Query 042631
Match_columns 66
No_of_seqs 109 out of 332
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 08:04:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042631.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042631hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3380 Predicted NAD/FAD-depe 99.8 5.3E-20 1.2E-24 134.3 4.8 60 2-66 17-79 (331)
2 PF13450 NAD_binding_8: NAD(P) 98.7 2.8E-08 6E-13 57.6 4.6 52 2-58 12-68 (68)
3 PF01593 Amino_oxidase: Flavin 98.3 1.5E-06 3.2E-11 59.3 5.0 55 2-59 7-64 (450)
4 TIGR03467 HpnE squalene-associ 98.1 5.3E-06 1.2E-10 58.4 5.2 54 2-58 3-59 (419)
5 PLN02576 protoporphyrinogen ox 98.0 7.5E-06 1.6E-10 60.2 3.6 52 2-58 28-83 (496)
6 TIGR00562 proto_IX_ox protopor 97.9 1.8E-05 3.9E-10 57.4 4.0 52 2-58 18-76 (462)
7 PRK11883 protoporphyrinogen ox 97.9 1.6E-05 3.5E-10 57.0 3.6 52 2-58 16-72 (451)
8 PRK07208 hypothetical protein; 97.7 5.4E-05 1.2E-09 55.5 4.9 53 2-59 20-75 (479)
9 PLN02268 probable polyamine ox 97.7 4.4E-05 9.5E-10 55.4 4.3 52 2-58 16-72 (435)
10 PRK12416 protoporphyrinogen ox 97.5 8.2E-05 1.8E-09 54.4 3.2 52 2-58 17-77 (463)
11 TIGR02731 phytoene_desat phyto 97.4 0.00036 7.7E-09 51.0 4.7 52 2-58 15-70 (453)
12 TIGR02734 crtI_fam phytoene de 97.3 0.00045 9.8E-09 51.1 4.5 51 2-58 14-67 (502)
13 PRK07233 hypothetical protein; 97.2 0.00037 8.1E-09 49.5 3.5 52 2-58 15-69 (434)
14 COG1233 Phytoene dehydrogenase 97.1 0.00071 1.5E-08 51.0 4.3 43 2-49 19-64 (487)
15 PLN02568 polyamine oxidase 97.1 0.00078 1.7E-08 51.8 4.5 52 2-58 21-81 (539)
16 TIGR02733 desat_CrtD C-3',4' d 97.1 0.00089 1.9E-08 49.6 4.5 52 2-58 17-73 (492)
17 KOG0029 Amine oxidase [Seconda 97.1 0.00098 2.1E-08 51.3 4.8 52 2-57 31-86 (501)
18 TIGR02732 zeta_caro_desat caro 96.9 0.0015 3.2E-08 49.1 4.3 52 2-58 15-70 (474)
19 PLN02676 polyamine oxidase 96.7 0.0026 5.6E-08 48.1 4.1 51 2-57 42-100 (487)
20 PLN02612 phytoene desaturase 96.6 0.0042 9.1E-08 47.8 5.1 52 2-58 109-164 (567)
21 PLN02529 lysine-specific histo 96.1 0.0081 1.8E-07 48.4 4.4 53 2-57 176-234 (738)
22 PLN02328 lysine-specific histo 96.0 0.0096 2.1E-07 48.5 4.0 53 2-57 254-312 (808)
23 PLN03000 amine oxidase 95.7 0.019 4.1E-07 47.3 4.9 53 2-57 200-258 (881)
24 COG1231 Monoamine oxidase [Ami 95.4 0.019 4.1E-07 44.4 3.5 51 2-57 23-76 (450)
25 TIGR02730 carot_isom carotene 95.1 0.028 6E-07 42.0 3.7 40 2-46 16-58 (493)
26 KOG0685 Flavin-containing amin 94.8 0.047 1E-06 42.8 4.2 50 2-56 37-91 (498)
27 COG1232 HemY Protoporphyrinoge 94.6 0.056 1.2E-06 41.4 4.1 52 2-58 16-72 (444)
28 PLN02487 zeta-carotene desatur 94.6 0.064 1.4E-06 41.9 4.5 53 2-58 91-146 (569)
29 TIGR00031 UDP-GALP_mutase UDP- 94.2 0.082 1.8E-06 39.4 4.1 56 1-60 16-74 (377)
30 COG3349 Uncharacterized conser 90.7 0.33 7.1E-06 37.9 3.5 52 2-57 16-70 (485)
31 PLN02976 amine oxidase 90.5 0.28 6E-06 43.2 3.3 41 2-46 709-752 (1713)
32 PTZ00363 rab-GDP dissociation 82.0 1.4 3.1E-05 33.4 2.8 48 1-51 19-87 (443)
33 PF02817 E3_binding: e3 bindin 79.9 2.3 5E-05 22.4 2.4 25 2-27 9-34 (39)
34 PRK13977 myosin-cross-reactive 77.6 3.8 8.3E-05 32.7 4.0 52 2-57 38-96 (576)
35 KOG1276 Protoporphyrinogen oxi 66.4 13 0.00028 29.5 4.5 53 2-58 27-87 (491)
36 COG1148 HdrA Heterodisulfide r 63.8 4.4 9.5E-05 32.7 1.5 24 2-28 140-166 (622)
37 PF05678 VQ: VQ motif; InterP 61.0 9.8 0.00021 19.2 2.1 21 41-61 5-25 (31)
38 PRK12775 putative trifunctiona 58.0 15 0.00033 30.8 3.8 22 2-26 446-470 (1006)
39 PRK12779 putative bifunctional 56.7 14 0.0003 30.8 3.3 22 2-26 322-346 (944)
40 COG0562 Glf UDP-galactopyranos 53.5 32 0.0007 26.4 4.6 55 1-58 16-74 (374)
41 COG1759 5-formaminoimidazole-4 46.0 26 0.00056 26.8 3.1 26 40-65 163-189 (361)
42 PF08672 APC2: Anaphase promot 43.9 14 0.0003 21.0 1.1 26 40-65 27-52 (60)
43 PF12342 DUF3640: Protein of u 42.9 13 0.00028 18.4 0.7 13 12-24 12-24 (26)
44 PF13463 HTH_27: Winged helix 39.8 12 0.00025 20.2 0.3 24 42-65 26-49 (68)
45 TIGR01316 gltA glutamate synth 39.6 51 0.0011 24.6 3.8 22 2-26 149-173 (449)
46 PF08410 DUF1737: Domain of un 38.8 48 0.001 18.7 2.8 21 43-63 8-29 (54)
47 smart00420 HTH_DEOR helix_turn 38.0 17 0.00036 18.2 0.8 25 41-65 21-45 (53)
48 PF01946 Thi4: Thi4 family; PD 36.9 23 0.00049 25.5 1.5 58 2-62 33-110 (230)
49 smart00345 HTH_GNTR helix_turn 36.7 19 0.00041 18.5 0.8 25 41-65 27-51 (60)
50 COG2072 TrkA Predicted flavopr 36.4 21 0.00046 26.9 1.4 55 1-60 23-93 (443)
51 PF10557 Cullin_Nedd8: Cullin 36.1 24 0.00053 19.9 1.3 28 38-65 34-61 (68)
52 PF09012 FeoC: FeoC like trans 34.8 13 0.00027 20.9 -0.0 25 41-65 21-45 (69)
53 PF01325 Fe_dep_repress: Iron 34.7 13 0.00029 20.7 0.1 25 41-65 29-53 (60)
54 smart00419 HTH_CRP helix_turn_ 33.9 20 0.00043 17.8 0.6 24 42-65 16-39 (48)
55 cd07377 WHTH_GntR Winged helix 33.9 22 0.00048 18.6 0.8 24 42-65 33-56 (66)
56 PF04468 PSP1: PSP1 C-terminal 33.8 41 0.0009 20.1 2.1 18 43-60 59-77 (88)
57 PF00743 FMO-like: Flavin-bind 33.7 28 0.00062 27.1 1.7 22 2-26 17-41 (531)
58 PF13545 HTH_Crp_2: Crp-like h 33.2 16 0.00034 20.2 0.2 25 41-65 35-59 (76)
59 PRK12831 putative oxidoreducta 32.8 81 0.0018 23.8 4.0 22 2-26 156-180 (464)
60 COG2907 Predicted NAD/FAD-bind 32.7 79 0.0017 24.8 3.9 46 10-58 33-82 (447)
61 PF13591 MerR_2: MerR HTH fami 32.0 38 0.00082 19.9 1.7 15 52-66 14-28 (84)
62 PRK12769 putative oxidoreducta 31.6 76 0.0017 24.9 3.8 23 2-27 343-368 (654)
63 PRK05704 dihydrolipoamide succ 31.3 33 0.00071 26.0 1.7 25 2-27 119-144 (407)
64 PRK10265 chaperone-modulator p 31.2 40 0.00086 20.6 1.8 15 52-66 21-35 (101)
65 PF12802 MarR_2: MarR family; 30.0 18 0.00039 19.1 0.1 23 43-65 30-52 (62)
66 COG0493 GltD NADPH-dependent g 29.9 35 0.00075 26.3 1.6 24 2-28 139-165 (457)
67 PRK12778 putative bifunctional 29.7 88 0.0019 25.0 3.9 22 2-26 447-471 (752)
68 PLN02172 flavin-containing mon 29.7 37 0.00081 25.8 1.7 23 2-27 26-51 (461)
69 smart00843 Ftsk_gamma This dom 29.4 54 0.0012 19.0 2.0 19 48-66 33-51 (63)
70 PRK12809 putative oxidoreducta 29.2 89 0.0019 24.6 3.8 22 2-26 326-350 (639)
71 PF13738 Pyr_redox_3: Pyridine 28.6 46 0.00099 21.1 1.8 24 2-28 13-40 (203)
72 PHA02591 hypothetical protein; 28.3 76 0.0016 19.6 2.6 24 40-63 37-60 (83)
73 TIGR01318 gltD_gamma_fam gluta 28.2 98 0.0021 23.3 3.7 22 2-26 157-181 (467)
74 COG0194 Gmk Guanylate kinase [ 28.1 46 0.001 23.3 1.9 30 25-57 36-65 (191)
75 cd03715 RT_ZFREV_like RT_ZFREV 27.7 56 0.0012 21.6 2.2 17 50-66 16-32 (210)
76 PF04304 DUF454: Protein of un 27.4 50 0.0011 18.5 1.7 18 47-64 7-24 (71)
77 PF09106 SelB-wing_2: Elongati 27.3 56 0.0012 17.8 1.8 18 48-65 34-51 (59)
78 PF12970 DUF3858: Domain of Un 27.3 30 0.00065 22.5 0.8 26 37-62 84-110 (116)
79 smart00521 CBF CCAAT-Binding t 27.1 30 0.00065 20.3 0.7 10 18-27 52-61 (62)
80 TIGR01317 GOGAT_sm_gam glutama 26.9 1E+02 0.0023 23.3 3.7 22 2-26 159-183 (485)
81 cd00092 HTH_CRP helix_turn_hel 26.8 32 0.00069 18.2 0.7 24 42-65 33-56 (67)
82 cd01645 RT_Rtv RT_Rtv: Reverse 26.6 60 0.0013 21.7 2.2 18 49-66 15-32 (213)
83 PF14178 YppF: YppF-like prote 26.3 72 0.0016 18.5 2.2 18 49-66 40-57 (60)
84 COG3233 Predicted deacetylase 26.2 71 0.0015 23.1 2.5 18 46-63 51-68 (233)
85 PF01047 MarR: MarR family; I 26.1 23 0.0005 18.6 0.1 25 41-65 24-48 (59)
86 PF09397 Ftsk_gamma: Ftsk gamm 25.2 41 0.00088 19.5 1.0 18 49-66 35-52 (65)
87 TIGR01349 PDHac_trf_mito pyruv 24.1 55 0.0012 25.0 1.8 26 2-28 145-171 (435)
88 PRK05249 soluble pyridine nucl 23.9 54 0.0012 24.1 1.7 24 2-28 21-47 (461)
89 PF03551 PadR: Transcriptional 23.4 69 0.0015 17.9 1.8 24 42-65 25-48 (75)
90 PF13412 HTH_24: Winged helix- 23.2 28 0.00062 17.8 0.1 20 46-65 29-48 (48)
91 PF13730 HTH_36: Helix-turn-he 22.6 84 0.0018 16.3 1.9 20 45-64 36-55 (55)
92 PRK13918 CRP/FNR family transc 22.5 47 0.001 21.2 1.0 28 38-65 153-180 (202)
93 TIGR01470 cysG_Nterm siroheme 22.1 15 0.00032 25.0 -1.5 37 22-62 17-53 (205)
94 PRK06416 dihydrolipoamide dehy 22.0 64 0.0014 23.8 1.7 23 2-28 20-45 (462)
95 smart00347 HTH_MARR helix_turn 21.9 55 0.0012 18.2 1.1 28 38-65 28-55 (101)
96 TIGR03257 met_CoM_red_bet meth 21.7 55 0.0012 25.5 1.4 34 15-48 363-407 (433)
97 PRK12814 putative NADPH-depend 21.6 1.6E+02 0.0035 23.3 3.9 22 2-26 209-233 (652)
98 PRK10402 DNA-binding transcrip 21.5 46 0.00099 22.1 0.8 25 41-65 176-200 (226)
99 PF02241 MCR_beta: Methyl-coen 21.4 39 0.00085 24.6 0.5 33 15-47 179-222 (255)
100 cd00537 MTHFR Methylenetetrahy 20.9 1.1E+02 0.0024 21.2 2.6 28 36-63 156-187 (274)
101 smart00418 HTH_ARSR helix_turn 20.9 56 0.0012 16.4 1.0 22 44-65 20-41 (66)
102 PF00890 FAD_binding_2: FAD bi 20.8 73 0.0016 22.8 1.8 25 2-31 15-42 (417)
103 COG4352 RPL13 Ribosomal protei 20.8 78 0.0017 20.6 1.7 49 4-66 65-113 (113)
104 PRK11857 dihydrolipoamide acet 20.7 69 0.0015 23.4 1.7 25 2-27 8-33 (306)
105 COG3571 Predicted hydrolase of 20.6 34 0.00074 24.2 0.1 35 15-49 92-130 (213)
106 TIGR01292 TRX_reduct thioredox 20.6 77 0.0017 21.1 1.8 23 2-28 16-41 (300)
107 PF01266 DAO: FAD dependent ox 20.5 62 0.0014 21.8 1.3 22 1-26 14-38 (358)
108 TIGR01347 sucB 2-oxoglutarate 20.3 72 0.0016 24.2 1.7 26 2-28 117-143 (403)
No 1
>COG3380 Predicted NAD/FAD-dependent oxidoreductase [General function prediction only]
Probab=99.80 E-value=5.3e-20 Score=134.34 Aligned_cols=60 Identities=32% Similarity=0.528 Sum_probs=56.9
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHHHHhCCcccC
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLINGWLERGLVRP 66 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~~~~~g~v~~ 66 (66)
|..|+++|++ ||| +||+||||+|||.++. .||||||||+++++.|.++|+.|.++|+|++
T Consensus 17 A~~L~~aG~~vtV~eK---g~GvGGRlAtRRl~~g--~~DhGAqYfk~~~~~F~~~Ve~~~~~glV~~ 79 (331)
T COG3380 17 AYALREAGREVTVFEK---GRGVGGRLATRRLDGG--RFDHGAQYFKPRDELFLRAVEALRDDGLVDV 79 (331)
T ss_pred HHHHHhcCcEEEEEEc---CCCcccchheeccCCc--cccccceeecCCchHHHHHHHHHHhCCceee
Confidence 6789999988 999 9999999999999987 5999999999999999999999999999864
No 2
>PF13450 NAD_binding_8: NAD(P)-binding Rossmann-like domain; PDB: 3KA7_A 1V0J_D 3INR_B 3KYB_B 3GF4_A 2BI8_A 3INT_B 1WAM_A 2BI7_A 3MJ4_G ....
Probab=98.72 E-value=2.8e-08 Score=57.56 Aligned_cols=52 Identities=35% Similarity=0.468 Sum_probs=44.7
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeee--CCHHHHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITV--NNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~--~~~~f~~~v~~~ 58 (66)
|..|+++|++ ||| ...+||+++|.+.++ ..+|+|+.+|.. .++.+.+++++|
T Consensus 12 A~~L~~~g~~v~v~E~---~~~~GG~~~~~~~~g--~~~d~g~~~~~~~~~~~~~~~l~~~L 68 (68)
T PF13450_consen 12 AYYLAKAGYRVTVFEK---NDRLGGRARSFRIPG--YRFDLGAHYFFPPDDYPNLFRLLREL 68 (68)
T ss_dssp HHHHHHTTSEEEEEES---SSSSSGGGCEEEETT--EEEETSS-SEEETTSCHHHHHHHHTT
T ss_pred HHHHHHCCCcEEEEec---CcccCcceeEEEECC--EEEeeccEEEeCCCCchHHHHHHcCC
Confidence 6789999988 999 999999999999866 479999999988 458898888874
No 3
>PF01593 Amino_oxidase: Flavin containing amine oxidoreductase This is a subset of the Pfam family; InterPro: IPR002937 This entry consists of various amine oxidases, including maize polyamine oxidase (PAO) [], L-amino acid oxidases (LAO) and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. In vertebrates MAO plays an important role in regulating the intracellular levels of amines via their oxidation; these include various neurotransmitters, neurotoxins and trace amines []. In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium []. PAOs in plants, bacteria and protozoa oxidise spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines []. Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid binding proteins and antibacterial glycoproteins.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2Z5U_A ....
Probab=98.29 E-value=1.5e-06 Score=59.34 Aligned_cols=55 Identities=24% Similarity=0.238 Sum_probs=45.2
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLINGWL 59 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~~~ 59 (66)
|..|+++|++ ||+ +..+|||+.|.+.+.....+|+|+.+|+..++.+..++.++.
T Consensus 7 A~~L~~~G~~v~vlEa---~~r~GGr~~t~~~~~~g~~~e~G~~~~~~~~~~~~~~~~~l~ 64 (450)
T PF01593_consen 7 AYYLAKAGYDVTVLEA---SDRVGGRIRTFRFDNPGFTFELGAHRFFGMYPNLLNLIDELG 64 (450)
T ss_dssp HHHHHHTTTEEEEEES---SSSSBTTS-EEEETTTTEEEESSS-EEETTSHHHHHHHHHHT
T ss_pred HHHHHhCCCCEEEEEc---CCCCCcceEEecCCccceeecCCcccccccchhhHHHHHHhh
Confidence 7889999988 999 999999999999983114799999999988887888888754
No 4
>TIGR03467 HpnE squalene-associated FAD-dependent desaturase. The sequences in this family are members of the pfam01593 superfamily of flavin-containing amine oxidases which include the phytoene desaturases. These sequences also include a FAD-dependent oxidoreductase domain, pfam01266. The genes of the family modeled here are generally in the same locus with genes involved in the biosynthesis and elaboration of squalene, the condensation product of the polyisoprenoid farnesyl pyrophosphate. This gene and its association with hopene biosynthesis in Zymomonas mobilis has been noted in the literature where the gene symbol hpnE was assigned. This gene is also found in contexts where the downstream conversion of squalene to hopenes is not evidence. The precise nature of the reaction catalyzed by this enzyme is unknown at this time.
Probab=98.13 E-value=5.3e-06 Score=58.40 Aligned_cols=54 Identities=26% Similarity=0.252 Sum_probs=47.2
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~~ 58 (66)
|..|+++|++ +|+ +.-+|||+.|-+.++....||.|+++|...++.+.++++++
T Consensus 3 A~~L~~~G~~v~vlEa---~~~~GG~~~t~~~~g~~~~~d~G~~~~~~~~~~~~~l~~~l 59 (419)
T TIGR03467 3 AVELARAGARVTLFEA---RPRLGGRARSFEDGGLGQTIDNGQHVLLGAYTNLLALLRRI 59 (419)
T ss_pred HHHHHhCCCceEEEec---CCCCCCceeEeecCCCCcceecCCEEEEcccHHHHHHHHHh
Confidence 7899999988 999 99999999999877543359999999998889998888875
No 5
>PLN02576 protoporphyrinogen oxidase
Probab=97.97 E-value=7.5e-06 Score=60.24 Aligned_cols=52 Identities=19% Similarity=0.226 Sum_probs=45.3
Q ss_pred hhHHHHC-CCc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHHH
Q 042631 2 ADYLRSR-GVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~-G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~~ 58 (66)
|..|.++ |++ +|+ +..+|||+.|.+.++. .||+|++.|...++.+..++++.
T Consensus 28 A~~L~~~~g~~v~vlEa---~~rvGGr~~t~~~~g~--~~d~G~~~~~~~~~~~~~l~~~g 83 (496)
T PLN02576 28 AYALASKHGVNVLVTEA---RDRVGGNITSVSEDGF--IWEEGPNSFQPSDPELTSAVDSG 83 (496)
T ss_pred HHHHHHhcCCCEEEEec---CCCCCCceeEeccCCe--EEecCCchhccCcHHHHHHHHcC
Confidence 6788888 877 999 9999999999998654 79999999999999888777763
No 6
>TIGR00562 proto_IX_ox protoporphyrinogen oxidase. This protein is a flavoprotein and has a beta-alpha-beta dinucleotide binding motif near the amino end.
Probab=97.86 E-value=1.8e-05 Score=57.41 Aligned_cols=52 Identities=15% Similarity=0.200 Sum_probs=45.5
Q ss_pred hhHHHHC----CCc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHHH
Q 042631 2 ADYLRSR----GVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~----G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~~ 58 (66)
|..|+++ |++ ||+ +..+|||+.|...++. .||.|++.|...++.+.++++++
T Consensus 18 A~~L~~~~~~~g~~v~vlE~---~~r~GG~~~t~~~~g~--~~e~G~~~~~~~~~~~~~l~~~l 76 (462)
T TIGR00562 18 AYYLEKEIPELPVELTLVEA---SDRVGGKIQTVKEDGY--LIERGPDSFLERKKSAPDLVKDL 76 (462)
T ss_pred HHHHHhcCCCCCCcEEEEEc---CCcCcceEEEEeeCCE--EEecCccccccCChHHHHHHHHc
Confidence 6788888 877 999 9999999999887654 69999999999999888888875
No 7
>PRK11883 protoporphyrinogen oxidase; Reviewed
Probab=97.86 E-value=1.6e-05 Score=57.01 Aligned_cols=52 Identities=15% Similarity=0.185 Sum_probs=44.0
Q ss_pred hhHHHHCC--Cc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHHH
Q 042631 2 ADYLRSRG--VR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~G--~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~~ 58 (66)
|..|+++| ++ ||+ +..+|||+.|.+..+. .+|+|++.|...++.+.++++++
T Consensus 16 A~~L~~~G~~~~V~vlEa---~~~~GGr~~t~~~~g~--~~d~G~~~~~~~~~~~~~l~~~l 72 (451)
T PRK11883 16 AYRLHKKGPDADITLLEA---SDRLGGKIQTVRKDGF--PIELGPESFLARKPSAPALVKEL 72 (451)
T ss_pred HHHHHHhCCCCCEEEEEc---CCCCcceEEEEeeCCe--EEecChHHhcCCcHHHHHHHHHc
Confidence 77899988 65 999 9999999999988765 69999998877777777777775
No 8
>PRK07208 hypothetical protein; Provisional
Probab=97.75 E-value=5.4e-05 Score=55.52 Aligned_cols=53 Identities=23% Similarity=0.200 Sum_probs=47.5
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLINGWL 59 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~~~ 59 (66)
|..|.++|++ +|+ +..+|||+.|...++. .+|.|++.|...++.+.++++++.
T Consensus 20 A~~L~~~g~~v~v~E~---~~~~GG~~~s~~~~g~--~~d~G~h~~~~~~~~~~~l~~~l~ 75 (479)
T PRK07208 20 AYELLKRGYPVTVLEA---DPVVGGISRTVTYKGN--RFDIGGHRFFSKSPEVMDLWNEIL 75 (479)
T ss_pred HHHHHHCCCcEEEEec---CCCCCceeeeeccCCc--eEccCCceeccCCHHHHHHHHHhc
Confidence 6789999988 999 9999999999887654 699999999999999999999985
No 9
>PLN02268 probable polyamine oxidase
Probab=97.74 E-value=4.4e-05 Score=55.36 Aligned_cols=52 Identities=19% Similarity=0.270 Sum_probs=41.4
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeee--CCHHHHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITV--NNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~--~~~~f~~~v~~~ 58 (66)
|+.|.++|++ +|+ +..+|||+.|.+..+. .+|.|+++|.- .++.+.++++++
T Consensus 16 A~~L~~~g~~v~vlEa---~~r~GGri~t~~~~g~--~~d~G~~~i~~~~~~~~~~~l~~~l 72 (435)
T PLN02268 16 ARALHDASFKVTLLES---RDRIGGRVHTDYSFGF--PVDMGASWLHGVCNENPLAPLIGRL 72 (435)
T ss_pred HHHHHhCCCeEEEEeC---CCCCCceeeecCcCCc--ccCCCCeeEeccCCCchHHHHHHHh
Confidence 7889999988 999 9999999999876554 69999999963 233366777664
No 10
>PRK12416 protoporphyrinogen oxidase; Provisional
Probab=97.52 E-value=8.2e-05 Score=54.44 Aligned_cols=52 Identities=23% Similarity=0.284 Sum_probs=44.0
Q ss_pred hhHHHHCC------Cc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHHH
Q 042631 2 ADYLRSRG------VR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~G------~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~~ 58 (66)
|..|+++| ++ +|+ +..+|||+.|.+..+. .+|+|++.|...++.+.++++++
T Consensus 17 A~~L~~~~~~~~~~~~V~vlEa---~~r~GGr~~T~~~~g~--~~e~G~~~i~~~~~~~~~l~~~l 77 (463)
T PRK12416 17 MFYLEKLKKDYNIDLNLILVEK---EEYLGGKIHSVEEKDF--IMESGADSIVARNEHVMPLVKDL 77 (463)
T ss_pred HHHHHhhhhccCCCccEEEEec---CCCccceEEEEeeCCE--EEecCcHHHhcCCHHHHHHHHHc
Confidence 67888752 44 999 9999999999987654 69999999988888888888886
No 11
>TIGR02731 phytoene_desat phytoene desaturase. Plants and cyanobacteria (and, supposedly, Chlorobium tepidum) have a conserved pathway from two molecules geranylgeranyl-PP to one of all-trans-lycopene. Members of this family are the enzyme pytoene desaturase (also called phytoene dehydrogenase). This model does not include the region of the chloroplast transit peptide in plants. A closely related family, excluded by this model, is zeta-carotene desaturase, another enzyme in the same pathway.
Probab=97.35 E-value=0.00036 Score=50.97 Aligned_cols=52 Identities=17% Similarity=0.253 Sum_probs=43.9
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceee-cCCCCeeecccCceeeeCCHHHHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRM-IRPQPQIFGHAAQFITVNNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr-~~~~~~~~DhGAqyft~~~~~f~~~v~~~ 58 (66)
|..|+++|++ +|+ +.-+|||+.|-+ .++. .+|+|.+.|....|.+.++++++
T Consensus 15 A~~L~~~G~~v~vlE~---~~~~GG~~~s~~~~~g~--~~d~G~~~~~~~~~~~~~l~~~l 70 (453)
T TIGR02731 15 AKYLADAGHTPIVLEA---RDVLGGKVAAWKDEDGD--WYETGLHIFFGAYPNMLQLLKEL 70 (453)
T ss_pred HHHHHHCCCcEEEEec---CCCCCCCcceeECCCCC--EEEcCcceeccCCchHHHHHHHc
Confidence 6789999988 999 999999998864 3443 69999999998889888888875
No 12
>TIGR02734 crtI_fam phytoene desaturase. Phytoene is converted to lycopene by desaturation at four (two symmetrical pairs of) sites. This is achieved by two enzymes (crtP and crtQ) in cyanobacteria (Gloeobacter being an exception) and plants, but by a single enzyme in most other bacteria and in fungi. This single enzyme is called the bacterial-type phytoene desaturase, or CrtI. Most members of this family, part of the larger Pfam family pfam01593, which also contains amino oxidases, are CrtI itself; it is likely that all members act on either phytoene or on related compounds such as dehydrosqualene, for carotenoid biosynthesis.
Probab=97.27 E-value=0.00045 Score=51.14 Aligned_cols=51 Identities=22% Similarity=0.127 Sum_probs=40.8
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~~ 58 (66)
|..|+++|++ +|| ..-+||++.|-+.++. .||.|+++++.. ..+.++++++
T Consensus 14 A~~La~~G~~V~VlE~---~~~~GG~~~t~~~~G~--~fD~G~~~~~~~-~~~~~l~~~l 67 (502)
T TIGR02734 14 AIRLAAAGIPVTVVEQ---RDKPGGRAGVLEDDGF--RFDTGPTVITMP-EALEELFALA 67 (502)
T ss_pred HHHHHhCCCcEEEEEC---CCCCcCceEEEecCCe--EEecCCeEEccc-cHHHHHHHHc
Confidence 6789999988 999 9999999999988765 799999999743 3455554543
No 13
>PRK07233 hypothetical protein; Provisional
Probab=97.22 E-value=0.00037 Score=49.53 Aligned_cols=52 Identities=23% Similarity=0.215 Sum_probs=45.6
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~~ 58 (66)
|..|+++|++ +|+ ..-+|||..|-+.++. .||.|...|...++.+.++++++
T Consensus 15 A~~L~~~G~~v~vlE~---~~~~GG~~~s~~~~g~--~~d~g~~~~~~~~~~~~~l~~~l 69 (434)
T PRK07233 15 AYRLAKRGHEVTVFEA---DDQLGGLAASFEFGGL--PIERFYHHIFKSDEALLELLDEL 69 (434)
T ss_pred HHHHHHCCCcEEEEEe---CCCCCCceeeeccCCc--chhhhhhhhccccHHHHHHHHHc
Confidence 6789999988 999 9999999999887765 69999998877888898988886
No 14
>COG1233 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=97.12 E-value=0.00071 Score=50.99 Aligned_cols=43 Identities=23% Similarity=0.417 Sum_probs=36.5
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNS 49 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~ 49 (66)
|..|+++|++ ||| ..-+|||++|....+. +||.|+-+++.-.+
T Consensus 19 Aa~LA~~G~~V~VlE~---~~~~GG~a~t~e~~Gf--~fd~G~~~~~~~~~ 64 (487)
T COG1233 19 AALLARAGLKVTVLEK---NDRVGGRARTFELDGF--RFDTGPSWYLMPDP 64 (487)
T ss_pred HHHHHhCCCEEEEEEe---cCCCCcceEEEeccce--EeccCcceeecCch
Confidence 6789999998 999 9999999999999865 79999866655443
No 15
>PLN02568 polyamine oxidase
Probab=97.11 E-value=0.00078 Score=51.83 Aligned_cols=52 Identities=17% Similarity=0.224 Sum_probs=40.8
Q ss_pred hhHHHHCC-----Cc---cccccCCCCcccccceeecCCCCeeecccCceeee-CCHHHHHHHHHH
Q 042631 2 ADYLRSRG-----VR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITV-NNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~G-----~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~-~~~~f~~~v~~~ 58 (66)
|+.|+++| ++ ||+ ..-+|||+.|.+..+. .||.|++++.- .++.+.++.+++
T Consensus 21 a~~L~~~g~~~~~~~v~v~E~---~~~~GGr~~t~~~~g~--~~d~G~~~~~g~~~~~~~~l~~~~ 81 (539)
T PLN02568 21 ANKLYTSSAANDMFELTVVEG---GDRIGGRINTSEFGGE--RIEMGATWIHGIGGSPVYKIAQEA 81 (539)
T ss_pred HHHHHhcccccCCceEEEEeC---CCCcCCeEEEEEeCCe--EEecCCceeCCCCCCHHHHHHHHh
Confidence 67888887 55 999 9999999999988765 69999999983 344555665554
No 16
>TIGR02733 desat_CrtD C-3',4' desaturase CrtD. Members of this family are slr1293, a carotenoid biosynthesis protein which was shown to be the C-3',4' desaturase (CrtD) of myxoxanthophyll biosynthesis in Synechocystis sp. strain PCC 6803, and close homologs (presumed to be functionally equivalent) from other cyanobacteria, where myxoxanthophyll biosynthesis is either known or expected. This enzyme can act on neurosporene and so presumably catalyzes the first step that is committed to myxoxanthophyll.
Probab=97.08 E-value=0.00089 Score=49.57 Aligned_cols=52 Identities=21% Similarity=0.204 Sum_probs=40.9
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeee--CCHHHHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITV--NNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~--~~~~f~~~v~~~ 58 (66)
|..|+++|++ +|| ..-+|||+.|-+.++. .||.|+.++.- ....+..+++++
T Consensus 17 a~~La~~G~~v~vlE~---~~~~GG~~~t~~~~G~--~fD~G~~~~~~~~~~~~~~~~~~~l 73 (492)
T TIGR02733 17 AALLAKRGYRVTLLEQ---HAQPGGCAGTFRRRGF--TFDVGATQVAGLEPGGIHARIFREL 73 (492)
T ss_pred HHHHHHCCCeEEEEec---CCCCCCccceeccCCE--EEeecceEEEecCcCCHHHHHHHHc
Confidence 6789999988 999 9999999999988654 79999999985 223355555443
No 17
>KOG0029 consensus Amine oxidase [Secondary metabolites biosynthesis, transport and catabolism]
Probab=97.08 E-value=0.00098 Score=51.29 Aligned_cols=52 Identities=21% Similarity=0.216 Sum_probs=42.4
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCH-HHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNS-RFCLLING 57 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~-~f~~~v~~ 57 (66)
|+.|.+.|++ +|. ...+|||+.|.+..... .+|.||++++-... -+.-+.++
T Consensus 31 ArqL~~~G~~V~VLEA---RdRvGGRI~t~~~~~~~-~vd~Gas~~~g~~~npl~~l~~q 86 (501)
T KOG0029|consen 31 ARQLQDFGFDVLVLEA---RDRVGGRIYTFKSEGGD-HVDLGASVLTGVYNNPLALLSKQ 86 (501)
T ss_pred HHHHHHcCCceEEEec---cCCcCceeEEEecCCCC-eeecCCceecCcCccHHHHHHHH
Confidence 8999999999 999 99999999999998765 59999999986554 34333333
No 18
>TIGR02732 zeta_caro_desat carotene 7,8-desaturase. Carotene 7,8-desaturase, also called zeta-carotene desaturase, catalyzes multiple steps in the pathway from geranylgeranyl-PP to all-trans-lycopene in plants and cyanobacteria. A similar enzyme and pathway is found in the green sulfur bacterium Chlorobium tepidum.
Probab=96.90 E-value=0.0015 Score=49.08 Aligned_cols=52 Identities=15% Similarity=0.112 Sum_probs=43.7
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceee-cCCCCeeecccCceeeeCCHHHHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRM-IRPQPQIFGHAAQFITVNNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr-~~~~~~~~DhGAqyft~~~~~f~~~v~~~ 58 (66)
|..|+++|++ ||+ +..+|||+.|-. .++. .+|+|.+.|....+.+.++++++
T Consensus 15 A~~L~~~G~~v~v~E~---~~~~GG~~~~~~~~~g~--~~d~G~~~~~~~~~~~~~~~~~l 70 (474)
T TIGR02732 15 AVELVDAGHEVDIYES---RSFIGGKVGSWVDGDGN--HIEMGLHVFFGCYANLFRLMKKV 70 (474)
T ss_pred HHHHHHCCCcEEEEEe---cCCCCceeeeeecCCCc--eEeeceEEecCchHHHHHHHHHc
Confidence 6789999988 999 999999999953 3443 69999999988888888888775
No 19
>PLN02676 polyamine oxidase
Probab=96.66 E-value=0.0026 Score=48.12 Aligned_cols=51 Identities=24% Similarity=0.333 Sum_probs=38.8
Q ss_pred hhHHHHCCC-c---cccccCCCCcccccceeecCCCCeeecccCceeee----CCHHHHHHHHH
Q 042631 2 ADYLRSRGV-R---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITV----NNSRFCLLING 57 (66)
Q Consensus 2 A~~L~~~G~-~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~----~~~~f~~~v~~ 57 (66)
|..|+++|+ + +|+ ...+|||+.|....+. .+|+|++++.. ..+.+.+++++
T Consensus 42 a~~L~~~g~~~v~vlE~---~~~~GG~~~~~~~~g~--~~d~g~~~~~~~~~~~~~~~~~l~~~ 100 (487)
T PLN02676 42 AKTLSEAGIEDILILEA---TDRIGGRMRKANFAGV--SVELGANWVEGVGGPESNPIWELANK 100 (487)
T ss_pred HHHHHHcCCCcEEEecC---CCCCCCcceeecCCCe--EEecCCEEEEcccCcccChHHHHHHh
Confidence 678999997 4 999 9999999999877554 69999999953 33344445443
No 20
>PLN02612 phytoene desaturase
Probab=96.64 E-value=0.0042 Score=47.80 Aligned_cols=52 Identities=17% Similarity=0.226 Sum_probs=43.6
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeec-CCCCeeecccCceeeeCCHHHHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMI-RPQPQIFGHAAQFITVNNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~-~~~~~~~DhGAqyft~~~~~f~~~v~~~ 58 (66)
|..|.++|++ +|+ ..-+||++.|-+. ++. .+|.|++.|....|.+.++++++
T Consensus 109 a~~l~~~g~~~~~~e~---~~~~gG~~~s~~~~~G~--~~D~G~h~~~g~~~~~~~ll~el 164 (567)
T PLN02612 109 AKYLADAGHKPILLEA---RDVLGGKVAAWKDEDGD--WYETGLHIFFGAYPNVQNLFGEL 164 (567)
T ss_pred HHHHHhcCCeEEEEec---CCCCCCcceeeEcCCCC--EEcCCceEEeCCCchHHHHHHHh
Confidence 6788999988 999 8889999998553 333 69999999998888888888876
No 21
>PLN02529 lysine-specific histone demethylase 1
Probab=96.15 E-value=0.0081 Score=48.38 Aligned_cols=53 Identities=21% Similarity=0.241 Sum_probs=39.8
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCC--CeeecccCceeeeCCHH-HHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQ--PQIFGHAAQFITVNNSR-FCLLING 57 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~--~~~~DhGAqyft~~~~~-f~~~v~~ 57 (66)
|+.|+++|++ ||+ ..-+|||+.|.+.... ...||.||++++-.... +..+.++
T Consensus 176 A~~l~~~g~~v~v~E~---~~~~GG~~~t~~~~~~g~~~~~DlGaswi~g~~~npl~~la~~ 234 (738)
T PLN02529 176 ARQLLSFGFKVVVLEG---RNRPGGRVYTQKMGRKGQFAAVDLGGSVITGIHANPLGVLARQ 234 (738)
T ss_pred HHHHHHcCCcEEEEec---CccCcCceeeecccCCCCceEEecCCeeccccccchHHHHHHH
Confidence 7889999988 999 9999999999987522 13699999999854321 4344443
No 22
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=95.96 E-value=0.0096 Score=48.51 Aligned_cols=53 Identities=21% Similarity=0.260 Sum_probs=40.8
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCC--eeecccCceeeeCC-HHHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQP--QIFGHAAQFITVNN-SRFCLLING 57 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~--~~~DhGAqyft~~~-~~f~~~v~~ 57 (66)
|..|.+.|++ +|+ ...+|||+.|....+.. ..+|+|+++++-.. .-+..++++
T Consensus 254 A~~L~~~g~~v~v~E~---~~r~GGr~~t~~~~g~~~~~~~d~Gas~i~g~~~npl~~l~~~ 312 (808)
T PLN02328 254 ARQLLSMGFKVVVLEG---RARPGGRVKTMKMKGDGVVAAADLGGSVLTGINGNPLGVLARQ 312 (808)
T ss_pred HHHHHHCCCcEEEEec---cccCCCcccccccCCCCcceeccCCceeecCCCccHHHHHHHH
Confidence 6788999988 999 99999999999886532 36899999998643 234445543
No 23
>PLN03000 amine oxidase
Probab=95.75 E-value=0.019 Score=47.32 Aligned_cols=53 Identities=15% Similarity=0.224 Sum_probs=40.9
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCC--CeeecccCceeeeCCHH-HHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQ--PQIFGHAAQFITVNNSR-FCLLING 57 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~--~~~~DhGAqyft~~~~~-f~~~v~~ 57 (66)
|+.|.+.|++ +|+ ...+|||+.|.+..+. ...+|.||++++-.... +..++++
T Consensus 200 A~~L~~~G~~V~VlE~---~~riGGRi~T~~~~g~~~~~~~DlGas~i~g~~~npl~~L~~q 258 (881)
T PLN03000 200 ARQLMRFGFKVTVLEG---RKRPGGRVYTKKMEANRVGAAADLGGSVLTGTLGNPLGIIARQ 258 (881)
T ss_pred HHHHHHCCCcEEEEEc---cCcCCCCcceecccCCCCceEeecCCeEEeCCCccHHHHHHHH
Confidence 6789999988 999 9999999999997642 24699999999876542 3334444
No 24
>COG1231 Monoamine oxidase [Amino acid transport and metabolism]
Probab=95.39 E-value=0.019 Score=44.42 Aligned_cols=51 Identities=18% Similarity=0.234 Sum_probs=42.6
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLING 57 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~ 57 (66)
|..|.++|++ +|. ...+|||+-|-|..+. ..|.|-||+....+.+..+.++
T Consensus 23 A~eL~kaG~~v~ilEa---r~r~GGR~~t~r~~~~--~~d~gG~~i~p~~~~~l~~~k~ 76 (450)
T COG1231 23 AYELKKAGYQVQILEA---RDRVGGRSLTARAGGE--YTDLGGQYINPTHDALLAYAKE 76 (450)
T ss_pred HHHHhhcCcEEEEEec---cCCcCceeEEEeccce--eeccCCcccCccchhhhhhHHh
Confidence 6789999998 999 9999999999998433 6899999999977776666543
No 25
>TIGR02730 carot_isom carotene isomerase. Members of this family, including sll0033 (crtH) of Synechocystis sp. PCC 6803, catalyze a cis-trans isomerization of carotenes to the all-trans lycopene, a reaction that can also occur non-enzymatically in light through photoisomerization.
Probab=95.14 E-value=0.028 Score=41.95 Aligned_cols=40 Identities=23% Similarity=0.129 Sum_probs=34.7
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeee
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITV 46 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~ 46 (66)
|..|+++|++ +|| ..-+||+++|-..++. .||.|+-+++-
T Consensus 16 A~~La~~G~~V~vlE~---~~~~GG~~~~~~~~G~--~fd~g~~~~~~ 58 (493)
T TIGR02730 16 ATQLAVKGAKVLVLER---YLIPGGSAGYFEREGY--RFDVGASMIFG 58 (493)
T ss_pred HHHHHHCCCcEEEEEC---CCCCCCceeEeccCCE--EEEecchhhee
Confidence 6789999988 999 9999999999877655 79999998763
No 26
>KOG0685 consensus Flavin-containing amine oxidase [Coenzyme transport and metabolism]
Probab=94.82 E-value=0.047 Score=42.77 Aligned_cols=50 Identities=22% Similarity=0.302 Sum_probs=38.6
Q ss_pred hhHHHHCCCc----cccccCCCCcccccceeecCCCCeeecccCceeee-CCHHHHHHHH
Q 042631 2 ADYLRSRGVR----FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITV-NNSRFCLLIN 56 (66)
Q Consensus 2 A~~L~~~G~~----fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~-~~~~f~~~v~ 56 (66)
|.+|.++|+. ||. +..+|||.-|-.-.+. .+|.||||+.= .+...-++++
T Consensus 37 A~rLle~gf~~~~IlEa---~dRIGGRI~ti~~~d~--~ielGAqwihG~~gNpVY~la~ 91 (498)
T KOG0685|consen 37 ATRLLENGFIDVLILEA---SDRIGGRIHTIPFADG--VIELGAQWIHGEEGNPVYELAK 91 (498)
T ss_pred HHHHHHhCCceEEEEEe---ccccCceEeeEEcCCC--eEeecceeecCCCCChHHHHHH
Confidence 6778877866 898 9999999999888777 69999999975 3333334444
No 27
>COG1232 HemY Protoporphyrinogen oxidase [Coenzyme metabolism]
Probab=94.58 E-value=0.056 Score=41.44 Aligned_cols=52 Identities=25% Similarity=0.378 Sum_probs=44.2
Q ss_pred hhHHHHCC--Cc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHHH
Q 042631 2 ADYLRSRG--VR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~G--~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~~ 58 (66)
|..|++++ ++ ||| +.-+||-+.|-..++. .||.|+..|-.+.++..+++.+|
T Consensus 16 Ay~L~k~~p~~~i~lfE~---~~r~GG~l~T~~~~G~--~~e~G~~~f~~~~~~~l~li~eL 72 (444)
T COG1232 16 AYRLQKAGPDVEVTLFEA---DDRVGGLLRTVKIDGF--LFERGPHHFLARKEEILDLIKEL 72 (444)
T ss_pred HHHHHHhCCCCcEEEEec---CCCCCceEEEEeeCCE--EEeechhheecchHHHHHHHHHh
Confidence 67899999 66 999 9999999999988776 69999999988867777777665
No 28
>PLN02487 zeta-carotene desaturase
Probab=94.57 E-value=0.064 Score=41.91 Aligned_cols=53 Identities=15% Similarity=0.127 Sum_probs=42.7
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~~ 58 (66)
|..|.++|++ ||+ ...+||++.|-+.... ..+|.|...|.-..+.+.++++++
T Consensus 91 a~~L~~~g~~v~i~E~---~~~~gG~~~s~~~~~g-~~~e~G~h~~~~~~~~~~~ll~~L 146 (569)
T PLN02487 91 AVELLDQGHEVDIYES---RPFIGGKVGSFVDKNG-NHIEMGLHVFFGCYNNLFRLMKKV 146 (569)
T ss_pred HHHHHhCCCeeEEEec---CCCCCCceeeeeecCC-cEEecceeEecCCcHHHHHHHHhc
Confidence 6789999988 999 9999999998863222 268999999987778788888765
No 29
>TIGR00031 UDP-GALP_mutase UDP-galactopyranose mutase. The gene is known as glf, ceoA, and rfbD. It is known experimentally in E. coli, Mycobacterium tuberculosis, and Klebsiella pneumoniae.
Probab=94.16 E-value=0.082 Score=39.42 Aligned_cols=56 Identities=18% Similarity=0.240 Sum_probs=43.7
Q ss_pred ChhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHHHHh
Q 042631 1 IADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLINGWLE 60 (66)
Q Consensus 1 ~A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~~~~ 60 (66)
+|..|++.|.+ +|| ...+||.+.|....+. ...+.|+..|...++.+..+++++.+
T Consensus 16 aA~~La~~G~~V~viEk---~~~iGG~~~~~~~~g~-~~~~~G~h~f~t~~~~v~~~~~~~~~ 74 (377)
T TIGR00031 16 LANILAQLNKRVLVVEK---RNHIGGNCYDEVDETI-LFHQYGPHIFHTNNQYVWDYISPFFE 74 (377)
T ss_pred HHHHHHhCCCeEEEEec---CCCCCCceeeecCCCc-eEEeecceeEecCcHHHHHHHHhhcc
Confidence 37788888877 999 9999999998765432 23589999998888887777777643
No 30
>COG3349 Uncharacterized conserved protein [Function unknown]
Probab=90.66 E-value=0.33 Score=37.92 Aligned_cols=52 Identities=19% Similarity=0.176 Sum_probs=43.2
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHH
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLING 57 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~ 57 (66)
|..|+++|++ +|. +.-+||.++|=+..+.. ...||--.|.-..+-.-+++++
T Consensus 16 a~~La~~g~~vt~~ea---~~~~GGk~~s~~~~dg~-~~E~glh~f~~~Y~n~~~ll~~ 70 (485)
T COG3349 16 AYELADAGYDVTLYEA---RDRLGGKVASWRDSDGN-HVEHGLHVFFGCYYNLLTLLKE 70 (485)
T ss_pred HHHHHhCCCceEEEec---cCccCceeeeeecCCCC-eeeeeeEEechhHHHHHHHhhh
Confidence 6789999998 999 99999999998886655 6999999998877655555554
No 31
>PLN02976 amine oxidase
Probab=90.53 E-value=0.28 Score=43.24 Aligned_cols=41 Identities=24% Similarity=0.286 Sum_probs=33.8
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecCCCCeeecccCceeee
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITV 46 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~ 46 (66)
|..|.++|++ ||+ +..+|||+.|.+.... +.+|+|+++++-
T Consensus 709 A~~L~~~G~~V~VlEa---~~~vGGri~t~~~~~g-~pvDlGas~i~G 752 (1713)
T PLN02976 709 ARHLQRQGFSVTVLEA---RSRIGGRVYTDRSSLS-VPVDLGASIITG 752 (1713)
T ss_pred HHHHHHCCCcEEEEee---ccCCCCceeeccccCC-ceeccCcEEEec
Confidence 6788999988 999 9999999999875322 368999999974
No 32
>PTZ00363 rab-GDP dissociation inhibitor; Provisional
Probab=81.98 E-value=1.4 Score=33.42 Aligned_cols=48 Identities=17% Similarity=0.236 Sum_probs=35.6
Q ss_pred ChhHHHHCCCc---cccccCCCCcccccceeecCC------------------CCeeecccCceeeeCCHHH
Q 042631 1 IADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRP------------------QPQIFGHAAQFITVNNSRF 51 (66)
Q Consensus 1 ~A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~------------------~~~~~DhGAqyft~~~~~f 51 (66)
+|..|+.+|.+ +|+ +.-.|||.+|-+... ..+.+|...+++-++++-.
T Consensus 19 lAa~Ls~~GkkVLhlD~---n~~yGG~~as~~l~~l~~~f~~~~~~~~~~~~~r~~~iDL~Pk~l~~~G~lv 87 (443)
T PTZ00363 19 LSGLLSVNGKKVLHMDR---NPYYGGESASLNLTQLYKKFKPGETPPESLGRNRDWNVDLIPKFIMASGELV 87 (443)
T ss_pred HHhhhhhCCCEEEEecC---CCCcCcccccccHHHHHHhhcccCCCchhcccccccccccCCeeeecCChHH
Confidence 47889999988 999 999999999864321 1245777777777776543
No 33
>PF02817 E3_binding: e3 binding domain; InterPro: IPR004167 A small domain of the E2 subunit of 2-oxo-acid dehydrogenases that is responsible for the binding of the E3 subunit. Proteins containing this domain include the branched-chain alpha-keto acid dehydrogenase complex of bacteria, which catalyses the overall conversion of alpha-keto acids to acyl-CoA and carbon dioxide; and the E-3 binding protein of eukaryotic pyruvate dehydrogenase.; GO: 0016746 transferase activity, transferring acyl groups, 0008152 metabolic process; PDB: 1BBL_A 1W4H_A 1BAL_A 2WXC_A 2BTH_A 2BTG_A 2CYU_A 2EQ7_C 2EQ8_C 3RNM_E ....
Probab=79.87 E-value=2.3 Score=22.37 Aligned_cols=25 Identities=32% Similarity=0.603 Sum_probs=15.7
Q ss_pred hhHHH-HCCCccccccCCCCcccccce
Q 042631 2 ADYLR-SRGVRFEDIWGNHGLGGRMRS 27 (66)
Q Consensus 2 A~~L~-~~G~~fEk~~g~rg~GGRmaT 27 (66)
|+.|+ +.|+++++|.|+ |++||..-
T Consensus 9 ar~la~e~gidl~~v~gt-G~~GrI~k 34 (39)
T PF02817_consen 9 ARKLAAELGIDLSQVKGT-GPGGRITK 34 (39)
T ss_dssp HHHHHHHTT--GGGSSSS-STTSBBCH
T ss_pred HHHHHHHcCCCccccccc-CCCCcEeH
Confidence 34444 688887777755 89998753
No 34
>PRK13977 myosin-cross-reactive antigen; Provisional
Probab=77.57 E-value=3.8 Score=32.67 Aligned_cols=52 Identities=13% Similarity=0.096 Sum_probs=34.6
Q ss_pred hhHHHHC----CCc---cccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHH
Q 042631 2 ADYLRSR----GVR---FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLING 57 (66)
Q Consensus 2 A~~L~~~----G~~---fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~ 57 (66)
|..|.+. |.+ ||| ..-+||++.+.........+|-|..+ ....+.+.++++.
T Consensus 38 A~~L~~dg~~~G~~VtIlEk---~~~~GG~~~~~~~~~~Gy~~~~G~~~-~~~y~~l~~ll~~ 96 (576)
T PRK13977 38 AVFLIRDGQMPGENITILEE---LDVPGGSLDGAGNPEKGYVARGGREM-ENHFECLWDLFRS 96 (576)
T ss_pred HHHHHHccCCCCCcEEEEeC---CCCCCCCccCcccccCCEEEECCCCc-cchHHHHHHHHHh
Confidence 5577775 445 999 99999999875533333468888664 4445566666544
No 35
>KOG1276 consensus Protoporphyrinogen oxidase [Coenzyme transport and metabolism]
Probab=66.36 E-value=13 Score=29.47 Aligned_cols=53 Identities=25% Similarity=0.339 Sum_probs=41.0
Q ss_pred hhHHHHCCCc-----cccccCCCCcccccceeecCCCCeeecccCceeeeCCH---HHHHHHHHH
Q 042631 2 ADYLRSRGVR-----FEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNS---RFCLLINGW 58 (66)
Q Consensus 2 A~~L~~~G~~-----fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~---~f~~~v~~~ 58 (66)
|..|+.++.+ ||+ +..+||-..|-|. ++.+.|+-|..-|+..+| +...+|++|
T Consensus 27 ay~L~r~~p~~~i~l~Ea---~~RvGGwirS~r~-~ng~ifE~GPrtlrpag~~g~~~l~lv~dL 87 (491)
T KOG1276|consen 27 AYYLARLGPDVTITLFEA---SPRVGGWIRSDRM-QNGFIFEEGPRTLRPAGPGGAETLDLVSDL 87 (491)
T ss_pred HHHHHhcCCCceEEEEec---CCcccceeeeccC-CCceeeccCCCccCcCCcchhHHHHHHHHc
Confidence 5678888755 999 9999999999332 233579999999999888 566666665
No 36
>COG1148 HdrA Heterodisulfide reductase, subunit A and related polyferredoxins [Energy production and conversion]
Probab=63.78 E-value=4.4 Score=32.72 Aligned_cols=24 Identities=33% Similarity=0.473 Sum_probs=21.4
Q ss_pred hhHHHHCCCc---cccccCCCCccccccee
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSR 28 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTR 28 (66)
|..|++.|+. .|| ..-+||||+.-
T Consensus 140 Al~La~~G~~v~LVEK---epsiGGrmak~ 166 (622)
T COG1148 140 ALELADMGFKVYLVEK---EPSIGGRMAKL 166 (622)
T ss_pred HHHHHHcCCeEEEEec---CCcccccHHhh
Confidence 5689999998 999 99999999864
No 37
>PF05678 VQ: VQ motif; InterPro: IPR008889 This short motif is found in a variety of plant proteins. These proteins vary greatly in length and are mostly composed of low complexity regions. They all conserve a short motif FXhVQChTG, where X is any amino acid and h is a hydrophobic amino acid. The function of this motif is uncertain, however one protein in this family has been found to bind the SigA sigma factor Q9LDH1 from SWISSPROT. It would seem plausible that this motif is needed for this activity and that this whole family might be involved in modulating plastid sigma factors.
Probab=61.05 E-value=9.8 Score=19.24 Aligned_cols=21 Identities=19% Similarity=0.238 Sum_probs=17.1
Q ss_pred CceeeeCCHHHHHHHHHHHhC
Q 042631 41 AQFITVNNSRFCLLINGWLER 61 (66)
Q Consensus 41 Aqyft~~~~~f~~~v~~~~~~ 61 (66)
..|+.++...|+++|++|-..
T Consensus 5 p~vi~~d~~~Fr~lVQ~LTG~ 25 (31)
T PF05678_consen 5 PTVIHTDPSNFRALVQRLTGA 25 (31)
T ss_pred CEEEEeCHHHHHHHHHHhHCc
Confidence 468888888999999998543
No 38
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=57.98 E-value=15 Score=30.75 Aligned_cols=22 Identities=36% Similarity=0.527 Sum_probs=18.8
Q ss_pred hhHHHHCCCc---cccccCCCCcccccc
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMR 26 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRma 26 (66)
|..|++.|++ ||+ ..-+||.|+
T Consensus 446 A~~La~~G~~VtV~E~---~~~~GG~l~ 470 (1006)
T PRK12775 446 AADLVKYGVDVTVYEA---LHVVGGVLQ 470 (1006)
T ss_pred HHHHHHcCCcEEEEec---CCCCcceee
Confidence 6789999988 999 888998765
No 39
>PRK12779 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Provisional
Probab=56.65 E-value=14 Score=30.82 Aligned_cols=22 Identities=45% Similarity=0.670 Sum_probs=19.4
Q ss_pred hhHHHHCCCc---cccccCCCCcccccc
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMR 26 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRma 26 (66)
|..|++.|++ ||+ ...+||-|.
T Consensus 322 A~~Lar~G~~VtVfE~---~~~~GG~l~ 346 (944)
T PRK12779 322 AYLLAVEGFPVTVFEA---FHDLGGVLR 346 (944)
T ss_pred HHHHHHCCCeEEEEee---CCCCCceEE
Confidence 6789999988 999 999999875
No 40
>COG0562 Glf UDP-galactopyranose mutase [Cell envelope biogenesis, outer membrane]
Probab=53.51 E-value=32 Score=26.41 Aligned_cols=55 Identities=18% Similarity=0.265 Sum_probs=43.5
Q ss_pred ChhHHHHCCCc---cccccCCCCcccccceeecCCCC-eeecccCceeeeCCHHHHHHHHHH
Q 042631 1 IADYLRSRGVR---FEDIWGNHGLGGRMRSRMIRPQP-QIFGHAAQFITVNNSRFCLLINGW 58 (66)
Q Consensus 1 ~A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~~~~-~~~DhGAqyft~~~~~f~~~v~~~ 58 (66)
||+.|++.|.. +|| ...+||-+=+..-+... ..=-+|+--|..++.+.-.+|...
T Consensus 16 ~A~~a~~~gk~VLIvek---R~HIGGNaYde~d~~tGIlvHkYGpHIFHT~~~~Vwdyv~~F 74 (374)
T COG0562 16 IAEVAAQLGKRVLIVEK---RNHIGGNAYDEADDQTGILVHKYGPHIFHTDNKRVWDYVNQF 74 (374)
T ss_pred HHHHHHHcCCEEEEEec---cccCCCccccccCCCCCeEEeeccCceeecCchHHHHHHhhh
Confidence 57888899987 999 99999999998865333 456789999999888666665543
No 41
>COG1759 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and metabolism]
Probab=46.03 E-value=26 Score=26.83 Aligned_cols=26 Identities=15% Similarity=0.364 Sum_probs=22.3
Q ss_pred cCceeeeCCH-HHHHHHHHHHhCCccc
Q 042631 40 AAQFITVNNS-RFCLLINGWLERGLVR 65 (66)
Q Consensus 40 GAqyft~~~~-~f~~~v~~~~~~g~v~ 65 (66)
|--||.++++ +|.+.++.+++.|++.
T Consensus 163 gRGyFiA~s~eef~ek~e~l~~~gvi~ 189 (361)
T COG1759 163 GRGYFIASSPEEFYEKAERLLKRGVIT 189 (361)
T ss_pred CceEEEEcCHHHHHHHHHHHHHcCCcc
Confidence 4569999887 8999999999999873
No 42
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=43.85 E-value=14 Score=21.02 Aligned_cols=26 Identities=8% Similarity=0.121 Sum_probs=18.7
Q ss_pred cCceeeeCCHHHHHHHHHHHhCCccc
Q 042631 40 AAQFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 40 GAqyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
+++++..+.++++++++.+.+.|.+.
T Consensus 27 ~~~~~~~s~~eL~~fL~~lv~e~~L~ 52 (60)
T PF08672_consen 27 DPGGYDISLEELQEFLDRLVEEGKLE 52 (60)
T ss_dssp GG--TT--HHHHHHHHHHHHHTTSEE
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCcEE
Confidence 45778888899999999999998763
No 43
>PF12342 DUF3640: Protein of unknown function (DUF3640) ; InterPro: IPR022101 This entry defines the N-terminal domain of the polyprotein of GB virus C; its function is not known.
Probab=42.91 E-value=13 Score=18.38 Aligned_cols=13 Identities=23% Similarity=0.268 Sum_probs=10.4
Q ss_pred cccccCCCCcccc
Q 042631 12 FEDIWGNHGLGGR 24 (66)
Q Consensus 12 fEk~~g~rg~GGR 24 (66)
+||=|+++|+.||
T Consensus 12 vdkdqwG~gv~G~ 24 (26)
T PF12342_consen 12 VDKDQWGPGVHGR 24 (26)
T ss_pred hcccccCCCcCCC
Confidence 6666789999887
No 44
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=39.76 E-value=12 Score=20.21 Aligned_cols=24 Identities=25% Similarity=0.400 Sum_probs=17.8
Q ss_pred ceeeeCCHHHHHHHHHHHhCCccc
Q 042631 42 QFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 42 qyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
+++..+.+...+.|+.|.+.|+|.
T Consensus 26 ~~~~~~~~~vs~~i~~L~~~glv~ 49 (68)
T PF13463_consen 26 ERLGISKSTVSRIIKKLEEKGLVE 49 (68)
T ss_dssp HHTT--HHHHHHHHHHHHHTTSEE
T ss_pred HHHCcCHHHHHHHHHHHHHCCCEE
Confidence 445556678889999999999983
No 45
>TIGR01316 gltA glutamate synthase (NADPH), homotetrameric. This protein is homologous to the small subunit of NADPH and NADH forms of glutamate synthase as found in eukaryotes and some bacteria. This protein is found in numerous species having no homolog of the glutamate synthase large subunit. The prototype of the family, from Pyrococcus sp. KOD1, was shown to be active as a homotetramer and to require NADPH.
Probab=39.59 E-value=51 Score=24.58 Aligned_cols=22 Identities=36% Similarity=0.456 Sum_probs=18.4
Q ss_pred hhHHHHCCCc---cccccCCCCcccccc
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMR 26 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRma 26 (66)
|..|++.|++ ||+ ...+||-|.
T Consensus 149 A~~l~~~G~~V~vie~---~~~~GG~l~ 173 (449)
T TIGR01316 149 ASELAKAGHSVTVFEA---LHKPGGVVT 173 (449)
T ss_pred HHHHHHCCCcEEEEec---CCCCCcEee
Confidence 6788899988 999 888998764
No 46
>PF08410 DUF1737: Domain of unknown function (DUF1737); InterPro: IPR013619 This domain of unknown function is found at the N terminus of bacterial and viral hypothetical proteins.
Probab=38.81 E-value=48 Score=18.72 Aligned_cols=21 Identities=29% Similarity=0.523 Sum_probs=16.8
Q ss_pred eeee-CCHHHHHHHHHHHhCCc
Q 042631 43 FITV-NNSRFCLLINGWLERGL 63 (66)
Q Consensus 43 yft~-~~~~f~~~v~~~~~~g~ 63 (66)
++|. ++.+|++.|.+.++.|+
T Consensus 8 ~lt~~d~~~fc~rVt~aL~~GW 29 (54)
T PF08410_consen 8 VLTGPDDSAFCHRVTEALNEGW 29 (54)
T ss_pred EEECCChHHHHHHHHHHHHcCC
Confidence 5665 44589999999999987
No 47
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=37.97 E-value=17 Score=18.17 Aligned_cols=25 Identities=24% Similarity=0.312 Sum_probs=19.5
Q ss_pred CceeeeCCHHHHHHHHHHHhCCccc
Q 042631 41 AQFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 41 Aqyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
++.|.++.+.+...++.|.+.|+|.
T Consensus 21 ~~~l~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 21 AELLGVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3455667778899999999999874
No 48
>PF01946 Thi4: Thi4 family; PDB: 1RP0_A 3FPZ_B 3JSK_K.
Probab=36.92 E-value=23 Score=25.52 Aligned_cols=58 Identities=19% Similarity=0.357 Sum_probs=30.3
Q ss_pred hhHHHHCCCc---cccccCCCCcccccc------eeec-CCCC--------e-eecccCceeeeCCHHHHH-HHHHHHhC
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMR------SRMI-RPQP--------Q-IFGHAAQFITVNNSRFCL-LINGWLER 61 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRma------TRr~-~~~~--------~-~~DhGAqyft~~~~~f~~-~v~~~~~~ 61 (66)
|..|+++|++ ||+ +..+||.|- ++-+ .... . .-|.+--|++++..+|.+ ++..-+++
T Consensus 33 A~~La~~g~kV~v~E~---~~~~GGg~~~Gg~lf~~iVVq~~a~~iL~elgi~y~~~~~g~~v~d~~~~~s~L~s~a~~a 109 (230)
T PF01946_consen 33 AYYLAKAGLKVAVIER---KLSPGGGMWGGGMLFNKIVVQEEADEILDELGIPYEEYGDGYYVADSVEFTSTLASKAIDA 109 (230)
T ss_dssp HHHHHHHTS-EEEEES---SSS-BTTTTS-CTT---EEEETTTHHHHHHHT---EE-SSEEEES-HHHHHHHHHHHHHTT
T ss_pred HHHHHHCCCeEEEEec---CCCCCccccccccccchhhhhhhHHHHHHhCCceeEEeCCeEEEEcHHHHHHHHHHHHhcC
Confidence 7889999998 998 777776653 3222 1100 0 224454466666667766 45555555
Q ss_pred C
Q 042631 62 G 62 (66)
Q Consensus 62 g 62 (66)
|
T Consensus 110 G 110 (230)
T PF01946_consen 110 G 110 (230)
T ss_dssp T
T ss_pred C
Confidence 4
No 49
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=36.66 E-value=19 Score=18.48 Aligned_cols=25 Identities=20% Similarity=0.218 Sum_probs=20.4
Q ss_pred CceeeeCCHHHHHHHHHHHhCCccc
Q 042631 41 AQFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 41 Aqyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
|+.|.++.+...+.++.|.+.|+|.
T Consensus 27 a~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 27 AAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 5566777788999999999999874
No 50
>COG2072 TrkA Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]
Probab=36.41 E-value=21 Score=26.89 Aligned_cols=55 Identities=22% Similarity=0.334 Sum_probs=34.5
Q ss_pred ChhHHHHCCCc----cccccCCCCcccc-----cceeecCCCCeeecccCceeeeC-C---H---HHHHHHHHHHh
Q 042631 1 IADYLRSRGVR----FEDIWGNHGLGGR-----MRSRMIRPQPQIFGHAAQFITVN-N---S---RFCLLINGWLE 60 (66)
Q Consensus 1 ~A~~L~~~G~~----fEk~~g~rg~GGR-----maTRr~~~~~~~~DhGAqyft~~-~---~---~f~~~v~~~~~ 60 (66)
+|..|+++|+. ||| ...+||= --+-+.+.. .+..+-+|++.. . + ....++.++++
T Consensus 23 aa~~L~~~g~~~~~i~Ek---~~~~Gg~W~~~ry~~l~~~~p--~~~~~~~~~p~~~~~~~~~~~~~~~y~~~~~~ 93 (443)
T COG2072 23 AAYALKQAGVPDFVIFEK---RDDVGGTWRYNRYPGLRLDSP--KWLLGFPFLPFRWDEAFAPFAEIKDYIKDYLE 93 (443)
T ss_pred HHHHHHHcCCCcEEEEEc---cCCcCCcchhccCCceEECCc--hheeccCCCccCCcccCCCcccHHHHHHHHHH
Confidence 47899999988 999 9899986 222233332 345577777763 1 1 24555555544
No 51
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=36.10 E-value=24 Score=19.91 Aligned_cols=28 Identities=11% Similarity=0.080 Sum_probs=20.2
Q ss_pred cccCceeeeCCHHHHHHHHHHHhCCccc
Q 042631 38 GHAAQFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 38 DhGAqyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
++=.+.|.++.+.|.+.++.|++.+.+.
T Consensus 34 ~~l~~~f~~~~~~ik~~Ie~LIekeyi~ 61 (68)
T PF10557_consen 34 EELKKRFPPSVSDIKKRIESLIEKEYIE 61 (68)
T ss_dssp HHTTTTS---HHHHHHHHHHHHHTTSEE
T ss_pred HHhcCCcCCCHHHHHHHHHHHHHhhhhh
Confidence 3334478899999999999999999875
No 52
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=34.83 E-value=13 Score=20.95 Aligned_cols=25 Identities=12% Similarity=0.316 Sum_probs=18.2
Q ss_pred CceeeeCCHHHHHHHHHHHhCCccc
Q 042631 41 AQFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 41 Aqyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
|.-|.++.+....+++.|+..|.|+
T Consensus 21 a~~~~~s~~~ve~mL~~l~~kG~I~ 45 (69)
T PF09012_consen 21 AREFGISPEAVEAMLEQLIRKGYIR 45 (69)
T ss_dssp HHHTT--HHHHHHHHHHHHCCTSCE
T ss_pred HHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 3445566678899999999999875
No 53
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=34.68 E-value=13 Score=20.72 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=20.4
Q ss_pred CceeeeCCHHHHHHHHHHHhCCccc
Q 042631 41 AQFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 41 Aqyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
|+.+.++.|..-+.+..|.+.|+|.
T Consensus 29 A~~L~vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 29 AERLGVSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp HHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHCCChHHHHHHHHHHHHCCCEE
Confidence 5677788889999999999999874
No 54
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=33.90 E-value=20 Score=17.79 Aligned_cols=24 Identities=8% Similarity=0.264 Sum_probs=18.8
Q ss_pred ceeeeCCHHHHHHHHHHHhCCccc
Q 042631 42 QFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 42 qyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
..+..+.+...+.++.|.+.|++.
T Consensus 16 ~~l~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 16 ELLGLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEE
Confidence 445556678889999999999874
No 55
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=33.86 E-value=22 Score=18.57 Aligned_cols=24 Identities=17% Similarity=0.181 Sum_probs=19.2
Q ss_pred ceeeeCCHHHHHHHHHHHhCCccc
Q 042631 42 QFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 42 qyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
+.|.++.+...+.+..|.+.|+|.
T Consensus 33 ~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 33 EELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEE
Confidence 345667778899999999999874
No 56
>PF04468 PSP1: PSP1 C-terminal conserved region; InterPro: IPR007557 The yeast polymerase suppressor 1 (PSP1) protein partially suppresses mutations in DNA polymerases alpha and delta []. The C-terminal half of PSP1 contains a domain, which is also found in several hypothetical proteins from both eukaryotic and prokaryotic sources: Crithidia fasciculata RBP45 and RBP33, subunits of the cycling sequence binding protein (CSBP) II. RBP45 and RBP33 proteins bind specifically to the cycling sequences present in several mRNAs that accumulate periodically during the cell cycle. RBP45 and RBP33 are phosphoproteins, which are phosphorylated differentially during progression through the cell cycle. Hypothetical proteins with high sequence similarity have been identified in other kinetoplastid organisms []. Bacillus subtilis yaaT protein, which plays a significant role in phosphorelay during initiation of sporulation. It is possible that the yaaT protein is also related to DNA replication. The sequence of the yaaT protein is widely conserved in prokaryotes (bacteria and archaea), but the functions of the protein are unknown []. The actual biological significance of the PSP1 C-terminal domain has not yet been clearly established.
Probab=33.78 E-value=41 Score=20.06 Aligned_cols=18 Identities=17% Similarity=0.289 Sum_probs=13.5
Q ss_pred eeeeCC-HHHHHHHHHHHh
Q 042631 43 FITVNN-SRFCLLINGWLE 60 (66)
Q Consensus 43 yft~~~-~~f~~~v~~~~~ 60 (66)
||++.+ .+|.+++.+|..
T Consensus 59 yy~a~~rvDFR~Lvr~L~~ 77 (88)
T PF04468_consen 59 YYTAESRVDFRELVRDLAR 77 (88)
T ss_pred EEEeCCcCcHHHHHHHHHH
Confidence 566654 489999999865
No 57
>PF00743 FMO-like: Flavin-binding monooxygenase-like; InterPro: IPR020946 Flavin-containing monooxygenases (FMOs) constitute a family of xenobiotic-metabolising enzymes []. Using an NADPH cofactor and FAD prosthetic group, these microsomal proteins catalyse the oxygenation of nucleophilic nitrogen, sulphur, phosphorous and selenium atoms in a range of structurally diverse compounds. FMOs have been implicated in the metabolism of a number of pharmaceuticals, pesticides and toxicants. In man, lack of hepatic FMO-catalysed trimethylamine metabolism results in trimethylaminuria (fish odour syndrome). Five mammalian forms of FMO are now known and have been designated FMO1-FMO5 [, , , , ]. This is a recent nomenclature based on comparison of amino acid sequences, and has been introduced in an attempt to eliminate confusion inherent in multiple, laboratory-specific designations and tissue-based classifications []. Following the determination of the complete nucleotide sequence of Saccharomyces cerevisiae (Baker's yeast) [], a novel gene was found to encode a protein with similarity to mammalian monooygenases.; GO: 0004499 flavin-containing monooxygenase activity, 0050660 flavin adenine dinucleotide binding, 0050661 NADP binding, 0055114 oxidation-reduction process; PDB: 2GVC_E 1VQW_B 2GV8_B 2XVI_B 2XVH_B 2XLS_A 2XLR_A 2XLU_D 2XLP_B 2XVE_A ....
Probab=33.74 E-value=28 Score=27.06 Aligned_cols=22 Identities=36% Similarity=0.647 Sum_probs=18.4
Q ss_pred hhHHHHCCCc---cccccCCCCcccccc
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMR 26 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRma 26 (66)
|+.|.+.|++ ||| +..+||--.
T Consensus 17 ~k~l~e~g~~~~~fE~---~~~iGG~W~ 41 (531)
T PF00743_consen 17 AKNLLEEGLEVTCFEK---SDDIGGLWR 41 (531)
T ss_dssp HHHHHHTT-EEEEEES---SSSSSGGGC
T ss_pred HHHHHHCCCCCeEEec---CCCCCccCe
Confidence 5788899998 999 999999765
No 58
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=33.23 E-value=16 Score=20.18 Aligned_cols=25 Identities=12% Similarity=0.372 Sum_probs=19.4
Q ss_pred CceeeeCCHHHHHHHHHHHhCCccc
Q 042631 41 AQFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 41 Aqyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
|.+..++.+.+.+.++.|.+.|++.
T Consensus 35 A~~~g~sr~tv~r~l~~l~~~g~I~ 59 (76)
T PF13545_consen 35 ADMLGVSRETVSRILKRLKDEGIIE 59 (76)
T ss_dssp HHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 4455556668889999999999874
No 59
>PRK12831 putative oxidoreductase; Provisional
Probab=32.83 E-value=81 Score=23.76 Aligned_cols=22 Identities=36% Similarity=0.439 Sum_probs=18.4
Q ss_pred hhHHHHCCCc---cccccCCCCcccccc
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMR 26 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRma 26 (66)
|..|++.|++ ||+ ..-+||-+.
T Consensus 156 A~~l~~~G~~V~v~e~---~~~~GG~l~ 180 (464)
T PRK12831 156 AGDLAKMGYDVTIFEA---LHEPGGVLV 180 (464)
T ss_pred HHHHHhCCCeEEEEec---CCCCCCeee
Confidence 6788899988 999 888998774
No 60
>COG2907 Predicted NAD/FAD-binding protein [General function prediction only]
Probab=32.69 E-value=79 Score=24.84 Aligned_cols=46 Identities=15% Similarity=0.138 Sum_probs=33.7
Q ss_pred Cc-cccccCCCCcccccceeecC--CCCeeecccCceeee-CCHHHHHHHHHH
Q 042631 10 VR-FEDIWGNHGLGGRMRSRMIR--PQPQIFGHAAQFITV-NNSRFCLLINGW 58 (66)
Q Consensus 10 ~~-fEk~~g~rg~GGRmaTRr~~--~~~~~~DhGAqyft~-~~~~f~~~v~~~ 58 (66)
++ ||. .+.+||+..|-..+ +....+|-|---++- +.|-+.++.+++
T Consensus 33 VTLfEA---~~rlGGha~Tv~~~~d~~g~~vDtGfiVyn~~tYpnl~~Lf~~i 82 (447)
T COG2907 33 VTLFEA---DRRLGGHANTVAGNTDGGGVFVDTGFIVYNERTYPNLTRLFKTI 82 (447)
T ss_pred eEEEec---cccccCccceeeccccCCceeecceeEEecCCCcchHHHHHHHc
Confidence 44 999 99999999998743 333568888655543 667788887775
No 61
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=31.97 E-value=38 Score=19.94 Aligned_cols=15 Identities=27% Similarity=0.561 Sum_probs=12.4
Q ss_pred HHHHHHHHhCCcccC
Q 042631 52 CLLINGWLERGLVRP 66 (66)
Q Consensus 52 ~~~v~~~~~~g~v~~ 66 (66)
.+++.+|.+.|+|.|
T Consensus 14 ~~~l~~lve~Gli~p 28 (84)
T PF13591_consen 14 PEFLRELVEEGLIEP 28 (84)
T ss_pred HHHHHHHHHCCCeee
Confidence 367899999999876
No 62
>PRK12769 putative oxidoreductase Fe-S binding subunit; Reviewed
Probab=31.59 E-value=76 Score=24.93 Aligned_cols=23 Identities=30% Similarity=0.570 Sum_probs=19.2
Q ss_pred hhHHHHCCCc---cccccCCCCcccccce
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRS 27 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaT 27 (66)
|..|++.|++ ||+ ..-+||.+..
T Consensus 343 A~~L~~~G~~V~V~E~---~~~~GG~l~~ 368 (654)
T PRK12769 343 ADVLARNGVAVTVYDR---HPEIGGLLTF 368 (654)
T ss_pred HHHHHHCCCeEEEEec---CCCCCceeee
Confidence 6788999988 999 8889997753
No 63
>PRK05704 dihydrolipoamide succinyltransferase; Validated
Probab=31.27 E-value=33 Score=25.96 Aligned_cols=25 Identities=32% Similarity=0.537 Sum_probs=18.0
Q ss_pred hhHHH-HCCCccccccCCCCcccccce
Q 042631 2 ADYLR-SRGVRFEDIWGNHGLGGRMRS 27 (66)
Q Consensus 2 A~~L~-~~G~~fEk~~g~rg~GGRmaT 27 (66)
|+.|+ +.|+++.+|.|+ |++||..-
T Consensus 119 aR~lA~e~gidl~~v~gt-G~~GrI~~ 144 (407)
T PRK05704 119 ARKLAAENGLDASAVKGT-GKGGRVTK 144 (407)
T ss_pred hhhHHhhcCCChhhCCCC-CCCCcccH
Confidence 56666 688887776655 88999843
No 64
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=31.16 E-value=40 Score=20.61 Aligned_cols=15 Identities=20% Similarity=0.306 Sum_probs=12.5
Q ss_pred HHHHHHHHhCCcccC
Q 042631 52 CLLINGWLERGLVRP 66 (66)
Q Consensus 52 ~~~v~~~~~~g~v~~ 66 (66)
.++|.+|.+.|++.|
T Consensus 21 ~~~l~eLve~GlIep 35 (101)
T PRK10265 21 EEELNEIVGLGVIEP 35 (101)
T ss_pred HHHHHHHHHCCCeec
Confidence 357899999999876
No 65
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=30.02 E-value=18 Score=19.11 Aligned_cols=23 Identities=17% Similarity=0.346 Sum_probs=17.2
Q ss_pred eeeeCCHHHHHHHHHHHhCCccc
Q 042631 43 FITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 43 yft~~~~~f~~~v~~~~~~g~v~ 65 (66)
.+..+.+.....|+.|.+.|+|.
T Consensus 30 ~l~~~~~~vs~~v~~L~~~Glv~ 52 (62)
T PF12802_consen 30 RLGISKSTVSRIVKRLEKKGLVE 52 (62)
T ss_dssp HHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHCcCHHHHHHHHHHHHHCCCEE
Confidence 33445567889999999999984
No 66
>COG0493 GltD NADPH-dependent glutamate synthase beta chain and related oxidoreductases [Amino acid transport and metabolism / General function prediction only]
Probab=29.91 E-value=35 Score=26.32 Aligned_cols=24 Identities=33% Similarity=0.268 Sum_probs=21.1
Q ss_pred hhHHHHCCCc---cccccCCCCccccccee
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSR 28 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTR 28 (66)
|..|+.+|++ ||+ ...+||+|..-
T Consensus 139 a~~L~~~G~~Vtv~e~---~~~~GGll~yG 165 (457)
T COG0493 139 ADDLSRAGHDVTVFER---VALDGGLLLYG 165 (457)
T ss_pred HHHHHhCCCeEEEeCC---cCCCceeEEec
Confidence 6789999988 999 99999998764
No 67
>PRK12778 putative bifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta; Provisional
Probab=29.72 E-value=88 Score=25.04 Aligned_cols=22 Identities=41% Similarity=0.684 Sum_probs=18.4
Q ss_pred hhHHHHCCCc---cccccCCCCcccccc
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMR 26 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRma 26 (66)
|..|++.|++ ||+ ..-+||-+.
T Consensus 447 A~~l~~~G~~V~v~e~---~~~~GG~l~ 471 (752)
T PRK12778 447 AGDLAKRGYDVTVFEA---LHEIGGVLK 471 (752)
T ss_pred HHHHHHCCCeEEEEec---CCCCCCeee
Confidence 6788999988 999 878888764
No 68
>PLN02172 flavin-containing monooxygenase FMO GS-OX
Probab=29.71 E-value=37 Score=25.78 Aligned_cols=23 Identities=35% Similarity=0.456 Sum_probs=19.9
Q ss_pred hhHHHHCCCc---cccccCCCCcccccce
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRS 27 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaT 27 (66)
|+.|.+.|++ ||+ +..+||...-
T Consensus 26 A~~l~~~G~~v~vfE~---~~~vGG~W~~ 51 (461)
T PLN02172 26 ARELRREGHTVVVFER---EKQVGGLWVY 51 (461)
T ss_pred HHHHHhcCCeEEEEec---CCCCcceeec
Confidence 6788999988 999 9999999854
No 69
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=29.40 E-value=54 Score=18.98 Aligned_cols=19 Identities=37% Similarity=0.515 Sum_probs=15.1
Q ss_pred CHHHHHHHHHHHhCCcccC
Q 042631 48 NSRFCLLINGWLERGLVRP 66 (66)
Q Consensus 48 ~~~f~~~v~~~~~~g~v~~ 66 (66)
..+=.++++.|.+.|+|.|
T Consensus 33 ynrAariid~lE~~GiV~p 51 (63)
T smart00843 33 YNRAARLIDQLEEEGIVGP 51 (63)
T ss_pred hhHHHHHHHHHHHCcCCCC
Confidence 3455679999999999876
No 70
>PRK12809 putative oxidoreductase Fe-S binding subunit; Reviewed
Probab=29.24 E-value=89 Score=24.58 Aligned_cols=22 Identities=36% Similarity=0.699 Sum_probs=18.3
Q ss_pred hhHHHHCCCc---cccccCCCCcccccc
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMR 26 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRma 26 (66)
|..|++.|++ ||+ ..-+||-+.
T Consensus 326 A~~L~~~G~~Vtv~e~---~~~~GG~l~ 350 (639)
T PRK12809 326 ADILARAGVQVDVFDR---HPEIGGMLT 350 (639)
T ss_pred HHHHHHcCCcEEEEeC---CCCCCCeee
Confidence 6788899988 999 888888764
No 71
>PF13738 Pyr_redox_3: Pyridine nucleotide-disulphide oxidoreductase; PDB: 3D1C_A 4A9W_B 2YLX_A 2YM2_A 2YLW_A 2YLR_A 2YM1_A 2YLS_A 1W4X_A 2YLT_A ....
Probab=28.60 E-value=46 Score=21.06 Aligned_cols=24 Identities=38% Similarity=0.488 Sum_probs=19.0
Q ss_pred hhHHHHCCCc----cccccCCCCccccccee
Q 042631 2 ADYLRSRGVR----FEDIWGNHGLGGRMRSR 28 (66)
Q Consensus 2 A~~L~~~G~~----fEk~~g~rg~GGRmaTR 28 (66)
|..|.++|++ ||+ ...+||.....
T Consensus 13 a~~l~~~g~~~v~v~e~---~~~~Gg~w~~~ 40 (203)
T PF13738_consen 13 AAHLLERGIDPVVVLER---NDRPGGVWRRY 40 (203)
T ss_dssp HHHHHHTT---EEEEES---SSSSTTHHHCH
T ss_pred HHHHHhCCCCcEEEEeC---CCCCCCeeEEe
Confidence 6788899987 999 98999999854
No 72
>PHA02591 hypothetical protein; Provisional
Probab=28.35 E-value=76 Score=19.59 Aligned_cols=24 Identities=4% Similarity=0.256 Sum_probs=21.0
Q ss_pred cCceeeeCCHHHHHHHHHHHhCCc
Q 042631 40 AAQFITVNNSRFCLLINGWLERGL 63 (66)
Q Consensus 40 GAqyft~~~~~f~~~v~~~~~~g~ 63 (66)
|..||--+.++..++..+|.+.|+
T Consensus 37 ~~ryfi~~~dd~~~vA~eL~eqGl 60 (83)
T PHA02591 37 QTRYFVESEDDLISVTHELARKGF 60 (83)
T ss_pred CEEEEEeccchHHHHHHHHHHcCC
Confidence 567998888899999999999986
No 73
>TIGR01318 gltD_gamma_fam glutamate synthase small subunit family protein, proteobacterial. This model represents one of three built for the NADPH-dependent or NADH-dependent glutamate synthase (EC 1.4.1.13 and 1.4.1.14, respectively) small subunit and homologs. TIGR01317 describes the small subunit (or equivalent region from longer forms) in eukaryotes, Gram-positive bacteria, and some other lineages, both NADH and NADPH-dependent. TIGR01316 describes a protein of similar length, from Archaea and a number of bacterial lineages, that forms glutamate synthase homotetramers without a large subunit. This model describes both glutatate synthase small subunit and closely related paralogs of unknown function from a number of gamma and alpha subdivision Proteobacteria, including E. coli.
Probab=28.21 E-value=98 Score=23.31 Aligned_cols=22 Identities=36% Similarity=0.691 Sum_probs=18.2
Q ss_pred hhHHHHCCCc---cccccCCCCcccccc
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMR 26 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRma 26 (66)
|..|++.|++ ||+ ..-+||.+.
T Consensus 157 A~~l~~~G~~V~i~e~---~~~~gG~l~ 181 (467)
T TIGR01318 157 ADILARAGVQVVVFDR---HPEIGGLLT 181 (467)
T ss_pred HHHHHHcCCeEEEEec---CCCCCceee
Confidence 6678888987 999 888999774
No 74
>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]
Probab=28.13 E-value=46 Score=23.27 Aligned_cols=30 Identities=23% Similarity=0.325 Sum_probs=22.6
Q ss_pred cceeecCCCCeeecccCceeeeCCHHHHHHHHH
Q 042631 25 MRSRMIRPQPQIFGHAAQFITVNNSRFCLLING 57 (66)
Q Consensus 25 maTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~ 57 (66)
+.||...+.. -+|--||-++.++|+++++.
T Consensus 36 ~TTR~pR~gE---v~G~dY~Fvs~~EF~~~i~~ 65 (191)
T COG0194 36 ATTRKPRPGE---VDGVDYFFVTEEEFEELIER 65 (191)
T ss_pred eccCCCCCCC---cCCceeEeCCHHHHHHHHhc
Confidence 4566555443 57999999999999998864
No 75
>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.
Probab=27.74 E-value=56 Score=21.61 Aligned_cols=17 Identities=29% Similarity=0.438 Sum_probs=14.6
Q ss_pred HHHHHHHHHHhCCcccC
Q 042631 50 RFCLLINGWLERGLVRP 66 (66)
Q Consensus 50 ~f~~~v~~~~~~g~v~~ 66 (66)
...+.|++++++|+++|
T Consensus 16 ~~~~~v~~ll~~G~I~~ 32 (210)
T cd03715 16 GITPHIQELLEAGILVP 32 (210)
T ss_pred HHHHHHHHHHHCCCeEC
Confidence 57789999999999875
No 76
>PF04304 DUF454: Protein of unknown function (DUF454); InterPro: IPR007401 This is a predicted membrane protein.
Probab=27.38 E-value=50 Score=18.45 Aligned_cols=18 Identities=28% Similarity=0.433 Sum_probs=15.3
Q ss_pred CCHHHHHHHHHHHhCCcc
Q 042631 47 NNSRFCLLINGWLERGLV 64 (66)
Q Consensus 47 ~~~~f~~~v~~~~~~g~v 64 (66)
+++-|...+++|.+.+.+
T Consensus 7 ~h~~~g~~I~~w~~~r~i 24 (71)
T PF04304_consen 7 NHRLFGPYIRNWEEHRGI 24 (71)
T ss_pred cCchhHHHHHHHHHCCCc
Confidence 578899999999988765
No 77
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=27.27 E-value=56 Score=17.77 Aligned_cols=18 Identities=17% Similarity=0.364 Sum_probs=15.3
Q ss_pred CHHHHHHHHHHHhCCccc
Q 042631 48 NSRFCLLINGWLERGLVR 65 (66)
Q Consensus 48 ~~~f~~~v~~~~~~g~v~ 65 (66)
.+.|..+++.|+++|.+.
T Consensus 34 ~k~~~~ll~~l~~~g~l~ 51 (59)
T PF09106_consen 34 PKLFNALLEALVAEGRLK 51 (59)
T ss_dssp HCCHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHHCCCee
Confidence 457999999999999874
No 78
>PF12970 DUF3858: Domain of Unknown Function with PDB structure (DUF3858); InterPro: IPR024544 This domain of unknown function is structurally similar to part of neuropilin-2. The proteins it occurs in have not yet been functionally characterised.; PDB: 3KD4_A.
Probab=27.26 E-value=30 Score=22.54 Aligned_cols=26 Identities=23% Similarity=0.397 Sum_probs=17.2
Q ss_pred ecccCceeeeCC-HHHHHHHHHHHhCC
Q 042631 37 FGHAAQFITVNN-SRFCLLINGWLERG 62 (66)
Q Consensus 37 ~DhGAqyft~~~-~~f~~~v~~~~~~g 62 (66)
.-.-=|-+|+.+ ++|.+++.+|.+.+
T Consensus 84 L~L~KqlitPaEY~afr~L~~eW~d~~ 110 (116)
T PF12970_consen 84 LELKKQLITPAEYPAFRSLMTEWTDVD 110 (116)
T ss_dssp EEE--SEE-HHHHHHHHHHHHHHH-GG
T ss_pred EEEeeeeeCchhHHHHHHHHHHhccCC
Confidence 556668888654 69999999998764
No 79
>smart00521 CBF CCAAT-Binding transcription Factor.
Probab=27.14 E-value=30 Score=20.30 Aligned_cols=10 Identities=40% Similarity=0.747 Sum_probs=8.2
Q ss_pred CCCcccccce
Q 042631 18 NHGLGGRMRS 27 (66)
Q Consensus 18 ~rg~GGRmaT 27 (66)
.||+|||.-|
T Consensus 52 ~Rg~gGRFl~ 61 (62)
T smart00521 52 PRGSGGRFLN 61 (62)
T ss_pred CcCCCCCCCC
Confidence 7999999754
No 80
>TIGR01317 GOGAT_sm_gam glutamate synthases, NADH/NADPH, small subunit. This model represents one of three built for the NADPH-dependent or NADH-dependent glutamate synthase (EC 1.4.1.13 and 1.4.1.14, respectively) small subunit or homologous region. TIGR01316 describes a family in several archaeal and deeply branched bacterial lineages of a homotetrameric form for which there is no large subunit. Another model describes glutamate synthase small subunit from gamma and some alpha subdivision Proteobacteria plus paralogs of unknown function. This model describes the small subunit, or homologous region of longer forms proteins, of eukaryotes, Gram-positive bacteria, cyanobacteria, and some other lineages. All members with known function participate in NADH or NADPH-dependent reactions to interconvert between glutamine plus 2-oxoglutarate and two molecules of glutamate.
Probab=26.92 E-value=1e+02 Score=23.32 Aligned_cols=22 Identities=36% Similarity=0.523 Sum_probs=18.1
Q ss_pred hhHHHHCCCc---cccccCCCCcccccc
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMR 26 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRma 26 (66)
|..|++.|++ ||+ ...+||.+.
T Consensus 159 A~~L~~~g~~V~v~e~---~~~~gG~l~ 183 (485)
T TIGR01317 159 ADQLNRAGHTVTVFER---EDRCGGLLM 183 (485)
T ss_pred HHHHHHcCCeEEEEec---CCCCCceee
Confidence 6788889987 999 888888764
No 81
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=26.77 E-value=32 Score=18.21 Aligned_cols=24 Identities=13% Similarity=0.332 Sum_probs=18.8
Q ss_pred ceeeeCCHHHHHHHHHHHhCCccc
Q 042631 42 QFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 42 qyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
+.+.++.+...+.++.|.+.|+|.
T Consensus 33 ~~~g~s~~tv~r~l~~L~~~g~i~ 56 (67)
T cd00092 33 DYLGLTRETVSRTLKELEEEGLIS 56 (67)
T ss_pred HHHCCCHHHHHHHHHHHHHCCCEE
Confidence 344556678889999999999874
No 82
>cd01645 RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.
Probab=26.58 E-value=60 Score=21.74 Aligned_cols=18 Identities=22% Similarity=0.442 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHhCCcccC
Q 042631 49 SRFCLLINGWLERGLVRP 66 (66)
Q Consensus 49 ~~f~~~v~~~~~~g~v~~ 66 (66)
+...+.|++|++.|+++|
T Consensus 15 ~~~~~~i~~ll~~g~I~~ 32 (213)
T cd01645 15 EALTELVTEQLKEGHIEP 32 (213)
T ss_pred HHHHHHHHHHHHCCceec
Confidence 367889999999999875
No 83
>PF14178 YppF: YppF-like protein
Probab=26.28 E-value=72 Score=18.53 Aligned_cols=18 Identities=22% Similarity=0.386 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHhCCcccC
Q 042631 49 SRFCLLINGWLERGLVRP 66 (66)
Q Consensus 49 ~~f~~~v~~~~~~g~v~~ 66 (66)
.+++.+|.+|...|.+.|
T Consensus 40 ~eYR~lvreLE~~GA~~p 57 (60)
T PF14178_consen 40 NEYRNLVRELEANGAVSP 57 (60)
T ss_pred HHHHHHHHHHHHhCCCCC
Confidence 479999999999998876
No 84
>COG3233 Predicted deacetylase [General function prediction only]
Probab=26.22 E-value=71 Score=23.13 Aligned_cols=18 Identities=28% Similarity=0.350 Sum_probs=15.6
Q ss_pred eCCHHHHHHHHHHHhCCc
Q 042631 46 VNNSRFCLLINGWLERGL 63 (66)
Q Consensus 46 ~~~~~f~~~v~~~~~~g~ 63 (66)
.+||+|++++.+..++|-
T Consensus 51 ~~d~rf~~~l~~r~e~Gd 68 (233)
T COG3233 51 SKDPRFVDLLTEREEEGD 68 (233)
T ss_pred ccChHHHHHHHHHHhcCC
Confidence 378899999999999874
No 85
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=26.15 E-value=23 Score=18.64 Aligned_cols=25 Identities=20% Similarity=0.365 Sum_probs=19.0
Q ss_pred CceeeeCCHHHHHHHHHHHhCCccc
Q 042631 41 AQFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 41 Aqyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
|.++.++.+..-.+++.|.+.|+|.
T Consensus 24 a~~~~~~~~~~t~~i~~L~~~g~I~ 48 (59)
T PF01047_consen 24 AEKLGISRSTVTRIIKRLEKKGLIE 48 (59)
T ss_dssp HHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHCCChhHHHHHHHHHHHCCCEE
Confidence 4455566778889999999999874
No 86
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=25.23 E-value=41 Score=19.49 Aligned_cols=18 Identities=33% Similarity=0.562 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHhCCcccC
Q 042631 49 SRFCLLINGWLERGLVRP 66 (66)
Q Consensus 49 ~~f~~~v~~~~~~g~v~~ 66 (66)
.+=.++++.|.+.|+|.|
T Consensus 35 nrAariid~LE~~GiVs~ 52 (65)
T PF09397_consen 35 NRAARIIDQLEEEGIVSP 52 (65)
T ss_dssp HHHHHHHHHHHHCTSBE-
T ss_pred HHHHHHHHHHHHCCCCCC
Confidence 355678999999999865
No 87
>TIGR01349 PDHac_trf_mito pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form. This model represents one of several closely related clades of the dihydrolipoamide acetyltransferase subunit of the pyruvate dehydrogenase complex. It includes sequences from mitochondria and from alpha and beta branches of the proteobacteria, as well as from some other bacteria. Sequences from Gram-positive bacteria are not included. The non-enzymatic homolog protein X, which serves as an E3 component binding protein, falls within the clade phylogenetically but is rejected by its low score.
Probab=24.14 E-value=55 Score=24.95 Aligned_cols=26 Identities=27% Similarity=0.574 Sum_probs=18.6
Q ss_pred hhHHH-HCCCccccccCCCCccccccee
Q 042631 2 ADYLR-SRGVRFEDIWGNHGLGGRMRSR 28 (66)
Q Consensus 2 A~~L~-~~G~~fEk~~g~rg~GGRmaTR 28 (66)
|+.|+ +.|+++++|.|+ |++||..-.
T Consensus 145 vR~lA~e~gvdl~~v~gt-G~~GrI~~~ 171 (435)
T TIGR01349 145 AKKLAKEKGIDLSAVAGS-GPNGRIVKK 171 (435)
T ss_pred HHHHHHHcCCCHhHCCCC-CCCCceeHH
Confidence 45666 688887777755 789998544
No 88
>PRK05249 soluble pyridine nucleotide transhydrogenase; Provisional
Probab=23.91 E-value=54 Score=24.07 Aligned_cols=24 Identities=25% Similarity=0.277 Sum_probs=19.9
Q ss_pred hhHHHHCCCc---cccccCCCCccccccee
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSR 28 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTR 28 (66)
|..|+++|.+ +|| ...+||.+..+
T Consensus 21 A~~la~~G~~v~liE~---~~~~GG~~~~~ 47 (461)
T PRK05249 21 AMQAAKLGKRVAVIER---YRNVGGGCTHT 47 (461)
T ss_pred HHHHHhCCCEEEEEec---ccccccccccc
Confidence 6788999988 999 88899987544
No 89
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=23.42 E-value=69 Score=17.87 Aligned_cols=24 Identities=17% Similarity=0.318 Sum_probs=20.4
Q ss_pred ceeeeCCHHHHHHHHHHHhCCccc
Q 042631 42 QFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 42 qyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
.++.++...+-..++.|.+.|+|.
T Consensus 25 ~~~~i~~g~lY~~L~~Le~~gli~ 48 (75)
T PF03551_consen 25 GFWKISPGSLYPALKRLEEEGLIE 48 (75)
T ss_dssp TTEETTHHHHHHHHHHHHHTTSEE
T ss_pred CCcccChhHHHHHHHHHHhCCCEE
Confidence 467788888999999999999985
No 90
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=23.18 E-value=28 Score=17.79 Aligned_cols=20 Identities=20% Similarity=0.365 Sum_probs=15.3
Q ss_pred eCCHHHHHHHHHHHhCCccc
Q 042631 46 VNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 46 ~~~~~f~~~v~~~~~~g~v~ 65 (66)
.+.+.....++.|.+.|+|+
T Consensus 29 is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 29 ISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp S-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHHHCcCcC
Confidence 45567888999999999874
No 91
>PF13730 HTH_36: Helix-turn-helix domain
Probab=22.64 E-value=84 Score=16.26 Aligned_cols=20 Identities=25% Similarity=0.300 Sum_probs=15.6
Q ss_pred eeCCHHHHHHHHHHHhCCcc
Q 042631 45 TVNNSRFCLLINGWLERGLV 64 (66)
Q Consensus 45 t~~~~~f~~~v~~~~~~g~v 64 (66)
.++....++.+++|.+.|++
T Consensus 36 g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 36 GVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CcCHHHHHHHHHHHHHCcCC
Confidence 34555788999999999975
No 92
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=22.55 E-value=47 Score=21.22 Aligned_cols=28 Identities=14% Similarity=0.164 Sum_probs=23.3
Q ss_pred cccCceeeeCCHHHHHHHHHHHhCCccc
Q 042631 38 GHAAQFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 38 DhGAqyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
..=|+|+.++-+.+.+.+.+|.+.|+|.
T Consensus 153 ~~iA~~lG~tretvsR~l~~l~~~g~I~ 180 (202)
T PRK13918 153 DELAAAVGSVRETVTKVIGELSREGYIR 180 (202)
T ss_pred HHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence 3447788888888999999999999875
No 93
>TIGR01470 cysG_Nterm siroheme synthase, N-terminal domain. This model represents a subfamily of CysG N-terminal region-related sequences. All sequences in the seed alignment for this model are N-terminal regions of known or predicted siroheme synthases. The C-terminal region of each is uroporphyrin-III C-methyltransferase (EC 2.1.1.107), which catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). The region represented by this model completes the process of oxidation and iron insertion to yield siroheme. Siroheme is a cofactor for nitrite and sulfite reductases, so siroheme synthase is CysG of cysteine biosynthesis in some organisms.
Probab=22.11 E-value=15 Score=25.00 Aligned_cols=37 Identities=24% Similarity=0.285 Sum_probs=24.2
Q ss_pred ccccceeecCCCCeeecccCceeeeCCHHHHHHHHHHHhCC
Q 042631 22 GGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLINGWLERG 62 (66)
Q Consensus 22 GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~~~~~g 62 (66)
||..+.|++.. -.+.||. +|+-+|++..-+.+|.+.|
T Consensus 17 gG~va~rk~~~---Ll~~ga~-VtVvsp~~~~~l~~l~~~~ 53 (205)
T TIGR01470 17 GGDVALRKARL---LLKAGAQ-LRVIAEELESELTLLAEQG 53 (205)
T ss_pred cCHHHHHHHHH---HHHCCCE-EEEEcCCCCHHHHHHHHcC
Confidence 67888887753 3677874 5665666666666666554
No 94
>PRK06416 dihydrolipoamide dehydrogenase; Reviewed
Probab=22.02 E-value=64 Score=23.76 Aligned_cols=23 Identities=30% Similarity=0.426 Sum_probs=18.9
Q ss_pred hhHHHHCCCc---cccccCCCCccccccee
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSR 28 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTR 28 (66)
|..|+++|.+ +|| .. +||.+..+
T Consensus 20 A~~aa~~G~~V~liE~---~~-~GG~c~~~ 45 (462)
T PRK06416 20 AIRAAQLGLKVAIVEK---EK-LGGTCLNR 45 (462)
T ss_pred HHHHHHCCCcEEEEec---cc-cccceeec
Confidence 6788899988 999 77 99987654
No 95
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=21.88 E-value=55 Score=18.20 Aligned_cols=28 Identities=21% Similarity=0.351 Sum_probs=21.9
Q ss_pred cccCceeeeCCHHHHHHHHHHHhCCccc
Q 042631 38 GHAAQFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 38 DhGAqyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
+.=++.+..+.+.....|+.|.+.|+|.
T Consensus 28 ~~la~~~~~s~~~i~~~l~~L~~~g~v~ 55 (101)
T smart00347 28 SELAKRLGVSPSTVTRVLDRLEKKGLIR 55 (101)
T ss_pred HHHHHHHCCCchhHHHHHHHHHHCCCeE
Confidence 3335566777888999999999999884
No 96
>TIGR03257 met_CoM_red_bet methyl-coenzyme M reductase, beta subunit. Members of this protein family are the beta subunit of methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis. Several methanogens have encode two such enzymes, designated I and II; this model does not separate the isozymes.
Probab=21.71 E-value=55 Score=25.48 Aligned_cols=34 Identities=18% Similarity=0.340 Sum_probs=24.5
Q ss_pred ccCCCCcc----cccceeecCCCC-------eeecccCceeeeCC
Q 042631 15 IWGNHGLG----GRMRSRMIRPQP-------QIFGHAAQFITVNN 48 (66)
Q Consensus 15 ~~g~rg~G----GRmaTRr~~~~~-------~~~DhGAqyft~~~ 48 (66)
|.|+.||| --.-||.+.+.. +..|-|.|+|++..
T Consensus 363 IYGGGGPGiFnGNHVVTRHskG~aiPcv~AAmalDAgTqmFSpe~ 407 (433)
T TIGR03257 363 IYGGGGPGIFNGNHVVTRHSKGFAIPCVCAAMALDAGTQMFSPES 407 (433)
T ss_pred cccCCCCccccCCeEEEecCCCcccchHHHHHhhccCCceecHHH
Confidence 57777875 356677776643 47899999998743
No 97
>PRK12814 putative NADPH-dependent glutamate synthase small subunit; Provisional
Probab=21.65 E-value=1.6e+02 Score=23.33 Aligned_cols=22 Identities=45% Similarity=0.726 Sum_probs=18.5
Q ss_pred hhHHHHCCCc---cccccCCCCcccccc
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMR 26 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRma 26 (66)
|..|++.|++ ||+ ..-+||.+.
T Consensus 209 A~~La~~G~~Vtv~e~---~~~~GG~l~ 233 (652)
T PRK12814 209 AYYLLRKGHDVTIFDA---NEQAGGMMR 233 (652)
T ss_pred HHHHHHCCCcEEEEec---CCCCCceee
Confidence 6788899988 999 888999774
No 98
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=21.53 E-value=46 Score=22.14 Aligned_cols=25 Identities=12% Similarity=0.493 Sum_probs=22.1
Q ss_pred CceeeeCCHHHHHHHHHHHhCCccc
Q 042631 41 AQFITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 41 Aqyft~~~~~f~~~v~~~~~~g~v~ 65 (66)
|+++.++.+...+.+.+|.+.|+|.
T Consensus 176 A~~lG~sretvsR~L~~L~~~G~I~ 200 (226)
T PRK10402 176 AEYLGVSYRHLLYVLAQFIQDGYLK 200 (226)
T ss_pred HHHHCCcHHHHHHHHHHHHHCCCEE
Confidence 7888888889999999999999875
No 99
>PF02241 MCR_beta: Methyl-coenzyme M reductase beta subunit, C-terminal domain; InterPro: IPR022679 Methyl-coenzyme M reductase (MCR) catalyses the reduction of methyl-coenzyme M (CH3-SCoM) and coenzyme B (HS-CoB) to methane and the corresponding heterosulphide CoM-S-S-CoB (2.8.4.1 from EC), the final step in methane biosynthesis. This reaction proceeds under anaerobic conditions by methanogenic Archaea [], and requires a nickel-porphinoid prosthetic group, coenzyme F430, which is in the EPR-detectable Ni(I) oxidation state in the active enzyme. Studies on a catalytically inactive enzyme aerobically co-crystallized with coenzyme M displayed a fully occupied coenzyme M-binding site with no alternate conformations. The binding of coenzyme M appears to induce specific conformational changes that suggests a molecular mechanism by which the enzyme ensures that methyl-coenzyme M enters the substrate channel prior to coenzyme B, as required by the active-site geometry []. MCR is a hexamer composed of 2 alpha, 2 beta, and 2 gamma subunits with two identical nickel porphinoid active sites, which form two long active site channels with F430 embedded at the bottom [, ]. This entry represents the C-terminal domain from the beta subunit of methyl-conenzyme M reductase (MCR). The C-terminal domain of MCR beta has an all-alpha fold with buried central helix. This entry is found in assocation with PF02783 from PFAM.; GO: 0050524 coenzyme-B sulfoethylthiotransferase activity; PDB: 1MRO_E 1HBM_B 3M30_B 3M32_B 1HBU_B 3M2U_E 3M2V_E 3M1V_B 1HBO_B 3POT_B ....
Probab=21.40 E-value=39 Score=24.55 Aligned_cols=33 Identities=18% Similarity=0.341 Sum_probs=19.1
Q ss_pred ccCCCCcc----cccceeecCCCC-------eeecccCceeeeC
Q 042631 15 IWGNHGLG----GRMRSRMIRPQP-------QIFGHAAQFITVN 47 (66)
Q Consensus 15 ~~g~rg~G----GRmaTRr~~~~~-------~~~DhGAqyft~~ 47 (66)
|.|+.||| --.-||.+.+.. +.+|-|.|+|++.
T Consensus 179 IYGGGGPGiFnGNHvVTRHskG~aiPcv~AA~~lDAgTqmFspe 222 (255)
T PF02241_consen 179 IYGGGGPGIFNGNHVVTRHSKGFAIPCVAAAMALDAGTQMFSPE 222 (255)
T ss_dssp SSS--SGGG--TTSTTT-SSSSSSHHHHHHHHHC-SS-SSS-HH
T ss_pred cccCCCCccccCCeEEEecCCCcccchHHHHHhhccCCceecHH
Confidence 56777775 356788777653 4789999999873
No 100
>cd00537 MTHFR Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase to convert homocysteine to methionine. The enzymatic mechanism is a ping-pong bi-bi mechanism, in which NAD(P)+ release precedes the binding of methylenetetrahydrofolate and the acceptor is free FAD. The family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from prokaryotes and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The bacterial enzyme is a homotetramer and NADH is the preferred reductant while the eukaryotic enzyme is a homodimer and NADPH is the preferred reductant. In humans, there are several clinically significant mutations in MTHFR that result in hyperhomocysteinemia, which is a risk factor for the development of cardiovascular disease.
Probab=20.95 E-value=1.1e+02 Score=21.24 Aligned_cols=28 Identities=21% Similarity=0.389 Sum_probs=21.6
Q ss_pred eecccCceeee----CCHHHHHHHHHHHhCCc
Q 042631 36 IFGHAAQFITV----NNSRFCLLINGWLERGL 63 (66)
Q Consensus 36 ~~DhGAqyft~----~~~~f~~~v~~~~~~g~ 63 (66)
-.|.||.||.. +.+.|.++++.+.+.|+
T Consensus 156 Ki~aGA~f~iTQ~~fd~~~~~~~~~~~~~~gi 187 (274)
T cd00537 156 KVDAGADFIITQLFFDNDAFLRFVDRCRAAGI 187 (274)
T ss_pred HHHCCCCEEeecccccHHHHHHHHHHHHHcCC
Confidence 35789999975 33588889999888874
No 101
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=20.90 E-value=56 Score=16.36 Aligned_cols=22 Identities=23% Similarity=0.312 Sum_probs=17.3
Q ss_pred eeeCCHHHHHHHHHHHhCCccc
Q 042631 44 ITVNNSRFCLLINGWLERGLVR 65 (66)
Q Consensus 44 ft~~~~~f~~~v~~~~~~g~v~ 65 (66)
+.++.+.....++.|.+.|++.
T Consensus 20 l~is~~~v~~~l~~L~~~g~i~ 41 (66)
T smart00418 20 LGLSQSTVSHHLKKLREAGLVE 41 (66)
T ss_pred HCCCHHHHHHHHHHHHHCCCee
Confidence 4456678889999999988874
No 102
>PF00890 FAD_binding_2: FAD binding domain of the Pfam family.; InterPro: IPR003953 In bacteria two distinct, membrane-bound, enzyme complexes are responsible for the interconversion of fumarate and succinate (1.3.99.1 from EC): fumarate reductase (Frd) is used in anaerobic growth, and succinate dehydrogenase (Sdh) is used in aerobic growth. Both complexes consist of two main components: a membrane-extrinsic component composed of a FAD-binding flavoprotein and an iron-sulphur protein; and an hydrophobic component composed of a membrane anchor protein and/or a cytochrome B. In eukaryotes mitochondrial succinate dehydrogenase (ubiquinone) (1.3.5.1 from EC) is an enzyme composed of two subunits: a FAD flavoprotein and and iron-sulphur protein. The flavoprotein subunit is a protein of about 60 to 70 Kd to which FAD is covalently bound to a histidine residue which is located in the N-terminal section of the protein []. The sequence around that histidine is well conserved in Frd and Sdh from various bacterial and eukaryotic species []. This family includes members that bind FAD such as the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase. ; GO: 0009055 electron carrier activity, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 2BS4_A 2BS3_A 2BS2_A 1E7P_J 1QLB_A 1KNR_A 1KNP_A 1CHU_A 2E5V_A 3AEF_A ....
Probab=20.83 E-value=73 Score=22.83 Aligned_cols=25 Identities=28% Similarity=0.319 Sum_probs=18.3
Q ss_pred hhHHHHCCCc---cccccCCCCcccccceeecC
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSRMIR 31 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTRr~~ 31 (66)
|..++++|.+ +|| +...|| +|....
T Consensus 15 A~~Aae~G~~V~lvek---~~~~gg--~~~~s~ 42 (417)
T PF00890_consen 15 AIEAAEAGAKVLLVEK---GPRLGG--SSAFSS 42 (417)
T ss_dssp HHHHHHTTT-EEEEES---SSGGGS--GGGGTC
T ss_pred HHHHhhhcCeEEEEEe---eccccc--cccccc
Confidence 5678899988 999 888888 554443
No 103
>COG4352 RPL13 Ribosomal protein L13E [Translation, ribosomal structure and biogenesis]
Probab=20.76 E-value=78 Score=20.56 Aligned_cols=49 Identities=24% Similarity=0.330 Sum_probs=31.3
Q ss_pred HHHHCCCccccccCCCCcccccceeecCCCCeeecccCceeeeCCHHHHHHHHHHHhCCcccC
Q 042631 4 YLRSRGVRFEDIWGNHGLGGRMRSRMIRPQPQIFGHAAQFITVNNSRFCLLINGWLERGLVRP 66 (66)
Q Consensus 4 ~L~~~G~~fEk~~g~rg~GGRmaTRr~~~~~~~~DhGAqyft~~~~~f~~~v~~~~~~g~v~~ 66 (66)
+|.++|++.++ .|-+|==.-+||.+..++.| +...+++.++++..++-|
T Consensus 65 El~aAGL~~~~---AR~LGI~VD~RRr~~~~en~-----------eal~k~ik~ll~~~~~~p 113 (113)
T COG4352 65 ELKAAGLSARK---ARTLGIAVDHRRRNRNPENF-----------EALVKRIKELLEKIIVFP 113 (113)
T ss_pred HHHHcCcCHHH---HHhhCcceehhhccCCHHHH-----------HHHHHHHHHHHhcCccCC
Confidence 57778888777 77776666666654332211 245667778888777654
No 104
>PRK11857 dihydrolipoamide acetyltransferase; Reviewed
Probab=20.71 E-value=69 Score=23.40 Aligned_cols=25 Identities=24% Similarity=0.384 Sum_probs=17.8
Q ss_pred hhHHH-HCCCccccccCCCCcccccce
Q 042631 2 ADYLR-SRGVRFEDIWGNHGLGGRMRS 27 (66)
Q Consensus 2 A~~L~-~~G~~fEk~~g~rg~GGRmaT 27 (66)
|+.|+ +.|++++.|.| -|++||..-
T Consensus 8 aR~lA~e~gvdl~~v~g-tG~~GrI~k 33 (306)
T PRK11857 8 ARALAKKLGIDISLLKG-SGRDGKILA 33 (306)
T ss_pred hHHHHHHcCCCHHHCCC-CCCCCceeH
Confidence 45555 68888777775 488999743
No 105
>COG3571 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]
Probab=20.62 E-value=34 Score=24.23 Aligned_cols=35 Identities=20% Similarity=0.301 Sum_probs=21.5
Q ss_pred ccCCCCcccccceeecCCCC----eeecccCceeeeCCH
Q 042631 15 IWGNHGLGGRMRSRMIRPQP----QIFGHAAQFITVNNS 49 (66)
Q Consensus 15 ~~g~rg~GGRmaTRr~~~~~----~~~DhGAqyft~~~~ 49 (66)
|.|++..||||+|-..++-. .-.=.|-+|.-+-.|
T Consensus 92 i~GGkSmGGR~aSmvade~~A~i~~L~clgYPfhppGKP 130 (213)
T COG3571 92 IIGGKSMGGRVASMVADELQAPIDGLVCLGYPFHPPGKP 130 (213)
T ss_pred eeccccccchHHHHHHHhhcCCcceEEEecCccCCCCCc
Confidence 45889999999997765321 123345566554443
No 106
>TIGR01292 TRX_reduct thioredoxin-disulfide reductase. This model describes thioredoxin-disulfide reductase, a member of the pyridine nucleotide-disulphide oxidoreductases (PFAM:PF00070).
Probab=20.57 E-value=77 Score=21.10 Aligned_cols=23 Identities=22% Similarity=0.406 Sum_probs=18.4
Q ss_pred hhHHHHCCCc---cccccCCCCccccccee
Q 042631 2 ADYLRSRGVR---FEDIWGNHGLGGRMRSR 28 (66)
Q Consensus 2 A~~L~~~G~~---fEk~~g~rg~GGRmaTR 28 (66)
|..|++.|++ +|+ .. +||++...
T Consensus 16 A~~l~~~g~~v~lie~---~~-~gg~~~~~ 41 (300)
T TIGR01292 16 AIYAARANLKTLIIEG---ME-PGGQLTTT 41 (300)
T ss_pred HHHHHHCCCCEEEEec---cC-CCcceeec
Confidence 6788899988 999 65 88987654
No 107
>PF01266 DAO: FAD dependent oxidoreductase; InterPro: IPR006076 This entry includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase (1.1.99.5 from EC), Sarcosine oxidase beta subunit (1.5.3.1 from EC), D-alanine oxidase (1.4.99.1 from EC), D-aspartate oxidase (1.4.3.1 from EC). D-amino acid oxidase (1.4.3.3 from EC) (DAMOX or DAO) is an FAD flavoenzyme that catalyzes the oxidation of neutral and basic D-amino acids into their corresponding keto acids. DAOs have been characterised and sequenced in fungi and vertebrates where they are known to be located in the peroxisomes. D-aspartate oxidase (1.4.3.1 from EC) (DASOX) [] is an enzyme, structurally related to DAO, which catalyzes the same reaction but is active only toward dicarboxylic D-amino acids. In DAO, a conserved histidine has been shown [] to be important for the enzyme's catalytic activity.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 2RGO_A 3NYE_A 3NYF_A 3NYC_A 3SM8_A 3SGL_A 3PVC_A 3DME_A 2GAH_B 3NLC_A ....
Probab=20.50 E-value=62 Score=21.76 Aligned_cols=22 Identities=27% Similarity=0.339 Sum_probs=17.3
Q ss_pred ChhHHHHCCCc---cccccCCCCcccccc
Q 042631 1 IADYLRSRGVR---FEDIWGNHGLGGRMR 26 (66)
Q Consensus 1 ~A~~L~~~G~~---fEk~~g~rg~GGRma 26 (66)
+|..|++.|++ +|+ . .+++-.|
T Consensus 14 ~A~~La~~G~~V~l~e~---~-~~~~~aS 38 (358)
T PF01266_consen 14 TAYELARRGHSVTLLER---G-DIGSGAS 38 (358)
T ss_dssp HHHHHHHTTSEEEEEES---S-STTSSGG
T ss_pred HHHHHHHCCCeEEEEee---c-ccccccc
Confidence 37899999988 999 7 7776444
No 108
>TIGR01347 sucB 2-oxoglutarate dehydrogenase complex dihydrolipoamide succinyltransferase (E2 component). dihydrolipoamide acetyltransferase. The seed for this model includes mitochondrial and Gram-negative bacterial forms. Mycobacterial candidates are highly derived, differ in having and extra copy of the lipoyl-binding domain at the N-terminus. They score below the trusted cutoff, but above the noise cutoff and above all examples of dihydrolipoamide acetyltransferase.
Probab=20.27 E-value=72 Score=24.17 Aligned_cols=26 Identities=27% Similarity=0.523 Sum_probs=18.2
Q ss_pred hhHHH-HCCCccccccCCCCccccccee
Q 042631 2 ADYLR-SRGVRFEDIWGNHGLGGRMRSR 28 (66)
Q Consensus 2 A~~L~-~~G~~fEk~~g~rg~GGRmaTR 28 (66)
|+.|+ +.|++++.|.| .|++||..-.
T Consensus 117 aR~lA~e~gvdl~~v~g-tG~~GrI~~~ 143 (403)
T TIGR01347 117 ARRLAKEHGIDLSAVPG-TGVTGRVTKE 143 (403)
T ss_pred hhhHHHHcCCChhhCCC-CCCCCcccHH
Confidence 45665 57888777666 4889998443
Done!