Query psy3877
Match_columns 145
No_of_seqs 190 out of 1142
Neff 7.8
Searched_HMMs 46136
Date Fri Aug 16 19:41:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3877.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3877hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02748 GerC3_HepT heptapren 100.0 1.5E-28 3.2E-33 196.8 15.5 135 5-142 179-317 (319)
2 PRK10888 octaprenyl diphosphat 100.0 3.4E-28 7.4E-33 195.0 16.3 138 3-142 178-321 (323)
3 PLN02857 octaprenyl-diphosphat 100.0 2.3E-28 5E-33 201.1 15.7 135 4-142 276-414 (416)
4 TIGR02749 prenyl_cyano solanes 100.0 2.9E-28 6.3E-33 195.4 15.8 135 4-142 182-320 (322)
5 CHL00151 preA prenyl transfera 100.0 3.2E-28 6.9E-33 195.2 15.6 135 4-142 183-321 (323)
6 PLN02890 geranyl diphosphate s 100.0 4.7E-28 1E-32 199.4 15.6 125 14-142 290-420 (422)
7 COG0142 IspA Geranylgeranyl py 99.9 6.2E-27 1.3E-31 187.7 14.9 135 3-142 181-320 (322)
8 KOG0777|consensus 99.9 1.3E-25 2.9E-30 170.1 11.0 143 1-143 168-310 (322)
9 PRK10581 geranyltranstransfera 99.9 3.2E-22 7E-27 159.0 10.7 104 3-142 189-297 (299)
10 KOG0776|consensus 99.9 9.1E-22 2E-26 158.8 10.9 120 13-138 262-381 (384)
11 PF00348 polyprenyl_synt: Poly 99.8 1.2E-20 2.6E-25 147.2 7.3 103 2-108 152-259 (260)
12 cd00685 Trans_IPPS_HT Trans-Is 99.8 4E-19 8.7E-24 138.4 11.6 99 3-141 156-258 (259)
13 cd00867 Trans_IPPS Trans-Isopr 99.6 2.4E-15 5.3E-20 114.8 10.7 50 14-64 148-197 (236)
14 KOG0711|consensus 99.5 2.9E-13 6.4E-18 106.9 10.0 110 14-126 217-328 (347)
15 cd00385 Isoprenoid_Biosyn_C1 I 98.8 1.3E-07 2.7E-12 70.3 11.9 98 14-138 142-241 (243)
16 cd00683 Trans_IPPS_HH Trans-Is 95.1 0.28 6E-06 38.2 9.4 87 13-124 140-226 (265)
17 PLN02632 phytoene synthase 94.9 0.31 6.6E-06 39.6 9.4 86 15-125 194-279 (334)
18 TIGR01559 squal_synth farnesyl 94.7 0.42 9.2E-06 38.9 9.8 101 2-127 148-251 (336)
19 TIGR03465 HpnD squalene syntha 94.4 0.7 1.5E-05 36.0 10.0 88 13-125 131-218 (266)
20 TIGR03464 HpnC squalene syntha 94.0 0.69 1.5E-05 36.1 9.4 86 15-125 134-219 (266)
21 PF00494 SQS_PSY: Squalene/phy 93.1 3.2 6.8E-05 32.1 11.6 91 15-129 141-232 (267)
22 COG1562 ERG9 Phytoene/squalene 84.6 12 0.00025 29.9 9.1 88 14-126 151-238 (288)
23 PF06783 UPF0239: Uncharacteri 80.9 2 4.4E-05 28.0 2.8 25 14-38 18-42 (85)
24 PF10820 DUF2543: Protein of u 66.1 3 6.4E-05 26.4 0.8 38 2-39 39-76 (81)
25 PRK10888 octaprenyl diphosphat 55.0 14 0.00029 29.9 3.1 34 17-62 69-102 (323)
26 COG0142 IspA Geranylgeranyl py 54.6 5.6 0.00012 32.1 0.8 31 22-64 76-106 (322)
27 PF06304 DUF1048: Protein of u 51.3 13 0.00027 25.2 2.0 33 16-48 30-67 (103)
28 KOG2114|consensus 48.7 79 0.0017 29.2 6.9 87 57-144 433-537 (933)
29 PRK13105 ubiA prenyltransferas 46.5 11 0.00025 29.9 1.4 33 25-68 173-205 (282)
30 KOG3330|consensus 44.2 18 0.00039 26.5 2.0 35 13-55 42-76 (183)
31 PF04358 DsrC: DsrC like prote 43.7 84 0.0018 21.4 5.1 53 87-141 46-105 (109)
32 cd00685 Trans_IPPS_HT Trans-Is 43.1 39 0.00085 26.0 3.9 20 17-36 44-63 (259)
33 TIGR02147 Fsuc_second hypothet 39.9 1.8E+02 0.004 22.9 7.2 66 59-125 124-216 (271)
34 PRK12872 ubiA prenyltransferas 39.5 15 0.00033 28.6 1.1 33 24-67 173-205 (285)
35 TIGR02749 prenyl_cyano solanes 34.3 49 0.0011 26.7 3.3 33 18-62 73-105 (322)
36 KOG2168|consensus 33.8 2.3E+02 0.005 26.3 7.5 106 28-136 298-406 (835)
37 PF10410 DnaB_bind: DnaB-helic 33.1 75 0.0016 18.2 3.2 30 110-139 23-52 (59)
38 PLN00012 chlorophyll synthetas 31.6 21 0.00046 29.5 0.8 33 23-66 263-295 (375)
39 cd02682 MIT_AAA_Arch MIT: doma 31.5 1.4E+02 0.003 18.9 4.9 17 102-118 50-66 (75)
40 CHL00151 preA prenyl transfera 31.4 63 0.0014 26.0 3.5 36 17-64 73-108 (323)
41 PLN02923 xylose isomerase 31.3 1.4E+02 0.003 25.6 5.4 52 16-67 401-457 (478)
42 PF10350 DUF2428: Putative dea 29.8 2.6E+02 0.0057 21.5 10.4 123 20-143 5-165 (255)
43 PF09053 CagZ: CagZ; InterPro 29.5 39 0.00084 24.2 1.7 11 21-31 142-152 (199)
44 PRK12465 xylose isomerase; Pro 28.9 1.6E+02 0.0036 25.0 5.5 51 16-66 367-422 (445)
45 PRK12884 ubiA prenyltransferas 28.1 66 0.0014 25.0 3.0 33 23-66 166-198 (279)
46 PRK00117 recX recombination re 27.9 2.2E+02 0.0047 20.0 6.0 39 73-112 30-68 (157)
47 PRK10581 geranyltranstransfera 27.9 60 0.0013 25.9 2.7 32 20-63 72-105 (299)
48 PF12193 Sulf_coat_C: Sulfolob 26.1 1.6E+02 0.0034 17.8 4.4 39 97-135 7-45 (69)
49 PRK10416 signal recognition pa 25.9 3.5E+02 0.0076 21.7 7.3 30 73-102 34-63 (318)
50 PRK13591 ubiA prenyltransferas 25.9 17 0.00037 29.4 -0.7 31 26-67 193-223 (307)
51 TIGR02056 ChlG chlorophyll syn 25.3 43 0.00094 26.7 1.5 32 24-66 195-226 (306)
52 COG2005 ModE N-terminal domain 25.2 68 0.0015 22.6 2.3 34 89-122 22-55 (130)
53 PF10776 DUF2600: Protein of u 24.7 2.1E+02 0.0046 23.4 5.4 45 98-142 250-294 (330)
54 PRK12883 ubiA prenyltransferas 24.7 53 0.0011 25.6 1.9 30 26-66 168-197 (277)
55 PRK10356 hypothetical protein; 24.4 1.6E+02 0.0034 23.6 4.4 68 59-127 85-154 (274)
56 PF06603 UpxZ: UpxZ family of 24.2 2.4E+02 0.0052 19.2 7.7 60 74-133 38-102 (106)
57 PF01040 UbiA: UbiA prenyltran 24.0 84 0.0018 23.5 2.9 34 22-66 156-189 (257)
58 PRK12875 ubiA prenyltransferas 23.8 55 0.0012 26.0 1.8 34 23-67 176-209 (282)
59 KOG0781|consensus 23.0 3.6E+02 0.0078 23.7 6.5 69 74-142 284-360 (587)
60 PRK12887 ubiA tocopherol phyty 22.5 1.3E+02 0.0028 24.1 3.7 34 23-67 193-226 (308)
61 TIGR01476 chlor_syn_BchG bacte 22.1 49 0.0011 25.9 1.2 30 26-66 175-204 (283)
62 PRK07566 bacteriochlorophyll/c 21.9 35 0.00076 27.3 0.4 29 27-66 204-232 (314)
63 PF14394 DUF4423: Domain of un 21.2 3.3E+02 0.0072 19.8 5.4 65 59-124 26-117 (171)
64 COG1575 MenA 1,4-dihydroxy-2-n 20.1 31 0.00068 27.8 -0.2 20 46-65 199-218 (303)
No 1
>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=99.96 E-value=1.5e-28 Score=196.83 Aligned_cols=135 Identities=16% Similarity=0.197 Sum_probs=114.7
Q ss_pred HHHhhcCCC----hHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHHHHh
Q psy3877 5 RLMQLFSDT----KSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQ 80 (145)
Q Consensus 5 rl~~~~~~~----~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~l~~ 80 (145)
++....++. .+.+.+||.++|+||||+||++||+++++.+|||.++||++||+|+|++++++..+....+..++.+
T Consensus 179 ~~ga~~ag~~~~~~~~l~~~g~~lG~aFQI~DDilD~~~~~~~~GK~~~~Dl~~gk~Tlp~l~al~~~~~~~~l~~~~~~ 258 (319)
T TIGR02748 179 QLGAIASGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGKPAGGDLLQGNVTLPVLYAMEDPFLKKRIEQVLEE 258 (319)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHccCCHHhhCCChhhHHhCCCchHHHHHHhcCcchhHHHHHHHcC
Confidence 344444443 3579999999999999999999999999999999999999999999999999865544467777765
Q ss_pred cCCCHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhhhcCCC
Q psy3877 81 RTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELLTWDTPD 142 (145)
Q Consensus 81 ~~~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~~~~~ll~~l~~~~~~~ 142 (145)
. +++++.+++++++++|++++|+.++++|.++|++.|+.+|.++.+..| ..+.+++.+|
T Consensus 259 ~--~~~~~~~~~~~i~~~g~~~~a~~~a~~~~~~A~~~L~~lp~~~~~~~L-~~l~~~~~~R 317 (319)
T TIGR02748 259 T--TAEEMEPLIEEVKKSDAIEYAYAVSDRYLKKALELLDGLPDGRAKKPL-QEIAKYIGKR 317 (319)
T ss_pred C--CHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHH-HHHHHHHHhc
Confidence 4 577889999999999999999999999999999999999999987665 5666666654
No 2
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=99.96 E-value=3.4e-28 Score=195.00 Aligned_cols=138 Identities=21% Similarity=0.285 Sum_probs=115.2
Q ss_pred HHHHHhhcCCC----hHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCc-hH-HHHH
Q psy3877 3 AIRLMQLFSDT----KSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPD-DR-QVIQ 76 (145)
Q Consensus 3 ~~rl~~~~~~~----~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~-~~-~l~~ 76 (145)
+++++...++. .+.+..||+++|+||||+||++||++++..+|||.|+||++||+|+|++++++..+. .+ .+..
T Consensus 178 ~~~~ga~lag~~~~~~~~l~~~g~~lG~aFQi~DD~ld~~~~~~~~GK~~g~Dl~~gk~Tlp~l~al~~~~~~~~~~l~~ 257 (323)
T PRK10888 178 AAQCSGILAGCTPEQEKGLQDYGRYLGTAFQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRT 257 (323)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHhhcccCChHhhCCCchhhhhcCCchHHHHHHHHhCCHHHHHHHHH
Confidence 44556666654 346999999999999999999999999999999999999999999999999997543 23 4666
Q ss_pred HHHhcCCCHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhhhcCCC
Q psy3877 77 ILRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELLTWDTPD 142 (145)
Q Consensus 77 ~l~~~~~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~~~~~ll~~l~~~~~~~ 142 (145)
++.++ ...+++.+++++++++|++++++..+++|.++|++.|+.+|+++.++.| ..+.+++.++
T Consensus 258 ~~~~~-~~~~~~~~~~~~l~~~g~~e~~~~~a~~~~~~A~~~L~~lp~~~~~~~L-~~l~~~~~~R 321 (323)
T PRK10888 258 AIEQG-NGRHLLEPVLEAMNACGSLEWTRQRAEEEADKAIAALQVLPDTPWREAL-IGLAHIAVQR 321 (323)
T ss_pred HHhCC-CCHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHH-HHHHHHHHhC
Confidence 66543 3456789999999999999999999999999999999999999988775 4666555544
No 3
>PLN02857 octaprenyl-diphosphate synthase
Probab=99.96 E-value=2.3e-28 Score=201.10 Aligned_cols=135 Identities=21% Similarity=0.341 Sum_probs=117.0
Q ss_pred HHHHhhcCCC----hHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHHHH
Q psy3877 4 IRLMQLFSDT----KSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILR 79 (145)
Q Consensus 4 ~rl~~~~~~~----~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~l~ 79 (145)
.++....++. .+.+.+||.++|+||||+||++||+++++.+|||.|+||++||+|+|+|++++..+ .+..++.
T Consensus 276 ~~~gallaga~~~~~~~l~~fG~~LGiAFQI~DDiLD~~~~~~~~GK~~g~DL~eGK~TlPli~al~~~~---~l~~~l~ 352 (416)
T PLN02857 276 TKSAAIFSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPAGSDLAKGNLTAPVIFALEKEP---ELREIIE 352 (416)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHhCCCcchhhhcCCccHHHHHHHhcCh---HHHHHHh
Confidence 3455555554 34699999999999999999999999999999999999999999999999998643 5777777
Q ss_pred hcCCCHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhhhcCCC
Q psy3877 80 QRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELLTWDTPD 142 (145)
Q Consensus 80 ~~~~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~~~~~ll~~l~~~~~~~ 142 (145)
+...+.+++.+++++++++|++++|++++++|.++|++.|+.||.++.+..| ..+.+++.++
T Consensus 353 ~~~~~~~~~~~~~~lv~~~Ggie~a~~~a~~~~~~A~~~L~~Lp~~~~~~~L-~~L~~~~~~R 414 (416)
T PLN02857 353 SEFCEEGSLEEAIELVNEGGGIERAQELAKEKADLAIQNLECLPRGAFRSSL-EDMVDYNLER 414 (416)
T ss_pred hccCCHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHH-HHHHHHHHhc
Confidence 7666778999999999999999999999999999999999999999888765 5666666654
No 4
>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=99.96 E-value=2.9e-28 Score=195.35 Aligned_cols=135 Identities=24% Similarity=0.356 Sum_probs=115.6
Q ss_pred HHHHhhcCCC----hHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHHHH
Q psy3877 4 IRLMQLFSDT----KSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILR 79 (145)
Q Consensus 4 ~rl~~~~~~~----~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~l~ 79 (145)
.++....++. .+.+.+||.++|+||||+||++||+++++.+|||.|+||++||+|+|++++++..+ .+..++.
T Consensus 182 ~~~ga~~ag~~~~~~~~l~~~G~~lG~aFQi~DDild~~~~~~~~GK~~g~Dl~~Gk~Tlp~l~al~~~~---~~~~~l~ 258 (322)
T TIGR02749 182 SKAAAVLSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPAGSDLMKGNLTAPVLFALEEEP---KLSELIE 258 (322)
T ss_pred HHHHHHHcCcCHHHHHHHHHHHHHHHHHHHHHHHhccCCCChHhhCCChhHHHhCCCchHHHHHHHhcCh---HHHHHHH
Confidence 3445555554 35799999999999999999999999999999999999999999999999998643 4566666
Q ss_pred hcCCCHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhhhcCCC
Q psy3877 80 QRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELLTWDTPD 142 (145)
Q Consensus 80 ~~~~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~~~~~ll~~l~~~~~~~ 142 (145)
+...+.+++.++++++.++|++++|++++++|.++|++.|+.+|+++.++.| ..+.+++.++
T Consensus 259 ~~~~~~~~~~~~~~~i~~~ga~~~a~~~~~~~~~~A~~~L~~lp~~~~~~~L-~~l~~~~~~R 320 (322)
T TIGR02749 259 REFSQKGDLEQALSLVRKSGGIKKARELAKEQAQLALQSLSFLPPSPPREAL-KELVHFVLSR 320 (322)
T ss_pred hccCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHH-HHHHHHHHhc
Confidence 6666778899999999999999999999999999999999999999888765 5666666554
No 5
>CHL00151 preA prenyl transferase; Reviewed
Probab=99.96 E-value=3.2e-28 Score=195.20 Aligned_cols=135 Identities=19% Similarity=0.288 Sum_probs=114.7
Q ss_pred HHHHhhcCCC----hHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHHHH
Q psy3877 4 IRLMQLFSDT----KSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILR 79 (145)
Q Consensus 4 ~rl~~~~~~~----~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~l~ 79 (145)
.++....++. .+.+++||.++|+||||+||++|++++++.+|||.|+||++||+|+|++++++..+ .+..++.
T Consensus 183 ~~~ga~lag~~~~~~~~l~~~G~~lG~aFQi~DDilD~~~~~~~~GK~~g~Dl~eGk~Tlp~l~al~~~~---~~~~~l~ 259 (323)
T CHL00151 183 CKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLTAPVLFALTQNS---KLAKLIE 259 (323)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHhhcccChhhhCCCchhhHhcCchHHHHHHHHhcCh---HHHHHHH
Confidence 3444444543 35799999999999999999999999999999999999999999999999998643 4555665
Q ss_pred hcCCCHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhhhcCCC
Q psy3877 80 QRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELLTWDTPD 142 (145)
Q Consensus 80 ~~~~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~~~~~ll~~l~~~~~~~ 142 (145)
+...+++++.+++++++++|++++|+.++++|.++|++.|+.+|.++.++.| ..+.+++..+
T Consensus 260 ~~~~~~~~~~~~~~~l~~~g~~~~a~~~a~~~~~~A~~~L~~lp~~~~~~~L-~~l~~~~~~R 321 (323)
T CHL00151 260 REFCETKDISQALQIIKETNGIEKAKDLALEHMQAAIQCLKFLPPSSAKDSL-IEIANFIINR 321 (323)
T ss_pred HhcCCHHHHHHHHHHHHHCCcHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHH-HHHHHHHHhc
Confidence 5555678899999999999999999999999999999999999999887775 5666666554
No 6
>PLN02890 geranyl diphosphate synthase
Probab=99.96 E-value=4.7e-28 Score=199.36 Aligned_cols=125 Identities=20% Similarity=0.223 Sum_probs=110.0
Q ss_pred hHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHHHHhcCCCHHHHHHHHH
Q psy3877 14 KSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTRDVEVKKYCIS 93 (145)
Q Consensus 14 ~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~l~~~~~~~~~~~~i~~ 93 (145)
.+.+++||+++|+||||+||++||+++++.+|||.|+||++||+|+|+|++++..+ .+..++.+...+++++.++++
T Consensus 290 ~~~l~~fG~~lGlAFQI~DDiLD~~g~~~~~GK~~g~DL~eGk~TlPvl~al~~~~---~l~~~l~~~~~~~~~v~~~~~ 366 (422)
T PLN02890 290 AVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGVITAPILFAMEEFP---QLREVVDRGFDNPANVDIALE 366 (422)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCChhhhCCCchhhHhcCCccHHHHHHHhcCH---HHHHHHhcccCCHHHHHHHHH
Confidence 35689999999999999999999999999999999999999999999999997533 466677766667788999999
Q ss_pred HHHHcChHHHHHHHHHHHHHHHHHHHhccCCCH------HHHHHHHHHhhhcCCC
Q psy3877 94 LLDRFGSFEHTREVLKELDVSARTEVARLGGNP------LLEAILDELLTWDTPD 142 (145)
Q Consensus 94 ~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~------~~~~ll~~l~~~~~~~ 142 (145)
++.++|++++|+.++++|.++|.+.|+.+|+++ .++.| ..+.+++.++
T Consensus 367 ~i~~~gaie~a~~la~~~~~~A~~~L~~lp~s~~~~~~~~r~~L-~~L~~~vi~R 420 (422)
T PLN02890 367 YLGKSRGIQRTRELAREHANLAAAAIESLPETDDEDVLTSRRAL-IDLTERVITR 420 (422)
T ss_pred HHHHcCHHHHHHHHHHHHHHHHHHHHHhCCCCccccchHHHHHH-HHHHHHHHhc
Confidence 999999999999999999999999999999987 67775 4666665554
No 7
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=99.95 E-value=6.2e-27 Score=187.68 Aligned_cols=135 Identities=23% Similarity=0.325 Sum_probs=114.5
Q ss_pred HHHHHhhcCCCh----HHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchH-HHHHH
Q psy3877 3 AIRLMQLFSDTK----SDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDR-QVIQI 77 (145)
Q Consensus 3 ~~rl~~~~~~~~----~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~-~l~~~ 77 (145)
+++++...++.. +.++.||.++|+||||+||+||+++++.++||++|+||++||.|+|++++++..++.. .+...
T Consensus 181 a~~~ga~la~~~~~~~~~l~~~g~~lGlaFQi~DDiLD~~~d~~~lGK~~g~Dl~~gK~T~p~l~~l~~~~~~~~~~~~~ 260 (322)
T COG0142 181 AAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEKANEDQKLLRIL 260 (322)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHhhHHHHHHHHhhcCCCChHHhCCCcchHHHcCCchHHHHHHHHcCchhhHHHHHH
Confidence 455666666653 7899999999999999999999999999999999999999999999999999875432 34444
Q ss_pred HHhcCCCHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhhhcCCC
Q psy3877 78 LRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELLTWDTPD 142 (145)
Q Consensus 78 l~~~~~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~~~~~ll~~l~~~~~~~ 142 (145)
+.+.. ++++++++++++|+++++...++.|.++|++.|+.+|+++.+..| ..++++++.+
T Consensus 261 ~~~~~----~~~~~~~~~~~~g~~~~~~~~a~~~~~~a~~~L~~l~~~~~~~~L-~~la~~i~~R 320 (322)
T COG0142 261 LEGGG----EVEEALELLRKSGAIEYAKNLAKTYVEKAKEALEKLPDSEAKEAL-LELADFIIKR 320 (322)
T ss_pred hhcch----HHHHHHHHHHHcchHHHHHHHHHHHHHHHHHHHHhCCCchHHHHH-HHHHHHHHhc
Confidence 44332 889999999999999999999999999999999999988888776 5777776655
No 8
>KOG0777|consensus
Probab=99.93 E-value=1.3e-25 Score=170.13 Aligned_cols=143 Identities=53% Similarity=0.833 Sum_probs=134.7
Q ss_pred ChHHHHHhhcCCChHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHHHHh
Q psy3877 1 MMAIRLMQLFSDTKSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQ 80 (145)
Q Consensus 1 ~~~~rl~~~~~~~~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~l~~ 80 (145)
||++|||+.+|...+.+..+-..+|+.|||+|||+++...+....|+++.||.|||.++|+|||+...++.+.++.++.+
T Consensus 168 ~La~rLMqlfS~~kedl~pl~n~LGl~fQIRDDY~NL~~keysenKsFaEDlTEGKfsFP~iHA~~t~~q~~Qvl~ILrq 247 (322)
T KOG0777|consen 168 RLALRLMQLFSHHKEDLVPLINLLGLIFQIRDDYLNLKDKEYSENKSFAEDLTEGKFSFPIIHALKTKGQTEQVLRILRQ 247 (322)
T ss_pred HHHHHHHHHHHhcchhHHHHHHHHhHhhhhhhhhccchhhhhhcccchhhhhccCccCCcchhhhhcCCchHHHHHHHHH
Confidence 58999999999999999999999999999999999999988888999999999999999999999877766789999999
Q ss_pred cCCCHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhhhcCCCC
Q psy3877 81 RTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELLTWDTPDS 143 (145)
Q Consensus 81 ~~~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~~~~~ll~~l~~~~~~~~ 143 (145)
++.+.+....++.+++..|+++||+...++...+|+..+.....+|+...|...+..|.+.++
T Consensus 248 RT~didiKkyci~~LEd~gSf~YTrn~l~~L~a~a~~~i~~~g~Npyl~~L~~hl~~~~~~~~ 310 (322)
T KOG0777|consen 248 RTSDIDIKKYCIQILEDTGSFAYTRNFLNQLVAEARSMIKNDGENPYLPDLASHLDTATNLHD 310 (322)
T ss_pred hhccchHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHhhhccch
Confidence 988878888999999999999999999999999999999999999999999999999887653
No 9
>PRK10581 geranyltranstransferase; Provisional
Probab=99.88 E-value=3.2e-22 Score=158.98 Aligned_cols=104 Identities=25% Similarity=0.339 Sum_probs=87.4
Q ss_pred HHHHHhhcCCC-----hHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHH
Q psy3877 3 AIRLMQLFSDT-----KSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQI 77 (145)
Q Consensus 3 ~~rl~~~~~~~-----~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~ 77 (145)
++.+....++. .+.+.+||.++|+||||+||++|++++++.+||+.|+|+++||.|+|+++++
T Consensus 189 ~~~~gailag~~~~~~~~~l~~~g~~lG~aFQI~DDilD~~g~~~~~GK~~g~Dl~~gk~T~p~l~~~------------ 256 (299)
T PRK10581 189 AVRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGL------------ 256 (299)
T ss_pred HHHHHHHHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHccccCChHHHCCCcchhhhcCCCCHHHHHHH------------
Confidence 34555555543 2568999999999999999999999999999999999999999999999865
Q ss_pred HHhcCCCHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhhhcCCC
Q psy3877 78 LRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELLTWDTPD 142 (145)
Q Consensus 78 l~~~~~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~~~~~ll~~l~~~~~~~ 142 (145)
+++...+++|.++|++.|+.+|.++..+..+..+.++++.|
T Consensus 257 ------------------------e~a~~~a~~~~~~A~~~l~~l~~~~~~~~~L~~l~~~~~~R 297 (299)
T PRK10581 257 ------------------------EQARKKARDLIDDARQSLDQLAAQSLDTSALEALANYIIQR 297 (299)
T ss_pred ------------------------HHHHHHHHHHHHHHHHHHHhCcCCchhHHHHHHHHHHHHhc
Confidence 46778999999999999999998776445556777777665
No 10
>KOG0776|consensus
Probab=99.87 E-value=9.1e-22 Score=158.81 Aligned_cols=120 Identities=18% Similarity=0.190 Sum_probs=100.4
Q ss_pred ChHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHHHHhcCCCHHHHHHHH
Q psy3877 13 TKSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTRDVEVKKYCI 92 (145)
Q Consensus 13 ~~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~l~~~~~~~~~~~~i~ 92 (145)
..+.+++||+++|++||+.||++||+...+..||+.|.|+..|+.|+|++++++..++ +...+.+...+..+..+..
T Consensus 262 v~e~~~~yGR~lGL~fQvvDDildftkss~elGK~ag~Dl~~g~lT~P~Lf~~e~~pe---~~e~l~~~~~e~~~~~~~~ 338 (384)
T KOG0776|consen 262 VIEAAFEYGRCLGLAFQVVDDILDFTKSSEELGKTAGKDLKAGKLTAPVLFALEKSPE---LREKLEREFSEPLDGFDAD 338 (384)
T ss_pred HHHHHHHHHHHHHHHHHHhhcccCcccchhhcCcchhhhhhhccccccchhhhhhChH---HHHHHHHhccccchhhHHH
Confidence 4689999999999999999999999999999999999999999999999999998764 4444444433333444455
Q ss_pred HHHHHcChHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhhh
Q psy3877 93 SLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELLTW 138 (145)
Q Consensus 93 ~~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~~~~~ll~~l~~~ 138 (145)
+++. ++..|..++++|.++|.+.|+.+|.++.|.+|.+..-.+
T Consensus 339 k~v~---~v~~a~~la~~~~~~Al~~l~~~p~s~ar~aL~~l~~~~ 381 (384)
T KOG0776|consen 339 KAVP---GVALAKYLARRHNNKALEALQSLPRSEARSALENLVLAV 381 (384)
T ss_pred HHHH---HHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHH
Confidence 5555 799999999999999999999999999999986554433
No 11
>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=99.83 E-value=1.2e-20 Score=147.16 Aligned_cols=103 Identities=26% Similarity=0.461 Sum_probs=81.9
Q ss_pred hHHHHHhhcCCCh----HHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCc-hHHHHH
Q psy3877 2 MAIRLMQLFSDTK----SDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPD-DRQVIQ 76 (145)
Q Consensus 2 ~~~rl~~~~~~~~----~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~-~~~l~~ 76 (145)
++.+++...++.+ +.++.||.++|+||||+||++|++++++.+||++|+||++||+|+|++++++..++ .+.+..
T Consensus 152 ~~~~~ga~lag~~~~~~~~l~~~g~~lG~afQi~DD~~d~~~~~~~~gK~~~~Dl~~gk~Tlp~~~al~~~~~~~~~~l~ 231 (260)
T PF00348_consen 152 LACQLGAILAGADEEQIEALREFGRHLGIAFQIRDDLLDLFGDEEELGKPVGSDLKEGKPTLPVLHALERAREELRELLQ 231 (260)
T ss_dssp HHHHHHHHHTTSGHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHSSTTTHHHHTTTSSHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhccchhHHHHHHHHHHHHHHHHHhhhhhhhhccCcHHHhcccchhHHhcCcccHHHHHHHHhCHHHHHHHHH
Confidence 4567777777765 68999999999999999999999999999999999999999999999999998532 223332
Q ss_pred HHHhcCCCHHHHHHHHHHHHHcChHHHHHHHH
Q psy3877 77 ILRQRTRDVEVKKYCISLLDRFGSFEHTREVL 108 (145)
Q Consensus 77 ~l~~~~~~~~~~~~i~~~l~~~g~~~~~~~~~ 108 (145)
..... .+.+.+.+.+..++.++++.+.+
T Consensus 232 ~~~~~----~~~~~~~~~~~~~~~~~~~~~~~ 259 (260)
T PF00348_consen 232 EAYGK----EDSEEALEIIAQTGALEYTRKFM 259 (260)
T ss_dssp HHHHH----SHHHHHHHHHHHHHHHTHHHHHH
T ss_pred HHHcc----cchHHHHHHHHHHHHHHHHHhhc
Confidence 22221 24456788888888999888765
No 12
>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases, head-to-tail. These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4) condensation reactions. This CD includes all-trans (E)-isoprenyl diphosphate synthases which synthesize various chain length (C10, C15, C20, C25, C30, C35, C40, C45, and C50) linear isoprenyl diphosphates from precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They catalyze the successive 1'-4 condensation of the 5-carbon IPP to allylic substrates geranyl-, farnesyl-, or geranylgeranyl-diphosphate. Isoprenoid chain elongation reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DDXX(XX
Probab=99.80 E-value=4e-19 Score=138.41 Aligned_cols=99 Identities=29% Similarity=0.403 Sum_probs=83.8
Q ss_pred HHHHHhhcCCC----hHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHHH
Q psy3877 3 AIRLMQLFSDT----KSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQIL 78 (145)
Q Consensus 3 ~~rl~~~~~~~----~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~l 78 (145)
+.++++..++. .+.+++||.++|++|||+||++|+++++..+||+.++||++||+|+|+++++
T Consensus 156 ~~~~~a~l~~~~~~~~~~l~~~g~~lG~afQi~DD~ld~~~~~~~~gK~~~~Di~~gk~T~~~~~~l------------- 222 (259)
T cd00685 156 APLLGALLAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLAL------------- 222 (259)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHhhcccCChHHHCCCcchHHHcCCchHHHHHHH-------------
Confidence 45566666653 4679999999999999999999999999999999999999999999999987
Q ss_pred HhcCCCHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhhhcCC
Q psy3877 79 RQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELLTWDTP 141 (145)
Q Consensus 79 ~~~~~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~~~~~ll~~l~~~~~~ 141 (145)
++.++.|.++|...|+.+|.++.+.. +..+.+++..
T Consensus 223 --------------------------~~~~~~~~~~a~~~l~~~~~~~~~~~-l~~~~~~~~~ 258 (259)
T cd00685 223 --------------------------RELAREYEEKALEALKALPESPAREA-LRALADFILE 258 (259)
T ss_pred --------------------------HHHHHHHHHHHHHHHHcCCCcHHHHH-HHHHHHHHHc
Confidence 67899999999999999998875544 4556665544
No 13
>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=99.63 E-value=2.4e-15 Score=114.82 Aligned_cols=50 Identities=30% Similarity=0.492 Sum_probs=48.2
Q ss_pred hHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHH
Q psy3877 14 KSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHA 64 (145)
Q Consensus 14 ~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~a 64 (145)
.+.+.+||.++|+||||+||++|++++...+|| +++||++||+|+|++++
T Consensus 148 ~~~~~~~~~~lG~a~Qi~dd~~D~~~d~~~~gk-~~~D~~~gr~tlp~~~~ 197 (236)
T cd00867 148 AEALKDYGRALGLAFQLTDDLLDVFGDAEELGK-VGSDLREGRITLPVILA 197 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccccCChHHHCc-cHHHHHcCCchHHHHHH
Confidence 378999999999999999999999999999999 99999999999999988
No 14
>KOG0711|consensus
Probab=99.48 E-value=2.9e-13 Score=106.90 Aligned_cols=110 Identities=16% Similarity=0.206 Sum_probs=90.8
Q ss_pred hHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCc-hHH-HHHHHHhcCCCHHHHHHH
Q psy3877 14 KSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPD-DRQ-VIQILRQRTRDVEVKKYC 91 (145)
Q Consensus 14 ~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~-~~~-l~~~l~~~~~~~~~~~~i 91 (145)
......+...+|..||++|||||++||++.+|| +|+||+++|+||.+.+|++..+. +.. +..-+.+ .+.+.+..+
T Consensus 217 ~~~~k~v~~~lg~~FQvQDDYLd~fgDp~vtgk-iGtDIqDnKCsWlv~~al~~~~~eq~~~l~~~yg~--~~~~~v~~v 293 (347)
T KOG0711|consen 217 HACEKKVLLLLGEYFQVQDDYLDCFGDPEVTGK-IGTDIQDNKCSWLVVKALQRASAEQYKILFENYGK--PEAEAVAKV 293 (347)
T ss_pred hhhHHHHHHHHHHHHhcchHHHHhcCChhhcCC-CCCccccCceeeehHHHHhhcCHHHHHHHHHhcCC--ccHHHHHHH
Confidence 456788999999999999999999999999998 78999999999999999999753 322 2333333 356778889
Q ss_pred HHHHHHcChHHHHHHHHHHHHHHHHHHHhccCCCH
Q psy3877 92 ISLLDRFGSFEHTREVLKELDVSARTEVARLGGNP 126 (145)
Q Consensus 92 ~~~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~ 126 (145)
..+.++.+....-...-..........|+.++.+.
T Consensus 294 k~ly~el~l~~~f~~yE~~~~~~Ik~~I~~~~~~~ 328 (347)
T KOG0711|consen 294 KALYKELHLPALFIEYEEGSYKKIKKLISQVDEDT 328 (347)
T ss_pred HHHHHHhccHHHHHHhhhhHHHHHHHHHHHccCCC
Confidence 99999999888777788888899999999887653
No 15
>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=98.80 E-value=1.3e-07 Score=70.34 Aligned_cols=98 Identities=26% Similarity=0.327 Sum_probs=74.5
Q ss_pred hHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHHHHhcCCCHHHHHHHHH
Q psy3877 14 KSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTRDVEVKKYCIS 93 (145)
Q Consensus 14 ~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~l~~~~~~~~~~~~i~~ 93 (145)
.+.+..++.++|++||+.||+.|+..+.... +|+.|+|.+++.+.....+.+ .
T Consensus 142 ~~~~~~~~~~~g~~~ql~nDl~~~~~e~~~~---------~~~~~l~~~~~~~~~~~~~~~------------------~ 194 (243)
T cd00385 142 LEALRKLGRALGLAFQLTNDLLDYEGDAERG---------EGKCTLPVLYALEYGVPAEDL------------------L 194 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccCCHHHh---------CCchHHHHHHHHHhCChhhHH------------------H
Confidence 6789999999999999999999998886421 579999999998875322111 1
Q ss_pred HHHHcChHHHHHHHHHHHHHHHHHHHhccCCCH--HHHHHHHHHhhh
Q psy3877 94 LLDRFGSFEHTREVLKELDVSARTEVARLGGNP--LLEAILDELLTW 138 (145)
Q Consensus 94 ~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~--~~~~ll~~l~~~ 138 (145)
.++.+++++.+...+..+.+++.+.+..+.... ....+...+.++
T Consensus 195 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 241 (243)
T cd00385 195 LVEKSGSLEEALEELAKLAEEALKELNELILSLPDVPRALLALALNL 241 (243)
T ss_pred HHHHCChHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHH
Confidence 677888999999999999999999988876542 344444444433
No 16
>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=95.09 E-value=0.28 Score=38.18 Aligned_cols=87 Identities=15% Similarity=0.087 Sum_probs=60.9
Q ss_pred ChHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHHHHhcCCCHHHHHHHH
Q psy3877 13 TKSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTRDVEVKKYCI 92 (145)
Q Consensus 13 ~~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~l~~~~~~~~~~~~i~ 92 (145)
..+....++.++|.|+|+.|=+.|+ +.|+..|.+.+|.=..-+..-..+.+ + .+..++ . +.
T Consensus 140 ~~~~~~~~A~~lG~AlqltnilRdv-----------~eD~~~gR~YlP~d~l~~~gv~~~~l---~-~~~~~~-~---~~ 200 (265)
T cd00683 140 SDEAALERARALGLALQLTNILRDV-----------GEDARRGRIYLPREELARFGVTLEDL---L-APENSP-A---FR 200 (265)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHH-----------HHHHccCCCcCCHHHHHHcCCCHHHH---c-CCCCCH-H---HH
Confidence 3567889999999999999988775 57888999999986665554221222 2 232232 2 22
Q ss_pred HHHHHcChHHHHHHHHHHHHHHHHHHHhccCC
Q psy3877 93 SLLDRFGSFEHTREVLKELDVSARTEVARLGG 124 (145)
Q Consensus 93 ~~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~ 124 (145)
. .+.+....++.+...|...+..+|.
T Consensus 201 ~------~~~~~~~~A~~~~~~a~~~~~~lp~ 226 (265)
T cd00683 201 A------LLRRLIARARAHYREALAGLAALPR 226 (265)
T ss_pred H------HHHHHHHHHHHHHHHHHHhHHhCCH
Confidence 2 2455566789999999999999984
No 17
>PLN02632 phytoene synthase
Probab=94.87 E-value=0.31 Score=39.59 Aligned_cols=86 Identities=16% Similarity=0.090 Sum_probs=57.0
Q ss_pred HHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHHHHhcCCCHHHHHHHHHH
Q psy3877 15 SDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTRDVEVKKYCISL 94 (145)
Q Consensus 15 ~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~l~~~~~~~~~~~~i~~~ 94 (145)
+.+...+.++|+|+|+.|=+.|+ +.|+..|.+-+|.=..-+..-..+. ++. +..++. . ..
T Consensus 194 ~~~~~~A~~lG~AlQltNILRDv-----------~eD~~~GRvYLP~e~L~~~Gv~~ed---l~~-~~~~~~-~---~~- 253 (334)
T PLN02632 194 ESVYNAALALGIANQLTNILRDV-----------GEDARRGRVYLPQDELAQFGLTDED---IFA-GKVTDK-W---RA- 253 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-----------HHHHhCCceeCCHHHHHHcCCCHHH---Hhc-CCCCHH-H---HH-
Confidence 55788999999999999988885 6888999999997655554311112 222 222322 2 12
Q ss_pred HHHcChHHHHHHHHHHHHHHHHHHHhccCCC
Q psy3877 95 LDRFGSFEHTREVLKELDVSARTEVARLGGN 125 (145)
Q Consensus 95 l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~ 125 (145)
.+.+-...++.|..+|...+..+|..
T Consensus 254 -----l~~~~~~~Ar~~~~~a~~~l~~lp~~ 279 (334)
T PLN02632 254 -----FMKFQIKRARMYFAEAEEGVSELDPA 279 (334)
T ss_pred -----HHHHHHHHHHHHHHHHHHhHhhCCHH
Confidence 13333456888888888888888754
No 18
>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=94.72 E-value=0.42 Score=38.94 Aligned_cols=101 Identities=14% Similarity=0.164 Sum_probs=63.6
Q ss_pred hHHHHHhhcCCCh---HHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHHH
Q psy3877 2 MAIRLMQLFSDTK---SDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQIL 78 (145)
Q Consensus 2 ~~~rl~~~~~~~~---~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~l 78 (145)
|.++|+...+..+ .....++..+|+|+|+.|=+.|+ +.|+.+|++=||-=-.-+.... +.. +
T Consensus 148 mlt~l~~~~~~~~~~~~~~~~~A~~lG~aLQlTNIlRDv-----------~ED~~~GR~YlP~e~l~~~g~~---~~d-l 212 (336)
T TIGR01559 148 GLSRLFVASGFEDPSLGESEALSNSMGLFLQKTNIIRDY-----------LEDINEGRMFWPREIWSKYAKK---LGD-F 212 (336)
T ss_pred HHHHHHhhcCCCCcchhhhHHHHHHHHHHHHHHHHHHHH-----------HhHHhCCCCCCCHHHHHHcCCC---HHH-h
Confidence 4556665432111 13468999999999999988875 5777889999996533333321 112 2
Q ss_pred HhcCCCHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHhccCCCHH
Q psy3877 79 RQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPL 127 (145)
Q Consensus 79 ~~~~~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~~ 127 (145)
..+..++. ... .++.-...+..|...|...+..+++.+.
T Consensus 213 ~~~~~~~~----~~~------~l~~lv~~A~~~~~~al~yl~~l~~~~~ 251 (336)
T TIGR01559 213 KKPENSDK----ALQ------CLNELVTNALHHATDCLTYLSRLRDQSI 251 (336)
T ss_pred cCccccHH----HHH------HHHHHHHHHHHHHHHHHHHHHhCCCcch
Confidence 22322222 222 3555667788899999999999976543
No 19
>TIGR03465 HpnD squalene synthase HpnD. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated.
Probab=94.36 E-value=0.7 Score=36.03 Aligned_cols=88 Identities=14% Similarity=0.086 Sum_probs=58.3
Q ss_pred ChHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHHHHhcCCCHHHHHHHH
Q psy3877 13 TKSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTRDVEVKKYCI 92 (145)
Q Consensus 13 ~~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~l~~~~~~~~~~~~i~ 92 (145)
.++.....+.++|.|+|+.|=+.|+ +.|+..|++.+|.=..-+..-..+.| + .+..++ .+.
T Consensus 131 ~~~~~~~~a~~lG~AlqltnilRdv-----------~eD~~~gR~ylP~~~l~~~gv~~~~l---~-~~~~~~-~~~--- 191 (266)
T TIGR03465 131 TDARTLEYAHHLGRALQLTNILRDV-----------GEDARRGRIYLPAEELQRFGVPAADI---L-EGRYSP-ALA--- 191 (266)
T ss_pred CChhHHHHHHHHHHHHHHHHHHHHh-----------HHHHhCCCeecCHHHHHHcCCCHHHh---c-CCCCCH-HHH---
Confidence 3466788999999999999987775 57888999999986655544222222 2 222222 222
Q ss_pred HHHHHcChHHHHHHHHHHHHHHHHHHHhccCCC
Q psy3877 93 SLLDRFGSFEHTREVLKELDVSARTEVARLGGN 125 (145)
Q Consensus 93 ~~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~ 125 (145)
. .+..-...++.+.+.|...+..+|..
T Consensus 192 ~------~~~~l~~~A~~~l~~a~~~~~~~p~~ 218 (266)
T TIGR03465 192 A------LCRFQAERARAHYAEADALLPACDRR 218 (266)
T ss_pred H------HHHHHHHHHHHHHHHHHHhhhhCCHh
Confidence 2 24444556788888888888888753
No 20
>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=94.04 E-value=0.69 Score=36.12 Aligned_cols=86 Identities=10% Similarity=0.086 Sum_probs=57.3
Q ss_pred HHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHHHHhcCCCHHHHHHHHHH
Q psy3877 15 SDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTRDVEVKKYCISL 94 (145)
Q Consensus 15 ~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~l~~~~~~~~~~~~i~~~ 94 (145)
.....++.++|.|+|+.|=+.|+ +.|+..|.+.+|.=..-+..-..+. ++. +..++ .+ ..
T Consensus 134 ~~~~~~A~~lG~AlQltniLRDl-----------~eD~~~gR~YLP~~~l~~~Gv~~ed---l~~-~~~~~-~~---~~- 193 (266)
T TIGR03464 134 PENVALSDAICTALQLINFWQDV-----------GVDYRKGRVYLPRDDLARFGVSEED---LAA-GRATP-AL---RE- 193 (266)
T ss_pred hhHHHHHHHHHHHHHHHHHHHhh-----------HHHHhcCCccCCHHHHHHcCCCHHH---Hhc-CCCCH-HH---HH-
Confidence 44567899999999999877773 6788889999997655554421122 222 22222 22 22
Q ss_pred HHHcChHHHHHHHHHHHHHHHHHHHhccCCC
Q psy3877 95 LDRFGSFEHTREVLKELDVSARTEVARLGGN 125 (145)
Q Consensus 95 l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~ 125 (145)
.+......++.+...|...+..+|..
T Consensus 194 -----~~~~~~~~A~~~~~~a~~~~~~lp~~ 219 (266)
T TIGR03464 194 -----LMAFEVSRTRALLDRGAPLAARVDGR 219 (266)
T ss_pred -----HHHHHHHHHHHHHHHHHHhHHhCCHh
Confidence 24555567888899999999988854
No 21
>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=93.07 E-value=3.2 Score=32.05 Aligned_cols=91 Identities=16% Similarity=0.143 Sum_probs=56.6
Q ss_pred HHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchh-HhhCcchHHHHHHHhcCCchHHHHHHHHhcCCCHHHHHHHHH
Q psy3877 15 SDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCED-LTEGKFSFPIIHAIQSRPDDRQVIQILRQRTRDVEVKKYCIS 93 (145)
Q Consensus 15 ~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~D-l~eGk~TlPli~al~~~~~~~~l~~~l~~~~~~~~~~~~i~~ 93 (145)
+.....+.++|.|+|+.|=+.|+ +.| ++.|++-+|.=..-+..-..+. ++.....++. +. .
T Consensus 141 ~~~~~~a~~lG~alql~nilRd~-----------~~D~~~~gR~ylP~d~l~~~gv~~~d---l~~~~~~~~~-~~---~ 202 (267)
T PF00494_consen 141 EAARDAARALGRALQLTNILRDI-----------PEDALRRGRIYLPLDDLRRFGVTPED---LLAGRPRSER-LR---A 202 (267)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTH-----------HHH-HHTT---S-HHHHHHTTSSHHH---HHHHG-GGHH-HH---H
T ss_pred hhHHHHHHHHHHHHHHHHHHHHh-----------HHHHHhcccccCCchhHHHcCCCHHH---HHhcccCCHH-HH---H
Confidence 57899999999999999877774 688 8899999998766554311112 2222211222 22 2
Q ss_pred HHHHcChHHHHHHHHHHHHHHHHHHHhccCCCHHHH
Q psy3877 94 LLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLE 129 (145)
Q Consensus 94 ~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~~~~ 129 (145)
.+......++.+.++|...+..+|+...+.
T Consensus 203 ------~~~~~~~~A~~~l~~a~~~~~~l~~~~~~~ 232 (267)
T PF00494_consen 203 ------LIRELAARARAHLDEARAGLSALPPPRARP 232 (267)
T ss_dssp ------HHHHHHHHHHHHHHHHHHGGGGS--TTHHH
T ss_pred ------HHHHHHHHHHHHHHHHHHHHHHcCCHhhhH
Confidence 244666788999999999999995443333
No 22
>COG1562 ERG9 Phytoene/squalene synthetase [Lipid metabolism]
Probab=84.60 E-value=12 Score=29.92 Aligned_cols=88 Identities=17% Similarity=0.192 Sum_probs=57.7
Q ss_pred hHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcCCchHHHHHHHHhcCCCHHHHHHHHH
Q psy3877 14 KSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTRDVEVKKYCIS 93 (145)
Q Consensus 14 ~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~~~~~~l~~~l~~~~~~~~~~~~i~~ 93 (145)
..........+|.|+|+.|=+.|+ +.|.++|++=+|.=-........ ..+. ++..+ + .+.+
T Consensus 151 ~~~~~~~a~~lG~A~QlvNilRdv-----------~eD~~~GrvylP~e~l~~~g~~~---~d~~-~~~~~-~---~~~~ 211 (288)
T COG1562 151 DAATRAYARGLGLALQLVNILRDV-----------GEDRRRGRVYLPAEELARFGVSE---ADLL-AGRVD-D---AFRE 211 (288)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHh-----------HHHHhCCcccCCHHHHHHhCCCH---HHHH-cccch-h---HHHH
Confidence 344555566699999999887774 78899999999965444443221 1121 12211 1 2333
Q ss_pred HHHHcChHHHHHHHHHHHHHHHHHHHhccCCCH
Q psy3877 94 LLDRFGSFEHTREVLKELDVSARTEVARLGGNP 126 (145)
Q Consensus 94 ~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~ 126 (145)
.+++-...++.+...|...+..+|...
T Consensus 212 ------~~~~~~~~ar~~~~~a~~~~~~lp~~~ 238 (288)
T COG1562 212 ------LMRFEADRARDHLAEARRGLPALPGRA 238 (288)
T ss_pred ------HHHHHHHHHHHHHHHHHHhhhhCCccc
Confidence 356666788999999999999998653
No 23
>PF06783 UPF0239: Uncharacterised protein family (UPF0239); InterPro: IPR009621 This is a group of transmembrane proteins of unknown function.; GO: 0016021 integral to membrane
Probab=80.89 E-value=2 Score=28.04 Aligned_cols=25 Identities=12% Similarity=0.060 Sum_probs=19.3
Q ss_pred hHHHHHHHHHHHHHHHHHhchhccc
Q psy3877 14 KSDFTTLAGILGLYFQVRDDYCNLC 38 (145)
Q Consensus 14 ~~~l~~~G~~lG~afQI~DD~lD~~ 38 (145)
-+.+-+||..+|-+||++==+-=++
T Consensus 18 ~e~llRYGLf~GAIFQliCilAiI~ 42 (85)
T PF06783_consen 18 FENLLRYGLFVGAIFQLICILAIIL 42 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHheee
Confidence 4678999999999999975444333
No 24
>PF10820 DUF2543: Protein of unknown function (DUF2543); InterPro: IPR020251 This entry contains proteins with no known function.
Probab=66.12 E-value=3 Score=26.36 Aligned_cols=38 Identities=24% Similarity=0.191 Sum_probs=33.9
Q ss_pred hHHHHHhhcCCChHHHHHHHHHHHHHHHHHhchhcccc
Q psy3877 2 MAIRLMQLFSDTKSDFTTLAGILGLYFQVRDDYCNLCS 39 (145)
Q Consensus 2 ~~~rl~~~~~~~~~~l~~~G~~lG~afQI~DD~lD~~~ 39 (145)
|+.|||-.+--+.++-...+...|+.-|=+||+-.|..
T Consensus 39 LitRLmnneeIsEeaQ~EMA~eAgi~~~rID~IA~fLN 76 (81)
T PF10820_consen 39 LITRLMNNEEISEEAQQEMASEAGIDEQRIDDIANFLN 76 (81)
T ss_pred HHHHHhccHhhhHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence 78899998888888889999999999999999988864
No 25
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=55.05 E-value=14 Score=29.91 Aligned_cols=34 Identities=18% Similarity=0.215 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHH
Q psy3877 17 FTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPII 62 (145)
Q Consensus 17 l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli 62 (145)
+..--+.+=.|..|.||+.| .+++|+|+.|+-..
T Consensus 69 ~A~avEllH~asLiHDDI~D------------~s~~RRG~pt~~~~ 102 (323)
T PRK10888 69 IAALIEFIHTATLLHDDVVD------------ESDMRRGKATANAA 102 (323)
T ss_pred HHHHHHHHHHHHHHHccccc------------CCcccCCCCCHHHH
Confidence 33444556778899999987 34556666654443
No 26
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=54.57 E-value=5.6 Score=32.09 Aligned_cols=31 Identities=19% Similarity=0.241 Sum_probs=23.2
Q ss_pred HHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHH
Q psy3877 22 GILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHA 64 (145)
Q Consensus 22 ~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~a 64 (145)
+.+=.+.=|.||++| .+|+|+|++|....|.
T Consensus 76 EliH~~SLiHDDvmD------------~s~~RRG~pt~~~~~g 106 (322)
T COG0142 76 ELIHTASLIHDDLMD------------DDDLRRGKPTVHAKFG 106 (322)
T ss_pred HHHHHHHHHHhhccc------------CCCccCCCCCchhHhc
Confidence 345567779999966 4678888888887763
No 27
>PF06304 DUF1048: Protein of unknown function (DUF1048); InterPro: IPR008316 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 2O3L_B 2HH6_A 2O4T_A.
Probab=51.28 E-value=13 Score=25.22 Aligned_cols=33 Identities=15% Similarity=0.212 Sum_probs=21.1
Q ss_pred HHHHHHHHHH-----HHHHHHhchhccccCchhcCCCc
Q psy3877 16 DFTTLAGILG-----LYFQVRDDYCNLCSKEYSENKSF 48 (145)
Q Consensus 16 ~l~~~G~~lG-----~afQI~DD~lD~~~~~~~~GK~~ 48 (145)
.+..|-.+.| -..+|.+|++|+|-.....|+++
T Consensus 30 ~i~~Yl~~~~~~~g~~~~~il~dildlfEe~aadG~~V 67 (103)
T PF06304_consen 30 AIQKYLWYFGPTDGRDMMEILSDILDLFEEAAADGKSV 67 (103)
T ss_dssp HHHHHHHHHTBSSHHHHHHHHHHHHHHHHHHHHTT--H
T ss_pred HHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHcCCCh
Confidence 3444444444 46799999999998766667654
No 28
>KOG2114|consensus
Probab=48.68 E-value=79 Score=29.24 Aligned_cols=87 Identities=8% Similarity=0.089 Sum_probs=55.3
Q ss_pred chHHHHHHHhcCCchHHHHHHHHhcCCCH--HHHHHHHHHHHHcChHHHHHHHHHHH----------------HHHHHHH
Q psy3877 57 FSFPIIHAIQSRPDDRQVIQILRQRTRDV--EVKKYCISLLDRFGSFEHTREVLKEL----------------DVSARTE 118 (145)
Q Consensus 57 ~TlPli~al~~~~~~~~l~~~l~~~~~~~--~~~~~i~~~l~~~g~~~~~~~~~~~~----------------~~~A~~~ 118 (145)
-|..++.++-...+.+.|...+++...+. -+++.+.+++++++-.+.+.-++..+ ..+|.+.
T Consensus 433 httlLLncYiKlkd~~kL~efI~~~~~g~~~fd~e~al~Ilr~snyl~~a~~LA~k~~~he~vl~ille~~~ny~eAl~y 512 (933)
T KOG2114|consen 433 HTTLLLNCYIKLKDVEKLTEFISKCDKGEWFFDVETALEILRKSNYLDEAELLATKFKKHEWVLDILLEDLHNYEEALRY 512 (933)
T ss_pred hHHHHHHHHHHhcchHHHHHHHhcCCCcceeeeHHHHHHHHHHhChHHHHHHHHHHhccCHHHHHHHHHHhcCHHHHHHH
Confidence 34445555544444446777776654221 14677899999999999988887765 4578888
Q ss_pred HhccCCCHHHHHHHHHHhhhcCCCCC
Q psy3877 119 VARLGGNPLLEAILDELLTWDTPDSP 144 (145)
Q Consensus 119 L~~lp~~~~~~~ll~~l~~~~~~~~~ 144 (145)
+..+|.++....+ .....+.-+..|
T Consensus 513 i~slp~~e~l~~l-~kyGk~Ll~h~P 537 (933)
T KOG2114|consen 513 ISSLPISELLRTL-NKYGKILLEHDP 537 (933)
T ss_pred HhcCCHHHHHHHH-HHHHHHHHhhCh
Confidence 8899987766553 344444433333
No 29
>PRK13105 ubiA prenyltransferase; Reviewed
Probab=46.48 E-value=11 Score=29.88 Aligned_cols=33 Identities=9% Similarity=0.095 Sum_probs=26.4
Q ss_pred HHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhcC
Q psy3877 25 GLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSR 68 (145)
Q Consensus 25 G~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~~ 68 (145)
..++.+.+|+.|+.+| -++|+.|+|+.+..+..
T Consensus 173 ~~a~~ii~~irDie~D-----------r~~G~~Tlpv~lG~~~a 205 (282)
T PRK13105 173 GMASHAFGAVQDVVAD-----------REAGIASIATVLGARRT 205 (282)
T ss_pred HHHHHHHHhCcchHhH-----------HHcCCccchHHhcHHHH
Confidence 6689999999997655 46789999999887653
No 30
>KOG3330|consensus
Probab=44.20 E-value=18 Score=26.52 Aligned_cols=35 Identities=17% Similarity=0.384 Sum_probs=27.8
Q ss_pred ChHHHHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhC
Q psy3877 13 TKSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEG 55 (145)
Q Consensus 13 ~~~~l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eG 55 (145)
.+..+.+.|.++|+ .++||+|-= ++-|.|.|+++-
T Consensus 42 Vn~qLdkMGyNiG~--RLiedFLAk------s~vpRC~dfret 76 (183)
T KOG3330|consen 42 VNKQLDKMGYNIGI--RLIEDFLAK------SNVPRCVDFRET 76 (183)
T ss_pred HHHHHHhccchhhH--HHHHHHHhh------cCCchhhhHHHH
Confidence 46789999999997 588998863 456789999874
No 31
>PF04358 DsrC: DsrC like protein; InterPro: IPR007453 DsrC (P45573 from SWISSPROT) has been observed to co-purify with Desulphovibrio vulgaris dissimilatory sulphite reductase []. However, DsrC appears to be only loosely associated to the sulphite reductase, which suggests that it may not be an integral part of the dissimilatory sulphite reductase. Many proteins in this entry are found in organisms such as Escherichia coli and Haemophilus influenzae which do not contain dissimilatory sulphite reductases but can synthesise assimilatory sirohaem sulphite and nitrite reductases. It is speculated that DsrC may be involved in the assembly, folding or stabilisation of sirohaem proteins []. The strictly conserved cysteine in the C terminus suggests that DsrC may have a catalytic function in the metabolism of sulphur compounds []. Also included in this entry is TusE, a partner to TusBCD in a sulphur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Many proteins in this entry are annotated as the third (gamma) subunit of dissimilatory sulphite reductase ; PDB: 2V4J_F 2A5W_C 1SAU_A 1JI8_A 1YX3_A.
Probab=43.72 E-value=84 Score=21.38 Aligned_cols=53 Identities=17% Similarity=0.268 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHcChHHHHHHHHHHHHHH-------HHHHHhccCCCHHHHHHHHHHhhhcCC
Q psy3877 87 VKKYCISLLDRFGSFEHTREVLKELDVS-------ARTEVARLGGNPLLEAILDELLTWDTP 141 (145)
Q Consensus 87 ~~~~i~~~l~~~g~~~~~~~~~~~~~~~-------A~~~L~~lp~~~~~~~ll~~l~~~~~~ 141 (145)
.+..+++...+.|..-..+.+++..... .+..-+-||.+|.+.+ ..++-..++
T Consensus 46 vI~flR~~y~~~~~~P~~R~l~K~~~~~~g~~~~~~k~L~~LFP~gP~k~a--~kiAGLPkP 105 (109)
T PF04358_consen 46 VIRFLRDYYQEYGVSPAIRMLIKALGEDLGEDKGNSKYLYQLFPGGPAKQA--CKIAGLPKP 105 (109)
T ss_dssp HHHHHHHHHHHHSS---HHHHHHHHHHHCSTT---HHHHHHHSTTHHHHCH--HHHHT-S--
T ss_pred HHHHHHHHHHHHCCCCcHHHHHHHHhhhcCCCchhHHHHHHHcCCCHHHHH--HHHhcCCCC
Confidence 4567788888899888888888887777 5555566898887765 455555443
No 32
>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=43.05 E-value=39 Score=26.01 Aligned_cols=20 Identities=20% Similarity=0.193 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHhchhc
Q psy3877 17 FTTLAGILGLYFQVRDDYCN 36 (145)
Q Consensus 17 l~~~G~~lG~afQI~DD~lD 36 (145)
+..--+.+=.|+-|.||+.|
T Consensus 44 la~aiEllh~asLIhDDI~D 63 (259)
T cd00685 44 LAAAIELLHTASLVHDDVMD 63 (259)
T ss_pred HHHHHHHHHHHHHHHhhhcc
Confidence 34444567788999999977
No 33
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=39.89 E-value=1.8e+02 Score=22.93 Aligned_cols=66 Identities=20% Similarity=0.256 Sum_probs=44.2
Q ss_pred HHHHHHHhcC-C---chHHHHHHHHhcCCCHHHHHHHHHHHHHcChHHH-----------------------HHHHHHHH
Q psy3877 59 FPIIHAIQSR-P---DDRQVIQILRQRTRDVEVKKYCISLLDRFGSFEH-----------------------TREVLKEL 111 (145)
Q Consensus 59 lPli~al~~~-~---~~~~l~~~l~~~~~~~~~~~~i~~~l~~~g~~~~-----------------------~~~~~~~~ 111 (145)
.|+|+.+-.. + +-.+|.+.+. +..+.++++..+++|.+.|-++. .+..-++.
T Consensus 124 ~~virel~~~~~~~~~~~~ia~~l~-p~is~~ev~~sL~~L~~~glikk~~~g~y~~t~~~l~~~~~~~~~avr~~h~q~ 202 (271)
T TIGR02147 124 NSVIRELLGVMPFADDPEELAKRCF-PKISAEQVKESLDLLERLGLIKKNEDGFYKQTDKAVSTGDEVIPLAVRQYQKQM 202 (271)
T ss_pred HHHHHHHhhcCCCCCCHHHHHHHhC-CCCCHHHHHHHHHHHHHCCCeeECCCCcEEeecceeecCCccchHHHHHHHHHH
Confidence 4666666532 1 1124555554 33467888899999999888755 45566677
Q ss_pred HHHHHHHHhccCCC
Q psy3877 112 DVSARTEVARLGGN 125 (145)
Q Consensus 112 ~~~A~~~L~~lp~~ 125 (145)
.+.|.++|+.+|.+
T Consensus 203 l~lA~~al~~~p~~ 216 (271)
T TIGR02147 203 IDLAKEALDALPPS 216 (271)
T ss_pred HHHHHHHHHhCCcc
Confidence 88899999988753
No 34
>PRK12872 ubiA prenyltransferase; Reviewed
Probab=39.49 E-value=15 Score=28.61 Aligned_cols=33 Identities=12% Similarity=0.146 Sum_probs=25.1
Q ss_pred HHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhc
Q psy3877 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQS 67 (145)
Q Consensus 24 lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~ 67 (145)
+-.++++..|+.|+.+| -+.|+.|+|+.+..+.
T Consensus 173 ~~~~~~~~~d~~D~e~D-----------~~~G~~Tlpv~lG~~~ 205 (285)
T PRK12872 173 KSFIREIVFDIKDIEGD-----------RKSGLKTLPIVLGKER 205 (285)
T ss_pred HHHHHHHHHhcccchhH-----------HHcCCcccchhcchHH
Confidence 45678888888886554 4678999999987654
No 35
>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=34.34 E-value=49 Score=26.65 Aligned_cols=33 Identities=15% Similarity=0.158 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHH
Q psy3877 18 TTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPII 62 (145)
Q Consensus 18 ~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli 62 (145)
...-+.+=.|.-|.||++| .+++|+|+.|.-..
T Consensus 73 A~avEliH~asLiHDDiiD------------~s~~RRG~pt~h~~ 105 (322)
T TIGR02749 73 AEITEMIHTASLVHDDVID------------ESDTRRGIETVHSL 105 (322)
T ss_pred HHHHHHHHHHHHHHccccc------------CccccCCCccHHHH
Confidence 3344566778899999988 34556666665544
No 36
>KOG2168|consensus
Probab=33.85 E-value=2.3e+02 Score=26.27 Aligned_cols=106 Identities=17% Similarity=0.105 Sum_probs=57.0
Q ss_pred HHHHhchhc--cccCchhcCCCcchhHhhC-cchHHHHHHHhcCCchHHHHHHHHhcCCCHHHHHHHHHHHHHcChHHHH
Q psy3877 28 FQVRDDYCN--LCSKEYSENKSFCEDLTEG-KFSFPIIHAIQSRPDDRQVIQILRQRTRDVEVKKYCISLLDRFGSFEHT 104 (145)
Q Consensus 28 fQI~DD~lD--~~~~~~~~GK~~g~Dl~eG-k~TlPli~al~~~~~~~~l~~~l~~~~~~~~~~~~i~~~l~~~g~~~~~ 104 (145)
+|.+.=+++ +.......|. .|+..+ .+.||++|.+-.+..-+.-.+.++......+.+......+..+.+-...
T Consensus 298 ~~~VrAfl~~~~~~~~~~~g~---~D~~~~~~P~W~~vyy~lR~G~lk~A~~~l~e~~~~~~~l~~~f~~y~~A~~~~~~ 374 (835)
T KOG2168|consen 298 YQKVRAFLNIKLQARNGSWGL---SDLEVINVPLWPLVYYLLRCGDLKAASQFLNENKDFFEKLAELFPTYFNAYAKNLS 374 (835)
T ss_pred HHHHHHHHHHHhcccccccCC---CcccccCccchHHHHHHHhhhhHHHHHHHHHHhhhhHHHHHHHHHHHHHhhhcCCC
Confidence 677777777 2233223344 555555 9999999988776543333344444333444444444333222222222
Q ss_pred HHHHHHHHHHHHHHHhccCCCHHHHHHHHHHh
Q psy3877 105 REVLKELDVSARTEVARLGGNPLLEAILDELL 136 (145)
Q Consensus 105 ~~~~~~~~~~A~~~L~~lp~~~~~~~ll~~l~ 136 (145)
..+=.++.-+-...+..-+.+|+|.++-..+.
T Consensus 375 ~~le~qlrl~~~~~l~~~~~DpyK~AvY~iig 406 (835)
T KOG2168|consen 375 SKLEKQLRLRLRSELGRNSTDPYKLAVYKIIG 406 (835)
T ss_pred ccccHHHHHHHHHHhccccCChHHHHHHHHHh
Confidence 33334455555556656677788877655543
No 37
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=33.10 E-value=75 Score=18.22 Aligned_cols=30 Identities=20% Similarity=0.019 Sum_probs=20.0
Q ss_pred HHHHHHHHHHhccCCCHHHHHHHHHHhhhc
Q psy3877 110 ELDVSARTEVARLGGNPLLEAILDELLTWD 139 (145)
Q Consensus 110 ~~~~~A~~~L~~lp~~~~~~~ll~~l~~~~ 139 (145)
++.+++...|..+|++-.++.++..+++.+
T Consensus 23 ~~~~~~~~~i~~i~~~i~r~~y~~~la~~~ 52 (59)
T PF10410_consen 23 EAVREAAPLIAQIPDPIERELYIRELAERL 52 (59)
T ss_dssp HHHHHHHHHHTT--SHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 455677778888887777777777777643
No 38
>PLN00012 chlorophyll synthetase; Provisional
Probab=31.55 E-value=21 Score=29.55 Aligned_cols=33 Identities=24% Similarity=0.424 Sum_probs=25.3
Q ss_pred HHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHh
Q psy3877 23 ILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ 66 (145)
Q Consensus 23 ~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~ 66 (145)
.+++++-+.+|+.|+- .|-+.|+.|+|+.+..+
T Consensus 263 l~~lai~ivnd~~Die-----------~Dr~aG~~TLpV~~G~~ 295 (375)
T PLN00012 263 IAGLGIAIVNDFKSIE-----------GDRALGLQSLPVAFGVE 295 (375)
T ss_pred HHHHHHHHHhhhcchh-----------hHHHcCCcccceeechH
Confidence 4677788899987764 45678899999987654
No 39
>cd02682 MIT_AAA_Arch MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in mostly archaebacterial AAA-ATPases. The molecular function of the MIT domain is unclear.
Probab=31.53 E-value=1.4e+02 Score=18.92 Aligned_cols=17 Identities=6% Similarity=-0.015 Sum_probs=7.7
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy3877 102 EHTREVLKELDVSARTE 118 (145)
Q Consensus 102 ~~~~~~~~~~~~~A~~~ 118 (145)
..-+..+.+|.++|...
T Consensus 50 ~~yr~ki~eY~~Rae~L 66 (75)
T cd02682 50 LIYEQMINEYKRRIEVL 66 (75)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33344444455544443
No 40
>CHL00151 preA prenyl transferase; Reviewed
Probab=31.41 E-value=63 Score=25.98 Aligned_cols=36 Identities=17% Similarity=0.159 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHH
Q psy3877 17 FTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHA 64 (145)
Q Consensus 17 l~~~G~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~a 64 (145)
+...-+.+=.|.-|.||+.| .+++|.|+.|+-..|.
T Consensus 73 ~A~aiEllH~asLiHDDi~D------------~s~~RRG~pt~h~~~G 108 (323)
T CHL00151 73 LAEITEIIHTASLVHDDVID------------ECSIRRGIPTVHKIFG 108 (323)
T ss_pred HHHHHHHHHHHHHHHccccc------------CccccCCCccHHHHhC
Confidence 44445567778899999977 3556666666555443
No 41
>PLN02923 xylose isomerase
Probab=31.34 E-value=1.4e+02 Score=25.64 Aligned_cols=52 Identities=21% Similarity=0.271 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHHHHhc--hhccccCch-hcCCCcchhHhhCcchHHHH--HHHhc
Q psy3877 16 DFTTLAGILGLYFQVRDD--YCNLCSKEY-SENKSFCEDLTEGKFSFPII--HAIQS 67 (145)
Q Consensus 16 ~l~~~G~~lG~afQI~DD--~lD~~~~~~-~~GK~~g~Dl~eGk~TlPli--~al~~ 67 (145)
.+..|++-+=.|-.|+.| +-++..+.+ ....+.|.+|.+|+.|+--+ |+++.
T Consensus 401 gMD~~A~gl~~Aa~l~ed~~l~~~~~~RYas~~~g~G~~i~~G~~~l~~l~~~a~~~ 457 (478)
T PLN02923 401 GMDTMARGLRNAAKLLEEGSLPELVRKRYASFDSELGAQIEAGKADFEELEKKALEW 457 (478)
T ss_pred HHHHHHHHHHHHHHHHhcccHHHHHHHHhccccchhchHHHcCcCCHHHHHHHHHhc
Confidence 456677777788888777 555544432 12345789999999999988 66654
No 42
>PF10350 DUF2428: Putative death-receptor fusion protein (DUF2428); InterPro: IPR019442 This domain is found in a family of proteins of unknown function that are conserved from plants to humans. Several of these proteins have been annotated as being HEAT repeat-containing proteins while others are designated as death-receptor interacting proteins, but neither of these has yet been confirmed. Aberrations in the genes encoding these proteins have been observed in benign thyroid adenomas [].
Probab=29.78 E-value=2.6e+02 Score=21.55 Aligned_cols=123 Identities=14% Similarity=0.127 Sum_probs=66.1
Q ss_pred HHHHHHHHHHHHhchhccccCchhcCC-----------CcchhHhhCcchHHHHHHHhcCCchHHHHH-HHH--------
Q psy3877 20 LAGILGLYFQVRDDYCNLCSKEYSENK-----------SFCEDLTEGKFSFPIIHAIQSRPDDRQVIQ-ILR-------- 79 (145)
Q Consensus 20 ~G~~lG~afQI~DD~lD~~~~~~~~GK-----------~~g~Dl~eGk~TlPli~al~~~~~~~~l~~-~l~-------- 79 (145)
+.+.+.+.++|.+=.+++..++.--|- +...+-........+.++...-.+...+.. ++.
T Consensus 5 ~~~ll~l~~~i~~~~~~vl~~~speg~~~~~~~~~~~~~~~~~~~~~~~q~il~~~Wr~iKE~s~Ll~~l~~~~~~~~~~ 84 (255)
T PF10350_consen 5 LNRLLSLCFRIWEFVLPVLCNDSPEGHLPEDEEDEEDNDEDEEDSSPSSQLILSCCWRSIKESSLLLGTLVEKIPLPPDS 84 (255)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCcCcCCccchhhhccccchhhhcCCcchHHHHHHHHHHHHHHHHHHHHHHhccccCcc
Confidence 445567777777777777655332232 111111223334444445443333223333 331
Q ss_pred -hcCCCHHHHHHHHH-------HHHHcChHHHHHHHHHHHHHHHH----HHHhccCCCHHHHHHHHHHhhh------cCC
Q psy3877 80 -QRTRDVEVKKYCIS-------LLDRFGSFEHTREVLKELDVSAR----TEVARLGGNPLLEAILDELLTW------DTP 141 (145)
Q Consensus 80 -~~~~~~~~~~~i~~-------~l~~~g~~~~~~~~~~~~~~~A~----~~L~~lp~~~~~~~ll~~l~~~------~~~ 141 (145)
....+.+.+..+-+ -++..|+++.+..-.....++.. ..+..+| ..+.+.+++.+.+- ++|
T Consensus 85 ~~~~ls~~~i~~ig~~l~~~L~~~rHrGAfe~~~~~f~~lc~~l~~~~~~~l~~LP-~~WL~~~l~~i~~~~~~~~~iTR 163 (255)
T PF10350_consen 85 SNSLLSPDQIEKIGELLIEQLLEIRHRGAFESVYPGFTALCRRLWSSNNPELSELP-EEWLDELLEAIESKGQQKLSITR 163 (255)
T ss_pred cccCCCHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHhcCCCchHHHhH-HHHHHHHHHHHhccccccccccc
Confidence 11224454444333 23456999999988888888777 4555554 45666777777666 567
Q ss_pred CC
Q psy3877 142 DS 143 (145)
Q Consensus 142 ~~ 143 (145)
||
T Consensus 164 RS 165 (255)
T PF10350_consen 164 RS 165 (255)
T ss_pred cc
Confidence 65
No 43
>PF09053 CagZ: CagZ; InterPro: IPR015139 Helicobacter pylori (Campylobacter pylori) clinical isolates can be classified into two types according to their degree of pathogenicity. Type I strains are associated with a severe disease pathology, express functional VacA (vacuolating cytotoxin A) and contain an insertion of 40 kb of foreign DNA: the cag (cytotoxin-associated gene) pathogenicity island (cagPAI). Type II strains lack the 40 kb insert, cagPAI. The cagPAI may be divided into two regions, cag I and cag II and contain approximately 16 and 15 genes, respectively. The cagPAI encodes a type IV secretion system (T4SS), which delivers CagA into the cytosol of gastric epithelial cells through a rigid needle structure covered by Cag7 or CagY, a VirB10-homologous protein, and CagT, a VirB7-homologous protein, at the base []. The CagA protein is the virulence factor that induces morphological changes in host cells, which may be associated with the development of peptic ulcer and gastric carcinoma []. CagZ is a 23 kDa protein consisting of a single compact L-shaped domain, composed of seven alpha-helices that run antiparallel to each other. 70% of the residues are in alpha-helix conformation and no beta-sheet is present. CagZ is essential for the translocation of the pathogenic protein CagA into host cells []. ; PDB: 1S2X_A.
Probab=29.49 E-value=39 Score=24.17 Aligned_cols=11 Identities=27% Similarity=0.697 Sum_probs=9.4
Q ss_pred HHHHHHHHHHH
Q psy3877 21 AGILGLYFQVR 31 (145)
Q Consensus 21 G~~lG~afQI~ 31 (145)
|.-+|+||||.
T Consensus 142 gnmmgvafqil 152 (199)
T PF09053_consen 142 GNMMGVAFQIL 152 (199)
T ss_dssp HHHHHHHHHHT
T ss_pred Cccceeeeeee
Confidence 67799999983
No 44
>PRK12465 xylose isomerase; Provisional
Probab=28.85 E-value=1.6e+02 Score=25.02 Aligned_cols=51 Identities=18% Similarity=0.175 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHHhc--hhccccCch-hcCCCcchhHhhCcchHHHH--HHHh
Q psy3877 16 DFTTLAGILGLYFQVRDD--YCNLCSKEY-SENKSFCEDLTEGKFSFPII--HAIQ 66 (145)
Q Consensus 16 ~l~~~G~~lG~afQI~DD--~lD~~~~~~-~~GK~~g~Dl~eGk~TlPli--~al~ 66 (145)
.+..|++-|=.|-.|+.| +-++..+.+ ....+.|.+|.+||.|+--+ |+++
T Consensus 367 gmD~~A~gl~~A~~~~ed~~~~~~~~~RY~s~~~~~g~~i~~g~~~l~~l~~~a~~ 422 (445)
T PRK12465 367 GMDAFARGLEVANALLTSSPLEQWRAERYASFDSGAGADFAAGKSTLADLAAHAAG 422 (445)
T ss_pred HHHHHHHHHHHHHHHHhcccHHHHHHHHhcccchhhChHHHcCcCCHHHHHHHHHc
Confidence 456677777788888877 555544432 12335689999999999988 6655
No 45
>PRK12884 ubiA prenyltransferase; Reviewed
Probab=28.08 E-value=66 Score=24.97 Aligned_cols=33 Identities=15% Similarity=0.188 Sum_probs=23.5
Q ss_pred HHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHh
Q psy3877 23 ILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ 66 (145)
Q Consensus 23 ~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~ 66 (145)
...+++++..|+.|.- +|-+.|+.|+|+.+.-+
T Consensus 166 ~~~~~~~~~~~~~D~e-----------~D~~~G~~Tl~v~~G~~ 198 (279)
T PRK12884 166 LMTLGREIMKDIEDVE-----------GDRLRGARTLAILYGEK 198 (279)
T ss_pred HHHHHHHHHHHhhhhh-----------hHHHcCCeeechHhcHH
Confidence 3445667777777753 56678899999988654
No 46
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=27.93 E-value=2.2e+02 Score=20.00 Aligned_cols=39 Identities=13% Similarity=0.139 Sum_probs=25.0
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHcChHHHHHHHHHHHH
Q psy3877 73 QVIQILRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELD 112 (145)
Q Consensus 73 ~l~~~l~~~~~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~ 112 (145)
+|...+.+...+++.+..+++.+.+.|-++.. ..++.++
T Consensus 30 el~~kL~~kg~~~~~i~~vl~~l~~~~~ldD~-~~a~~~~ 68 (157)
T PRK00117 30 ELRRKLAAKGFSEEVIEAVLDRLKEEGLLDDE-RFAESFV 68 (157)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHH-HHHHHHH
Confidence 56666666666677777788877777666554 3344333
No 47
>PRK10581 geranyltranstransferase; Provisional
Probab=27.89 E-value=60 Score=25.91 Aligned_cols=32 Identities=19% Similarity=0.258 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHhch--hccccCchhcCCCcchhHhhCcchHHHHH
Q psy3877 20 LAGILGLYFQVRDDY--CNLCSKEYSENKSFCEDLTEGKFSFPIIH 63 (145)
Q Consensus 20 ~G~~lG~afQI~DD~--lD~~~~~~~~GK~~g~Dl~eGk~TlPli~ 63 (145)
--+.+=.|.-|.||+ +| .+|+|.|++|.-..|
T Consensus 72 avEliH~aSLiHDDip~~D------------~s~~RRG~pt~h~~~ 105 (299)
T PRK10581 72 AVECIHAYSLIHDDLPAMD------------DDDLRRGLPTCHVKF 105 (299)
T ss_pred HHHHHHHHHHHHcCccccc------------CCCccCCCcChHHHh
Confidence 334566788999999 87 355566666655543
No 48
>PF12193 Sulf_coat_C: Sulfolobus virus coat protein C terminal; InterPro: IPR022014 This domain family is found in viruses, and is approximately 70 amino acids in length. It is the C-terminal of a coat protein in sulfolobus viruses. ; PDB: 3F2E_A.
Probab=26.13 E-value=1.6e+02 Score=17.82 Aligned_cols=39 Identities=18% Similarity=0.477 Sum_probs=16.8
Q ss_pred HcChHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHH
Q psy3877 97 RFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDEL 135 (145)
Q Consensus 97 ~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~~~~~ll~~l 135 (145)
+.|...-.+...+.+.-+..++|..+...|+..-+++.+
T Consensus 7 qygvtgpnraiyqgfglkvaralnr~g~gpalvnmingl 45 (69)
T PF12193_consen 7 QYGVTGPNRAIYQGFGLKVARALNRIGSGPALVNMINGL 45 (69)
T ss_dssp HHT--GGGHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHH
T ss_pred hhcCCCccHHHHHhhhHHHHHHHHhcCCchHHHHHHhhh
Confidence 344444444444444444445555555555444444433
No 49
>PRK10416 signal recognition particle-docking protein FtsY; Provisional
Probab=25.92 E-value=3.5e+02 Score=21.74 Aligned_cols=30 Identities=10% Similarity=-0.015 Sum_probs=17.9
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHcChHH
Q psy3877 73 QVIQILRQRTRDVEVKKYCISLLDRFGSFE 102 (145)
Q Consensus 73 ~l~~~l~~~~~~~~~~~~i~~~l~~~g~~~ 102 (145)
.+.+++.++..+++.+.++.+.+.+.+.-.
T Consensus 34 ~~~~l~~~~~~~~~~~~~l~~~L~~~dv~~ 63 (318)
T PRK10416 34 GINGLFAKKKIDEDLLEELEELLIEADVGV 63 (318)
T ss_pred HHHHHhCCCCCCHHHHHHHHHHHHHCCCCH
Confidence 344555444446666777777777776533
No 50
>PRK13591 ubiA prenyltransferase; Provisional
Probab=25.86 E-value=17 Score=29.37 Aligned_cols=31 Identities=16% Similarity=0.180 Sum_probs=22.5
Q ss_pred HHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhc
Q psy3877 26 LYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQS 67 (145)
Q Consensus 26 ~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~ 67 (145)
.+..+.+|+.|+-+ |-++|+.|+|+.+..+.
T Consensus 193 ~~~~iindirDiEG-----------Dr~~G~kTLPV~lG~~~ 223 (307)
T PRK13591 193 FINSCVYDFKDVKG-----------DTLAGIKTLPVSLGEQK 223 (307)
T ss_pred HHHHHHHHhhhhHh-----------HHHcCCeeEEEEECHHH
Confidence 34457888888654 55788999999876554
No 51
>TIGR02056 ChlG chlorophyll synthase, ChlG. This model represents the strictly cyanobacterial and plant-specific chlorophyll synthase ChlG. ChlG is the enzyme (esterase) which attaches the side chain moiety onto chlorophyllide a. Both geranylgeranyl and phytyl pyrophosphates are substrates to varying degrees in enzymes from different sources. Thus, ChlG may act as the final or penultimate step in chlorophyll biosynthesis (along with the geranylgeranyl reductase, ChlP).
Probab=25.26 E-value=43 Score=26.69 Aligned_cols=32 Identities=25% Similarity=0.395 Sum_probs=22.2
Q ss_pred HHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHh
Q psy3877 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ 66 (145)
Q Consensus 24 lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~ 66 (145)
...++-+.+|+.|+ -+|.+.|+.|+|+.+..+
T Consensus 195 ~~~~i~~~n~~~D~-----------e~D~~~G~~Tlpv~lG~~ 226 (306)
T TIGR02056 195 AGLGIAIVNDFKSV-----------EGDRALGLQSLPVAFGIE 226 (306)
T ss_pred HHHHHHHHHHccCh-----------HHHHHcCCcCcchhcChH
Confidence 34445567777765 356678999999987654
No 52
>COG2005 ModE N-terminal domain of molybdenum-binding protein [General function prediction only]
Probab=25.17 E-value=68 Score=22.64 Aligned_cols=34 Identities=15% Similarity=0.016 Sum_probs=27.2
Q ss_pred HHHHHHHHHcChHHHHHHHHHHHHHHHHHHHhcc
Q psy3877 89 KYCISLLDRFGSFEHTREVLKELDVSARTEVARL 122 (145)
Q Consensus 89 ~~i~~~l~~~g~~~~~~~~~~~~~~~A~~~L~~l 122 (145)
-+++..|.++|++..+-..+.--...|+..|+.+
T Consensus 22 ~~LL~~I~etGSIs~AAk~~GiSYk~AW~~i~~~ 55 (130)
T COG2005 22 IELLKAIAETGSISAAAKAAGISYKSAWDYIKAL 55 (130)
T ss_pred HHHHHHHHHhCCHHHHHHHcCCCHHHHHHHHHHH
Confidence 3588899999999999888887777777777643
No 53
>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=24.73 E-value=2.1e+02 Score=23.43 Aligned_cols=45 Identities=24% Similarity=0.187 Sum_probs=35.8
Q ss_pred cChHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhhhcCCC
Q psy3877 98 FGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELLTWDTPD 142 (145)
Q Consensus 98 ~g~~~~~~~~~~~~~~~A~~~L~~lp~~~~~~~ll~~l~~~~~~~ 142 (145)
++..+.+.+.+..+.++|.+.+..+|.....+.+...|..++--|
T Consensus 250 Y~~~~~~~~Rl~~f~~~A~~~~~~Lp~~~fHr~iv~GLla~YLSD 294 (330)
T PF10776_consen 250 YPDEEEMEERLKYFVEKALEQASRLPYPKFHRMIVRGLLAMYLSD 294 (330)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHhCC
Confidence 345667778888999999999999998887777777777666555
No 54
>PRK12883 ubiA prenyltransferase UbiA-like protein; Reviewed
Probab=24.68 E-value=53 Score=25.59 Aligned_cols=30 Identities=20% Similarity=0.294 Sum_probs=21.2
Q ss_pred HHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHh
Q psy3877 26 LYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ 66 (145)
Q Consensus 26 ~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~ 66 (145)
.++.+.+|+.|+. .|-+.|+.|+|+.+..+
T Consensus 168 ~~~~~~~~~~D~e-----------~D~~~G~~Tlpv~~G~~ 197 (277)
T PRK12883 168 VAREIMKDIEDIE-----------GDKAKGAKTLPIIIGKK 197 (277)
T ss_pred HHHHHHhhhhhhc-----------cHHHcCCcCcChHhcHH
Confidence 4555667766643 46678899999988654
No 55
>PRK10356 hypothetical protein; Provisional
Probab=24.37 E-value=1.6e+02 Score=23.56 Aligned_cols=68 Identities=10% Similarity=-0.000 Sum_probs=39.9
Q ss_pred HHHHHHHhcC--CchHHHHHHHHhcCCCHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHhccCCCHH
Q psy3877 59 FPIIHAIQSR--PDDRQVIQILRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPL 127 (145)
Q Consensus 59 lPli~al~~~--~~~~~l~~~l~~~~~~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~A~~~L~~lp~~~~ 127 (145)
+|+|-..+.. .++..|..+..+...+.++..++..+.+++++-. .........+..+.-++.+|.+-.
T Consensus 85 ~P~I~~~N~~I~~eR~~L~~l~~~~~ls~~e~~~L~~la~~Ykv~~-~~~~~~~~~~~LL~RVDiIP~slv 154 (274)
T PRK10356 85 MPYITSQNAAITAERNWLISKQYQGQWSPAERARLKDIAKRYKVKW-SGNTRKIPWNTLLERVDIIPTSMV 154 (274)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHcCCCc-CCCcchhhHHHHHHHhCcCCHHHH
Confidence 4666665543 2233566665555567788888888888888641 111122233555666777776543
No 56
>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=24.25 E-value=2.4e+02 Score=19.20 Aligned_cols=60 Identities=17% Similarity=0.172 Sum_probs=43.4
Q ss_pred HHHHHHhcCCC-HHHHHHHHHHHHHcChHHHH----HHHHHHHHHHHHHHHhccCCCHHHHHHHH
Q psy3877 74 VIQILRQRTRD-VEVKKYCISLLDRFGSFEHT----REVLKELDVSARTEVARLGGNPLLEAILD 133 (145)
Q Consensus 74 l~~~l~~~~~~-~~~~~~i~~~l~~~g~~~~~----~~~~~~~~~~A~~~L~~lp~~~~~~~ll~ 133 (145)
...++..+..+ +++..-+..++..+++.=|. .+..+...+++++.|+.+|.|..+-.|+.
T Consensus 38 ~~~Ly~~~G~t~EeeA~lCLaLLmGYnat~yd~geke~~~Q~vL~Rs~~vL~~Lp~SlLK~~Llt 102 (106)
T PF06603_consen 38 SNDLYSQHGSTPEEEANLCLALLMGYNATIYDNGEKEEKKQEVLDRSWEVLDKLPASLLKVQLLT 102 (106)
T ss_pred HHHHHhccCCCHHHHHHHHHHHHHhccchhhhCccHHHHHHHHHHHHHHHHHhCCcHHHHHHHHH
Confidence 34555555544 45556688888877766554 46677788999999999999998887763
No 57
>PF01040 UbiA: UbiA prenyltransferase family; InterPro: IPR000537 The UbiA family of prenyltransferases includes bacterial 4-hydroxybenzoate octaprenyltransferase (gene ubiA); yeast mitochondrial para-hydroxybenzoate--polyprenyltransferase (gene COQ2); and protohaem IX farnesyltransferase (haem O synthase) from yeast and mammals(gene COX10), and from bacteria (genes cyoE or ctaB) [, ]. These are integral membrane proteins, which probably contain seven transmembrane segments. The signature is also found in cytochrome C oxidase assembly factor. The complexity of cytochrome C oxidase requires assistance in building the complex, and this is carried out by the cytochrome C oxidase assembly factor.; GO: 0004659 prenyltransferase activity, 0016021 integral to membrane
Probab=24.00 E-value=84 Score=23.49 Aligned_cols=34 Identities=15% Similarity=0.230 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHh
Q psy3877 22 GILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ 66 (145)
Q Consensus 22 ~~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~ 66 (145)
--++.+....+|+.|+.+ |-+.|+.|+|+.+..+
T Consensus 156 ~~~~~~~~~~~~~~D~~~-----------D~~~g~~Tl~v~~G~~ 189 (257)
T PF01040_consen 156 FLLIFAIMFFNDIRDIEG-----------DRKAGRRTLPVLLGEK 189 (257)
T ss_pred HHHHHHHHHHHHhhhHHH-----------HHHcCCcchHHHHHHH
Confidence 456777778888888654 4567899999988543
No 58
>PRK12875 ubiA prenyltransferase; Reviewed
Probab=23.81 E-value=55 Score=25.95 Aligned_cols=34 Identities=6% Similarity=0.028 Sum_probs=24.6
Q ss_pred HHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhc
Q psy3877 23 ILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQS 67 (145)
Q Consensus 23 ~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~ 67 (145)
...+++.+.+++.|+ -.|-+.|+.|+|+.+..+.
T Consensus 176 l~~~~~~~in~i~Di-----------e~D~~aGi~Tlav~lG~~~ 209 (282)
T PRK12875 176 LWAMGMHTFSAIPDI-----------EPDRAAGIRTTATVLGERR 209 (282)
T ss_pred HHHHHHHHHHhccCH-----------HHHHHcCCccchhhccHhh
Confidence 455666777877775 3566788999999876543
No 59
>KOG0781|consensus
Probab=22.98 E-value=3.6e+02 Score=23.73 Aligned_cols=69 Identities=14% Similarity=0.147 Sum_probs=46.0
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHc-ChHHHHHHHHHHHHHHHHHHHh-----ccC--CCHHHHHHHHHHhhhcCCC
Q psy3877 74 VIQILRQRTRDVEVKKYCISLLDRF-GSFEHTREVLKELDVSARTEVA-----RLG--GNPLLEAILDELLTWDTPD 142 (145)
Q Consensus 74 l~~~l~~~~~~~~~~~~i~~~l~~~-g~~~~~~~~~~~~~~~A~~~L~-----~lp--~~~~~~~ll~~l~~~~~~~ 142 (145)
+..+++++..+++++.-+++-++++ =.-.-|.+.+..+.+.....|+ .|. .+..++++.+.|..+++|.
T Consensus 284 fkglvG~K~L~eeDL~pvL~kM~ehLitKNVA~eiA~~LcEsV~a~Legkkv~sfs~V~~Tvk~Al~daLvQILTP~ 360 (587)
T KOG0781|consen 284 FKGLVGSKSLSEEDLNPVLDKMTEHLITKNVAAEIAEKLCESVAASLEGKKVGSFSTVESTVKEALRDALVQILTPQ 360 (587)
T ss_pred HHhhcccccccHhhhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhhhcccccchHHHHHHHHHHHHHHHHHcCCC
Confidence 4556666777778777777776654 1223345566666666666665 343 4677889999999999874
No 60
>PRK12887 ubiA tocopherol phytyltransferase; Reviewed
Probab=22.45 E-value=1.3e+02 Score=24.10 Aligned_cols=34 Identities=12% Similarity=0.109 Sum_probs=25.4
Q ss_pred HHHHHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHhc
Q psy3877 23 ILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQS 67 (145)
Q Consensus 23 ~lG~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~~ 67 (145)
-.-.++.+.+|+.|.- +|.+.|+.|+|+.+..+.
T Consensus 193 ~~~~~~~l~~di~D~e-----------gD~~~Gi~Tlav~lG~~~ 226 (308)
T PRK12887 193 VFTFAIAIFKDIPDME-----------GDRQYQITTFTLRLGKQA 226 (308)
T ss_pred HHHHHHHHHHhccchh-----------hHHHcCCcchhHHHhHHH
Confidence 4556778888888864 455788999999987654
No 61
>TIGR01476 chlor_syn_BchG bacteriochlorophyll/chlorophyll synthetase. This model describes a subfamily of a large family of polyprenyltransferases (pfam01040) that also includes 4-hydroxybenzoate octaprenyltransferase and protoheme IX farnesyltransferase (heme O synthase). Members of this family are found exclusively in photosynthetic organisms, including a single copy in Arabidopsis thaliana.
Probab=22.14 E-value=49 Score=25.88 Aligned_cols=30 Identities=17% Similarity=0.238 Sum_probs=21.9
Q ss_pred HHHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHh
Q psy3877 26 LYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ 66 (145)
Q Consensus 26 ~afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~ 66 (145)
.++.+.+|+.|+- +|.+.|+.|+|+.+.-+
T Consensus 175 ~~i~~~nd~~D~~-----------~D~~~G~~Tl~v~lG~~ 204 (283)
T TIGR01476 175 HGIMTLNDFKSVE-----------GDRQLGLRSLPVMIGVK 204 (283)
T ss_pred HHHHHHHhccchh-----------hHHHcCCcCcceEEcHH
Confidence 3467788888764 55678899999987654
No 62
>PRK07566 bacteriochlorophyll/chlorophyll a synthase; Reviewed
Probab=21.88 E-value=35 Score=27.35 Aligned_cols=29 Identities=17% Similarity=0.233 Sum_probs=21.7
Q ss_pred HHHHHhchhccccCchhcCCCcchhHhhCcchHHHHHHHh
Q psy3877 27 YFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ 66 (145)
Q Consensus 27 afQI~DD~lD~~~~~~~~GK~~g~Dl~eGk~TlPli~al~ 66 (145)
++.+.+|+.|.. +|.+.|+.|+|+.+..+
T Consensus 204 ~~~~~~d~~D~e-----------~D~~aG~~Tlpv~~G~~ 232 (314)
T PRK07566 204 GIMTLNDFKSVE-----------GDRQLGLRSLPVVFGEK 232 (314)
T ss_pred HHHHHHHHHHhH-----------hHHHcCCcccceeEcHH
Confidence 357788888753 56678899999987644
No 63
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=21.17 E-value=3.3e+02 Score=19.77 Aligned_cols=65 Identities=20% Similarity=0.316 Sum_probs=41.1
Q ss_pred HHHHHHHhcC-C---chHHHHHHHHhcCCCHHHHHHHHHHHHHcChHHH-----------------------HHHHHHHH
Q psy3877 59 FPIIHAIQSR-P---DDRQVIQILRQRTRDVEVKKYCISLLDRFGSFEH-----------------------TREVLKEL 111 (145)
Q Consensus 59 lPli~al~~~-~---~~~~l~~~l~~~~~~~~~~~~i~~~l~~~g~~~~-----------------------~~~~~~~~ 111 (145)
.|+|+.+-.. + +-.+|.+-+. +..+.++++..+++|.+.|.++. .+..-++.
T Consensus 26 ~~~ir~l~~l~~~~~d~~~iak~l~-p~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~~l~~~~~~~~~avr~~h~q~ 104 (171)
T PF14394_consen 26 HPAIRELLPLMPFAPDPEWIAKRLR-PKISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDKSLTTSSEIPSEAVRSYHKQM 104 (171)
T ss_pred HHHHHHHhhcCCCCCCHHHHHHHhc-CCCCHHHHHHHHHHHHHCCCeEECCCCcEEEecceeeCCCCCcHHHHHHHHHHH
Confidence 4666666543 1 1224555544 33467778888888888776543 34455667
Q ss_pred HHHHHHHHhccCC
Q psy3877 112 DVSARTEVARLGG 124 (145)
Q Consensus 112 ~~~A~~~L~~lp~ 124 (145)
.+.|.++|+.+|.
T Consensus 105 ~~lA~~al~~~p~ 117 (171)
T PF14394_consen 105 LELAQEALDRVPP 117 (171)
T ss_pred HHHHHHHHHhCCc
Confidence 8889999998774
No 64
>COG1575 MenA 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism]
Probab=20.12 E-value=31 Score=27.85 Aligned_cols=20 Identities=20% Similarity=0.478 Sum_probs=15.7
Q ss_pred CCcchhHhhCcchHHHHHHH
Q psy3877 46 KSFCEDLTEGKFSFPIIHAI 65 (145)
Q Consensus 46 K~~g~Dl~eGk~TlPli~al 65 (145)
...-+|.++||+|+|+...-
T Consensus 199 rDie~D~~~gk~TLavrLG~ 218 (303)
T COG1575 199 RDIEEDIRNGKYTLAVRLGR 218 (303)
T ss_pred ccchhHHhcCCcceeeeecc
Confidence 44568999999999987543
Done!