Query 040006
Match_columns 129
No_of_seqs 103 out of 689
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 04:10:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040006.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040006hhsearch_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 100.0 3E-35 6.5E-40 254.2 13.9 127 1-129 552-680 (784)
2 cd00684 Terpene_cyclase_plant_ 100.0 3.6E-34 7.8E-39 240.3 14.1 129 1-129 319-447 (542)
3 cd00868 Terpene_cyclase_C1 Ter 99.9 8.5E-21 1.8E-25 145.8 13.4 129 1-129 85-213 (284)
4 PF03936 Terpene_synth_C: Terp 99.8 2.3E-19 5E-24 136.9 11.9 128 1-128 99-227 (270)
5 PLN02592 ent-copalyl diphospha 99.8 1.5E-19 3.2E-24 156.9 10.4 107 1-129 608-721 (800)
6 cd00687 Terpene_cyclase_nonpla 99.6 6E-16 1.3E-20 120.8 7.2 115 10-129 105-219 (303)
7 cd00385 Isoprenoid_Biosyn_C1 I 99.0 3.3E-09 7.1E-14 77.6 9.4 115 7-129 52-166 (243)
8 cd00867 Trans_IPPS Trans-Isopr 93.7 0.95 2.1E-05 33.7 9.4 85 39-128 86-171 (236)
9 COG0864 NikR Predicted transcr 88.1 1.6 3.4E-05 31.0 5.2 50 24-83 16-65 (136)
10 cd00685 Trans_IPPS_HT Trans-Is 86.6 9.6 0.00021 29.1 9.3 86 38-128 108-194 (259)
11 TIGR02749 prenyl_cyano solanes 84.3 18 0.00039 28.9 10.1 86 38-128 133-219 (322)
12 PLN02890 geranyl diphosphate s 83.3 14 0.00031 30.9 9.4 87 38-128 227-313 (422)
13 TIGR02748 GerC3_HepT heptapren 78.7 29 0.00064 27.6 9.5 85 38-128 129-215 (319)
14 COG0142 IspA Geranylgeranyl py 76.8 29 0.00062 27.7 8.9 86 38-128 134-219 (322)
15 PLN02857 octaprenyl-diphosphat 72.5 40 0.00087 28.1 9.0 87 38-128 227-313 (416)
16 PF05772 NinB: NinB protein; 67.3 5.9 0.00013 27.7 2.6 57 20-80 43-100 (127)
17 COG2443 Sss1 Preprotein transl 66.7 16 0.00034 22.7 4.1 21 64-84 25-45 (65)
18 PRK00630 nickel responsive reg 66.5 20 0.00043 25.7 5.3 36 24-63 22-57 (148)
19 PRK10888 octaprenyl diphosphat 65.8 67 0.0015 25.6 11.0 85 38-128 130-216 (323)
20 COG4860 Uncharacterized protei 60.2 34 0.00073 24.7 5.4 59 14-80 27-90 (170)
21 PRK01002 nickel responsive reg 53.3 43 0.00093 23.6 5.1 36 24-63 16-51 (141)
22 CHL00151 preA prenyl transfera 48.3 1.4E+02 0.003 23.8 9.8 85 39-128 135-220 (323)
23 PF04545 Sigma70_r4: Sigma-70, 46.2 41 0.00089 18.7 3.4 29 5-33 1-32 (50)
24 PF13060 DUF3921: Protein of u 45.5 63 0.0014 19.0 5.8 43 13-57 6-48 (58)
25 PRK09400 secE preprotein trans 44.0 51 0.0011 20.0 3.7 20 64-83 24-43 (61)
26 PF08281 Sigma70_r4_2: Sigma-7 43.3 31 0.00068 19.4 2.6 27 4-30 6-35 (54)
27 PF00348 polyprenyl_synt: Poly 42.4 1.5E+02 0.0033 22.5 9.8 60 64-127 130-190 (260)
28 PRK14744 leu operon leader pep 40.9 12 0.00025 19.1 0.4 18 109-126 10-27 (28)
29 TIGR02793 nikR nickel-responsi 40.4 95 0.0021 21.6 5.1 36 24-63 12-47 (129)
30 PRK04460 nickel responsive reg 39.9 98 0.0021 21.8 5.2 36 24-63 14-49 (137)
31 cd00686 Terpene_cyclase_cis_tr 36.6 1.4E+02 0.0031 24.5 6.2 114 6-128 103-230 (357)
32 PF15265 FAM196: FAM196 family 36.5 22 0.00047 30.6 1.6 22 18-39 412-434 (514)
33 PF14162 YozD: YozD-like prote 36.1 30 0.00066 20.6 1.7 21 62-82 23-43 (57)
34 PRK12520 RNA polymerase sigma 35.7 93 0.002 22.1 4.7 50 4-54 127-179 (191)
35 COG4572 ChaB Putative cation t 35.6 24 0.00053 22.3 1.3 21 7-27 15-35 (76)
36 PF11433 DUF3198: Protein of u 34.2 99 0.0021 18.0 4.0 29 20-48 19-49 (51)
37 PF09824 ArsR: ArsR transcript 34.2 73 0.0016 23.2 3.8 58 13-78 19-81 (160)
38 TIGR03001 Sig-70_gmx1 RNA poly 33.0 2.1E+02 0.0045 21.8 6.4 46 4-50 157-205 (244)
39 TIGR02394 rpoS_proteo RNA poly 32.5 95 0.002 24.0 4.5 55 4-60 218-279 (285)
40 PRK14562 haloacid dehalogenase 32.1 2E+02 0.0044 21.4 6.1 29 42-71 78-106 (204)
41 PF06330 TRI5: Trichodiene syn 31.9 2.1E+02 0.0044 23.8 6.5 83 38-128 145-230 (376)
42 PRK02967 nickel responsive reg 31.7 1.5E+02 0.0032 20.9 5.0 36 24-63 13-48 (139)
43 TIGR00327 secE_euk_arch protei 31.5 49 0.0011 20.2 2.2 20 64-83 20-39 (61)
44 PRK12530 RNA polymerase sigma 28.9 1.3E+02 0.0029 21.4 4.6 46 4-50 130-178 (189)
45 PF14502 HTH_41: Helix-turn-he 27.9 94 0.002 18.1 2.9 26 63-88 3-28 (48)
46 KOG3094 Predicted membrane pro 27.9 71 0.0015 25.3 3.0 61 41-110 107-171 (284)
47 PRK12525 RNA polymerase sigma 27.8 1.2E+02 0.0026 21.1 4.1 46 5-51 115-163 (168)
48 KOG4713 Cyclin-dependent kinas 27.7 1.4E+02 0.003 22.3 4.3 47 14-60 134-185 (189)
49 PRK09642 RNA polymerase sigma 27.6 1.5E+02 0.0032 20.3 4.5 45 4-49 102-149 (160)
50 COG2524 Predicted transcriptio 27.2 2.9E+02 0.0063 22.0 6.3 66 8-79 3-79 (294)
51 PF13337 Lon_2: Putative ATP-d 26.9 17 0.00037 30.8 -0.6 59 64-122 277-341 (457)
52 TIGR02835 spore_sigmaE RNA pol 25.8 1.1E+02 0.0023 22.9 3.7 32 4-35 174-212 (234)
53 PRK07037 extracytoplasmic-func 25.8 1.5E+02 0.0032 20.3 4.2 44 5-49 106-152 (163)
54 cd07957 Anticodon_Ia_Met Antic 25.7 1.9E+02 0.004 18.7 4.5 45 14-59 39-83 (129)
55 PHA02046 hypothetical protein 25.7 67 0.0015 21.4 2.2 20 49-68 16-35 (99)
56 COG0783 Dps DNA-binding ferrit 24.9 2.2E+02 0.0049 20.5 5.0 36 1-36 39-76 (156)
57 PF02236 Viral_DNA_bi: Viral D 24.9 2E+02 0.0044 18.7 4.9 29 45-76 35-63 (86)
58 PF14629 ORC4_C: Origin recogn 24.6 1.5E+02 0.0033 21.5 4.3 41 15-55 122-168 (203)
59 PF01484 Col_cuticle_N: Nemato 24.2 1.2E+02 0.0025 17.0 2.9 12 38-49 41-52 (53)
60 PF13837 Myb_DNA-bind_4: Myb/S 24.1 1.8E+02 0.0039 17.8 4.6 38 23-60 36-73 (90)
61 PRK12537 RNA polymerase sigma 23.8 1.1E+02 0.0024 21.6 3.3 44 4-48 129-175 (182)
62 PF00494 SQS_PSY: Squalene/phy 23.4 3.2E+02 0.007 20.5 7.4 45 47-94 93-137 (267)
63 KOG0085 G protein subunit Galp 23.2 2.1E+02 0.0044 22.8 4.8 34 50-83 156-190 (359)
64 cd00683 Trans_IPPS_HH Trans-Is 23.1 3.4E+02 0.0073 20.5 7.3 45 46-93 94-138 (265)
65 PRK11923 algU RNA polymerase s 22.9 1E+02 0.0023 21.8 3.0 53 5-57 135-192 (193)
66 KOG4420 Uncharacterized conser 22.6 4.1E+02 0.0089 21.3 7.3 72 7-79 197-278 (325)
67 PF02186 TFIIE_beta: TFIIE bet 22.5 52 0.0011 20.1 1.2 15 97-111 34-48 (65)
68 PF09921 DUF2153: Uncharacteri 22.1 2.9E+02 0.0062 19.4 5.5 47 18-64 10-56 (126)
69 PF14278 TetR_C_8: Transcripti 22.1 1.7E+02 0.0038 16.9 5.8 29 31-59 22-50 (77)
70 PRK08301 sporulation sigma fac 21.6 1.6E+02 0.0034 21.8 3.9 44 4-48 174-224 (234)
71 PLN03223 Polycystin cation cha 21.6 2.5E+02 0.0054 27.7 5.7 24 38-67 1438-1461(1634)
72 PRK12531 RNA polymerase sigma 21.5 1.6E+02 0.0034 21.1 3.8 46 5-51 138-186 (194)
73 TIGR03486 cas_csx13_C CRISPR-a 21.4 2.9E+02 0.0062 20.0 4.9 60 13-72 54-124 (152)
74 PRK12529 RNA polymerase sigma 21.1 1.5E+02 0.0033 20.8 3.6 45 4-49 123-170 (178)
75 PF11732 Thoc2: Transcription- 20.8 90 0.0019 19.9 2.0 27 100-126 15-41 (77)
76 PF02197 RIIa: Regulatory subu 20.8 1.6E+02 0.0034 15.9 4.1 31 21-51 4-34 (38)
77 PRK01250 inorganic pyrophospha 20.7 72 0.0016 23.5 1.8 53 3-55 121-174 (176)
78 PRK09647 RNA polymerase sigma 20.6 2E+02 0.0042 21.0 4.2 45 5-50 135-182 (203)
79 PF08843 DUF1814: Nucleotidyl 20.2 2.7E+02 0.0058 19.9 4.8 30 44-75 204-233 (233)
80 PRK12515 RNA polymerase sigma 20.1 1.4E+02 0.0031 21.1 3.3 31 5-35 128-161 (189)
No 1
>PLN02279 ent-kaur-16-ene synthase
Probab=100.00 E-value=3e-35 Score=254.19 Aligned_cols=127 Identities=26% Similarity=0.423 Sum_probs=121.2
Q ss_pred CCcc-ccCcCChhHHHHHHHHHHHHHHHHHH-HHhhcCcchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhh
Q 040006 1 WDIG-HIDALPEYMKFIFKTLIGVYSEAEEE-LSKERRSYSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLR 78 (129)
Q Consensus 1 WD~~-~~~~Lpeymk~~f~~l~~~~~e~~~~-~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~ 78 (129)
||++ +++.||+|||+||.+|+++++|++.+ +.+||+ ++++|+|++|++++++|++||||+++||+||++|||+||.+
T Consensus 552 WD~~~~~~~lpeymki~f~aL~~t~nei~~~~~~~qGr-~v~~~l~~aW~~ll~ayl~EAeW~~~g~vPT~eEYL~na~v 630 (784)
T PLN02279 552 WDVNGSPDFCSEQVEIIFSALRSTISEIGDKAFTWQGR-NVTSHIIKIWLDLLKSMLTEAQWSSNKSTPTLDEYMTNAYV 630 (784)
T ss_pred hccccchhhCcHHHHHHHHHHHHHHHHHHHHHHHHcCc-hHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhhchh
Confidence 9998 67999999999999999999999986 557777 99999999999999999999999999999999999999999
Q ss_pred hhchhHHHHHHHHhcCCCCChHHHhhhcCchHHHHHHHHHHHHhcccccCC
Q 040006 79 SIGFLPIAVASFIFMGDIASREIFEWEMSNPKIIIAAETIFRFLDDIAGHK 129 (129)
Q Consensus 79 s~g~~~~~~~s~~~~g~~~~~e~~~~~~~~p~i~~~~~~i~RL~nDi~s~~ 129 (129)
|+|++++++++++++|+.+|+++++| .++|+|+++++.|+||+|||+||+
T Consensus 631 S~~l~~i~l~~~~~~G~~l~eev~e~-~~~~~L~~l~s~I~RLlNDI~S~e 680 (784)
T PLN02279 631 SFALGPIVLPALYLVGPKLSEEVVDS-PELHKLYKLMSTCGRLLNDIRGFK 680 (784)
T ss_pred hhhhHHHHHHHHHHhCCCCCHHHHhC-cchhHHHHHHHHHHHHHHhccccH
Confidence 99999999999999999999999999 599999999999999999999985
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=100.00 E-value=3.6e-34 Score=240.34 Aligned_cols=129 Identities=49% Similarity=0.848 Sum_probs=126.0
Q ss_pred CCccccCcCChhHHHHHHHHHHHHHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhhh
Q 040006 1 WDIGHIDALPEYMKFIFKTLIGVYSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRSI 80 (129)
Q Consensus 1 WD~~~~~~Lpeymk~~f~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s~ 80 (129)
||.+++++||+|||+||++++++++|+++++.++++++.++|++++|+++++||++||+|+++||+||++|||+|+.+|+
T Consensus 319 wd~~~~~~lPe~mk~~~~al~~~~~ei~~~~~~~~~~~~~~~~~~~~~~~~~a~l~EA~w~~~g~vPt~eEYl~~~~~S~ 398 (542)
T cd00684 319 WDISAIDQLPEYMKIVFKALLNTVNEIEEELLKEGGSYVVPYLKEAWKDLVKAYLVEAKWAHEGYVPTFEEYMENALVSI 398 (542)
T ss_pred ccccchhhccHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHhhhhHHh
Confidence 89999999999999999999999999999999998889999999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHHhcCCCCChHHHhhhcCchHHHHHHHHHHHHhcccccCC
Q 040006 81 GFLPIAVASFIFMGDIASREIFEWEMSNPKIIIAAETIFRFLDDIAGHK 129 (129)
Q Consensus 81 g~~~~~~~s~~~~g~~~~~e~~~~~~~~p~i~~~~~~i~RL~nDi~s~~ 129 (129)
|+++++.+++++||+.+|+++++|+...|+|+++++.++||+||++||+
T Consensus 399 g~~~~~~~~~~~~g~~l~~e~~e~~~~~~~l~~~~~~i~rL~NDi~S~~ 447 (542)
T cd00684 399 GLGPLLLTSFLGMGDILTEEAFEWLESRPKLVRASSTIGRLMNDIATYE 447 (542)
T ss_pred hHHHHHHHHHHhcCCCCCHHHHHHHhccHHHHHHHHHHHHHhcChhhhH
Confidence 9999999999999999999999999888999999999999999999985
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=99.86 E-value=8.5e-21 Score=145.77 Aligned_cols=129 Identities=50% Similarity=0.806 Sum_probs=119.2
Q ss_pred CCccccCcCChhHHHHHHHHHHHHHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhhh
Q 040006 1 WDIGHIDALPEYMKFIFKTLIGVYSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRSI 80 (129)
Q Consensus 1 WD~~~~~~Lpeymk~~f~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s~ 80 (129)
|+....+.+|++++.++++++++.+++...+.++++......+++.|.+++++++.||+|+.+|++|+++||+.++..|+
T Consensus 85 ~~~~~~~~~p~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~e~~~~~~~~~p~~~eYl~~R~~~~ 164 (284)
T cd00868 85 WDISAIDELPEYMKPVFKALYDLVNEIEEELAKEGGSESLPYLKEAWKDLLRAYLVEAKWANEGYVPSFEEYLENRRVSI 164 (284)
T ss_pred cChhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHhceehh
Confidence 56667789999999999999999999998777766668889999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHHhcCCCCChHHHhhhcCchHHHHHHHHHHHHhcccccCC
Q 040006 81 GFLPIAVASFIFMGDIASREIFEWEMSNPKIIIAAETIFRFLDDIAGHK 129 (129)
Q Consensus 81 g~~~~~~~s~~~~g~~~~~e~~~~~~~~p~i~~~~~~i~RL~nDi~s~~ 129 (129)
|.++.+....+++|..+|++.+.+.....++.++++.+++|+||+.||+
T Consensus 165 g~~~~~~l~~~~~g~~l~~~~~~~~~~~~~l~~~~~~~~~l~NDl~S~~ 213 (284)
T cd00868 165 GYPPLLALSFLGMGDILPEEAFEWLPSYPKLVRASSTIGRLLNDIASYE 213 (284)
T ss_pred hHHHHHHHHHHHcCCCCCHHHHHHhhhhHHHHHHHHHHHHHhccchHHH
Confidence 9999999999999999998666677899999999999999999999974
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=99.81 E-value=2.3e-19 Score=136.90 Aligned_cols=128 Identities=24% Similarity=0.374 Sum_probs=114.6
Q ss_pred CCccccCcCChhHHHHHHHHHHHHHHHHHHHHhh-cCcchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhh
Q 040006 1 WDIGHIDALPEYMKFIFKTLIGVYSEAEEELSKE-RRSYSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRS 79 (129)
Q Consensus 1 WD~~~~~~Lpeymk~~f~~l~~~~~e~~~~~~~~-~~~~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s 79 (129)
||+...+.+|++++.++.++.++++++...+.+. ++.+..+++++.|.++++++++|++|+..|++||++||++.+..|
T Consensus 99 ~~~~~~~~~~~~~~~~~~~l~d~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~ps~eeYl~~R~~t 178 (270)
T PF03936_consen 99 WDPNSGDPLPDPDKPLFRALADIWNRIAARMSPAQRRRDQIKRFRNSWREYLNAYLWEARWRERGRIPSLEEYLEMRRHT 178 (270)
T ss_dssp TSSGGGGGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS--SHHHHHHHHHHH
T ss_pred ccccccccccchhHHHHHHHHHHHHHHHHHhhhhhcccHHhhHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHhcccc
Confidence 5566778999999999999999999998765555 443588999999999999999999999999999999999999999
Q ss_pred hchhHHHHHHHHhcCCCCChHHHhhhcCchHHHHHHHHHHHHhcccccC
Q 040006 80 IGFLPIAVASFIFMGDIASREIFEWEMSNPKIIIAAETIFRFLDDIAGH 128 (129)
Q Consensus 80 ~g~~~~~~~s~~~~g~~~~~e~~~~~~~~p~i~~~~~~i~RL~nDi~s~ 128 (129)
+|.++++....+++|...++...+++.+.|.+.++++.+++|.|||.||
T Consensus 179 ~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~NDl~S~ 227 (270)
T PF03936_consen 179 SGVYPCLALIEFALEFALGELPPEVLEHPPMLRRLAADIIRLVNDLYSY 227 (270)
T ss_dssp TSHHHHHHHHHHHCSSCHTHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccHHHHHHHHhCCCccccccHHHHHhchHHHHHHHHHHHHhcccchh
Confidence 9999999999999987788888888888899999999999999999987
No 5
>PLN02592 ent-copalyl diphosphate synthase
Probab=99.81 E-value=1.5e-19 Score=156.91 Aligned_cols=107 Identities=17% Similarity=0.146 Sum_probs=92.3
Q ss_pred CCccccCcCCh------hHHHHHHHHHHHHHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHh
Q 040006 1 WDIGHIDALPE------YMKFIFKTLIGVYSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKS 74 (129)
Q Consensus 1 WD~~~~~~Lpe------ymk~~f~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~ 74 (129)
||.+++++||+ |||+||.+|||++||++.++.+.++.++++|++++|.++|+ +|.++|+
T Consensus 608 Wd~~~~~~lp~~~~~~~~mki~f~aLy~tineia~~a~~~qGr~v~~~L~~~W~~l~~------~w~~~g~--------- 672 (800)
T PLN02592 608 SDHHFNDRNMRRSGSVKTGEELVGLLLGTLNQLSLDALEAHGRDISHLLRHAWEMWLL------KWLLEGD--------- 672 (800)
T ss_pred cCchhhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHH------HHHhcCc---------
Confidence 89999999998 99999999999999998754444444999999999999999 6666665
Q ss_pred hhhhhhchhHHHHHHHH-hcCCCCChHHHhhhcCchHHHHHHHHHHHHhcccccCC
Q 040006 75 VSLRSIGFLPIAVASFI-FMGDIASREIFEWEMSNPKIIIAAETIFRFLDDIAGHK 129 (129)
Q Consensus 75 ~~~~s~g~~~~~~~s~~-~~g~~~~~e~~~~~~~~p~i~~~~~~i~RL~nDi~s~~ 129 (129)
+|+|.+.+++++++ .+|..+++++++ +|++.++++++.||+||++|++
T Consensus 673 ---~s~~~~~ilv~~~~l~~g~~lsee~l~----~~~~~~l~~li~Rl~nDl~t~~ 721 (800)
T PLN02592 673 ---GRQGEAELLVKTINLTAGRSLSEELLA----HPQYEQLAQLTNRICYQLGHYK 721 (800)
T ss_pred ---eeccchhhHHHHHHHhcCCCCCHHHcc----chhHHHHHHHHHHHHHhhhHHh
Confidence 45677778888888 459999999996 6899999999999999999974
No 6
>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=99.63 E-value=6e-16 Score=120.77 Aligned_cols=115 Identities=17% Similarity=0.093 Sum_probs=99.4
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhhhchhHHHHHH
Q 040006 10 PEYMKFIFKTLIGVYSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRSIGFLPIAVAS 89 (129)
Q Consensus 10 peymk~~f~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s~g~~~~~~~s 89 (129)
|+....+..++.+....+...+.. ...+.+++.|.+++.+++.|++|+.+|++||++||++++..|+|..+++...
T Consensus 105 ~~~~~p~~~~~~d~~~r~~~~~~~----~~~~r~~~~~~~~~~a~~~e~~~~~~~~~psl~eYl~~R~~~~g~~~~~~l~ 180 (303)
T cd00687 105 PDDATPLEFGLADLWRRTLARMSA----EWFNRFAHYTEDYFDAYIWEGKNRLNGHVPDVAEYLEMRRFNIGADPCLGLS 180 (303)
T ss_pred CCCCCHHHHHHHHHHHHhccCCCH----HHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhhhcccccccHHHH
Confidence 367778888888888877654322 3457889999999999999999999999999999999999999999999999
Q ss_pred HHhcCCCCChHHHhhhcCchHHHHHHHHHHHHhcccccCC
Q 040006 90 FIFMGDIASREIFEWEMSNPKIIIAAETIFRFLDDIAGHK 129 (129)
Q Consensus 90 ~~~~g~~~~~e~~~~~~~~p~i~~~~~~i~RL~nDi~s~~ 129 (129)
.+++|..++.++.+. ....++.++++.+++|+|||.||+
T Consensus 181 ~~~~g~~lp~~~~~~-~~~~~l~~~~~~~~~l~NDl~S~~ 219 (303)
T cd00687 181 EFIGGPEVPAAVRLD-PVMRALEALASDAIALVNDIYSYE 219 (303)
T ss_pred HHhcCCCCCHHHHhC-hHHHHHHHHHHHHHHHHHHHHhhH
Confidence 999998899988776 445679999999999999999984
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=99.00 E-value=3.3e-09 Score=77.56 Aligned_cols=115 Identities=21% Similarity=0.245 Sum_probs=90.2
Q ss_pred CcCChhHHHHHHHHHHHHHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhhhchhHHH
Q 040006 7 DALPEYMKFIFKTLIGVYSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRSIGFLPIA 86 (129)
Q Consensus 7 ~~Lpeymk~~f~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s~g~~~~~ 86 (129)
...|..+...+..+.+.+.++..... ......+++.+.+++.++..|+.|..+ +.||++||+.....++|.. +.
T Consensus 52 ~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~g~~~d~~~~~~-~~~t~~ey~~~~~~~t~~~-~~ 125 (243)
T cd00385 52 DGLPEAILAGDLLLADAFEELAREGS----PEALEILAEALLDLLEGQLLDLKWRRE-YVPTLEEYLEYCRYKTAGL-VG 125 (243)
T ss_pred cCchHHHHHHHHHHHHHHHHHHhCCC----HHHHHHHHHHHHHHHHHHHHHHHhccC-CCCCHHHHHHHHHHhHHHH-HH
Confidence 45778888888888888888764321 355778899999999999999999877 8999999999999998444 44
Q ss_pred HHHHHhcCCCCChHHHhhhcCchHHHHHHHHHHHHhcccccCC
Q 040006 87 VASFIFMGDIASREIFEWEMSNPKIIIAAETIFRFLDDIAGHK 129 (129)
Q Consensus 87 ~~s~~~~g~~~~~e~~~~~~~~p~i~~~~~~i~RL~nDi~s~~ 129 (129)
..+.++++...++ ..+.....++.+..+.+.+|.||+.++.
T Consensus 126 ~~~~~~~~~~~~~--~~~~~~~~~~~~~~g~~~ql~nDl~~~~ 166 (243)
T cd00385 126 ALCLLGAGLSGGE--AELLEALRKLGRALGLAFQLTNDLLDYE 166 (243)
T ss_pred HHHHHHHHHhCCC--HHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 5555655554444 5555666789999999999999998863
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=93.73 E-value=0.95 Score=33.69 Aligned_cols=85 Identities=14% Similarity=0.118 Sum_probs=60.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhh-hhchhHHHHHHHHhcCCCCChHHHhhhcCchHHHHHHHH
Q 040006 39 SIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLR-SIGFLPIAVASFIFMGDIASREIFEWEMSNPKIIIAAET 117 (129)
Q Consensus 39 ~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~-s~g~~~~~~~s~~~~g~~~~~e~~~~~~~~p~i~~~~~~ 117 (129)
......+...+++.+...+..|..+ ..||.++|++...- |+++....+......+.. +.+..+-+ .++.+..++
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 4556678889999999999999654 57899999999987 666554444333333332 33333333 467899999
Q ss_pred HHHHhcccccC
Q 040006 118 IFRFLDDIAGH 128 (129)
Q Consensus 118 i~RL~nDi~s~ 128 (129)
...+.||+..+
T Consensus 161 a~Qi~dd~~D~ 171 (236)
T cd00867 161 AFQLTDDLLDV 171 (236)
T ss_pred HHHHHHHhccc
Confidence 99999999764
No 9
>COG0864 NikR Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]
Probab=88.15 E-value=1.6 Score=30.98 Aligned_cols=50 Identities=16% Similarity=0.274 Sum_probs=32.8
Q ss_pred HHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhhhchh
Q 040006 24 YSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRSIGFL 83 (129)
Q Consensus 24 ~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s~g~~ 83 (129)
++|+++.+.+.|.+.+- +..++.++.|++|.+|.+.. |-+..|.++..+.
T Consensus 16 l~elD~~i~~rg~~sRS----E~IrdAir~yl~e~~~~~~~------~~~~~G~i~vvy~ 65 (136)
T COG0864 16 LEELDELIEERGYSSRS----ELIRDALREYLEEYRWLEDI------EGERAGVITVVYD 65 (136)
T ss_pred HHHHHHHHHHcCCCcHH----HHHHHHHHHHHHHhhhhccc------cceeEEEEEEEEc
Confidence 66666666656665665 44677889999999998765 3344455544443
No 10
>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases, head-to-tail. These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4) condensation reactions. This CD includes all-trans (E)-isoprenyl diphosphate synthases which synthesize various chain length (C10, C15, C20, C25, C30, C35, C40, C45, and C50) linear isoprenyl diphosphates from precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They catalyze the successive 1'-4 condensation of the 5-carbon IPP to allylic substrates geranyl-, farnesyl-, or geranylgeranyl-diphosphate. Isoprenoid chain elongation reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DDXX(XX
Probab=86.60 E-value=9.6 Score=29.12 Aligned_cols=86 Identities=16% Similarity=0.038 Sum_probs=58.7
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhhhchhHHHHHHHHhc-CCCCChHHHhhhcCchHHHHHHH
Q 040006 38 YSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRSIGFLPIAVASFIFM-GDIASREIFEWEMSNPKIIIAAE 116 (129)
Q Consensus 38 ~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s~g~~~~~~~s~~~~-g~~~~~e~~~~~~~~p~i~~~~~ 116 (129)
..+..+-+....++.+-..+..|... ..||.++|++...--+|.....++...++ +. .+.+..+-+ -++-+..+
T Consensus 108 ~~~~~~~~~~~~~~~GQ~~d~~~~~~-~~~~~~~y~~~~~~KT~~l~~~~~~~~a~l~~-~~~~~~~~l---~~~g~~lG 182 (259)
T cd00685 108 RALELFSEAILELVEGQLLDLLSEYD-TDVTEEEYLRIIRLKTAALFAAAPLLGALLAG-ADEEEAEAL---KRFGRNLG 182 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCC-CCCCHHHHHHHHHHhHHHHHHHHHHHHHHHcC-CCHHHHHHH---HHHHHHHH
Confidence 44556667788899999999999654 57999999998877777664433322222 11 133343333 46889999
Q ss_pred HHHHHhcccccC
Q 040006 117 TIFRFLDDIAGH 128 (129)
Q Consensus 117 ~i~RL~nDi~s~ 128 (129)
+..-+.||+..+
T Consensus 183 ~afQi~DD~ld~ 194 (259)
T cd00685 183 LAFQIQDDILDL 194 (259)
T ss_pred HHHHHHHHhhcc
Confidence 999999997653
No 11
>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=84.26 E-value=18 Score=28.89 Aligned_cols=86 Identities=10% Similarity=-0.015 Sum_probs=56.7
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhhhchhHHHHHHHHh-cCCCCChHHHhhhcCchHHHHHHH
Q 040006 38 YSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRSIGFLPIAVASFIF-MGDIASREIFEWEMSNPKIIIAAE 116 (129)
Q Consensus 38 ~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s~g~~~~~~~s~~~-~g~~~~~e~~~~~~~~p~i~~~~~ 116 (129)
..+..+-+...+++.+-+.+..+..+ ..+|.++|++...-=+|.-.-.++ .+| +--..+++..+-+ -++-+..+
T Consensus 133 ~~~~~~~~~~~~~~~Gq~~~~~~~~~-~~~~~~~y~~~~~~KTa~L~~~~~-~~ga~~ag~~~~~~~~l---~~~G~~lG 207 (322)
T TIGR02749 133 EVVKLISKVITDFAEGEIKQGLNQFD-SDLSLEDYLEKSFYKTASLVAASS-KAAAVLSDVPSQVANDL---YEYGKHLG 207 (322)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcccC-CCCCHHHHHHHHHccHHHHHHHHH-HHHHHHcCcCHHHHHHH---HHHHHHHH
Confidence 45566677788899998888877543 457999999876655554433222 222 1112345555444 35788999
Q ss_pred HHHHHhcccccC
Q 040006 117 TIFRFLDDIAGH 128 (129)
Q Consensus 117 ~i~RL~nDi~s~ 128 (129)
+...+.||+..+
T Consensus 208 ~aFQi~DDild~ 219 (322)
T TIGR02749 208 LAFQVVDDILDF 219 (322)
T ss_pred HHHHHHHHhccC
Confidence 999999999764
No 12
>PLN02890 geranyl diphosphate synthase
Probab=83.28 E-value=14 Score=30.87 Aligned_cols=87 Identities=13% Similarity=0.020 Sum_probs=60.0
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhhhchhHHHHHHHHhcCCCCChHHHhhhcCchHHHHHHHH
Q 040006 38 YSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRSIGFLPIAVASFIFMGDIASREIFEWEMSNPKIIIAAET 117 (129)
Q Consensus 38 ~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s~g~~~~~~~s~~~~g~~~~~e~~~~~~~~p~i~~~~~~ 117 (129)
.++..+-++...++.+-+.+..|.. ...+|.++|++...--+|.-...++..-++--..+++..+.+ -++-+..++
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 4566777888999999999999864 456899999987665555543333222222112355666554 367889999
Q ss_pred HHHHhcccccC
Q 040006 118 IFRFLDDIAGH 128 (129)
Q Consensus 118 i~RL~nDi~s~ 128 (129)
...+.||+-.+
T Consensus 303 AFQI~DDiLD~ 313 (422)
T PLN02890 303 AFQLIDDVLDF 313 (422)
T ss_pred HHHHHHHHHhh
Confidence 99999998654
No 13
>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=78.71 E-value=29 Score=27.56 Aligned_cols=85 Identities=14% Similarity=0.022 Sum_probs=56.9
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhhhchhHHHHHHHHhc--CCCCChHHHhhhcCchHHHHHH
Q 040006 38 YSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRSIGFLPIAVASFIFM--GDIASREIFEWEMSNPKIIIAA 115 (129)
Q Consensus 38 ~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s~g~~~~~~~s~~~~--g~~~~~e~~~~~~~~p~i~~~~ 115 (129)
..+..+-+...+++.+-..+..|.. +..++.++|++...--+|.....+ +.+|. +. .+.+..+-+ -++-+..
T Consensus 129 ~~~~~~~~~~~~~~~Gq~~~~~~~~-~~~~~~~~Y~~~i~~KTa~L~~~~-~~~ga~~ag-~~~~~~~~l---~~~g~~l 202 (319)
T TIGR02748 129 RAHQILSHTIVEVCRGEIEQIKDKY-NFDQNLRTYLRRIKRKTALLIAAS-CQLGAIASG-ANEAIVKKL---YWFGYYV 202 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHcC-CCHHHHHHH---HHHHHHH
Confidence 3456667778889999888888854 446799999988776666553332 23332 22 234444433 3578899
Q ss_pred HHHHHHhcccccC
Q 040006 116 ETIFRFLDDIAGH 128 (129)
Q Consensus 116 ~~i~RL~nDi~s~ 128 (129)
++...+.||+..+
T Consensus 203 G~aFQI~DDilD~ 215 (319)
T TIGR02748 203 GMSYQITDDILDF 215 (319)
T ss_pred HHHHHHHHHHHHc
Confidence 9999999998654
No 14
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=76.78 E-value=29 Score=27.72 Aligned_cols=86 Identities=19% Similarity=0.067 Sum_probs=60.6
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhhhchhHHHHHHHHhcCCCCChHHHhhhcCchHHHHHHHH
Q 040006 38 YSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRSIGFLPIAVASFIFMGDIASREIFEWEMSNPKIIIAAET 117 (129)
Q Consensus 38 ~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s~g~~~~~~~s~~~~g~~~~~e~~~~~~~~p~i~~~~~~ 117 (129)
.....+.+....+|.+-..+..+.++. +|.++|++.-.-=+|.-.-.++-.-++--..+++..+.+ -.+-+..++
T Consensus 134 ~~~~~~~~~~~~~~~GQ~lDl~~~~~~--~t~e~y~~~i~~KTa~L~~~a~~~ga~la~~~~~~~~~l---~~~g~~lGl 208 (322)
T COG0142 134 EAIKALAEAINGLCGGQALDLAFENKP--VTLEEYLRVIELKTAALFAAAAVLGAILAGADEELLEAL---EDYGRNLGL 208 (322)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHccCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHH---HHHHHHhhH
Confidence 355667788899999999999987655 999999997776665554433322222112235666665 357899999
Q ss_pred HHHHhcccccC
Q 040006 118 IFRFLDDIAGH 128 (129)
Q Consensus 118 i~RL~nDi~s~ 128 (129)
..-+.||+-.+
T Consensus 209 aFQi~DDiLD~ 219 (322)
T COG0142 209 AFQIQDDILDI 219 (322)
T ss_pred HHHHHHHhhcC
Confidence 99999998654
No 15
>PLN02857 octaprenyl-diphosphate synthase
Probab=72.54 E-value=40 Score=28.12 Aligned_cols=87 Identities=16% Similarity=0.030 Sum_probs=57.6
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhhhchhHHHHHHHHhcCCCCChHHHhhhcCchHHHHHHHH
Q 040006 38 YSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRSIGFLPIAVASFIFMGDIASREIFEWEMSNPKIIIAAET 117 (129)
Q Consensus 38 ~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s~g~~~~~~~s~~~~g~~~~~e~~~~~~~~p~i~~~~~~ 117 (129)
..+..+.+...+++.+-+.+..+.. +..++.++|++...-=+|.-...++..-++--..+++..+-+ -++-+..++
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 4556667778888888888888764 445799999997776665554333222111112355555554 457888999
Q ss_pred HHHHhcccccC
Q 040006 118 IFRFLDDIAGH 128 (129)
Q Consensus 118 i~RL~nDi~s~ 128 (129)
...+.||+..+
T Consensus 303 AFQI~DDiLD~ 313 (416)
T PLN02857 303 AFQVVDDILDF 313 (416)
T ss_pred HHHHHHHHHhh
Confidence 99999998654
No 16
>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=67.30 E-value=5.9 Score=27.72 Aligned_cols=57 Identities=16% Similarity=0.233 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHH-HHHhhhhhhh
Q 040006 20 LIGVYSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMD-EYKSVSLRSI 80 (129)
Q Consensus 20 l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~e-EYm~~~~~s~ 80 (129)
+.-.+.||++-+...|+ .+-.+.||+++.+-+.-++.....-+|.+| |+...+.-|+
T Consensus 43 lwa~l~dIs~qv~~~G~----k~~~e~WK~~~~~~~~~~~~~~~~~~~gl~Gg~v~~g~sTs 100 (127)
T PF05772_consen 43 LWAMLGDISRQVEWNGR----KLDPEDWKELFTAAFLIATGEEQRVVPGLDGGFVVLGESTS 100 (127)
T ss_dssp HHHHHHHHHHH--BTTB-------HHHHHHHHHHHH-----S--EEEE-TTSSEEEE---TT
T ss_pred HHHHHHHHHHHhHhcCc----cCCHHHHHHHHHHHHhhhccchhhhccCCCCCeEEEeeech
Confidence 34467888887777777 556688999999999666665556677766 5544444333
No 17
>COG2443 Sss1 Preprotein translocase subunit Sss1 [Intracellular trafficking and secretion]
Probab=66.70 E-value=16 Score=22.69 Aligned_cols=21 Identities=14% Similarity=0.097 Sum_probs=16.5
Q ss_pred CCCCCHHHHHhhhhhhhchhH
Q 040006 64 GYVPSMDEYKSVSLRSIGFLP 84 (129)
Q Consensus 64 ~~iPt~eEYm~~~~~s~g~~~ 84 (129)
-..|+-|||...+.++..+-.
T Consensus 25 arKP~~eEy~~~aKi~~~Gi~ 45 (65)
T COG2443 25 ARKPDWEEYSKIAKITGLGIL 45 (65)
T ss_pred HhCCCHHHHHHHHHHHHHHHH
Confidence 458999999999998765443
No 18
>PRK00630 nickel responsive regulator; Provisional
Probab=66.49 E-value=20 Score=25.72 Aligned_cols=36 Identities=17% Similarity=0.347 Sum_probs=25.0
Q ss_pred HHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHhcC
Q 040006 24 YSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKWLNE 63 (129)
Q Consensus 24 ~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~~ 63 (129)
.+++++.+...|-.++- +++++++|.|+.|.+|...
T Consensus 22 l~~lD~~~~~~gy~sRS----e~Ir~~iR~~l~e~~~~~~ 57 (148)
T PRK00630 22 LDELDNRIIKNGYSSRS----ELVRDLIREKLVEDNWAED 57 (148)
T ss_pred HHHHHHHHHHcCCCCHH----HHHHHHHHHHHHHhhhhcc
Confidence 56666555555544454 4578889999999999753
No 19
>PRK10888 octaprenyl diphosphate synthase; Provisional
Probab=65.83 E-value=67 Score=25.63 Aligned_cols=85 Identities=12% Similarity=-0.031 Sum_probs=57.6
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhhhchhHHHHHHHHhc--CCCCChHHHhhhcCchHHHHHH
Q 040006 38 YSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRSIGFLPIAVASFIFM--GDIASREIFEWEMSNPKIIIAA 115 (129)
Q Consensus 38 ~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s~g~~~~~~~s~~~~--g~~~~~e~~~~~~~~p~i~~~~ 115 (129)
..+..+-+....++.+-..+..|.. +..+|.++|++...--+|...-.+ +.+|. +. .+.+..+-+ -++-+..
T Consensus 130 ~~~~~~~~~~~~~~~Gq~~d~~~~~-~~~~s~~~y~~~i~~KTa~lf~~~-~~~ga~lag-~~~~~~~~l---~~~g~~l 203 (323)
T PRK10888 130 KVLEVMSEAVNVIAEGEVLQLMNVN-DPDITEENYMRVIYSKTARLFEAA-AQCSGILAG-CTPEQEKGL---QDYGRYL 203 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHcC-CCHHHHHHH---HHHHHHH
Confidence 4456667778889998888888854 345899999998776666553332 33332 22 244444433 3578899
Q ss_pred HHHHHHhcccccC
Q 040006 116 ETIFRFLDDIAGH 128 (129)
Q Consensus 116 ~~i~RL~nDi~s~ 128 (129)
++..-+.||+..+
T Consensus 204 G~aFQi~DD~ld~ 216 (323)
T PRK10888 204 GTAFQLIDDLLDY 216 (323)
T ss_pred HHHHHHHHHhhcc
Confidence 9999999998754
No 20
>COG4860 Uncharacterized protein conserved in archaea [Function unknown]
Probab=60.22 E-value=34 Score=24.74 Aligned_cols=59 Identities=22% Similarity=0.279 Sum_probs=36.6
Q ss_pred HHHHHHHHH---HHHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHh--cCCCCCCHHHHHhhhhhhh
Q 040006 14 KFIFKTLIG---VYSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKWL--NEGYVPSMDEYKSVSLRSI 80 (129)
Q Consensus 14 k~~f~~l~~---~~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~--~~~~iPt~eEYm~~~~~s~ 80 (129)
|-+|.+|.. |..|+|+...++|+ ..+.++ =++=|-|++|+ .+|..|.-+=|-.-.-|++
T Consensus 27 rKl~~aLstgW~T~~eiee~iG~eg~-RaL~iL-------kkagmlEtqWr~p~~G~kPeKeYHtsYt~Vqi 90 (170)
T COG4860 27 RKLLLALSTGWITLPEIEEKIGKEGR-RALLIL-------KKAGMLETQWRTPSNGQKPEKEYHTSYTNVQI 90 (170)
T ss_pred HHHHHHHhhcceeHHHHHHHhchhhH-HHHHHH-------HhhcchhheeeccCCCCCchhhhhhheeeEEE
Confidence 344444433 56788877777777 344444 45667899998 5688898554444444443
No 21
>PRK01002 nickel responsive regulator; Provisional
Probab=53.32 E-value=43 Score=23.63 Aligned_cols=36 Identities=17% Similarity=0.389 Sum_probs=24.3
Q ss_pred HHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHhcC
Q 040006 24 YSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKWLNE 63 (129)
Q Consensus 24 ~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~~ 63 (129)
++++++-+.++|-.++- ++.++.++.|+.|.+|..+
T Consensus 16 l~~lD~~~~~~g~~sRS----e~Ir~air~~l~~~~~~~~ 51 (141)
T PRK01002 16 LGEFDEIIEERGYASRS----EGIRDAIRDYIIKYKWMNS 51 (141)
T ss_pred HHHHHHHHHHcCCCCHH----HHHHHHHHHHHHHhhhccC
Confidence 56666555556533444 4577888999999999654
No 22
>CHL00151 preA prenyl transferase; Reviewed
Probab=48.30 E-value=1.4e+02 Score=23.76 Aligned_cols=85 Identities=12% Similarity=-0.008 Sum_probs=53.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhhhchhHHHHHHHHhc-CCCCChHHHhhhcCchHHHHHHHH
Q 040006 39 SIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRSIGFLPIAVASFIFM-GDIASREIFEWEMSNPKIIIAAET 117 (129)
Q Consensus 39 ~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s~g~~~~~~~s~~~~-g~~~~~e~~~~~~~~p~i~~~~~~ 117 (129)
....+.+...+++.+-+.+..+.. ..-+|.++|+....-=+|...-.++..-++ +. .+.+..+-+ -++-+..++
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 455667777888888777776643 345799999997554444443322211111 22 244444444 467889999
Q ss_pred HHHHhcccccC
Q 040006 118 IFRFLDDIAGH 128 (129)
Q Consensus 118 i~RL~nDi~s~ 128 (129)
...+.||+-.+
T Consensus 210 aFQi~DDilD~ 220 (323)
T CHL00151 210 AFQIIDDVLDI 220 (323)
T ss_pred HHHHHHHHhhc
Confidence 99999998654
No 23
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=46.23 E-value=41 Score=18.74 Aligned_cols=29 Identities=21% Similarity=0.224 Sum_probs=19.0
Q ss_pred ccCcCChhHHHHHHHHHH---HHHHHHHHHHh
Q 040006 5 HIDALPEYMKFIFKTLIG---VYSEAEEELSK 33 (129)
Q Consensus 5 ~~~~Lpeymk~~f~~l~~---~~~e~~~~~~~ 33 (129)
++++||+--+-+....|- ++.||++.+..
T Consensus 1 Al~~L~~~er~vi~~~y~~~~t~~eIa~~lg~ 32 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRYFEGLTLEEIAERLGI 32 (50)
T ss_dssp HHCTS-HHHHHHHHHHHTST-SHHHHHHHHTS
T ss_pred ChhhCCHHHHHHHHHHhcCCCCHHHHHHHHCC
Confidence 468899887777777763 57777655433
No 24
>PF13060 DUF3921: Protein of unknown function (DUF3921)
Probab=45.46 E-value=63 Score=18.99 Aligned_cols=43 Identities=16% Similarity=0.179 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHH
Q 040006 13 MKFIFKTLIGVYSEAEEELSKERRSYSIQYAIRSFQELVMKYFCE 57 (129)
Q Consensus 13 mk~~f~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~E 57 (129)
|..+-+++-.+++|+.+++..+|- +..-+.++=.+++.+.--|
T Consensus 6 lsmiqkaih~tydelgkei~~~g~--~~d~i~kaqeeylsals~e 48 (58)
T PF13060_consen 6 LSMIQKAIHRTYDELGKEIDLQGV--IADEIQKAQEEYLSALSHE 48 (58)
T ss_pred HHHHHHHHHHhHHHHhHHhhhcch--HHHHHHHHHHHHHHHhhHH
Confidence 567888999999999999888874 5555566666666555444
No 25
>PRK09400 secE preprotein translocase subunit SecE; Reviewed
Probab=44.01 E-value=51 Score=20.03 Aligned_cols=20 Identities=15% Similarity=0.039 Sum_probs=15.5
Q ss_pred CCCCCHHHHHhhhhhhhchh
Q 040006 64 GYVPSMDEYKSVSLRSIGFL 83 (129)
Q Consensus 64 ~~iPt~eEYm~~~~~s~g~~ 83 (129)
-..|+-+||...+.++.-+-
T Consensus 24 ~~KPd~~Ef~~ia~~~~iG~ 43 (61)
T PRK09400 24 ARKPTREEFLLVAKVTGLGI 43 (61)
T ss_pred hcCCCHHHHHHHHHHHHHHH
Confidence 45799999999998775433
No 26
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=43.28 E-value=31 Score=19.42 Aligned_cols=27 Identities=30% Similarity=0.283 Sum_probs=17.9
Q ss_pred cccCcCChhHHHHHHHHHH---HHHHHHHH
Q 040006 4 GHIDALPEYMKFIFKTLIG---VYSEAEEE 30 (129)
Q Consensus 4 ~~~~~Lpeymk~~f~~l~~---~~~e~~~~ 30 (129)
.++..||+..+.+|.-.|- ++.||++.
T Consensus 6 ~~l~~L~~~~r~i~~l~~~~g~s~~eIa~~ 35 (54)
T PF08281_consen 6 QALAQLPERQREIFLLRYFQGMSYAEIAEI 35 (54)
T ss_dssp HHHHCS-HHHHHHHHHHHTS---HHHHHHH
T ss_pred HHHHCCCHHHHHHHHHHHHHCcCHHHHHHH
Confidence 3678899999988877653 56666654
No 27
>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=42.39 E-value=1.5e+02 Score=22.52 Aligned_cols=60 Identities=18% Similarity=0.134 Sum_probs=40.3
Q ss_pred CCCCCHHHHHhhhhhhhchhHHHHHHHHhc-CCCCChHHHhhhcCchHHHHHHHHHHHHhccccc
Q 040006 64 GYVPSMDEYKSVSLRSIGFLPIAVASFIFM-GDIASREIFEWEMSNPKIIIAAETIFRFLDDIAG 127 (129)
Q Consensus 64 ~~iPt~eEYm~~~~~s~g~~~~~~~s~~~~-g~~~~~e~~~~~~~~p~i~~~~~~i~RL~nDi~s 127 (129)
+..+|.++|++...--+|...-..+..-++ +. .+.+..+-+ -++-+..++...+.||+..
T Consensus 130 ~~~~~~~~y~~i~~~KTg~l~~~~~~~ga~lag-~~~~~~~~l---~~~g~~lG~afQi~DD~~d 190 (260)
T PF00348_consen 130 DKDPTEEEYLEIIRLKTGSLFALACQLGAILAG-ADEEQIEAL---REFGRHLGIAFQIRDDLLD 190 (260)
T ss_dssp TSSTSHHHHHHHHHHHTHHHHHHHHHHHHHHTT-SGHHHHHHH---HHHHHHHHHHHHHHHHHHH
T ss_pred cccccHHHHHHHHhhcchHHHHHHHHHHHHhcc-chhHHHHHH---HHHHHHHHHHHhhhhhhhh
Confidence 348899999998887777664333222222 22 345555554 4688999999999999854
No 28
>PRK14744 leu operon leader peptide; Provisional
Probab=40.85 E-value=12 Score=19.12 Aligned_cols=18 Identities=17% Similarity=-0.092 Sum_probs=15.3
Q ss_pred hHHHHHHHHHHHHhcccc
Q 040006 109 PKIIIAAETIFRFLDDIA 126 (129)
Q Consensus 109 p~i~~~~~~i~RL~nDi~ 126 (129)
+-++.+++.=+|+.+||+
T Consensus 10 lLLLNA~~lRGR~v~giQ 27 (28)
T PRK14744 10 LLLLNAFIVRGRPVGGIQ 27 (28)
T ss_pred HHHhhhHhhcCccccccc
Confidence 457889999999999986
No 29
>TIGR02793 nikR nickel-responsive transcriptional regulator NikR. Three members of the seed for this model, from Escherichia coli, Pseudomonas putida, and Brucella melitensis, are found associated with a nickel ABC transporter operon that acts to import nickel for use as a cofactor in urease or hydrogenase. These proteins, with characterized nickel-binding and DNA-binding domains, act as nickel-responsive transcriptional regulators. In the larger family of full-length homologs, most others both lack proximity to the nickel ABC transporter operon and form a separate clade. Several of the homologs not within the scope of this model, but rather scoring between the trusted and noise cutoffs, have been shown to bind nickel, copper, or both, and to regulate genes in response to nickel.
Probab=40.42 E-value=95 Score=21.60 Aligned_cols=36 Identities=3% Similarity=0.027 Sum_probs=23.9
Q ss_pred HHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHhcC
Q 040006 24 YSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKWLNE 63 (129)
Q Consensus 24 ~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~~ 63 (129)
++++++-+...|=.++- ++.++++|.|+.|-+|...
T Consensus 12 l~~lD~~~~~~g~~~RS----e~ir~~ir~~l~e~~~~~~ 47 (129)
T TIGR02793 12 LETLDRLIARRGYQNRS----EAIRDLLRSGLQQEAAEQH 47 (129)
T ss_pred HHHHHHHHHHcCCCCHH----HHHHHHHHHHHHHhhhhcC
Confidence 55555555555533444 5577889999999999654
No 30
>PRK04460 nickel responsive regulator; Provisional
Probab=39.93 E-value=98 Score=21.79 Aligned_cols=36 Identities=11% Similarity=0.346 Sum_probs=23.9
Q ss_pred HHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHhcC
Q 040006 24 YSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKWLNE 63 (129)
Q Consensus 24 ~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~~ 63 (129)
++++++.+...|=.++- ++.++.+|.|+.|.+|...
T Consensus 14 l~~lD~~~~~~gy~sRS----e~ird~ir~~l~e~~~~~~ 49 (137)
T PRK04460 14 LEKFDELIEEKGYQNRS----EAIRDLIRDFLVEHEWEEG 49 (137)
T ss_pred HHHHHHHHHHcCCCCHH----HHHHHHHHHHHHHhhhhcC
Confidence 55565555555522333 5578889999999999754
No 31
>cd00686 Terpene_cyclase_cis_trans_C1 Cis, Trans, Terpene Cyclases, Class 1. This CD includes the terpenoid cyclase, trichodiene synthase, which catalyzes the cyclization of farnesyl diphosphate (FPP) to trichodiene using a cis-trans pathway, and is the first committed step in the biosynthesis of trichothecene toxins and antibiotics. As with other enzymes with the 'terpenoid synthase fold', this enzyme has two conserved metal binding motifs that coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP. 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 as homodimers and are found in several genera of fungi.
Probab=36.59 E-value=1.4e+02 Score=24.53 Aligned_cols=114 Identities=18% Similarity=0.147 Sum_probs=58.4
Q ss_pred cCcCChhHHHHHHHHHH----------HHHHH-HHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHh
Q 040006 6 IDALPEYMKFIFKTLIG----------VYSEA-EEELSKERRSYSIQYAIRSFQELVMKYFCEAKWLNEGYVPSMDEYKS 74 (129)
Q Consensus 6 ~~~Lpeymk~~f~~l~~----------~~~e~-~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~ 74 (129)
.++..+.|+.++.-|.. .+++. .+-+..-|. ++-.-+.+.--+.+.+-..|.. +-+.-|.-.+|-.
T Consensus 103 ~~e~~~~m~~f~~dL~~G~~qkhP~l~~v~~~l~~~lr~fGp-F~s~~IikSTLdFv~g~~iEq~--nf~~~p~A~~fP~ 179 (357)
T cd00686 103 KDDPYPTMVNYFDDLQAGREQAHPWWALVNEHFPNVLRHFGP-FCSLNLIRSTLDFFEGCWIEQY--NFGGFPGSHDYPQ 179 (357)
T ss_pred ccccchHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHHHHhhh-hhHHHHHHHHHHHHHHHHHhhh--ccCCCCCCcccch
Confidence 46667778887777654 12222 222222233 5555566666677777777755 2344565455544
Q ss_pred hhhhhhchhHHHHHHHHhcCCCCChHHHhhhcCchHHHHHHHHH---HHHhcccccC
Q 040006 75 VSLRSIGFLPIAVASFIFMGDIASREIFEWEMSNPKIIIAAETI---FRFLDDIAGH 128 (129)
Q Consensus 75 ~~~~s~g~~~~~~~s~~~~g~~~~~e~~~~~~~~p~i~~~~~~i---~RL~nDi~s~ 128 (129)
.-..=+|.+=...+ |++-.+..++... +..+.-+...+ .=.+|||-||
T Consensus 180 ylR~ksGl~E~yA~-FiFPk~~FpE~~~-----~~qi~~AIp~~~~~i~~~NDILSF 230 (357)
T cd00686 180 FLRRMNGLGHCVGA-SLWPKEQFNERSL-----FLEITSAIAQMENWMVWVNDLMSF 230 (357)
T ss_pred HHHhccCCcceeEE-EecchhhCchHhh-----HHHhhHHHHHHHHHHHhhhhhhhe
Confidence 44444454433332 3433333333222 22233344433 3478999876
No 32
>PF15265 FAM196: FAM196 family
Probab=36.48 E-value=22 Score=30.59 Aligned_cols=22 Identities=41% Similarity=0.631 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHH-HHHhhcCcch
Q 040006 18 KTLIGVYSEAEE-ELSKERRSYS 39 (129)
Q Consensus 18 ~~l~~~~~e~~~-~~~~~~~~~~ 39 (129)
+.|+|++.|+|+ ++.++|++|+
T Consensus 412 KVLLnVIQDLEKgeA~rEGrsYR 434 (514)
T PF15265_consen 412 KVLLNVIQDLEKGEAHREGRSYR 434 (514)
T ss_pred HHHHHHHHHHHhhhccccccccc
Confidence 568999999997 7999999874
No 33
>PF14162 YozD: YozD-like protein
Probab=36.11 E-value=30 Score=20.55 Aligned_cols=21 Identities=24% Similarity=0.610 Sum_probs=17.5
Q ss_pred cCCCCCCHHHHHhhhhhhhch
Q 040006 62 NEGYVPSMDEYKSVSLRSIGF 82 (129)
Q Consensus 62 ~~~~iPt~eEYm~~~~~s~g~ 82 (129)
..||+|+-+|--+.|.++.-+
T Consensus 23 kRGyvP~e~El~eiADItFeY 43 (57)
T PF14162_consen 23 KRGYVPTEEELEEIADITFEY 43 (57)
T ss_pred HccCCCcHHHHHHHHHHHHHH
Confidence 469999999998888888744
No 34
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=35.73 E-value=93 Score=22.14 Aligned_cols=50 Identities=18% Similarity=0.042 Sum_probs=30.2
Q ss_pred cccCcCChhHHHHHHHHH---HHHHHHHHHHHhhcCcchHHHHHHHHHHHHHHH
Q 040006 4 GHIDALPEYMKFIFKTLI---GVYSEAEEELSKERRSYSIQYAIRSFQELVMKY 54 (129)
Q Consensus 4 ~~~~~Lpeymk~~f~~l~---~~~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ay 54 (129)
.++++||+..+-+|..-+ -++.||+..+.-..+ .+...+.++-+.+-+.+
T Consensus 127 ~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~-tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 127 ACVDRLPPRTGRVFMMREWLELETEEICQELQITAT-NAWVLLYRARMRLRECL 179 (191)
T ss_pred HHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHH-HHHHHHHHHHHHHHHHH
Confidence 367789998888886654 257777765444443 44455555555554433
No 35
>COG4572 ChaB Putative cation transport regulator [General function prediction only]
Probab=35.55 E-value=24 Score=22.27 Aligned_cols=21 Identities=24% Similarity=0.257 Sum_probs=16.8
Q ss_pred CcCChhHHHHHHHHHHHHHHH
Q 040006 7 DALPEYMKFIFKTLIGVYSEA 27 (129)
Q Consensus 7 ~~Lpeymk~~f~~l~~~~~e~ 27 (129)
++||+..+.+|.+.||.--+-
T Consensus 15 ~~lp~haqdiy~~afnsA~e~ 35 (76)
T COG4572 15 HQLPSHAQDIYKAAFNSAWEQ 35 (76)
T ss_pred HHhHHHHHHHHHHHHHHHHhh
Confidence 478999999999999865443
No 36
>PF11433 DUF3198: Protein of unknown function (DUF3198); InterPro: IPR024504 This domain is found at the C-terminal of a family of archaeal proteins annotated as membrane proteins.; PDB: 1X9B_A.
Probab=34.21 E-value=99 Score=18.02 Aligned_cols=29 Identities=17% Similarity=0.284 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHhhcCcch--HHHHHHHHH
Q 040006 20 LIGVYSEAEEELSKERRSYS--IQYAIRSFQ 48 (129)
Q Consensus 20 l~~~~~e~~~~~~~~~~~~~--~~~~~~~~~ 48 (129)
+.+-.+|+|+-..+-|++|. +.-.|+.|+
T Consensus 19 Fv~nL~ELE~is~rlg~~Y~~~LeeaK~kWk 49 (51)
T PF11433_consen 19 FVRNLTELERISKRLGKSYQIRLEEAKEKWK 49 (51)
T ss_dssp HHHHHHHHHHHHHHH-SHHHHHHHHHHHHH-
T ss_pred HHHhHHHHHHHHHHHchHHHHHHHHHHHhhc
Confidence 34556777776677777754 456677775
No 37
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=34.21 E-value=73 Score=23.23 Aligned_cols=58 Identities=26% Similarity=0.260 Sum_probs=33.6
Q ss_pred HHHHHHHHHH---HHHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHhc--CCCCCCHHHHHhhhhh
Q 040006 13 MKFIFKTLIG---VYSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKWLN--EGYVPSMDEYKSVSLR 78 (129)
Q Consensus 13 mk~~f~~l~~---~~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~--~~~iPt~eEYm~~~~~ 78 (129)
-|-+|..|.+ |..|+++....+++ ++..-|=++-|.|.+|+- .|..|.-+=+-.-+.+
T Consensus 19 ~kkV~~~Ls~~W~T~~El~e~~G~d~~--------~~L~~LkK~gLiE~qWrmP~pG~kPeKEYhtsYs~v 81 (160)
T PF09824_consen 19 YKKVYDELSKGWMTEEELEEKYGKDVR--------ESLLILKKGGLIESQWRMPEPGEKPEKEYHTSYSKV 81 (160)
T ss_pred HHHHHHHHHhccCCHHHHHHHHCcCHH--------HHHHHHHHcCchhhccccCCCCCCchHHHHhhHhhe
Confidence 4555666654 56666655544442 445555678899999984 3556764433333333
No 38
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=33.05 E-value=2.1e+02 Score=21.76 Aligned_cols=46 Identities=11% Similarity=0.127 Sum_probs=28.6
Q ss_pred cccCcCChhHHHHHHHHHH---HHHHHHHHHHhhcCcchHHHHHHHHHHH
Q 040006 4 GHIDALPEYMKFIFKTLIG---VYSEAEEELSKERRSYSIQYAIRSFQEL 50 (129)
Q Consensus 4 ~~~~~Lpeymk~~f~~l~~---~~~e~~~~~~~~~~~~~~~~~~~~~~~l 50 (129)
.++++||+-.|-+|..-+- ++.||+..+....+ .+...+.++-+.+
T Consensus 157 ~aL~~Lp~~~R~v~~L~~~eg~S~~EIA~~Lgis~~-TVk~rl~RAr~~L 205 (244)
T TIGR03001 157 EALAALSERERHLLRLHFVDGLSMDRIGAMYQVHRS-TVSRWVAQARERL 205 (244)
T ss_pred HHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHH-HHHHHHHHHHHHH
Confidence 4678899988888877653 68888766554444 3334444444433
No 39
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=32.48 E-value=95 Score=24.00 Aligned_cols=55 Identities=11% Similarity=0.132 Sum_probs=35.4
Q ss_pred cccCcCChhHHHHHHHHH-------HHHHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHH
Q 040006 4 GHIDALPEYMKFIFKTLI-------GVYSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKW 60 (129)
Q Consensus 4 ~~~~~Lpeymk~~f~~l~-------~~~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW 60 (129)
.+++.||+..|.++...| -++.||+..+.-..+ .+...+.++.+ .++..|.+..|
T Consensus 218 ~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~-tVk~~l~rAlk-kLr~~l~~~~~ 279 (285)
T TIGR02394 218 AWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRE-RVRQIQVEALK-KLRRILERDGV 279 (285)
T ss_pred HHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHH-HHHHHHHHHHH-HHHHHHHHhhh
Confidence 468899999999888765 278899876554433 44455555554 33445554444
No 40
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=32.12 E-value=2e+02 Score=21.43 Aligned_cols=29 Identities=31% Similarity=0.374 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCCHHH
Q 040006 42 YAIRSFQELVMKYFCEAKWLNEGYVPSMDE 71 (129)
Q Consensus 42 ~~~~~~~~l~~ayl~EakW~~~~~iPt~eE 71 (129)
+...+.++++.|..- ..|..++.+||.+|
T Consensus 78 ~~~~~lQEyvEA~~f-~~~l~~~~l~s~ee 106 (204)
T PRK14562 78 YVGTALQEYVEALLV-YSLLFENKIPSPEE 106 (204)
T ss_pred hcchHHHHHHHHHHH-HHHHcCCCCCCHHH
Confidence 444456666666554 56888888998887
No 41
>PF06330 TRI5: Trichodiene synthase (TRI5); InterPro: IPR024652 This family consists of several fungal trichodiene synthase proteins (EC:4.2.3.6). TRI5 encodes the enzyme trichodiene synthase, which has been shown to catalyse the first step in the trichothecene pathways of Fusarium and Trichothecium species [, ].; GO: 0045482 trichodiene synthase activity, 0016106 sesquiterpenoid biosynthetic process; PDB: 1YYT_A 2PS5_A 2AEL_A 1YYS_A 1YJ4_A 2Q9Y_A 2PS4_A 2AEK_B 1KIY_B 2PS7_A ....
Probab=31.95 E-value=2.1e+02 Score=23.82 Aligned_cols=83 Identities=14% Similarity=0.277 Sum_probs=39.6
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhcCCCCC---CHHHHHhhhhhhhchhHHHHHHHHhcCCCCChHHHhhhcCchHHHHH
Q 040006 38 YSIQYAIRSFQELVMKYFCEAKWLNEGYVP---SMDEYKSVSLRSIGFLPIAVASFIFMGDIASREIFEWEMSNPKIIIA 114 (129)
Q Consensus 38 ~~~~~~~~~~~~l~~ayl~EakW~~~~~iP---t~eEYm~~~~~s~g~~~~~~~s~~~~g~~~~~e~~~~~~~~p~i~~~ 114 (129)
++-+-+.++--+.+.+...|.+=+ +-.| .|=+|++ .=+|.....+ .|++-.+..++... + ..+-..+--
T Consensus 145 f~anmI~~STLdFi~g~~LE~~~f--~~~p~A~~FP~fLR---~ktGlsEaYA-~FiFPk~~fpe~~~-~-~~y~~AIpd 216 (376)
T PF06330_consen 145 FCANMIVKSTLDFINGCWLEQKNF--HGSPGAPDFPDFLR---RKTGLSEAYA-FFIFPKALFPEVEY-F-IQYTPAIPD 216 (376)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTT------TT-TTHHHHHH---HHHH-HHHHH-HHT--TTTS-TTTT-H-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhhcccC--CCCCCCccccHHHH---hccCcchhhe-eeecccccCChHHH-H-HHHHHHHHH
Confidence 666777777788888888887632 2234 4556654 3344444433 24444443333211 1 111112223
Q ss_pred HHHHHHHhcccccC
Q 040006 115 AETIFRFLDDIAGH 128 (129)
Q Consensus 115 ~~~i~RL~nDi~s~ 128 (129)
.+.+.=+.|||-||
T Consensus 217 l~~fi~~~NDILSF 230 (376)
T PF06330_consen 217 LMRFINYVNDILSF 230 (376)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHhhhhHHHH
Confidence 33344488898764
No 42
>PRK02967 nickel responsive regulator; Provisional
Probab=31.73 E-value=1.5e+02 Score=20.91 Aligned_cols=36 Identities=3% Similarity=0.107 Sum_probs=24.0
Q ss_pred HHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHhcC
Q 040006 24 YSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKWLNE 63 (129)
Q Consensus 24 ~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~~ 63 (129)
.+++++-+...|=.++- ++.++++|.++.|.+|...
T Consensus 13 l~~lD~~~~~~gy~sRS----eaIrd~iR~~l~~~~~~~~ 48 (139)
T PRK02967 13 LETLDSLIARRGYQNRS----EAIRDLLRAALAQERTQEH 48 (139)
T ss_pred HHHHHHHHHHcCCCCHh----HHHHHHHHHHHHHhhhhcc
Confidence 55565555555522343 5578889999999999754
No 43
>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=31.47 E-value=49 Score=20.16 Aligned_cols=20 Identities=20% Similarity=0.130 Sum_probs=16.0
Q ss_pred CCCCCHHHHHhhhhhhhchh
Q 040006 64 GYVPSMDEYKSVSLRSIGFL 83 (129)
Q Consensus 64 ~~iPt~eEYm~~~~~s~g~~ 83 (129)
-..|+-+||...+.++.-+-
T Consensus 20 ~~KPd~~Ef~~iak~t~iG~ 39 (61)
T TIGR00327 20 CKKPDLEEYLKVAKVTGIGI 39 (61)
T ss_pred hcCCCHHHHHHHHHHHHHHH
Confidence 46899999999999776443
No 44
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=28.89 E-value=1.3e+02 Score=21.44 Aligned_cols=46 Identities=13% Similarity=0.022 Sum_probs=27.8
Q ss_pred cccCcCChhHHHHHHHHHH---HHHHHHHHHHhhcCcchHHHHHHHHHHH
Q 040006 4 GHIDALPEYMKFIFKTLIG---VYSEAEEELSKERRSYSIQYAIRSFQEL 50 (129)
Q Consensus 4 ~~~~~Lpeymk~~f~~l~~---~~~e~~~~~~~~~~~~~~~~~~~~~~~l 50 (129)
.++++||+-.|-+|..-+- ++.||+..+.-..+ .+..++.++-+.+
T Consensus 130 ~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~-tVk~~l~RAr~~L 178 (189)
T PRK12530 130 ACLNHLPAQQARVFMMREYLELSSEQICQECDISTS-NLHVLLYRARLQL 178 (189)
T ss_pred HHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHCCCHH-HHHHHHHHHHHHH
Confidence 3678889888888776542 57777765444333 3444555555433
No 45
>PF14502 HTH_41: Helix-turn-helix domain
Probab=27.92 E-value=94 Score=18.06 Aligned_cols=26 Identities=23% Similarity=0.275 Sum_probs=20.7
Q ss_pred CCCCCCHHHHHhhhhhhhchhHHHHH
Q 040006 63 EGYVPSMDEYKSVSLRSIGFLPIAVA 88 (129)
Q Consensus 63 ~~~iPt~eEYm~~~~~s~g~~~~~~~ 88 (129)
...+||.+||-+-=.+|.|.....+.
T Consensus 3 GdRi~tI~e~~~~~~vs~GtiQ~Alk 28 (48)
T PF14502_consen 3 GDRIPTISEYSEKFGVSRGTIQNALK 28 (48)
T ss_pred CcccCCHHHHHHHhCcchhHHHHHHH
Confidence 45699999998888888887776554
No 46
>KOG3094 consensus Predicted membrane protein [Function unknown]
Probab=27.87 E-value=71 Score=25.28 Aligned_cols=61 Identities=10% Similarity=0.053 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHH----HhhhhhhhchhHHHHHHHHhcCCCCChHHHhhhcCchH
Q 040006 41 QYAIRSFQELVMKYFCEAKWLNEGYVPSMDEY----KSVSLRSIGFLPIAVASFIFMGDIASREIFEWEMSNPK 110 (129)
Q Consensus 41 ~~~~~~~~~l~~ayl~EakW~~~~~iPt~eEY----m~~~~~s~g~~~~~~~s~~~~g~~~~~e~~~~~~~~p~ 110 (129)
+|+.+.|..... ++++.|.-++= |-.-.++.+...++.....|+....+.|.+.|..+.--
T Consensus 107 Pf~hk~W~~~~~---------~~~~~PPr~DvNaPDLYiP~MafiTYIll~gl~lGlqg~FsPE~Lg~~~s~al 171 (284)
T KOG3094|consen 107 PFLHKDWTRIYE---------RESPLPPRYDVNAPDLYIPLMAFITYILLAGLLLGLQGRFSPEALGILASKAL 171 (284)
T ss_pred eecCcchhhhhc---------ccCCCCccccCCCcchhhhHHHHHHHHHHHHHHhhhccCCCHHHHHHHHHHHH
Confidence 455555655444 67888866553 33456778888999999999988889999999755433
No 47
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=27.78 E-value=1.2e+02 Score=21.08 Aligned_cols=46 Identities=22% Similarity=0.225 Sum_probs=28.5
Q ss_pred ccCcCChhHHHHHHHHH-H--HHHHHHHHHHhhcCcchHHHHHHHHHHHH
Q 040006 5 HIDALPEYMKFIFKTLI-G--VYSEAEEELSKERRSYSIQYAIRSFQELV 51 (129)
Q Consensus 5 ~~~~Lpeymk~~f~~l~-~--~~~e~~~~~~~~~~~~~~~~~~~~~~~l~ 51 (129)
+++.||+-.+.+|.-.+ + +++||++.+.-..+ .+...++++.+.+.
T Consensus 115 ~l~~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~-tV~~~l~ra~~~~~ 163 (168)
T PRK12525 115 LLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLS-RIHQYMVEAFKCCY 163 (168)
T ss_pred HHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHH-HHHHHHHHHHHHHH
Confidence 56778888888876643 2 57777766544333 45556666665443
No 48
>KOG4713 consensus Cyclin-dependent kinase 2-associated protein [Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning]
Probab=27.72 E-value=1.4e+02 Score=22.27 Aligned_cols=47 Identities=17% Similarity=0.205 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhh--cCcchHHHHHH---HHHHHHHHHHHHHHH
Q 040006 14 KFIFKTLIGVYSEAEEELSKE--RRSYSIQYAIR---SFQELVMKYFCEAKW 60 (129)
Q Consensus 14 k~~f~~l~~~~~e~~~~~~~~--~~~~~~~~~~~---~~~~l~~ayl~EakW 60 (129)
..-|..|++.++||.+++... |......-||+ .=+.++|..|+|++=
T Consensus 134 ~~kY~~LL~vieEmgkeirpTyagsks~~ERLKr~I~hAR~lVRecl~etE~ 185 (189)
T KOG4713|consen 134 QTKYADLLSVIEEMGKEIRPTYAGSKSAMERLKRDIIHARLLVRECLQETER 185 (189)
T ss_pred chHHHHHHHHHHHHhcccCccccccccHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 356888999999998776554 22133344444 336789999999874
No 49
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=27.58 E-value=1.5e+02 Score=20.28 Aligned_cols=45 Identities=16% Similarity=0.073 Sum_probs=27.4
Q ss_pred cccCcCChhHHHHHHHHH-H--HHHHHHHHHHhhcCcchHHHHHHHHHH
Q 040006 4 GHIDALPEYMKFIFKTLI-G--VYSEAEEELSKERRSYSIQYAIRSFQE 49 (129)
Q Consensus 4 ~~~~~Lpeymk~~f~~l~-~--~~~e~~~~~~~~~~~~~~~~~~~~~~~ 49 (129)
.+++.||+..+-+|..-+ . .+.||++.+....+ .+...+.++-+.
T Consensus 102 ~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~-tV~~~l~Rar~~ 149 (160)
T PRK09642 102 QKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVK-TVEMKLYRARKW 149 (160)
T ss_pred HHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHH-HHHHHHHHHHHH
Confidence 357789988888776554 2 57777766554444 344444444443
No 50
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=27.21 E-value=2.9e+02 Score=22.04 Aligned_cols=66 Identities=24% Similarity=0.355 Sum_probs=38.3
Q ss_pred cCChhHHHHHHHHHHHHH---------HHHHHHHhhcCcchHHHHHHHHHHHHHH-HHHHHH-HhcCCCCCCHHHHHhhh
Q 040006 8 ALPEYMKFIFKTLIGVYS---------EAEEELSKERRSYSIQYAIRSFQELVMK-YFCEAK-WLNEGYVPSMDEYKSVS 76 (129)
Q Consensus 8 ~Lpeymk~~f~~l~~~~~---------e~~~~~~~~~~~~~~~~~~~~~~~l~~a-yl~Eak-W~~~~~iPt~eEYm~~~ 76 (129)
.|..--|-+.++|.+.|+ |+++.+.++.+ .+ |.+++ .+|| =|.|-+ ==+.||+||.+-|=..+
T Consensus 3 ~LT~~QkeIL~aLi~LY~~~~r~IKgeeIA~~l~rnpG-TV----RNqmq-~LkaLgLVegvpGPkGGY~PT~kAYe~L~ 76 (294)
T COG2524 3 ELTSSQKEILQALINLYRRKKRPIKGEEIAEVLNRNPG-TV----RNQMQ-SLKALGLVEGVPGPKGGYKPTSKAYEALS 76 (294)
T ss_pred cccHHHHHHHHHHHHHHHhcCCCcchHHHHHHHccCcc-hH----HHHHH-HHHhcCccccccCCCCCccccHHHHHHhc
Confidence 466667788889988886 45555555544 22 22222 2222 133322 12679999999996555
Q ss_pred hhh
Q 040006 77 LRS 79 (129)
Q Consensus 77 ~~s 79 (129)
.-+
T Consensus 77 iqt 79 (294)
T COG2524 77 IQT 79 (294)
T ss_pred cCC
Confidence 544
No 51
>PF13337 Lon_2: Putative ATP-dependent Lon protease
Probab=26.91 E-value=17 Score=30.81 Aligned_cols=59 Identities=24% Similarity=0.184 Sum_probs=36.8
Q ss_pred CCCCCHHHHHhhhhhhhch-hHHHHHHHHhcCCCC-ChHHH----hhhcCchHHHHHHHHHHHHh
Q 040006 64 GYVPSMDEYKSVSLRSIGF-LPIAVASFIFMGDIA-SREIF----EWEMSNPKIIIAAETIFRFL 122 (129)
Q Consensus 64 ~~iPt~eEYm~~~~~s~g~-~~~~~~s~~~~g~~~-~~e~~----~~~~~~p~i~~~~~~i~RL~ 122 (129)
.-+..+..||++|.-|-|. ......|++++|+.- +-+.+ .-+...|+..+-++.+-|+-
T Consensus 277 d~i~imK~YMesG~fsRG~~~i~a~as~vf~GNi~~~v~~~~~~~~lf~~lP~~~~DsAflDRiH 341 (457)
T PF13337_consen 277 DEIQIMKDYMESGSFSRGKEEINADASMVFVGNINQSVENMLKTSHLFEPLPEEMRDSAFLDRIH 341 (457)
T ss_pred HHHHHHHHHHhccceeecccccccceeEEEEcCcCCcchhccccchhhhhcCHHHHHHHHHhHhh
Confidence 3356678888888888777 344456777888742 11111 22234488888888877764
No 52
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=25.81 E-value=1.1e+02 Score=22.85 Aligned_cols=32 Identities=16% Similarity=0.128 Sum_probs=23.3
Q ss_pred cccCcCChhHHHHHHHHH-------HHHHHHHHHHHhhc
Q 040006 4 GHIDALPEYMKFIFKTLI-------GVYSEAEEELSKER 35 (129)
Q Consensus 4 ~~~~~Lpeymk~~f~~l~-------~~~~e~~~~~~~~~ 35 (129)
.++++||+..|.++.--+ -++.||+..+....
T Consensus 174 ~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~ 212 (234)
T TIGR02835 174 KALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQ 212 (234)
T ss_pred HHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCH
Confidence 467899999999888765 37888876544433
No 53
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=25.79 E-value=1.5e+02 Score=20.29 Aligned_cols=44 Identities=11% Similarity=0.157 Sum_probs=27.2
Q ss_pred ccCcCChhHHHHHHHHH-H--HHHHHHHHHHhhcCcchHHHHHHHHHH
Q 040006 5 HIDALPEYMKFIFKTLI-G--VYSEAEEELSKERRSYSIQYAIRSFQE 49 (129)
Q Consensus 5 ~~~~Lpeymk~~f~~l~-~--~~~e~~~~~~~~~~~~~~~~~~~~~~~ 49 (129)
+++.||+..+.+|...+ . .+.||++.+....+ .+..++.++.+.
T Consensus 106 ~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~-tV~~~l~ra~~~ 152 (163)
T PRK07037 106 ALSELPARTRYAFEMYRLHGETQKDIARELGVSPT-LVNFMIRDALVH 152 (163)
T ss_pred HHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHH-HHHHHHHHHHHH
Confidence 56789998888886543 2 57777765544443 344455555543
No 54
>cd07957 Anticodon_Ia_Met Anticodon-binding domain of methionyl tRNA synthetases. This domain is found in methionyl tRNA synthetases (MetRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon (CAU). MetRS catalyzes the transfer of methionine to the 3'-end of its tRNA.
Probab=25.68 E-value=1.9e+02 Score=18.69 Aligned_cols=45 Identities=11% Similarity=0.124 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHH
Q 040006 14 KFIFKTLIGVYSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAK 59 (129)
Q Consensus 14 k~~f~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~Eak 59 (129)
+-+...+..++.+++..+..-.=...+..+.+. .+.+..|++..|
T Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~-~~~~n~y~~~~k 83 (129)
T cd07957 39 EELLEEAEELLEEVAEAMEELEFRKALEEIMEL-ARAANKYIDETA 83 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHH-HHHHHhhhccCC
Confidence 556777788888887766432111223333322 245565655443
No 55
>PHA02046 hypothetical protein
Probab=25.68 E-value=67 Score=21.40 Aligned_cols=20 Identities=25% Similarity=0.335 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHhcCCCCCC
Q 040006 49 ELVMKYFCEAKWLNEGYVPS 68 (129)
Q Consensus 49 ~l~~ayl~EakW~~~~~iPt 68 (129)
-++.+...|.+|.+++-+|-
T Consensus 16 ~~a~~l~~e~~~~re~eiPl 35 (99)
T PHA02046 16 LVCTAIEREFKWYRENDIPL 35 (99)
T ss_pred HHHHHHHHHHHHHHhcCCCC
Confidence 45677888999999999883
No 56
>COG0783 Dps DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]
Probab=24.89 E-value=2.2e+02 Score=20.46 Aligned_cols=36 Identities=17% Similarity=0.296 Sum_probs=21.9
Q ss_pred CCccccCc--CChhHHHHHHHHHHHHHHHHHHHHhhcC
Q 040006 1 WDIGHIDA--LPEYMKFIFKTLIGVYSEAEEELSKERR 36 (129)
Q Consensus 1 WD~~~~~~--Lpeymk~~f~~l~~~~~e~~~~~~~~~~ 36 (129)
|+..+.+. |=+.+.-.|..+.+.++|+++.+..-|+
T Consensus 39 WnV~G~~F~~lHe~~ee~y~el~~~~DeiAERi~~LGg 76 (156)
T COG0783 39 WNVKGPNFFALHEKLEELYEELAEHVDEIAERIRALGG 76 (156)
T ss_pred cceeCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 44444442 3355666777777777777766666666
No 57
>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=24.86 E-value=2e+02 Score=18.65 Aligned_cols=29 Identities=21% Similarity=0.386 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhh
Q 040006 45 RSFQELVMKYFCEAKWLNEGYVPSMDEYKSVS 76 (129)
Q Consensus 45 ~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~ 76 (129)
+.|+++|.+|+.|.+= +--+||.-+-...
T Consensus 35 e~~~Ki~~~~l~~~k~---~~~LTFSS~KSf~ 63 (86)
T PF02236_consen 35 ECFRKICQTWLNEEKR---GLQLTFSSQKSFT 63 (86)
T ss_dssp HHHHHHHHHHHHHHHT---T---SS--HHHHH
T ss_pred HHHHHHHHHHHHhcCc---CCCcceechHHHH
Confidence 7899999999999872 3334777665443
No 58
>PF14629 ORC4_C: Origin recognition complex (ORC) subunit 4 C-terminus
Probab=24.62 E-value=1.5e+02 Score=21.49 Aligned_cols=41 Identities=15% Similarity=0.318 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHhh------cCcchHHHHHHHHHHHHHHHH
Q 040006 15 FIFKTLIGVYSEAEEELSKE------RRSYSIQYAIRSFQELVMKYF 55 (129)
Q Consensus 15 ~~f~~l~~~~~e~~~~~~~~------~~~~~~~~~~~~~~~l~~ayl 55 (129)
+=|..+|+.|.++.+..... .+.+..+-++++|..|+.--+
T Consensus 122 ~NF~~vy~EY~~~~~~~~~~~~~~~~~~~~~k~v~~~a~E~L~~l~L 168 (203)
T PF14629_consen 122 FNFEMVYDEYKKFAKSYNSSSAIVGTIKVWSKPVALKAWEHLLSLEL 168 (203)
T ss_pred ccHHHHHHHHHHHHHhhccccccccccccCCHHHHHHHHHHHHHCCC
Confidence 34677777777777654554 333566778889988887444
No 59
>PF01484 Col_cuticle_N: Nematode cuticle collagen N-terminal domain; InterPro: IPR002486 The function of this domain is unknown. It is found in the N-terminal region of nematode cuticle collagens (see IPR008160 from INTERPRO). Cuticle is a tough elastic structure secreted by hypodermal cells and is primarily composed of collagen proteins [, ].; GO: 0042302 structural constituent of cuticle
Probab=24.16 E-value=1.2e+02 Score=16.99 Aligned_cols=12 Identities=8% Similarity=-0.014 Sum_probs=6.7
Q ss_pred chHHHHHHHHHH
Q 040006 38 YSIQYAIRSFQE 49 (129)
Q Consensus 38 ~~~~~~~~~~~~ 49 (129)
.......+.|++
T Consensus 41 ~fk~~s~d~W~~ 52 (53)
T PF01484_consen 41 EFKEISDDAWNE 52 (53)
T ss_pred HHHHHHHHHHhh
Confidence 334455666765
No 60
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=24.10 E-value=1.8e+02 Score=17.81 Aligned_cols=38 Identities=21% Similarity=0.226 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHH
Q 040006 23 VYSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKW 60 (129)
Q Consensus 23 ~~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW 60 (129)
...+|+.++...|-.....-.+.-|+.|.+.|-..-.+
T Consensus 36 ~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~k~~ 73 (90)
T PF13837_consen 36 VWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKIKDR 73 (90)
T ss_dssp HHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCSSSS
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 57778877776664334567788899999988865543
No 61
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=23.82 E-value=1.1e+02 Score=21.60 Aligned_cols=44 Identities=11% Similarity=0.039 Sum_probs=26.7
Q ss_pred cccCcCChhHHHHHHHHH---HHHHHHHHHHHhhcCcchHHHHHHHHH
Q 040006 4 GHIDALPEYMKFIFKTLI---GVYSEAEEELSKERRSYSIQYAIRSFQ 48 (129)
Q Consensus 4 ~~~~~Lpeymk~~f~~l~---~~~~e~~~~~~~~~~~~~~~~~~~~~~ 48 (129)
.+++.||+-.|-+|..-+ -.+.||++.+....+ .+..++.++-+
T Consensus 129 ~~l~~L~~~~r~i~~l~~~~~~s~~eIA~~lgis~~-tV~~~l~ra~~ 175 (182)
T PRK12537 129 RCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLG-TVKAWIKRSLK 175 (182)
T ss_pred HHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChh-hHHHHHHHHHH
Confidence 467889988888776654 257777765544444 34444444443
No 62
>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=23.41 E-value=3.2e+02 Score=20.46 Aligned_cols=45 Identities=9% Similarity=-0.018 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhhhchhHHHHHHHHhcC
Q 040006 47 FQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRSIGFLPIAVASFIFMG 94 (129)
Q Consensus 47 ~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s~g~~~~~~~s~~~~g 94 (129)
+.+++.++. .+....-.||++|...-..-++|....++...++..
T Consensus 93 l~~li~~~~---~dl~~~~~~t~~~L~~Y~~~vag~vg~l~~~~~~~~ 137 (267)
T PF00494_consen 93 LLELIDGME---MDLEFTPYETFADLERYCYYVAGSVGLLLLQLLGAH 137 (267)
T ss_dssp HHHHHHHHH---HCTT-S--SSHHHHHHHHHHHTHHHHHHHHHHHHSS
T ss_pred HHHHHHHhc---ccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 344444444 233335578999999999988888888777777664
No 63
>KOG0085 consensus G protein subunit Galphaq/Galphay, small G protein superfamily [Signal transduction mechanisms]
Probab=23.19 E-value=2.1e+02 Score=22.80 Aligned_cols=34 Identities=18% Similarity=0.426 Sum_probs=26.0
Q ss_pred HHHHHHHHHH-HhcCCCCCCHHHHHhhhhhhhchh
Q 040006 50 LVMKYFCEAK-WLNEGYVPSMDEYKSVSLRSIGFL 83 (129)
Q Consensus 50 l~~ayl~Eak-W~~~~~iPt~eEYm~~~~~s~g~~ 83 (129)
-++-|+.... -...+|+||-.+-|.+...++|..
T Consensus 156 SakYylsdldria~~~ylPTqQDvLRvRvPTTGi~ 190 (359)
T KOG0085|consen 156 SAKYYLSDLDRIATPGYLPTQQDVLRVRVPTTGII 190 (359)
T ss_pred hhhHHhhhhhhhcCcccCcchhhhheeecCcccce
Confidence 4555666644 345699999999999999999864
No 64
>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=23.12 E-value=3.4e+02 Score=20.54 Aligned_cols=45 Identities=11% Similarity=0.182 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCHHHHHhhhhhhhchhHHHHHHHHhc
Q 040006 46 SFQELVMKYFCEAKWLNEGYVPSMDEYKSVSLRSIGFLPIAVASFIFM 93 (129)
Q Consensus 46 ~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~~~s~g~~~~~~~s~~~~ 93 (129)
.+.+++.++-.... ....||++|...-..-+.|....++...++.
T Consensus 94 ~~~~li~g~~~Dl~---~~~~~t~~eL~~Y~~~vAg~vg~l~~~i~~~ 138 (265)
T cd00683 94 PFRDLLAGMAMDLD---KRRYETLDELDEYCYYVAGVVGLMLLRVFGA 138 (265)
T ss_pred HHHHHHHHHHHhCC---CCCCCCHHHHHHHHHHhHHHHHHHHHHHhCC
Confidence 35566666664444 3567899888777777777666666666643
No 65
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=22.92 E-value=1e+02 Score=21.83 Aligned_cols=53 Identities=15% Similarity=0.182 Sum_probs=25.7
Q ss_pred ccCcCChhHHHHHHHH-HH--HHHHHHHHHHhhcCc--chHHHHHHHHHHHHHHHHHH
Q 040006 5 HIDALPEYMKFIFKTL-IG--VYSEAEEELSKERRS--YSIQYAIRSFQELVMKYFCE 57 (129)
Q Consensus 5 ~~~~Lpeymk~~f~~l-~~--~~~e~~~~~~~~~~~--~~~~~~~~~~~~l~~ayl~E 57 (129)
+++.||+--+-+|.-- ++ .++||++.+....+. ..+.-.++..++.++.|++|
T Consensus 135 ~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~~~ 192 (193)
T PRK11923 135 TIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQPLLQE 192 (193)
T ss_pred HHHhCCHHHhHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4566776655555442 22 466776554443331 22333444455555555543
No 66
>KOG4420 consensus Uncharacterized conserved protein (Ganglioside-induced differentiation associated protein 1, GDAP1) [Function unknown]
Probab=22.61 E-value=4.1e+02 Score=21.33 Aligned_cols=72 Identities=22% Similarity=0.337 Sum_probs=45.2
Q ss_pred CcCChhHHHHHHHHHHHHHHHHHHHHhhc--------CcchHHH--HHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhhh
Q 040006 7 DALPEYMKFIFKTLIGVYSEAEEELSKER--------RSYSIQY--AIRSFQELVMKYFCEAKWLNEGYVPSMDEYKSVS 76 (129)
Q Consensus 7 ~~Lpeymk~~f~~l~~~~~e~~~~~~~~~--------~~~~~~~--~~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~~ 76 (129)
+..|.|+|-+-..+..+.+++|.++.++. ..+.+.- +.-...++-.-=+.+--| ..|..|.+++|-+--
T Consensus 197 hdd~s~lkkild~l~~~Ld~VEteLe~r~~~~~wL~G~efslADVsLg~~LhRL~~Lg~e~~yw-~~gsrpnle~Yf~rv 275 (325)
T KOG4420|consen 197 HDDVSYLKKILDELAMVLDQVETELEKRKLCELWLCGCEFSLADVSLGATLHRLKFLGLEKKYW-EDGSRPNLESYFERV 275 (325)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHhhccccceeeccccchHHHHHHHHHHHHHHHcccHHHhc-ccCCCccHHHHHHHH
Confidence 45788999999999999999999888843 3232211 111122222222333446 569999999997644
Q ss_pred hhh
Q 040006 77 LRS 79 (129)
Q Consensus 77 ~~s 79 (129)
.--
T Consensus 276 rrR 278 (325)
T KOG4420|consen 276 RRR 278 (325)
T ss_pred Hhh
Confidence 433
No 67
>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=22.48 E-value=52 Score=20.13 Aligned_cols=15 Identities=33% Similarity=0.760 Sum_probs=9.3
Q ss_pred CChHHHhhhcCchHH
Q 040006 97 ASREIFEWEMSNPKI 111 (129)
Q Consensus 97 ~~~e~~~~~~~~p~i 111 (129)
+.+..++|+.++|+|
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 356788888777764
No 68
>PF09921 DUF2153: Uncharacterized protein conserved in archaea (DUF2153); InterPro: IPR014450 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=22.13 E-value=2.9e+02 Score=19.37 Aligned_cols=47 Identities=19% Similarity=0.334 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHHhhcCcchHHHHHHHHHHHHHHHHHHHHHhcCC
Q 040006 18 KTLIGVYSEAEEELSKERRSYSIQYAIRSFQELVMKYFCEAKWLNEG 64 (129)
Q Consensus 18 ~~l~~~~~e~~~~~~~~~~~~~~~~~~~~~~~l~~ayl~EakW~~~~ 64 (129)
+.++++++++++.+....|-..+-..+-++..+.|.--.--.|..+-
T Consensus 10 k~~l~~~~~~e~~~~~~DRL~LIl~sr~afqhm~RTlKaFd~WLqdP 56 (126)
T PF09921_consen 10 KRLLETFKKHEKNVESADRLDLILSSRAAFQHMMRTLKAFDQWLQDP 56 (126)
T ss_pred HHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHcCc
Confidence 56788899998877776665555566667766666555555788764
No 69
>PF14278 TetR_C_8: Transcriptional regulator C-terminal region
Probab=22.12 E-value=1.7e+02 Score=16.87 Aligned_cols=29 Identities=17% Similarity=0.162 Sum_probs=16.6
Q ss_pred HHhhcCcchHHHHHHHHHHHHHHHHHHHH
Q 040006 31 LSKERRSYSIQYAIRSFQELVMKYFCEAK 59 (129)
Q Consensus 31 ~~~~~~~~~~~~~~~~~~~l~~ayl~Eak 59 (129)
+..+|...-...+++.+++.+..++.+..
T Consensus 22 l~~~~~~~f~~~l~~~~~~~~~~~~~~~~ 50 (77)
T PF14278_consen 22 LSPNGDPNFQERLKELIKEWITEYINENS 50 (77)
T ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34444434556677777777666664433
No 70
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=21.63 E-value=1.6e+02 Score=21.79 Aligned_cols=44 Identities=16% Similarity=0.184 Sum_probs=27.8
Q ss_pred cccCcCChhHHHHHHHHH-----H--HHHHHHHHHHhhcCcchHHHHHHHHH
Q 040006 4 GHIDALPEYMKFIFKTLI-----G--VYSEAEEELSKERRSYSIQYAIRSFQ 48 (129)
Q Consensus 4 ~~~~~Lpeymk~~f~~l~-----~--~~~e~~~~~~~~~~~~~~~~~~~~~~ 48 (129)
.++++||+-.|-+|..-+ + ++.||+..+....+ .+-..+.++.+
T Consensus 174 ~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~-tVk~~~~rA~~ 224 (234)
T PRK08301 174 KALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQS-YISRLEKRIIK 224 (234)
T ss_pred HHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHH-HHHHHHHHHHH
Confidence 367889999999998866 2 68888766544333 33334444433
No 71
>PLN03223 Polycystin cation channel protein; Provisional
Probab=21.57 E-value=2.5e+02 Score=27.65 Aligned_cols=24 Identities=8% Similarity=0.315 Sum_probs=18.7
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 040006 38 YSIQYAIRSFQELVMKYFCEAKWLNEGYVP 67 (129)
Q Consensus 38 ~~~~~~~~~~~~l~~ayl~EakW~~~~~iP 67 (129)
-..+|+++.|+.++| .|+...|+|
T Consensus 1438 EIvDfm~~rfrslL~------g~~~~~~i~ 1461 (1634)
T PLN03223 1438 ELFPMLRDKWRSMFK------GWFYKNHIP 1461 (1634)
T ss_pred HHHHHHHHHHHHHHh------hhcccccCC
Confidence 467899999999997 366666666
No 72
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=21.52 E-value=1.6e+02 Score=21.09 Aligned_cols=46 Identities=11% Similarity=0.090 Sum_probs=26.7
Q ss_pred ccCcCChhHHHHHHHHH-H--HHHHHHHHHHhhcCcchHHHHHHHHHHHH
Q 040006 5 HIDALPEYMKFIFKTLI-G--VYSEAEEELSKERRSYSIQYAIRSFQELV 51 (129)
Q Consensus 5 ~~~~Lpeymk~~f~~l~-~--~~~e~~~~~~~~~~~~~~~~~~~~~~~l~ 51 (129)
++.+||+--+-+|.-.+ + ++.||++.+.-..+ .+...+..+-+.+-
T Consensus 138 ~l~~Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~-tVk~rl~ra~~~Lr 186 (194)
T PRK12531 138 FLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLG-TVKSRLRLAVEKLR 186 (194)
T ss_pred HHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHH-HHHHHHHHHHHHHH
Confidence 46678887777776543 2 67777765544443 44444444444433
No 73
>TIGR03486 cas_csx13_C CRISPR-associated protein, Cas_csx13 family, C-terminal region. Members of this family are found among cas (CRISPR-Associated) genes close to CRISPR repeats in Leptospira interrogans (a spirochete), Myxococcus xanthus (a delta-proteobacterium), and Lyngbya sp. PCC 8106 (a cyanobacterium). It is found with other cas genes in Anabaena variabilis ATCC 29413. In Lyngbya sp., the protein is split into two tandem genes. This model corresponds to the C-terminal region or upstream gene; the N-terminal region is modelled by TIGR03485. CRISPR/cas systems are associated with prokaryotic acquired resistance to phage and other exogenous DNA.
Probab=21.44 E-value=2.9e+02 Score=20.01 Aligned_cols=60 Identities=17% Similarity=0.287 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhc---CcchHHHHH-HHHHHHHHHHHHHH-------HHhcCCCCCCHHHH
Q 040006 13 MKFIFKTLIGVYSEAEEELSKER---RSYSIQYAI-RSFQELVMKYFCEA-------KWLNEGYVPSMDEY 72 (129)
Q Consensus 13 mk~~f~~l~~~~~e~~~~~~~~~---~~~~~~~~~-~~~~~l~~ayl~Ea-------kW~~~~~iPt~eEY 72 (129)
++.|-.++-.++..|.....+.| .+.....-. +.-..+.+++-.|. =|.+.|..|+++|+
T Consensus 54 iqa~HeAlr~~~~qI~~~tk~~g~~~~~~~~e~e~erir~~l~r~kt~~~fr~~i~df~srAg~~~~Lqe~ 124 (152)
T TIGR03486 54 VQSFHEALRRIYAKIASHTKRRGSETLGDRWKRENERIYSSLARAKTSEQFRTFIADLWARAGRIPSLQEH 124 (152)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhcccchhHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHccCCcchHHH
Confidence 34444555556666655544423 222222221 12233444443331 27889999999988
No 74
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=21.10 E-value=1.5e+02 Score=20.83 Aligned_cols=45 Identities=13% Similarity=0.139 Sum_probs=26.8
Q ss_pred cccCcCChhHHHHHHHHH-H--HHHHHHHHHHhhcCcchHHHHHHHHHH
Q 040006 4 GHIDALPEYMKFIFKTLI-G--VYSEAEEELSKERRSYSIQYAIRSFQE 49 (129)
Q Consensus 4 ~~~~~Lpeymk~~f~~l~-~--~~~e~~~~~~~~~~~~~~~~~~~~~~~ 49 (129)
.++++||+.-+.+|.--+ + ++.||+..+..-.+ .+..++..+.+.
T Consensus 123 ~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~-tVk~~l~rAl~~ 170 (178)
T PRK12529 123 ALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALP-TVKKYIHQAYVT 170 (178)
T ss_pred HHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHH-HHHHHHHHHHHH
Confidence 367889988888887643 2 67777765444333 343444444443
No 75
>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=20.82 E-value=90 Score=19.89 Aligned_cols=27 Identities=15% Similarity=0.228 Sum_probs=19.6
Q ss_pred HHHhhhcCchHHHHHHHHHHHHhcccc
Q 040006 100 EIFEWEMSNPKIIIAAETIFRFLDDIA 126 (129)
Q Consensus 100 e~~~~~~~~p~i~~~~~~i~RL~nDi~ 126 (129)
.++..+.++++++..+....|.++|++
T Consensus 15 ~il~Qie~YdNli~~vVe~~ky~t~l~ 41 (77)
T PF11732_consen 15 VILSQIESYDNLIEPVVESLKYFTDLG 41 (77)
T ss_pred HHHHHHHHhhhhHHHHHHHHhhcchhh
Confidence 456667777888888877777777653
No 76
>PF02197 RIIa: Regulatory subunit of type II PKA R-subunit; InterPro: IPR003117 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. In the absence of cAMP, Protein Kinase A (PKA) exists as an equimolar tetramer of regulatory (R) and catalytic (C) subunits []. In addition to its role as an inhibitor of the C subunit, the R subunit anchors the holoenzyme to specific intracellular locations and prevents the C subunit from entering the nucleus. All R subunits have a conserved domain structure consisting of the N-terminal dimerization domain, inhibitory region, cAMP-binding domain A and cAMP-binding domain B. R subunits interact with C subunits primarily through the inhibitory site. The cAMP-binding domains show extensive sequence similarity and bind cAMP cooperatively. Two types of regulatory (R) subunits exist - types I and I - which differ in molecular weight, sequence, autophosphorylation cabaility, cellular location and tissue distribution. Types I and II were further sub-divided into alpha and beta subtypes, based mainly on sequence similarity. This entry represents types I-alpha, I-beta, II-alpha and II-beta regulatory subunits of PKA proteins. These subunits contain the dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).; GO: 0008603 cAMP-dependent protein kinase regulator activity, 0007165 signal transduction; PDB: 2IZY_E 1R2A_A 1L6E_A 2IZX_B 2KYG_A 2EZW_B 3IM4_B 3IM3_A 4F9K_C 2HWN_B ....
Probab=20.78 E-value=1.6e+02 Score=15.88 Aligned_cols=31 Identities=23% Similarity=0.312 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHhhcCcchHHHHHHHHHHHH
Q 040006 21 IGVYSEAEEELSKERRSYSIQYAIRSFQELV 51 (129)
Q Consensus 21 ~~~~~e~~~~~~~~~~~~~~~~~~~~~~~l~ 51 (129)
-+.++++..++.+++-.+++.|..+-+.++.
T Consensus 4 ~~lL~~~~~~vl~~qP~Di~~F~a~yF~~L~ 34 (38)
T PF02197_consen 4 QELLKEFTREVLREQPDDILQFAADYFEKLE 34 (38)
T ss_dssp HHHHHHHHHHHHHH--S-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCCcHHHHHHHHHHHHH
Confidence 3567788888777777788888777665543
No 77
>PRK01250 inorganic pyrophosphatase; Provisional
Probab=20.67 E-value=72 Score=23.51 Aligned_cols=53 Identities=21% Similarity=0.211 Sum_probs=32.0
Q ss_pred ccccCcCChhHHHHHHHHHHHHHHHH-HHHHhhcCcchHHHHHHHHHHHHHHHH
Q 040006 3 IGHIDALPEYMKFIFKTLIGVYSEAE-EELSKERRSYSIQYAIRSFQELVMKYF 55 (129)
Q Consensus 3 ~~~~~~Lpeymk~~f~~l~~~~~e~~-~~~~~~~~~~~~~~~~~~~~~l~~ayl 55 (129)
+..++.||..+.---+.+|..|+.++ ....+-++..-...+++..++-.+.|.
T Consensus 121 i~dl~dl~~~~l~eI~~fF~~YK~le~gk~~~v~g~~~~~~A~~~I~~~~~~y~ 174 (176)
T PRK01250 121 IKDVNDLPELLKAQIKHFFEHYKDLEKGKWVKVEGWGGAEEAKAEIVEAIERAK 174 (176)
T ss_pred cCChHHCCHHHHHHHHHHHHHhcCCCCCCCEEecCccCHHHHHHHHHHHHHHHh
Confidence 35677788877666677777777775 222222333445666666666666553
No 78
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=20.63 E-value=2e+02 Score=21.03 Aligned_cols=45 Identities=20% Similarity=0.117 Sum_probs=27.3
Q ss_pred ccCcCChhHHHHHHHHHH---HHHHHHHHHHhhcCcchHHHHHHHHHHH
Q 040006 5 HIDALPEYMKFIFKTLIG---VYSEAEEELSKERRSYSIQYAIRSFQEL 50 (129)
Q Consensus 5 ~~~~Lpeymk~~f~~l~~---~~~e~~~~~~~~~~~~~~~~~~~~~~~l 50 (129)
+++.||+..+-+|...+- .+.||++.+....+ .+..++.++-+.+
T Consensus 135 ~L~~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~-tV~~~l~RArk~L 182 (203)
T PRK09647 135 ALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLG-TVRSRIHRGRQQL 182 (203)
T ss_pred HHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHH-HHHHHHHHHHHHH
Confidence 567888888888766542 57777765544443 4444555554433
No 79
>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=20.21 E-value=2.7e+02 Score=19.93 Aligned_cols=30 Identities=13% Similarity=0.070 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCHHHHHhh
Q 040006 44 IRSFQELVMKYFCEAKWLNEGYVPSMDEYKSV 75 (129)
Q Consensus 44 ~~~~~~l~~ayl~EakW~~~~~iPt~eEYm~~ 75 (129)
++.|.....++.....+ .+..|+||+++++
T Consensus 204 ~~~~~~~~~~~~~~~~~--~~~~~~f~~~~~~ 233 (233)
T PF08843_consen 204 REFWQRDYEAMRDALLY--AGDLPDFDDALAR 233 (233)
T ss_pred HHHHHHHHHHhHhhhhc--cCCCcCHHHHhcC
Confidence 56677666666655443 5789999999864
No 80
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=20.13 E-value=1.4e+02 Score=21.11 Aligned_cols=31 Identities=13% Similarity=0.037 Sum_probs=20.1
Q ss_pred ccCcCChhHHHHHHHHHH---HHHHHHHHHHhhc
Q 040006 5 HIDALPEYMKFIFKTLIG---VYSEAEEELSKER 35 (129)
Q Consensus 5 ~~~~Lpeymk~~f~~l~~---~~~e~~~~~~~~~ 35 (129)
+++.||+..+.+|..-+- .++||+..+....
T Consensus 128 ~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~ 161 (189)
T PRK12515 128 CLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPE 161 (189)
T ss_pred HHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCH
Confidence 577889888888754332 5777776544433
Done!