Query 028006
Match_columns 215
No_of_seqs 165 out of 794
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 04:49:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028006.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028006hhsearch_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 1.7E-55 3.6E-60 408.5 24.0 210 1-212 331-542 (542)
2 PLN02279 ent-kaur-16-ene synth 100.0 2.8E-55 6.2E-60 416.8 22.7 209 1-215 565-778 (784)
3 PLN02150 terpene synthase/cycl 100.0 4.9E-37 1.1E-41 223.6 10.3 94 121-215 1-96 (96)
4 cd00868 Terpene_cyclase_C1 Ter 100.0 3.9E-32 8.5E-37 231.9 20.9 187 1-188 97-284 (284)
5 PF03936 Terpene_synth_C: Terp 100.0 3.7E-29 8E-34 212.1 13.7 158 2-160 112-270 (270)
6 cd00687 Terpene_cyclase_nonpla 99.9 8.7E-27 1.9E-31 201.7 14.4 157 3-165 110-267 (303)
7 PLN02592 ent-copalyl diphospha 99.9 2.3E-25 5E-30 212.1 17.3 171 1-214 626-800 (800)
8 cd00385 Isoprenoid_Biosyn_C1 I 99.7 4.1E-17 8.9E-22 133.4 12.5 169 5-182 62-243 (243)
9 cd00686 Terpene_cyclase_cis_tr 97.6 0.00069 1.5E-08 59.5 10.8 128 26-162 145-276 (357)
10 PF06330 TRI5: Trichodiene syn 97.5 0.0018 4E-08 57.6 11.5 134 24-163 143-277 (376)
11 cd00867 Trans_IPPS Trans-Isopr 95.7 0.42 9.1E-06 39.4 13.2 118 27-161 86-214 (236)
12 PLN02890 geranyl diphosphate s 93.5 3.8 8.3E-05 37.5 14.6 92 23-119 224-315 (422)
13 TIGR02749 prenyl_cyano solanes 93.3 5.4 0.00012 35.1 16.6 91 23-118 130-220 (322)
14 PLN02857 octaprenyl-diphosphat 93.2 3.9 8.5E-05 37.4 14.2 88 26-118 227-314 (416)
15 cd00685 Trans_IPPS_HT Trans-Is 93.2 2.4 5.1E-05 35.9 12.1 121 26-161 108-239 (259)
16 TIGR02748 GerC3_HepT heptapren 91.1 10 0.00022 33.3 16.0 87 26-118 129-216 (319)
17 PF00494 SQS_PSY: Squalene/phy 88.8 11 0.00023 31.8 11.8 134 32-179 90-236 (267)
18 COG0142 IspA Geranylgeranyl py 88.4 17 0.00036 32.0 15.0 108 26-139 134-251 (322)
19 KOG1719 Dual specificity phosp 84.7 0.8 1.7E-05 36.3 2.4 63 95-161 90-165 (183)
20 TIGR03465 HpnD squalene syntha 84.5 24 0.00051 29.9 13.7 133 35-182 87-228 (266)
21 PRK10888 octaprenyl diphosphat 83.2 31 0.00068 30.3 17.1 90 23-118 127-217 (323)
22 COG3707 AmiR Response regulato 82.0 1.2 2.6E-05 36.3 2.6 49 105-153 125-174 (194)
23 CHL00151 preA prenyl transfera 81.0 38 0.00082 29.7 15.0 89 26-119 134-222 (323)
24 PF03861 ANTAR: ANTAR domain; 78.9 1.8 3.9E-05 27.9 2.2 28 126-153 15-42 (56)
25 PF13060 DUF3921: Protein of u 77.0 11 0.00024 23.7 5.2 44 2-47 7-50 (58)
26 PRK10581 geranyltranstransfera 76.9 42 0.00092 29.1 10.8 112 36-161 152-276 (299)
27 PF12368 DUF3650: Protein of u 70.3 3.5 7.6E-05 22.9 1.6 18 132-149 9-26 (28)
28 PF00348 polyprenyl_synt: Poly 68.2 72 0.0016 26.8 11.3 65 52-120 130-194 (260)
29 smart00463 SMR Small MutS-rela 64.6 9.7 0.00021 25.9 3.3 23 137-159 7-29 (80)
30 smart00400 ZnF_CHCC zinc finge 64.2 7.7 0.00017 24.7 2.6 25 124-148 30-54 (55)
31 PF01713 Smr: Smr domain; Int 61.3 10 0.00022 26.1 2.9 24 137-160 4-27 (83)
32 COG1308 EGD2 Transcription fac 59.3 9.5 0.00021 28.8 2.6 23 128-150 86-108 (122)
33 cd00683 Trans_IPPS_HH Trans-Is 58.6 1.1E+02 0.0024 25.7 13.3 132 33-183 93-238 (265)
34 TIGR03464 HpnC squalene syntha 58.1 1.1E+02 0.0025 25.7 13.0 119 51-181 101-228 (266)
35 PLN02632 phytoene synthase 57.3 1.4E+02 0.003 26.4 13.8 134 35-180 142-287 (334)
36 COG2443 Sss1 Preprotein transl 55.2 42 0.00091 22.5 4.9 21 53-73 26-46 (65)
37 PF06603 UpxZ: UpxZ family of 54.2 22 0.00047 26.1 3.7 72 98-177 25-99 (106)
38 COG1093 SUI2 Translation initi 53.6 21 0.00046 30.6 4.1 65 116-183 96-170 (269)
39 PF05772 NinB: NinB protein; 53.4 12 0.00026 28.5 2.4 58 8-69 43-101 (127)
40 PRK14562 haloacid dehalogenase 45.6 1E+02 0.0022 25.3 6.9 29 30-59 78-106 (204)
41 PRK06369 nac nascent polypepti 44.8 21 0.00045 26.8 2.4 27 124-150 74-100 (115)
42 COG0864 NikR Predicted transcr 43.8 65 0.0014 24.8 5.1 37 12-52 16-52 (136)
43 TIGR00264 alpha-NAC-related pr 42.6 24 0.00052 26.5 2.5 24 127-150 79-102 (116)
44 PF13189 Cytidylate_kin2: Cyti 42.2 8.6 0.00019 30.6 0.1 35 130-165 128-162 (179)
45 PTZ00393 protein tyrosine phos 41.6 22 0.00047 30.1 2.4 29 123-151 181-209 (241)
46 PF10397 ADSL_C: Adenylosuccin 41.2 38 0.00082 23.2 3.2 30 129-158 8-37 (81)
47 PF03701 UPF0181: Uncharacteri 38.7 50 0.0011 21.0 3.1 45 111-157 2-46 (51)
48 KOG1766 Enhancer of rudimentar 38.5 1.3E+02 0.0029 21.7 5.6 60 140-206 24-88 (104)
49 PF01807 zf-CHC2: CHC2 zinc fi 38.2 25 0.00055 25.1 2.0 29 125-153 62-90 (97)
50 KOG0776 Geranylgeranyl pyropho 37.8 2.6E+02 0.0056 25.5 8.6 100 19-123 189-292 (384)
51 COG4860 Uncharacterized protei 37.1 36 0.00077 26.6 2.7 58 2-67 27-89 (170)
52 COG5442 FlaF Flagellar biosynt 34.6 1.4E+02 0.003 22.0 5.3 71 110-181 9-82 (115)
53 PF13798 PCYCGC: Protein of un 33.5 45 0.00098 26.4 2.8 32 134-172 127-158 (158)
54 COG3140 Uncharacterized protei 29.1 38 0.00082 21.9 1.4 48 112-161 3-50 (60)
55 PRK12793 flaF flagellar biosyn 27.5 2.6E+02 0.0057 20.8 6.3 45 138-183 39-84 (115)
56 PHA02896 A-type inclusion like 27.5 1E+02 0.0023 29.1 4.5 47 136-185 3-49 (616)
57 smart00195 DSPc Dual specifici 27.2 54 0.0012 24.3 2.3 24 127-150 93-117 (138)
58 KOG3730 Acyl-CoA:dihydroxyacte 26.9 1E+02 0.0022 29.1 4.3 55 125-188 76-130 (685)
59 PF05402 PqqD: Coenzyme PQQ sy 26.4 1.4E+02 0.003 19.2 4.0 31 126-156 32-62 (68)
60 PRK05114 hypothetical protein; 26.4 88 0.0019 20.5 2.8 45 111-157 2-46 (59)
61 PTZ00242 protein tyrosine phos 24.6 53 0.0011 25.9 1.9 28 124-151 110-138 (166)
62 PF11433 DUF3198: Protein of u 24.5 1.6E+02 0.0034 18.5 3.5 30 7-36 18-49 (51)
63 KOG1720 Protein tyrosine phosp 24.4 62 0.0013 27.0 2.3 28 124-151 159-187 (225)
64 PF00584 SecE: SecE/Sec61-gamm 24.3 1.2E+02 0.0026 19.1 3.3 26 55-80 19-44 (57)
65 PF12550 GCR1_C: Transcription 24.0 83 0.0018 21.6 2.6 25 126-150 55-79 (81)
66 PF02061 Lambda_CIII: Lambda P 23.2 1.9E+02 0.004 17.6 4.5 28 138-165 12-41 (45)
67 PRK04946 hypothetical protein; 22.0 1.1E+02 0.0024 24.7 3.3 44 112-157 69-121 (181)
68 KOG4061 DMQ mono-oxygenase/Ubi 22.0 1.9E+02 0.0042 23.5 4.6 51 132-183 66-120 (217)
69 cd00751 thiolase Thiolase are 21.4 1E+02 0.0023 27.5 3.4 39 127-165 153-191 (386)
70 PRK08470 adenylosuccinate lyas 20.9 4.8E+02 0.01 24.0 7.6 72 87-159 304-386 (442)
71 PF00782 DSPc: Dual specificit 20.9 77 0.0017 23.2 2.1 24 127-150 88-112 (133)
72 PF12668 DUF3791: Protein of u 20.6 1E+02 0.0022 20.0 2.4 23 128-150 6-28 (62)
73 PF14278 TetR_C_8: Transcripti 20.2 2.4E+02 0.0052 17.9 4.3 25 19-43 22-46 (77)
No 1
>cd00684 Terpene_cyclase_plant_C1 Plant Terpene Cyclases, Class 1. This CD includes a diverse group of monomeric plant terpene cyclases (Tspa-Tspf) that convert the acyclic isoprenoid diphosphates, geranyl diphosphate (GPP), farnesyl diphosphate (FPP), or geranylgeranyl diphosphate (GGPP) into cyclic monoterpenes, diterpenes, or sesquiterpenes, respectively; a few form acyclic species. Terpnoid cyclases are soluble enzymes localized to the cytosol (sesquiterpene synthases) or plastids (mono- and diterpene synthases). All monoterpene and diterpene synthases have restrict substrate specificity, however, some sesquiterpene synthases can accept both FPP and GPP. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl diphosphates, via bridging Mg2+ ions (K+ preferred by gymnosperm cyclases), inducing conformational changes such that an N-terminal regi
Probab=100.00 E-value=1.7e-55 Score=408.50 Aligned_cols=210 Identities=48% Similarity=0.798 Sum_probs=205.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHh
Q 028006 1 MKFIVKALLDIYREAEEELAKEGRSYGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVD 80 (215)
Q Consensus 1 mk~~~~~l~~~~~e~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~ 80 (215)
||+||.+|+++++|++.++.++|+++.+.|+++.|++++++|++||+|+++|++||++|||++|.+|+|+++++++++++
T Consensus 331 mk~~~~al~~~~~ei~~~~~~~~~~~~~~~~~~~~~~~~~a~l~EA~w~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~ 410 (542)
T cd00684 331 MKIVFKALLNTVNEIEEELLKEGGSYVVPYLKEAWKDLVKAYLVEAKWAHEGYVPTFEEYMENALVSIGLGPLLLTSFLG 410 (542)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhhhhHHhhHHHHHHHHHHh
Confidence 68999999999999999999999989999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCCCChhhhhhhhcchHHHHHHHHHHHHhcCcccchHhhhcCCCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHHHHH
Q 028006 81 LGDFIATKDNFECILKNAKSLKATETIGRLMDDIAGYKFEQKRGHNPSAVECYKNQHGVSEEEAVKELLLEVANSWKDIN 160 (215)
Q Consensus 81 ~g~~l~~~e~~~~~~~~~~i~~~~~~i~rL~NDi~S~~~E~~~G~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ln 160 (215)
+|+.+ |+++++|+...|+|+++++.++||+||++||++|+++|+++|+|.|||+|+|+|+|+|+++++++++++||++|
T Consensus 411 ~g~~l-~~e~~e~~~~~~~l~~~~~~i~rL~NDi~S~~kE~~rGdv~n~V~~ymke~g~s~eeA~~~i~~~ie~~wk~ln 489 (542)
T cd00684 411 MGDIL-TEEAFEWLESRPKLVRASSTIGRLMNDIATYEDEMKRGDVASSIECYMKEYGVSEEEAREEIKKMIEDAWKELN 489 (542)
T ss_pred cCCCC-CHHHHHHHhccHHHHHHHHHHHHHhcChhhhHHHHhcCCcccHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 99999 99999998777999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCC-CCCCHHHHHHHHHHhhhhhhhcccCCCCCCCchh-HHHHHHHHcccc
Q 028006 161 EELLNP-TTVPLPMLQRLLYFARSGHFIYDDGHDRYTHSLM-MKRQVALLLTEP 212 (215)
Q Consensus 161 ~e~l~~-~~~p~~~~~~~ln~aR~~~~~Y~~~~Dg~t~~~~-~k~~i~~l~~~p 212 (215)
++++++ +.+|++|+++++|++|+++++|+++ ||||.|+. +|++|++||++|
T Consensus 490 ~e~l~~~~~~p~~~~~~~~n~~r~~~~~Y~~~-D~~t~~~~~~~~~i~~ll~~p 542 (542)
T cd00684 490 EEFLKPSSDVPRPIKQRFLNLARVIDVFYKEG-DGFTHPEGEIKDHITSLLFEP 542 (542)
T ss_pred HHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCC-CCCCCccHHHHHHHHHHhcCC
Confidence 999998 7899999999999999999999999 99999966 999999999998
No 2
>PLN02279 ent-kaur-16-ene synthase
Probab=100.00 E-value=2.8e-55 Score=416.78 Aligned_cols=209 Identities=24% Similarity=0.354 Sum_probs=199.9
Q ss_pred CHHHHHHHHHHHHHHHHH-HHHhCCCchhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHH
Q 028006 1 MKFIVKALLDIYREAEEE-LAKEGRSYGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFV 79 (215)
Q Consensus 1 mk~~~~~l~~~~~e~~~~-~~~~g~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~ 79 (215)
||+||++||+++||++.+ +.+||+ ++++|++++|++++++|++||+|+++|++||++|||+++.+|+|+++++.++++
T Consensus 565 mki~f~aL~~t~nei~~~~~~~qGr-~v~~~l~~aW~~ll~ayl~EAeW~~~g~vPT~eEYL~na~vS~~l~~i~l~~~~ 643 (784)
T PLN02279 565 VEIIFSALRSTISEIGDKAFTWQGR-NVTSHIIKIWLDLLKSMLTEAQWSSNKSTPTLDEYMTNAYVSFALGPIVLPALY 643 (784)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCc-hHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhhchhhhhhHHHHHHHHH
Confidence 799999999999999987 567777 999999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCCCChhhhhhhhcchHHHHHHHHHHHHhcCcccchHhhhcCCCcchhhHHhhcC--CCCHHHHHHHHHHHHHHHHH
Q 028006 80 DLGDFIATKDNFECILKNAKSLKATETIGRLMDDIAGYKFEQKRGHNPSAVECYKNQH--GVSEEEAVKELLLEVANSWK 157 (215)
Q Consensus 80 ~~g~~l~~~e~~~~~~~~~~i~~~~~~i~rL~NDi~S~~~E~~~G~~~n~V~~ym~e~--g~s~eeA~~~i~~~i~~~wk 157 (215)
++|+.+ |+++++| .++|+|+++++.++||+|||+||++|++|||+ |+|+|||+|+ |+|+|||+++++++++++||
T Consensus 644 ~~G~~l-~eev~e~-~~~~~L~~l~s~I~RLlNDI~S~e~E~~rG~~-nsV~cYMke~~~gvSeEEAi~~i~~~Ie~~wK 720 (784)
T PLN02279 644 LVGPKL-SEEVVDS-PELHKLYKLMSTCGRLLNDIRGFKRESKEGKL-NAVSLHMIHGNGNSTEEEAIESMKGLIESQRR 720 (784)
T ss_pred HhCCCC-CHHHHhC-cchhHHHHHHHHHHHHHHhccccHhHHhCCCc-ceehhhhccCCCCCCHHHHHHHHHHHHHHHHH
Confidence 999999 9999999 59999999999999999999999999999998 9999999987 89999999999999999999
Q ss_pred HHHHhhcCC--CCCCHHHHHHHHHHhhhhhhhcccCCCCCCCchhHHHHHHHHcccccCC
Q 028006 158 DINEELLNP--TTVPLPMLQRLLYFARSGHFIYDDGHDRYTHSLMMKRQVALLLTEPLAI 215 (215)
Q Consensus 158 ~ln~e~l~~--~~~p~~~~~~~ln~aR~~~~~Y~~~~Dg~t~~~~~k~~i~~l~~~p~~i 215 (215)
+||++++++ +.+|++|+++++|++|+++++|+++ ||||.+ .||++|++||++||++
T Consensus 721 eLn~~~l~~~~~~vp~~~~~~~ln~aR~~~~~Y~~~-Dgyt~~-~~k~~i~~ll~ePi~l 778 (784)
T PLN02279 721 ELLRLVLQEKGSNVPRECKDLFWKMSKVLHLFYRKD-DGFTSN-DMMSLVKSVIYEPVSL 778 (784)
T ss_pred HHHHHHhccCCCCCCHHHHHHHHHHHHhhhhheeCC-CCCChH-HHHHHHHHHhccCCcC
Confidence 999999974 5799999999999999999999999 999964 7999999999999985
No 3
>PLN02150 terpene synthase/cyclase family protein
Probab=100.00 E-value=4.9e-37 Score=223.57 Aligned_cols=94 Identities=37% Similarity=0.602 Sum_probs=91.0
Q ss_pred hhcCCCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhhhhhhh-cccCCCCCCCch
Q 028006 121 QKRGHNPSAVECYKNQHGVSEEEAVKELLLEVANSWKDINEELLNPTTVPLPMLQRLLYFARSGHFI-YDDGHDRYTHSL 199 (215)
Q Consensus 121 ~~~G~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ln~e~l~~~~~p~~~~~~~ln~aR~~~~~-Y~~~~Dg~t~~~ 199 (215)
|+|||++|+|+|||||||+|+|||+++++++++++||+||+|+++++++|.+++++++|+||+++|+ |++| ||||.++
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 5799999999999999999999999999999999999999999999999999999999999999999 9999 9999886
Q ss_pred h-HHHHHHHHcccccCC
Q 028006 200 M-MKRQVALLLTEPLAI 215 (215)
Q Consensus 200 ~-~k~~i~~l~~~p~~i 215 (215)
. +|++|++||++|+|+
T Consensus 80 ~~~K~~I~sLlv~pi~i 96 (96)
T PLN02150 80 GKLKDLITSLFFHPLPL 96 (96)
T ss_pred HHHHHHHHHHhccCCCC
Confidence 5 999999999999986
No 4
>cd00868 Terpene_cyclase_C1 Terpene cyclases, Class 1. Terpene cyclases, Class 1 (C1) of the class 1 family of isoprenoid biosynthesis enzymes, which share the 'isoprenoid synthase fold' and convert linear, all-trans, isoprenoids, geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate into numerous cyclic forms of monoterpenes, diterpenes, and sesquiterpenes. Also included in this CD are the cis-trans terpene cyclases such as trichodiene synthase. The class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational ch
Probab=100.00 E-value=3.9e-32 Score=231.90 Aligned_cols=187 Identities=44% Similarity=0.727 Sum_probs=173.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHh
Q 028006 1 MKFIVKALLDIYREAEEELAKEGRSYGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVD 80 (215)
Q Consensus 1 mk~~~~~l~~~~~e~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~ 80 (215)
++.++.+++++.+++...+.++++.....++++.|.+++.++.+|++|+..|++||++||+.+|+.|+|+.+++.+++++
T Consensus 97 ~~~~~~~l~d~~~r~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~e~~~~~~~~~p~~~eYl~~R~~~~g~~~~~~l~~~~ 176 (284)
T cd00868 97 MKPVFKALYDLVNEIEEELAKEGGSESLPYLKEAWKDLLRAYLVEAKWANEGYVPSFEEYLENRRVSIGYPPLLALSFLG 176 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHhceehhhHHHHHHHHHHH
Confidence 36799999999999998888777768899999999999999999999999999999999999999999999999999999
Q ss_pred hCCCCCChhhhhhhhcchHHHHHHHHHHHHhcCcccchHhhhcCCCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHHHHH
Q 028006 81 LGDFIATKDNFECILKNAKSLKATETIGRLMDDIAGYKFEQKRGHNPSAVECYKNQHGVSEEEAVKELLLEVANSWKDIN 160 (215)
Q Consensus 81 ~g~~l~~~e~~~~~~~~~~i~~~~~~i~rL~NDi~S~~~E~~~G~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ln 160 (215)
+|..+ |++.+.+.+..+.+.+.++.+++|+||++||+||+.+|+.+|+|.|||+++|+|.++|++++.++++++|++++
T Consensus 177 ~g~~l-~~~~~~~~~~~~~l~~~~~~~~~l~NDl~S~~kE~~~g~~~N~v~vl~~~~~~~~~eA~~~~~~~~~~~~~~~~ 255 (284)
T cd00868 177 MGDIL-PEEAFEWLPSYPKLVRASSTIGRLLNDIASYEKEIARGEVANSVECYMKEYGVSEEEALEELRKMIEEAWKELN 255 (284)
T ss_pred cCCCC-CHHHHHHhhhhHHHHHHHHHHHHHhccchHHHHHHccCCcccHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHH
Confidence 99999 98444445788999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCC-CCCCHHHHHHHHHHhhhhhhhc
Q 028006 161 EELLNP-TTVPLPMLQRLLYFARSGHFIY 188 (215)
Q Consensus 161 ~e~l~~-~~~p~~~~~~~ln~aR~~~~~Y 188 (215)
+.+.+. ++.|..+++.+.|.+|.....|
T Consensus 256 ~~~~~~~~~~~~~~~~~l~~~~~g~~~w~ 284 (284)
T cd00868 256 EEVLKLSSDVPRAVLETLLNLARGIYVWY 284 (284)
T ss_pred HHHhcCCCCCCHHHHHHHHHHHHhhhhcC
Confidence 999974 4688999999999999887654
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=99.96 E-value=3.7e-29 Score=212.09 Aligned_cols=158 Identities=25% Similarity=0.328 Sum_probs=143.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHh-CCCchhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHh
Q 028006 2 KFIVKALLDIYREAEEELAKE-GRSYGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVD 80 (215)
Q Consensus 2 k~~~~~l~~~~~e~~~~~~~~-g~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~ 80 (215)
+.++.++.++++++...+.+. ++.+..+++++.|.+|+.++++|++|+..|++||++||++.|+.|+|+.+++.+..++
T Consensus 112 ~~~~~~l~d~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~ps~eeYl~~R~~t~g~~~~~~l~~~~ 191 (270)
T PF03936_consen 112 KPLFRALADIWNRIAARMSPAQRRRDQIKRFRNSWREYLNAYLWEARWRERGRIPSLEEYLEMRRHTSGVYPCLALIEFA 191 (270)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS--SHHHHHHHHHHHTSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhhhhhcccHHhhHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHhccccccccHHHHHHHHh
Confidence 568899999999998766555 4435788999999999999999999999999999999999999999999999999999
Q ss_pred hCCCCCChhhhhhhhcchHHHHHHHHHHHHhcCcccchHhhhcCCCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHHHHH
Q 028006 81 LGDFIATKDNFECILKNAKSLKATETIGRLMDDIAGYKFEQKRGHNPSAVECYKNQHGVSEEEAVKELLLEVANSWKDIN 160 (215)
Q Consensus 81 ~g~~l~~~e~~~~~~~~~~i~~~~~~i~rL~NDi~S~~~E~~~G~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ln 160 (215)
+|..+ ++...+++...|.+.++++.+++|.|||.||+||+++|+..|.|.|+|+++|+|.|+|++++.+++++++++||
T Consensus 192 ~~~~~-~~~~~~~~~~~~~l~~~~~~~~~l~NDl~S~~KE~~~g~~~N~v~~l~~~~~~s~e~A~~~v~~~~~~~~~efn 270 (270)
T PF03936_consen 192 LEFAL-GELPPEVLEHPPMLRRLAADIIRLVNDLYSYKKEIARGDVHNLVVVLMNEHGLSLEEAVDEVAEMINECIREFN 270 (270)
T ss_dssp CSSCH-THHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCSHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCcc-ccccHHHHHhchHHHHHHHHHHHHhcccchhhcchhhcccccHHHHhhhhcCCCHHHHHHHHHHHHHHHHHhcC
Confidence 97777 76666776677789999999999999999999999999999999999999999999999999999999999998
No 6
>cd00687 Terpene_cyclase_nonplant_C1 Non-plant Terpene Cyclases, Class 1. This CD includes terpenoid cyclases such as pentalenene synthase and aristolochene synthase which, using an all-trans pathway, catalyze the ionization of farnesyl diphosphate, followed by the formation of a macrocyclic intermediate by bond formation between C1 with either C10 (aristolochene synthase) or C11 (pentalenene synthase), resulting in production of tricyclic hydrocarbon pentalenene or bicyclic hydrocarbon aristolochene. As with other enzymes with the 'terpenoid synthase fold', they have two conserved metal binding motifs, proposed to coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP to the enzymes. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function in the monomeric form and are found in
Probab=99.94 E-value=8.7e-27 Score=201.67 Aligned_cols=157 Identities=18% Similarity=0.105 Sum_probs=139.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhhC
Q 028006 3 FIVKALLDIYREAEEELAKEGRSYGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDLG 82 (215)
Q Consensus 3 ~~~~~l~~~~~e~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g 82 (215)
.+..++.++...+.... ......++++.|.+|+.++++|++|+.+|++||++||+++|+.|+|+.+++.++.+++|
T Consensus 110 p~~~~~~d~~~r~~~~~----~~~~~~r~~~~~~~~~~a~~~e~~~~~~~~~psl~eYl~~R~~~~g~~~~~~l~~~~~g 185 (303)
T cd00687 110 PLEFGLADLWRRTLARM----SAEWFNRFAHYTEDYFDAYIWEGKNRLNGHVPDVAEYLEMRRFNIGADPCLGLSEFIGG 185 (303)
T ss_pred HHHHHHHHHHHHhccCC----CHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhhhcccccccHHHHHHhcC
Confidence 45566666666665442 23456899999999999999999999999999999999999999999999999999999
Q ss_pred CCCCChhhhhhhhcchHHHHHHHHHHHHhcCcccchHhh-hcCCCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHHHHHH
Q 028006 83 DFIATKDNFECILKNAKSLKATETIGRLMDDIAGYKFEQ-KRGHNPSAVECYKNQHGVSEEEAVKELLLEVANSWKDINE 161 (215)
Q Consensus 83 ~~l~~~e~~~~~~~~~~i~~~~~~i~rL~NDi~S~~~E~-~~G~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ln~ 161 (215)
..+ |+++.+. +...++.++++.+++|+|||+||+||+ +.|+.+|+|.|+|+++|+|.|+|++++.++++++++++.+
T Consensus 186 ~~l-p~~~~~~-~~~~~l~~~~~~~~~l~NDl~S~~KE~~~~g~~~N~V~vl~~~~g~s~~eA~~~~~~~~~~~~~~f~~ 263 (303)
T cd00687 186 PEV-PAAVRLD-PVMRALEALASDAIALVNDIYSYEKEIKANGEVHNLVKVLAEEHGLSLEEAISVVRDMHNERITQFEE 263 (303)
T ss_pred CCC-CHHHHhC-hHHHHHHHHHHHHHHHHHHHHhhHHHHHhCCccchHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 999 9888776 456679999999999999999999999 8999999999999999999999999999999999988876
Q ss_pred hhcC
Q 028006 162 ELLN 165 (215)
Q Consensus 162 e~l~ 165 (215)
..-.
T Consensus 264 ~~~~ 267 (303)
T cd00687 264 LEAS 267 (303)
T ss_pred HHHh
Confidence 5543
No 7
>PLN02592 ent-copalyl diphosphate synthase
Probab=99.93 E-value=2.3e-25 Score=212.11 Aligned_cols=171 Identities=15% Similarity=0.195 Sum_probs=144.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHH-
Q 028006 1 MKFIVKALLDIYREAEEELAKEGRSYGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFV- 79 (215)
Q Consensus 1 mk~~~~~l~~~~~e~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~- 79 (215)
||+||.+|||++||++.++.+.++.++++|++++|.++++ +|..+|+ +|+|...+++.+++
T Consensus 626 mki~f~aLy~tineia~~a~~~qGr~v~~~L~~~W~~l~~------~w~~~g~------------~s~~~~~ilv~~~~l 687 (800)
T PLN02592 626 GEELVGLLLGTLNQLSLDALEAHGRDISHLLRHAWEMWLL------KWLLEGD------------GRQGEAELLVKTINL 687 (800)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHH------HHHhcCc------------eeccchhhHHHHHHH
Confidence 6899999999999998765444444999999999999999 6777766 34466666666666
Q ss_pred hhCCCCCChhhhhhhhcchHHHHHHHHHHHHhcCcccchHhhhcCCCcchhhHHhhcCC-CCHHHHHHHHHHHHHHHHHH
Q 028006 80 DLGDFIATKDNFECILKNAKSLKATETIGRLMDDIAGYKFEQKRGHNPSAVECYKNQHG-VSEEEAVKELLLEVANSWKD 158 (215)
Q Consensus 80 ~~g~~l~~~e~~~~~~~~~~i~~~~~~i~rL~NDi~S~~~E~~~G~~~n~V~~ym~e~g-~s~eeA~~~i~~~i~~~wk~ 158 (215)
.+|..+ |+++++ +|.+.++++.+.||+||++|+++|+.. .| +|+ +|.+++.+.++.++++
T Consensus 688 ~~g~~l-see~l~----~~~~~~l~~li~Rl~nDl~t~~~e~~~-------------~~~~~~-~a~~~~~~~ie~~~~e 748 (800)
T PLN02592 688 TAGRSL-SEELLA----HPQYEQLAQLTNRICYQLGHYKKNKVH-------------INTYNP-EEKSKTTPSIESDMQE 748 (800)
T ss_pred hcCCCC-CHHHcc----chhHHHHHHHHHHHHHhhhHHhhhccc-------------CCcccH-HHHHHHHHHHHHHHHH
Confidence 559999 999876 588999999999999999999998841 23 455 8999999999999999
Q ss_pred HHHhhcC-C-CCCCHHHHHHHHHHhhhhhhhcccCCCCCCCchhHHHHHHHHcccccC
Q 028006 159 INEELLN-P-TTVPLPMLQRLLYFARSGHFIYDDGHDRYTHSLMMKRQVALLLTEPLA 214 (215)
Q Consensus 159 ln~e~l~-~-~~~p~~~~~~~ln~aR~~~~~Y~~~~Dg~t~~~~~k~~i~~l~~~p~~ 214 (215)
|.+.+++ . +.+|++|++++|+++| +||.. ||+.|..|++||+.+|++||+
T Consensus 749 L~~lvl~~~~~~vp~~cK~~f~~~~k---~fy~~---~~~~~~~~~~~i~~vl~epv~ 800 (800)
T PLN02592 749 LVQLVLQNSSDDIDPVIKQTFLMVAK---SFYYA---AYCDPGTINYHIAKVLFERVA 800 (800)
T ss_pred HHHHHhhcCCCCCCHHHHHHHHHHHH---HHHHh---hcCCHHHHHHHHHHHhCCCCC
Confidence 9999997 3 5699999999999999 66763 899998899999999999985
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=99.73 E-value=4.1e-17 Score=133.39 Aligned_cols=169 Identities=24% Similarity=0.281 Sum_probs=135.0
Q ss_pred HHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhhCCC
Q 028006 5 VKALLDIYREAEEELAKEGRSYGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDLGDF 84 (215)
Q Consensus 5 ~~~l~~~~~e~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~ 84 (215)
+..+.+.+.++... ........+++.|.+++.|+..|+.|... ..||++||+..+..++ +.++...+..+++..
T Consensus 62 ~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~g~~~d~~~~~~-~~~t~~ey~~~~~~~t-~~~~~~~~~~~~~~~ 135 (243)
T cd00385 62 DLLLADAFEELARE----GSPEALEILAEALLDLLEGQLLDLKWRRE-YVPTLEEYLEYCRYKT-AGLVGALCLLGAGLS 135 (243)
T ss_pred HHHHHHHHHHHHhC----CCHHHHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHHhH-HHHHHHHHHHHHHHh
Confidence 34445555554432 22356789999999999999999999876 8999999999999998 555556666666666
Q ss_pred CCChhhhhhhhcchHHHHHHHHHHHHhcCcccchHhhhcC-CCcchhhHHhhcCCC------------CHHHHHHHHHHH
Q 028006 85 IATKDNFECILKNAKSLKATETIGRLMDDIAGYKFEQKRG-HNPSAVECYKNQHGV------------SEEEAVKELLLE 151 (215)
Q Consensus 85 l~~~e~~~~~~~~~~i~~~~~~i~rL~NDi~S~~~E~~~G-~~~n~V~~ym~e~g~------------s~eeA~~~i~~~ 151 (215)
. ++ ..+.+....+...++.+.+|.||+.|+.+|.++| +..|++.++|+++|+ +.++|.+++.++
T Consensus 136 ~-~~--~~~~~~~~~~~~~~g~~~ql~nDl~~~~~e~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~ 212 (243)
T cd00385 136 G-GE--AELLEALRKLGRALGLAFQLTNDLLDYEGDAERGEGKCTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKL 212 (243)
T ss_pred C-CC--HHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHhCCchHHHHHHHHHhCChhhHHHHHHHCChHHHHHHHHHHH
Confidence 6 65 3444566778899999999999999999999986 677999999999998 889999999999
Q ss_pred HHHHHHHHHHhhcCCCCCCHHHHHHHHHHhh
Q 028006 152 VANSWKDINEELLNPTTVPLPMLQRLLYFAR 182 (215)
Q Consensus 152 i~~~wk~ln~e~l~~~~~p~~~~~~~ln~aR 182 (215)
++++|+++++........+..+++.+.++.|
T Consensus 213 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (243)
T cd00385 213 AEEALKELNELILSLPDVPRALLALALNLYR 243 (243)
T ss_pred HHHHHHHHhcCCCCcHHHHHHHHHHHHHHhC
Confidence 9999999998777533456678887777654
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=97.62 E-value=0.00069 Score=59.49 Aligned_cols=128 Identities=19% Similarity=0.115 Sum_probs=85.5
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhhCCCCCChhhhhhhhcchHHHHHH-
Q 028006 26 YGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDLGDFIATKDNFECILKNAKSLKAT- 104 (215)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~~e~~~~~~~~~~i~~~~- 104 (215)
+.-.-+.++--+++.+.+-|... -+.-|.-.+|-...+.=+|.+-..+++. . |++.|.-...+..+.-+.
T Consensus 145 F~s~~IikSTLdFv~g~~iEq~n--f~~~p~A~~fP~ylR~ksGl~E~yA~Fi------F-Pk~~FpE~~~~~qi~~AIp 215 (357)
T cd00686 145 FCSLNLIRSTLDFFEGCWIEQYN--FGGFPGSHDYPQFLRRMNGLGHCVGASL------W-PKEQFNERSLFLEITSAIA 215 (357)
T ss_pred hhHHHHHHHHHHHHHHHHHhhhc--cCCCCCCcccchHHHhccCCcceeEEEe------c-chhhCchHhhHHHhhHHHH
Confidence 66666777788889998888663 3346655666666666666655544332 2 444433222222222233
Q ss_pred --HHHHHHhcCcccchHhhhc-CCCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHh
Q 028006 105 --ETIGRLMDDIAGYKFEQKR-GHNPSAVECYKNQHGVSEEEAVKELLLEVANSWKDINEE 162 (215)
Q Consensus 105 --~~i~rL~NDi~S~~~E~~~-G~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ln~e 162 (215)
....-++|||.||=||.-. ++..|.|.-|.+.+|+|..+|.+.+..-.-.+-+++..-
T Consensus 216 ~~~~~i~~~NDILSFYKEe~~~~E~~n~V~Nya~~~GiS~~eAL~~lt~dTv~~s~rv~~V 276 (357)
T cd00686 216 QMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVAV 276 (357)
T ss_pred HHHHHHHhhhhhhheehhhcccccccchHHHhhhhcCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455689999999999854 566799999999999999999998877777777666554
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=97.46 E-value=0.0018 Score=57.60 Aligned_cols=134 Identities=16% Similarity=0.162 Sum_probs=80.1
Q ss_pred CCchhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhhCCCCCChhhhhhhhcchHHHHH
Q 028006 24 RSYGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDLGDFIATKDNFECILKNAKSLKA 103 (215)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~~e~~~~~~~~~~i~~~ 103 (215)
++++-+-+.++--+++.+..-|.+.. .-.|.-..|-..-+.=+|...+.+...+- .... |+.. ....+-..+-.
T Consensus 143 gpf~anmI~~STLdFi~g~~LE~~~f--~~~p~A~~FP~fLR~ktGlsEaYA~FiFP-k~~f-pe~~--~~~~y~~AIpd 216 (376)
T PF06330_consen 143 GPFCANMIVKSTLDFINGCWLEQKNF--HGSPGAPDFPDFLRRKTGLSEAYAFFIFP-KALF-PEVE--YFIQYTPAIPD 216 (376)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHTTT------TT-TTHHHHHHHHHH-HHHHHHHT---TTTS--TTT--THHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHhhcccC--CCCCCCccccHHHHhccCcchhheeeecc-cccC-ChHH--HHHHHHHHHHH
Confidence 33666777888888999998887542 22343333333344456666655544331 1222 3221 11111123344
Q ss_pred HHHHHHHhcCcccchHhhh-cCCCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 028006 104 TETIGRLMDDIAGYKFEQK-RGHNPSAVECYKNQHGVSEEEAVKELLLEVANSWKDINEEL 163 (215)
Q Consensus 104 ~~~i~rL~NDi~S~~~E~~-~G~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ln~e~ 163 (215)
....+-++|||.||=||.- .|+..|.|.-+-.-+|+|.-+|.+.+.+..-++-+++.+-.
T Consensus 217 l~~fi~~~NDILSFYKE~l~a~E~~NyI~n~A~~~g~S~~eaL~~l~~eti~a~~rv~~vL 277 (376)
T PF06330_consen 217 LMRFINYVNDILSFYKEELVAGETGNYIHNRARVHGVSILEALRELTDETIEAVERVRRVL 277 (376)
T ss_dssp HHHHHHHHHHHHHHHHHHTTSSSSSSHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhhhhHHHHHHhhcccccccchhhhhhhccCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4556679999999999977 78889999888888899999999988776666666655543
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=95.70 E-value=0.42 Score=39.44 Aligned_cols=118 Identities=14% Similarity=0.075 Sum_probs=77.5
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhh-hhhhHHHHHHHHHhhCCCCCChhhhhhhhcchHHHHHHH
Q 028006 27 GIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALR-SIGLRTLAVASFVDLGDFIATKDNFECILKNAKSLKATE 105 (215)
Q Consensus 27 ~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~-s~g~~~~~~~~~~~~g~~l~~~e~~~~~~~~~~i~~~~~ 105 (215)
....+.+....++.|...+..|... ..||+++|++.... |.+.....+......+.. +++..+. ..++-+..+
T Consensus 86 ~~~~~~~~~~~~~~Gq~~Dl~~~~~-~~~t~~~y~~~~~~Kta~l~~~~~~~~~~~~~~--~~~~~~~---~~~~~~~lG 159 (236)
T cd00867 86 ALELFAEALRELLEGQALDLEFERD-TYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGA--DDEQAEA---LKDYGRALG 159 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHhccHHHHHHHHHHHHHHcCc--CHHHHHH---HHHHHHHHH
Confidence 4566778889999999999888543 57899999999887 665544433332222322 3222232 355678889
Q ss_pred HHHHHhcCcccchHhh----------hcCCCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHHHHHH
Q 028006 106 TIGRLMDDIAGYKFEQ----------KRGHNPSAVECYKNQHGVSEEEAVKELLLEVANSWKDINE 161 (215)
Q Consensus 106 ~i~rL~NDi~S~~~E~----------~~G~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ln~ 161 (215)
...-+.||+..+.... .+|.. +...+++ .+.+.+..+++++.+..
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 9999999999886554 55555 5555555 55566666666655543
No 12
>PLN02890 geranyl diphosphate synthase
Probab=93.53 E-value=3.8 Score=37.52 Aligned_cols=92 Identities=9% Similarity=-0.075 Sum_probs=61.6
Q ss_pred CCCchhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhhCCCCCChhhhhhhhcchHHHH
Q 028006 23 GRSYGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDLGDFIATKDNFECILKNAKSLK 102 (215)
Q Consensus 23 g~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~~e~~~~~~~~~~i~~ 102 (215)
+....+..+-++...++.|-+.+..|.. ...+|.++|++....-+|.-+..++..-++--.. +++..+.+ -.+-+
T Consensus 224 ~~~~~~~~~s~a~~~l~~Gq~ld~~~~~-~~~~s~~~Yl~~i~~KTa~Lf~~s~~~gAilaga-~~~~~~~l---~~fG~ 298 (422)
T PLN02890 224 KNTEVVSLLATAVEHLVTGETMQITSSR-EQRRSMDYYMQKTYYKTASLISNSCKAVAILAGQ-TAEVAVLA---FEYGR 298 (422)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCc-CHHHHHHH---HHHHH
Confidence 4445677788888999999999988864 4568999999876555555543332222221123 55554443 45677
Q ss_pred HHHHHHHHhcCcccchH
Q 028006 103 ATETIGRLMDDIAGYKF 119 (215)
Q Consensus 103 ~~~~i~rL~NDi~S~~~ 119 (215)
..+...-+.||+..|.-
T Consensus 299 ~lGlAFQI~DDiLD~~g 315 (422)
T PLN02890 299 NLGLAFQLIDDVLDFTG 315 (422)
T ss_pred HHHHHHHHHHHHHhhcC
Confidence 88889999999998853
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=93.28 E-value=5.4 Score=35.09 Aligned_cols=91 Identities=7% Similarity=-0.006 Sum_probs=58.0
Q ss_pred CCCchhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhhCCCCCChhhhhhhhcchHHHH
Q 028006 23 GRSYGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDLGDFIATKDNFECILKNAKSLK 102 (215)
Q Consensus 23 g~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~~e~~~~~~~~~~i~~ 102 (215)
+....+..+.+....++.+-+.+..|.. ...+|.++|++.-..=+|.-+..++..-++--.. +++..+.+ -.+-+
T Consensus 130 ~~~~~~~~~~~~~~~~~~Gq~~~~~~~~-~~~~~~~~y~~~~~~KTa~L~~~~~~~ga~~ag~-~~~~~~~l---~~~G~ 204 (322)
T TIGR02749 130 ENLEVVKLISKVITDFAEGEIKQGLNQF-DSDLSLEDYLEKSFYKTASLVAASSKAAAVLSDV-PSQVANDL---YEYGK 204 (322)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHccc-CCCCCHHHHHHHHHccHHHHHHHHHHHHHHHcCc-CHHHHHHH---HHHHH
Confidence 3334566777777888888887777643 3457999999876555555443332222221123 54444433 55677
Q ss_pred HHHHHHHHhcCcccch
Q 028006 103 ATETIGRLMDDIAGYK 118 (215)
Q Consensus 103 ~~~~i~rL~NDi~S~~ 118 (215)
..+...-+.||+..+.
T Consensus 205 ~lG~aFQi~DDild~~ 220 (322)
T TIGR02749 205 HLGLAFQVVDDILDFT 220 (322)
T ss_pred HHHHHHHHHHHhccCC
Confidence 8899999999998875
No 14
>PLN02857 octaprenyl-diphosphate synthase
Probab=93.20 E-value=3.9 Score=37.39 Aligned_cols=88 Identities=16% Similarity=0.064 Sum_probs=57.4
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhhCCCCCChhhhhhhhcchHHHHHHH
Q 028006 26 YGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDLGDFIATKDNFECILKNAKSLKATE 105 (215)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~~e~~~~~~~~~~i~~~~~ 105 (215)
..+..+.+...+++.+-+.+..|.. +..+|.++|++....=+|.-+..++..-++--.. +++..+.+ .++-+..+
T Consensus 227 ~~~~~~s~~~~~l~~Gei~q~~~~~-~~~~s~~~Yl~~i~~KTa~L~~~a~~~gallaga-~~~~~~~l---~~fG~~LG 301 (416)
T PLN02857 227 EVIKLISQVIKDFASGEIKQASSLF-DCDVTLDEYLLKSYYKTASLIAASTKSAAIFSGV-DSSVKEQM---YEYGKNLG 301 (416)
T ss_pred HHHHHHHHHHHHHHhhHHHHHhccc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCC-CHHHHHHH---HHHHHHHH
Confidence 4566677778888888777777754 4457999999986655555544332222111123 54544443 55677888
Q ss_pred HHHHHhcCcccch
Q 028006 106 TIGRLMDDIAGYK 118 (215)
Q Consensus 106 ~i~rL~NDi~S~~ 118 (215)
...-+.||+..+.
T Consensus 302 iAFQI~DDiLD~~ 314 (416)
T PLN02857 302 LAFQVVDDILDFT 314 (416)
T ss_pred HHHHHHHHHHhhc
Confidence 9999999999876
No 15
>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=93.20 E-value=2.4 Score=35.89 Aligned_cols=121 Identities=11% Similarity=-0.039 Sum_probs=77.5
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhhCCCCCChhhhhhhhcchHHHHHHH
Q 028006 26 YGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDLGDFIATKDNFECILKNAKSLKATE 105 (215)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~~e~~~~~~~~~~i~~~~~ 105 (215)
..+..+.+.+...+.+-..+..|... ..||.++|++....-+|.-+..++...++--.. +++..+. ..++-+..+
T Consensus 108 ~~~~~~~~~~~~~~~GQ~~d~~~~~~-~~~~~~~y~~~~~~KT~~l~~~~~~~~a~l~~~-~~~~~~~---l~~~g~~lG 182 (259)
T cd00685 108 RALELFSEAILELVEGQLLDLLSEYD-TDVTEEEYLRIIRLKTAALFAAAPLLGALLAGA-DEEEAEA---LKRFGRNLG 182 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCC-CCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCC-CHHHHHH---HHHHHHHHH
Confidence 45666777788888888888888543 579999999998777776655443322221112 3333332 355778888
Q ss_pred HHHHHhcCcccchHhh-----------hcCCCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHHHHHH
Q 028006 106 TIGRLMDDIAGYKFEQ-----------KRGHNPSAVECYKNQHGVSEEEAVKELLLEVANSWKDINE 161 (215)
Q Consensus 106 ~i~rL~NDi~S~~~E~-----------~~G~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ln~ 161 (215)
...-+.||+..+.... ..|.. |...+|.. .+.+...++++++.+..
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 8999999988775432 22333 45444444 56677777777766663
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=91.06 E-value=10 Score=33.27 Aligned_cols=87 Identities=11% Similarity=-0.033 Sum_probs=56.8
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhhC-CCCCChhhhhhhhcchHHHHHH
Q 028006 26 YGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDLG-DFIATKDNFECILKNAKSLKAT 104 (215)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g-~~l~~~e~~~~~~~~~~i~~~~ 104 (215)
..+..+.+.....+.|-..+..|.. +.-+|.++|++.-..-+|.-+..+ +..|.- -.. +++..+.+ -.+-+..
T Consensus 129 ~~~~~~~~~~~~~~~Gq~~~~~~~~-~~~~~~~~Y~~~i~~KTa~L~~~~-~~~ga~~ag~-~~~~~~~l---~~~g~~l 202 (319)
T TIGR02748 129 RAHQILSHTIVEVCRGEIEQIKDKY-NFDQNLRTYLRRIKRKTALLIAAS-CQLGAIASGA-NEAIVKKL---YWFGYYV 202 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHcCC-CHHHHHHH---HHHHHHH
Confidence 4566777788888999888887743 445799999988766666554332 222221 112 43333332 4566788
Q ss_pred HHHHHHhcCcccch
Q 028006 105 ETIGRLMDDIAGYK 118 (215)
Q Consensus 105 ~~i~rL~NDi~S~~ 118 (215)
+...-+.||+..+.
T Consensus 203 G~aFQI~DDilD~~ 216 (319)
T TIGR02748 203 GMSYQITDDILDFV 216 (319)
T ss_pred HHHHHHHHHHHHcc
Confidence 88999999998775
No 17
>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=88.79 E-value=11 Score=31.80 Aligned_cols=134 Identities=13% Similarity=0.037 Sum_probs=69.2
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhhCCCCCCh-hhhhhhhcchHHHHHHHHHHHH
Q 028006 32 KQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDLGDFIATK-DNFECILKNAKSLKATETIGRL 110 (215)
Q Consensus 32 ~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~~-e~~~~~~~~~~i~~~~~~i~rL 110 (215)
++.+.+++.++. .+.....++|++|+......++|......+..++.. - ++ +..+. ....+...-+
T Consensus 90 ~~~l~~li~~~~---~dl~~~~~~t~~~L~~Y~~~vag~vg~l~~~~~~~~--~-~~~~~~~~-------a~~lG~alql 156 (267)
T PF00494_consen 90 REPLLELIDGME---MDLEFTPYETFADLERYCYYVAGSVGLLLLQLLGAH--D-PDEAARDA-------ARALGRALQL 156 (267)
T ss_dssp HHHHHHHHHHHH---HCTT-S--SSHHHHHHHHHHHTHHHHHHHHHHHHSS--T-SHHHHHHH-------HHHHHHHHHH
T ss_pred HHHHHHHHHHhc---ccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccc--c-chhhHHHH-------HHHHHHHHHH
Confidence 444566666663 333335678999999988888887776666655542 1 22 22232 3344444444
Q ss_pred hcCcccchHh-hhcCCCcchhhHHhhcCCCCHHHHHHH----------HHHHHHHHHHHHHHhhcCCCCC-CHHHHHHHH
Q 028006 111 MDDIAGYKFE-QKRGHNPSAVECYKNQHGVSEEEAVKE----------LLLEVANSWKDINEELLNPTTV-PLPMLQRLL 178 (215)
Q Consensus 111 ~NDi~S~~~E-~~~G~~~n~V~~ym~e~g~s~eeA~~~----------i~~~i~~~wk~ln~e~l~~~~~-p~~~~~~~l 178 (215)
.|=+...... ..+|.+- .=.=.|.++|+|.++-... +..+++.+...+.+..--...+ |..+...+.
T Consensus 157 ~nilRd~~~D~~~~gR~y-lP~d~l~~~gv~~~dl~~~~~~~~~~~~~~~~~~~~A~~~l~~a~~~~~~l~~~~~~~~~~ 235 (267)
T PF00494_consen 157 TNILRDIPEDALRRGRIY-LPLDDLRRFGVTPEDLLAGRPRSERLRALIRELAARARAHLDEARAGLSALPPPRARPAVA 235 (267)
T ss_dssp HHHHHTHHHH-HHTT----S-HHHHHHTTSSHHHHHHHG-GGHHHHHHHHHHHHHHHHHHHHHHHGGGGS--TTHHHHHH
T ss_pred HHHHHHhHHHHHhccccc-CCchhHHHcCCCHHHHHhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHhhhHHHH
Confidence 4444444455 4566531 1123567899988865432 4555555555555444333446 443443333
Q ss_pred H
Q 028006 179 Y 179 (215)
Q Consensus 179 n 179 (215)
-
T Consensus 236 ~ 236 (267)
T PF00494_consen 236 A 236 (267)
T ss_dssp H
T ss_pred H
Confidence 3
No 18
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=88.44 E-value=17 Score=31.99 Aligned_cols=108 Identities=14% Similarity=0.026 Sum_probs=71.9
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhhCCCCCChhhhhhhhcchHHHHHHH
Q 028006 26 YGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDLGDFIATKDNFECILKNAKSLKATE 105 (215)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~~e~~~~~~~~~~i~~~~~ 105 (215)
.....+.+.+..++.+-..+-.|.... +|.++|++.-..=+|.-+.++...-++--.. +++..+.+ ..+-+..+
T Consensus 134 ~~~~~~~~~~~~~~~GQ~lDl~~~~~~--~t~e~y~~~i~~KTa~L~~~a~~~ga~la~~-~~~~~~~l---~~~g~~lG 207 (322)
T COG0142 134 EAIKALAEAINGLCGGQALDLAFENKP--VTLEEYLRVIELKTAALFAAAAVLGAILAGA-DEELLEAL---EDYGRNLG 207 (322)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHccCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHcCC-CHHHHHHH---HHHHHHhh
Confidence 456677788889999988888875544 9999999987666666655443333321222 44444443 55678889
Q ss_pred HHHHHhcCcccchHhh-hcCCC---------cchhhHHhhcCCC
Q 028006 106 TIGRLMDDIAGYKFEQ-KRGHN---------PSAVECYKNQHGV 139 (215)
Q Consensus 106 ~i~rL~NDi~S~~~E~-~~G~~---------~n~V~~ym~e~g~ 139 (215)
+..-+.||+..+.-+. .-|.. .++..+|.-+.+-
T Consensus 208 laFQi~DDiLD~~~d~~~lGK~~g~Dl~~gK~T~p~l~~l~~~~ 251 (322)
T COG0142 208 LAFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEKAN 251 (322)
T ss_pred HHHHHHHHhhcCCCChHHhCCCcchHHHcCCchHHHHHHHHcCc
Confidence 9999999999887542 22332 3666677766643
No 19
>KOG1719 consensus Dual specificity phosphatase [Defense mechanisms]
Probab=84.66 E-value=0.8 Score=36.25 Aligned_cols=63 Identities=25% Similarity=0.279 Sum_probs=41.8
Q ss_pred hcchHHHHHHHHHHHHhcCcccchHh------hhcCCCcchhhHHhhcC-CCCHHHHHHHHHHH------HHHHHHHHHH
Q 028006 95 LKNAKSLKATETIGRLMDDIAGYKFE------QKRGHNPSAVECYKNQH-GVSEEEAVKELLLE------VANSWKDINE 161 (215)
Q Consensus 95 ~~~~~i~~~~~~i~rL~NDi~S~~~E------~~~G~~~n~V~~ym~e~-g~s~eeA~~~i~~~------i~~~wk~ln~ 161 (215)
++..+|.+++.-|. -.+|..+= -.||..+..|.||+-++ +.|.++|++++++. -...|+-+++
T Consensus 90 Ps~~~i~~aVeFi~----k~asLGktvYVHCKAGRtRSaTvV~cYLmq~~~wtpe~A~~~vr~iRp~VlL~~~Qw~~l~e 165 (183)
T KOG1719|consen 90 PSLENIQKAVEFIH----KNASLGKTVYVHCKAGRTRSATVVACYLMQHKNWTPEAAVEHVRKIRPRVLLRPAQWDVLKE 165 (183)
T ss_pred CCHHHHHHHHHHHH----hccccCCeEEEEecCCCccchhhhhhhhhhhcCCCHHHHHHHHHhcCcceeecHHHHHHHHH
Confidence 34445555554443 33444432 35777889999999888 99999999999883 3345655544
No 20
>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=84.52 E-value=24 Score=29.89 Aligned_cols=133 Identities=14% Similarity=0.002 Sum_probs=65.1
Q ss_pred HHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhhCCCCCChhhhhhhhcchHHHHHHHHHHHHhcCc
Q 028006 35 MQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDLGDFIATKDNFECILKNAKSLKATETIGRLMDDI 114 (215)
Q Consensus 35 ~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~~e~~~~~~~~~~i~~~~~~i~rL~NDi 114 (215)
+.+++.++. ........+|++|+......+.|.-..+++..+ |.. ++..... ....+...-|.|=+
T Consensus 87 ~~~li~g~~---~Dl~~~~~~t~~dL~~Y~~~vAg~vg~l~~~ll--g~~--~~~~~~~-------a~~lG~Alqltnil 152 (266)
T TIGR03465 87 FLEVIDGME---MDLEQTRYPDFAELDLYCDRVAGAVGRLSARIF--GAT--DARTLEY-------AHHLGRALQLTNIL 152 (266)
T ss_pred HHHHHHHHH---HHcCCCCCCCHHHHHHHHHHhHHHHHHHHHHHh--CCC--ChhHHHH-------HHHHHHHHHHHHHH
Confidence 444455542 222334567999988877766666555444444 321 2222222 22223333333322
Q ss_pred ccchHhhhcCCCcchhhHHhhcCCCCHH---------HHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhh
Q 028006 115 AGYKFEQKRGHNPSAVECYKNQHGVSEE---------EAVKELLLEVANSWKDINEELLNPTTVPLPMLQRLLYFAR 182 (215)
Q Consensus 115 ~S~~~E~~~G~~~n~V~~ym~e~g~s~e---------eA~~~i~~~i~~~wk~ln~e~l~~~~~p~~~~~~~ln~aR 182 (215)
.......++|.+ -.=.=-|.++|+|.+ ....-+..+++.+...+.+..--...+|......++-.++
T Consensus 153 Rdv~eD~~~gR~-ylP~~~l~~~gv~~~~l~~~~~~~~~~~~~~~l~~~A~~~l~~a~~~~~~~p~~~~~~~~~~~~ 228 (266)
T TIGR03465 153 RDVGEDARRGRI-YLPAEELQRFGVPAADILEGRYSPALAALCRFQAERARAHYAEADALLPACDRRAQRAARAMAA 228 (266)
T ss_pred HHhHHHHhCCCe-ecCHHHHHHcCCCHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhCCHhhhHHHHHHHH
Confidence 222333456754 111224577898876 3345556666666655555433234577644444444433
No 21
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=83.20 E-value=31 Score=30.29 Aligned_cols=90 Identities=12% Similarity=-0.070 Sum_probs=58.4
Q ss_pred CCCchhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhh-CCCCCChhhhhhhhcchHHH
Q 028006 23 GRSYGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDL-GDFIATKDNFECILKNAKSL 101 (215)
Q Consensus 23 g~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~-g~~l~~~e~~~~~~~~~~i~ 101 (215)
+....+..+.+.....+.+-..+..|.. +.-+|.++|++....=+|.-+..+ +..+. --.. +++..+. ...+-
T Consensus 127 ~~~~~~~~~~~~~~~~~~Gq~~d~~~~~-~~~~s~~~y~~~i~~KTa~lf~~~-~~~ga~lag~-~~~~~~~---l~~~g 200 (323)
T PRK10888 127 GSLKVLEVMSEAVNVIAEGEVLQLMNVN-DPDITEENYMRVIYSKTARLFEAA-AQCSGILAGC-TPEQEKG---LQDYG 200 (323)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHcCC-CHHHHHH---HHHHH
Confidence 3334566677778888888888877743 345899999998766666554333 22222 1112 4343333 34567
Q ss_pred HHHHHHHHHhcCcccch
Q 028006 102 KATETIGRLMDDIAGYK 118 (215)
Q Consensus 102 ~~~~~i~rL~NDi~S~~ 118 (215)
+..+...-+.||+..+.
T Consensus 201 ~~lG~aFQi~DD~ld~~ 217 (323)
T PRK10888 201 RYLGTAFQLIDDLLDYS 217 (323)
T ss_pred HHHHHHHHHHHHhhccc
Confidence 88888999999998885
No 22
>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]
Probab=82.00 E-value=1.2 Score=36.34 Aligned_cols=49 Identities=27% Similarity=0.175 Sum_probs=35.0
Q ss_pred HHHHHHhcCcccchHhhhcCC-CcchhhHHhhcCCCCHHHHHHHHHHHHH
Q 028006 105 ETIGRLMDDIAGYKFEQKRGH-NPSAVECYKNQHGVSEEEAVKELLLEVA 153 (215)
Q Consensus 105 ~~i~rL~NDi~S~~~E~~~G~-~~n~V~~ym~e~g~s~eeA~~~i~~~i~ 153 (215)
...-.|--|+..+++..+.-. +.-+=.+.|+.+|+|++||+++++++-=
T Consensus 125 ~~~~~L~~el~~~k~~L~~rK~ierAKglLM~~~g~sE~EAy~~lR~~AM 174 (194)
T COG3707 125 EERRALRRELAKLKDRLEERKVIERAKGLLMKRRGLSEEEAYKLLRRTAM 174 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 334556667777776654332 3445568999999999999999998643
No 23
>CHL00151 preA prenyl transferase; Reviewed
Probab=81.05 E-value=38 Score=29.73 Aligned_cols=89 Identities=7% Similarity=-0.065 Sum_probs=55.4
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhhCCCCCChhhhhhhhcchHHHHHHH
Q 028006 26 YGIPYAKQMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDLGDFIATKDNFECILKNAKSLKATE 105 (215)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~~e~~~~~~~~~~i~~~~~ 105 (215)
.....+.+....++.+-..+..|.. ..-+|.++|+.....=+|.-+..++..-++--.. +++..+. ...+-+..+
T Consensus 134 ~~~~~~~~~~~~l~~G~~~~~~~~~-~~~~~~~~yl~~i~~KTa~L~~~~~~~ga~lag~-~~~~~~~---l~~~G~~lG 208 (323)
T CHL00151 134 EVVKLISKVITDFAEGEIRQGLVQF-DTTLSILNYIEKSFYKTASLIAASCKAAALLSDA-DEKDHND---FYLYGKHLG 208 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCC-CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHcCC-CHHHHHH---HHHHHHHHH
Confidence 4566777788888888877766642 3457899999975444444443322222221113 4443333 355778889
Q ss_pred HHHHHhcCcccchH
Q 028006 106 TIGRLMDDIAGYKF 119 (215)
Q Consensus 106 ~i~rL~NDi~S~~~ 119 (215)
...-+.||+..+.-
T Consensus 209 ~aFQi~DDilD~~~ 222 (323)
T CHL00151 209 LAFQIIDDVLDITS 222 (323)
T ss_pred HHHHHHHHHhhccc
Confidence 99999999998753
No 24
>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=78.95 E-value=1.8 Score=27.85 Aligned_cols=28 Identities=25% Similarity=0.189 Sum_probs=21.5
Q ss_pred CcchhhHHhhcCCCCHHHHHHHHHHHHH
Q 028006 126 NPSAVECYKNQHGVSEEEAVKELLLEVA 153 (215)
Q Consensus 126 ~~n~V~~ym~e~g~s~eeA~~~i~~~i~ 153 (215)
+.-++.+.|..+|+|+++|.+.+++.-.
T Consensus 15 I~~AkgiLm~~~g~~e~~A~~~Lr~~Am 42 (56)
T PF03861_consen 15 IEQAKGILMARYGLSEDEAYRLLRRQAM 42 (56)
T ss_dssp HHHHHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 4467789999999999999999988654
No 25
>PF13060 DUF3921: Protein of unknown function (DUF3921)
Probab=77.03 E-value=11 Score=23.74 Aligned_cols=44 Identities=20% Similarity=0.201 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHHHHH
Q 028006 2 KFIVKALLDIYREAEEELAKEGRSYGIPYAKQMMQELIILYFTEAK 47 (215)
Q Consensus 2 k~~~~~l~~~~~e~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~Ea~ 47 (215)
.++-+++-.|++|+.+++..||- ..+-+.++-++|+.+.-.|.-
T Consensus 7 smiqkaih~tydelgkei~~~g~--~~d~i~kaqeeylsals~et~ 50 (58)
T PF13060_consen 7 SMIQKAIHRTYDELGKEIDLQGV--IADEIQKAQEEYLSALSHETL 50 (58)
T ss_pred HHHHHHHHHhHHHHhHHhhhcch--HHHHHHHHHHHHHHHhhHHHH
Confidence 45678999999999999988884 677788888888888766643
No 26
>PRK10581 geranyltranstransferase; Provisional
Probab=76.94 E-value=42 Score=29.15 Aligned_cols=112 Identities=9% Similarity=-0.013 Sum_probs=68.3
Q ss_pred HHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHh--hCCCCCChhhhhhhhcchHHHHHHHHHHHHhcC
Q 028006 36 QELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVD--LGDFIATKDNFECILKNAKSLKATETIGRLMDD 113 (215)
Q Consensus 36 ~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~--~g~~l~~~e~~~~~~~~~~i~~~~~~i~rL~ND 113 (215)
..++.|-..+..|.. ..+|.++|++.-..=+|.-+..++ ..+ ++..- +++..+.+ .++-+..+...-+.||
T Consensus 152 ~~l~~GQ~ld~~~~~--~~~~~~~y~~i~~~KTa~L~~~~~-~~gailag~~-~~~~~~~l---~~~g~~lG~aFQI~DD 224 (299)
T PRK10581 152 AGMCGGQALDLEAEG--KQVPLDALERIHRHKTGALIRAAV-RLGALSAGDK-GRRALPVL---DRYAESIGLAFQVQDD 224 (299)
T ss_pred chhhHhhHHHHhccC--CCCCHHHHHHHHHHhhHHHHHHHH-HHHHHHcCCC-cHHHHHHH---HHHHHHHHHHHHHHHH
Confidence 346677777777743 468999999876544444443222 222 12111 22333433 5577888999999999
Q ss_pred cccchHh-h----------hcCCCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHHHHHH
Q 028006 114 IAGYKFE-Q----------KRGHNPSAVECYKNQHGVSEEEAVKELLLEVANSWKDINE 161 (215)
Q Consensus 114 i~S~~~E-~----------~~G~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ln~ 161 (215)
+..+.-. . ..|.. +.+.++- .|.|.+.+++.++++.+.+..
T Consensus 225 ilD~~g~~~~~GK~~g~Dl~~gk~-T~p~l~~------~e~a~~~a~~~~~~A~~~l~~ 276 (299)
T PRK10581 225 ILDVVGDTATLGKRQGADQQLGKS-TYPALLG------LEQARKKARDLIDDARQSLDQ 276 (299)
T ss_pred HccccCChHHHCCCcchhhhcCCC-CHHHHHH------HHHHHHHHHHHHHHHHHHHHh
Confidence 9988432 1 22333 4544442 478888899999988877664
No 27
>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=70.26 E-value=3.5 Score=22.92 Aligned_cols=18 Identities=44% Similarity=0.711 Sum_probs=14.7
Q ss_pred HHhhcCCCCHHHHHHHHH
Q 028006 132 CYKNQHGVSEEEAVKELL 149 (215)
Q Consensus 132 ~ym~e~g~s~eeA~~~i~ 149 (215)
-|.++||+|.||..+.+.
T Consensus 9 rYV~eh~ls~ee~~~RL~ 26 (28)
T PF12368_consen 9 RYVKEHGLSEEEVAERLA 26 (28)
T ss_pred hhHHhcCCCHHHHHHHHH
Confidence 589999999999776654
No 28
>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=68.21 E-value=72 Score=26.82 Aligned_cols=65 Identities=12% Similarity=0.008 Sum_probs=42.1
Q ss_pred CCCCChHHhhhhhhhhhhhHHHHHHHHHhhCCCCCChhhhhhhhcchHHHHHHHHHHHHhcCcccchHh
Q 028006 52 GYVPTFDEYKSVALRSIGLRTLAVASFVDLGDFIATKDNFECILKNAKSLKATETIGRLMDDIAGYKFE 120 (215)
Q Consensus 52 ~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~~e~~~~~~~~~~i~~~~~~i~rL~NDi~S~~~E 120 (215)
+..+|.++|++.-..-+|.-+...+..-++--.. +++..+. ...+-+..+...-+.||+..+...
T Consensus 130 ~~~~~~~~y~~i~~~KTg~l~~~~~~~ga~lag~-~~~~~~~---l~~~g~~lG~afQi~DD~~d~~~~ 194 (260)
T PF00348_consen 130 DKDPTEEEYLEIIRLKTGSLFALACQLGAILAGA-DEEQIEA---LREFGRHLGIAFQIRDDLLDLFGD 194 (260)
T ss_dssp TSSTSHHHHHHHHHHHTHHHHHHHHHHHHHHTTS-GHHHHHH---HHHHHHHHHHHHHHHHHHHHHHSH
T ss_pred cccccHHHHHHHHhhcchHHHHHHHHHHHHhccc-hhHHHHH---HHHHHHHHHHHHhhhhhhhhccCc
Confidence 3478999999998777776644333322221123 4344343 356778889999999999888743
No 29
>smart00463 SMR Small MutS-related domain.
Probab=64.58 E-value=9.7 Score=25.94 Aligned_cols=23 Identities=30% Similarity=0.266 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHH
Q 028006 137 HGVSEEEAVKELLLEVANSWKDI 159 (215)
Q Consensus 137 ~g~s~eeA~~~i~~~i~~~wk~l 159 (215)
||++.++|+..+...++++++.-
T Consensus 7 HG~~~~eA~~~l~~~l~~~~~~~ 29 (80)
T smart00463 7 HGLTVEEALTALDKFLNNARLKG 29 (80)
T ss_pred CCCCHHHHHHHHHHHHHHHHHcC
Confidence 79999999999999999988653
No 30
>smart00400 ZnF_CHCC zinc finger.
Probab=64.22 E-value=7.7 Score=24.68 Aligned_cols=25 Identities=28% Similarity=0.283 Sum_probs=20.9
Q ss_pred CCCcchhhHHhhcCCCCHHHHHHHH
Q 028006 124 GHNPSAVECYKNQHGVSEEEAVKEL 148 (215)
Q Consensus 124 G~~~n~V~~ym~e~g~s~eeA~~~i 148 (215)
|...+.|..+|+-+|+|-.||++.+
T Consensus 30 g~gGd~i~fv~~~~~~sf~eA~~~L 54 (55)
T smart00400 30 GAGGNVISFLMKYDKLSFVEAVKKL 54 (55)
T ss_pred CCCCCHHHHHHHHHCcCHHHHHHHh
Confidence 4445889999998899999999865
No 31
>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=61.31 E-value=10 Score=26.07 Aligned_cols=24 Identities=25% Similarity=0.257 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q 028006 137 HGVSEEEAVKELLLEVANSWKDIN 160 (215)
Q Consensus 137 ~g~s~eeA~~~i~~~i~~~wk~ln 160 (215)
||++.+||...+.+.++++|+.-.
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 32
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=59.34 E-value=9.5 Score=28.80 Aligned_cols=23 Identities=39% Similarity=0.434 Sum_probs=19.3
Q ss_pred chhhHHhhcCCCCHHHHHHHHHH
Q 028006 128 SAVECYKNQHGVSEEEAVKELLL 150 (215)
Q Consensus 128 n~V~~ym~e~g~s~eeA~~~i~~ 150 (215)
-=|.+.|.|.|+|.++|++.+.+
T Consensus 86 eDIkLV~eQa~VsreeA~kAL~e 108 (122)
T COG1308 86 EDIKLVMEQAGVSREEAIKALEE 108 (122)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHH
Confidence 34789999999999999987754
No 33
>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=58.63 E-value=1.1e+02 Score=25.67 Aligned_cols=132 Identities=17% Similarity=0.156 Sum_probs=64.8
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhhCCCCCChhhhhhhhcchHHHHHHHH---HHH
Q 028006 33 QMMQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDLGDFIATKDNFECILKNAKSLKATET---IGR 109 (215)
Q Consensus 33 ~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~~e~~~~~~~~~~i~~~~~~---i~r 109 (215)
+.+.+++.++... ......||++|.......+.|.--.+++..++.+ - +++.... ....+. ++.
T Consensus 93 ~~~~~li~g~~~D---l~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~~~~--~-~~~~~~~-------A~~lG~Alqltn 159 (265)
T cd00683 93 EPFRDLLAGMAMD---LDKRRYETLDELDEYCYYVAGVVGLMLLRVFGAS--S-DEAALER-------ARALGLALQLTN 159 (265)
T ss_pred HHHHHHHHHHHHh---CCCCCCCCHHHHHHHHHHhHHHHHHHHHHHhCCC--C-ChHHHHH-------HHHHHHHHHHHH
Confidence 3345555555322 2345678998877777666665554444444321 2 2222222 222222 333
Q ss_pred HhcCcccchHhhhcCCC--cchhhHHhhcCCCCHHHH---------HHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHH
Q 028006 110 LMDDIAGYKFEQKRGHN--PSAVECYKNQHGVSEEEA---------VKELLLEVANSWKDINEELLNPTTVPLPMLQRLL 178 (215)
Q Consensus 110 L~NDi~S~~~E~~~G~~--~n~V~~ym~e~g~s~eeA---------~~~i~~~i~~~wk~ln~e~l~~~~~p~~~~~~~l 178 (215)
++-|+. ...++|-+ +. =-|.++|+|.++- ..-+..+++.+.+-+....-....+|....-.++
T Consensus 160 ilRdv~---eD~~~gR~YlP~---d~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~ 233 (265)
T cd00683 160 ILRDVG---EDARRGRIYLPR---EELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAALPRRSRFCVR 233 (265)
T ss_pred HHHHHH---HHHccCCCcCCH---HHHHHcCCCHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCCHhhHHHHH
Confidence 344544 33355543 32 2367788887653 2445556666665555444333457765444444
Q ss_pred HHhhh
Q 028006 179 YFARS 183 (215)
Q Consensus 179 n~aR~ 183 (215)
-++.+
T Consensus 234 ~~~~~ 238 (265)
T cd00683 234 AAAML 238 (265)
T ss_pred HHHHH
Confidence 44433
No 34
>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=58.12 E-value=1.1e+02 Score=25.73 Aligned_cols=119 Identities=14% Similarity=0.069 Sum_probs=56.0
Q ss_pred CCCCCChHHhhhhhhhhhhhHHHHHHHHHhhCCCCCChhhhhhhhcchHHHHHHHHHHHHhcCcccchHhhhcCCCcchh
Q 028006 51 KGYVPTFDEYKSVALRSIGLRTLAVASFVDLGDFIATKDNFECILKNAKSLKATETIGRLMDDIAGYKFEQKRGHNPSAV 130 (215)
Q Consensus 51 ~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~~e~~~~~~~~~~i~~~~~~i~rL~NDi~S~~~E~~~G~~~n~V 130 (215)
....+|++|.......++|.--.+++..++.+. + +....... +-. +--++-++-|+. ....+|.+- .=
T Consensus 101 ~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~g~~~---~-~~~~~A~~---lG~-AlQltniLRDl~---eD~~~gR~Y-LP 168 (266)
T TIGR03464 101 VTRYATWAELLDYCRYSANPVGRLVLDLYGASD---P-ENVALSDA---ICT-ALQLINFWQDVG---VDYRKGRVY-LP 168 (266)
T ss_pred CCCCCCHHHHHHHHHHhHHHHHHHHHHHcCCCC---h-hHHHHHHH---HHH-HHHHHHHHHhhH---HHHhcCCcc-CC
Confidence 345679998888877777666655555443221 1 21221111 111 112233344543 333456431 11
Q ss_pred hHHhhcCCCCHHHHH---------HHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHh
Q 028006 131 ECYKNQHGVSEEEAV---------KELLLEVANSWKDINEELLNPTTVPLPMLQRLLYFA 181 (215)
Q Consensus 131 ~~ym~e~g~s~eeA~---------~~i~~~i~~~wk~ln~e~l~~~~~p~~~~~~~ln~a 181 (215)
.=.|.++|+|.|+-. .-+..+++.+...+.+..--...+|..+.-.++-++
T Consensus 169 ~~~l~~~Gv~~edl~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~ 228 (266)
T TIGR03464 169 RDDLARFGVSEEDLAAGRATPALRELMAFEVSRTRALLDRGAPLAARVDGRLGLELALIV 228 (266)
T ss_pred HHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCCHhhhHHHHHHH
Confidence 124678899976533 333344444444433332222357765555544444
No 35
>PLN02632 phytoene synthase
Probab=57.25 E-value=1.4e+02 Score=26.38 Aligned_cols=134 Identities=13% Similarity=0.096 Sum_probs=62.9
Q ss_pred HHHHHHHHHHHHHHHhCCCCCChHHhhhhhhhhhhhHHHHHHHHHhhCCCCCChhhhhhhhcchHHHHHHHH---HHHHh
Q 028006 35 MQELIILYFTEAKWLYKGYVPTFDEYKSVALRSIGLRTLAVASFVDLGDFIATKDNFECILKNAKSLKATET---IGRLM 111 (215)
Q Consensus 35 ~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~~e~~~~~~~~~~i~~~~~~---i~rL~ 111 (215)
+.+++.++... ......+|++|+......+.|.--.+++..++..... + ...+++ .+.-...+. ++-++
T Consensus 142 ~~~li~g~~~D---l~~~~~~t~~eL~~Ycy~vAgtVG~l~l~vlg~~~~~-~-~~~~~~---~~~A~~lG~AlQltNIL 213 (334)
T PLN02632 142 FRDMIEGMRMD---LVKSRYENFDELYLYCYYVAGTVGLMSVPVMGIAPES-K-ASTESV---YNAALALGIANQLTNIL 213 (334)
T ss_pred HHHHHHHHHHH---hccCCCCCHHHHHHHHHHhhHHHHHHHHHHhCCCCcc-c-cchHHH---HHHHHHHHHHHHHHHHH
Confidence 34455555322 2234567888888877666665555444444432211 1 111111 111122233 33344
Q ss_pred cCcccchHhhhcCCCcchhhHHhhcCCCCHHHH---------HHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHH
Q 028006 112 DDIAGYKFEQKRGHNPSAVECYKNQHGVSEEEA---------VKELLLEVANSWKDINEELLNPTTVPLPMLQRLLYF 180 (215)
Q Consensus 112 NDi~S~~~E~~~G~~~n~V~~ym~e~g~s~eeA---------~~~i~~~i~~~wk~ln~e~l~~~~~p~~~~~~~ln~ 180 (215)
-|+. ...++|.+- .=.=-|.++|+|.++- ..-+..+++.+..-+.+..---..+|..+.-.+.=.
T Consensus 214 RDv~---eD~~~GRvY-LP~e~L~~~Gv~~edl~~~~~~~~~~~l~~~~~~~Ar~~~~~a~~~l~~lp~~~r~~v~~a 287 (334)
T PLN02632 214 RDVG---EDARRGRVY-LPQDELAQFGLTDEDIFAGKVTDKWRAFMKFQIKRARMYFAEAEEGVSELDPASRWPVWAS 287 (334)
T ss_pred HHHH---HHHhCCcee-CCHHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhHhhCCHHhHHHHHHH
Confidence 4554 445666531 1112467899998873 234455555555444443322235776554333333
No 36
>COG2443 Sss1 Preprotein translocase subunit Sss1 [Intracellular trafficking and secretion]
Probab=55.23 E-value=42 Score=22.51 Aligned_cols=21 Identities=24% Similarity=0.184 Sum_probs=15.9
Q ss_pred CCCChHHhhhhhhhhhhhHHH
Q 028006 53 YVPTFDEYKSVALRSIGLRTL 73 (215)
Q Consensus 53 ~~Ps~eEYl~~~~~s~g~~~~ 73 (215)
..||-|||.+.+.++...-.+
T Consensus 26 rKP~~eEy~~~aKi~~~Gi~l 46 (65)
T COG2443 26 RKPDWEEYSKIAKITGLGILL 46 (65)
T ss_pred hCCCHHHHHHHHHHHHHHHHH
Confidence 479999999998877644433
No 37
>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=54.20 E-value=22 Score=26.13 Aligned_cols=72 Identities=8% Similarity=0.074 Sum_probs=43.5
Q ss_pred hHHHHHHHHHHHHhcCcccchHhhhcCCCcchhhHHhhcCCCCH---HHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHH
Q 028006 98 AKSLKATETIGRLMDDIAGYKFEQKRGHNPSAVECYKNQHGVSE---EEAVKELLLEVANSWKDINEELLNPTTVPLPML 174 (215)
Q Consensus 98 ~~i~~~~~~i~rL~NDi~S~~~E~~~G~~~n~V~~ym~e~g~s~---eeA~~~i~~~i~~~wk~ln~e~l~~~~~p~~~~ 174 (215)
..+.+.-..+.+.+||+++.+-+-... -||.---.+.-+++|. -|.-++++..++.+|.-+. .+|.+++
T Consensus 25 D~~~rLN~ev~~~~~~Ly~~~G~t~Ee-eA~lCLaLLmGYnat~yd~geke~~~Q~vL~Rs~~vL~-------~Lp~SlL 96 (106)
T PF06603_consen 25 DDFSRLNKEVYEQSNDLYSQHGSTPEE-EANLCLALLMGYNATIYDNGEKEEKKQEVLDRSWEVLD-------KLPASLL 96 (106)
T ss_pred HHHHHHhHHHHHHHHHHHhccCCCHHH-HHHHHHHHHHhccchhhhCccHHHHHHHHHHHHHHHHH-------hCCcHHH
Confidence 347788888999999999874221111 1333322222344433 2334577888999997766 4777766
Q ss_pred HHH
Q 028006 175 QRL 177 (215)
Q Consensus 175 ~~~ 177 (215)
+.=
T Consensus 97 K~~ 99 (106)
T PF06603_consen 97 KVQ 99 (106)
T ss_pred HHH
Confidence 643
No 38
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=53.62 E-value=21 Score=30.57 Aligned_cols=65 Identities=25% Similarity=0.280 Sum_probs=49.8
Q ss_pred cchHhhhcCCCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHhh----------cCCCCCCHHHHHHHHHHhhh
Q 028006 116 GYKFEQKRGHNPSAVECYKNQHGVSEEEAVKELLLEVANSWKDINEEL----------LNPTTVPLPMLQRLLYFARS 183 (215)
Q Consensus 116 S~~~E~~~G~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ln~e~----------l~~~~~p~~~~~~~ln~aR~ 183 (215)
.|++||. .++..+..+...|.+.++|.+++.--+++.|-++-..| |...++|...+..+.++||=
T Consensus 96 ~wk~~qk---a~klle~aaekl~~~~ee~~~~vg~~L~e~fG~~y~aFE~aa~~g~~~l~~~~~~~~~~~~l~e~a~e 170 (269)
T COG1093 96 EWKKEQK---ADKLLELAAEKLGKDLEEAYEEVGWKLEEEFGSLYDAFEAAAKEGGEVLDDEGVPEEWKEVLKEIARE 170 (269)
T ss_pred HHHHHHH---HHHHHHHHHHHhCCCHHHHHHHHhHHHHHHhCCHHHHHHHHHhcCCcccccCCCCHHHHHHHHHHHHh
Confidence 3456665 35778888889999999999999988888776654433 33457888999999999983
No 39
>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=53.43 E-value=12 Score=28.50 Aligned_cols=58 Identities=17% Similarity=0.192 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHHHHHHHhCCCCCChH-Hhhhhhhhhhh
Q 028006 8 LLDIYREAEEELAKEGRSYGIPYAKQMMQELIILYFTEAKWLYKGYVPTFD-EYKSVALRSIG 69 (215)
Q Consensus 8 l~~~~~e~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~e-EYl~~~~~s~g 69 (215)
++-.+.||++-+.-.|+ .+-.+.|++++.+.+.-++.....-+|.++ |+...|..|+-
T Consensus 43 lwa~l~dIs~qv~~~G~----k~~~e~WK~~~~~~~~~~~~~~~~~~~gl~Gg~v~~g~sTsk 101 (127)
T PF05772_consen 43 LWAMLGDISRQVEWNGR----KLDPEDWKELFTAAFLIATGEEQRVVPGLDGGFVVLGESTSK 101 (127)
T ss_dssp HHHHHHHHHHH--BTTB-------HHHHHHHHHHHH-----S--EEEE-TTSSEEEE---TTT
T ss_pred HHHHHHHHHHHhHhcCc----cCCHHHHHHHHHHHHhhhccchhhhccCCCCCeEEEeeechh
Confidence 45577788877777776 566788999999988666666556678777 66655554443
No 40
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=45.61 E-value=1e+02 Score=25.26 Aligned_cols=29 Identities=21% Similarity=0.425 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCChHH
Q 028006 30 YAKQMMQELIILYFTEAKWLYKGYVPTFDE 59 (215)
Q Consensus 30 ~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eE 59 (215)
++....++|+.|..- ..|...|.+||.+|
T Consensus 78 ~~~~~lQEyvEA~~f-~~~l~~~~l~s~ee 106 (204)
T PRK14562 78 YVGTALQEYVEALLV-YSLLFENKIPSPEE 106 (204)
T ss_pred hcchHHHHHHHHHHH-HHHHcCCCCCCHHH
Confidence 444455666666533 56777788888777
No 41
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=44.76 E-value=21 Score=26.75 Aligned_cols=27 Identities=41% Similarity=0.341 Sum_probs=22.0
Q ss_pred CCCcchhhHHhhcCCCCHHHHHHHHHH
Q 028006 124 GHNPSAVECYKNQHGVSEEEAVKELLL 150 (215)
Q Consensus 124 G~~~n~V~~ym~e~g~s~eeA~~~i~~ 150 (215)
|-...-|...|.+.|+|.++|++.+.+
T Consensus 74 ~i~~edI~lv~~q~gvs~~~A~~AL~~ 100 (115)
T PRK06369 74 EIPEEDIELVAEQTGVSEEEARKALEE 100 (115)
T ss_pred CCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 334577899999999999999987754
No 42
>COG0864 NikR Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]
Probab=43.82 E-value=65 Score=24.82 Aligned_cols=37 Identities=22% Similarity=0.370 Sum_probs=22.4
Q ss_pred HHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHHHHHHHhCC
Q 028006 12 YREAEEELAKEGRSYGIPYAKQMMQELIILYFTEAKWLYKG 52 (215)
Q Consensus 12 ~~e~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~ 52 (215)
++|+.+.+.+.|.+++-.. ..+-++.|++|.+|....
T Consensus 16 l~elD~~i~~rg~~sRSE~----IrdAir~yl~e~~~~~~~ 52 (136)
T COG0864 16 LEELDELIEERGYSSRSEL----IRDALREYLEEYRWLEDI 52 (136)
T ss_pred HHHHHHHHHHcCCCcHHHH----HHHHHHHHHHHhhhhccc
Confidence 3444444454566565544 455566778888997654
No 43
>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=42.60 E-value=24 Score=26.47 Aligned_cols=24 Identities=33% Similarity=0.286 Sum_probs=20.4
Q ss_pred cchhhHHhhcCCCCHHHHHHHHHH
Q 028006 127 PSAVECYKNQHGVSEEEAVKELLL 150 (215)
Q Consensus 127 ~n~V~~ym~e~g~s~eeA~~~i~~ 150 (215)
..-|...|.+.|+|.++|++.+.+
T Consensus 79 ~eDI~lV~eq~gvs~e~A~~AL~~ 102 (116)
T TIGR00264 79 EDDIELVMKQCNVSKEEARRALEE 102 (116)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHH
Confidence 467899999999999999987764
No 44
>PF13189 Cytidylate_kin2: Cytidylate kinase-like family; PDB: 3FDI_A.
Probab=42.18 E-value=8.6 Score=30.58 Aligned_cols=35 Identities=26% Similarity=0.215 Sum_probs=24.8
Q ss_pred hhHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHhhcC
Q 028006 130 VECYKNQHGVSEEEAVKELLLEVANSWKDINEELLN 165 (215)
Q Consensus 130 V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ln~e~l~ 165 (215)
|.=.|+.+|+|+++|.+.+.+ .+...+..-+.+..
T Consensus 128 v~ri~~~~~~s~~~A~~~i~~-~D~~R~~~~~~~~~ 162 (179)
T PF13189_consen 128 VERIMEREGISEEEAEKLIKK-EDKRRRAYYKYYTG 162 (179)
T ss_dssp HHHHHHHHT--HHHHHHHHHH-HHHHHHHHHHHH-S
T ss_pred HHHHHHHcCCCHHHHHHHHHH-HHHHHHHHHHHHhC
Confidence 455677789999999999877 77777777777764
No 45
>PTZ00393 protein tyrosine phosphatase; Provisional
Probab=41.63 E-value=22 Score=30.13 Aligned_cols=29 Identities=14% Similarity=0.117 Sum_probs=24.1
Q ss_pred cCCCcchhhHHhhcCCCCHHHHHHHHHHH
Q 028006 123 RGHNPSAVECYKNQHGVSEEEAVKELLLE 151 (215)
Q Consensus 123 ~G~~~n~V~~ym~e~g~s~eeA~~~i~~~ 151 (215)
.|-.+-.+.+||-++|++.+||++.+++.
T Consensus 181 lGRTGtl~AayLI~~GmspeeAI~~VR~~ 209 (241)
T PTZ00393 181 LGRAPVLASIVLIEFGMDPIDAIVFIRDR 209 (241)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 34456788899999999999999999873
No 46
>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=41.19 E-value=38 Score=23.25 Aligned_cols=30 Identities=17% Similarity=0.298 Sum_probs=24.6
Q ss_pred hhhHHhhcCCCCHHHHHHHHHHHHHHHHHH
Q 028006 129 AVECYKNQHGVSEEEAVKELLLEVANSWKD 158 (215)
Q Consensus 129 ~V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ 158 (215)
.|...+-+.|++.|+|.+.+++...++|+.
T Consensus 8 ~v~~~L~~~G~gR~~Ah~lv~~~a~~a~~~ 37 (81)
T PF10397_consen 8 RVMLALAEKGLGRQEAHELVQEAAMEAWEN 37 (81)
T ss_dssp HHHHHHHHTTH-HHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHHHHHHH
Confidence 455666688999999999999999999964
No 47
>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=38.71 E-value=50 Score=20.98 Aligned_cols=45 Identities=16% Similarity=0.297 Sum_probs=29.7
Q ss_pred hcCcccchHhhhcCCCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHH
Q 028006 111 MDDIAGYKFEQKRGHNPSAVECYKNQHGVSEEEAVKELLLEVANSWK 157 (215)
Q Consensus 111 ~NDi~S~~~E~~~G~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk 157 (215)
.||+-+...|+..--+ -=|.-.|. .|+|.-||+..+-..+.+.-+
T Consensus 2 ~~~lp~LtHeeQQ~Av-E~Iq~LMa-qGmSsgEAI~~VA~~iRe~~~ 46 (51)
T PF03701_consen 2 FNDLPSLTHEEQQQAV-ERIQELMA-QGMSSGEAIAIVAQEIREEHQ 46 (51)
T ss_pred CCCCCCCCHHHHHHHH-HHHHHHHH-hcccHHHHHHHHHHHHHHHHH
Confidence 3666666666554222 22445665 799999999998888876553
No 48
>KOG1766 consensus Enhancer of rudimentary [General function prediction only]
Probab=38.52 E-value=1.3e+02 Score=21.72 Aligned_cols=60 Identities=17% Similarity=0.202 Sum_probs=40.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCH-----HHHHHHHHHhhhhhhhcccCCCCCCCchhHHHHHH
Q 028006 140 SEEEAVKELLLEVANSWKDINEELLNPTTVPL-----PMLQRLLYFARSGHFIYDDGHDRYTHSLMMKRQVA 206 (215)
Q Consensus 140 s~eeA~~~i~~~i~~~wk~ln~e~l~~~~~p~-----~~~~~~ln~aR~~~~~Y~~~~Dg~t~~~~~k~~i~ 206 (215)
|.-||++-+.+|-|+.-|+.| |+.-|. .+-+++=.++-+...+|+.. -| |....-|+.|+
T Consensus 24 sv~e~megiCk~yEe~Lkk~n-----Ps~~~ITYDIsqlfeFiD~L~DlS~lVy~~~-t~-tY~pynk~wIK 88 (104)
T KOG1766|consen 24 SVTECMEGICKMYEEHLKKKN-----PSAPPITYDISQLFEFIDDLADLSMLVYNRE-TG-TYIPYNKDWIK 88 (104)
T ss_pred hHHHHHHHHHHHHHHHHHhcC-----CCCCCcceeHHHHHHHHHHHhhhhhhheecc-cc-cccCccHHHHH
Confidence 667899999999998888887 433222 55667777888888999877 44 43322344444
No 49
>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=38.21 E-value=25 Score=25.13 Aligned_cols=29 Identities=28% Similarity=0.239 Sum_probs=20.5
Q ss_pred CCcchhhHHhhcCCCCHHHHHHHHHHHHH
Q 028006 125 HNPSAVECYKNQHGVSEEEAVKELLLEVA 153 (215)
Q Consensus 125 ~~~n~V~~ym~e~g~s~eeA~~~i~~~i~ 153 (215)
...|+|..+|+-+|+|-.||++.+.++..
T Consensus 62 ~~Gd~i~~v~~~~~~~f~eAv~~l~~~~~ 90 (97)
T PF01807_consen 62 KGGDVIDFVMKYEGCSFKEAVKWLAEEFG 90 (97)
T ss_dssp -EE-HHHHHHHHHT--HHHHHHHHHHHHT
T ss_pred CCCcHHhHHHHHhCCCHHHHHHHHHHHhC
Confidence 33588999999889999999998877543
No 50
>KOG0776 consensus Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism]
Probab=37.78 E-value=2.6e+02 Score=25.46 Aligned_cols=100 Identities=13% Similarity=0.062 Sum_probs=66.5
Q ss_pred HHHhCCCchhhHHHHHHHHHHHHHHHHHHHHhCCCC--C-ChHHhhhhhhhhhhhHHHHHHHHHh-hCCCCCChhhhhhh
Q 028006 19 LAKEGRSYGIPYAKQMMQELIILYFTEAKWLYKGYV--P-TFDEYKSVALRSIGLRTLAVASFVD-LGDFIATKDNFECI 94 (215)
Q Consensus 19 ~~~~g~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~--P-s~eEYl~~~~~s~g~~~~~~~~~~~-~g~~l~~~e~~~~~ 94 (215)
++.-+...++..+..+.++++++-..|..-..+|.- + .+|+|...-.-.+|.-+...+-.-+ +| .- ++++.+.+
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-GG-SEEVIEAA 266 (384)
T ss_pred HHhccCchHHHHHHHHHHHHHHhhhhcccccccccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHHc-CC-CHHHHHHH
Confidence 344455577888899999999999887665432232 2 5788877776666665543222111 23 24 66777765
Q ss_pred hcchHHHHHHHHHHHHhcCcccchHhhhc
Q 028006 95 LKNAKSLKATETIGRLMDDIAGYKFEQKR 123 (215)
Q Consensus 95 ~~~~~i~~~~~~i~rL~NDi~S~~~E~~~ 123 (215)
. +.-+..++..-+++||..+.+....
T Consensus 267 ~---~yGR~lGL~fQvvDDildftkss~e 292 (384)
T KOG0776|consen 267 F---EYGRCLGLAFQVVDDILDFTKSSEE 292 (384)
T ss_pred H---HHHHHHHHHHHHhhcccCcccchhh
Confidence 3 3567889999999999999987654
No 51
>COG4860 Uncharacterized protein conserved in archaea [Function unknown]
Probab=37.13 E-value=36 Score=26.57 Aligned_cols=58 Identities=26% Similarity=0.296 Sum_probs=36.5
Q ss_pred HHHHHHHHH---HHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHHHHHHHh--CCCCCChHHhhhhhhhh
Q 028006 2 KFIVKALLD---IYREAEEELAKEGRSYGIPYAKQMMQELIILYFTEAKWLY--KGYVPTFDEYKSVALRS 67 (215)
Q Consensus 2 k~~~~~l~~---~~~e~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~Ea~w~~--~~~~Ps~eEYl~~~~~s 67 (215)
|.+|.+|.. |.-||++...++|++ .+.+++ ++=+-|++|+. +|..|.-+-+-....+.
T Consensus 27 rKl~~aLstgW~T~~eiee~iG~eg~R-aL~iLk-------kagmlEtqWr~p~~G~kPeKeYHtsYt~Vq 89 (170)
T COG4860 27 RKLLLALSTGWITLPEIEEKIGKEGRR-ALLILK-------KAGMLETQWRTPSNGQKPEKEYHTSYTNVQ 89 (170)
T ss_pred HHHHHHHhhcceeHHHHHHHhchhhHH-HHHHHH-------hhcchhheeeccCCCCCchhhhhhheeeEE
Confidence 345555543 777888888888873 454444 45577899983 47788755444444433
No 52
>COG5442 FlaF Flagellar biosynthesis regulator FlaF [Cell motility and secretion]
Probab=34.59 E-value=1.4e+02 Score=21.97 Aligned_cols=71 Identities=18% Similarity=0.331 Sum_probs=48.5
Q ss_pred HhcCcccchHhhhcCCCcchhhHHh--hcCCCCHHHHHHHHHHHHHHHHHHHHHhhcCC-CCCCHHHHHHHHHHh
Q 028006 110 LMDDIAGYKFEQKRGHNPSAVECYK--NQHGVSEEEAVKELLLEVANSWKDINEELLNP-TTVPLPMLQRLLYFA 181 (215)
Q Consensus 110 L~NDi~S~~~E~~~G~~~n~V~~ym--~e~g~s~eeA~~~i~~~i~~~wk~ln~e~l~~-~~~p~~~~~~~ln~a 181 (215)
.++|=++-.++.+++-+.-+|...- +..|-..-+|++.+. ....-|-.+.+.+-.| +++|+.+.--.+.++
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 4566666677777777766665332 233545566776664 4788999999999887 679997776665554
No 53
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=33.50 E-value=45 Score=26.37 Aligned_cols=32 Identities=31% Similarity=0.516 Sum_probs=21.4
Q ss_pred hhcCCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHH
Q 028006 134 KNQHGVSEEEAVKELLLEVANSWKDINEELLNPTTVPLP 172 (215)
Q Consensus 134 m~e~g~s~eeA~~~i~~~i~~~wk~ln~e~l~~~~~p~~ 172 (215)
|++.|.| .++|++.|++.||+ .+.+|++-|+|
T Consensus 127 ~~~~Gks----~~eIR~~ID~kYk~---g~~~pTpTp~P 158 (158)
T PF13798_consen 127 MYQEGKS----PKEIRQYIDEKYKE---GYAKPTPTPMP 158 (158)
T ss_pred HHHcCCC----HHHHHHHHHHHHHh---CCCCCCCCCCC
Confidence 4455555 45678889999964 37778776654
No 54
>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.13 E-value=38 Score=21.94 Aligned_cols=48 Identities=19% Similarity=0.237 Sum_probs=31.3
Q ss_pred cCcccchHhhhcCCCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHHHHHH
Q 028006 112 DDIAGYKFEQKRGHNPSAVECYKNQHGVSEEEAVKELLLEVANSWKDINE 161 (215)
Q Consensus 112 NDi~S~~~E~~~G~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ln~ 161 (215)
+++-|.-.|+..--+ --|.=+|. .|+|--||+.-+.+.+.+.-|..|+
T Consensus 3 ~~lp~LtHeqQQ~AV-E~Iq~lMa-eGmSsGEAIa~VA~elRe~hk~~~~ 50 (60)
T COG3140 3 AGLPSLTHEQQQKAV-ERIQELMA-EGMSSGEAIALVAQELRENHKGENR 50 (60)
T ss_pred CccccccHHHHHHHH-HHHHHHHH-ccccchhHHHHHHHHHHHHhccccc
Confidence 555666666654333 22445665 5899999999888888776665554
No 55
>PRK12793 flaF flagellar biosynthesis regulatory protein FlaF; Reviewed
Probab=27.50 E-value=2.6e+02 Score=20.80 Aligned_cols=45 Identities=22% Similarity=0.396 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhhcCC-CCCCHHHHHHHHHHhhh
Q 028006 138 GVSEEEAVKELLLEVANSWKDINEELLNP-TTVPLPMLQRLLYFARS 183 (215)
Q Consensus 138 g~s~eeA~~~i~~~i~~~wk~ln~e~l~~-~~~p~~~~~~~ln~aR~ 183 (215)
|.+..++++.+.. -..-|--|-..+..| +++|..++.-.++++=.
T Consensus 39 ~~~~~~~~eAL~~-NrrLWt~~~~Dl~~p~N~LP~eLRa~lisL~~f 84 (115)
T PRK12793 39 GAYSREAIEALYF-TRRLWTVLIEDLGSPENALPEELRADLISIGLW 84 (115)
T ss_pred CCChHHHHHHHHH-HHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHH
Confidence 3334444444443 667899999999987 67999999999998853
No 56
>PHA02896 A-type inclusion like protein; Provisional
Probab=27.46 E-value=1e+02 Score=29.08 Aligned_cols=47 Identities=9% Similarity=0.166 Sum_probs=38.4
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhhhhh
Q 028006 136 QHGVSEEEAVKELLLEVANSWKDINEELLNPTTVPLPMLQRLLYFARSGH 185 (215)
Q Consensus 136 e~g~s~eeA~~~i~~~i~~~wk~ln~e~l~~~~~p~~~~~~~ln~aR~~~ 185 (215)
..||..|.-+..+..+|++.| |++.-+.+.+|+.-.+.+=|+.|-.-
T Consensus 3 ~~~~giEKcV~eFkSlVertW---nk~Lns~SCIpRk~RKiIRNILR~YI 49 (616)
T PHA02896 3 RDGCGIDKCIRKFESLIIRTW---DHDLNERSFLNRKDRKIIRNIFRCFI 49 (616)
T ss_pred ccccChHHHHHHHHHHHHHhh---CCccccccCcCHHHHHHHHHHHHHHH
Confidence 458889999999999999999 33333457899999999999999653
No 57
>smart00195 DSPc Dual specificity phosphatase, catalytic domain.
Probab=27.25 E-value=54 Score=24.26 Aligned_cols=24 Identities=13% Similarity=0.091 Sum_probs=18.1
Q ss_pred cchhhHH-hhcCCCCHHHHHHHHHH
Q 028006 127 PSAVECY-KNQHGVSEEEAVKELLL 150 (215)
Q Consensus 127 ~n~V~~y-m~e~g~s~eeA~~~i~~ 150 (215)
+..+.+| |+..|.|.++|++.++.
T Consensus 93 ~~v~~~yl~~~~~~~~~~A~~~v~~ 117 (138)
T smart00195 93 ATLIIAYLMKYRNLSLNDAYDFVKD 117 (138)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 3556676 55679999999998864
No 58
>KOG3730 consensus Acyl-CoA:dihydroxyactetone-phosphate acyltransferase DHAPAT [Lipid transport and metabolism]
Probab=26.95 E-value=1e+02 Score=29.06 Aligned_cols=55 Identities=18% Similarity=0.122 Sum_probs=37.4
Q ss_pred CCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhhhhhhhc
Q 028006 125 HNPSAVECYKNQHGVSEEEAVKELLLEVANSWKDINEELLNPTTVPLPMLQRLLYFARSGHFIY 188 (215)
Q Consensus 125 ~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ln~e~l~~~~~p~~~~~~~ln~aR~~~~~Y 188 (215)
.+.+.|+=|-++.|+|.+.-.+++++++++---++|-. .+.-..+-+++++.=+|
T Consensus 76 ~~~sVi~~~~kes~~s~d~~r~ea~eIlDEmsh~~nl~---------~IR~cg~ai~ki~k~i~ 130 (685)
T KOG3730|consen 76 KLRSVIEHYAKESGTSLDQMRREAREILDEMSHDRNLA---------IIRWCGIAITKIGKRIC 130 (685)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhcchH---------HHHHHHHHHHHHHHHHh
Confidence 35688999999999999988888888887655554432 23334455555555444
No 59
>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=26.41 E-value=1.4e+02 Score=19.19 Aligned_cols=31 Identities=16% Similarity=0.104 Sum_probs=22.7
Q ss_pred CcchhhHHhhcCCCCHHHHHHHHHHHHHHHH
Q 028006 126 NPSAVECYKNQHGVSEEEAVKELLLEVANSW 156 (215)
Q Consensus 126 ~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~w 156 (215)
+...+.....+++++.+++.+.+...+++-.
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 4567777778889999999888888887654
No 60
>PRK05114 hypothetical protein; Provisional
Probab=26.35 E-value=88 Score=20.45 Aligned_cols=45 Identities=16% Similarity=0.228 Sum_probs=28.7
Q ss_pred hcCcccchHhhhcCCCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHH
Q 028006 111 MDDIAGYKFEQKRGHNPSAVECYKNQHGVSEEEAVKELLLEVANSWK 157 (215)
Q Consensus 111 ~NDi~S~~~E~~~G~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk 157 (215)
.||+-+...|+..--+ -=|.-.|. .|+|--||+..+...+.+..+
T Consensus 2 ~~~lp~LtHeeQQ~AV-ErIq~LMa-qGmSsgEAI~~VA~eiRe~~~ 46 (59)
T PRK05114 2 FAGLPSLTHEQQQKAV-ERIQELMA-QGMSSGEAIALVAEELRANHQ 46 (59)
T ss_pred CCCcccCCHHHHHHHH-HHHHHHHH-ccccHHHHHHHHHHHHHHHHh
Confidence 3555555555443222 23455665 689999999999888876553
No 61
>PTZ00242 protein tyrosine phosphatase; Provisional
Probab=24.56 E-value=53 Score=25.90 Aligned_cols=28 Identities=21% Similarity=0.157 Sum_probs=21.7
Q ss_pred CCCcchhhHHhhcCC-CCHHHHHHHHHHH
Q 028006 124 GHNPSAVECYKNQHG-VSEEEAVKELLLE 151 (215)
Q Consensus 124 G~~~n~V~~ym~e~g-~s~eeA~~~i~~~ 151 (215)
|-.+..+.||+.++| +|.++|++.+++.
T Consensus 110 gRSgt~~a~yL~~~~~~s~~eAi~~vr~~ 138 (166)
T PTZ00242 110 GRAPILVALALVEYGGMEPLDAVGFVREK 138 (166)
T ss_pred CHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence 334577889998874 9999999888763
No 62
>PF11433 DUF3198: Protein of unknown function (DUF3198); InterPro: IPR024504 This domain is found at the C-terminal of a family of archaeal proteins annotated as membrane proteins.; PDB: 1X9B_A.
Probab=24.48 E-value=1.6e+02 Score=18.48 Aligned_cols=30 Identities=23% Similarity=0.290 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHhCCCc--hhhHHHHHHH
Q 028006 7 ALLDIYREAEEELAKEGRSY--GIPYAKQMMQ 36 (215)
Q Consensus 7 ~l~~~~~e~~~~~~~~g~~~--~~~~~~~~~~ 36 (215)
.+.+..+|+|.-..+-|++| .++-.++.|+
T Consensus 18 ~Fv~nL~ELE~is~rlg~~Y~~~LeeaK~kWk 49 (51)
T PF11433_consen 18 VFVRNLTELERISKRLGKSYQIRLEEAKEKWK 49 (51)
T ss_dssp HHHHHHHHHHHHHHHH-SHHHHHHHHHHHHH-
T ss_pred HHHHhHHHHHHHHHHHchHHHHHHHHHHHhhc
Confidence 34566677776666668765 3445566664
No 63
>KOG1720 consensus Protein tyrosine phosphatase CDC14 [Defense mechanisms]
Probab=24.37 E-value=62 Score=26.98 Aligned_cols=28 Identities=25% Similarity=0.464 Sum_probs=22.2
Q ss_pred CCCcchhhHHhh-cCCCCHHHHHHHHHHH
Q 028006 124 GHNPSAVECYKN-QHGVSEEEAVKELLLE 151 (215)
Q Consensus 124 G~~~n~V~~ym~-e~g~s~eeA~~~i~~~ 151 (215)
|...-.|.|||- ++|+|..||++.++.+
T Consensus 159 GRTG~liAc~lmy~~g~ta~eaI~~lR~~ 187 (225)
T KOG1720|consen 159 GRTGTLIACYLMYEYGMTAGEAIAWLRIC 187 (225)
T ss_pred CchhHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence 445678999875 6699999999988763
No 64
>PF00584 SecE: SecE/Sec61-gamma subunits of protein translocation complex; InterPro: IPR001901 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion []. SecE, part of the main SecYEG translocase complex, is ~106 residues in length, and spans the inner membrane of the Gram-negative bacterial envelope. Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. In eukaryotes, the evolutionary related protein sec61-gamma plays a role in protein translocation through the endoplasmic reticulum; it is part of a trimeric complex that also consist of sec61-alpha and beta []. Both secE and sec61-gamma are small proteins of about 60 to 90 amino acids that contain a single transmembrane region at their C-terminal extremity (Escherichia coli secE is an exception, in that it possess an extra N-terminal segment of 60 residues that contains two additional transmembrane domains) [].; GO: 0006605 protein targeting, 0006886 intracellular protein transport, 0016020 membrane; PDB: 3J01_B 2WW9_B 2WWA_B 3DL8_C 2WWB_B 3DIN_G 2ZJS_E 2ZQP_E.
Probab=24.32 E-value=1.2e+02 Score=19.13 Aligned_cols=26 Identities=12% Similarity=0.031 Sum_probs=18.3
Q ss_pred CChHHhhhhhhhhhhhHHHHHHHHHh
Q 028006 55 PTFDEYKSVALRSIGLRTLAVASFVD 80 (215)
Q Consensus 55 Ps~eEYl~~~~~s~g~~~~~~~~~~~ 80 (215)
||-+|..+........-.......++
T Consensus 19 P~~~e~~~~t~~Vl~~~~i~~~~~~~ 44 (57)
T PF00584_consen 19 PSRKELLKSTIIVLVFVIIFGLFFFL 44 (57)
T ss_dssp CCTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999877666655555544443
No 65
>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=24.05 E-value=83 Score=21.62 Aligned_cols=25 Identities=36% Similarity=0.376 Sum_probs=18.9
Q ss_pred CcchhhHHhhcCCCCHHHHHHHHHH
Q 028006 126 NPSAVECYKNQHGVSEEEAVKELLL 150 (215)
Q Consensus 126 ~~n~V~~ym~e~g~s~eeA~~~i~~ 150 (215)
+-+.|.-+..+.|.|.++|++.+..
T Consensus 55 Ii~~I~~l~~~~g~~~~~ai~~le~ 79 (81)
T PF12550_consen 55 IIDFIERLANERGISEEEAIEILEE 79 (81)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 3456665577889999999988754
No 66
>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=23.20 E-value=1.9e+02 Score=17.61 Aligned_cols=28 Identities=18% Similarity=0.416 Sum_probs=20.8
Q ss_pred CCC--HHHHHHHHHHHHHHHHHHHHHhhcC
Q 028006 138 GVS--EEEAVKELLLEVANSWKDINEELLN 165 (215)
Q Consensus 138 g~s--~eeA~~~i~~~i~~~wk~ln~e~l~ 165 (215)
|++ -|.-.+.+..-+.+.||++-+-.-+
T Consensus 12 G~~ql~ESLLdrItRklr~gwKRl~~iLnQ 41 (45)
T PF02061_consen 12 GCPQLSESLLDRITRKLRDGWKRLWDILNQ 41 (45)
T ss_pred CCchhhHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 555 4667889999999999998754433
No 67
>PRK04946 hypothetical protein; Provisional
Probab=22.03 E-value=1.1e+02 Score=24.67 Aligned_cols=44 Identities=27% Similarity=0.352 Sum_probs=31.3
Q ss_pred cCcccchHh---------hhcCCCcchhhHHhhcCCCCHHHHHHHHHHHHHHHHH
Q 028006 112 DDIAGYKFE---------QKRGHNPSAVECYKNQHGVSEEEAVKELLLEVANSWK 157 (215)
Q Consensus 112 NDi~S~~~E---------~~~G~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk 157 (215)
+|..+|.++ ..+|+.. ++.-+-=||.+.+||.+.+...+.++.+
T Consensus 69 ~~~l~y~r~Gv~~~~~k~Lr~G~~~--~~~~LDLhG~~~eeA~~~L~~fl~~a~~ 121 (181)
T PRK04946 69 EGPVRYVREDVDHFELKKLRRGDYS--PELFLDLHGLTQLQAKQELGALIAACRK 121 (181)
T ss_pred CCceEEecCCCCHHHHHHhhCCCCC--CceEEECCCCCHHHHHHHHHHHHHHHHH
Confidence 355556544 5678763 3333445799999999999999998885
No 68
>KOG4061 consensus DMQ mono-oxygenase/Ubiquinone biosynthesis protein COQ7/CLK-1/CAT5 [General function prediction only]
Probab=22.01 E-value=1.9e+02 Score=23.51 Aligned_cols=51 Identities=22% Similarity=0.197 Sum_probs=41.6
Q ss_pred HHhhcC----CCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhhh
Q 028006 132 CYKNQH----GVSEEEAVKELLLEVANSWKDINEELLNPTTVPLPMLQRLLYFARS 183 (215)
Q Consensus 132 ~ym~e~----g~s~eeA~~~i~~~i~~~wk~ln~e~l~~~~~p~~~~~~~ln~aR~ 183 (215)
+|.-|+ +.+..-.++++.+.=.+.-+.||+..++ .+|+..++..+||.+-.
T Consensus 66 IYaGQ~avL~~~~vgpvi~hmWdqEk~Hl~tf~~l~~k-~rVrpT~l~P~w~vagf 120 (217)
T KOG4061|consen 66 IYAGQMAVLQGTSVGPVIKHMWDQEKEHLKTFENLALK-HRVRPTVLTPLWNVAGF 120 (217)
T ss_pred hhhchhhhhcCCCchhHHHHHHHHHHHHHHHHHHHHHH-ccCCchhhhhHHHHHHH
Confidence 355544 4578888999999999999999998887 57999999999998853
No 69
>cd00751 thiolase Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and eukaryotes (cytosol, microbodies and mitochondria). There are 2 functional different classes: thiolase-I (3-ketoacyl-CoA thiolase) and thiolase-II (acetoacetyl-CoA thiolase). Thiolase-I can cleave longer fatty acid molecules and plays an important role in the beta-oxidative degradation of fatty acids. Thiolase-II has a high substrate specificity. Although it can cleave acetoacyl-CoA, its main function is the synthesis of acetoacyl-CoA from two molecules of acetyl-CoA, which gives it importance in several biosynthetic pathways.
Probab=21.41 E-value=1e+02 Score=27.46 Aligned_cols=39 Identities=15% Similarity=0.054 Sum_probs=31.5
Q ss_pred cchhhHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHhhcC
Q 028006 127 PSAVECYKNQHGVSEEEAVKELLLEVANSWKDINEELLN 165 (215)
Q Consensus 127 ~n~V~~ym~e~g~s~eeA~~~i~~~i~~~wk~ln~e~l~ 165 (215)
+..-+-||++||+|.|+--....+...++|+-.|...+.
T Consensus 153 a~~a~~~~~~yg~tre~la~vav~~~~~a~~~~~~~~~~ 191 (386)
T cd00751 153 GITAENVAEKYGISREEQDEFALRSHQRAAAAQEAGRFK 191 (386)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHcCCCc
Confidence 355678999999999987777778888999888776664
No 70
>PRK08470 adenylosuccinate lyase; Provisional
Probab=20.92 E-value=4.8e+02 Score=23.98 Aligned_cols=72 Identities=18% Similarity=0.216 Sum_probs=49.4
Q ss_pred ChhhhhhhhcchHHHHHHHHHHHHhcCccc---chHh-----h--hcCCC-cchhhHHhhcCCCCHHHHHHHHHHHHHHH
Q 028006 87 TKDNFECILKNAKSLKATETIGRLMDDIAG---YKFE-----Q--KRGHN-PSAVECYKNQHGVSEEEAVKELLLEVANS 155 (215)
Q Consensus 87 ~~e~~~~~~~~~~i~~~~~~i~rL~NDi~S---~~~E-----~--~~G~~-~n~V~~ym~e~g~s~eeA~~~i~~~i~~~ 155 (215)
.....+| ...|..+..+....++++++.+ ...| . ..|-. +..|...+...|++.++|.+.+++....+
T Consensus 304 ~~~~~e~-~~l~~~~~~~~~~l~~~~~~l~~l~v~~~rm~~nl~~~~g~~~ae~l~~~L~~~G~~~~~Ah~~V~~~~~~a 382 (442)
T PRK08470 304 SHSSVER-FILPDAFITTDFMLHRLNNVIENLVVYPENMMKNLNLTGGLVFSQRVLLELPKKGVSREDAYKIVQRNAMKV 382 (442)
T ss_pred chhHHHh-hhHHHHHHHHHHHHHHHHHHHccCEECHHHHHHHHHhccChHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 4344455 2457777777777777776654 2222 1 23443 55566667677999999999999999999
Q ss_pred HHHH
Q 028006 156 WKDI 159 (215)
Q Consensus 156 wk~l 159 (215)
|+++
T Consensus 383 ~~~~ 386 (442)
T PRK08470 383 WEDL 386 (442)
T ss_pred HHHh
Confidence 9884
No 71
>PF00782 DSPc: Dual specificity phosphatase, catalytic domain; InterPro: IPR000340 Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; 3.1.3.48 from EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [, ]. The PTP superfamily can be divided into four subfamilies []: (1) pTyr-specific phosphatases (2) dual specificity phosphatases (dTyr and dSer/dThr) (3) Cdc25 phosphatases (dTyr and/or dThr) (4) LMW (low molecular weight) phosphatases Based on their cellular localisation, PTPases are also classified as: Receptor-like, which are transmembrane receptors that contain PTPase domains [] Non-receptor (intracellular) PTPases [] All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif []. Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry represents dual specificity protein-tyrosine phosphatases. Ser/Thr and Tyr dual specificity phosphatases are a group of enzymes with both Ser/Thr (3.1.3.16 from EC) and tyrosine specific protein phosphatase (3.1.3.48 from EC) activity able to remove both the serine/threonine or tyrosine-bound phosphate group from a wide range of phosphoproteins, including a number of enzymes which have been phosphorylated under the action of a kinase. Dual specificity protein phosphatases (DSPs) regulate mitogenic signal transduction and control the cell cycle. The crystal structure of a human DSP, vaccinia H1-related phosphatase (or VHR), has been determined at 2.1 angstrom resolution []. A shallow active site pocket in VHR allows for the hydrolysis of phosphorylated serine, threonine, or tyrosine protein residues, whereas the deeper active site of protein tyrosine phosphatases (PTPs) restricts substrate specificity to only phosphotyrosine. Positively charged crevices near the active site may explain the enzyme's preference for substrates with two phosphorylated residues. The VHR structure defines a conserved structural scaffold for both DSPs and PTPs. A "recognition region" connecting helix alpha1 to strand beta1, may determine differences in substrate specificity between VHR, the PTPs, and other DSPs. These proteins may also have inactive phosphatase domains, and dependent on the domain composition this loss of catalytic activity has different effects on protein function. Inactive single domain phosphatases can still specifically bind substrates, and protect again dephosphorylation, while the inactive domains of tandem phosphatases can be further subdivided into two classes. Those which bind phosphorylated tyrosine residues may recruit multi-phosphorylated substrates for the adjacent active domains and are more conserved, while the other class have accumulated several variable amino acid substitutions and have a complete loss of tyrosine binding capability. The second class shows a release of evolutionary constraint for the sites around the catalytic centre, which emphasises a difference in function from the first group. There is a region of higher conservation common to both classes, suggesting a new regulatory centre [].; GO: 0008138 protein tyrosine/serine/threonine phosphatase activity, 0006470 protein dephosphorylation; PDB: 2G6Z_A 1MKP_A 1YZ4_A 2P4D_A 1M3G_A 1ZZW_A 2OUD_A 2HXP_A 3LJ8_A 1OHD_A ....
Probab=20.89 E-value=77 Score=23.17 Aligned_cols=24 Identities=25% Similarity=0.317 Sum_probs=18.7
Q ss_pred cchhhHHhhc-CCCCHHHHHHHHHH
Q 028006 127 PSAVECYKNQ-HGVSEEEAVKELLL 150 (215)
Q Consensus 127 ~n~V~~ym~e-~g~s~eeA~~~i~~ 150 (215)
+..+.+|+-. +|+|.++|++.++.
T Consensus 88 ~~v~~ayLm~~~~~~~~~A~~~v~~ 112 (133)
T PF00782_consen 88 GAVAAAYLMKKNGMSLEEAIEYVRS 112 (133)
T ss_dssp HHHHHHHHHHHHTSSHHHHHHHHHH
T ss_pred hHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4667776665 59999999998865
No 72
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=20.63 E-value=1e+02 Score=19.96 Aligned_cols=23 Identities=22% Similarity=0.229 Sum_probs=18.7
Q ss_pred chhhHHhhcCCCCHHHHHHHHHH
Q 028006 128 SAVECYKNQHGVSEEEAVKELLL 150 (215)
Q Consensus 128 n~V~~ym~e~g~s~eeA~~~i~~ 150 (215)
..|+.|.+..|+|.++|.+.+.+
T Consensus 6 ~~Ie~~A~~~~~s~~ea~~~~~~ 28 (62)
T PF12668_consen 6 FCIEEFAKKLNISGEEAYNYFKR 28 (62)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHH
Confidence 35777888889999999988765
No 73
>PF14278 TetR_C_8: Transcriptional regulator C-terminal region
Probab=20.19 E-value=2.4e+02 Score=17.93 Aligned_cols=25 Identities=24% Similarity=0.323 Sum_probs=13.7
Q ss_pred HHHhCCCchhhHHHHHHHHHHHHHH
Q 028006 19 LAKEGRSYGIPYAKQMMQELIILYF 43 (215)
Q Consensus 19 ~~~~g~~~~~~~~~~~~~~~~~~~~ 43 (215)
+..+|...-...+++.+++.+....
T Consensus 22 l~~~~~~~f~~~l~~~~~~~~~~~~ 46 (77)
T PF14278_consen 22 LSPNGDPNFQERLKELIKEWITEYI 46 (77)
T ss_pred HCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 3444443455666666666665554
Done!