Query 036976
Match_columns 243
No_of_seqs 139 out of 1276
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 07:18:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036976.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036976hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR03464 HpnC squalene syntha 100.0 8.4E-56 1.8E-60 382.5 26.6 225 1-231 12-266 (266)
2 PLN02632 phytoene synthase 100.0 1.8E-55 3.8E-60 390.8 27.7 234 1-234 67-329 (334)
3 TIGR03465 HpnD squalene syntha 100.0 1.7E-54 3.7E-59 374.4 26.6 226 1-232 12-266 (266)
4 cd00683 Trans_IPPS_HH Trans-Is 100.0 1.9E-51 4E-56 355.3 24.1 217 1-222 18-265 (265)
5 PF00494 SQS_PSY: Squalene/phy 100.0 5.4E-48 1.2E-52 333.8 18.7 217 1-221 12-267 (267)
6 COG1562 ERG9 Phytoene/squalene 100.0 1.3E-45 2.8E-50 319.9 23.3 229 1-234 28-287 (288)
7 TIGR01559 squal_synth farnesyl 100.0 3.7E-36 8E-41 265.9 22.5 226 2-228 21-293 (336)
8 KOG4411 Phytoene/squalene synt 100.0 1.9E-31 4E-36 217.5 21.9 223 2-231 30-289 (292)
9 cd00867 Trans_IPPS Trans-Isopr 99.6 1.5E-15 3.2E-20 128.7 8.5 151 7-182 22-220 (236)
10 cd00385 Isoprenoid_Biosyn_C1 I 99.5 7.5E-14 1.6E-18 116.2 7.7 129 54-182 95-228 (243)
11 KOG1459 Squalene synthetase [L 99.5 2.4E-13 5.3E-18 118.3 10.5 222 7-236 153-405 (413)
12 KOG1459 Squalene synthetase [L 99.1 3.6E-10 7.7E-15 98.7 8.1 164 61-226 153-317 (413)
13 PLN02890 geranyl diphosphate s 95.7 0.32 6.9E-06 44.9 13.2 124 62-185 253-399 (422)
14 TIGR02749 prenyl_cyano solanes 95.5 0.24 5.1E-06 44.2 11.5 121 64-184 161-304 (322)
15 PLN02857 octaprenyl-diphosphat 95.2 0.24 5.3E-06 45.6 10.9 122 64-185 255-399 (416)
16 CHL00151 preA prenyl transfera 95.1 0.26 5.6E-06 43.9 10.5 121 64-184 162-305 (323)
17 PRK10888 octaprenyl diphosphat 94.9 0.46 1E-05 42.4 11.4 122 62-184 156-305 (323)
18 TIGR02748 GerC3_HepT heptapren 94.5 0.51 1.1E-05 42.0 10.9 123 63-185 156-302 (319)
19 cd00685 Trans_IPPS_HT Trans-Is 94.2 0.86 1.9E-05 39.1 11.3 117 54-185 124-244 (259)
20 PRK10581 geranyltranstransfera 93.9 0.6 1.3E-05 41.1 10.0 110 63-184 168-280 (299)
21 COG0142 IspA Geranylgeranyl py 89.0 12 0.00026 33.3 12.8 129 54-182 150-302 (322)
22 PF00348 polyprenyl_synt: Poly 87.4 11 0.00023 32.3 11.1 71 55-125 123-195 (260)
23 KOG0776 Geranylgeranyl pyropho 82.0 24 0.00053 32.2 11.0 122 56-185 223-369 (384)
24 TIGR01439 lp_hng_hel_AbrB loop 66.7 2.9 6.3E-05 25.0 0.9 21 126-146 5-25 (43)
25 cd00684 Terpene_cyclase_plant_ 56.7 1.9E+02 0.004 27.7 14.7 108 59-175 380-492 (542)
26 PF07899 Frigida: Frigida-like 55.6 83 0.0018 27.7 8.3 112 19-174 113-226 (290)
27 PRK02899 adaptor protein; Prov 53.5 21 0.00046 29.4 4.1 43 128-172 11-53 (197)
28 COG0819 TenA Putative transcri 42.4 1.5E+02 0.0032 24.9 7.5 64 134-208 87-151 (218)
29 COG1575 MenA 1,4-dihydroxy-2-n 40.0 11 0.00023 33.4 0.3 23 113-135 193-215 (303)
30 PF04014 Antitoxin-MazE: Antid 38.7 17 0.00037 22.4 1.0 23 126-148 5-27 (47)
31 PRK02315 adaptor protein; Prov 36.3 49 0.0011 28.0 3.8 42 128-171 11-52 (233)
32 PF03070 TENA_THI-4: TENA/THI- 34.5 2.4E+02 0.0053 22.6 7.7 63 134-207 80-143 (210)
33 cd00687 Terpene_cyclase_nonpla 34.3 3E+02 0.0065 23.6 16.8 135 35-178 109-268 (303)
34 PHA01083 hypothetical protein 31.6 1.2E+02 0.0025 24.0 4.8 61 102-169 20-90 (149)
35 cd03025 DsbA_FrnE_like DsbA fa 27.4 1.8E+02 0.0039 22.9 5.6 36 134-169 129-164 (193)
36 TIGR02235 menA_cyano-plnt 1,4- 26.6 32 0.00068 30.1 1.0 27 109-135 174-200 (285)
37 TIGR00242 mraZ protein. Member 26.2 30 0.00065 26.9 0.8 33 118-151 76-108 (142)
38 PF15496 DUF4646: Domain of un 26.0 59 0.0013 24.7 2.3 29 120-148 24-53 (123)
39 PF11020 DUF2610: Domain of un 25.2 89 0.0019 21.9 2.8 51 28-78 19-80 (82)
40 COG2002 AbrB Regulators of sta 24.8 36 0.00077 24.1 0.9 23 126-148 12-34 (89)
41 cd07321 Extradiol_Dioxygenase_ 24.3 45 0.00098 23.1 1.3 34 114-147 5-40 (77)
42 cd07922 CarBa CarBa is the A s 23.9 48 0.001 23.3 1.3 34 114-147 6-41 (81)
43 PLN02922 prenyltransferase 23.3 41 0.00089 29.9 1.1 27 109-135 201-227 (315)
44 COG5204 SPT4 Transcription elo 23.1 39 0.00084 24.5 0.7 17 119-135 90-107 (112)
45 PF13351 DUF4099: Protein of u 23.1 61 0.0013 22.8 1.8 18 132-149 6-23 (85)
46 PF05389 MecA: Negative regula 22.9 28 0.00061 29.0 0.0 43 127-171 10-52 (220)
47 COG5140 UFD1 Ubiquitin fusion- 22.2 29 0.00063 29.7 -0.0 25 125-149 89-113 (331)
48 PF01323 DSBA: DSBA-like thior 21.8 1.4E+02 0.0029 23.5 3.9 36 134-169 127-162 (193)
49 KOG1666 V-SNARE [Intracellular 20.3 3.7E+02 0.008 22.6 6.0 46 160-205 41-86 (220)
No 1
>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=100.00 E-value=8.4e-56 Score=382.51 Aligned_cols=225 Identities=30% Similarity=0.429 Sum_probs=215.4
Q ss_pred CCCCChhhhHHHHHHH----------------------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhCCCCHH-----
Q 036976 1 ALLMTEERRKAIWAIC----------------------VLDRWEERLQDIFYGRPYDMLDAALTDAVFKFPLDIK----- 53 (243)
Q Consensus 1 ~lllp~~~R~~~~aly----------------------~L~~w~~~l~~~~~g~~~~pv~~aL~~~i~~~~l~~~----- 53 (243)
++|+|+++|+++++|| +|+||+++++++++|.+.|||..+|.+++++++||.+
T Consensus 12 ~~~lp~~~R~~~~alYAf~R~~Ddi~D~~~~~~~~~~~~L~~wr~~l~~~~~g~~~~pv~~aL~~~~~~~~l~~~~~~~l 91 (266)
T TIGR03464 12 SLLLPARLRAPIHAVYAFARTADDIADEGDGSAEERLALLDDFRAELDAIYSGEPAAPVFVALARTVQRHGLPIEPFLDL 91 (266)
T ss_pred HHhCCHHHHHHHHHHHHHHHHHHHhccCCCCChHHHHHHHHHHHHHHHHHhCCCCCChHHHHHHHHHHHcCCChHHHHHH
Confidence 4689999999999999 5999999999999998899999999999999999987
Q ss_pred ---hhccCCCCCCCCHHHHHHHHHHhhhHHHHHHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhhhhCCCc
Q 036976 54 ---MRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRV 130 (243)
Q Consensus 54 ---~~~Dl~~~~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D~~~gR~ 130 (243)
|++|+.+.+|+|++||+.|||+|||+||+|+++++|..+.. ..++|.++|.|+|+|||||||++|+++|||
T Consensus 92 i~~~~~Dl~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~g~~~~~------~~~~A~~lG~AlQltniLRDl~eD~~~gR~ 165 (266)
T TIGR03464 92 LDAFRQDVVVTRYATWAELLDYCRYSANPVGRLVLDLYGASDPE------NVALSDAICTALQLINFWQDVGVDYRKGRV 165 (266)
T ss_pred HHHHHHhccCCCCCCHHHHHHHHHHhHHHHHHHHHHHcCCCChh------HHHHHHHHHHHHHHHHHHHhhHHHHhcCCc
Confidence 89999999999999999999999999999999999975432 468899999999999999999999999999
Q ss_pred ccCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcCccCChHHHHHHHHHHHHHHHHHHCCCCC
Q 036976 131 YLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYDN 210 (243)
Q Consensus 131 YlP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~~~~~iL~~l~~~~~~~ 210 (243)
|||.|+|++||++++++.++..++++++++++++++|+++|.+|+.+++.+|+++++++.+++.+|+.+|++|+++||++
T Consensus 166 YLP~~~l~~~Gv~~edl~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~~y~~iL~~l~~~~~~~ 245 (266)
T TIGR03464 166 YLPRDDLARFGVSEEDLAAGRATPALRELMAFEVSRTRALLDRGAPLAARVDGRLGLELALIVRGGLRILEKIERQGYDV 245 (266)
T ss_pred cCCHHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCCHhhhHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcccChHHHHHHHHHHHH
Q 036976 211 LTKRAYVGRMKKYLMLPQAYN 231 (243)
Q Consensus 211 ~~~r~~ls~~~k~~~~~~a~~ 231 (243)
|++|+++|+++|+|++++++|
T Consensus 246 ~~~r~~~~~~~kl~~~~~a~~ 266 (266)
T TIGR03464 246 LRERPKLGKFDWAGLLLRALW 266 (266)
T ss_pred CCCCCcCCHHHHHHHHHHHhC
Confidence 999999999999999999874
No 2
>PLN02632 phytoene synthase
Probab=100.00 E-value=1.8e-55 Score=390.76 Aligned_cols=234 Identities=75% Similarity=1.207 Sum_probs=220.0
Q ss_pred CCCCChhhhHHHHHHH---------------------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhCCCCHH------
Q 036976 1 ALLMTEERRKAIWAIC---------------------VLDRWEERLQDIFYGRPYDMLDAALTDAVFKFPLDIK------ 53 (243)
Q Consensus 1 ~lllp~~~R~~~~aly---------------------~L~~w~~~l~~~~~g~~~~pv~~aL~~~i~~~~l~~~------ 53 (243)
++|+|+++|+++++|| +|+||++.++++++|.+.||+..+|.+++++++|+.+
T Consensus 67 ~~lLP~~~R~ai~alYAf~R~~DdI~D~~~~~~~~~~~L~~w~~~l~~~~~g~~~~pv~~aL~~~~~~~~L~~~~~~~li 146 (334)
T PLN02632 67 TLLMTPERRKAIWAIYVWCRRTDELVDGPNASHITPAALDRWEARLEDLFDGRPYDMLDAALADTVSKFPLDIQPFRDMI 146 (334)
T ss_pred HHhCCHHHHHHHHHHHHHHHHHhHHhcCCCCChhhHHHHHHHHHHHHHHhCCCCCChHHHHHHHHHHHCCCChHHHHHHH
Confidence 4689999999999999 7999999999999999899999999999999999987
Q ss_pred --hhccCCCCCCCCHHHHHHHHHHhhhHHHHHHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhhhhCCCcc
Q 036976 54 --MRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVY 131 (243)
Q Consensus 54 --~~~Dl~~~~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D~~~gR~Y 131 (243)
|++|++..+|+|++||+.|||+|||+||+|+++++|..+......+.+.+.|.++|.|+|+|||||||++|+++||||
T Consensus 147 ~g~~~Dl~~~~~~t~~eL~~Ycy~vAgtVG~l~l~vlg~~~~~~~~~~~~~~~A~~lG~AlQltNILRDv~eD~~~GRvY 226 (334)
T PLN02632 147 EGMRMDLVKSRYENFDELYLYCYYVAGTVGLMSVPVMGIAPESKASTESVYNAALALGIANQLTNILRDVGEDARRGRVY 226 (334)
T ss_pred HHHHHHhccCCCCCHHHHHHHHHHhhHHHHHHHHHHhCCCCccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcee
Confidence 899999999999999999999999999999999999754221112345789999999999999999999999999999
Q ss_pred cCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcCccCChHHHHHHHHHHHHHHHHHHCCCCCC
Q 036976 132 LPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYDNL 211 (243)
Q Consensus 132 lP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~~~~~iL~~l~~~~~~~~ 211 (243)
||.|+|++||++++++.++..++++++++++++++|+.||++|+.++..+|+++++++.+++.+|+.||++|+++||++|
T Consensus 227 LP~e~L~~~Gv~~edl~~~~~~~~~~~l~~~~~~~Ar~~~~~a~~~l~~lp~~~r~~v~~a~~~y~~iL~~i~~~~~~v~ 306 (334)
T PLN02632 227 LPQDELAQFGLTDEDIFAGKVTDKWRAFMKFQIKRARMYFAEAEEGVSELDPASRWPVWASLLLYRQILDAIEANDYDNF 306 (334)
T ss_pred CCHHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhHhhCCHHhHHHHHHHHHHHHHHHHHHHHcCCCcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcccChHHHHHHHHHHHHhhc
Q 036976 212 TKRAYVGRMKKYLMLPQAYNRTQ 234 (243)
Q Consensus 212 ~~r~~ls~~~k~~~~~~a~~~~~ 234 (243)
++|+++|+++|+|+++++++++.
T Consensus 307 ~~R~~l~~~~Kl~~~~~~~~~~~ 329 (334)
T PLN02632 307 TKRAYVGKWKKLLALPLAYARAL 329 (334)
T ss_pred CCCCccCHHHHHHHHHHHHHhhc
Confidence 99999999999999999987754
No 3
>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=100.00 E-value=1.7e-54 Score=374.42 Aligned_cols=226 Identities=32% Similarity=0.537 Sum_probs=216.1
Q ss_pred CCCCChhhhHHHHHHH---------------------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhCCCCHH------
Q 036976 1 ALLMTEERRKAIWAIC---------------------VLDRWEERLQDIFYGRPYDMLDAALTDAVFKFPLDIK------ 53 (243)
Q Consensus 1 ~lllp~~~R~~~~aly---------------------~L~~w~~~l~~~~~g~~~~pv~~aL~~~i~~~~l~~~------ 53 (243)
++|+|+++|+++++|| +|+||++.++.++.|.+.|||+.+|.+++++++++.+
T Consensus 12 ~~~lp~~~R~~~~alYaf~r~~d~i~D~~~~~~~~~~~L~~w~~~l~~~~~g~~~~pv~~al~~~~~~~~l~~~~~~~li 91 (266)
T TIGR03465 12 MRLLPPERRRAMTALYAFCREVDDIVDEDSDPEVAQAKLAWWRAEIDRLYAGAPSHPVARALADPARRFDLPQEDFLEVI 91 (266)
T ss_pred HHHCCHHHHHHHHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHHHHhCCCCCChHHHHHHHHHHHcCCCHHHHHHHH
Confidence 3689999999999999 9999999999999999999999999999999999987
Q ss_pred --hhccCCCCCCCCHHHHHHHHHHhhhHHHHHHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhhhhCCCcc
Q 036976 54 --MRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVY 131 (243)
Q Consensus 54 --~~~Dl~~~~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D~~~gR~Y 131 (243)
|++|++..+|+|++||+.||++|||+||.|+++++|..++ .+.+.|+++|.|+|+||||||+++|+.+||||
T Consensus 92 ~g~~~Dl~~~~~~t~~dL~~Y~~~vAg~vg~l~~~llg~~~~------~~~~~a~~lG~AlqltnilRdv~eD~~~gR~y 165 (266)
T TIGR03465 92 DGMEMDLEQTRYPDFAELDLYCDRVAGAVGRLSARIFGATDA------RTLEYAHHLGRALQLTNILRDVGEDARRGRIY 165 (266)
T ss_pred HHHHHHcCCCCCCCHHHHHHHHHHhHHHHHHHHHHHhCCCCh------hHHHHHHHHHHHHHHHHHHHHhHHHHhCCCee
Confidence 8999999999999999999999999999999999996432 25789999999999999999999999999999
Q ss_pred cCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcCccCChHHHHHHHHHHHHHHHHHHCCCCCC
Q 036976 132 LPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYDNL 211 (243)
Q Consensus 132 lP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~~~~~iL~~l~~~~~~~~ 211 (243)
||.|+|++||+++++|.++..++++++++++++++|+.||++|+++++.+|++.+.++.+++.+|+.||++|+++||++|
T Consensus 166 lP~~~l~~~gv~~~~l~~~~~~~~~~~~~~~l~~~A~~~l~~a~~~~~~~p~~~~~~~~~~~~~~~~iL~~i~~~~~~~~ 245 (266)
T TIGR03465 166 LPAEELQRFGVPAADILEGRYSPALAALCRFQAERARAHYAEADALLPACDRRAQRAARAMAAIYRALLDEIEADGFQVL 245 (266)
T ss_pred cCHHHHHHcCCCHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhCCHhhhHHHHHHHHHHHHHHHHHHHCCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcccChHHHHHHHHHHHHh
Q 036976 212 TKRAYVGRMKKYLMLPQAYNR 232 (243)
Q Consensus 212 ~~r~~ls~~~k~~~~~~a~~~ 232 (243)
++|+++|+++|+|++|+++++
T Consensus 246 ~~r~~~~~~~k~~~~~~~~~~ 266 (266)
T TIGR03465 246 RQRVSLTPLRKLWIALRTWLR 266 (266)
T ss_pred CCCCcCCHHHHHHHHHHHHhC
Confidence 999999999999999998754
No 4
>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=100.00 E-value=1.9e-51 Score=355.31 Aligned_cols=217 Identities=40% Similarity=0.664 Sum_probs=205.4
Q ss_pred CCCCChhhhHHHHHHH----------------------HHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHhCCCCHH----
Q 036976 1 ALLMTEERRKAIWAIC----------------------VLDRWEERLQDIFYGR-PYDMLDAALTDAVFKFPLDIK---- 53 (243)
Q Consensus 1 ~lllp~~~R~~~~aly----------------------~L~~w~~~l~~~~~g~-~~~pv~~aL~~~i~~~~l~~~---- 53 (243)
++|+|+++|+++++|| +|+||++.+++++.|. +.|||+.+|.+++++++|+.+
T Consensus 18 ~~~lp~~~R~~~~alYaf~r~~Ddi~D~~~~~~~~~~~~L~~w~~~l~~~~~~~~~~~pv~~al~~~~~~~~l~~~~~~~ 97 (265)
T cd00683 18 SRLLPPELRRAVCALYAFCRAADDIVDDPAAPPDEKLALLDAFRAELDAAYWGGAPTHPVLRALADLARRYGIPREPFRD 97 (265)
T ss_pred HHhCCHHHHHHHHHHHHHHHHHHhhhhCCCCCchhHHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHcCCCHHHHHH
Confidence 3689999999999999 8999999999999964 579999999999999999987
Q ss_pred ----hhccCCCCCCCCHHHHHHHHHHhhhHHHHHHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhhhhCCC
Q 036976 54 ----MRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGR 129 (243)
Q Consensus 54 ----~~~Dl~~~~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D~~~gR 129 (243)
|++|++..+|+|++||+.||++|||+||+|+++++|.... +...++|.++|.|+|+||||||+++|+++||
T Consensus 98 li~g~~~Dl~~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~~~~~~-----~~~~~~A~~lG~AlqltnilRdv~eD~~~gR 172 (265)
T cd00683 98 LLAGMAMDLDKRRYETLDELDEYCYYVAGVVGLMLLRVFGASSD-----EAALERARALGLALQLTNILRDVGEDARRGR 172 (265)
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHHHhHHHHHHHHHHHhCCCCC-----hHHHHHHHHHHHHHHHHHHHHHHHHHHccCC
Confidence 9999999999999999999999999999999999997211 2357899999999999999999999999999
Q ss_pred cccCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcCccCChHHHHHHHHHHHHHHHHHHCCCC
Q 036976 130 VYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYD 209 (243)
Q Consensus 130 ~YlP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~~~~~iL~~l~~~~~~ 209 (243)
||||.|+|++||++++++.++..++++++++++++++|+.||.+|+++++.+|++.++++.+++.+|+.++++|+++||+
T Consensus 173 ~YlP~d~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~~y~~il~~i~~~~~~ 252 (265)
T cd00683 173 IYLPREELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAALPRRSRFCVRAAAMLYRTILDEIEARGYD 252 (265)
T ss_pred CcCCHHHHHHcCCCHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCCHhhHHHHHHHHHHHHHHHHHHHHCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcccChHHH
Q 036976 210 NLTKRAYVGRMKK 222 (243)
Q Consensus 210 ~~~~r~~ls~~~k 222 (243)
+|++|+++|+++|
T Consensus 253 ~~~~r~~~~~~~k 265 (265)
T cd00683 253 VLSVRVRVPKARK 265 (265)
T ss_pred CCCCCCCCCCCCC
Confidence 9999999998765
No 5
>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=100.00 E-value=5.4e-48 Score=333.79 Aligned_cols=217 Identities=36% Similarity=0.624 Sum_probs=186.2
Q ss_pred CCCCChhhhHHHHHHH---------------------HHHHHHHHHHHHHcC------CCCCHHHHHHHHHHHhCCCCHH
Q 036976 1 ALLMTEERRKAIWAIC---------------------VLDRWEERLQDIFYG------RPYDMLDAALTDAVFKFPLDIK 53 (243)
Q Consensus 1 ~lllp~~~R~~~~aly---------------------~L~~w~~~l~~~~~g------~~~~pv~~aL~~~i~~~~l~~~ 53 (243)
++|+|++.|+++++|| +|+||++.++.++.+ .+.|||+.+|.++++.++++.+
T Consensus 12 ~~~lP~~~R~~~~alyaf~r~~d~i~D~~~~~~~~~~~L~~w~~~l~~~~~~~~~~~~~~~~pv~~~l~~~~~~~~l~~~ 91 (267)
T PF00494_consen 12 SLLLPKEKRPAVFALYAFCRELDDIVDEPSDPEEARARLQWWRDALNSIFASYEDSLPEPSHPVARALADLVRRYGLPRE 91 (267)
T ss_dssp HTTS-HHHHHHHHHHHHHHHHHHHHHHCTSS-HSCHHHHHHHHHHHHHHHH-TSTHHHSSHHHHHHHHHHHHCCSHHHHH
T ss_pred HHHCCHHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHHHHHHHhhhhhhccCCCcCHHHHHHHHHHHHHhhhHH
Confidence 3789999999999999 799999999999942 3458999999999999999887
Q ss_pred --------hhccCCCCCCCCHHHHHHHHHHhhhHHHHHHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhh-
Q 036976 54 --------MRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGED- 124 (243)
Q Consensus 54 --------~~~Dl~~~~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D- 124 (243)
|++|++..+|+|++||+.||++|||+||+|+++++|..++. +.+.++|.++|.|+|+||||||+++|
T Consensus 92 ~l~~li~~~~~dl~~~~~~t~~~L~~Y~~~vag~vg~l~~~~~~~~~~~----~~~~~~a~~lG~alql~nilRd~~~D~ 167 (267)
T PF00494_consen 92 PLLELIDGMEMDLEFTPYETFADLERYCYYVAGSVGLLLLQLLGAHDPD----EAARDAARALGRALQLTNILRDIPEDA 167 (267)
T ss_dssp HHHHHHHHHHHCTT-S--SSHHHHHHHHHHHTHHHHHHHHHHHHSSTSH----HHHHHHHHHHHHHHHHHHHHHTHHHH-
T ss_pred HHHHHHHHhcccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccccch----hhHHHHHHHHHHHHHHHHHHHHhHHHH
Confidence 99999999999999999999999999999999999984221 24689999999999999999999999
Q ss_pred hhCCCcccCHhhHHhCCCChHhhhhcc-CCHHHHHHHHHHHHHHHHHHHHHHHchhhc-CccCChHHHHHHHHHHHHHHH
Q 036976 125 ASRGRVYLPQDKLAQFVLCDKDVFARK-VTDNWREFMKEQIKRARTFFNMAEEGASQL-DKDSRWPVWSSLLIYREILDA 202 (243)
Q Consensus 125 ~~~gR~YlP~~~l~~~gv~~~~l~~~~-~~~~~~~l~~~~~~~A~~~~~~a~~~~~~l-p~~~~~~~~~~~~~~~~iL~~ 202 (243)
+++||||||.|+|++||++++++.++. .++++++++.+++.+|++++.+|++++..+ |+++++++.+++.+|..+|++
T Consensus 168 ~~~gR~ylP~d~l~~~gv~~~dl~~~~~~~~~~~~~~~~~~~~A~~~l~~a~~~~~~l~~~~~~~~~~~~~~~~~~~l~~ 247 (267)
T PF00494_consen 168 LRRGRIYLPLDDLRRFGVTPEDLLAGRPRSERLRALIRELAARARAHLDEARAGLSALPPPRARPAVAAAAALYRAILDK 247 (267)
T ss_dssp HHTT---S-HHHHHHTTSSHHHHHHHG-GGHHHHHHHHHHHHHHHHHHHHHHHGGGGS--TTHHHHHHHHHHHHHHHHHH
T ss_pred HhcccccCCchhHHHcCCCHHHHHhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHhhhHHHHHHHHHHHHHHHH
Confidence 899999999999999999999999886 888899999999999999999999999999 777999989999999999999
Q ss_pred HHHCCCC-CCCCCcccChHH
Q 036976 203 IEENDYD-NLTKRAYVGRMK 221 (243)
Q Consensus 203 l~~~~~~-~~~~r~~ls~~~ 221 (243)
|+++||+ +|++|+++|+++
T Consensus 248 l~~~~~~~v~~~r~~~~~~r 267 (267)
T PF00494_consen 248 LERNGYDPVFQRRVKVSKWR 267 (267)
T ss_dssp HHHTTT--GSSS-----HH-
T ss_pred HHcCCCcccCCCCCcCCCCC
Confidence 9999999 889999999874
No 6
>COG1562 ERG9 Phytoene/squalene synthetase [Lipid metabolism]
Probab=100.00 E-value=1.3e-45 Score=319.91 Aligned_cols=229 Identities=39% Similarity=0.639 Sum_probs=211.2
Q ss_pred CCCCChhhhHHHHHHH---------------------HHHHHHHHHHHHHcCCC--CCHHHHHHHHHHHhCCCCHH----
Q 036976 1 ALLMTEERRKAIWAIC---------------------VLDRWEERLQDIFYGRP--YDMLDAALTDAVFKFPLDIK---- 53 (243)
Q Consensus 1 ~lllp~~~R~~~~aly---------------------~L~~w~~~l~~~~~g~~--~~pv~~aL~~~i~~~~l~~~---- 53 (243)
++|+|+++|++++++| .+.+|+.++...++|.+ .|||..+|.+++.+|+++.+
T Consensus 28 ~~~lp~~~R~av~alYa~~R~~Ddv~D~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~pv~~al~~~~~~~~~~~~~~~~ 107 (288)
T COG1562 28 ILLLPPEKREAVWALYAFCREADDVVDGVSDPDLPAEILLAWRRELDGDFSGQPASDHPVLAALVEVARRFGLPREAFPA 107 (288)
T ss_pred HHhCCHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHhccccCCCcccCHHHHHHHHHHHHcCCCHHHHHH
Confidence 4689999999999999 44556666666666654 79999999999999999987
Q ss_pred ----hhccCCCCCCCCHHHHHHHHHHhhhHHHHHHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhhhhCCC
Q 036976 54 ----MRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGR 129 (243)
Q Consensus 54 ----~~~Dl~~~~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D~~~gR 129 (243)
|++|+...+|.|++||+.||++|||+||.|++.|+|..... ...+.|..+|.|+|+||||||++||..+||
T Consensus 108 ~~da~~~Dl~~~~y~~~~eL~~Yc~~vAg~vG~l~~~Il~~~~~~-----~~~~~a~~lG~A~QlvNilRdv~eD~~~Gr 182 (288)
T COG1562 108 LIDAMRMDLDRTRYLDFEELEEYCYGVAGAVGLLLARILGPDKDA-----ATRAYARGLGLALQLVNILRDVGEDRRRGR 182 (288)
T ss_pred HHHHHHHHhhhccccCHHHHHHHHHHhHHHHHHHHHHHhCcccch-----hhHHHHHHHHHHHHHHHHHHHhHHHHhCCc
Confidence 99999999999999999999999999999999999985321 245678889999999999999999999999
Q ss_pred cccCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcCccCChHHHHHHHHHHHHHHHHHHCCCC
Q 036976 130 VYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYD 209 (243)
Q Consensus 130 ~YlP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~~~~~iL~~l~~~~~~ 209 (243)
+|||.|+|.+||++.+++.++.++++++.+++.++++|+.++..|+.+++.+|.++++++.++..+|..++.++++++++
T Consensus 183 vylP~e~l~~~g~~~~d~~~~~~~~~~~~~~~~~~~~ar~~~~~a~~~~~~lp~~~~~~~~~~~~~~~~~~~~i~a~~~~ 262 (288)
T COG1562 183 VYLPAEELARFGVSEADLLAGRVDDAFRELMRFEADRARDHLAEARRGLPALPGRAQLAVLAAALLYAYLLDAIEADPAD 262 (288)
T ss_pred ccCCHHHHHHhCCCHHHHHcccchhHHHHHHHHHHHHHHHHHHHHHHhhhhCCccccchhhHHHHHHHHHHHHHHccchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcccChHHHHHHHHHHHHhhc
Q 036976 210 NLTKRAYVGRMKKYLMLPQAYNRTQ 234 (243)
Q Consensus 210 ~~~~r~~ls~~~k~~~~~~a~~~~~ 234 (243)
+|++++.+++++|+|+++++.+++.
T Consensus 263 vl~~~~~l~~~~~~~~~~~~~~~~~ 287 (288)
T COG1562 263 VLSQRAVLPKLRKLWLLLKAWLRGF 287 (288)
T ss_pred hhccCcccCcchHHHHHHHHHHhcc
Confidence 9999999999999999999988764
No 7
>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=100.00 E-value=3.7e-36 Score=265.95 Aligned_cols=226 Identities=17% Similarity=0.113 Sum_probs=175.8
Q ss_pred CCCChhhhHHHHHHH-------------------HHHHHHHHHHHHHcCC-----CCCHH----HHHHHHHHHhC-CCCH
Q 036976 2 LLMTEERRKAIWAIC-------------------VLDRWEERLQDIFYGR-----PYDML----DAALTDAVFKF-PLDI 52 (243)
Q Consensus 2 lllp~~~R~~~~aly-------------------~L~~w~~~l~~~~~g~-----~~~pv----~~aL~~~i~~~-~l~~ 52 (243)
.+||+++|++++++| ++.+|+.-.+.++.+. ..||. ...+...+..+ .++.
T Consensus 21 ~~Lp~~lR~aV~~~Yl~cR~~DdIeDd~~~~~~~kl~~l~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~v~~~~~~l~~ 100 (336)
T TIGR01559 21 QELPPELRNAVCIFYLVLRALDTVEDDMTISVDKKIPLLRDFHEKIYDPDWRFTESDNEKDRQVLDDFPVVSLEFLKLKP 100 (336)
T ss_pred HHcCHHHHHHHHHHHHHHHhccccccCCCCCHHHHHHHHHHHHHHHhccCcccCCCCChhhHHHHHhchHHHHHHHhcCH
Confidence 578999999999999 5655555555544421 11443 33344444444 2332
Q ss_pred H---------------hhccCCCCCC--CCHHHHHHHHHHhhhHHHHHHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHH
Q 036976 53 K---------------MRMDTRKFRY--ENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLT 115 (243)
Q Consensus 53 ~---------------~~~Dl~~~~~--~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~ 115 (243)
. |++|+...+| +|++||+.|||+|||+||.|+++|++.............+.|.++|.|||+|
T Consensus 101 ~~~~~I~~~~~~M~~GMa~dl~~~~~~~~T~~dL~~YCy~VAG~VG~mlt~l~~~~~~~~~~~~~~~~~A~~lG~aLQlT 180 (336)
T TIGR01559 101 KYQEVIADITRRMGNGMADFIDKEVTNEQTVGDYDKYCHYVAGLVGIGLSRLFVASGFEDPSLGESEALSNSMGLFLQKT 180 (336)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCcCCCCCHHHHHHHHhccccHHHHHHHHHHhhcCCCCcchhhhHHHHHHHHHHHHHH
Confidence 1 8899999999 9999999999999999999999999642100000011368899999999999
Q ss_pred HHHHhhhhhhhCCCcccCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcCccC-ChHHHHHHH
Q 036976 116 NFLRDVGEDASRGRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDS-RWPVWSSLL 194 (243)
Q Consensus 116 nilRDi~~D~~~gR~YlP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp~~~-~~~~~~~~~ 194 (243)
|||||++||+.+||||||.|+|.+||++.+++..+.+++++.+++.+++.+|+.|+..|..++..++..+ +.....+..
T Consensus 181 NIlRDv~ED~~~GR~YlP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~~al~yl~~l~~~~~~~fcaip~~ 260 (336)
T TIGR01559 181 NIIRDYLEDINEGRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELVTNALHHATDCLTYLSRLRDQSIFNFCAIPQV 260 (336)
T ss_pred HHHHHHHhHHhCCCCCCCHHHHHHcCCCHHHhcCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999886654 223334455
Q ss_pred HHHHHHHHHHHCCCCCCCCCcccChHHHHHHHHH
Q 036976 195 IYREILDAIEENDYDNLTKRAYVGRMKKYLMLPQ 228 (243)
Q Consensus 195 ~~~~iL~~l~~~~~~~~~~r~~ls~~~k~~~~~~ 228 (243)
+.-..|+.+.++ .++|++.+++++..-..++.+
T Consensus 261 mAi~TL~~~~~n-~~~~~~~VKi~r~~~~~~~~~ 293 (336)
T TIGR01559 261 MAIATLALCYNN-PQVFQGNVKIRKGTTVKLILD 293 (336)
T ss_pred HHHHHHHHHhcC-hhhcCCCceecHHHHHHHHHH
Confidence 667888888554 579999999988777777654
No 8
>KOG4411 consensus Phytoene/squalene synthetase [Lipid transport and metabolism]
Probab=100.00 E-value=1.9e-31 Score=217.51 Aligned_cols=223 Identities=18% Similarity=0.217 Sum_probs=194.0
Q ss_pred CCCChhhhHHHHHHH----------------------HHHHHHHHHHHHHcCCC----CCHHHHHHHHHHHhCCCCHH--
Q 036976 2 LLMTEERRKAIWAIC----------------------VLDRWEERLQDIFYGRP----YDMLDAALTDAVFKFPLDIK-- 53 (243)
Q Consensus 2 lllp~~~R~~~~aly----------------------~L~~w~~~l~~~~~g~~----~~pv~~aL~~~i~~~~l~~~-- 53 (243)
+.+|.+.|.+.++|. ||+||+|.|+.+|.-.| +|||+++|..++..+++...
T Consensus 30 l~lp~e~r~aafaLrAfNVE~ar~~~d~~~~p~ia~mRL~fW~daIdk~y~~~p~~v~~qPva~aL~~~~~~~~~nk~~L 109 (292)
T KOG4411|consen 30 LELPTEMRKAAFALRAFNVELARIKVDTRKGPAIAMMRLQFWKDAIDKIYGISPLPVPRQPVAIALCSFAAGHNANKDML 109 (292)
T ss_pred HhCcHHHHHHHHHHHHhhHHHHHHhhccccCcHHHHHHHHHHHHHHHHHcCCCCCCCCCcHHHHHHHHHHhccccCHHHH
Confidence 467999999999997 99999999999998665 58999999999999999876
Q ss_pred ------hhccCCCCCCCCHHHHHHHHHHhhhHHHHHHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhhhhC
Q 036976 54 ------MRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASR 127 (243)
Q Consensus 54 ------~~~Dl~~~~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D~~~ 127 (243)
++.|.....|++..||++|.+.+-|++.++.++..|..... +.++|.|+|.|.+++|+||.++...++
T Consensus 110 ~rlV~aR~r~~~d~~fesI~eLeeY~e~TissLL~l~l~agg~~~~~------AdhaAshlGkA~gia~llrs~p~~~~r 183 (292)
T KOG4411|consen 110 LRLVEARQRTIGDRQFESINELEEYGESTISSLLCLQLDAGGKVLPM------ADHAASHLGKAYGIANLLRSTPPLLAR 183 (292)
T ss_pred HHHHHHhhcCCcccchHHHHHHHHHHHhHHHHHHHHHHHhcCccccc------hHHHHHHHhHHHHHHHHHHhccHHHhC
Confidence 67788889999999999999999999999999999975432 468999999999999999999999999
Q ss_pred CCcccCHhhHHhCCCChHhh-hhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcCccCChHHHHHHHHHHHHHHHHHHC
Q 036976 128 GRVYLPQDKLAQFVLCDKDV-FARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEEN 206 (243)
Q Consensus 128 gR~YlP~~~l~~~gv~~~~l-~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~~~~~iL~~l~~~ 206 (243)
|..|||.|.|..||++++++ .++...+++..++.+++..|+.|+-.|++.++.+|+..|+++... .....+|+.|+++
T Consensus 184 ~~~~iPadv~~lhGvtq~~il~~k~~~~g~~~~~fd~as~an~hL~~AR~l~~kVP~~vrp~ll~t-v~td~~l~~l~k~ 262 (292)
T KOG4411|consen 184 GIVLIPADVMSLHGVTQLDILYKKKKLDGMVGMTFDLASEANRHLIDARSLIEKVPKAVRPALLAT-VTTDYILKTLEKN 262 (292)
T ss_pred CCccccHHHHHHcCCCHHHHHhhccchhhhhhHHHHHHHHHHHHHHHHHhHhhhCCHHHHHHHHHh-hhHHHHHHHHHHc
Confidence 99999999999999999665 466788899999999999999999999999999999999987655 6789999999999
Q ss_pred CCCCCCC-CcccChH-HHHHHHHHHHH
Q 036976 207 DYDNLTK-RAYVGRM-KKYLMLPQAYN 231 (243)
Q Consensus 207 ~~~~~~~-r~~ls~~-~k~~~~~~a~~ 231 (243)
+||++++ ++.-.++ -...+.|+.+.
T Consensus 263 nfdi~~p~~~~R~~L~lp~lLfw~sl~ 289 (292)
T KOG4411|consen 263 NFDIYSPHLQRRNPLLLPSLLFWRSLC 289 (292)
T ss_pred cccccCHhhhcCCcccccHHHHHHHHH
Confidence 9999986 3433333 22334455543
No 9
>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=99.61 E-value=1.5e-15 Score=128.69 Aligned_cols=151 Identities=27% Similarity=0.307 Sum_probs=113.1
Q ss_pred hhhHHHHHHH---------------------HHHH-HHHHHHHHHcCCCCCHHHHHHHHHHH-----hCCCCHH------
Q 036976 7 ERRKAIWAIC---------------------VLDR-WEERLQDIFYGRPYDMLDAALTDAVF-----KFPLDIK------ 53 (243)
Q Consensus 7 ~~R~~~~aly---------------------~L~~-w~~~l~~~~~g~~~~pv~~aL~~~i~-----~~~l~~~------ 53 (243)
..+.++..|| ...| |.+.+. +..| .+++..++..+.+ .+++..+
T Consensus 22 ~~a~ave~l~~~~li~DDI~D~~~~rrg~~~~~~~~~g~~~a-i~~g--d~l~~~a~~~l~~~~~~~~~~~~~~~~~~~~ 98 (236)
T cd00867 22 RLAAAVELLHAASLVHDDIVDDSDLRRGKPTAHLRRFGNALA-ILAG--DYLLARAFQLLARLGYPRALELFAEALRELL 98 (236)
T ss_pred HHHHHHHHHHHHHHHHcccccCCccCCCCccHhHHhhCHhHH-HHHH--HHHHHHHHHHHHhCChHHHHHHHHHHHHHHH
Confidence 7888999999 3334 444433 2222 3678888877766 3333333
Q ss_pred --hhccCCCCC--CCCHHHHHHHHHH-hhhHHHHHHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhhh---
Q 036976 54 --MRMDTRKFR--YENLQELYLYCYY-VAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDA--- 125 (243)
Q Consensus 54 --~~~Dl~~~~--~~t~~dL~~Y~~~-~Ag~vg~l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D~--- 125 (243)
+.+|+...+ +.|++++..||++ ||+.+|.++..++.....+....+.+.+++.++|.|+|++|.++|+.+|.
T Consensus 99 ~Gq~~Dl~~~~~~~~t~~~y~~~~~~Kta~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lG~a~Qi~dd~~D~~~d~~~~ 178 (236)
T cd00867 99 EGQALDLEFERDTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDDLLDVFGDAEEL 178 (236)
T ss_pred HHHHHHHHhccCCCCCHHHHHHHHHhccHHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHHHHHHHHhccccCChHHH
Confidence 777887776 9999999999999 99999998887765432221223457789999999999999999998888
Q ss_pred -------hCCCcccCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcC
Q 036976 126 -------SRGRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLD 182 (243)
Q Consensus 126 -------~~gR~YlP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp 182 (243)
.+||+|+|.+.+ .+.+.+.+++++..+.+.....|
T Consensus 179 gk~~~D~~~gr~tlp~~~~----------------------~~~~~~~~~~~~~~~~~~~~~~~ 220 (236)
T cd00867 179 GKVGSDLREGRITLPVILA----------------------RERAAEYAEEAYAALEALPPSLP 220 (236)
T ss_pred CccHHHHHcCCchHHHHHH----------------------HHHHHHHHHHHHHHHHhCCCCch
Confidence 899999999988 56677778888888877766655
No 10
>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1. Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoter
Probab=99.48 E-value=7.5e-14 Score=116.22 Aligned_cols=129 Identities=26% Similarity=0.297 Sum_probs=109.4
Q ss_pred hhccCCCCC--CCCHHHHHHHHHHh-hhHHHHHHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhhhhC--C
Q 036976 54 MRMDTRKFR--YENLQELYLYCYYV-AGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASR--G 128 (243)
Q Consensus 54 ~~~Dl~~~~--~~t~~dL~~Y~~~~-Ag~vg~l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D~~~--g 128 (243)
+..|+.... ++|++|+..||+.+ ++.++.++....+.........+.....+.++|.++|++|.++|+..|.+. |
T Consensus 95 ~~~d~~~~~~~~~t~~ey~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ql~nDl~~~~~e~~~~~~ 174 (243)
T cd00385 95 QLLDLKWRREYVPTLEEYLEYCRYKTAGLVGALCLLGAGLSGGEAELLEALRKLGRALGLAFQLTNDLLDYEGDAERGEG 174 (243)
T ss_pred HHHHHHhccCCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHhCC
Confidence 555666554 89999999999999 888888887776653222222345788999999999999999999999987 8
Q ss_pred CcccCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcC
Q 036976 129 RVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLD 182 (243)
Q Consensus 129 R~YlP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp 182 (243)
++++|...+.++|++.+++.....++.+.++++.+...+++.+.+..+....+|
T Consensus 175 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~ 228 (243)
T cd00385 175 KCTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKLAEEALKELNELILSLP 228 (243)
T ss_pred chHHHHHHHHHhCChhhHHHHHHHCChHHHHHHHHHHHHHHHHHHHhcCCCCcH
Confidence 999999999999999999998899999999999999999999999888777665
No 11
>KOG1459 consensus Squalene synthetase [Lipid transport and metabolism]
Probab=99.48 E-value=2.4e-13 Score=118.28 Aligned_cols=222 Identities=30% Similarity=0.377 Sum_probs=174.3
Q ss_pred hhhHHHHHHH---------------------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhCCC------CHH---hhc
Q 036976 7 ERRKAIWAIC---------------------VLDRWEERLQDIFYGRPYDMLDAALTDAVFKFPL------DIK---MRM 56 (243)
Q Consensus 7 ~~R~~~~aly---------------------~L~~w~~~l~~~~~g~~~~pv~~aL~~~i~~~~l------~~~---~~~ 56 (243)
+.++++++.| +|+.|....+++++|.+-.-.-..+.+...+... |.+ +.+
T Consensus 153 ~~v~ti~d~d~yChyvagLVg~glsrlf~~s~le~~~~~~e~l~ns~glfLqktnIirdy~ed~~d~r~Fwp~eIwg~y~ 232 (413)
T KOG1459|consen 153 EEVETIWDYDVYCHYVAGLVGIGLSRLFTASKLEDLLARLEQLSNSMGLFLQKTNIIRDYLEDPVDGRPFWPREIWGKYM 232 (413)
T ss_pred HHHhHHHHHHHHHHHHHHhhCCchHhhhhHHHHhhhhhhHHHHhcccchHHHHhHHHHHHHhccccCCccChHHHHHHHH
Confidence 4478888887 7778888888888886532222233333333322 333 777
Q ss_pred c-CCCCCCCCHHHHHHHHHHhhhHHHHHHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhhhhCCCcccCHh
Q 036976 57 D-TRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLPQD 135 (243)
Q Consensus 57 D-l~~~~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D~~~gR~YlP~~ 135 (243)
| +..-++++.+|+--||...+++.|.|-...+ ...-+....+++...|--.+++-+.|+++++.++|..+|+++||.
T Consensus 233 d~L~d~~~~en~dl~l~Cln~m~tnaL~hv~d~-l~yls~l~~qsvfnfcaipqimai~Tlal~~nn~dvfrG~Vklrk- 310 (413)
T KOG1459|consen 233 DKLKDFRYPENDDLALQCLNEMVTNALMHVPDV-LTYLSKLRTQSVFNFCAIPQIMAIATLALCYNNEDVFRGNVKLRK- 310 (413)
T ss_pred HHHHhhhCccchhHHHHHHHHHHHHHhhccHHH-HHHHhhcccHHHHHHHHHHHHHHHHHHHHHhcCHhHhccceeecC-
Confidence 8 8888999999999999999999999965554 221222334567889999999999999999999999999999998
Q ss_pred hHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcCccCChHHHHHHHHHHHHHHHHHHCCCCCCCCCc
Q 036976 136 KLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDYDNLTKRA 215 (243)
Q Consensus 136 ~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~~~~~iL~~l~~~~~~~~~~r~ 215 (243)
|.+.+.+.+++..+++++++.....+++..++.+.+..-.|.-...+.+......|+. .+.+..+.++.|.+|+
T Consensus 311 -----Gl~~~~I~~~k~~~~v~~~f~~y~~~i~~k~d~~dpnflklsask~~qv~esl~~~~~-~~~il~n~~~~f~k~~ 384 (413)
T KOG1459|consen 311 -----GLAVELILASKTMDKVRNIFYMYLRDIRMKFDEADPNFLKLSASKTEQVWESLLLYRR-PDEILANRYNNFTKRI 384 (413)
T ss_pred -----CchHHHHHhcccHHHHHHHHHHHHHHHHhhCCccCCCchhhhhhhHHHHHHHHHHhhc-cccccccccccccchh
Confidence 9999999999999999999999999999999998877555555556666655555554 8888999999999999
Q ss_pred ccChHHHHHHHHHHHHhhccC
Q 036976 216 YVGRMKKYLMLPQAYNRTQSK 236 (243)
Q Consensus 216 ~ls~~~k~~~~~~a~~~~~~~ 236 (243)
.+....++..+..++.+..++
T Consensus 385 ~v~~V~~i~al~~ay~~~v~~ 405 (413)
T KOG1459|consen 385 YVGFVKKIAALPLAYAKSVSK 405 (413)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 999999988888888887665
No 12
>KOG1459 consensus Squalene synthetase [Lipid transport and metabolism]
Probab=99.08 E-value=3.6e-10 Score=98.75 Aligned_cols=164 Identities=20% Similarity=0.173 Sum_probs=123.6
Q ss_pred CCCCCHHHHHHHHHHhhhHHHHHHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhhhhCCCcccCHhhHHhC
Q 036976 61 FRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDASRGRVYLPQDKLAQF 140 (243)
Q Consensus 61 ~~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D~~~gR~YlP~~~l~~~ 140 (243)
...+|..|...||++|||-||.=.++++-...-.. ......+.++.+|..||-|||+||..||...||-+.|.|+..++
T Consensus 153 ~~v~ti~d~d~yChyvagLVg~glsrlf~~s~le~-~~~~~e~l~ns~glfLqktnIirdy~ed~~d~r~Fwp~eIwg~y 231 (413)
T KOG1459|consen 153 EEVETIWDYDVYCHYVAGLVGIGLSRLFTASKLED-LLARLEQLSNSMGLFLQKTNIIRDYLEDPVDGRPFWPREIWGKY 231 (413)
T ss_pred HHHhHHHHHHHHHHHHHHhhCCchHhhhhHHHHhh-hhhhHHHHhcccchHHHHhHHHHHHHhccccCCccChHHHHHHH
Confidence 45889999999999999999999988886521100 11234678999999999999999999999999999999999988
Q ss_pred CCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcCccCChHHHHHHH-HHHHHHHHHHHCCCCCCCCCcccCh
Q 036976 141 VLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLL-IYREILDAIEENDYDNLTKRAYVGR 219 (243)
Q Consensus 141 gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~-~~~~iL~~l~~~~~~~~~~r~~ls~ 219 (243)
--.-+|+....+++..-.++.+++..|..|-..+......+...+-.-+-++-. +....| .+.-+|-++|+.++++++
T Consensus 232 ~d~L~d~~~~en~dl~l~Cln~m~tnaL~hv~d~l~yls~l~~qsvfnfcaipqimai~Tl-al~~nn~dvfrG~Vklrk 310 (413)
T KOG1459|consen 232 MDKLKDFRYPENDDLALQCLNEMVTNALMHVPDVLTYLSKLRTQSVFNFCAIPQIMAIATL-ALCYNNEDVFRGNVKLRK 310 (413)
T ss_pred HHHHHhhhCccchhHHHHHHHHHHHHHhhccHHHHHHHhhcccHHHHHHHHHHHHHHHHHH-HHHhcCHhHhccceeecC
Confidence 545678888888888889999999999999988877666665554332211111 222233 345688899999999887
Q ss_pred HHHHHHH
Q 036976 220 MKKYLML 226 (243)
Q Consensus 220 ~~k~~~~ 226 (243)
..-..++
T Consensus 311 Gl~~~~I 317 (413)
T KOG1459|consen 311 GLAVELI 317 (413)
T ss_pred CchHHHH
Confidence 5444333
No 13
>PLN02890 geranyl diphosphate synthase
Probab=95.66 E-value=0.32 Score=44.95 Aligned_cols=124 Identities=17% Similarity=0.115 Sum_probs=76.6
Q ss_pred CCCCHHHHHHHHHHhhhHHHHHHHhhhCCC-CCCCchhhhhHHHHHHHHHHHHHHHHHHhh-----------hhhhhCCC
Q 036976 62 RYENLQELYLYCYYVAGTVGLMSVPVMGIA-PDSSSSAQSIYNGALNLGVGNQLTNFLRDV-----------GEDASRGR 129 (243)
Q Consensus 62 ~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~-~~~~~~~~~~~~~a~~lG~alql~nilRDi-----------~~D~~~gR 129 (243)
.-.|++++..-.+.-.+++...++++-+.- ..+....+.+..+..++|.|+|+.+=+-|+ +.|+..|.
T Consensus 253 ~~~s~~~Yl~~i~~KTa~Lf~~s~~~gAilaga~~~~~~~l~~fG~~lGlAFQI~DDiLD~~g~~~~~GK~~g~DL~eGk 332 (422)
T PLN02890 253 QRRSMDYYMQKTYYKTASLISNSCKAVAILAGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGV 332 (422)
T ss_pred CCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCChhhhCCCchhhHhcCC
Confidence 345778877777777777777776654321 111112234678999999999999988886 46788899
Q ss_pred cccCHhhHHhCCCChHhhhh-ccC-CHHHHHH---------HHHHHHHHHHHHHHHHHchhhcCccC
Q 036976 130 VYLPQDKLAQFVLCDKDVFA-RKV-TDNWREF---------MKEQIKRARTFFNMAEEGASQLDKDS 185 (243)
Q Consensus 130 ~YlP~~~l~~~gv~~~~l~~-~~~-~~~~~~l---------~~~~~~~A~~~~~~a~~~~~~lp~~~ 185 (243)
+-+|.=..-+..-....+.. +.. ...+..+ +.+-.+.|++|.++|.+.+..+|...
T Consensus 333 ~TlPvl~al~~~~~l~~~l~~~~~~~~~v~~~~~~i~~~gaie~a~~la~~~~~~A~~~L~~lp~s~ 399 (422)
T PLN02890 333 ITAPILFAMEEFPQLREVVDRGFDNPANVDIALEYLGKSRGIQRTRELAREHANLAAAAIESLPETD 399 (422)
T ss_pred ccHHHHHHHhcCHHHHHHHhcccCCHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHHhCCCCc
Confidence 88887543322111112221 111 2223222 33344568889999999888888764
No 14
>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=95.47 E-value=0.24 Score=44.16 Aligned_cols=121 Identities=17% Similarity=0.163 Sum_probs=72.2
Q ss_pred CCHHHHHHHHHHhhhHHHHHHHhhhCCC-CCCCchhhhhHHHHHHHHHHHHHHHHHHh-----------hhhhhhCCCcc
Q 036976 64 ENLQELYLYCYYVAGTVGLMSVPVMGIA-PDSSSSAQSIYNGALNLGVGNQLTNFLRD-----------VGEDASRGRVY 131 (243)
Q Consensus 64 ~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~-~~~~~~~~~~~~~a~~lG~alql~nilRD-----------i~~D~~~gR~Y 131 (243)
.+.+++..-++.-.+++...++++-..- ..+....+.+.+++.++|.|+|+.+=+.| ++.|+..|.+-
T Consensus 161 ~~~~~y~~~~~~KTa~L~~~~~~~ga~~ag~~~~~~~~l~~~G~~lG~aFQi~DDild~~~~~~~~GK~~g~Dl~~Gk~T 240 (322)
T TIGR02749 161 LSLEDYLEKSFYKTASLVAASSKAAAVLSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPAGSDLMKGNLT 240 (322)
T ss_pred CCHHHHHHHHHccHHHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHHHHHHHHHhccCCCChHhhCCChhHHHhCCCch
Confidence 4677776666666677766666553321 11112234577899999999999988877 56888999998
Q ss_pred cCHhhHHhCCCChHhhhhc-c-CCHHHHHH---------HHHHHHHHHHHHHHHHHchhhcCcc
Q 036976 132 LPQDKLAQFVLCDKDVFAR-K-VTDNWREF---------MKEQIKRARTFFNMAEEGASQLDKD 184 (243)
Q Consensus 132 lP~~~l~~~gv~~~~l~~~-~-~~~~~~~l---------~~~~~~~A~~~~~~a~~~~~~lp~~ 184 (243)
+|.=..-+..-....++.. . ....+..+ +..--+.++++.++|.+.+..+|..
T Consensus 241 lp~l~al~~~~~~~~~l~~~~~~~~~~~~~~~~i~~~ga~~~a~~~~~~~~~~A~~~L~~lp~~ 304 (322)
T TIGR02749 241 APVLFALEEEPKLSELIEREFSQKGDLEQALSLVRKSGGIKKARELAKEQAQLALQSLSFLPPS 304 (322)
T ss_pred HHHHHHHhcChHHHHHHHhccCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 8864332221111122211 1 11222222 2333445777888888888888775
No 15
>PLN02857 octaprenyl-diphosphate synthase
Probab=95.23 E-value=0.24 Score=45.65 Aligned_cols=122 Identities=19% Similarity=0.218 Sum_probs=72.9
Q ss_pred CCHHHHHHHHHHhhhHHHHHHHhhhCC-CCCCCchhhhhHHHHHHHHHHHHHHHHHHhh-----------hhhhhCCCcc
Q 036976 64 ENLQELYLYCYYVAGTVGLMSVPVMGI-APDSSSSAQSIYNGALNLGVGNQLTNFLRDV-----------GEDASRGRVY 131 (243)
Q Consensus 64 ~t~~dL~~Y~~~~Ag~vg~l~~~l~g~-~~~~~~~~~~~~~~a~~lG~alql~nilRDi-----------~~D~~~gR~Y 131 (243)
.|.+++..-.+.-.+++...++++-.. ...+....+.+.++..++|.|+|+.+=+.|+ +.|+..|.+-
T Consensus 255 ~s~~~Yl~~i~~KTa~L~~~a~~~gallaga~~~~~~~l~~fG~~LGiAFQI~DDiLD~~~~~~~~GK~~g~DL~eGK~T 334 (416)
T PLN02857 255 VTLDEYLLKSYYKTASLIAASTKSAAIFSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPAGSDLAKGNLT 334 (416)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHhCCCcchhhhcCCcc
Confidence 467777766666677776666655332 1111122345778999999999999888884 5788899998
Q ss_pred cCHhhHHhCCCChHhhhhcc--CCHHHHHH---------HHHHHHHHHHHHHHHHHchhhcCccC
Q 036976 132 LPQDKLAQFVLCDKDVFARK--VTDNWREF---------MKEQIKRARTFFNMAEEGASQLDKDS 185 (243)
Q Consensus 132 lP~~~l~~~gv~~~~l~~~~--~~~~~~~l---------~~~~~~~A~~~~~~a~~~~~~lp~~~ 185 (243)
+|.=.--+..-....++... .++.+.++ +++--+.|+++.++|.+.+..+|.+.
T Consensus 335 lPli~al~~~~~l~~~l~~~~~~~~~~~~~~~lv~~~Ggie~a~~~a~~~~~~A~~~L~~Lp~~~ 399 (416)
T PLN02857 335 APVIFALEKEPELREIIESEFCEEGSLEEAIELVNEGGGIERAQELAKEKADLAIQNLECLPRGA 399 (416)
T ss_pred HHHHHHHhcChHHHHHHhhccCCHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHHhCCCCH
Confidence 88643211111111222211 12223332 22333457888888888888888753
No 16
>CHL00151 preA prenyl transferase; Reviewed
Probab=95.10 E-value=0.26 Score=43.93 Aligned_cols=121 Identities=12% Similarity=0.091 Sum_probs=69.9
Q ss_pred CCHHHHHHHHHHhhhHHHHHHHhhhCC-CCCCCchhhhhHHHHHHHHHHHHHHHHHHhh-----------hhhhhCCCcc
Q 036976 64 ENLQELYLYCYYVAGTVGLMSVPVMGI-APDSSSSAQSIYNGALNLGVGNQLTNFLRDV-----------GEDASRGRVY 131 (243)
Q Consensus 64 ~t~~dL~~Y~~~~Ag~vg~l~~~l~g~-~~~~~~~~~~~~~~a~~lG~alql~nilRDi-----------~~D~~~gR~Y 131 (243)
.|.++...=++.-.|++..+++.+-.. ...+....+.+..+..++|.|+|+.+=+-|+ +.|+..|++-
T Consensus 162 ~~~~~yl~~i~~KTa~L~~~~~~~ga~lag~~~~~~~~l~~~G~~lG~aFQi~DDilD~~~~~~~~GK~~g~Dl~eGk~T 241 (323)
T CHL00151 162 LSILNYIEKSFYKTASLIAASCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLT 241 (323)
T ss_pred CCHHHHHHHHHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHhhcccChhhhCCCchhhHhcCchH
Confidence 455555554445555666665544322 1111122345778999999999999888874 6788899998
Q ss_pred cCHhhHHhCCCChHhhhh-cc-CCHHHHHH---------HHHHHHHHHHHHHHHHHchhhcCcc
Q 036976 132 LPQDKLAQFVLCDKDVFA-RK-VTDNWREF---------MKEQIKRARTFFNMAEEGASQLDKD 184 (243)
Q Consensus 132 lP~~~l~~~gv~~~~l~~-~~-~~~~~~~l---------~~~~~~~A~~~~~~a~~~~~~lp~~ 184 (243)
+|.=..-+..-....+.. .. ..+.+..+ +.+--+.++.|.++|.+.+..+|..
T Consensus 242 lp~l~al~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~g~~~~a~~~a~~~~~~A~~~L~~lp~~ 305 (323)
T CHL00151 242 APVLFALTQNSKLAKLIEREFCETKDISQALQIIKETNGIEKAKDLALEHMQAAIQCLKFLPPS 305 (323)
T ss_pred HHHHHHHhcChHHHHHHHHhcCCHHHHHHHHHHHHHCCcHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 885433221111111111 11 12223333 3344456788888888888888765
No 17
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=94.87 E-value=0.46 Score=42.35 Aligned_cols=122 Identities=15% Similarity=0.088 Sum_probs=76.5
Q ss_pred CCCCHHHHHHHHHHhhhHHHHHHHhhhCCC-CCCCchhhhhHHHHHHHHHHHHHHHHHHhh-----------hhhhhCCC
Q 036976 62 RYENLQELYLYCYYVAGTVGLMSVPVMGIA-PDSSSSAQSIYNGALNLGVGNQLTNFLRDV-----------GEDASRGR 129 (243)
Q Consensus 62 ~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~-~~~~~~~~~~~~~a~~lG~alql~nilRDi-----------~~D~~~gR 129 (243)
.-.|.+++..-++.-.|++..+++.+-+.- ..+....+.+..++.++|.|+|+.+=+-|+ +.|+..|.
T Consensus 156 ~~~s~~~y~~~i~~KTa~lf~~~~~~ga~lag~~~~~~~~l~~~g~~lG~aFQi~DD~ld~~~~~~~~GK~~g~Dl~~gk 235 (323)
T PRK10888 156 PDITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRYLGTAFQLIDDLLDYSADGETLGKNVGDDLNEGK 235 (323)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHhhcccCChHhhCCCchhhhhcCC
Confidence 446888888888888888888877765321 111112334678999999999999888776 67888999
Q ss_pred cccCHhhHHhCCCChH--h-h---hhccC-CHHHHHH---------HHHHHHHHHHHHHHHHHchhhcCcc
Q 036976 130 VYLPQDKLAQFVLCDK--D-V---FARKV-TDNWREF---------MKEQIKRARTFFNMAEEGASQLDKD 184 (243)
Q Consensus 130 ~YlP~~~l~~~gv~~~--~-l---~~~~~-~~~~~~l---------~~~~~~~A~~~~~~a~~~~~~lp~~ 184 (243)
+-+|.=..-+. .+++ . + ..... .+.+..+ +.+-.+.|+.+.++|.+.+..+|..
T Consensus 236 ~Tlp~l~al~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~g~~e~~~~~a~~~~~~A~~~L~~lp~~ 305 (323)
T PRK10888 236 PTLPLLHAMHH-GTPEQAAMIRTAIEQGNGRHLLEPVLEAMNACGSLEWTRQRAEEEADKAIAALQVLPDT 305 (323)
T ss_pred chHHHHHHHHh-CCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 98885433222 1221 1 1 11111 1222222 2233345778888888888888865
No 18
>TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II. Members of this family are component II of the heterodimeric heptaprenyl diphosphate synthase. The trusted cutoff was set such that all members identified are encoded near to a recognizable gene for component I (in Pfam family pfam07307). This enzyme acts in menaquinone-7 isoprenoid side chain biosynthesis.
Probab=94.54 E-value=0.51 Score=41.97 Aligned_cols=123 Identities=16% Similarity=0.153 Sum_probs=75.3
Q ss_pred CCCHHHHHHHHHHhhhHHHHHHHhhhCCC-CCCCchhhhhHHHHHHHHHHHHHHHHHHhh-----------hhhhhCCCc
Q 036976 63 YENLQELYLYCYYVAGTVGLMSVPVMGIA-PDSSSSAQSIYNGALNLGVGNQLTNFLRDV-----------GEDASRGRV 130 (243)
Q Consensus 63 ~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~-~~~~~~~~~~~~~a~~lG~alql~nilRDi-----------~~D~~~gR~ 130 (243)
-.+.+++..-++.-.|++...++.+-..- ..+....+.+.+++.++|.|+|+.|=+.|+ +.|+..|..
T Consensus 156 ~~~~~~Y~~~i~~KTa~L~~~~~~~ga~~ag~~~~~~~~l~~~g~~lG~aFQI~DDilD~~~~~~~~GK~~~~Dl~~gk~ 235 (319)
T TIGR02748 156 DQNLRTYLRRIKRKTALLIAASCQLGAIASGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGKPAGGDLLQGNV 235 (319)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHccCCHHhhCCChhhHHhCCCc
Confidence 35777877777777777777666553221 111112234678999999999999988886 478888999
Q ss_pred ccCHhhHHhCCCChHhh---hhccCCHHHHHHHH---------HHHHHHHHHHHHHHHchhhcCccC
Q 036976 131 YLPQDKLAQFVLCDKDV---FARKVTDNWREFMK---------EQIKRARTFFNMAEEGASQLDKDS 185 (243)
Q Consensus 131 YlP~~~l~~~gv~~~~l---~~~~~~~~~~~l~~---------~~~~~A~~~~~~a~~~~~~lp~~~ 185 (243)
-+|.=..-+..-..+.+ .....+..+..++. .-...++.+.++|.+.+..+|...
T Consensus 236 Tlp~l~al~~~~~~~~l~~~~~~~~~~~~~~~~~~i~~~g~~~~a~~~a~~~~~~A~~~L~~lp~~~ 302 (319)
T TIGR02748 236 TLPVLYAMEDPFLKKRIEQVLEETTAEEMEPLIEEVKKSDAIEYAYAVSDRYLKKALELLDGLPDGR 302 (319)
T ss_pred hHHHHHHhcCcchhHHHHHHHcCCCHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHhcCCCCH
Confidence 88876554321111111 11112223333322 233457888888888888887653
No 19
>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases, head-to-tail. These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4) condensation reactions. This CD includes all-trans (E)-isoprenyl diphosphate synthases which synthesize various chain length (C10, C15, C20, C25, C30, C35, C40, C45, and C50) linear isoprenyl diphosphates from precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They catalyze the successive 1'-4 condensation of the 5-carbon IPP to allylic substrates geranyl-, farnesyl-, or geranylgeranyl-diphosphate. Isoprenoid chain elongation reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DDXX(XX
Probab=94.18 E-value=0.86 Score=39.08 Aligned_cols=117 Identities=15% Similarity=0.050 Sum_probs=72.9
Q ss_pred hhccCCCC--CCCCHHHHHHHHHHhhhHHHHHHHhhhCCC-CCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhhhh-CCC
Q 036976 54 MRMDTRKF--RYENLQELYLYCYYVAGTVGLMSVPVMGIA-PDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDAS-RGR 129 (243)
Q Consensus 54 ~~~Dl~~~--~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~-~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D~~-~gR 129 (243)
+..|+... .-.|++++..-+..-.|+...+++.+.+.- ..+....+.+.+++.++|.++|+.|=+.|+-.|.. .|+
T Consensus 124 Q~~d~~~~~~~~~~~~~y~~~~~~KT~~l~~~~~~~~a~l~~~~~~~~~~l~~~g~~lG~afQi~DD~ld~~~~~~~~gK 203 (259)
T cd00685 124 QLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGK 203 (259)
T ss_pred HHHHHHccCCCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHhhcccCChHHHCC
Confidence 33455443 257899999888888888877776655431 11122334578899999999999998888754331 122
Q ss_pred cccCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcCccC
Q 036976 130 VYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDS 185 (243)
Q Consensus 130 ~YlP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp~~~ 185 (243)
- ..+|+.+++.+=.+.-++ -+.++.+.++|...+..+|...
T Consensus 204 ~------------~~~Di~~gk~T~~~~~~l---~~~~~~~~~~a~~~l~~~~~~~ 244 (259)
T cd00685 204 P------------VGSDLREGKCTLPVLLAL---RELAREYEEKALEALKALPESP 244 (259)
T ss_pred C------------cchHHHcCCchHHHHHHH---HHHHHHHHHHHHHHHHcCCCcH
Confidence 1 123444444433222222 5667777888888887787654
No 20
>PRK10581 geranyltranstransferase; Provisional
Probab=93.94 E-value=0.6 Score=41.15 Aligned_cols=110 Identities=19% Similarity=0.120 Sum_probs=69.2
Q ss_pred CCCHHHHHHHHHHhhhHHHHHHHhhhCCC-CCCC-chhhhhHHHHHHHHHHHHHHHHHHhhhhhh-hCCCcccCHhhHHh
Q 036976 63 YENLQELYLYCYYVAGTVGLMSVPVMGIA-PDSS-SSAQSIYNGALNLGVGNQLTNFLRDVGEDA-SRGRVYLPQDKLAQ 139 (243)
Q Consensus 63 ~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~-~~~~-~~~~~~~~~a~~lG~alql~nilRDi~~D~-~~gR~YlP~~~l~~ 139 (243)
..+.+++..-++.=.|++..+++.+-+.- ..+. ...+.+.+++.++|.|+|+.+=+.|+-.|. ..|.-
T Consensus 168 ~~~~~~y~~i~~~KTa~L~~~~~~~gailag~~~~~~~~~l~~~g~~lG~aFQI~DDilD~~g~~~~~GK~--------- 238 (299)
T PRK10581 168 QVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLGKR--------- 238 (299)
T ss_pred CCCHHHHHHHHHHhhHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHccccCChHHHCCC---------
Confidence 45788888888877777877766554321 1111 123456789999999999999998874332 11211
Q ss_pred CCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHHHchhhcCcc
Q 036976 140 FVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAEEGASQLDKD 184 (243)
Q Consensus 140 ~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp~~ 184 (243)
.-+|+.+|+.+-.+-..++.--+.++++.++|.+.+..+|..
T Consensus 239 ---~g~Dl~~gk~T~p~l~~~e~a~~~a~~~~~~A~~~l~~l~~~ 280 (299)
T PRK10581 239 ---QGADQQLGKSTYPALLGLEQARKKARDLIDDARQSLDQLAAQ 280 (299)
T ss_pred ---cchhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCC
Confidence 113444444443333345556677888889988888888764
No 21
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=89.02 E-value=12 Score=33.30 Aligned_cols=129 Identities=16% Similarity=0.082 Sum_probs=77.8
Q ss_pred hhccCCCCC-CCCHHHHHHHHHHhhhHHHHHHHhhhCCC-CCCCchhhhhHHHHHHHHHHHHHHHHHHhhh---------
Q 036976 54 MRMDTRKFR-YENLQELYLYCYYVAGTVGLMSVPVMGIA-PDSSSSAQSIYNGALNLGVGNQLTNFLRDVG--------- 122 (243)
Q Consensus 54 ~~~Dl~~~~-~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~-~~~~~~~~~~~~~a~~lG~alql~nilRDi~--------- 122 (243)
...|+.... ..|.+++..=.+.=.|+....++.+.+.- .......+.+..++..+|.|+|+.+=+-|+-
T Consensus 150 Q~lDl~~~~~~~t~e~y~~~i~~KTa~L~~~a~~~ga~la~~~~~~~~~l~~~g~~lGlaFQi~DDiLD~~~d~~~lGK~ 229 (322)
T COG0142 150 QALDLAFENKPVTLEEYLRVIELKTAALFAAAAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEELGKP 229 (322)
T ss_pred HHHHHHccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhHHHHHHHHhhcCCCChHHhCCC
Confidence 444554332 27888888777777788877777766542 2222334568899999999999998877765
Q ss_pred --hhhhCCCcccCHhhHHhCCCChHhh-hhcc-CCHHHHHHHH---------HHHHHHHHHHHHHHHchhhcC
Q 036976 123 --EDASRGRVYLPQDKLAQFVLCDKDV-FARK-VTDNWREFMK---------EQIKRARTFFNMAEEGASQLD 182 (243)
Q Consensus 123 --~D~~~gR~YlP~~~l~~~gv~~~~l-~~~~-~~~~~~~l~~---------~~~~~A~~~~~~a~~~~~~lp 182 (243)
.|+..|.+-+|.-..-+.+-..... .... ....+..+.. .-...+..+.++|.+.++.+|
T Consensus 230 ~g~Dl~~gK~T~p~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~a~~~~~~a~~~L~~l~ 302 (322)
T COG0142 230 VGSDLKEGKPTLPVLLALEKANEDQKLLRILLEGGGEVEEALELLRKSGAIEYAKNLAKTYVEKAKEALEKLP 302 (322)
T ss_pred cchHHHcCCchHHHHHHHHcCchhhHHHHHHhhcchHHHHHHHHHHHcchHHHHHHHHHHHHHHHHHHHHhCC
Confidence 4566677777766544443221111 1000 0002222222 222347888888888888788
No 22
>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=87.36 E-value=11 Score=32.32 Aligned_cols=71 Identities=15% Similarity=0.132 Sum_probs=51.5
Q ss_pred hccCCCC-CCCCHHHHHHHHHHhhhHHHHHHHhhhCC-CCCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhhh
Q 036976 55 RMDTRKF-RYENLQELYLYCYYVAGTVGLMSVPVMGI-APDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDA 125 (243)
Q Consensus 55 ~~Dl~~~-~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~-~~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D~ 125 (243)
..|+... .-.|++++..-++.-.|++..+++++... ...+....+.+..++.++|.|+|+.|=+.|+-.|-
T Consensus 123 ~~d~~~~~~~~~~~~y~~i~~~KTg~l~~~~~~~ga~lag~~~~~~~~l~~~g~~lG~afQi~DD~~d~~~~~ 195 (260)
T PF00348_consen 123 ALDLANEDKDPTEEEYLEIIRLKTGSLFALACQLGAILAGADEEQIEALREFGRHLGIAFQIRDDLLDLFGDE 195 (260)
T ss_dssp HHHHHTTTSSTSHHHHHHHHHHHTHHHHHHHHHHHHHHTTSGHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHH
T ss_pred hhccccccccccHHHHHHHHhhcchHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHhhhhhhhhccCcH
Confidence 3344332 36789999999999999999998877643 11222233557789999999999999888887553
No 23
>KOG0776 consensus Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism]
Probab=81.98 E-value=24 Score=32.18 Aligned_cols=122 Identities=16% Similarity=0.174 Sum_probs=69.2
Q ss_pred ccCCCCCCCCHHHHHHHHHHhhhHHHH---HHHhhhCCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhh-----------
Q 036976 56 MDTRKFRYENLQELYLYCYYVAGTVGL---MSVPVMGIAPDSSSSAQSIYNGALNLGVGNQLTNFLRDV----------- 121 (243)
Q Consensus 56 ~Dl~~~~~~t~~dL~~Y~~~~Ag~vg~---l~~~l~g~~~~~~~~~~~~~~~a~~lG~alql~nilRDi----------- 121 (243)
.|++..+++.+.. =-..-.+++.. .+.-|+|-.++ ...+.+.+|++++|.++|+++=+-|.
T Consensus 223 ~d~~~~~~e~~e~---~~~~KTAsLla~Sc~~~aILgg~s~--ev~e~~~~yGR~lGL~fQvvDDildftkss~elGK~a 297 (384)
T KOG0776|consen 223 LDLDDVGLEYLEF---KTLLKTASLLAKSCVAAAILGGGSE--EVIEAAFEYGRCLGLAFQVVDDILDFTKSSEELGKTA 297 (384)
T ss_pred cccCCcchHHHHH---HHHHHHHHHHHHHHHHHHHHcCCCH--HHHHHHHHHHHHHHHHHHHhhcccCcccchhhcCcch
Confidence 3555444443333 33333333333 33455664322 23456789999999999999876664
Q ss_pred hhhhhCCCcccCH----hhHHhCCCChHhhhhc-------cCCHHHHHHHHHHHHHHHHHHHHHHHchhhcCccC
Q 036976 122 GEDASRGRVYLPQ----DKLAQFVLCDKDVFAR-------KVTDNWREFMKEQIKRARTFFNMAEEGASQLDKDS 185 (243)
Q Consensus 122 ~~D~~~gR~YlP~----~~l~~~gv~~~~l~~~-------~~~~~~~~l~~~~~~~A~~~~~~a~~~~~~lp~~~ 185 (243)
+.|+..|-+-=|. |.-.++ .+.|.++ ....++...+..-...|++|-++|.+.+..+|+..
T Consensus 298 g~Dl~~g~lT~P~Lf~~e~~pe~---~e~l~~~~~e~~~~~~~~k~v~~v~~a~~la~~~~~~Al~~l~~~p~s~ 369 (384)
T KOG0776|consen 298 GKDLKAGKLTAPVLFALEKSPEL---REKLEREFSEPLDGFDADKAVPGVALAKYLARRHNNKALEALQSLPRSE 369 (384)
T ss_pred hhhhhhccccccchhhhhhChHH---HHHHHHhccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCch
Confidence 3466666653332 332222 1122221 22334555677777788899999988888788764
No 24
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=66.72 E-value=2.9 Score=24.96 Aligned_cols=21 Identities=19% Similarity=0.491 Sum_probs=18.3
Q ss_pred hCCCcccCHhhHHhCCCChHh
Q 036976 126 SRGRVYLPQDKLAQFVLCDKD 146 (243)
Q Consensus 126 ~~gR~YlP~~~l~~~gv~~~~ 146 (243)
++||+.||.++.++.|+...+
T Consensus 5 ~kgri~iP~~~r~~l~~~~gd 25 (43)
T TIGR01439 5 KKGQIVIPKEIREKLGLKEGD 25 (43)
T ss_pred cCCeEEecHHHHHHcCcCCCC
Confidence 589999999999999988654
No 25
>cd00684 Terpene_cyclase_plant_C1 Plant Terpene Cyclases, Class 1. This CD includes a diverse group of monomeric plant terpene cyclases (Tspa-Tspf) that convert the acyclic isoprenoid diphosphates, geranyl diphosphate (GPP), farnesyl diphosphate (FPP), or geranylgeranyl diphosphate (GGPP) into cyclic monoterpenes, diterpenes, or sesquiterpenes, respectively; a few form acyclic species. Terpnoid cyclases are soluble enzymes localized to the cytosol (sesquiterpene synthases) or plastids (mono- and diterpene synthases). All monoterpene and diterpene synthases have restrict substrate specificity, however, some sesquiterpene synthases can accept both FPP and GPP. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl diphosphates, via bridging Mg2+ ions (K+ preferred by gymnosperm cyclases), inducing conformational changes such that an N-terminal regi
Probab=56.74 E-value=1.9e+02 Score=27.74 Aligned_cols=108 Identities=14% Similarity=0.083 Sum_probs=63.5
Q ss_pred CCCCCCCHHHHHHHHHHhhhHHHHHHHhhhCCCCCCCch-hh--h-hHHHHHHHHHHHHHHHHHHhhhhhhhCCCc-ccC
Q 036976 59 RKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSS-AQ--S-IYNGALNLGVGNQLTNFLRDVGEDASRGRV-YLP 133 (243)
Q Consensus 59 ~~~~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~~~~~~~-~~--~-~~~~a~~lG~alql~nilRDi~~D~~~gR~-YlP 133 (243)
.....+|++|.......++|.--.++.-.+|..+..... .+ . ........+....+.|=+........+|.+ =.-
T Consensus 380 ~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~e~~e~~~~~~~l~~~~~~i~rL~NDi~S~~kE~~rGdv~n~V 459 (542)
T cd00684 380 HEGYVPTFEEYMENALVSIGLGPLLLTSFLGMGDILTEEAFEWLESRPKLVRASSTIGRLMNDIATYEDEMKRGDVASSI 459 (542)
T ss_pred hcCCCCCHHHHHhhhhHHhhHHHHHHHHHHhcCCCCCHHHHHHHhccHHHHHHHHHHHHHhcChhhhHHHHhcCCcccHH
Confidence 345678999988888777665555555445443211100 00 0 012222334445555555556666677874 566
Q ss_pred HhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHHH
Q 036976 134 QDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMAE 175 (243)
Q Consensus 134 ~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a~ 175 (243)
.-.|+++|+|.++ ..+-+..+++.+.+.+.+..
T Consensus 460 ~~ymke~g~s~ee---------A~~~i~~~ie~~wk~ln~e~ 492 (542)
T cd00684 460 ECYMKEYGVSEEE---------AREEIKKMIEDAWKELNEEF 492 (542)
T ss_pred HHHHHhcCCCHHH---------HHHHHHHHHHHHHHHHHHHH
Confidence 6788999998765 34456777777777777643
No 26
>PF07899 Frigida: Frigida-like protein; InterPro: IPR012474 This family is composed of plant proteins that are similar to FRIGIDA protein expressed by Arabidopsis thaliana (Mouse-ear cress) (Q9FDW0 from SWISSPROT). This protein is probably nuclear and is required for the regulation of flowering time in the late-flowering phenotype. It is known to increase RNA levels of flowering locus C. Allelic variation at the FRIGIDA locus is a major determinant of natural variation in flowering time [].
Probab=55.64 E-value=83 Score=27.66 Aligned_cols=112 Identities=16% Similarity=0.197 Sum_probs=74.2
Q ss_pred HHHHHHHHHHHcCCC-CCHHHHHHHHHHHhCCCCHHhhccCCCCCCCCHHHHHHHHHHhhhHHHHHHHhhhCCCCCCCch
Q 036976 19 DRWEERLQDIFYGRP-YDMLDAALTDAVFKFPLDIKMRMDTRKFRYENLQELYLYCYYVAGTVGLMSVPVMGIAPDSSSS 97 (243)
Q Consensus 19 ~~w~~~l~~~~~g~~-~~pv~~aL~~~i~~~~l~~~~~~Dl~~~~~~t~~dL~~Y~~~~Ag~vg~l~~~l~g~~~~~~~~ 97 (243)
..|+..+. .+.. ...-+.+|...+..|+|..+ | |.+||..+...++.
T Consensus 113 ~~WK~~l~---~~~~~~~lea~gFL~lla~fgi~s~---------F-d~del~~Lv~~va~------------------- 160 (290)
T PF07899_consen 113 EEWKSKLD---GVNNENSLEALGFLQLLAAFGIVSE---------F-DEDELLKLVVSVAR------------------- 160 (290)
T ss_pred HHHHHHHH---hcccCCCHHHHHHHHHHHHcCCccc---------c-CHHHHHHHHHHhcc-------------------
Confidence 46999887 2222 24677899999999999853 2 34565544433331
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHhhhhhh-hCCCcccCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHHHH
Q 036976 98 AQSIYNGALNLGVGNQLTNFLRDVGEDA-SRGRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFNMA 174 (243)
Q Consensus 98 ~~~~~~~a~~lG~alql~nilRDi~~D~-~~gR~YlP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~~a 174 (243)
.+-+..|+.++++++-+.|+-+.+ .+|+..-.-...-.||++.. .+| ..+++..++.++.-....
T Consensus 161 ----~~~a~~L~~sLgl~~k~~d~V~~LI~~g~~ieAv~fi~~f~L~dk------fpP--v~lLk~yl~~~k~~~~~~ 226 (290)
T PF07899_consen 161 ----RKQAPELCRSLGLSDKMPDIVEKLIKKGKQIEAVRFIYAFGLVDK------FPP--VPLLKSYLEDSKKAAKRI 226 (290)
T ss_pred ----hHhhHHHHHHcCchhhhHHHHHHHHHCCCccchHHHHHHHcCCCC------CCC--HHHHHHHHHHHHHHHHHH
Confidence 244778999999999999999999 77777667777777887752 222 235555555555554443
No 27
>PRK02899 adaptor protein; Provisional
Probab=53.48 E-value=21 Score=29.44 Aligned_cols=43 Identities=14% Similarity=0.306 Sum_probs=36.9
Q ss_pred CCcccCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHHH
Q 036976 128 GRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFFN 172 (243)
Q Consensus 128 gR~YlP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~~ 172 (243)
=||+|-.++|...|++.+||+. ++++..++...+.+.|..-+.
T Consensus 11 Irv~it~~DL~eRgi~~~dL~~--n~~k~e~lF~~mm~Ea~~e~~ 53 (197)
T PRK02899 11 IKIFLTFDDLSERGLTKEDLWR--DAPKVHQLFRDMMQEANKELG 53 (197)
T ss_pred EEEEEeHHHHHHcCCCHHHHhc--CcHHHHHHHHHHHHHhhhccC
Confidence 4899999999999999999986 568899999999998865443
No 28
>COG0819 TenA Putative transcription activator [Transcription]
Probab=42.37 E-value=1.5e+02 Score=24.93 Aligned_cols=64 Identities=9% Similarity=0.086 Sum_probs=45.8
Q ss_pred HhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHH-HHHHHHchhhcCccCChHHHHHHHHHHHHHHHHHHCCC
Q 036976 134 QDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTF-FNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEENDY 208 (243)
Q Consensus 134 ~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~-~~~a~~~~~~lp~~~~~~~~~~~~~~~~iL~~l~~~~~ 208 (243)
...+++.|++.+++.+.+.++......+.+...+..- +.... .++.....+|..+..++.+.+.
T Consensus 87 ~~~~~~lgis~~~~~~~~~~~~~~aYt~ym~~~~~~g~~~~~~-----------aAl~PC~~~Y~eig~~~~~~~~ 151 (218)
T COG0819 87 ERLAEELGISLDELLKTEPSPANKAYTRYLLDTAYSGSFAELL-----------AALLPCLWGYAEIGKRLKAKPR 151 (218)
T ss_pred HHHHHHhCCCHHHHHhcCCCchHHHHHHHHHHHHhcCCHHHHH-----------HHHHHHHHHHHHHHHHHHhccc
Confidence 3468889999999999999999888888887765432 22221 2344555678888888877664
No 29
>COG1575 MenA 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism]
Probab=39.96 E-value=11 Score=33.35 Aligned_cols=23 Identities=39% Similarity=0.520 Sum_probs=19.7
Q ss_pred HHHHHHHhhhhhhhCCCcccCHh
Q 036976 113 QLTNFLRDVGEDASRGRVYLPQD 135 (243)
Q Consensus 113 ql~nilRDi~~D~~~gR~YlP~~ 135 (243)
=++|.+||+.+|.+.||.-+|--
T Consensus 193 l~aNNirDie~D~~~gk~TLavr 215 (303)
T COG1575 193 LLANNLRDIEEDIRNGKYTLAVR 215 (303)
T ss_pred HHhcccccchhHHhcCCcceeee
Confidence 36788999999999999888765
No 30
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=38.71 E-value=17 Score=22.35 Aligned_cols=23 Identities=22% Similarity=0.336 Sum_probs=18.1
Q ss_pred hCCCcccCHhhHHhCCCChHhhh
Q 036976 126 SRGRVYLPQDKLAQFVLCDKDVF 148 (243)
Q Consensus 126 ~~gR~YlP~~~l~~~gv~~~~l~ 148 (243)
+.+++.||.++.++.|+.+.|-.
T Consensus 5 ~s~~v~iPk~~~~~l~l~~Gd~v 27 (47)
T PF04014_consen 5 NSGQVTIPKEIREKLGLKPGDEV 27 (47)
T ss_dssp TCSEEEE-HHHHHHTTSSTTTEE
T ss_pred CCceEECCHHHHHHcCCCCCCEE
Confidence 46789999999999999887643
No 31
>PRK02315 adaptor protein; Provisional
Probab=36.29 E-value=49 Score=28.03 Aligned_cols=42 Identities=14% Similarity=0.178 Sum_probs=36.3
Q ss_pred CCcccCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHH
Q 036976 128 GRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFF 171 (243)
Q Consensus 128 gR~YlP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~ 171 (243)
=||+|-.++|+..|++..+|+- ++++..++...+.+.|..-.
T Consensus 11 IRv~it~~DL~eRGi~~~dL~~--n~~k~e~fF~~mm~Ea~~e~ 52 (233)
T PRK02315 11 IKVFITYDDLEERGFEREDLLY--NREKIEEFFYSMMDEVDEED 52 (233)
T ss_pred EEEEecHHHHHHcCCCHHHHhc--CcHHHHHHHHHHHHHhcccc
Confidence 4899999999999999999985 56889999999999886543
No 32
>PF03070 TENA_THI-4: TENA/THI-4/PQQC family; InterPro: IPR004305 Proteins containing this domain are found in all the three major phyla of life: archaebacteria, eubacteria, and eukaryotes. In Bacillus subtilis, TENA is one of a number of proteins that enhance the expression of extracellular enzymes, such as alkaline protease, neutral protease and levansucrase []. The THI-4 protein, which is involved in thiamine biosynthesis, also contains this domain. The C-terminal part of these proteins consistently show significant sequence similarity to TENA proteins. This similarity was first noted with the Neurospora crassa THI-4 []. The exact molecular function of this domain is uncertain.; PDB: 2RD3_D 3RM5_B 1UDD_D 1Z72_B 3HML_A 3HLX_A 3HNH_A 3DDE_B 3OQL_A 2A6B_A ....
Probab=34.48 E-value=2.4e+02 Score=22.59 Aligned_cols=63 Identities=16% Similarity=0.111 Sum_probs=44.4
Q ss_pred HhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHH-HHHHHHHchhhcCccCChHHHHHHHHHHHHHHHHHHCC
Q 036976 134 QDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRART-FFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEEND 207 (243)
Q Consensus 134 ~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~-~~~~a~~~~~~lp~~~~~~~~~~~~~~~~iL~~l~~~~ 207 (243)
.+.++++|++.+++.+.+.+|..+..+..+...+.. .+..+. .++.....+|..+.+.+.+..
T Consensus 80 ~~~~~~~gi~~~~~~~~~~~p~~~~y~~~l~~~a~~~~~~~~l-----------~al~pc~~~Y~~~~~~~~~~~ 143 (210)
T PF03070_consen 80 EDFAEELGISREDLENIEPSPATRAYTDFLLSLAQTGSLAEGL-----------AALLPCEWIYAEIGKRLAEKL 143 (210)
T ss_dssp HHHHHHTTSHHHHHHHSTC-HHHHHHHHHHHHHHHHSSHHHHH-----------HHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHhCCCHHHHHhhhhhhHHHHHHHHHHHHhccCCHHHHH-----------HHHHHHHHHHHHHHHHHhccc
Confidence 677889999999998888999999998888877643 233322 234455567777777776543
No 33
>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=34.27 E-value=3e+02 Score=23.60 Aligned_cols=135 Identities=12% Similarity=0.040 Sum_probs=79.2
Q ss_pred CHHHHHHHHHHHhCC--CCHH-----------------hhc-cCCCCCCCCHHHHHHHHHHhhhHHHHHH-Hh-hhCCC-
Q 036976 35 DMLDAALTDAVFKFP--LDIK-----------------MRM-DTRKFRYENLQELYLYCYYVAGTVGLMS-VP-VMGIA- 91 (243)
Q Consensus 35 ~pv~~aL~~~i~~~~--l~~~-----------------~~~-Dl~~~~~~t~~dL~~Y~~~~Ag~vg~l~-~~-l~g~~- 91 (243)
.|+..++.+...+.. .+.. .+. .-.....+|+++...+-..+.|....+. +. ++|..
T Consensus 109 ~p~~~~~~d~~~r~~~~~~~~~~~r~~~~~~~~~~a~~~e~~~~~~~~~psl~eYl~~R~~~~g~~~~~~l~~~~~g~~l 188 (303)
T cd00687 109 TPLEFGLADLWRRTLARMSAEWFNRFAHYTEDYFDAYIWEGKNRLNGHVPDVAEYLEMRRFNIGADPCLGLSEFIGGPEV 188 (303)
T ss_pred CHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhhhcccccccHHHHHHhcCCCC
Confidence 688888888876543 2222 111 2223456788887776666655443322 22 23432
Q ss_pred CCCCchhhhhHHHHHHHHHHHHHHHHHHhhhhhh-hCCCc-ccCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHH
Q 036976 92 PDSSSSAQSIYNGALNLGVGNQLTNFLRDVGEDA-SRGRV-YLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRART 169 (243)
Q Consensus 92 ~~~~~~~~~~~~~a~~lG~alql~nilRDi~~D~-~~gR~-YlP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~ 169 (243)
+......+.+...-...+....++|=|-....+. +.|.+ =+-.=+|+++|+|.++ ..+.+..++.....
T Consensus 189 p~~~~~~~~~~~l~~~~~~~~~l~NDl~S~~KE~~~~g~~~N~V~vl~~~~g~s~~e---------A~~~~~~~~~~~~~ 259 (303)
T cd00687 189 PAAVRLDPVMRALEALASDAIALVNDIYSYEKEIKANGEVHNLVKVLAEEHGLSLEE---------AISVVRDMHNERIT 259 (303)
T ss_pred CHHHHhChHHHHHHHHHHHHHHHHHHHHhhHHHHHhCCccchHHHHHHHHcCCCHHH---------HHHHHHHHHHHHHH
Confidence 1111112334556667788888888888888888 78874 4555577788888765 23345555666666
Q ss_pred HHHHHHHch
Q 036976 170 FFNMAEEGA 178 (243)
Q Consensus 170 ~~~~a~~~~ 178 (243)
.|.+..+.+
T Consensus 260 ~f~~~~~~l 268 (303)
T cd00687 260 QFEELEASL 268 (303)
T ss_pred HHHHHHHhc
Confidence 666665544
No 34
>PHA01083 hypothetical protein
Probab=31.65 E-value=1.2e+02 Score=23.95 Aligned_cols=61 Identities=16% Similarity=0.172 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhCC-CcccCHhhHHh----CCCChHhhhh-----ccCCHHHHHHHHHHHHHHHH
Q 036976 102 YNGALNLGVGNQLTNFLRDVGEDASRG-RVYLPQDKLAQ----FVLCDKDVFA-----RKVTDNWREFMKEQIKRART 169 (243)
Q Consensus 102 ~~~a~~lG~alql~nilRDi~~D~~~g-R~YlP~~~l~~----~gv~~~~l~~-----~~~~~~~~~l~~~~~~~A~~ 169 (243)
...|..||+-=|.+. +.+.| |.|+|.+.... .|++++...- ...+|+.+++++..+.+...
T Consensus 20 kqLA~~LGVs~q~IS-------~~R~G~r~~i~de~A~~LAe~aGiDp~eall~i~aDraetp~~kalWesIaKKlng 90 (149)
T PHA01083 20 KQIAHDLGVSPQKIS-------KMRTGVRTYISDEEAIFLAESAGIDPEIALLGCHADRNENPRAKAIWESIAKKQNG 90 (149)
T ss_pred HHHHHHhCCCHHHHH-------HHHcCCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhc
Confidence 456777777666654 55689 99999986544 6999886643 34788888888888776544
No 35
>cd03025 DsbA_FrnE_like DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
Probab=27.39 E-value=1.8e+02 Score=22.91 Aligned_cols=36 Identities=17% Similarity=0.182 Sum_probs=26.1
Q ss_pred HhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHH
Q 036976 134 QDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRART 169 (243)
Q Consensus 134 ~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~ 169 (243)
.++..+.|++.+++...-.++..++.++...+.|.+
T Consensus 129 ~~ia~~~Gld~~~~~~~~~s~~~~~~l~~~~~~a~~ 164 (193)
T cd03025 129 RELAIELGLDVEEFLEDFQSDEAKQAIQEDQKLARE 164 (193)
T ss_pred HHHHHHcCCCHHHHHHHHcChHHHHHHHHHHHHHHH
Confidence 356678999999988877777777666666555543
No 36
>TIGR02235 menA_cyano-plnt 1,4-dihydroxy-2-naphthoate phytyltransferase. This family of phytyltransferases, found in plants and cyanobacteria, are involved in the biosythesis of phylloquinone (Vitamin K1). Phylloquinone is a critical component of photosystem I. The closely related MenA enzyme from bacteria transfers a prenyl group (which only differs in the saturation of the isoprenyl groups) in the biosynthesis of menaquinone. Activity towards both substrates in certain organisms should be considered a possibility.
Probab=26.61 E-value=32 Score=30.10 Aligned_cols=27 Identities=11% Similarity=0.075 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHhhhhhhhCCCcccCHh
Q 036976 109 GVGNQLTNFLRDVGEDASRGRVYLPQD 135 (243)
Q Consensus 109 G~alql~nilRDi~~D~~~gR~YlP~~ 135 (243)
..+.-++|-+||+.+|.+.||.-+|--
T Consensus 174 ~~~iL~~Nn~rD~e~D~~~Gk~TL~v~ 200 (285)
T TIGR02235 174 TTLILFCSHFHQVEDDLAHGKRSPVVR 200 (285)
T ss_pred HHHHHHhcCCccchhHHHcCCcceehe
Confidence 457788999999999999999988765
No 37
>TIGR00242 mraZ protein. Members of this family contain two tandem copies of a domain described by pfam02381. This protein often is found with other genes of the dcw (division cell wall) gene cluster, including mraW, ftsI, murE, murF, ftsW, murG, etc.
Probab=26.24 E-value=30 Score=26.87 Aligned_cols=33 Identities=18% Similarity=0.218 Sum_probs=25.4
Q ss_pred HHhhhhhhhCCCcccCHhhHHhCCCChHhhhhcc
Q 036976 118 LRDVGEDASRGRVYLPQDKLAQFVLCDKDVFARK 151 (243)
Q Consensus 118 lRDi~~D~~~gR~YlP~~~l~~~gv~~~~l~~~~ 151 (243)
..++.-| ++|||-||....+..|++.+-+.-|.
T Consensus 76 a~~~~~D-~~GRi~iP~~lr~~a~l~k~vv~vG~ 108 (142)
T TIGR00242 76 ATECEMD-TAGRVLIANNLRNHAKLEKEIVLIGQ 108 (142)
T ss_pred CeeeeeC-CCCeEeCCHHHHHHhCCCCcEEEEeC
Confidence 3444444 48999999999999999987776553
No 38
>PF15496 DUF4646: Domain of unknown function (DUF4646)
Probab=26.01 E-value=59 Score=24.66 Aligned_cols=29 Identities=24% Similarity=0.243 Sum_probs=20.4
Q ss_pred hhhhhhhCCCcccC-HhhHHhCCCChHhhh
Q 036976 120 DVGEDASRGRVYLP-QDKLAQFVLCDKDVF 148 (243)
Q Consensus 120 Di~~D~~~gR~YlP-~~~l~~~gv~~~~l~ 148 (243)
..+..+..|--|+| -+.|..|+|+++|..
T Consensus 24 s~s~~l~~gFp~~~~P~~l~~~DVs~eDW~ 53 (123)
T PF15496_consen 24 SRSDSLSSGFPYLYPPPPLASHDVSEEDWT 53 (123)
T ss_pred ecCCccccCCCCcCCCchhhhcCCCHHHHH
Confidence 33555677777763 445799999999953
No 39
>PF11020 DUF2610: Domain of unknown function (DUF2610); InterPro: IPR021277 This family is conserved in Proteobacteria. One member is annotated as being elongation factor P but this could not be confirmed.
Probab=25.21 E-value=89 Score=21.91 Aligned_cols=51 Identities=24% Similarity=0.143 Sum_probs=29.2
Q ss_pred HHcCCC---CCHHHHHHHHHHH--hCCCCHH------hhccCCCCCCCCHHHHHHHHHHhhh
Q 036976 28 IFYGRP---YDMLDAALTDAVF--KFPLDIK------MRMDTRKFRYENLQELYLYCYYVAG 78 (243)
Q Consensus 28 ~~~g~~---~~pv~~aL~~~i~--~~~l~~~------~~~Dl~~~~~~t~~dL~~Y~~~~Ag 78 (243)
+|-|.| .||+-.......+ ...+|.+ .-.+|...-=-.|+||..|+-.+|.
T Consensus 19 iYIG~P~~~~HPl~~Q~~WLskeRgG~IP~~V~~sl~kL~~La~~N~v~feeLc~YAL~~a~ 80 (82)
T PF11020_consen 19 IYIGEPKPDHHPLQFQATWLSKERGGQIPEKVMDSLSKLYKLAKENNVSFEELCVYALGVAQ 80 (82)
T ss_pred EEeCCCCCCCCchHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 456766 3788776666553 3446665 2233433333456777777766653
No 40
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=24.82 E-value=36 Score=24.14 Aligned_cols=23 Identities=17% Similarity=0.481 Sum_probs=20.6
Q ss_pred hCCCcccCHhhHHhCCCChHhhh
Q 036976 126 SRGRVYLPQDKLAQFVLCDKDVF 148 (243)
Q Consensus 126 ~~gR~YlP~~~l~~~gv~~~~l~ 148 (243)
.+||+.||.++=+.+|+.+.|.+
T Consensus 12 ~~GqIvIPkeiR~~lgi~~Gd~l 34 (89)
T COG2002 12 RKGQIVIPKEIREALGIKEGDVL 34 (89)
T ss_pred cCceEEecHHHHHHhCCCCCCEE
Confidence 58999999999999999998764
No 41
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=24.27 E-value=45 Score=23.06 Aligned_cols=34 Identities=21% Similarity=0.307 Sum_probs=24.0
Q ss_pred HHHHHHhhhhhhh-CCCc-ccCHhhHHhCCCChHhh
Q 036976 114 LTNFLRDVGEDAS-RGRV-YLPQDKLAQFVLCDKDV 147 (243)
Q Consensus 114 l~nilRDi~~D~~-~gR~-YlP~~~l~~~gv~~~~l 147 (243)
+-|++.....|.+ +.|. ==|...|+++|+|+++.
T Consensus 5 ~~~~~~~~~~~~~~re~f~~dp~a~~~~~~Lt~eE~ 40 (77)
T cd07321 5 LEKLLEQLLVKPEVKERFKADPEAVLAEYGLTPEEK 40 (77)
T ss_pred HHHHHHHHhcCHHHHHHHHhCHHHHHHHcCCCHHHH
Confidence 3566777776663 3333 24999999999999875
No 42
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=23.93 E-value=48 Score=23.33 Aligned_cols=34 Identities=9% Similarity=0.241 Sum_probs=23.9
Q ss_pred HHHHHHhhhhhhhCCCccc--CHhhHHhCCCChHhh
Q 036976 114 LTNFLRDVGEDASRGRVYL--PQDKLAQFVLCDKDV 147 (243)
Q Consensus 114 l~nilRDi~~D~~~gR~Yl--P~~~l~~~gv~~~~l 147 (243)
+--++.++..|...-.-|+ |+..++++|+|+++.
T Consensus 6 ~nrli~~L~~dp~~rerF~~DPea~~~~~gLt~eE~ 41 (81)
T cd07922 6 VNRLIQELFKDPGLIERFQDDPSAVFEEYGLTPAER 41 (81)
T ss_pred HHHHHHHHhcCHHHHHHHHHCHHHHHHHcCCCHHHH
Confidence 4456667777774333343 999999999999874
No 43
>PLN02922 prenyltransferase
Probab=23.27 E-value=41 Score=29.86 Aligned_cols=27 Identities=7% Similarity=0.053 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHhhhhhhhCCCcccCHh
Q 036976 109 GVGNQLTNFLRDVGEDASRGRVYLPQD 135 (243)
Q Consensus 109 G~alql~nilRDi~~D~~~gR~YlP~~ 135 (243)
..+..++|-+||+.+|.+.||--+|--
T Consensus 201 ~~~iL~~Nn~rD~e~D~~~Gk~TL~v~ 227 (315)
T PLN02922 201 TTLILFCSHFHQIDGDRAVGKMSPLVR 227 (315)
T ss_pred HHHHHHHccCcchhhHHHcCccceeeE
Confidence 346778899999999999999877765
No 44
>COG5204 SPT4 Transcription elongation factor SPT4 [Transcription]
Probab=23.13 E-value=39 Score=24.55 Aligned_cols=17 Identities=47% Similarity=0.870 Sum_probs=13.8
Q ss_pred Hhhhhhh-hCCCcccCHh
Q 036976 119 RDVGEDA-SRGRVYLPQD 135 (243)
Q Consensus 119 RDi~~D~-~~gR~YlP~~ 135 (243)
-|+-+|+ .+||+|-|.+
T Consensus 90 edvve~L~~~g~~Y~pR~ 107 (112)
T COG5204 90 EDVVEDLEQHGRIYYPRT 107 (112)
T ss_pred HHHHHHHHHhCccccCCC
Confidence 4777888 6899999975
No 45
>PF13351 DUF4099: Protein of unknown function (DUF4099)
Probab=23.10 E-value=61 Score=22.84 Aligned_cols=18 Identities=17% Similarity=0.370 Sum_probs=15.9
Q ss_pred cCHhhHHhCCCChHhhhh
Q 036976 132 LPQDKLAQFVLCDKDVFA 149 (243)
Q Consensus 132 lP~~~l~~~gv~~~~l~~ 149 (243)
||=+.|+++|++.+.|..
T Consensus 6 i~w~~L~~~Gi~ke~Le~ 23 (85)
T PF13351_consen 6 IPWEELEKFGISKEMLEK 23 (85)
T ss_pred CCHHHHHHcCCCHHHhhC
Confidence 688899999999999876
No 46
>PF05389 MecA: Negative regulator of genetic competence (MecA); InterPro: IPR008681 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. This family contains several bacterial MecA proteins. In complex media competence development is poor, and there is little or no expression of late competence genes. Overexpression of MecA inhibits comG transcription [, , ]. MecA enables the recognition and targeting of unfolded and aggregated proteins to the ClpC protease or to other proteins involved in proteolysis. Acts negatively in the development of competence by binding ComK and recruiting it to the ClpCP protease. When overexpressed, inhibits sporulation. Also involved in Spx degradation by ClpC. ; PDB: 3JTP_C 2Y1R_O 3PXI_c 3PXG_b 3JTO_D 3JTN_A.
Probab=22.90 E-value=28 Score=29.04 Aligned_cols=43 Identities=14% Similarity=0.165 Sum_probs=0.0
Q ss_pred CCCcccCHhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHHHH
Q 036976 127 RGRVYLPQDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRARTFF 171 (243)
Q Consensus 127 ~gR~YlP~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~~~ 171 (243)
.=||+|-.++|...|++..||.. ++++..++...+.+.|..-.
T Consensus 10 tIr~~it~~DL~~rgi~~~dl~~--~~~k~e~fF~~ileea~~e~ 52 (220)
T PF05389_consen 10 TIRCTITNEDLEERGISLLDLWY--NSEKIEEFFYSILEEADEEH 52 (220)
T ss_dssp ---------------------------------------------
T ss_pred EEEEEEeHHHHHHcCCCHHHHhc--CcHHHHHHHHHHHHHhcccc
Confidence 34899999999999999999986 57778888888888875543
No 47
>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=22.23 E-value=29 Score=29.70 Aligned_cols=25 Identities=32% Similarity=0.521 Sum_probs=22.5
Q ss_pred hhCCCcccCHhhHHhCCCChHhhhh
Q 036976 125 ASRGRVYLPQDKLAQFVLCDKDVFA 149 (243)
Q Consensus 125 ~~~gR~YlP~~~l~~~gv~~~~l~~ 149 (243)
++.||+|||.=+|+.-++.+.|+..
T Consensus 89 aEEGrVylP~WMm~tLs~epgdlv~ 113 (331)
T COG5140 89 AEEGRVYLPSWMMQTLSMEPGDLVV 113 (331)
T ss_pred ecCCcEeehHHHHHhccCCCCcEEE
Confidence 4689999999999999999999865
No 48
>PF01323 DSBA: DSBA-like thioredoxin domain; InterPro: IPR001853 DSBA is a sub-family of the Thioredoxin family []. The efficient and correct folding of bacterial disulphide bonded proteins in vivo is dependent upon a class of periplasmic oxidoreductase proteins called DsbA, after the Escherichia coli enzyme. The bacterial protein-folding factor DsbA is the most oxidizing of the thioredoxin family. DsbA catalyses disulphide-bond formation during the folding of secreted proteins. The extremely oxidizing nature of DsbA has been proposed to result from either domain motion or stabilising active-site interactions in the reduced form. DsbA's highly oxidizing nature is a result of hydrogen bond, electrostatic and helix-dipole interactions that favour the thiolate over the disulphide at the active site []. In the pathogenic bacterium Vibrio cholerae, the DsbA homologue (TcpG) is responsible for the folding, maturation and secretion of virulence factors. While the overall architecture of TcpG and DsbA is similar and the surface features are retained in TcpG, there are significant differences. For example, the kinked active site helix results from a three-residue loop in DsbA, but is caused by a proline in TcpG (making TcpG more similar to thioredoxin in this respect). Furthermore, the proposed peptide binding groove of TcpG is substantially shortened compared with that of DsbA due to a six-residue deletion. Also, the hydrophobic pocket of TcpG is more shallow and the acidic patch is much less extensive than that of E. coli DsbA [].; GO: 0015035 protein disulfide oxidoreductase activity; PDB: 3GL5_A 3DKS_D 3RPP_C 3RPN_B 1YZX_A 3L9V_C 2IMD_A 2IME_A 2IMF_A 2B3S_B ....
Probab=21.84 E-value=1.4e+02 Score=23.54 Aligned_cols=36 Identities=14% Similarity=0.053 Sum_probs=26.5
Q ss_pred HhhHHhCCCChHhhhhccCCHHHHHHHHHHHHHHHH
Q 036976 134 QDKLAQFVLCDKDVFARKVTDNWREFMKEQIKRART 169 (243)
Q Consensus 134 ~~~l~~~gv~~~~l~~~~~~~~~~~l~~~~~~~A~~ 169 (243)
.+.+++.|++.+++...-.++.+++.++...+.|.+
T Consensus 127 ~~~~~~~Gld~~~~~~~~~~~~~~~~~~~~~~~a~~ 162 (193)
T PF01323_consen 127 AEIAEEAGLDPDEFDAALDSPEVKAALEEDTAEARQ 162 (193)
T ss_dssp HHHHHHTT--HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHcCCcHHHHHHHhcchHHHHHHHHHHHHHHH
Confidence 567888999999988877888888777777666654
No 49
>KOG1666 consensus V-SNARE [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.34 E-value=3.7e+02 Score=22.58 Aligned_cols=46 Identities=15% Similarity=0.261 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHHHHHchhhcCccCChHHHHHHHHHHHHHHHHHH
Q 036976 160 MKEQIKRARTFFNMAEEGASQLDKDSRWPVWSSLLIYREILDAIEE 205 (243)
Q Consensus 160 ~~~~~~~A~~~~~~a~~~~~~lp~~~~~~~~~~~~~~~~iL~~l~~ 205 (243)
++...+.|...+.+-.-.+..+|+..+..+..=..-|+.-|++++.
T Consensus 41 i~~~leEa~ell~qMdlEvr~lp~~~Rs~~~~KlR~yksdl~~l~~ 86 (220)
T KOG1666|consen 41 IDSKLEEANELLDQMDLEVRELPPNFRSSYLSKLREYKSDLKKLKR 86 (220)
T ss_pred HHHhHHHHHHHHHHHHHHHHhCCchhhhHHHHHHHHHHHHHHHHHH
Confidence 5777788888888888778889999988887777788877777654
Done!