~~~~~~~~l~~~~~~~~~l~NDl~S~~kE~~~g~~~N~v~vl~~~~~~~~~e 238 (284)
T cd00868 160 RRVSIGYPPLLALSFLGMGDI-LPEEAFEWLPSYPKLVRASSTIGRLLNDIASYEKEIARGEVANSVECYMKEYGVSEEE 238 (284)
T ss_pred ceehhhHHHHHHHHHHHcCCC-CCHHHHHHhhhhHHHHHHHHHHHHHhccchHHHHHHccCCcccHHHHHHhccCCCHHH
Confidence 999999999999999999999 9984444447889999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCC-CCCCHHHHHHHHHHhhhhhhhc
Q 040645 162 AVKELLLEVADSWKDINEELLNP-TTASLPTLQRVLYFARSGHFIY 206 (233)
Q Consensus 162 A~~~i~~~i~~~~k~ln~e~l~~-~~~p~~~~~~~~n~~R~~~~~Y 206 (233)
|++++.++++++|++|++.+.+. ++.|+.+++.+.|.+|.....|
T Consensus 239 A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~g~~~w~ 284 (284)
T cd00868 239 ALEELRKMIEEAWKELNEEVLKLSSDVPRAVLETLLNLARGIYVWY 284 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhhhhcC
Confidence 99999999999999999999974 3688999999999999877665
No 4
>PLN02150 terpene synthase/cyclase family protein
Probab=100.00 E-value=2.8e-35 Score=218.42 Aligned_cols=94 Identities=36% Similarity=0.592 Sum_probs=90.9
Q ss_pred hhcCCccchhHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhhhhhhh-cccCCCCCCCch
Q 040645 139 QKRGHIPSAVECYKNQHGVSEEEAVKELLLEVADSWKDINEELLNPTTASLPTLQRVLYFARSGHFI-YDDGHDRYTHSL 217 (233)
Q Consensus 139 ~~~G~~~n~V~~yM~e~g~s~eeA~~~i~~~i~~~~k~ln~e~l~~~~~p~~~~~~~~n~~R~~~~~-Y~~~~D~~t~~~ 217 (233)
++|||++|+|+|||||||+|+|||+++++++|+++||+||+|+|+++++|++++++++|+||+++++ |+++ ||||.++
T Consensus 1 ~~rg~vaSsIeCYMke~g~seeeA~~~i~~li~~~WK~iN~e~l~~~~~p~~~~~~~~NlaR~~~~~~Y~~~-Dg~t~~~ 79 (96)
T PLN02150 1 MRRGEVANGVNCYMKQHGVTKEEAVSELKKMIRDNYKIVMEEFLTIKDVPRPVLVRCLNLARLIDVYCYNEG-DGFTYPH 79 (96)
T ss_pred CCCCcchHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHhheecCC-CCCCCCc
Confidence 5789999999999999999999999999999999999999999999999999999999999999999 9999 9999876
Q ss_pred h-HHHHHHHHcccccCC
Q 040645 218 M-MKRQVALLLTEPLAI 233 (233)
Q Consensus 218 ~-~k~~i~~l~~~pi~~ 233 (233)
. +|++|++||++||++
T Consensus 80 ~~~K~~I~sLlv~pi~i 96 (96)
T PLN02150 80 GKLKDLITSLFFHPLPL 96 (96)
T ss_pred HHHHHHHHHHhccCCCC
Confidence 5 999999999999986
No 5
>PF03936 Terpene_synth_C: Terpene synthase family, metal binding domain; InterPro: IPR005630 Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C10) synthases, sesquiterpene (C15) synthases and the diterpene (C20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf []. Tpsa includes vetispiridiene synthase Q39979 from SWISSPROT, 5-epi- aristolochene synthase, Q40577 from SWISSPROT and (+)-delta-cadinene synthase P93665 from SWISSPROT . Tpsb includes (-)-limonene synthase, Q40322 from SWISSPROT. Tpsc includes copalyl diphosphate synthase (kaurene synthase A), O04408 from SWISSPROT. Tpsd includes taxadiene synthase, Q41594 from SWISSPROT, pinene synthase, O24475 from SWISSPROT and myrcene synthase, O24474 from SWISSPROT. Tpse includes ent-kaurene synthase B Q39548 from SWISSPROT. Tpsf includes linalool synthase Q9ZPN5 from SWISSPROT. In the fungus Phaeosphaeria sp. (strain L487) the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein [].; GO: 0000287 magnesium ion binding, 0016829 lyase activity; PDB: 3PYB_A 3PYA_A 3G4F_A 3G4D_B 3CKE_A 2OA6_D 2E4O_B 3BNY_B 3BNX_A 3LG5_A ....
Probab=99.97 E-value=1.2e-31 Score=231.72 Aligned_cols=176 Identities=27% Similarity=0.406 Sum_probs=160.3
Q ss_pred ccccccCCCCcCCCChhHHHHHHHHHHHHHHHHHHHHHh-cCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHh
Q 040645 2 VLTKKWDIGLIDTLPEYMKFIFKALLDIYREAEEELAKE-RRSYGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKS 80 (233)
Q Consensus 2 ~ai~RWD~~~~~~lpe~mk~~f~~l~~~~~e~~~~~~~~-~~~~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~ 80 (233)
++++|||+...+.+|++++.++.++.++++++...+.+. ++.+..++++++|.+++.++++|++|+..|++||++||++
T Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~ps~eeYl~ 173 (270)
T PF03936_consen 94 DAVERWDPNSGDPLPDPDKPLFRALADIWNRIAARMSPAQRRRDQIKRFRNSWREYLNAYLWEARWRERGRIPSLEEYLE 173 (270)
T ss_dssp HHHHHTSSGGGGGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS--SHHHHHH
T ss_pred HHHhcccccccccccchhHHHHHHHHHHHHHHHHHhhhhhcccHHhhHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHH
Confidence 468899998888999999999999999999998766655 4435888999999999999999999999999999999999
Q ss_pred hhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHHHHHHHhhCccchhhhhhcCCccchhHHHhhcCCCCHH
Q 040645 81 VALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQTIVRFMDDIAGYKFEQKRGHIPSAVECYKNQHGVSEE 160 (233)
Q Consensus 81 ~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~G~~~n~V~~yM~e~g~s~e 160 (233)
.|+.|+|+.+++.+..+++|.. +++...+++.+.|.+.++++.+++|.|||+||+||+++|+..|.|.++|+++|+|.|
T Consensus 174 ~R~~t~g~~~~~~l~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~~l~NDl~S~~KE~~~g~~~N~v~~l~~~~~~s~e 252 (270)
T PF03936_consen 174 MRRHTSGVYPCLALIEFALEFA-LGELPPEVLEHPPMLRRLAADIIRLVNDLYSYKKEIARGDVHNLVVVLMNEHGLSLE 252 (270)
T ss_dssp HHHHHTSHHHHHHHHHHHCSSC-HTHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCSHHHHHHHHHTHHHH
T ss_pred hccccccccHHHHHHHHhCCCc-cccccHHHHHhchHHHHHHHHHHHHhcccchhhcchhhcccccHHHHhhhhcCCCHH
Confidence 9999999999999999999776 776666666666789999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 040645 161 EAVKELLLEVADSWKDIN 178 (233)
Q Consensus 161 eA~~~i~~~i~~~~k~ln 178 (233)
+|++++.+++++++++||
T Consensus 253 ~A~~~v~~~~~~~~~efn 270 (270)
T PF03936_consen 253 EAVDEVAEMINECIREFN 270 (270)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhcC
Confidence 999999999999999998
No 6
>PLN02592 ent-copalyl diphosphate synthase
Probab=99.97 E-value=8.8e-30 Score=247.01 Aligned_cols=185 Identities=14% Similarity=0.148 Sum_probs=159.1
Q ss_pred cccCCCCcCCCCh------hHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHH
Q 040645 5 KKWDIGLIDTLPE------YMKFIFKALLDIYREAEEELAKERRSYGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEY 78 (233)
Q Consensus 5 ~RWD~~~~~~lpe------~mk~~f~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEY 78 (233)
+|||.+++++||+ |||+||.+||+|+||++.++.+.+|.++.+|++++|.++++ +|..+|+
T Consensus 606 ~rWd~~~~~~lp~~~~~~~~mki~f~aLy~tineia~~a~~~qGr~v~~~L~~~W~~l~~------~w~~~g~------- 672 (800)
T PLN02592 606 RRSDHHFNDRNMRRSGSVKTGEELVGLLLGTLNQLSLDALEAHGRDISHLLRHAWEMWLL------KWLLEGD------- 672 (800)
T ss_pred cccCchhhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHH------HHHhcCc-------
Confidence 4999999999988 99999999999999999765655555999999999999999 6777666
Q ss_pred HhhhhhhcchHHHHHHHHH-hcCCCCCChhhhhhhhcchHHHHHHHHHHHHhhCccchhhhhhcCCccchhHHHhhcCC-
Q 040645 79 KSVALRSIGFLPVAVASFV-DLGDFIATKDNFECILKNAKSVKATQTIVRFMDDIAGYKFEQKRGHIPSAVECYKNQHG- 156 (233)
Q Consensus 79 l~~~~~s~g~~~~~~~~~~-~~g~~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~G~~~n~V~~yM~e~g- 156 (233)
.|+|...+++++++ .+|.. +|+++++ +|.+.+.++.+.||+||++|+++|... .|
T Consensus 673 -----~s~~~~~ilv~~~~l~~g~~-lsee~l~----~~~~~~l~~li~Rl~nDl~t~~~e~~~-------------~~~ 729 (800)
T PLN02592 673 -----GRQGEAELLVKTINLTAGRS-LSEELLA----HPQYEQLAQLTNRICYQLGHYKKNKVH-------------INT 729 (800)
T ss_pred -----eeccchhhHHHHHHHhcCCC-CCHHHcc----chhHHHHHHHHHHHHHhhhHHhhhccc-------------CCc
Confidence 44566666777777 55999 9998876 588999999999999999999998841 23
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhhcC-C-CCCCHHHHHHHHHHhhhhhhhcccCCCCCCCchhHHHHHHHHcccccC
Q 040645 157 VSEEEAVKELLLEVADSWKDINEELLN-P-TTASLPTLQRVLYFARSGHFIYDDGHDRYTHSLMMKRQVALLLTEPLA 232 (233)
Q Consensus 157 ~s~eeA~~~i~~~i~~~~k~ln~e~l~-~-~~~p~~~~~~~~n~~R~~~~~Y~~~~D~~t~~~~~k~~i~~l~~~pi~ 232 (233)
.++ +|.+++.+.|+.++++|.+.+++ . +.+|++||+.||+++| +||.. ||+.|+.|+++|..++++||.
T Consensus 730 ~~~-~a~~~~~~~ie~~~~eL~~lvl~~~~~~vp~~cK~~f~~~~k---~fy~~---~~~~~~~~~~~i~~vl~epv~ 800 (800)
T PLN02592 730 YNP-EEKSKTTPSIESDMQELVQLVLQNSSDDIDPVIKQTFLMVAK---SFYYA---AYCDPGTINYHIAKVLFERVA 800 (800)
T ss_pred ccH-HHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHH---HHHHh---hcCCHHHHHHHHHHHhCCCCC
Confidence 455 89999999999999999999997 3 4699999999999999 56663 899998899999999999985
No 7
>cd00687 Terpene_cyclase_nonplant_C1 Non-plant Terpene Cyclases, Class 1. This CD includes terpenoid cyclases such as pentalenene synthase and aristolochene synthase which, using an all-trans pathway, catalyze the ionization of farnesyl diphosphate, followed by the formation of a macrocyclic intermediate by bond formation between C1 with either C10 (aristolochene synthase) or C11 (pentalenene synthase), resulting in production of tricyclic hydrocarbon pentalenene or bicyclic hydrocarbon aristolochene. As with other enzymes with the 'terpenoid synthase fold', they have two conserved metal binding motifs, proposed to coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP to the enzymes. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function in the monomeric form and are found in
Probab=99.95 E-value=3.8e-27 Score=207.87 Aligned_cols=161 Identities=18% Similarity=0.143 Sum_probs=146.0
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhhhhhhcchHHHHHHH
Q 040645 16 PEYMKFIFKALLDIYREAEEELAKERRSYGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSVALRSIGFLPVAVAS 95 (233)
Q Consensus 16 pe~mk~~f~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~s~g~~~~~~~~ 95 (233)
|+....+..++.++...+.... +.....++++.|.+++.++++|++|+.+|++||++||+++|+.|+|+.+++.++
T Consensus 105 ~~~~~p~~~~~~d~~~r~~~~~----~~~~~~r~~~~~~~~~~a~~~e~~~~~~~~~psl~eYl~~R~~~~g~~~~~~l~ 180 (303)
T cd00687 105 PDDATPLEFGLADLWRRTLARM----SAEWFNRFAHYTEDYFDAYIWEGKNRLNGHVPDVAEYLEMRRFNIGADPCLGLS 180 (303)
T ss_pred CCCCCHHHHHHHHHHHHhccCC----CHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhhhcccccccHHHH
Confidence 5788888888888888876543 234568999999999999999999999999999999999999999999999999
Q ss_pred HHhcCCCCCChhhhhhhhcchHHHHHHHHHHHHhhCccchhhhh-hcCCccchhHHHhhcCCCCHHHHHHHHHHHHHHHH
Q 040645 96 FVDLGDFIATKDNFECILKNAKSVKATQTIVRFMDDIAGYKFEQ-KRGHIPSAVECYKNQHGVSEEEAVKELLLEVADSW 174 (233)
Q Consensus 96 ~~~~g~~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~-~~G~~~n~V~~yM~e~g~s~eeA~~~i~~~i~~~~ 174 (233)
.+++|.. +|+++.+. +...++.++++.+++|+|||+||+||+ +.|+.+|+|.|+|+++|+|.|+|++++.+++++++
T Consensus 181 ~~~~g~~-lp~~~~~~-~~~~~l~~~~~~~~~l~NDl~S~~KE~~~~g~~~N~V~vl~~~~g~s~~eA~~~~~~~~~~~~ 258 (303)
T cd00687 181 EFIGGPE-VPAAVRLD-PVMRALEALASDAIALVNDIYSYEKEIKANGEVHNLVKVLAEEHGLSLEEAISVVRDMHNERI 258 (303)
T ss_pred HHhcCCC-CCHHHHhC-hHHHHHHHHHHHHHHHHHHHHhhHHHHHhCCccchHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 9999999 99988877 566789999999999999999999999 89999999999999999999999999999999999
Q ss_pred HHHHHhhc
Q 040645 175 KDINEELL 182 (233)
Q Consensus 175 k~ln~e~l 182 (233)
+++.+..-
T Consensus 259 ~~f~~~~~ 266 (303)
T cd00687 259 TQFEELEA 266 (303)
T ss_pred HHHHHHHH
Confidence 88876554
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=99.75 E-value=1.7e-17 Score=138.23 Aligned_cols=179 Identities=22% Similarity=0.247 Sum_probs=148.8
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhhhhhhcchHHHH
Q 040645 13 DTLPEYMKFIFKALLDIYREAEEELAKERRSYGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSVALRSIGFLPVA 92 (233)
Q Consensus 13 ~~lpe~mk~~f~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~s~g~~~~~ 92 (233)
...|..+...+..+.+.++++.... .......+++.|.+++.|+..|+.|+.+ ++||++||+..+..++ +.++.
T Consensus 52 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~g~~~d~~~~~~-~~~t~~ey~~~~~~~t-~~~~~ 125 (243)
T cd00385 52 DGLPEAILAGDLLLADAFEELAREG----SPEALEILAEALLDLLEGQLLDLKWRRE-YVPTLEEYLEYCRYKT-AGLVG 125 (243)
T ss_pred cCchHHHHHHHHHHHHHHHHHHhCC----CHHHHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHHhH-HHHHH
Confidence 4678888888888888888886432 2356789999999999999999999977 8999999999999998 55555
Q ss_pred HHHHHhcCCCCCChhhhhhhhcchHHHHHHHHHHHHhhCccchhhhhhcC-CccchhHHHhhcCCC------------CH
Q 040645 93 VASFVDLGDFIATKDNFECILKNAKSVKATQTIVRFMDDIAGYKFEQKRG-HIPSAVECYKNQHGV------------SE 159 (233)
Q Consensus 93 ~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~G-~~~n~V~~yM~e~g~------------s~ 159 (233)
.+...+++.. .++ ..+.+...++...++.+.+|.||+.|+.+|.++| +..|++.++|+++|+ +.
T Consensus 126 ~~~~~~~~~~-~~~--~~~~~~~~~~~~~~g~~~ql~nDl~~~~~e~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 202 (243)
T cd00385 126 ALCLLGAGLS-GGE--AELLEALRKLGRALGLAFQLTNDLLDYEGDAERGEGKCTLPVLYALEYGVPAEDLLLVEKSGSL 202 (243)
T ss_pred HHHHHHHHHh-CCC--HHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHhCCchHHHHHHHHHhCChhhHHHHHHHCChH
Confidence 6666666666 665 3344566789999999999999999999999986 667999999999998 88
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhh
Q 040645 160 EEAVKELLLEVADSWKDINEELLNPTTASLPTLQRVLYFAR 200 (233)
Q Consensus 160 eeA~~~i~~~i~~~~k~ln~e~l~~~~~p~~~~~~~~n~~R 200 (233)
++|.+++..+++++++++++......+.++.+++.+.++.|
T Consensus 203 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (243)
T cd00385 203 EEALEELAKLAEEALKELNELILSLPDVPRALLALALNLYR 243 (243)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhC
Confidence 99999999999999999998877644467788888877764
No 9
>cd00686 Terpene_cyclase_cis_trans_C1 Cis, Trans, Terpene Cyclases, Class 1. This CD includes the terpenoid cyclase, trichodiene synthase, which catalyzes the cyclization of farnesyl diphosphate (FPP) to trichodiene using a cis-trans pathway, and is the first committed step in the biosynthesis of trichothecene toxins and antibiotics. As with other enzymes with the 'terpenoid synthase fold', this enzyme has two conserved metal binding motifs that coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function as homodimers and are found in several genera of fungi.
Probab=97.60 E-value=0.0015 Score=58.62 Aligned_cols=164 Identities=16% Similarity=0.128 Sum_probs=105.2
Q ss_pred cCCCChhHHHHHHHHHH----------HHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhh
Q 040645 12 IDTLPEYMKFIFKALLD----------IYREAEEELAKERRSYGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSV 81 (233)
Q Consensus 12 ~~~lpe~mk~~f~~l~~----------~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~ 81 (233)
.+...+.|+.++.-|.. -+++.=..+.+.=|.+.-.-+.++--+++.+..-|.... +.-|.-.+|-..
T Consensus 103 ~~e~~~~m~~f~~dL~~G~~qkhP~l~~v~~~l~~~lr~fGpF~s~~IikSTLdFv~g~~iEq~nf--~~~p~A~~fP~y 180 (357)
T cd00686 103 KDDPYPTMVNYFDDLQAGREQAHPWWALVNEHFPNVLRHFGPFCSLNLIRSTLDFFEGCWIEQYNF--GGFPGSHDYPQF 180 (357)
T ss_pred ccccchHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHhhhcc--CCCCCCcccchH
Confidence 45666788888877643 333332222222233566667777778888888886643 336766677776
Q ss_pred hhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHH---HHHHHhhCccchhhhhhc-CCccchhHHHhhcCCC
Q 040645 82 ALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQ---TIVRFMDDIAGYKFEQKR-GHIPSAVECYKNQHGV 157 (233)
Q Consensus 82 ~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~---~i~rL~NDi~S~~~E~~~-G~~~n~V~~yM~e~g~ 157 (233)
.+.=+|.+-..+.+. -|++.|.-.+.+..+..+.. ...-++|||.||=||... ++..|.|.-|-+.+|+
T Consensus 181 lR~ksGl~E~yA~Fi-------FPk~~FpE~~~~~qi~~AIp~~~~~i~~~NDILSFYKEe~~~~E~~n~V~Nya~~~Gi 253 (357)
T cd00686 181 LRRMNGLGHCVGASL-------WPKEQFNERSLFLEITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEI 253 (357)
T ss_pred HHhccCCcceeEEEe-------cchhhCchHhhHHHhhHHHHHHHHHHHhhhhhhheehhhcccccccchHHHhhhhcCC
Confidence 776677665544322 34333332222333333444 455699999999999854 4567999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhhcCCC
Q 040645 158 SEEEAVKELLLEVADSWKDINEELLNPT 185 (233)
Q Consensus 158 s~eeA~~~i~~~i~~~~k~ln~e~l~~~ 185 (233)
|..+|.+.+..-.-.+-+++.+ .|++.
T Consensus 254 S~~eAL~~lt~dTv~~s~rv~~-VLse~ 280 (357)
T cd00686 254 SLHEALEKLTQDTLHSSKQMVA-VFSDK 280 (357)
T ss_pred CHHHHHHHHHHHHHHHHHHHHH-HhcCC
Confidence 9999999888777777777654 45543
No 10
>PF06330 TRI5: Trichodiene synthase (TRI5); InterPro: IPR024652 This family consists of several fungal trichodiene synthase proteins (EC:4.2.3.6). TRI5 encodes the enzyme trichodiene synthase, which has been shown to catalyse the first step in the trichothecene pathways of Fusarium and Trichothecium species [, ].; GO: 0045482 trichodiene synthase activity, 0016106 sesquiterpenoid biosynthetic process; PDB: 1YYT_A 2PS5_A 2AEL_A 1YYS_A 1YJ4_A 2Q9Y_A 2PS4_A 2AEK_B 1KIY_B 2PS7_A ....
Probab=97.10 E-value=0.011 Score=53.72 Aligned_cols=132 Identities=15% Similarity=0.196 Sum_probs=79.5
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHH
Q 040645 44 YGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQ 123 (233)
Q Consensus 44 ~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~ 123 (233)
+..+-+.++--+++.+..-|++..+ -.|.-..|-..-+.=+|.....+.+.+ -... -|+.. ....+-..+-...
T Consensus 145 f~anmI~~STLdFi~g~~LE~~~f~--~~p~A~~FP~fLR~ktGlsEaYA~FiF-Pk~~-fpe~~--~~~~y~~AIpdl~ 218 (376)
T PF06330_consen 145 FCANMIVKSTLDFINGCWLEQKNFH--GSPGAPDFPDFLRRKTGLSEAYAFFIF-PKAL-FPEVE--YFIQYTPAIPDLM 218 (376)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTT------TT-TTHHHHHHHHHH-HHHHHHHT---TTT-S-TTT--THHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhhcccCC--CCCCCccccHHHHhccCcchhheeeec-cccc-CChHH--HHHHHHHHHHHHH
Confidence 5566677777888998888876432 234333444444555566655554322 2222 33321 1111222444555
Q ss_pred HHHHHhhCccchhhhhh-cCCccchhHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 040645 124 TIVRFMDDIAGYKFEQK-RGHIPSAVECYKNQHGVSEEEAVKELLLEVADSWKDINEEL 181 (233)
Q Consensus 124 ~i~rL~NDi~S~~~E~~-~G~~~n~V~~yM~e~g~s~eeA~~~i~~~i~~~~k~ln~e~ 181 (233)
.++-++|||.||=||.- .|+..|.|.-+-.-+|+|..+|...+.+..-.+-+++.+-.
T Consensus 219 ~fi~~~NDILSFYKE~l~a~E~~NyI~n~A~~~g~S~~eaL~~l~~eti~a~~rv~~vL 277 (376)
T PF06330_consen 219 RFINYVNDILSFYKEELVAGETGNYIHNRARVHGVSILEALRELTDETIEAVERVRRVL 277 (376)
T ss_dssp HHHHHHHHHHHHHHHHTTSSSSSSHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhhhhHHHHHHhhcccccccchhhhhhhccCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 56679999999999977 78889999888888899999999998766666666665443
No 11
>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates
Probab=95.91 E-value=0.31 Score=41.01 Aligned_cols=118 Identities=12% Similarity=0.125 Sum_probs=80.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhhhhh-hcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHH
Q 040645 45 GISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSVALR-SIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQ 123 (233)
Q Consensus 45 ~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~-s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~ 123 (233)
....+.+....++.+...+..|... ..||+++|.+.... |+++....+......+. -+++..+ ...++.+..+
T Consensus 86 ~~~~~~~~~~~~~~Gq~~Dl~~~~~-~~~t~~~y~~~~~~Kta~l~~~~~~~~~~~~~--~~~~~~~---~~~~~~~~lG 159 (236)
T cd00867 86 ALELFAEALRELLEGQALDLEFERD-TYETLDEYLEYCRYKTAGLVGLLCLLGAGLSG--ADDEQAE---ALKDYGRALG 159 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHhccHHHHHHHHHHHHHHcC--cCHHHHH---HHHHHHHHHH
Confidence 4566778889999999999888654 57899999999988 66554443333333332 2333333 3357788999
Q ss_pred HHHHHhhCccchhhhh----------hcCCccchhHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHH
Q 040645 124 TIVRFMDDIAGYKFEQ----------KRGHIPSAVECYKNQHGVSEEEAVKELLLEVADSWKDINE 179 (233)
Q Consensus 124 ~i~rL~NDi~S~~~E~----------~~G~~~n~V~~yM~e~g~s~eeA~~~i~~~i~~~~k~ln~ 179 (233)
....+.||+..+.... ++|.. +....++ .+.+.+..+++.+.+..
T Consensus 160 ~a~Qi~dd~~D~~~d~~~~gk~~~D~~~gr~-tlp~~~~----------~~~~~~~~~~~~~~~~~ 214 (236)
T cd00867 160 LAFQLTDDLLDVFGDAEELGKVGSDLREGRI-TLPVILA----------RERAAEYAEEAYAALEA 214 (236)
T ss_pred HHHHHHHHhccccCChHHHCccHHHHHcCCc-hHHHHHH----------HHHHHHHHHHHHHHHHh
Confidence 9999999999886644 55554 5555555 56666667767666543
No 12
>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=94.19 E-value=2.1 Score=36.87 Aligned_cols=121 Identities=12% Similarity=-0.005 Sum_probs=80.2
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHH
Q 040645 44 YGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQ 123 (233)
Q Consensus 44 ~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~ 123 (233)
.....+.+....++.+-..+..|... ..||.++|++....-+|.....+....++--. .+++..+. ..++.+..+
T Consensus 108 ~~~~~~~~~~~~~~~GQ~~d~~~~~~-~~~~~~~y~~~~~~KT~~l~~~~~~~~a~l~~-~~~~~~~~---l~~~g~~lG 182 (259)
T cd00685 108 RALELFSEAILELVEGQLLDLLSEYD-TDVTEEEYLRIIRLKTAALFAAAPLLGALLAG-ADEEEAEA---LKRFGRNLG 182 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCC-CCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcC-CCHHHHHH---HHHHHHHHH
Confidence 45667777888889998888888654 57999999999887777765544433322112 33443333 367888899
Q ss_pred HHHHHhhCccchhhh-----------hhcCCccchhHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHH
Q 040645 124 TIVRFMDDIAGYKFE-----------QKRGHIPSAVECYKNQHGVSEEEAVKELLLEVADSWKDINE 179 (233)
Q Consensus 124 ~i~rL~NDi~S~~~E-----------~~~G~~~n~V~~yM~e~g~s~eeA~~~i~~~i~~~~k~ln~ 179 (233)
...-+.||+..+... ...|.. |...++.. .+.++..++++++.+..
T Consensus 183 ~afQi~DD~ld~~~~~~~~gK~~~~Di~~gk~-T~~~~~~l---------~~~~~~~~~~a~~~l~~ 239 (259)
T cd00685 183 LAFQIQDDILDLFGDPETLGKPVGSDLREGKC-TLPVLLAL---------RELAREYEEKALEALKA 239 (259)
T ss_pred HHHHHHHHhhcccCChHHHCCCcchHHHcCCc-hHHHHHHH---------HHHHHHHHHHHHHHHHc
Confidence 999999998877532 223433 55444443 56777777777777653
No 13
>TIGR02749 prenyl_cyano solanesyl diphosphate synthase. Members of this family all are from cyanobacteria or plastid-containing eukaryotes. A member from Arabidopsis (where both plastoquinone and ubiquinone contain the C(45) prenyl moiety) was characterized by heterologous expression as a solanesyl diphosphate synthase.
Probab=93.33 E-value=5 Score=35.97 Aligned_cols=88 Identities=9% Similarity=0.006 Sum_probs=58.4
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHH
Q 040645 44 YGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQ 123 (233)
Q Consensus 44 ~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~ 123 (233)
.....+.+....++.+-+.+..+... ..+|.++|++.-..=+|..+..++..-++--. .+++..+. ..++-+..+
T Consensus 133 ~~~~~~~~~~~~~~~Gq~~~~~~~~~-~~~~~~~y~~~~~~KTa~L~~~~~~~ga~~ag-~~~~~~~~---l~~~G~~lG 207 (322)
T TIGR02749 133 EVVKLISKVITDFAEGEIKQGLNQFD-SDLSLEDYLEKSFYKTASLVAASSKAAAVLSD-VPSQVAND---LYEYGKHLG 207 (322)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcccC-CCCCHHHHHHHHHccHHHHHHHHHHHHHHHcC-cCHHHHHH---HHHHHHHHH
Confidence 45667777788888888777766533 34799999987665555554333222222122 45554444 367888999
Q ss_pred HHHHHhhCccchh
Q 040645 124 TIVRFMDDIAGYK 136 (233)
Q Consensus 124 ~i~rL~NDi~S~~ 136 (233)
...-+.||+..+.
T Consensus 208 ~aFQi~DDild~~ 220 (322)
T TIGR02749 208 LAFQVVDDILDFT 220 (322)
T ss_pred HHHHHHHHhccCC
Confidence 9999999998875
No 14
>PLN02890 geranyl diphosphate synthase
Probab=92.28 E-value=6 Score=36.98 Aligned_cols=91 Identities=11% Similarity=-0.021 Sum_probs=62.5
Q ss_pred CcchHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHH
Q 040645 42 RSYGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKA 121 (233)
Q Consensus 42 ~~~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~ 121 (233)
...++..+-++...++.+-+.+..|.. ...+|.++|++....-+|.....++..-++--. .+++..+.+ -.+-+.
T Consensus 225 ~~~~~~~~s~a~~~l~~Gq~ld~~~~~-~~~~s~~~Yl~~i~~KTa~Lf~~s~~~gAilag-a~~~~~~~l---~~fG~~ 299 (422)
T PLN02890 225 NTEVVSLLATAVEHLVTGETMQITSSR-EQRRSMDYYMQKTYYKTASLISNSCKAVAILAG-QTAEVAVLA---FEYGRN 299 (422)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcC-cCHHHHHHH---HHHHHH
Confidence 335677888888999999998988864 346899999987665555554333222221112 455555443 567888
Q ss_pred HHHHHHHhhCccchhh
Q 040645 122 TQTIVRFMDDIAGYKF 137 (233)
Q Consensus 122 ~~~i~rL~NDi~S~~~ 137 (233)
.+...-+.||+..|.-
T Consensus 300 lGlAFQI~DDiLD~~g 315 (422)
T PLN02890 300 LGLAFQLIDDVLDFTG 315 (422)
T ss_pred HHHHHHHHHHHHhhcC
Confidence 9999999999998853
No 15
>PLN02857 octaprenyl-diphosphate synthase
Probab=92.27 E-value=4.1 Score=38.01 Aligned_cols=88 Identities=16% Similarity=0.061 Sum_probs=58.8
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHH
Q 040645 44 YGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQ 123 (233)
Q Consensus 44 ~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~ 123 (233)
.+...+.+...+++.+-+.+..+.. +.-+|.++|++....=+|.....+...-++--. .+++..+. ..++-+..+
T Consensus 227 ~~~~~~s~~~~~l~~Gei~q~~~~~-~~~~s~~~Yl~~i~~KTa~L~~~a~~~gallag-a~~~~~~~---l~~fG~~LG 301 (416)
T PLN02857 227 EVIKLISQVIKDFASGEIKQASSLF-DCDVTLDEYLLKSYYKTASLIAASTKSAAIFSG-VDSSVKEQ---MYEYGKNLG 301 (416)
T ss_pred HHHHHHHHHHHHHHhhHHHHHhccc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcC-CCHHHHHH---HHHHHHHHH
Confidence 4566777778888888777777754 345799999987766665554333222211112 45554444 367888899
Q ss_pred HHHHHhhCccchh
Q 040645 124 TIVRFMDDIAGYK 136 (233)
Q Consensus 124 ~i~rL~NDi~S~~ 136 (233)
...-+.||+..+.
T Consensus 302 iAFQI~DDiLD~~ 314 (416)
T PLN02857 302 LAFQVVDDILDFT 314 (416)
T ss_pred HHHHHHHHHHhhc
Confidence 9999999999876
No 16
>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=91.10 E-value=9.9 Score=33.98 Aligned_cols=104 Identities=13% Similarity=0.024 Sum_probs=66.2
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhhhhhhcchHHHHHHHHHh-cCCCCCChhhhhhhhcchHHHHHH
Q 040645 44 YGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSVALRSIGFLPVAVASFVD-LGDFIATKDNFECILKNAKSVKAT 122 (233)
Q Consensus 44 ~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~s~g~~~~~~~~~~~-~g~~~l~~e~~~~~~~~~~l~~~~ 122 (233)
..+..+.++...++.+-..+..|.. +.-+|.++|++.-..-+|..+..++..-+ ++ . .+++..+. ..++-+..
T Consensus 129 ~~~~~~~~~~~~~~~Gq~~~~~~~~-~~~~~~~~Y~~~i~~KTa~L~~~~~~~ga~~a-g-~~~~~~~~---l~~~g~~l 202 (319)
T TIGR02748 129 RAHQILSHTIVEVCRGEIEQIKDKY-NFDQNLRTYLRRIKRKTALLIAASCQLGAIAS-G-ANEAIVKK---LYWFGYYV 202 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHc-C-CCHHHHHH---HHHHHHHH
Confidence 4566777888889999888887753 34579999998776666655433321111 12 2 34443333 35677889
Q ss_pred HHHHHHhhCccchhhh-----------hhcCCccchhHHHhhc
Q 040645 123 QTIVRFMDDIAGYKFE-----------QKRGHIPSAVECYKNQ 154 (233)
Q Consensus 123 ~~i~rL~NDi~S~~~E-----------~~~G~~~n~V~~yM~e 154 (233)
+...-+.||+..+.-. ..+|.. ++..+|..+
T Consensus 203 G~aFQI~DDilD~~~~~~~~GK~~~~Dl~~gk~-Tlp~l~al~ 244 (319)
T TIGR02748 203 GMSYQITDDILDFVGTEEELGKPAGGDLLQGNV-TLPVLYAME 244 (319)
T ss_pred HHHHHHHHHHHHccCCHHhhCCChhhHHhCCCc-hHHHHHHhc
Confidence 9999999999877532 334444 665556554
No 17
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=89.29 E-value=16 Score=32.78 Aligned_cols=109 Identities=15% Similarity=0.065 Sum_probs=73.6
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHH
Q 040645 44 YGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQ 123 (233)
Q Consensus 44 ~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~ 123 (233)
.....+.+....++.+-..+-.+.... +|.++|++.-..=+|.....+...-++--. .+++..+.+ ..+-+...
T Consensus 134 ~~~~~~~~~~~~~~~GQ~lDl~~~~~~--~t~e~y~~~i~~KTa~L~~~a~~~ga~la~-~~~~~~~~l---~~~g~~lG 207 (322)
T COG0142 134 EAIKALAEAINGLCGGQALDLAFENKP--VTLEEYLRVIELKTAALFAAAAVLGAILAG-ADEELLEAL---EDYGRNLG 207 (322)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHccCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHcC-CCHHHHHHH---HHHHHHhh
Confidence 456777888888999988888876555 999999998876666665544433332222 344555544 66888999
Q ss_pred HHHHHhhCccchhhh-hhcCCc---------cchhHHHhhcCCCC
Q 040645 124 TIVRFMDDIAGYKFE-QKRGHI---------PSAVECYKNQHGVS 158 (233)
Q Consensus 124 ~i~rL~NDi~S~~~E-~~~G~~---------~n~V~~yM~e~g~s 158 (233)
..+-+.||+..+.-+ ..-|+. .+...++.-+.+..
T Consensus 208 laFQi~DDiLD~~~d~~~lGK~~g~Dl~~gK~T~p~l~~l~~~~~ 252 (322)
T COG0142 208 LAFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEKANE 252 (322)
T ss_pred HHHHHHHHhhcCCCChHHhCCCcchHHHcCCchHHHHHHHHcCch
Confidence 999999999888753 222332 36666776665443
No 18
>PF00494 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR002060 Squalene synthase 2.5.1.21 from EC (farnesyl-diphosphate farnesyltransferase) (SQS) and Phytoene synthase 2.5.1.32 from EC (PSY) share a number of functional similarities. These similarities are also reflected at the level of their primary structure [, , ]. In particular three well conserved regions are shared by SQS and PSY; they could be involved in substrate binding and/or the catalytic mechanism. SQS catalyzes the conversion of two molecules of farnesyl diphosphate (FPP) into squalene. It is the first committed step in the cholesterol biosynthetic pathway. The reaction carried out by SQS is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of FPP to form presqualene diphosphate; this intermediate is then rearranged in a NADP-dependent reduction, to form squalene: 2 FPP -> presqualene diphosphate + NADP -> squalene SQS is found in eukaryotes. In yeast it is encoded by the ERG9 gene, in mammals by the FDFT1 gene. SQS seems to be membrane-bound. PSY catalyzes the conversion of two molecules of geranylgeranyl diphosphate (GGPP) into phytoene. It is the second step in the biosynthesis of carotenoids from isopentenyl diphosphate. The reaction carried out by PSY is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of GGPP to form prephytoene diphosphate; this intermediate is then rearranged to form phytoene. 2 GGPP -> prephytoene diphosphate -> phytoene PSY is found in all organisms that synthesize carotenoids: plants and photosynthetic bacteria as well as some non- photosynthetic bacteria and fungi. In bacteria PSY is encoded by the gene crtB. In plants PSY is localized in the chloroplast.; GO: 0016740 transferase activity, 0009058 biosynthetic process; PDB: 3NRI_A 3NPR_A 2ZCR_A 2ZCP_B 4F6V_A 4EA0_A 3ACW_A 4F6X_A 3VJE_B 3ACX_A ....
Probab=88.72 E-value=11 Score=32.35 Aligned_cols=121 Identities=11% Similarity=0.055 Sum_probs=62.9
Q ss_pred hCCCCCCHHHHHhhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHHHHHHHhhCccchhhh-hhcCCccc
Q 040645 68 YKGYIPSFDEYKSVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQTIVRFMDDIAGYKFE-QKRGHIPS 146 (233)
Q Consensus 68 ~~~~iPt~eEYl~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E-~~~G~~~n 146 (233)
....++|++|+......++|....+++..++..+. - ++.. ......+...-+.|=+...... ..+|-+-
T Consensus 105 ~~~~~~t~~~L~~Y~~~vag~vg~l~~~~~~~~~~-~-~~~~-------~~a~~lG~alql~nilRd~~~D~~~~gR~y- 174 (267)
T PF00494_consen 105 EFTPYETFADLERYCYYVAGSVGLLLLQLLGAHDP-D-EAAR-------DAARALGRALQLTNILRDIPEDALRRGRIY- 174 (267)
T ss_dssp T-S--SSHHHHHHHHHHHTHHHHHHHHHHHHSSTS-H-HHHH-------HHHHHHHHHHHHHHHHHTHHHH-HHTT----
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccccc-h-hhHH-------HHHHHHHHHHHHHHHHHHhHHHHHhccccc-
Confidence 33567899999999988888877766666554322 1 1222 3334445545555555555556 5666541
Q ss_pred hhHHHhhcCCCCHHHHHHH----------HHHHHHHHHHHHHHhhcCCCCC-CHHHHHHHHHH
Q 040645 147 AVECYKNQHGVSEEEAVKE----------LLLEVADSWKDINEELLNPTTA-SLPTLQRVLYF 198 (233)
Q Consensus 147 ~V~~yM~e~g~s~eeA~~~----------i~~~i~~~~k~ln~e~l~~~~~-p~~~~~~~~n~ 198 (233)
.=.=.|.+||+|.++-.+. +..+++.+...+.+..---..+ |..+...+.-.
T Consensus 175 lP~d~l~~~gv~~~dl~~~~~~~~~~~~~~~~~~~~A~~~l~~a~~~~~~l~~~~~~~~~~~~ 237 (267)
T PF00494_consen 175 LPLDDLRRFGVTPEDLLAGRPRSERLRALIRELAARARAHLDEARAGLSALPPPRARPAVAAA 237 (267)
T ss_dssp S-HHHHHHTTSSHHHHHHHG-GGHHHHHHHHHHHHHHHHHHHHHHHGGGGS--TTHHHHHHHH
T ss_pred CCchhHHHcCCCHHHHHhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHhhhHHHHHH
Confidence 1122567889988865432 4455555555444433222346 44344433333
No 19
>TIGR03465 HpnD squalene synthase HpnD. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated.
Probab=88.60 E-value=15 Score=31.70 Aligned_cols=121 Identities=12% Similarity=0.076 Sum_probs=62.5
Q ss_pred CCCCCCHHHHHhhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHHHHHHHhhCccchhhhhhcCCccchh
Q 040645 69 KGYIPSFDEYKSVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQTIVRFMDDIAGYKFEQKRGHIPSAV 148 (233)
Q Consensus 69 ~~~iPt~eEYl~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~G~~~n~V 148 (233)
...++|++|+......+.|....+++..+ |.. +++... .....+...-|.|=+........+|-+ -.=
T Consensus 100 ~~~~~t~~dL~~Y~~~vAg~vg~l~~~ll--g~~--~~~~~~-------~a~~lG~AlqltnilRdv~eD~~~gR~-ylP 167 (266)
T TIGR03465 100 QTRYPDFAELDLYCDRVAGAVGRLSARIF--GAT--DARTLE-------YAHHLGRALQLTNILRDVGEDARRGRI-YLP 167 (266)
T ss_pred CCCCCCHHHHHHHHHHhHHHHHHHHHHHh--CCC--ChhHHH-------HHHHHHHHHHHHHHHHHhHHHHhCCCe-ecC
Confidence 45677999988888777776666555443 322 222222 223333333333333333344556654 111
Q ss_pred HHHhhcCCCCHHH---------HHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhhh
Q 040645 149 ECYKNQHGVSEEE---------AVKELLLEVADSWKDINEELLNPTTASLPTLQRVLYFARS 201 (233)
Q Consensus 149 ~~yM~e~g~s~ee---------A~~~i~~~i~~~~k~ln~e~l~~~~~p~~~~~~~~n~~R~ 201 (233)
.=.|.++|+|.++ ...-+..+++.+...+.+..--...+|......++-.+++
T Consensus 168 ~~~l~~~gv~~~~l~~~~~~~~~~~~~~~l~~~A~~~l~~a~~~~~~~p~~~~~~~~~~~~~ 229 (266)
T TIGR03465 168 AEELQRFGVPAADILEGRYSPALAALCRFQAERARAHYAEADALLPACDRRAQRAARAMAAI 229 (266)
T ss_pred HHHHHHcCCCHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhCCHhhhHHHHHHHHH
Confidence 2245778988763 4455566666666555444322345776555444444433
No 20
>CHL00151 preA prenyl transferase; Reviewed
Probab=84.60 E-value=29 Score=31.02 Aligned_cols=89 Identities=10% Similarity=-0.019 Sum_probs=55.9
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHH
Q 040645 44 YGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQ 123 (233)
Q Consensus 44 ~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~ 123 (233)
.....+.+....++.+-..+..+.. ..-+|.++|+.....=+|...-.++..-++--. .+++..+. ..++-+..+
T Consensus 134 ~~~~~~~~~~~~l~~G~~~~~~~~~-~~~~~~~~yl~~i~~KTa~L~~~~~~~ga~lag-~~~~~~~~---l~~~G~~lG 208 (323)
T CHL00151 134 EVVKLISKVITDFAEGEIRQGLVQF-DTTLSILNYIEKSFYKTASLIAASCKAAALLSD-ADEKDHND---FYLYGKHLG 208 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCC-CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHcC-CCHHHHHH---HHHHHHHHH
Confidence 3456677788888888777766642 334789999996544444444322222221112 44444333 367888999
Q ss_pred HHHHHhhCccchhh
Q 040645 124 TIVRFMDDIAGYKF 137 (233)
Q Consensus 124 ~i~rL~NDi~S~~~ 137 (233)
...-+.||+..+.-
T Consensus 209 ~aFQi~DDilD~~~ 222 (323)
T CHL00151 209 LAFQIIDDVLDITS 222 (323)
T ss_pred HHHHHHHHHhhccc
Confidence 99999999998753
No 21
>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=82.78 E-value=30 Score=29.73 Aligned_cols=134 Identities=15% Similarity=0.128 Sum_probs=66.6
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCHHHHHhhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHHHHHHHhhC
Q 040645 52 TMQELIMLYFTEAKWLYKGYIPSFDEYKSVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQTIVRFMDD 131 (233)
Q Consensus 52 ~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~~i~rL~ND 131 (233)
.+.+++.++.+. ......||++|.......+.|+.-.+++..++.+ . +++.. +.....+...-|.|=
T Consensus 94 ~~~~li~g~~~D---l~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~~~~-~--~~~~~-------~~A~~lG~Alqltni 160 (265)
T cd00683 94 PFRDLLAGMAMD---LDKRRYETLDELDEYCYYVAGVVGLMLLRVFGAS-S--DEAAL-------ERARALGLALQLTNI 160 (265)
T ss_pred HHHHHHHHHHHh---CCCCCCCCHHHHHHHHHHhHHHHHHHHHHHhCCC-C--ChHHH-------HHHHHHHHHHHHHHH
Confidence 344455555322 2345678998888888777776665555444321 1 22222 222333333333332
Q ss_pred ccchhhhhhcCCc--cchhHHHhhcCCCCHHHH---------HHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhh
Q 040645 132 IAGYKFEQKRGHI--PSAVECYKNQHGVSEEEA---------VKELLLEVADSWKDINEELLNPTTASLPTLQRVLYFAR 200 (233)
Q Consensus 132 i~S~~~E~~~G~~--~n~V~~yM~e~g~s~eeA---------~~~i~~~i~~~~k~ln~e~l~~~~~p~~~~~~~~n~~R 200 (233)
+.......++|-+ +.- -|.++|+|.++- ..-+..+++.+.+.+....-....+|....-.++-++.
T Consensus 161 lRdv~eD~~~gR~YlP~d---~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~ 237 (265)
T cd00683 161 LRDVGEDARRGRIYLPRE---ELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAALPRRSRFCVRAAAM 237 (265)
T ss_pred HHHHHHHHccCCCcCCHH---HHHHcCCCHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCCHhhHHHHHHHHH
Confidence 2222333455543 222 367788887652 24455566666555544433334577655555555544
Q ss_pred h
Q 040645 201 S 201 (233)
Q Consensus 201 ~ 201 (233)
+
T Consensus 238 ~ 238 (265)
T cd00683 238 L 238 (265)
T ss_pred H
Confidence 4
No 22
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=80.43 E-value=43 Score=30.01 Aligned_cols=91 Identities=11% Similarity=-0.023 Sum_probs=59.8
Q ss_pred cCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHH
Q 040645 41 RRSYGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVK 120 (233)
Q Consensus 41 ~~~~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~ 120 (233)
+....+..+.+....++.+-..+..|.. +.-+|.++|++....=+|.....++..-++--. .+++..+. ...+-+
T Consensus 127 ~~~~~~~~~~~~~~~~~~Gq~~d~~~~~-~~~~s~~~y~~~i~~KTa~lf~~~~~~ga~lag-~~~~~~~~---l~~~g~ 201 (323)
T PRK10888 127 GSLKVLEVMSEAVNVIAEGEVLQLMNVN-DPDITEENYMRVIYSKTARLFEAAAQCSGILAG-CTPEQEKG---LQDYGR 201 (323)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHcC-CCHHHHHH---HHHHHH
Confidence 3334566777788888888888887754 345799999998776666664333221111112 34443333 357888
Q ss_pred HHHHHHHHhhCccchh
Q 040645 121 ATQTIVRFMDDIAGYK 136 (233)
Q Consensus 121 ~~~~i~rL~NDi~S~~ 136 (233)
..+...-+.||+..+.
T Consensus 202 ~lG~aFQi~DD~ld~~ 217 (323)
T PRK10888 202 YLGTAFQLIDDLLDYS 217 (323)
T ss_pred HHHHHHHHHHHhhccc
Confidence 8999999999998885
No 23
>KOG1719 consensus Dual specificity phosphatase [Defense mechanisms]
Probab=77.85 E-value=1.9 Score=34.84 Aligned_cols=53 Identities=25% Similarity=0.206 Sum_probs=35.8
Q ss_pred hcchHHHHHHHHHHHHhhCccchhhh------hhcCCccchhHHHhhcC-CCCHHHHHHHHHHH
Q 040645 113 LKNAKSVKATQTIVRFMDDIAGYKFE------QKRGHIPSAVECYKNQH-GVSEEEAVKELLLE 169 (233)
Q Consensus 113 ~~~~~l~~~~~~i~rL~NDi~S~~~E------~~~G~~~n~V~~yM~e~-g~s~eeA~~~i~~~ 169 (233)
++..+|.+++.-| +-.+|..+= -.||-.+..|.||+-++ +.|.++|++++++.
T Consensus 90 Ps~~~i~~aVeFi----~k~asLGktvYVHCKAGRtRSaTvV~cYLmq~~~wtpe~A~~~vr~i 149 (183)
T KOG1719|consen 90 PSLENIQKAVEFI----HKNASLGKTVYVHCKAGRTRSATVVACYLMQHKNWTPEAAVEHVRKI 149 (183)
T ss_pred CCHHHHHHHHHHH----HhccccCCeEEEEecCCCccchhhhhhhhhhhcCCCHHHHHHHHHhc
Confidence 3444555555544 333344332 35666689999999888 89999999999873
No 24
>PRK10581 geranyltranstransferase; Provisional
Probab=77.27 E-value=34 Score=30.30 Aligned_cols=113 Identities=12% Similarity=0.002 Sum_probs=69.8
Q ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHhhhhhhcchHHHHHHHHH-hcCCCCCChhhhhhhhcchHHHHHHHHHHHHhhCc
Q 040645 54 QELIMLYFTEAKWLYKGYIPSFDEYKSVALRSIGFLPVAVASFV-DLGDFIATKDNFECILKNAKSVKATQTIVRFMDDI 132 (233)
Q Consensus 54 ~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~s~g~~~~~~~~~~-~~g~~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi 132 (233)
..++.+-..+..|.. ..+|.++|++.-..=+|.....+...- .++.. -+++..+. ..++-+..+..+-+.||+
T Consensus 152 ~~l~~GQ~ld~~~~~--~~~~~~~y~~i~~~KTa~L~~~~~~~gailag~-~~~~~~~~---l~~~g~~lG~aFQI~DDi 225 (299)
T PRK10581 152 AGMCGGQALDLEAEG--KQVPLDALERIHRHKTGALIRAAVRLGALSAGD-KGRRALPV---LDRYAESIGLAFQVQDDI 225 (299)
T ss_pred chhhHhhHHHHhccC--CCCCHHHHHHHHHHhhHHHHHHHHHHHHHHcCC-CcHHHHHH---HHHHHHHHHHHHHHHHHH
Confidence 346777777777753 468999999876544444433222111 12221 12233333 367888999999999999
Q ss_pred cchhhh-----------hhcCCccchhHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHH
Q 040645 133 AGYKFE-----------QKRGHIPSAVECYKNQHGVSEEEAVKELLLEVADSWKDINE 179 (233)
Q Consensus 133 ~S~~~E-----------~~~G~~~n~V~~yM~e~g~s~eeA~~~i~~~i~~~~k~ln~ 179 (233)
..+.-. ...|.. +.+.++ ..+.|.+.+++.++++.+.+..
T Consensus 226 lD~~g~~~~~GK~~g~Dl~~gk~-T~p~l~------~~e~a~~~a~~~~~~A~~~l~~ 276 (299)
T PRK10581 226 LDVVGDTATLGKRQGADQQLGKS-TYPALL------GLEQARKKARDLIDDARQSLDQ 276 (299)
T ss_pred ccccCChHHHCCCcchhhhcCCC-CHHHHH------HHHHHHHHHHHHHHHHHHHHHh
Confidence 987432 223333 444443 2478899999999999877754
No 25
>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]
Probab=75.13 E-value=2.8 Score=34.94 Aligned_cols=49 Identities=24% Similarity=0.201 Sum_probs=34.3
Q ss_pred HHHHhhCccchhhhhhcCCc-cchhHHHhhcCCCCHHHHHHHHHHHHHHH
Q 040645 125 IVRFMDDIAGYKFEQKRGHI-PSAVECYKNQHGVSEEEAVKELLLEVADS 173 (233)
Q Consensus 125 i~rL~NDi~S~~~E~~~G~~-~n~V~~yM~e~g~s~eeA~~~i~~~i~~~ 173 (233)
.-.|--|+..+++..+.-++ .-+=.+.|+.+|+|++||+++++++--+.
T Consensus 127 ~~~L~~el~~~k~~L~~rK~ierAKglLM~~~g~sE~EAy~~lR~~AM~R 176 (194)
T COG3707 127 RRALRRELAKLKDRLEERKVIERAKGLLMKRRGLSEEEAYKLLRRTAMDR 176 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhc
Confidence 44566677777765443332 34455799999999999999999865443
No 26
>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=73.86 E-value=2.9 Score=27.39 Aligned_cols=30 Identities=27% Similarity=0.246 Sum_probs=22.7
Q ss_pred ccchhHHHhhcCCCCHHHHHHHHHHHHHHH
Q 040645 144 IPSAVECYKNQHGVSEEEAVKELLLEVADS 173 (233)
Q Consensus 144 ~~n~V~~yM~e~g~s~eeA~~~i~~~i~~~ 173 (233)
+.-++.+.|..+|+|+++|.+.+++.-.+.
T Consensus 15 I~~AkgiLm~~~g~~e~~A~~~Lr~~Am~~ 44 (56)
T PF03861_consen 15 IEQAKGILMARYGLSEDEAYRLLRRQAMRR 44 (56)
T ss_dssp HHHHHHHHHHHHT--HHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHhCcCHHHHHHHHHHHHHHc
Confidence 456778899999999999999998865543
No 27
>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=73.84 E-value=57 Score=27.98 Aligned_cols=64 Identities=14% Similarity=0.051 Sum_probs=43.3
Q ss_pred CCCCCHHHHHhhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHHHHHHHhhCccchhh
Q 040645 70 GYIPSFDEYKSVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQTIVRFMDDIAGYKF 137 (233)
Q Consensus 70 ~~iPt~eEYl~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~ 137 (233)
+..+|.++|++.-..-+|......+..-++--. .+++..+. ..++.+..+...-+.||+..+..
T Consensus 130 ~~~~~~~~y~~i~~~KTg~l~~~~~~~ga~lag-~~~~~~~~---l~~~g~~lG~afQi~DD~~d~~~ 193 (260)
T PF00348_consen 130 DKDPTEEEYLEIIRLKTGSLFALACQLGAILAG-ADEEQIEA---LREFGRHLGIAFQIRDDLLDLFG 193 (260)
T ss_dssp TSSTSHHHHHHHHHHHTHHHHHHHHHHHHHHTT-SGHHHHHH---HHHHHHHHHHHHHHHHHHHHHHS
T ss_pred cccccHHHHHHHHhhcchHHHHHHHHHHHHhcc-chhHHHHH---HHHHHHHHHHHHhhhhhhhhccC
Confidence 447899999998887777764433322222112 44444444 36788899999999999988874
No 28
>PF13060 DUF3921: Protein of unknown function (DUF3921)
Probab=73.58 E-value=21 Score=22.93 Aligned_cols=45 Identities=18% Similarity=0.184 Sum_probs=34.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHH
Q 040645 18 YMKFIFKALLDIYREAEEELAKERRSYGISYAKQTMQELIMLYFTEA 64 (233)
Q Consensus 18 ~mk~~f~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~Ea 64 (233)
.|..+-+++..|+.|+++++..|| -+.+-+.++=.+|+.+.-.|.
T Consensus 5 qlsmiqkaih~tydelgkei~~~g--~~~d~i~kaqeeylsals~et 49 (58)
T PF13060_consen 5 QLSMIQKAIHRTYDELGKEIDLQG--VIADEIQKAQEEYLSALSHET 49 (58)
T ss_pred HHHHHHHHHHHhHHHHhHHhhhcc--hHHHHHHHHHHHHHHHhhHHH
Confidence 366788999999999999988877 355666677777777765554
No 29
>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=72.26 E-value=64 Score=27.84 Aligned_cols=121 Identities=13% Similarity=0.081 Sum_probs=58.5
Q ss_pred CCCCCCHHHHHhhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHHHHHHHhhCccchhhhhhcCCccchh
Q 040645 69 KGYIPSFDEYKSVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQTIVRFMDDIAGYKFEQKRGHIPSAV 148 (233)
Q Consensus 69 ~~~iPt~eEYl~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~G~~~n~V 148 (233)
....+|++|.......++|+.-.+++..++.+.. +.... ....+...-|.|=+........+|-+ -.=
T Consensus 101 ~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~g~~~~----~~~~~-------A~~lG~AlQltniLRDl~eD~~~gR~-YLP 168 (266)
T TIGR03464 101 VTRYATWAELLDYCRYSANPVGRLVLDLYGASDP----ENVAL-------SDAICTALQLINFWQDVGVDYRKGRV-YLP 168 (266)
T ss_pred CCCCCCHHHHHHHHHHhHHHHHHHHHHHcCCCCh----hHHHH-------HHHHHHHHHHHHHHHhhHHHHhcCCc-cCC
Confidence 4457799998888887777776666554433221 21111 22222222222222222233445643 111
Q ss_pred HHHhhcCCCCHHHHH---------HHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhhh
Q 040645 149 ECYKNQHGVSEEEAV---------KELLLEVADSWKDINEELLNPTTASLPTLQRVLYFARS 201 (233)
Q Consensus 149 ~~yM~e~g~s~eeA~---------~~i~~~i~~~~k~ln~e~l~~~~~p~~~~~~~~n~~R~ 201 (233)
.=.|.++|+|.|+-. .-+..++..+...+.+..---..+|..+.-.++-++++
T Consensus 169 ~~~l~~~Gv~~edl~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~~ 230 (266)
T TIGR03464 169 RDDLARFGVSEEDLAAGRATPALRELMAFEVSRTRALLDRGAPLAARVDGRLGLELALIVRG 230 (266)
T ss_pred HHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCCHhhhHHHHHHHHH
Confidence 124678899976632 33344444444433332211234776655554444433
No 30
>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=69.61 E-value=3.5 Score=23.36 Aligned_cols=18 Identities=44% Similarity=0.711 Sum_probs=15.0
Q ss_pred HHhhcCCCCHHHHHHHHH
Q 040645 150 CYKNQHGVSEEEAVKELL 167 (233)
Q Consensus 150 ~yM~e~g~s~eeA~~~i~ 167 (233)
.|.++||+|.||..+.+.
T Consensus 9 rYV~eh~ls~ee~~~RL~ 26 (28)
T PF12368_consen 9 RYVKEHGLSEEEVAERLA 26 (28)
T ss_pred hhHHhcCCCHHHHHHHHH
Confidence 588999999999777664
No 31
>PLN02632 phytoene synthase
Probab=66.16 E-value=1e+02 Score=27.77 Aligned_cols=138 Identities=11% Similarity=0.070 Sum_probs=65.7
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCHHHHHhhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHHHHHHHhhCc
Q 040645 53 MQELIMLYFTEAKWLYKGYIPSFDEYKSVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQTIVRFMDDI 132 (233)
Q Consensus 53 ~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi 132 (233)
+.+++.++.... .....+|++|+......+.|+.-.+++..++.... .+. ..++. .+.....+...-|.|=+
T Consensus 142 ~~~li~g~~~Dl---~~~~~~t~~eL~~Ycy~vAgtVG~l~l~vlg~~~~-~~~-~~~~~---~~~A~~lG~AlQltNIL 213 (334)
T PLN02632 142 FRDMIEGMRMDL---VKSRYENFDELYLYCYYVAGTVGLMSVPVMGIAPE-SKA-STESV---YNAALALGIANQLTNIL 213 (334)
T ss_pred HHHHHHHHHHHh---ccCCCCCHHHHHHHHHHhhHHHHHHHHHHhCCCCc-ccc-chHHH---HHHHHHHHHHHHHHHHH
Confidence 344555553222 23467799998888877777666655544433221 110 00111 12222333333333333
Q ss_pred cchhhhhhcCCccchhHHHhhcCCCCHHHH---------HHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHh
Q 040645 133 AGYKFEQKRGHIPSAVECYKNQHGVSEEEA---------VKELLLEVADSWKDINEELLNPTTASLPTLQRVLYFA 199 (233)
Q Consensus 133 ~S~~~E~~~G~~~n~V~~yM~e~g~s~eeA---------~~~i~~~i~~~~k~ln~e~l~~~~~p~~~~~~~~n~~ 199 (233)
........+|-+ -.=.=.|.++|+|.++- ..-+..+++.+..-+.+..---..+|..+.-.++=.+
T Consensus 214 RDv~eD~~~GRv-YLP~e~L~~~Gv~~edl~~~~~~~~~~~l~~~~~~~Ar~~~~~a~~~l~~lp~~~r~~v~~a~ 288 (334)
T PLN02632 214 RDVGEDARRGRV-YLPQDELAQFGLTDEDIFAGKVTDKWRAFMKFQIKRARMYFAEAEEGVSELDPASRWPVWASL 288 (334)
T ss_pred HHHHHHHhCCce-eCCHHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhHhhCCHHhHHHHHHHH
Confidence 333344566653 11112467889998872 3344455555554443332112347765553333333
No 32
>smart00463 SMR Small MutS-related domain.
Probab=59.20 E-value=13 Score=25.71 Aligned_cols=23 Identities=26% Similarity=0.242 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHH
Q 040645 155 HGVSEEEAVKELLLEVADSWKDI 177 (233)
Q Consensus 155 ~g~s~eeA~~~i~~~i~~~~k~l 177 (233)
||++.++|+..+...++++++.-
T Consensus 7 HG~~~~eA~~~l~~~l~~~~~~~ 29 (80)
T smart00463 7 HGLTVEEALTALDKFLNNARLKG 29 (80)
T ss_pred CCCCHHHHHHHHHHHHHHHHHcC
Confidence 69999999999999999998754
No 33
>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=58.67 E-value=16 Score=23.72 Aligned_cols=45 Identities=18% Similarity=0.361 Sum_probs=31.7
Q ss_pred hhCccchhhhhhcCCccchhHHHhhcCCCCHHHHHHHHHHHHHHHHH
Q 040645 129 MDDIAGYKFEQKRGHIPSAVECYKNQHGVSEEEAVKELLLEVADSWK 175 (233)
Q Consensus 129 ~NDi~S~~~E~~~G~~~n~V~~yM~e~g~s~eeA~~~i~~~i~~~~k 175 (233)
.||+-++..|+.+--+ --|.-.|.+ |+|--||+..|...|++.-+
T Consensus 2 ~~~lp~LtHeeQQ~Av-E~Iq~LMaq-GmSsgEAI~~VA~~iRe~~~ 46 (51)
T PF03701_consen 2 FNDLPSLTHEEQQQAV-ERIQELMAQ-GMSSGEAIAIVAQEIREEHQ 46 (51)
T ss_pred CCCCCCCCHHHHHHHH-HHHHHHHHh-cccHHHHHHHHHHHHHHHHH
Confidence 3677776666654333 345567754 99999999999998887654
No 34
>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=57.58 E-value=12 Score=26.11 Aligned_cols=24 Identities=25% Similarity=0.282 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q 040645 155 HGVSEEEAVKELLLEVADSWKDIN 178 (233)
Q Consensus 155 ~g~s~eeA~~~i~~~i~~~~k~ln 178 (233)
||++.+||...+.+.++++++.-.
T Consensus 4 HG~~~~eA~~~l~~~l~~~~~~~~ 27 (83)
T PF01713_consen 4 HGLTVEEALRALEEFLDEARQRGI 27 (83)
T ss_dssp TTS-HHHHHHHHHHHHHHHHHTTH
T ss_pred CCCcHHHHHHHHHHHHHHHHHcCC
Confidence 799999999999999999986544
No 35
>smart00400 ZnF_CHCC zinc finger.
Probab=57.50 E-value=11 Score=24.38 Aligned_cols=25 Identities=28% Similarity=0.218 Sum_probs=20.8
Q ss_pred CCccchhHHHhhcCCCCHHHHHHHH
Q 040645 142 GHIPSAVECYKNQHGVSEEEAVKEL 166 (233)
Q Consensus 142 G~~~n~V~~yM~e~g~s~eeA~~~i 166 (233)
|...++|..+|+-+|+|-.||++.+
T Consensus 30 g~gGd~i~fv~~~~~~sf~eA~~~L 54 (55)
T smart00400 30 GAGGNVISFLMKYDKLSFVEAVKKL 54 (55)
T ss_pred CCCCCHHHHHHHHHCcCHHHHHHHh
Confidence 3445889999998899999999875
No 36
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=55.46 E-value=85 Score=26.23 Aligned_cols=30 Identities=27% Similarity=0.455 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCCCCHHH
Q 040645 47 SYAKQTMQELIMLYFTEAKWLYKGYIPSFDE 77 (233)
Q Consensus 47 ~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eE 77 (233)
.++....++|+.|..- ..|...|.+||.+|
T Consensus 77 ~~~~~~lQEyvEA~~f-~~~l~~~~l~s~ee 106 (204)
T PRK14562 77 GYVGTALQEYVEALLV-YSLLFENKIPSPEE 106 (204)
T ss_pred hhcchHHHHHHHHHHH-HHHHcCCCCCCHHH
Confidence 4555566777766543 67888888888888
No 37
>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=52.50 E-value=1.8e+02 Score=26.35 Aligned_cols=123 Identities=15% Similarity=0.131 Sum_probs=78.0
Q ss_pred hCCCCCCHHHHHhhhhhhcchHHHHHHHHHhcCCCCCChhhhhhhhcchHHHHHHHHHHHHhhCccchhhhhhcCCccch
Q 040645 68 YKGYIPSFDEYKSVALRSIGFLPVAVASFVDLGDFIATKDNFECILKNAKSVKATQTIVRFMDDIAGYKFEQKRGHIPSA 147 (233)
Q Consensus 68 ~~~~iPt~eEYl~~~~~s~g~~~~~~~~~~~~g~~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~~E~~~G~~~n~ 147 (233)
+.+..|.++=| +.+..|.+.--++++.-++..+. ++++..+.+. ..-.-..+-+-.|++=....+.+...|+. |.
T Consensus 172 ~~~~~p~l~W~-EfaAatGSTLgIF~L~a~A~~p~-~t~~~a~~i~--~aYFPwI~gLHILLDy~IDq~EDr~~GdL-NF 246 (330)
T PF10776_consen 172 HRDKYPELEWW-EFAAATGSTLGIFALFAYAADPD-LTPEDAEKIK--DAYFPWICGLHILLDYFIDQEEDREGGDL-NF 246 (330)
T ss_pred hhhcCCCccHH-HHHHHhccHHHHHHHHHHHcCCC-CCHHHHHHHH--HcccHHHHHHHHHHHHHhhhHhHhcCCCc-ee
Confidence 34556654433 34444555555556666677777 8887766652 22333455566677777777777888887 99
Q ss_pred hHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhhhhhhhcccC
Q 040645 148 VECYKNQHGVSEEEAVKELLLEVADSWKDINEELLNPTTASLPTLQRVLYFARSGHFIYDDG 209 (233)
Q Consensus 148 V~~yM~e~g~s~eeA~~~i~~~i~~~~k~ln~e~l~~~~~p~~~~~~~~n~~R~~~~~Y~~~ 209 (233)
|..|- +.+++.+++...++++-+...+ +|.+--.+.++ |.+--+|-.+
T Consensus 247 v~YY~-----~~~~~~~Rl~~f~~~A~~~~~~-------Lp~~~fHr~iv--~GLla~YLSD 294 (330)
T PF10776_consen 247 VFYYP-----DEEEMEERLKYFVEKALEQASR-------LPYPKFHRMIV--RGLLAMYLSD 294 (330)
T ss_pred eeeCC-----CHHHHHHHHHHHHHHHHHHHHh-------CCCchHHHHHH--HHHHHHHhCC
Confidence 97543 5799999999999999877653 55544444433 3344567666
No 38
>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.22 E-value=9.8 Score=25.09 Aligned_cols=48 Identities=19% Similarity=0.295 Sum_probs=33.6
Q ss_pred hCccchhhhhhcCCccchhHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHH
Q 040645 130 DDIAGYKFEQKRGHIPSAVECYKNQHGVSEEEAVKELLLEVADSWKDINE 179 (233)
Q Consensus 130 NDi~S~~~E~~~G~~~n~V~~yM~e~g~s~eeA~~~i~~~i~~~~k~ln~ 179 (233)
+++.|+-.|+.+--+ --|.-+|.| |+|--||+..+...+++.-|..|+
T Consensus 3 ~~lp~LtHeqQQ~AV-E~Iq~lMae-GmSsGEAIa~VA~elRe~hk~~~~ 50 (60)
T COG3140 3 AGLPSLTHEQQQKAV-ERIQELMAE-GMSSGEAIALVAQELRENHKGENR 50 (60)
T ss_pred CccccccHHHHHHHH-HHHHHHHHc-cccchhHHHHHHHHHHHHhccccc
Confidence 556666667665444 345567765 899999999999888877665543
No 39
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=51.50 E-value=15 Score=28.33 Aligned_cols=23 Identities=39% Similarity=0.434 Sum_probs=19.3
Q ss_pred chhHHHhhcCCCCHHHHHHHHHH
Q 040645 146 SAVECYKNQHGVSEEEAVKELLL 168 (233)
Q Consensus 146 n~V~~yM~e~g~s~eeA~~~i~~ 168 (233)
-=|.+.|.|-|+|.++|++.+.+
T Consensus 86 eDIkLV~eQa~VsreeA~kAL~e 108 (122)
T COG1308 86 EDIKLVMEQAGVSREEAIKALEE 108 (122)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHH
Confidence 34789999999999999987754
No 40
>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=48.38 E-value=7.3 Score=30.27 Aligned_cols=56 Identities=13% Similarity=0.165 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHH-HHHhhhhhhc
Q 040645 27 LDIYREAEEELAKERRSYGISYAKQTMQELIMLYFTEAKWLYKGYIPSFD-EYKSVALRSI 86 (233)
Q Consensus 27 ~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~e-EYl~~~~~s~ 86 (233)
.-.+.+|++.+...|+ .+-.+.|++++.+.+.-++.....-+|.++ |+...|..|+
T Consensus 44 wa~l~dIs~qv~~~G~----k~~~e~WK~~~~~~~~~~~~~~~~~~~gl~Gg~v~~g~sTs 100 (127)
T PF05772_consen 44 WAMLGDISRQVEWNGR----KLDPEDWKELFTAAFLIATGEEQRVVPGLDGGFVVLGESTS 100 (127)
T ss_dssp HHHHHHHHHH--BTTB-------HHHHHHHHHHHH-----S--EEEE-TTSSEEEE---TT
T ss_pred HHHHHHHHHHhHhcCc----cCCHHHHHHHHHHHHhhhccchhhhccCCCCCeEEEeeech
Confidence 4567788887777776 456688999999888666666666677766 5554444443
No 41
>COG2443 Sss1 Preprotein translocase subunit Sss1 [Intracellular trafficking and secretion]
Probab=48.30 E-value=51 Score=22.55 Aligned_cols=23 Identities=17% Similarity=0.183 Sum_probs=17.2
Q ss_pred CCCCCHHHHHhhhhhhcchHHHH
Q 040645 70 GYIPSFDEYKSVALRSIGFLPVA 92 (233)
Q Consensus 70 ~~iPt~eEYl~~~~~s~g~~~~~ 92 (233)
-..||-|||.+.+.++...-.++
T Consensus 25 arKP~~eEy~~~aKi~~~Gi~li 47 (65)
T COG2443 25 ARKPDWEEYSKIAKITGLGILLI 47 (65)
T ss_pred HhCCCHHHHHHHHHHHHHHHHHH
Confidence 34799999999998776554443
No 42
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=46.36 E-value=22 Score=28.70 Aligned_cols=25 Identities=28% Similarity=0.510 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCCHH
Q 040645 163 VKELLLEVADSWKDINEELLNPTTASLP 190 (233)
Q Consensus 163 ~~~i~~~i~~~~k~ln~e~l~~~~~p~~ 190 (233)
.++|++.|++.|| +.+.+||+-|+|
T Consensus 134 ~~eIR~~ID~kYk---~g~~~pTpTp~P 158 (158)
T PF13798_consen 134 PKEIRQYIDEKYK---EGYAKPTPTPMP 158 (158)
T ss_pred HHHHHHHHHHHHH---hCCCCCCCCCCC
Confidence 4578899999997 458888777764
No 43
>COG4860 Uncharacterized protein conserved in archaea [Function unknown]
Probab=46.09 E-value=32 Score=27.37 Aligned_cols=51 Identities=25% Similarity=0.313 Sum_probs=33.2
Q ss_pred hHHHHHHHHHH---HHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHh--CCCCCCHH
Q 040645 18 YMKFIFKALLD---IYREAEEELAKERRSYGISYAKQTMQELIMLYFTEAKWLY--KGYIPSFD 76 (233)
Q Consensus 18 ~mk~~f~~l~~---~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~Ea~w~~--~~~iPt~e 76 (233)
--|.+|.+|.. |.-+|++.+.++|+ ..+.+++ ++=+-|++|+. +|..|.-+
T Consensus 25 t~rKl~~aLstgW~T~~eiee~iG~eg~-RaL~iLk-------kagmlEtqWr~p~~G~kPeKe 80 (170)
T COG4860 25 TKRKLLLALSTGWITLPEIEEKIGKEGR-RALLILK-------KAGMLETQWRTPSNGQKPEKE 80 (170)
T ss_pred HHHHHHHHHhhcceeHHHHHHHhchhhH-HHHHHHH-------hhcchhheeeccCCCCCchhh
Confidence 34455555544 77788888888887 3444444 45567899984 57788733
No 44
>PRK05114 hypothetical protein; Provisional
Probab=43.96 E-value=33 Score=22.85 Aligned_cols=45 Identities=18% Similarity=0.279 Sum_probs=30.6
Q ss_pred hhCccchhhhhhcCCccchhHHHhhcCCCCHHHHHHHHHHHHHHHHH
Q 040645 129 MDDIAGYKFEQKRGHIPSAVECYKNQHGVSEEEAVKELLLEVADSWK 175 (233)
Q Consensus 129 ~NDi~S~~~E~~~G~~~n~V~~yM~e~g~s~eeA~~~i~~~i~~~~k 175 (233)
.||+-++..|+.+--+ --|.-.|.+ |+|--||+..+...|++..+
T Consensus 2 ~~~lp~LtHeeQQ~AV-ErIq~LMaq-GmSsgEAI~~VA~eiRe~~~ 46 (59)
T PRK05114 2 FAGLPSLTHEQQQKAV-ERIQELMAQ-GMSSGEAIALVAEELRANHQ 46 (59)
T ss_pred CCCcccCCHHHHHHHH-HHHHHHHHc-cccHHHHHHHHHHHHHHHHh
Confidence 3555555555544333 445667764 99999999999998887654
No 45
>PF10397 ADSL_C: Adenylosuccinate lyase C-terminus; InterPro: IPR019468 Adenylosuccinate lyase catalyses two steps in the synthesis of purine nucleotides: the conversion of succinylaminoimidazole-carboxamide ribotide into aminoimidazole-carboxamide ribotide (the fifth step of de novo IMP biosynthesis); the formation of adenosine monophosphate (AMP) from adenylosuccinate (the final step in the synthesis of AMP from IMP) []. This entry represents the C-terminal, seven alpha-helical, domain of adenylosuccinate lyase [].; PDB: 1YIS_A 1C3U_B 1C3C_A 3C8T_A 2PFM_B 1RE5_D 1Q5N_A 2VD6_D 2J91_B 2X75_A.
Probab=42.94 E-value=33 Score=24.02 Aligned_cols=29 Identities=17% Similarity=0.304 Sum_probs=24.4
Q ss_pred hhHHHhhcCCCCHHHHHHHHHHHHHHHHH
Q 040645 147 AVECYKNQHGVSEEEAVKELLLEVADSWK 175 (233)
Q Consensus 147 ~V~~yM~e~g~s~eeA~~~i~~~i~~~~k 175 (233)
.|...+-+.|++.|+|.+.|++...++|+
T Consensus 8 ~v~~~L~~~G~gR~~Ah~lv~~~a~~a~~ 36 (81)
T PF10397_consen 8 RVMLALAEKGLGRQEAHELVQEAAMEAWE 36 (81)
T ss_dssp HHHHHHHHTTH-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHHHHHH
Confidence 45566778899999999999999999996
No 46
>PF02061 Lambda_CIII: Lambda Phage CIII; InterPro: IPR013056 Bacteriophage lambda regulatory protein CIII is a small protein that plays a role in stabilising the CII transcriptional activator, via a mechanism that is not yet fully understood [, ]. Stabilised CII activates CI, the gene for the repressor protein that prevents transcription of proteins required for lytic development. The central portion of the protein is well conserved and is both necessary and sufficient for the activity of the protein []. Comparative analysis of the CIII sequence in lambda, Bacteriophage HK022 and the lambdoid Enterobacteria phage P22 has led to the suggestion that this central region assumes an amphipathic alpha-helical structure []. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=42.45 E-value=80 Score=19.58 Aligned_cols=26 Identities=23% Similarity=0.509 Sum_probs=20.5
Q ss_pred CCC--HHHHHHHHHHHHHHHHHHHHHhh
Q 040645 156 GVS--EEEAVKELLLEVADSWKDINEEL 181 (233)
Q Consensus 156 g~s--~eeA~~~i~~~i~~~~k~ln~e~ 181 (233)
|++ -|.-.+.|.+-+++.||++-+-.
T Consensus 12 G~~ql~ESLLdrItRklr~gwKRl~~iL 39 (45)
T PF02061_consen 12 GCPQLSESLLDRITRKLRDGWKRLWDIL 39 (45)
T ss_pred CCchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 565 56778999999999999986543
No 47
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=41.12 E-value=47 Score=29.04 Aligned_cols=65 Identities=22% Similarity=0.210 Sum_probs=49.0
Q ss_pred chhhhhhcCCccchhHHHhhcCCCCHHHHHHHHHHHHHHHHHHHH----------HhhcCCCCCCHHHHHHHHHHhhh
Q 040645 134 GYKFEQKRGHIPSAVECYKNQHGVSEEEAVKELLLEVADSWKDIN----------EELLNPTTASLPTLQRVLYFARS 201 (233)
Q Consensus 134 S~~~E~~~G~~~n~V~~yM~e~g~s~eeA~~~i~~~i~~~~k~ln----------~e~l~~~~~p~~~~~~~~n~~R~ 201 (233)
.|++||+- ++.+...+...|.+.++|..++.--+++.+-++- .++|...++|...+..+.++||=
T Consensus 96 ~wk~~qka---~klle~aaekl~~~~ee~~~~vg~~L~e~fG~~y~aFE~aa~~g~~~l~~~~~~~~~~~~l~e~a~e 170 (269)
T COG1093 96 EWKKEQKA---DKLLELAAEKLGKDLEEAYEEVGWKLEEEFGSLYDAFEAAAKEGGEVLDDEGVPEEWKEVLKEIARE 170 (269)
T ss_pred HHHHHHHH---HHHHHHHHHHhCCCHHHHHHHHhHHHHHHhCCHHHHHHHHHhcCCcccccCCCCHHHHHHHHHHHHh
Confidence 45666663 5778888888899999999999988887765543 23334456888999999999873
No 48
>KOG3284 consensus Vacuolar sorting protein VPS28 [Intracellular trafficking, secretion, and vesicular transport]
Probab=40.21 E-value=1.3e+02 Score=25.17 Aligned_cols=65 Identities=11% Similarity=0.065 Sum_probs=42.5
Q ss_pred CCChhHHHHHHHHHHHHHHHHHHHHHhcCc-----chHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHhhhhhhc
Q 040645 14 TLPEYMKFIFKALLDIYREAEEELAKERRS-----YGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKSVALRSI 86 (233)
Q Consensus 14 ~lpe~mk~~f~~l~~~~~e~~~~~~~~~~~-----~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~~~~~s~ 86 (233)
+.=|.|..+| +++++++..|++..++.-+ .--..++..|+..++... ...+||+|+|-+.-+...
T Consensus 22 E~~enlseLy-aIi~ale~LEKAyirD~is~sey~s~c~kLi~Q~k~~~~~~~-------~~~f~SiE~Fc~kyrl~c 91 (213)
T KOG3284|consen 22 EVYENLSELY-AIIKALEQLEKAYIRDCISPSEYTSECSKLIVQYKVAFRSVQ-------GTEFPSIEDFCKKYRLDC 91 (213)
T ss_pred HHHHHHHHHH-HHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHhc-------ccccCcHHHHHHHHccCC
Confidence 3346676676 6788999999998886542 123445666776666542 237999999976554443
No 49
>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=38.71 E-value=72 Score=23.90 Aligned_cols=71 Identities=7% Similarity=0.017 Sum_probs=45.6
Q ss_pred hHHHHHHHHHHHHhhCccchhhhhhcCCccchhHHHhhcCCCCH---HHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHH
Q 040645 116 AKSVKATQTIVRFMDDIAGYKFEQKRGHIPSAVECYKNQHGVSE---EEAVKELLLEVADSWKDINEELLNPTTASLPTL 192 (233)
Q Consensus 116 ~~l~~~~~~i~rL~NDi~S~~~E~~~G~~~n~V~~yM~e~g~s~---eeA~~~i~~~i~~~~k~ln~e~l~~~~~p~~~~ 192 (233)
-.+.+.-..+.+.+||+++.+-+-.. +-||.-...+.-+++|. -|--++++..++.+|.-+. .+|.+++
T Consensus 25 D~~~rLN~ev~~~~~~Ly~~~G~t~E-eeA~lCLaLLmGYnat~yd~geke~~~Q~vL~Rs~~vL~-------~Lp~SlL 96 (106)
T PF06603_consen 25 DDFSRLNKEVYEQSNDLYSQHGSTPE-EEANLCLALLMGYNATIYDNGEKEEKKQEVLDRSWEVLD-------KLPASLL 96 (106)
T ss_pred HHHHHHhHHHHHHHHHHHhccCCCHH-HHHHHHHHHHHhccchhhhCccHHHHHHHHHHHHHHHHH-------hCCcHHH
Confidence 35778888899999999987432111 11455444444455543 3445688999999998775 3776665
Q ss_pred HH
Q 040645 193 QR 194 (233)
Q Consensus 193 ~~ 194 (233)
+.
T Consensus 97 K~ 98 (106)
T PF06603_consen 97 KV 98 (106)
T ss_pred HH
Confidence 54
No 50
>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=38.70 E-value=26 Score=25.57 Aligned_cols=30 Identities=30% Similarity=0.250 Sum_probs=20.7
Q ss_pred CCccchhHHHhhcCCCCHHHHHHHHHHHHH
Q 040645 142 GHIPSAVECYKNQHGVSEEEAVKELLLEVA 171 (233)
Q Consensus 142 G~~~n~V~~yM~e~g~s~eeA~~~i~~~i~ 171 (233)
|...|+|..+|+-.|+|-.||++.+.+...
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 334588999998889999999999887653
No 51
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=36.29 E-value=33 Score=26.21 Aligned_cols=27 Identities=41% Similarity=0.320 Sum_probs=21.7
Q ss_pred CCccchhHHHhhcCCCCHHHHHHHHHH
Q 040645 142 GHIPSAVECYKNQHGVSEEEAVKELLL 168 (233)
Q Consensus 142 G~~~n~V~~yM~e~g~s~eeA~~~i~~ 168 (233)
|-...-|.+.|.+.|+|.++|++.+.+
T Consensus 74 ~i~~edI~lv~~q~gvs~~~A~~AL~~ 100 (115)
T PRK06369 74 EIPEEDIELVAEQTGVSEEEARKALEE 100 (115)
T ss_pred CCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 333567899999999999999987764
No 52
>PF13189 Cytidylate_kin2: Cytidylate kinase-like family; PDB: 3FDI_A.
Probab=34.90 E-value=13 Score=30.08 Aligned_cols=37 Identities=24% Similarity=0.171 Sum_probs=25.6
Q ss_pred chhHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHhhcC
Q 040645 146 SAVECYKNQHGVSEEEAVKELLLEVADSWKDINEELLN 183 (233)
Q Consensus 146 n~V~~yM~e~g~s~eeA~~~i~~~i~~~~k~ln~e~l~ 183 (233)
.-|.-.|+.+|+|.++|.+.+.+ .+...+.+-+.+..
T Consensus 126 ~Rv~ri~~~~~~s~~~A~~~i~~-~D~~R~~~~~~~~~ 162 (179)
T PF13189_consen 126 FRVERIMEREGISEEEAEKLIKK-EDKRRRAYYKYYTG 162 (179)
T ss_dssp HHHHHHHHHHT--HHHHHHHHHH-HHHHHHHHHHHH-S
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH-HHHHHHHHHHHHhC
Confidence 44666788889999999999888 66677777666664
No 53
>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=34.32 E-value=37 Score=25.94 Aligned_cols=24 Identities=33% Similarity=0.286 Sum_probs=20.2
Q ss_pred cchhHHHhhcCCCCHHHHHHHHHH
Q 040645 145 PSAVECYKNQHGVSEEEAVKELLL 168 (233)
Q Consensus 145 ~n~V~~yM~e~g~s~eeA~~~i~~ 168 (233)
..-|.+.|.+.|+|.++|++.+.+
T Consensus 79 ~eDI~lV~eq~gvs~e~A~~AL~~ 102 (116)
T TIGR00264 79 EDDIELVMKQCNVSKEEARRALEE 102 (116)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHH
Confidence 466889999999999999987764
No 54
>PTZ00393 protein tyrosine phosphatase; Provisional
Probab=34.00 E-value=35 Score=29.49 Aligned_cols=39 Identities=8% Similarity=0.009 Sum_probs=27.8
Q ss_pred ccchhHHHhhcCCCCHHHHHHHHHHH----HHHHHHHHHHhhc
Q 040645 144 IPSAVECYKNQHGVSEEEAVKELLLE----VADSWKDINEELL 182 (233)
Q Consensus 144 ~~n~V~~yM~e~g~s~eeA~~~i~~~----i~~~~k~ln~e~l 182 (233)
.+-.+.+||-++|++.++|++.++.. +.....++.+.|-
T Consensus 184 TGtl~AayLI~~GmspeeAI~~VR~~RPgAIn~~Q~~fL~~y~ 226 (241)
T PTZ00393 184 APVLASIVLIEFGMDPIDAIVFIRDRRKGAINKRQLQFLKAYK 226 (241)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Confidence 35778899999999999999999873 3334444444443
No 55
>cd00737 endolysin_autolysin Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell walls. Similarly, bacteria produce autolysins to facilitate the biosynthesis of its cell wall hetropolymer peptidoglycan and cell division. Both endolysin and autolysin enzymes cleave the glycosidic beta 1,4-bonds between the N-acetylmuramic acid and the N-acetylglucosamine of the peptidoglycan.
Probab=31.98 E-value=2.3e+02 Score=21.52 Aligned_cols=52 Identities=15% Similarity=0.302 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhhhhhhhcccCCCCCCC
Q 040645 156 GVSEEEAVKELLLEVADSWKDINEELLNPTTASLPTLQRVLYFARSGHFIYDDGHDRYTH 215 (233)
Q Consensus 156 g~s~eeA~~~i~~~i~~~~k~ln~e~l~~~~~p~~~~~~~~n~~R~~~~~Y~~~~D~~t~ 215 (233)
.+|.++|.+-+.+.++...+.++..+ +.++|..-....+++ .|+-|..++..
T Consensus 42 ~iT~~qa~~ll~~dl~~~~~~v~~~~--~~~l~~~~~dALvs~------ayN~G~~~~~~ 93 (133)
T cd00737 42 TITEEQADALLAKDLAKAERAVNRAV--KVPLTQNQFDALVSF------AFNVGAGAFRT 93 (133)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHh------hhhcCcccccc
Confidence 58999999999999999998876544 234665444443333 35555344443
No 56
>KOG0776 consensus Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism]
Probab=31.95 E-value=3.2e+02 Score=25.35 Aligned_cols=100 Identities=14% Similarity=0.096 Sum_probs=66.8
Q ss_pred HHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCC---CHHHHHhhhhhhcchHHHHHHHH-HhcCCCCCChhhhhhh
Q 040645 37 LAKERRSYGISYAKQTMQELIMLYFTEAKWLYKGYIP---SFDEYKSVALRSIGFLPVAVASF-VDLGDFIATKDNFECI 112 (233)
Q Consensus 37 ~~~~~~~~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iP---t~eEYl~~~~~s~g~~~~~~~~~-~~~g~~~l~~e~~~~~ 112 (233)
+..-+..-+.+.+..+..+++++-..+..-..+|.-+ .+++|...-.-.+|.-+-..+-. .-+| . -++++.+.+
T Consensus 189 la~l~n~~v~elm~~aI~dLv~ge~~~~~~~~~~~d~~~~~~e~~e~~~~~KTAsLla~Sc~~~aILg-g-~s~ev~e~~ 266 (384)
T KOG0776|consen 189 LASLENPVVVELMASAIADLVRGEFTQGLVAGEGLDLDDVGLEYLEFKTLLKTASLLAKSCVAAAILG-G-GSEEVIEAA 266 (384)
T ss_pred HHhccCchHHHHHHHHHHHHHHhhhhcccccccccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHc-C-CCHHHHHHH
Confidence 3334444677888889999999988777665433433 57778776666555544222211 1233 3 567777775
Q ss_pred hcchHHHHHHHHHHHHhhCccchhhhhhc
Q 040645 113 LKNAKSVKATQTIVRFMDDIAGYKFEQKR 141 (233)
Q Consensus 113 ~~~~~l~~~~~~i~rL~NDi~S~~~E~~~ 141 (233)
-+.-+..+...-+++||..+.+....
T Consensus 267 ---~~yGR~lGL~fQvvDDildftkss~e 292 (384)
T KOG0776|consen 267 ---FEYGRCLGLAFQVVDDILDFTKSSEE 292 (384)
T ss_pred ---HHHHHHHHHHHHHhhcccCcccchhh
Confidence 46778999999999999999876543
No 57
>COG0864 NikR Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]
Probab=31.93 E-value=1.2e+02 Score=23.73 Aligned_cols=43 Identities=23% Similarity=0.399 Sum_probs=27.0
Q ss_pred CCChhHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhCC
Q 040645 14 TLPEYMKFIFKALLDIYREAEEELAKERRSYGISYAKQTMQELIMLYFTEAKWLYKG 70 (233)
Q Consensus 14 ~lpe~mk~~f~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~Ea~w~~~~ 70 (233)
.||+.+ ++.++++ +.+.|..++-+. .++.++.|++|-+|....
T Consensus 10 SLp~~L-------l~elD~~---i~~rg~~sRSE~----IrdAir~yl~e~~~~~~~ 52 (136)
T COG0864 10 SLPEEL-------LEELDEL---IEERGYSSRSEL----IRDALREYLEEYRWLEDI 52 (136)
T ss_pred ECcHHH-------HHHHHHH---HHHcCCCcHHHH----HHHHHHHHHHHhhhhccc
Confidence 477765 5555555 444555555544 455667778888998754
No 58
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=30.99 E-value=95 Score=20.40 Aligned_cols=31 Identities=16% Similarity=0.163 Sum_probs=22.7
Q ss_pred ccchhHHHhhcCCCCHHHHHHHHHHHHHHHH
Q 040645 144 IPSAVECYKNQHGVSEEEAVKELLLEVADSW 174 (233)
Q Consensus 144 ~~n~V~~yM~e~g~s~eeA~~~i~~~i~~~~ 174 (233)
+..++.....+++++.+++.+.+...+++-.
T Consensus 32 ~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~ 62 (68)
T PF05402_consen 32 VEEIVDALAEEYDVDPEEAEEDVEEFLEQLR 62 (68)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 4567777777889999999888888887655
No 59
>KOG4713 consensus Cyclin-dependent kinase 2-associated protein [Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning]
Probab=29.37 E-value=97 Score=25.45 Aligned_cols=48 Identities=15% Similarity=0.218 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHh--cCcchHHHHHHHH---HHHHHHHHHHHHHH
Q 040645 20 KFIFKALLDIYREAEEELAKE--RRSYGISYAKQTM---QELIMLYFTEAKWL 67 (233)
Q Consensus 20 k~~f~~l~~~~~e~~~~~~~~--~~~~~~~~~~~~~---~~~~~a~~~Ea~w~ 67 (233)
..-|..|++.++|+.+++..- |.....+++|.-. +.+++.+++|++-.
T Consensus 134 ~~kY~~LL~vieEmgkeirpTyagsks~~ERLKr~I~hAR~lVRecl~etE~~ 186 (189)
T KOG4713|consen 134 QTKYADLLSVIEEMGKEIRPTYAGSKSAMERLKRDIIHARLLVRECLQETERA 186 (189)
T ss_pred chHHHHHHHHHHHHhcccCccccccccHHHHHHhhHHHHHHHHHHHHHHHHHh
Confidence 456788999999998876542 4335667776644 66999999998754
No 60
>PRK12793 flaF flagellar biosynthesis regulatory protein FlaF; Reviewed
Probab=28.21 E-value=2.7e+02 Score=21.16 Aligned_cols=42 Identities=17% Similarity=0.262 Sum_probs=31.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhhcCC-CCCCHHHHHHHHHHhh
Q 040645 158 SEEEAVKELLLEVADSWKDINEELLNP-TTASLPTLQRVLYFAR 200 (233)
Q Consensus 158 s~eeA~~~i~~~i~~~~k~ln~e~l~~-~~~p~~~~~~~~n~~R 200 (233)
+..++++.+.. -..-|-.|-.++..| +++|..++.-+++++=
T Consensus 41 ~~~~~~eAL~~-NrrLWt~~~~Dl~~p~N~LP~eLRa~lisL~~ 83 (115)
T PRK12793 41 YSREAIEALYF-TRRLWTVLIEDLGSPENALPEELRADLISIGL 83 (115)
T ss_pred ChHHHHHHHHH-HHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHH
Confidence 33444433333 566899999999998 6799999999999884
No 61
>PF02970 TBCA: Tubulin binding cofactor A; InterPro: IPR004226 The folding pathway of tubulins includes highly specific interactions with a series of cofactors (A, B, C, D and E) after they are released from the eukaryotic chaperonin CCT. Cofactors A and D capture and stabilise tubulin in a quasi-native conformation. Cofactor E binds to the cofactor D-tubulin complex, and interaction with cofactor C then causes the release of tubulin poypeptides in the native state. This family is the tubulin-specific chaperone A.; GO: 0051082 unfolded protein binding, 0007021 tubulin complex assembly, 0005874 microtubule; PDB: 3MXZ_A 1QSD_A 1H7C_A.
Probab=25.49 E-value=2.5e+02 Score=20.18 Aligned_cols=59 Identities=19% Similarity=0.318 Sum_probs=37.7
Q ss_pred HHHHHHHHHhhCccchhhhhhcCCccchhHHHhhcCCCC------HHHHHHHHHHHHHHHHHHHHHhh
Q 040645 120 KATQTIVRFMDDIAGYKFEQKRGHIPSAVECYKNQHGVS------EEEAVKELLLEVADSWKDINEEL 181 (233)
Q Consensus 120 ~~~~~i~rL~NDi~S~~~E~~~G~~~n~V~~yM~e~g~s------~eeA~~~i~~~i~~~~k~ln~e~ 181 (233)
-.++.+-||+.|..+|++|.... ..-|. =|+..|-. .++++++...||-++-++|...+
T Consensus 4 Ikt~~vkRL~KE~~~Y~kE~~~q--~~rle-~~k~~~~de~~iKkq~~vl~Et~~mipd~~~RL~~a~ 68 (90)
T PF02970_consen 4 IKTGVVKRLLKEEASYEKEVEEQ--EARLE-KMKAEGEDEYDIKKQEEVLEETKMMIPDCQQRLEKAV 68 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH--HHHHH-HHHHCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ehHHHHHHHHHHHHHHHHHHHHH--HHHHH-HHHhcCCcHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 35678899999999999996532 12233 23333432 25677777777777777665433
No 62
>PHA02896 A-type inclusion like protein; Provisional
Probab=25.24 E-value=1.2e+02 Score=29.21 Aligned_cols=45 Identities=9% Similarity=0.226 Sum_probs=37.4
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhhh
Q 040645 154 QHGVSEEEAVKELLLEVADSWKDINEELLNPTTASLPTLQRVLYFARS 201 (233)
Q Consensus 154 e~g~s~eeA~~~i~~~i~~~~k~ln~e~l~~~~~p~~~~~~~~n~~R~ 201 (233)
..|+.+|..+..+..+|++.|. ++.-+.+.+|+.-..++=|+-|-
T Consensus 3 ~~~~giEKcV~eFkSlVertWn---k~Lns~SCIpRk~RKiIRNILR~ 47 (616)
T PHA02896 3 RDGCGIDKCIRKFESLIIRTWD---HDLNERSFLNRKDRKIIRNIFRC 47 (616)
T ss_pred ccccChHHHHHHHHHHHHHhhC---CccccccCcCHHHHHHHHHHHHH
Confidence 3588999999999999999993 44444578999999999999985
No 63
>KOG2099 consensus Glycogen phosphorylase [Carbohydrate transport and metabolism]
Probab=23.75 E-value=30 Score=33.83 Aligned_cols=34 Identities=15% Similarity=0.469 Sum_probs=27.0
Q ss_pred ccccccCCCCcCC-CChhHHHHHHHHHHHHHHHHH
Q 040645 2 VLTKKWDIGLIDT-LPEYMKFIFKALLDIYREAEE 35 (233)
Q Consensus 2 ~ai~RWD~~~~~~-lpe~mk~~f~~l~~~~~e~~~ 35 (233)
+|.|||-.+.++. ||-+++|+|..=...++.+..
T Consensus 383 EALErWp~~L~e~LLPRHleIIy~In~~~l~~i~~ 417 (843)
T KOG2099|consen 383 EALERWPVSLMEKLLPRHLEIIYEINQRFLQTVAA 417 (843)
T ss_pred HHHHHhhHHHHHHhhhHHHHHHHHHHHHHHHHHHH
Confidence 6899999998875 599999999876666666644
No 64
>PRK08470 adenylosuccinate lyase; Provisional
Probab=23.73 E-value=3.5e+02 Score=25.36 Aligned_cols=73 Identities=18% Similarity=0.238 Sum_probs=50.9
Q ss_pred CChhhhhhhhcchHHHHHHHHHHHHhhCccchh---hh-----h--hcCCc-cchhHHHhhcCCCCHHHHHHHHHHHHHH
Q 040645 104 ATKDNFECILKNAKSVKATQTIVRFMDDIAGYK---FE-----Q--KRGHI-PSAVECYKNQHGVSEEEAVKELLLEVAD 172 (233)
Q Consensus 104 l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~---~E-----~--~~G~~-~n~V~~yM~e~g~s~eeA~~~i~~~i~~ 172 (233)
+.....+| ...|..+..+....++++++.+-- .| . ..|-. +..|...+..+|++.++|.+.+++....
T Consensus 303 ~~~~~~e~-~~l~~~~~~~~~~l~~~~~~l~~l~v~~~rm~~nl~~~~g~~~ae~l~~~L~~~G~~~~~Ah~~V~~~~~~ 381 (442)
T PRK08470 303 ISHSSVER-FILPDAFITTDFMLHRLNNVIENLVVYPENMMKNLNLTGGLVFSQRVLLELPKKGVSREDAYKIVQRNAMK 381 (442)
T ss_pred CchhHHHh-hhHHHHHHHHHHHHHHHHHHHccCEECHHHHHHHHHhccChHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 44444455 245778888888888877765421 11 2 23444 5666667767799999999999999999
Q ss_pred HHHHH
Q 040645 173 SWKDI 177 (233)
Q Consensus 173 ~~k~l 177 (233)
+|+++
T Consensus 382 a~~~~ 386 (442)
T PRK08470 382 VWEDL 386 (442)
T ss_pred HHHHh
Confidence 99884
No 65
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=23.38 E-value=1.9e+02 Score=24.60 Aligned_cols=70 Identities=10% Similarity=0.026 Sum_probs=38.2
Q ss_pred CCcCCCChhHHHHHHHHHH---HHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHh
Q 040645 10 GLIDTLPEYMKFIFKALLD---IYREAEEELAKERRSYGISYAKQTMQELIMLYFTEAKWLYKGYIPSFDEYKS 80 (233)
Q Consensus 10 ~~~~~lpe~mk~~f~~l~~---~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~Ea~w~~~~~iPt~eEYl~ 80 (233)
.++++||+..+.+|..-+- ++.||+..+...-+ .+..++..+.+.+-+.+-.+.-=+-+-+.|-+|.++.
T Consensus 157 ~aL~~Lp~~~R~v~~L~~~eg~S~~EIA~~Lgis~~-TVk~rl~RAr~~Lr~~l~~~~~~~~~~~~~~~~~~~~ 229 (244)
T TIGR03001 157 EALAALSERERHLLRLHFVDGLSMDRIGAMYQVHRS-TVSRWVAQARERLLERTRRRLAERLKLSSPELESLLG 229 (244)
T ss_pred HHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHH-HHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHH
Confidence 4677888888877776653 77888776544333 3334444444433333322222233345556666653
No 66
>PF12469 DUF3692: CRISPR-associated protein ; InterPro: IPR024615 This uncharacterised N-terminal domain family is typically between 101 and 138 amino acids in length. ; PDB: 3UNG_C 4DOZ_A 3UR3_C.
Probab=21.75 E-value=91 Score=23.50 Aligned_cols=41 Identities=24% Similarity=0.396 Sum_probs=25.9
Q ss_pred hcCCccchhHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 040645 140 KRGHIPSAVECYKNQHGVSEEEAVKELLLEVADSWKDINEEL 181 (233)
Q Consensus 140 ~~G~~~n~V~~yM~e~g~s~eeA~~~i~~~i~~~~k~ln~e~ 181 (233)
.+..++|-+...+-. +-..++..+++++.+++.|+++-+.+
T Consensus 77 ~~~~~Pnr~~a~~p~-~~~~~~~~~~~k~~~~~~w~~i~~~v 117 (117)
T PF12469_consen 77 PRAGIPNRFLAIVPG-DEEAEELAEEAKEAIREAWKEIAEKV 117 (117)
T ss_dssp GSB---SEEEEEEET-TT-HHHHHHHHHHHHHHHHHHHHH--
T ss_pred cccCCCceeeeecCc-hhHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 333447777544432 22578999999999999999987643
No 67
>KOG2077 consensus JNK/SAPK-associated protein-1 [Signal transduction mechanisms]
Probab=21.41 E-value=2.2e+02 Score=28.03 Aligned_cols=92 Identities=15% Similarity=0.172 Sum_probs=52.5
Q ss_pred hhhhhhhcchHHHHHHHHHHHHhhCcc------chhhhhhcCCccch--hHHHhhcCCCCHHHHHHHHHHHHHHHHHHHH
Q 040645 107 DNFECILKNAKSVKATQTIVRFMDDIA------GYKFEQKRGHIPSA--VECYKNQHGVSEEEAVKELLLEVADSWKDIN 178 (233)
Q Consensus 107 e~~~~~~~~~~l~~~~~~i~rL~NDi~------S~~~E~~~G~~~n~--V~~yM~e~g~s~eeA~~~i~~~i~~~~k~ln 178 (233)
|+-+-+..+..|+..-+.+--.-||+. +.+++.-||..-.. +..=|.+.---.||-++.++....++.++
T Consensus 302 EVeNLilENsqLLetKNALNiVKNDLIakVDeL~~E~~vLrgElea~kqak~Klee~i~elEEElk~~k~ea~~ar~~-- 379 (832)
T KOG2077|consen 302 EVENLILENSQLLETKNALNIVKNDLIAKVDELTCEKDVLRGELEAVKQAKLKLEEKIRELEEELKKAKAEAEDARQK-- 379 (832)
T ss_pred HHHHHHHhhHHHHhhhhHHHHHHHHHHHHHHhhccHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--
Confidence 344445566778877777777778875 45666677765221 11222222222344444444444444432
Q ss_pred HhhcC--CCCCCHHHHHHH--HHHhhhh
Q 040645 179 EELLN--PTTASLPTLQRV--LYFARSG 202 (233)
Q Consensus 179 ~e~l~--~~~~p~~~~~~~--~n~~R~~ 202 (233)
... .+.+|++-.++| ..|+||+
T Consensus 380 --~~~~e~ddiPmAqRkRFTRvEMaRVL 405 (832)
T KOG2077|consen 380 --AKDDEDDDIPMAQRKRFTRVEMARVL 405 (832)
T ss_pred --hcccccccccHHHHhhhHHHHHHHHH
Confidence 333 367999998887 5788875
No 68
>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=20.97 E-value=4e+02 Score=21.37 Aligned_cols=13 Identities=46% Similarity=0.864 Sum_probs=10.8
Q ss_pred HHhCCCCCCHHHH
Q 040645 66 WLYKGYIPSFDEY 78 (233)
Q Consensus 66 w~~~~~iPt~eEY 78 (233)
|...|..||++|.
T Consensus 112 ~srAg~~~~Lqe~ 124 (152)
T TIGR03486 112 WARAGRIPSLQEH 124 (152)
T ss_pred HHHccCCcchHHH
Confidence 6788999999876
No 69
>PF12550 GCR1_C: Transcriptional activator of glycolytic enzymes; InterPro: IPR022210 This domain family is found in eukaryotes, and is approximately 80 amino acids in length. This family is activates the transcription of glycolytic enzymes.
Probab=20.57 E-value=1e+02 Score=21.53 Aligned_cols=25 Identities=40% Similarity=0.466 Sum_probs=19.1
Q ss_pred ccchhHHHhhcCCCCHHHHHHHHHH
Q 040645 144 IPSAVECYKNQHGVSEEEAVKELLL 168 (233)
Q Consensus 144 ~~n~V~~yM~e~g~s~eeA~~~i~~ 168 (233)
+-+.|.-+.++.|.|.++|++.+..
T Consensus 55 Ii~~I~~l~~~~g~~~~~ai~~le~ 79 (81)
T PF12550_consen 55 IIDFIERLANERGISEEEAIEILEE 79 (81)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4466665577789999999988764
No 70
>COG5442 FlaF Flagellar biosynthesis regulator FlaF [Cell motility and secretion]
Probab=20.52 E-value=3.7e+02 Score=20.16 Aligned_cols=71 Identities=15% Similarity=0.267 Sum_probs=45.7
Q ss_pred HhhCccchhhhhhcCCccchhHHHhh--cCCCCHHHHHHHHHHHHHHHHHHHHHhhcCC-CCCCHHHHHHHHHHh
Q 040645 128 FMDDIAGYKFEQKRGHIPSAVECYKN--QHGVSEEEAVKELLLEVADSWKDINEELLNP-TTASLPTLQRVLYFA 199 (233)
Q Consensus 128 L~NDi~S~~~E~~~G~~~n~V~~yM~--e~g~s~eeA~~~i~~~i~~~~k~ln~e~l~~-~~~p~~~~~~~~n~~ 199 (233)
.++|=++.-|+..++-+.-+|...-. ..|-..-+|++.+. -...-|-.|.+.+=.| +++|+.+.--.+.++
T Consensus 9 vm~~~va~akdRer~~ltRsiall~aa~a~~~~sre~IeAl~-ftrrvW~~fieDl~~pdNqLp~ELRAnlISig 82 (115)
T COG5442 9 VMEDGVASAKDRERQLLTRSIALLDAARAPGDDSREAIEALY-FTRRVWTRFIEDLGSPDNQLPMELRANLISIG 82 (115)
T ss_pred HHhhhhhhHHHHHHHHHHHHHHHHHHHhccchhHHHHHHHHH-HHHHHHHHHHHHhcCccccccHHHHHHHHHHH
Confidence 35565566667777766555543222 22444455665543 3678899999999887 679998876666554
No 71
>TIGR03515 GldC gliding motility-associated protein GldC. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldC is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldC do not abolish the gliding phenotype but do impair it. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.
Probab=20.33 E-value=3.8e+02 Score=20.14 Aligned_cols=41 Identities=12% Similarity=0.185 Sum_probs=24.8
Q ss_pred CCC-hhHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHH
Q 040645 14 TLP-EYMKFIFKALLDIYREAEEELAKERRSYGISYAKQTMQELIMLY 60 (233)
Q Consensus 14 ~lp-e~mk~~f~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~a~ 60 (233)
..| +.||.+|. .|+-.+++-+.+-.+ -....+.++++|.-+
T Consensus 59 dMpVdEMK~Ff~---qtl~~maDT~~rAT~---d~kma~~m~dfcd~f 100 (108)
T TIGR03515 59 DMPVDEMKRFFI---ETLGGMADTFLNATG---DEKMAEDIKDLCDRL 100 (108)
T ss_pred cCcHHHHHHHHH---HHHHHHHHHHHHhcC---cHHHHHHHHHHHHHH
Confidence 567 88999995 455555555555444 234455566666554
Done!