Query 025155
Match_columns 257
No_of_seqs 59 out of 61
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 03:11:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025155.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025155hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02343 allene oxide cyclase 100.0 9E-112 2E-116 742.0 21.0 194 60-257 36-229 (229)
2 PF06351 Allene_ox_cyc: Allene 100.0 1E-106 3E-111 688.9 14.5 176 77-255 1-176 (176)
3 PF03018 Dirigent: Dirigent-li 98.8 1.8E-07 4E-12 77.0 12.9 87 114-204 33-126 (144)
4 cd06186 NOX_Duox_like_FAD_NADP 61.3 6.9 0.00015 31.9 2.4 13 180-192 107-119 (210)
5 COG0543 UbiB 2-polyprenylpheno 52.9 9.6 0.00021 33.5 2.0 23 169-191 91-119 (252)
6 PF08030 NAD_binding_6: Ferric 47.8 9.2 0.0002 29.7 1.0 12 180-191 2-13 (156)
7 cd00322 FNR_like Ferredoxin re 47.5 17 0.00036 29.4 2.4 25 168-192 80-110 (223)
8 PRK05802 hypothetical protein; 46.3 15 0.00033 33.7 2.3 26 167-192 149-185 (320)
9 cd06187 O2ase_reductase_like T 43.4 19 0.00042 29.5 2.3 12 180-191 99-110 (224)
10 PF04004 Leo1: Leo1-like prote 41.7 1.9E+02 0.0042 24.6 8.1 62 131-193 38-113 (171)
11 cd06183 cyt_b5_reduct_like Cyt 41.6 19 0.00041 29.5 2.0 12 180-191 105-116 (234)
12 cd06191 FNR_iron_sulfur_bindin 39.8 24 0.00051 29.4 2.3 12 180-191 103-114 (231)
13 cd06184 flavohem_like_fad_nad_ 38.3 24 0.00052 29.7 2.1 25 168-192 96-126 (247)
14 cd06196 FNR_like_1 Ferredoxin 38.2 25 0.00055 28.9 2.2 23 169-191 87-111 (218)
15 cd06197 FNR_like_2 FAD/NAD(P) 37.3 27 0.00059 29.6 2.3 13 179-191 125-137 (220)
16 PTZ00274 cytochrome b5 reducta 36.6 28 0.00061 32.3 2.5 24 168-191 142-171 (325)
17 cd06190 T4MO_e_transfer_like T 36.0 28 0.00061 28.9 2.2 23 169-191 81-109 (232)
18 PRK08564 5'-methylthioadenosin 35.8 33 0.00071 31.3 2.7 55 181-235 8-69 (267)
19 KOG0534 NADH-cytochrome b-5 re 35.6 28 0.00061 32.6 2.3 25 167-191 138-168 (286)
20 cd06220 DHOD_e_trans_like2 FAD 33.1 36 0.00078 28.8 2.4 23 169-191 74-100 (233)
21 cd06209 BenDO_FAD_NAD Benzoate 32.6 35 0.00075 28.4 2.2 13 180-192 103-115 (228)
22 cd06198 FNR_like_3 NAD(P) bind 32.5 36 0.00079 28.0 2.3 14 179-192 95-108 (216)
23 cd06195 FNR1 Ferredoxin-NADP+ 31.8 35 0.00076 28.7 2.1 12 180-191 102-113 (241)
24 cd06217 FNR_iron_sulfur_bindin 31.6 41 0.00088 27.8 2.4 12 180-191 108-119 (235)
25 PF13363 BetaGal_dom3: Beta-ga 31.5 32 0.0007 26.8 1.7 23 167-189 16-42 (79)
26 PRK00054 dihydroorotate dehydr 31.0 40 0.00087 28.9 2.4 24 168-191 85-114 (250)
27 cd06192 DHOD_e_trans_like FAD/ 30.0 43 0.00093 28.4 2.4 24 168-191 80-109 (243)
28 cd06213 oxygenase_e_transfer_s 29.1 45 0.00097 27.8 2.3 12 180-191 101-112 (227)
29 PRK08345 cytochrome-c3 hydroge 29.1 45 0.00097 29.7 2.4 25 168-192 90-121 (289)
30 PRK07609 CDP-6-deoxy-delta-3,4 28.6 45 0.00098 29.8 2.4 25 168-192 187-217 (339)
31 cd06215 FNR_iron_sulfur_bindin 28.5 48 0.001 27.3 2.4 13 180-192 104-116 (231)
32 cd06216 FNR_iron_sulfur_bindin 28.4 43 0.00093 28.2 2.1 13 180-192 123-135 (243)
33 PRK08051 fre FMN reductase; Va 27.7 52 0.0011 27.8 2.5 12 180-191 103-114 (232)
34 PLN02292 ferric-chelate reduct 27.7 43 0.00093 34.9 2.3 24 169-192 415-444 (702)
35 PRK07823 5'-methylthioadenosin 27.5 50 0.0011 30.3 2.5 38 182-220 7-49 (264)
36 smart00797 AHS2 Allophanate hy 27.3 62 0.0013 30.0 3.1 21 169-189 33-54 (280)
37 cd06212 monooxygenase_like The 27.3 49 0.0011 27.6 2.2 13 180-192 104-116 (232)
38 PLN02844 oxidoreductase/ferric 26.5 46 0.001 34.8 2.3 23 169-191 407-435 (722)
39 cd06194 FNR_N-term_Iron_sulfur 26.3 58 0.0013 26.9 2.5 24 168-191 79-109 (222)
40 TIGR01697 PNPH-PUNA-XAPA inosi 26.1 43 0.00092 29.6 1.8 36 183-220 2-52 (248)
41 TIGR02911 sulfite_red_B sulfit 26.0 56 0.0012 28.6 2.5 24 168-191 81-111 (261)
42 PLN02631 ferric-chelate reduct 25.8 52 0.0011 34.3 2.5 24 168-191 395-424 (699)
43 cd06221 sulfite_reductase_like 25.6 57 0.0012 28.2 2.4 25 168-192 80-111 (253)
44 PLN03116 ferredoxin--NADP+ red 25.4 59 0.0013 29.3 2.5 24 168-191 137-168 (307)
45 cd06189 flavin_oxioreductase N 24.5 56 0.0012 27.1 2.1 13 180-192 99-111 (224)
46 PRK06171 sorbitol-6-phosphate 24.1 46 0.001 27.7 1.5 20 172-191 1-20 (266)
47 cd06188 NADH_quinone_reductase 24.0 63 0.0014 28.3 2.4 12 180-191 151-162 (283)
48 cd06211 phenol_2-monooxygenase 23.5 63 0.0014 27.2 2.2 12 180-191 110-121 (238)
49 PRK13838 conjugal transfer pil 23.4 2.2E+02 0.0047 24.6 5.5 44 113-157 51-102 (176)
50 cd06210 MMO_FAD_NAD_binding Me 23.1 64 0.0014 26.9 2.2 12 180-191 109-120 (236)
51 PTZ00319 NADH-cytochrome B5 re 22.1 70 0.0015 28.8 2.3 11 181-191 168-178 (300)
52 cd06219 DHOD_e_trans_like1 FAD 21.2 73 0.0016 27.4 2.2 22 170-191 83-109 (248)
53 PRK08221 anaerobic sulfite red 21.1 75 0.0016 27.9 2.3 12 180-191 102-113 (263)
54 PRK13289 bifunctional nitric o 21.0 77 0.0017 28.9 2.4 24 168-191 244-273 (399)
55 TIGR02160 PA_CoA_Oxy5 phenylac 20.8 67 0.0015 28.9 2.0 12 180-191 110-121 (352)
56 cd06193 siderophore_interactin 20.8 77 0.0017 27.0 2.2 24 168-191 104-132 (235)
57 cd06218 DHOD_e_trans FAD/NAD b 20.5 81 0.0018 27.2 2.3 13 180-192 99-111 (246)
58 PF02141 DENN: DENN (AEX-3) do 20.5 16 0.00035 30.2 -1.9 31 201-235 127-157 (185)
No 1
>PLN02343 allene oxide cyclase
Probab=100.00 E-value=8.5e-112 Score=741.99 Aligned_cols=194 Identities=75% Similarity=1.225 Sum_probs=190.1
Q ss_pred CccceeEEeeCCCCCCCCCCccccceeEEEEEEecccCCCCcceEeeCCCcccccccCccccccccccccccceeceeee
Q 025155 60 NVTTKAFFFNKPSSQPDSSRPANNKVQELFVYEINERDRNSPAILKLSQKPEHLTIGDLVPFTNKLYTGDLQKRIGITAG 139 (257)
Q Consensus 60 ~~~~~~~~~~~~~~~~~~~~p~~~kvqel~vyeiNE~dr~SPa~L~ls~k~~~nslGDlVpFsNkLY~g~l~kRiGitaG 139 (257)
..++++|+|++++. ++++|+ |||||+|||||||||+|||||||++|+++|+|||||||+||||+|||+||||||||
T Consensus 36 ~~s~~~~~~~~~~~--~~~~p~--kvQel~VYEiNErDR~SPa~L~ls~k~~~~sLGDlVPFsNKlY~g~L~kRlGiTaG 111 (229)
T PLN02343 36 NLTVTRALFSNKAN--ENPRPT--KVQELSVYEINERDRGSPAFLKLSKKSVENALGDLVPFTNKLYTGDLKKRLGITAG 111 (229)
T ss_pred cccceeeeeccccc--CCCCCc--eeEEEEEEEeccccCCCcceEEcccCcccccccceeccccccccchhhhhhcccce
Confidence 34578999999987 889999 99999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEeeccCCCCCEEEEEEEEEeecCceEEEeceeccccccEEEEeccceeeeeeeeEEEEEEeeeceeEEEEEEeccC
Q 025155 140 LCVLIKHEPEKKGDRFEAIYSFYFGDYGHISVQGAYLTYEDTYLAVTGGSGIFEGVYGQVKLHQIVFPYKLFYTFYLKGV 219 (257)
Q Consensus 140 ~Cvliq~~pek~GdryEa~ySfyFGDyGhISvqGpylt~eDtyLAVTGGTGiFeGa~GqVkL~qivfPfklfYtFyLkgi 219 (257)
+|++|||+|||+||||||||||||||||||||||||+||||||||||||+||||||||||||||||||||||||||||||
T Consensus 112 ~Cvliq~~pek~gDryEa~ySfyfGDyGHisvqGpyltyeDt~LaiTGGsGiFega~GqvkL~qivfPfKlfYTFyLkGi 191 (229)
T PLN02343 112 LCVLIQHVPEKKGDRYEAIYSFYFGDYGHISVQGPYLTYEDTYLAITGGSGIFEGAYGQVKLHQIVFPFKLFYTFYLKGI 191 (229)
T ss_pred eEEEEEeccccCCceeEEEEEEEecCcceeEEeccccccccceEEeecCcceeecceeEEEEeeeeeeeeeEEEEEeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCChhhhhcCCCCCCCCCccChhhhccCCccccCCCCC
Q 025155 220 ADLPQELLVKPVEPSPTVEAAPAAKATEPHAAISNFTN 257 (257)
Q Consensus 220 ~dlp~el~~~~v~ps~~vep~p~aka~~p~a~~~nft~ 257 (257)
||||+||+++||+|||+|||+|+|||||||++++||||
T Consensus 192 ~dLP~eL~~~~v~Ps~~Vep~p~Aka~~p~~~~~nfT~ 229 (229)
T PLN02343 192 PDLPEELTGTPVPPSPDVEPAPEAKACEPSSVIPNFTN 229 (229)
T ss_pred ccchHHHhCCCCCCCCCCCcChhHhhcCCCccccccCC
Confidence 99999999999999999999999999999999999997
No 2
>PF06351 Allene_ox_cyc: Allene oxide cyclase; InterPro: IPR009410 This family consists of several plant specific allene oxide cyclase proteins (5.3.99.6 from EC). The allene oxide cyclase (AOC)-catalysed step in jasmonate (JA) biosynthesis is important in the wound response of tomato [].; GO: 0016853 isomerase activity, 0009507 chloroplast; PDB: 2GIN_A 2DIO_B 2BRJ_B 2Q4I_B 1Z8K_A 1ZVC_A.
Probab=100.00 E-value=1.2e-106 Score=688.87 Aligned_cols=176 Identities=83% Similarity=1.345 Sum_probs=137.9
Q ss_pred CCCccccceeEEEEEEecccCCCCcceEeeCCCcccccccCccccccccccccccceeceeeeeEEEEeeccCCCCCEEE
Q 025155 77 SSRPANNKVQELFVYEINERDRNSPAILKLSQKPEHLTIGDLVPFTNKLYTGDLQKRIGITAGLCVLIKHEPEKKGDRFE 156 (257)
Q Consensus 77 ~~~p~~~kvqel~vyeiNE~dr~SPa~L~ls~k~~~nslGDlVpFsNkLY~g~l~kRiGitaG~Cvliq~~pek~GdryE 156 (257)
+++|+ |||||+|||||||||+||||||||||++ |+|||||||+||||+||||+|||||+|+|++|||+|||+|||||
T Consensus 1 ~~~p~--kvqel~vyeiNErdR~SPa~L~ls~k~~-nslGDlvpFsNklY~g~l~~rlGitaG~Cvliq~~p~k~GdryE 77 (176)
T PF06351_consen 1 SSRPT--KVQELSVYEINERDRGSPAYLRLSQKSV-NSLGDLVPFSNKLYDGDLQKRLGITAGICVLIQHVPEKKGDRYE 77 (176)
T ss_dssp ---------EEEEEEEE--S-S--S--B--SSSSS-S-TT-EEEEEEEEEETTSS-EEEEEEEEEEEEEEECCCTEEEEE
T ss_pred CCCcc--ceEEEEEEEEcccccCCCcEEEcccccc-hhcccccccccccccchhhhhhcccceEEEEEEeccccCCceEE
Confidence 46788 9999999999999999999999999999 99999999999999999999999999999999999999999999
Q ss_pred EEEEEEeecCceEEEeceeccccccEEEEeccceeeeeeeeEEEEEEeeeceeEEEEEEeccCCCChhhhhcCCCCCCCC
Q 025155 157 AIYSFYFGDYGHISVQGAYLTYEDTYLAVTGGSGIFEGVYGQVKLHQIVFPYKLFYTFYLKGVADLPQELLVKPVEPSPT 236 (257)
Q Consensus 157 a~ySfyFGDyGhISvqGpylt~eDtyLAVTGGTGiFeGa~GqVkL~qivfPfklfYtFyLkgi~dlp~el~~~~v~ps~~ 236 (257)
|+|||||||||||||||||+|||||||||||||||||||||||||||||||||||||||||||||||+||+++||+|||+
T Consensus 78 aiySfyfGdyGhISvqGpy~t~eDtyLAVTGGtGiF~g~~GqVkL~qivfPfKlfYTFylkGi~dLP~el~~~~v~Ps~~ 157 (176)
T PF06351_consen 78 AIYSFYFGDYGHISVQGPYLTYEDTYLAVTGGTGIFEGVYGQVKLHQIVFPFKLFYTFYLKGIPDLPEELLGKPVEPSPA 157 (176)
T ss_dssp EEEEEE-GGGEEEEEEEEEETTS-EEEEEEEEEETTTT-EEEEEEEEEETTTEEEEEEEEES-S---GGGHS-----STT
T ss_pred EEEEEEecccceEEEecccccccceeEEEeccCceeecceEEEEEEEeecceEEEEEEEecccccccHHHhCCCCCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccChhhhccCCccccCCC
Q 025155 237 VEAAPAAKATEPHAAISNF 255 (257)
Q Consensus 237 vep~p~aka~~p~a~~~nf 255 (257)
|||+|+||||||||+++||
T Consensus 158 vep~p~Aka~~p~a~~~nf 176 (176)
T PF06351_consen 158 VEPSPAAKACEPHAVIPNF 176 (176)
T ss_dssp ----HHHHCT-GGGB-TT-
T ss_pred CCcChHHhhcCCcccccCC
Confidence 9999999999999999998
No 3
>PF03018 Dirigent: Dirigent-like protein; InterPro: IPR004265 This family contains a number of proteins which are induced during disease response in plants.
Probab=98.77 E-value=1.8e-07 Score=76.98 Aligned_cols=87 Identities=30% Similarity=0.411 Sum_probs=76.2
Q ss_pred cccCccccccccccccc--cceeceeeeeEEEEeeccCCCCCEEEEEEEEEeecC---c-eEEEeceec-cccccEEEEe
Q 025155 114 TIGDLVPFTNKLYTGDL--QKRIGITAGLCVLIKHEPEKKGDRFEAIYSFYFGDY---G-HISVQGAYL-TYEDTYLAVT 186 (257)
Q Consensus 114 slGDlVpFsNkLY~g~l--~kRiGitaG~Cvliq~~pek~GdryEa~ySfyFGDy---G-hISvqGpyl-t~eDtyLAVT 186 (257)
..|+++-|.++|++|-. -+.||--+|+.+.- ...|..+-..+++.|-+. | +|+|+|... .-+..-+||+
T Consensus 33 ~FG~~~V~D~~lt~gp~~~S~~VGraqG~~~~~----s~~~~~~~~~~~~vF~~g~~~GStl~v~G~~~~~~~~~e~~VV 108 (144)
T PF03018_consen 33 GFGTVVVFDDPLTEGPDPDSKLVGRAQGFYVSA----SLDGSSWFMSFTLVFEDGEYNGSTLSVMGRDPFFEPVRELAVV 108 (144)
T ss_pred CCcEEEEEeeceEcCCCCCCccceEEEEEEEee----cccCccEEEEEEEEEEecccCCCeEEEeCCCcccCcccEEeEe
Confidence 78999999999998854 78999999999996 456788999999999772 6 899999985 4466799999
Q ss_pred ccceeeeeeeeEEEEEEe
Q 025155 187 GGSGIFEGVYGQVKLHQI 204 (257)
Q Consensus 187 GGTGiFeGa~GqVkL~qi 204 (257)
||||-|+.|+|.+++..+
T Consensus 109 GGTG~Fr~ArG~~~~~~~ 126 (144)
T PF03018_consen 109 GGTGEFRMARGYAKLRTV 126 (144)
T ss_pred cCCCeEcceEEEEEEEEE
Confidence 999999999999999887
No 4
>cd06186 NOX_Duox_like_FAD_NADP NADPH oxidase (NOX) catalyzes the generation of reactive oxygen species (ROS) such as superoxide and hydrogen peroxide. ROS were originally identified as bactericidal agents in phagocytes, but are now also implicated in cell signaling and metabolism. NOX has a 6-alpha helix heme-binding transmembrane domain fused to a flavoprotein with the nucleotide binding domain located in the cytoplasm. Duox enzymes link a peroxidase domain to the NOX domain via a single transmembrane and EF-hand Ca2+ binding sites. The flavoprotein module has a ferredoxin like FAD/NADPH binding domain. In classical phagocytic NOX2, electron transfer occurs from NADPH to FAD to the heme of cytb to oxygen leading to superoxide formation.
Probab=61.35 E-value=6.9 Score=31.88 Aligned_cols=13 Identities=62% Similarity=0.889 Sum_probs=11.2
Q ss_pred ccEEEEeccceee
Q 025155 180 DTYLAVTGGSGIF 192 (257)
Q Consensus 180 DtyLAVTGGTGiF 192 (257)
+..+-|.||+||=
T Consensus 107 ~~~vliagG~GIt 119 (210)
T cd06186 107 DNVLLVAGGSGIT 119 (210)
T ss_pred CeEEEEeccccHh
Confidence 5789999999983
No 5
>COG0543 UbiB 2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases [Coenzyme metabolism / Energy production and conversion]
Probab=52.93 E-value=9.6 Score=33.50 Aligned_cols=23 Identities=35% Similarity=0.440 Sum_probs=19.4
Q ss_pred EEEeceecccccc------EEEEecccee
Q 025155 169 ISVQGAYLTYEDT------YLAVTGGSGI 191 (257)
Q Consensus 169 ISvqGpylt~eDt------yLAVTGGTGi 191 (257)
|.+.|||=+.-+- .|.|-||+|+
T Consensus 91 i~v~GP~G~~~~~~~~~~~vlliagGtG~ 119 (252)
T COG0543 91 IRVRGPLGNGFLREKIGKPVLLIAGGTGI 119 (252)
T ss_pred EEEEcCCCCCccccccCCcEEEEecccCH
Confidence 8999999876332 8999999998
No 6
>PF08030 NAD_binding_6: Ferric reductase NAD binding domain; InterPro: IPR013121 This entry contains ferric reductase NAD binding proteins.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3A1F_A.
Probab=47.78 E-value=9.2 Score=29.72 Aligned_cols=12 Identities=58% Similarity=0.963 Sum_probs=10.6
Q ss_pred ccEEEEecccee
Q 025155 180 DTYLAVTGGSGI 191 (257)
Q Consensus 180 DtyLAVTGGTGi 191 (257)
|+.+.|.||+||
T Consensus 2 ~~vvlvAGG~GI 13 (156)
T PF08030_consen 2 DNVVLVAGGSGI 13 (156)
T ss_dssp SEEEEEEEGGGH
T ss_pred CEEEEEecCcCH
Confidence 678899999997
No 7
>cd00322 FNR_like Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in
Probab=47.47 E-value=17 Score=29.38 Aligned_cols=25 Identities=24% Similarity=0.458 Sum_probs=17.1
Q ss_pred eEEEeceeccc------cccEEEEeccceee
Q 025155 168 HISVQGAYLTY------EDTYLAVTGGSGIF 192 (257)
Q Consensus 168 hISvqGpylt~------eDtyLAVTGGTGiF 192 (257)
.|.+.||+=++ .+.++.|.||+||=
T Consensus 80 ~v~i~gP~G~~~~~~~~~~~~v~ia~G~Gia 110 (223)
T cd00322 80 EVEVSGPGGDFFLPLEESGPVVLIAGGIGIT 110 (223)
T ss_pred EEEEECCCcccccCcccCCcEEEEecCCchh
Confidence 45555555443 35689999999984
No 8
>PRK05802 hypothetical protein; Provisional
Probab=46.25 E-value=15 Score=33.72 Aligned_cols=26 Identities=27% Similarity=0.469 Sum_probs=19.1
Q ss_pred ceEEEecee----ccc-------cccEEEEeccceee
Q 025155 167 GHISVQGAY----LTY-------EDTYLAVTGGSGIF 192 (257)
Q Consensus 167 GhISvqGpy----lt~-------eDtyLAVTGGTGiF 192 (257)
..|.|.||| +.. ....+.|.||+||-
T Consensus 149 d~l~v~GP~GnG~F~l~~~~~~~~~~~llIaGGiGIa 185 (320)
T PRK05802 149 DEILLRGPYWNGILGLKNIKSTKNGKSLVIARGIGQA 185 (320)
T ss_pred CEEEEeCCCCcCcCCcccccccCCCeEEEEEeEEeHH
Confidence 368999997 321 23689999999983
No 9
>cd06187 O2ase_reductase_like The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S] ferredoxin center (fused to the FAD/NADH domain and/or discrete) to the oxygenase. Dioxygenases add both atoms of oxygen to the substrate, while mono-oxygenases (aka mixed oxygenases) add one atom to the substrate and one atom to water. In dioxygenases, Class I enzymes are 2 component, containing a reductase with Rieske type [2Fe-2S] redox centers and an oxygenase. Class II are 3 component, having discrete flavin and ferredoxin proteins and an oxygenase. Class III have 2 [2Fe-2S] centers, one fused to the flavin domain and the other separate.
Probab=43.41 E-value=19 Score=29.51 Aligned_cols=12 Identities=33% Similarity=0.861 Sum_probs=10.6
Q ss_pred ccEEEEecccee
Q 025155 180 DTYLAVTGGSGI 191 (257)
Q Consensus 180 DtyLAVTGGTGi 191 (257)
+.++.|.||+||
T Consensus 99 ~~~lliagG~GI 110 (224)
T cd06187 99 RPVLCIAGGTGL 110 (224)
T ss_pred CCEEEEecCcCH
Confidence 468999999998
No 10
>PF04004 Leo1: Leo1-like protein; InterPro: IPR007149 Members of this family are part of the Paf1/RNA polymerase II complex [, ]. The Paf1 complex probably functions during the elongation phase of transcription [].
Probab=41.69 E-value=1.9e+02 Score=24.64 Aligned_cols=62 Identities=23% Similarity=0.483 Sum_probs=41.1
Q ss_pred cceeceeeeeEEEEeeccCCCCC----------EEE-EEEEEEeecCceEEEeceecccc--ccEEEEeccc-eeee
Q 025155 131 QKRIGITAGLCVLIKHEPEKKGD----------RFE-AIYSFYFGDYGHISVQGAYLTYE--DTYLAVTGGS-GIFE 193 (257)
Q Consensus 131 ~kRiGitaG~Cvliq~~pek~Gd----------ryE-a~ySfyFGDyGhISvqGpylt~e--DtyLAVTGGT-GiFe 193 (257)
..|+-...-.+|+-...+...|. ||+ -.+|+..|| -+.-|+..|-..+ .+||+|--++ ++++
T Consensus 38 ~~~~~~~~~ntIRWR~~~~~~g~~~~eSNAriVrWsDGS~sL~iG~-E~fdi~~~~~~~~~~~~~L~~~~~~~~~l~ 113 (171)
T PF04004_consen 38 RERLKLKVENTIRWRYSPDETGEKVKESNARIVRWSDGSLSLHIGN-EVFDIQKKYPLVQDDHNYLFVRHGSSGVLQ 113 (171)
T ss_pred hhhhccccccEEEEeecCCCCCCEeeecccEEEEEcCCceEEEecc-EEEEeccccccccCCcceEEEEcCCcceEE
Confidence 45555655566776666656665 566 788999996 4666645554444 3899998774 6665
No 11
>cd06183 cyt_b5_reduct_like Cytochrome b5 reductase catalyzes the reduction of 2 molecules of cytochrome b5 using NADH as an electron donor. Like ferredoxin reductases, these proteins have an N-terminal FAD binding subdomain and a C-terminal NADH binding subdomain, separated by a cleft, which accepts FAD. The NADH-binding moiety interacts with part of the FAD and resembles a Rossmann fold. However, NAD is bound differently than in canonical Rossmann fold proteins. Nitrate reductases, flavoproteins similar to pyridine nucleotide cytochrome reductases, catalyze the reduction of nitrate to nitrite. The enzyme can be divided into three functional fragments that bind the cofactors molybdopterin, heme-iron, and FAD/NADH.
Probab=41.60 E-value=19 Score=29.54 Aligned_cols=12 Identities=33% Similarity=0.650 Sum_probs=10.8
Q ss_pred ccEEEEecccee
Q 025155 180 DTYLAVTGGSGI 191 (257)
Q Consensus 180 DtyLAVTGGTGi 191 (257)
+.++.|.||+||
T Consensus 105 ~~~vliagGtGi 116 (234)
T cd06183 105 KHIGMIAGGTGI 116 (234)
T ss_pred cEEEEEcCCcch
Confidence 568999999999
No 12
>cd06191 FNR_iron_sulfur_binding Iron-sulfur binding Ferredoxin Reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with a C-terminal iron-sulfur binding cluster domain. FNR was intially identified as a chloroplast reductase activity catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methnae assimilation in a variety of organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in
Probab=39.79 E-value=24 Score=29.42 Aligned_cols=12 Identities=58% Similarity=0.955 Sum_probs=10.8
Q ss_pred ccEEEEecccee
Q 025155 180 DTYLAVTGGSGI 191 (257)
Q Consensus 180 DtyLAVTGGTGi 191 (257)
+.++.|.||+||
T Consensus 103 ~~~lliagG~Gi 114 (231)
T cd06191 103 GRYLLVAAGSGI 114 (231)
T ss_pred CcEEEEecCccH
Confidence 578999999998
No 13
>cd06184 flavohem_like_fad_nad_binding FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The hemoglobin domain adopts a globin fold with an embedded heme molecule. Flavohemoglobins also have a C-terminal reductase domain with bindiing sites for FAD and NAD(P)H. This domain catalyzes the conversion of NO + O2 + NAD(P)H to NO3- + NAD(P)+. Instead of the oxygen transport function of hemoglobins, flavohemoglobins seem to act in NO dioxygenation and NO signalling.
Probab=38.30 E-value=24 Score=29.69 Aligned_cols=25 Identities=16% Similarity=0.349 Sum_probs=17.7
Q ss_pred eEEEeceeccc------cccEEEEeccceee
Q 025155 168 HISVQGAYLTY------EDTYLAVTGGSGIF 192 (257)
Q Consensus 168 hISvqGpylt~------eDtyLAVTGGTGiF 192 (257)
.+.|.|||=.+ .+.++.|.|||||-
T Consensus 96 ~v~i~gP~G~~~~~~~~~~~llliagGtGia 126 (247)
T cd06184 96 VLEVSAPAGDFVLDEASDRPLVLISAGVGIT 126 (247)
T ss_pred EEEEEcCCCceECCCCCCCcEEEEeccccHh
Confidence 56677775432 24689999999983
No 14
>cd06196 FNR_like_1 Ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which varies in orientation with respect to the NAD(P) binding domain. The N-terminal region may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) which then transfers a hydride ion to convert NADP+ to NADPH.
Probab=38.16 E-value=25 Score=28.89 Aligned_cols=23 Identities=17% Similarity=0.450 Sum_probs=14.8
Q ss_pred EEEeceeccc--cccEEEEecccee
Q 025155 169 ISVQGAYLTY--EDTYLAVTGGSGI 191 (257)
Q Consensus 169 ISvqGpylt~--eDtyLAVTGGTGi 191 (257)
|.+.|||=++ .+..+.|.||+||
T Consensus 87 v~i~gP~G~~~~~~~~vlia~GtGi 111 (218)
T cd06196 87 LLIEDPWGAIEYKGPGVFIAGGAGI 111 (218)
T ss_pred EEEECCccceEecCceEEEecCCCc
Confidence 4444444433 2467899999997
No 15
>cd06197 FNR_like_2 FAD/NAD(P) binding domain of ferredoxin reductase-like proteins. Ferredoxin reductase (FNR) was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and have a variety of physiological functions in a variety of organisms including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which varies in orientation with respect to the NAD(P) binding domain. The N-terminal moeity
Probab=37.31 E-value=27 Score=29.62 Aligned_cols=13 Identities=38% Similarity=0.716 Sum_probs=11.3
Q ss_pred cccEEEEecccee
Q 025155 179 EDTYLAVTGGSGI 191 (257)
Q Consensus 179 eDtyLAVTGGTGi 191 (257)
.+..+.|.||+||
T Consensus 125 ~~~illIagG~GI 137 (220)
T cd06197 125 ERKMVWIAGGVGI 137 (220)
T ss_pred CceEEEEecccch
Confidence 4578999999998
No 16
>PTZ00274 cytochrome b5 reductase; Provisional
Probab=36.58 E-value=28 Score=32.27 Aligned_cols=24 Identities=13% Similarity=0.325 Sum_probs=17.5
Q ss_pred eEEEeceeccc--c----ccEEEEecccee
Q 025155 168 HISVQGAYLTY--E----DTYLAVTGGSGI 191 (257)
Q Consensus 168 hISvqGpylt~--e----DtyLAVTGGTGi 191 (257)
.|.|.||+.++ + +.++.|.|||||
T Consensus 142 ~v~v~GP~f~~~~~~~~~~~lvlIAGGsGI 171 (325)
T PTZ00274 142 KLLFRSVTFKIQYRPNRWKHVGMIAGGTGF 171 (325)
T ss_pred EEEEeCCeeecccCCCCCceEEEEeCCcch
Confidence 56677775543 1 458999999998
No 17
>cd06190 T4MO_e_transfer_like Toluene-4-monoxygenase electron transfer component of Pseudomonas mendocina hydroxylates toluene and forms p-cresol as part of a three component toluene-4-monoxygenase system. Electron transfer is from NADH to an NADH:ferredoxin oxidoreductase (TmoF in P. mendocina) to ferredoxin to an iron-containing oxygenase. TmoF is homologous to other mono- and dioxygenase systems within the ferredoxin reductase family.
Probab=36.02 E-value=28 Score=28.91 Aligned_cols=23 Identities=26% Similarity=0.653 Sum_probs=15.8
Q ss_pred EEEeceeccc------cccEEEEecccee
Q 025155 169 ISVQGAYLTY------EDTYLAVTGGSGI 191 (257)
Q Consensus 169 ISvqGpylt~------eDtyLAVTGGTGi 191 (257)
|.|.|||=++ .+.++.|.||+||
T Consensus 81 v~v~gP~G~~~~~~~~~~~illIagG~Gi 109 (232)
T cd06190 81 LELDGPYGLAYLRPDEDRDIVCIAGGSGL 109 (232)
T ss_pred EEEECCcccceecCCCCCcEEEEeeCcCH
Confidence 5566665432 3468999999997
No 18
>PRK08564 5'-methylthioadenosine phosphorylase II; Reviewed
Probab=35.79 E-value=33 Score=31.34 Aligned_cols=55 Identities=24% Similarity=0.461 Sum_probs=31.4
Q ss_pred cEEEEeccceeee-eeeeEEEEEEeeeceeE----EEEEEeccCC--CChhhhhcCCCCCCC
Q 025155 181 TYLAVTGGSGIFE-GVYGQVKLHQIVFPYKL----FYTFYLKGVA--DLPQELLVKPVEPSP 235 (257)
Q Consensus 181 tyLAVTGGTGiFe-Ga~GqVkL~qivfPfkl----fYtFyLkgi~--dlp~el~~~~v~ps~ 235 (257)
.-+||.||||+++ |.-...+-..+.-||.- +.--+|.|.+ =||+.=..-..+|+.
T Consensus 8 ~~igiIgGSGl~~~~~l~~~~~~~~~tpyg~p~~~l~~g~l~g~~v~~l~RhGr~H~y~~~~ 69 (267)
T PRK08564 8 ASIGIIGGSGLYDPGIFENSKEVKVYTPYGEPSDNIIIGEIEGVEVAFLPRHGRGHRIPPHK 69 (267)
T ss_pred ceEEEEecCCCCCCcccccceeeeEEcCCCCCccCEEEEEECCEEEEEEeCCCCCcccCCcc
Confidence 3689999999987 44344444566678862 3334566654 333332333444443
No 19
>KOG0534 consensus NADH-cytochrome b-5 reductase [Coenzyme transport and metabolism; Energy production and conversion]
Probab=35.57 E-value=28 Score=32.61 Aligned_cols=25 Identities=20% Similarity=0.511 Sum_probs=19.7
Q ss_pred ceEEEeceeccc--c----ccEEEEecccee
Q 025155 167 GHISVQGAYLTY--E----DTYLAVTGGSGI 191 (257)
Q Consensus 167 GhISvqGpylt~--e----DtyLAVTGGTGi 191 (257)
..|.|.||.-++ + .....|.|||||
T Consensus 138 d~ve~rGP~G~~~~~~~~~~~l~miAgGtGI 168 (286)
T KOG0534|consen 138 DTVEFRGPIGEFKYDPQKAKHLGMIAGGTGI 168 (286)
T ss_pred CEEEEecCccceEecCCCcceEEEEecccch
Confidence 468899997655 2 458899999998
No 20
>cd06220 DHOD_e_trans_like2 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity, as well as 3 cofactors: FMN, FAD, and an [2Fe-2S] cluster.
Probab=33.07 E-value=36 Score=28.81 Aligned_cols=23 Identities=30% Similarity=0.634 Sum_probs=15.6
Q ss_pred EEEeceecc---c-cccEEEEecccee
Q 025155 169 ISVQGAYLT---Y-EDTYLAVTGGSGI 191 (257)
Q Consensus 169 ISvqGpylt---~-eDtyLAVTGGTGi 191 (257)
|.+.|||=+ . .+..+.|.||+||
T Consensus 74 v~i~gP~G~~f~~~~~~~vliAgGtGi 100 (233)
T cd06220 74 LGIRGPYGNGFELVGGKVLLIGGGIGI 100 (233)
T ss_pred EEEECcCCCCccCCCCeEEEEecCcCh
Confidence 445555422 1 4678999999997
No 21
>cd06209 BenDO_FAD_NAD Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal ferredoxin at the end fused to an FAD/NADP(P) domain. In dioxygenase FAD/NAD(P) binding domain, the reductase transfers 2 electrons from NAD(P)H to the oxygenase which insert into an aromatic substrate, an initial step in microbial aerobic degradation of aromatic rings. Flavin oxidoreductases use flavins as substrates, unlike flavoenzymes which have a flavin prosthetic group.
Probab=32.64 E-value=35 Score=28.38 Aligned_cols=13 Identities=31% Similarity=0.700 Sum_probs=11.0
Q ss_pred ccEEEEeccceee
Q 025155 180 DTYLAVTGGSGIF 192 (257)
Q Consensus 180 DtyLAVTGGTGiF 192 (257)
+.++.|.||+||=
T Consensus 103 ~~~vlia~GtGIa 115 (228)
T cd06209 103 RPLLMLAGGTGLA 115 (228)
T ss_pred CeEEEEEcccCHh
Confidence 5689999999983
No 22
>cd06198 FNR_like_3 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P) binding domain. The N-terminal domain may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) which then transfers a hydride ion to convert NADP+ to NADPH.
Probab=32.49 E-value=36 Score=28.01 Aligned_cols=14 Identities=29% Similarity=0.498 Sum_probs=11.7
Q ss_pred cccEEEEeccceee
Q 025155 179 EDTYLAVTGGSGIF 192 (257)
Q Consensus 179 eDtyLAVTGGTGiF 192 (257)
.+.++.|.||+||=
T Consensus 95 ~~~~vlia~GtGia 108 (216)
T cd06198 95 RARQIWIAGGIGIT 108 (216)
T ss_pred CceEEEEccccCHH
Confidence 35789999999984
No 23
>cd06195 FNR1 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH.
Probab=31.77 E-value=35 Score=28.69 Aligned_cols=12 Identities=25% Similarity=0.512 Sum_probs=10.7
Q ss_pred ccEEEEecccee
Q 025155 180 DTYLAVTGGSGI 191 (257)
Q Consensus 180 DtyLAVTGGTGi 191 (257)
+..+-|.||+||
T Consensus 102 ~~~vlIagGtGi 113 (241)
T cd06195 102 KRLWLLATGTGI 113 (241)
T ss_pred ceEEEEeeccch
Confidence 568999999998
No 24
>cd06217 FNR_iron_sulfur_binding_3 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap between the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form
Probab=31.64 E-value=41 Score=27.84 Aligned_cols=12 Identities=50% Similarity=0.908 Sum_probs=10.7
Q ss_pred ccEEEEecccee
Q 025155 180 DTYLAVTGGSGI 191 (257)
Q Consensus 180 DtyLAVTGGTGi 191 (257)
+.++.|.||+||
T Consensus 108 ~~~vliagG~Gi 119 (235)
T cd06217 108 DPVVLLAGGSGI 119 (235)
T ss_pred ceEEEEecCcCc
Confidence 568899999999
No 25
>PF13363 BetaGal_dom3: Beta-galactosidase, domain 3; PDB: 3OGS_A 3OGV_A 3OGR_A 3OG2_A 1TG7_A 1XC6_A.
Probab=31.52 E-value=32 Score=26.84 Aligned_cols=23 Identities=30% Similarity=0.557 Sum_probs=16.5
Q ss_pred ceEEEeceec----cccccEEEEeccc
Q 025155 167 GHISVQGAYL----TYEDTYLAVTGGS 189 (257)
Q Consensus 167 GhISvqGpyl----t~eDtyLAVTGGT 189 (257)
.+|-|+|||| ..++.-|+++|=.
T Consensus 16 ~~vlV~GpyLVRsAsv~g~tL~L~GD~ 42 (79)
T PF13363_consen 16 NSVLVKGPYLVRSASVSGSTLSLTGDF 42 (79)
T ss_dssp HB-EEE-SSEEEEEEEETTEEEEEEEB
T ss_pred CCEEEECCcEEEEEEEcCCEEEEEeec
Confidence 3899999999 4577889988843
No 26
>PRK00054 dihydroorotate dehydrogenase electron transfer subunit; Reviewed
Probab=31.02 E-value=40 Score=28.90 Aligned_cols=24 Identities=25% Similarity=0.472 Sum_probs=17.0
Q ss_pred eEEEeceecc---c--c-ccEEEEecccee
Q 025155 168 HISVQGAYLT---Y--E-DTYLAVTGGSGI 191 (257)
Q Consensus 168 hISvqGpylt---~--e-DtyLAVTGGTGi 191 (257)
.|.|.|||=+ . + +.++.|.||+||
T Consensus 85 ~v~i~gP~G~~f~l~~~~~~~vlIagG~Gi 114 (250)
T PRK00054 85 ELDIRGPLGNGFDLEEIGGKVLLVGGGIGV 114 (250)
T ss_pred EEEEEcccCCCCCCCCCCCeEEEEeccccH
Confidence 4667777632 2 2 468999999997
No 27
>cd06192 DHOD_e_trans_like FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity, as well as NAD binding. NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal domain may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD (formi
Probab=29.96 E-value=43 Score=28.35 Aligned_cols=24 Identities=33% Similarity=0.494 Sum_probs=16.9
Q ss_pred eEEEeceecc------ccccEEEEecccee
Q 025155 168 HISVQGAYLT------YEDTYLAVTGGSGI 191 (257)
Q Consensus 168 hISvqGpylt------~eDtyLAVTGGTGi 191 (257)
.|.|.|||=+ ..+.++.|.||+||
T Consensus 80 ~l~i~gP~G~~~~~~~~~~~~lliagGtGi 109 (243)
T cd06192 80 KLDVMGPLGNGFEGPKKGGTVLLVAGGIGL 109 (243)
T ss_pred EEEEEccCCCCCccCCCCCEEEEEeCcccH
Confidence 5667777522 13468999999998
No 28
>cd06213 oxygenase_e_transfer_subunit The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S] ferredoxin center (fused to the FAD/NADH domain and/or discrete) to the oxygenase. Dioxygenases add both atoms of oxygen to the substrate while mono-oxygenases add one atom to the substrate and one atom to water. In dioxygenases, Class I enzymes are 2 component, containing a reductase with Rieske type [2Fe-2S] redox centers and an oxygenase. Class II are 3 component, having discrete flavin and ferredoxin proteins and an oxygenase. Class III have 2 [2Fe-2S] centers, one fused to the flavin domain and the other separate.
Probab=29.10 E-value=45 Score=27.79 Aligned_cols=12 Identities=42% Similarity=0.891 Sum_probs=10.8
Q ss_pred ccEEEEecccee
Q 025155 180 DTYLAVTGGSGI 191 (257)
Q Consensus 180 DtyLAVTGGTGi 191 (257)
+.++.|.||+||
T Consensus 101 ~~~lliagG~Gi 112 (227)
T cd06213 101 APILCIAGGSGL 112 (227)
T ss_pred CcEEEEecccch
Confidence 578999999998
No 29
>PRK08345 cytochrome-c3 hydrogenase subunit gamma; Provisional
Probab=29.08 E-value=45 Score=29.66 Aligned_cols=25 Identities=28% Similarity=0.534 Sum_probs=17.5
Q ss_pred eEEEeceecc---cc----ccEEEEeccceee
Q 025155 168 HISVQGAYLT---YE----DTYLAVTGGSGIF 192 (257)
Q Consensus 168 hISvqGpylt---~e----DtyLAVTGGTGiF 192 (257)
.|.|.|||=. .. +.++.|.||+||=
T Consensus 90 ~v~v~gP~G~~f~~~~~~~~~~llIAgGtGIa 121 (289)
T PRK08345 90 IVGVRGPYGNGFPVDEMEGMDLLLIAGGLGMA 121 (289)
T ss_pred EEEEeCCCCCCCCcccccCceEEEEecccchh
Confidence 4677777632 21 3689999999984
No 30
>PRK07609 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated
Probab=28.56 E-value=45 Score=29.84 Aligned_cols=25 Identities=16% Similarity=0.464 Sum_probs=16.6
Q ss_pred eEEEeceeccc------cccEEEEeccceee
Q 025155 168 HISVQGAYLTY------EDTYLAVTGGSGIF 192 (257)
Q Consensus 168 hISvqGpylt~------eDtyLAVTGGTGiF 192 (257)
.|.+.|||=++ .+.++.|.||+||-
T Consensus 187 ~v~v~gP~G~~~~~~~~~~~ivlIagGtGia 217 (339)
T PRK07609 187 ILRIEGPLGTFFLREDSDKPIVLLASGTGFA 217 (339)
T ss_pred EEEEEcCceeEEecCCCCCCEEEEecCcChh
Confidence 35566665332 23589999999983
No 31
>cd06215 FNR_iron_sulfur_binding_1 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal portion of the FAD/NAD binding domain contains most of the NADP(H) binding residues and the N-terminal sub-domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. In this ferredoxin like sub-group, the FAD/NAD sub-domains is typically fused to a C-terminal iron-sulfur binding domain. Iron-sulfur pr
Probab=28.51 E-value=48 Score=27.34 Aligned_cols=13 Identities=46% Similarity=0.733 Sum_probs=11.2
Q ss_pred ccEEEEeccceee
Q 025155 180 DTYLAVTGGSGIF 192 (257)
Q Consensus 180 DtyLAVTGGTGiF 192 (257)
+.++.|.||+||-
T Consensus 104 ~~~vlIagG~Gia 116 (231)
T cd06215 104 DKLLLLSAGSGIT 116 (231)
T ss_pred CcEEEEecCcCcc
Confidence 5789999999975
No 32
>cd06216 FNR_iron_sulfur_binding_2 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to for
Probab=28.35 E-value=43 Score=28.19 Aligned_cols=13 Identities=38% Similarity=0.598 Sum_probs=10.9
Q ss_pred ccEEEEeccceee
Q 025155 180 DTYLAVTGGSGIF 192 (257)
Q Consensus 180 DtyLAVTGGTGiF 192 (257)
+.++.|.||+||=
T Consensus 123 ~~~v~iagG~Gia 135 (243)
T cd06216 123 PRLLLIAAGSGIT 135 (243)
T ss_pred CCEEEEecCccHh
Confidence 4689999999973
No 33
>PRK08051 fre FMN reductase; Validated
Probab=27.71 E-value=52 Score=27.82 Aligned_cols=12 Identities=33% Similarity=0.794 Sum_probs=10.8
Q ss_pred ccEEEEecccee
Q 025155 180 DTYLAVTGGSGI 191 (257)
Q Consensus 180 DtyLAVTGGTGi 191 (257)
+.++.|.||+||
T Consensus 103 ~~~vliagG~Gi 114 (232)
T PRK08051 103 RPLLLIAGGTGF 114 (232)
T ss_pred CcEEEEecCcCc
Confidence 469999999998
No 34
>PLN02292 ferric-chelate reductase
Probab=27.69 E-value=43 Score=34.89 Aligned_cols=24 Identities=42% Similarity=0.742 Sum_probs=17.5
Q ss_pred EEEeceecc------ccccEEEEeccceee
Q 025155 169 ISVQGAYLT------YEDTYLAVTGGSGIF 192 (257)
Q Consensus 169 ISvqGpylt------~eDtyLAVTGGTGiF 192 (257)
+.|+|||=. ..|+.+.|.||+||=
T Consensus 415 V~VeGPYG~~~~~~~~~~~vvlIAGGiGIT 444 (702)
T PLN02292 415 VSVEGPYGPASTDFLRHESLVMVSGGSGIT 444 (702)
T ss_pred EEEECCccCCccccccCCcEEEEEeccCHH
Confidence 567777642 236899999999983
No 35
>PRK07823 5'-methylthioadenosine phosphorylase; Validated
Probab=27.48 E-value=50 Score=30.35 Aligned_cols=38 Identities=24% Similarity=0.260 Sum_probs=26.2
Q ss_pred EEEEeccceeeeeee-eEEEEEEeeeceeE----EEEEEeccCC
Q 025155 182 YLAVTGGSGIFEGVY-GQVKLHQIVFPYKL----FYTFYLKGVA 220 (257)
Q Consensus 182 yLAVTGGTGiFeGa~-GqVkL~qivfPfkl----fYtFyLkgi~ 220 (257)
-+||.||||++.-+. +.++ ..+.-||.- +.-.+|.|.+
T Consensus 7 ~igII~GSGl~~l~~~~~~~-~~~~tpyg~~sg~l~~G~l~g~~ 49 (264)
T PRK07823 7 MLGVIGGSGFYSFFGSDARE-VNVDTPYGPPSAPITIGEVGGRR 49 (264)
T ss_pred eEEEEeccccchhhccccee-eEEeccCCCCCCCEEEEEECCEE
Confidence 689999999998776 4333 456668863 4445677764
No 36
>smart00797 AHS2 Allophanate hydrolase subunit 2. This domain represents subunit 2 of allophanate hydrolase (AHS2).
Probab=27.32 E-value=62 Score=29.96 Aligned_cols=21 Identities=33% Similarity=0.659 Sum_probs=14.3
Q ss_pred EEEeceeccc-cccEEEEeccc
Q 025155 169 ISVQGAYLTY-EDTYLAVTGGS 189 (257)
Q Consensus 169 ISvqGpylt~-eDtyLAVTGGT 189 (257)
|+..|+-+.+ +|+++||||+-
T Consensus 33 it~gg~~l~f~~~~~iAitGA~ 54 (280)
T smart00797 33 ITLGGPTLRFTADAVIALTGAD 54 (280)
T ss_pred EecCcEEEEECCCcEEEEeCCC
Confidence 3444665655 78899999864
No 37
>cd06212 monooxygenase_like The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. These flavoprotein monooxygenases use molecular oxygen as a substrate and require reduced FAD. One atom of oxygen is incorportated into the aromatic compond, while the other is used to form a molecule of water. In contrast dioxygenases add both atoms of oxygen to the substrate.
Probab=27.29 E-value=49 Score=27.56 Aligned_cols=13 Identities=31% Similarity=0.613 Sum_probs=11.1
Q ss_pred ccEEEEeccceee
Q 025155 180 DTYLAVTGGSGIF 192 (257)
Q Consensus 180 DtyLAVTGGTGiF 192 (257)
+..+.|.||+||-
T Consensus 104 ~~~l~iagG~Gia 116 (232)
T cd06212 104 RPIVLIGGGSGMA 116 (232)
T ss_pred CcEEEEecCcchh
Confidence 4789999999984
No 38
>PLN02844 oxidoreductase/ferric-chelate reductase
Probab=26.53 E-value=46 Score=34.80 Aligned_cols=23 Identities=39% Similarity=0.717 Sum_probs=16.3
Q ss_pred EEEeceeccc------cccEEEEecccee
Q 025155 169 ISVQGAYLTY------EDTYLAVTGGSGI 191 (257)
Q Consensus 169 ISvqGpylt~------eDtyLAVTGGTGi 191 (257)
+.|.|||=+. .|..+-|.||+||
T Consensus 407 v~VeGPYG~~s~~~~~~~~lVLIAGGiGI 435 (722)
T PLN02844 407 VAIEGPYGPASVDFLRYDSLLLVAGGIGI 435 (722)
T ss_pred EEEECCccCCCCCccCCCeEEEEEcCcCH
Confidence 4555555432 2689999999998
No 39
>cd06194 FNR_N-term_Iron_sulfur_binding Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an N-terminal Iron-Sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second e
Probab=26.34 E-value=58 Score=26.87 Aligned_cols=24 Identities=29% Similarity=0.537 Sum_probs=16.9
Q ss_pred eEEEeceeccc-------cccEEEEecccee
Q 025155 168 HISVQGAYLTY-------EDTYLAVTGGSGI 191 (257)
Q Consensus 168 hISvqGpylt~-------eDtyLAVTGGTGi 191 (257)
.|.|.|||=++ .+..+.|.||+||
T Consensus 79 ~v~i~gP~G~~~~~~~~~~~~~v~iagG~Gi 109 (222)
T cd06194 79 ALRLQGPFGQAFYRPEYGEGPLLLVGAGTGL 109 (222)
T ss_pred EEEEecCcCCeeccCCCCCCCEEEEecCcch
Confidence 46677776432 2468899999998
No 40
>TIGR01697 PNPH-PUNA-XAPA inosine guanosine and xanthosine phosphorylase family. Sequences from Clostridium and Thermotoga fall between these last two clades and are uncharacterized with respect to substrate range and operon.
Probab=26.14 E-value=43 Score=29.58 Aligned_cols=36 Identities=28% Similarity=0.336 Sum_probs=25.6
Q ss_pred EEEeccceeeeeeeeEEEEEEeeeceeE---------------EEEEEeccCC
Q 025155 183 LAVTGGSGIFEGVYGQVKLHQIVFPYKL---------------FYTFYLKGVA 220 (257)
Q Consensus 183 LAVTGGTGiFeGa~GqVkL~qivfPfkl---------------fYtFyLkgi~ 220 (257)
++|.||||+++.. ..+ .+.+.-|++- ||.-.++|.+
T Consensus 2 ~~ii~gsg~~~~~-~~~-~~~~~~~~~~~p~~~~~~~~~~~~~~~~G~~~g~~ 52 (248)
T TIGR01697 2 VAIILGSGLGALA-DQV-EDAVIIPYEKIPGFPVSTVVGHAGELVFGRLGGKP 52 (248)
T ss_pred EEEEeeCCcchhh-hhc-ccceEeeCccCCCCCCcccCCCCccEEEEEECCEE
Confidence 6899999999966 333 5556667752 8888888753
No 41
>TIGR02911 sulfite_red_B sulfite reductase, subunit B. Members of this protein family include the B subunit, one of three subunits, of the anaerobic sulfite reductase of Salmonella, and close homologs from various Clostridum species, where the three-gene neighborhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms as seen in Clostridium pasteurianum.
Probab=25.96 E-value=56 Score=28.60 Aligned_cols=24 Identities=25% Similarity=0.630 Sum_probs=16.5
Q ss_pred eEEEeceecc---c----cccEEEEecccee
Q 025155 168 HISVQGAYLT---Y----EDTYLAVTGGSGI 191 (257)
Q Consensus 168 hISvqGpylt---~----eDtyLAVTGGTGi 191 (257)
.|.|.|||=+ . .+.++.|.||+||
T Consensus 81 ~v~i~gP~G~~f~~~~~~~~~~llIAgGtGI 111 (261)
T TIGR02911 81 NLFLRGPYGNGFDVDNYKHKELVVVAGGTGV 111 (261)
T ss_pred EEEEecCCCCCcccCccCCceEEEEecccCc
Confidence 4566777522 2 2368999999998
No 42
>PLN02631 ferric-chelate reductase
Probab=25.80 E-value=52 Score=34.35 Aligned_cols=24 Identities=38% Similarity=0.729 Sum_probs=17.3
Q ss_pred eEEEeceec----c--ccccEEEEecccee
Q 025155 168 HISVQGAYL----T--YEDTYLAVTGGSGI 191 (257)
Q Consensus 168 hISvqGpyl----t--~eDtyLAVTGGTGi 191 (257)
.+.|.|||= + -.|+.+.|.||+||
T Consensus 395 ~V~VeGPYG~~~~~~~~~~~vVlIAGGsGI 424 (699)
T PLN02631 395 EVSTEGPYGPNSFDVSRHNSLILVSGGSGI 424 (699)
T ss_pred EEEEECCCCCCCCCcCCCCcEEEEEeCcCh
Confidence 366667773 1 13679999999997
No 43
>cd06221 sulfite_reductase_like Anaerobic sulfite reductase contains an FAD and NADPH binding module with structural similarity to ferredoxin reductase and sequence similarity to dihydroorotate dehydrogenases. Clostridium pasteurianum inducible dissimilatory type sulfite reductase is linked to ferredoxin and reduces NH2OH and SeO3 at a lesser rate than it's normal substate SO3(2-). Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+.
Probab=25.59 E-value=57 Score=28.23 Aligned_cols=25 Identities=24% Similarity=0.510 Sum_probs=17.0
Q ss_pred eEEEeceecc---c----cccEEEEeccceee
Q 025155 168 HISVQGAYLT---Y----EDTYLAVTGGSGIF 192 (257)
Q Consensus 168 hISvqGpylt---~----eDtyLAVTGGTGiF 192 (257)
.|.+.|||=+ . .+..+.|.||+||-
T Consensus 80 ~v~i~gP~G~~f~~~~~~~~~iv~IA~G~Git 111 (253)
T cd06221 80 TVGLRGPFGNGFPVEEMKGKDLLLVAGGLGLA 111 (253)
T ss_pred EEEEECCcCCCcccccccCCeEEEEccccchh
Confidence 4666666522 1 24689999999973
No 44
>PLN03116 ferredoxin--NADP+ reductase; Provisional
Probab=25.39 E-value=59 Score=29.26 Aligned_cols=24 Identities=25% Similarity=0.434 Sum_probs=16.5
Q ss_pred eEEEeceeccc--------cccEEEEecccee
Q 025155 168 HISVQGAYLTY--------EDTYLAVTGGSGI 191 (257)
Q Consensus 168 hISvqGpylt~--------eDtyLAVTGGTGi 191 (257)
.|.|.||+=++ .+..+.|-|||||
T Consensus 137 ~v~v~gP~G~f~~~~~~~~~~~~vlIAgGtGI 168 (307)
T PLN03116 137 KVQITGPSGKVMLLPEEDPNATHIMVATGTGI 168 (307)
T ss_pred EEEEEEecCCceeCCCCCCCCcEEEEecCccH
Confidence 46777773321 2368999999997
No 45
>cd06189 flavin_oxioreductase NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN, or riboflavin via NAD(P)H. Flavin is used as a substrate, rather than a tightly bound prosthetic group as in flavoenzymes; weaker binding is due to the absence of a binding site for the AMP moeity of FAD.
Probab=24.51 E-value=56 Score=27.14 Aligned_cols=13 Identities=23% Similarity=0.644 Sum_probs=11.0
Q ss_pred ccEEEEeccceee
Q 025155 180 DTYLAVTGGSGIF 192 (257)
Q Consensus 180 DtyLAVTGGTGiF 192 (257)
+.++.|.||+||-
T Consensus 99 ~~ivliagG~Gia 111 (224)
T cd06189 99 RPLILIAGGTGFA 111 (224)
T ss_pred CCEEEEecCcCHH
Confidence 4689999999983
No 46
>PRK06171 sorbitol-6-phosphate 2-dehydrogenase; Provisional
Probab=24.10 E-value=46 Score=27.67 Aligned_cols=20 Identities=30% Similarity=0.446 Sum_probs=15.7
Q ss_pred eceeccccccEEEEecccee
Q 025155 172 QGAYLTYEDTYLAVTGGSGI 191 (257)
Q Consensus 172 qGpylt~eDtyLAVTGGTGi 191 (257)
|+++++.++....||||+|-
T Consensus 1 ~~~~~~l~~k~vlItG~s~g 20 (266)
T PRK06171 1 MQDWLNLQGKIIIVTGGSSG 20 (266)
T ss_pred CcccccCCCCEEEEeCCCCh
Confidence 45677788888899999864
No 47
>cd06188 NADH_quinone_reductase Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase, and has NADH and FAD binding sites. (Na+-NQR) is distinct from H+-translocating NADH:quinone oxidoreductases and noncoupled NADH:quinone oxidoreductases. The NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal domain of this group typically contains an iron-sulfur cluster binding domain.
Probab=24.03 E-value=63 Score=28.27 Aligned_cols=12 Identities=25% Similarity=0.675 Sum_probs=10.5
Q ss_pred ccEEEEecccee
Q 025155 180 DTYLAVTGGSGI 191 (257)
Q Consensus 180 DtyLAVTGGTGi 191 (257)
+.++.|.||+||
T Consensus 151 ~~~vlIAgGtGI 162 (283)
T cd06188 151 REMVFIGGGAGM 162 (283)
T ss_pred CcEEEEEecccH
Confidence 468999999998
No 48
>cd06211 phenol_2-monooxygenase_like Phenol 2-monooxygenase (phenol hydroxylase) is a flavoprotein monooxygenase, able to use molecular oxygen as a substrate in the microbial degredation of phenol. This protein is encoded by a single gene and uses a tightly bound FAD cofactor in the NAD(P)H dependent conversion of phenol and O2 to catechol and H2O. This group is related to the NAD binding ferredoxin reductases.
Probab=23.48 E-value=63 Score=27.18 Aligned_cols=12 Identities=33% Similarity=0.780 Sum_probs=10.6
Q ss_pred ccEEEEecccee
Q 025155 180 DTYLAVTGGSGI 191 (257)
Q Consensus 180 DtyLAVTGGTGi 191 (257)
+..+.|.||+||
T Consensus 110 ~~~v~iagG~Gi 121 (238)
T cd06211 110 RPIIFIAGGSGL 121 (238)
T ss_pred CCEEEEeCCcCH
Confidence 568999999997
No 49
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=23.37 E-value=2.2e+02 Score=24.58 Aligned_cols=44 Identities=32% Similarity=0.470 Sum_probs=25.6
Q ss_pred ccccCccccccc---cccccccceeceeeeeE-----EEEeeccCCCCCEEEE
Q 025155 113 LTIGDLVPFTNK---LYTGDLQKRIGITAGLC-----VLIKHEPEKKGDRFEA 157 (257)
Q Consensus 113 nslGDlVpFsNk---LY~g~l~kRiGitaG~C-----vliq~~pek~GdryEa 157 (257)
-..||+|-|..+ .++.+.+ |--+..|.| .+++.+-...||+.+.
T Consensus 51 ~~rGDiVvf~~P~~~~~~~a~~-r~yl~~g~~p~~~~~~iKRViglpGD~V~i 102 (176)
T PRK13838 51 VAVGDLVFICPPETAAFREARE-RGYLRRGLCPGGFAPLIKTVAALAGQRVEI 102 (176)
T ss_pred CCCCcEEEEECCchhhhhhhhh-cccccccccccCCCceEEEEEEeCCcEEEE
Confidence 467888888632 2332222 223445555 4677777777887763
No 50
>cd06210 MMO_FAD_NAD_binding Methane monooxygenase (MMO) reductase of methanotrophs catalyzes the NADH-dependent hydroxylation of methane to methanol. This multicomponent enzyme mediates electron transfer via a hydroxylase (MMOH), a coupling protein, and a reductase which is comprised of an N-terminal [2Fe-2S] ferredoxin domain, an FAD binding subdomain, and an NADH binding subdomain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. Dioxygenases add both atom of oxygen to the substrate, while mono-oxygenases add one atom to the substrate and one atom to water.
Probab=23.14 E-value=64 Score=26.88 Aligned_cols=12 Identities=33% Similarity=0.642 Sum_probs=10.3
Q ss_pred ccEEEEecccee
Q 025155 180 DTYLAVTGGSGI 191 (257)
Q Consensus 180 DtyLAVTGGTGi 191 (257)
+..+-|.||+||
T Consensus 109 ~~~vliagGtGi 120 (236)
T cd06210 109 RPRWFVAGGTGL 120 (236)
T ss_pred ccEEEEccCcch
Confidence 457889999998
No 51
>PTZ00319 NADH-cytochrome B5 reductase; Provisional
Probab=22.08 E-value=70 Score=28.83 Aligned_cols=11 Identities=36% Similarity=0.993 Sum_probs=9.8
Q ss_pred cEEEEecccee
Q 025155 181 TYLAVTGGSGI 191 (257)
Q Consensus 181 tyLAVTGGTGi 191 (257)
.++.|-||+||
T Consensus 168 ~illIAgGtGI 178 (300)
T PTZ00319 168 AFAMIAGGTGI 178 (300)
T ss_pred eEEEEecCccc
Confidence 58899999998
No 52
>cd06219 DHOD_e_trans_like1 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity, as well as NAD binding. NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal domain may contain a flavin prosthetic group, as in flavoenzymes, or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD,
Probab=21.22 E-value=73 Score=27.39 Aligned_cols=22 Identities=36% Similarity=0.385 Sum_probs=15.3
Q ss_pred EEeceeccc-----cccEEEEecccee
Q 025155 170 SVQGAYLTY-----EDTYLAVTGGSGI 191 (257)
Q Consensus 170 SvqGpylt~-----eDtyLAVTGGTGi 191 (257)
.+.|||=++ .+..+-|.||+||
T Consensus 83 ~i~gP~G~~~~~~~~~~~lliagG~Gi 109 (248)
T cd06219 83 DVVGPLGKPSEIENYGTVVFVGGGVGI 109 (248)
T ss_pred eeecCCCCCeecCCCCeEEEEeCcccH
Confidence 466665221 3468999999997
No 53
>PRK08221 anaerobic sulfite reductase subunit B; Provisional
Probab=21.15 E-value=75 Score=27.86 Aligned_cols=12 Identities=33% Similarity=0.880 Sum_probs=10.5
Q ss_pred ccEEEEecccee
Q 025155 180 DTYLAVTGGSGI 191 (257)
Q Consensus 180 DtyLAVTGGTGi 191 (257)
+.++-|-||+||
T Consensus 102 ~~~llIAgGtGI 113 (263)
T PRK08221 102 KELIVVAGGTGV 113 (263)
T ss_pred ccEEEEcccccH
Confidence 368999999997
No 54
>PRK13289 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional
Probab=20.98 E-value=77 Score=28.92 Aligned_cols=24 Identities=17% Similarity=0.440 Sum_probs=16.1
Q ss_pred eEEEeceeccc------cccEEEEecccee
Q 025155 168 HISVQGAYLTY------EDTYLAVTGGSGI 191 (257)
Q Consensus 168 hISvqGpylt~------eDtyLAVTGGTGi 191 (257)
.|.|.|||=.+ .+.++.|.|||||
T Consensus 244 ~v~v~gP~G~f~l~~~~~~~~vlIagGtGI 273 (399)
T PRK13289 244 VLELAAPAGDFFLDVASDTPVVLISGGVGI 273 (399)
T ss_pred EEEEEcCccccccCCCCCCcEEEEecCccH
Confidence 45566664322 2368999999997
No 55
>TIGR02160 PA_CoA_Oxy5 phenylacetate-CoA oxygenase/reductase, PaaK subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=20.84 E-value=67 Score=28.91 Aligned_cols=12 Identities=58% Similarity=0.991 Sum_probs=10.6
Q ss_pred ccEEEEecccee
Q 025155 180 DTYLAVTGGSGI 191 (257)
Q Consensus 180 DtyLAVTGGTGi 191 (257)
+.++-|.||+||
T Consensus 110 ~~~lliagG~GI 121 (352)
T TIGR02160 110 GHYVAVAAGSGI 121 (352)
T ss_pred ccEEEEeccccH
Confidence 568999999997
No 56
>cd06193 siderophore_interacting Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from transferrin and lactoferrin for bacterial uptake, contributing to pathogen virulence. Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hy
Probab=20.77 E-value=77 Score=26.96 Aligned_cols=24 Identities=17% Similarity=0.360 Sum_probs=17.0
Q ss_pred eEEEeceeccc-----cccEEEEecccee
Q 025155 168 HISVQGAYLTY-----EDTYLAVTGGSGI 191 (257)
Q Consensus 168 hISvqGpylt~-----eDtyLAVTGGTGi 191 (257)
.|.+.||+=++ .+.++.|-|||||
T Consensus 104 ~v~v~gP~G~~~~~~~~~~~vlia~GtGi 132 (235)
T cd06193 104 TLGIAGPGGSFLPPPDADWYLLAGDETAL 132 (235)
T ss_pred EEEEECCCCCCCCCCCcceEEEEeccchH
Confidence 56666665444 2358999999997
No 57
>cd06218 DHOD_e_trans FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity, as well as 3 cofactors: FMN, FAD, and an [2Fe-2S] cluster.
Probab=20.52 E-value=81 Score=27.16 Aligned_cols=13 Identities=46% Similarity=0.613 Sum_probs=10.9
Q ss_pred ccEEEEeccceee
Q 025155 180 DTYLAVTGGSGIF 192 (257)
Q Consensus 180 DtyLAVTGGTGiF 192 (257)
+..+-|.|||||=
T Consensus 99 ~~~vlIagGtGIa 111 (246)
T cd06218 99 GKVLLVGGGIGIA 111 (246)
T ss_pred CcEEEEecccCHH
Confidence 4689999999983
No 58
>PF02141 DENN: DENN (AEX-3) domain; InterPro: IPR001194 The human serine- and leucine-rich DENN protein possesses a RGD cellular adhesion motif and a leucine-zipper-like motif associated with protein dimerization, and shows partial homology to the receptor binding domain of tumor necrosis factor alpha. DENN is virtually identical to MADD, a human MAP kinase-activating death domain protein that interacts with type I tumor necrosis factor receptor. DENN displays significant homology to Rab3 GEP, a rat GDP/GTP exchange protein specific for Rab3 small G proteins implicated in intracellular vesicle trafficking. DENN also exhibits strong similarity to Caenorhabditis elegans AEX-3, which interacts with Rab3 to regulate synaptic vesicle release []. The DENN domain is always encircled on both sides by more divergent domains, known as uDENN (IPR005113 from INTERPRO) and dDENN (IPR005112 from INTERPRO), which could play a key role in DENN function.; PDB: 3TW8_A.
Probab=20.46 E-value=16 Score=30.19 Aligned_cols=31 Identities=26% Similarity=0.575 Sum_probs=17.1
Q ss_pred EEEeeeceeEEEEEEeccCCCChhhhhcCCCCCCC
Q 025155 201 LHQIVFPYKLFYTFYLKGVADLPQELLVKPVEPSP 235 (257)
Q Consensus 201 L~qivfPfklfYtFyLkgi~dlp~el~~~~v~ps~ 235 (257)
+.++++||+|-..| ||-||.+|+.---.|.|
T Consensus 127 l~~ll~Pf~w~~~~----ip~LP~~l~~~l~aP~P 157 (185)
T PF02141_consen 127 LLSLLYPFQWQHVY----IPVLPPSLLDYLEAPTP 157 (185)
T ss_dssp HHHTTTTS---SEE----ESS--GGGGGGGG-SS-
T ss_pred HHHHccCcccCceE----EeecCHHHHhhcCCCCC
Confidence 46788888888887 78888877665544443
Done!