Query psy1305
Match_columns 68
No_of_seqs 149 out of 1254
Neff 10.0
Searched_HMMs 46136
Date Fri Aug 16 18:09:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1305.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1305hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02771 Acyl-CoA_dh_N: Acyl-C 99.8 3.4E-18 7.4E-23 86.6 5.7 68 1-68 6-73 (113)
2 KOG0141|consensus 99.7 2.2E-17 4.7E-22 95.7 5.7 68 1-68 47-116 (421)
3 KOG0139|consensus 99.7 2.2E-16 4.8E-21 92.3 6.0 67 2-68 44-110 (398)
4 cd01157 MCAD Medium chain acyl 99.6 1.8E-15 4E-20 89.4 6.8 67 2-68 8-74 (378)
5 KOG0140|consensus 99.6 3.1E-15 6.8E-20 86.8 6.8 67 2-68 35-101 (408)
6 cd01160 LCAD Long chain acyl-C 99.6 3.1E-15 6.8E-20 88.2 6.9 68 1-68 5-72 (372)
7 PRK03354 crotonobetainyl-CoA d 99.6 7.3E-15 1.6E-19 87.1 7.2 68 1-68 11-79 (380)
8 TIGR03207 cyc_hxne_CoA_dh cycl 99.6 7.8E-15 1.7E-19 86.7 6.8 67 2-68 8-74 (372)
9 cd01151 GCD Glutaryl-CoA dehyd 99.6 9.5E-15 2E-19 86.7 7.2 66 2-68 20-85 (386)
10 TIGR03203 pimD_small pimeloyl- 99.6 1.1E-14 2.3E-19 86.5 7.1 68 1-68 10-79 (378)
11 cd01156 IVD Isovaleryl-CoA deh 99.6 1.1E-14 2.4E-19 85.9 7.0 67 2-68 9-75 (376)
12 PTZ00461 isovaleryl-CoA dehydr 99.6 1.6E-14 3.4E-19 86.4 7.0 67 2-68 44-110 (410)
13 cd01162 IBD Isobutyryl-CoA deh 99.6 1.5E-14 3.2E-19 85.6 6.7 68 1-68 7-74 (375)
14 cd01155 ACAD_FadE2 Acyl-CoA de 99.5 2.3E-14 5E-19 85.3 6.3 68 1-68 5-83 (394)
15 PLN02519 isovaleryl-CoA dehydr 99.5 3.7E-14 8E-19 84.7 6.6 67 2-68 33-101 (404)
16 PRK12341 putative acyl-CoA deh 99.5 6.1E-14 1.3E-18 83.2 7.4 67 2-68 12-79 (381)
17 TIGR03204 pimC_large pimeloyl- 99.5 9.4E-14 2E-18 82.9 6.9 68 1-68 10-82 (395)
18 cd01158 SCAD_SBCAD Short chain 99.5 9.2E-14 2E-18 81.9 6.7 67 2-68 6-72 (373)
19 cd01161 VLCAD Very long chain 99.5 1.8E-13 3.8E-18 81.9 6.5 65 2-68 34-98 (409)
20 cd01153 ACAD_fadE5 Putative ac 99.5 3.9E-13 8.4E-18 80.4 7.1 67 2-68 1-78 (407)
21 PLN02526 acyl-coenzyme A oxida 99.4 5.6E-13 1.2E-17 80.0 7.1 66 2-68 36-101 (412)
22 cd01152 ACAD_fadE6_17_26 Putat 99.4 4.1E-13 8.9E-18 79.6 4.9 68 1-68 5-77 (380)
23 cd01163 DszC Dibenzothiophene 99.4 1.4E-12 3.1E-17 77.2 6.6 63 5-68 2-64 (377)
24 cd01159 NcnH Naphthocyclinone 99.3 4.5E-12 9.7E-17 75.0 6.3 62 6-68 3-64 (370)
25 PRK13026 acyl-CoA dehydrogenas 99.3 8.2E-12 1.8E-16 79.7 6.4 66 2-67 78-149 (774)
26 PTZ00456 acyl-CoA dehydrogenas 99.3 1.5E-11 3.2E-16 77.2 6.8 65 2-66 63-139 (622)
27 PRK09463 fadE acyl-CoA dehydro 99.2 5.5E-11 1.2E-15 76.1 7.3 45 24-68 107-151 (777)
28 PLN02876 acyl-CoA dehydrogenas 99.2 1.3E-10 2.7E-15 74.8 6.9 68 1-68 408-508 (822)
29 COG1960 CaiA Acyl-CoA dehydrog 99.2 1.1E-10 2.4E-15 69.5 6.1 67 2-68 12-81 (393)
30 KOG0138|consensus 98.9 4.2E-09 9E-14 61.8 5.4 66 2-68 62-127 (432)
31 KOG0137|consensus 98.5 2.9E-07 6.2E-12 57.6 4.6 49 19-67 102-150 (634)
32 PTZ00457 acyl-CoA dehydrogenas 98.4 4.6E-07 9.9E-12 56.5 4.0 38 31-68 55-93 (520)
33 PLN02636 acyl-coenzyme A oxida 97.5 0.00038 8.2E-09 45.1 5.6 61 2-68 68-132 (686)
34 cd01154 AidB Proteins involved 97.5 0.00041 8.9E-09 42.3 5.0 46 6-53 37-91 (418)
35 PLN02312 acyl-CoA oxidase 93.5 0.17 3.7E-06 33.3 4.0 43 23-68 102-144 (680)
36 KOG1469|consensus 91.1 0.24 5.1E-06 29.7 2.3 40 29-68 30-71 (392)
37 cd00567 ACAD Acyl-CoA dehydrog 87.1 1.6 3.4E-05 25.6 3.8 37 2-38 6-42 (327)
38 COG4953 PbpC Membrane carboxyp 75.4 23 0.0005 24.1 6.4 40 28-68 405-452 (733)
39 PF09652 Cas_VVA1548: Putative 74.2 6.1 0.00013 19.8 2.7 37 25-61 40-80 (93)
40 PF10597 U5_2-snRNA_bdg: U5-sn 69.8 1.7 3.8E-05 23.0 0.3 11 44-54 109-119 (135)
41 PF01870 Hjc: Archaeal hollida 66.8 6.9 0.00015 19.2 2.0 23 29-51 4-26 (88)
42 cd00072 GYF GYF domain: contai 64.9 12 0.00026 16.7 2.9 36 24-59 14-49 (57)
43 PF07355 GRDB: Glycine/sarcosi 64.4 18 0.00039 22.5 3.8 44 23-66 287-332 (349)
44 TIGR01917 gly_red_sel_B glycin 56.6 21 0.00046 22.8 3.2 44 23-66 283-328 (431)
45 COG3931 Predicted N-formylglut 52.0 9.2 0.0002 22.5 1.1 18 42-59 32-49 (263)
46 PF00650 CRAL_TRIO: CRAL/TRIO 51.2 8 0.00017 20.1 0.8 11 42-52 149-159 (159)
47 cd01709 RT_like_1 RT_like_1: A 50.9 12 0.00026 23.2 1.5 12 44-55 296-307 (346)
48 TIGR01918 various_sel_PB selen 50.5 29 0.00063 22.2 3.2 44 23-66 283-328 (431)
49 PF10431 ClpB_D2-small: C-term 47.1 32 0.00069 16.1 3.4 56 4-64 4-62 (81)
50 PF10546 P63C: P63C domain; I 45.7 40 0.00088 16.9 3.2 26 7-38 3-28 (94)
51 PF07862 Nif11: Nitrogen fixat 45.4 27 0.00059 14.8 4.1 39 3-41 3-42 (49)
52 PF05788 Orbi_VP1: Orbivirus R 45.1 10 0.00022 27.0 0.7 22 42-63 913-934 (1301)
53 PF15187 Augurin: Oesophageal 43.9 43 0.00094 17.2 2.7 37 4-40 26-62 (114)
54 PF12627 PolyA_pol_RNAbd: Prob 40.5 18 0.0004 16.0 1.0 23 25-47 37-59 (64)
55 COG4840 Uncharacterized protei 39.8 37 0.0008 16.0 1.9 16 53-68 53-68 (71)
56 PHA00435 capsid assembly prote 39.7 57 0.0012 19.8 3.1 28 18-45 147-174 (306)
57 COG4705 Uncharacterized membra 39.1 31 0.00068 20.1 1.9 20 43-62 215-234 (258)
58 PHA02087 hypothetical protein 38.3 8.9 0.00019 18.1 -0.2 32 27-58 31-72 (83)
59 TIGR03826 YvyF flagellar opero 38.0 68 0.0015 17.2 3.9 38 4-41 33-72 (137)
60 PF05046 Img2: Mitochondrial l 37.5 16 0.00034 17.9 0.5 39 2-40 41-87 (87)
61 TIGR03541 reg_near_HchA LuxR f 37.4 24 0.00052 20.1 1.4 19 29-47 101-119 (232)
62 TIGR03798 ocin_TIGR03798 bacte 34.8 51 0.0011 14.9 3.9 38 4-41 2-40 (64)
63 PF11314 DUF3117: Protein of u 34.1 44 0.00095 14.7 1.6 27 41-67 19-48 (51)
64 PF13101 DUF3945: Protein of u 33.9 47 0.001 14.9 1.8 22 42-63 23-44 (59)
65 PF11248 DUF3046: Protein of u 32.1 62 0.0013 15.0 2.1 16 23-38 41-56 (63)
66 cd00170 SEC14 Sec14p-like lipi 31.6 18 0.00039 18.3 0.2 20 32-52 138-157 (157)
67 PF02518 HATPase_c: Histidine 31.2 71 0.0015 15.4 2.8 41 26-66 48-88 (111)
68 PRK10857 DNA-binding transcrip 30.9 33 0.00072 18.7 1.2 25 27-52 41-65 (164)
69 TIGR02010 IscR iron-sulfur clu 30.0 24 0.00053 18.3 0.6 25 27-52 41-65 (135)
70 TIGR02625 YiiL_rotase L-rhamno 29.6 49 0.0011 16.7 1.6 21 25-45 21-41 (102)
71 PF06569 DUF1128: Protein of u 29.4 69 0.0015 15.3 2.0 16 53-68 53-68 (71)
72 PF08343 RNR_N: Ribonucleotide 28.8 81 0.0017 15.3 2.6 17 3-19 23-39 (82)
73 KOG3490|consensus 28.4 66 0.0014 16.6 1.9 19 24-42 84-102 (111)
74 PF07370 DUF1489: Protein of u 28.0 77 0.0017 17.1 2.2 17 25-41 121-137 (137)
75 PF14278 TetR_C_8: Transcripti 27.9 68 0.0015 14.2 2.3 6 7-12 35-40 (77)
76 PF08564 CDC37_C: Cdc37 C term 27.6 70 0.0015 16.2 1.9 16 29-44 53-68 (99)
77 PTZ00304 NADH dehydrogenase [u 27.5 69 0.0015 20.8 2.3 24 27-56 59-82 (461)
78 smart00516 SEC14 Domain in hom 27.3 25 0.00055 18.1 0.3 12 42-53 146-157 (158)
79 PRK09303 adaptive-response sen 26.9 1.6E+02 0.0034 18.0 3.7 41 25-66 315-355 (380)
80 PF14542 Acetyltransf_CG: GCN5 26.5 51 0.0011 15.5 1.3 22 43-64 28-49 (78)
81 PF10073 DUF2312: Uncharacteri 26.3 89 0.0019 15.0 2.7 10 3-12 3-12 (74)
82 COG5458 Uncharacterized conser 25.9 84 0.0018 16.7 2.1 16 26-41 129-144 (144)
83 PRK06035 3-hydroxyacyl-CoA deh 25.5 1.5E+02 0.0033 17.4 3.9 27 27-54 260-287 (291)
84 TIGR01913 bet_lambda phage rec 25.5 22 0.00048 20.0 -0.1 27 26-52 155-181 (188)
85 PF09859 Oxygenase-NA: Oxygena 25.4 1.4E+02 0.003 16.8 4.3 41 3-43 15-62 (173)
86 COG1640 MalQ 4-alpha-glucanotr 24.9 71 0.0015 21.1 2.0 23 24-46 353-375 (520)
87 COG2964 Uncharacterized protei 24.9 1.6E+02 0.0034 17.3 3.9 15 29-43 176-190 (220)
88 KOG1471|consensus 24.7 39 0.00084 20.0 0.8 12 44-55 248-259 (317)
89 PF08013 Tagatose_6_P_K: Tagat 24.0 99 0.0021 20.0 2.5 21 47-67 54-75 (424)
90 PF02382 RTX: RTX N-terminal d 24.0 94 0.002 21.1 2.4 27 41-67 45-72 (653)
91 PF15519 RBM39linker: linker b 23.9 26 0.00056 16.6 0.0 20 48-67 7-26 (73)
92 COG1591 Holliday junction reso 23.4 63 0.0014 17.4 1.4 24 26-49 8-31 (137)
93 TIGR03562 osmo_induc_OsmC pero 23.4 1.3E+02 0.0028 15.8 2.6 21 42-62 29-50 (135)
94 PF13309 HTH_22: HTH domain 22.8 95 0.0021 14.1 2.3 16 29-44 27-42 (64)
95 PRK13694 hypothetical protein; 22.7 1.1E+02 0.0025 15.0 2.4 9 4-12 12-20 (83)
96 PF11909 NdhN: NADH-quinone ox 22.6 96 0.0021 17.0 1.9 20 29-48 8-27 (154)
97 PLN03244 alpha-amylase; Provis 22.5 58 0.0013 22.9 1.4 20 38-57 588-607 (872)
98 PF14433 SUKH-3: SUKH-3 immuni 22.4 91 0.002 16.3 1.9 13 29-41 2-14 (142)
99 PF04458 DUF505: Protein of un 22.4 1.1E+02 0.0024 20.7 2.5 20 23-42 101-120 (591)
100 PF03682 UPF0158: Uncharacteri 22.3 84 0.0018 17.2 1.8 8 28-35 150-157 (163)
101 PF15552 DUF4657: Domain of un 22.1 61 0.0013 19.6 1.3 18 51-68 123-141 (301)
102 PRK15053 dpiB sensor histidine 21.9 2.2E+02 0.0049 18.1 4.0 39 25-65 478-516 (545)
103 TIGR03563 perox_SACOL1771 pero 21.9 1.3E+02 0.0029 15.6 2.4 20 42-61 27-48 (138)
104 COG0219 CspR Predicted rRNA me 21.8 1.3E+02 0.0028 16.6 2.4 40 24-66 105-146 (155)
105 TIGR00217 malQ 4-alpha-glucano 21.7 1E+02 0.0022 20.3 2.2 24 24-47 361-384 (513)
106 COG0386 BtuE Glutathione perox 21.7 1E+02 0.0022 17.1 2.0 26 29-54 47-73 (162)
107 PRK13596 NADH dehydrogenase I 21.4 1E+02 0.0023 19.8 2.2 24 27-56 39-62 (433)
108 PF07927 YcfA: YcfA-like prote 21.4 90 0.002 13.3 1.7 14 29-42 2-15 (56)
109 TIGR03059 psaOeuk photosystem 21.3 93 0.002 15.1 1.6 20 48-67 21-40 (82)
110 COG4558 ChuT ABC-type hemin tr 20.9 1.1E+02 0.0025 18.7 2.2 27 26-52 109-135 (300)
111 PRK11278 NADH dehydrogenase I 20.7 1.1E+02 0.0023 19.9 2.2 24 27-56 47-70 (448)
112 cd08801 Death_UNC5D Death doma 20.5 1.4E+02 0.003 15.1 2.2 14 55-68 62-75 (98)
113 PF07098 DUF1360: Protein of u 20.4 1E+02 0.0022 15.8 1.7 19 3-21 15-33 (105)
114 COG3185 4-hydroxyphenylpyruvat 20.2 1E+02 0.0022 19.5 1.9 21 29-49 257-277 (363)
No 1
>PF02771 Acyl-CoA_dh_N: Acyl-CoA dehydrogenase, N-terminal domain; InterPro: IPR006092 Mammalian Co-A dehydrogenases (1.3.99.3 from EC) are enzymes that catalyse the first step in each cycle of beta-oxidation in mitochondion. Acyl-CoA dehydrogenases [, , ] catalyze the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with concommitant reduction of enzyme-bound FAD. Reoxidation of the flavin involves transfer of electrons to ETF (electron transfering flavoprotein). These enzymes are homodimers containing one molecule of FAD. The monomeric enzyme is folded into three domains of approximately equal size. The N-terminal and the C-terminal are mainly alpha-helices packed together, and the middle domain consists of two orthogonal beta-sheets. The flavin ring is buried in the crevise between two alpha-helical domains and the beta-sheet of one subunit, and the adenosine pyrophosphate moiety is stretched into the subunit junction with one formed by two C-terminal domains []. The N-terminal domain of Acyl-CoA dehydrogenase is an all-alpha domain, on dimerisation, the N-terminal of one molecule extends into the other dimer and lies on the surface of the molecule.; GO: 0003995 acyl-CoA dehydrogenase activity, 0055114 oxidation-reduction process; PDB: 2WBI_B 1SIQ_A 1SIR_A 2R0N_A 2R0M_A 2DVL_A 1UKW_B 3MDD_B 1UDY_C 3MDE_B ....
Probab=99.75 E-value=3.4e-18 Score=86.57 Aligned_cols=68 Identities=43% Similarity=0.794 Sum_probs=63.0
Q ss_pred CHHHHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 1 MLQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
++++.+++|+++++.|...++|.++.+|+++|+++++.||+++.+|++|||.++++.+.+++.+++++
T Consensus 6 ~l~~~~~~~~~~~~~~~~~~~d~~~~~p~~~~~~l~~~G~~~~~~p~~~GG~~~~~~~~~~~~e~l~~ 73 (113)
T PF02771_consen 6 ALREEAREFAEEEIAPHAAEWDEDGRFPREVWRALGEAGLLGLAVPEEYGGLGLSPLELAIVLEELAR 73 (113)
T ss_dssp HHHHHHHHHHHHHTHHHHHHHHHHTSCHHHHHHHHHHTTTTSTTSCGGGTSEB-THHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHchHHHHHHHHhCCCCHHHHHHHHHHHHhhhhccccccCcchhhhhHHHHHHhhhh
Confidence 37899999999999999999988889999999999999999999999999999999999999999874
No 2
>KOG0141|consensus
Probab=99.71 E-value=2.2e-17 Score=95.74 Aligned_cols=68 Identities=43% Similarity=0.692 Sum_probs=64.8
Q ss_pred CHHHHHHHHHHhhhchhHHHhhhhCCCC--HHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 1 MLQKTCRDFAQQELKPIAAKLDKEHLFP--ADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
++++++++|+++++.|.+.++|....|+ +++|+++++.|+++++.|++|||.|+++...++++||++|
T Consensus 47 ~~r~sv~kF~qeelaP~a~eidk~n~~~~~r~~WkklG~~gllGita~~~~GG~G~~y~~h~ivmEE~sr 116 (421)
T KOG0141|consen 47 QLRESVRKFFQEELAPHASEIDKANEFKDLREFWKKLGKQGLLGITAPEEYGGSGGGYLSHCIVMEEISR 116 (421)
T ss_pred HHHHHHHHHHHHhhcchhhhhhhcCCcchHHHHHHHhhhcCcccccchhhhCCCchhHHHHHHHHHHHHh
Confidence 3789999999999999999999999994 8999999999999999999999999999999999999986
No 3
>KOG0139|consensus
Probab=99.67 E-value=2.2e-16 Score=92.26 Aligned_cols=67 Identities=55% Similarity=0.873 Sum_probs=65.2
Q ss_pred HHHHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++.+++|+.+.+.|..+++|+++.+|..+++.+.++|++++.+|++|||.|.++..+.+++||+++
T Consensus 44 l~~tvrkfa~~~i~Plv~~mD~~~~~~~~v~k~~fe~Glmgv~vpeeyGGsG~df~~~~~v~EEisk 110 (398)
T KOG0139|consen 44 LQKTVRKFAQEEIKPLVREMDRESRYPASVIKGLFELGLMGVEVPEEYGGSGLDFFAAAIVIEEISK 110 (398)
T ss_pred HHHHHHHHHHHhcchHHHhhhhhccCCHHHHHHHhhcCcceeecChhhCCCchhHHHHHHHHHHHhc
Confidence 6789999999999999999999999999999999999999999999999999999999999999985
No 4
>cd01157 MCAD Medium chain acyl-CoA dehydrogenase. MCADs are mitochondrial beta-oxidation enzymes, which catalyze the alpha,beta dehydrogenation of the corresponding medium chain acyl-CoA by FAD, which becomes reduced. The reduced form of MCAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. MCAD is a homotetramer.
Probab=99.62 E-value=1.8e-15 Score=89.35 Aligned_cols=67 Identities=40% Similarity=0.618 Sum_probs=63.4
Q ss_pred HHHHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++.+++|+++++.|...++|..+.+|.++|+.+.+.||+++.+|++|||.|++..+.+.+.+++++
T Consensus 8 l~~~~~~~~~~~~~~~~~~~d~~~~~p~~~~~~l~~~G~~~~~vP~~~GG~g~~~~~~~~v~e~l~~ 74 (378)
T cd01157 8 FQETARKFAREEIIPVAAEYDKSGEYPWPLIKRAWELGLMNTHIPEDCGGLGLGTFDTCLITEELAY 74 (378)
T ss_pred HHHHHHHHHHHhcccchHHHHhhCCCCHHHHHHHHhCCCCCcCCChhhCCCCCCHHHHHHHHHHHHh
Confidence 6899999999999998888888888999999999999999999999999999999999999999974
No 5
>KOG0140|consensus
Probab=99.61 E-value=3.1e-15 Score=86.80 Aligned_cols=67 Identities=39% Similarity=0.645 Sum_probs=64.8
Q ss_pred HHHHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++.+++|.++++.|.+.++|..+.||.+++++..++|+.+..+|++|||.|++..+.+++.|+|++
T Consensus 35 ~q~~A~kFa~~e~~P~aae~Dk~ge~P~~iirkA~~lG~~~~~ip~~~GG~Gls~l~t~lI~E~Lay 101 (408)
T KOG0140|consen 35 FQEAARKFAKDEMIPNAAEYDKSGEFPWEIIRKAHELGFMNTYIPEDYGGLGLSRLDTCLIFEALAY 101 (408)
T ss_pred HHHHHHHHHHHhhccchhhhcccCCCcHHHHHHHHHcccCcccCccccCCCCchhHHHHHHHHHHHc
Confidence 6789999999999999999999999999999999999999999999999999999999999999974
No 6
>cd01160 LCAD Long chain acyl-CoA dehydrogenase. LCAD is an acyl-CoA dehydrogenases (ACAD), which is found in the mitochondria of eukaryotes and in some prokaryotes. It catalyzes the alpha, beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of LCAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. LCAD acts as a homodimer.
Probab=99.61 E-value=3.1e-15 Score=88.16 Aligned_cols=68 Identities=35% Similarity=0.558 Sum_probs=63.6
Q ss_pred CHHHHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 1 MLQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
++++.+++|+++++.|...++|.++.+|+++|+.+.+.||+++.+|++|||.|+++.+.+.+.+++++
T Consensus 5 ~l~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~l~~~G~~~~~vP~~~GG~g~~~~~~~~~~e~la~ 72 (372)
T cd01160 5 AFRDVVRRFFAKEVAPFHHEWEKAGEVPREVWRKAGEQGLLGVGFPEEYGGIGGDLLSAAVLWEELAR 72 (372)
T ss_pred HHHHHHHHHHHHhCchhHHHHHhhCCCCHHHHHHHHhCCCCCCCCCHHHCCCCCCHHHHHHHHHHHHH
Confidence 36899999999999988888888888999999999999999999999999999999999999999875
No 7
>PRK03354 crotonobetainyl-CoA dehydrogenase; Validated
Probab=99.59 E-value=7.3e-15 Score=87.07 Aligned_cols=68 Identities=22% Similarity=0.418 Sum_probs=61.7
Q ss_pred CHHHHHHHHHHhhh-chhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 1 MLQKTCRDFAQQEL-KPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 1 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
++++.+++|+.+++ .+...++|..+.+|.++|+.|.+.||+++.+|++|||.|+++.+.+.+.+++++
T Consensus 11 ~~~~~~r~~~~~~~~~~~~~~~d~~~~~p~~~~~~l~~~Gl~~~~vP~~~GG~g~~~~~~~~~~~~la~ 79 (380)
T PRK03354 11 LFVAGIRELMASENWEAYFAECDRDSVYPERFVKALADMGIDSLLIPEEHGGLDAGFVTLAAVWMELGR 79 (380)
T ss_pred HHHHHHHHHHHhccCChhHHHHHhhCCCCHHHHHHHHHCCCCccCCChhhCCCCCCHHHHHHHHHHHHh
Confidence 37899999999876 466667888888999999999999999999999999999999999999999975
No 8
>TIGR03207 cyc_hxne_CoA_dh cyclohexanecarboxyl-CoA dehydrogenase. Cyclohex-1-ene-1carboxyl-CoA is an intermediate in the anaerobic degradation of benzoyl-CoA derived from varioius aromatic compounds, in Rhodopseudomonas palustris but not Thauera aromatica. The aliphatic compound cyclohexanecarboxylate, can be converted to the same intermediate in two steps. The first step is its ligation to coenzyme A. The second is the action of this enzyme, cyclohexanecarboxyl-CoA dehydrogenase.
Probab=99.58 E-value=7.8e-15 Score=86.66 Aligned_cols=67 Identities=33% Similarity=0.572 Sum_probs=63.2
Q ss_pred HHHHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++.+++|+++.+.|...+.|..+.+|+++|+.+.+.||+++.+|++|||.|+++.+.+.+.+++++
T Consensus 8 l~~~~~~~~~~~~~p~~~~~d~~~~~~~~~~~~l~~~G~~~l~vP~~~GG~g~~~~~~~~~~e~la~ 74 (372)
T TIGR03207 8 LADTARRFARERIAPGFKERDKTRVLDRELMRDMGEMGFIGPELPEEHGGLGMGCLAAGVIHEQIAR 74 (372)
T ss_pred HHHHHHHHHHHhcCcchHHHHhhCCCCHHHHHHHHHCCCCcccCChhHCCCCCCHHHHHHHHHHHHh
Confidence 6799999999999998888888888999999999999999999999999999999999999999975
No 9
>cd01151 GCD Glutaryl-CoA dehydrogenase. Glutaryl-CoA dehydrogenase (GCD). GCD is an acyl-CoA dehydrogenase, which catalyzes the oxidative decarboxylation of glutaryl-CoA to crotonyl-CoA and carbon dioxide in the catabolism of lysine, hydroxylysine, and tryptophan. It uses electron transfer flavoprotein (ETF) as an electron acceptor. GCD is a homotetramer. GCD deficiency leads to a severe neurological disorder in humans.
Probab=99.58 E-value=9.5e-15 Score=86.69 Aligned_cols=66 Identities=33% Similarity=0.607 Sum_probs=61.9
Q ss_pred HHHHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++.+++|+++++.|...+.|..+.+|.++|+++.+.||+++ +|++|||.|+++.+...+.+++++
T Consensus 20 ~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~l~~~Gl~~~-vP~~~GG~g~~~~~~~~v~e~l~~ 85 (386)
T cd01151 20 IRDTAREFCQEELAPRVLEAYREEKFDRKIIEEMGELGLLGA-TIKGYGCAGLSSVAYGLIAREVER 85 (386)
T ss_pred HHHHHHHHHHHhcCccHHHHHHhCCCCHHHHHHHHHCCCCcc-CccccCCCCCCHHHHHHHHHHHHh
Confidence 678999999999999888888888899999999999999999 999999999999999999999874
No 10
>TIGR03203 pimD_small pimeloyl-CoA dehydrogenase, small subunit. Members of this protein family are the PimD proteins of species such as Rhodopseudomonas palustris, Bradyrhizobium japonicum. The pimFABCDE operon encodes proteins for the metabolism of straight chain dicarboxylates of seven to fourteen carbons. Especially relevant is pimeloyl-CoA, basis of the gene symbol, as it is a catabolite of benzoyl-CoA degradation, which occurs in Rhodopseudomonas palustris.
Probab=99.58 E-value=1.1e-14 Score=86.54 Aligned_cols=68 Identities=18% Similarity=0.294 Sum_probs=60.5
Q ss_pred CHHHHHHHHHHhhhchhHH--HhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 1 MLQKTCRDFAQQELKPIAA--KLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
++++.+++|+++++.+... .+|..+.||+++|+.+.+.||+++.+|++|||.|++..+.+++.|++++
T Consensus 10 ~l~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~l~e~G~~~l~vPe~~GG~G~~~~~~~~v~eel~~ 79 (378)
T TIGR03203 10 LLKESVEGLLKTSYDFDSRKKYQKEKGGWSKAVWGKLAEQGLLGLPFSEADGGFGAGSVETMIVMEALGK 79 (378)
T ss_pred HHHHHHHHHHHhhCCHHHHHHHHhccCCCCHHHHHHHHHCCCcccccchhcCCCCCCHHHHHHHHHHHhC
Confidence 3789999999998876543 3466778999999999999999999999999999999999999999975
No 11
>cd01156 IVD Isovaleryl-CoA dehydrogenase. Isovaleryl-CoA dehydrogenase (IVD) is an is an acyl-CoA dehydrogenase, which catalyzes the third step in leucine catabolism, the conversion of isovaleryl-CoA (3-methylbutyryl-CoA) into 3-methylcrotonyl-CoA. IVD is a homotetramer and has the greatest affinity for small branched chain substrates.
Probab=99.57 E-value=1.1e-14 Score=85.93 Aligned_cols=67 Identities=48% Similarity=0.897 Sum_probs=63.0
Q ss_pred HHHHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++.+++|+++++.|.+.+.|..+.+|+++|+.+.+.||+++.+|++|||.|+++.+...+.+++++
T Consensus 9 l~~~~~~~~~~~~~~~a~~~d~~~~~~~~~~~~l~~~Gl~~~~vP~e~GG~g~~~~~~~~~~e~la~ 75 (376)
T cd01156 9 LRQSVREFAQKEIAPLAAKIDRDNEFPRDLWRKMGKLGLLGITAPEEYGGSGMGYLAHVIIMEEISR 75 (376)
T ss_pred HHHHHHHHHHHhcCcchHHHHhhCCCCHHHHHHHHhCCCCcccCCHhhCCCCCCHHHHHHHHHHHhc
Confidence 6899999999999998888888888999999999999999999999999999999999999999875
No 12
>PTZ00461 isovaleryl-CoA dehydrogenase; Provisional
Probab=99.56 E-value=1.6e-14 Score=86.42 Aligned_cols=67 Identities=36% Similarity=0.560 Sum_probs=63.0
Q ss_pred HHHHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++.+++|+.+++.|.+.+.|..+.+|+++|+.+.+.||+++.+|++|||.|+++.+...+.+++++
T Consensus 44 l~~~~~~~~~~~~~~~a~~~d~~~~~~~~~~~~l~~~Gl~~l~vP~~~GG~g~~~~~~~~~~e~la~ 110 (410)
T PTZ00461 44 LRETVAKFSREVVDKHAREDDINMHFNRDLFKQLGDLGVMGVTVPEADGGAGMDAVAAVIIHHELSK 110 (410)
T ss_pred HHHHHHHHHHHhCCccHHHHhhhCCCCHHHHHHHHHCCCCcccCChhhCCCCCCHHHHHHHHHHHHh
Confidence 6789999999999998888888889999999999999999999999999999999999999999875
No 13
>cd01162 IBD Isobutyryl-CoA dehydrogenase. Isobutyryl-CoA dehydrogenase (IBD) catalyzes the alpha, beta- dehydrogenation of short branched chain acyl-CoA intermediates in valine catabolism. It is predicted to be a homotetramer.
Probab=99.56 E-value=1.5e-14 Score=85.55 Aligned_cols=68 Identities=32% Similarity=0.659 Sum_probs=63.5
Q ss_pred CHHHHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 1 MLQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
++++.+++|+++++.|.+.++|..+.+|+++|+.+.+.||+++.+|++|||.|++..+.+.+.+++++
T Consensus 7 ~l~~~~~~~~~~~~~~~a~~~d~~~~~p~~~~~~l~~~Gl~~~~vP~~~GG~g~~~~~~~~~~~~l~~ 74 (375)
T cd01162 7 AIQEVARAFAAKEMAPHAADWDQKKHFPVDVLRKAAELGFGGIYIRDDVGGSGLSRLDASIIFEALST 74 (375)
T ss_pred HHHHHHHHHHHHhCCcchhhHHhhCCCCHHHHHHHHHCCCCCcCCCHhhCCCCCCHHHHHHHHHHHHh
Confidence 37899999999999998888888889999999999999999999999999999999999999999874
No 14
>cd01155 ACAD_FadE2 Acyl-CoA dehydrogenases similar to fadE2. FadE2-like Acyl-CoA dehydrogenase (ACAD). Acyl-CoA dehydrogenases (ACAD) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACAD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. ACAD's are generally homotetramers and have an active site glutamate at a conserved position.
Probab=99.54 E-value=2.3e-14 Score=85.28 Aligned_cols=68 Identities=21% Similarity=0.243 Sum_probs=58.9
Q ss_pred CHHHHHHHHHHhhhchhHHHhhhh-----------CCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 1 MLQKTCRDFAQQELKPIAAKLDKE-----------HLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
++++.+++|+++++.|...++|+. ..+++++|+.+++.||+++.+|++|||.|+++.+.+.+.|++++
T Consensus 5 ~~~~~~r~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~l~~P~~~GG~g~~~~~~~~v~e~l~~ 83 (394)
T cd01155 5 ELRARVKAFMEEHVYPAEQEFLEYYAEGGDRWWTPPPIIEKLKAKAKAEGLWNLFLPEVSGLSGLTNLEYAYLAEETGR 83 (394)
T ss_pred HHHHHHHHHHHHhcCccHHHHHhhcccccccccCCchhHHHHHHHHHhCCCCCCCCChhhCCCCcCHHHHHHHHHHHhh
Confidence 378999999999999987777643 12336899999999999999999999999999999999999974
No 15
>PLN02519 isovaleryl-CoA dehydrogenase
Probab=99.53 E-value=3.7e-14 Score=84.73 Aligned_cols=67 Identities=40% Similarity=0.688 Sum_probs=62.0
Q ss_pred HHHHHHHHHHhhhchhHHHhhhhCCCCHH--HHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDKEHLFPAD--QIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++.+++|+++++.|...++|..+.+|.+ +|+.|.+.||+++.+|++|||.|+++.+.+.+.+++++
T Consensus 33 ~~~~~~~~~~~~~~~~a~~~d~~~~~p~~~~~~~~l~~~G~~~~~vP~e~GG~g~~~~~~~~v~e~la~ 101 (404)
T PLN02519 33 FKESVQQFAQENIAPHAAAIDATNSFPKDVNLWKLMGDFNLHGITAPEEYGGLGLGYLYHCIAMEEISR 101 (404)
T ss_pred HHHHHHHHHHHhCCcchHHHHhcCCCCchHHHHHHHHHCCCCcccCChhhCCCCCCHHHHHHHHHHHhh
Confidence 67899999999999988888888888865 79999999999999999999999999999999999975
No 16
>PRK12341 putative acyl-CoA dehydrogenase; Provisional
Probab=99.53 E-value=6.1e-14 Score=83.16 Aligned_cols=67 Identities=21% Similarity=0.396 Sum_probs=61.4
Q ss_pred HHHHHHHHHHhhhc-hhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQELK-PIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++.++.|+.+.+. +...++|+.+.+|.++|+.+.+.||+++.+|++|||.|+++.+.+.+.+++++
T Consensus 12 ~~~~~~~~~~~~~~~~~~~~~d~~~~~p~~~~~~l~~~Gl~~~~vP~~~GG~g~~~~~~~~~~e~la~ 79 (381)
T PRK12341 12 LLASIRELITRNFPEEYFRTCDENGTYPREFMRALADNGISMLGVPEEFGGTPADYVTQMLVLEEVSK 79 (381)
T ss_pred HHHHHHHHHHHhcCchhHHHHHHhCCCCHHHHHHHHHCCCCCcCCChhhCCCCcCHHHHHHHHHHHhh
Confidence 67899999999886 46677888888999999999999999999999999999999999999999975
No 17
>TIGR03204 pimC_large pimeloyl-CoA dehydrogenase, large subunit. Members of this protein family are the PimC proteins of species such as Rhodopseudomonas palustris and Bradyrhizobium japonicum. The pimFABCDE operon encodes proteins for the metabolism of straight chain dicarboxylates of seven to fourteen carbons. Especially relevant is pimeloyl-CoA, basis of the gene symbol, as it is a catabolite of benzoyl-CoA degradation, which occurs in Rhodopseudomonas palustris.
Probab=99.51 E-value=9.4e-14 Score=82.88 Aligned_cols=68 Identities=15% Similarity=0.199 Sum_probs=57.9
Q ss_pred CHHHHHHHHHHhhhchhHHHh-hhhCCCCH----HHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 1 MLQKTCRDFAQQELKPIAAKL-DKEHLFPA----DQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~----~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
++++++++|+.+++.|...+. .....+|. ++|+.+.+.||+++.+|++|||.|+++.+.+.+.|++++
T Consensus 10 ~l~~~~r~f~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~l~e~G~~gl~vPe~~GG~G~~~~~~~~v~eelg~ 82 (395)
T TIGR03204 10 AFRDEVRSFFKDNVPADTRQKLVEGRHLTKDEMVTWWRILNKKGWGVSHWPKQYGGTGWTSVQHYIFNEELQS 82 (395)
T ss_pred HHHHHHHHHHHHhCChhhhhhhhccCCCChHHHHHHHHHHHhCCCCCCCCCcccCCCCCCHHHHHHHHHHHHh
Confidence 378999999999998865443 23334563 899999999999999999999999999999999999975
No 18
>cd01158 SCAD_SBCAD Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases. Short chain acyl-CoA dehydrogenase (SCAD). SCAD is a mitochondrial beta-oxidation enzyme. It catalyzes the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of SCAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. This subgroup also contains the eukaryotic short/branched chain acyl-CoA dehydrogenase(SBCAD), the bacterial butyryl-CoA dehydorgenase(BCAD) and 2-methylbutyryl-CoA dehydrogenase, which is involved in isoleucine catabolism. These enzymes are homotetramers.
Probab=99.50 E-value=9.2e-14 Score=81.89 Aligned_cols=67 Identities=52% Similarity=0.929 Sum_probs=62.5
Q ss_pred HHHHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++.+++|+.+++.+.+.+.|..+.+|.++|+.+.+.||+++.+|++|||.|.++.+.+.+.+++++
T Consensus 6 ~~~~~~~~~~~~~~~~a~~~d~~~~~~~~~~~~l~~~Gl~~l~vP~e~GG~g~~~~~~~~v~~~l~~ 72 (373)
T cd01158 6 IRKTVRDFAEKEIAPLAAEMDEKGEFPREVIKEMAELGLMGIPIPEEYGGAGLDFLAYAIAIEELAK 72 (373)
T ss_pred HHHHHHHHHHHhcccchHHHhhcCCCCHHHHHHHHhCCCCcccCCHHHCCCCCCHHHHHHHHHHHHh
Confidence 6889999999989888888888888999999999999999999999999999999999999999874
No 19
>cd01161 VLCAD Very long chain acyl-CoA dehydrogenase. VLCAD is an acyl-CoA dehydrogenase (ACAD), which is found in the mitochondria of eukaryotes and in some bacteria. It catalyzes the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. VLCAD acts as a homodimer.
Probab=99.47 E-value=1.8e-13 Score=81.89 Aligned_cols=65 Identities=31% Similarity=0.482 Sum_probs=59.4
Q ss_pred HHHHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++.+++|+++++.|. .++..+.+|.++|+.+.+.||+++.+|++|||.|++..+...+.+++++
T Consensus 34 l~~~~~~~~~~~~~~~--~~d~~~~~~~~~~~~l~~~Gl~~l~vP~~~GG~g~~~~~~~~v~e~l~~ 98 (409)
T cd01161 34 LVGPVEKFFEEVNDPA--KNDQLEKIPRKTLTQLKELGLFGLQVPEEYGGLGLNNTQYARLAEIVGM 98 (409)
T ss_pred HHHHHHHHHHHhCCch--hhccccCCCHHHHHHHHhCCCCCCCCChhhCCCCCCHHHHHHHHHHHhh
Confidence 6799999999998875 3566778999999999999999999999999999999999999999975
No 20
>cd01153 ACAD_fadE5 Putative acyl-CoA dehydrogenases similar to fadE5. Putative acyl-CoA dehydrogenase (ACAD). Mitochondrial acyl-CoA dehydrogenases (ACAD) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. The mitochondrial ACD's are generally homotetramers and have an active site glutamate at a conserved position.
Probab=99.46 E-value=3.9e-13 Score=80.45 Aligned_cols=67 Identities=27% Similarity=0.440 Sum_probs=60.4
Q ss_pred HHHHHHHHHHhhhchhHHHhhhhCC--------CC---HHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDKEHL--------FP---ADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~--------~~---~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++++++|+.+.+.|.+.++|.+.. || .++|+.|.+.||+++.+|++|||.|+++.+...+.+++++
T Consensus 1 ~~~~~~~~~~~~~~~~a~~~d~~~~~~~~~~~~~p~~~~e~~~~l~~~Gl~~~~vP~e~GG~g~~~~~~~~~~e~l~~ 78 (407)
T cd01153 1 VLEEVARLAENVLAPLNADGDREGPVFDDGRVVVPPPFKEALDAFAEAGWMALGVPEEYGGQGLPITVYSALAEIFSR 78 (407)
T ss_pred ChHHHHHHHHHHhhhhHHhHhccCCcccCCceEcChhHHHHHHHHHHCCCCCCCCccccCCCCCCHHHHHHHHHHHHh
Confidence 4789999999999998888887654 88 6789999999999999999999999999999999999874
No 21
>PLN02526 acyl-coenzyme A oxidase
Probab=99.44 E-value=5.6e-13 Score=79.95 Aligned_cols=66 Identities=35% Similarity=0.572 Sum_probs=60.6
Q ss_pred HHHHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++.+++|+++++.|...+.+....+|.++|+++.+.||+++.+ ++|||.|+++.+.+.+++++++
T Consensus 36 l~~~~~~f~~~~~~~~~~~~~~~~~~p~~~~~~l~~~G~~~~~v-~~~GG~G~~~~~~~~~~e~la~ 101 (412)
T PLN02526 36 LRKRVRECMEKEVAPIMTEYWEKAEFPFHIIPKLGSLGIAGGTI-KGYGCPGLSITASAIATAEVAR 101 (412)
T ss_pred HHHHHHHHHHHhcccchHHHHHhCCCCHHHHHHHHHCCCCcCcc-cccCCCCcCHHHHHHHHHHHHh
Confidence 68899999999998887776667789999999999999999999 9999999999999999999975
No 22
>cd01152 ACAD_fadE6_17_26 Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26. Putative acyl-CoA dehydrogenases (ACAD). Mitochondrial acyl-CoA dehydrogenases (ACAD) catalyze the alpha, beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. The mitochondrial ACD's are generally homotetramers and have an active site glutamate at a conserved position.
Probab=99.41 E-value=4.1e-13 Score=79.63 Aligned_cols=68 Identities=21% Similarity=0.238 Sum_probs=59.5
Q ss_pred CHHHHHHHHHHhhhchhHHH-----hhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 1 MLQKTCRDFAQQELKPIAAK-----LDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
++++.+++|+++++.|.... ++..+.+|.++++.|.+.||+++.+|++|||.|+++.+.+.+.+++++
T Consensus 5 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Gl~~l~vP~~~GG~g~~~~~~~~~~e~l~~ 77 (380)
T cd01152 5 AFRAEVRAWLAAHLPPELREESALGYREGREDRRRWQRALAAAGWAAPGWPKEYGGRGASLMEQLIFREEMAA 77 (380)
T ss_pred HHHHHHHHHHHhcCCccccccccccccccchHHHHHHHHHHhCCCCccCCChhhCCCCCCHHHHHHHHHHHHh
Confidence 36889999999999886532 244567899999999999999999999999999999999999999874
No 23
>cd01163 DszC Dibenzothiophene (DBT) desulfurization enzyme C. DszC is a flavin reductase dependent enzyme, which catalyzes the first two steps of DBT desulfurization in mesophilic bacteria. DszC converts DBT to DBT-sulfoxide, which is then converted to DBT-sulfone. Bacteria with this enzyme are candidates for the removal of organic sulfur compounds from fossil fuels, which pollute the environment. An equivalent enzyme tdsC, is found in thermophilic bacteria. This alignment also contains a closely related uncharacterized subgroup.
Probab=99.40 E-value=1.4e-12 Score=77.19 Aligned_cols=63 Identities=29% Similarity=0.393 Sum_probs=56.5
Q ss_pred HHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 5 TCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
.+++++. .+.+.+.++|+.+.+|.++|+.+.+.||+++.+|++|||.|+++.+...+.+++++
T Consensus 2 ~~~~~~~-~~~~~a~~~d~~~~~p~~~~~~l~~~G~~~l~vP~~~GG~g~~~~~~~~~~e~la~ 64 (377)
T cd01163 2 RARPLAA-RIAEGAAERDRQRGLPYEEVALLRQSGLGTLRVPKEYGGLGASLPDLYEVVRELAA 64 (377)
T ss_pred hHHHHHH-HHhhhhhhhhhcCCCCHHHHHHHHHCCCccccCchhhCCCCCCHHHHHHHHHHHHh
Confidence 3556665 47788888999999999999999999999999999999999999999999999975
No 24
>cd01159 NcnH Naphthocyclinone hydroxylase. Naphthocyclinone is an aromatic polyketide and an antibiotic, which is active against Gram-positive bacteria. Polyketides are secondary metabolites, which have important biological functions such as antitumor, immunosupressive or antibiotic activities. NcnH is a hydroxylase involved in the biosynthesis of naphthocyclinone and possibly other polyketides.
Probab=99.34 E-value=4.5e-12 Score=74.98 Aligned_cols=62 Identities=21% Similarity=0.447 Sum_probs=55.5
Q ss_pred HHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 6 CRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
++++++. +.+.+.++|.++.||.++|+.+++.||+++.+|++|||.|+++.+.+.+.+++++
T Consensus 3 ~~~~~~~-~~~~a~~~d~~~~~p~~~~~~l~~~Gl~~~~vP~e~GG~g~~~~~~~~~~e~la~ 64 (370)
T cd01159 3 AEDLAPL-IRERAPEAERARRLPDEVVRALREIGFFRMFVPKRYGGLEGDFAEFAEAIATLAE 64 (370)
T ss_pred HHHHHHH-HHHhHHHHHHcCCCCHHHHHHHHHCChHhhCCchhcCCCCCCHHHHHHHHHHHHh
Confidence 3445553 7788888999999999999999999999999999999999999999999999975
No 25
>PRK13026 acyl-CoA dehydrogenase; Reviewed
Probab=99.31 E-value=8.2e-12 Score=79.69 Aligned_cols=66 Identities=21% Similarity=0.425 Sum_probs=55.1
Q ss_pred HHHHHHHHHHhhhchh---HHHh---hhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHh
Q psy1305 2 LQKTCRDFAQQELKPI---AAKL---DKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIA 67 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~---~~~~---~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~ 67 (68)
+.++-++|+++.+.+. ..++ ++.+.+|+++|+.+++.||+++.+|++|||.|++..+.+.++++++
T Consensus 78 l~~eeq~fl~~~v~~l~~~~~e~~~~~~~~~~P~evw~~Lae~Gl~gl~IPeeyGGlG~s~~~~a~V~eela 149 (774)
T PRK13026 78 LTAEEQAFIDNEVETLLTMLDDWDIVQNRKDLPPEVWDYLKKEGFFALIIPKEYGGKGFSAYANSTIVSKIA 149 (774)
T ss_pred cCHHHHHHHHHHHHHHHhhhhhhhhhhhhcCCCHHHHHHHHHCCCCcCCCChhhCCCCCCHHHHHHHHHHHH
Confidence 3456777877776664 3333 3467899999999999999999999999999999999999999986
No 26
>PTZ00456 acyl-CoA dehydrogenase; Provisional
Probab=99.29 E-value=1.5e-11 Score=77.20 Aligned_cols=65 Identities=29% Similarity=0.389 Sum_probs=54.7
Q ss_pred HHHHHHHHHHhhhchhHHHhhhhCCC---------C---HHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHH
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDKEHLF---------P---ADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEI 66 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~---------~---~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l 66 (68)
+++++++|+.+++.|...+.|+++.+ | +++|+.+.+.||+++.+|++|||.|++......+.|.+
T Consensus 63 il~~a~~fa~~~~~p~~~~~D~~~~~~~~~g~v~~p~g~~e~~~~l~e~G~~~l~~Pee~GG~Gl~~~~~~~~~E~~ 139 (622)
T PTZ00456 63 LLEEASKLATQTLLPLYESSDSEGCVLLKDGNVTTPKGFKEAYQALKAGGWTGISEPEEYGGQALPLSVGFITRELM 139 (622)
T ss_pred HHHHHHHHHHHhcccchhhHhhccCccccCCcccCChhHHHHHHHHHHcCCCCCCCCcccCCCCcCHHHHHHHHHHH
Confidence 68999999999999988888876543 5 58999999999999999999999999987555555544
No 27
>PRK09463 fadE acyl-CoA dehydrogenase; Reviewed
Probab=99.23 E-value=5.5e-11 Score=76.08 Aligned_cols=45 Identities=20% Similarity=0.443 Sum_probs=42.5
Q ss_pred hCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 24 EHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 24 ~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
.+.+|+++|+.+++.||+++.+|++|||.|++..+.+.+.+++++
T Consensus 107 ~~~~P~e~w~~L~e~G~~gl~IPeeyGG~Gls~~~~a~v~eeLg~ 151 (777)
T PRK09463 107 LADLPPEVWQFIKEHGFFGMIIPKEYGGLEFSAYAHSRVLQKLAS 151 (777)
T ss_pred ccCCCHHHHHHHHHCCCCcCCCchhhCCCCCCHHHHHHHHHHHHh
Confidence 368999999999999999999999999999999999999999874
No 28
>PLN02876 acyl-CoA dehydrogenase
Probab=99.17 E-value=1.3e-10 Score=74.78 Aligned_cols=68 Identities=24% Similarity=0.394 Sum_probs=56.8
Q ss_pred CHHHHHHHHHHhhhchhHHHhhhh-------CCCC-HHHHHHHH-HcCCCcccCCcc-----------------------
Q psy1305 1 MLQKTCRDFAQQELKPIAAKLDKE-------HLFP-ADQIKKLG-ALGLMGVLVDEE----------------------- 48 (68)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~-~~~~~~l~-~~G~~~~~~p~~----------------------- 48 (68)
++++++++|+++++.|...++++. ..+| .+.|+++. +.||+++.+|++
T Consensus 408 ~l~~~~~~f~~~~~~p~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~G~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~ 487 (822)
T PLN02876 408 ELRKKLIKFMEDHIYPMENEFYKLAQSSSRWTVHPEEERLKELAKKEGLWNLWIPLDSAARARKLLFEDNKHMVSGDSAD 487 (822)
T ss_pred HHHHHHHHHHHHHccCccHHHHhhcccccccccCcchHHHHHHHHHcCcccCCCCchhhhhhhhcccccccccccccccc
Confidence 378999999999988876665532 1377 57777775 999999999995
Q ss_pred -cCCCCCCHHHHHHHHHHHhC
Q psy1305 49 -YGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 49 -~GG~g~~~~~~~~~~e~l~~ 68 (68)
|||.|+++.+.+.+.|++++
T Consensus 488 ~~GG~G~~~~~~~~~~Eelg~ 508 (822)
T PLN02876 488 QLLGAGLSNLEYGYLCEIMGR 508 (822)
T ss_pred cCCCCCCCHHHHHHHHHHHhc
Confidence 99999999999999999975
No 29
>COG1960 CaiA Acyl-CoA dehydrogenases [Lipid metabolism]
Probab=99.17 E-value=1.1e-10 Score=69.46 Aligned_cols=67 Identities=40% Similarity=0.783 Sum_probs=60.1
Q ss_pred HHHHHHHHHHhhhchhHHHhhh---hCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDK---EHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++.+++|+.+.+.|...+.+. ...+|+++++.+.+.|++++.+|++|||.+.+......+.+++++
T Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~l~~~G~~~~~~p~e~GG~~~~~~~~~~~~e~l~~ 81 (393)
T COG1960 12 LRAEVREFAEEELAPEAAEIDRRIEDERFPRELLRALAEAGLLGLTIPEEYGGLGLSPLEQAAVLEELAR 81 (393)
T ss_pred HHHHHHHHHHHhcCcchhhhhhhcccccCHHHHHHHHHhCCcccCCCChhhCCCCcchhHHHHHHHHHHh
Confidence 5678999999989877776665 578889999999999999999999999999999999999999874
No 30
>KOG0138|consensus
Probab=98.91 E-value=4.2e-09 Score=61.79 Aligned_cols=66 Identities=24% Similarity=0.606 Sum_probs=62.5
Q ss_pred HHHHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++.+|++|++++.|+..+..++..|++++..+++..|+++..+ +.||..|.+.+.+.++..|+.|
T Consensus 62 ir~~~Reycq~~l~Prvtea~r~e~F~~~i~pemGsmGvlG~ti-kGYGCaG~S~vaygl~~rEveR 127 (432)
T KOG0138|consen 62 IRDTFREYCQERLMPRVTEANRNEVFDREIIPEMGSMGVLGPTI-KGYGCAGVSSVAYGLLAREVER 127 (432)
T ss_pred HHHHHHHHHHHHhhhHHHHHhhhccCChhhhhhhhccccccCcc-cCcCCCchHHHHHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999999 8999999999999999998864
No 31
>KOG0137|consensus
Probab=98.48 E-value=2.9e-07 Score=57.63 Aligned_cols=49 Identities=27% Similarity=0.380 Sum_probs=44.2
Q ss_pred HHhhhhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHh
Q psy1305 19 AKLDKEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIA 67 (68)
Q Consensus 19 ~~~~~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~ 67 (68)
+..|..+..++..++.|++.|++++.+|.+|+|.|+++.++..+.|.++
T Consensus 102 ~k~d~~~~~~~~t~e~l~elG~fgl~v~~e~~G~G~~ntq~arl~e~~~ 150 (634)
T KOG0137|consen 102 KKNDKLGKIEETTLEALRELGLFGLQVPSEFDGLGFCNTQYARLFEIVS 150 (634)
T ss_pred hhhhhhcccchhHHHHHHHhCceeeccCcccCccccchHHHHHHhhccc
Confidence 4466677889999999999999999999999999999999999988764
No 32
>PTZ00457 acyl-CoA dehydrogenase; Provisional
Probab=98.40 E-value=4.6e-07 Score=56.46 Aligned_cols=38 Identities=32% Similarity=0.439 Sum_probs=33.9
Q ss_pred HHHHHHHc-CCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 31 QIKKLGAL-GLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 31 ~~~~l~~~-G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+-+.+.++ ||+++.+|++|||.|++..+.+.+.|++++
T Consensus 55 ~~~~~~~l~Gl~gl~vPeeyGG~Gl~~~~~a~v~Eelgr 93 (520)
T PTZ00457 55 IRSNDKILGNLYGARIATEYGGLGLGHTAHALIYEEVGT 93 (520)
T ss_pred HHhchHhcCCccCCCCChhhCCCCCCHHHHHHHHHHHHh
Confidence 33367788 999999999999999999999999999975
No 33
>PLN02636 acyl-coenzyme A oxidase
Probab=97.52 E-value=0.00038 Score=45.06 Aligned_cols=61 Identities=13% Similarity=0.151 Sum_probs=48.7
Q ss_pred HHHHHHHHHHhhh---chhHHHhhhhCCCC-HHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 2 LQKTCRDFAQQEL---KPIAAKLDKEHLFP-ADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 2 ~~~~~~~~~~~~~---~~~~~~~~~~~~~~-~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+++.+++|+.+.+ .|....+++.+.++ +++++.+.+.|++++.+|++ ++.+...+.|++++
T Consensus 68 ~r~~v~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~~~~~g~~~~~~~~~------~~~~~~~~~e~l~~ 132 (686)
T PLN02636 68 IQEKIYEFFNSRPDLQTPVEISKDEHRELCMRQLTGLVREAGIRPMKYLVE------DPAKYFAITEAVGS 132 (686)
T ss_pred HHHHHHHHHHhCccccCCchhhHHHhhhhHHHHHHHHHHhcCccccccccC------CHHHHHHHHHHHHh
Confidence 5788999988774 56566677677788 88999999999999999875 67778888887753
No 34
>cd01154 AidB Proteins involved in DNA damage response, similar to the AidB gene product. AidB is one of several genes involved in the SOS adaptive response to DNA alkylation damage, whose expression is activated by the Ada protein. Its function has not been entirely elucidated; however, it is similar in sequence and function to acyl-CoA dehydrogenases. It has been proposed that aidB directly destroys DNA alkylating agents such as nitrosoguanidines (nitrosated amides) or their reaction intermediates.
Probab=97.45 E-value=0.00041 Score=42.28 Aligned_cols=46 Identities=15% Similarity=0.230 Sum_probs=33.9
Q ss_pred HHHHHHhhhchhHHHhhhhCC------CC---HHHHHHHHHcCCCcccCCcccCCCC
Q psy1305 6 CRDFAQQELKPIAAKLDKEHL------FP---ADQIKKLGALGLMGVLVDEEYGGAG 53 (68)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~------~~---~~~~~~l~~~G~~~~~~p~~~GG~g 53 (68)
..++++++ .|....+|..+. +| +++++.+.+.||+++ +|.++|+.|
T Consensus 37 ~~~~a~~~-~P~~~~~d~~g~r~~~v~~~~~~~~~~~~~~~~G~~~~-~~~~~~~~g 91 (418)
T cd01154 37 LARLADRN-PPVLEMWDRWGRRVDRVWVHPAWHALMRRLIEEGVINI-EDGPAGEGR 91 (418)
T ss_pred HHHHhhcC-CCcccCCCCCCCcCCeEEeCHHHHHHHHHHHHcCCccC-CchhhCCCc
Confidence 34455555 577777887777 77 789999999999999 666666544
No 35
>PLN02312 acyl-CoA oxidase
Probab=93.49 E-value=0.17 Score=33.28 Aligned_cols=43 Identities=19% Similarity=0.173 Sum_probs=32.7
Q ss_pred hhCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHHhC
Q psy1305 23 KEHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 23 ~~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+...++.+.++.+.+.|+++..+|++ |.+ +......+.|++++
T Consensus 102 ~~~~~~~~~~~~l~~~g~~~~~~pe~--g~~-~~~~~~~~~Eel~~ 144 (680)
T PLN02312 102 QQREITMKRILYLLERGVFRGWLTET--GPE-AELRKLALLEVIGI 144 (680)
T ss_pred HHHHhHHHHHHHHHHhhhcCCCCCCC--CCc-cHHHHHHHHHHHHH
Confidence 34456778999999999999999985 333 57777788887763
No 36
>KOG1469|consensus
Probab=91.07 E-value=0.24 Score=29.68 Aligned_cols=40 Identities=18% Similarity=0.209 Sum_probs=32.2
Q ss_pred HHHHHHHHHcCCCcccCCc--ccCCCCCCHHHHHHHHHHHhC
Q psy1305 29 ADQIKKLGALGLMGVLVDE--EYGGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 29 ~~~~~~l~~~G~~~~~~p~--~~GG~g~~~~~~~~~~e~l~~ 68 (68)
+.+-+..+..|++++.+|. +--|.|++.+++..+.|.+++
T Consensus 30 ekLKE~aK~eGlWNLFlp~~~qkyg~GLtnveYa~icElmGr 71 (392)
T KOG1469|consen 30 EKLKEMAKVEGLWNLFLPAVSQKYGAGLTNVEYAHICELMGR 71 (392)
T ss_pred HHHHHHHHhcchHHhhhHHHHHhhccCccchhHHHHHHHhcc
Confidence 3455555669999999995 335899999999999999875
No 37
>cd00567 ACAD Acyl-CoA dehydrogenase. Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast, AXO catalyzes a different oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities. The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isob
Probab=87.11 E-value=1.6 Score=25.61 Aligned_cols=37 Identities=32% Similarity=0.522 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHc
Q psy1305 2 LQKTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGAL 38 (68)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 38 (68)
+++.+++|+.+++.+.....+....++++.++.++..
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 42 (327)
T cd00567 6 LRDSAREFAAEELEPYARERRETPEEPWELLAELGLL 42 (327)
T ss_pred HHHHHHHHHHHhccccHHhHHhhCCCCHHHHHHHHHH
Confidence 6789999999988887765555444555555444443
No 38
>COG4953 PbpC Membrane carboxypeptidase/penicillin-binding protein PbpC [Cell envelope biogenesis, outer membrane]
Probab=75.37 E-value=23 Score=24.13 Aligned_cols=40 Identities=25% Similarity=0.380 Sum_probs=34.0
Q ss_pred CHHHHHHHHHcCCCcccCCccc--------CCCCCCHHHHHHHHHHHhC
Q psy1305 28 PADQIKKLGALGLMGVLVDEEY--------GGAGLDTLALHVAMEEIAQ 68 (68)
Q Consensus 28 ~~~~~~~l~~~G~~~~~~p~~~--------GG~g~~~~~~~~~~e~l~~ 68 (68)
|..+...|..+|+ .+..|+.+ ||.|.++.+.+.+...+++
T Consensus 405 p~rf~~rl~~ag~-~L~~P~~~~~GLsLiLGg~gi~L~dLa~lYa~lAn 452 (733)
T COG4953 405 PPRFAARLRQAGV-HLYLPEGAAPGLSLILGGAGITLEDLAQLYAALAN 452 (733)
T ss_pred hHHHHHHHHhCCC-CCCCCCccCCCeeEEecCCcccHHHHHHHHHHHhc
Confidence 6789999999999 78888874 7999999999988777653
No 39
>PF09652 Cas_VVA1548: Putative CRISPR-associated protein (Cas_VVA1548); InterPro: IPR013443 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved region of about 95 amino acids found exclusively in species with CRISPR repeats. In all bacterial species that contain this entry, the genes encoding the proteins are in the midst of a cluster of cas genes.
Probab=74.16 E-value=6.1 Score=19.79 Aligned_cols=37 Identities=14% Similarity=0.206 Sum_probs=32.0
Q ss_pred CCCCHHHHHHHHHcCC----CcccCCcccCCCCCCHHHHHH
Q psy1305 25 HLFPADQIKKLGALGL----MGVLVDEEYGGAGLDTLALHV 61 (68)
Q Consensus 25 ~~~~~~~~~~l~~~G~----~~~~~p~~~GG~g~~~~~~~~ 61 (68)
|..|-.+...+.+.|. +.+.+|.+.=|.+++..++..
T Consensus 40 GtLPvhLaA~vc~kGa~y~~L~l~lp~e~RG~ELsae~m~~ 80 (93)
T PF09652_consen 40 GTLPVHLAAEVCEKGARYYHLSLDLPAEQRGRELSAEQMRA 80 (93)
T ss_pred EeCcHHHHHHHHhCCcEEEEEEccCChHHcCCcccHHHHHh
Confidence 5789999999999998 788999999999999876643
No 40
>PF10597 U5_2-snRNA_bdg: U5-snRNA binding site 2 of PrP8; InterPro: IPR019581 The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis []. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor [].
Probab=69.75 E-value=1.7 Score=23.05 Aligned_cols=11 Identities=36% Similarity=0.773 Sum_probs=9.1
Q ss_pred cCCcccCCCCC
Q psy1305 44 LVDEEYGGAGL 54 (68)
Q Consensus 44 ~~p~~~GG~g~ 54 (68)
--|++.||+|+
T Consensus 109 YtPKElGGLGM 119 (135)
T PF10597_consen 109 YTPKELGGLGM 119 (135)
T ss_pred cChhhccccce
Confidence 35899999987
No 41
>PF01870 Hjc: Archaeal holliday junction resolvase (hjc); InterPro: IPR002732 This entry represents Holliday junction resolvases (hjc gene) and related proteins, primarily from archaeal species []. The Holliday junction is an essential intermediate of homologous recombination. Holliday junctions are four-stranded DNA complexes that are formed during recombination and related DNA repair events. In the presence of divalent cations, these junctions exist predominantly as the stacked-X form in which the double-helical segments are coaxially stacked and twisted by 60 degrees in a right-handed direction across the junction cross-over. In this structure, the stacked arms resemble two adjacent double-helices, but are linked at the junction by two common strands that cross-over between the duplexes []. During homologous recombination, genetic information is physically exchanged between parental DNAs via crossing single strands of the same polarity within the four-way Holliday structure. This process is terminated by the endonucleolytic activity of resolvases, which convert the four-way DNA back to two double strands.; PDB: 2WJ0_A 2WIZ_B 2WIW_B 2WCW_C 2WCZ_A 1HH1_A 1GEF_D 1IPI_B 2EO0_B 1OB9_A ....
Probab=66.85 E-value=6.9 Score=19.25 Aligned_cols=23 Identities=26% Similarity=0.244 Sum_probs=19.1
Q ss_pred HHHHHHHHHcCCCcccCCcccCC
Q psy1305 29 ADQIKKLGALGLMGVLVDEEYGG 51 (68)
Q Consensus 29 ~~~~~~l~~~G~~~~~~p~~~GG 51 (68)
+++.+.|.+.|+..+..|...++
T Consensus 4 rel~~~L~~~Gf~v~R~~~Sg~~ 26 (88)
T PF01870_consen 4 RELVKILWERGFAVVRAAGSGGG 26 (88)
T ss_dssp HHHHHHHHHTT-EEEEBSCCSSS
T ss_pred HHHHHHHHhCCcEEEEecCCCCc
Confidence 57899999999999999987665
No 42
>cd00072 GYF GYF domain: contains conserved Gly-Tyr-Phe residues; Proline-binding domain in CD2-binding and other proteins. Involved in signaling lymphocyte activity. Also present in other unrelated proteins (mainly unknown) derived from diverse eukaryotic species.
Probab=64.94 E-value=12 Score=16.73 Aligned_cols=36 Identities=17% Similarity=0.078 Sum_probs=27.9
Q ss_pred hCCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHH
Q psy1305 24 EHLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLAL 59 (68)
Q Consensus 24 ~~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~ 59 (68)
.|+|+.+-+....+.|++...++-...|.+.+....
T Consensus 14 qGPF~~~~M~~W~~~gyF~~~l~vr~~~~~~~f~~l 49 (57)
T cd00072 14 QGPFSASQMLQWYQAGYFPDGLQVRRLDNGGEFYTL 49 (57)
T ss_pred cCCcCHHHHHHHHHCCCCCCCeEEEECCCCCCcEEH
Confidence 578999999999999999999987766544444333
No 43
>PF07355 GRDB: Glycine/sarcosine/betaine reductase selenoprotein B (GRDB); InterPro: IPR022787 This entry represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. All members are expected to contain an internal UGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon. ; GO: 0030699 glycine reductase activity, 0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor, 0055114 oxidation-reduction process, 0030700 glycine reductase complex
Probab=64.41 E-value=18 Score=22.47 Aligned_cols=44 Identities=27% Similarity=0.448 Sum_probs=31.0
Q ss_pred hhCCCCHHHHHHHHHcCCCcccCCcccC--CCCCCHHHHHHHHHHH
Q psy1305 23 KEHLFPADQIKKLGALGLMGVLVDEEYG--GAGLDTLALHVAMEEI 66 (68)
Q Consensus 23 ~~~~~~~~~~~~l~~~G~~~~~~p~~~G--G~g~~~~~~~~~~e~l 66 (68)
.+.-+|-+.+++|.+.|.++-..|.-|+ |.|-+....-....++
T Consensus 287 ~N~v~PlD~LreL~~EG~IG~l~~~~yst~G~gt~~~~~~~~g~eI 332 (349)
T PF07355_consen 287 PNRVFPLDRLRELEKEGVIGSLAPYFYSTMGNGTAVANAKRFGPEI 332 (349)
T ss_pred CCeeeeHHHHHHHHHcCCcccccCeeEEcCCCCccHHHHHHHHHHH
Confidence 3456889999999999999999998886 4444444433344443
No 44
>TIGR01917 gly_red_sel_B glycine reductase, selenoprotein B. Glycine reductase is a complex with two selenoprotein subunits, A and B. This model represents the glycine reductase selenoprotein B. Closely related to it, but excluded from this model, are selenoprotein B subunits of betaine reductase and sarcosine reductase. All contain selenocysteine incorporated during translation at a specific UGA codon.
Probab=56.55 E-value=21 Score=22.80 Aligned_cols=44 Identities=20% Similarity=0.323 Sum_probs=30.5
Q ss_pred hhCCCCHHHHHHHHHcCCCcccCCcccCC--CCCCHHHHHHHHHHH
Q psy1305 23 KEHLFPADQIKKLGALGLMGVLVDEEYGG--AGLDTLALHVAMEEI 66 (68)
Q Consensus 23 ~~~~~~~~~~~~l~~~G~~~~~~p~~~GG--~g~~~~~~~~~~e~l 66 (68)
.+.-+|-+.+++|.+.|.++-..|.-|+= .|-+........+++
T Consensus 283 pn~v~PlD~LreLe~EG~IG~l~~~fy~t~G~gt~~~~a~~~g~eI 328 (431)
T TIGR01917 283 ADRVIPVDVLRDLEKEGKIGELFKYFYSTTGNGTAVANSKQFAKEF 328 (431)
T ss_pred CCeeeeHHHHHHHHHcCCcccccCeeEEccCCCccHHHHHHHHHHH
Confidence 34457889999999999999999888863 333333333444444
No 45
>COG3931 Predicted N-formylglutamate amidohydrolase [Amino acid transport and metabolism]
Probab=51.99 E-value=9.2 Score=22.54 Aligned_cols=18 Identities=33% Similarity=0.468 Sum_probs=14.3
Q ss_pred cccCCcccCCCCCCHHHH
Q psy1305 42 GVLVDEEYGGAGLDTLAL 59 (68)
Q Consensus 42 ~~~~p~~~GG~g~~~~~~ 59 (68)
+-.+|.+||.+|++...+
T Consensus 32 s~~lP~~~g~LGL~~~~~ 49 (263)
T COG3931 32 SNHLPAEYGTLGLPAEAF 49 (263)
T ss_pred hccCCHhHhccCCCHHHH
Confidence 346899999999987654
No 46
>PF00650 CRAL_TRIO: CRAL/TRIO domain; InterPro: IPR001251 This entry defines the C-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1OLM_E 1O6U_E 3Q8G_A 3B7Q_B 3B7Z_A ....
Probab=51.20 E-value=8 Score=20.09 Aligned_cols=11 Identities=36% Similarity=0.585 Sum_probs=8.2
Q ss_pred cccCCcccCCC
Q psy1305 42 GVLVDEEYGGA 52 (68)
Q Consensus 42 ~~~~p~~~GG~ 52 (68)
.-.+|++|||.
T Consensus 149 ~~~lP~~~GG~ 159 (159)
T PF00650_consen 149 PEQLPVEYGGT 159 (159)
T ss_dssp GGGSBGGGTSS
T ss_pred HhHCchhcCCC
Confidence 44788999883
No 47
>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs). 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.
Probab=50.88 E-value=12 Score=23.19 Aligned_cols=12 Identities=50% Similarity=0.825 Sum_probs=9.6
Q ss_pred cCCcccCCCCCC
Q psy1305 44 LVDEEYGGAGLD 55 (68)
Q Consensus 44 ~~p~~~GG~g~~ 55 (68)
.+|.++||+|+.
T Consensus 296 ~~P~~lGGL~l~ 307 (346)
T cd01709 296 YFPEELGGLGLK 307 (346)
T ss_pred eChhhcCCcccC
Confidence 467888999983
No 48
>TIGR01918 various_sel_PB selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family. This model represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. This model is built in fragment mode to assist in recognizing fragmentary translations. All members are expected to contain an internal TGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon.
Probab=50.55 E-value=29 Score=22.22 Aligned_cols=44 Identities=20% Similarity=0.348 Sum_probs=29.8
Q ss_pred hhCCCCHHHHHHHHHcCCCcccCCcccC--CCCCCHHHHHHHHHHH
Q psy1305 23 KEHLFPADQIKKLGALGLMGVLVDEEYG--GAGLDTLALHVAMEEI 66 (68)
Q Consensus 23 ~~~~~~~~~~~~l~~~G~~~~~~p~~~G--G~g~~~~~~~~~~e~l 66 (68)
.+.-+|-+.+++|.+.|.++-..|.-|+ |.|-+....-....++
T Consensus 283 pn~v~PlD~LreLekEG~IG~L~~~fyst~G~gt~~~~a~~~g~eI 328 (431)
T TIGR01918 283 PDRVVPVDVLRDYEKEGKIGELHEYFYSTVGNGTTVAESKQFAKEF 328 (431)
T ss_pred CCeeeeHHHHHHHHHcCCcccccCeeEEcCCCCchHHHHHHHHHHH
Confidence 3446789999999999999998888885 3333333333333333
No 49
>PF10431 ClpB_D2-small: C-terminal, D2-small domain, of ClpB protein ; InterPro: IPR019489 Most Clp ATPases form complexes with peptidase subunits and are involved in protein degradation, though some, such as ClpB, do not associate with peptidases and are involved in protein disaggregation []. This entry represents the C-terminal domain of Clp ATPases, often referred to as the D2-small domain, which forms a mixed alpha-beta structure. Compared with the adjacent AAA D1-small domain (IPR003959 from INTERPRO) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit, thereby providing enough binding energy to stabilise the functional assembly [].; PDB: 3HWS_A 3HTE_F 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 3PXI_A 1R6B_X ....
Probab=47.12 E-value=32 Score=16.07 Aligned_cols=56 Identities=20% Similarity=0.270 Sum_probs=32.5
Q ss_pred HHHHHHHHhhhchhHHHhhhhC---CCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHH
Q psy1305 4 KTCRDFAQQELKPIAAKLDKEH---LFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAME 64 (68)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e 64 (68)
+.+.+.+...+..........+ .+.+++.+.+.+.|+- .+||..++.-.-...+..
T Consensus 4 ~~l~~I~~~~l~~l~~~l~~~~i~l~~~~~~~~~l~~~~~~-----~~~GAR~l~r~i~~~i~~ 62 (81)
T PF10431_consen 4 EDLEKIADLQLKKLNERLKEKGIELEFDDAVVDYLAEKGYD-----PEYGARPLRRIIEREIEP 62 (81)
T ss_dssp HHHHHHHHSHHHHHHHHHHHTTEEEEE-HHHHHHHHHHHHH-----TTTTTTCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCeEEecHHHHHHHHHhCcc-----cCCCHHHHHHHHHHHHHH
Confidence 4455555555554444433322 4678899999988733 478888775554444433
No 50
>PF10546 P63C: P63C domain; InterPro: IPR018874 This entry represents the C-terminal domain from p63 (Q94MQ6 from SWISSPROT), one of the proteins of Myxococcus phage Mx8. The function of these proteins are unknown [].
Probab=45.73 E-value=40 Score=16.88 Aligned_cols=26 Identities=23% Similarity=0.446 Sum_probs=16.4
Q ss_pred HHHHHhhhchhHHHhhhhCCCCHHHHHHHHHc
Q psy1305 7 RDFAQQELKPIAAKLDKEHLFPADQIKKLGAL 38 (68)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 38 (68)
+.|+++++.+.. ..||.++++++..+
T Consensus 3 ~~yi~~e~~~W~------K~FPd~fY~el~RL 28 (94)
T PF10546_consen 3 EAYIAEEARPWE------KRFPDEFYEELYRL 28 (94)
T ss_pred HHHHHHHHHHHH------HHCCHHHHHHHHHH
Confidence 455555554432 35788888888774
No 51
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=45.35 E-value=27 Score=14.77 Aligned_cols=39 Identities=13% Similarity=0.107 Sum_probs=23.8
Q ss_pred HHHHHHHHHhhhc-hhHHHhhhhCCCCHHHHHHHHHcCCC
Q psy1305 3 QKTCRDFAQQELK-PIAAKLDKEHLFPADQIKKLGALGLM 41 (68)
Q Consensus 3 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~G~~ 41 (68)
.+.+.+|+...-. |..++--..-.-+.++++...+.|+-
T Consensus 3 ~~~l~~Fl~~~~~d~~l~~~l~~~~~~~e~~~lA~~~Gy~ 42 (49)
T PF07862_consen 3 IESLKAFLEKVKSDPELREQLKACQNPEEVVALAREAGYD 42 (49)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHhcCCHHHHHHHHHHcCCC
Confidence 4678888876443 22232222233568888888888874
No 52
>PF05788 Orbi_VP1: Orbivirus RNA-dependent RNA polymerase (VP1); InterPro: IPR008723 This family consists of the RNA-dependent RNA polymerase protein VP1 from the Orbivirus. VP1 may have both enzymatic and structural roles in the virus life cycle [].; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=45.12 E-value=10 Score=27.03 Aligned_cols=22 Identities=32% Similarity=0.537 Sum_probs=18.3
Q ss_pred cccCCcccCCCCCCHHHHHHHH
Q psy1305 42 GVLVDEEYGGAGLDTLALHVAM 63 (68)
Q Consensus 42 ~~~~p~~~GG~g~~~~~~~~~~ 63 (68)
.+.+|.+|||.|..+....+++
T Consensus 913 ~ly~P~~wnGyGahP~AlNiVm 934 (1301)
T PF05788_consen 913 ALYVPVEWNGYGAHPAALNIVM 934 (1301)
T ss_pred eEEeecccCCccCChhHhhccc
Confidence 5678999999999998777654
No 53
>PF15187 Augurin: Oesophageal cancer-related gene 4
Probab=43.89 E-value=43 Score=17.18 Aligned_cols=37 Identities=8% Similarity=0.097 Sum_probs=22.4
Q ss_pred HHHHHHHHhhhchhHHHhhhhCCCCHHHHHHHHHcCC
Q psy1305 4 KTCRDFAQQELKPIAAKLDKEHLFPADQIKKLGALGL 40 (68)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~ 40 (68)
..+++|+...-.+..+-||...+-...|++.+-=.|+
T Consensus 26 skAkeFL~~l~R~kR~lWDRsrPdVQQW~qQFlYmGF 62 (114)
T PF15187_consen 26 SKAKEFLASLKRQKRQLWDRSRPDVQQWYQQFLYMGF 62 (114)
T ss_pred HHHHHHHHHhhhHHHhhhccCCHHHHHHHHHHHHhcc
Confidence 3567777765555556677665444566666665555
No 54
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=40.53 E-value=18 Score=15.97 Aligned_cols=23 Identities=30% Similarity=0.437 Sum_probs=19.6
Q ss_pred CCCCHHHHHHHHHcCCCcccCCc
Q psy1305 25 HLFPADQIKKLGALGLMGVLVDE 47 (68)
Q Consensus 25 ~~~~~~~~~~l~~~G~~~~~~p~ 47 (68)
+..|...++.+.+.|++...+|+
T Consensus 37 ~~~~~~~~~~l~~~gll~~ifP~ 59 (64)
T PF12627_consen 37 SPNPSRAFKLLDELGLLEYIFPE 59 (64)
T ss_dssp STTHHHHHHHHHHTTCHHHHSTT
T ss_pred CCCHHHHHHHHHHcCCHHHHCcc
Confidence 56778999999999999888874
No 55
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.78 E-value=37 Score=16.01 Aligned_cols=16 Identities=6% Similarity=0.306 Sum_probs=11.3
Q ss_pred CCCHHHHHHHHHHHhC
Q psy1305 53 GLDTLALHVAMEEIAQ 68 (68)
Q Consensus 53 g~~~~~~~~~~e~l~~ 68 (68)
.+|+.+...+.+++++
T Consensus 53 nfSpsEmqaiA~eL~r 68 (71)
T COG4840 53 NFSPSEMQAIADELGR 68 (71)
T ss_pred cCCHHHHHHHHHHHHH
Confidence 3467777788887764
No 56
>PHA00435 capsid assembly protein
Probab=39.72 E-value=57 Score=19.82 Aligned_cols=28 Identities=21% Similarity=0.309 Sum_probs=23.6
Q ss_pred HHHhhhhCCCCHHHHHHHHHcCCCcccC
Q psy1305 18 AAKLDKEHLFPADQIKKLGALGLMGVLV 45 (68)
Q Consensus 18 ~~~~~~~~~~~~~~~~~l~~~G~~~~~~ 45 (68)
..++++++.+..+-+++|.+.||..-.+
T Consensus 147 ~aEY~~~g~LSeeSY~~La~AGysR~fV 174 (306)
T PHA00435 147 QAEYEEEGGLSEESYAELAAAGYSKAFV 174 (306)
T ss_pred HHHHHhcCCcCHHHHHHHHHcCCcHHHH
Confidence 4567788999999999999999987655
No 57
>COG4705 Uncharacterized membrane-anchored protein conserved in bacteria [Function unknown]
Probab=39.13 E-value=31 Score=20.12 Aligned_cols=20 Identities=30% Similarity=0.378 Sum_probs=14.1
Q ss_pred ccCCcccCCCCCCHHHHHHH
Q psy1305 43 VLVDEEYGGAGLDTLALHVA 62 (68)
Q Consensus 43 ~~~p~~~GG~g~~~~~~~~~ 62 (68)
+.-|-+|||.|++..-.+.+
T Consensus 215 Ltkp~~~GGl~lgt~~aSli 234 (258)
T COG4705 215 LTKPIKYGGLGLGTGYASLI 234 (258)
T ss_pred hcCCcccCCcCcchhHHHHH
Confidence 35688999999876554443
No 58
>PHA02087 hypothetical protein
Probab=38.25 E-value=8.9 Score=18.13 Aligned_cols=32 Identities=19% Similarity=0.262 Sum_probs=21.8
Q ss_pred CCHHHHHHHH----------HcCCCcccCCcccCCCCCCHHH
Q psy1305 27 FPADQIKKLG----------ALGLMGVLVDEEYGGAGLDTLA 58 (68)
Q Consensus 27 ~~~~~~~~l~----------~~G~~~~~~p~~~GG~g~~~~~ 58 (68)
.|.++|..+- ++.-..+-+|++-||.|.+..+
T Consensus 31 mpdefw~~~d~nk~v~y~lvdsdg~~ielpe~~ggggi~fdd 72 (83)
T PHA02087 31 MPDEFWAKFDPNKLVQYMLVDSDGVKIELPESEGGGGITFDD 72 (83)
T ss_pred CcHHHHhcCCCccceeEEEEcCCCcEEECCcccCCCceeecc
Confidence 4677776554 4444467889999998886553
No 59
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=37.97 E-value=68 Score=17.22 Aligned_cols=38 Identities=13% Similarity=0.135 Sum_probs=22.2
Q ss_pred HHHHHHHHhhhc--hhHHHhhhhCCCCHHHHHHHHHcCCC
Q psy1305 4 KTCRDFAQQELK--PIAAKLDKEHLFPADQIKKLGALGLM 41 (68)
Q Consensus 4 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~l~~~G~~ 41 (68)
+.|++|+.++-. ....+..+.-..+.+.+..+.+.|=+
T Consensus 33 ~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL 72 (137)
T TIGR03826 33 EKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRL 72 (137)
T ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCe
Confidence 568888887665 33445444445666666555555433
No 60
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=37.50 E-value=16 Score=17.86 Aligned_cols=39 Identities=21% Similarity=0.234 Sum_probs=21.3
Q ss_pred HHHHHHHHHHhhhc--------hhHHHhhhhCCCCHHHHHHHHHcCC
Q psy1305 2 LQKTCRDFAQQELK--------PIAAKLDKEHLFPADQIKKLGALGL 40 (68)
Q Consensus 2 ~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~l~~~G~ 40 (68)
+++.+++++..... +......-.|.+..++.+.|.+.||
T Consensus 41 L~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~~~~Vk~wL~~~GF 87 (87)
T PF05046_consen 41 LKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGDHVEEVKKWLLEKGF 87 (87)
T ss_pred HHHHHHHHhhhhcCCCcceEEeecCCEEEEcCccHHHHHHHHHHCcC
Confidence 45666666654332 1111222345666778778877775
No 61
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=37.36 E-value=24 Score=20.13 Aligned_cols=19 Identities=16% Similarity=0.242 Sum_probs=16.4
Q ss_pred HHHHHHHHHcCCCcccCCc
Q psy1305 29 ADQIKKLGALGLMGVLVDE 47 (68)
Q Consensus 29 ~~~~~~l~~~G~~~~~~p~ 47 (68)
+.++....+.|+.|+.+|-
T Consensus 101 ~~~~~~a~~~g~~G~t~Pv 119 (232)
T TIGR03541 101 YRVVRNPSGRGVHGLQVPV 119 (232)
T ss_pred hHHHHHHHHcCCCcEEEeE
Confidence 4799999999998899984
No 62
>TIGR03798 ocin_TIGR03798 bacteriocin propeptide, TIGR03798 family. This model describes a conserved, fairly long (about 65 residue) propeptide region for a family of putative microcins, that is, bacteriocins of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain.
Probab=34.85 E-value=51 Score=14.88 Aligned_cols=38 Identities=16% Similarity=0.150 Sum_probs=20.9
Q ss_pred HHHHHHHHhhhc-hhHHHhhhhCCCCHHHHHHHHHcCCC
Q psy1305 4 KTCRDFAQQELK-PIAAKLDKEHLFPADQIKKLGALGLM 41 (68)
Q Consensus 4 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~G~~ 41 (68)
+.++.|+..... |..+.--....-+.++++...+.|+-
T Consensus 2 e~l~~Fl~~~~~d~~L~~~l~~~~~~e~~~~lA~~~Gf~ 40 (64)
T TIGR03798 2 EQLKAFLEKVKTDPDLREKLKAAEDPEDRVAIAKEAGFE 40 (64)
T ss_pred HHHHHHHHHHHcCHHHHHHHHHcCCHHHHHHHHHHcCCC
Confidence 456777766443 22222112223367788888777764
No 63
>PF11314 DUF3117: Protein of unknown function (DUF3117); InterPro: IPR021465 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=34.11 E-value=44 Score=14.70 Aligned_cols=27 Identities=22% Similarity=0.138 Sum_probs=20.6
Q ss_pred CcccCCcccCCC---CCCHHHHHHHHHHHh
Q psy1305 41 MGVLVDEEYGGA---GLDTLALHVAMEEIA 67 (68)
Q Consensus 41 ~~~~~p~~~GG~---g~~~~~~~~~~e~l~ 67 (68)
.-+.+|-+.||. .++..+...+.+.+.
T Consensus 19 ivmRvPleGGGRLVvEl~~~Ea~~L~~~l~ 48 (51)
T PF11314_consen 19 IVMRVPLEGGGRLVVELNPDEAKELGEALK 48 (51)
T ss_pred EEEEEecCCCcEEEEEeCHHHHHHHHHHHH
Confidence 456788888885 888888888777663
No 64
>PF13101 DUF3945: Protein of unknown function (DUF3945)
Probab=33.91 E-value=47 Score=14.89 Aligned_cols=22 Identities=9% Similarity=0.068 Sum_probs=16.9
Q ss_pred cccCCcccCCCCCCHHHHHHHH
Q psy1305 42 GVLVDEEYGGAGLDTLALHVAM 63 (68)
Q Consensus 42 ~~~~p~~~GG~g~~~~~~~~~~ 63 (68)
.+.+|...+|..++..+...+.
T Consensus 23 ~i~ip~~i~g~~Ls~~q~~~L~ 44 (59)
T PF13101_consen 23 KIRIPDKIKGVELSPEQKEDLR 44 (59)
T ss_pred cccccceecCccCCHHHHHHHH
Confidence 3678899999999987766553
No 65
>PF11248 DUF3046: Protein of unknown function (DUF3046); InterPro: IPR021408 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=32.12 E-value=62 Score=15.02 Aligned_cols=16 Identities=19% Similarity=0.175 Sum_probs=12.3
Q ss_pred hhCCCCHHHHHHHHHc
Q psy1305 23 KEHLFPADQIKKLGAL 38 (68)
Q Consensus 23 ~~~~~~~~~~~~l~~~ 38 (68)
+.|.-|+++|..+++.
T Consensus 41 ~~G~dpr~VW~AlC~~ 56 (63)
T PF11248_consen 41 EAGVDPRDVWRALCDA 56 (63)
T ss_pred HcCCCHHHHHHHHHHH
Confidence 4566789999999873
No 66
>cd00170 SEC14 Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=31.60 E-value=18 Score=18.34 Aligned_cols=20 Identities=30% Similarity=0.411 Sum_probs=11.5
Q ss_pred HHHHHHcCCCcccCCcccCCC
Q psy1305 32 IKKLGALGLMGVLVDEEYGGA 52 (68)
Q Consensus 32 ~~~l~~~G~~~~~~p~~~GG~ 52 (68)
+..|.+. +-.-.+|.+|||.
T Consensus 138 ~~~L~~~-i~~~~Lp~~~GG~ 157 (157)
T cd00170 138 KEELLKY-IDKEQLPEEYGGT 157 (157)
T ss_pred HHHHHhh-CChhhCcHhhCCC
Confidence 3344432 3345788888883
No 67
>PF02518 HATPase_c: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; InterPro: IPR003594 This domain is found in several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases [], heat shock protein HSP90 [, , ], phytochrome-like ATPases and DNA mismatch repair proteins. The fold of this domain consists of two layers, alpha/beta, which contains an 8-stranded mixed beta-sheet. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0005524 ATP binding; PDB: 3JZ3_A 3DGE_A 2C2A_A 2BU5_A 2BU8_A 2BU6_A 2BU7_A 2BU2_A 2BTZ_A 3K99_D ....
Probab=31.19 E-value=71 Score=15.41 Aligned_cols=41 Identities=17% Similarity=0.175 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHH
Q psy1305 26 LFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEI 66 (68)
Q Consensus 26 ~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l 66 (68)
.+|.+.++.+.+..+..-.-....+|.|+.+.-...+++.+
T Consensus 48 gi~~~~l~~~~~~~~~~~~~~~~~~g~GlGL~~~~~~~~~~ 88 (111)
T PF02518_consen 48 GIPPEELEKLFEPFFTSDKSETSISGHGLGLYIVKQIAERH 88 (111)
T ss_dssp STTHHHHHHHCSTTSHSSSSSGGSSSSSHHHHHHHHHHHHT
T ss_pred cccccccccchhhcccccccccccCCCChHHHHHHHHHHHC
Confidence 47888888887766665543345567777776666665544
No 68
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=30.88 E-value=33 Score=18.74 Aligned_cols=25 Identities=24% Similarity=0.347 Sum_probs=18.3
Q ss_pred CCHHHHHHHHHcCCCcccCCcccCCC
Q psy1305 27 FPADQIKKLGALGLMGVLVDEEYGGA 52 (68)
Q Consensus 27 ~~~~~~~~l~~~G~~~~~~p~~~GG~ 52 (68)
+-..+++.|.+.|+... .....||.
T Consensus 41 ~l~kIl~~L~~aGLv~s-~rG~~GGy 65 (164)
T PRK10857 41 YLEQLFSRLRKNGLVSS-VRGPGGGY 65 (164)
T ss_pred HHHHHHHHHHHCCCEEe-CCCCCCCe
Confidence 34678999999999986 43455665
No 69
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=29.97 E-value=24 Score=18.34 Aligned_cols=25 Identities=28% Similarity=0.351 Sum_probs=17.3
Q ss_pred CCHHHHHHHHHcCCCcccCCcccCCC
Q psy1305 27 FPADQIKKLGALGLMGVLVDEEYGGA 52 (68)
Q Consensus 27 ~~~~~~~~l~~~G~~~~~~p~~~GG~ 52 (68)
+-..+++.|.+.|+... .....||.
T Consensus 41 ~l~kil~~L~~~glv~s-~~G~~Ggy 65 (135)
T TIGR02010 41 YLEQLFAKLRKAGLVKS-VRGPGGGY 65 (135)
T ss_pred HHHHHHHHHHHCCceEE-EeCCCCCE
Confidence 33678899999999865 33445664
No 70
>TIGR02625 YiiL_rotase L-rhamnose 1-epimerase. Members of this protein family are rhamnose mutarotase from Escherichia coli, previously designated YiiL as an uncharacterized protein, and close homologs also associated with rhamnose dissimilation operons in other bacterial genomes. Mutarotase is a term for an epimerase that changes optical activity. This enzyme was shown experimentally to interconvert alpha and beta stereoisomers of the pyranose form of L-rhamnose. The crystal structure of this small (104 amino acid) protein shows a locally asymmetric dimer with active site residues of His, Tyr, and Trp.
Probab=29.63 E-value=49 Score=16.71 Aligned_cols=21 Identities=10% Similarity=-0.002 Sum_probs=18.3
Q ss_pred CCCCHHHHHHHHHcCCCcccC
Q psy1305 25 HLFPADQIKKLGALGLMGVLV 45 (68)
Q Consensus 25 ~~~~~~~~~~l~~~G~~~~~~ 45 (68)
....+++.+.|+++|+..+.|
T Consensus 21 ~~vWPEv~~~L~~~Gi~~ysI 41 (102)
T TIGR02625 21 NEIWPELKEVLKSHGAHNYSI 41 (102)
T ss_pred HccCHHHHHHHHHCCCeEEEE
Confidence 367899999999999998876
No 71
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=29.43 E-value=69 Score=15.25 Aligned_cols=16 Identities=19% Similarity=0.349 Sum_probs=11.6
Q ss_pred CCCHHHHHHHHHHHhC
Q psy1305 53 GLDTLALHVAMEEIAQ 68 (68)
Q Consensus 53 g~~~~~~~~~~e~l~~ 68 (68)
-+|+.+.-.+.+|||+
T Consensus 53 ~fS~sEm~aI~~ELG~ 68 (71)
T PF06569_consen 53 SFSPSEMQAIAEELGQ 68 (71)
T ss_pred CCCHHHHHHHHHHHHh
Confidence 3467788888888874
No 72
>PF08343 RNR_N: Ribonucleotide reductase N-terminal; InterPro: IPR013554 This domain is found at the N terminus of bacterial ribonucleoside-diphosphate reductases (ribonucleotide reductases, RNRs) which catalyse the formation of deoxyribonucleotides []. It occurs together with the RNR all-alpha domain (IPR013509 from INTERPRO) and the RNR barrel domain (IPR000788 from INTERPRO). ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0006260 DNA replication, 0055114 oxidation-reduction process, 0005971 ribonucleoside-diphosphate reductase complex; PDB: 1PEM_A 2BQ1_E 1PEU_A 1PEQ_A 1PEO_A.
Probab=28.81 E-value=81 Score=15.32 Aligned_cols=17 Identities=12% Similarity=0.436 Sum_probs=12.9
Q ss_pred HHHHHHHHHhhhchhHH
Q psy1305 3 QKTCRDFAQQELKPIAA 19 (68)
Q Consensus 3 ~~~~~~~~~~~~~~~~~ 19 (68)
++++++|+.++|.|...
T Consensus 23 ~eA~~~y~~~~V~pnt~ 39 (82)
T PF08343_consen 23 KEAVRAYFKEHVNPNTV 39 (82)
T ss_dssp HHHHHHHHHHTTGGGB-
T ss_pred HHHHHHHHHHhccccee
Confidence 46789999998888643
No 73
>KOG3490|consensus
Probab=28.38 E-value=66 Score=16.62 Aligned_cols=19 Identities=16% Similarity=0.364 Sum_probs=16.2
Q ss_pred hCCCCHHHHHHHHHcCCCc
Q psy1305 24 EHLFPADQIKKLGALGLMG 42 (68)
Q Consensus 24 ~~~~~~~~~~~l~~~G~~~ 42 (68)
++..|.++++.+...|+.-
T Consensus 84 sG~Lpe~~v~~l~~~g~~Y 102 (111)
T KOG3490|consen 84 SGVLPEEVVESLKSRGVHY 102 (111)
T ss_pred cccCCHHHHHHHHhcceee
Confidence 4788999999999998754
No 74
>PF07370 DUF1489: Protein of unknown function (DUF1489); InterPro: IPR008320 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.95 E-value=77 Score=17.10 Aligned_cols=17 Identities=29% Similarity=0.628 Sum_probs=14.8
Q ss_pred CCCCHHHHHHHHHcCCC
Q psy1305 25 HLFPADQIKKLGALGLM 41 (68)
Q Consensus 25 ~~~~~~~~~~l~~~G~~ 41 (68)
...|.++.++|++.|++
T Consensus 121 ~~lP~~L~~eL~eLGll 137 (137)
T PF07370_consen 121 DELPPELRRELAELGLL 137 (137)
T ss_pred ccCCHHHHHHHHHhcCC
Confidence 46899999999999985
No 75
>PF14278 TetR_C_8: Transcriptional regulator C-terminal region
Probab=27.94 E-value=68 Score=14.16 Aligned_cols=6 Identities=0% Similarity=0.545 Sum_probs=2.2
Q ss_pred HHHHHh
Q psy1305 7 RDFAQQ 12 (68)
Q Consensus 7 ~~~~~~ 12 (68)
++.+.+
T Consensus 35 ~~~~~~ 40 (77)
T PF14278_consen 35 KELIKE 40 (77)
T ss_pred HHHHHH
Confidence 333333
No 76
>PF08564 CDC37_C: Cdc37 C terminal domain; InterPro: IPR013873 Cdc37 is a protein required for the activity of numerous eukaryotic protein kinases. This entry corresponds to the C-terminal domain whose function is unclear. It is found C-terminal to the Hsp90 chaperone (heat shock protein 90) binding domain IPR013874 from INTERPRO and the N-terminal kinase binding domain of Cdc37 IPR013855 from INTERPRO []. ; PDB: 1US7_B.
Probab=27.60 E-value=70 Score=16.18 Aligned_cols=16 Identities=6% Similarity=0.034 Sum_probs=12.4
Q ss_pred HHHHHHHHHcCCCccc
Q psy1305 29 ADQIKKLGALGLMGVL 44 (68)
Q Consensus 29 ~~~~~~l~~~G~~~~~ 44 (68)
..+++.|.++|++++.
T Consensus 53 E~~v~~~~esGi~~~~ 68 (99)
T PF08564_consen 53 EYHVERCIESGIWSPE 68 (99)
T ss_dssp HHHHHHHHHTTSS--T
T ss_pred HHHHHHHHhCCccccc
Confidence 5789999999999874
No 77
>PTZ00304 NADH dehydrogenase [ubiquinone] flavoprotein 1; Provisional
Probab=27.45 E-value=69 Score=20.78 Aligned_cols=24 Identities=33% Similarity=0.414 Sum_probs=19.1
Q ss_pred CCHHHHHHHHHcCCCcccCCcccCCCCCCH
Q psy1305 27 FPADQIKKLGALGLMGVLVDEEYGGAGLDT 56 (68)
Q Consensus 27 ~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~ 56 (68)
-|.++++.+.++|+.+. ||.|++.
T Consensus 59 ~p~~ii~~Vk~aGL~Gr------GGAGFPT 82 (461)
T PTZ00304 59 GHDWIIDEIKKSGLRGR------GGAGFPS 82 (461)
T ss_pred CHHHHHHHHHHhCCCCC------CCcCCch
Confidence 46789999999999875 6777654
No 78
>smart00516 SEC14 Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p). Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and the RasGAP, neurofibromin (NF1). Lipid-binding domain. The SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=27.32 E-value=25 Score=18.14 Aligned_cols=12 Identities=33% Similarity=0.351 Sum_probs=9.0
Q ss_pred cccCCcccCCCC
Q psy1305 42 GVLVDEEYGGAG 53 (68)
Q Consensus 42 ~~~~p~~~GG~g 53 (68)
.-.+|.+|||..
T Consensus 146 ~~~lP~~~GG~~ 157 (158)
T smart00516 146 PEQLPEELGGTL 157 (158)
T ss_pred HhhCcHhhCCCC
Confidence 446899999863
No 79
>PRK09303 adaptive-response sensory kinase; Validated
Probab=26.87 E-value=1.6e+02 Score=18.04 Aligned_cols=41 Identities=12% Similarity=0.030 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHHH
Q psy1305 25 HLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEEI 66 (68)
Q Consensus 25 ~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~l 66 (68)
..+|.+....+.+-.+-.-. ....+|.|+.+.-...+++.+
T Consensus 315 ~GI~~~~~~~iF~pf~~~~~-~~~~~G~GLGL~i~~~iv~~~ 355 (380)
T PRK09303 315 PGIPEEEQERIFEDRVRLPR-DEGTEGYGIGLSVCRRIVRVH 355 (380)
T ss_pred CCCCHHHHHHHccCceeCCC-CCCCCcccccHHHHHHHHHHc
Confidence 35777777777665443222 345568888877766666654
No 80
>PF14542 Acetyltransf_CG: GCN5-related N-acetyl-transferase; PDB: 2H5M_A 2Q44_A 1XMT_A 2Q4Y_A 2IL4_A 2EVN_A 1R57_A.
Probab=26.50 E-value=51 Score=15.50 Aligned_cols=22 Identities=23% Similarity=0.373 Sum_probs=14.0
Q ss_pred ccCCcccCCCCCCHHHHHHHHH
Q psy1305 43 VLVDEEYGGAGLDTLALHVAME 64 (68)
Q Consensus 43 ~~~p~~~GG~g~~~~~~~~~~e 64 (68)
..+|.++.|.|+.....-.+++
T Consensus 28 T~V~~~~rGqGia~~L~~~~l~ 49 (78)
T PF14542_consen 28 TEVPPELRGQGIAKKLVEAALD 49 (78)
T ss_dssp EEE-CSSSTTTHHHHHHHHHHH
T ss_pred EEECccccCCcHHHHHHHHHHH
Confidence 3578889999886655544444
No 81
>PF10073 DUF2312: Uncharacterized protein conserved in bacteria (DUF2312); InterPro: IPR018753 This entry is represented by Azospirillum phage Cd, Gp10. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family of hypothetical bacterial proteins have no known function.
Probab=26.35 E-value=89 Score=15.01 Aligned_cols=10 Identities=20% Similarity=0.484 Sum_probs=5.7
Q ss_pred HHHHHHHHHh
Q psy1305 3 QKTCRDFAQQ 12 (68)
Q Consensus 3 ~~~~~~~~~~ 12 (68)
.+.++.|++.
T Consensus 3 ~~~Lr~~ieR 12 (74)
T PF10073_consen 3 AEQLRQFIER 12 (74)
T ss_pred HHHHHHHHHH
Confidence 3556666654
No 82
>COG5458 Uncharacterized conserved protein [Function unknown]
Probab=25.88 E-value=84 Score=16.69 Aligned_cols=16 Identities=44% Similarity=0.711 Sum_probs=13.7
Q ss_pred CCCHHHHHHHHHcCCC
Q psy1305 26 LFPADQIKKLGALGLM 41 (68)
Q Consensus 26 ~~~~~~~~~l~~~G~~ 41 (68)
..|.++.+++++.|++
T Consensus 129 ~mP~dLrreLaeLGll 144 (144)
T COG5458 129 DMPADLRRELAELGLL 144 (144)
T ss_pred cCCHHHHHHHHHhccC
Confidence 5788999999999975
No 83
>PRK06035 3-hydroxyacyl-CoA dehydrogenase; Validated
Probab=25.53 E-value=1.5e+02 Score=17.41 Aligned_cols=27 Identities=26% Similarity=0.497 Sum_probs=21.0
Q ss_pred CCHHHHHHHHHcCCCcccCCcccC-CCCC
Q psy1305 27 FPADQIKKLGALGLMGVLVDEEYG-GAGL 54 (68)
Q Consensus 27 ~~~~~~~~l~~~G~~~~~~p~~~G-G~g~ 54 (68)
.|.++++.+.+.|.++..-|+ || |.|+
T Consensus 260 ~~~~~l~~~v~~g~~G~k~~~-~~~g~Gf 287 (291)
T PRK06035 260 IPPNSLKQMVLNGYVGDKKVK-YGSKGGW 287 (291)
T ss_pred CccHHHHHHHHCCCCcCCCCC-CCCCcee
Confidence 367889999999999988764 57 6664
No 84
>TIGR01913 bet_lambda phage recombination protein Bet. This model represents the phage recombination protein Bet from a number of phage, including phage lambda. All members of this family are found in phage genomes or in putative prophage regions of bacterial genomes.
Probab=25.53 E-value=22 Score=20.03 Aligned_cols=27 Identities=19% Similarity=0.426 Sum_probs=23.0
Q ss_pred CCCHHHHHHHHHcCCCcccCCcccCCC
Q psy1305 26 LFPADQIKKLGALGLMGVLVDEEYGGA 52 (68)
Q Consensus 26 ~~~~~~~~~l~~~G~~~~~~p~~~GG~ 52 (68)
..|..-+++++...-+...+|+++||.
T Consensus 155 ~~P~~Ml~K~A~~qALR~AFPe~~~g~ 181 (188)
T TIGR01913 155 SMPRTMLRKCAEAQALRLAFPEQFGGI 181 (188)
T ss_pred hCHHHHHHHHHHHHHHHHhchhhhcCc
Confidence 356788899999999999999999885
No 85
>PF09859 Oxygenase-NA: Oxygenase, catalysing oxidative methylation of damaged DNA; InterPro: IPR018655 This family of various hypothetical prokaryotic proteins, has no known function.
Probab=25.44 E-value=1.4e+02 Score=16.84 Aligned_cols=41 Identities=22% Similarity=0.359 Sum_probs=26.5
Q ss_pred HHHHHHHHHhhhchhHHHhhh----hCCCC---HHHHHHHHHcCCCcc
Q psy1305 3 QKTCRDFAQQELKPIAAKLDK----EHLFP---ADQIKKLGALGLMGV 43 (68)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~----~~~~~---~~~~~~l~~~G~~~~ 43 (68)
...+++-+-..+.|.++.|.+ +..|| .++++.+.++|=..+
T Consensus 15 ~~~lR~~lY~~LapiAnrW~~~L~~~~~yP~~~~~fl~~ch~aGQ~rp 62 (173)
T PF09859_consen 15 LQALREALYPRLAPIANRWNERLGIDARYPATLAEFLARCHAAGQTRP 62 (173)
T ss_pred HHHHHHHHhHHhHHHHHHHHHHhCCCCCCCccHHHHHHHHHhccCCCC
Confidence 344555555567777776653 34677 568888888886654
No 86
>COG1640 MalQ 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]
Probab=24.91 E-value=71 Score=21.12 Aligned_cols=23 Identities=26% Similarity=0.316 Sum_probs=20.6
Q ss_pred hCCCCHHHHHHHHHcCCCcccCC
Q psy1305 24 EHLFPADQIKKLGALGLMGVLVD 46 (68)
Q Consensus 24 ~~~~~~~~~~~l~~~G~~~~~~p 46 (68)
-|.+|.++.+.+...|+.++.|+
T Consensus 353 LGtvp~eV~~~l~~~gi~g~kIl 375 (520)
T COG1640 353 LGTVPAEVRDLLAHLGIPGMKIL 375 (520)
T ss_pred cCCCCHHHHHHHHHcCCCceEEE
Confidence 37889999999999999999876
No 87
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.86 E-value=1.6e+02 Score=17.31 Aligned_cols=15 Identities=20% Similarity=0.383 Sum_probs=13.1
Q ss_pred HHHHHHHHHcCCCcc
Q psy1305 29 ADQIKKLGALGLMGV 43 (68)
Q Consensus 29 ~~~~~~l~~~G~~~~ 43 (68)
++++++|.+.|+|.+
T Consensus 176 reiV~~L~EkGiF~l 190 (220)
T COG2964 176 REIVKALYEKGIFNL 190 (220)
T ss_pred HHHHHHHHhcCccch
Confidence 679999999999975
No 88
>KOG1471|consensus
Probab=24.70 E-value=39 Score=20.02 Aligned_cols=12 Identities=50% Similarity=0.833 Sum_probs=9.6
Q ss_pred cCCcccCCCCCC
Q psy1305 44 LVDEEYGGAGLD 55 (68)
Q Consensus 44 ~~p~~~GG~g~~ 55 (68)
.+|++|||...+
T Consensus 248 ~LP~~yGG~~~~ 259 (317)
T KOG1471|consen 248 VLPEEYGGTCGD 259 (317)
T ss_pred hCccccCCCccc
Confidence 689999997655
No 89
>PF08013 Tagatose_6_P_K: Tagatose 6 phosphate kinase; InterPro: IPR012062 Escherichia coli and other enteric bacteria contain two closely related D-tagatose 1,6-bisphosphate (TagBP)-specific aldolases involved in catabolism of galactitol (genes gatY gatZ) and of N-acetyl-galactosamine and D-galactosamine (genes kbaY, kbaZ, also called agaY, agaZ). The catalytic subunits GatY/KbaY alone are sufficient to show aldolase activity and contain most or all of the residues that have been identified as essential in substrate/product recognition and catalysis for class II aldolases [, ]. However, these aldolases differ from other Class II aldolases (which are homodimeric enzymes) in that they require subunits GatZ/KbaZ for full activity and for good in vivo and in vitro stability. The Z subunits alone do not show any aldolase activity []. It should be noted that the previous suggestion of a tagatose 6P-kinase function for AgaZ [] and other members of this family turned out to be erroneous [, ].; GO: 0019402 galactitol metabolic process; PDB: 2FIQ_A 3TXV_A.
Probab=24.02 E-value=99 Score=19.95 Aligned_cols=21 Identities=29% Similarity=0.574 Sum_probs=15.1
Q ss_pred cccCCC-CCCHHHHHHHHHHHh
Q psy1305 47 EEYGGA-GLDTLALHVAMEEIA 67 (68)
Q Consensus 47 ~~~GG~-g~~~~~~~~~~e~l~ 67 (68)
..+||. |+++.++...+.+++
T Consensus 54 nq~GGYTGmtP~dF~~~V~~iA 75 (424)
T PF08013_consen 54 NQFGGYTGMTPADFRDFVREIA 75 (424)
T ss_dssp STT-TTTTB-HHHHHHHHHHHH
T ss_pred cccCCcCCCCHHHHHHHHHHHH
Confidence 356885 999999998888775
No 90
>PF02382 RTX: RTX N-terminal domain; InterPro: IPR018504 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior []. Four principal exotoxin secretion systems have been described. In the type II and IV secretion systems, toxins are first exported to the periplasm by way of a cleaved N-terminal signal sequence; a second set of proteins is used for extracellular transport (type II), or the C terminus of the exotoxin itself is used (type IV). Type III secretion involves at least 20 molecules that assemble into a needle; effector proteins are then translocated through this without need of a signal sequence. In the Type I system, a complete channel is formed through both membranes, and the secretion signal is carried on the C terminus of the exotoxin. The RTX (repeats in toxin) family of cytolytic toxins belong to the Type I secretion system, and are important virulence factors in Gram-negative bacteria. As well as the C-terminal signal sequence, several glycine-rich repeats are also found. These are essential for binding calcium, and are critical for the biological activity of the secreted toxins []. All RTX toxin operons exist in the order rtxCABD, RtxA protein being the structural component of the exotoxin, both RtxB and D being required for its export from the bacterial cell; RtxC is an acyl-carrier-protein-dependent acyl- modification enzyme, required to convert RtxA to its active form []. Escherichia coli haemolysin (HlyA) is often quoted as the model for RTX toxins. Recent work on its relative rtxC gene product HlyC [] has revealed that it provides the acylation aspect for post-translational modification of two internal lysine residues in the HlyA protein. To cause pathogenicity, the HlyA toxin must first bind Ca2+ ions to the set of glycine-rich repeats and then be activated by HlyC []. This has been demonstrated both in vitro and in vivo. A number of the sequences in this family are metallopeptidases belonging to MEROPS peptidase family M10 (clan MA(M)), subfamily M10B: serralysin, epralysin and unassigned peptidases.; GO: 0005509 calcium ion binding, 0009405 pathogenesis, 0005576 extracellular region
Probab=24.00 E-value=94 Score=21.10 Aligned_cols=27 Identities=19% Similarity=0.314 Sum_probs=23.0
Q ss_pred CcccCCcccCC-CCCCHHHHHHHHHHHh
Q psy1305 41 MGVLVDEEYGG-AGLDTLALHVAMEEIA 67 (68)
Q Consensus 41 ~~~~~p~~~GG-~g~~~~~~~~~~e~l~ 67 (68)
+-+.+|++|-+ .|-++-+.+-..++|+
T Consensus 45 LiL~IPKdYd~~~GngLndLVKAAdeLG 72 (653)
T PF02382_consen 45 LILYIPKDYDASQGNGLNDLVKAADELG 72 (653)
T ss_pred EEEEcccccccccCccHHHHHHHHHHcC
Confidence 45678999977 8999999999999886
No 91
>PF15519 RBM39linker: linker between RRM2 and RRM3 domains in RBM39 protein; PDB: 3S6E_A 2LQ5_A.
Probab=23.92 E-value=26 Score=16.58 Aligned_cols=20 Identities=25% Similarity=0.464 Sum_probs=0.0
Q ss_pred ccCCCCCCHHHHHHHHHHHh
Q psy1305 48 EYGGAGLDTLALHVAMEEIA 67 (68)
Q Consensus 48 ~~GG~g~~~~~~~~~~e~l~ 67 (68)
+-||..++......++..|+
T Consensus 7 d~~G~~l~a~sR~~LM~KLA 26 (73)
T PF15519_consen 7 DRGGVNLNATSRAALMAKLA 26 (73)
T ss_dssp --------------------
T ss_pred cccccccccccccccccccc
Confidence 44666666666666655554
No 92
>COG1591 Holliday junction resolvase - archaeal type [DNA replication, recombination, and repair]
Probab=23.43 E-value=63 Score=17.44 Aligned_cols=24 Identities=17% Similarity=0.109 Sum_probs=20.6
Q ss_pred CCCHHHHHHHHHcCCCcccCCccc
Q psy1305 26 LFPADQIKKLGALGLMGVLVDEEY 49 (68)
Q Consensus 26 ~~~~~~~~~l~~~G~~~~~~p~~~ 49 (68)
.+-+++++.|.+.|+-.+..|.+.
T Consensus 8 ~~EReLv~~L~e~GfAvvR~paSG 31 (137)
T COG1591 8 RFERELVRILWERGFAVVRAPASG 31 (137)
T ss_pred hHHHHHHHHHHhcCceEEEcccCC
Confidence 345799999999999999998775
No 93
>TIGR03562 osmo_induc_OsmC peroxiredoxin, OsmC subfamily. Pfam model pfam02566, OsmC-like protein, contains several deeply split clades of homologous proteins. The clade modeled here includes the protein OsmC, or osmotically induced protein C. The member from Thermus thermophilus was shown to have hydroperoxide peroxidase activity. In many species, this protein is induced by stress and helps resist oxidative stress.
Probab=23.37 E-value=1.3e+02 Score=15.85 Aligned_cols=21 Identities=14% Similarity=0.159 Sum_probs=13.1
Q ss_pred cccCCcccCC-CCCCHHHHHHH
Q psy1305 42 GVLVDEEYGG-AGLDTLALHVA 62 (68)
Q Consensus 42 ~~~~p~~~GG-~g~~~~~~~~~ 62 (68)
.+..|+++|| .|.++.++...
T Consensus 29 ~~s~p~~~~~~~G~nPeeLLla 50 (135)
T TIGR03562 29 PYSFKTRFEDGPGTNPEELIAA 50 (135)
T ss_pred ccccCcccCCCCCCCHHHHHHH
Confidence 3456888865 46677766543
No 94
>PF13309 HTH_22: HTH domain
Probab=22.80 E-value=95 Score=14.07 Aligned_cols=16 Identities=13% Similarity=0.250 Sum_probs=13.1
Q ss_pred HHHHHHHHHcCCCccc
Q psy1305 29 ADQIKKLGALGLMGVL 44 (68)
Q Consensus 29 ~~~~~~l~~~G~~~~~ 44 (68)
.++++.|.+.|+|.+-
T Consensus 27 ~~iV~~L~~~G~F~lK 42 (64)
T PF13309_consen 27 KEIVRQLYEKGIFLLK 42 (64)
T ss_pred HHHHHHHHHCCCcccC
Confidence 4789999999999763
No 95
>PRK13694 hypothetical protein; Provisional
Probab=22.72 E-value=1.1e+02 Score=14.99 Aligned_cols=9 Identities=22% Similarity=0.501 Sum_probs=4.8
Q ss_pred HHHHHHHHh
Q psy1305 4 KTCRDFAQQ 12 (68)
Q Consensus 4 ~~~~~~~~~ 12 (68)
+.++.|+..
T Consensus 12 ~~Lr~fIER 20 (83)
T PRK13694 12 EQLRAFIER 20 (83)
T ss_pred HHHHHHHHH
Confidence 455566543
No 96
>PF11909 NdhN: NADH-quinone oxidoreductase cyanobacterial subunit N; InterPro: IPR020874 NAD(P)H-quinone oxidoreductase (NDH-1) shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. It couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. NDH-1 can be composed of about 15 different subunits, although different subcomplexes with different compositions have been identified which probably have different functions. This entry represents subunit N. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process, 0016020 membrane
Probab=22.55 E-value=96 Score=17.02 Aligned_cols=20 Identities=25% Similarity=0.297 Sum_probs=13.6
Q ss_pred HHHHHHHHHcCCCcccCCcc
Q psy1305 29 ADQIKKLGALGLMGVLVDEE 48 (68)
Q Consensus 29 ~~~~~~l~~~G~~~~~~p~~ 48 (68)
+.+++.+-+.|-+++..|-+
T Consensus 8 ~~f~rdlEk~gaLavy~PlE 27 (154)
T PF11909_consen 8 KKFIRDLEKSGALAVYAPLE 27 (154)
T ss_pred hHHHHHHHHcCceEEEcCCc
Confidence 45666777777777777755
No 97
>PLN03244 alpha-amylase; Provisional
Probab=22.48 E-value=58 Score=22.90 Aligned_cols=20 Identities=25% Similarity=0.308 Sum_probs=17.5
Q ss_pred cCCCcccCCcccCCCCCCHH
Q psy1305 38 LGLMGVLVDEEYGGAGLDTL 57 (68)
Q Consensus 38 ~G~~~~~~p~~~GG~g~~~~ 57 (68)
.++.+++.|.+.||+|+++.
T Consensus 588 S~~P~vt~Pv~~GGLGFDYK 607 (872)
T PLN03244 588 TYYPGLCEPTSQGGLGFDYY 607 (872)
T ss_pred CCCcCccccCCCCCCCccce
Confidence 58889999999999999865
No 98
>PF14433 SUKH-3: SUKH-3 immunity protein
Probab=22.41 E-value=91 Score=16.29 Aligned_cols=13 Identities=31% Similarity=0.309 Sum_probs=8.1
Q ss_pred HHHHHHHHHcCCC
Q psy1305 29 ADQIKKLGALGLM 41 (68)
Q Consensus 29 ~~~~~~l~~~G~~ 41 (68)
+++.+.|.++||.
T Consensus 2 ~~v~~~L~~aGW~ 14 (142)
T PF14433_consen 2 EKVIELLRAAGWY 14 (142)
T ss_pred HHHHHHHHHcCCC
Confidence 4556666666666
No 99
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=22.37 E-value=1.1e+02 Score=20.66 Aligned_cols=20 Identities=20% Similarity=0.137 Sum_probs=15.9
Q ss_pred hhCCCCHHHHHHHHHcCCCc
Q psy1305 23 KEHLFPADQIKKLGALGLMG 42 (68)
Q Consensus 23 ~~~~~~~~~~~~l~~~G~~~ 42 (68)
.++..|..+.+.|.+.||.-
T Consensus 101 ~~g~v~~~~~e~L~ERGlA~ 120 (591)
T PF04458_consen 101 EAGRVPPVWNEALEERGLAE 120 (591)
T ss_pred HhCcCChHHHHHHHHccchh
Confidence 34778888999999988864
No 100
>PF03682 UPF0158: Uncharacterised protein family (UPF0158); InterPro: IPR005361 This is a small family of hypothetical bacterial proteins of unknown function.
Probab=22.31 E-value=84 Score=17.23 Aligned_cols=8 Identities=50% Similarity=0.883 Sum_probs=3.3
Q ss_pred CHHHHHHH
Q psy1305 28 PADQIKKL 35 (68)
Q Consensus 28 ~~~~~~~l 35 (68)
|+.+++.+
T Consensus 150 ~~~~~~~~ 157 (163)
T PF03682_consen 150 PKDILEKL 157 (163)
T ss_pred hHHHHhhc
Confidence 34444433
No 101
>PF15552 DUF4657: Domain of unknown function (DUF4657)
Probab=22.09 E-value=61 Score=19.55 Aligned_cols=18 Identities=39% Similarity=0.687 Sum_probs=13.7
Q ss_pred CCCCCHH-HHHHHHHHHhC
Q psy1305 51 GAGLDTL-ALHVAMEEIAQ 68 (68)
Q Consensus 51 G~g~~~~-~~~~~~e~l~~ 68 (68)
|.|+.+. +.|++.|.|++
T Consensus 123 GQGLRYLEHLCLvLEqMAr 141 (301)
T PF15552_consen 123 GQGLRYLEHLCLVLEQMAR 141 (301)
T ss_pred CccHHHHHHHHHHHHHHHH
Confidence 7788877 56788888874
No 102
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=21.95 E-value=2.2e+02 Score=18.09 Aligned_cols=39 Identities=15% Similarity=0.153 Sum_probs=24.6
Q ss_pred CCCCHHHHHHHHHcCCCcccCCcccCCCCCCHHHHHHHHHH
Q psy1305 25 HLFPADQIKKLGALGLMGVLVDEEYGGAGLDTLALHVAMEE 65 (68)
Q Consensus 25 ~~~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~~~~~~~~e~ 65 (68)
..+|++..+.+.+.|+.. -+.+.||.|+.+.-...+++.
T Consensus 478 ~Gi~~~~~~~iF~~~~~t--k~~~~~g~GlGL~ivk~iv~~ 516 (545)
T PRK15053 478 CGVPESLRDKIFEQGVST--RADEPGEHGIGLYLIASYVTR 516 (545)
T ss_pred CCcCHHHHHHHhCCCCCC--CCCCCCCceeCHHHHHHHHHH
Confidence 357788888888877752 334556666666555555444
No 103
>TIGR03563 perox_SACOL1771 peroxiredoxin, SACOL1771 subfamily. This protein family belongs to the OsmC/Ohr family (pfam02566, OsmC-like protein) of peroxiredoxins.
Probab=21.86 E-value=1.3e+02 Score=15.56 Aligned_cols=20 Identities=15% Similarity=0.340 Sum_probs=13.6
Q ss_pred cccCCcccCCC--CCCHHHHHH
Q psy1305 42 GVLVDEEYGGA--GLDTLALHV 61 (68)
Q Consensus 42 ~~~~p~~~GG~--g~~~~~~~~ 61 (68)
-+..|.++||. |.++.++..
T Consensus 27 ~~d~p~~~gG~~~g~nP~elll 48 (138)
T TIGR03563 27 QISIPKEMDGPGVGTNPDEMLL 48 (138)
T ss_pred cccCccccCCCCCCCCHHHHHH
Confidence 35578889885 567776654
No 104
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=21.78 E-value=1.3e+02 Score=16.63 Aligned_cols=40 Identities=10% Similarity=0.074 Sum_probs=25.9
Q ss_pred hCCCCHHHHHHHHHcCCCcccCCccc--CCCCCCHHHHHHHHHHH
Q psy1305 24 EHLFPADQIKKLGALGLMGVLVDEEY--GGAGLDTLALHVAMEEI 66 (68)
Q Consensus 24 ~~~~~~~~~~~l~~~G~~~~~~p~~~--GG~g~~~~~~~~~~e~l 66 (68)
+...|.++++..-+. .+.+|-.. ..+.++..-.+++.|.+
T Consensus 105 s~GLP~~i~~~~~~~---~irIPm~~~~RSLNLsnsvavv~yEa~ 146 (155)
T COG0219 105 SRGLPEEILDAAPDR---CIRIPMRPGVRSLNLSNTVAVVLYEAL 146 (155)
T ss_pred CCCCCHHHHHhCccc---eEEeccCCCCccchHHHHHHHHHHHHH
Confidence 346788998888887 44455443 34566666666666654
No 105
>TIGR00217 malQ 4-alpha-glucanotransferase. This enzyme is known as amylomaltase and disproportionating enzyme.
Probab=21.71 E-value=1e+02 Score=20.29 Aligned_cols=24 Identities=13% Similarity=0.070 Sum_probs=20.9
Q ss_pred hCCCCHHHHHHHHHcCCCcccCCc
Q psy1305 24 EHLFPADQIKKLGALGLMGVLVDE 47 (68)
Q Consensus 24 ~~~~~~~~~~~l~~~G~~~~~~p~ 47 (68)
-|.+|+++.+.+.+.|+.++.|..
T Consensus 361 LG~v~~~Vr~ll~~~gipGmkVl~ 384 (513)
T TIGR00217 361 LGTVPEEVSRLRDEFNFPGMKVLY 384 (513)
T ss_pred CCCCCHHHHHHHHHcCCCCceEeE
Confidence 367899999999999999998764
No 106
>COG0386 BtuE Glutathione peroxidase [Posttranslational modification, protein turnover, chaperones]
Probab=21.67 E-value=1e+02 Score=17.14 Aligned_cols=26 Identities=19% Similarity=0.233 Sum_probs=22.0
Q ss_pred HHHHHHHHHcCCCcccCC-cccCCCCC
Q psy1305 29 ADQIKKLGALGLMGVLVD-EEYGGAGL 54 (68)
Q Consensus 29 ~~~~~~l~~~G~~~~~~p-~~~GG~g~ 54 (68)
..++++..+.|+.-+.+| .+++|.+-
T Consensus 47 e~Ly~ky~~~Gf~VLgFPcNQF~~QEP 73 (162)
T COG0386 47 EALYKKYKDKGFEVLGFPCNQFGGQEP 73 (162)
T ss_pred HHHHHHHhhCCcEEEeccccccccCCC
Confidence 578999999999999999 57777654
No 107
>PRK13596 NADH dehydrogenase I subunit F; Provisional
Probab=21.38 E-value=1e+02 Score=19.80 Aligned_cols=24 Identities=42% Similarity=0.479 Sum_probs=18.9
Q ss_pred CCHHHHHHHHHcCCCcccCCcccCCCCCCH
Q psy1305 27 FPADQIKKLGALGLMGVLVDEEYGGAGLDT 56 (68)
Q Consensus 27 ~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~ 56 (68)
-|.++++.+.++|+.+. ||.|++.
T Consensus 39 ~~~~l~~~v~~aGl~Gr------GGAGFPt 62 (433)
T PRK13596 39 GRDWIIEEMKASGLRGR------GGAGFPT 62 (433)
T ss_pred CHHHHHHHHHHcCCCCC------CCCcchh
Confidence 46789999999999875 6766654
No 108
>PF07927 YcfA: YcfA-like protein; InterPro: IPR012933 This entry represents UPF0395, which contains viral, archaeal and bacterial proteins. It includes YncN of Escherichia coli K12. Most of these proteins are hypothetical proteins of unknown function. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1WHZ_A.
Probab=21.36 E-value=90 Score=13.28 Aligned_cols=14 Identities=29% Similarity=0.311 Sum_probs=9.0
Q ss_pred HHHHHHHHHcCCCc
Q psy1305 29 ADQIKKLGALGLMG 42 (68)
Q Consensus 29 ~~~~~~l~~~G~~~ 42 (68)
+++.+.|.+.||.-
T Consensus 2 ~el~k~L~~~G~~~ 15 (56)
T PF07927_consen 2 RELIKLLEKAGFEE 15 (56)
T ss_dssp HHHHHHHHHTT-EE
T ss_pred hHHHHHHHHCCCEE
Confidence 46777777777763
No 109
>TIGR03059 psaOeuk photosystem I protein PsaO. Members of this family are the PsaO protein of photosystem I. This protein is found in chloroplasts but not in Cyanobacteria.
Probab=21.34 E-value=93 Score=15.08 Aligned_cols=20 Identities=35% Similarity=0.431 Sum_probs=13.5
Q ss_pred ccCCCCCCHHHHHHHHHHHh
Q psy1305 48 EYGGAGLDTLALHVAMEEIA 67 (68)
Q Consensus 48 ~~GG~g~~~~~~~~~~e~l~ 67 (68)
.++|..++-.-...+-++++
T Consensus 21 ~~~g~SLtglF~~sIg~~LA 40 (82)
T TIGR03059 21 LYGGKSLTGLFASSIGENLA 40 (82)
T ss_pred ccCCchHHHHHHHHHHHHHh
Confidence 56777777666666666665
No 110
>COG4558 ChuT ABC-type hemin transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=20.86 E-value=1.1e+02 Score=18.72 Aligned_cols=27 Identities=30% Similarity=0.187 Sum_probs=22.8
Q ss_pred CCCHHHHHHHHHcCCCcccCCcccCCC
Q psy1305 26 LFPADQIKKLGALGLMGVLVDEEYGGA 52 (68)
Q Consensus 26 ~~~~~~~~~l~~~G~~~~~~p~~~GG~ 52 (68)
.-|.++++.++..|+-...+|.++...
T Consensus 109 aGP~~vl~qLraagV~vv~v~~~~~~~ 135 (300)
T COG4558 109 AGPATVLDQLRAAGVPVVTVPEQPTLD 135 (300)
T ss_pred cCcHHHHHHHHHcCCcEEEcCCCCCHH
Confidence 457899999999999999999776543
No 111
>PRK11278 NADH dehydrogenase I subunit F; Provisional
Probab=20.69 E-value=1.1e+02 Score=19.87 Aligned_cols=24 Identities=38% Similarity=0.707 Sum_probs=18.7
Q ss_pred CCHHHHHHHHHcCCCcccCCcccCCCCCCH
Q psy1305 27 FPADQIKKLGALGLMGVLVDEEYGGAGLDT 56 (68)
Q Consensus 27 ~~~~~~~~l~~~G~~~~~~p~~~GG~g~~~ 56 (68)
-|.++++.+.++|+.+. ||.|++.
T Consensus 47 ~~~~li~~v~~aGl~Gr------GGAgFPt 70 (448)
T PRK11278 47 SPDEIVNQVKDAGLKGR------GGAGFST 70 (448)
T ss_pred CHHHHHHHHHHcCcCcC------CCCccch
Confidence 36789999999999875 6666654
No 112
>cd08801 Death_UNC5D Death domain found in Uncoordinated-5D. Death Domain (DD) found in Uncoordinated-5D (UNC5D). UNC5D is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=20.45 E-value=1.4e+02 Score=15.13 Aligned_cols=14 Identities=43% Similarity=0.527 Sum_probs=10.2
Q ss_pred CHHHHHHHHHHHhC
Q psy1305 55 DTLALHVAMEEIAQ 68 (68)
Q Consensus 55 ~~~~~~~~~e~l~~ 68 (68)
++...+.+++|||+
T Consensus 62 ~L~~La~aleeiGr 75 (98)
T cd08801 62 DLDSLACALEEIGR 75 (98)
T ss_pred CHHHHHHHHHHhCc
Confidence 46777777888775
No 113
>PF07098 DUF1360: Protein of unknown function (DUF1360); InterPro: IPR010773 This entry is represented by Mycobacterium phage PG1, Gp7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial proteins of around 115 residues in length. Members of this family are found in Bacillus species and Streptomyces coelicolor, the function of the family is unknown.
Probab=20.38 E-value=1e+02 Score=15.79 Aligned_cols=19 Identities=0% Similarity=-0.067 Sum_probs=9.9
Q ss_pred HHHHHHHHHhhhchhHHHh
Q psy1305 3 QKTCRDFAQQELKPIAAKL 21 (68)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~ 21 (68)
.|+|-+|++.-+.....+.
T Consensus 15 ~D~It~~lR~pF~~~~~~~ 33 (105)
T PF07098_consen 15 KDKITSPLRAPFTRRVEEA 33 (105)
T ss_pred HhhhhHHHHHHHHHHhhcc
Confidence 3666666665444333333
No 114
>COG3185 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]
Probab=20.18 E-value=1e+02 Score=19.48 Aligned_cols=21 Identities=19% Similarity=0.249 Sum_probs=15.6
Q ss_pred HHHHHHHHHcCCCcccCCccc
Q psy1305 29 ADQIKKLGALGLMGVLVDEEY 49 (68)
Q Consensus 29 ~~~~~~l~~~G~~~~~~p~~~ 49 (68)
-+.++++.+.|+--+.+|+-|
T Consensus 257 ~~tv~~lr~rG~~fl~ip~tY 277 (363)
T COG3185 257 YATVAALRERGVKFLPIPETY 277 (363)
T ss_pred HHHHHHHHHcCCccCCCchhH
Confidence 356677778888887787766
Done!