Query psy6224
Match_columns 82
No_of_seqs 35 out of 37
Neff 2.9
Searched_HMMs 46136
Date Fri Aug 16 20:53:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6224.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6224hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4232|consensus 99.5 2E-16 4.4E-21 128.8 -3.1 73 4-81 313-386 (430)
2 cd03507 Delta12-FADS-like The 98.1 6E-07 1.3E-11 65.2 0.1 68 4-76 153-221 (222)
3 cd03506 Delta6-FADS-like The D 97.8 3.3E-06 7.1E-11 59.7 -0.5 65 14-81 127-192 (204)
4 PF00487 FA_desaturase: Fatty 97.8 4.9E-06 1.1E-10 55.3 0.1 53 28-81 186-239 (257)
5 PLN02505 omega-6 fatty acid de 96.7 0.00049 1.1E-08 55.0 0.4 61 16-82 272-334 (381)
6 PLN03198 delta6-acyl-lipid des 95.8 0.00097 2.1E-08 55.2 -2.2 62 13-81 419-481 (526)
7 PLN02498 omega-3 fatty acid de 95.4 0.0064 1.4E-07 50.3 1.1 57 20-82 334-391 (450)
8 PLN02598 omega-6 fatty acid de 95.1 0.0043 9.3E-08 50.3 -0.7 62 16-82 297-360 (421)
9 PLN03199 delta6-acyl-lipid des 92.0 0.034 7.4E-07 45.2 -0.7 63 14-80 369-436 (485)
10 cd03511 Rhizopine-oxygenase-li 91.8 0.046 9.9E-07 40.4 -0.2 24 58-81 243-266 (285)
11 cd03510 Rhizobitoxine-FADS-lik 91.7 0.052 1.1E-06 38.4 0.1 25 58-82 149-173 (175)
12 COG3239 DesA Fatty acid desatu 91.3 0.032 6.9E-07 43.5 -1.5 49 32-81 240-289 (343)
13 cd03514 CrtR_beta-carotene-hyd 90.4 0.081 1.8E-06 38.2 0.0 23 59-81 173-195 (207)
14 cd03513 CrtW_beta-carotene-ket 89.6 0.086 1.9E-06 39.4 -0.4 65 3-80 159-224 (225)
15 PF12073 DUF3553: Protein of u 86.7 0.4 8.7E-06 29.9 1.3 22 26-47 3-26 (52)
16 cd01060 Membrane-FADS-like The 86.0 0.23 5E-06 31.0 -0.0 14 57-70 108-122 (122)
17 cd03509 DesA_FADS-like Fatty a 84.7 0.32 6.9E-06 37.2 0.2 24 59-82 228-251 (288)
18 cd03508 Delta4-sphingolipid-FA 77.8 0.82 1.8E-05 35.2 0.3 28 55-82 225-252 (289)
19 PLN02579 sphingolipid delta-4 73.9 1.1 2.5E-05 35.2 0.2 28 55-82 253-280 (323)
20 PF00067 p450: Cytochrome P450 51.2 6.4 0.00014 27.9 0.5 23 12-34 365-387 (463)
21 smart00546 CUE Domain that may 41.6 6.4 0.00014 21.8 -0.5 19 63-81 7-25 (43)
22 PLN02500 cytochrome P450 90B1 37.4 15 0.00033 28.5 0.8 24 11-34 385-408 (490)
23 PLN02687 flavonoid 3'-monooxyg 34.7 17 0.00036 28.6 0.6 24 11-34 399-422 (517)
24 PLN02220 delta-9 acyl-lipid de 34.5 8.1 0.00018 30.4 -1.2 20 52-71 233-254 (299)
25 PTZ00404 cytochrome P450; Prov 33.8 17 0.00037 28.0 0.5 23 12-34 387-409 (482)
26 PF10848 DUF2655: Protein of u 33.5 30 0.00065 23.3 1.6 52 13-64 16-76 (82)
27 PLN03141 3-epi-6-deoxocathaste 32.9 19 0.00041 27.7 0.7 24 11-34 356-379 (452)
28 PF00799 Gemini_AL1: Geminivir 32.2 11 0.00024 26.0 -0.7 10 33-42 104-113 (114)
29 PLN02655 ent-kaurene oxidase 30.8 20 0.00043 27.8 0.5 25 11-35 363-387 (466)
30 cd03505 Delta9-FADS-like The D 29.8 9.4 0.0002 28.0 -1.4 21 51-71 125-147 (178)
31 PLN03112 cytochrome P450 famil 28.1 25 0.00054 27.4 0.6 26 11-36 398-423 (514)
32 PF05304 DUF728: Protein of un 27.9 19 0.00041 25.3 -0.1 12 30-41 90-101 (103)
33 PF02845 CUE: CUE domain; Int 27.2 18 0.00039 20.0 -0.3 18 64-81 7-24 (42)
34 KOG3635|consensus 27.1 21 0.00045 33.4 -0.0 26 19-44 123-148 (1150)
35 PRK15137 DNA-specific endonucl 25.5 26 0.00057 27.4 0.3 9 64-72 118-126 (235)
36 TIGR00622 ssl1 transcription f 25.5 27 0.00059 24.5 0.3 10 63-72 33-42 (112)
37 PLN02774 brassinosteroid-6-oxi 24.9 28 0.00061 26.9 0.3 24 11-34 368-391 (463)
38 PF04231 Endonuclease_1: Endon 24.5 22 0.00049 26.7 -0.2 9 64-72 106-114 (218)
39 COG2124 CypX Cytochrome P450 [ 23.8 32 0.00069 26.8 0.5 24 11-34 321-344 (411)
40 PLN02302 ent-kaurenoic acid ox 23.1 34 0.00074 26.1 0.5 24 11-34 392-415 (490)
41 COG1398 OLE1 Fatty-acid desatu 22.9 61 0.0013 26.3 1.9 22 51-72 224-248 (289)
42 PLN02183 ferulate 5-hydroxylas 22.0 40 0.00088 26.5 0.7 24 11-34 405-428 (516)
43 PLN02196 abscisic acid 8'-hydr 20.8 34 0.00075 26.5 0.1 23 12-34 369-391 (463)
No 1
>KOG4232|consensus
Probab=99.54 E-value=2e-16 Score=128.79 Aligned_cols=73 Identities=29% Similarity=0.470 Sum_probs=65.7
Q ss_pred eeehhhhhhcccccccCCCccCCCCCCCCCCCceeeeeeehcccccc-cceeeEeeecCchhhhhccCCCCcccccccc
Q psy6224 4 WGSFLFAVIGVNAAHHHPDIFHQGDTPREDRDWGINQIDAVRSRPDE-RNQFIVLTTFGEHTLHHLFPTIDHCFLHIAH 81 (82)
Q Consensus 4 ~~Sf~F~~iGl~AaHHhp~ifhdGD~~r~d~DwGi~qldtv~dR~d~-~s~F~vlt~FGdH~LHHLFPTlDH~~L~~~~ 81 (82)
.++++|..+ ++++|+.|+|||+|+ ++ +||+.+|++|++||.+. .+++++. .+|.++.||||||++++-|+-++
T Consensus 313 ~~~~s~~v~-l~~nH~~~~i~~~~~-i~--~dw~~~Q~~tT~n~~~~~f~dwl~g-hln~qieHHLFPtmpr~nL~~v~ 386 (430)
T KOG4232|consen 313 FSSWSFWVT-LTMNHIDPEIYHEGD-IR--RDWFSLQLATTINVGPSKFSDWLSG-HLNFQIEHHLFPTMPRHNLNKVA 386 (430)
T ss_pred HHHHHHHHH-HhhhccchhhccCCc-ch--hhHHHHHHhhccccCchhHHHHHHh-hhhhhHHhhcCCCCCccchHHHH
Confidence 445555555 999999999999999 77 99999999999999999 9999999 99999999999999999987653
No 2
>cd03507 Delta12-FADS-like The Delta12 Fatty Acid Desaturase (Delta12-FADS)-like CD includes the integral-membrane enzymes, delta-12 acyl-lipid desaturases, oleate 12-hydroxylases, omega3 and omega6 fatty acid desaturases, and other related proteins, found in a wide range of organisms including higher plants, green algae, diatoms, nematodes, fungi, and bacteria. The expression of these proteins appears to be temperature dependent: decreases in temperature result in increased levels of fatty acid desaturation within membrane lipids subsequently altering cell membrane fluidity. An important enzyme for the production of polyunsaturates in plants is the oleate delta-12 desaturase (Arabidopsis FAD2) of the endoplasmic reticulum. This enzyme accepts l-acyl-2-oleoyl-sn-glycero-3-phosphocholine as substrate and requires NADH:cytochrome b oxidoreductase, cytochrome b, and oxygen for activity. FAD2 converts oleate(18:1) to linoleate (18:2) and is closely related to oleate 12-hydroxylase which cat
Probab=98.11 E-value=6e-07 Score=65.20 Aligned_cols=68 Identities=21% Similarity=0.283 Sum_probs=53.8
Q ss_pred eeehhhhhhcccccccCCCccCCCCCCCCCCCceeeeeeehcccccc-cceeeEeeecCchhhhhccCCCCccc
Q psy6224 4 WGSFLFAVIGVNAAHHHPDIFHQGDTPREDRDWGINQIDAVRSRPDE-RNQFIVLTTFGEHTLHHLFPTIDHCF 76 (82)
Q Consensus 4 ~~Sf~F~~iGl~AaHHhp~ifhdGD~~r~d~DwGi~qldtv~dR~d~-~s~F~vlt~FGdH~LHHLFPTlDH~~ 76 (82)
+.++..+ +.+-.-|.+|++-++++ ++.+|+..|+.+.+||+.. ...++.- ++|.|..|||||++-+..
T Consensus 153 ~~~~~l~-~~t~l~H~~~~~~~~~~---~~w~~~~~q~~~t~~~~~~~~~~~l~~-~i~~hv~HHlfP~iP~y~ 221 (222)
T cd03507 153 VVNAWLV-LITYLQHTFPDIPWYRA---DEWNFAQAGLLGTVDRDYGGWLNWLTH-IIGTHVAHHLFPRIPHYN 221 (222)
T ss_pred HHHHHHH-eeeEecCCCCCCCCcCc---cccchhhhcceeeeeccccHHHHHHhc-CCCcccchhcCCCCCcCc
Confidence 3455555 77888999999988876 6678889999999999655 4455555 999999999999986653
No 3
>cd03506 Delta6-FADS-like The Delta6 Fatty Acid Desaturase (Delta6-FADS)-like CD includes the integral-membrane enzymes: delta-4, delta-5, delta-6, delta-8, delta-8-sphingolipid, and delta-11 desaturases found in vertebrates, higher plants, fungi, and bacteria. These desaturases are required for the synthesis of highly unsaturated fatty acids (HUFAs), which are mainly esterified into phospholipids and contribute to maintaining membrane fluidity. While HUFAs may be required for cold tolerance in bacteria, plants and fish, the primary role of HUFAs in mammals is cell signaling. These enzymes are described as front-end desaturases because they introduce a double bond between the pre-exiting double bond and the carboxyl (front) end of the fatty acid. Various substrates are involved, with both acyl-coenzyme A (CoA) and acyl-lipid desaturases present in this CD. Acyl-lipid desaturases are localized in the membranes of cyanobacterial thylakoid, plant endoplasmic reticulum (ER), and plastid; an
Probab=97.81 E-value=3.3e-06 Score=59.67 Aligned_cols=65 Identities=17% Similarity=0.206 Sum_probs=50.1
Q ss_pred ccccccCCCccCCCCCCCCCCCceeeeeeehcccccc-cceeeEeeecCchhhhhccCCCCcccccccc
Q psy6224 14 VNAAHHHPDIFHQGDTPREDRDWGINQIDAVRSRPDE-RNQFIVLTTFGEHTLHHLFPTIDHCFLHIAH 81 (82)
Q Consensus 14 l~AaHHhp~ifhdGD~~r~d~DwGi~qldtv~dR~d~-~s~F~vlt~FGdH~LHHLFPTlDH~~L~~~~ 81 (82)
+...|...++....+ +++.||...|+.|.+|+... ...++ .-+++-|+.|||||++-+..||++.
T Consensus 127 ~~~~H~~~~~~~~~~--~~~~~w~~~q~~tt~~~~~~~~~~~l-~ggln~qieHHLfP~ip~~~l~~~~ 192 (204)
T cd03506 127 FQLNHFGMPVEDPPG--ESKNDWLERQVLTTRNITGSPFLDWL-HGGLNYQIEHHLFPTMPRHNYPKVA 192 (204)
T ss_pred eecccccccccCCCC--CcccCHHHHHHhCcccCCCCCHHHHH-hcchhhHHHHhcCCCchhhhHHHHH
Confidence 446677777776411 36779999999999999544 44444 4688999999999999999999864
No 4
>PF00487 FA_desaturase: Fatty acid desaturase This entry is only a subset of the Pfam family.; InterPro: IPR005804 Fatty acid desaturases are enzymes that catalyse the insertion of a double bond at the delta position of fatty acids. There seem to be two distinct families of fatty acid desaturases which do not seem to be evolutionary related. Family 1 is composed of: Stearoyl-CoA desaturase (SCD) (1.14.19.1 from EC) []. Family 2 is composed of: Bacterial fatty acid desaturases. Plant stearoyl-acyl-carrier-protein desaturase (1.14.19.1 from EC) [], this enzyme catalyzes the introduction of a double bond at the delta(9) position of steraoyl-ACP to produce oleoyl-ACP. This enzyme is responsible for the conversion of saturated fatty acids to unsaturated fatty acids in the synthesis of vegetable oils. Cyanobacterial DesA [], an enzyme that can introduce a second cis double bond at the delta(12) position of fatty acid bound to membranes glycerolipids. DesA is involved in chilling tolerance; the phase transition temperature of lipids of cellular membranes being dependent on the degree of unsaturation of fatty acids of the membrane lipids. This entry contains fatty acid desaturases belonging to Family 1. ; GO: 0006629 lipid metabolic process
Probab=97.80 E-value=4.9e-06 Score=55.27 Aligned_cols=53 Identities=25% Similarity=0.355 Sum_probs=41.7
Q ss_pred CCCCCCCCceeeeeeehcccccc-cceeeEeeecCchhhhhccCCCCcccccccc
Q psy6224 28 DTPREDRDWGINQIDAVRSRPDE-RNQFIVLTTFGEHTLHHLFPTIDHCFLHIAH 81 (82)
Q Consensus 28 D~~r~d~DwGi~qldtv~dR~d~-~s~F~vlt~FGdH~LHHLFPTlDH~~L~~~~ 81 (82)
+...++.+|..-|+.+..+.... ...+ ..-++|-|+.||+||++....||++.
T Consensus 186 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~H~~HHl~P~vp~~~l~~~~ 239 (257)
T PF00487_consen 186 DDNEDTRDFYYRQLPGSSNVHNSWWLNW-LTGGLNYHIEHHLFPGVPWYNLPEAH 239 (257)
T ss_pred cccccccceecccccccccccCchhhhc-cccCCCChHHhCCCCCcCHHHHHHHH
Confidence 44457788999999988886555 3344 46678999999999999999999874
No 5
>PLN02505 omega-6 fatty acid desaturase
Probab=96.69 E-value=0.00049 Score=55.04 Aligned_cols=61 Identities=28% Similarity=0.421 Sum_probs=48.8
Q ss_pred ccccCCCccCCCCCCCCCCCceeeeeeehcccccc-cceeeEeeecC-chhhhhccCCCCccccccccC
Q psy6224 16 AAHHHPDIFHQGDTPREDRDWGINQIDAVRSRPDE-RNQFIVLTTFG-EHTLHHLFPTIDHCFLHIAHE 82 (82)
Q Consensus 16 AaHHhp~ifhdGD~~r~d~DwGi~qldtv~dR~d~-~s~F~vlt~FG-dH~LHHLFPTlDH~~L~~~~~ 82 (82)
.=|.+|++.+..+ ++.+|---||.| +|| +. .-.+ .+-+.| .|..|||||.+-+--|++|.|
T Consensus 272 lqHt~~~ip~~~~---~~W~~~rgAl~t-vdr-~yg~~~~-l~h~I~~~Hv~HHl~srIP~Y~l~eA~~ 334 (381)
T PLN02505 272 LQHTHPALPHYDS---SEWDWLRGALAT-VDR-DYGILNK-VFHNITDTHVAHHLFSTMPHYHAMEATK 334 (381)
T ss_pred HhccCCCCCccCC---CCcChhhcccee-ccC-cchHHHH-HHccCCcccchhhccCCCCCCCHHHHHH
Confidence 4588999999866 888899999977 788 44 2222 456666 999999999999999999964
No 6
>PLN03198 delta6-acyl-lipid desaturase; Provisional
Probab=95.84 E-value=0.00097 Score=55.17 Aligned_cols=62 Identities=19% Similarity=0.303 Sum_probs=46.7
Q ss_pred cccccccCCCccCCCCCCCCCCCceeeeeeehcccccc-cceeeEeeecCchhhhhccCCCCcccccccc
Q psy6224 13 GVNAAHHHPDIFHQGDTPREDRDWGINQIDAVRSRPDE-RNQFIVLTTFGEHTLHHLFPTIDHCFLHIAH 81 (82)
Q Consensus 13 Gl~AaHHhp~ifhdGD~~r~d~DwGi~qldtv~dR~d~-~s~F~vlt~FGdH~LHHLFPTlDH~~L~~~~ 81 (82)
=+...|-..+++ .++.||-..|+.|.+|=..- ...| ..-+.+-|+-|||||++-+..||+|.
T Consensus 419 vF~lnH~~~~v~------~~~~dw~~~Qv~tT~n~~~~~~~~w-f~GGLN~QiEHHLFP~iP~~~l~~i~ 481 (526)
T PLN03198 419 VFVLSHNGMEVY------NKSKEFVNAQIVSTRDIKANIFNDW-FTGGLNRQIEHHLFPTMPRHNLNKIA 481 (526)
T ss_pred hhhccccCCCCC------CCCcCHHHHHHhcCcCcCCchHHHH-hhcCCcccchhhcCCCCchhhHHHHh
Confidence 366778887775 12338999999999885422 3333 34678999999999999999999874
No 7
>PLN02498 omega-3 fatty acid desaturase
Probab=95.40 E-value=0.0064 Score=50.33 Aligned_cols=57 Identities=25% Similarity=0.343 Sum_probs=41.6
Q ss_pred CCCccCCCCCCCCCCCceeeeeeehcccccc-cceeeEeeecCchhhhhccCCCCccccccccC
Q psy6224 20 HPDIFHQGDTPREDRDWGINQIDAVRSRPDE-RNQFIVLTTFGEHTLHHLFPTIDHCFLHIAHE 82 (82)
Q Consensus 20 hp~ifhdGD~~r~d~DwGi~qldtv~dR~d~-~s~F~vlt~FGdH~LHHLFPTlDH~~L~~~~~ 82 (82)
+|++=+-.+ ++.+|---|| +.+|| |. +-.+ ..-+-|.|..|||||.+-|--|++|.|
T Consensus 334 ~~~iP~y~~---~eWs~~rGaL-~TvDR-~yg~i~~-l~H~I~tHV~HHlf~~IPhYhl~eAt~ 391 (450)
T PLN02498 334 EDKLPWYRG---KEWSYLRGGL-TTLDR-DYGWINN-IHHDIGTHVIHHLFPQIPHYHLVEATE 391 (450)
T ss_pred CCCCCCCCC---CCcchhhccc-eeecC-cccchhh-hhcCcccchhhhccCCCCCcCHHHHHH
Confidence 466654433 5777777788 68899 65 3333 233678999999999999999999864
No 8
>PLN02598 omega-6 fatty acid desaturase
Probab=95.12 E-value=0.0043 Score=50.31 Aligned_cols=62 Identities=21% Similarity=0.252 Sum_probs=43.1
Q ss_pred ccccCCCccCCCCCCCCCCCceeeeeeehcccccc--cceeeEeeecCchhhhhccCCCCccccccccC
Q psy6224 16 AAHHHPDIFHQGDTPREDRDWGINQIDAVRSRPDE--RNQFIVLTTFGEHTLHHLFPTIDHCFLHIAHE 82 (82)
Q Consensus 16 AaHHhp~ifhdGD~~r~d~DwGi~qldtv~dR~d~--~s~F~vlt~FGdH~LHHLFPTlDH~~L~~~~~ 82 (82)
.-|.+|++-++.+ ++.+|.--|+...++| |. +..+ ..=+.|-|..|||||++-+..||++.+
T Consensus 297 lhHt~p~ip~~~~---~eW~~~~~al~~Tv~~-~~~~~~~~-L~hnIn~HV~HHLfP~IP~Y~lpea~~ 360 (421)
T PLN02598 297 VHHTAPHIPFKQA---REWNAAQAQLNGTVHC-DYPAWIEF-LCHDISVHIPHHISSKIPSYNLRKAHA 360 (421)
T ss_pred HhhcCCCCCcccc---ccccHhhhhhcCceec-CCcHHHHH-HHcCCccchhhhcCCCCCcchHHHHHH
Confidence 4577888877433 4444444566667777 44 3222 445778999999999999999998853
No 9
>PLN03199 delta6-acyl-lipid desaturase-like protein; Provisional
Probab=92.03 E-value=0.034 Score=45.21 Aligned_cols=63 Identities=17% Similarity=0.230 Sum_probs=44.0
Q ss_pred ccccccCCCccCCCCCCCCCCCceeeeeeehccccc-cc--cee--eEeeecCchhhhhccCCCCccccccc
Q psy6224 14 VNAAHHHPDIFHQGDTPREDRDWGINQIDAVRSRPD-ER--NQF--IVLTTFGEHTLHHLFPTIDHCFLHIA 80 (82)
Q Consensus 14 l~AaHHhp~ifhdGD~~r~d~DwGi~qldtv~dR~d-~~--s~F--~vlt~FGdH~LHHLFPTlDH~~L~~~ 80 (82)
+..+|..-+++.+ + +..||...|+.|.+|=.- .+ |.| ...-..+-+.-|||||++-|..+|++
T Consensus 369 f~l~H~~~~~~~~-~---~~~d~~~~Qv~TT~n~~~~~~~~s~~~~wf~GGLN~QIEHHLFP~mp~~~y~~i 436 (485)
T PLN03199 369 FGLGHNGMATYDA-D---ARPDFWKLQVTTTRNIIGGHGFPQAFVDWFCGGLQYQVDHHLFPMLPRHNIAKC 436 (485)
T ss_pred EecCCccccccCC-C---CCccHHHHHHHhccCccCCCCCcchHHHHHhccchhhhhhhcCCCCchhhHHhh
Confidence 4567776666533 3 344899999999987631 00 222 22356788999999999999999875
No 10
>cd03511 Rhizopine-oxygenase-like This CD includes the putative hydrocarbon oxygenase, MocD, a bacterial rhizopine (3-O-methyl-scyllo-inosamine, 3-O-MSI) oxygenase, and other related proteins. It has been proposed that MocD, MocE (Rieske-like ferredoxin), and MocF (ferredoxin reductase) under the regulation of MocR, act in concert to form a ferredoxin oxygenase system that demethylates 3-O-MSI to form scyllo-inosamine. This domain family appears to be structurally related to the membrane fatty acid desaturases and the alkane hydroxylases. They all share in common extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within homologs, stearoyl CoA d
Probab=91.75 E-value=0.046 Score=40.39 Aligned_cols=24 Identities=25% Similarity=0.437 Sum_probs=21.9
Q ss_pred eecCchhhhhccCCCCcccccccc
Q psy6224 58 TTFGEHTLHHLFPTIDHCFLHIAH 81 (82)
Q Consensus 58 t~FGdH~LHHLFPTlDH~~L~~~~ 81 (82)
-++|-|+-||+||++-+..||++.
T Consensus 243 ~n~nyH~eHHl~P~vP~y~Lp~~h 266 (285)
T cd03511 243 WNMPYHAEHHMYPSVPFHALPKLH 266 (285)
T ss_pred cCCchHHHHhcCCCCcHhHHHHHH
Confidence 588999999999999999999865
No 11
>cd03510 Rhizobitoxine-FADS-like This CD includes the dihydrorhizobitoxine fatty acid desaturase (RtxC) characterized in Bradyrhizobium japonicum USDA110, and other related proteins. Dihydrorhizobitoxine desaturase is reported to be involved in the final step of rhizobitoxine biosynthesis. This domain family appears to be structurally related to the membrane fatty acid desaturases and the alkane hydroxylases. They all share in common extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXX(X)HH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within homologs, stearoyl CoA desaturase and alkane hydroxylase.
Probab=91.74 E-value=0.052 Score=38.38 Aligned_cols=25 Identities=36% Similarity=0.538 Sum_probs=22.2
Q ss_pred eecCchhhhhccCCCCccccccccC
Q psy6224 58 TTFGEHTLHHLFPTIDHCFLHIAHE 82 (82)
Q Consensus 58 t~FGdH~LHHLFPTlDH~~L~~~~~ 82 (82)
-++|-|..|||||++-.-.||++++
T Consensus 149 ~~~~YH~eHHl~P~vP~~~Lp~~h~ 173 (175)
T cd03510 149 HNINYHLEHHLFPAVPFYNLPKAHR 173 (175)
T ss_pred cCCcHHHHHhCCcCCchhhHHHHHH
Confidence 4899999999999999999988753
No 12
>COG3239 DesA Fatty acid desaturase [Lipid metabolism]
Probab=91.27 E-value=0.032 Score=43.52 Aligned_cols=49 Identities=29% Similarity=0.401 Sum_probs=37.5
Q ss_pred CCCCceeeeeeehcccccc-cceeeEeeecCchhhhhccCCCCcccccccc
Q psy6224 32 EDRDWGINQIDAVRSRPDE-RNQFIVLTTFGEHTLHHLFPTIDHCFLHIAH 81 (82)
Q Consensus 32 ~d~DwGi~qldtv~dR~d~-~s~F~vlt~FGdH~LHHLFPTlDH~~L~~~~ 81 (82)
+|.+|..-|+.+.++. +. +-.-...=+.|-|..|||||.|-.-.||++.
T Consensus 240 ~d~~~~~~~l~~~~~~-~~~~~~~~l~~n~nyH~~HHl~P~vP~y~lp~~~ 289 (343)
T COG3239 240 EDWQWSDRALNARSNV-DAPPLLRFLTGNINYHVEHHLFPDVPWYRLPRAH 289 (343)
T ss_pred ccchHHHHHHhccCcc-CchHHHHHhcCCccccHhhhCCCCCchhhHHHHH
Confidence 6777798998877633 33 3333455689999999999999999998875
No 13
>cd03514 CrtR_beta-carotene-hydroxylase Beta-carotene hydroxylase (CrtR), the carotenoid zeaxanthin biosynthetic enzyme catalyzes the addition of hydroxyl groups to the beta-ionone rings of beta-carotene to form zeaxanthin and is found in bacteria and red algae. Carotenoids are important natural pigments; zeaxanthin and lutein are the only dietary carotenoids that accumulate in the macular region of the retina and lens. It is proposed that these carotenoids protect ocular tissues against photooxidative damage. CrtR does not show overall amino acid sequence similarity to the beta-carotene hydroxylases similar to CrtZ, an astaxanthin biosynthetic beta-carotene hydroxylase. However, CrtR does show sequence similarity to the green alga, Haematococcus pluvialis, beta-carotene ketolase (CrtW), which converts beta-carotene to canthaxanthin. Sequences of the CrtR_beta-carotene-hydroxylase domain family, as well as, the CrtW_beta-carotene-ketolase domain family appear to be structurally related
Probab=90.44 E-value=0.081 Score=38.23 Aligned_cols=23 Identities=30% Similarity=0.355 Sum_probs=20.3
Q ss_pred ecCchhhhhccCCCCcccccccc
Q psy6224 59 TFGEHTLHHLFPTIDHCFLHIAH 81 (82)
Q Consensus 59 ~FGdH~LHHLFPTlDH~~L~~~~ 81 (82)
+.|-|.-|||||.+-+..||+|.
T Consensus 173 ~~nyH~~HHL~P~IP~y~Lp~a~ 195 (207)
T cd03514 173 GQNYHLVHHLWPSIPWYRYPEAY 195 (207)
T ss_pred CCchhHHHhCCCCCchhhhHHHH
Confidence 34589999999999999999986
No 14
>cd03513 CrtW_beta-carotene-ketolase Beta-carotene ketolase/oxygenase (CrtW, also known as CrtO), the carotenoid astaxanthin biosynthetic enzyme, initially catalyzes the addition of two keto groups to carbons C4 and C4' of beta-carotene. Carotenoids are important natural pigments produced by many microorganisms and plants. Astaxanthin is reported to be an antioxidant, an anti-cancer agent, and an immune system stimulant. A number of bacteria and green algae can convert beta-carotene into astaxanthin by using several ketocarotenoids as intermediates and CrtW and a beta-carotene hydroxylase (CrtZ). CrtW initially converts beta-carotene to canthaxanthin via echinenone, and CrtZ initially mediates the conversion of beta-carotene to zeaxanthin via beta-cryptoxanthin. After a few more intermediates are formed, CrtW and CrtZ act in combination to produce astaxanthin. Sequences of this domain family appear to be structurally related to membrane fatty acid desaturases and alkane hydroxylases. Th
Probab=89.61 E-value=0.086 Score=39.41 Aligned_cols=65 Identities=25% Similarity=0.202 Sum_probs=39.2
Q ss_pred eeeehhhhhhcccccccCCCccCCCCCCCCCCCceeeeeeehcccc-cccceeeEeeecCchhhhhccCCCCccccccc
Q psy6224 3 GWGSFLFAVIGVNAAHHHPDIFHQGDTPREDRDWGINQIDAVRSRP-DERNQFIVLTTFGEHTLHHLFPTIDHCFLHIA 80 (82)
Q Consensus 3 ~~~Sf~F~~iGl~AaHHhp~ifhdGD~~r~d~DwGi~qldtv~dR~-d~~s~F~vlt~FGdH~LHHLFPTlDH~~L~~~ 80 (82)
+++|+.-+++|=+-.|+.++. +..+.. ..+..+ -.+-.|+.--+||-|.-||+||.+-.-.||+|
T Consensus 159 l~~~~~l~~f~T~lpH~~~~~------~~~~~~-------~a~~~~~~~~~~~l~c~~fgyH~eHH~fP~~Pw~~Lp~~ 224 (225)
T cd03513 159 ILSSLQLFYFGTWLPHRPGRG------GFADRH-------RARSSRLSPVLSFLTCYHFGYHHEHHLSPSTPWWRLPEL 224 (225)
T ss_pred HHHHHHHHHHHhhcCCCCCCC------CCCCcc-------cceecCccHHHHHHHHHhcCcchhhccCCCCCcccCccc
Confidence 457777788888877875441 111111 111110 01222222236999999999999999999987
No 15
>PF12073 DUF3553: Protein of unknown function (DUF3553); InterPro: IPR021938 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 60 amino acids in length. This protein has two conserved sequence motifs: GQVQS and TVNF.
Probab=86.70 E-value=0.4 Score=29.92 Aligned_cols=22 Identities=32% Similarity=0.602 Sum_probs=18.3
Q ss_pred CCCCCC--CCCCceeeeeeehccc
Q psy6224 26 QGDTPR--EDRDWGINQIDAVRSR 47 (82)
Q Consensus 26 dGD~~r--~d~DwGi~qldtv~dR 47 (82)
.|+..| +-.|||+-|+++.++.
T Consensus 3 pG~~VrHP~~pdWG~GqVqS~i~~ 26 (52)
T PF12073_consen 3 PGMLVRHPDHPDWGIGQVQSNIGG 26 (52)
T ss_pred CCCEEeCCCCCCCcceEEEEecCC
Confidence 577666 7889999999998776
No 16
>cd01060 Membrane-FADS-like The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the exception of archaea. Membrane FADSs are non-heme, iron-containing, oxygen-dependent enzymes involved in regioselective introduction of double bonds in fatty acyl aliphatic chains. They play an important role in the maintenance of the proper structure and functioning of biological membranes. Alkane hydroxylases are bacterial, integral-membrane di-iron enzymes that share a requirement for iron and oxygen for activity similar to that of membrane FADSs, and are involved in the initial oxidation of inactivated alkanes. Beta-carotene ketolase and beta-carotene hydroxylase are carotenoid biosynthetic enzymes for astaxanthin and zeaxanthin, respectively. This superfamily domain has extensive hydrophobic regions that would
Probab=85.97 E-value=0.23 Score=31.01 Aligned_cols=14 Identities=64% Similarity=1.084 Sum_probs=11.9
Q ss_pred eee-cCchhhhhccC
Q psy6224 57 LTT-FGEHTLHHLFP 70 (82)
Q Consensus 57 lt~-FGdH~LHHLFP 70 (82)
+++ ++-|..|||||
T Consensus 108 ~~~g~~~H~~HHl~P 122 (122)
T cd01060 108 LTGGLGYHNEHHLFP 122 (122)
T ss_pred HhcccccccccccCc
Confidence 344 89999999999
No 17
>cd03509 DesA_FADS-like Fatty acid desaturase protein family subgroup, a delta-12 acyl-lipid desaturase-like, DesA-like, yet uncharacterized subgroup of membrane fatty acid desaturase proteins found in alpha-, beta-, and gamma-proteobacteria. Sequences of this domain family appear to be structurally related to membrane fatty acid desaturases and alkane hydroxylases. They all share in common extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within homologs, stearoyl CoA desaturase and alkane hydroxylase.
Probab=84.69 E-value=0.32 Score=37.23 Aligned_cols=24 Identities=25% Similarity=0.234 Sum_probs=22.2
Q ss_pred ecCchhhhhccCCCCccccccccC
Q psy6224 59 TFGEHTLHHLFPTIDHCFLHIAHE 82 (82)
Q Consensus 59 ~FGdH~LHHLFPTlDH~~L~~~~~ 82 (82)
+-|-|.-||++|.+-...||+|++
T Consensus 228 ninyH~~HH~~P~vP~y~Lp~~h~ 251 (288)
T cd03509 228 NNNLHVVHHDLPTLPWYDLPRLYR 251 (288)
T ss_pred cCCchHhhcCCCCCCcccHHHHHH
Confidence 889999999999999999999863
No 18
>cd03508 Delta4-sphingolipid-FADS-like The Delta4-sphingolipid Fatty Acid Desaturase (Delta4-sphingolipid-FADS)-like CD includes the integral-membrane enzymes, dihydroceramide Delta-4 desaturase, involved in the synthesis of sphingosine; and the human membrane fatty acid (lipid) desaturase (MLD), reported to modulate biosynthesis of the epidermal growth factor receptor; and other related proteins. These proteins are found in various eukaryotes including vertebrates, higher plants, and fungi. Studies show that MLD is localized to the endoplasmic reticulum. As with other members of this superfamily, this domain family has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for
Probab=77.84 E-value=0.82 Score=35.22 Aligned_cols=28 Identities=29% Similarity=0.354 Sum_probs=23.9
Q ss_pred eEeeecCchhhhhccCCCCccccccccC
Q psy6224 55 IVLTTFGEHTLHHLFPTIDHCFLHIAHE 82 (82)
Q Consensus 55 ~vlt~FGdH~LHHLFPTlDH~~L~~~~~ 82 (82)
...-+-|-|.-||+||++-.-.||+|.+
T Consensus 225 ~~~~n~~yH~~HH~~p~iP~~~Lp~~~~ 252 (289)
T cd03508 225 LLTFNVGYHNEHHDFPYIPGTRLPKLRK 252 (289)
T ss_pred HHhhccChHHHhcCCCCCCcccHHHHHH
Confidence 3455789999999999999999999863
No 19
>PLN02579 sphingolipid delta-4 desaturase
Probab=73.95 E-value=1.1 Score=35.17 Aligned_cols=28 Identities=36% Similarity=0.493 Sum_probs=24.0
Q ss_pred eEeeecCchhhhhccCCCCccccccccC
Q psy6224 55 IVLTTFGEHTLHHLFPTIDHCFLHIAHE 82 (82)
Q Consensus 55 ~vlt~FGdH~LHHLFPTlDH~~L~~~~~ 82 (82)
.+.=+-|-|.-||+||.+--..||+|.+
T Consensus 253 ~l~~NigYH~eHH~fP~IP~~~Lp~l~~ 280 (323)
T PLN02579 253 LLTWNVGYHNEHHDFPRIPGSKLHKVKE 280 (323)
T ss_pred HHhhcccccHhhcCCCCCchhhHHHHHH
Confidence 3445789999999999999999999864
No 20
>PF00067 p450: Cytochrome P450 p450 superfamily signature b-class p450 signature mitochondrial p450 signature E-class p450 group I signature E-class p450 group II signature E-class p450 group IV signature; InterPro: IPR001128 Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus). Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains. Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity. Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes. More information about these proteins can be found at Protein of the Month: Cytochrome P450 [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 0020037 heme binding, 0055114 oxidation-reduction process; PDB: 2RFC_B 2RFB_A 3EJB_H 3EJE_H 3EJD_H 1N6B_A 1NR6_A 1DT6_A 3EL3_A 3DBG_B ....
Probab=51.25 E-value=6.4 Score=27.86 Aligned_cols=23 Identities=26% Similarity=0.517 Sum_probs=17.7
Q ss_pred hcccccccCCCccCCCCCCCCCC
Q psy6224 12 IGVNAAHHHPDIFHQGDTPREDR 34 (82)
Q Consensus 12 iGl~AaHHhp~ifhdGD~~r~d~ 34 (82)
+...++|++|++|.|.+..++++
T Consensus 365 ~~~~~~~~d~~~~~dp~~F~P~R 387 (463)
T PF00067_consen 365 VSIYALHRDPEYFPDPDEFDPER 387 (463)
T ss_dssp EEHHHHTTSTTTSSSTTS--TTG
T ss_pred ccccccccccccccccccccccc
Confidence 34678999999999999888766
No 21
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=41.64 E-value=6.4 Score=21.84 Aligned_cols=19 Identities=26% Similarity=0.609 Sum_probs=15.2
Q ss_pred hhhhhccCCCCcccccccc
Q psy6224 63 HTLHHLFPTIDHCFLHIAH 81 (82)
Q Consensus 63 H~LHHLFPTlDH~~L~~~~ 81 (82)
..|.=|||.++...+..|.
T Consensus 7 ~~L~~mFP~l~~~~I~~~L 25 (43)
T smart00546 7 HDLKDMFPNLDEEVIKAVL 25 (43)
T ss_pred HHHHHHCCCCCHHHHHHHH
Confidence 3567799999999887764
No 22
>PLN02500 cytochrome P450 90B1
Probab=37.44 E-value=15 Score=28.51 Aligned_cols=24 Identities=17% Similarity=0.156 Sum_probs=19.8
Q ss_pred hhcccccccCCCccCCCCCCCCCC
Q psy6224 11 VIGVNAAHHHPDIFHQGDTPREDR 34 (82)
Q Consensus 11 ~iGl~AaHHhp~ifhdGD~~r~d~ 34 (82)
++...|.||+|++|.|-+..++++
T Consensus 385 ~~~~~~~hrdp~~~~dP~~F~PeR 408 (490)
T PLN02500 385 LPVIAAVHLDSSLYDQPQLFNPWR 408 (490)
T ss_pred EechhhcccCcccCCCccccChhh
Confidence 456778999999999998887665
No 23
>PLN02687 flavonoid 3'-monooxygenase
Probab=34.74 E-value=17 Score=28.65 Aligned_cols=24 Identities=25% Similarity=0.318 Sum_probs=19.9
Q ss_pred hhcccccccCCCccCCCCCCCCCC
Q psy6224 11 VIGVNAAHHHPDIFHQGDTPREDR 34 (82)
Q Consensus 11 ~iGl~AaHHhp~ifhdGD~~r~d~ 34 (82)
++...++||+|++|.|.++.++++
T Consensus 399 ~~~~~~~h~d~~~~~dp~~F~PeR 422 (517)
T PLN02687 399 LVNVWAIARDPEQWPDPLEFRPDR 422 (517)
T ss_pred EEecHHhcCCcccCCCcccCCchh
Confidence 456778999999999999888665
No 24
>PLN02220 delta-9 acyl-lipid desaturase
Probab=34.49 E-value=8.1 Score=30.41 Aligned_cols=20 Identities=40% Similarity=0.649 Sum_probs=16.3
Q ss_pred ceeeEeeecCc--hhhhhccCC
Q psy6224 52 NQFIVLTTFGE--HTLHHLFPT 71 (82)
Q Consensus 52 s~F~vlt~FGd--H~LHHLFPT 71 (82)
+-++.+-+||+ |--||-||.
T Consensus 233 ~~~lallt~GEgwHNnHHafP~ 254 (299)
T PLN02220 233 VWWLSLFTMGESWHNNHHAFES 254 (299)
T ss_pred hHHHHHHhccccccccccCCcc
Confidence 45567778887 999999996
No 25
>PTZ00404 cytochrome P450; Provisional
Probab=33.83 E-value=17 Score=28.03 Aligned_cols=23 Identities=13% Similarity=0.166 Sum_probs=19.1
Q ss_pred hcccccccCCCccCCCCCCCCCC
Q psy6224 12 IGVNAAHHHPDIFHQGDTPREDR 34 (82)
Q Consensus 12 iGl~AaHHhp~ifhdGD~~r~d~ 34 (82)
+...|.|++|++|.|-++.++++
T Consensus 387 ~~~~a~hrdp~~~~dP~~F~PeR 409 (482)
T PTZ00404 387 INYYSLGRNEKYFENPEQFDPSR 409 (482)
T ss_pred eeHHHhhCCccccCCccccCccc
Confidence 44568899999999999988665
No 26
>PF10848 DUF2655: Protein of unknown function (DUF2655); InterPro: IPR020371 This entry contains proteins with no known function.
Probab=33.46 E-value=30 Score=23.30 Aligned_cols=52 Identities=29% Similarity=0.473 Sum_probs=32.1
Q ss_pred cccccccCCCccCC-CC--CCCC---CCCceeeeeeehcccccc---cceeeEeeecCchh
Q psy6224 13 GVNAAHHHPDIFHQ-GD--TPRE---DRDWGINQIDAVRSRPDE---RNQFIVLTTFGEHT 64 (82)
Q Consensus 13 Gl~AaHHhp~ifhd-GD--~~r~---d~DwGi~qldtv~dR~d~---~s~F~vlt~FGdH~ 64 (82)
|-..+|-.|++|-. |. -+++ -.|--++.-=-|-||+|- ...|+|||+||.-+
T Consensus 16 ~kq~g~yspe~~~~tgkdcnpqpanclkd~~vlrhccv~drs~kmg~s~~~~vlt~~~~et 76 (82)
T PF10848_consen 16 KKQPGHYSPEIFPSTGKDCNPQPANCLKDQYVLRHCCVDDRSDKMGYSAKFLVLTSMDTET 76 (82)
T ss_pred ccCCCCcCccccccCCCCCCCCchhhhhhhhhhhhhcccCCCcccCceEEEEEEEecCcch
Confidence 44567888888753 21 1111 123334445567789887 56789999999643
No 27
>PLN03141 3-epi-6-deoxocathasterone 23-monooxygenase; Provisional
Probab=32.88 E-value=19 Score=27.67 Aligned_cols=24 Identities=8% Similarity=-0.000 Sum_probs=20.1
Q ss_pred hhcccccccCCCccCCCCCCCCCC
Q psy6224 11 VIGVNAAHHHPDIFHQGDTPREDR 34 (82)
Q Consensus 11 ~iGl~AaHHhp~ifhdGD~~r~d~ 34 (82)
++.+.++|++|++|.|-+..++++
T Consensus 356 ~~~~~~~~~d~~~~~dP~~F~PeR 379 (452)
T PLN03141 356 LAYFRSVHLDEENYDNPYQFNPWR 379 (452)
T ss_pred EEehHhccCCchhcCCccccCccc
Confidence 456789999999999999888655
No 28
>PF00799 Gemini_AL1: Geminivirus Rep catalytic domain; InterPro: IPR022690 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity. The AL1 proteins encodes the replication initiator protein (Rep) of geminiviruses, which is a replicon-specific initiator enzyme and is an essential component of the replisome []. For geminivirus Rep protein, this N-terminal region is crucial for origin recognition and DNA cleavage and nucleotidyl transfer []. It is found in association with PF08283 from PFAM. ; GO: 0006260 DNA replication; PDB: 1L5I_A 1L2M_A.
Probab=32.19 E-value=11 Score=26.00 Aligned_cols=10 Identities=50% Similarity=0.866 Sum_probs=4.1
Q ss_pred CCCceeeeee
Q psy6224 33 DRDWGINQID 42 (82)
Q Consensus 33 d~DwGi~qld 42 (82)
.++||.+|+|
T Consensus 104 ~~e~G~fq~~ 113 (114)
T PF00799_consen 104 YIEWGTFQID 113 (114)
T ss_dssp EEEEC-----
T ss_pred EEeeeeEecC
Confidence 5789999987
No 29
>PLN02655 ent-kaurene oxidase
Probab=30.83 E-value=20 Score=27.76 Aligned_cols=25 Identities=8% Similarity=0.106 Sum_probs=20.5
Q ss_pred hhcccccccCCCccCCCCCCCCCCC
Q psy6224 11 VIGVNAAHHHPDIFHQGDTPREDRD 35 (82)
Q Consensus 11 ~iGl~AaHHhp~ifhdGD~~r~d~D 35 (82)
++...++||+|++|.|-++.++++=
T Consensus 363 ~~~~~~~~~d~~~~~~p~~F~PeR~ 387 (466)
T PLN02655 363 AINIYGCNMDKKRWENPEEWDPERF 387 (466)
T ss_pred EecHHHhcCCcccCCChhccCcccc
Confidence 4677899999999999888876653
No 30
>cd03505 Delta9-FADS-like The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide range of bacteria. These enzymes play essential roles in fatty acid metabolism and the regulation of cell membrane fluidity. Acyl-CoA desaturases are the enzymes involved in the CoA-bound desaturation of fatty acids. Mammalian stearoyl-CoA delta-9 desaturase is a key enzyme in the biosynthesis of monounsaturated fatty acids, and in yeast, the delta-9 acyl-CoA desaturase (OLE1) reaction accounts for all de nova unsaturated fatty acid production in Saccharomyces cerevisiae. These non-heme, iron-containing, ER membrane-bound enzymes are part of a three-component enzyme system involving cytochrome b5, cytochrome b5 reductase, and the delta-9 fatty acid desaturase. This complex catalyzes the NADH- and oxygen-dependent i
Probab=29.82 E-value=9.4 Score=27.97 Aligned_cols=21 Identities=52% Similarity=0.926 Sum_probs=16.5
Q ss_pred cceeeEeeecCc--hhhhhccCC
Q psy6224 51 RNQFIVLTTFGE--HTLHHLFPT 71 (82)
Q Consensus 51 ~s~F~vlt~FGd--H~LHHLFPT 71 (82)
.+-++.+-+||+ |--||.||.
T Consensus 125 n~~~~~llt~GEg~HNnHHafP~ 147 (178)
T cd03505 125 NNWWVALLTFGEGWHNNHHAFPG 147 (178)
T ss_pred hhHHHHHHHccccccccccCCcc
Confidence 455577777877 999999995
No 31
>PLN03112 cytochrome P450 family protein; Provisional
Probab=28.10 E-value=25 Score=27.43 Aligned_cols=26 Identities=19% Similarity=0.470 Sum_probs=21.8
Q ss_pred hhcccccccCCCccCCCCCCCCCCCc
Q psy6224 11 VIGVNAAHHHPDIFHQGDTPREDRDW 36 (82)
Q Consensus 11 ~iGl~AaHHhp~ifhdGD~~r~d~Dw 36 (82)
++...+.||+|++|.|-++.++++-|
T Consensus 398 ~~~~~~~h~d~~~~~dP~~F~PeRf~ 423 (514)
T PLN03112 398 FINTHGLGRNTKIWDDVEEFRPERHW 423 (514)
T ss_pred EEehHHhhCCcccCCChhhcCCcccC
Confidence 45778899999999988888887755
No 32
>PF05304 DUF728: Protein of unknown function (DUF728); InterPro: IPR007968 This entry is represented by the Tobacco rattle virus, 16kDa protein; it is a family of uncharacterised viral proteins.
Probab=27.90 E-value=19 Score=25.30 Aligned_cols=12 Identities=42% Similarity=0.869 Sum_probs=10.3
Q ss_pred CCCCCCceeeee
Q psy6224 30 PREDRDWGINQI 41 (82)
Q Consensus 30 ~r~d~DwGi~ql 41 (82)
.|.|+|+||-||
T Consensus 90 ~RDDi~fGl~~L 101 (103)
T PF05304_consen 90 FRDDIDFGLDQL 101 (103)
T ss_pred hhccCccchhhh
Confidence 468999999887
No 33
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=27.19 E-value=18 Score=20.03 Aligned_cols=18 Identities=22% Similarity=0.534 Sum_probs=13.1
Q ss_pred hhhhccCCCCcccccccc
Q psy6224 64 TLHHLFPTIDHCFLHIAH 81 (82)
Q Consensus 64 ~LHHLFPTlDH~~L~~~~ 81 (82)
.|-=|||.++...|..|.
T Consensus 7 ~L~~mFP~~~~~~I~~~L 24 (42)
T PF02845_consen 7 QLQEMFPDLDREVIEAVL 24 (42)
T ss_dssp HHHHHSSSS-HHHHHHHH
T ss_pred HHHHHCCCCCHHHHHHHH
Confidence 456689999998887664
No 34
>KOG3635|consensus
Probab=27.14 E-value=21 Score=33.40 Aligned_cols=26 Identities=46% Similarity=0.631 Sum_probs=22.4
Q ss_pred cCCCccCCCCCCCCCCCceeeeeeeh
Q psy6224 19 HHPDIFHQGDTPREDRDWGINQIDAV 44 (82)
Q Consensus 19 Hhp~ifhdGD~~r~d~DwGi~qldtv 44 (82)
|.--+.|-|+++-.|-+||=.|+|||
T Consensus 123 HsKf~~~Tg~~v~~d~~wgHLQiDav 148 (1150)
T KOG3635|consen 123 HSKFNVHTGGTVVGDEEWGHLQIDAV 148 (1150)
T ss_pred HHHhcccCCCcccChhhccceehhHH
Confidence 34457789999999999999999997
No 35
>PRK15137 DNA-specific endonuclease I; Provisional
Probab=25.53 E-value=26 Score=27.37 Aligned_cols=9 Identities=44% Similarity=0.874 Sum_probs=7.3
Q ss_pred hhhhccCCC
Q psy6224 64 TLHHLFPTI 72 (82)
Q Consensus 64 ~LHHLFPTl 72 (82)
=||||+|+.
T Consensus 118 DLHnL~Pa~ 126 (235)
T PRK15137 118 DMHNLQPAI 126 (235)
T ss_pred ccccccccc
Confidence 389999985
No 36
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.46 E-value=27 Score=24.45 Aligned_cols=10 Identities=50% Similarity=0.976 Sum_probs=7.6
Q ss_pred hhhhhccCCC
Q psy6224 63 HTLHHLFPTI 72 (82)
Q Consensus 63 H~LHHLFPTl 72 (82)
-..|||||--
T Consensus 33 RSyHHLfPl~ 42 (112)
T TIGR00622 33 RSYHHLFPLK 42 (112)
T ss_pred HhhhccCCCc
Confidence 4579999954
No 37
>PLN02774 brassinosteroid-6-oxidase
Probab=24.89 E-value=28 Score=26.94 Aligned_cols=24 Identities=13% Similarity=0.018 Sum_probs=20.1
Q ss_pred hhcccccccCCCccCCCCCCCCCC
Q psy6224 11 VIGVNAAHHHPDIFHQGDTPREDR 34 (82)
Q Consensus 11 ~iGl~AaHHhp~ifhdGD~~r~d~ 34 (82)
++...+.|+||++|.|-+..++++
T Consensus 368 ~~~~~~~~rdp~~~~dP~~F~PeR 391 (463)
T PLN02774 368 YVYTREINYDPFLYPDPMTFNPWR 391 (463)
T ss_pred EEehHHhcCCcccCCChhccCchh
Confidence 456678999999999999888765
No 38
>PF04231 Endonuclease_1: Endonuclease I; InterPro: IPR007346 Bacterial periplasmic or secreted (3.1.21.1 from EC) Escherichia coli endonuclease I (EndoI) is a sequence independent endonuclease located in the periplasm. It is inhibited by different RNA species. It is thought to normally generate double strand breaks in DNA, except in the presence of high salt concentrations and RNA, when it generates single strand breaks in DNA. Its biological role is unknown []. Other family members are known to be extracellular []. This family also includes a non-specific, Mg2+-activated ribonuclease precursor (Q03091 from SWISSPROT) [].; GO: 0004518 nuclease activity; PDB: 1OUO_A 1OUP_B 2IVK_C 2VND_A 2PU3_A 2G7F_A 2G7E_A.
Probab=24.53 E-value=22 Score=26.73 Aligned_cols=9 Identities=44% Similarity=0.608 Sum_probs=7.1
Q ss_pred hhhhccCCC
Q psy6224 64 TLHHLFPTI 72 (82)
Q Consensus 64 ~LHHLFPTl 72 (82)
=||||||+.
T Consensus 106 DlH~L~pa~ 114 (218)
T PF04231_consen 106 DLHNLRPAD 114 (218)
T ss_dssp -GGGEEEEE
T ss_pred cccceeccc
Confidence 489999985
No 39
>COG2124 CypX Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=23.84 E-value=32 Score=26.78 Aligned_cols=24 Identities=25% Similarity=0.577 Sum_probs=20.1
Q ss_pred hhcccccccCCCccCCCCCCCCCC
Q psy6224 11 VIGVNAAHHHPDIFHQGDTPREDR 34 (82)
Q Consensus 11 ~iGl~AaHHhp~ifhdGD~~r~d~ 34 (82)
++.+.+|||+|+.|-+-|..+.++
T Consensus 321 ~~~~~~anrDp~~f~~P~~F~p~R 344 (411)
T COG2124 321 LLSIGAANRDPEVFPDPDEFDPER 344 (411)
T ss_pred EecHhhhcCChhhCCChhhcCCCC
Confidence 456779999999999999888665
No 40
>PLN02302 ent-kaurenoic acid oxidase
Probab=23.13 E-value=34 Score=26.14 Aligned_cols=24 Identities=13% Similarity=0.278 Sum_probs=19.5
Q ss_pred hhcccccccCCCccCCCCCCCCCC
Q psy6224 11 VIGVNAAHHHPDIFHQGDTPREDR 34 (82)
Q Consensus 11 ~iGl~AaHHhp~ifhdGD~~r~d~ 34 (82)
.+...+.|++|++|.|-+..++++
T Consensus 392 ~~~~~~~~rd~~~~~dP~~F~PeR 415 (490)
T PLN02302 392 LAWFRQVHMDPEVYPNPKEFDPSR 415 (490)
T ss_pred EeeHHHhcCCcccCCCccccChhh
Confidence 345668999999999999888665
No 41
>COG1398 OLE1 Fatty-acid desaturase [Lipid metabolism]
Probab=22.88 E-value=61 Score=26.28 Aligned_cols=22 Identities=55% Similarity=0.972 Sum_probs=16.3
Q ss_pred ccee-eEeeecCc--hhhhhccCCC
Q psy6224 51 RNQF-IVLTTFGE--HTLHHLFPTI 72 (82)
Q Consensus 51 ~s~F-~vlt~FGd--H~LHHLFPTl 72 (82)
.|++ ..|..||+ |--||-||+-
T Consensus 224 rN~ww~al~t~GEgwHNnHHafp~~ 248 (289)
T COG1398 224 RNCWWVALVTFGEGWHNNHHAFPNS 248 (289)
T ss_pred cceeEEEEeecccccccccccCcch
Confidence 5555 55667765 9999999984
No 42
>PLN02183 ferulate 5-hydroxylase
Probab=21.98 E-value=40 Score=26.54 Aligned_cols=24 Identities=21% Similarity=0.246 Sum_probs=19.7
Q ss_pred hhcccccccCCCccCCCCCCCCCC
Q psy6224 11 VIGVNAAHHHPDIFHQGDTPREDR 34 (82)
Q Consensus 11 ~iGl~AaHHhp~ifhdGD~~r~d~ 34 (82)
++...+.||+|++|.|-+..++++
T Consensus 405 ~~~~~~~hrd~~~~~dP~~F~PeR 428 (516)
T PLN02183 405 MINAWAIGRDKNSWEDPDTFKPSR 428 (516)
T ss_pred EEehhhhcCCccccCCccccCchh
Confidence 355678999999999999887665
No 43
>PLN02196 abscisic acid 8'-hydroxylase
Probab=20.80 E-value=34 Score=26.52 Aligned_cols=23 Identities=26% Similarity=0.291 Sum_probs=19.3
Q ss_pred hcccccccCCCccCCCCCCCCCC
Q psy6224 12 IGVNAAHHHPDIFHQGDTPREDR 34 (82)
Q Consensus 12 iGl~AaHHhp~ifhdGD~~r~d~ 34 (82)
+...++|++|++|.|-+..++++
T Consensus 369 ~~~~~~~rd~~~~~dP~~F~PeR 391 (463)
T PLN02196 369 PLFRNIHHSADIFSDPGKFDPSR 391 (463)
T ss_pred eeHHHhcCCchhcCCcCccChhh
Confidence 45668999999999999888766
Done!