Query 028137
Match_columns 213
No_of_seqs 225 out of 807
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 06:49:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028137.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028137hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01559 squal_synth farnesyl 100.0 7.6E-56 1.6E-60 403.1 16.9 164 1-167 173-336 (336)
2 KOG1459 Squalene synthetase [L 100.0 1.1E-49 2.3E-54 361.7 16.3 199 1-208 199-402 (413)
3 COG1562 ERG9 Phytoene/squalene 99.9 1.5E-25 3.3E-30 200.7 10.4 124 1-127 161-284 (288)
4 TIGR03465 HpnD squalene syntha 99.9 1.2E-24 2.7E-29 190.7 12.6 121 1-125 142-263 (266)
5 TIGR03464 HpnC squalene syntha 99.9 2.3E-24 4.9E-29 189.4 12.6 121 1-125 143-264 (266)
6 PLN02632 phytoene synthase 99.9 8.9E-24 1.9E-28 192.2 12.6 121 1-125 203-324 (334)
7 PF00494 SQS_PSY: Squalene/phy 99.9 8.6E-24 1.9E-28 183.6 10.5 114 1-117 150-267 (267)
8 cd00683 Trans_IPPS_HH Trans-Is 99.9 9.7E-24 2.1E-28 184.3 9.9 112 1-117 151-264 (265)
9 cd00385 Isoprenoid_Biosyn_C1 I 98.2 2E-06 4.3E-11 70.0 4.6 77 1-78 152-228 (243)
10 cd00867 Trans_IPPS Trans-Isopr 98.1 3.2E-06 6.9E-11 71.8 4.7 53 1-78 158-220 (236)
11 KOG4411 Phytoene/squalene synt 97.7 0.00028 6E-09 62.6 9.2 104 1-109 164-269 (292)
12 KOG1459 Squalene synthetase [L 95.7 0.011 2.3E-07 55.5 3.9 102 2-118 285-391 (413)
13 CHL00151 preA prenyl transfera 64.8 9.9 0.00022 34.6 4.4 77 1-80 207-305 (323)
14 PRK10581 geranyltranstransfera 50.8 28 0.00061 31.5 4.8 66 1-80 215-280 (299)
15 TIGR02749 prenyl_cyano solanes 45.7 34 0.00073 31.2 4.5 77 1-80 206-304 (322)
16 TIGR02609 doc_partner putative 43.2 67 0.0015 23.1 4.9 50 26-75 12-73 (74)
17 PLN02857 octaprenyl-diphosphat 42.0 38 0.00082 32.4 4.4 77 1-81 300-399 (416)
18 PRK02899 adaptor protein; Prov 39.2 38 0.00082 29.0 3.6 43 23-67 10-52 (197)
19 TIGR01439 lp_hng_hel_AbrB loop 34.7 25 0.00055 21.7 1.4 20 23-42 6-25 (43)
20 PF13990 YjcZ: YjcZ-like prote 33.4 44 0.00094 30.4 3.1 46 21-70 146-193 (270)
21 PLN02890 geranyl diphosphate s 31.4 71 0.0015 30.7 4.4 77 1-80 300-398 (422)
22 KOG0713 Molecular chaperone (D 29.3 93 0.002 29.2 4.6 58 125-185 27-84 (336)
23 PRK10888 octaprenyl diphosphat 27.9 1.6E+02 0.0035 26.8 6.0 77 1-81 203-306 (323)
24 PRK02315 adaptor protein; Prov 26.4 80 0.0017 27.7 3.5 42 23-66 10-51 (233)
25 PRK06246 fumarate hydratase; P 24.4 1.3E+02 0.0029 27.4 4.7 63 6-81 8-70 (280)
26 PF05961 Chordopox_A13L: Chord 22.6 1.2E+02 0.0025 22.2 3.1 22 190-211 7-28 (68)
27 COG2002 AbrB Regulators of sta 22.3 53 0.0012 24.3 1.4 22 23-44 13-34 (89)
28 KOG0811 SNARE protein PEP12/VA 22.2 1.8E+02 0.0038 26.5 4.9 56 126-187 187-245 (269)
29 cd00685 Trans_IPPS_HT Trans-Is 21.9 1.4E+02 0.003 25.9 4.2 64 1-81 181-244 (259)
30 TIGR00722 ttdA_fumA_fumB hydro 21.8 1.4E+02 0.003 27.2 4.2 61 8-81 2-62 (273)
31 PF12179 IKKbetaNEMObind: I-ka 20.9 63 0.0014 21.0 1.3 15 5-19 13-27 (38)
32 TIGR02748 GerC3_HepT heptapren 20.1 2.4E+02 0.0052 25.6 5.4 77 1-80 202-301 (319)
No 1
>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=7.6e-56 Score=403.07 Aligned_cols=164 Identities=64% Similarity=1.071 Sum_probs=162.4
Q ss_pred CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137 1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH 80 (213)
Q Consensus 1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~ 80 (213)
||+|||+|||||||+||++ +||+|||+|+|++||++.+|+.+|++++++.+|+++|+.+|+.||++|+.|++.++++
T Consensus 173 lG~aLQlTNIlRDv~ED~~---~GR~YlP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~~al~yl~~l~~~ 249 (336)
T TIGR01559 173 MGLFLQKTNIIRDYLEDIN---EGRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELVTNALHHATDCLTYLSRLRDQ 249 (336)
T ss_pred HHHHHHHHHHHHHHHhHHh---CCCCCCCHHHHHHcCCCHHHhcCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence 7999999999999999998 7999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhHHHHHHHHHHHHHHcCCCCCCCccccCHHHHHHHHHHhCChHHHHHHHHHHHHhhccccCCCCCCHHHHHHHH
Q 028137 81 AIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRV 160 (213)
Q Consensus 81 s~f~fcaip~~maiatL~~i~~n~~Vf~~rVKi~r~~~~~l~~~~~~~~~v~~~f~~~~~~i~~k~~~~dp~~~~~~~~~ 160 (213)
++|+||+||++||++||++|++|++||+++|||||++++++|++|+|+.+|+.+|++|+++|++|++|+||||.+|++.|
T Consensus 250 ~~~~fcaip~~mAi~TL~~~~~n~~~~~~~VKi~r~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~dp~~~~~~~~~ 329 (336)
T TIGR01559 250 SIFNFCAIPQVMAIATLALCYNNPQVFQGNVKIRKGTTVKLILDSTNMPAVYDIFYRYARKIYHKIDPNDPNFSKTLIII 329 (336)
T ss_pred chhHHHHHHHHHHHHHHHHHhcChhhcCCCceecHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHh
Q 028137 161 EAIQKAC 167 (213)
Q Consensus 161 ~~i~~~~ 167 (213)
++|+|+|
T Consensus 330 ~~~~~~~ 336 (336)
T TIGR01559 330 SKIEQQC 336 (336)
T ss_pred HHHHHhC
Confidence 9999997
No 2
>KOG1459 consensus Squalene synthetase [Lipid transport and metabolism]
Probab=100.00 E-value=1.1e-49 Score=361.71 Aligned_cols=199 Identities=51% Similarity=0.818 Sum_probs=186.7
Q ss_pred CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137 1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH 80 (213)
Q Consensus 1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~ 80 (213)
||+|||+|||||||.||.. .||.|||+|||++|..+++|+..|+|++.+++|+++|+++|+.|.++++.|++.++.+
T Consensus 199 ~glfLqktnIirdy~ed~~---d~r~Fwp~eIwg~y~d~L~d~~~~en~dl~l~Cln~m~tnaL~hv~d~l~yls~l~~q 275 (413)
T KOG1459|consen 199 MGLFLQKTNIIRDYLEDPV---DGRPFWPREIWGKYMDKLKDFRYPENDDLALQCLNEMVTNALMHVPDVLTYLSKLRTQ 275 (413)
T ss_pred cchHHHHhHHHHHHHhccc---cCCccChHHHHHHHHHHHHhhhCccchhHHHHHHHHHHHHHhhccHHHHHHHhhcccH
Confidence 7999999999999999999 6999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhHHHHHHHHHHHHHHcCCCCCCCccccCHHHHHHHHHHhCChHHHHHHHHHHHHhhccccCCCCCC-----HHH
Q 028137 81 AIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYDFSNILKPKINKNDPN-----ATK 155 (213)
Q Consensus 81 s~f~fcaip~~maiatL~~i~~n~~Vf~~rVKi~r~~~~~l~~~~~~~~~v~~~f~~~~~~i~~k~~~~dp~-----~~~ 155 (213)
|+|+||||||+||++||++|+||.+||+|+||||||.++.+|+.++|+.+|+.+|++|.++|+.|++++||| ..+
T Consensus 276 svfnfcaipqimai~Tlal~~nn~dvfrG~VklrkGl~~~~I~~~k~~~~v~~~f~~y~~~i~~k~d~~dpnflklsask 355 (413)
T KOG1459|consen 276 SVFNFCAIPQIMAIATLALCYNNEDVFRGNVKLRKGLAVELILASKTMDKVRNIFYMYLRDIRMKFDEADPNFLKLSASK 355 (413)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCHhHhccceeecCCchHHHHHhcccHHHHHHHHHHHHHHHHhhCCccCCCchhhhhhh
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999 667
Q ss_pred HHHHHHHHHHHhhhccccccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHhh
Q 028137 156 TLSRVEAIQKACMDSGVLNKRKSYIIQSELRYSSTMIVIFFIILAIIFSYLSS 208 (213)
Q Consensus 156 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 208 (213)
|.+..+++.+.|.+.+.++++..+..+ +..+.++++++|+.|+|...
T Consensus 356 ~~qv~esl~~~~~~~~il~n~~~~f~k------~~~v~~V~~i~al~~ay~~~ 402 (413)
T KOG1459|consen 356 TEQVWESLLLYRRPDEILANRYNNFTK------RIYVGFVKKIAALPLAYAKS 402 (413)
T ss_pred HHHHHHHHHHhhccccccccccccccc------hhHHHHHHHHHHHHHHHHHH
Confidence 777788888899999999988554211 56677889999999999854
No 3
>COG1562 ERG9 Phytoene/squalene synthetase [Lipid metabolism]
Probab=99.92 E-value=1.5e-25 Score=200.69 Aligned_cols=124 Identities=20% Similarity=0.161 Sum_probs=119.6
Q ss_pred CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137 1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH 80 (213)
Q Consensus 1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~ 80 (213)
||+|+|+||||||++||.. +||+|||+|+|++||++.+|+.++.+++.+..|+++++.+|+.|+.+|..+++.+|.+
T Consensus 161 lG~A~QlvNilRdv~eD~~---~GrvylP~e~l~~~g~~~~d~~~~~~~~~~~~~~~~~~~~ar~~~~~a~~~~~~lp~~ 237 (288)
T COG1562 161 LGLALQLVNILRDVGEDRR---RGRVYLPAEELARFGVSEADLLAGRVDDAFRELMRFEADRARDHLAEARRGLPALPGR 237 (288)
T ss_pred HHHHHHHHHHHHHhHHHHh---CCcccCCHHHHHHhCCCHHHHHcccchhHHHHHHHHHHHHHHHHHHHHHHhhhhCCcc
Confidence 6999999999999999999 8999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhHHHHHHHHHHHHHHcCCCCCCCccccCHHHHHHHHHHhCC
Q 028137 81 AIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNN 127 (213)
Q Consensus 81 s~f~fcaip~~maiatL~~i~~n~~Vf~~rVKi~r~~~~~l~~~~~~ 127 (213)
+.+.||++|+++++.+.++..++.+||+++++++++++++++.++..
T Consensus 238 ~~~~~~~~~~~~~~~~~~i~a~~~~vl~~~~~l~~~~~~~~~~~~~~ 284 (288)
T COG1562 238 AQLAVLAAALLYAYLLDAIEADPADVLSQRAVLPKLRKLWLLLKAWL 284 (288)
T ss_pred ccchhhHHHHHHHHHHHHHHccchhhhccCcccCcchHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999987753
No 4
>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=99.92 E-value=1.2e-24 Score=190.70 Aligned_cols=121 Identities=21% Similarity=0.167 Sum_probs=113.5
Q ss_pred CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137 1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH 80 (213)
Q Consensus 1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~ 80 (213)
+|.|||+||||||+.||++ +||+|||.|+|.+||++.+|+..+++++++..++++++.+|+.||.+|..++..+|..
T Consensus 142 lG~AlqltnilRdv~eD~~---~gR~ylP~~~l~~~gv~~~~l~~~~~~~~~~~~~~~l~~~A~~~l~~a~~~~~~~p~~ 218 (266)
T TIGR03465 142 LGRALQLTNILRDVGEDAR---RGRIYLPAEELQRFGVPAADILEGRYSPALAALCRFQAERARAHYAEADALLPACDRR 218 (266)
T ss_pred HHHHHHHHHHHHHhHHHHh---CCCeecCHHHHHHcCCCHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhCCHh
Confidence 6999999999999999999 8999999999999999999999999999999999999999999999999999999976
Q ss_pred hhhhhhhHHHHHHHHHHHHH-HcCCCCCCCccccCHHHHHHHHHHh
Q 028137 81 AIFRFCAIPQIMAIGTLALC-YNNIEVFRGVVKMRRGLTAKVIDRT 125 (213)
Q Consensus 81 s~f~fcaip~~maiatL~~i-~~n~~Vf~~rVKi~r~~~~~l~~~~ 125 (213)
+. .+|.++..++.++|..+ .+|++||++++++++.++.+++.++
T Consensus 219 ~~-~~~~~~~~~~~~iL~~i~~~~~~~~~~r~~~~~~~k~~~~~~~ 263 (266)
T TIGR03465 219 AQ-RAARAMAAIYRALLDEIEADGFQVLRQRVSLTPLRKLWIALRT 263 (266)
T ss_pred hh-HHHHHHHHHHHHHHHHHHHCCCCCCCCCCcCCHHHHHHHHHHH
Confidence 53 47888999999999988 5789999999999999999988765
No 5
>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=99.91 E-value=2.3e-24 Score=189.45 Aligned_cols=121 Identities=17% Similarity=0.083 Sum_probs=110.8
Q ss_pred CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137 1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH 80 (213)
Q Consensus 1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~ 80 (213)
+|.|||+|||+||++||++ +||+|||.|++.+||++.+|+..+..++++.+++.+++.+|+.||.+|..++..+|..
T Consensus 143 lG~AlQltniLRDl~eD~~---~gR~YLP~~~l~~~Gv~~edl~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~ 219 (266)
T TIGR03464 143 ICTALQLINFWQDVGVDYR---KGRVYLPRDDLARFGVSEEDLAAGRATPALRELMAFEVSRTRALLDRGAPLAARVDGR 219 (266)
T ss_pred HHHHHHHHHHHHhhHHHHh---cCCccCCHHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCCHh
Confidence 6999999999999999999 8999999999999999999999999999999999999999999999999999999876
Q ss_pred hhhhhhhHHHHHHHHHHHHH-HcCCCCCCCccccCHHHHHHHHHHh
Q 028137 81 AIFRFCAIPQIMAIGTLALC-YNNIEVFRGVVKMRRGLTAKVIDRT 125 (213)
Q Consensus 81 s~f~fcaip~~maiatL~~i-~~n~~Vf~~rVKi~r~~~~~l~~~~ 125 (213)
+. .++..+..++.++|..+ .++++||++++++++.++.+++.++
T Consensus 220 ~~-~~~~~~~~~y~~iL~~l~~~~~~~~~~r~~~~~~~kl~~~~~a 264 (266)
T TIGR03464 220 LG-LELALIVRGGLRILEKIERQGYDVLRERPKLGKFDWAGLLLRA 264 (266)
T ss_pred hh-HHHHHHHHHHHHHHHHHHHcCCCCCCCCCcCCHHHHHHHHHHH
Confidence 53 35566677777899888 5799999999999999999998764
No 6
>PLN02632 phytoene synthase
Probab=99.90 E-value=8.9e-24 Score=192.18 Aligned_cols=121 Identities=18% Similarity=0.146 Sum_probs=110.2
Q ss_pred CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137 1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH 80 (213)
Q Consensus 1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~ 80 (213)
||.|||+|||+||++||++ +||+|||.|+|.+||++.+|+..+.+++++.+++.+++.+|+.||.+|..++..+|..
T Consensus 203 lG~AlQltNILRDv~eD~~---~GRvYLP~e~L~~~Gv~~edl~~~~~~~~~~~l~~~~~~~Ar~~~~~a~~~l~~lp~~ 279 (334)
T PLN02632 203 LGIANQLTNILRDVGEDAR---RGRVYLPQDELAQFGLTDEDIFAGKVTDKWRAFMKFQIKRARMYFAEAEEGVSELDPA 279 (334)
T ss_pred HHHHHHHHHHHHHHHHHHh---CCceeCCHHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhHhhCCHH
Confidence 6999999999999999998 8999999999999999999999999999999999999999999999999999999987
Q ss_pred hhhhhhhHHHHHHHHHHHHH-HcCCCCCCCccccCHHHHHHHHHHh
Q 028137 81 AIFRFCAIPQIMAIGTLALC-YNNIEVFRGVVKMRRGLTAKVIDRT 125 (213)
Q Consensus 81 s~f~fcaip~~maiatL~~i-~~n~~Vf~~rVKi~r~~~~~l~~~~ 125 (213)
+. ..+.++..++-++|..+ .+|++||++|+.+++.++++++.++
T Consensus 280 ~r-~~v~~a~~~y~~iL~~i~~~~~~v~~~R~~l~~~~Kl~~~~~~ 324 (334)
T PLN02632 280 SR-WPVWASLLLYRQILDAIEANDYDNFTKRAYVGKWKKLLALPLA 324 (334)
T ss_pred hH-HHHHHHHHHHHHHHHHHHHcCCCcCCCCCccCHHHHHHHHHHH
Confidence 63 24456666666789888 6799999999999999999988655
No 7
>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=99.90 E-value=8.6e-24 Score=183.64 Aligned_cols=114 Identities=25% Similarity=0.296 Sum_probs=93.5
Q ss_pred CcchHHHHHhhhchHhh-hhcCCCCcccccHHHHHhhcCChhhhcccc-ccHHHHHHHHHHHHHHHHHHHHHHHhHHccc
Q 028137 1 MGLFLQKTNIIRDYLED-INEIPKCRMFWPREIWSKYVNKLEDLKYEE-NSDKAVQCLNDMVTNALMHVEDCLKYMSALR 78 (213)
Q Consensus 1 lGlaLQlTNILRDv~ED-~~e~p~GRiY~P~eil~k~g~~~~dl~~~~-~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~ 78 (213)
+|.|||+||||||++|| +. +||+|||.|+|.+||++++|+..+. .++++..++.+++.+|+.|+.+|..++..++
T Consensus 150 lG~alql~nilRd~~~D~~~---~gR~ylP~d~l~~~gv~~~dl~~~~~~~~~~~~~~~~~~~~A~~~l~~a~~~~~~l~ 226 (267)
T PF00494_consen 150 LGRALQLTNILRDIPEDALR---RGRIYLPLDDLRRFGVTPEDLLAGRPRSERLRALIRELAARARAHLDEARAGLSALP 226 (267)
T ss_dssp HHHHHHHHHHHHTHHHH-HH---TT---S-HHHHHHTTSSHHHHHHHG-GGHHHHHHHHHHHHHHHHHHHHHHHGGGGS-
T ss_pred HHHHHHHHHHHHHhHHHHHh---cccccCCchhHHHcCCCHHHHHhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 59999999999999999 78 7999999999999999999998876 7777999999999999999999999999996
Q ss_pred hhhhhhhhhHHHHHHHHHHHHH-HcCCC-CCCCccccCHHH
Q 028137 79 DHAIFRFCAIPQIMAIGTLALC-YNNIE-VFRGVVKMRRGL 117 (213)
Q Consensus 79 ~~s~f~fcaip~~maiatL~~i-~~n~~-Vf~~rVKi~r~~ 117 (213)
++..+.+|.+|..++.++|+.+ .+|++ ||++|++++|++
T Consensus 227 ~~~~~~~~~~~~~~~~~~l~~l~~~~~~~v~~~r~~~~~~r 267 (267)
T PF00494_consen 227 PPRARPAVAAAAALYRAILDKLERNGYDPVFQRRVKVSKWR 267 (267)
T ss_dssp -TTHHHHHHHHHHHHHHHHHHHHHTTT--GSSS-----HH-
T ss_pred CHhhhHHHHHHHHHHHHHHHHHHcCCCcccCCCCCcCCCCC
Confidence 6666778999999999999988 56888 899999999974
No 8
>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=99.90 E-value=9.7e-24 Score=184.35 Aligned_cols=112 Identities=31% Similarity=0.421 Sum_probs=103.4
Q ss_pred CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137 1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH 80 (213)
Q Consensus 1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~ 80 (213)
+|.|||+||||||++||++ +||+|||.|+|.+||++.+|+..+..++++.+++.+++..|+.||..|..++..+|..
T Consensus 151 lG~AlqltnilRdv~eD~~---~gR~YlP~d~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~ 227 (265)
T cd00683 151 LGLALQLTNILRDVGEDAR---RGRIYLPREELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAALPRR 227 (265)
T ss_pred HHHHHHHHHHHHHHHHHHc---cCCCcCCHHHHHHcCCCHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCCHh
Confidence 6999999999999999998 8999999999999999999999999999999999999999999999999999999976
Q ss_pred hhhhhhhHHHHHHHH-HHHHH-HcCCCCCCCccccCHHH
Q 028137 81 AIFRFCAIPQIMAIG-TLALC-YNNIEVFRGVVKMRRGL 117 (213)
Q Consensus 81 s~f~fcaip~~maia-tL~~i-~~n~~Vf~~rVKi~r~~ 117 (213)
+ ++|++|+++.+. +|..+ .+++++|++++.+++.+
T Consensus 228 ~--~~~~~~~~~~y~~il~~i~~~~~~~~~~r~~~~~~~ 264 (265)
T cd00683 228 S--RFCVRAAAMLYRTILDEIEARGYDVLSVRVRVPKAR 264 (265)
T ss_pred h--HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Confidence 5 689999999876 56677 57899999999888754
No 9
>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=98.18 E-value=2e-06 Score=69.98 Aligned_cols=77 Identities=23% Similarity=0.210 Sum_probs=66.3
Q ss_pred CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccc
Q 028137 1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALR 78 (213)
Q Consensus 1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~ 78 (213)
+|.++|++|.++|+..|.... .||+++|...+.+++.+.+++......+...++++.+...+..++.+..+....++
T Consensus 152 ~g~~~ql~nDl~~~~~e~~~~-~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~ 228 (243)
T cd00385 152 LGLAFQLTNDLLDYEGDAERG-EGKCTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKLAEEALKELNELILSLP 228 (243)
T ss_pred HHHHHHHHHHHHhccCCHHHh-CCchHHHHHHHHHhCChhhHHHHHHHCChHHHHHHHHHHHHHHHHHHHhcCCCCcH
Confidence 589999999999999999821 18999999999999999988888887888888888888888888888888777664
No 10
>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=98.12 E-value=3.2e-06 Score=71.79 Aligned_cols=53 Identities=19% Similarity=0.122 Sum_probs=41.2
Q ss_pred CcchHHHHHhhhchHhhh----------hcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHH
Q 028137 1 MGLFLQKTNIIRDYLEDI----------NEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDC 70 (213)
Q Consensus 1 lGlaLQlTNILRDv~ED~----------~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~a 70 (213)
+|+|+|++|++||+.+|. . .||+|||.+.+ .+.+...+..++..+
T Consensus 158 lG~a~Qi~dd~~D~~~d~~~~gk~~~D~~---~gr~tlp~~~~----------------------~~~~~~~~~~~~~~~ 212 (236)
T cd00867 158 LGLAFQLTDDLLDVFGDAEELGKVGSDLR---EGRITLPVILA----------------------RERAAEYAEEAYAAL 212 (236)
T ss_pred HHHHHHHHHHhccccCChHHHCccHHHHH---cCCchHHHHHH----------------------HHHHHHHHHHHHHHH
Confidence 699999999999999888 6 69999999977 445555666666666
Q ss_pred HHhHHccc
Q 028137 71 LKYMSALR 78 (213)
Q Consensus 71 l~yl~~l~ 78 (213)
..+....+
T Consensus 213 ~~~~~~~~ 220 (236)
T cd00867 213 EALPPSLP 220 (236)
T ss_pred HhCCCCch
Confidence 66655543
No 11
>KOG4411 consensus Phytoene/squalene synthetase [Lipid transport and metabolism]
Probab=97.67 E-value=0.00028 Score=62.57 Aligned_cols=104 Identities=15% Similarity=0.158 Sum_probs=83.8
Q ss_pred CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhh-ccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccch
Q 028137 1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDL-KYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRD 79 (213)
Q Consensus 1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl-~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~ 79 (213)
+|.|--+.|.||-..=-.. +|-.|+|.|+++.||++..|+ .+....++...|..+++..|-+|..+|.+....+|.
T Consensus 164 lGkA~gia~llrs~p~~~~---r~~~~iPadv~~lhGvtq~~il~~k~~~~g~~~~~fd~as~an~hL~~AR~l~~kVP~ 240 (292)
T KOG4411|consen 164 LGKAYGIANLLRSTPPLLA---RGIVLIPADVMSLHGVTQLDILYKKKKLDGMVGMTFDLASEANRHLIDARSLIEKVPK 240 (292)
T ss_pred HhHHHHHHHHHHhccHHHh---CCCccccHHHHHHcCCCHHHHHhhccchhhhhhHHHHHHHHHHHHHHHHHhHhhhCCH
Confidence 5888889999999999888 899999999999999999665 456667889999999999999999999999999988
Q ss_pred hhhhhhhhHHHHHHHHHHHHH-HcCCCCCCC
Q 028137 80 HAIFRFCAIPQIMAIGTLALC-YNNIEVFRG 109 (213)
Q Consensus 80 ~s~f~fcaip~~maiatL~~i-~~n~~Vf~~ 109 (213)
+. +......+---.+|+.+ .+|+++|+.
T Consensus 241 ~v--rp~ll~tv~td~~l~~l~k~nfdi~~p 269 (292)
T KOG4411|consen 241 AV--RPALLATVTTDYILKTLEKNNFDIYSP 269 (292)
T ss_pred HH--HHHHHHhhhHHHHHHHHHHccccccCH
Confidence 75 22222222223457666 689999985
No 12
>KOG1459 consensus Squalene synthetase [Lipid transport and metabolism]
Probab=95.73 E-value=0.011 Score=55.48 Aligned_cols=102 Identities=11% Similarity=-0.010 Sum_probs=74.1
Q ss_pred cchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchhh
Q 028137 2 GLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHA 81 (213)
Q Consensus 2 GlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~s 81 (213)
|.+=|.||+++|..||+- +||+++|+ |.+.+++....+.++....+-....++...++++....-.+.-.+
T Consensus 285 qimai~Tlal~~nn~dvf---rG~Vklrk------Gl~~~~I~~~k~~~~v~~~f~~y~~~i~~k~d~~dpnflklsask 355 (413)
T KOG1459|consen 285 QIMAIATLALCYNNEDVF---RGNVKLRK------GLAVELILASKTMDKVRNIFYMYLRDIRMKFDEADPNFLKLSASK 355 (413)
T ss_pred HHHHHHHHHHHhcCHhHh---ccceeecC------CchHHHHHhcccHHHHHHHHHHHHHHHHhhCCccCCCchhhhhhh
Confidence 566789999999999999 89999999 888899999999999999999999999888887766644443222
Q ss_pred hhhhhhHHHHHHH----HHHHHH-HcCCCCCCCccccCHHHH
Q 028137 82 IFRFCAIPQIMAI----GTLALC-YNNIEVFRGVVKMRRGLT 118 (213)
Q Consensus 82 ~f~fcaip~~mai----atL~~i-~~n~~Vf~~rVKi~r~~~ 118 (213)
+-++++- .....+ .|.++.|++++.+..-.+
T Consensus 356 ------~~qv~esl~~~~~~~~il~n~~~~f~k~~~v~~V~~ 391 (413)
T KOG1459|consen 356 ------TEQVWESLLLYRRPDEILANRYNNFTKRIYVGFVKK 391 (413)
T ss_pred ------HHHHHHHHHHhhccccccccccccccchhHHHHHHH
Confidence 1223322 223444 345577877666655443
No 13
>CHL00151 preA prenyl transferase; Reviewed
Probab=64.82 E-value=9.9 Score=34.62 Aligned_cols=77 Identities=18% Similarity=0.216 Sum_probs=43.0
Q ss_pred CcchHHHHHhhhch-----------HhhhhcCCCCcccccHHHHHhhcCChhh-hc----cccccHHHHHH------HHH
Q 028137 1 MGLFLQKTNIIRDY-----------LEDINEIPKCRMFWPREIWSKYVNKLED-LK----YEENSDKAVQC------LND 58 (213)
Q Consensus 1 lGlaLQlTNILRDv-----------~ED~~e~p~GRiY~P~eil~k~g~~~~d-l~----~~~~~~~~~~l------l~~ 58 (213)
+|+|+|+.+=+-|+ +.|+. .|..=||-=..-+....... +. .++.-..+++. +++
T Consensus 207 lG~aFQi~DDilD~~~~~~~~GK~~g~Dl~---eGk~Tlp~l~al~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~g~~~~ 283 (323)
T CHL00151 207 LGLAFQIIDDVLDITSSTESLGKPIGSDLK---NGNLTAPVLFALTQNSKLAKLIEREFCETKDISQALQIIKETNGIEK 283 (323)
T ss_pred HHHHHHHHHHHhhcccChhhhCCCchhhHh---cCchHHHHHHHHhcChHHHHHHHHhcCCHHHHHHHHHHHHHCCcHHH
Confidence 69999999877775 56777 47777773211110000000 00 11111112222 345
Q ss_pred HHHHHHHHHHHHHHhHHccchh
Q 028137 59 MVTNALMHVEDCLKYMSALRDH 80 (213)
Q Consensus 59 lv~~A~~h~~~al~yl~~l~~~ 80 (213)
.-..|.+|.++|++.+..+|..
T Consensus 284 a~~~a~~~~~~A~~~L~~lp~~ 305 (323)
T CHL00151 284 AKDLALEHMQAAIQCLKFLPPS 305 (323)
T ss_pred HHHHHHHHHHHHHHHHHhCCCC
Confidence 5566888889999999888754
No 14
>PRK10581 geranyltranstransferase; Provisional
Probab=50.79 E-value=28 Score=31.47 Aligned_cols=66 Identities=20% Similarity=0.202 Sum_probs=45.7
Q ss_pred CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137 1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH 80 (213)
Q Consensus 1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~ 80 (213)
+|+++|+.+=+.|+..|-+ .++|- .-+|+.++..+=..+..+++.-..|.+|+++|.+.+..++..
T Consensus 215 lG~aFQI~DDilD~~g~~~------------~~GK~--~g~Dl~~gk~T~p~l~~~e~a~~~a~~~~~~A~~~l~~l~~~ 280 (299)
T PRK10581 215 IGLAFQVQDDILDVVGDTA------------TLGKR--QGADQQLGKSTYPALLGLEQARKKARDLIDDARQSLDQLAAQ 280 (299)
T ss_pred HHHHHHHHHHHccccCChH------------HHCCC--cchhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCC
Confidence 5899998877777654433 24442 125666666655556667777788999999999999988753
No 15
>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=45.67 E-value=34 Score=31.23 Aligned_cols=77 Identities=21% Similarity=0.144 Sum_probs=40.8
Q ss_pred CcchHHHHHhhhc-----------hHhhhhcCCCCcccccHHHHHhhcCChhhhc-----cccccHHHHHH------HHH
Q 028137 1 MGLFLQKTNIIRD-----------YLEDINEIPKCRMFWPREIWSKYVNKLEDLK-----YEENSDKAVQC------LND 58 (213)
Q Consensus 1 lGlaLQlTNILRD-----------v~ED~~e~p~GRiY~P~eil~k~g~~~~dl~-----~~~~~~~~~~l------l~~ 58 (213)
+|+|+|+.+=+.| +++|+. .|.+=||-=..-+..-....+. .++.-+.+.+. ++.
T Consensus 206 lG~aFQi~DDild~~~~~~~~GK~~g~Dl~---~Gk~Tlp~l~al~~~~~~~~~l~~~~~~~~~~~~~~~~i~~~ga~~~ 282 (322)
T TIGR02749 206 LGLAFQVVDDILDFTGSTEQLGKPAGSDLM---KGNLTAPVLFALEEEPKLSELIEREFSQKGDLEQALSLVRKSGGIKK 282 (322)
T ss_pred HHHHHHHHHHhccCCCChHhhCCChhHHHh---CCCchHHHHHHHhcChHHHHHHHhccCCHHHHHHHHHHHHHCCHHHH
Confidence 5999999988877 467777 4766666422111100000110 11111122222 334
Q ss_pred HHHHHHHHHHHHHHhHHccchh
Q 028137 59 MVTNALMHVEDCLKYMSALRDH 80 (213)
Q Consensus 59 lv~~A~~h~~~al~yl~~l~~~ 80 (213)
.-..|.++.++|.+.+..+|+.
T Consensus 283 a~~~~~~~~~~A~~~L~~lp~~ 304 (322)
T TIGR02749 283 ARELAKEQAQLALQSLSFLPPS 304 (322)
T ss_pred HHHHHHHHHHHHHHHHHhCCCC
Confidence 4445677778888888877654
No 16
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=43.24 E-value=67 Score=23.07 Aligned_cols=50 Identities=16% Similarity=0.169 Sum_probs=35.7
Q ss_pred ccccHHHHHhhcCChhhhc-----------ccccc-HHHHHHHHHHHHHHHHHHHHHHHhHH
Q 028137 26 MFWPREIWSKYVNKLEDLK-----------YEENS-DKAVQCLNDMVTNALMHVEDCLKYMS 75 (213)
Q Consensus 26 iY~P~eil~k~g~~~~dl~-----------~~~~~-~~~~~ll~~lv~~A~~h~~~al~yl~ 75 (213)
+-+|++++.+.|+...|-. .+... +.+-.-+...++.+.+-|++++.-|+
T Consensus 12 vtIPk~i~~~lgl~~Gd~v~v~~~~~~iii~~~~~~~~~~~~~~~~~~~~~~~y~~~l~~La 73 (74)
T TIGR02609 12 VTLPKEVLESLGLKEGDTLYVDEEEGGLKLKRFDEGKELEKKMQMAVERAMSKYDEALKELA 73 (74)
T ss_pred EEECHHHHHHcCcCCCCEEEEEEECCEEEEEECCCCccHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5689999999998776532 12222 35556666688899999999988764
No 17
>PLN02857 octaprenyl-diphosphate synthase
Probab=42.03 E-value=38 Score=32.38 Aligned_cols=77 Identities=19% Similarity=0.233 Sum_probs=41.8
Q ss_pred CcchHHHHHhhhch-----------HhhhhcCCCCcccccHHH-HHhhcCChhhhc-----cccccHHHHHH------HH
Q 028137 1 MGLFLQKTNIIRDY-----------LEDINEIPKCRMFWPREI-WSKYVNKLEDLK-----YEENSDKAVQC------LN 57 (213)
Q Consensus 1 lGlaLQlTNILRDv-----------~ED~~e~p~GRiY~P~ei-l~k~g~~~~dl~-----~~~~~~~~~~l------l~ 57 (213)
+|+++|+.+=+.|+ ++|+. .|..=||-=. +++ .-...++. .++.-+.+++. ++
T Consensus 300 LGiAFQI~DDiLD~~~~~~~~GK~~g~DL~---eGK~TlPli~al~~-~~~l~~~l~~~~~~~~~~~~~~~lv~~~Ggie 375 (416)
T PLN02857 300 LGLAFQVVDDILDFTQSTEQLGKPAGSDLA---KGNLTAPVIFALEK-EPELREIIESEFCEEGSLEEAIELVNEGGGIE 375 (416)
T ss_pred HHHHHHHHHHHHhhcCCHHHhCCCcchhhh---cCCccHHHHHHHhc-ChHHHHHHhhccCCHHHHHHHHHHHHHcCHHH
Confidence 59999999877775 57777 4777666421 111 00001111 11111222222 23
Q ss_pred HHHHHHHHHHHHHHHhHHccchhh
Q 028137 58 DMVTNALMHVEDCLKYMSALRDHA 81 (213)
Q Consensus 58 ~lv~~A~~h~~~al~yl~~l~~~s 81 (213)
+-...|.++.+.|++.+..+|...
T Consensus 376 ~a~~~a~~~~~~A~~~L~~Lp~~~ 399 (416)
T PLN02857 376 RAQELAKEKADLAIQNLECLPRGA 399 (416)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCH
Confidence 334457778888888888887543
No 18
>PRK02899 adaptor protein; Provisional
Probab=39.17 E-value=38 Score=29.03 Aligned_cols=43 Identities=26% Similarity=0.220 Sum_probs=36.9
Q ss_pred CCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHH
Q 028137 23 KCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHV 67 (213)
Q Consensus 23 ~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~ 67 (213)
.=||++-.+.|...|.+..||.. +++++.+++.+|...|..-.
T Consensus 10 tIrv~it~~DL~eRgi~~~dL~~--n~~k~e~lF~~mm~Ea~~e~ 52 (197)
T PRK02899 10 KIKIFLTFDDLSERGLTKEDLWR--DAPKVHQLFRDMMQEANKEL 52 (197)
T ss_pred eEEEEEeHHHHHHcCCCHHHHhc--CcHHHHHHHHHHHHHhhhcc
Confidence 34899999999999999999986 56899999999999886533
No 19
>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=34.74 E-value=25 Score=21.74 Aligned_cols=20 Identities=35% Similarity=0.355 Sum_probs=17.0
Q ss_pred CCcccccHHHHHhhcCChhh
Q 028137 23 KCRMFWPREIWSKYVNKLED 42 (213)
Q Consensus 23 ~GRiY~P~eil~k~g~~~~d 42 (213)
.||+-+|.++....+.+..|
T Consensus 6 kgri~iP~~~r~~l~~~~gd 25 (43)
T TIGR01439 6 KGQIVIPKEIREKLGLKEGD 25 (43)
T ss_pred CCeEEecHHHHHHcCcCCCC
Confidence 59999999999999876554
No 20
>PF13990 YjcZ: YjcZ-like protein
Probab=33.44 E-value=44 Score=30.45 Aligned_cols=46 Identities=15% Similarity=0.196 Sum_probs=29.3
Q ss_pred CCCCcccccHHH--HHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHH
Q 028137 21 IPKCRMFWPREI--WSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDC 70 (213)
Q Consensus 21 ~p~GRiY~P~ei--l~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~a 70 (213)
.|.||||.--|. |+.||.- ..-.+.+....++..+...|-++..+.
T Consensus 146 S~agRcyvaLEeL~WGaFGd~----~Rl~~~~~~~~l~~~lr~~a~~~La~~ 193 (270)
T PF13990_consen 146 SPAGRCYVALEELRWGAFGDA----CRLGNPPVRTMLLDNLRDKATEQLAQD 193 (270)
T ss_pred CcchhHHHHHHHHhcchhHHH----HHcCChhHHHHHHHHHHHHHHHHHHHh
Confidence 367999998885 8888833 223344566666666666665555544
No 21
>PLN02890 geranyl diphosphate synthase
Probab=31.42 E-value=71 Score=30.66 Aligned_cols=77 Identities=18% Similarity=0.186 Sum_probs=42.3
Q ss_pred CcchHHHHHhhhchH-----------hhhhcCCCCcccccHHHHHhhcCChhhh-c----cccccHHHHH------HHHH
Q 028137 1 MGLFLQKTNIIRDYL-----------EDINEIPKCRMFWPREIWSKYVNKLEDL-K----YEENSDKAVQ------CLND 58 (213)
Q Consensus 1 lGlaLQlTNILRDv~-----------ED~~e~p~GRiY~P~eil~k~g~~~~dl-~----~~~~~~~~~~------ll~~ 58 (213)
+|+|+|+.+=+-|+. .|+. .|.+=||-=..-+.......+ . .++.-+.+++ .++.
T Consensus 300 lGlAFQI~DDiLD~~g~~~~~GK~~g~DL~---eGk~TlPvl~al~~~~~l~~~l~~~~~~~~~v~~~~~~i~~~gaie~ 376 (422)
T PLN02890 300 LGLAFQLIDDVLDFTGTSASLGKGSLSDIR---HGVITAPILFAMEEFPQLREVVDRGFDNPANVDIALEYLGKSRGIQR 376 (422)
T ss_pred HHHHHHHHHHHHhhcCChhhhCCCchhhHh---cCCccHHHHHHHhcCHHHHHHHhcccCCHHHHHHHHHHHHHcCHHHH
Confidence 599999998888873 6676 376656643211110000011 1 1111112222 2334
Q ss_pred HHHHHHHHHHHHHHhHHccchh
Q 028137 59 MVTNALMHVEDCLKYMSALRDH 80 (213)
Q Consensus 59 lv~~A~~h~~~al~yl~~l~~~ 80 (213)
--..|.+|.+.|.+.+..+|+.
T Consensus 377 a~~la~~~~~~A~~~L~~lp~s 398 (422)
T PLN02890 377 TRELAREHANLAAAAIESLPET 398 (422)
T ss_pred HHHHHHHHHHHHHHHHHhCCCC
Confidence 4455888888899998888754
No 22
>KOG0713 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=29.29 E-value=93 Score=29.22 Aligned_cols=58 Identities=24% Similarity=0.335 Sum_probs=44.1
Q ss_pred hCChHHHHHHHHHHHHhhccccCCCCCCHHHHHHHHHHHHHHhhhccccccccchhhhhhh
Q 028137 125 TNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYIIQSEL 185 (213)
Q Consensus 125 ~~~~~~v~~~f~~~~~~i~~k~~~~dp~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~ 185 (213)
.-|-+.++.+|++.|-+.|-=-+|+||++..--+.+...=..-.+ ..+|++|...++.
T Consensus 27 ~Asd~eIKkAYRKLALk~HPDkNpddp~A~e~F~~in~AYEVLsD---pekRk~YD~~GEe 84 (336)
T KOG0713|consen 27 NASDQEIKKAYRKLALKYHPDKNPDDPNANEKFKEINAAYEVLSD---PEKRKHYDTYGEE 84 (336)
T ss_pred CCCHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHHhcC---HHHHHHHHhhhHh
Confidence 357888999999999999998899999998877777665554433 3467777655544
No 23
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=27.90 E-value=1.6e+02 Score=26.85 Aligned_cols=77 Identities=16% Similarity=0.076 Sum_probs=43.3
Q ss_pred CcchHHHHHhhhch-----------HhhhhcCCCCcccccHHHHHhhcCChh------hhcc-ccccHHHHHH-------
Q 028137 1 MGLFLQKTNIIRDY-----------LEDINEIPKCRMFWPREIWSKYVNKLE------DLKY-EENSDKAVQC------- 55 (213)
Q Consensus 1 lGlaLQlTNILRDv-----------~ED~~e~p~GRiY~P~eil~k~g~~~~------dl~~-~~~~~~~~~l------- 55 (213)
+|+|+|+.+=+-|+ +.|+. .|.+=||-=..-+.+ +.+ .+.. +...+...++
T Consensus 203 lG~aFQi~DD~ld~~~~~~~~GK~~g~Dl~---~gk~Tlp~l~al~~~-~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~ 278 (323)
T PRK10888 203 LGTAFQLIDDLLDYSADGETLGKNVGDDLN---EGKPTLPLLHAMHHG-TPEQAAMIRTAIEQGNGRHLLEPVLEAMNAC 278 (323)
T ss_pred HHHHHHHHHHhhcccCChHhhCCCchhhhh---cCCchHHHHHHHHhC-CHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc
Confidence 59999999888776 67777 487777732211111 111 1111 1111111122
Q ss_pred --HHHHHHHHHHHHHHHHHhHHccchhh
Q 028137 56 --LNDMVTNALMHVEDCLKYMSALRDHA 81 (213)
Q Consensus 56 --l~~lv~~A~~h~~~al~yl~~l~~~s 81 (213)
++.-...|.+|.+.|.+.+..+|+..
T Consensus 279 g~~e~~~~~a~~~~~~A~~~L~~lp~~~ 306 (323)
T PRK10888 279 GSLEWTRQRAEEEADKAIAALQVLPDTP 306 (323)
T ss_pred ChHHHHHHHHHHHHHHHHHHHhcCCCCH
Confidence 33344557788888888888887643
No 24
>PRK02315 adaptor protein; Provisional
Probab=26.35 E-value=80 Score=27.66 Aligned_cols=42 Identities=19% Similarity=0.203 Sum_probs=36.2
Q ss_pred CCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHH
Q 028137 23 KCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMH 66 (213)
Q Consensus 23 ~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h 66 (213)
.=||++-.+.|...|.+..||.. |++++.+++.+|+..|..-
T Consensus 10 tIRv~it~~DL~eRGi~~~dL~~--n~~k~e~fF~~mm~Ea~~e 51 (233)
T PRK02315 10 TIKVFITYDDLEERGFEREDLLY--NREKIEEFFYSMMDEVDEE 51 (233)
T ss_pred eEEEEecHHHHHHcCCCHHHHhc--CcHHHHHHHHHHHHHhccc
Confidence 35899999999999999999984 6688999999999888553
No 25
>PRK06246 fumarate hydratase; Provisional
Probab=24.38 E-value=1.3e+02 Score=27.36 Aligned_cols=63 Identities=14% Similarity=0.197 Sum_probs=43.9
Q ss_pred HHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchhh
Q 028137 6 QKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHA 81 (213)
Q Consensus 6 QlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~s 81 (213)
.+++.++|...++. .+||.|..+... +..+.|.++-+...++.+++|+.---+ ..++..++.+
T Consensus 8 ~i~~~v~~~~~~a~------~~lp~Dv~~~l~----~a~~~E~s~~ak~~l~~ileN~~iA~~---~~~P~CQDTG 70 (280)
T PRK06246 8 DIIEAVAELCIEAN------YYLPDDVKEALK----KAYEKEESPIGKEILKAILENAEIAKE---EQVPLCQDTG 70 (280)
T ss_pred HHHHHHHHHHHHHH------hhCCHHHHHHHH----HHHHhccChhHHHHHHHHHHHHHHHhc---CCCccccCCC
Confidence 36667777777777 899999988753 455667778888899999988865333 3344444443
No 26
>PF05961 Chordopox_A13L: Chordopoxvirus A13L protein; InterPro: IPR009236 This family consists of A13L proteins from the Chordopoxviruses. A13L or p8 is one of the three most abundant membrane proteins of the intracellular mature Vaccinia virus [].
Probab=22.56 E-value=1.2e+02 Score=22.21 Aligned_cols=22 Identities=18% Similarity=0.351 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHHhhccC
Q 028137 190 TMIVIFFIILAIIFSYLSSTRA 211 (213)
Q Consensus 190 ~~~~~~~~~~~~~~~~~~~~~~ 211 (213)
++++|+.++.+|+++.+.+++.
T Consensus 7 Li~ICVaii~lIlY~iYnr~~~ 28 (68)
T PF05961_consen 7 LIIICVAIIGLILYGIYNRKKT 28 (68)
T ss_pred HHHHHHHHHHHHHHHHHhcccc
Confidence 4567888999999998877654
No 27
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=22.27 E-value=53 Score=24.32 Aligned_cols=22 Identities=27% Similarity=0.267 Sum_probs=19.4
Q ss_pred CCcccccHHHHHhhcCChhhhc
Q 028137 23 KCRMFWPREIWSKYVNKLEDLK 44 (213)
Q Consensus 23 ~GRiY~P~eil~k~g~~~~dl~ 44 (213)
.||+.+|.++-.++|.+..|..
T Consensus 13 ~GqIvIPkeiR~~lgi~~Gd~l 34 (89)
T COG2002 13 KGQIVIPKEIREALGIKEGDVL 34 (89)
T ss_pred CceEEecHHHHHHhCCCCCCEE
Confidence 5999999999999999887654
No 28
>KOG0811 consensus SNARE protein PEP12/VAM3/Syntaxin 7/Syntaxin 17 [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.19 E-value=1.8e+02 Score=26.47 Aligned_cols=56 Identities=18% Similarity=0.236 Sum_probs=32.8
Q ss_pred CChHHHHHHHHHHHHhhccccCCC---CCCHHHHHHHHHHHHHHhhhccccccccchhhhhhhhh
Q 028137 126 NNMTDVYLAFYDFSNILKPKINKN---DPNATKTLSRVEAIQKACMDSGVLNKRKSYIIQSELRY 187 (213)
Q Consensus 126 ~~~~~v~~~f~~~~~~i~~k~~~~---dp~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~ 187 (213)
.++.+|-.||.+++..+|..-..- +-|...++..+. +--+ -|.+...|.....+.+
T Consensus 187 ~dI~dvN~IFkdL~~lV~eQG~~VDsIe~nve~a~~nve---qg~~---~L~kA~~yq~~~~k~~ 245 (269)
T KOG0811|consen 187 ADIIDVNEIFKDLGSLVHEQGELVDSIEANVENASVNVE---QGTE---NLRKAAKYQRKARKKK 245 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhHHhHHHHHHHHHHHHHH---HHHH---HHHHHHHHHHHhcCch
Confidence 568899999999999999864332 233333332222 2211 2445555666666555
No 29
>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=21.86 E-value=1.4e+02 Score=25.87 Aligned_cols=64 Identities=23% Similarity=0.173 Sum_probs=39.1
Q ss_pred CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137 1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH 80 (213)
Q Consensus 1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~ 80 (213)
+|+++|+.|=+.|+..|-. .++|- ..+|+.++..+=-.+-++ -..+..|.+++...+..++.+
T Consensus 181 lG~afQi~DD~ld~~~~~~------------~~gK~--~~~Di~~gk~T~~~~~~l---~~~~~~~~~~a~~~l~~~~~~ 243 (259)
T cd00685 181 LGLAFQIQDDILDLFGDPE------------TLGKP--VGSDLREGKCTLPVLLAL---RELAREYEEKALEALKALPES 243 (259)
T ss_pred HHHHHHHHHHhhcccCChH------------HHCCC--cchHHHcCCchHHHHHHH---HHHHHHHHHHHHHHHHcCCCc
Confidence 5899998887776654432 12221 125666555443233222 567778888899999888765
Q ss_pred h
Q 028137 81 A 81 (213)
Q Consensus 81 s 81 (213)
+
T Consensus 244 ~ 244 (259)
T cd00685 244 P 244 (259)
T ss_pred H
Confidence 3
No 30
>TIGR00722 ttdA_fumA_fumB hydro-lyases, Fe-S type, tartrate/fumarate subfamily, alpha region. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase. This model represents a subset of closely related proteins or modules, including the E. coli tartrate dehydratase alpha chain and the N-terminal region of the class I fumarase (where the C-terminal region is homologous to the tartrate dehydratase beta chain). The activity of archaeal proteins in this subfamily has not been established.
Probab=21.84 E-value=1.4e+02 Score=27.18 Aligned_cols=61 Identities=13% Similarity=0.178 Sum_probs=43.2
Q ss_pred HHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchhh
Q 028137 8 TNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHA 81 (213)
Q Consensus 8 TNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~s 81 (213)
|+.++|...++. .+||.|+.... .+-.+.+.++-+.+.++.+++|+.---. ..++..++.+
T Consensus 2 ~~~v~~~~~~a~------~~lp~Dv~~al----~~a~~~E~s~~ak~~l~~ileN~~iA~~---~~~P~CQDTG 62 (273)
T TIGR00722 2 TEAVKEAIKEAV------TRLPEDVVDAI----KEAYDREESEIAKINLEAILDNIEIAEK---LGVPVCQDTG 62 (273)
T ss_pred HHHHHHHHHHHH------hhCCHHHHHHH----HHHHhhcCCHHHHHHHHHHHHHHHHHhc---CCCccccCCC
Confidence 566777777777 89999998875 3445667778888899999999875333 3344444443
No 31
>PF12179 IKKbetaNEMObind: I-kappa-kinase-beta NEMO binding domain; InterPro: IPR022007 This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with PF00069 from PFAM. These proteins are involved in inflammatory reactions. They cause release of NF-kappa-B into the nucleus of inflammatory cells and upregulation of transcription of proinflammatory cytokines. They perform this function by phosphorylating I-kappa-B proteins which are targeted for degradation to release NF-kappa-B. This kinase (I-kappa-kinase-beta) is found in association with IKK-alpha and NEMO (NF-kappa-B essential modulator). This domain is the binding site of IKK-beta for NEMO. ; GO: 0008384 IkappaB kinase activity; PDB: 3BRT_C 3BRV_C.
Probab=20.89 E-value=63 Score=21.03 Aligned_cols=15 Identities=13% Similarity=0.355 Sum_probs=12.4
Q ss_pred HHHHHhhhchHhhhh
Q 028137 5 LQKTNIIRDYLEDIN 19 (213)
Q Consensus 5 LQlTNILRDv~ED~~ 19 (213)
=|+||+++|..++-+
T Consensus 13 sqL~s~mqdt~~Eq~ 27 (38)
T PF12179_consen 13 SQLESLMQDTMKEQD 27 (38)
T ss_dssp HHHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHHhc
Confidence 499999999887654
No 32
>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=20.08 E-value=2.4e+02 Score=25.59 Aligned_cols=77 Identities=16% Similarity=0.161 Sum_probs=40.5
Q ss_pred CcchHHHHHhhhchH-----------hhhhcCCCCcccccHHHHHhhcCC---hhhhccccccHH---HHHHH------H
Q 028137 1 MGLFLQKTNIIRDYL-----------EDINEIPKCRMFWPREIWSKYVNK---LEDLKYEENSDK---AVQCL------N 57 (213)
Q Consensus 1 lGlaLQlTNILRDv~-----------ED~~e~p~GRiY~P~eil~k~g~~---~~dl~~~~~~~~---~~~ll------~ 57 (213)
+|+++|+.|=+.|+. .|+. .|..=||-=..-+.... ...+......+. +.+.+ +
T Consensus 202 lG~aFQI~DDilD~~~~~~~~GK~~~~Dl~---~gk~Tlp~l~al~~~~~~~~l~~~~~~~~~~~~~~~~~~i~~~g~~~ 278 (319)
T TIGR02748 202 VGMSYQITDDILDFVGTEEELGKPAGGDLL---QGNVTLPVLYAMEDPFLKKRIEQVLEETTAEEMEPLIEEVKKSDAIE 278 (319)
T ss_pred HHHHHHHHHHHHHccCCHHhhCCChhhHHh---CCCchHHHHHHhcCcchhHHHHHHHcCCCHHHHHHHHHHHHHcCcHH
Confidence 599999999888874 6676 47666664322211000 001111111111 22222 2
Q ss_pred HHHHHHHHHHHHHHHhHHccchh
Q 028137 58 DMVTNALMHVEDCLKYMSALRDH 80 (213)
Q Consensus 58 ~lv~~A~~h~~~al~yl~~l~~~ 80 (213)
.-...|.++.+.|++.+..+|..
T Consensus 279 ~a~~~a~~~~~~A~~~L~~lp~~ 301 (319)
T TIGR02748 279 YAYAVSDRYLKKALELLDGLPDG 301 (319)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCC
Confidence 23344677778888888887653
Done!