Query psy5533
Match_columns 136
No_of_seqs 110 out of 1083
Neff 8.8
Searched_HMMs 46136
Date Fri Aug 16 20:00:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5533.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5533hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02890 geranyl diphosphate s 100.0 1.9E-32 4.2E-37 212.3 14.4 136 1-136 281-422 (422)
2 TIGR02749 prenyl_cyano solanes 100.0 2.4E-32 5.3E-37 206.7 14.5 136 1-136 187-322 (322)
3 PLN02857 octaprenyl-diphosphat 100.0 2.8E-32 6.1E-37 211.4 14.5 136 1-136 281-416 (416)
4 CHL00151 preA prenyl transfera 100.0 4.6E-32 1E-36 205.4 14.3 135 1-135 188-322 (323)
5 TIGR02748 GerC3_HepT heptapren 100.0 6.1E-31 1.3E-35 199.0 14.8 135 1-136 183-319 (319)
6 PRK10888 octaprenyl diphosphat 100.0 1.1E-30 2.4E-35 197.7 14.7 136 1-136 184-323 (323)
7 COG0142 IspA Geranylgeranyl py 100.0 7.4E-30 1.6E-34 193.2 14.0 136 1-136 187-322 (322)
8 KOG0776|consensus 99.9 1.1E-26 2.4E-31 176.1 11.6 131 1-134 254-384 (384)
9 PRK10581 geranyltranstransfera 99.9 8.3E-26 1.8E-30 169.6 11.0 102 2-136 196-299 (299)
10 cd00685 Trans_IPPS_HT Trans-Is 99.9 2.4E-22 5.2E-27 148.2 10.7 97 2-134 163-259 (259)
11 PF00348 polyprenyl_synt: Poly 99.9 1.6E-22 3.5E-27 149.3 3.8 101 1-101 159-259 (260)
12 cd00867 Trans_IPPS Trans-Isopr 99.7 2.6E-17 5.6E-22 119.5 10.1 95 2-134 140-236 (236)
13 KOG0777|consensus 99.6 2.3E-15 4.9E-20 107.7 9.8 114 12-125 183-299 (322)
14 KOG0711|consensus 99.6 2.5E-15 5.4E-20 111.5 9.2 134 2-136 208-347 (347)
15 cd00385 Isoprenoid_Biosyn_C1 I 98.9 1E-07 2.2E-12 67.8 12.3 102 6-131 138-241 (243)
16 PF00494 SQS_PSY: Squalene/phy 92.7 3 6.4E-05 30.7 10.4 90 11-121 141-231 (267)
17 cd00683 Trans_IPPS_HH Trans-Is 91.2 4 8.7E-05 30.1 9.7 85 12-118 143-227 (265)
18 PF06783 UPF0239: Uncharacteri 90.9 0.39 8.5E-06 29.5 3.3 25 7-31 15-39 (85)
19 PLN02632 phytoene synthase 90.4 4.9 0.00011 31.0 9.8 86 11-118 194-279 (334)
20 TIGR03464 HpnC squalene syntha 89.5 7 0.00015 29.0 9.9 83 14-118 137-219 (266)
21 TIGR01559 squal_synth farnesyl 89.3 4.4 9.5E-05 31.4 8.7 84 13-118 166-249 (336)
22 TIGR03465 HpnD squalene syntha 88.1 5.6 0.00012 29.4 8.4 85 12-118 134-218 (266)
23 cd00685 Trans_IPPS_HT Trans-Is 83.9 14 0.00029 27.2 8.6 25 8-32 39-63 (259)
24 TIGR02748 GerC3_HepT heptapren 83.6 17 0.00038 27.7 9.3 29 4-32 59-87 (319)
25 PRK10888 octaprenyl diphosphat 83.1 13 0.00028 28.5 8.5 28 5-32 61-88 (323)
26 PF00348 polyprenyl_synt: Poly 81.7 15 0.00033 27.0 8.2 29 4-32 29-57 (260)
27 TIGR02749 prenyl_cyano solanes 77.0 31 0.00067 26.4 8.8 21 12-32 71-91 (322)
28 KOG3330|consensus 71.0 4.5 9.7E-05 27.9 2.5 38 6-51 39-76 (183)
29 COG0142 IspA Geranylgeranyl py 70.4 15 0.00032 28.2 5.6 30 18-59 76-105 (322)
30 CHL00151 preA prenyl transfera 65.5 20 0.00043 27.5 5.4 35 13-59 73-107 (323)
31 PLN02890 geranyl diphosphate s 64.6 67 0.0015 25.8 8.3 22 11-32 164-185 (422)
32 PHA02130 hypothetical protein 60.9 10 0.00023 22.1 2.4 31 28-58 32-64 (81)
33 PRK13105 ubiA prenyltransferas 53.6 25 0.00054 26.5 4.0 32 21-63 173-204 (282)
34 PRK12872 ubiA prenyltransferas 49.9 13 0.00027 27.7 2.0 31 21-62 174-204 (285)
35 PF06304 DUF1048: Protein of u 47.1 15 0.00032 23.5 1.7 33 12-44 30-67 (103)
36 COG1562 ERG9 Phytoene/squalene 46.8 1.3E+02 0.0027 22.9 8.1 85 13-119 154-238 (288)
37 PRK12465 xylose isomerase; Pro 42.7 1.2E+02 0.0026 24.5 6.4 53 10-62 365-422 (445)
38 PLN00012 chlorophyll synthetas 42.2 19 0.00041 28.3 2.0 32 19-61 263-294 (375)
39 PRK13591 ubiA prenyltransferas 41.8 10 0.00022 29.0 0.4 26 24-60 195-220 (307)
40 PRK10581 geranyltranstransfera 41.4 1.6E+02 0.0034 22.4 8.0 42 6-59 62-105 (299)
41 PF09053 CagZ: CagZ; InterPro 36.5 27 0.00058 23.5 1.7 11 17-27 142-152 (199)
42 COG0571 Rnc dsRNA-specific rib 36.1 1.8E+02 0.0038 21.5 8.4 51 80-130 122-173 (235)
43 PLN02923 xylose isomerase 36.0 1.6E+02 0.0034 24.0 6.1 54 10-63 399-457 (478)
44 PHA02603 nrdC.11 hypothetical 34.5 1.8E+02 0.004 22.6 6.1 22 113-134 302-323 (330)
45 TIGR02056 ChlG chlorophyll syn 33.4 43 0.00094 25.4 2.7 32 20-62 195-226 (306)
46 PF06603 UpxZ: UpxZ family of 32.7 1.1E+02 0.0024 19.6 4.0 48 79-126 51-102 (106)
47 cd00687 Terpene_cyclase_nonpla 32.5 2.1E+02 0.0045 21.2 9.4 25 12-36 197-221 (303)
48 PLN02857 octaprenyl-diphosphat 32.4 1.2E+02 0.0027 24.2 5.1 23 10-32 163-185 (416)
49 PRK01194 V-type ATP synthase s 30.1 1.6E+02 0.0036 20.6 5.0 38 94-131 75-113 (185)
50 COG2005 ModE N-terminal domain 29.8 32 0.00069 23.0 1.2 35 81-115 21-55 (130)
51 PRK12875 ubiA prenyltransferas 29.5 1.4E+02 0.003 22.5 4.7 31 19-60 176-206 (282)
52 TIGR01476 chlor_syn_BchG bacte 29.3 32 0.0007 25.6 1.4 28 22-60 175-202 (283)
53 PLN02878 homogentisate phytylt 28.5 88 0.0019 23.7 3.5 34 16-60 164-197 (280)
54 PF01040 UbiA: UbiA prenyltran 28.4 1.7E+02 0.0036 20.9 5.0 35 14-59 152-186 (257)
55 PF10759 DUF2587: Protein of u 26.0 2.1E+02 0.0045 19.7 4.6 33 81-113 39-71 (169)
56 PF04716 ETC_C1_NDUFA5: ETC co 25.8 1.3E+02 0.0029 16.9 4.9 33 98-130 4-37 (57)
57 PRK12887 ubiA tocopherol phyty 25.5 1.9E+02 0.004 22.1 4.9 33 19-62 193-225 (308)
58 cd00867 Trans_IPPS Trans-Isopr 25.5 2.5E+02 0.0054 19.8 8.9 29 4-32 14-42 (236)
59 PF03623 Focal_AT: Focal adhes 25.4 1.7E+02 0.0037 19.8 4.1 33 5-37 33-65 (139)
60 PF05546 She9_MDM33: She9 / Md 24.7 2.6E+02 0.0057 20.2 5.2 107 8-115 6-125 (207)
61 PRK03963 V-type ATP synthase s 24.3 2.4E+02 0.0053 19.6 5.1 33 98-130 80-112 (198)
62 PRK12883 ubiA prenyltransferas 24.2 1.7E+02 0.0037 21.7 4.4 29 22-61 168-196 (277)
63 PRK12884 ubiA prenyltransferas 24.1 99 0.0021 22.8 3.2 36 16-62 163-198 (279)
64 PF10776 DUF2600: Protein of u 23.7 1.5E+02 0.0032 23.1 4.0 32 89-120 248-279 (330)
65 PF10244 MRP-L51: Mitochondria 23.0 48 0.001 20.8 1.1 24 27-55 19-42 (94)
66 PRK07566 bacteriochlorophyll/c 22.7 35 0.00075 26.0 0.5 29 23-62 204-232 (314)
67 PHA03046 Hypothetical protein; 22.6 2.5E+02 0.0054 18.8 5.0 60 70-130 73-134 (142)
68 PF11433 DUF3198: Protein of u 22.5 1.5E+02 0.0032 16.2 3.0 21 9-29 22-42 (51)
69 KOG2114|consensus 21.5 3.6E+02 0.0078 24.0 6.1 51 80-130 465-531 (933)
70 PRK12882 ubiA prenyltransferas 20.3 1.4E+02 0.003 22.1 3.3 30 22-62 171-200 (276)
71 PF10047 DUF2281: Protein of u 20.3 1.3E+02 0.0028 17.3 2.5 27 107-134 4-30 (66)
No 1
>PLN02890 geranyl diphosphate synthase
Probab=100.00 E-value=1.9e-32 Score=212.32 Aligned_cols=136 Identities=43% Similarity=0.760 Sum_probs=126.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhh
Q psy5533 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGD 80 (136)
Q Consensus 1 i~ag~~~~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~ 80 (136)
+++|++++.+..+++||.++|+||||+||++||+++++.+|||.++|+++||+|+|++++++..+.+..++.+...++++
T Consensus 281 ilaga~~~~~~~l~~fG~~lGlAFQI~DDiLD~~g~~~~~GK~~g~DL~eGk~TlPvl~al~~~~~l~~~l~~~~~~~~~ 360 (422)
T PLN02890 281 ILAGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGVITAPILFAMEEFPQLREVVDRGFDNPAN 360 (422)
T ss_pred HHcCcCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCChhhhCCCchhhHhcCCccHHHHHHHhcCHHHHHHHhcccCCHHH
Confidence 46899999999999999999999999999999999999999999999999999999999998766666677666678889
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcCCCCH------HHHHHHHHHHHHHccCC
Q psy5533 81 VEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESP------YQKGLVVLTDLVLNRMK 136 (136)
Q Consensus 81 ~~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~~------~~~~L~~l~~~~~~r~~ 136 (136)
++++.++|.++|++++|+..+++|.++|.+.|+.+|+++ .+..|..|++++.+|.+
T Consensus 361 v~~~~~~i~~~gaie~a~~la~~~~~~A~~~L~~lp~s~~~~~~~~r~~L~~L~~~vi~R~k 422 (422)
T PLN02890 361 VDIALEYLGKSRGIQRTRELAREHANLAAAAIESLPETDDEDVLTSRRALIDLTERVITRNK 422 (422)
T ss_pred HHHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHHhCCCCccccchHHHHHHHHHHHHHHhccC
Confidence 999999999999999999999999999999999999876 68999999999999975
No 2
>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=100.00 E-value=2.4e-32 Score=206.74 Aligned_cols=136 Identities=40% Similarity=0.674 Sum_probs=127.0
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhh
Q psy5533 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGD 80 (136)
Q Consensus 1 i~ag~~~~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~ 80 (136)
+++|++++.++.+++||.++|+||||+||++|++++++.+|||.++|+.+||+|+|++++++..+.....+.+...++++
T Consensus 187 ~~ag~~~~~~~~l~~~G~~lG~aFQi~DDild~~~~~~~~GK~~g~Dl~~Gk~Tlp~l~al~~~~~~~~~l~~~~~~~~~ 266 (322)
T TIGR02749 187 VLSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPAGSDLMKGNLTAPVLFALEEEPKLSELIEREFSQKGD 266 (322)
T ss_pred HHcCcCHHHHHHHHHHHHHHHHHHHHHHHhccCCCChHhhCCChhHHHhCCCchHHHHHHHhcChHHHHHHHhccCCHHH
Confidence 36789999999999999999999999999999999999999999999999999999999998766666677666677889
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHccCC
Q psy5533 81 VEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPYQKGLVVLTDLVLNRMK 136 (136)
Q Consensus 81 ~~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~~~~~~L~~l~~~~~~r~~ 136 (136)
++++.++|..+|+++++++.+++|.++|.+.|+.+|+++.+..|..|++++.+|.+
T Consensus 267 ~~~~~~~i~~~ga~~~a~~~~~~~~~~A~~~L~~lp~~~~~~~L~~l~~~~~~R~~ 322 (322)
T TIGR02749 267 LEQALSLVRKSGGIKKARELAKEQAQLALQSLSFLPPSPPREALKELVHFVLSRLY 322 (322)
T ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhcCC
Confidence 99999999999999999999999999999999999999889999999999999975
No 3
>PLN02857 octaprenyl-diphosphate synthase
Probab=100.00 E-value=2.8e-32 Score=211.40 Aligned_cols=136 Identities=40% Similarity=0.678 Sum_probs=128.1
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhh
Q psy5533 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGD 80 (136)
Q Consensus 1 i~ag~~~~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~ 80 (136)
+++|++++.++.+.+||.++|+||||+||++|++++++.+|||.++|+.+||+|+|++++++..+.+..++.....++++
T Consensus 281 llaga~~~~~~~l~~fG~~LGiAFQI~DDiLD~~~~~~~~GK~~g~DL~eGK~TlPli~al~~~~~l~~~l~~~~~~~~~ 360 (416)
T PLN02857 281 IFSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPAGSDLAKGNLTAPVIFALEKEPELREIIESEFCEEGS 360 (416)
T ss_pred HHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHhCCCcchhhhcCCccHHHHHHHhcChHHHHHHhhccCCHHH
Confidence 36899999999999999999999999999999999999999999999999999999999999877677777777778899
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHccCC
Q psy5533 81 VEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPYQKGLVVLTDLVLNRMK 136 (136)
Q Consensus 81 ~~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~~~~~~L~~l~~~~~~r~~ 136 (136)
+++++++|.++|+++++++.+++|.++|++.|+.+|.+..+..|..|++++.+|.+
T Consensus 361 ~~~~~~lv~~~Ggie~a~~~a~~~~~~A~~~L~~Lp~~~~~~~L~~L~~~~~~R~~ 416 (416)
T PLN02857 361 LEEAIELVNEGGGIERAQELAKEKADLAIQNLECLPRGAFRSSLEDMVDYNLERIY 416 (416)
T ss_pred HHHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhccC
Confidence 99999999999999999999999999999999999998888999999999999974
No 4
>CHL00151 preA prenyl transferase; Reviewed
Probab=100.00 E-value=4.6e-32 Score=205.41 Aligned_cols=135 Identities=37% Similarity=0.634 Sum_probs=125.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhh
Q psy5533 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGD 80 (136)
Q Consensus 1 i~ag~~~~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~ 80 (136)
+++|++++.++.+++||.++|+||||+||++|++++++.+|||.|+|+++||+|+|++++++..+.....+.+...++++
T Consensus 188 ~lag~~~~~~~~l~~~G~~lG~aFQi~DDilD~~~~~~~~GK~~g~Dl~eGk~Tlp~l~al~~~~~~~~~l~~~~~~~~~ 267 (323)
T CHL00151 188 LLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLTAPVLFALTQNSKLAKLIEREFCETKD 267 (323)
T ss_pred HHcCCCHHHHHHHHHHHHHHHHHHHHHHHHhhcccChhhhCCCchhhHhcCchHHHHHHHHhcChHHHHHHHHhcCCHHH
Confidence 36889999999999999999999999999999999999999999999999999999999998766666666666667889
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHccC
Q psy5533 81 VEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPYQKGLVVLTDLVLNRM 135 (136)
Q Consensus 81 ~~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~~~~~~L~~l~~~~~~r~ 135 (136)
++++.+++.++|++++|+..+++|.++|.+.|+.+|.++.+..|..|++++.+|.
T Consensus 268 ~~~~~~~l~~~g~~~~a~~~a~~~~~~A~~~L~~lp~~~~~~~L~~l~~~~~~R~ 322 (323)
T CHL00151 268 ISQALQIIKETNGIEKAKDLALEHMQAAIQCLKFLPPSSAKDSLIEIANFIINRL 322 (323)
T ss_pred HHHHHHHHHHCCcHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhcc
Confidence 9999999999999999999999999999999999999888999999999999985
No 5
>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=99.97 E-value=6.1e-31 Score=199.01 Aligned_cols=135 Identities=27% Similarity=0.443 Sum_probs=120.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhh--cCCh
Q psy5533 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRR--FQEP 78 (136)
Q Consensus 1 i~ag~~~~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~--~~~~ 78 (136)
++||++++.++.+++||.++|+||||+||++||+++++.+|||.++|+.+||+|+|++++++..+ ....+... ..++
T Consensus 183 ~~ag~~~~~~~~l~~~g~~lG~aFQI~DDilD~~~~~~~~GK~~~~Dl~~gk~Tlp~l~al~~~~-~~~~l~~~~~~~~~ 261 (319)
T TIGR02748 183 IASGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGKPAGGDLLQGNVTLPVLYAMEDPF-LKKRIEQVLEETTA 261 (319)
T ss_pred HHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHccCCHHhhCCChhhHHhCCCchHHHHHHhcCcc-hhHHHHHHHcCCCH
Confidence 36789999999999999999999999999999999999999999999999999999999998544 33333221 1267
Q ss_pred hhHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHccCC
Q psy5533 79 GDVEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPYQKGLVVLTDLVLNRMK 136 (136)
Q Consensus 79 ~~~~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~~~~~~L~~l~~~~~~r~~ 136 (136)
.++.++.++|..+|++++|+.++++|.++|++.|+.+|+++.+..|..+++++.+|.+
T Consensus 262 ~~~~~~~~~i~~~g~~~~a~~~a~~~~~~A~~~L~~lp~~~~~~~L~~l~~~~~~R~~ 319 (319)
T TIGR02748 262 EEMEPLIEEVKKSDAIEYAYAVSDRYLKKALELLDGLPDGRAKKPLQEIAKYIGKRKY 319 (319)
T ss_pred HHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhccC
Confidence 8899999999999999999999999999999999999998889999999999999974
No 6
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=99.97 E-value=1.1e-30 Score=197.75 Aligned_cols=136 Identities=29% Similarity=0.435 Sum_probs=121.7
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCc-chHHHHh---hcC
Q psy5533 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPE-LNPMIMR---RFQ 76 (136)
Q Consensus 1 i~ag~~~~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~-~~~~l~~---~~~ 76 (136)
++||++++.+..+++||+++|+||||+||++||+++++.+|||.|+|+.+||+|+|++++++..++ ....+.. ...
T Consensus 184 ~lag~~~~~~~~l~~~g~~lG~aFQi~DD~ld~~~~~~~~GK~~g~Dl~~gk~Tlp~l~al~~~~~~~~~~l~~~~~~~~ 263 (323)
T PRK10888 184 ILAGCTPEQEKGLQDYGRYLGTAFQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRTAIEQGN 263 (323)
T ss_pred HHcCCCHHHHHHHHHHHHHHHHHHHHHHHhhcccCChHhhCCCchhhhhcCCchHHHHHHHHhCCHHHHHHHHHHHhCCC
Confidence 368999999999999999999999999999999999999999999999999999999999997654 3333322 223
Q ss_pred ChhhHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHccCC
Q psy5533 77 EPGDVEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPYQKGLVVLTDLVLNRMK 136 (136)
Q Consensus 77 ~~~~~~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~~~~~~L~~l~~~~~~r~~ 136 (136)
.++++.++.+++.++|++++++..+++|.++|.+.|+.+|+++.+..|..|++++.+|..
T Consensus 264 ~~~~~~~~~~~l~~~g~~e~~~~~a~~~~~~A~~~L~~lp~~~~~~~L~~l~~~~~~R~~ 323 (323)
T PRK10888 264 GRHLLEPVLEAMNACGSLEWTRQRAEEEADKAIAALQVLPDTPWREALIGLAHIAVQRDR 323 (323)
T ss_pred CHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhCcC
Confidence 456789999999999999999999999999999999999999889999999999999964
No 7
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=99.97 E-value=7.4e-30 Score=193.22 Aligned_cols=136 Identities=38% Similarity=0.585 Sum_probs=121.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhh
Q psy5533 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGD 80 (136)
Q Consensus 1 i~ag~~~~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~ 80 (136)
+++|++++..+.++.||.++|+||||+||++|+++++.++|||+|+|+.+||+|+|++++++.+++....+........+
T Consensus 187 ~la~~~~~~~~~l~~~g~~lGlaFQi~DDiLD~~~d~~~lGK~~g~Dl~~gK~T~p~l~~l~~~~~~~~~~~~~~~~~~~ 266 (322)
T COG0142 187 ILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEKANEDQKLLRILLEGGGE 266 (322)
T ss_pred HHcCCCHHHHHHHHHHHHHhhHHHHHHHHhhcCCCChHHhCCCcchHHHcCCchHHHHHHHHcCchhhHHHHHHhhcchH
Confidence 46889999999999999999999999999999999999999999999999999999999999987643333222222229
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHccCC
Q psy5533 81 VEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPYQKGLVVLTDLVLNRMK 136 (136)
Q Consensus 81 ~~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~~~~~~L~~l~~~~~~r~~ 136 (136)
++++.+++.++|+++++...++.|.++|.+.|+.+|++..+..|..+++++.+|.+
T Consensus 267 ~~~~~~~~~~~g~~~~~~~~a~~~~~~a~~~L~~l~~~~~~~~L~~la~~i~~R~~ 322 (322)
T COG0142 267 VEEALELLRKSGAIEYAKNLAKTYVEKAKEALEKLPDSEAKEALLELADFIIKRKY 322 (322)
T ss_pred HHHHHHHHHHcchHHHHHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHhccC
Confidence 99999999999999999999999999999999999987899999999999999974
No 8
>KOG0776|consensus
Probab=99.94 E-value=1.1e-26 Score=176.10 Aligned_cols=131 Identities=47% Similarity=0.679 Sum_probs=124.7
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhh
Q psy5533 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGD 80 (136)
Q Consensus 1 i~ag~~~~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~ 80 (136)
|++|.+++..+.+++||+++|++||+.||++|+....+..||+.+.|+..|+.|+|+++++++.++..+.+.+.+..+.+
T Consensus 254 ILgg~s~ev~e~~~~yGR~lGL~fQvvDDildftkss~elGK~ag~Dl~~g~lT~P~Lf~~e~~pe~~e~l~~~~~e~~~ 333 (384)
T KOG0776|consen 254 ILGGGSEEVIEAAFEYGRCLGLAFQVVDDILDFTKSSEELGKTAGKDLKAGKLTAPVLFALEKSPELREKLEREFSEPLD 333 (384)
T ss_pred HHcCCCHHHHHHHHHHHHHHHHHHHHhhcccCcccchhhcCcchhhhhhhccccccchhhhhhChHHHHHHHHhccccch
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999988888878
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHcc
Q psy5533 81 VEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPYQKGLVVLTDLVLNR 134 (136)
Q Consensus 81 ~~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~~~~~~L~~l~~~~~~r 134 (136)
.....+.+. ++..+...+++|.++|++.|+.+|++++|+.|++|+..+..|
T Consensus 334 ~~~~~k~v~---~v~~a~~la~~~~~~Al~~l~~~p~s~ar~aL~~l~~~~~~r 384 (384)
T KOG0776|consen 334 GFDADKAVP---GVALAKYLARRHNNKALEALQSLPRSEARSALENLVLAVLTR 384 (384)
T ss_pred hhHHHHHHH---HHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHhcC
Confidence 888777776 899999999999999999999999999999999999998876
No 9
>PRK10581 geranyltranstransferase; Provisional
Probab=99.93 E-value=8.3e-26 Score=169.57 Aligned_cols=102 Identities=32% Similarity=0.495 Sum_probs=94.5
Q ss_pred CCCCC-HHHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhh
Q psy5533 2 LGGAD-DKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGD 80 (136)
Q Consensus 2 ~ag~~-~~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~ 80 (136)
++|++ ++.++.+.+||.++|+||||+||++|++++++.+|||.++|+.+||+|+|+++
T Consensus 196 lag~~~~~~~~~l~~~g~~lG~aFQI~DDilD~~g~~~~~GK~~g~Dl~~gk~T~p~l~--------------------- 254 (299)
T PRK10581 196 SAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALL--------------------- 254 (299)
T ss_pred HcCCCcHHHHHHHHHHHHHHHHHHHHHHHHccccCChHHHCCCcchhhhcCCCCHHHHH---------------------
Confidence 56776 46789999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcCCCCHH-HHHHHHHHHHHHccCC
Q psy5533 81 VEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPY-QKGLVVLTDLVLNRMK 136 (136)
Q Consensus 81 ~~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~~~-~~~L~~l~~~~~~r~~ 136 (136)
+++++++.+++|.++|.+.|+.+|+++. +..|..|++++.+|.+
T Consensus 255 ------------~~e~a~~~a~~~~~~A~~~l~~l~~~~~~~~~L~~l~~~~~~R~~ 299 (299)
T PRK10581 255 ------------GLEQARKKARDLIDDARQSLDQLAAQSLDTSALEALANYIIQRDK 299 (299)
T ss_pred ------------HHHHHHHHHHHHHHHHHHHHHhCcCCchhHHHHHHHHHHHHhccC
Confidence 7889999999999999999999997654 7889999999999974
No 10
>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=99.88 E-value=2.4e-22 Score=148.24 Aligned_cols=97 Identities=42% Similarity=0.697 Sum_probs=90.5
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhhH
Q psy5533 2 LGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGDV 81 (136)
Q Consensus 2 ~ag~~~~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~~ 81 (136)
++|++++.+..+++||.++|++|||+||++|++++++.+||+.++|+.+||+|+|+++++
T Consensus 163 l~~~~~~~~~~l~~~g~~lG~afQi~DD~ld~~~~~~~~gK~~~~Di~~gk~T~~~~~~l-------------------- 222 (259)
T cd00685 163 LAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLAL-------------------- 222 (259)
T ss_pred HcCCCHHHHHHHHHHHHHHHHHHHHHHHhhcccCChHHHCCCcchHHHcCCchHHHHHHH--------------------
Confidence 578889999999999999999999999999999999999999999999999999999954
Q ss_pred HHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHcc
Q psy5533 82 EKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPYQKGLVVLTDLVLNR 134 (136)
Q Consensus 82 ~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~~~~~~L~~l~~~~~~r 134 (136)
++.+..|.++|...|+.+|++..+..|..+++++.+|
T Consensus 223 ----------------~~~~~~~~~~a~~~l~~~~~~~~~~~l~~~~~~~~~r 259 (259)
T cd00685 223 ----------------RELAREYEEKALEALKALPESPAREALRALADFILER 259 (259)
T ss_pred ----------------HHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHcC
Confidence 7889999999999999999877788899999999887
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=99.86 E-value=1.6e-22 Score=149.29 Aligned_cols=101 Identities=40% Similarity=0.600 Sum_probs=84.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhh
Q psy5533 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGD 80 (136)
Q Consensus 1 i~ag~~~~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~ 80 (136)
+++|++++.++.+++||.++|+||||+||++|++++++..||+.++||.+||+|+|++++++..++....+........+
T Consensus 159 ~lag~~~~~~~~l~~~g~~lG~afQi~DD~~d~~~~~~~~gK~~~~Dl~~gk~Tlp~~~al~~~~~~~~~~l~~~~~~~~ 238 (260)
T PF00348_consen 159 ILAGADEEQIEALREFGRHLGIAFQIRDDLLDLFGDEEELGKPVGSDLKEGKPTLPVLHALERAREELRELLQEAYGKED 238 (260)
T ss_dssp HHTTSGHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHSSTTTHHHHTTTSSHHHHHHHHHHHHHHHHHHHHHHHHSH
T ss_pred HhccchhHHHHHHHHHHHHHHHHHhhhhhhhhccCcHHHhcccchhHHhcCcccHHHHHHHHhCHHHHHHHHHHHHcccc
Confidence 36889999999999999999999999999999999999999999999999999999999999976654444333333446
Q ss_pred HHHHHHHHHhcCHHHHHHHHH
Q psy5533 81 VEKAFEFVHKSQGLEQTKFLA 101 (136)
Q Consensus 81 ~~~i~~~i~~~g~~~~~~~~~ 101 (136)
.+.+.+.+..++.++++++.+
T Consensus 239 ~~~~~~~~~~~~~~~~~~~~~ 259 (260)
T PF00348_consen 239 SEEALEIIAQTGALEYTRKFM 259 (260)
T ss_dssp HHHHHHHHHHHHHHTHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHhhc
Confidence 677777777778888777654
No 12
>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates
Probab=99.73 E-value=2.6e-17 Score=119.46 Aligned_cols=95 Identities=40% Similarity=0.624 Sum_probs=81.2
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhhH
Q psy5533 2 LGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGDV 81 (136)
Q Consensus 2 ~ag~~~~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~~ 81 (136)
++|.+++..+.+..||.++|+||||.||++|++++.+.+|| .++|+.+||+|+|++++
T Consensus 140 ~~~~~~~~~~~~~~~~~~lG~a~Qi~dd~~D~~~d~~~~gk-~~~D~~~gr~tlp~~~~--------------------- 197 (236)
T cd00867 140 LSGADDEQAEALKDYGRALGLAFQLTDDLLDVFGDAEELGK-VGSDLREGRITLPVILA--------------------- 197 (236)
T ss_pred HcCcCHHHHHHHHHHHHHHHHHHHHHHHhccccCChHHHCc-cHHHHHcCCchHHHHHH---------------------
Confidence 46777888999999999999999999999999999999999 99999999999999983
Q ss_pred HHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcCCCCH--HHHHHHHHHHHHHcc
Q psy5533 82 EKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESP--YQKGLVVLTDLVLNR 134 (136)
Q Consensus 82 ~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~~--~~~~L~~l~~~~~~r 134 (136)
.+.+..+.+++...+..+++.. .+..+..++..+.+|
T Consensus 198 ----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r 236 (236)
T cd00867 198 ----------------RERAAEYAEEAYAALEALPPSLPRARRALIALADFLYRR 236 (236)
T ss_pred ----------------HHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhC
Confidence 5666777777877777776543 466788888888765
No 13
>KOG0777|consensus
Probab=99.64 E-value=2.3e-15 Score=107.70 Aligned_cols=114 Identities=19% Similarity=0.249 Sum_probs=93.2
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchH---HHHhhcCChhhHHHHHHHH
Q psy5533 12 VAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNP---MIMRRFQEPGDVEKAFEFV 88 (136)
Q Consensus 12 ~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~---~l~~~~~~~~~~~~i~~~i 88 (136)
.+..+-..+|+.|||+|||+++..-+.+..|+.+.|+.|||.++|+++|+...++-.+ ++.++..+.+-...+++++
T Consensus 183 dl~pl~n~LGl~fQIRDDY~NL~~keysenKsFaEDlTEGKfsFP~iHA~~t~~q~~Qvl~ILrqRT~didiKkyci~~L 262 (322)
T KOG0777|consen 183 DLVPLINLLGLIFQIRDDYLNLKDKEYSENKSFAEDLTEGKFSFPIIHALKTKGQTEQVLRILRQRTSDIDIKKYCIQIL 262 (322)
T ss_pred hHHHHHHHHhHhhhhhhhhccchhhhhhcccchhhhhccCccCCcchhhhhcCCchHHHHHHHHHhhccchHHHHHHHHH
Confidence 3455667899999999999999887777899999999999999999999977665433 4444444445557899999
Q ss_pred HhcCHHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHH
Q psy5533 89 HKSQGLEQTKFLARKHCVEAVRLASGLAESPYQKGLV 125 (136)
Q Consensus 89 ~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~~~~~~L~ 125 (136)
++.|++++++..+++...+|.+.++....+++-..|.
T Consensus 263 Ed~gSf~YTrn~l~~L~a~a~~~i~~~g~Npyl~~L~ 299 (322)
T KOG0777|consen 263 EDTGSFAYTRNFLNQLVAEARSMIKNDGENPYLPDLA 299 (322)
T ss_pred HHcccHHHHHHHHHHHHHHHHHHHHhcCCCcchHHHH
Confidence 9999999999999999999999999887665544443
No 14
>KOG0711|consensus
Probab=99.62 E-value=2.5e-15 Score=111.47 Aligned_cols=134 Identities=19% Similarity=0.155 Sum_probs=110.4
Q ss_pred CCC-CCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcch-HHHHhhc--CC
Q psy5533 2 LGG-ADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELN-PMIMRRF--QE 77 (136)
Q Consensus 2 ~ag-~~~~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~-~~l~~~~--~~ 77 (136)
+|| ++.+.......+-..+|..||++|||+|++||++.+|| +|.||.++|+||.+++|+++++..+ +++..++ ..
T Consensus 208 ~ag~~~~k~~~~~k~v~~~lg~~FQvQDDYLd~fgDp~vtgk-iGtDIqDnKCsWlv~~al~~~~~eq~~~l~~~yg~~~ 286 (347)
T KOG0711|consen 208 LAGIANLKEHACEKKVLLLLGEYFQVQDDYLDCFGDPEVTGK-IGTDIQDNKCSWLVVKALQRASAEQYKILFENYGKPE 286 (347)
T ss_pred HhhhhhHHHhhhHHHHHHHHHHHHhcchHHHHhcCChhhcCC-CCCccccCceeeehHHHHhhcCHHHHHHHHHhcCCcc
Confidence 455 57778889999999999999999999999999999998 5899999999999999999987644 4554444 46
Q ss_pred hhhHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcCCCC--HHHHHHHHHHHHHHccCC
Q psy5533 78 PGDVEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAES--PYQKGLVVLTDLVLNRMK 136 (136)
Q Consensus 78 ~~~~~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~--~~~~~L~~l~~~~~~r~~ 136 (136)
++.++.+..+..+.+....-.+.-..........|+.++.+ .....+-.++..+.+|++
T Consensus 287 ~~~v~~vk~ly~el~l~~~f~~yE~~~~~~Ik~~I~~~~~~~~~~~~v~t~fl~kiykr~k 347 (347)
T KOG0711|consen 287 AEAVAKVKALYKELHLPALFIEYEEGSYKKIKKLISQVDEDTGVKVKVGTSFLNKIYKRSK 347 (347)
T ss_pred HHHHHHHHHHHHHhccHHHHHHhhhhHHHHHHHHHHHccCCCcchhhhHHHHHHHHHhhcC
Confidence 67889999999999887777777777888888888877654 344556678999999875
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=98.85 E-value=1e-07 Score=67.78 Aligned_cols=102 Identities=32% Similarity=0.381 Sum_probs=76.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhhHHHHH
Q psy5533 6 DDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGDVEKAF 85 (136)
Q Consensus 6 ~~~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~~~~i~ 85 (136)
+.+....+..+|.++|++||+.||+.|+.++.... +|+.|+|.+++.+......+.+
T Consensus 138 ~~~~~~~~~~~~~~~g~~~ql~nDl~~~~~e~~~~---------~~~~~l~~~~~~~~~~~~~~~~-------------- 194 (243)
T cd00385 138 EAELLEALRKLGRALGLAFQLTNDLLDYEGDAERG---------EGKCTLPVLYALEYGVPAEDLL-------------- 194 (243)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHh---------CCchHHHHHHHHHhCChhhHHH--------------
Confidence 35678899999999999999999999998776431 4789999999877654322211
Q ss_pred HHHHhcCHHHHHHHHHHHHHHHHHHHhhcCCCCH--HHHHHHHHHHHH
Q psy5533 86 EFVHKSQGLEQTKFLARKHCVEAVRLASGLAESP--YQKGLVVLTDLV 131 (136)
Q Consensus 86 ~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~~--~~~~L~~l~~~~ 131 (136)
.+..++.++.+...+..+.++++..+..+.... ....+...+..+
T Consensus 195 -~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 241 (243)
T cd00385 195 -LVEKSGSLEEALEELAKLAEEALKELNELILSLPDVPRALLALALNL 241 (243)
T ss_pred -HHHHCChHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHH
Confidence 666778899999999999999999998876542 344454444443
No 16
>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=92.69 E-value=3 Score=30.67 Aligned_cols=90 Identities=24% Similarity=0.157 Sum_probs=52.9
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchh-HhhCcccHHHHHHhhcCCcchHHHHhhcCChhhHHHHHHHHH
Q psy5533 11 EVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAAD-LKLGLATAPVLFACEKFPELNPMIMRRFQEPGDVEKAFEFVH 89 (136)
Q Consensus 11 ~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~D-i~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~~~~i~~~i~ 89 (136)
......+.++|.|+|+.|=+.|+ +.| ...|++-+|.=..-+..-...+++.....+ ..+..
T Consensus 141 ~~~~~~a~~lG~alql~nilRd~-----------~~D~~~~gR~ylP~d~l~~~gv~~~dl~~~~~~~-~~~~~------ 202 (267)
T PF00494_consen 141 EAARDAARALGRALQLTNILRDI-----------PEDALRRGRIYLPLDDLRRFGVTPEDLLAGRPRS-ERLRA------ 202 (267)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTH-----------HHH-HHTT---S-HHHHHHTTSSHHHHHHHG-GG-HHHHH------
T ss_pred hhHHHHHHHHHHHHHHHHHHHHh-----------HHHHHhcccccCCchhHHHcCCCHHHHHhcccCC-HHHHH------
Confidence 46788899999999999888885 457 678888888765433221112222111011 11222
Q ss_pred hcCHHHHHHHHHHHHHHHHHHHhhcCCCCHHH
Q psy5533 90 KSQGLEQTKFLARKHCVEAVRLASGLAESPYQ 121 (136)
Q Consensus 90 ~~g~~~~~~~~~~~~~~~A~~~l~~l~~~~~~ 121 (136)
.+......++.+..+|...+..+|+...+
T Consensus 203 ---~~~~~~~~A~~~l~~a~~~~~~l~~~~~~ 231 (267)
T PF00494_consen 203 ---LIRELAARARAHLDEARAGLSALPPPRAR 231 (267)
T ss_dssp ---HHHHHHHHHHHHHHHHHHGGGGS--TTHH
T ss_pred ---HHHHHHHHHHHHHHHHHHHHHHcCCHhhh
Confidence 34566778889999999999999554333
No 17
>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=91.23 E-value=4 Score=30.09 Aligned_cols=85 Identities=25% Similarity=0.175 Sum_probs=54.5
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhhHHHHHHHHHhc
Q psy5533 12 VAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGDVEKAFEFVHKS 91 (136)
Q Consensus 12 ~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~~~~i~~~i~~~ 91 (136)
.+..++.++|.|+|+.|=+.|+- .|...|++.+|.=..-+..-...+++.. . ..+.+..
T Consensus 143 ~~~~~A~~lG~AlqltnilRdv~-----------eD~~~gR~YlP~d~l~~~gv~~~~l~~~-~-~~~~~~~-------- 201 (265)
T cd00683 143 AALERARALGLALQLTNILRDVG-----------EDARRGRIYLPREELARFGVTLEDLLAP-E-NSPAFRA-------- 201 (265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-----------HHHccCCCcCCHHHHHHcCCCHHHHcCC-C-CCHHHHH--------
Confidence 45688999999999999888863 4566788888875433322122222211 1 1112222
Q ss_pred CHHHHHHHHHHHHHHHHHHHhhcCCCC
Q psy5533 92 QGLEQTKFLARKHCVEAVRLASGLAES 118 (136)
Q Consensus 92 g~~~~~~~~~~~~~~~A~~~l~~l~~~ 118 (136)
.+......++.+...|...+..+|..
T Consensus 202 -~~~~~~~~A~~~~~~a~~~~~~lp~~ 227 (265)
T cd00683 202 -LLRRLIARARAHYREALAGLAALPRR 227 (265)
T ss_pred -HHHHHHHHHHHHHHHHHHhHHhCCHh
Confidence 34556667889999999999999853
No 18
>PF06783 UPF0239: Uncharacterised protein family (UPF0239); InterPro: IPR009621 This is a group of transmembrane proteins of unknown function.; GO: 0016021 integral to membrane
Probab=90.93 E-value=0.39 Score=29.46 Aligned_cols=25 Identities=32% Similarity=0.442 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhh
Q psy5533 7 DKLSEVAFEYGRNLGIAFQLVDDLL 31 (136)
Q Consensus 7 ~~~~~~l~~~G~~lG~afQi~DDll 31 (136)
+...+.+-+||..+|-.||+.==+-
T Consensus 15 et~~e~llRYGLf~GAIFQliCilA 39 (85)
T PF06783_consen 15 ETFFENLLRYGLFVGAIFQLICILA 39 (85)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4568899999999999999975443
No 19
>PLN02632 phytoene synthase
Probab=90.44 E-value=4.9 Score=30.96 Aligned_cols=86 Identities=21% Similarity=0.075 Sum_probs=53.7
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhhHHHHHHHHHh
Q psy5533 11 EVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGDVEKAFEFVHK 90 (136)
Q Consensus 11 ~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~~~~i~~~i~~ 90 (136)
+.+...+.++|+|+|+.|=+.|+ +.|...|++-+|.=..-+..-...+++... .+ ..+..
T Consensus 194 ~~~~~~A~~lG~AlQltNILRDv-----------~eD~~~GRvYLP~e~L~~~Gv~~edl~~~~-~~-~~~~~------- 253 (334)
T PLN02632 194 ESVYNAALALGIANQLTNILRDV-----------GEDARRGRVYLPQDELAQFGLTDEDIFAGK-VT-DKWRA------- 253 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-----------HHHHhCCceeCCHHHHHHcCCCHHHHhcCC-CC-HHHHH-------
Confidence 45678899999999999988886 457778888888654333221122222111 11 11111
Q ss_pred cCHHHHHHHHHHHHHHHHHHHhhcCCCC
Q psy5533 91 SQGLEQTKFLARKHCVEAVRLASGLAES 118 (136)
Q Consensus 91 ~g~~~~~~~~~~~~~~~A~~~l~~l~~~ 118 (136)
.+......++.|..+|...+..+|..
T Consensus 254 --l~~~~~~~Ar~~~~~a~~~l~~lp~~ 279 (334)
T PLN02632 254 --FMKFQIKRARMYFAEAEEGVSELDPA 279 (334)
T ss_pred --HHHHHHHHHHHHHHHHHHhHhhCCHH
Confidence 23333466888888888888888864
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=89.48 E-value=7 Score=28.96 Aligned_cols=83 Identities=12% Similarity=-0.002 Sum_probs=51.1
Q ss_pred HHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhhHHHHHHHHHhcCH
Q psy5533 14 FEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGDVEKAFEFVHKSQG 93 (136)
Q Consensus 14 ~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~~~~i~~~i~~~g~ 93 (136)
..++.++|.|+|+.|=+.|+ +.|...|++-+|.=..-+..-...+++.. ..+ ..+.. .
T Consensus 137 ~~~A~~lG~AlQltniLRDl-----------~eD~~~gR~YLP~~~l~~~Gv~~edl~~~-~~~-~~~~~---------~ 194 (266)
T TIGR03464 137 VALSDAICTALQLINFWQDV-----------GVDYRKGRVYLPRDDLARFGVSEEDLAAG-RAT-PALRE---------L 194 (266)
T ss_pred HHHHHHHHHHHHHHHHHHhh-----------HHHHhcCCccCCHHHHHHcCCCHHHHhcC-CCC-HHHHH---------H
Confidence 46788999999999888885 35666788888864432221111122211 111 11111 2
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCC
Q psy5533 94 LEQTKFLARKHCVEAVRLASGLAES 118 (136)
Q Consensus 94 ~~~~~~~~~~~~~~A~~~l~~l~~~ 118 (136)
+......++.+..+|...+..+|..
T Consensus 195 ~~~~~~~A~~~~~~a~~~~~~lp~~ 219 (266)
T TIGR03464 195 MAFEVSRTRALLDRGAPLAARVDGR 219 (266)
T ss_pred HHHHHHHHHHHHHHHHHhHHhCCHh
Confidence 4455566788899999999888754
No 21
>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=89.35 E-value=4.4 Score=31.37 Aligned_cols=84 Identities=18% Similarity=0.258 Sum_probs=50.9
Q ss_pred HHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhhHHHHHHHHHhcC
Q psy5533 13 AFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGDVEKAFEFVHKSQ 92 (136)
Q Consensus 13 l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~~~~i~~~i~~~g 92 (136)
...++..+|+|+|+.|=+.|+. .|+..|+.=+|.=-.-+...+..++. . ++.......
T Consensus 166 ~~~~A~~lG~aLQlTNIlRDv~-----------ED~~~GR~YlP~e~l~~~g~~~~dl~-~----~~~~~~~~~------ 223 (336)
T TIGR01559 166 SEALSNSMGLFLQKTNIIRDYL-----------EDINEGRMFWPREIWSKYAKKLGDFK-K----PENSDKALQ------ 223 (336)
T ss_pred hHHHHHHHHHHHHHHHHHHHHH-----------hHHhCCCCCCCHHHHHHcCCCHHHhc-C----ccccHHHHH------
Confidence 4689999999999999998874 45566777777442222111111111 1 111111111
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCC
Q psy5533 93 GLEQTKFLARKHCVEAVRLASGLAES 118 (136)
Q Consensus 93 ~~~~~~~~~~~~~~~A~~~l~~l~~~ 118 (136)
.++.....+..|...|+..+..+++.
T Consensus 224 ~l~~lv~~A~~~~~~al~yl~~l~~~ 249 (336)
T TIGR01559 224 CLNELVTNALHHATDCLTYLSRLRDQ 249 (336)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence 34555667888889999999888664
No 22
>TIGR03465 HpnD squalene synthase HpnD. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated.
Probab=88.09 E-value=5.6 Score=29.40 Aligned_cols=85 Identities=21% Similarity=0.111 Sum_probs=52.3
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhhHHHHHHHHHhc
Q psy5533 12 VAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGDVEKAFEFVHKS 91 (136)
Q Consensus 12 ~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~~~~i~~~i~~~ 91 (136)
.....+.++|.|+|+.|=+.|+ +.|+..|++.+|.=..-+..-...++... ..+ ..+..
T Consensus 134 ~~~~~a~~lG~AlqltnilRdv-----------~eD~~~gR~ylP~~~l~~~gv~~~~l~~~-~~~-~~~~~-------- 192 (266)
T TIGR03465 134 RTLEYAHHLGRALQLTNILRDV-----------GEDARRGRIYLPAEELQRFGVPAADILEG-RYS-PALAA-------- 192 (266)
T ss_pred hHHHHHHHHHHHHHHHHHHHHh-----------HHHHhCCCeecCHHHHHHcCCCHHHhcCC-CCC-HHHHH--------
Confidence 3567899999999999988886 35677788888875433322111122111 111 11221
Q ss_pred CHHHHHHHHHHHHHHHHHHHhhcCCCC
Q psy5533 92 QGLEQTKFLARKHCVEAVRLASGLAES 118 (136)
Q Consensus 92 g~~~~~~~~~~~~~~~A~~~l~~l~~~ 118 (136)
.+......++.+..+|...+..+|..
T Consensus 193 -~~~~l~~~A~~~l~~a~~~~~~~p~~ 218 (266)
T TIGR03465 193 -LCRFQAERARAHYAEADALLPACDRR 218 (266)
T ss_pred -HHHHHHHHHHHHHHHHHHhhhhCCHh
Confidence 24445566778888888888888753
No 23
>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=83.87 E-value=14 Score=27.22 Aligned_cols=25 Identities=20% Similarity=0.029 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhh
Q psy5533 8 KLSEVAFEYGRNLGIAFQLVDDLLD 32 (136)
Q Consensus 8 ~~~~~l~~~G~~lG~afQi~DDlld 32 (136)
+....+..--+.+=.|+-|.||++|
T Consensus 39 ~~~~~la~aiEllh~asLIhDDI~D 63 (259)
T cd00685 39 EAALRLAAAIELLHTASLVHDDVMD 63 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 5555666667778889999999988
No 24
>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=83.59 E-value=17 Score=27.73 Aligned_cols=29 Identities=17% Similarity=0.030 Sum_probs=19.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy5533 4 GADDKLSEVAFEYGRNLGIAFQLVDDLLD 32 (136)
Q Consensus 4 g~~~~~~~~l~~~G~~lG~afQi~DDlld 32 (136)
|.+.+....+...-+.+=.|.=|-||++|
T Consensus 59 ~~~~~~~~~~A~aiEliH~asLiHDDI~D 87 (319)
T TIGR02748 59 DYDLDAIKHVAVALELIHMASLVHDDVID 87 (319)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHhccccC
Confidence 33444444455555667778889999988
No 25
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=83.12 E-value=13 Score=28.49 Aligned_cols=28 Identities=18% Similarity=0.063 Sum_probs=18.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy5533 5 ADDKLSEVAFEYGRNLGIAFQLVDDLLD 32 (136)
Q Consensus 5 ~~~~~~~~l~~~G~~lG~afQi~DDlld 32 (136)
.+.+....+..--+.+=.|..|-||++|
T Consensus 61 ~~~~~~~~~A~avEllH~asLiHDDI~D 88 (323)
T PRK10888 61 YQGNAHVTIAALIEFIHTATLLHDDVVD 88 (323)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHccccc
Confidence 3334344455555667778899999988
No 26
>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=81.72 E-value=15 Score=26.96 Aligned_cols=29 Identities=21% Similarity=0.166 Sum_probs=21.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy5533 4 GADDKLSEVAFEYGRNLGIAFQLVDDLLD 32 (136)
Q Consensus 4 g~~~~~~~~l~~~G~~lG~afQi~DDlld 32 (136)
|.+.+....+...-+.+=.|+=|.||++|
T Consensus 29 ~~~~~~~~~~a~avEliH~asLIhDDI~D 57 (260)
T PF00348_consen 29 GGDPEKAIPLAAAVELIHAASLIHDDIID 57 (260)
T ss_dssp TCHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 34455566667777778889999999988
No 27
>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=77.00 E-value=31 Score=26.44 Aligned_cols=21 Identities=24% Similarity=0.189 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHhhhhh
Q psy5533 12 VAFEYGRNLGIAFQLVDDLLD 32 (136)
Q Consensus 12 ~l~~~G~~lG~afQi~DDlld 32 (136)
.+..--+.+=.|.-|-||++|
T Consensus 71 ~~A~avEliH~asLiHDDiiD 91 (322)
T TIGR02749 71 RLAEITEMIHTASLVHDDVID 91 (322)
T ss_pred HHHHHHHHHHHHHHHHccccc
Confidence 344455666678889999988
No 28
>KOG3330|consensus
Probab=71.04 E-value=4.5 Score=27.92 Aligned_cols=38 Identities=24% Similarity=0.452 Sum_probs=29.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhC
Q psy5533 6 DDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLG 51 (136)
Q Consensus 6 ~~~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~g 51 (136)
.++...+|.+.|.++|+ .+.||++-= ++-|+|.|+++-
T Consensus 39 ~e~Vn~qLdkMGyNiG~--RLiedFLAk------s~vpRC~dfret 76 (183)
T KOG3330|consen 39 PEDVNKQLDKMGYNIGI--RLIEDFLAK------SNVPRCVDFRET 76 (183)
T ss_pred HHHHHHHHHhccchhhH--HHHHHHHhh------cCCchhhhHHHH
Confidence 34567799999999997 578888762 366889999863
No 29
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=70.40 E-value=15 Score=28.16 Aligned_cols=30 Identities=33% Similarity=0.430 Sum_probs=19.3
Q ss_pred HHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHH
Q psy5533 18 RNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLF 59 (136)
Q Consensus 18 ~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~ 59 (136)
+.+=.+.=|-||++| . +|++.|++|....|
T Consensus 76 EliH~~SLiHDDvmD--~----------s~~RRG~pt~~~~~ 105 (322)
T COG0142 76 ELIHTASLIHDDLMD--D----------DDLRRGKPTVHAKF 105 (322)
T ss_pred HHHHHHHHHHhhccc--C----------CCccCCCCCchhHh
Confidence 334455567899977 2 35666777777666
No 30
>CHL00151 preA prenyl transferase; Reviewed
Probab=65.45 E-value=20 Score=27.46 Aligned_cols=35 Identities=23% Similarity=0.354 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHH
Q psy5533 13 AFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLF 59 (136)
Q Consensus 13 l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~ 59 (136)
+...-+.+=.|.-|-||++| + ++++.|++|....|
T Consensus 73 ~A~aiEllH~asLiHDDi~D--~----------s~~RRG~pt~h~~~ 107 (323)
T CHL00151 73 LAEITEIIHTASLVHDDVID--E----------CSIRRGIPTVHKIF 107 (323)
T ss_pred HHHHHHHHHHHHHHHccccc--C----------ccccCCCccHHHHh
Confidence 34445556667788999988 2 34555666655444
No 31
>PLN02890 geranyl diphosphate synthase
Probab=64.59 E-value=67 Score=25.80 Aligned_cols=22 Identities=32% Similarity=0.317 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHhhhhh
Q psy5533 11 EVAFEYGRNLGIAFQLVDDLLD 32 (136)
Q Consensus 11 ~~l~~~G~~lG~afQi~DDlld 32 (136)
-.+...-+.+=.|.-|-||++|
T Consensus 164 ~~~AaavEliH~ASLVHDDIiD 185 (422)
T PLN02890 164 QNIAEITEMIHVASLLHDDVLD 185 (422)
T ss_pred HHHHHHHHHHHHHHHHHccccc
Confidence 3455566677788899999988
No 32
>PHA02130 hypothetical protein
Probab=60.86 E-value=10 Score=22.11 Aligned_cols=31 Identities=26% Similarity=0.246 Sum_probs=18.7
Q ss_pred hhhhhh-cCCccccCC-CCchhHhhCcccHHHH
Q psy5533 28 DDLLDF-ISSSDAMGK-PTAADLKLGLATAPVL 58 (136)
Q Consensus 28 DDlld~-~~~~~~~GK-~~~~Di~~gk~Tlp~l 58 (136)
||++++ |.+.--+|- |..+||.+||-|+..-
T Consensus 32 ddil~ipfkstv~w~lcp~~qdi~ngke~fvwn 64 (81)
T PHA02130 32 DDILSIPFKSTVYWDLCPYAQDIHNGKENFVWN 64 (81)
T ss_pred cchhcccccceeeeccCcchhhhhcCcceeehh
Confidence 567776 222222333 6778999999887543
No 33
>PRK13105 ubiA prenyltransferase; Reviewed
Probab=53.60 E-value=25 Score=26.55 Aligned_cols=32 Identities=19% Similarity=0.428 Sum_probs=24.5
Q ss_pred HHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhc
Q psy5533 21 GIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEK 63 (136)
Q Consensus 21 G~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~ 63 (136)
..++.+.+++.|+-+ |-.+|+.|+|+.+-.+.
T Consensus 173 ~~a~~ii~~irDie~-----------Dr~~G~~Tlpv~lG~~~ 204 (282)
T PRK13105 173 GMASHAFGAVQDVVA-----------DREAGIASIATVLGARR 204 (282)
T ss_pred HHHHHHHHhCcchHh-----------HHHcCCccchHHhcHHH
Confidence 568889999888754 45578999999985443
No 34
>PRK12872 ubiA prenyltransferase; Reviewed
Probab=49.87 E-value=13 Score=27.69 Aligned_cols=31 Identities=32% Similarity=0.437 Sum_probs=23.0
Q ss_pred HHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhh
Q psy5533 21 GIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACE 62 (136)
Q Consensus 21 G~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~ 62 (136)
-.+.++..|+.|.-+ |-..|++|+|+.+-.+
T Consensus 174 ~~~~~~~~d~~D~e~-----------D~~~G~~Tlpv~lG~~ 204 (285)
T PRK12872 174 SFIREIVFDIKDIEG-----------DRKSGLKTLPIVLGKE 204 (285)
T ss_pred HHHHHHHHhcccchh-----------HHHcCCcccchhcchH
Confidence 457778888888654 4557999999998544
No 35
>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=47.12 E-value=15 Score=23.50 Aligned_cols=33 Identities=24% Similarity=0.413 Sum_probs=21.7
Q ss_pred HHHHHHHHHH-----HHHHHHhhhhhhcCCccccCCCC
Q psy5533 12 VAFEYGRNLG-----IAFQLVDDLLDFISSSDAMGKPT 44 (136)
Q Consensus 12 ~l~~~G~~lG-----~afQi~DDlld~~~~~~~~GK~~ 44 (136)
.+..|-.++| -..+|.+|++|+|......|+++
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 46799999999998777667763
No 36
>COG1562 ERG9 Phytoene/squalene synthetase [Lipid metabolism]
Probab=46.81 E-value=1.3e+02 Score=22.87 Aligned_cols=85 Identities=26% Similarity=0.228 Sum_probs=50.7
Q ss_pred HHHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhhcCCcchHHHHhhcCChhhHHHHHHHHHhcC
Q psy5533 13 AFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGDVEKAFEFVHKSQ 92 (136)
Q Consensus 13 l~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~~~~~~~~~l~~~~~~~~~~~~i~~~i~~~g 92 (136)
.......+|.|+|+.+=+.|+ +.|...|+.=+|.=-.-+...+..+....... +.+. .
T Consensus 154 ~~~~a~~lG~A~QlvNilRdv-----------~eD~~~GrvylP~e~l~~~g~~~~d~~~~~~~--~~~~---~------ 211 (288)
T COG1562 154 TRAYARGLGLALQLVNILRDV-----------GEDRRRGRVYLPAEELARFGVSEADLLAGRVD--DAFR---E------ 211 (288)
T ss_pred hHHHHHHHHHHHHHHHHHHHh-----------HHHHhCCcccCCHHHHHHhCCCHHHHHcccch--hHHH---H------
Confidence 344455599999999888885 56777888777744322222222222211100 1111 1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCCH
Q psy5533 93 GLEQTKFLARKHCVEAVRLASGLAESP 119 (136)
Q Consensus 93 ~~~~~~~~~~~~~~~A~~~l~~l~~~~ 119 (136)
.+++.....+.+...|...+..+|...
T Consensus 212 ~~~~~~~~ar~~~~~a~~~~~~lp~~~ 238 (288)
T COG1562 212 LMRFEADRARDHLAEARRGLPALPGRA 238 (288)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhCCccc
Confidence 355566778888889999998888643
No 37
>PRK12465 xylose isomerase; Provisional
Probab=42.73 E-value=1.2e+02 Score=24.49 Aligned_cols=53 Identities=21% Similarity=0.210 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHHHHHHhh--hhhhcCCcc-ccCCCCchhHhhCcccHHHH--HHhh
Q psy5533 10 SEVAFEYGRNLGIAFQLVDD--LLDFISSSD-AMGKPTAADLKLGLATAPVL--FACE 62 (136)
Q Consensus 10 ~~~l~~~G~~lG~afQi~DD--lld~~~~~~-~~GK~~~~Di~~gk~Tlp~l--~a~~ 62 (136)
+.-+..|++-+=.|-.|..| +.++..+.. ++-.+.|.+|.+||.|+--+ |+++
T Consensus 365 i~gmD~~A~gl~~A~~~~ed~~~~~~~~~RY~s~~~~~g~~i~~g~~~l~~l~~~a~~ 422 (445)
T PRK12465 365 IGGMDAFARGLEVANALLTSSPLEQWRAERYASFDSGAGADFAAGKSTLADLAAHAAG 422 (445)
T ss_pred HHHHHHHHHHHHHHHHHHhcccHHHHHHHHhcccchhhChHHHcCcCCHHHHHHHHHc
Confidence 34566778888889999877 666554442 23345688999999999988 6655
No 38
>PLN00012 chlorophyll synthetase; Provisional
Probab=42.19 E-value=19 Score=28.34 Aligned_cols=32 Identities=31% Similarity=0.553 Sum_probs=24.5
Q ss_pred HHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHh
Q psy5533 19 NLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFAC 61 (136)
Q Consensus 19 ~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~ 61 (136)
-+++++-+.+|+.|+-+ |-+.|++|+|+.+-.
T Consensus 263 l~~lai~ivnd~~Die~-----------Dr~aG~~TLpV~~G~ 294 (375)
T PLN00012 263 IAGLGIAIVNDFKSIEG-----------DRALGLQSLPVAFGV 294 (375)
T ss_pred HHHHHHHHHhhhcchhh-----------HHHcCCcccceeech
Confidence 46777888999888643 566789999998743
No 39
>PRK13591 ubiA prenyltransferase; Provisional
Probab=41.85 E-value=10 Score=29.05 Aligned_cols=26 Identities=31% Similarity=0.331 Sum_probs=20.0
Q ss_pred HHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHH
Q psy5533 24 FQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFA 60 (136)
Q Consensus 24 fQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a 60 (136)
..+.+|+.|..+ |..+|+.|+|+.+-
T Consensus 195 ~~iindirDiEG-----------Dr~~G~kTLPV~lG 220 (307)
T PRK13591 195 NSCVYDFKDVKG-----------DTLAGIKTLPVSLG 220 (307)
T ss_pred HHHHHHhhhhHh-----------HHHcCCeeEEEEEC
Confidence 347789888754 56679999999983
No 40
>PRK10581 geranyltranstransferase; Provisional
Probab=41.42 E-value=1.6e+02 Score=22.39 Aligned_cols=42 Identities=26% Similarity=0.309 Sum_probs=25.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhhh--hhhcCCccccCCCCchhHhhCcccHHHHH
Q psy5533 6 DDKLSEVAFEYGRNLGIAFQLVDDL--LDFISSSDAMGKPTAADLKLGLATAPVLF 59 (136)
Q Consensus 6 ~~~~~~~l~~~G~~lG~afQi~DDl--ld~~~~~~~~GK~~~~Di~~gk~Tlp~l~ 59 (136)
+.+....+..--+.+=.|.-|-||+ +| ++ |++.|++|....|
T Consensus 62 ~~~~~~~~A~avEliH~aSLiHDDip~~D--~s----------~~RRG~pt~h~~~ 105 (299)
T PRK10581 62 STNTLDAPAAAVECIHAYSLIHDDLPAMD--DD----------DLRRGLPTCHVKF 105 (299)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHcCccccc--CC----------CccCCCcChHHHh
Confidence 4344444455556666778899999 88 33 4555666655544
No 41
>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=36.54 E-value=27 Score=23.49 Aligned_cols=11 Identities=45% Similarity=1.026 Sum_probs=9.7
Q ss_pred HHHHHHHHHHH
Q psy5533 17 GRNLGIAFQLV 27 (136)
Q Consensus 17 G~~lG~afQi~ 27 (136)
|..+|+||||.
T Consensus 142 gnmmgvafqil 152 (199)
T PF09053_consen 142 GNMMGVAFQIL 152 (199)
T ss_dssp HHHHHHHHHHT
T ss_pred Cccceeeeeee
Confidence 77899999995
No 42
>COG0571 Rnc dsRNA-specific ribonuclease [Transcription]
Probab=36.12 E-value=1.8e+02 Score=21.46 Aligned_cols=51 Identities=14% Similarity=0.067 Sum_probs=38.2
Q ss_pred hHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcCCC-CHHHHHHHHHHHH
Q psy5533 80 DVEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAE-SPYQKGLVVLTDL 130 (136)
Q Consensus 80 ~~~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l~~-~~~~~~L~~l~~~ 130 (136)
-++.++.-+.--++++.++..+..+...-+..+...+. ..++..|++++..
T Consensus 122 ~~EAligAiylD~g~~~~~~~i~~l~~~~~~~~~~~~~~~D~Kt~LQe~~q~ 173 (235)
T COG0571 122 AFEALIGAIYLDSGLEAARKFILKLFLPRLEEIDAGDQFKDPKTRLQELLQA 173 (235)
T ss_pred HHHHHHHHHHHhCChHHHHHHHHHHHHHHHhhccccccccChhHHHHHHHHh
Confidence 35555555555555999999999999999998877664 5678888887753
No 43
>PLN02923 xylose isomerase
Probab=36.04 E-value=1.6e+02 Score=24.00 Aligned_cols=54 Identities=20% Similarity=0.164 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHHHHHHhh--hhhhcCCcc-ccCCCCchhHhhCcccHHHH--HHhhc
Q psy5533 10 SEVAFEYGRNLGIAFQLVDD--LLDFISSSD-AMGKPTAADLKLGLATAPVL--FACEK 63 (136)
Q Consensus 10 ~~~l~~~G~~lG~afQi~DD--lld~~~~~~-~~GK~~~~Di~~gk~Tlp~l--~a~~~ 63 (136)
+.-+..|++-+=.|-.|..| +.++..+.+ .+-.+.|.+|.+||.|+--+ |+++.
T Consensus 399 I~gMD~~A~gl~~Aa~l~ed~~l~~~~~~RYas~~~g~G~~i~~G~~~l~~l~~~a~~~ 457 (478)
T PLN02923 399 ISGMDTMARGLRNAAKLLEEGSLPELVRKRYASFDSELGAQIEAGKADFEELEKKALEW 457 (478)
T ss_pred HHHHHHHHHHHHHHHHHHhcccHHHHHHHHhccccchhchHHHcCcCCHHHHHHHHHhc
Confidence 44566788888889999877 666555442 23445688999999999988 66554
No 44
>PHA02603 nrdC.11 hypothetical protein; Provisional
Probab=34.49 E-value=1.8e+02 Score=22.62 Aligned_cols=22 Identities=9% Similarity=-0.032 Sum_probs=15.2
Q ss_pred hcCCCCHHHHHHHHHHHHHHcc
Q psy5533 113 SGLAESPYQKGLVVLTDLVLNR 134 (136)
Q Consensus 113 ~~l~~~~~~~~L~~l~~~~~~r 134 (136)
..+|+.+......+++..+..+
T Consensus 302 s~LP~~pD~~~i~~~l~~vy~~ 323 (330)
T PHA02603 302 NGMPQKVDMEFWDDFLEEVYLE 323 (330)
T ss_pred CCCCCCcCHHHHHHHHHHHHHH
Confidence 4788877677777777766543
No 45
>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=33.43 E-value=43 Score=25.39 Aligned_cols=32 Identities=34% Similarity=0.599 Sum_probs=22.2
Q ss_pred HHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhh
Q psy5533 20 LGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACE 62 (136)
Q Consensus 20 lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~ 62 (136)
+..+.-+.+|+.|+- +|.+.|++|+|+.+-.+
T Consensus 195 ~~~~i~~~n~~~D~e-----------~D~~~G~~Tlpv~lG~~ 226 (306)
T TIGR02056 195 AGLGIAIVNDFKSVE-----------GDRALGLQSLPVAFGIE 226 (306)
T ss_pred HHHHHHHHHHccChH-----------HHHHcCCcCcchhcChH
Confidence 344555778877764 46677999999987433
No 46
>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=32.71 E-value=1.1e+02 Score=19.58 Aligned_cols=48 Identities=6% Similarity=-0.014 Sum_probs=33.2
Q ss_pred hhHHHHHHHHHhcCHHHH----HHHHHHHHHHHHHHHhhcCCCCHHHHHHHH
Q psy5533 79 GDVEKAFEFVHKSQGLEQ----TKFLARKHCVEAVRLASGLAESPYQKGLVV 126 (136)
Q Consensus 79 ~~~~~i~~~i~~~g~~~~----~~~~~~~~~~~A~~~l~~l~~~~~~~~L~~ 126 (136)
++..-...++..+++.=+ -.+.++...++++..|+.+|++--|-.|..
T Consensus 51 eeA~lCLaLLmGYnat~yd~geke~~~Q~vL~Rs~~vL~~Lp~SlLK~~Llt 102 (106)
T PF06603_consen 51 EEANLCLALLMGYNATIYDNGEKEEKKQEVLDRSWEVLDKLPASLLKVQLLT 102 (106)
T ss_pred HHHHHHHHHHHhccchhhhCccHHHHHHHHHHHHHHHHHhCCcHHHHHHHHH
Confidence 344556666666655433 356777889999999999999876655543
No 47
>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=32.45 E-value=2.1e+02 Score=21.20 Aligned_cols=25 Identities=20% Similarity=0.189 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhcCC
Q psy5533 12 VAFEYGRNLGIAFQLVDDLLDFISS 36 (136)
Q Consensus 12 ~l~~~G~~lG~afQi~DDlld~~~~ 36 (136)
.+..+-...+...-+.||+..|-.+
T Consensus 197 ~~~~l~~~~~~~~~l~NDl~S~~KE 221 (303)
T cd00687 197 VMRALEALASDAIALVNDIYSYEKE 221 (303)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhHHH
Confidence 3667777888888888998887543
No 48
>PLN02857 octaprenyl-diphosphate synthase
Probab=32.37 E-value=1.2e+02 Score=24.24 Aligned_cols=23 Identities=26% Similarity=0.208 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhh
Q psy5533 10 SEVAFEYGRNLGIAFQLVDDLLD 32 (136)
Q Consensus 10 ~~~l~~~G~~lG~afQi~DDlld 32 (136)
.-.+...-+.+=.|.=|-||++|
T Consensus 163 ~~~lAaaiEliH~ASLIHDDI~D 185 (416)
T PLN02857 163 HRRLAEITEMIHTASLIHDDVLD 185 (416)
T ss_pred HHHHHHHHHHHHHHHHHHCcccc
Confidence 33445555666677789999988
No 49
>PRK01194 V-type ATP synthase subunit E; Provisional
Probab=30.11 E-value=1.6e+02 Score=20.56 Aligned_cols=38 Identities=11% Similarity=0.081 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCC-CCHHHHHHHHHHHHH
Q psy5533 94 LEQTKFLARKHCVEAVRLASGLA-ESPYQKGLVVLTDLV 131 (136)
Q Consensus 94 ~~~~~~~~~~~~~~A~~~l~~l~-~~~~~~~L~~l~~~~ 131 (136)
+..=.++++..+++|.+.|..+| +..+...|..|+...
T Consensus 75 L~aree~I~~v~~~a~e~L~~l~~~~~Y~~~L~~LI~~a 113 (185)
T PRK01194 75 REKRREILKDYLDIAYEHLMNITKSKEYDSILNKMIEVA 113 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHcccCCchHHHHHHHHHHHH
Confidence 33446888899999999999999 467888998887654
No 50
>COG2005 ModE N-terminal domain of molybdenum-binding protein [General function prediction only]
Probab=29.84 E-value=32 Score=22.98 Aligned_cols=35 Identities=9% Similarity=-0.002 Sum_probs=27.9
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcC
Q psy5533 81 VEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGL 115 (136)
Q Consensus 81 ~~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l 115 (136)
.-++++.|.++|++..|.+.+.-....|+..|+.+
T Consensus 21 ~~~LL~~I~etGSIs~AAk~~GiSYk~AW~~i~~~ 55 (130)
T COG2005 21 RIELLKAIAETGSISAAAKAAGISYKSAWDYIKAL 55 (130)
T ss_pred HHHHHHHHHHhCCHHHHHHHcCCCHHHHHHHHHHH
Confidence 34677888999999999988888778888777644
No 51
>PRK12875 ubiA prenyltransferase; Reviewed
Probab=29.55 E-value=1.4e+02 Score=22.54 Aligned_cols=31 Identities=13% Similarity=0.247 Sum_probs=22.3
Q ss_pred HHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHH
Q psy5533 19 NLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFA 60 (136)
Q Consensus 19 ~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a 60 (136)
.+.+++.+.+++.|+- .|.+.|++|+|+.+-
T Consensus 176 l~~~~~~~in~i~Die-----------~D~~aGi~Tlav~lG 206 (282)
T PRK12875 176 LWAMGMHTFSAIPDIE-----------PDRAAGIRTTATVLG 206 (282)
T ss_pred HHHHHHHHHHhccCHH-----------HHHHcCCccchhhcc
Confidence 4456667777777753 466789999999983
No 52
>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=29.27 E-value=32 Score=25.60 Aligned_cols=28 Identities=25% Similarity=0.449 Sum_probs=20.4
Q ss_pred HHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHH
Q psy5533 22 IAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFA 60 (136)
Q Consensus 22 ~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a 60 (136)
.+.-+.+|+.|+- +|...|++|+|+.+-
T Consensus 175 ~~i~~~nd~~D~~-----------~D~~~G~~Tl~v~lG 202 (283)
T TIGR01476 175 HGIMTLNDFKSVE-----------GDRQLGLRSLPVMIG 202 (283)
T ss_pred HHHHHHHhccchh-----------hHHHcCCcCcceEEc
Confidence 3456788888864 456678999999873
No 53
>PLN02878 homogentisate phytyltransferase
Probab=28.54 E-value=88 Score=23.72 Aligned_cols=34 Identities=15% Similarity=0.250 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHH
Q psy5533 16 YGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFA 60 (136)
Q Consensus 16 ~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a 60 (136)
|-.-+..+.-+..|+.|+-|| -..|..|+|+.+-
T Consensus 164 f~~~f~~~i~i~KDi~DieGD-----------~~~Gi~Tlpv~lG 197 (280)
T PLN02878 164 FMCFFSVVIALFKDIPDVEGD-----------RIFGIRSFSVRLG 197 (280)
T ss_pred HHHHHHHHHHHHhhCcCchhH-----------HHCCCceechhhC
Confidence 334444555588898887654 4568899999983
No 54
>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=28.37 E-value=1.7e+02 Score=20.85 Aligned_cols=35 Identities=31% Similarity=0.299 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHH
Q psy5533 14 FEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLF 59 (136)
Q Consensus 14 ~~~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~ 59 (136)
.-+.--++.+....+|+.|+.+ |.+.|+.|+|+.+
T Consensus 152 ~~~~~~~~~~~~~~~~~~D~~~-----------D~~~g~~Tl~v~~ 186 (257)
T PF01040_consen 152 AIFFFLLIFAIMFFNDIRDIEG-----------DRKAGRRTLPVLL 186 (257)
T ss_pred HHHHHHHHHHHHHHHHhhhHHH-----------HHHcCCcchHHHH
Confidence 3344567777788888888754 4556889999987
No 55
>PF10759 DUF2587: Protein of unknown function (DUF2587); InterPro: IPR019695 This entry represents proteins found Actinobacteria sp. The function is not known.
Probab=25.97 E-value=2.1e+02 Score=19.73 Aligned_cols=33 Identities=12% Similarity=0.078 Sum_probs=23.3
Q ss_pred HHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhh
Q psy5533 81 VEKAFEFVHKSQGLEQTKFLARKHCVEAVRLAS 113 (136)
Q Consensus 81 ~~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~ 113 (136)
++.+++-|+...--+.++..+.+.++..++.|+
T Consensus 39 ikqLLEEVraApLDeAsR~RL~eIH~~SI~ELe 71 (169)
T PF10759_consen 39 IKQLLEEVRAAPLDEASRNRLREIHERSIKELE 71 (169)
T ss_pred HHHHHHHHHcCcCCHHHHHHHHHHHHHHHHHHH
Confidence 445555566666667778888888888887775
No 56
>PF04716 ETC_C1_NDUFA5: ETC complex I subunit conserved region; InterPro: IPR006806 This is a family of eukaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC) (1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 29.9 kDa protein. The conserved region is found at the N terminus of the member proteins [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022904 respiratory electron transport chain, 0005743 mitochondrial inner membrane
Probab=25.81 E-value=1.3e+02 Score=16.86 Aligned_cols=33 Identities=9% Similarity=0.078 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHhhcCCCC-HHHHHHHHHHHH
Q psy5533 98 KFLARKHCVEAVRLASGLAES-PYQKGLVVLTDL 130 (136)
Q Consensus 98 ~~~~~~~~~~A~~~l~~l~~~-~~~~~L~~l~~~ 130 (136)
+..+....++.++.|+.+|.+ .+|..-..++..
T Consensus 4 r~~L~~lY~~~L~~L~~~P~~a~YR~~tE~it~~ 37 (57)
T PF04716_consen 4 REALISLYNKTLKALKKIPEDAAYRQYTEAITKH 37 (57)
T ss_pred HHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHH
Confidence 445666778888999999974 578887777764
No 57
>PRK12887 ubiA tocopherol phytyltransferase; Reviewed
Probab=25.52 E-value=1.9e+02 Score=22.06 Aligned_cols=33 Identities=15% Similarity=0.236 Sum_probs=23.6
Q ss_pred HHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhh
Q psy5533 19 NLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACE 62 (136)
Q Consensus 19 ~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~ 62 (136)
-+-.++.+..|+.|.-+ |...|+.|+|+.+-.+
T Consensus 193 ~~~~~~~l~~di~D~eg-----------D~~~Gi~Tlav~lG~~ 225 (308)
T PRK12887 193 VFTFAIAIFKDIPDMEG-----------DRQYQITTFTLRLGKQ 225 (308)
T ss_pred HHHHHHHHHHhccchhh-----------HHHcCCcchhHHHhHH
Confidence 34456677788888643 5667999999998443
No 58
>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=25.48 E-value=2.5e+02 Score=19.82 Aligned_cols=29 Identities=24% Similarity=0.126 Sum_probs=21.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy5533 4 GADDKLSEVAFEYGRNLGIAFQLVDDLLD 32 (136)
Q Consensus 4 g~~~~~~~~l~~~G~~lG~afQi~DDlld 32 (136)
|.+.+....+..--+.+=.+.-+.||+.|
T Consensus 14 ~~~~~~~~~~a~ave~l~~~~li~DDI~D 42 (236)
T cd00867 14 GGDLEAALRLAAAVELLHAASLVHDDIVD 42 (236)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHccccc
Confidence 44455555667777778888899999988
No 59
>PF03623 Focal_AT: Focal adhesion targeting region; InterPro: IPR005189 Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signalling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal "focal adhesion targeting" (FAT) region is necessary and sufficient for localizing FAK to focal adhesions. The crystal structure of FAT shows it forms a four-helix bundle that resembles those found in two other proteins involved in cell adhesion, alpha-catenin and vinculin []. The binding of FAT to the focal adhesion protein, paxillin, requires the integrity of the helical bundle, whereas binding to another focal adhesion protein, talin, does not.; GO: 0004713 protein tyrosine kinase activity, 0004871 signal transducer activity, 0006468 protein phosphorylation, 0007172 signal complex assembly, 0005925 focal adhesion; PDB: 1K05_C 1OW8_C 1OW7_C 3S9O_C 3B71_B 1K04_A 1OW6_C 3GM1_B 3GM3_A 3GM2_A ....
Probab=25.39 E-value=1.7e+02 Score=19.78 Aligned_cols=33 Identities=21% Similarity=0.252 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCc
Q psy5533 5 ADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSS 37 (136)
Q Consensus 5 ~~~~~~~~l~~~G~~lG~afQi~DDlld~~~~~ 37 (136)
.+++++...+.+|..++-.++..|++++.+++.
T Consensus 33 ~~~~y~~~VK~VG~~Lr~Ll~sVd~~~~~l~~s 65 (139)
T PF03623_consen 33 KPEEYVDLVKNVGLALRDLLTSVDQILPSLPSS 65 (139)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHGGGSHTT
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHhhccCCHH
Confidence 356789999999999999999999999998654
No 60
>PF05546 She9_MDM33: She9 / Mdm33 family; InterPro: IPR008839 Members of this family are mitochondrial inner membrane proteins with a role in inner mitochondrial membrane organisation and biogenesis []. The yeast Mdm33 protein assembles into an oligomeric complex in the inner membrane where it performs homotypic protein-protein interactions. It has been suggested that Mdm33 plays a distinct role, possibly involved in fission of the mitochondrial inner membrane [].
Probab=24.68 E-value=2.6e+02 Score=20.22 Aligned_cols=107 Identities=19% Similarity=0.173 Sum_probs=66.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhcCCccccCCC----------CchhHhhCcccHHHHHHhhcCC--cchHHHHhhc
Q psy5533 8 KLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKP----------TAADLKLGLATAPVLFACEKFP--ELNPMIMRRF 75 (136)
Q Consensus 8 ~~~~~l~~~G~~lG~afQi~DDlld~~~~~~~~GK~----------~~~Di~~gk~Tlp~l~a~~~~~--~~~~~l~~~~ 75 (136)
.....+..+-..+..|-|-.||+-+|.+=.. +-+. .-..+++.|.+|--...-...+ +..+++.+..
T Consensus 6 ~~~~~~d~lq~~i~~as~~lNd~TGYs~Ie~-LK~~i~~~E~~l~~~r~~~~~aK~~Y~~ai~~Rs~sQrEvn~LLqRK~ 84 (207)
T PF05546_consen 6 KLSFYMDSLQETIFTASQALNDVTGYSEIEK-LKKSIEELEDELEAARQEVREAKAAYDDAIQQRSSSQREVNELLQRKH 84 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccChHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 3445677777888899999999888754221 1110 0112223333333332222222 2345666544
Q ss_pred C-ChhhHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcC
Q psy5533 76 Q-EPGDVEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGL 115 (136)
Q Consensus 76 ~-~~~~~~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l 115 (136)
. ++.|+++.-+++..-.+.+.....+..-+..|....+..
T Consensus 85 sWs~~DleRFT~Lyr~dH~~e~~e~~ak~~l~~aE~~~e~~ 125 (207)
T PF05546_consen 85 SWSPADLERFTELYRNDHENEQAEEEAKEALEEAEEKVEEA 125 (207)
T ss_pred CCChHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 4 899999999999988888888888888877777766544
No 61
>PRK03963 V-type ATP synthase subunit E; Provisional
Probab=24.31 E-value=2.4e+02 Score=19.58 Aligned_cols=33 Identities=21% Similarity=0.116 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHH
Q psy5533 98 KFLARKHCVEAVRLASGLAESPYQKGLVVLTDL 130 (136)
Q Consensus 98 ~~~~~~~~~~A~~~l~~l~~~~~~~~L~~l~~~ 130 (136)
.++++..++++.+.|..+++..++.+|..++..
T Consensus 80 ~el~~~v~~~a~~~l~~~~~~~Y~~~l~~li~~ 112 (198)
T PRK03963 80 EELISEVLEAVRERLAELPEDEYFETLKALTKE 112 (198)
T ss_pred HHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHH
Confidence 466677777788888888777777777777554
No 62
>PRK12883 ubiA prenyltransferase UbiA-like protein; Reviewed
Probab=24.21 E-value=1.7e+02 Score=21.66 Aligned_cols=29 Identities=24% Similarity=0.412 Sum_probs=20.0
Q ss_pred HHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHh
Q psy5533 22 IAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFAC 61 (136)
Q Consensus 22 ~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~ 61 (136)
.+..+.+|+.|+- .|.+.|++|+|+.+-.
T Consensus 168 ~~~~~~~~~~D~e-----------~D~~~G~~Tlpv~~G~ 196 (277)
T PRK12883 168 VAREIMKDIEDIE-----------GDKAKGAKTLPIIIGK 196 (277)
T ss_pred HHHHHHhhhhhhc-----------cHHHcCCcCcChHhcH
Confidence 3555667776653 3566799999999843
No 63
>PRK12884 ubiA prenyltransferase; Reviewed
Probab=24.09 E-value=99 Score=22.84 Aligned_cols=36 Identities=17% Similarity=0.236 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhh
Q psy5533 16 YGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACE 62 (136)
Q Consensus 16 ~G~~lG~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~ 62 (136)
+.--..+++++..|+.|.- .|-+.|++|+|+.+-.+
T Consensus 163 ~~~~~~~~~~~~~~~~D~e-----------~D~~~G~~Tl~v~~G~~ 198 (279)
T PRK12884 163 MAFLMTLGREIMKDIEDVE-----------GDRLRGARTLAILYGEK 198 (279)
T ss_pred HHHHHHHHHHHHHHhhhhh-----------hHHHcCCeeechHhcHH
Confidence 3444456677777877754 35667899999988443
No 64
>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=23.70 E-value=1.5e+02 Score=23.11 Aligned_cols=32 Identities=16% Similarity=0.049 Sum_probs=24.7
Q ss_pred HhcCHHHHHHHHHHHHHHHHHHHhhcCCCCHH
Q psy5533 89 HKSQGLEQTKFLARKHCVEAVRLASGLAESPY 120 (136)
Q Consensus 89 ~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~~~ 120 (136)
.=++..+.+.+.+....++|.+.+..||....
T Consensus 248 ~YY~~~~~~~~Rl~~f~~~A~~~~~~Lp~~~f 279 (330)
T PF10776_consen 248 FYYPDEEEMEERLKYFVEKALEQASRLPYPKF 279 (330)
T ss_pred eeCCCHHHHHHHHHHHHHHHHHHHHhCCCchH
Confidence 33445677788888899999999999997653
No 65
>PF10244 MRP-L51: Mitochondrial ribosomal subunit; InterPro: IPR019373 MRP-L51 is a family of small proteins from the intact 55 S mitochondrial ribosome []. It has otherwise been referred to as bMRP-64 []. The exact function of this family is not known.
Probab=23.01 E-value=48 Score=20.76 Aligned_cols=24 Identities=21% Similarity=0.379 Sum_probs=15.3
Q ss_pred HhhhhhhcCCccccCCCCchhHhhCcccH
Q psy5533 27 VDDLLDFISSSDAMGKPTAADLKLGLATA 55 (136)
Q Consensus 27 ~DDlld~~~~~~~~GK~~~~Di~~gk~Tl 55 (136)
++|++|+.||.. ---.|+.-| +++
T Consensus 19 qnDyIdILGd~~----~hP~~l~~~-P~W 42 (94)
T PF10244_consen 19 QNDYIDILGDGK----LHPKDLIYG-PSW 42 (94)
T ss_pred CcccccccCCCC----cCHHHHhcC-cHH
Confidence 589999999853 222456555 443
No 66
>PRK07566 bacteriochlorophyll/chlorophyll a synthase; Reviewed
Probab=22.67 E-value=35 Score=26.03 Aligned_cols=29 Identities=28% Similarity=0.495 Sum_probs=21.1
Q ss_pred HHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhh
Q psy5533 23 AFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACE 62 (136)
Q Consensus 23 afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~ 62 (136)
++-+.+|+.|.. +|.+.|++|+|+.+-.+
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 357788888864 46667899999987443
No 67
>PHA03046 Hypothetical protein; Provisional
Probab=22.65 E-value=2.5e+02 Score=18.85 Aligned_cols=60 Identities=20% Similarity=0.265 Sum_probs=36.0
Q ss_pred HHHhhcCChhhHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhhcCCCC--HHHHHHHHHHHH
Q psy5533 70 MIMRRFQEPGDVEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAES--PYQKGLVVLTDL 130 (136)
Q Consensus 70 ~l~~~~~~~~~~~~i~~~i~~~g~~~~~~~~~~~~~~~A~~~l~~l~~~--~~~~~L~~l~~~ 130 (136)
++...+... +.-.+..++.+...+++-.+..-..+...-..|..|+.. ..+..+..|+..
T Consensus 73 ILkDsFI~~-d~~~iKd~vlRL~vlEK~~~~~i~~c~~~~~~i~RLE~H~ETlRk~Ml~L~kK 134 (142)
T PHA03046 73 ILKDSFIHK-DEMDIKDFVLRLLVLEKLFQLSIKRCKSLNNIIKRLENHTETVRKNMITLSKK 134 (142)
T ss_pred HHhhhccch-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 333444332 334566677777778877777777777777777777653 235555555544
No 68
>PF11433 DUF3198: Protein of unknown function (DUF3198); InterPro: IPR024504 This domain is found at the C-terminal of a family of archaeal proteins annotated as membrane proteins.; PDB: 1X9B_A.
Probab=22.51 E-value=1.5e+02 Score=16.18 Aligned_cols=21 Identities=14% Similarity=0.126 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhh
Q psy5533 9 LSEVAFEYGRNLGIAFQLVDD 29 (136)
Q Consensus 9 ~~~~l~~~G~~lG~afQi~DD 29 (136)
....|.++...+|-.||++-|
T Consensus 22 nL~ELE~is~rlg~~Y~~~Le 42 (51)
T PF11433_consen 22 NLTELERISKRLGKSYQIRLE 42 (51)
T ss_dssp HHHHHHHHHHHH-SHHHHHHH
T ss_pred hHHHHHHHHHHHchHHHHHHH
Confidence 345788899999999999854
No 69
>KOG2114|consensus
Probab=21.50 E-value=3.6e+02 Score=24.05 Aligned_cols=51 Identities=35% Similarity=0.421 Sum_probs=37.0
Q ss_pred hHHHHHHHHHhcCHHHHHHHHHHHH----------------HHHHHHHhhcCCCCHHHHHHHHHHHH
Q psy5533 80 DVEKAFEFVHKSQGLEQTKFLARKH----------------CVEAVRLASGLAESPYQKGLVVLTDL 130 (136)
Q Consensus 80 ~~~~i~~~i~~~g~~~~~~~~~~~~----------------~~~A~~~l~~l~~~~~~~~L~~l~~~ 130 (136)
|++.+.+++.+++-.+.|.-++..+ ..+|+..+..+|+++.-..+...-..
T Consensus 465 d~e~al~Ilr~snyl~~a~~LA~k~~~he~vl~ille~~~ny~eAl~yi~slp~~e~l~~l~kyGk~ 531 (933)
T KOG2114|consen 465 DVETALEILRKSNYLDEAELLATKFKKHEWVLDILLEDLHNYEEALRYISSLPISELLRTLNKYGKI 531 (933)
T ss_pred eHHHHHHHHHHhChHHHHHHHHHHhccCHHHHHHHHHHhcCHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence 6888999999999888887666554 45788888899887655555444333
No 70
>PRK12882 ubiA prenyltransferase; Reviewed
Probab=20.34 E-value=1.4e+02 Score=22.08 Aligned_cols=30 Identities=27% Similarity=0.438 Sum_probs=20.0
Q ss_pred HHHHHHhhhhhhcCCccccCCCCchhHhhCcccHHHHHHhh
Q psy5533 22 IAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACE 62 (136)
Q Consensus 22 ~afQi~DDlld~~~~~~~~GK~~~~Di~~gk~Tlp~l~a~~ 62 (136)
+++-+.+|+.|.- .|.+.|.+|+|+.+-.+
T Consensus 171 ~~~~~~~~~~D~e-----------~D~~~G~~tlpv~~G~~ 200 (276)
T PRK12882 171 LAREIIKDVEDIE-----------GDRAEGARTLPILIGVR 200 (276)
T ss_pred HHHHHHhhhhhhh-----------hHHHcCCccccHHhhHH
Confidence 4555556666643 46667999999988443
No 71
>PF10047 DUF2281: Protein of unknown function (DUF2281); InterPro: IPR018739 This domain is found in putative uncharacterised proteins, though some proteins contaning this domain are described as a transcritional regulator of the Xre family.
Probab=20.32 E-value=1.3e+02 Score=17.26 Aligned_cols=27 Identities=19% Similarity=0.352 Sum_probs=17.6
Q ss_pred HHHHHhhcCCCCHHHHHHHHHHHHHHcc
Q psy5533 107 EAVRLASGLAESPYQKGLVVLTDLVLNR 134 (136)
Q Consensus 107 ~A~~~l~~l~~~~~~~~L~~l~~~~~~r 134 (136)
+..+.+..||+. ....+..+++++..+
T Consensus 4 ~l~~~i~~LP~~-~~~Evldfi~fL~~k 30 (66)
T PF10047_consen 4 ELLEKIQQLPEE-LQQEVLDFIEFLLQK 30 (66)
T ss_pred HHHHHHHHCCHH-HHHHHHHHHHHHHHh
Confidence 345566777753 456677778777665
Done!