Query 025080
Match_columns 258
No_of_seqs 169 out of 813
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 02:31:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025080.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025080hhsearch_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 2E-68 4.4E-73 510.5 23.5 255 1-255 286-542 (542)
2 PLN02279 ent-kaur-16-ene synth 100.0 4.2E-68 9.1E-73 519.4 21.3 255 1-258 519-778 (784)
3 cd00868 Terpene_cyclase_C1 Ter 100.0 1.9E-43 4.2E-48 312.0 20.5 232 1-232 52-284 (284)
4 PF03936 Terpene_synth_C: Terp 100.0 1.3E-39 2.9E-44 285.5 10.6 204 1-204 66-270 (270)
5 PLN02592 ent-copalyl diphospha 100.0 2.5E-38 5.3E-43 309.2 18.8 216 1-257 567-800 (800)
6 cd00687 Terpene_cyclase_nonpla 100.0 4.7E-35 1E-39 261.7 13.7 202 2-208 63-266 (303)
7 PLN02150 terpene synthase/cycl 100.0 9.3E-35 2E-39 216.8 10.3 94 165-258 1-96 (96)
8 cd00385 Isoprenoid_Biosyn_C1 I 99.9 4.2E-22 9.2E-27 168.9 8.1 211 2-226 20-243 (243)
9 cd00686 Terpene_cyclase_cis_tr 98.4 9.1E-06 2E-10 72.9 13.2 182 5-209 93-278 (357)
10 PF06330 TRI5: Trichodiene syn 98.3 4.4E-06 9.5E-11 76.0 8.9 181 5-207 93-277 (376)
11 cd00867 Trans_IPPS Trans-Isopr 94.2 0.56 1.2E-05 40.0 10.2 117 73-205 87-214 (236)
12 PF00494 SQS_PSY: Squalene/phy 92.0 0.71 1.5E-05 40.3 7.6 157 8-190 30-192 (267)
13 TIGR02749 prenyl_cyano solanes 90.4 8.7 0.00019 34.8 13.3 87 72-162 134-220 (322)
14 TIGR03465 HpnD squalene syntha 89.2 14 0.00031 32.2 13.6 135 77-225 84-227 (266)
15 PLN02890 geranyl diphosphate s 89.0 7.2 0.00016 36.8 11.8 89 71-163 227-315 (422)
16 cd00685 Trans_IPPS_HT Trans-Is 88.7 3.8 8.2E-05 35.7 9.3 120 72-205 109-239 (259)
17 PLN02857 octaprenyl-diphosphat 88.5 5.5 0.00012 37.5 10.7 87 72-162 228-314 (416)
18 TIGR02748 GerC3_HepT heptapren 87.2 20 0.00042 32.4 13.2 86 72-162 130-216 (319)
19 KOG1719 Dual specificity phosp 83.6 1 2.2E-05 36.5 2.6 40 166-205 119-165 (183)
20 COG0142 IspA Geranylgeranyl py 82.7 23 0.0005 32.0 11.5 108 72-184 135-252 (322)
21 cd00683 Trans_IPPS_HH Trans-Is 81.9 34 0.00073 29.7 14.3 184 10-226 38-237 (265)
22 PRK10888 octaprenyl diphosphat 81.2 42 0.00091 30.4 13.4 86 72-162 131-217 (323)
23 PF03861 ANTAR: ANTAR domain; 80.4 1.9 4.2E-05 28.4 2.7 30 169-198 14-43 (56)
24 COG3707 AmiR Response regulato 79.9 2.1 4.6E-05 35.8 3.4 50 149-198 125-175 (194)
25 PLN02632 phytoene synthase 78.4 53 0.0012 29.9 12.8 153 8-187 85-241 (334)
26 CHL00151 preA prenyl transfera 77.4 47 0.001 30.0 11.8 86 73-162 136-221 (323)
27 TIGR03464 HpnC squalene syntha 77.0 50 0.0011 28.8 14.7 147 9-188 31-182 (266)
28 PF12368 DUF3650: Protein of u 74.2 2.8 6E-05 23.8 1.7 18 176-193 9-26 (28)
29 smart00400 ZnF_CHCC zinc finge 60.0 11 0.00024 24.5 2.9 25 168-192 30-54 (55)
30 PRK10581 geranyltranstransfera 59.4 56 0.0012 29.3 8.1 111 82-205 153-276 (299)
31 smart00463 SMR Small MutS-rela 58.2 14 0.00031 25.8 3.3 24 181-204 7-30 (80)
32 PF01713 Smr: Smr domain; Int 56.1 13 0.00029 26.2 2.9 27 181-207 4-30 (83)
33 COG1093 SUI2 Translation initi 54.6 28 0.00062 30.6 5.1 64 160-226 96-169 (269)
34 PF00348 polyprenyl_synt: Poly 53.5 1.5E+02 0.0032 25.7 9.7 65 97-164 130-194 (260)
35 PF13060 DUF3921: Protein of u 52.8 57 0.0012 21.0 4.9 45 45-91 5-49 (58)
36 PF03701 UPF0181: Uncharacteri 49.7 34 0.00074 22.2 3.6 44 156-201 3-46 (51)
37 COG1308 EGD2 Transcription fac 44.8 26 0.00055 27.2 3.0 23 172-194 86-108 (122)
38 PTZ00393 protein tyrosine phos 44.5 23 0.0005 30.8 3.0 29 167-195 181-209 (241)
39 PF00156 Pribosyltran: Phospho 42.6 11 0.00023 28.4 0.6 21 8-28 91-111 (125)
40 COG2236 Predicted phosphoribos 42.1 15 0.00033 30.8 1.5 23 8-30 90-112 (192)
41 PF01807 zf-CHC2: CHC2 zinc fi 42.1 28 0.00061 25.6 2.8 29 169-197 62-90 (97)
42 PRK09177 xanthine-guanine phos 41.7 11 0.00024 30.4 0.6 22 8-29 87-108 (156)
43 PF05772 NinB: NinB protein; 40.5 25 0.00054 27.5 2.4 60 52-115 42-102 (127)
44 PF10397 ADSL_C: Adenylosuccin 37.9 53 0.0012 23.1 3.7 30 173-202 8-37 (81)
45 PF10776 DUF2600: Protein of u 36.1 3.4E+02 0.0074 24.8 14.1 116 118-252 194-311 (330)
46 PRK05114 hypothetical protein; 34.3 77 0.0017 21.2 3.6 44 156-201 3-46 (59)
47 PRK05205 bifunctional pyrimidi 33.3 20 0.00044 29.3 0.9 20 8-27 98-117 (176)
48 COG2443 Sss1 Preprotein transl 33.2 50 0.0011 22.7 2.7 21 97-117 25-45 (65)
49 KOG1766 Enhancer of rudimentar 33.1 1.9E+02 0.0042 21.4 5.8 61 184-250 24-89 (104)
50 PRK06369 nac nascent polypepti 32.9 47 0.001 25.5 2.8 27 168-194 74-100 (115)
51 KOG3730 Acyl-CoA:dihydroxyacte 31.0 1.9E+02 0.0042 27.9 6.9 75 169-255 76-151 (685)
52 PF05402 PqqD: Coenzyme PQQ sy 31.0 1.4E+02 0.003 19.7 4.8 32 170-201 32-63 (68)
53 TIGR00264 alpha-NAC-related pr 30.8 55 0.0012 25.1 2.9 24 171-194 79-102 (116)
54 PF11989 Dsl1_C: Retrograde tr 29.9 4.1E+02 0.0089 23.8 11.1 28 227-255 244-272 (291)
55 PRK09162 hypoxanthine-guanine 29.7 24 0.00051 29.1 0.8 22 8-29 100-121 (181)
56 PF13189 Cytidylate_kin2: Cyti 29.3 30 0.00065 28.2 1.3 37 172-209 126-162 (179)
57 COG3140 Uncharacterized protei 28.9 52 0.0011 21.7 2.1 48 156-205 3-50 (60)
58 PRK14562 haloacid dehalogenase 28.4 1.7E+02 0.0038 24.6 5.8 55 49-104 52-106 (204)
59 PF13798 PCYCGC: Protein of un 28.1 87 0.0019 25.4 3.7 34 176-216 125-158 (158)
60 smart00195 DSPc Dual specifici 28.0 65 0.0014 24.6 3.0 24 171-194 93-117 (138)
61 KOG1720 Protein tyrosine phosp 27.9 60 0.0013 27.8 2.8 29 167-195 158-187 (225)
62 TIGR01203 HGPRTase hypoxanthin 27.6 28 0.0006 28.3 0.8 21 8-28 87-107 (166)
63 PRK15423 hypoxanthine phosphor 27.2 31 0.00067 28.5 1.0 22 8-29 95-116 (178)
64 TIGR01559 squal_synth farnesyl 27.1 4.9E+02 0.011 23.8 17.4 167 75-252 105-291 (336)
65 cd07977 TFIIE_beta_winged_heli 26.0 76 0.0016 22.3 2.7 33 168-201 9-45 (75)
66 PHA03369 capsid maturational p 25.8 75 0.0016 31.3 3.4 29 217-249 301-329 (663)
67 PTZ00242 protein tyrosine phos 25.8 65 0.0014 26.1 2.7 28 168-195 110-138 (166)
68 KOG3231 Predicted assembly/vac 25.5 46 0.001 27.2 1.7 22 10-31 144-165 (208)
69 KOG2077 JNK/SAPK-associated pr 25.3 1.5E+02 0.0032 29.3 5.2 88 137-228 306-405 (832)
70 PF06883 RNA_pol_Rpa2_4: RNA p 25.3 22 0.00047 23.8 -0.2 32 18-49 3-34 (58)
71 PF12668 DUF3791: Protein of u 24.6 92 0.002 20.7 2.9 23 172-194 6-28 (62)
72 TIGR01090 apt adenine phosphor 24.5 37 0.0008 27.5 1.0 22 8-29 112-133 (169)
73 PRK07322 adenine phosphoribosy 24.3 38 0.00081 27.8 1.0 21 7-27 122-142 (178)
74 PRK02304 adenine phosphoribosy 24.2 42 0.0009 27.3 1.3 22 8-29 117-138 (175)
75 COG2096 cob(I)alamin adenosylt 23.2 2.1E+02 0.0046 23.8 5.2 20 13-32 30-49 (184)
76 PF06603 UpxZ: UpxZ family of 22.5 2E+02 0.0043 21.7 4.4 70 142-220 25-98 (106)
77 KOG4061 DMQ mono-oxygenase/Ubi 22.0 1.7E+02 0.0038 24.4 4.4 49 177-226 67-119 (217)
78 PF12550 GCR1_C: Transcription 21.9 79 0.0017 22.3 2.2 28 167-194 52-79 (81)
79 TIGR01367 pyrE_Therm orotate p 21.7 44 0.00096 27.7 1.0 21 8-28 108-128 (187)
80 PF00782 DSPc: Dual specificit 21.5 81 0.0018 23.8 2.4 24 171-194 88-112 (133)
81 PF07637 PSD5: Protein of unkn 21.1 2.4E+02 0.0052 18.9 4.4 54 188-255 3-56 (64)
82 PRK07199 phosphoribosylpyropho 20.8 47 0.001 29.8 1.0 20 8-27 214-233 (301)
83 PF12909 DUF3832: Protein of u 20.4 2.7E+02 0.0058 20.3 4.7 27 181-207 31-57 (89)
84 PLN02297 ribose-phosphate pyro 20.2 47 0.001 30.3 0.9 21 8-28 233-253 (326)
85 cd00127 DSPc Dual specificity 20.1 1.3E+02 0.0028 22.7 3.3 20 175-194 101-120 (139)
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=2e-68 Score=510.52 Aligned_cols=255 Identities=53% Similarity=0.882 Sum_probs=250.1
Q ss_pred CceeeeehheeccccCCCCCHHHHHHHHHHHHhccCcccCCCChhHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHH
Q 025080 1 MTKTIYTASIIDDTFDAYGFFEELKLLAEAVQRWDIGAMDILPEYMKVLYKALLDTFNEIEQDLAKEGRSSYLPYGKEKM 80 (258)
Q Consensus 1 ~aK~~~~~~~~DD~~D~~gt~eel~~~~~ai~rWd~~~~~~lp~~~k~~~~al~~~~~e~~~~~~~~~~~~~~~~~~~~~ 80 (258)
+||+++|+|++||+||.|||++|++.||+||+|||.++++++|+|||++|.++++++++++.++.++++++++.|++++|
T Consensus 286 ~aK~~~l~~~iDD~fD~~gt~eEl~~ft~ai~rwd~~~~~~lPe~mk~~~~al~~~~~ei~~~~~~~~~~~~~~~~~~~~ 365 (542)
T cd00684 286 LAKTIALITVIDDTYDVYGTLEELELFTEAVERWDISAIDQLPEYMKIVFKALLNTVNEIEEELLKEGGSYVVPYLKEAW 365 (542)
T ss_pred HHHHHHHHhhhHhhhccCCCHHHHHHHHHHHHhccccchhhccHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHH
Confidence 48999999999999999999999999999999999999999999999999999999999999999999989999999999
Q ss_pred HHHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhHHHHhcCccc
Q 025080 81 QELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVICRLRNDIVS 160 (258)
Q Consensus 81 ~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S 160 (258)
++++++|++||+|+++|++||++||+++|.+|+|++++++++++++|+.+|+++++|+..+|+|+++++.++||+|||.|
T Consensus 366 ~~~~~a~l~EA~w~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~e~~e~~~~~~~l~~~~~~i~rL~NDi~S 445 (542)
T cd00684 366 KDLVKAYLVEAKWAHEGYVPTFEEYMENALVSIGLGPLLLTSFLGMGDILTEEAFEWLESRPKLVRASSTIGRLMNDIAT 445 (542)
T ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHhhhhHHhhHHHHHHHHHHhcCCCCCHHHHHHHhccHHHHHHHHHHHHHhcChhh
Confidence 99999999999999999999999999999999999999999999999999999999987779999999999999999999
Q ss_pred hHHHhhcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhhcCC-CCCcHHHHHHHHhhhhhhhhhhccCCCCC
Q 025080 161 QQFEQKRGHIASGVECYIKQYGVSAEEVVTVFTEEVENAWKDMNEEFLKP-TAFPVALIERPFNIARVIEFLNKKGDWYT 239 (258)
Q Consensus 161 ~~kE~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ln~~~l~~-~~~p~~~~~~~~n~~R~~~~~Y~~~D~~t 239 (258)
|++|+++|+++|+|.|||+|+|+|+|+|+++++++++++||++|++++++ +.+|++|+++++|++|+++++|+++||||
T Consensus 446 ~~kE~~rGdv~n~V~~ymke~g~s~eeA~~~i~~~ie~~wk~ln~e~l~~~~~~p~~~~~~~~n~~r~~~~~Y~~~D~~t 525 (542)
T cd00684 446 YEDEMKRGDVASSIECYMKEYGVSEEEAREEIKKMIEDAWKELNEEFLKPSSDVPRPIKQRFLNLARVIDVFYKEGDGFT 525 (542)
T ss_pred hHHHHhcCCcccHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCCCCC
Confidence 99999999999999999999999999999999999999999999999997 78999999999999999999999999999
Q ss_pred Cc-HHHHHHHHhhcccc
Q 025080 240 HS-HAIKDQIAAVLRDP 255 (258)
Q Consensus 240 ~~-~~~~~~i~~l~~~p 255 (258)
.| ..+|++|++||++|
T Consensus 526 ~~~~~~~~~i~~ll~~p 542 (542)
T cd00684 526 HPEGEIKDHITSLLFEP 542 (542)
T ss_pred CccHHHHHHHHHHhcCC
Confidence 99 78999999999998
No 2
>PLN02279 ent-kaur-16-ene synthase
Probab=100.00 E-value=4.2e-68 Score=519.42 Aligned_cols=255 Identities=22% Similarity=0.309 Sum_probs=244.4
Q ss_pred CceeeeehheeccccCCCCCHHHHHHHHHHHHhccCc-ccCCCChhHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHH
Q 025080 1 MTKTIYTASIIDDTFDAYGFFEELKLLAEAVQRWDIG-AMDILPEYMKVLYKALLDTFNEIEQDLAKEGRSSYLPYGKEK 79 (258)
Q Consensus 1 ~aK~~~~~~~~DD~~D~~gt~eel~~~~~ai~rWd~~-~~~~lp~~~k~~~~al~~~~~e~~~~~~~~~~~~~~~~~~~~ 79 (258)
+||.+++++++||+||+|||.|||+.||+||+|||.+ ..+.+|+|||+||.+++++++|++.++.+.+|+++++|++++
T Consensus 519 ~aK~~~L~tviDD~fD~yGt~eEL~~ft~aVeRWD~~~~~~~lpeymki~f~aL~~t~nei~~~~~~~qGr~v~~~l~~a 598 (784)
T PLN02279 519 WAKNGVLTTVVDDFFDVGGSEEELENLIQLVEKWDVNGSPDFCSEQVEIIFSALRSTISEIGDKAFTWQGRNVTSHIIKI 598 (784)
T ss_pred HHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHhccccchhhCcHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHH
Confidence 4899999999999999999999999999999999999 569999999999999999999999998766777999999999
Q ss_pred HHHHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhHHHHhcCcc
Q 025080 80 MQELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVICRLRNDIV 159 (258)
Q Consensus 80 ~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~ 159 (258)
|++++++|++||+|+.+||+||++|||+++.+|+|+.++...+.+++|..+|+++++| +++|+|+++++.++||+|||+
T Consensus 599 W~~ll~ayl~EAeW~~~g~vPT~eEYL~na~vS~~l~~i~l~~~~~~G~~l~eev~e~-~~~~~L~~l~s~I~RLlNDI~ 677 (784)
T PLN02279 599 WLDLLKSMLTEAQWSSNKSTPTLDEYMTNAYVSFALGPIVLPALYLVGPKLSEEVVDS-PELHKLYKLMSTCGRLLNDIR 677 (784)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHhhchhhhhhHHHHHHHHHHhCCCCCHHHHhC-cchhHHHHHHHHHHHHHHhcc
Confidence 9999999999999999999999999999999999999988888889999999999999 699999999999999999999
Q ss_pred chHHHhhcCCcchhHHHHHhhC--CCCHHHHHHHHHHHHHHHHHHHHHhhcCC--CCCcHHHHHHHHhhhhhhhhhhccC
Q 025080 160 SQQFEQKRGHIASGVECYIKQY--GVSAEEVVTVFTEEVENAWKDMNEEFLKP--TAFPVALIERPFNIARVIEFLNKKG 235 (258)
Q Consensus 160 S~~kE~~~g~~~n~V~~ym~e~--g~s~eeA~~~i~~~i~~~~k~ln~~~l~~--~~~p~~~~~~~~n~~R~~~~~Y~~~ 235 (258)
||++|+++|++ |+|+|||+|+ |+|+|||+++++++|+++||+||++++++ +.+|++|++++||++|++++||+++
T Consensus 678 S~e~E~~rG~~-nsV~cYMke~~~gvSeEEAi~~i~~~Ie~~wKeLn~~~l~~~~~~vp~~~~~~~ln~aR~~~~~Y~~~ 756 (784)
T PLN02279 678 GFKRESKEGKL-NAVSLHMIHGNGNSTEEEAIESMKGLIESQRRELLRLVLQEKGSNVPRECKDLFWKMSKVLHLFYRKD 756 (784)
T ss_pred ccHhHHhCCCc-ceehhhhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHhhhhheeCC
Confidence 99999999998 9999999987 89999999999999999999999999963 5799999999999999999999999
Q ss_pred CCCCCcHHHHHHHHhhcccccCC
Q 025080 236 DWYTHSHAIKDQIAAVLRDPVTI 258 (258)
Q Consensus 236 D~~t~~~~~~~~i~~l~~~p~~~ 258 (258)
||||.+ +||++|++||++||++
T Consensus 757 Dgyt~~-~~k~~i~~ll~ePi~l 778 (784)
T PLN02279 757 DGFTSN-DMMSLVKSVIYEPVSL 778 (784)
T ss_pred CCCChH-HHHHHHHHHhccCCcC
Confidence 999975 7999999999999974
No 3
>cd00868 Terpene_cyclase_C1 Terpene cyclases, Class 1. Terpene cyclases, Class 1 (C1) of the class 1 family of isoprenoid biosynthesis enzymes, which share the 'isoprenoid synthase fold' and convert linear, all-trans, isoprenoids, geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate into numerous cyclic forms of monoterpenes, diterpenes, and sesquiterpenes. Also included in this CD are the cis-trans terpene cyclases such as trichodiene synthase. The class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational ch
Probab=100.00 E-value=1.9e-43 Score=311.99 Aligned_cols=232 Identities=52% Similarity=0.839 Sum_probs=218.3
Q ss_pred CceeeeehheeccccCCCCCHHHHHHHHHHHHhccCcccCCCChhHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHH
Q 025080 1 MTKTIYTASIIDDTFDAYGFFEELKLLAEAVQRWDIGAMDILPEYMKVLYKALLDTFNEIEQDLAKEGRSSYLPYGKEKM 80 (258)
Q Consensus 1 ~aK~~~~~~~~DD~~D~~gt~eel~~~~~ai~rWd~~~~~~lp~~~k~~~~al~~~~~e~~~~~~~~~~~~~~~~~~~~~ 80 (258)
+||+++|+|++||+||.+++.+++..++++++||+....+.+|+++++++.++.+++++++..+.+.+++....++++.|
T Consensus 52 ~a~~~~~~f~~DD~~D~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~r~~~~~ 131 (284)
T cd00868 52 LAKTIALLTVIDDTYDDYGTLEELELFTEAVERWDISAIDELPEYMKPVFKALYDLVNEIEEELAKEGGSESLPYLKEAW 131 (284)
T ss_pred HHHHHHHHHHHHhccccCCCHHHHHHHHHHHHhcChhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHH
Confidence 47899999999999999999999999999999999998999999999999999999999999998877777899999999
Q ss_pred HHHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhHHHHhcCccc
Q 025080 81 QELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVICRLRNDIVS 160 (258)
Q Consensus 81 ~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S 160 (258)
..|++++.+|++|+..|++||++||+++|+.|+|+.++++++++++|..+|++.+.+.+..+++.+.++.+++|+||++|
T Consensus 132 ~~~~~~~~~e~~~~~~~~~p~~~eYl~~R~~~~g~~~~~~l~~~~~g~~l~~~~~~~~~~~~~l~~~~~~~~~l~NDl~S 211 (284)
T cd00868 132 KDLLRAYLVEAKWANEGYVPSFEEYLENRRVSIGYPPLLALSFLGMGDILPEEAFEWLPSYPKLVRASSTIGRLLNDIAS 211 (284)
T ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHhceehhhHHHHHHHHHHHcCCCCCHHHHHHhhhhHHHHHHHHHHHHHhccchH
Confidence 99999999999999999999999999999999999999999999999999984444448889999999999999999999
Q ss_pred hHHHhhcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhhcC-CCCCcHHHHHHHHhhhhhhhhhh
Q 025080 161 QQFEQKRGHIASGVECYIKQYGVSAEEVVTVFTEEVENAWKDMNEEFLK-PTAFPVALIERPFNIARVIEFLN 232 (258)
Q Consensus 161 ~~kE~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ln~~~l~-~~~~p~~~~~~~~n~~R~~~~~Y 232 (258)
|+||+.+|+.+|+|.|||+++|+|.|+|++++.+++++++++|++...+ +++.|+.+++.+.|.+|.....|
T Consensus 212 ~~kE~~~g~~~N~v~vl~~~~~~~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~g~~~w~ 284 (284)
T cd00868 212 YEKEIARGEVANSVECYMKEYGVSEEEALEELRKMIEEAWKELNEEVLKLSSDVPRAVLETLLNLARGIYVWY 284 (284)
T ss_pred HHHHHccCCcccHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhhhhcC
Confidence 9999999999999999999999999999999999999999999999997 34688999999999999877654
No 4
>PF03936 Terpene_synth_C: Terpene synthase family, metal binding domain; InterPro: IPR005630 Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C10) synthases, sesquiterpene (C15) synthases and the diterpene (C20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf []. Tpsa includes vetispiridiene synthase Q39979 from SWISSPROT, 5-epi- aristolochene synthase, Q40577 from SWISSPROT and (+)-delta-cadinene synthase P93665 from SWISSPROT . Tpsb includes (-)-limonene synthase, Q40322 from SWISSPROT. Tpsc includes copalyl diphosphate synthase (kaurene synthase A), O04408 from SWISSPROT. Tpsd includes taxadiene synthase, Q41594 from SWISSPROT, pinene synthase, O24475 from SWISSPROT and myrcene synthase, O24474 from SWISSPROT. Tpse includes ent-kaurene synthase B Q39548 from SWISSPROT. Tpsf includes linalool synthase Q9ZPN5 from SWISSPROT. In the fungus Phaeosphaeria sp. (strain L487) the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein [].; GO: 0000287 magnesium ion binding, 0016829 lyase activity; PDB: 3PYB_A 3PYA_A 3G4F_A 3G4D_B 3CKE_A 2OA6_D 2E4O_B 3BNY_B 3BNX_A 3LG5_A ....
Probab=100.00 E-value=1.3e-39 Score=285.47 Aligned_cols=204 Identities=26% Similarity=0.382 Sum_probs=187.2
Q ss_pred CceeeeehheeccccCCCCCHHHHHHHHHHHHhccCcccCCCChhHHHHHHHHHHHHHHHHHHHHHhCCC-CcccchHHH
Q 025080 1 MTKTIYTASIIDDTFDAYGFFEELKLLAEAVQRWDIGAMDILPEYMKVLYKALLDTFNEIEQDLAKEGRS-SYLPYGKEK 79 (258)
Q Consensus 1 ~aK~~~~~~~~DD~~D~~gt~eel~~~~~ai~rWd~~~~~~lp~~~k~~~~al~~~~~e~~~~~~~~~~~-~~~~~~~~~ 79 (258)
+||+++|+|++||+||.+|+.++++.|+++++||+......+|+..++++.++.++++++...+.+.+++ +..++|+++
T Consensus 66 ~a~~~~w~f~~DD~~D~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~~~~~~~ 145 (270)
T PF03936_consen 66 AADWMAWLFIFDDFFDDGGSAEELEALTDAVERWDPNSGDPLPDPDKPLFRALADIWNRIAARMSPAQRRRDQIKRFRNS 145 (270)
T ss_dssp HHHHHHHHHHHHHHHHTTSHHHHHHHHHHHHHHTSSGGGGGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHhhchheeeeeeccccccchHHHHHHHHHHhcccccccccccchhHHHHHHHHHHHHHHHHHhhhhhcccHHhhHHHHH
Confidence 3789999999999999999999999999999999988888999999999999999999999888765432 356789999
Q ss_pred HHHHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhHHHHhcCcc
Q 025080 80 MQELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVICRLRNDIV 159 (258)
Q Consensus 80 ~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~ 159 (258)
|.+|++++.+|++|+..|++||++||+++|+.|+|+.+++.+.++++|..+++...+++...+.+.++++.+++|+|||+
T Consensus 146 ~~~~~~~~~~e~~~~~~~~~ps~eeYl~~R~~t~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~NDl~ 225 (270)
T PF03936_consen 146 WREYLNAYLWEARWRERGRIPSLEEYLEMRRHTSGVYPCLALIEFALEFALGELPPEVLEHPPMLRRLAADIIRLVNDLY 225 (270)
T ss_dssp HHHHHHHHHHHHHHHHTTS--SHHHHHHHHHHHTSHHHHHHHHHHHCSSCHTHHHHHHHHTTHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhccCCCCCHHHHHHhccccccccHHHHHHHHhCCCccccccHHHHHhchHHHHHHHHHHHHhcccc
Confidence 99999999999999999999999999999999999999999999999776776666666667779999999999999999
Q ss_pred chHHHhhcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHH
Q 025080 160 SQQFEQKRGHIASGVECYIKQYGVSAEEVVTVFTEEVENAWKDMN 204 (258)
Q Consensus 160 S~~kE~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ln 204 (258)
||+||+++|+.+|.|.|+|+++|+|.|+|++++.+++++++++||
T Consensus 226 S~~KE~~~g~~~N~v~~l~~~~~~s~e~A~~~v~~~~~~~~~efn 270 (270)
T PF03936_consen 226 SYKKEIARGDVHNLVVVLMNEHGLSLEEAVDEVAEMINECIREFN 270 (270)
T ss_dssp HHHHHHHTTSCCSHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhcchhhcccccHHHHhhhhcCCCHHHHHHHHHHHHHHHHHhcC
Confidence 999999999999999999999999999999999999999999998
No 5
>PLN02592 ent-copalyl diphosphate synthase
Probab=100.00 E-value=2.5e-38 Score=309.16 Aligned_cols=216 Identities=16% Similarity=0.127 Sum_probs=191.9
Q ss_pred CceeeeehheeccccCCCCCHHHHHHHHHHHH--------hccCcccCCCCh------hHHHHHHHHHHHHHHHHHHHHH
Q 025080 1 MTKTIYTASIIDDTFDAYGFFEELKLLAEAVQ--------RWDIGAMDILPE------YMKVLYKALLDTFNEIEQDLAK 66 (258)
Q Consensus 1 ~aK~~~~~~~~DD~~D~~gt~eel~~~~~ai~--------rWd~~~~~~lp~------~~k~~~~al~~~~~e~~~~~~~ 66 (258)
+||.+++++++||+||+|||+|||+.||++|+ |||.++.++||+ |||+||.+|+++.||++.++.+
T Consensus 567 ~aK~~~LitviDD~fD~yGt~eEl~~ft~~v~~~~~~~~~rWd~~~~~~lp~~~~~~~~mki~f~aLy~tineia~~a~~ 646 (800)
T PLN02592 567 WAKTTVLVEAISSYFNKETSSKQRRAFLHEFGYGYKINGRRSDHHFNDRNMRRSGSVKTGEELVGLLLGTLNQLSLDALE 646 (800)
T ss_pred HHHHHHHHHhhcccccCCCCHHHHHHHHHHHHhcccccccccCchhhhcccccccchhHHHHHHHHHHHHHHHHHHHHHH
Confidence 48999999999999999999999999999997 899999999988 9999999999999999999999
Q ss_pred hCCCCcccchHHHHHHHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHh-hcCCCCChhhhhhccCchhHH
Q 025080 67 EGRSSYLPYGKEKMQELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFL-GMCDVANKEAFEWISKDPKIS 145 (258)
Q Consensus 67 ~~~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~-~~g~~l~~e~~~~~~~~~~l~ 145 (258)
.||+++.++++++|.++++ +|..+|+ +|+|...++..+++ .+|..+|+++++ +|++.
T Consensus 647 ~qGr~v~~~L~~~W~~l~~------~w~~~g~------------~s~~~~~ilv~~~~l~~g~~lsee~l~----~~~~~ 704 (800)
T PLN02592 647 AHGRDISHLLRHAWEMWLL------KWLLEGD------------GRQGEAELLVKTINLTAGRSLSEELLA----HPQYE 704 (800)
T ss_pred HhCccHHHHHHHHHHHHHH------HHHhcCc------------eeccchhhHHHHHHHhcCCCCCHHHcc----chhHH
Confidence 9999999999999999999 5666665 34566656666666 569999998886 58899
Q ss_pred HHHHhHHHHhcCccchHHHhhcCCcchhHHHHHhhCC-CCHHHHHHHHHHHHHHHHHHHHHhhcC-C-CCCcHHHHHHHH
Q 025080 146 TASSVICRLRNDIVSQQFEQKRGHIASGVECYIKQYG-VSAEEVVTVFTEEVENAWKDMNEEFLK-P-TAFPVALIERPF 222 (258)
Q Consensus 146 ~~~~~i~rL~NDi~S~~kE~~~g~~~n~V~~ym~e~g-~s~eeA~~~i~~~i~~~~k~ln~~~l~-~-~~~p~~~~~~~~ 222 (258)
+.++.+.||+||++|+++|... .| +|+ +|.+++.+.|+.++++|.+.+++ . +.+|++||++||
T Consensus 705 ~l~~li~Rl~nDl~t~~~e~~~-------------~~~~~~-~a~~~~~~~ie~~~~eL~~lvl~~~~~~vp~~cK~~f~ 770 (800)
T PLN02592 705 QLAQLTNRICYQLGHYKKNKVH-------------INTYNP-EEKSKTTPSIESDMQELVQLVLQNSSDDIDPVIKQTFL 770 (800)
T ss_pred HHHHHHHHHHHhhhHHhhhccc-------------CCcccH-HHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHH
Confidence 9999999999999999998841 33 455 89999999999999999999997 3 569999999999
Q ss_pred hhhhhhhhhhccCCCCCCcHHHHHHHHhhcccccC
Q 025080 223 NIARVIEFLNKKGDWYTHSHAIKDQIAAVLRDPVT 257 (258)
Q Consensus 223 n~~R~~~~~Y~~~D~~t~~~~~~~~i~~l~~~p~~ 257 (258)
+++| +||.. ||+.|.+|++||.+++++||.
T Consensus 771 ~~~k---~fy~~--~~~~~~~~~~~i~~vl~epv~ 800 (800)
T PLN02592 771 MVAK---SFYYA--AYCDPGTINYHIAKVLFERVA 800 (800)
T ss_pred HHHH---HHHHh--hcCCHHHHHHHHHHHhCCCCC
Confidence 9999 46666 999999999999999999984
No 6
>cd00687 Terpene_cyclase_nonplant_C1 Non-plant Terpene Cyclases, Class 1. This CD includes terpenoid cyclases such as pentalenene synthase and aristolochene synthase which, using an all-trans pathway, catalyze the ionization of farnesyl diphosphate, followed by the formation of a macrocyclic intermediate by bond formation between C1 with either C10 (aristolochene synthase) or C11 (pentalenene synthase), resulting in production of tricyclic hydrocarbon pentalenene or bicyclic hydrocarbon aristolochene. As with other enzymes with the 'terpenoid synthase fold', they have two conserved metal binding motifs, proposed to coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP to the enzymes. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function in the monomeric form and are found in
Probab=100.00 E-value=4.7e-35 Score=261.69 Aligned_cols=202 Identities=16% Similarity=0.049 Sum_probs=180.6
Q ss_pred ceeeeehheeccccCCC-CCHHHHHHHHHHHHhccCcccCCCChhHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHH
Q 025080 2 TKTIYTASIIDDTFDAY-GFFEELKLLAEAVQRWDIGAMDILPEYMKVLYKALLDTFNEIEQDLAKEGRSSYLPYGKEKM 80 (258)
Q Consensus 2 aK~~~~~~~~DD~~D~~-gt~eel~~~~~ai~rWd~~~~~~lp~~~k~~~~al~~~~~e~~~~~~~~~~~~~~~~~~~~~ 80 (258)
++++.|+|++||+||.. +++++++.+++.+.++.......-|....++..++.+++.++...+.. ...++|++.|
T Consensus 63 ~~~~~w~f~~DD~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~d~~~r~~~~~~~----~~~~r~~~~~ 138 (303)
T cd00687 63 ADLMAWLFVFDDLLDRDQKSPEDGEAGVTRLLDILRGDGLDSPDDATPLEFGLADLWRRTLARMSA----EWFNRFAHYT 138 (303)
T ss_pred HHHHHHHHHhcccCCccccCHHHHHHHHHHHHhccCCCCCCCCCCCCHHHHHHHHHHHHhccCCCH----HHHHHHHHHH
Confidence 57889999999999987 599999999999988655422222578889999999999999876532 3457899999
Q ss_pred HHHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhHHHHhcCccc
Q 025080 81 QELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVICRLRNDIVS 160 (258)
Q Consensus 81 ~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S 160 (258)
.+|+.++++|++|+.+|++||++||+++|+.|+|+.+++.++++++|..+|+++.+. +...++.++++.+++|+|||+|
T Consensus 139 ~~~~~a~~~e~~~~~~~~~psl~eYl~~R~~~~g~~~~~~l~~~~~g~~lp~~~~~~-~~~~~l~~~~~~~~~l~NDl~S 217 (303)
T cd00687 139 EDYFDAYIWEGKNRLNGHVPDVAEYLEMRRFNIGADPCLGLSEFIGGPEVPAAVRLD-PVMRALEALASDAIALVNDIYS 217 (303)
T ss_pred HHHHHHHHHHHHHHhcCCCcCHHHHHHHhhhcccccccHHHHHHhcCCCCCHHHHhC-hHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999999988877 5667799999999999999999
Q ss_pred hHHHh-hcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhhc
Q 025080 161 QQFEQ-KRGHIASGVECYIKQYGVSAEEVVTVFTEEVENAWKDMNEEFL 208 (258)
Q Consensus 161 ~~kE~-~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ln~~~l 208 (258)
|+||+ +.|+.+|+|.|+|+++|+|.|+|++++.++++++++++.+.--
T Consensus 218 ~~KE~~~~g~~~N~V~vl~~~~g~s~~eA~~~~~~~~~~~~~~f~~~~~ 266 (303)
T cd00687 218 YEKEIKANGEVHNLVKVLAEEHGLSLEEAISVVRDMHNERITQFEELEA 266 (303)
T ss_pred hHHHHHhCCccchHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999 8999999999999999999999999999999999988876553
No 7
>PLN02150 terpene synthase/cyclase family protein
Probab=100.00 E-value=9.3e-35 Score=216.77 Aligned_cols=94 Identities=34% Similarity=0.629 Sum_probs=91.3
Q ss_pred hhcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHhhhhhhhhh-hccCCCCCCc-H
Q 025080 165 QKRGHIASGVECYIKQYGVSAEEVVTVFTEEVENAWKDMNEEFLKPTAFPVALIERPFNIARVIEFL-NKKGDWYTHS-H 242 (258)
Q Consensus 165 ~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ln~~~l~~~~~p~~~~~~~~n~~R~~~~~-Y~~~D~~t~~-~ 242 (258)
++|||++|+|+|||||||+|+|||+++++++|+++||++|+|+|+++++|.+++++++|+||+++++ |+++||||.+ .
T Consensus 1 ~~rg~vaSsIeCYMke~g~seeeA~~~i~~li~~~WK~iN~e~l~~~~~p~~~~~~~~NlaR~~~~~~Y~~~Dg~t~~~~ 80 (96)
T PLN02150 1 MRRGEVANGVNCYMKQHGVTKEEAVSELKKMIRDNYKIVMEEFLTIKDVPRPVLVRCLNLARLIDVYCYNEGDGFTYPHG 80 (96)
T ss_pred CCCCcchHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHhheecCCCCCCCCcH
Confidence 5799999999999999999999999999999999999999999999999999999999999999999 9999999988 7
Q ss_pred HHHHHHHhhcccccCC
Q 025080 243 AIKDQIAAVLRDPVTI 258 (258)
Q Consensus 243 ~~~~~i~~l~~~p~~~ 258 (258)
.+|++|++||++||++
T Consensus 81 ~~K~~I~sLlv~pi~i 96 (96)
T PLN02150 81 KLKDLITSLFFHPLPL 96 (96)
T ss_pred HHHHHHHHHhccCCCC
Confidence 8999999999999986
No 8
>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1. Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoter
Probab=99.86 E-value=4.2e-22 Score=168.87 Aligned_cols=211 Identities=27% Similarity=0.324 Sum_probs=170.9
Q ss_pred ceeeeehheeccccCCCCCHHHHHHHHHHHHhccCcccCCCChhHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHHH
Q 025080 2 TKTIYTASIIDDTFDAYGFFEELKLLAEAVQRWDIGAMDILPEYMKVLYKALLDTFNEIEQDLAKEGRSSYLPYGKEKMQ 81 (258)
Q Consensus 2 aK~~~~~~~~DD~~D~~gt~eel~~~~~ai~rWd~~~~~~lp~~~k~~~~al~~~~~e~~~~~~~~~~~~~~~~~~~~~~ 81 (258)
+++..|.+++||++|..++..+.......+ .....|..+.+....+.+.++++..... .....++.+.|.
T Consensus 20 ~~~~~~~~~~DDi~D~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~ 89 (243)
T cd00385 20 EKLHAASLVHDDIVDDSGTRRGLPTAHLAV------AIDGLPEAILAGDLLLADAFEELAREGS----PEALEILAEALL 89 (243)
T ss_pred HHHHHHHHHHhhcccCCCCCCCchhhhhhH------HhcCchHHHHHHHHHHHHHHHHHHhCCC----HHHHHHHHHHHH
Confidence 567789999999999888766665554433 2345677888888999999999875422 234678999999
Q ss_pred HHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhHHHHhcCccch
Q 025080 82 ELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVICRLRNDIVSQ 161 (258)
Q Consensus 82 ~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~ 161 (258)
+++.++.+|+.|+.. +.||++||++++..++ +.++..++..+++...|+ ..+.+...++...++.+.+|.||+.|+
T Consensus 90 ~~~~g~~~d~~~~~~-~~~t~~ey~~~~~~~t-~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~g~~~ql~nDl~~~ 165 (243)
T cd00385 90 DLLEGQLLDLKWRRE-YVPTLEEYLEYCRYKT-AGLVGALCLLGAGLSGGE--AELLEALRKLGRALGLAFQLTNDLLDY 165 (243)
T ss_pred HHHHHHHHHHHhccC-CCCCHHHHHHHHHHhH-HHHHHHHHHHHHHHhCCC--HHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999877 8999999999999998 455556666666666665 333355677889999999999999999
Q ss_pred HHHhhcC-CcchhHHHHHhhCCC------------CHHHHHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHhhhh
Q 025080 162 QFEQKRG-HIASGVECYIKQYGV------------SAEEVVTVFTEEVENAWKDMNEEFLKPTAFPVALIERPFNIAR 226 (258)
Q Consensus 162 ~kE~~~g-~~~n~V~~ym~e~g~------------s~eeA~~~i~~~i~~~~k~ln~~~l~~~~~p~~~~~~~~n~~R 226 (258)
.+|.++| +..|++.++|+++|+ +.++|.+++.++++++++++++........+..+++.+.+++|
T Consensus 166 ~~e~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (243)
T cd00385 166 EGDAERGEGKCTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKLAEEALKELNELILSLPDVPRALLALALNLYR 243 (243)
T ss_pred cCCHHHhCCchHHHHHHHHHhCChhhHHHHHHHCChHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhC
Confidence 9999986 678999999999999 8899999999999999999998777633456778888777654
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=98.36 E-value=9.1e-06 Score=72.90 Aligned_cols=182 Identities=16% Similarity=0.064 Sum_probs=116.0
Q ss_pred eeehheeccccCCCCCHHHHHHHHHHHHhccCcccCCCChhHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHHHHHH
Q 025080 5 IYTASIIDDTFDAYGFFEELKLLAEAVQRWDIGAMDILPEYMKVLYKALLDTFNEIEQDLAKEGRSSYLPYGKEKMQELV 84 (258)
Q Consensus 5 ~~~~~~~DD~~D~~gt~eel~~~~~ai~rWd~~~~~~lp~~~k~~~~al~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (258)
.+.++++||.-|... +.++.|.+-+.. ..... .|+...+.+.+..+.+. -|+++-.-+.++.-+++
T Consensus 93 ~tY~~~lDD~~~e~~--~~m~~f~~dL~~---G~~qk-----hP~l~~v~~~l~~~lr~----fGpF~s~~IikSTLdFv 158 (357)
T cd00686 93 YTYTLVLDDSKDDPY--PTMVNYFDDLQA---GREQA-----HPWWALVNEHFPNVLRH----FGPFCSLNLIRSTLDFF 158 (357)
T ss_pred HheeeEecccccccc--hHHHHHHHHHhc---CCCCC-----CcHHHHHHHHHHHHHHH----hhhhhHHHHHHHHHHHH
Confidence 456789999977554 667777776663 11111 13333333333333322 24444556777788899
Q ss_pred HHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHH---HHhHHHHhcCccch
Q 025080 85 QMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTA---SSVICRLRNDIVSQ 161 (258)
Q Consensus 85 ~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~---~~~i~rL~NDi~S~ 161 (258)
.+..-|... -+.-|.-.+|-...+.=+|..=..+...+ |++.+.-...+..+..+ ....+-++|||.||
T Consensus 159 ~g~~iEq~n--f~~~p~A~~fP~ylR~ksGl~E~yA~FiF------Pk~~FpE~~~~~qi~~AIp~~~~~i~~~NDILSF 230 (357)
T cd00686 159 EGCWIEQYN--FGGFPGSHDYPQFLRRMNGLGHCVGASLW------PKEQFNERSLFLEITSAIAQMENWMVWVNDLMSF 230 (357)
T ss_pred HHHHHhhhc--cCCCCCCcccchHHHhccCCcceeEEEec------chhhCchHhhHHHhhHHHHHHHHHHHhhhhhhhe
Confidence 999999763 34477777787777777776655443322 44333222222333333 33456699999999
Q ss_pred HHHhhc-CCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhhcC
Q 025080 162 QFEQKR-GHIASGVECYIKQYGVSAEEVVTVFTEEVENAWKDMNEEFLK 209 (258)
Q Consensus 162 ~kE~~~-g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ln~~~l~ 209 (258)
=||.-. ++-.|.|.-|.+.+|+|..+|+..+.+-.-.+-+++.+- |.
T Consensus 231 YKEe~~~~E~~n~V~Nya~~~GiS~~eAL~~lt~dTv~~s~rv~~V-Ls 278 (357)
T cd00686 231 YKEFDDERDQISLVKNYVVSDEISLHEALEKLTQDTLHSSKQMVAV-FS 278 (357)
T ss_pred ehhhcccccccchHHHhhhhcCCCHHHHHHHHHHHHHHHHHHHHHH-hc
Confidence 999854 556788888888899999999998888777777776554 44
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=98.26 E-value=4.4e-06 Score=75.98 Aligned_cols=181 Identities=13% Similarity=0.045 Sum_probs=109.1
Q ss_pred eeehheeccccCCCCCHHHHHHHHHHHHhccCcccCCCChhHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHHHHHH
Q 025080 5 IYTASIIDDTFDAYGFFEELKLLAEAVQRWDIGAMDILPEYMKVLYKALLDTFNEIEQDLAKEGRSSYLPYGKEKMQELV 84 (258)
Q Consensus 5 ~~~~~~~DD~~D~~gt~eel~~~~~ai~rWd~~~~~~lp~~~k~~~~al~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (258)
.++++.+||.++.. .+++..|.+.+-. ++-++ .++...+.+.+.++ .+.-++.+-+-+..+.-+++
T Consensus 93 T~yvi~iDD~~~~~--~~~l~~F~~~l~~------Gq~Q~--~p~L~~~~~~L~~~----~~~fgpf~anmI~~STLdFi 158 (376)
T PF06330_consen 93 TTYVIIIDDSSQEP--SDDLRTFHQRLIL------GQPQK--HPLLDGFASLLREM----WRHFGPFCANMIVKSTLDFI 158 (376)
T ss_dssp HHHHHHHTT--S-S--HHHHTTHHHHHHH------T---S--SHHHHHHHHHHHHH----HTTS-HHHHHHHHHHHHHHH
T ss_pred HHHHHhcccccccc--cHHHHHHHHHHhc------CCCCC--CHHHHHHHHHHHHH----HHHcchHHHHHHHHHHHHHH
Confidence 46788999997766 4788888776653 11111 13444444444433 33344455667778888999
Q ss_pred HHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchh---HHHHHHhHHHHhcCccch
Q 025080 85 QMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPK---ISTASSVICRLRNDIVSQ 161 (258)
Q Consensus 85 ~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~---l~~~~~~i~rL~NDi~S~ 161 (258)
.+..-|++.. +-.|.-..|-...+.=+|+..+.+...+ -....|+. ..+.. .+--....+-++|||.||
T Consensus 159 ~g~~LE~~~f--~~~p~A~~FP~fLR~ktGlsEaYA~FiF-Pk~~fpe~-----~~~~~y~~AIpdl~~fi~~~NDILSF 230 (376)
T PF06330_consen 159 NGCWLEQKNF--HGSPGAPDFPDFLRRKTGLSEAYAFFIF-PKALFPEV-----EYFIQYTPAIPDLMRFINYVNDILSF 230 (376)
T ss_dssp HHHHHHTTT------TT-TTHHHHHHHHHH-HHHHHHHT---TTTS-TT-----TTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhhcccC--CCCCCCccccHHHHhccCcchhheeeec-ccccCChH-----HHHHHHHHHHHHHHHHHHhhhhHHHH
Confidence 9999887642 3345555566666666677666555433 12222321 22233 334455566799999999
Q ss_pred HHHhh-cCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 025080 162 QFEQK-RGHIASGVECYIKQYGVSAEEVVTVFTEEVENAWKDMNEEF 207 (258)
Q Consensus 162 ~kE~~-~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ln~~~ 207 (258)
=||.- .|+..|.|.-+-.-+|+|.-+|+..+.+-.-++.+++.+-.
T Consensus 231 YKE~l~a~E~~NyI~n~A~~~g~S~~eaL~~l~~eti~a~~rv~~vL 277 (376)
T PF06330_consen 231 YKEELVAGETGNYIHNRARVHGVSILEALRELTDETIEAVERVRRVL 277 (376)
T ss_dssp HHHHTTSSSSSSHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHhhcccccccchhhhhhhccCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99987 78889999888888899999999998777777766655543
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=94.21 E-value=0.56 Score=39.95 Aligned_cols=117 Identities=19% Similarity=0.159 Sum_probs=75.4
Q ss_pred ccchHHHHHHHHHHHHHHHHHhhCCCCCChhhhhccccc-cccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhH
Q 025080 73 LPYGKEKMQELVQMYFVQAKWFSEGYVPTWDEYYPVGLV-SCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVI 151 (258)
Q Consensus 73 ~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~-s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i 151 (258)
...+.+.+..++.+...+..|... ..||.++|.+.-.. |++..-..+......+. -+++..+. ..++.+..+..
T Consensus 87 ~~~~~~~~~~~~~Gq~~Dl~~~~~-~~~t~~~y~~~~~~Kta~l~~~~~~~~~~~~~-~~~~~~~~---~~~~~~~lG~a 161 (236)
T cd00867 87 LELFAEALRELLEGQALDLEFERD-TYETLDEYLEYCRYKTAGLVGLLCLLGAGLSG-ADDEQAEA---LKDYGRALGLA 161 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHhccHHHHHHHHHHHHHHcC-cCHHHHHH---HHHHHHHHHHH
Confidence 445677788999999999888654 57999999999887 66654333322222222 22222322 25567888899
Q ss_pred HHHhcCccchHHHh----------hcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHH
Q 025080 152 CRLRNDIVSQQFEQ----------KRGHIASGVECYIKQYGVSAEEVVTVFTEEVENAWKDMNE 205 (258)
Q Consensus 152 ~rL~NDi~S~~kE~----------~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ln~ 205 (258)
..+.||+..+.... ++|.. +...+++ .+.+.+..+++++.+..
T Consensus 162 ~Qi~dd~~D~~~d~~~~gk~~~D~~~gr~-tlp~~~~----------~~~~~~~~~~~~~~~~~ 214 (236)
T cd00867 162 FQLTDDLLDVFGDAEELGKVGSDLREGRI-TLPVILA----------RERAAEYAEEAYAALEA 214 (236)
T ss_pred HHHHHHhccccCChHHHCccHHHHHcCCc-hHHHHHH----------HHHHHHHHHHHHHHHHh
Confidence 99999999886544 45554 5555555 55566666666655543
No 12
>PF00494 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR002060 Squalene synthase 2.5.1.21 from EC (farnesyl-diphosphate farnesyltransferase) (SQS) and Phytoene synthase 2.5.1.32 from EC (PSY) share a number of functional similarities. These similarities are also reflected at the level of their primary structure [, , ]. In particular three well conserved regions are shared by SQS and PSY; they could be involved in substrate binding and/or the catalytic mechanism. SQS catalyzes the conversion of two molecules of farnesyl diphosphate (FPP) into squalene. It is the first committed step in the cholesterol biosynthetic pathway. The reaction carried out by SQS is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of FPP to form presqualene diphosphate; this intermediate is then rearranged in a NADP-dependent reduction, to form squalene: 2 FPP -> presqualene diphosphate + NADP -> squalene SQS is found in eukaryotes. In yeast it is encoded by the ERG9 gene, in mammals by the FDFT1 gene. SQS seems to be membrane-bound. PSY catalyzes the conversion of two molecules of geranylgeranyl diphosphate (GGPP) into phytoene. It is the second step in the biosynthesis of carotenoids from isopentenyl diphosphate. The reaction carried out by PSY is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of GGPP to form prephytoene diphosphate; this intermediate is then rearranged to form phytoene. 2 GGPP -> prephytoene diphosphate -> phytoene PSY is found in all organisms that synthesize carotenoids: plants and photosynthetic bacteria as well as some non- photosynthetic bacteria and fungi. In bacteria PSY is encoded by the gene crtB. In plants PSY is localized in the chloroplast.; GO: 0016740 transferase activity, 0009058 biosynthetic process; PDB: 3NRI_A 3NPR_A 2ZCR_A 2ZCP_B 4F6V_A 4EA0_A 3ACW_A 4F6X_A 3VJE_B 3ACX_A ....
Probab=91.98 E-value=0.71 Score=40.26 Aligned_cols=157 Identities=19% Similarity=0.174 Sum_probs=83.2
Q ss_pred hheeccccCCCCCH----HHHHHHHHHHHhccCcccCCCChhHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHHHHH
Q 025080 8 ASIIDDTFDAYGFF----EELKLLAEAVQRWDIGAMDILPEYMKVLYKALLDTFNEIEQDLAKEGRSSYLPYGKEKMQEL 83 (258)
Q Consensus 8 ~~~~DD~~D~~gt~----eel~~~~~ai~rWd~~~~~~lp~~~k~~~~al~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~ 83 (258)
.-.+||+-|....+ ..|+-+-+++.+.-.+..+..+....++..++..+..... .-++.+.++
T Consensus 30 ~r~~d~i~D~~~~~~~~~~~L~~w~~~l~~~~~~~~~~~~~~~~pv~~~l~~~~~~~~-------------l~~~~l~~l 96 (267)
T PF00494_consen 30 CRELDDIVDEPSDPEEARARLQWWRDALNSIFASYEDSLPEPSHPVARALADLVRRYG-------------LPREPLLEL 96 (267)
T ss_dssp HHHHHHHHHCTSS-HSCHHHHHHHHHHHHHHHH-TSTHHHSSHHHHHHHHHHHHCCSH-------------HHHHHHHHH
T ss_pred HHHHhhccccchhhHHHHHHHHHHHHHHHHHhhhhhhccCCCcCHHHHHHHHHHHHHh-------------hhHHHHHHH
Confidence 34567777765532 2344455555543222122334445566666666553322 234557778
Q ss_pred HHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCCh-hhhhhccCchhHHHHHHhHHHHhcCccchH
Q 025080 84 VQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANK-EAFEWISKDPKISTASSVICRLRNDIVSQQ 162 (258)
Q Consensus 84 ~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~-e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~ 162 (258)
+.++.+. .....++|++|+..+...++|....+.+..++.. -++ +.. +.....+..+-+.|=+....
T Consensus 97 i~~~~~d---l~~~~~~t~~~L~~Y~~~vag~vg~l~~~~~~~~--~~~~~~~-------~~a~~lG~alql~nilRd~~ 164 (267)
T PF00494_consen 97 IDGMEMD---LEFTPYETFADLERYCYYVAGSVGLLLLQLLGAH--DPDEAAR-------DAARALGRALQLTNILRDIP 164 (267)
T ss_dssp HHHHHHC---TT-S--SSHHHHHHHHHHHTHHHHHHHHHHHHSS--TSHHHHH-------HHHHHHHHHHHHHHHHHTHH
T ss_pred HHHhccc---ccCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccc--cchhhHH-------HHHHHHHHHHHHHHHHHHhH
Confidence 8887433 3335688999999998888887666665555432 122 122 23344455555555555555
Q ss_pred HH-hhcCCcchhHHHHHhhCCCCHHHHHH
Q 025080 163 FE-QKRGHIASGVECYIKQYGVSAEEVVT 190 (258)
Q Consensus 163 kE-~~~g~~~n~V~~ym~e~g~s~eeA~~ 190 (258)
.. ..+|.+-==- =.|.++|+|.++-.+
T Consensus 165 ~D~~~~gR~ylP~-d~l~~~gv~~~dl~~ 192 (267)
T PF00494_consen 165 EDALRRGRIYLPL-DDLRRFGVTPEDLLA 192 (267)
T ss_dssp HH-HHTT---S-H-HHHHHTTSSHHHHHH
T ss_pred HHHHhcccccCCc-hhHHHcCCCHHHHHh
Confidence 66 5666541111 256789999887543
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=90.44 E-value=8.7 Score=34.80 Aligned_cols=87 Identities=6% Similarity=0.014 Sum_probs=54.8
Q ss_pred cccchHHHHHHHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhH
Q 025080 72 YLPYGKEKMQELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVI 151 (258)
Q Consensus 72 ~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i 151 (258)
....+.+....++.+-+.+..+... ..+|.++|++.-..=+|.-+..++..-++--..+++..+.+ -++-......
T Consensus 134 ~~~~~~~~~~~~~~Gq~~~~~~~~~-~~~~~~~y~~~~~~KTa~L~~~~~~~ga~~ag~~~~~~~~l---~~~G~~lG~a 209 (322)
T TIGR02749 134 VVKLISKVITDFAEGEIKQGLNQFD-SDLSLEDYLEKSFYKTASLVAASSKAAAVLSDVPSQVANDL---YEYGKHLGLA 209 (322)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcccC-CCCCHHHHHHHHHccHHHHHHHHHHHHHHHcCcCHHHHHHH---HHHHHHHHHH
Confidence 4556667777888888777766433 35799999987655555444332221111122355444443 5567788889
Q ss_pred HHHhcCccchH
Q 025080 152 CRLRNDIVSQQ 162 (258)
Q Consensus 152 ~rL~NDi~S~~ 162 (258)
.-+.||+..+.
T Consensus 210 FQi~DDild~~ 220 (322)
T TIGR02749 210 FQVVDDILDFT 220 (322)
T ss_pred HHHHHHhccCC
Confidence 99999998875
No 14
>TIGR03465 HpnD squalene synthase HpnD. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated.
Probab=89.23 E-value=14 Score=32.22 Aligned_cols=135 Identities=13% Similarity=0.076 Sum_probs=68.6
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhHHHHhc
Q 025080 77 KEKMQELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVICRLRN 156 (258)
Q Consensus 77 ~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~N 156 (258)
++.+.+++.++.+.. .....+|++|+..+...++|.-..+++..+ |.. ++.. .......+...-|.|
T Consensus 84 ~~~~~~li~g~~~Dl---~~~~~~t~~dL~~Y~~~vAg~vg~l~~~ll--g~~-~~~~-------~~~a~~lG~Alqltn 150 (266)
T TIGR03465 84 QEDFLEVIDGMEMDL---EQTRYPDFAELDLYCDRVAGAVGRLSARIF--GAT-DART-------LEYAHHLGRALQLTN 150 (266)
T ss_pred HHHHHHHHHHHHHHc---CCCCCCCHHHHHHHHHHhHHHHHHHHHHHh--CCC-ChhH-------HHHHHHHHHHHHHHH
Confidence 355777777775333 345678999988887777766555444443 321 1111 122333344444444
Q ss_pred CccchHHHhhcCCcchhHHHHHhhCCCCHHH---------HHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHhhh
Q 025080 157 DIVSQQFEQKRGHIASGVECYIKQYGVSAEE---------VVTVFTEEVENAWKDMNEEFLKPTAFPVALIERPFNIA 225 (258)
Q Consensus 157 Di~S~~kE~~~g~~~n~V~~ym~e~g~s~ee---------A~~~i~~~i~~~~k~ln~~~l~~~~~p~~~~~~~~n~~ 225 (258)
=+.......++|.+- .=.=.|.++|+|.++ ...-+..+++.+...+.+..-.-..+|......++-.+
T Consensus 151 ilRdv~eD~~~gR~y-lP~~~l~~~gv~~~~l~~~~~~~~~~~~~~~l~~~A~~~l~~a~~~~~~~p~~~~~~~~~~~ 227 (266)
T TIGR03465 151 ILRDVGEDARRGRIY-LPAEELQRFGVPAADILEGRYSPALAALCRFQAERARAHYAEADALLPACDRRAQRAARAMA 227 (266)
T ss_pred HHHHhHHHHhCCCee-cCHHHHHHcCCCHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhCCHhhhHHHHHHH
Confidence 333334445677641 111245678998774 33444555555554444332222457764444444333
No 15
>PLN02890 geranyl diphosphate synthase
Probab=88.95 E-value=7.2 Score=36.79 Aligned_cols=89 Identities=9% Similarity=-0.017 Sum_probs=58.8
Q ss_pred CcccchHHHHHHHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHh
Q 025080 71 SYLPYGKEKMQELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSV 150 (258)
Q Consensus 71 ~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~ 150 (258)
.++..+.++...++.+-..+..|.. ...+|.++|++....-+|.-+..++..-++--..+++..+.+ -++-+....
T Consensus 227 ~~~~~~s~a~~~l~~Gq~ld~~~~~-~~~~s~~~Yl~~i~~KTa~Lf~~s~~~gAilaga~~~~~~~l---~~fG~~lGl 302 (422)
T PLN02890 227 EVVSLLATAVEHLVTGETMQITSSR-EQRRSMDYYMQKTYYKTASLISNSCKAVAILAGQTAEVAVLA---FEYGRNLGL 302 (422)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCcCHHHHHHH---HHHHHHHHH
Confidence 3566778888899999998988864 346899999987655555444333222111112355555443 456678888
Q ss_pred HHHHhcCccchHH
Q 025080 151 ICRLRNDIVSQQF 163 (258)
Q Consensus 151 i~rL~NDi~S~~k 163 (258)
..-+.||+..|.-
T Consensus 303 AFQI~DDiLD~~g 315 (422)
T PLN02890 303 AFQLIDDVLDFTG 315 (422)
T ss_pred HHHHHHHHHhhcC
Confidence 8899999998753
No 16
>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=88.69 E-value=3.8 Score=35.72 Aligned_cols=120 Identities=15% Similarity=0.064 Sum_probs=74.3
Q ss_pred cccchHHHHHHHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhH
Q 025080 72 YLPYGKEKMQELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVI 151 (258)
Q Consensus 72 ~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i 151 (258)
....+.+.+...+.+...+..|... ..||.++|++....-+|.....+....++--..+++..+. ..++-...+..
T Consensus 109 ~~~~~~~~~~~~~~GQ~~d~~~~~~-~~~~~~~y~~~~~~KT~~l~~~~~~~~a~l~~~~~~~~~~---l~~~g~~lG~a 184 (259)
T cd00685 109 ALELFSEAILELVEGQLLDLLSEYD-TDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEA---LKRFGRNLGLA 184 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCC-CCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHH---HHHHHHHHHHH
Confidence 4556677778888888888888654 5799999999987777766543332222111123443333 25677788888
Q ss_pred HHHhcCccchHHH-----------hhcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHH
Q 025080 152 CRLRNDIVSQQFE-----------QKRGHIASGVECYIKQYGVSAEEVVTVFTEEVENAWKDMNE 205 (258)
Q Consensus 152 ~rL~NDi~S~~kE-----------~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ln~ 205 (258)
.-+.||+..+... ...|.. |...++.. .+.+...++++++.+..
T Consensus 185 fQi~DD~ld~~~~~~~~gK~~~~Di~~gk~-T~~~~~~l---------~~~~~~~~~~a~~~l~~ 239 (259)
T cd00685 185 FQIQDDILDLFGDPETLGKPVGSDLREGKC-TLPVLLAL---------RELAREYEEKALEALKA 239 (259)
T ss_pred HHHHHHhhcccCChHHHCCCcchHHHcCCc-hHHHHHHH---------HHHHHHHHHHHHHHHHc
Confidence 8999998876532 223333 44444443 45566666767666553
No 17
>PLN02857 octaprenyl-diphosphate synthase
Probab=88.47 E-value=5.5 Score=37.50 Aligned_cols=87 Identities=11% Similarity=0.080 Sum_probs=54.7
Q ss_pred cccchHHHHHHHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhH
Q 025080 72 YLPYGKEKMQELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVI 151 (258)
Q Consensus 72 ~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i 151 (258)
.+..+.+...+++.+-+.+..+.. +.-+|.++|++....=+|.-+..++..-++--..+++..+.+ .++-+.....
T Consensus 228 ~~~~~s~~~~~l~~Gei~q~~~~~-~~~~s~~~Yl~~i~~KTa~L~~~a~~~gallaga~~~~~~~l---~~fG~~LGiA 303 (416)
T PLN02857 228 VIKLISQVIKDFASGEIKQASSLF-DCDVTLDEYLLKSYYKTASLIAASTKSAAIFSGVDSSVKEQM---YEYGKNLGLA 303 (416)
T ss_pred HHHHHHHHHHHHHhhHHHHHhccc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHHH---HHHHHHHHHH
Confidence 345566667777777777777654 445799999998665555444332211111112355544433 5567788888
Q ss_pred HHHhcCccchH
Q 025080 152 CRLRNDIVSQQ 162 (258)
Q Consensus 152 ~rL~NDi~S~~ 162 (258)
.-+.||+..+.
T Consensus 304 FQI~DDiLD~~ 314 (416)
T PLN02857 304 FQVVDDILDFT 314 (416)
T ss_pred HHHHHHHHhhc
Confidence 89999999875
No 18
>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=87.19 E-value=20 Score=32.44 Aligned_cols=86 Identities=13% Similarity=0.022 Sum_probs=55.2
Q ss_pred cccchHHHHHHHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhc-CCCCChhhhhhccCchhHHHHHHh
Q 025080 72 YLPYGKEKMQELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGM-CDVANKEAFEWISKDPKISTASSV 150 (258)
Q Consensus 72 ~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~-g~~l~~e~~~~~~~~~~l~~~~~~ 150 (258)
.+..+.++....+.+-..+..|.. +..+|.++|++.-..-+|.-+..++ ..|. --..+++..+.+ .++-+..+.
T Consensus 130 ~~~~~~~~~~~~~~Gq~~~~~~~~-~~~~~~~~Y~~~i~~KTa~L~~~~~-~~ga~~ag~~~~~~~~l---~~~g~~lG~ 204 (319)
T TIGR02748 130 AHQILSHTIVEVCRGEIEQIKDKY-NFDQNLRTYLRRIKRKTALLIAASC-QLGAIASGANEAIVKKL---YWFGYYVGM 204 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHcCCCHHHHHHH---HHHHHHHHH
Confidence 455677778888888888887753 3457999999887666665443322 2221 012244433332 456677888
Q ss_pred HHHHhcCccchH
Q 025080 151 ICRLRNDIVSQQ 162 (258)
Q Consensus 151 i~rL~NDi~S~~ 162 (258)
..-+.||+..+.
T Consensus 205 aFQI~DDilD~~ 216 (319)
T TIGR02748 205 SYQITDDILDFV 216 (319)
T ss_pred HHHHHHHHHHcc
Confidence 899999998775
No 19
>KOG1719 consensus Dual specificity phosphatase [Defense mechanisms]
Probab=83.61 E-value=1 Score=36.54 Aligned_cols=40 Identities=25% Similarity=0.380 Sum_probs=31.3
Q ss_pred hcCCcchhHHHHHhhC-CCCHHHHHHHHHHH------HHHHHHHHHH
Q 025080 166 KRGHIASGVECYIKQY-GVSAEEVVTVFTEE------VENAWKDMNE 205 (258)
Q Consensus 166 ~~g~~~n~V~~ym~e~-g~s~eeA~~~i~~~------i~~~~k~ln~ 205 (258)
.||..+..|.||+-++ |.|.++|++++++. ....|+.+++
T Consensus 119 GRtRSaTvV~cYLmq~~~wtpe~A~~~vr~iRp~VlL~~~Qw~~l~e 165 (183)
T KOG1719|consen 119 GRTRSATVVACYLMQHKNWTPEAAVEHVRKIRPRVLLRPAQWDVLKE 165 (183)
T ss_pred CCccchhhhhhhhhhhcCCCHHHHHHHHHhcCcceeecHHHHHHHHH
Confidence 4677789999998887 99999999999873 3455655554
No 20
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=82.68 E-value=23 Score=32.04 Aligned_cols=108 Identities=12% Similarity=0.070 Sum_probs=69.0
Q ss_pred cccchHHHHHHHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhH
Q 025080 72 YLPYGKEKMQELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVI 151 (258)
Q Consensus 72 ~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i 151 (258)
....+.+....++.+...+-.+.... +|.++|++.-..=+|.-...+...-++--..+++..+.+ ..+-+.....
T Consensus 135 ~~~~~~~~~~~~~~GQ~lDl~~~~~~--~t~e~y~~~i~~KTa~L~~~a~~~ga~la~~~~~~~~~l---~~~g~~lGla 209 (322)
T COG0142 135 AIKALAEAINGLCGGQALDLAFENKP--VTLEEYLRVIELKTAALFAAAAVLGAILAGADEELLEAL---EDYGRNLGLA 209 (322)
T ss_pred HHHHHHHHHHHHHHhHHHHHHccCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHH---HHHHHHhhHH
Confidence 35567777888888888888876555 999999999766666554433322221112234555543 5567888899
Q ss_pred HHHhcCccchHHHh-hcCCc---------chhHHHHHhhCCCC
Q 025080 152 CRLRNDIVSQQFEQ-KRGHI---------ASGVECYIKQYGVS 184 (258)
Q Consensus 152 ~rL~NDi~S~~kE~-~~g~~---------~n~V~~ym~e~g~s 184 (258)
.-+.|||..+.-+. .-|.. .+...++.-+++-.
T Consensus 210 FQi~DDiLD~~~d~~~lGK~~g~Dl~~gK~T~p~l~~l~~~~~ 252 (322)
T COG0142 210 FQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEKANE 252 (322)
T ss_pred HHHHHHhhcCCCChHHhCCCcchHHHcCCchHHHHHHHHcCch
Confidence 99999999887532 22221 36666676666433
No 21
>cd00683 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases, head-to-head. These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes
Probab=81.92 E-value=34 Score=29.75 Aligned_cols=184 Identities=17% Similarity=0.159 Sum_probs=91.1
Q ss_pred eeccccCCCCCH-----HHHHHHHHHHHhccCcccCCCChhHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHHHHHH
Q 025080 10 IIDDTFDAYGFF-----EELKLLAEAVQRWDIGAMDILPEYMKVLYKALLDTFNEIEQDLAKEGRSSYLPYGKEKMQELV 84 (258)
Q Consensus 10 ~~DD~~D~~gt~-----eel~~~~~ai~rWd~~~~~~lp~~~k~~~~al~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (258)
.+||+-|..... ..|+.+.+++++-... .-| -.++..++.++..+. + .-++.+.+++
T Consensus 38 ~~Ddi~D~~~~~~~~~~~~L~~w~~~l~~~~~~---~~~--~~pv~~al~~~~~~~--------~-----l~~~~~~~li 99 (265)
T cd00683 38 AADDIVDDPAAPPDEKLALLDAFRAELDAAYWG---GAP--THPVLRALADLARRY--------G-----IPREPFRDLL 99 (265)
T ss_pred HHHhhhhCCCCCchhHHHHHHHHHHHHHHHHcC---CCC--CChHHHHHHHHHHHc--------C-----CCHHHHHHHH
Confidence 478888865422 3344444444432111 111 136666666655421 1 2345677888
Q ss_pred HHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhHHHHhcCccchHHH
Q 025080 85 QMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVICRLRNDIVSQQFE 164 (258)
Q Consensus 85 ~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~kE 164 (258)
.++..... ....||++|.......+.|..-.+++..++.+ -+++. .+.....+...-|.|=+......
T Consensus 100 ~g~~~Dl~---~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~~~~--~~~~~-------~~~A~~lG~AlqltnilRdv~eD 167 (265)
T cd00683 100 AGMAMDLD---KRRYETLDELDEYCYYVAGVVGLMLLRVFGAS--SDEAA-------LERARALGLALQLTNILRDVGED 167 (265)
T ss_pred HHHHHhCC---CCCCCCHHHHHHHHHHhHHHHHHHHHHHhCCC--CChHH-------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 88864444 45678998877777766665544444444321 11111 12233334434444433333444
Q ss_pred hhcCCc--chhHHHHHhhCCCCHHHHH---------HHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHhhhh
Q 025080 165 QKRGHI--ASGVECYIKQYGVSAEEVV---------TVFTEEVENAWKDMNEEFLKPTAFPVALIERPFNIAR 226 (258)
Q Consensus 165 ~~~g~~--~n~V~~ym~e~g~s~eeA~---------~~i~~~i~~~~k~ln~~~l~~~~~p~~~~~~~~n~~R 226 (258)
.++|-+ +.- -|.++|+|.++-. .-+..+++.+.+.+....-.-..+|....-.++-++.
T Consensus 168 ~~~gR~YlP~d---~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~ 237 (265)
T cd00683 168 ARRGRIYLPRE---ELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAALPRRSRFCVRAAAM 237 (265)
T ss_pred HccCCCcCCHH---HHHHcCCCHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCCHhhHHHHHHHHH
Confidence 556653 222 3678899886632 3344455555444443332224577544444444433
No 22
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=81.20 E-value=42 Score=30.39 Aligned_cols=86 Identities=12% Similarity=-0.045 Sum_probs=55.2
Q ss_pred cccchHHHHHHHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhc-CCCCChhhhhhccCchhHHHHHHh
Q 025080 72 YLPYGKEKMQELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGM-CDVANKEAFEWISKDPKISTASSV 150 (258)
Q Consensus 72 ~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~-g~~l~~e~~~~~~~~~~l~~~~~~ 150 (258)
.+..+.++....+.+-..+..|.. +.-+|.++|++....-+|..+..++ ..+. --..+++..+. ..++-+..+.
T Consensus 131 ~~~~~~~~~~~~~~Gq~~d~~~~~-~~~~s~~~y~~~i~~KTa~lf~~~~-~~ga~lag~~~~~~~~---l~~~g~~lG~ 205 (323)
T PRK10888 131 VLEVMSEAVNVIAEGEVLQLMNVN-DPDITEENYMRVIYSKTARLFEAAA-QCSGILAGCTPEQEKG---LQDYGRYLGT 205 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHcCCCHHHHHH---HHHHHHHHHH
Confidence 455667777788888888877754 3458999999987666655543322 2221 11234443333 2456778888
Q ss_pred HHHHhcCccchH
Q 025080 151 ICRLRNDIVSQQ 162 (258)
Q Consensus 151 i~rL~NDi~S~~ 162 (258)
..-+.||+..+.
T Consensus 206 aFQi~DD~ld~~ 217 (323)
T PRK10888 206 AFQLIDDLLDYS 217 (323)
T ss_pred HHHHHHHhhccc
Confidence 889999998885
No 23
>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=80.36 E-value=1.9 Score=28.40 Aligned_cols=30 Identities=17% Similarity=0.338 Sum_probs=23.0
Q ss_pred CcchhHHHHHhhCCCCHHHHHHHHHHHHHH
Q 025080 169 HIASGVECYIKQYGVSAEEVVTVFTEEVEN 198 (258)
Q Consensus 169 ~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~ 198 (258)
-+.-++.++|..+|+|+++|.+.++..-.+
T Consensus 14 ~I~~AkgiLm~~~g~~e~~A~~~Lr~~Am~ 43 (56)
T PF03861_consen 14 VIEQAKGILMARYGLSEDEAYRLLRRQAMR 43 (56)
T ss_dssp HHHHHHHHHHHHHT--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence 456788899999999999999998876544
No 24
>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]
Probab=79.91 E-value=2.1 Score=35.82 Aligned_cols=50 Identities=16% Similarity=0.185 Sum_probs=35.5
Q ss_pred HhHHHHhcCccchHHHhhcC-CcchhHHHHHhhCCCCHHHHHHHHHHHHHH
Q 025080 149 SVICRLRNDIVSQQFEQKRG-HIASGVECYIKQYGVSAEEVVTVFTEEVEN 198 (258)
Q Consensus 149 ~~i~rL~NDi~S~~kE~~~g-~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~ 198 (258)
...-.|--++..+|+..+.- .+.-+=.++|+++|+|++||+++++++--+
T Consensus 125 ~~~~~L~~el~~~k~~L~~rK~ierAKglLM~~~g~sE~EAy~~lR~~AM~ 175 (194)
T COG3707 125 EERRALRRELAKLKDRLEERKVIERAKGLLMKRRGLSEEEAYKLLRRTAMD 175 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh
Confidence 33455666777777664433 234555689999999999999999987543
No 25
>PLN02632 phytoene synthase
Probab=78.36 E-value=53 Score=29.88 Aligned_cols=153 Identities=16% Similarity=0.192 Sum_probs=74.7
Q ss_pred hheeccccCCCCCH----HHHHHHHHHHHhccCcccCCCChhHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHHHHH
Q 025080 8 ASIIDDTFDAYGFF----EELKLLAEAVQRWDIGAMDILPEYMKVLYKALLDTFNEIEQDLAKEGRSSYLPYGKEKMQEL 83 (258)
Q Consensus 8 ~~~~DD~~D~~gt~----eel~~~~~ai~rWd~~~~~~lp~~~k~~~~al~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~ 83 (258)
.-.+||+=|..... ..|+.+-+.+++-- +.-|. .++..++.++..+.. --++.+.++
T Consensus 85 ~R~~DdI~D~~~~~~~~~~~L~~w~~~l~~~~----~g~~~--~pv~~aL~~~~~~~~-------------L~~~~~~~l 145 (334)
T PLN02632 85 CRRTDELVDGPNASHITPAALDRWEARLEDLF----DGRPY--DMLDAALADTVSKFP-------------LDIQPFRDM 145 (334)
T ss_pred HHHHhHHhcCCCCChhhHHHHHHHHHHHHHHh----CCCCC--ChHHHHHHHHHHHCC-------------CChHHHHHH
Confidence 34578888865432 23444444443311 11121 256666666554331 123456777
Q ss_pred HHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhHHHHhcCccchHH
Q 025080 84 VQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVICRLRNDIVSQQF 163 (258)
Q Consensus 84 ~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~k 163 (258)
+.++..... ....+|++|+..+...++|.--.+++..++.....+. ..++. .+.....+...-|.|=+.....
T Consensus 146 i~g~~~Dl~---~~~~~t~~eL~~Ycy~vAgtVG~l~l~vlg~~~~~~~-~~~~~---~~~A~~lG~AlQltNILRDv~e 218 (334)
T PLN02632 146 IEGMRMDLV---KSRYENFDELYLYCYYVAGTVGLMSVPVMGIAPESKA-STESV---YNAALALGIANQLTNILRDVGE 218 (334)
T ss_pred HHHHHHHhc---cCCCCCHHHHHHHHHHhhHHHHHHHHHHhCCCCcccc-chHHH---HHHHHHHHHHHHHHHHHHHHHH
Confidence 888754332 3467798888888776666555444444433221110 00111 1222233443444443333344
Q ss_pred HhhcCCcchhHHHHHhhCCCCHHH
Q 025080 164 EQKRGHIASGVECYIKQYGVSAEE 187 (258)
Q Consensus 164 E~~~g~~~n~V~~ym~e~g~s~ee 187 (258)
...+|.+- +=.=.|.++|+|.++
T Consensus 219 D~~~GRvY-LP~e~L~~~Gv~~ed 241 (334)
T PLN02632 219 DARRGRVY-LPQDELAQFGLTDED 241 (334)
T ss_pred HHhCCcee-CCHHHHHHcCCCHHH
Confidence 55677541 101246789999887
No 26
>CHL00151 preA prenyl transferase; Reviewed
Probab=77.45 E-value=47 Score=30.00 Aligned_cols=86 Identities=6% Similarity=-0.029 Sum_probs=52.0
Q ss_pred ccchHHHHHHHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhHH
Q 025080 73 LPYGKEKMQELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVIC 152 (258)
Q Consensus 73 ~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~ 152 (258)
...+.+....++.+-..+..|.. ..-+|.++|+..-..=+|.-+..++..-++--..+++..+. ..++-...+...
T Consensus 136 ~~~~~~~~~~l~~G~~~~~~~~~-~~~~~~~~yl~~i~~KTa~L~~~~~~~ga~lag~~~~~~~~---l~~~G~~lG~aF 211 (323)
T CHL00151 136 VKLISKVITDFAEGEIRQGLVQF-DTTLSILNYIEKSFYKTASLIAASCKAAALLSDADEKDHND---FYLYGKHLGLAF 211 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCC-CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHcCCCHHHHHH---HHHHHHHHHHHH
Confidence 44567777778888777766543 34578999999744444433332221111111234443333 255677888899
Q ss_pred HHhcCccchH
Q 025080 153 RLRNDIVSQQ 162 (258)
Q Consensus 153 rL~NDi~S~~ 162 (258)
-+.||+..+.
T Consensus 212 Qi~DDilD~~ 221 (323)
T CHL00151 212 QIIDDVLDIT 221 (323)
T ss_pred HHHHHHhhcc
Confidence 9999999875
No 27
>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=76.95 E-value=50 Score=28.82 Aligned_cols=147 Identities=20% Similarity=0.183 Sum_probs=72.1
Q ss_pred heeccccCCC-CCHHH----HHHHHHHHHhccCcccCCCChhHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHHHHH
Q 025080 9 SIIDDTFDAY-GFFEE----LKLLAEAVQRWDIGAMDILPEYMKVLYKALLDTFNEIEQDLAKEGRSSYLPYGKEKMQEL 83 (258)
Q Consensus 9 ~~~DD~~D~~-gt~ee----l~~~~~ai~rWd~~~~~~lp~~~k~~~~al~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~ 83 (258)
=.+||+-|.. +++++ |+.+-+.++.-. ..-| -.|+..++.++..+. + + =++.+.++
T Consensus 31 R~~Ddi~D~~~~~~~~~~~~L~~wr~~l~~~~----~g~~--~~pv~~aL~~~~~~~--------~---l--~~~~~~~l 91 (266)
T TIGR03464 31 RTADDIADEGDGSAEERLALLDDFRAELDAIY----SGEP--AAPVFVALARTVQRH--------G---L--PIEPFLDL 91 (266)
T ss_pred HHHHHhccCCCCChHHHHHHHHHHHHHHHHHh----CCCC--CChHHHHHHHHHHHc--------C---C--ChHHHHHH
Confidence 3578888874 44443 444444443211 1112 235666776666532 1 1 13456667
Q ss_pred HHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhHHHHhcCccchHH
Q 025080 84 VQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVICRLRNDIVSQQF 163 (258)
Q Consensus 84 ~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~k 163 (258)
+.++... ......+|++|...+...++|.--.+++..++.+. + +.. +.....+...-|.|=+.....
T Consensus 92 i~~~~~D---l~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~g~~~--~-~~~-------~~A~~lG~AlQltniLRDl~e 158 (266)
T TIGR03464 92 LDAFRQD---VVVTRYATWAELLDYCRYSANPVGRLVLDLYGASD--P-ENV-------ALSDAICTALQLINFWQDVGV 158 (266)
T ss_pred HHHHHHh---ccCCCCCCHHHHHHHHHHhHHHHHHHHHHHcCCCC--h-hHH-------HHHHHHHHHHHHHHHHHhhHH
Confidence 7776322 23455779998888887777766555544443221 1 111 112223333333332222233
Q ss_pred HhhcCCcchhHHHHHhhCCCCHHHH
Q 025080 164 EQKRGHIASGVECYIKQYGVSAEEV 188 (258)
Q Consensus 164 E~~~g~~~n~V~~ym~e~g~s~eeA 188 (258)
...+|.+- +=.=.|.++|+|.++-
T Consensus 159 D~~~gR~Y-LP~~~l~~~Gv~~edl 182 (266)
T TIGR03464 159 DYRKGRVY-LPRDDLARFGVSEEDL 182 (266)
T ss_pred HHhcCCcc-CCHHHHHHcCCCHHHH
Confidence 34456531 1012467899998763
No 28
>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=74.17 E-value=2.8 Score=23.78 Aligned_cols=18 Identities=39% Similarity=0.615 Sum_probs=14.7
Q ss_pred HHHhhCCCCHHHHHHHHH
Q 025080 176 CYIKQYGVSAEEVVTVFT 193 (258)
Q Consensus 176 ~ym~e~g~s~eeA~~~i~ 193 (258)
-|.++||+|.||....+.
T Consensus 9 rYV~eh~ls~ee~~~RL~ 26 (28)
T PF12368_consen 9 RYVKEHGLSEEEVAERLA 26 (28)
T ss_pred hhHHhcCCCHHHHHHHHH
Confidence 589999999999766554
No 29
>smart00400 ZnF_CHCC zinc finger.
Probab=59.98 E-value=11 Score=24.50 Aligned_cols=25 Identities=20% Similarity=0.126 Sum_probs=20.9
Q ss_pred CCcchhHHHHHhhCCCCHHHHHHHH
Q 025080 168 GHIASGVECYIKQYGVSAEEVVTVF 192 (258)
Q Consensus 168 g~~~n~V~~ym~e~g~s~eeA~~~i 192 (258)
|.-.|+|..+|+-.|+|-.||++.+
T Consensus 30 g~gGd~i~fv~~~~~~sf~eA~~~L 54 (55)
T smart00400 30 GAGGNVISFLMKYDKLSFVEAVKKL 54 (55)
T ss_pred CCCCCHHHHHHHHHCcCHHHHHHHh
Confidence 4445889999998899999999875
No 30
>PRK10581 geranyltranstransferase; Provisional
Probab=59.42 E-value=56 Score=29.26 Aligned_cols=111 Identities=11% Similarity=0.099 Sum_probs=66.1
Q ss_pred HHHHHHHHHHHHhhCCCCCChhhhhccccccccchhhHHHH--HhhcCCCCChhhhhhccCchhHHHHHHhHHHHhcCcc
Q 025080 82 ELVQMYFVQAKWFSEGYVPTWDEYYPVGLVSCGYFMLATNS--FLGMCDVANKEAFEWISKDPKISTASSVICRLRNDIV 159 (258)
Q Consensus 82 ~~~~~~~~Ea~w~~~~~~Ps~eEYl~~~~~s~g~~~~~~~~--~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~ 159 (258)
.++.+...+..|.. ..+|.++|++.-..=+|.-+..++. -+..|. -+++..+.+ .++-+......-+.||+.
T Consensus 153 ~l~~GQ~ld~~~~~--~~~~~~~y~~i~~~KTa~L~~~~~~~gailag~-~~~~~~~~l---~~~g~~lG~aFQI~DDil 226 (299)
T PRK10581 153 GMCGGQALDLEAEG--KQVPLDALERIHRHKTGALIRAAVRLGALSAGD-KGRRALPVL---DRYAESIGLAFQVQDDIL 226 (299)
T ss_pred hhhHhhHHHHhccC--CCCCHHHHHHHHHHhhHHHHHHHHHHHHHHcCC-CcHHHHHHH---HHHHHHHHHHHHHHHHHc
Confidence 46667766777743 4689999998755444433332221 111221 122333332 567788888999999999
Q ss_pred chHHH-----------hhcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHH
Q 025080 160 SQQFE-----------QKRGHIASGVECYIKQYGVSAEEVVTVFTEEVENAWKDMNE 205 (258)
Q Consensus 160 S~~kE-----------~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ln~ 205 (258)
.+... ...|.. +.+.++ ..+.|.+.+++.++++.+.+..
T Consensus 227 D~~g~~~~~GK~~g~Dl~~gk~-T~p~l~------~~e~a~~~a~~~~~~A~~~l~~ 276 (299)
T PRK10581 227 DVVGDTATLGKRQGADQQLGKS-TYPALL------GLEQARKKARDLIDDARQSLDQ 276 (299)
T ss_pred cccCChHHHCCCcchhhhcCCC-CHHHHH------HHHHHHHHHHHHHHHHHHHHHh
Confidence 87422 222333 444443 2467888888888888877664
No 31
>smart00463 SMR Small MutS-related domain.
Probab=58.20 E-value=14 Score=25.83 Aligned_cols=24 Identities=25% Similarity=0.252 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q 025080 181 YGVSAEEVVTVFTEEVENAWKDMN 204 (258)
Q Consensus 181 ~g~s~eeA~~~i~~~i~~~~k~ln 204 (258)
||++.++|+..+...++++++.-.
T Consensus 7 HG~~~~eA~~~l~~~l~~~~~~~~ 30 (80)
T smart00463 7 HGLTVEEALTALDKFLNNARLKGL 30 (80)
T ss_pred CCCCHHHHHHHHHHHHHHHHHcCC
Confidence 799999999999999999997643
No 32
>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=56.15 E-value=13 Score=26.17 Aligned_cols=27 Identities=22% Similarity=0.316 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 025080 181 YGVSAEEVVTVFTEEVENAWKDMNEEF 207 (258)
Q Consensus 181 ~g~s~eeA~~~i~~~i~~~~k~ln~~~ 207 (258)
||++.+||...+.+.++++++.-...+
T Consensus 4 HG~~~~eA~~~l~~~l~~~~~~~~~~~ 30 (83)
T PF01713_consen 4 HGLTVEEALRALEEFLDEARQRGIREL 30 (83)
T ss_dssp TTS-HHHHHHHHHHHHHHHHHTTHSEE
T ss_pred CCCcHHHHHHHHHHHHHHHHHcCCCEE
Confidence 799999999999999999997655444
No 33
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=54.61 E-value=28 Score=30.57 Aligned_cols=64 Identities=23% Similarity=0.192 Sum_probs=49.3
Q ss_pred chHHHhhcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHH----------HhhcCCCCCcHHHHHHHHhhhh
Q 025080 160 SQQFEQKRGHIASGVECYIKQYGVSAEEVVTVFTEEVENAWKDMN----------EEFLKPTAFPVALIERPFNIAR 226 (258)
Q Consensus 160 S~~kE~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ln----------~~~l~~~~~p~~~~~~~~n~~R 226 (258)
-|++||+ .++.+...+...|.+.++|..+++--+++.+-.+- .+.|.+.++|.-.+..+.++||
T Consensus 96 ~wk~~qk---a~klle~aaekl~~~~ee~~~~vg~~L~e~fG~~y~aFE~aa~~g~~~l~~~~~~~~~~~~l~e~a~ 169 (269)
T COG1093 96 EWKKEQK---ADKLLELAAEKLGKDLEEAYEEVGWKLEEEFGSLYDAFEAAAKEGGEVLDDEGVPEEWKEVLKEIAR 169 (269)
T ss_pred HHHHHHH---HHHHHHHHHHHhCCCHHHHHHHHhHHHHHHhCCHHHHHHHHHhcCCcccccCCCCHHHHHHHHHHHH
Confidence 3466665 35888888888899999999999988887775543 3344445788888999999887
No 34
>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=53.52 E-value=1.5e+02 Score=25.66 Aligned_cols=65 Identities=15% Similarity=0.210 Sum_probs=42.2
Q ss_pred CCCCChhhhhccccccccchhhHHHHHhhcCCCCChhhhhhccCchhHHHHHHhHHHHhcCccchHHH
Q 025080 97 GYVPTWDEYYPVGLVSCGYFMLATNSFLGMCDVANKEAFEWISKDPKISTASSVICRLRNDIVSQQFE 164 (258)
Q Consensus 97 ~~~Ps~eEYl~~~~~s~g~~~~~~~~~~~~g~~l~~e~~~~~~~~~~l~~~~~~i~rL~NDi~S~~kE 164 (258)
+..+|.++|++.-..-+|.-+..++..-++--..+++..+.+ .++-.......-+.||+..+...
T Consensus 130 ~~~~~~~~y~~i~~~KTg~l~~~~~~~ga~lag~~~~~~~~l---~~~g~~lG~afQi~DD~~d~~~~ 194 (260)
T PF00348_consen 130 DKDPTEEEYLEIIRLKTGSLFALACQLGAILAGADEEQIEAL---REFGRHLGIAFQIRDDLLDLFGD 194 (260)
T ss_dssp TSSTSHHHHHHHHHHHTHHHHHHHHHHHHHHTTSGHHHHHHH---HHHHHHHHHHHHHHHHHHHHHSH
T ss_pred cccccHHHHHHHHhhcchHHHHHHHHHHHHhccchhHHHHHH---HHHHHHHHHHHhhhhhhhhccCc
Confidence 448899999999877777664433322221112334444433 56778889999999999988753
No 35
>PF13060 DUF3921: Protein of unknown function (DUF3921)
Probab=52.81 E-value=57 Score=21.00 Aligned_cols=45 Identities=13% Similarity=0.239 Sum_probs=33.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHHHHHHHHHHHHH
Q 025080 45 YMKVLYKALLDTFNEIEQDLAKEGRSSYLPYGKEKMQELVQMYFVQA 91 (258)
Q Consensus 45 ~~k~~~~al~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ea 91 (258)
.|..+-.++..+++|++.++..+|- ..+-+.++-++|+.+.-.|.
T Consensus 5 qlsmiqkaih~tydelgkei~~~g~--~~d~i~kaqeeylsals~et 49 (58)
T PF13060_consen 5 QLSMIQKAIHRTYDELGKEIDLQGV--IADEIQKAQEEYLSALSHET 49 (58)
T ss_pred HHHHHHHHHHHhHHHHhHHhhhcch--HHHHHHHHHHHHHHHhhHHH
Confidence 3556778999999999999877553 45667777778887776654
No 36
>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=49.67 E-value=34 Score=22.18 Aligned_cols=44 Identities=18% Similarity=0.407 Sum_probs=29.4
Q ss_pred cCccchHHHhhcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHH
Q 025080 156 NDIVSQQFEQKRGHIASGVECYIKQYGVSAEEVVTVFTEEVENAWK 201 (258)
Q Consensus 156 NDi~S~~kE~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k 201 (258)
||+-+.-.|+..--+ -=|.-+| ..|+|.-||+..+...|.+..+
T Consensus 3 ~~lp~LtHeeQQ~Av-E~Iq~LM-aqGmSsgEAI~~VA~~iRe~~~ 46 (51)
T PF03701_consen 3 NDLPSLTHEEQQQAV-ERIQELM-AQGMSSGEAIAIVAQEIREEHQ 46 (51)
T ss_pred CCCCCCCHHHHHHHH-HHHHHHH-HhcccHHHHHHHHHHHHHHHHH
Confidence 566555555443222 2345577 4799999999999988887654
No 37
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=44.80 E-value=26 Score=27.17 Aligned_cols=23 Identities=30% Similarity=0.492 Sum_probs=18.7
Q ss_pred hhHHHHHhhCCCCHHHHHHHHHH
Q 025080 172 SGVECYIKQYGVSAEEVVTVFTE 194 (258)
Q Consensus 172 n~V~~ym~e~g~s~eeA~~~i~~ 194 (258)
-=|.+.|.|-|+|.++|++.+.+
T Consensus 86 eDIkLV~eQa~VsreeA~kAL~e 108 (122)
T COG1308 86 EDIKLVMEQAGVSREEAIKALEE 108 (122)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHH
Confidence 34788999999999999887654
No 38
>PTZ00393 protein tyrosine phosphatase; Provisional
Probab=44.55 E-value=23 Score=30.81 Aligned_cols=29 Identities=7% Similarity=0.242 Sum_probs=24.3
Q ss_pred cCCcchhHHHHHhhCCCCHHHHHHHHHHH
Q 025080 167 RGHIASGVECYIKQYGVSAEEVVTVFTEE 195 (258)
Q Consensus 167 ~g~~~n~V~~ym~e~g~s~eeA~~~i~~~ 195 (258)
.|-.+.++.+||-++|+|.++|++.++..
T Consensus 181 lGRTGtl~AayLI~~GmspeeAI~~VR~~ 209 (241)
T PTZ00393 181 LGRAPVLASIVLIEFGMDPIDAIVFIRDR 209 (241)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 34456888999999999999999999874
No 39
>PF00156 Pribosyltran: Phosphoribosyl transferase domain; InterPro: IPR000836 The name PRT comes from phosphoribosyltransferase (PRTase) enzymes, which carry out phosphoryl transfer reactions on 5-phosphoribosyl-alpha1-pyrophosphate PRPP, an activated form of ribose-5-phosphate. Members of Phosphoribosyltransferase (PRT) are catalytic and are regulatory proteins involved in nucleotide synthesis and salvage []. This includes a range of diverse phosphoribosyl transferase enzymes including adenine phosphoribosyltransferase (2.4.2.7 from EC); hypoxanthine-guanine-xanthine phosphoribosyltransferase; hypoxanthine phosphoribosyltransferase (2.4.2.8 from EC); ribose-phosphate pyrophosphokinase (2.7.6.1 from EC); amidophosphoribosyltransferase (2.4.2.14 from EC); orotate phosphoribosyltransferase (2.4.2.10 from EC);uracil phosphoribosyltransferase (2.4.2.9 from EC); and xanthine-guanine phosphoribosyltransferase (2.4.2.22 from EC). Not all PRT proteins are enzymes. For example, in some bacteria PRT proteins regulate the expression of purine and pyrimidine synthetic genes. Members of PRT are defined by the protein fold and by a short 13-residue sequence motif, The motif consists of four hydrophobic amino acids, two acidic amino acids and seven amino acids of variable character, usually including glycine and threonine. The motif has been predicted to be a PRPP-binding site in advance of structural information [, ]. Apart of this motif, different PRT proteins have a low level of sequence identity, less than 15%. The PRT sequence motif is only found in PRTases from the nucleotide synthesis and salvage pathways. Other PRTases, from the tryptophan, histidine and nicotinamide synthetic and salvage pathways, lack the PRT sequence motif and appear to be unrelated to each other and unrelated to the PRT family.; GO: 0009116 nucleoside metabolic process; PDB: 2JBH_A 1Y0B_D 2FXV_B 1GPH_1 1AO0_D 1ORO_B 1VCH_C 2WNS_A 2PRZ_B 2PS1_A ....
Probab=42.62 E-value=11 Score=28.37 Aligned_cols=21 Identities=33% Similarity=0.393 Sum_probs=16.8
Q ss_pred hheeccccCCCCCHHHHHHHH
Q 025080 8 ASIIDDTFDAYGFFEELKLLA 28 (258)
Q Consensus 8 ~~~~DD~~D~~gt~eel~~~~ 28 (258)
+.++||++|.++|+.++..+.
T Consensus 91 vliVDDvi~tG~Tl~~~~~~L 111 (125)
T PF00156_consen 91 VLIVDDVIDTGGTLKEAIELL 111 (125)
T ss_dssp EEEEEEEESSSHHHHHHHHHH
T ss_pred EEEEeeeEcccHHHHHHHHHH
Confidence 468999999999988865543
No 40
>COG2236 Predicted phosphoribosyltransferases [General function prediction only]
Probab=42.12 E-value=15 Score=30.81 Aligned_cols=23 Identities=22% Similarity=0.086 Sum_probs=18.7
Q ss_pred hheeccccCCCCCHHHHHHHHHH
Q 025080 8 ASIIDDTFDAYGFFEELKLLAEA 30 (258)
Q Consensus 8 ~~~~DD~~D~~gt~eel~~~~~a 30 (258)
+.++||+.|++.|++.+..+.+.
T Consensus 90 VLIVDDI~DTG~Tl~~a~~~l~~ 112 (192)
T COG2236 90 VLIVDDIVDTGETLELALEELKK 112 (192)
T ss_pred EEEEecccCchHhHHHHHHHHHh
Confidence 35799999999999888776654
No 41
>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=42.06 E-value=28 Score=25.60 Aligned_cols=29 Identities=24% Similarity=0.236 Sum_probs=20.9
Q ss_pred CcchhHHHHHhhCCCCHHHHHHHHHHHHH
Q 025080 169 HIASGVECYIKQYGVSAEEVVTVFTEEVE 197 (258)
Q Consensus 169 ~~~n~V~~ym~e~g~s~eeA~~~i~~~i~ 197 (258)
.-.|+|..+|+-.|+|-.||++.+.++..
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 34588999998889999999999987654
No 42
>PRK09177 xanthine-guanine phosphoribosyltransferase; Validated
Probab=41.72 E-value=11 Score=30.41 Aligned_cols=22 Identities=18% Similarity=0.238 Sum_probs=18.0
Q ss_pred hheeccccCCCCCHHHHHHHHH
Q 025080 8 ASIIDDTFDAYGFFEELKLLAE 29 (258)
Q Consensus 8 ~~~~DD~~D~~gt~eel~~~~~ 29 (258)
+.++||+.|.++|+.++.....
T Consensus 87 VLIVDDIiDTG~Tl~~v~~~l~ 108 (156)
T PRK09177 87 FLVVDDLVDTGGTARAVREMYP 108 (156)
T ss_pred EEEEeeeeCCHHHHHHHHHHHh
Confidence 4578999999999999876654
No 43
>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=40.52 E-value=25 Score=27.51 Aligned_cols=60 Identities=18% Similarity=0.221 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHhCCCCcccchHHHHHHHHHHHHHHHHHhhCCCCCChh-hhhccccccccc
Q 025080 52 ALLDTFNEIEQDLAKEGRSSYLPYGKEKMQELVQMYFVQAKWFSEGYVPTWD-EYYPVGLVSCGY 115 (258)
Q Consensus 52 al~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~e-EYl~~~~~s~g~ 115 (258)
.++....+|++.+.-. | ..+-.+.|++++.+.+.-++.....-+|.++ |+...|..|+-+
T Consensus 42 ~lwa~l~dIs~qv~~~-G---~k~~~e~WK~~~~~~~~~~~~~~~~~~~gl~Gg~v~~g~sTskm 102 (127)
T PF05772_consen 42 KLWAMLGDISRQVEWN-G---RKLDPEDWKELFTAAFLIATGEEQRVVPGLDGGFVVLGESTSKM 102 (127)
T ss_dssp HHHHHHHHHHHH--BT-T---B---HHHHHHHHHHHH-----S--EEEE-TTSSEEEE---TTT-
T ss_pred HHHHHHHHHHHHhHhc-C---ccCCHHHHHHHHHHHHhhhccchhhhccCCCCCeEEEeeechhh
Confidence 3456778887765443 3 3478899999999988777766666678777 666666555543
No 44
>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=37.90 E-value=53 Score=23.11 Aligned_cols=30 Identities=20% Similarity=0.387 Sum_probs=24.4
Q ss_pred hHHHHHhhCCCCHHHHHHHHHHHHHHHHHH
Q 025080 173 GVECYIKQYGVSAEEVVTVFTEEVENAWKD 202 (258)
Q Consensus 173 ~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ 202 (258)
.|...+-+.|++.|+|.+.+++...++|+.
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 355566678999999999999999999964
No 45
>PF10776 DUF2600: Protein of unknown function (DUF2600); InterPro: IPR019712 This is a bacterial family of proteins. Some members in the family are annotated as YtpB, however no function is currently known.
Probab=36.14 E-value=3.4e+02 Score=24.81 Aligned_cols=116 Identities=16% Similarity=0.093 Sum_probs=67.2
Q ss_pred hHHHHHhhcCCCCChhhhhhcc--CchhHHHHHHhHHHHhcCccchHHHhhcCCcchhHHHHHhhCCCCHHHHHHHHHHH
Q 025080 118 LATNSFLGMCDVANKEAFEWIS--KDPKISTASSVICRLRNDIVSQQFEQKRGHIASGVECYIKQYGVSAEEVVTVFTEE 195 (258)
Q Consensus 118 ~~~~~~~~~g~~l~~e~~~~~~--~~~~l~~~~~~i~rL~NDi~S~~kE~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~ 195 (258)
++++.-++..+.++++..+.+. .+|=+ +-+--|++=....+.+...|+. |.|..|- +.+++.+.+.-.
T Consensus 194 IF~L~a~A~~p~~t~~~a~~i~~aYFPwI----~gLHILLDy~IDq~EDr~~GdL-NFv~YY~-----~~~~~~~Rl~~f 263 (330)
T PF10776_consen 194 IFALFAYAADPDLTPEDAEKIKDAYFPWI----CGLHILLDYFIDQEEDREGGDL-NFVFYYP-----DEEEMEERLKYF 263 (330)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHcccHHH----HHHHHHHHHHhhhHhHhcCCCc-eeeeeCC-----CHHHHHHHHHHH
Confidence 3444455667778887776653 12333 3334444444555555666666 9997443 889999999999
Q ss_pred HHHHHHHHHHhhcCCCCCcHHHHHHHHhhhhhhhhhhccCCCCCCcHHHHHHHHhhc
Q 025080 196 VENAWKDMNEEFLKPTAFPVALIERPFNIARVIEFLNKKGDWYTHSHAIKDQIAAVL 252 (258)
Q Consensus 196 i~~~~k~ln~~~l~~~~~p~~~~~~~~n~~R~~~~~Y~~~D~~t~~~~~~~~i~~l~ 252 (258)
++++-+...+ +|.+--.+.+ .|.+--+|-.++.-.....++..-+.|+
T Consensus 264 ~~~A~~~~~~-------Lp~~~fHr~i--v~GLla~YLSD~K~~~~~~~~~~ak~Ll 311 (330)
T PF10776_consen 264 VEKALEQASR-------LPYPKFHRMI--VRGLLAMYLSDPKVRSQPNVRPVAKRLL 311 (330)
T ss_pred HHHHHHHHHh-------CCCchHHHHH--HHHHHHHHhCCHhhccchhhHHHHHHHH
Confidence 9999977663 5543332322 3334457866655333333344444443
No 46
>PRK05114 hypothetical protein; Provisional
Probab=34.33 E-value=77 Score=21.18 Aligned_cols=44 Identities=18% Similarity=0.331 Sum_probs=28.1
Q ss_pred cCccchHHHhhcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHH
Q 025080 156 NDIVSQQFEQKRGHIASGVECYIKQYGVSAEEVVTVFTEEVENAWK 201 (258)
Q Consensus 156 NDi~S~~kE~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k 201 (258)
||+-++-.|+..--+ -=|.-+| ..|+|--||+..+...|.+..+
T Consensus 3 ~~lp~LtHeeQQ~AV-ErIq~LM-aqGmSsgEAI~~VA~eiRe~~~ 46 (59)
T PRK05114 3 AGLPSLTHEQQQKAV-ERIQELM-AQGMSSGEAIALVAEELRANHQ 46 (59)
T ss_pred CCcccCCHHHHHHHH-HHHHHHH-HccccHHHHHHHHHHHHHHHHh
Confidence 444444444333222 3355577 4799999999999998887654
No 47
>PRK05205 bifunctional pyrimidine regulatory protein PyrR uracil phosphoribosyltransferase; Provisional
Probab=33.31 E-value=20 Score=29.27 Aligned_cols=20 Identities=10% Similarity=-0.012 Sum_probs=16.2
Q ss_pred hheeccccCCCCCHHHHHHH
Q 025080 8 ASIIDDTFDAYGFFEELKLL 27 (258)
Q Consensus 8 ~~~~DD~~D~~gt~eel~~~ 27 (258)
+.++||+.|.++|+.++...
T Consensus 98 VLIVDDIidTG~Tl~~~~~~ 117 (176)
T PRK05205 98 VILVDDVLYTGRTIRAALDA 117 (176)
T ss_pred EEEEecccCcHHHHHHHHHH
Confidence 46799999999998886543
No 48
>COG2443 Sss1 Preprotein translocase subunit Sss1 [Intracellular trafficking and secretion]
Probab=33.24 E-value=50 Score=22.67 Aligned_cols=21 Identities=19% Similarity=0.475 Sum_probs=16.1
Q ss_pred CCCCChhhhhccccccccchh
Q 025080 97 GYVPTWDEYYPVGLVSCGYFM 117 (258)
Q Consensus 97 ~~~Ps~eEYl~~~~~s~g~~~ 117 (258)
-..||-|||.+.+.++.....
T Consensus 25 arKP~~eEy~~~aKi~~~Gi~ 45 (65)
T COG2443 25 ARKPDWEEYSKIAKITGLGIL 45 (65)
T ss_pred HhCCCHHHHHHHHHHHHHHHH
Confidence 457999999999987765443
No 49
>KOG1766 consensus Enhancer of rudimentary [General function prediction only]
Probab=33.11 E-value=1.9e+02 Score=21.40 Aligned_cols=61 Identities=23% Similarity=0.158 Sum_probs=41.2
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhhcCCCCCc-----HHHHHHHHhhhhhhhhhhccCCCCCCcHHHHHHHHh
Q 025080 184 SAEEVVTVFTEEVENAWKDMNEEFLKPTAFP-----VALIERPFNIARVIEFLNKKGDWYTHSHAIKDQIAA 250 (258)
Q Consensus 184 s~eeA~~~i~~~i~~~~k~ln~~~l~~~~~p-----~~~~~~~~n~~R~~~~~Y~~~D~~t~~~~~~~~i~~ 250 (258)
|.-||.+-+.+|-++..|+.| |+.-| ..+-+++=.++-+..++|...-+-..| --|++||.
T Consensus 24 sv~e~megiCk~yEe~Lkk~n-----Ps~~~ITYDIsqlfeFiD~L~DlS~lVy~~~t~tY~p-ynk~wIKe 89 (104)
T KOG1766|consen 24 SVTECMEGICKMYEEHLKKKN-----PSAPPITYDISQLFEFIDDLADLSMLVYNRETGTYIP-YNKDWIKE 89 (104)
T ss_pred hHHHHHHHHHHHHHHHHHhcC-----CCCCCcceeHHHHHHHHHHHhhhhhhheecccccccC-ccHHHHHH
Confidence 567889999999999888876 43222 255667777888888889877554444 12444443
No 50
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=32.95 E-value=47 Score=25.49 Aligned_cols=27 Identities=30% Similarity=0.288 Sum_probs=21.7
Q ss_pred CCcchhHHHHHhhCCCCHHHHHHHHHH
Q 025080 168 GHIASGVECYIKQYGVSAEEVVTVFTE 194 (258)
Q Consensus 168 g~~~n~V~~ym~e~g~s~eeA~~~i~~ 194 (258)
|-...-|...|.+.|+|.++|++.+.+
T Consensus 74 ~i~~edI~lv~~q~gvs~~~A~~AL~~ 100 (115)
T PRK06369 74 EIPEEDIELVAEQTGVSEEEARKALEE 100 (115)
T ss_pred CCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 444577899999999999999887654
No 51
>KOG3730 consensus Acyl-CoA:dihydroxyactetone-phosphate acyltransferase DHAPAT [Lipid transport and metabolism]
Probab=30.99 E-value=1.9e+02 Score=27.93 Aligned_cols=75 Identities=16% Similarity=0.166 Sum_probs=47.5
Q ss_pred CcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHhhhhhhhhhhccCCCCCCc-HHHHHH
Q 025080 169 HIASGVECYIKQYGVSAEEVVTVFTEEVENAWKDMNEEFLKPTAFPVALIERPFNIARVIEFLNKKGDWYTHS-HAIKDQ 247 (258)
Q Consensus 169 ~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ln~~~l~~~~~p~~~~~~~~n~~R~~~~~Y~~~D~~t~~-~~~~~~ 247 (258)
.+++.|.-|-++.|.|.+.-.+++++++++--.++|-.- +.-..+-+++++.=+| ||+... ..|.+.
T Consensus 76 ~~~sVi~~~~kes~~s~d~~r~ea~eIlDEmsh~~nl~~---------IR~cg~ai~ki~k~i~---dg~yVNe~~~~~v 143 (685)
T KOG3730|consen 76 KLRSVIEHYAKESGTSLDQMRREAREILDEMSHDRNLAI---------IRWCGIAITKIGKRIC---DGFYVNEASMANV 143 (685)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhcchHH---------HHHHHHHHHHHHHHHh---cceeECHHHHHHH
Confidence 457999999999999999988888888887666655322 2223355555543333 666654 445544
Q ss_pred HHhhcccc
Q 025080 248 IAAVLRDP 255 (258)
Q Consensus 248 i~~l~~~p 255 (258)
=+..=-+|
T Consensus 144 r~~~~k~p 151 (685)
T KOG3730|consen 144 RKDMGKCP 151 (685)
T ss_pred HHHhccCC
Confidence 44443444
No 52
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=30.96 E-value=1.4e+02 Score=19.73 Aligned_cols=32 Identities=22% Similarity=0.275 Sum_probs=23.5
Q ss_pred cchhHHHHHhhCCCCHHHHHHHHHHHHHHHHH
Q 025080 170 IASGVECYIKQYGVSAEEVVTVFTEEVENAWK 201 (258)
Q Consensus 170 ~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k 201 (258)
+..++..+..+++++.+++.+.+...+++..+
T Consensus 32 ~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~ 63 (68)
T PF05402_consen 32 VEEIVDALAEEYDVDPEEAEEDVEEFLEQLRE 63 (68)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 45777777888899999998888888876653
No 53
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=30.81 E-value=55 Score=25.15 Aligned_cols=24 Identities=33% Similarity=0.403 Sum_probs=19.9
Q ss_pred chhHHHHHhhCCCCHHHHHHHHHH
Q 025080 171 ASGVECYIKQYGVSAEEVVTVFTE 194 (258)
Q Consensus 171 ~n~V~~ym~e~g~s~eeA~~~i~~ 194 (258)
..-|...|.+.|+|.++|++.+.+
T Consensus 79 ~eDI~lV~eq~gvs~e~A~~AL~~ 102 (116)
T TIGR00264 79 EDDIELVMKQCNVSKEEARRALEE 102 (116)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHH
Confidence 466888999999999999887653
No 54
>PF11989 Dsl1_C: Retrograde transport protein Dsl1 C terminal; InterPro: IPR021876 Dsl1 is a peripheral membrane protein required for transport between the Golgi and the endoplasmic reticulum []. It is localised to the ER membrane, and in vitro it specifically binds to coatomer, the major component of the protein coat of COPI vesicles []. Binding sites for coatomer are found on a disorganised region between the C and N termini of Dsl1 []. The C-terminal domain is involved in binding to the Sec39 subunit of the Dsl1p complex []. The N-terminal complexes with another subunit of the Dsl1p complex called Tip20 which forms heterodimers by pairing the N termini of each protein []. ; PDB: 3K8P_C.
Probab=29.85 E-value=4.1e+02 Score=23.81 Aligned_cols=28 Identities=21% Similarity=0.534 Sum_probs=17.8
Q ss_pred hhhhhhccCCCCCCc-HHHHHHHHhhcccc
Q 025080 227 VIEFLNKKGDWYTHS-HAIKDQIAAVLRDP 255 (258)
Q Consensus 227 ~~~~~Y~~~D~~t~~-~~~~~~i~~l~~~p 255 (258)
+|+.|| +||=|-.+ .++-+.|++||.+.
T Consensus 244 Im~~Fy-~Gel~~fsTdElI~lIkslFadS 272 (291)
T PF11989_consen 244 IMEMFY-QGELYDFSTDELIQLIKSLFADS 272 (291)
T ss_dssp HHHHHH-TTGGGGS-HHHHHHHHHHHS---
T ss_pred HHHHHh-cCchhcccHHHHHHHHHHHhcCC
Confidence 355555 55555566 89999999999873
No 55
>PRK09162 hypoxanthine-guanine phosphoribosyltransferase; Provisional
Probab=29.70 E-value=24 Score=29.08 Aligned_cols=22 Identities=14% Similarity=0.170 Sum_probs=17.3
Q ss_pred hheeccccCCCCCHHHHHHHHH
Q 025080 8 ASIIDDTFDAYGFFEELKLLAE 29 (258)
Q Consensus 8 ~~~~DD~~D~~gt~eel~~~~~ 29 (258)
+.++||+.|.+.|+.++.....
T Consensus 100 VLIVDDIidTG~Tl~~~~~~Lk 121 (181)
T PRK09162 100 VLVVDDILDEGHTLAAIRDRCL 121 (181)
T ss_pred EEEEccccCcHHHHHHHHHHHH
Confidence 4568999999999988765543
No 56
>PF13189 Cytidylate_kin2: Cytidylate kinase-like family; PDB: 3FDI_A.
Probab=29.31 E-value=30 Score=28.23 Aligned_cols=37 Identities=16% Similarity=0.233 Sum_probs=24.7
Q ss_pred hhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhhcC
Q 025080 172 SGVECYIKQYGVSAEEVVTVFTEEVENAWKDMNEEFLK 209 (258)
Q Consensus 172 n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ln~~~l~ 209 (258)
.=|.-.|+.+|+|.++|.+.+.+ .+...+.+-+.+..
T Consensus 126 ~Rv~ri~~~~~~s~~~A~~~i~~-~D~~R~~~~~~~~~ 162 (179)
T PF13189_consen 126 FRVERIMEREGISEEEAEKLIKK-EDKRRRAYYKYYTG 162 (179)
T ss_dssp HHHHHHHHHHT--HHHHHHHHHH-HHHHHHHHHHHH-S
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH-HHHHHHHHHHHHhC
Confidence 34556777889999999987776 66677676666664
No 57
>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.94 E-value=52 Score=21.75 Aligned_cols=48 Identities=19% Similarity=0.318 Sum_probs=31.6
Q ss_pred cCccchHHHhhcCCcchhHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHH
Q 025080 156 NDIVSQQFEQKRGHIASGVECYIKQYGVSAEEVVTVFTEEVENAWKDMNE 205 (258)
Q Consensus 156 NDi~S~~kE~~~g~~~n~V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ln~ 205 (258)
+++.|.-.|+...-+ --|+=+|. .|+|--||+..+...+.+.-|.-|+
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 455555556554433 33455674 5899999999998888877665543
No 58
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=28.40 E-value=1.7e+02 Score=24.59 Aligned_cols=55 Identities=24% Similarity=0.297 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCcccchHHHHHHHHHHHHHHHHHhhCCCCCChhh
Q 025080 49 LYKALLDTFNEIEQDLAKEGRSSYLPYGKEKMQELVQMYFVQAKWFSEGYVPTWDE 104 (258)
Q Consensus 49 ~~~al~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ea~w~~~~~~Ps~eE 104 (258)
.....-+.++++...+....--....++..++++|+.+..- ..|...|.+||.+|
T Consensus 52 ~l~~a~~~~~~l~~~~~~~~~~~y~~~~~~~lQEyvEA~~f-~~~l~~~~l~s~ee 106 (204)
T PRK14562 52 LLKEAEELVKELKELLKDHPELYYAGYVGTALQEYVEALLV-YSLLFENKIPSPEE 106 (204)
T ss_pred HHHHHHHHHHHHHHHhccCchhhhhhhcchHHHHHHHHHHH-HHHHcCCCCCCHHH
Confidence 34444455555555443311111134666677888887654 78888999999998
No 59
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=28.11 E-value=87 Score=25.43 Aligned_cols=34 Identities=24% Similarity=0.447 Sum_probs=23.4
Q ss_pred HHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCcHH
Q 025080 176 CYIKQYGVSAEEVVTVFTEEVENAWKDMNEEFLKPTAFPVA 216 (258)
Q Consensus 176 ~ym~e~g~s~eeA~~~i~~~i~~~~k~ln~~~l~~~~~p~~ 216 (258)
.-|++.|.|.. +|++.|++.||+ -+.+|++-|+|
T Consensus 125 ~~~~~~Gks~~----eIR~~ID~kYk~---g~~~pTpTp~P 158 (158)
T PF13798_consen 125 VQMYQEGKSPK----EIRQYIDEKYKE---GYAKPTPTPMP 158 (158)
T ss_pred HHHHHcCCCHH----HHHHHHHHHHHh---CCCCCCCCCCC
Confidence 35667777754 589999999964 26777666543
No 60
>smart00195 DSPc Dual specificity phosphatase, catalytic domain.
Probab=28.00 E-value=65 Score=24.58 Aligned_cols=24 Identities=17% Similarity=0.268 Sum_probs=18.0
Q ss_pred chhHHHH-HhhCCCCHHHHHHHHHH
Q 025080 171 ASGVECY-IKQYGVSAEEVVTVFTE 194 (258)
Q Consensus 171 ~n~V~~y-m~e~g~s~eeA~~~i~~ 194 (258)
+..+.+| |+..|.|.++|++.++.
T Consensus 93 ~~v~~~yl~~~~~~~~~~A~~~v~~ 117 (138)
T smart00195 93 ATLIIAYLMKYRNLSLNDAYDFVKD 117 (138)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 3556666 66679999999998853
No 61
>KOG1720 consensus Protein tyrosine phosphatase CDC14 [Defense mechanisms]
Probab=27.89 E-value=60 Score=27.75 Aligned_cols=29 Identities=24% Similarity=0.547 Sum_probs=22.8
Q ss_pred cCCcchhHHHHHh-hCCCCHHHHHHHHHHH
Q 025080 167 RGHIASGVECYIK-QYGVSAEEVVTVFTEE 195 (258)
Q Consensus 167 ~g~~~n~V~~ym~-e~g~s~eeA~~~i~~~ 195 (258)
-|...-+|.|||- ++|+|..||++.++.+
T Consensus 158 lGRTG~liAc~lmy~~g~ta~eaI~~lR~~ 187 (225)
T KOG1720|consen 158 LGRTGTLIACYLMYEYGMTAGEAIAWLRIC 187 (225)
T ss_pred CCchhHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence 4555688999864 5699999999988753
No 62
>TIGR01203 HGPRTase hypoxanthine phosphoribosyltransferase. Sequence differences as small as a single residue can affect whether members of this family act on hypoxanthine and guanine or hypoxanthine only. The designation of this model as equivalog reflects hypoxanthine specificity and does not reflect whether or not guanine can replace hypoxanthine.
Probab=27.62 E-value=28 Score=28.26 Aligned_cols=21 Identities=24% Similarity=0.135 Sum_probs=17.0
Q ss_pred hheeccccCCCCCHHHHHHHH
Q 025080 8 ASIIDDTFDAYGFFEELKLLA 28 (258)
Q Consensus 8 ~~~~DD~~D~~gt~eel~~~~ 28 (258)
+.++||+.|.++|+.++....
T Consensus 87 vlivDDii~TG~Tl~~~~~~l 107 (166)
T TIGR01203 87 VLIVEDIVDTGLTLQYLLDLL 107 (166)
T ss_pred EEEEeeeeCcHHHHHHHHHHH
Confidence 567999999999988875543
No 63
>PRK15423 hypoxanthine phosphoribosyltransferase; Provisional
Probab=27.24 E-value=31 Score=28.47 Aligned_cols=22 Identities=14% Similarity=0.302 Sum_probs=17.6
Q ss_pred hheeccccCCCCCHHHHHHHHH
Q 025080 8 ASIIDDTFDAYGFFEELKLLAE 29 (258)
Q Consensus 8 ~~~~DD~~D~~gt~eel~~~~~ 29 (258)
+.++||+.|++.|+..+..+..
T Consensus 95 VLlVDDIiDTG~TL~~l~~~l~ 116 (178)
T PRK15423 95 VLIVEDIIDSGNTLSKVREILS 116 (178)
T ss_pred EEEEeeecCchHHHHHHHHHHH
Confidence 4579999999999988766643
No 64
>TIGR01559 squal_synth farnesyl-diphosphate farnesyltransferase. This model describes farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes. This family is related to phytoene synthases. Tentatively identified archaeal homologs (excluded from this model) lack the C-terminal predicted transmembrane region universally conserved among members of this family.
Probab=27.10 E-value=4.9e+02 Score=23.77 Aligned_cols=167 Identities=8% Similarity=0.068 Sum_probs=82.0
Q ss_pred chHHHHHHHHHHHHHHHHHhhCCCC--CChhhhhccccccccchhhHHHHHh-hcCCCCChhhhhhccCchhHHHHHHhH
Q 025080 75 YGKEKMQELVQMYFVQAKWFSEGYV--PTWDEYYPVGLVSCGYFMLATNSFL-GMCDVANKEAFEWISKDPKISTASSVI 151 (258)
Q Consensus 75 ~~~~~~~~~~~~~~~Ea~w~~~~~~--Ps~eEYl~~~~~s~g~~~~~~~~~~-~~g~~l~~e~~~~~~~~~~l~~~~~~i 151 (258)
.+++..+++..++. .+...... +|++||...-....|+-=...+-.+ ..|..-+. .. ..++.-...+..
T Consensus 105 ~I~~~~~~M~~GMa---~dl~~~~~~~~T~~dL~~YCy~VAG~VG~mlt~l~~~~~~~~~~--~~---~~~~~A~~lG~a 176 (336)
T TIGR01559 105 VIADITRRMGNGMA---DFIDKEVTNEQTVGDYDKYCHYVAGLVGIGLSRLFVASGFEDPS--LG---ESEALSNSMGLF 176 (336)
T ss_pred HHHHHHHHHHHHHH---HHHhcCcCCCCCHHHHHHHHhccccHHHHHHHHHHhhcCCCCcc--hh---hhHHHHHHHHHH
Confidence 34455566667773 33322222 7877766665544443322222222 22211111 00 113344555555
Q ss_pred HHHhcCccchHHHhhcCCc--chhHHHHHhhCCCCH---------HHHHHHHHHHHHHHHHHHHHhh--c---CCCCCcH
Q 025080 152 CRLRNDIVSQQFEQKRGHI--ASGVECYIKQYGVSA---------EEVVTVFTEEVENAWKDMNEEF--L---KPTAFPV 215 (258)
Q Consensus 152 ~rL~NDi~S~~kE~~~g~~--~n~V~~ym~e~g~s~---------eeA~~~i~~~i~~~~k~ln~~~--l---~~~~~p~ 215 (258)
.-+.|=|..+..+.++|-+ +-- -+.++|++. +.+..-+.+++..++..+.+.. + ++..+=.
T Consensus 177 LQlTNIlRDv~ED~~~GR~YlP~e---~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~~al~yl~~l~~~~~~~ 253 (336)
T TIGR01559 177 LQKTNIIRDYLEDINEGRMFWPRE---IWSKYAKKLGDFKKPENSDKALQCLNELVTNALHHATDCLTYLSRLRDQSIFN 253 (336)
T ss_pred HHHHHHHHHHHhHHhCCCCCCCHH---HHHHcCCCHHHhcCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcchhH
Confidence 5666655555555555543 211 244567654 4566777888888886655432 2 2222333
Q ss_pred HHHHHHHhhhhhhhhhhccCCCCCCc-HHHHHHHHhhc
Q 025080 216 ALIERPFNIARVIEFLNKKGDWYTHS-HAIKDQIAAVL 252 (258)
Q Consensus 216 ~~~~~~~n~~R~~~~~Y~~~D~~t~~-~~~~~~i~~l~ 252 (258)
.|.-..+-..-++..+|++.+-|... +-=|..+..++
T Consensus 254 fcaip~~mAi~TL~~~~~n~~~~~~~VKi~r~~~~~~~ 291 (336)
T TIGR01559 254 FCAIPQVMAIATLALCYNNPQVFQGNVKIRKGTTVKLI 291 (336)
T ss_pred HHHHHHHHHHHHHHHHhcChhhcCCCceecHHHHHHHH
Confidence 45544444445566678777655543 33344444444
No 65
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=25.97 E-value=76 Score=22.27 Aligned_cols=33 Identities=18% Similarity=0.384 Sum_probs=22.5
Q ss_pred CCcchhHHHHHhhCC---CCHHHHHHHHH-HHHHHHHH
Q 025080 168 GHIASGVECYIKQYG---VSAEEVVTVFT-EEVENAWK 201 (258)
Q Consensus 168 g~~~n~V~~ym~e~g---~s~eeA~~~i~-~~i~~~~k 201 (258)
+.++-+|. |||+++ +|.+|-.+++. --+....+
T Consensus 9 t~l~~aV~-ymK~r~~~Plt~~EIl~~ls~~d~~~~~~ 45 (75)
T cd07977 9 TQLAKIVD-YMKKRHQHPLTLDEILDYLSLLDIGPKLK 45 (75)
T ss_pred hhHHHHHH-HHHhcCCCCccHHHHHHHHhccCccHHHH
Confidence 45567787 999887 78888877777 33433333
No 66
>PHA03369 capsid maturational protease; Provisional
Probab=25.80 E-value=75 Score=31.29 Aligned_cols=29 Identities=17% Similarity=0.262 Sum_probs=21.2
Q ss_pred HHHHHHhhhhhhhhhhccCCCCCCcHHHHHHHH
Q 025080 217 LIERPFNIARVIEFLNKKGDWYTHSHAIKDQIA 249 (258)
Q Consensus 217 ~~~~~~n~~R~~~~~Y~~~D~~t~~~~~~~~i~ 249 (258)
+.+.+.|+.|++..+|++.|+ ..+++|++
T Consensus 301 ~~~ql~~~~k~l~~~~~~kde----~v~~~yl~ 329 (663)
T PHA03369 301 LADQLNNLYKLLRTIYKHKDE----TVIEQYLI 329 (663)
T ss_pred HHHHHHHHHHHHHHhccCccc----hHHHHHHH
Confidence 344677888888999999988 34565553
No 67
>PTZ00242 protein tyrosine phosphatase; Provisional
Probab=25.79 E-value=65 Score=26.11 Aligned_cols=28 Identities=21% Similarity=0.318 Sum_probs=21.7
Q ss_pred CCcchhHHHHHhhC-CCCHHHHHHHHHHH
Q 025080 168 GHIASGVECYIKQY-GVSAEEVVTVFTEE 195 (258)
Q Consensus 168 g~~~n~V~~ym~e~-g~s~eeA~~~i~~~ 195 (258)
|-.+..+.||+-++ |+|.++|++.++..
T Consensus 110 gRSgt~~a~yL~~~~~~s~~eAi~~vr~~ 138 (166)
T PTZ00242 110 GRAPILVALALVEYGGMEPLDAVGFVREK 138 (166)
T ss_pred CHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence 33457788898887 49999999988754
No 68
>KOG3231 consensus Predicted assembly/vacuolar sorting protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.51 E-value=46 Score=27.23 Aligned_cols=22 Identities=32% Similarity=0.409 Sum_probs=16.9
Q ss_pred eeccccCCCCCHHHHHHHHHHH
Q 025080 10 IIDDTFDAYGFFEELKLLAEAV 31 (258)
Q Consensus 10 ~~DD~~D~~gt~eel~~~~~ai 31 (258)
.+||++|+.|.-||-+..++-+
T Consensus 144 TLDdild~sgDeeEs~aiVNqV 165 (208)
T KOG3231|consen 144 TLDDILDGSGDEEESQAIVNQV 165 (208)
T ss_pred hHHHHhcCCCcHHHHHHHHHHH
Confidence 4799999999999876655433
No 69
>KOG2077 consensus JNK/SAPK-associated protein-1 [Signal transduction mechanisms]
Probab=25.31 E-value=1.5e+02 Score=29.32 Aligned_cols=88 Identities=18% Similarity=0.256 Sum_probs=48.0
Q ss_pred hccCchhHHHHHHhHHHHhcCcc------chHHHhhcCCcchh--HHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhhc
Q 025080 137 WISKDPKISTASSVICRLRNDIV------SQQFEQKRGHIASG--VECYIKQYGVSAEEVVTVFTEEVENAWKDMNEEFL 208 (258)
Q Consensus 137 ~~~~~~~l~~~~~~i~rL~NDi~------S~~kE~~~g~~~n~--V~~ym~e~g~s~eeA~~~i~~~i~~~~k~ln~~~l 208 (258)
-+..+..|+..-+.+--.-||+. +.+++.-||..-.. +..=|.+..--.||-++.++....++.++ +.
T Consensus 306 LilENsqLLetKNALNiVKNDLIakVDeL~~E~~vLrgElea~kqak~Klee~i~elEEElk~~k~ea~~ar~~----~~ 381 (832)
T KOG2077|consen 306 LILENSQLLETKNALNIVKNDLIAKVDELTCEKDVLRGELEAVKQAKLKLEEKIRELEEELKKAKAEAEDARQK----AK 381 (832)
T ss_pred HHHhhHHHHhhhhHHHHHHHHHHHHHHhhccHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh----hc
Confidence 34455667666666666667764 44566666665221 12222222222344444444444444422 33
Q ss_pred C--CCCCcHHHHHHH--Hhhhhhh
Q 025080 209 K--PTAFPVALIERP--FNIARVI 228 (258)
Q Consensus 209 ~--~~~~p~~~~~~~--~n~~R~~ 228 (258)
. .+.+|++-.++| ..|+|++
T Consensus 382 ~~e~ddiPmAqRkRFTRvEMaRVL 405 (832)
T KOG2077|consen 382 DDEDDDIPMAQRKRFTRVEMARVL 405 (832)
T ss_pred ccccccccHHHHhhhHHHHHHHHH
Confidence 3 467999998888 7888875
No 70
>PF06883 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific domain ; InterPro: IPR009674 This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=25.28 E-value=22 Score=23.80 Aligned_cols=32 Identities=16% Similarity=0.199 Sum_probs=26.0
Q ss_pred CCCHHHHHHHHHHHHhccCcccCCCChhHHHH
Q 025080 18 YGFFEELKLLAEAVQRWDIGAMDILPEYMKVL 49 (258)
Q Consensus 18 ~gt~eel~~~~~ai~rWd~~~~~~lp~~~k~~ 49 (258)
+-+.++++.+.+.+++|.......+|..+.+.
T Consensus 3 ~~~~~~a~~~~~~LR~~Kv~~~~~vP~~lEI~ 34 (58)
T PF06883_consen 3 YVSPEEAEQIADQLRYLKVEGEHGVPPTLEIG 34 (58)
T ss_pred eecHHHHHHHHHHHHHHHHcCCCCCCCceEEE
Confidence 44788999999999999888777888777654
No 71
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=24.58 E-value=92 Score=20.73 Aligned_cols=23 Identities=26% Similarity=0.395 Sum_probs=19.0
Q ss_pred hhHHHHHhhCCCCHHHHHHHHHH
Q 025080 172 SGVECYIKQYGVSAEEVVTVFTE 194 (258)
Q Consensus 172 n~V~~ym~e~g~s~eeA~~~i~~ 194 (258)
.+|+.|-+.+|+|.++|.+.+.+
T Consensus 6 ~~Ie~~A~~~~~s~~ea~~~~~~ 28 (62)
T PF12668_consen 6 FCIEEFAKKLNISGEEAYNYFKR 28 (62)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHH
Confidence 46788888889999999987764
No 72
>TIGR01090 apt adenine phosphoribosyltransferase. A phylogenetic analysis suggested omitting the bi-directional best hit homologs from the spirochetes from the seed for this model and making only tentative predictions of adenine phosphoribosyltransferase function for this lineage.
Probab=24.53 E-value=37 Score=27.47 Aligned_cols=22 Identities=27% Similarity=0.262 Sum_probs=17.4
Q ss_pred hheeccccCCCCCHHHHHHHHH
Q 025080 8 ASIIDDTFDAYGFFEELKLLAE 29 (258)
Q Consensus 8 ~~~~DD~~D~~gt~eel~~~~~ 29 (258)
+.++||+++.++|+.++.....
T Consensus 112 VLIVDDIitTG~Tl~~a~~~L~ 133 (169)
T TIGR01090 112 VLIVDDLLATGGTAEATDELIR 133 (169)
T ss_pred EEEEeccccchHHHHHHHHHHH
Confidence 4578999999999888765543
No 73
>PRK07322 adenine phosphoribosyltransferase; Provisional
Probab=24.35 E-value=38 Score=27.80 Aligned_cols=21 Identities=29% Similarity=0.445 Sum_probs=16.8
Q ss_pred ehheeccccCCCCCHHHHHHH
Q 025080 7 TASIIDDTFDAYGFFEELKLL 27 (258)
Q Consensus 7 ~~~~~DD~~D~~gt~eel~~~ 27 (258)
-+.++||+++.++|+.++...
T Consensus 122 ~VLIVDDiitTG~Tl~aa~~~ 142 (178)
T PRK07322 122 RVAIVDDVVSTGGTLTALERL 142 (178)
T ss_pred EEEEEeccccccHHHHHHHHH
Confidence 457899999999998876544
No 74
>PRK02304 adenine phosphoribosyltransferase; Provisional
Probab=24.19 E-value=42 Score=27.31 Aligned_cols=22 Identities=32% Similarity=0.342 Sum_probs=16.9
Q ss_pred hheeccccCCCCCHHHHHHHHH
Q 025080 8 ASIIDDTFDAYGFFEELKLLAE 29 (258)
Q Consensus 8 ~~~~DD~~D~~gt~eel~~~~~ 29 (258)
+.++||+++.++|+.++....+
T Consensus 117 VLIVDDivtTG~Tl~~~~~~l~ 138 (175)
T PRK02304 117 VLIVDDLLATGGTLEAAIKLLE 138 (175)
T ss_pred EEEEeCCccccHHHHHHHHHHH
Confidence 4579999999999877655443
No 75
>COG2096 cob(I)alamin adenosyltransferase [Coenzyme transport and metabolism]
Probab=23.23 E-value=2.1e+02 Score=23.83 Aligned_cols=20 Identities=25% Similarity=0.473 Sum_probs=16.1
Q ss_pred cccCCCCCHHHHHHHHHHHH
Q 025080 13 DTFDAYGFFEELKLLAEAVQ 32 (258)
Q Consensus 13 D~~D~~gt~eel~~~~~ai~ 32 (258)
..-..|||.||+..|.-...
T Consensus 30 ~rVeayGtlDElNs~IG~A~ 49 (184)
T COG2096 30 PRVEAYGTLDELNSFIGLAR 49 (184)
T ss_pred ceeeeeccHHHHHHHHHHHH
Confidence 34568999999999987665
No 76
>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=22.52 E-value=2e+02 Score=21.68 Aligned_cols=70 Identities=17% Similarity=0.270 Sum_probs=42.6
Q ss_pred hhHHHHHHhHHHHhcCccchHHHhhcCCcchh-HHHHHhhCCCCH---HHHHHHHHHHHHHHHHHHHHhhcCCCCCcHHH
Q 025080 142 PKISTASSVICRLRNDIVSQQFEQKRGHIASG-VECYIKQYGVSA---EEVVTVFTEEVENAWKDMNEEFLKPTAFPVAL 217 (258)
Q Consensus 142 ~~l~~~~~~i~rL~NDi~S~~kE~~~g~~~n~-V~~ym~e~g~s~---eeA~~~i~~~i~~~~k~ln~~~l~~~~~p~~~ 217 (258)
..+.+.-..+.+.+||+++.+-+-... -||. +.++| -+++|. -|--++++..++.+|..+.+ +|.++
T Consensus 25 D~~~rLN~ev~~~~~~Ly~~~G~t~Ee-eA~lCLaLLm-GYnat~yd~geke~~~Q~vL~Rs~~vL~~-------Lp~Sl 95 (106)
T PF06603_consen 25 DDFSRLNKEVYEQSNDLYSQHGSTPEE-EANLCLALLM-GYNATIYDNGEKEEKKQEVLDRSWEVLDK-------LPASL 95 (106)
T ss_pred HHHHHHhHHHHHHHHHHHhccCCCHHH-HHHHHHHHHH-hccchhhhCccHHHHHHHHHHHHHHHHHh-------CCcHH
Confidence 346677778889999999874322111 1343 33333 344432 23445788889999977763 77766
Q ss_pred HHH
Q 025080 218 IER 220 (258)
Q Consensus 218 ~~~ 220 (258)
++.
T Consensus 96 LK~ 98 (106)
T PF06603_consen 96 LKV 98 (106)
T ss_pred HHH
Confidence 654
No 77
>KOG4061 consensus DMQ mono-oxygenase/Ubiquinone biosynthesis protein COQ7/CLK-1/CAT5 [General function prediction only]
Probab=21.99 E-value=1.7e+02 Score=24.35 Aligned_cols=49 Identities=20% Similarity=0.279 Sum_probs=40.9
Q ss_pred HHhhC----CCCHHHHHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHhhhh
Q 025080 177 YIKQY----GVSAEEVVTVFTEEVENAWKDMNEEFLKPTAFPVALIERPFNIAR 226 (258)
Q Consensus 177 ym~e~----g~s~eeA~~~i~~~i~~~~k~ln~~~l~~~~~p~~~~~~~~n~~R 226 (258)
|.-|+ +.+.--.++++.+.=.+..+.||+..++ .+|+..++..+||.+-
T Consensus 67 YaGQ~avL~~~~vgpvi~hmWdqEk~Hl~tf~~l~~k-~rVrpT~l~P~w~vag 119 (217)
T KOG4061|consen 67 YAGQMAVLQGTSVGPVIKHMWDQEKEHLKTFENLALK-HRVRPTVLTPLWNVAG 119 (217)
T ss_pred hhchhhhhcCCCchhHHHHHHHHHHHHHHHHHHHHHH-ccCCchhhhhHHHHHH
Confidence 55554 4678888999999999999999998887 5799999999999874
No 78
>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=21.94 E-value=79 Score=22.31 Aligned_cols=28 Identities=29% Similarity=0.421 Sum_probs=21.0
Q ss_pred cCCcchhHHHHHhhCCCCHHHHHHHHHH
Q 025080 167 RGHIASGVECYIKQYGVSAEEVVTVFTE 194 (258)
Q Consensus 167 ~g~~~n~V~~ym~e~g~s~eeA~~~i~~ 194 (258)
|-.+-+.|.-+..+.|+|.++|++.+..
T Consensus 52 RK~Ii~~I~~l~~~~g~~~~~ai~~le~ 79 (81)
T PF12550_consen 52 RKVIIDFIERLANERGISEEEAIEILEE 79 (81)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4445567776677889999999987754
No 79
>TIGR01367 pyrE_Therm orotate phosphoribosyltransferase, Thermus family. This model represents a distinct clade of orotate phosphoribosyltransferases. Members include the experimentally determined example from Thermus aquaticus and additional examples from Caulobacter crescentus, Helicobacter pylori, Mesorhizobium loti, and related species.
Probab=21.74 E-value=44 Score=27.69 Aligned_cols=21 Identities=14% Similarity=0.037 Sum_probs=16.8
Q ss_pred hheeccccCCCCCHHHHHHHH
Q 025080 8 ASIIDDTFDAYGFFEELKLLA 28 (258)
Q Consensus 8 ~~~~DD~~D~~gt~eel~~~~ 28 (258)
+.++||+.|.++|+.++....
T Consensus 108 VLIVDDIi~TG~Tl~~a~~~l 128 (187)
T TIGR01367 108 FVAVEDVVTTGGSLLEAIRAI 128 (187)
T ss_pred EEEEEeeecchHHHHHHHHHH
Confidence 457999999999988875543
No 80
>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=21.50 E-value=81 Score=23.77 Aligned_cols=24 Identities=21% Similarity=0.372 Sum_probs=18.3
Q ss_pred chhHHHHHhh-CCCCHHHHHHHHHH
Q 025080 171 ASGVECYIKQ-YGVSAEEVVTVFTE 194 (258)
Q Consensus 171 ~n~V~~ym~e-~g~s~eeA~~~i~~ 194 (258)
+.++.+|+-. +|+|.++|+++++.
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 4666676555 59999999998854
No 81
>PF07637 PSD5: Protein of unknown function (DUF1595); InterPro: IPR013043 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013039 from INTERPRO and IPR013042 from INTERPRO.
Probab=21.09 E-value=2.4e+02 Score=18.86 Aligned_cols=54 Identities=15% Similarity=0.325 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHhhhhhhhhhhccCCCCCCcHHHHHHHHhhcccc
Q 025080 188 VVTVFTEEVENAWKDMNEEFLKPTAFPVALIERPFNIARVIEFLNKKGDWYTHSHAIKDQIAAVLRDP 255 (258)
Q Consensus 188 A~~~i~~~i~~~~k~ln~~~l~~~~~p~~~~~~~~n~~R~~~~~Y~~~D~~t~~~~~~~~i~~l~~~p 255 (258)
|.+-+......+|+ .+++..=++..+.+..- -++.|++|. ..++..++.+|..|
T Consensus 3 a~~~l~~Fa~rAfR---------Rp~~~~e~~~~~~~~~~---~~~~g~~~~--~a~~~~l~aiL~SP 56 (64)
T PF07637_consen 3 AREILRRFARRAFR---------RPLTDEEVDRYLALYDS---ARAQGEDFE--EALKEALQAILCSP 56 (64)
T ss_pred HHHHHHHHHHHHhC---------CCCCHHHHHHHHHHHHH---HHHcCCCHH--HHHHHHHHHHHcCc
Confidence 33444555555553 35666556666665543 244555544 57999999999888
No 82
>PRK07199 phosphoribosylpyrophosphate synthetase; Provisional
Probab=20.82 E-value=47 Score=29.82 Aligned_cols=20 Identities=15% Similarity=0.094 Sum_probs=15.8
Q ss_pred hheeccccCCCCCHHHHHHH
Q 025080 8 ASIIDDTFDAYGFFEELKLL 27 (258)
Q Consensus 8 ~~~~DD~~D~~gt~eel~~~ 27 (258)
+.++||++|.+||+.++...
T Consensus 214 vIIVDDIidTG~Tl~~aa~~ 233 (301)
T PRK07199 214 PVLVDDIVSTGRTLIEAARQ 233 (301)
T ss_pred EEEEecccCcHHHHHHHHHH
Confidence 45799999999998776433
No 83
>PF12909 DUF3832: Protein of unknown function (DUF3832); InterPro: IPR024308 This domain found in bacteria and Acanthamoeba polyphaga mimivirus (APMV) L591 protein has no known function. In Q0AZ30 from SWISSPROT and other uncharacterised proteins this domain is found C-terminal, while the N terminus shows remote homology to the bacterial toxin/antitoxin 'addiction module' (PF12910 from PFAM).; PDB: 3K6Q_C.
Probab=20.37 E-value=2.7e+02 Score=20.30 Aligned_cols=27 Identities=22% Similarity=0.362 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 025080 181 YGVSAEEVVTVFTEEVENAWKDMNEEF 207 (258)
Q Consensus 181 ~g~s~eeA~~~i~~~i~~~~k~ln~~~ 207 (258)
.|-|.|+|++.+.+.+.+--++...++
T Consensus 31 ~g~T~eeA~~~lie~l~dYAedy~~~~ 57 (89)
T PF12909_consen 31 NGPTLEEAIEDLIEDLRDYAEDYMNRF 57 (89)
T ss_dssp EESSHHHHHHHHHHHHHHHHHHHHHTH
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999988888777766554
No 84
>PLN02297 ribose-phosphate pyrophosphokinase
Probab=20.20 E-value=47 Score=30.28 Aligned_cols=21 Identities=24% Similarity=0.290 Sum_probs=16.4
Q ss_pred hheeccccCCCCCHHHHHHHH
Q 025080 8 ASIIDDTFDAYGFFEELKLLA 28 (258)
Q Consensus 8 ~~~~DD~~D~~gt~eel~~~~ 28 (258)
+.++||++|.+||+.++....
T Consensus 233 vlIVDDIidTG~Tl~~aa~~L 253 (326)
T PLN02297 233 VVIVDDLVQSGGTLIECQKVL 253 (326)
T ss_pred EEEEecccCcHHHHHHHHHHH
Confidence 457999999999988865443
No 85
>cd00127 DSPc Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or Cdc25-like.
Probab=20.07 E-value=1.3e+02 Score=22.67 Aligned_cols=20 Identities=20% Similarity=0.301 Sum_probs=16.3
Q ss_pred HHHHhhCCCCHHHHHHHHHH
Q 025080 175 ECYIKQYGVSAEEVVTVFTE 194 (258)
Q Consensus 175 ~~ym~e~g~s~eeA~~~i~~ 194 (258)
..+|+..|++.++|++++++
T Consensus 101 ~~l~~~~~~~~~~a~~~vr~ 120 (139)
T cd00127 101 AYLMKTLGLSLREAYEFVKS 120 (139)
T ss_pred HHHHHHcCCCHHHHHHHHHH
Confidence 45677779999999999876
Done!