Query 041900
Match_columns 101
No_of_seqs 123 out of 688
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 11:52:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041900.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041900hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02279 ent-kaur-16-ene synth 99.9 1.9E-27 4.1E-32 194.7 9.4 97 3-101 584-680 (784)
2 cd00684 Terpene_cyclase_plant_ 99.9 5.1E-27 1.1E-31 186.2 9.3 100 2-101 348-447 (542)
3 cd00868 Terpene_cyclase_C1 Ter 99.7 3.3E-17 7E-22 118.8 8.9 95 7-101 119-213 (284)
4 PF03936 Terpene_synth_C: Terp 99.7 3.3E-17 7.1E-22 118.1 7.1 91 10-100 137-227 (270)
5 cd00687 Terpene_cyclase_nonpla 99.7 1E-16 2.2E-21 118.2 7.0 91 10-101 129-219 (303)
6 PLN02592 ent-copalyl diphospha 99.2 4.5E-11 9.7E-16 98.9 6.4 76 3-101 645-721 (800)
7 cd00385 Isoprenoid_Biosyn_C1 I 98.9 2.3E-09 4.9E-14 74.0 6.4 88 10-101 79-166 (243)
8 cd00867 Trans_IPPS Trans-Isopr 95.0 0.3 6.5E-06 34.5 8.5 85 11-100 86-171 (236)
9 cd00685 Trans_IPPS_HT Trans-Is 89.7 3.7 8E-05 29.8 8.2 87 10-100 108-194 (259)
10 TIGR02749 prenyl_cyano solanes 87.0 7 0.00015 29.6 8.5 87 10-100 133-219 (322)
11 PLN02890 geranyl diphosphate s 86.2 5.8 0.00013 31.5 7.9 87 10-100 227-313 (422)
12 TIGR02748 GerC3_HepT heptapren 82.3 12 0.00025 28.3 7.8 86 10-100 129-215 (319)
13 COG0142 IspA Geranylgeranyl py 81.7 13 0.00029 28.1 8.0 85 11-100 135-219 (322)
14 PRK10888 octaprenyl diphosphat 78.3 24 0.00052 26.8 8.4 85 11-100 131-216 (323)
15 PLN02857 octaprenyl-diphosphat 77.4 17 0.00037 28.8 7.5 87 10-100 227-313 (416)
16 COG2443 Sss1 Preprotein transl 71.4 10 0.00023 22.4 3.9 22 36-57 25-46 (65)
17 CHL00151 preA prenyl transfera 63.5 62 0.0013 24.4 8.2 85 11-100 135-220 (323)
18 PF00348 polyprenyl_synt: Poly 56.9 72 0.0016 23.0 7.9 76 21-99 114-190 (260)
19 PRK09400 secE preprotein trans 56.2 34 0.00074 19.8 4.1 20 36-55 24-43 (61)
20 PF14162 YozD: YozD-like prote 49.6 46 0.001 18.9 3.8 33 21-55 12-44 (57)
21 COG0864 NikR Predicted transcr 42.5 29 0.00063 23.3 2.7 27 6-36 26-52 (136)
22 PRK14744 leu operon leader pep 42.4 11 0.00023 18.5 0.4 18 81-98 10-27 (28)
23 PF13337 Lon_2: Putative ATP-d 41.5 6.4 0.00014 31.6 -0.7 57 34-93 275-340 (457)
24 PHA02046 hypothetical protein 40.4 28 0.0006 22.2 2.1 21 20-40 15-35 (99)
25 PF02186 TFIIE_beta: TFIIE bet 37.9 18 0.00039 21.2 1.0 15 69-83 34-48 (65)
26 cd00923 Cyt_c_Oxidase_Va Cytoc 37.8 21 0.00046 23.0 1.3 19 81-99 42-60 (103)
27 KOG4077 Cytochrome c oxidase, 36.4 21 0.00046 24.3 1.2 20 80-99 83-102 (149)
28 PF05772 NinB: NinB protein; 35.4 18 0.00038 24.1 0.7 40 13-52 60-100 (127)
29 TIGR00327 secE_euk_arch protei 34.5 53 0.0011 19.1 2.6 21 36-56 20-40 (61)
30 cd00683 Trans_IPPS_HH Trans-Is 33.5 1.8E+02 0.004 20.9 6.7 45 17-64 93-137 (265)
31 PRK10581 geranyltranstransfera 32.4 2E+02 0.0044 21.5 6.1 75 20-100 152-228 (299)
32 PF02284 COX5A: Cytochrome c o 31.7 28 0.00061 22.6 1.2 19 81-99 45-63 (108)
33 KOG1774 Small nuclear ribonucl 31.2 17 0.00037 22.5 0.1 18 32-49 37-54 (88)
34 PF02236 Viral_DNA_bi: Viral D 29.7 1.4E+02 0.0031 18.5 4.8 30 17-49 35-64 (86)
35 PF00494 SQS_PSY: Squalene/phy 29.5 2.1E+02 0.0046 20.4 6.9 48 16-66 90-137 (267)
36 PF00584 SecE: SecE/Sec61-gamm 28.7 55 0.0012 18.1 2.0 27 38-64 18-44 (57)
37 PF09435 DUF2015: Fungal prote 27.9 86 0.0019 21.0 3.0 46 12-57 19-70 (128)
38 PRK14562 haloacid dehalogenase 27.8 2.2E+02 0.0048 20.2 5.4 28 15-43 79-106 (204)
39 TIGR03760 ICE_TraI_Pfluor inte 27.3 48 0.001 23.9 1.9 22 65-86 166-187 (218)
40 PF08843 DUF1814: Nucleotidyl 26.6 87 0.0019 21.3 3.1 30 16-47 204-233 (233)
41 PLN00179 acyl- [acyl-carrier p 26.1 68 0.0015 25.4 2.6 61 12-74 65-133 (390)
42 PF13224 DUF4032: Domain of un 25.6 12 0.00027 26.0 -1.3 12 90-101 78-89 (165)
43 KOG0777 Geranylgeranyl pyropho 23.8 1E+02 0.0022 23.2 3.1 82 10-98 121-202 (322)
44 PF07914 DUF1679: Protein of u 23.7 3.7E+02 0.008 21.2 6.9 78 16-98 324-407 (414)
45 PF14502 HTH_41: Helix-turn-he 23.6 1.1E+02 0.0024 17.0 2.5 26 35-60 3-28 (48)
46 PF08054 Leu_leader: Leucine o 22.3 49 0.0011 16.3 0.8 18 82-99 11-28 (28)
47 PF07514 TraI_2: Putative heli 22.3 97 0.0021 23.6 2.8 25 62-86 172-197 (327)
48 PF11732 Thoc2: Transcription- 22.2 69 0.0015 19.5 1.7 27 72-98 15-41 (77)
49 PF13926 DUF4211: Domain of un 21.3 1.5E+02 0.0033 19.7 3.4 71 11-83 32-106 (153)
50 COG1049 AcnB Aconitase B [Ener 21.2 55 0.0012 27.8 1.4 14 35-48 808-821 (852)
51 cd08574 GDPD_GDE_2_3_6 Glycero 20.1 69 0.0015 23.1 1.6 18 32-49 107-124 (252)
52 PF03389 MobA_MobL: MobA/MobL 20.0 1.1E+02 0.0025 21.7 2.7 23 10-32 162-184 (216)
No 1
>PLN02279 ent-kaur-16-ene synthase
Probab=99.94 E-value=1.9e-27 Score=194.71 Aligned_cols=97 Identities=27% Similarity=0.320 Sum_probs=92.7
Q ss_pred hhhhCCccHHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHhcCCCcchhhhhhccCCcH
Q 041900 3 LASQGKLYRLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVGMGDIVTKESFEWLFSNPR 82 (101)
Q Consensus 3 ~~~~~~~~~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~~~~e~~~w~~~~p~ 82 (101)
+.+||+ ++++|+|++|++++++|++||+|+++||+||+||||+||.+|+|++++++++++++|+.+|+|+++| .++|+
T Consensus 584 ~~~qGr-~v~~~l~~aW~~ll~ayl~EAeW~~~g~vPT~eEYL~na~vS~~l~~i~l~~~~~~G~~l~eev~e~-~~~~~ 661 (784)
T PLN02279 584 FTWQGR-NVTSHIIKIWLDLLKSMLTEAQWSSNKSTPTLDEYMTNAYVSFALGPIVLPALYLVGPKLSEEVVDS-PELHK 661 (784)
T ss_pred HHHcCc-hHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhhchhhhhhHHHHHHHHHHhCCCCCHHHHhC-cchhH
Confidence 346777 9999999999999999999999999999999999999999999999999999999999999999999 69999
Q ss_pred HHHHHHHHHHHhcccccCC
Q 041900 83 SVRASSAVNRLMNDIMSHK 101 (101)
Q Consensus 83 i~~~~~~i~RL~nDi~s~~ 101 (101)
|+++++.|+||+|||+||+
T Consensus 662 L~~l~s~I~RLlNDI~S~e 680 (784)
T PLN02279 662 LYKLMSTCGRLLNDIRGFK 680 (784)
T ss_pred HHHHHHHHHHHHHhccccH
Confidence 9999999999999999985
No 2
>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=99.94 E-value=5.1e-27 Score=186.20 Aligned_cols=100 Identities=55% Similarity=0.867 Sum_probs=95.7
Q ss_pred hhhhhCCccHHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHhcCCCcchhhhhhccCCc
Q 041900 2 DLASQGKLYRLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVGMGDIVTKESFEWLFSNP 81 (101)
Q Consensus 2 ~~~~~~~~~~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~~~~e~~~w~~~~p 81 (101)
++.++++.+.+.|++++|++++++|++||+|+++||+||++|||+++.+|+|+++++++++++||+.+|+++++|+..+|
T Consensus 348 ~~~~~~~~~~~~~~~~~~~~~~~a~l~EA~w~~~g~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~l~~e~~e~~~~~~ 427 (542)
T cd00684 348 ELLKEGGSYVVPYLKEAWKDLVKAYLVEAKWAHEGYVPTFEEYMENALVSIGLGPLLLTSFLGMGDILTEEAFEWLESRP 427 (542)
T ss_pred HHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhhhhHHhhHHHHHHHHHHhcCCCCCHHHHHHHhccH
Confidence 45677777999999999999999999999999999999999999999999999999999999999999999999998889
Q ss_pred HHHHHHHHHHHHhcccccCC
Q 041900 82 RSVRASSAVNRLMNDIMSHK 101 (101)
Q Consensus 82 ~i~~~~~~i~RL~nDi~s~~ 101 (101)
+|+++++.|+||+|||+||+
T Consensus 428 ~l~~~~~~i~rL~NDi~S~~ 447 (542)
T cd00684 428 KLVRASSTIGRLMNDIATYE 447 (542)
T ss_pred HHHHHHHHHHHHhcChhhhH
Confidence 99999999999999999985
No 3
>cd00868 Terpene_cyclase_C1 Terpene cyclases, Class 1. Terpene cyclases, Class 1 (C1) of the class 1 family of isoprenoid biosynthesis enzymes, which share the 'isoprenoid synthase fold' and convert linear, all-trans, isoprenoids, geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate into numerous cyclic forms of monoterpenes, diterpenes, and sesquiterpenes. Also included in this CD are the cis-trans terpene cyclases such as trichodiene synthase. The class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational ch
Probab=99.72 E-value=3.3e-17 Score=118.84 Aligned_cols=95 Identities=49% Similarity=0.837 Sum_probs=87.7
Q ss_pred CCccHHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHhcCCCcchhhhhhccCCcHHHHH
Q 041900 7 GKLYRLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVGMGDIVTKESFEWLFSNPRSVRA 86 (101)
Q Consensus 7 ~~~~~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~~~~e~~~w~~~~p~i~~~ 86 (101)
++......+++.|.+++++++.|++|+..|++||++||+.++..|+|.++.+....+++|..+|++.+.+....++++++
T Consensus 119 ~~~~~~~r~~~~~~~~~~~~~~e~~~~~~~~~p~~~eYl~~R~~~~g~~~~~~l~~~~~g~~l~~~~~~~~~~~~~l~~~ 198 (284)
T cd00868 119 GGSESLPYLKEAWKDLLRAYLVEAKWANEGYVPSFEEYLENRRVSIGYPPLLALSFLGMGDILPEEAFEWLPSYPKLVRA 198 (284)
T ss_pred cCchHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHhceehhhHHHHHHHHHHHcCCCCCHHHHHHhhhhHHHHHH
Confidence 34367889999999999999999999999999999999999999999999999999999999998666666899999999
Q ss_pred HHHHHHHhcccccCC
Q 041900 87 SSAVNRLMNDIMSHK 101 (101)
Q Consensus 87 ~~~i~RL~nDi~s~~ 101 (101)
++.+++|+||+.||+
T Consensus 199 ~~~~~~l~NDl~S~~ 213 (284)
T cd00868 199 SSTIGRLLNDIASYE 213 (284)
T ss_pred HHHHHHHhccchHHH
Confidence 999999999999974
No 4
>PF03936 Terpene_synth_C: Terpene synthase family, metal binding domain; InterPro: IPR005630 Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C10) synthases, sesquiterpene (C15) synthases and the diterpene (C20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf []. Tpsa includes vetispiridiene synthase Q39979 from SWISSPROT, 5-epi- aristolochene synthase, Q40577 from SWISSPROT and (+)-delta-cadinene synthase P93665 from SWISSPROT . Tpsb includes (-)-limonene synthase, Q40322 from SWISSPROT. Tpsc includes copalyl diphosphate synthase (kaurene synthase A), O04408 from SWISSPROT. Tpsd includes taxadiene synthase, Q41594 from SWISSPROT, pinene synthase, O24475 from SWISSPROT and myrcene synthase, O24474 from SWISSPROT. Tpse includes ent-kaurene synthase B Q39548 from SWISSPROT. Tpsf includes linalool synthase Q9ZPN5 from SWISSPROT. In the fungus Phaeosphaeria sp. (strain L487) the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein [].; GO: 0000287 magnesium ion binding, 0016829 lyase activity; PDB: 3PYB_A 3PYA_A 3G4F_A 3G4D_B 3CKE_A 2OA6_D 2E4O_B 3BNY_B 3BNX_A 3LG5_A ....
Probab=99.70 E-value=3.3e-17 Score=118.06 Aligned_cols=91 Identities=21% Similarity=0.320 Sum_probs=83.0
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHhcCCCcchhhhhhccCCcHHHHHHHH
Q 041900 10 YRLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVGMGDIVTKESFEWLFSNPRSVRASSA 89 (101)
Q Consensus 10 ~~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~~~~e~~~w~~~~p~i~~~~~~ 89 (101)
+..+++++.|.++++++++|++|+..|++||++||++++..|+|.++++....++||...+++..+++.+.|.+.++++.
T Consensus 137 ~~~~~~~~~~~~~~~~~~~e~~~~~~~~~ps~eeYl~~R~~t~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 216 (270)
T PF03936_consen 137 DQIKRFRNSWREYLNAYLWEARWRERGRIPSLEEYLEMRRHTSGVYPCLALIEFALEFALGELPPEVLEHPPMLRRLAAD 216 (270)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTTS--SHHHHHHHHHHHTSHHHHHHHHHHHCSSCHTHHHHHHHHTTHHHHHHHHH
T ss_pred HHhhHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHhccccccccHHHHHHHHhCCCccccccHHHHHhchHHHHHHHH
Confidence 35678999999999999999999999999999999999999999999999999999877788888888888899999999
Q ss_pred HHHHhcccccC
Q 041900 90 VNRLMNDIMSH 100 (101)
Q Consensus 90 i~RL~nDi~s~ 100 (101)
+++|.|||.||
T Consensus 217 ~~~l~NDl~S~ 227 (270)
T PF03936_consen 217 IIRLVNDLYSY 227 (270)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHhcccchh
Confidence 99999999987
No 5
>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=99.68 E-value=1e-16 Score=118.18 Aligned_cols=91 Identities=19% Similarity=0.070 Sum_probs=83.3
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHhcCCCcchhhhhhccCCcHHHHHHHH
Q 041900 10 YRLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVGMGDIVTKESFEWLFSNPRSVRASSA 89 (101)
Q Consensus 10 ~~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~~~~e~~~w~~~~p~i~~~~~~ 89 (101)
.-.+++++.|.+++.+++.|++|+.++++||++||++++..|+|..+++....+++|..+|+++.+. ....++.++++.
T Consensus 129 ~~~~r~~~~~~~~~~a~~~e~~~~~~~~~psl~eYl~~R~~~~g~~~~~~l~~~~~g~~lp~~~~~~-~~~~~l~~~~~~ 207 (303)
T cd00687 129 EWFNRFAHYTEDYFDAYIWEGKNRLNGHVPDVAEYLEMRRFNIGADPCLGLSEFIGGPEVPAAVRLD-PVMRALEALASD 207 (303)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhhhcccccccHHHHHHhcCCCCCHHHHhC-hHHHHHHHHHHH
Confidence 3468899999999999999999999999999999999999999999999999999999999988776 445669999999
Q ss_pred HHHHhcccccCC
Q 041900 90 VNRLMNDIMSHK 101 (101)
Q Consensus 90 i~RL~nDi~s~~ 101 (101)
+++|+|||.||+
T Consensus 208 ~~~l~NDl~S~~ 219 (303)
T cd00687 208 AIALVNDIYSYE 219 (303)
T ss_pred HHHHHHHHHhhH
Confidence 999999999984
No 6
>PLN02592 ent-copalyl diphosphate synthase
Probab=99.17 E-value=4.5e-11 Score=98.93 Aligned_cols=76 Identities=17% Similarity=0.214 Sum_probs=63.8
Q ss_pred hhhhCCccHHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHH-hcCCCcchhhhhhccCCc
Q 041900 3 LASQGKLYRLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFV-GMGDIVTKESFEWLFSNP 81 (101)
Q Consensus 3 ~~~~~~~~~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~-~~g~~~~~e~~~w~~~~p 81 (101)
+..||+ ++++|++++|.++|+ +|.++|+ +|+|.+.+++++++ .+|+.+++|+++ +|
T Consensus 645 ~~~qGr-~v~~~L~~~W~~l~~------~w~~~g~------------~s~~~~~ilv~~~~l~~g~~lsee~l~----~~ 701 (800)
T PLN02592 645 LEAHGR-DISHLLRHAWEMWLL------KWLLEGD------------GRQGEAELLVKTINLTAGRSLSEELLA----HP 701 (800)
T ss_pred HHHhCc-cHHHHHHHHHHHHHH------HHHhcCc------------eeccchhhHHHHHHHhcCCCCCHHHcc----ch
Confidence 345666 999999999999999 6666665 45577777888888 559999999997 59
Q ss_pred HHHHHHHHHHHHhcccccCC
Q 041900 82 RSVRASSAVNRLMNDIMSHK 101 (101)
Q Consensus 82 ~i~~~~~~i~RL~nDi~s~~ 101 (101)
++.++++.+.||+||++|++
T Consensus 702 ~~~~l~~li~Rl~nDl~t~~ 721 (800)
T PLN02592 702 QYEQLAQLTNRICYQLGHYK 721 (800)
T ss_pred hHHHHHHHHHHHHHhhhHHh
Confidence 99999999999999999974
No 7
>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=98.95 E-value=2.3e-09 Score=74.00 Aligned_cols=88 Identities=25% Similarity=0.395 Sum_probs=71.5
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHhcCCCcchhhhhhccCCcHHHHHHHH
Q 041900 10 YRLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVGMGDIVTKESFEWLFSNPRSVRASSA 89 (101)
Q Consensus 10 ~~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~~~~e~~~w~~~~p~i~~~~~~ 89 (101)
.....+++.|.+++.++..|+.|..+ +.||++||+..+..++ +.++...+..+++...++ ..+.....++.+..+.
T Consensus 79 ~~~~~~~~~~~~~~~g~~~d~~~~~~-~~~t~~ey~~~~~~~t-~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~g~ 154 (243)
T cd00385 79 EALEILAEALLDLLEGQLLDLKWRRE-YVPTLEEYLEYCRYKT-AGLVGALCLLGAGLSGGE--AELLEALRKLGRALGL 154 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHHhH-HHHHHHHHHHHHHHhCCC--HHHHHHHHHHHHHHHH
Confidence 34778899999999999999999877 8999999999999998 444555556666655554 4554666788899999
Q ss_pred HHHHhcccccCC
Q 041900 90 VNRLMNDIMSHK 101 (101)
Q Consensus 90 i~RL~nDi~s~~ 101 (101)
+.+|.||+.++.
T Consensus 155 ~~ql~nDl~~~~ 166 (243)
T cd00385 155 AFQLTNDLLDYE 166 (243)
T ss_pred HHHHHHHHHhcc
Confidence 999999998873
No 8
>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates
Probab=94.98 E-value=0.3 Score=34.48 Aligned_cols=85 Identities=21% Similarity=0.230 Sum_probs=58.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhh-hcchhhHHHHHHHhcCCCcchhhhhhccCCcHHHHHHHH
Q 041900 11 RLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALV-TSACPILSTISFVGMGDIVTKESFEWLFSNPRSVRASSA 89 (101)
Q Consensus 11 ~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~-S~g~~~~~~~~~~~~g~~~~~e~~~w~~~~p~i~~~~~~ 89 (101)
....+.+...+++.+...+..|..+ ..||+++|++...- |.+.....+......+.. +++..+.+ .++.+..++
T Consensus 86 ~~~~~~~~~~~~~~Gq~~Dl~~~~~-~~~t~~~y~~~~~~Kta~l~~~~~~~~~~~~~~-~~~~~~~~---~~~~~~lG~ 160 (236)
T cd00867 86 ALELFAEALRELLEGQALDLEFERD-TYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGA-DDEQAEAL---KDYGRALGL 160 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHhccHHHHHHHHHHHHHHcCc-CHHHHHHH---HHHHHHHHH
Confidence 4566778889999999999999654 57899999999887 665554433333322322 22223222 457788999
Q ss_pred HHHHhcccccC
Q 041900 90 VNRLMNDIMSH 100 (101)
Q Consensus 90 i~RL~nDi~s~ 100 (101)
..-+.||+..+
T Consensus 161 a~Qi~dd~~D~ 171 (236)
T cd00867 161 AFQLTDDLLDV 171 (236)
T ss_pred HHHHHHHhccc
Confidence 99999998754
No 9
>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=89.69 E-value=3.7 Score=29.78 Aligned_cols=87 Identities=20% Similarity=0.130 Sum_probs=57.2
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHhcCCCcchhhhhhccCCcHHHHHHHH
Q 041900 10 YRLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVGMGDIVTKESFEWLFSNPRSVRASSA 89 (101)
Q Consensus 10 ~~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~~~~e~~~w~~~~p~i~~~~~~ 89 (101)
..+..+-+...+++.+-..+..|... ..||.++|++...--+|.....++...++--..+++..+-+ -++-+..++
T Consensus 108 ~~~~~~~~~~~~~~~GQ~~d~~~~~~-~~~~~~~y~~~~~~KT~~l~~~~~~~~a~l~~~~~~~~~~l---~~~g~~lG~ 183 (259)
T cd00685 108 RALELFSEAILELVEGQLLDLLSEYD-TDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEAL---KRFGRNLGL 183 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCC-CCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHHH---HHHHHHHHH
Confidence 34666777888999999999999654 57999999999877777654433322221111123333222 447788888
Q ss_pred HHHHhcccccC
Q 041900 90 VNRLMNDIMSH 100 (101)
Q Consensus 90 i~RL~nDi~s~ 100 (101)
..-+.||+..+
T Consensus 184 afQi~DD~ld~ 194 (259)
T cd00685 184 AFQIQDDILDL 194 (259)
T ss_pred HHHHHHHhhcc
Confidence 88899997643
No 10
>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=87.04 E-value=7 Score=29.57 Aligned_cols=87 Identities=7% Similarity=0.059 Sum_probs=55.2
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHhcCCCcchhhhhhccCCcHHHHHHHH
Q 041900 10 YRLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVGMGDIVTKESFEWLFSNPRSVRASSA 89 (101)
Q Consensus 10 ~~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~~~~e~~~w~~~~p~i~~~~~~ 89 (101)
..+..+-+...+++.+-+.+..|..+ ..+|.++|++...--+|.-.-.++..-++--..+++..+.+ -++-+..++
T Consensus 133 ~~~~~~~~~~~~~~~Gq~~~~~~~~~-~~~~~~~y~~~~~~KTa~L~~~~~~~ga~~ag~~~~~~~~l---~~~G~~lG~ 208 (322)
T TIGR02749 133 EVVKLISKVITDFAEGEIKQGLNQFD-SDLSLEDYLEKSFYKTASLVAASSKAAAVLSDVPSQVANDL---YEYGKHLGL 208 (322)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcccC-CCCCHHHHHHHHHccHHHHHHHHHHHHHHHcCcCHHHHHHH---HHHHHHHHH
Confidence 34666777788899998888877543 45899999997665555443222211111122344444443 346778999
Q ss_pred HHHHhcccccC
Q 041900 90 VNRLMNDIMSH 100 (101)
Q Consensus 90 i~RL~nDi~s~ 100 (101)
..-+.||+..+
T Consensus 209 aFQi~DDild~ 219 (322)
T TIGR02749 209 AFQVVDDILDF 219 (322)
T ss_pred HHHHHHHhccC
Confidence 99999998654
No 11
>PLN02890 geranyl diphosphate synthase
Probab=86.20 E-value=5.8 Score=31.45 Aligned_cols=87 Identities=16% Similarity=0.090 Sum_probs=58.4
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHhcCCCcchhhhhhccCCcHHHHHHHH
Q 041900 10 YRLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVGMGDIVTKESFEWLFSNPRSVRASSA 89 (101)
Q Consensus 10 ~~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~~~~e~~~w~~~~p~i~~~~~~ 89 (101)
..+..+-++..+++.+-+.+..|.. +..+|.++|++...--+|.-...++..-++--..+++..+.+ -++-+..++
T Consensus 227 ~~~~~~s~a~~~l~~Gq~ld~~~~~-~~~~s~~~Yl~~i~~KTa~Lf~~s~~~gAilaga~~~~~~~l---~~fG~~lGl 302 (422)
T PLN02890 227 EVVSLLATAVEHLVTGETMQITSSR-EQRRSMDYYMQKTYYKTASLISNSCKAVAILAGQTAEVAVLA---FEYGRNLGL 302 (422)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCcCHHHHHHH---HHHHHHHHH
Confidence 4567778888999999999999974 456899999987655555443322222111112345555554 357788899
Q ss_pred HHHHhcccccC
Q 041900 90 VNRLMNDIMSH 100 (101)
Q Consensus 90 i~RL~nDi~s~ 100 (101)
..-+.||+-.+
T Consensus 303 AFQI~DDiLD~ 313 (422)
T PLN02890 303 AFQLIDDVLDF 313 (422)
T ss_pred HHHHHHHHHhh
Confidence 99999998654
No 12
>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=82.31 E-value=12 Score=28.32 Aligned_cols=86 Identities=10% Similarity=0.042 Sum_probs=55.1
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHhc-CCCcchhhhhhccCCcHHHHHHH
Q 041900 10 YRLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVGM-GDIVTKESFEWLFSNPRSVRASS 88 (101)
Q Consensus 10 ~~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~-g~~~~~e~~~w~~~~p~i~~~~~ 88 (101)
..+..+-++..+++.+-..+..|.. +..+|.++|++...--+|.-...+ +.+|. --..+++..+-+ -++-+..+
T Consensus 129 ~~~~~~~~~~~~~~~Gq~~~~~~~~-~~~~~~~~Y~~~i~~KTa~L~~~~-~~~ga~~ag~~~~~~~~l---~~~g~~lG 203 (319)
T TIGR02748 129 RAHQILSHTIVEVCRGEIEQIKDKY-NFDQNLRTYLRRIKRKTALLIAAS-CQLGAIASGANEAIVKKL---YWFGYYVG 203 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHcCCCHHHHHHH---HHHHHHHH
Confidence 3466677788899999998988853 446799999998766666543322 22221 011233333332 34667888
Q ss_pred HHHHHhcccccC
Q 041900 89 AVNRLMNDIMSH 100 (101)
Q Consensus 89 ~i~RL~nDi~s~ 100 (101)
+..-+.||+..+
T Consensus 204 ~aFQI~DDilD~ 215 (319)
T TIGR02748 204 MSYQITDDILDF 215 (319)
T ss_pred HHHHHHHHHHHc
Confidence 888999998643
No 13
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=81.74 E-value=13 Score=28.09 Aligned_cols=85 Identities=16% Similarity=0.175 Sum_probs=58.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHhcCCCcchhhhhhccCCcHHHHHHHHH
Q 041900 11 RLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVGMGDIVTKESFEWLFSNPRSVRASSAV 90 (101)
Q Consensus 11 ~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~~~~e~~~w~~~~p~i~~~~~~i 90 (101)
.+..+.+....++.+-..+..+.++. +|.|+|++.-.-=+|.-...++-.-++--..+++..+.+ -.+-+..++.
T Consensus 135 ~~~~~~~~~~~~~~GQ~lDl~~~~~~--~t~e~y~~~i~~KTa~L~~~a~~~ga~la~~~~~~~~~l---~~~g~~lGla 209 (322)
T COG0142 135 AIKALAEAINGLCGGQALDLAFENKP--VTLEEYLRVIELKTAALFAAAAVLGAILAGADEELLEAL---EDYGRNLGLA 209 (322)
T ss_pred HHHHHHHHHHHHHHhHHHHHHccCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHH---HHHHHHhhHH
Confidence 46677788999999999999997666 999999998666555443333222222111224555554 3377888999
Q ss_pred HHHhcccccC
Q 041900 91 NRLMNDIMSH 100 (101)
Q Consensus 91 ~RL~nDi~s~ 100 (101)
.=+.||+-.+
T Consensus 210 FQi~DDiLD~ 219 (322)
T COG0142 210 FQIQDDILDI 219 (322)
T ss_pred HHHHHHhhcC
Confidence 9999998654
No 14
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=78.28 E-value=24 Score=26.75 Aligned_cols=85 Identities=16% Similarity=0.074 Sum_probs=54.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHhc-CCCcchhhhhhccCCcHHHHHHHH
Q 041900 11 RLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVGM-GDIVTKESFEWLFSNPRSVRASSA 89 (101)
Q Consensus 11 ~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~-g~~~~~e~~~w~~~~p~i~~~~~~ 89 (101)
.+..+-++...++.+-..+..|.. +..+|.++|+....--+|...-.+ +.+|. --..+++..+-+ -++-+..++
T Consensus 131 ~~~~~~~~~~~~~~Gq~~d~~~~~-~~~~s~~~y~~~i~~KTa~lf~~~-~~~ga~lag~~~~~~~~l---~~~g~~lG~ 205 (323)
T PRK10888 131 VLEVMSEAVNVIAEGEVLQLMNVN-DPDITEENYMRVIYSKTARLFEAA-AQCSGILAGCTPEQEKGL---QDYGRYLGT 205 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHcCCCHHHHHHH---HHHHHHHHH
Confidence 455667778889999998888854 345899999998766666553322 22221 011233333332 347778888
Q ss_pred HHHHhcccccC
Q 041900 90 VNRLMNDIMSH 100 (101)
Q Consensus 90 i~RL~nDi~s~ 100 (101)
..=+.||+..+
T Consensus 206 aFQi~DD~ld~ 216 (323)
T PRK10888 206 AFQLIDDLLDY 216 (323)
T ss_pred HHHHHHHhhcc
Confidence 88889998654
No 15
>PLN02857 octaprenyl-diphosphate synthase
Probab=77.37 E-value=17 Score=28.79 Aligned_cols=87 Identities=14% Similarity=0.119 Sum_probs=55.6
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHhcCCCcchhhhhhccCCcHHHHHHHH
Q 041900 10 YRLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVGMGDIVTKESFEWLFSNPRSVRASSA 89 (101)
Q Consensus 10 ~~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~~~~e~~~w~~~~p~i~~~~~~ 89 (101)
..+..+.++..+++.+-+.+..+.. +..++.++|++...--+|.-...++..-++--..+++..+-+ -++-+..++
T Consensus 227 ~~~~~~s~~~~~l~~Gei~q~~~~~-~~~~s~~~Yl~~i~~KTa~L~~~a~~~gallaga~~~~~~~l---~~fG~~LGi 302 (416)
T PLN02857 227 EVIKLISQVIKDFASGEIKQASSLF-DCDVTLDEYLLKSYYKTASLIAASTKSAAIFSGVDSSVKEQM---YEYGKNLGL 302 (416)
T ss_pred HHHHHHHHHHHHHHhhHHHHHhccc-CCCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcCCCHHHHHHH---HHHHHHHHH
Confidence 3466677778888999888888764 446799999998766555443322211111122344444443 446778888
Q ss_pred HHHHhcccccC
Q 041900 90 VNRLMNDIMSH 100 (101)
Q Consensus 90 i~RL~nDi~s~ 100 (101)
..-+.||+..+
T Consensus 303 AFQI~DDiLD~ 313 (416)
T PLN02857 303 AFQVVDDILDF 313 (416)
T ss_pred HHHHHHHHHhh
Confidence 88889998654
No 16
>COG2443 Sss1 Preprotein translocase subunit Sss1 [Intracellular trafficking and secretion]
Probab=71.36 E-value=10 Score=22.43 Aligned_cols=22 Identities=27% Similarity=0.363 Sum_probs=17.3
Q ss_pred CcccChHHHhhhhhhhcchhhH
Q 041900 36 NYVPTVDEYMAVALVTSACPIL 57 (101)
Q Consensus 36 ~~vPt~eEYl~~~~~S~g~~~~ 57 (101)
-.+||-|||...+.++..+..+
T Consensus 25 arKP~~eEy~~~aKi~~~Gi~l 46 (65)
T COG2443 25 ARKPDWEEYSKIAKITGLGILL 46 (65)
T ss_pred HhCCCHHHHHHHHHHHHHHHHH
Confidence 5689999999999987655443
No 17
>CHL00151 preA prenyl transferase; Reviewed
Probab=63.53 E-value=62 Score=24.41 Aligned_cols=85 Identities=6% Similarity=0.105 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHh-cCCCcchhhhhhccCCcHHHHHHHH
Q 041900 11 RLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVG-MGDIVTKESFEWLFSNPRSVRASSA 89 (101)
Q Consensus 11 ~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~-~g~~~~~e~~~w~~~~p~i~~~~~~ 89 (101)
.+..+.++..+++.+-+.+..|.. ...+|.++|+....-=+|.-.-.++..-+ ++. .+++..+.+ -++-+..++
T Consensus 135 ~~~~~~~~~~~l~~G~~~~~~~~~-~~~~~~~~yl~~i~~KTa~L~~~~~~~ga~lag-~~~~~~~~l---~~~G~~lG~ 209 (323)
T CHL00151 135 VVKLISKVITDFAEGEIRQGLVQF-DTTLSILNYIEKSFYKTASLIAASCKAAALLSD-ADEKDHNDF---YLYGKHLGL 209 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCC-CCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHcC-CCHHHHHHH---HHHHHHHHH
Confidence 456677888889999888877743 34579999999744444433322221111 121 233434333 347778899
Q ss_pred HHHHhcccccC
Q 041900 90 VNRLMNDIMSH 100 (101)
Q Consensus 90 i~RL~nDi~s~ 100 (101)
..-+.||+-.+
T Consensus 210 aFQi~DDilD~ 220 (323)
T CHL00151 210 AFQIIDDVLDI 220 (323)
T ss_pred HHHHHHHHhhc
Confidence 99999998654
No 18
>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=56.88 E-value=72 Score=23.03 Aligned_cols=76 Identities=14% Similarity=0.167 Sum_probs=44.2
Q ss_pred HHHHHHHHHHH-HhcCCcccChHHHhhhhhhhcchhhHHHHHHHhcCCCcchhhhhhccCCcHHHHHHHHHHHHhccccc
Q 041900 21 NLVKHYLFEAK-WCHQNYVPTVDEYMAVALVTSACPILSTISFVGMGDIVTKESFEWLFSNPRSVRASSAVNRLMNDIMS 99 (101)
Q Consensus 21 ~l~~~yl~Eak-W~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~~~~e~~~w~~~~p~i~~~~~~i~RL~nDi~s 99 (101)
..+++..-+.. ....+..+|.++|++...--+|.....++..-++=-..+.+..+-+ -++-+..++..-+.||+..
T Consensus 114 ~~~~~~~~q~~d~~~~~~~~~~~~y~~i~~~KTg~l~~~~~~~ga~lag~~~~~~~~l---~~~g~~lG~afQi~DD~~d 190 (260)
T PF00348_consen 114 ALIEGEIGQALDLANEDKDPTEEEYLEIIRLKTGSLFALACQLGAILAGADEEQIEAL---REFGRHLGIAFQIRDDLLD 190 (260)
T ss_dssp HHHHHHHHHHHHHHTTTSSTSHHHHHHHHHHHTHHHHHHHHHHHHHHTTSGHHHHHHH---HHHHHHHHHHHHHHHHHHH
T ss_pred hcccceeehhhccccccccccHHHHHHHHhhcchHHHHHHHHHHHHhccchhHHHHHH---HHHHHHHHHHHhhhhhhhh
Confidence 34444433332 2223448899999999887777663333222222112334444443 4577888899999999753
No 19
>PRK09400 secE preprotein translocase subunit SecE; Reviewed
Probab=56.17 E-value=34 Score=19.84 Aligned_cols=20 Identities=35% Similarity=0.360 Sum_probs=15.8
Q ss_pred CcccChHHHhhhhhhhcchh
Q 041900 36 NYVPTVDEYMAVALVTSACP 55 (101)
Q Consensus 36 ~~vPt~eEYl~~~~~S~g~~ 55 (101)
-.+|+-+||...+.++.-+.
T Consensus 24 ~~KPd~~Ef~~ia~~~~iG~ 43 (61)
T PRK09400 24 ARKPTREEFLLVAKVTGLGI 43 (61)
T ss_pred hcCCCHHHHHHHHHHHHHHH
Confidence 45799999999998775443
No 20
>PF14162 YozD: YozD-like protein
Probab=49.61 E-value=46 Score=18.94 Aligned_cols=33 Identities=24% Similarity=0.388 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchh
Q 041900 21 NLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACP 55 (101)
Q Consensus 21 ~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~ 55 (101)
+++.-|..|.- .+||+|+-+|--+.+.++.-+-
T Consensus 12 EIAefFy~eL~--kRGyvP~e~El~eiADItFeYl 44 (57)
T PF14162_consen 12 EIAEFFYHELV--KRGYVPTEEELEEIADITFEYL 44 (57)
T ss_pred HHHHHHHHHHH--HccCCCcHHHHHHHHHHHHHHH
Confidence 45555566543 4699999999999998887543
No 21
>COG0864 NikR Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]
Probab=42.54 E-value=29 Score=23.34 Aligned_cols=27 Identities=26% Similarity=0.511 Sum_probs=19.9
Q ss_pred hCCccHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 041900 6 QGKLYRLHYAKEAMKNLVKHYLFEAKWCHQN 36 (101)
Q Consensus 6 ~~~~~~~~~~k~~~~~l~~~yl~EakW~~~~ 36 (101)
.|.+.+- +..++.++.|++|.+|.+..
T Consensus 26 rg~~sRS----E~IrdAir~yl~e~~~~~~~ 52 (136)
T COG0864 26 RGYSSRS----ELIRDALREYLEEYRWLEDI 52 (136)
T ss_pred cCCCcHH----HHHHHHHHHHHHHhhhhccc
Confidence 4444444 45678899999999998765
No 22
>PRK14744 leu operon leader peptide; Provisional
Probab=42.37 E-value=11 Score=18.46 Aligned_cols=18 Identities=17% Similarity=-0.010 Sum_probs=15.0
Q ss_pred cHHHHHHHHHHHHhcccc
Q 041900 81 PRSVRASSAVNRLMNDIM 98 (101)
Q Consensus 81 p~i~~~~~~i~RL~nDi~ 98 (101)
+-++.|++.-+|+.+||+
T Consensus 10 lLLLNA~~lRGR~v~giQ 27 (28)
T PRK14744 10 LLLLNAFIVRGRPVGGIQ 27 (28)
T ss_pred HHHhhhHhhcCccccccc
Confidence 456788999999999986
No 23
>PF13337 Lon_2: Putative ATP-dependent Lon protease
Probab=41.53 E-value=6.4 Score=31.62 Aligned_cols=57 Identities=25% Similarity=0.397 Sum_probs=39.1
Q ss_pred cCCcccChHHHhhhhhhhcchh-hHHHHHHHhcCCCc--------chhhhhhccCCcHHHHHHHHHHHH
Q 041900 34 HQNYVPTVDEYMAVALVTSACP-ILSTISFVGMGDIV--------TKESFEWLFSNPRSVRASSAVNRL 93 (101)
Q Consensus 34 ~~~~vPt~eEYl~~~~~S~g~~-~~~~~~~~~~g~~~--------~~e~~~w~~~~p~i~~~~~~i~RL 93 (101)
+..-++.+..||++|.-|-|.. ....++++++|+.- +.+.|+ .-|+.++-++.+=|+
T Consensus 275 d~d~i~imK~YMesG~fsRG~~~i~a~as~vf~GNi~~~v~~~~~~~~lf~---~lP~~~~DsAflDRi 340 (457)
T PF13337_consen 275 DKDEIQIMKDYMESGSFSRGKEEINADASMVFVGNINQSVENMLKTSHLFE---PLPEEMRDSAFLDRI 340 (457)
T ss_pred ChHHHHHHHHHHhccceeecccccccceeEEEEcCcCCcchhccccchhhh---hcCHHHHHHHHHhHh
Confidence 3445678999999999999884 44566777788753 123333 348888877777775
No 24
>PHA02046 hypothetical protein
Probab=40.41 E-value=28 Score=22.17 Aligned_cols=21 Identities=24% Similarity=0.374 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHhcCCcccC
Q 041900 20 KNLVKHYLFEAKWCHQNYVPT 40 (101)
Q Consensus 20 ~~l~~~yl~EakW~~~~~vPt 40 (101)
.-++.+...|.+|+.++.+|-
T Consensus 15 ~~~a~~l~~e~~~~re~eiPl 35 (99)
T PHA02046 15 ELVCTAIEREFKWYRENDIPL 35 (99)
T ss_pred HHHHHHHHHHHHHHHhcCCCC
Confidence 346778889999999999883
No 25
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=37.94 E-value=18 Score=21.18 Aligned_cols=15 Identities=33% Similarity=0.685 Sum_probs=9.3
Q ss_pred cchhhhhhccCCcHH
Q 041900 69 VTKESFEWLFSNPRS 83 (101)
Q Consensus 69 ~~~e~~~w~~~~p~i 83 (101)
+.+..++|+.++|+|
T Consensus 34 ~~~~~~~~Lk~npKI 48 (65)
T PF02186_consen 34 IGKKLKQWLKNNPKI 48 (65)
T ss_dssp S-HHHHHHHHH-TTE
T ss_pred CCHHHHHHHHcCCCE
Confidence 345678888877775
No 26
>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.
Probab=37.80 E-value=21 Score=23.00 Aligned_cols=19 Identities=26% Similarity=0.399 Sum_probs=17.2
Q ss_pred cHHHHHHHHHHHHhccccc
Q 041900 81 PRSVRASSAVNRLMNDIMS 99 (101)
Q Consensus 81 p~i~~~~~~i~RL~nDi~s 99 (101)
|+|+.++=..||=+||.++
T Consensus 42 P~ii~aaLrAcRRvND~al 60 (103)
T cd00923 42 PKVIEAALRACRRVNDFAL 60 (103)
T ss_pred cHHHHHHHHHHHHhhhHHH
Confidence 9999999999999999864
No 27
>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]
Probab=36.43 E-value=21 Score=24.29 Aligned_cols=20 Identities=25% Similarity=0.454 Sum_probs=18.0
Q ss_pred CcHHHHHHHHHHHHhccccc
Q 041900 80 NPRSVRASSAVNRLMNDIMS 99 (101)
Q Consensus 80 ~p~i~~~~~~i~RL~nDi~s 99 (101)
.|++++++-..+|=.||+++
T Consensus 83 ~pkvIEaaLRA~RRvNDfa~ 102 (149)
T KOG4077|consen 83 SPKVIEAALRACRRVNDFAT 102 (149)
T ss_pred ChHHHHHHHHHHHHhccHHH
Confidence 39999999999999999875
No 28
>PF05772 NinB: NinB protein; InterPro: IPR008711 The ninR region of Bacteriophage lambda contains two recombination genes, orf (ninB) and rap (ninG), that have roles when the RecF and RecBCD recombination pathways of Escherichia coli, respectively, operate on phage lambda []. Genetic recombination in phage lambda relies on DNA end processing by Exo to expose 3'-tailed strands for annealing and exchange by beta protein. Phage lambda encodes an additional recombinase, NinB (Orf), which participates in the early stages of recombination by supplying a function equivalent to the E. coli RecFOR complex. These host enzymes assist loading of the RecA strand exchange protein onto ssDNA coated with ssDNA-binding protein. NinB has two structural domains with unusual folds, and exists as an intertwined dimer [].; PDB: 1PC6_B.
Probab=35.38 E-value=18 Score=24.12 Aligned_cols=40 Identities=25% Similarity=0.268 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCcccChH-HHhhhhhhhc
Q 041900 13 HYAKEAMKNLVKHYLFEAKWCHQNYVPTVD-EYMAVALVTS 52 (101)
Q Consensus 13 ~~~k~~~~~l~~~yl~EakW~~~~~vPt~e-EYl~~~~~S~ 52 (101)
.+-.+.|++++.+-+.-++.....-+|.+| |+...+.-|+
T Consensus 60 k~~~e~WK~~~~~~~~~~~~~~~~~~~gl~Gg~v~~g~sTs 100 (127)
T PF05772_consen 60 KLDPEDWKELFTAAFLIATGEEQRVVPGLDGGFVVLGESTS 100 (127)
T ss_dssp ---HHHHHHHHHHHH-----S--EEEE-TTSSEEEE---TT
T ss_pred cCCHHHHHHHHHHHHhhhccchhhhccCCCCCeEEEeeech
Confidence 556678998888888666665556677766 5554444333
No 29
>TIGR00327 secE_euk_arch protein translocase SEC61 complex gamma subunit, archaeal and eukaryotic. This model describes archaeal SEC61-like and eukaryotic SEC61 but not bacterial secE proteins, for which a Pfam pfam00584 (SecE) has been created.
Probab=34.54 E-value=53 Score=19.11 Aligned_cols=21 Identities=38% Similarity=0.460 Sum_probs=16.5
Q ss_pred CcccChHHHhhhhhhhcchhh
Q 041900 36 NYVPTVDEYMAVALVTSACPI 56 (101)
Q Consensus 36 ~~vPt~eEYl~~~~~S~g~~~ 56 (101)
-..|+-+||...+.++.-+..
T Consensus 20 ~~KPd~~Ef~~iak~t~iG~~ 40 (61)
T TIGR00327 20 CKKPDLEEYLKVAKVTGIGII 40 (61)
T ss_pred hcCCCHHHHHHHHHHHHHHHH
Confidence 468999999999987764443
No 30
>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=33.50 E-value=1.8e+02 Score=20.86 Aligned_cols=45 Identities=16% Similarity=0.216 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHh
Q 041900 17 EAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVG 64 (101)
Q Consensus 17 ~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~ 64 (101)
+.+.+++.++-.... ....||++|...-..-+.|....+++..++
T Consensus 93 ~~~~~li~g~~~Dl~---~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~~ 137 (265)
T cd00683 93 EPFRDLLAGMAMDLD---KRRYETLDELDEYCYYVAGVVGLMLLRVFG 137 (265)
T ss_pred HHHHHHHHHHHHhCC---CCCCCCHHHHHHHHHHhHHHHHHHHHHHhC
Confidence 446677777765554 356779887777777777766665655554
No 31
>PRK10581 geranyltranstransferase; Provisional
Probab=32.42 E-value=2e+02 Score=21.50 Aligned_cols=75 Identities=9% Similarity=0.052 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHh--cCCCcchhhhhhccCCcHHHHHHHHHHHHhccc
Q 041900 20 KNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVG--MGDIVTKESFEWLFSNPRSVRASSAVNRLMNDI 97 (101)
Q Consensus 20 ~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~--~g~~~~~e~~~w~~~~p~i~~~~~~i~RL~nDi 97 (101)
..++.+-..+..|.. ..+|.++|++...-=+|.-...+ +.+| ++..-+++..+.+ -++-+..++..=+.||+
T Consensus 152 ~~l~~GQ~ld~~~~~--~~~~~~~y~~i~~~KTa~L~~~~-~~~gailag~~~~~~~~~l---~~~g~~lG~aFQI~DDi 225 (299)
T PRK10581 152 AGMCGGQALDLEAEG--KQVPLDALERIHRHKTGALIRAA-VRLGALSAGDKGRRALPVL---DRYAESIGLAFQVQDDI 225 (299)
T ss_pred chhhHhhHHHHhccC--CCCCHHHHHHHHHHhhHHHHHHH-HHHHHHHcCCCcHHHHHHH---HHHHHHHHHHHHHHHHH
Confidence 457788888888854 46899999987654444332222 1222 2222122334443 34777888888889998
Q ss_pred ccC
Q 041900 98 MSH 100 (101)
Q Consensus 98 ~s~ 100 (101)
-.+
T Consensus 226 lD~ 228 (299)
T PRK10581 226 LDV 228 (299)
T ss_pred ccc
Confidence 654
No 32
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=31.69 E-value=28 Score=22.63 Aligned_cols=19 Identities=26% Similarity=0.385 Sum_probs=16.2
Q ss_pred cHHHHHHHHHHHHhccccc
Q 041900 81 PRSVRASSAVNRLMNDIMS 99 (101)
Q Consensus 81 p~i~~~~~~i~RL~nDi~s 99 (101)
|+|+.++=..||=+||.++
T Consensus 45 P~ii~aALrAcRRvND~a~ 63 (108)
T PF02284_consen 45 PKIIEAALRACRRVNDFAL 63 (108)
T ss_dssp HHHHHHHHHHHHHTT-HHH
T ss_pred hHHHHHHHHHHHHhhhHHH
Confidence 9999999999999999864
No 33
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification]
Probab=31.23 E-value=17 Score=22.54 Aligned_cols=18 Identities=28% Similarity=0.399 Sum_probs=14.1
Q ss_pred HhcCCcccChHHHhhhhh
Q 041900 32 WCHQNYVPTVDEYMAVAL 49 (101)
Q Consensus 32 W~~~~~vPt~eEYl~~~~ 49 (101)
-+.+|++--|||||..-.
T Consensus 37 ~rieG~IvGFDEyMNvVl 54 (88)
T KOG1774|consen 37 LRIEGRIVGFDEYMNLVL 54 (88)
T ss_pred cEEeEEEechHHhhhhhh
Confidence 456799999999997643
No 34
>PF02236 Viral_DNA_bi: Viral DNA-binding protein, all alpha domain; InterPro: IPR003176 This domain represents the N-terminal domain of the viral DNA-binding protein, a multi functional protein involved in DNA replication and transcription control.; GO: 0003677 DNA binding, 0006260 DNA replication, 0006351 transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ADU_A 1ADV_B 2WB0_X 2WAZ_X 1ANV_A.
Probab=29.65 E-value=1.4e+02 Score=18.47 Aligned_cols=30 Identities=17% Similarity=0.259 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHhcCCcccChHHHhhhhh
Q 041900 17 EAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVAL 49 (101)
Q Consensus 17 ~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~ 49 (101)
+.|+++|.+|+.|.+ .+--+||.-+-+...
T Consensus 35 e~~~Ki~~~~l~~~k---~~~~LTFSS~KSf~~ 64 (86)
T PF02236_consen 35 ECFRKICQTWLNEEK---RGLQLTFSSQKSFTH 64 (86)
T ss_dssp HHHHHHHHHHHHHHH---TT---SS--HHHHHH
T ss_pred HHHHHHHHHHHHhcC---cCCCcceechHHHHH
Confidence 679999999999977 233458877755543
No 35
>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=29.55 E-value=2.1e+02 Score=20.37 Aligned_cols=48 Identities=10% Similarity=0.112 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHhcC
Q 041900 16 KEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVGMG 66 (101)
Q Consensus 16 k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g 66 (101)
++.+.+++.++.+. ....-.+|++|...-..-+.|.....+...++..
T Consensus 90 ~~~l~~li~~~~~d---l~~~~~~t~~~L~~Y~~~vag~vg~l~~~~~~~~ 137 (267)
T PF00494_consen 90 REPLLELIDGMEMD---LEFTPYETFADLERYCYYVAGSVGLLLLQLLGAH 137 (267)
T ss_dssp HHHHHHHHHHHHHC---TT-S--SSHHHHHHHHHHHTHHHHHHHHHHHHSS
T ss_pred HHHHHHHHHHhccc---ccCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 45566667776644 3335578999999999988888877777777653
No 36
>PF00584 SecE: SecE/Sec61-gamma subunits of protein translocation complex; InterPro: IPR001901 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion []. SecE, part of the main SecYEG translocase complex, is ~106 residues in length, and spans the inner membrane of the Gram-negative bacterial envelope. Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. In eukaryotes, the evolutionary related protein sec61-gamma plays a role in protein translocation through the endoplasmic reticulum; it is part of a trimeric complex that also consist of sec61-alpha and beta []. Both secE and sec61-gamma are small proteins of about 60 to 90 amino acids that contain a single transmembrane region at their C-terminal extremity (Escherichia coli secE is an exception, in that it possess an extra N-terminal segment of 60 residues that contains two additional transmembrane domains) [].; GO: 0006605 protein targeting, 0006886 intracellular protein transport, 0016020 membrane; PDB: 3J01_B 2WW9_B 2WWA_B 3DL8_C 2WWB_B 3DIN_G 2ZJS_E 2ZQP_E.
Probab=28.71 E-value=55 Score=18.09 Aligned_cols=27 Identities=15% Similarity=0.218 Sum_probs=19.5
Q ss_pred ccChHHHhhhhhhhcchhhHHHHHHHh
Q 041900 38 VPTVDEYMAVALVTSACPILSTISFVG 64 (101)
Q Consensus 38 vPt~eEYl~~~~~S~g~~~~~~~~~~~ 64 (101)
=||-+|..+.+.+....-.++...+.+
T Consensus 18 WP~~~e~~~~t~~Vl~~~~i~~~~~~~ 44 (57)
T PF00584_consen 18 WPSRKELLKSTIIVLVFVIIFGLFFFL 44 (57)
T ss_dssp CCCTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 399999999988877766655544443
No 37
>PF09435 DUF2015: Fungal protein of unknown function (DUF2015); InterPro: IPR018559 This entry represents uncharacterised proteins found in fungi.
Probab=27.90 E-value=86 Score=21.00 Aligned_cols=46 Identities=13% Similarity=0.251 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHHHHHH---HHhcCCccc---ChHHHhhhhhhhcchhhH
Q 041900 12 LHYAKEAMKNLVKHYLFEA---KWCHQNYVP---TVDEYMAVALVTSACPIL 57 (101)
Q Consensus 12 ~~~~k~~~~~l~~~yl~Ea---kW~~~~~vP---t~eEYl~~~~~S~g~~~~ 57 (101)
+.+.+..|..+..-+..+. .++.-.+.| ||++=++.|..|+..-+.
T Consensus 19 lf~~R~r~~~~~~~~~~~~~~~~~~~y~~l~~~~sF~~D~eaGLsSs~FDl~ 70 (128)
T PF09435_consen 19 LFFTRHRWLPLLPRYRSRLLRIRSYFYSRLPLNSSFEDDIEAGLSSSNFDLS 70 (128)
T ss_pred HHHHHHHHHhhchhhhhhhccccccccccCCCCCCHHHHHHccccccccChh
Confidence 4456667777766666553 344457788 899999999988876654
No 38
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=27.79 E-value=2.2e+02 Score=20.16 Aligned_cols=28 Identities=21% Similarity=0.360 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCcccChHH
Q 041900 15 AKEAMKNLVKHYLFEAKWCHQNYVPTVDE 43 (101)
Q Consensus 15 ~k~~~~~l~~~yl~EakW~~~~~vPt~eE 43 (101)
...+.++++.|..- ..|..++.+||.+|
T Consensus 79 ~~~~lQEyvEA~~f-~~~l~~~~l~s~ee 106 (204)
T PRK14562 79 VGTALQEYVEALLV-YSLLFENKIPSPEE 106 (204)
T ss_pred cchHHHHHHHHHHH-HHHHcCCCCCCHHH
Confidence 34445556555554 55777777777777
No 39
>TIGR03760 ICE_TraI_Pfluor integrating conjugative element relaxase, PFL_4751 family. Members of this protein family are the TraI putative relaxases required for transfer by a subclass of integrating conjugative elements (ICE) as found in Pseudomonas fluorescens Pf-5, and understood from study of two related ICE, SXT and R391. This model represents the N-terminal domain. Note that no homology is detected to the similarly named TraI relaxase of the F plasmid.
Probab=27.29 E-value=48 Score=23.88 Aligned_cols=22 Identities=27% Similarity=0.585 Sum_probs=18.6
Q ss_pred cCCCcchhhhhhccCCcHHHHH
Q 041900 65 MGDIVTKESFEWLFSNPRSVRA 86 (101)
Q Consensus 65 ~g~~~~~e~~~w~~~~p~i~~~ 86 (101)
.+..+|++++.|+.++|++...
T Consensus 166 a~~llp~~~l~wL~~~p~v~~~ 187 (218)
T TIGR03760 166 APRLLPAEALAWLSSNPEVLAT 187 (218)
T ss_pred HHHhCCHHHHHHHHhChHHHHH
Confidence 4678999999999999987653
No 40
>PF08843 DUF1814: Nucleotidyl transferase of unknown function (DUF1814); InterPro: IPR014942 This large group of proteins are largely uncharacterised. Some are annotated as abortive infective proteins but support for this annotation could not be found.
Probab=26.56 E-value=87 Score=21.34 Aligned_cols=30 Identities=13% Similarity=0.105 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHhcCCcccChHHHhhh
Q 041900 16 KEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAV 47 (101)
Q Consensus 16 k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~ 47 (101)
++.|+....++.....+ .+..|+||+++.+
T Consensus 204 ~~~~~~~~~~~~~~~~~--~~~~~~f~~~~~~ 233 (233)
T PF08843_consen 204 REFWQRDYEAMRDALLY--AGDLPDFDDALAR 233 (233)
T ss_pred HHHHHHHHHHhHhhhhc--cCCCcCHHHHhcC
Confidence 45566655555544443 5778899998764
No 41
>PLN00179 acyl- [acyl-carrier protein] desaturase
Probab=26.06 E-value=68 Score=25.39 Aligned_cols=61 Identities=18% Similarity=0.322 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHHHHH--HHHHhcCCccc--ChHHHhhhhh----hhcchhhHHHHHHHhcCCCcchhhh
Q 041900 12 LHYAKEAMKNLVKHYLF--EAKWCHQNYVP--TVDEYMAVAL----VTSACPILSTISFVGMGDIVTKESF 74 (101)
Q Consensus 12 ~~~~k~~~~~l~~~yl~--EakW~~~~~vP--t~eEYl~~~~----~S~g~~~~~~~~~~~~g~~~~~e~~ 74 (101)
+..+-..-.+.+.-+|. |..|.-..|+| .-+.|...+. ...+.+.....+++ |+.+|+|.+
T Consensus 65 l~~LE~~ve~~l~~hL~pvek~WqPhDflP~~~~~~F~~~v~~lr~~~~~Lpd~~~v~Lv--gdmiTEeaL 133 (390)
T PLN00179 65 FKSLEGWAEENLLPLLKPVEKSWQPQDFLPDPASEGFYDQVKELRERAAELPDDYFVVLV--GDMITEEAL 133 (390)
T ss_pred HHHHHHHHHHHHHHHhchHhhccCccccCCCCccCChHHHHhhhhHhhcCCChhhhhhhh--hcchhhhcc
Confidence 33333334566677777 66799999999 2455544333 55666655554444 799999988
No 42
>PF13224 DUF4032: Domain of unknown function (DUF4032)
Probab=25.61 E-value=12 Score=26.03 Aligned_cols=12 Identities=50% Similarity=0.670 Sum_probs=9.0
Q ss_pred HHHHhcccccCC
Q 041900 90 VNRLMNDIMSHK 101 (101)
Q Consensus 90 i~RL~nDi~s~~ 101 (101)
.-||+|||.+|+
T Consensus 78 ArrlLndi~~yr 89 (165)
T PF13224_consen 78 ARRLLNDIDSYR 89 (165)
T ss_pred HHHHHHHHHHHH
Confidence 348999998763
No 43
>KOG0777 consensus Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism]
Probab=23.78 E-value=1e+02 Score=23.17 Aligned_cols=82 Identities=9% Similarity=0.118 Sum_probs=53.5
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHhcCCcccChHHHhhhhhhhcchhhHHHHHHHhcCCCcchhhhhhccCCcHHHHHHHH
Q 041900 10 YRLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVDEYMAVALVTSACPILSTISFVGMGDIVTKESFEWLFSNPRSVRASSA 89 (101)
Q Consensus 10 ~~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~eEYl~~~~~S~g~~~~~~~~~~~~g~~~~~e~~~w~~~~p~i~~~~~~ 89 (101)
..+.-+-+..-++-++.=-+.-||+.=..||-++|...-+--+|+-.-++.-+. +-.+ .+=.+..+++...+.
T Consensus 121 ~a~kifteqLleLHrGQGldIYWRD~~tcPtee~Yk~Mv~~KTGGLF~La~rLM---qlfS----~~kedl~pl~n~LGl 193 (322)
T KOG0777|consen 121 NAIKIFTEQLLELHRGQGLDIYWRDFLTCPTEEMYKNMVMNKTGGLFRLALRLM---QLFS----HHKEDLVPLINLLGL 193 (322)
T ss_pred hHHHHHHHHHHHHhcCCCcceeeeccCcCCCHHHHHHHHHHhcccHHHHHHHHH---HHHH----hcchhHHHHHHHHhH
Confidence 445555666667777777788899988899999999988777765543332221 1111 111233567788888
Q ss_pred HHHHhcccc
Q 041900 90 VNRLMNDIM 98 (101)
Q Consensus 90 i~RL~nDi~ 98 (101)
+..+-||-.
T Consensus 194 ~fQIRDDY~ 202 (322)
T KOG0777|consen 194 IFQIRDDYL 202 (322)
T ss_pred hhhhhhhhc
Confidence 888888743
No 44
>PF07914 DUF1679: Protein of unknown function (DUF1679); InterPro: IPR012877 This region is found in a number of Caenorhabditis elegans and Caenorhabditis briggsae proteins, in one case (Q19034 from SWISSPROT) as a repeat. In many of the family members, this region is associated with the CHK region described by SMART as being found in zinc finger-C4 and HLH domain-containing kinases. In fact, one member of this family (Q9GUC1 from SWISSPROT) is annotated as being a member of the nuclear hormone receptor family, and contains regions typical of such proteins (IPR000536 from INTERPRO, IPR008946 from INTERPRO, and IPR001628 from INTERPRO).
Probab=23.66 E-value=3.7e+02 Score=21.17 Aligned_cols=78 Identities=14% Similarity=0.095 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHHHH-H-hcCCccc-ChHHHhhhhhhhcchhhHHHHHHHh--cCC-CcchhhhhhccCCcHHHHHHHH
Q 041900 16 KEAMKNLVKHYLFEAK-W-CHQNYVP-TVDEYMAVALVTSACPILSTISFVG--MGD-IVTKESFEWLFSNPRSVRASSA 89 (101)
Q Consensus 16 k~~~~~l~~~yl~Eak-W-~~~~~vP-t~eEYl~~~~~S~g~~~~~~~~~~~--~g~-~~~~e~~~w~~~~p~i~~~~~~ 89 (101)
|+.|..+++.|...-. = .+.+..| |+|+-.+.-..-.-...++....++ +.. ..+++.-+-. .-.....
T Consensus 324 R~~~~~lL~~Yy~~f~~~l~~~~~~PfT~eqL~~sY~l~fp~~al~~lp~~~~~~~~~~~~~e~k~~~-----~~~~~~K 398 (414)
T PF07914_consen 324 REHTEELLEYYYDTFTEALEDGGKAPFTLEQLKDSYRLYFPFGALFLLPGIGPFIDMKKISEEEKEER-----REEMMDK 398 (414)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHH-----HHHHHHH
Confidence 4556666666654422 2 2345788 9988766554433333222222221 111 2222222211 1245667
Q ss_pred HHHHhcccc
Q 041900 90 VNRLMNDIM 98 (101)
Q Consensus 90 i~RL~nDi~ 98 (101)
+..++.||.
T Consensus 399 ~~gilEDi~ 407 (414)
T PF07914_consen 399 AIGILEDIE 407 (414)
T ss_pred HHHHHHHHH
Confidence 777888874
No 45
>PF14502 HTH_41: Helix-turn-helix domain
Probab=23.59 E-value=1.1e+02 Score=16.96 Aligned_cols=26 Identities=19% Similarity=0.165 Sum_probs=20.2
Q ss_pred CCcccChHHHhhhhhhhcchhhHHHH
Q 041900 35 QNYVPTVDEYMAVALVTSACPILSTI 60 (101)
Q Consensus 35 ~~~vPt~eEYl~~~~~S~g~~~~~~~ 60 (101)
.+.+||.+||-+-=-+|.|...-.+.
T Consensus 3 GdRi~tI~e~~~~~~vs~GtiQ~Alk 28 (48)
T PF14502_consen 3 GDRIPTISEYSEKFGVSRGTIQNALK 28 (48)
T ss_pred CcccCCHHHHHHHhCcchhHHHHHHH
Confidence 46799999998888888887665544
No 46
>PF08054 Leu_leader: Leucine operon leader peptide; InterPro: IPR012570 This family consists of the leucine operon leader peptide. The leucine operon is involved in the control of the biosynthesis of leucine. Four adjacent leucine codons within the leucine leader RNA are critically important in transcription attenuation-mediated control of leucine operon expression in bacteria. The leader RNA contains translational start and stop signals, a cluster of four leucine codons and overlapping regions of dyad symmetry that are capable of forming stem-and-loop structures [].; GO: 0009098 leucine biosynthetic process
Probab=22.34 E-value=49 Score=16.28 Aligned_cols=18 Identities=22% Similarity=0.139 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHhccccc
Q 041900 82 RSVRASSAVNRLMNDIMS 99 (101)
Q Consensus 82 ~i~~~~~~i~RL~nDi~s 99 (101)
-++.|+..=+|+.+|+++
T Consensus 11 LLLnA~~~RGrlvg~~q~ 28 (28)
T PF08054_consen 11 LLLNAFLVRGRLVGGIQH 28 (28)
T ss_pred HHHHHHHHcCcccccccC
Confidence 466788888888888763
No 47
>PF07514 TraI_2: Putative helicase; InterPro: IPR011119 The members of this family are restricted to the proteobacteria. Some members have been annotated as helicase, conjugative relaxase or nickase. The majority contain an HD domain, which is found in a superfamily of enzymes with a predicted or known phosphohydrolase activity. These enzymes appear to be involved in the nucleic acid metabolism, signal transduction and possibly other functions in bacteria.
Probab=22.27 E-value=97 Score=23.65 Aligned_cols=25 Identities=24% Similarity=0.456 Sum_probs=20.0
Q ss_pred HHhcCCCcchhhhhhccC-CcHHHHH
Q 041900 62 FVGMGDIVTKESFEWLFS-NPRSVRA 86 (101)
Q Consensus 62 ~~~~g~~~~~e~~~w~~~-~p~i~~~ 86 (101)
.+.....+|++.+.|+.+ .|++...
T Consensus 172 ~~l~~~llp~~~l~wL~~~~p~v~~~ 197 (327)
T PF07514_consen 172 ALLAPRLLPPEALAWLSSGDPEVLSA 197 (327)
T ss_pred HHHHHHhCCHHHHHHHccCChHHHHH
Confidence 344467899999999999 9998764
No 48
>PF11732 Thoc2: Transcription- and export-related complex subunit; InterPro: IPR021726 The THO/TREX complex is the transcription- and export-related complex associated with spliceosomes that preferentially deal with spliced mRNAs as opposed to unspliced mRNAs. Thoc2 plays a role in RNA polymerase II (RNA pol II)-dependent transcription and is required for the stability of DNA repeats []. In humans, the TRE complex is comprised of the exon-junction-associated proteins Aly/REF and UAP56 together with the THO proteins THOC1 (hHpr1/p84), Thoc2 (hRlr1), THOC3 (hTex1), THOC5 (fSAP79), THOC6 (fSAP35), and THOC7 (fSAP24). Although much evidence indicates that the function of the TREX complex as an adaptor between the mRNA and components of the export machinery is conserved among eukaryotes, in Drosophila the majority of mRNAs can be exported from the nucleus independently of the THO complex []. This entry represents a conserved domain found towards the N terminus of these proteins.
Probab=22.23 E-value=69 Score=19.45 Aligned_cols=27 Identities=7% Similarity=-0.002 Sum_probs=19.1
Q ss_pred hhhhhccCCcHHHHHHHHHHHHhcccc
Q 041900 72 ESFEWLFSNPRSVRASSAVNRLMNDIM 98 (101)
Q Consensus 72 e~~~w~~~~p~i~~~~~~i~RL~nDi~ 98 (101)
.++..+.+|++++..+....|.++|++
T Consensus 15 ~il~Qie~YdNli~~vVe~~ky~t~l~ 41 (77)
T PF11732_consen 15 VILSQIESYDNLIEPVVESLKYFTDLG 41 (77)
T ss_pred HHHHHHHHhhhhHHHHHHHHhhcchhh
Confidence 455666777888887777777777653
No 49
>PF13926 DUF4211: Domain of unknown function (DUF4211)
Probab=21.26 E-value=1.5e+02 Score=19.69 Aligned_cols=71 Identities=15% Similarity=0.097 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCcccChH----HHhhhhhhhcchhhHHHHHHHhcCCCcchhhhhhccCCcHH
Q 041900 11 RLHYAKEAMKNLVKHYLFEAKWCHQNYVPTVD----EYMAVALVTSACPILSTISFVGMGDIVTKESFEWLFSNPRS 83 (101)
Q Consensus 11 ~~~~~k~~~~~l~~~yl~EakW~~~~~vPt~e----EYl~~~~~S~g~~~~~~~~~~~~g~~~~~e~~~w~~~~p~i 83 (101)
...-+|+.|+.+++.++.-|= +.++..++. ||+..++--+=..+.-..--+...-..+.+..+++.++|.+
T Consensus 32 ~~~~~k~~F~~~ve~lv~~al--dp~f~~~l~~~~de~fl~a~~~id~~~~~~~~~l~~ss~W~~~f~~aL~~~P~l 106 (153)
T PF13926_consen 32 STQPLKEHFKIYVEWLVSNAL--DPDFLQELEDERDEYFLPALKKIDDELQGRKDSLLSSSAWKPDFKKALETYPEL 106 (153)
T ss_pred hhhhHHHHHHHHHHHHHHHHc--CHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhceeeeccCCHHHHHHHHHCCCe
Confidence 344566677777776665443 344555553 77777666655443333333333445567778888888876
No 50
>COG1049 AcnB Aconitase B [Energy production and conversion]
Probab=21.24 E-value=55 Score=27.83 Aligned_cols=14 Identities=50% Similarity=0.788 Sum_probs=11.9
Q ss_pred CCcccChHHHhhhh
Q 041900 35 QNYVPTVDEYMAVA 48 (101)
Q Consensus 35 ~~~vPt~eEYl~~~ 48 (101)
-|.+||.|||+..-
T Consensus 808 LGkiPt~eEY~~~v 821 (852)
T COG1049 808 LGKIPTVEEYMAYV 821 (852)
T ss_pred HcCCCCHHHHHHHH
Confidence 49999999998764
No 51
>cd08574 GDPD_GDE_2_3_6 Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2, GDE3, GDE6-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian glycerophosphodiester phosphodiesterase domain-containing protein subtype 5 (GDE2), subtype 2 (GDE3), subtype 1 (GDE6), and their eukaryotic homologs. Mammalian GDE2, GDE3, and GDE6 show very high sequence similarity to each other and have been classified into the same family. Although they are all transmembrane proteins, based on different pattern of tissue distribution, these enzymes might display diverse cellular functions. Mammalian GDE2 is primarily expressed in mature neurons. It selectively hydrolyzes glycerophosphocholine (GPC) and mainly functions in a complex with an antioxidant scavenger peroxiredoxin1 (Prdx1) to control motor neuron differentiation in the spinal cord. Mammalian GDE3 is specifically expressed in bo
Probab=20.15 E-value=69 Score=23.08 Aligned_cols=18 Identities=17% Similarity=0.296 Sum_probs=13.6
Q ss_pred HhcCCcccChHHHhhhhh
Q 041900 32 WCHQNYVPTVDEYMAVAL 49 (101)
Q Consensus 32 W~~~~~vPt~eEYl~~~~ 49 (101)
+.....+|||+|+++...
T Consensus 107 ~~~~~~IPtL~evl~~~~ 124 (252)
T cd08574 107 EAGNQSIPSLAELLRLAK 124 (252)
T ss_pred hcCCCCCCCHHHHHHHHH
Confidence 344567999999998654
No 52
>PF03389 MobA_MobL: MobA/MobL family; InterPro: IPR005053 This entry represents a domain found at the N terminus of MobA in Escherichia coli, and MobL in Thiobacillus ferrooxidans (Acidithiobacillus ferrooxidans), as well as in conjugal transfer protein TraA. MobA and MobL are mobilisation proteins, which are essential for specific plasmid transfer.; GO: 0009291 unidirectional conjugation; PDB: 2NS6_A.
Probab=20.01 E-value=1.1e+02 Score=21.73 Aligned_cols=23 Identities=22% Similarity=0.088 Sum_probs=19.5
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHH
Q 041900 10 YRLHYAKEAMKNLVKHYLFEAKW 32 (101)
Q Consensus 10 ~~~~~~k~~~~~l~~~yl~EakW 32 (101)
.-+..+++.|.++++.+|.++.-
T Consensus 162 ~~l~~~R~~Wa~~~N~~L~~~g~ 184 (216)
T PF03389_consen 162 ETLERWREQWADLCNAALERAGL 184 (216)
T ss_dssp THHHHHHHHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHHHHHHHHHHhcc
Confidence 45789999999999999988764
Done!