Query 029918
Match_columns 185
No_of_seqs 166 out of 1104
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 05:42:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029918.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029918hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0325 Predicted enzyme with 100.0 2.2E-58 4.8E-63 392.5 15.3 147 35-185 2-162 (228)
2 cd06822 PLPDE_III_YBL036c_euk 100.0 7.8E-55 1.7E-59 370.0 15.7 145 37-185 2-161 (227)
3 KOG3157 Proline synthetase co- 100.0 4.9E-55 1.1E-59 368.9 13.5 147 38-185 9-169 (244)
4 TIGR00044 pyridoxal phosphate 100.0 2.7E-36 5.8E-41 254.2 16.6 148 34-185 2-163 (229)
5 cd06824 PLPDE_III_Yggs_like Py 100.0 1E-29 2.2E-34 212.8 16.5 146 36-185 2-161 (224)
6 cd00635 PLPDE_III_YBL036c_like 99.8 4.5E-20 9.7E-25 153.8 16.1 146 36-185 1-159 (222)
7 cd06815 PLPDE_III_AR_like_1 Ty 99.6 1.3E-14 2.7E-19 129.0 13.7 136 33-185 8-157 (353)
8 cd00430 PLPDE_III_AR Type III 99.6 1.1E-14 2.4E-19 128.8 13.2 135 33-185 8-159 (367)
9 PF01168 Ala_racemase_N: Alani 99.6 6.9E-15 1.5E-19 120.4 10.9 133 40-185 3-151 (218)
10 TIGR00492 alr alanine racemase 99.4 1.1E-11 2.4E-16 110.1 13.7 135 33-185 9-161 (367)
11 cd06821 PLPDE_III_D-TA Type II 99.3 1.2E-11 2.6E-16 109.2 9.3 139 33-185 16-170 (361)
12 PRK00053 alr alanine racemase; 99.3 4.9E-11 1.1E-15 106.0 13.0 132 33-185 10-160 (363)
13 cd06808 PLPDE_III Type III Pyr 99.2 1.5E-10 3.3E-15 93.3 11.1 134 37-185 2-149 (211)
14 cd06820 PLPDE_III_LS_D-TA_like 99.2 1.1E-10 2.5E-15 102.8 9.5 138 33-185 10-163 (353)
15 cd07376 PLPDE_III_DSD_D-TA_lik 99.1 4.1E-10 8.9E-15 98.9 10.6 136 36-185 2-154 (345)
16 cd06811 PLPDE_III_yhfX_like Ty 99.1 2.3E-09 4.9E-14 97.0 12.6 136 33-184 35-191 (382)
17 PRK13340 alanine racemase; Rev 98.5 1.3E-06 2.9E-11 79.4 12.9 136 33-185 47-201 (406)
18 cd06819 PLPDE_III_LS_D-TA Type 98.5 1.1E-06 2.4E-11 77.5 10.0 138 33-185 14-167 (358)
19 cd06818 PLPDE_III_cryptic_DSD 98.4 3.2E-06 6.8E-11 76.2 12.5 140 33-185 10-166 (382)
20 cd06826 PLPDE_III_AR2 Type III 98.3 1.4E-05 3E-10 71.7 13.4 135 33-185 8-162 (365)
21 cd06843 PLPDE_III_PvsE_like Ty 98.1 6.9E-05 1.5E-09 66.9 14.2 138 33-185 9-171 (377)
22 cd06827 PLPDE_III_AR_proteobac 98.1 4.3E-05 9.4E-10 68.6 12.6 131 33-185 8-155 (354)
23 cd06839 PLPDE_III_Btrk_like Ty 98.1 6.8E-05 1.5E-09 66.6 12.8 138 33-185 14-176 (382)
24 cd06810 PLPDE_III_ODC_DapDC_li 98.1 7.6E-05 1.6E-09 65.8 12.4 135 34-185 9-169 (368)
25 cd06828 PLPDE_III_DapDC Type I 98.0 0.00025 5.5E-09 62.6 13.9 139 33-185 10-174 (373)
26 TIGR01048 lysA diaminopimelate 97.9 0.00034 7.4E-09 63.1 14.0 138 33-185 32-196 (417)
27 cd06825 PLPDE_III_VanT Type II 97.8 0.00045 9.8E-09 62.3 12.8 130 33-185 8-154 (368)
28 cd06817 PLPDE_III_DSD Type III 97.8 0.00032 7E-09 64.1 11.5 141 33-185 13-175 (389)
29 PRK11930 putative bifunctional 97.7 0.00073 1.6E-08 66.6 13.9 134 40-185 466-617 (822)
30 cd06814 PLPDE_III_DSD_D-TA_lik 97.7 0.00086 1.9E-08 61.0 12.8 137 33-185 16-175 (379)
31 cd06812 PLPDE_III_DSD_D-TA_lik 97.6 0.001 2.3E-08 59.2 12.2 138 33-185 13-166 (374)
32 PRK03646 dadX alanine racemase 97.5 0.0019 4.1E-08 58.2 12.7 130 33-185 10-157 (355)
33 cd06813 PLPDE_III_DSD_D-TA_lik 97.4 0.0025 5.5E-08 57.7 12.5 136 33-185 18-180 (388)
34 cd06842 PLPDE_III_Y4yA_like Ty 97.4 0.0033 7.2E-08 57.6 13.4 139 33-185 17-174 (423)
35 PLN02537 diaminopimelate decar 97.2 0.0076 1.7E-07 54.7 13.0 137 33-185 25-189 (410)
36 TIGR03099 dCO2ase_PEP1 pyridox 96.9 0.025 5.5E-07 50.9 12.9 124 33-172 32-168 (398)
37 cd06841 PLPDE_III_MccE_like Ty 96.8 0.032 6.9E-07 50.0 13.0 139 33-185 14-173 (379)
38 COG3457 Predicted amino acid r 96.7 0.044 9.5E-07 50.1 13.1 116 60-183 28-160 (353)
39 cd00622 PLPDE_III_ODC Type III 95.5 0.33 7.2E-06 43.0 12.3 133 33-185 9-160 (362)
40 COG0787 Alr Alanine racemase [ 95.5 0.39 8.5E-06 44.2 13.0 134 33-185 11-162 (360)
41 COG3616 Predicted amino acid a 91.1 4.3 9.4E-05 37.6 11.9 135 41-185 26-179 (368)
42 TIGR03619 F420_Rv2161c probabl 89.8 0.68 1.5E-05 39.6 5.2 49 38-86 188-242 (246)
43 PRK11165 diaminopimelate decar 82.0 17 0.00037 33.4 10.5 113 62-184 48-189 (420)
44 TIGR01047 nspC carboxynorsperm 81.4 42 0.00091 30.5 13.4 123 33-172 10-146 (380)
45 COG0019 LysA Diaminopimelate d 80.7 36 0.00078 31.6 12.0 134 33-184 34-195 (394)
46 cd06836 PLPDE_III_ODC_DapDC_li 79.6 47 0.001 30.0 13.9 108 60-173 27-149 (379)
47 PF02784 Orn_Arg_deC_N: Pyrido 79.0 37 0.00081 28.5 11.4 111 41-164 3-117 (251)
48 TIGR03856 F420_MSMEG_2906 prob 76.9 6.3 0.00014 34.0 5.6 46 38-85 181-226 (249)
49 TIGR02356 adenyl_thiF thiazole 75.1 12 0.00025 31.0 6.5 67 82-151 68-136 (202)
50 cd06830 PLPDE_III_ADC Type III 74.6 69 0.0015 29.3 15.6 145 33-183 12-190 (409)
51 cd01483 E1_enzyme_family Super 73.9 17 0.00036 27.8 6.7 66 83-151 47-114 (143)
52 cd06829 PLPDE_III_CANSDC Type 72.4 70 0.0015 28.4 13.2 102 59-172 25-142 (346)
53 cd01487 E1_ThiF_like E1_ThiF_l 68.9 22 0.00048 28.8 6.8 87 59-150 24-112 (174)
54 cd01485 E1-1_like Ubiquitin ac 62.3 33 0.00072 28.3 6.7 65 84-151 70-138 (198)
55 cd06831 PLPDE_III_ODC_like_AZI 60.6 1.4E+02 0.003 27.4 12.6 119 33-172 20-147 (394)
56 TIGR02355 moeB molybdopterin s 58.3 36 0.00079 29.1 6.4 65 84-151 73-139 (240)
57 PRK05690 molybdopterin biosynt 54.8 38 0.00083 29.0 6.0 66 83-151 80-147 (245)
58 cd00757 ThiF_MoeB_HesA_family 53.5 49 0.0011 27.7 6.4 65 84-151 70-136 (228)
59 cd01492 Aos1_SUMO Ubiquitin ac 52.5 69 0.0015 26.4 7.0 65 83-151 69-135 (197)
60 PRK08644 thiamine biosynthesis 51.2 59 0.0013 27.2 6.4 87 59-150 53-141 (212)
61 TIGR02354 thiF_fam2 thiamine b 48.5 79 0.0017 26.3 6.8 97 47-150 36-134 (200)
62 PF00072 Response_reg: Respons 48.4 17 0.00036 25.4 2.3 28 59-86 70-97 (112)
63 COG1210 GalU UDP-glucose pyrop 48.2 23 0.0005 32.1 3.7 114 60-177 15-177 (291)
64 PRK05600 thiamine biosynthesis 47.9 55 0.0012 29.9 6.2 67 82-151 88-156 (370)
65 PLN02439 arginine decarboxylas 44.8 3.1E+02 0.0067 26.8 15.5 137 34-172 7-162 (559)
66 PF00899 ThiF: ThiF family; I 40.0 1.3E+02 0.0027 22.8 6.3 65 84-151 51-117 (135)
67 PRK05354 arginine decarboxylas 39.4 4E+02 0.0087 26.5 14.6 134 33-172 71-225 (634)
68 PRK07878 molybdopterin biosynt 38.1 1.2E+02 0.0026 27.7 6.9 67 82-151 89-157 (392)
69 PRK08762 molybdopterin biosynt 37.7 1.2E+02 0.0026 27.4 6.7 88 60-151 137-250 (376)
70 TIGR03854 F420_MSMEG_3544 prob 31.1 1.2E+02 0.0026 26.5 5.4 24 39-62 186-209 (290)
71 TIGR01273 speA arginine decarb 31.1 5.4E+02 0.012 25.6 14.8 134 33-172 64-218 (624)
72 PF10498 IFT57: Intra-flagella 30.5 99 0.0022 28.5 5.0 20 8-27 255-274 (359)
73 cd01489 Uba2_SUMO Ubiquitin ac 28.5 3.5E+02 0.0075 24.4 8.0 67 82-151 46-115 (312)
74 cd01573 modD_like ModD; Quinol 28.3 1.9E+02 0.0041 25.4 6.2 72 63-138 185-261 (272)
75 PRK08223 hypothetical protein; 27.8 2.2E+02 0.0048 25.5 6.6 67 82-151 74-144 (287)
76 cd06840 PLPDE_III_Bif_AspK_Dap 26.2 4.8E+02 0.01 23.4 11.5 101 61-172 36-153 (368)
77 PLN00064 photosystem II protei 25.9 3.1E+02 0.0067 23.0 6.6 65 17-90 74-141 (166)
78 PRK07411 hypothetical protein; 25.7 2.4E+02 0.0051 25.9 6.6 67 82-151 85-153 (390)
79 TIGR03044 PS_II_psb27 photosys 24.3 3.4E+02 0.0074 22.0 6.4 72 17-98 45-121 (135)
80 TIGR03857 F420_MSMEG_2249 prob 23.5 1.2E+02 0.0026 27.0 4.2 27 39-65 184-210 (329)
81 KOG4196 bZIP transcription fac 23.4 2.5E+02 0.0054 22.8 5.5 57 3-63 74-130 (135)
82 PRK05597 molybdopterin biosynt 23.1 2.8E+02 0.006 25.1 6.4 65 84-151 77-143 (355)
83 COG0205 PfkA 6-phosphofructoki 21.0 75 0.0016 29.3 2.4 32 87-118 237-268 (347)
84 TIGR03860 FMN_nitrolo FMN-depe 20.7 1.1E+02 0.0023 28.3 3.3 26 39-64 240-265 (422)
85 PLN00035 histone H4; Provision 20.1 3.9E+02 0.0085 20.6 5.8 40 38-88 61-101 (103)
No 1
>COG0325 Predicted enzyme with a TIM-barrel fold [General function prediction only]
Probab=100.00 E-value=2.2e-58 Score=392.45 Aligned_cols=147 Identities=46% Similarity=0.626 Sum_probs=140.2
Q ss_pred HHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHHcCCcccccccHHHHHHHHhcCCC--CceEEEEec
Q 029918 35 VAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPD--DLEWHFIGN 112 (185)
Q Consensus 35 ~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~--~i~WHfIG~ 112 (185)
++.+||..|+++|.++|.++||+|++|+|||||||+|+++|++||++|+|+||||||||+.+|++.|++ +|.|||||+
T Consensus 2 ~i~~nl~~v~~~I~~a~~~a~R~~~~V~LvAVSK~~~~~~I~~~~~aG~r~fGENrvQe~~~K~~~l~~~~~i~WHfIG~ 81 (228)
T COG0325 2 DIKENLAAVRERIAAAAERAGRNPGSVTLVAVSKTVPAEDIREAYEAGQRHFGENRVQEALDKIEALKDLPDIEWHFIGP 81 (228)
T ss_pred cHHHHHHHHHHHHHHHHHHcCCCCCcEEEEEEeCCCCHHHHHHHHHcCChhhcchHHHHHHHHHHhcCcCCCeEEEEech
Confidence 478999999999999999999999999999999999999999999999999999999999999999987 499999999
Q ss_pred ccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCccccc------------ccCCcccc
Q 029918 113 LQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECF------------IKCSWSHS 180 (185)
Q Consensus 113 LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~------------~~~~~l~l 180 (185)
|||||+|+++ ++|+|||||||+|||.+|++++...+ ++++||||||+|+|+||||+ ..||+|.+
T Consensus 82 LQsNK~k~v~---~~~~~ihSlDr~klA~~l~kra~~~~-~~l~v~iQVNi~~E~sK~G~~~~e~~~~~~~~~~~~~L~l 157 (228)
T COG0325 82 LQSNKVKLVA---ENFDWIHSLDRLKLAKELNKRALELP-KPLNVLIQVNISGEESKSGVPPEELDELAQEVQELPNLEL 157 (228)
T ss_pred hhhhHHHHHH---hhcceeeecCHHHHHHHHHHHHHhCC-CCceEEEEEecCCccccCCCCHHHHHHHHHHHHhCCCCeE
Confidence 9999999999 89999999999999999999887654 58999999999999999996 36999999
Q ss_pred cccCC
Q 029918 181 CLLMI 185 (185)
Q Consensus 181 ~g~m~ 185 (185)
.|||+
T Consensus 158 ~GLM~ 162 (228)
T COG0325 158 RGLMT 162 (228)
T ss_pred eEEEe
Confidence 99996
No 2
>cd06822 PLPDE_III_YBL036c_euk Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins. This subfamily contains mostly uncharacterized eukaryotic proteins with similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity. Some members of this subfamily are also referred to as PROSC (Proline synthetase co-transcribed bacterial homolog)
Probab=100.00 E-value=7.8e-55 Score=370.00 Aligned_cols=145 Identities=54% Similarity=0.843 Sum_probs=136.1
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHHcCCcccccccHHHHHHHHhcCCCCceEEEEeccccc
Q 029918 37 ATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQSN 116 (185)
Q Consensus 37 ~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~~i~WHfIG~LQsN 116 (185)
.+||..|+++|.++|.+ |+|++|+|||||||+|+++|++||++|+++||||||||+.+|++.|+++|+||||||||||
T Consensus 2 ~~~l~~i~~~i~~a~~~--r~~~~v~LvaVsK~~~~~~i~~~~~~G~~~fGENrvQe~~~K~~~l~~~i~wHfIG~LQ~N 79 (227)
T cd06822 2 IANLKRIRQAVKRASKK--LPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVQELIEKAPDLPIDIKWHFIGHLQSN 79 (227)
T ss_pred hHHHHHHHHHHHHHHHh--CCCCCcEEEEEECCCCHHHHHHHHHcCCccccCcHHHHHHHHHHhccCCceEEEECCCchh
Confidence 57999999999999988 8899999999999999999999999999999999999999999999878999999999999
Q ss_pred chHHHhhcCCCccEEEecCcHHHHHHHHHHHHhc--CCCCccEEEEEeCCCCCccccc------------c-cCCccccc
Q 029918 117 KVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETM--GRKPLKVLVQVNTSGEEYGECF------------I-KCSWSHSC 181 (185)
Q Consensus 117 Kvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~--~~~~l~VLIQVNis~E~sKsG~------------~-~~~~l~l~ 181 (185)
|+|+++ .+++|+|||||||+++|++|++++.+. + .+++||||||+++|++|+|+ . .||+|+|.
T Consensus 80 K~k~i~-~~~~~~~ihsvDs~~la~~L~~~a~~~~~~-~~~~VlIqVn~g~e~~K~Gv~~~e~~~l~~~i~~~~~~L~l~ 157 (227)
T cd06822 80 KVKKLL-KVPNLYMVETVDSEKLADKLNKAWEKLGER-EPLKVMVQVNTSGEESKSGLEPSEAVELVKHIIEECPNLKFS 157 (227)
T ss_pred hHHHHh-ccccccEEEecCCHHHHHHHHHHHHHhcCC-CCCcEEEEEeCCCCCCCCCCCHHHHHHHHHHHHhhCCCceEE
Confidence 999996 115999999999999999999999876 5 68999999999999999997 2 79999999
Q ss_pred ccCC
Q 029918 182 LLMI 185 (185)
Q Consensus 182 g~m~ 185 (185)
||||
T Consensus 158 GLMt 161 (227)
T cd06822 158 GLMT 161 (227)
T ss_pred EEEe
Confidence 9997
No 3
>KOG3157 consensus Proline synthetase co-transcribed protein [General function prediction only]
Probab=100.00 E-value=4.9e-55 Score=368.88 Aligned_cols=147 Identities=56% Similarity=0.832 Sum_probs=140.7
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHHcCCcccccccHHHHHHHHhcCCCCceEEEEecccccc
Q 029918 38 TALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQSNK 117 (185)
Q Consensus 38 ~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~~i~WHfIG~LQsNK 117 (185)
..|..|.+||++++.+++|+...++|||||||+|++.|.+||++|+|+||||||||+.+|++.||+||+|||||||||||
T Consensus 9 ~~L~~v~~rv~qa~~~~~r~~~~~rlvaVSKtKPa~~i~~~Y~~GqR~FGENYVQEl~eKap~lp~DI~WHFIG~lQsnK 88 (244)
T KOG3157|consen 9 SALRAVIERVQQAVNQRPRDENAVRLVAVSKTKPASLIIEAYDAGQRHFGENYVQELIEKAPLLPDDIKWHFIGHLQSNK 88 (244)
T ss_pred HHHHHHHHHHHHHHHhccccccceEEEEeecCCcHHHHHHHHHcCcChhhHHHHHHHHHhcccCcccceeeeechhhhcc
Confidence 46889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCC-CCccEEEEEeCCCCCcccccc-------------cCCccccccc
Q 029918 118 VKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGR-KPLKVLVQVNTSGEEYGECFI-------------KCSWSHSCLL 183 (185)
Q Consensus 118 vk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~-~~l~VLIQVNis~E~sKsG~~-------------~~~~l~l~g~ 183 (185)
+|+++ ++|++++||||||.|+|..||+.+.+.+. .|+.||||||||||++|||+. .|++|+|.||
T Consensus 89 ~kkl~-svpnL~~vetVDseK~A~~ld~a~~k~g~~~PL~V~VQvNTSGEd~K~Giepse~~~l~~~i~~~c~nL~f~Gl 167 (244)
T KOG3157|consen 89 CKKLL-SVPNLYSVETVDSEKKARKLDSAWSKLGPDNPLKVLVQVNTSGEDSKSGIEPSEAPELAEHIKSECKNLKFSGL 167 (244)
T ss_pred cchhc-cCCceEEEEecchHHHHHHHHHHHHhcCCCCCeEEEEEeecCCccccCCCChhhhHHHHHHHHHhCCcceeeee
Confidence 99998 58999999999999999999999998764 599999999999999999973 4999999999
Q ss_pred CC
Q 029918 184 MI 185 (185)
Q Consensus 184 m~ 185 (185)
||
T Consensus 168 MT 169 (244)
T KOG3157|consen 168 MT 169 (244)
T ss_pred EE
Confidence 97
No 4
>TIGR00044 pyridoxal phosphate enzyme, YggS family. Members of this protein family include YggS from Escherichia coli and YBL036C, an uncharacterized pyridoxal protein of Saccharomyces cerevisiae.
Probab=100.00 E-value=2.7e-36 Score=254.22 Aligned_cols=148 Identities=42% Similarity=0.621 Sum_probs=138.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHHcCCcccccccHHHHHHHHhcCCC--CceEEEEe
Q 029918 34 GVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPD--DLEWHFIG 111 (185)
Q Consensus 34 ~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~--~i~WHfIG 111 (185)
.++.+||+.|+++|..+|.++||+|.+++|+||||+.+++.|..++++|+++|||||+||+.+|+..|++ ++.|||||
T Consensus 2 ~~~~~~~~~i~~~i~~~~~~~~~~~~~~~l~aV~K~~~~~~i~~l~~~G~~~fg~~~~~Ea~~k~~~lr~~~~~~~~~ig 81 (229)
T TIGR00044 2 SDIIHYLEDIKTKIEAANTHVNRNPSKVKLLAVSKTKPASAIQIAYDAGQRAFGENYVQELVEKIKLLEDLGKLEWHFIG 81 (229)
T ss_pred hhHHHHHHHHHHHHHHHHHHcCCCcCCeEEEEEECCCCHHHHHHHHHcCCccccEEcHHHHHHHHHHhcccCCceEEEEC
Confidence 4678999999999999999999999999999999999999999999999999999999999999998864 58999999
Q ss_pred cccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc------------cCCccc
Q 029918 112 NLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI------------KCSWSH 179 (185)
Q Consensus 112 ~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~------------~~~~l~ 179 (185)
|+|+||.++++ ..++++++|||++.++.|++.+.+.+ ++++|+||||++++.++.||. .||+|+
T Consensus 82 ~~q~~~~~~~~---~~~~l~~~vds~~~~~~l~~~a~~~~-~~~~V~l~vdtg~gm~R~G~~~~e~~~~~~~i~~~~~l~ 157 (229)
T TIGR00044 82 PLQSNKDRLVV---ENFDWVHTIDSLKIAKKLNEQREKLQ-PPLNVLLQINISDEESKSGIQPEELLELAIQIEELKHLK 157 (229)
T ss_pred CCcchHHHHHh---hhcCEEEEECCHHHHHHHHHHHHhcC-CCceEEEEEECCCCCCCCCCCHHHHHHHHHHHhcCCCCe
Confidence 99999999998 78999999999999999999998765 689999999999999999983 599999
Q ss_pred ccccCC
Q 029918 180 SCLLMI 185 (185)
Q Consensus 180 l~g~m~ 185 (185)
+.||||
T Consensus 158 l~Gl~t 163 (229)
T TIGR00044 158 LRGLMT 163 (229)
T ss_pred EEEEEE
Confidence 999996
No 5
>cd06824 PLPDE_III_Yggs_like Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins. This subfamily contains mainly uncharacterized proteobacterial proteins with similarity to the hypothetical Escherichia coli protein YggS, a homolog of yeast YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. Like yeast YBL036c, Yggs is a single domain monomeric protein with a typical TIM-barrel fold. Its structure, which shows a covalently-bound PLP cofactor, is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. YggS has not been characterized extensively and its biological function is still unkonwn.
Probab=99.97 E-value=1e-29 Score=212.83 Aligned_cols=146 Identities=47% Similarity=0.638 Sum_probs=135.4
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHHcCCcccccccHHHHHHHHhcCCC--CceEEEEecc
Q 029918 36 AATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPD--DLEWHFIGNL 113 (185)
Q Consensus 36 i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~--~i~WHfIG~L 113 (185)
+.+|+..|.++|+.+|.++||+|++++|+||+|+|+++.|..++++|++.||+|++||+.+|+..|.+ .+.|||||++
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~aVvKahG~~~v~~~~~~G~~~fgva~~~Ea~~k~~~Lr~~g~~~~~~lg~~ 81 (224)
T cd06824 2 IAENLAQVKQRIAQAAKQAGRDPSSVQLLAVSKTKPADAIREAYAAGQRHFGENYVQEALEKIEALRDLQDIEWHFIGPI 81 (224)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCcCCeEEEEEECCCCHHHHHHHHHcCCcccCcChHHHHHHHHHHhccCCCeeEEEEcCc
Confidence 46799999999999999999999999999999999999999999999999999999999999999976 4899999999
Q ss_pred cccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc------------cCCccccc
Q 029918 114 QSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI------------KCSWSHSC 181 (185)
Q Consensus 114 QsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~------------~~~~l~l~ 181 (185)
|.||..+.+ ...+++++|||++.++.|++.+.+.+ .+++|+|+||+++..++.||. .+|+|++.
T Consensus 82 ~~~~~~~~~---~~~~~~~~I~s~~~~~~l~~~a~~~g-~~~~v~l~id~~~Gm~R~Gi~~~~~~~~~~~i~~~~~l~l~ 157 (224)
T cd06824 82 QSNKTKLIA---ENFDWVHSVDRLKIAKRLNDQRPAGL-PPLNVCIQVNISGEDSKSGVAPEDAAELAEAISQLPNLRLR 157 (224)
T ss_pred hhhhHHHHH---hhCCEEEecCCHHHHHHHHHHHHhcC-CCCcEEEEEEcCCCCCCCCCCHHHHHHHHHHHhcCCCCcEE
Confidence 999988887 57899999999999999999987654 579999999999999999983 48999999
Q ss_pred ccCC
Q 029918 182 LLMI 185 (185)
Q Consensus 182 g~m~ 185 (185)
|||+
T Consensus 158 Gl~t 161 (224)
T cd06824 158 GLMA 161 (224)
T ss_pred EEEE
Confidence 9996
No 6
>cd00635 PLPDE_III_YBL036c_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins. This family contains mostly uncharacterized proteins, widely distributed among eukaryotes, bacteria and archaea, that bear similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity.
Probab=99.85 E-value=4.5e-20 Score=153.79 Aligned_cols=146 Identities=48% Similarity=0.665 Sum_probs=131.8
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHHcCCcccccccHHHHHHHHhcCCC-CceEEEEeccc
Q 029918 36 AATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPD-DLEWHFIGNLQ 114 (185)
Q Consensus 36 i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~-~i~WHfIG~LQ 114 (185)
+.+|++.++..|+...+.++|.+..++++||+|+|.+..|..++++|++.||.++++|+....+.+.+ .+.|+|||++|
T Consensus 1 ~~~~~~~l~~Ni~~~~~~~~~~~~~~~l~avvK~hg~~~va~~~~~G~~~f~va~l~Ea~~lr~~~~~~~~~~~llg~~~ 80 (222)
T cd00635 1 IAENLEEVRERIAAAAERAGRDPDEVTLVAVSKTVPAEAIREAIEAGQRDFGENRVQEALDKAEELPDPDIEWHFIGHLQ 80 (222)
T ss_pred ChHHHHHHHHHHHHHHHHcCCCcCCeEEEEEECCCCHHHHHHHHHcCCcccCCCcHHHHHHHHHHccCCCceEEEECccc
Confidence 35899999999999999998888889999999999999999999999999999999999998777654 58899999999
Q ss_pred ccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc------------cCCcccccc
Q 029918 115 SNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI------------KCSWSHSCL 182 (185)
Q Consensus 115 sNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~------------~~~~l~l~g 182 (185)
.++++.++ .+.+++.||||+..++.|++.+.+.+ ++++|+|.||++.+.++.|+. .+|+|.+.|
T Consensus 81 ~~~~~~~~---~~~~~~~~v~s~~~l~~l~~~a~~~~-~~~~v~lkvdtG~~~~R~G~~~~~~~~~~~~i~~~~~l~~~G 156 (222)
T cd00635 81 TNKVKYAV---RLFDLIHSVDSLKLAEELNKRAEKEG-RVLDVLVQVNIGGEESKSGVAPEELEELLEEIAALPNLRIRG 156 (222)
T ss_pred cccHHHHH---hhCCEEEEcCCHHHHHHHHHHHHhcC-CCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHHcCCCCcEEE
Confidence 99999998 56789999999999999999987665 689999999998889999983 489999999
Q ss_pred cCC
Q 029918 183 LMI 185 (185)
Q Consensus 183 ~m~ 185 (185)
+|+
T Consensus 157 i~s 159 (222)
T cd00635 157 LMT 159 (222)
T ss_pred EEE
Confidence 985
No 7
>cd06815 PLPDE_III_AR_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1. This subfamily is composed of uncharacterized bacterial proteins with similarity to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.
Probab=99.60 E-value=1.3e-14 Score=129.02 Aligned_cols=136 Identities=12% Similarity=0.092 Sum_probs=107.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCC-C-HHHHHHHHHcCCcccccccHHHHHHHHhcCCCCceEEEE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTK-P-VSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFI 110 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~-p-~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~~i~WHfI 110 (185)
.+.|..|++.+++.. + +.+++|+||+|+. . ++.++.++++|++.||.++++|+. ++....-...||++
T Consensus 8 l~al~~Ni~~i~~~~-------~--~~~~~l~~vvKa~hg~~~va~~l~~~G~~~f~va~i~EA~-~lr~~G~~~~illl 77 (353)
T cd06815 8 LSKIRHNAKVLVELC-------K--SRGIEVTGVTKVVCGDPEIAEALLEGGITHLADSRIENLK-KLKDLGISGPKMLL 77 (353)
T ss_pred HHHHHHHHHHHHHHH-------h--hcCCEEEEEEcccCCCHHHHHHHHHcCCCEEEeccHHHHH-HHHhcCCCCCEEEE
Confidence 345566666665443 2 2468999999997 3 677777889999999999999997 55544323489999
Q ss_pred ecccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc------------cCCcc
Q 029918 111 GNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI------------KCSWS 178 (185)
Q Consensus 111 G~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~------------~~~~l 178 (185)
|.+|.++++.++ .+ ..+-.++|++.|+.|++.+.+.+ ++++|+|+||++. ++.||. .+++|
T Consensus 78 g~~~~~~~~~~~---~~-~~~~~i~s~~~~~~l~~~a~~~~-~~~~vhlkvDtGm--~R~G~~~~e~~~~~~~i~~~~~l 150 (353)
T cd06815 78 RIPMLSEVEDVV---KY-ADISLNSELETIKALSEEAKKQG-KIHKIILMVDLGD--LREGVLPEDLLDFVEEILKLPGI 150 (353)
T ss_pred CCCCHHHHHHHH---hh-cceeccChHHHHHHHHHHHHHcC-CccceEEEEecCC--CccccCHHHHHHHHHHHhCCCCc
Confidence 999999999998 33 34566889999999999987665 5799999999986 899973 48999
Q ss_pred cccccCC
Q 029918 179 HSCLLMI 185 (185)
Q Consensus 179 ~l~g~m~ 185 (185)
++.|+||
T Consensus 151 ~~~Gi~t 157 (353)
T cd06815 151 ELVGIGT 157 (353)
T ss_pred EEEeccc
Confidence 9999976
No 8
>cd00430 PLPDE_III_AR Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase. This family includes predominantly bacterial alanine racemases (AR), some serine racemases (SerRac), and putative bifunctional enzymes containing N-terminal UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase (murF) and C-terminal AR domains. These proteins are fold type III PLP-dependent enzymes that play essential roles in peptidoglycan biosynthesis. AR catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. SerRac converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. murF catalyzes the addition of D-Ala-D-Ala to UDPMurNAc-tripeptide, the final step in the synthesis of the cytoplasmic precursor of bacterial cell wall peptidoglycan. Members of this family contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with activ
Probab=99.60 E-value=1.1e-14 Score=128.75 Aligned_cols=135 Identities=17% Similarity=0.151 Sum_probs=111.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecC----CCHHHH-HHHHHcCCcccccccHHHHHHHHhcCCCCceE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKT----KPVSVI-RQVYEAGHRCFGENYVQEIVEKAAQLPDDLEW 107 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt----~p~e~I-~~a~~~G~r~FGENrvQEl~~K~~~L~~~i~W 107 (185)
.+.|..|++.+++.+ +..+++.+|+|+ |+...| +.+.++|++.||.++++|+........ +..|
T Consensus 8 ~~~i~~N~~~l~~~~----------~~~~~l~~vvKan~yGhg~~~i~~~l~~~G~~~~~vas~~Ea~~~~~~g~-~~~i 76 (367)
T cd00430 8 LDALRHNLRVIRRLL----------GPGTKIMAVVKADAYGHGAVEVAKALEEAGADYFAVATLEEALELREAGI-TAPI 76 (367)
T ss_pred HHHHHHHHHHHHHhC----------CCCCEEEEEEeeccccCcHHHHHHHHHHCCCCEEEECcHHHHHHHHhcCC-CCCE
Confidence 455667777766554 226899999999 556666 567789999999999999999887653 3579
Q ss_pred EEEecccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc------------cC
Q 029918 108 HFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI------------KC 175 (185)
Q Consensus 108 HfIG~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~------------~~ 175 (185)
+++|+++.++++.++ . ..++.+|||++.++.|++.+.+.+ .+++|+|+||++. +|.|+. .+
T Consensus 77 ~~~~~~~~~~~~~~~---~-~~i~~~vds~~~l~~l~~~a~~~~-~~~~v~l~vdtG~--~R~G~~~~e~~~~~~~i~~~ 149 (367)
T cd00430 77 LVLGGTPPEEAEEAI---E-YDLTPTVSSLEQAEALSAAAARLG-KTLKVHLKIDTGM--GRLGFRPEEAEELLEALKAL 149 (367)
T ss_pred EEEeCCCHHHHHHHH---H-cCCEEEECCHHHHHHHHHHHHHcC-CceEEEEEEcCCC--CCCCCCHHHHHHHHHHHHhC
Confidence 999999999999998 3 367899999999999999987654 5789999999975 999973 47
Q ss_pred CcccccccCC
Q 029918 176 SWSHSCLLMI 185 (185)
Q Consensus 176 ~~l~l~g~m~ 185 (185)
++|++.|||+
T Consensus 150 ~~l~~~Gi~~ 159 (367)
T cd00430 150 PGLELEGVFT 159 (367)
T ss_pred CCceEEEEEE
Confidence 9999999985
No 9
>PF01168 Ala_racemase_N: Alanine racemase, N-terminal domain; InterPro: IPR001608 Alanine racemase plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins containing this domain are found in both prokaryotes and eukaryotes [,]. The molecular structure of alanine racemase from Bacillus stearothermophilus was determined by X-ray crystallography to a resolution of 1.9 A []. The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N terminus, and a C-terminal domain essentially composed of beta-strands. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C terminus of the first beta-strand of the alpha/beta barrel. This domain is also found in the PROSC (proline synthetase co-transcribed bacterial homolog) family of proteins, which are not known to have alanine racemase activity.; PDB: 3KW3_A 1B54_A 1CT5_A 2ODO_B 2RJG_A 3B8V_D 2RJH_D 3B8T_D 3B8W_B 3B8U_A ....
Probab=99.60 E-value=6.9e-15 Score=120.43 Aligned_cols=133 Identities=20% Similarity=0.228 Sum_probs=106.8
Q ss_pred HHHHHHHHHHHHHHcCCCCCCeEEEEeecC--CCHHHHHHHH-Hc-CCcccccccHHHHHHHHhcCCCCceEEEEecccc
Q 029918 40 LRSVIQRVHQAAERSSRPPDRIRIVAVSKT--KPVSVIRQVY-EA-GHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQS 115 (185)
Q Consensus 40 l~~V~~rI~~a~~~~gR~p~~V~LvAVSKt--~p~e~I~~a~-~~-G~r~FGENrvQEl~~K~~~L~~~i~WHfIG~LQs 115 (185)
+..++..|+...+.+ ++ ..+|++|+|+ .+.+.++.+. .+ |++.||.++++|+..=.+.. ..|+++|+++.
T Consensus 3 l~al~~Ni~~~~~~~-~~--~~~l~~vvK~~ayg~~~~~~~~~~~~g~~~~~va~~~Ea~~lr~~g---~~il~l~~~~~ 76 (218)
T PF01168_consen 3 LDALRHNIRKIRQRA-GP--GTKLRAVVKANAYGHGIVRVAKALAEGIDGFAVATLEEAEELREAG---APILVLGPIPP 76 (218)
T ss_dssp HHHHHHHHHHHHHHH-CT--TSEEEEE-HHHHHTTHHHHHHHHHHHTCSEEEESSHHHHHHHHHTT---SEEEEESESTG
T ss_pred HHHHHHHHHHHHHHc-CC--CCEEEEEEcCCCcCccHHHHHHHHhcCCCEEEEeeHHHhhhHHhcC---CceEEEcCCCh
Confidence 344455555555555 22 5789999999 7777777777 55 89999999999998544433 67999999999
Q ss_pred cchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc------------cCCccccccc
Q 029918 116 NKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI------------KCSWSHSCLL 183 (185)
Q Consensus 116 NKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~------------~~~~l~l~g~ 183 (185)
++++.++ ++ +++.+|||++.++.|++.+.+.+ .+++|+|+||++.. +.||. .+|++++.|+
T Consensus 77 ~~~~~~~---~~-~~~~~v~s~~~~~~l~~~~~~~~-~~~~v~l~vdtG~~--R~G~~~~~~~~l~~~i~~~~~l~l~Gl 149 (218)
T PF01168_consen 77 EELEELV---EY-NIIPTVDSLEQLEALSKAAKKQG-KPLKVHLKVDTGMG--RLGVRPEELEELAEAIKALPNLRLEGL 149 (218)
T ss_dssp GGHHHHH---HT-TEEEEE-SHHHHHHHHHHHHHHT-STEEEEEEBESSSS--SSSBECHHHHHHHHHHHHTTTEEEEEE
T ss_pred hhHHHHh---hC-cEEEEEchhhHHHHHHHHHHHcC-CceEEEEeeccccc--ccCCCHHHHHHHHHHHhcCCCceEeeE
Confidence 9999999 56 99999999999999999998765 68999999999887 88873 4899999999
Q ss_pred CC
Q 029918 184 MI 185 (185)
Q Consensus 184 m~ 185 (185)
|+
T Consensus 150 ~t 151 (218)
T PF01168_consen 150 MT 151 (218)
T ss_dssp EE
T ss_pred ec
Confidence 96
No 10
>TIGR00492 alr alanine racemase. This enzyme interconverts L-alanine and D-alanine. Its primary function is to generate D-alanine for cell wall formation. With D-alanine-D-alanine ligase, it makes up the D-alanine branch of the peptidoglycan biosynthetic route. It is a monomer with one pyridoxal phosphate per subunit. In E. coli, the ortholog is duplicated so that a second isozyme, DadX, is present. DadX, a paralog of the biosynthetic Alr, is induced by D- or L-alanine and is involved in catabolism.
Probab=99.37 E-value=1.1e-11 Score=110.13 Aligned_cols=135 Identities=15% Similarity=0.131 Sum_probs=106.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCC----CHHHH-HHHHHcCCcccccccHHHHHHHHhcCCCCceE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTK----PVSVI-RQVYEAGHRCFGENYVQEIVEKAAQLPDDLEW 107 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~----p~e~I-~~a~~~G~r~FGENrvQEl~~K~~~L~~~i~W 107 (185)
.+.|..|++.+++.+ +..++|++|+|.- ....| +.++++|++.|+.++++|+..-...- -+..|
T Consensus 9 l~~l~~N~~~i~~~~----------~~~~~i~~vvKAnaYGhg~~~i~~~l~~~G~~~~~vas~~Ea~~lr~~G-~~~~i 77 (367)
T TIGR00492 9 LAALKHNLSAIRNHI----------GPKSKIMAVVKANAYGHGLIEVAKTLLQAGADYFGVANLEEAITLRKAG-ITAPI 77 (367)
T ss_pred HHHHHHHHHHHHHhc----------CCCCEEEEEEEcCCccCcHHHHHHHHHHCCCCEEEECcHHHHHHHHhcC-CCCCE
Confidence 455677777776554 2357999999995 45555 66678999999999999988765432 24579
Q ss_pred EEEecccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc------------cC
Q 029918 108 HFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI------------KC 175 (185)
Q Consensus 108 HfIG~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~------------~~ 175 (185)
+++|+.+...+..++ ..+++.+|||++.++.|++.+.+.+ ++++|+|+||++. ++.|+. .+
T Consensus 78 lvl~~~~~~~~~~~~----~~~l~~~v~s~~~l~~l~~~a~~~~-~~~~V~l~VdtGm--~R~Gi~~~e~~~~~~~i~~~ 150 (367)
T TIGR00492 78 LLLGGFFAEDLKILA----AWDLTTTVHSVEQLQALEEALLKEP-KRLKVHLKIDTGM--NRLGVKPDEAALFVQKLRQL 150 (367)
T ss_pred EEEeCCCHHHHHHHH----HcCCEEEECCHHHHHHHHHHHHHcC-CceEEEEEeeCCC--CCCCCChHHHHHHHHHHHhC
Confidence 999999866677666 3567999999999999999987664 5789999999985 999973 48
Q ss_pred Cccc-ccccCC
Q 029918 176 SWSH-SCLLMI 185 (185)
Q Consensus 176 ~~l~-l~g~m~ 185 (185)
|+|+ +.|+|+
T Consensus 151 ~~l~~l~Gi~t 161 (367)
T TIGR00492 151 KKFLELEGIFS 161 (367)
T ss_pred CCCCCceEEEc
Confidence 9999 999986
No 11
>cd06821 PLPDE_III_D-TA Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme D-Threonine Aldolase. D-threonine aldolase (D-TA, EC 4.3.1.18) reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. Its activity is present in several genera of bacteria but not in fungi. It requires PLP and a divalent cation such as Co2+, Ni2+, Mn2+, or Mg2+ as cofactors for catalytic activity and thermal stability. Members of this subfamily show similarity to bacterial alanine racemase (AR), a fold type III PLP-dependent enzyme which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on its similarity to AR, it is possible that low specificity D-TAs also form dimers in solution. Experimental data show that
Probab=99.29 E-value=1.2e-11 Score=109.25 Aligned_cols=139 Identities=21% Similarity=0.153 Sum_probs=107.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHH-HHHcCCcccccccHHHHHHHHhcCCCC--ceEEE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQ-VYEAGHRCFGENYVQEIVEKAAQLPDD--LEWHF 109 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~-a~~~G~r~FGENrvQEl~~K~~~L~~~--i~WHf 109 (185)
.+.+..|++.+++.+ + ..++|.+|.|+++...|.. ++++|...|+.++++|+......--++ +.||+
T Consensus 16 ~~~l~~Ni~~~~~~~-------~---~~~~l~~~vKah~~~~i~~~~~~~G~~~~~vas~~Ea~~~~~~G~~~ill~~~~ 85 (361)
T cd06821 16 PDRIEENIRRMIRMA-------G---DPQRLRPHVKTHKMAEIVRLQLEAGITKFKCATIAEAEMLAEAGAPDVLLAYPL 85 (361)
T ss_pred HHHHHHHHHHHHHHH-------h---cCCCccccchhhcCHHHHHHHHhcCCCcEEEecHHHHHHHHHcCCCeEEEeCCC
Confidence 556667776666554 2 1348999999998877555 668999999999999999887752233 56999
Q ss_pred EecccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc-------------cCC
Q 029918 110 IGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI-------------KCS 176 (185)
Q Consensus 110 IG~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~-------------~~~ 176 (185)
+|+.+.+.++.+. ..+...++.+|||++.++.|++.+.+.+ .+++|+|+||++. ++.|+. .+|
T Consensus 86 ~~~~~~~~~~l~~-~~~~~~~~~~Vds~~~l~~l~~~a~~~~-~~~~V~l~Vd~G~--~R~Gv~~~~~~~~l~~~i~~~~ 161 (361)
T cd06821 86 VGPNIERFLELAK-KYPGTRFSALVDDLEAAEALSAAAGSAG-LTLSVLLDVNTGM--NRTGIAPGEDAEELYRAIATLP 161 (361)
T ss_pred CHHHHHHHHHHHh-hCCCCeEEEEECCHHHHHHHHHHHHHcC-CeEEEEEEeCCCC--CcCCCCChHHHHHHHHHHhhCC
Confidence 9998888887665 1223567899999999999999998765 6899999999974 677762 479
Q ss_pred cccccccCC
Q 029918 177 WSHSCLLMI 185 (185)
Q Consensus 177 ~l~l~g~m~ 185 (185)
+|+|.|||+
T Consensus 162 ~l~l~Gl~~ 170 (361)
T cd06821 162 GLVLAGLHA 170 (361)
T ss_pred CceEeeEEe
Confidence 999999984
No 12
>PRK00053 alr alanine racemase; Reviewed
Probab=99.29 E-value=4.9e-11 Score=106.05 Aligned_cols=132 Identities=18% Similarity=0.294 Sum_probs=101.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecC----CCHHHHHHHH-HcCCcccccccHHHHHHHHhc-CCCCce
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKT----KPVSVIRQVY-EAGHRCFGENYVQEIVEKAAQ-LPDDLE 106 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt----~p~e~I~~a~-~~G~r~FGENrvQEl~~K~~~-L~~~i~ 106 (185)
.+.|..|++.+++.+ +..++|++|+|. |....|..++ ++|++.||.++++|+...... ++.+|
T Consensus 10 l~~l~~N~~~i~~~~----------~~~~~i~~vvKanaYghg~~~i~~~l~~~G~~~~~vas~~Ea~~l~~~G~~~~i- 78 (363)
T PRK00053 10 LDALRHNLRQIRKHA----------PPKSKLMAVVKANAYGHGAVEVAKTLLEAGADGFGVATLEEALELREAGITAPI- 78 (363)
T ss_pred HHHHHHHHHHHHHhC----------CCCCEEEEEEeeccccCcHHHHHHHHHHCCCCEEEECcHHHHHHHHhcCCCCCE-
Confidence 556777777776665 235899999996 7788888776 689999999999999988775 33343
Q ss_pred EEEEec-ccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc------------
Q 029918 107 WHFIGN-LQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI------------ 173 (185)
Q Consensus 107 WHfIG~-LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~------------ 173 (185)
-+.|+ .-..+++.++ . .+++.+|||++.++.|++. +.+ ++++|+|+||++. ++.||.
T Consensus 79 -l~l~~~~~~~e~~~~~---~-~~i~~~v~s~~~l~~l~~~--~~~-~~~~V~l~vdtG~--~R~Gi~~~e~~~~~~~i~ 148 (363)
T PRK00053 79 -LILGGFFPAEDLPLII---A-YNLTTAVHSLEQLEALEKA--ELG-KPLKVHLKIDTGM--HRLGVRPEEAEAALERLL 148 (363)
T ss_pred -EEEeCCCCHHHHHHHH---H-cCCEEEECCHHHHHHHHHh--ccC-CCeEEEEEecCCC--CcCCCCHHHHHHHHHHHH
Confidence 22333 2335788877 2 5678999999999999985 343 5799999999984 899973
Q ss_pred cCCcccccccCC
Q 029918 174 KCSWSHSCLLMI 185 (185)
Q Consensus 174 ~~~~l~l~g~m~ 185 (185)
.+|+|.+.|||+
T Consensus 149 ~~~~l~l~Gi~t 160 (363)
T PRK00053 149 ACPNVRLEGIFS 160 (363)
T ss_pred hCCCCceEEEEe
Confidence 489999999986
No 13
>cd06808 PLPDE_III Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes. The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these p
Probab=99.21 E-value=1.5e-10 Score=93.34 Aligned_cols=134 Identities=17% Similarity=0.148 Sum_probs=103.9
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHH-HHHHHcCCcccccccHHHHHHHHhcCCCCceEEEEeccc-
Q 029918 37 ATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVI-RQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQ- 114 (185)
Q Consensus 37 ~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I-~~a~~~G~r~FGENrvQEl~~K~~~L~~~i~WHfIG~LQ- 114 (185)
..|++.+++.+ +..+++.+|+|+.+...| +.++++ ...|+-++.+|+..-...-.++.+|+|.|+.+
T Consensus 2 ~~N~~~i~~~~----------~~~~~i~~~vKan~~~~i~~~~~~~-~~~~~v~s~~E~~~~~~~g~~~~~I~~~~~~~~ 70 (211)
T cd06808 2 RHNYRRLREAA----------PAGITLFAVVKANANPEVARTLAAL-GTGFDVASLGEALLLRAAGIPPEPILFLGPCKQ 70 (211)
T ss_pred hHHHHHHHHhC----------CCCCEEEEEEecCCCHHHHHHHHHc-CCcEEEcCHHHHHHHHHcCCCHHHEEEcCCCCC
Confidence 45666665554 226899999999995555 445555 78999999999998766533346799999999
Q ss_pred ccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc------------cCCcccccc
Q 029918 115 SNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI------------KCSWSHSCL 182 (185)
Q Consensus 115 sNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~------------~~~~l~l~g 182 (185)
.+.++.++ ..-..+-+|||++-+..|++.+.+.+ .+++|+|+||++...+|.|+. .++++.|.|
T Consensus 71 ~~~l~~~~---~~~~~~~~ids~~~l~~l~~~~~~~~-~~~~v~lrv~~g~~~~R~G~~~~e~~~~~~~i~~~~~l~l~G 146 (211)
T cd06808 71 VSELEDAA---EQGVIVVTVDSLEELEKLEEAALKAG-PPARVLLRIDTGDENGKFGVRPEELKALLERAKELPHLRLVG 146 (211)
T ss_pred HHHHHHHH---HcCCCEEEeCCHHHHHHHHHHHHHhC-CCceEEEEEcCCCCCCCCCCCHHHHHHHHHHHHhCCCCcEEE
Confidence 68899888 44234458999999999998887665 578999999997667999973 478899999
Q ss_pred cCC
Q 029918 183 LMI 185 (185)
Q Consensus 183 ~m~ 185 (185)
||+
T Consensus 147 l~~ 149 (211)
T cd06808 147 LHT 149 (211)
T ss_pred EEE
Confidence 985
No 14
>cd06820 PLPDE_III_LS_D-TA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Low Specificity D-Threonine Aldolase-like. This subfamily is composed of uncharacterized bacterial proteins with similarity to low specificity D-threonine aldolase (D-TA), which is a fold type III PLP-dependent enzyme that catalyzes the interconversion between D-threonine/D-allo-threonine and glycine plus acetaldehyde. Both PLP and divalent cations (eg. Mn2+) are required for catalytic activity. Low specificity D-TAs show similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on its similarity to AR, it is possible that low specificity D-TAs also form dimers in solution. Experimental data show that the monomeric form of low specificity D-TAs exh
Probab=99.18 E-value=1.1e-10 Score=102.77 Aligned_cols=138 Identities=17% Similarity=0.180 Sum_probs=109.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHH-HHHcCCcccccccHHHHHHHHhc-CCC-CceEEE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQ-VYEAGHRCFGENYVQEIVEKAAQ-LPD-DLEWHF 109 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~-a~~~G~r~FGENrvQEl~~K~~~-L~~-~i~WHf 109 (185)
.+.+..|++.+++... +..++|.+++|+++...|.. +.++|+..|+-.+++|+..-... +++ -+-||+
T Consensus 10 ~~~l~~Ni~~~~~~~~---------~~~v~l~~~~K~h~~~~i~~~~~~~G~~~~~vas~~Ea~~~~~~G~~~i~i~~~~ 80 (353)
T cd06820 10 LDRLERNIARMQAYAD---------AHGLSLRPHIKTHKSPEIARLQLAAGAIGITVATVGEAEVMADAGLSDIFIAYPI 80 (353)
T ss_pred HHHHHHHHHHHHHHHH---------HcCCccccccccccCHHHHHHHHhCCCCCEEEeeHHHHHHHHHCCCCeEEEECCc
Confidence 4556777777766542 23589999999999887754 55789999999999999765543 222 267999
Q ss_pred EecccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc-------------cCC
Q 029918 110 IGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI-------------KCS 176 (185)
Q Consensus 110 IG~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~-------------~~~ 176 (185)
+|+-+.+++..++ ...+++.+|||++.++.|++.+.+.+ .+++|+|+||++. ++.|+. .+|
T Consensus 81 ~~~~~~~~l~~l~---~~~~~~~~vds~~~l~~L~~~a~~~~-~~~~V~l~vd~G~--~R~Gv~~~~~~~~l~~~i~~~~ 154 (353)
T cd06820 81 VGRQKLERLRALA---ERVTLSVGVDSAEVARGLAEVAEGAG-RPLEVLVEVDSGM--NRCGVQTPEDAVALARAIASAP 154 (353)
T ss_pred CCHHHHHHHHHHh---cCCCEEEEECCHHHHHHHHHHHHhcC-CeeEEEEEECCCC--CcCCCCChHHHHHHHHHHHhCC
Confidence 9999888888887 56789999999999999999998765 6899999999973 777863 379
Q ss_pred cccccccCC
Q 029918 177 WSHSCLLMI 185 (185)
Q Consensus 177 ~l~l~g~m~ 185 (185)
+|+|.|+|+
T Consensus 155 ~l~l~Gi~~ 163 (353)
T cd06820 155 GLRFRGIFT 163 (353)
T ss_pred CcEEEEEEe
Confidence 999999985
No 15
>cd07376 PLPDE_III_DSD_D-TA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase. This family includes eukaryotic D-serine dehydratases (DSD), cryptic DSDs from bacteria, D-threonine aldolases (D-TA), low specificity D-TAs, and similar uncharacterized proteins. DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. Members of this family are fold type III PLP-dependent enzymes, similar to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on similarity to AR, it is poss
Probab=99.12 E-value=4.1e-10 Score=98.93 Aligned_cols=136 Identities=15% Similarity=0.134 Sum_probs=102.5
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHH-HHHHHcCCcccccccHHHHHHHHhcCCCCceEEEEeccc
Q 029918 36 AATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVI-RQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQ 114 (185)
Q Consensus 36 i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I-~~a~~~G~r~FGENrvQEl~~K~~~L~~~i~WHfIG~LQ 114 (185)
|..|++.+++.+. +..++|.+|+|+++..+| +.+.++|++.|+.++++|+......-..+| .+-|+++
T Consensus 2 l~~Ni~~~~~~~~---------~~~~~l~~vvKah~~~~v~~~l~~~G~~~~~vat~~Ea~~l~~~G~~~I--li~~~~~ 70 (345)
T cd07376 2 LEANISRMAARAR---------ASGVRLRPHVKTHKSPELAQRQLAAGARGVTVATLAEAETFAEAGVKDI--LMAYPLV 70 (345)
T ss_pred hHHHHHHHHHHHH---------HcCCccccccchhcCHHHHHHHHhCCCCcEEEecHHHHHHHHHcCCCeE--EEECCcC
Confidence 4567777766542 235899999999999765 446788999999999999998876533333 3446998
Q ss_pred -ccchHHHhhcCC-CccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc--------------cCCcc
Q 029918 115 -SNKVKPLLAGVP-NLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI--------------KCSWS 178 (185)
Q Consensus 115 -sNKvk~~~~~~~-~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~--------------~~~~l 178 (185)
.+|++.++.... ..++.-+|||++-++.|++.+.+.+ .+++|+|+||++. ++.||. .+++|
T Consensus 71 ~~~~~~~~~~l~~~~~~i~~~Vds~~~l~~l~~~a~~~~-~~~~V~l~ID~G~--~R~Gv~~~~~~~l~~~~~i~~~~~l 147 (345)
T cd07376 71 GPAAIARLAGLLRQEAEFHVLVDSPEALAALAAFAAAHG-VRLRVMLEVDVGG--HRSGVRPEEAAALALADAVQASPGL 147 (345)
T ss_pred CHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHHHHhcC-CeeEEEEEeCCCC--CcCCCCCcHHHHHHHHHHhccCCCe
Confidence 789888862111 1334557999999999999987665 6899999999875 677863 47899
Q ss_pred cccccCC
Q 029918 179 HSCLLMI 185 (185)
Q Consensus 179 ~l~g~m~ 185 (185)
+|.|||+
T Consensus 148 ~l~Gl~~ 154 (345)
T cd07376 148 RLAGVMA 154 (345)
T ss_pred EEeEEEe
Confidence 9999985
No 16
>cd06811 PLPDE_III_yhfX_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX. This subfamily is composed of the uncharacterized protein yhfX from Escherichia coli K-12 and similar bacterial proteins. These proteins are homologous to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.
Probab=99.05 E-value=2.3e-09 Score=96.97 Aligned_cols=136 Identities=16% Similarity=0.088 Sum_probs=105.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCC--CHHHHHHHHHcCCcccccccHHHHHHHHhcCCCCceEEEE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTK--PVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFI 110 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~--p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~~i~WHfI 110 (185)
.+.|.+|++.+++... +..++|.+|+|.. .++-++.+.++|++.|+--.+.|+..=.+ ..+.||.|
T Consensus 35 l~~I~~N~~~l~~~~~---------~~~~~l~~vvKAna~~~~ia~~l~~~G~~g~~vas~~Ea~~lr~---aGi~~~~I 102 (382)
T cd06811 35 LDQIEENARLLAETAE---------KYGIELYFMTKQFGRNPFLARALLEAGIPGAVAVDFKEARALHE---AGLPLGHV 102 (382)
T ss_pred HHHHHHHHHHHHHHHh---------hCCCEEEEEEccCCCCHHHHHHHHHcCCCeEeEecHHHHHHHHH---cCCCHHhE
Confidence 6667777777765541 1257999999997 66777777889999888888888864322 25779999
Q ss_pred eccc---ccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCC----ccccc-----------
Q 029918 111 GNLQ---SNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEE----YGECF----------- 172 (185)
Q Consensus 111 G~LQ---sNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~----sKsG~----------- 172 (185)
|+++ .++++.++ .....+.+|||+..+++|++.+.+.+ ++++|+|.||++.+. ++.||
T Consensus 103 ~~l~~~~~~el~~~v---~~~~~~i~V~s~~~l~~L~~~A~~~g-~~~~V~LrVdtg~~ri~~g~~~G~~~~e~~~~~~~ 178 (382)
T cd06811 103 GHLVQIPRHQVPAVL---AMRPEVITVYSLEKAREISDAAVELG-RVQDVLLRVYGDEDTLYPGQEGGFPLEELPAVLAA 178 (382)
T ss_pred EEccCCCHHHHHHHH---HcCCCEEEECCHHHHHHHHHHHHHcC-CceEEEEEEECCCCccccCccceecHHHHHHHHHH
Confidence 9887 68899888 44334799999999999999987765 689999999987664 46687
Q ss_pred -ccCCcccccccC
Q 029918 173 -IKCSWSHSCLLM 184 (185)
Q Consensus 173 -~~~~~l~l~g~m 184 (185)
..+++|++.|++
T Consensus 179 i~~l~~l~l~Git 191 (382)
T cd06811 179 IKALPGIRIAGLT 191 (382)
T ss_pred HHcCCCcEEEeEc
Confidence 247999999985
No 17
>PRK13340 alanine racemase; Reviewed
Probab=98.54 E-value=1.3e-06 Score=79.37 Aligned_cols=136 Identities=13% Similarity=0.191 Sum_probs=97.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCC----HHH-HHHHHHcCCcccccccHHHHHHHHhcCCCCceE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKP----VSV-IRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEW 107 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p----~e~-I~~a~~~G~r~FGENrvQEl~~K~~~L~~~i~W 107 (185)
.+.|..|++.+++.+ +...++.+|.|..+ ... .+.++++|+..|+=..+.|+..=...-.++...
T Consensus 47 l~ai~~N~~~i~~~~----------~~~~~i~~vvKAnaYG~G~~~va~~l~~~G~~~~~Vas~~Ea~~lr~~G~~~~il 116 (406)
T PRK13340 47 PGAFRHNIKTLRSLL----------ANKSKVCAVMKADAYGHGIELLMPSIIKANVPCIGIASNEEARRVRELGFTGQLL 116 (406)
T ss_pred HHHHHHHHHHHHHhC----------CCCCEEEEEEccccccccHHHHHHHHHHCCCCEEEEccHHHHHHHHhCCCCCCEE
Confidence 556666776665443 22369999999976 333 456668999999999999997544431122334
Q ss_pred EEEecccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc--------------
Q 029918 108 HFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI-------------- 173 (185)
Q Consensus 108 HfIG~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~-------------- 173 (185)
-|=|+ ....+..++. ..+.-+|||+..++.|++.+.+.+ ++++|+|+||++| .++.||.
T Consensus 117 vl~~~-~~~el~~~~~----~~l~~~v~s~~~l~~l~~~a~~~~-~~~~V~LkVDt~G-m~R~G~~~~e~~~~~~~~~l~ 189 (406)
T PRK13340 117 RVRSA-SPAEIEQALR----YDLEELIGDDEQAKLLAAIAKKNG-KPIDIHLALNSGG-MSRNGLDMSTARGKWEALRIA 189 (406)
T ss_pred EECCC-CHHHHHHHHH----cCCEEEECCHHHHHHHHHHHHHcC-CceEEEEEECCCC-CCCcCCChhhhhHHHHHHHHH
Confidence 44333 5566777762 345678999999999999887654 6899999999966 8898872
Q ss_pred cCCcccccccCC
Q 029918 174 KCSWSHSCLLMI 185 (185)
Q Consensus 174 ~~~~l~l~g~m~ 185 (185)
.+++|++.|+|+
T Consensus 190 ~~~~l~l~Gi~t 201 (406)
T PRK13340 190 TLPSLGIVGIMT 201 (406)
T ss_pred hCCCccEEEEEE
Confidence 378999999985
No 18
>cd06819 PLPDE_III_LS_D-TA Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Low Specificity D-Threonine Aldolase. Low specificity D-threonine aldolase (Low specificity D-TA, EC 4.3.1.18), encoded by dtaAS gene from Arthrobacter sp. strain DK-38, is the prototype of this subfamily. Low specificity D-TAs are fold type III PLP-dependent enzymes that catalyze the interconversion between D-threonine/D-allo-threonine and glycine plus acetaldehyde. Both PLP and divalent cations (eg. Mn2+) are required for catalytic activity. Members of this subfamily show similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on its similarity to AR, it is possible that low specificity D-TAs also form dimers in solution. Experimental data show that t
Probab=98.47 E-value=1.1e-06 Score=77.54 Aligned_cols=138 Identities=15% Similarity=0.088 Sum_probs=96.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHH-HHcCCcccccccHHHHHHHHhcCCCCc--eEEE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQV-YEAGHRCFGENYVQEIVEKAAQLPDDL--EWHF 109 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a-~~~G~r~FGENrvQEl~~K~~~L~~~i--~WHf 109 (185)
.+.|..|++.+++.+. . ..+++.++.|+++...|..+ .++|+..|+-.+++|+..=...=-+++ -+.+
T Consensus 14 ~~~l~~N~~~l~~~~~----~-----~~~~l~~~~K~h~~~~i~~~~~~~G~~~~~vas~~Ea~~~~~~G~~~ili~~~~ 84 (358)
T cd06819 14 LDALERNIKRMAAFAK----A-----HGVRLRPHAKTHKCPAIARRQIAAGAVGVCCQKLSEAEVMAAAGIRDILITNEV 84 (358)
T ss_pred HHHHHHHHHHHHHHHH----H-----cCCcccccchhhcCHHHHHHHHhCCCCcEEEccHHHHHHHHHCCCCeEEEECCc
Confidence 5667777777766552 1 24678899999998776654 577999999999999974322101122 1223
Q ss_pred EecccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc-------------cCC
Q 029918 110 IGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI-------------KCS 176 (185)
Q Consensus 110 IG~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~-------------~~~ 176 (185)
+|+--...+-.++ ....+.-+|||++-++.|++.+.+.+ .+++|+|+||++. ++.|+. .+|
T Consensus 85 ~~~~~~~~~~~~~---~~~~i~~~vDs~~~l~~l~~~a~~~~-~~~~V~l~vd~G~--~R~Gv~~~~~~~~l~~~i~~~~ 158 (358)
T cd06819 85 VGPAKIARLAALA---RRAPLIVCVDHPDNVRALAAAAVEAG-VRLDVLVEIDVGQ--GRCGVPPGEAALALARTIAALP 158 (358)
T ss_pred CCHHHHHHHHHHh---cCCCEEEEECCHHHHHHHHHHHHhcC-CceEEEEEECCCC--CcCCCCChHHHHHHHHHHHhCC
Confidence 3443233333333 34568899999999999999998765 6899999999864 577763 478
Q ss_pred cccccccCC
Q 029918 177 WSHSCLLMI 185 (185)
Q Consensus 177 ~l~l~g~m~ 185 (185)
+|+|.|+|.
T Consensus 159 ~l~l~Gi~~ 167 (358)
T cd06819 159 GLRFAGLQA 167 (358)
T ss_pred CceEeEEEe
Confidence 999999963
No 19
>cd06818 PLPDE_III_cryptic_DSD Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bacterial Cryptic D-Serine Dehydratase. This subfamily is composed of Burkholderia cepacia cryptic D-serine dehydratase (cryptic DSD), which is also called D-serine deaminase, and similar bacterial proteins. Members of this subfamily are fold type III PLP-dependent enzymes with similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as dimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on similarity, it is possible cryptic DSDs may also form dimers. Cryptic DSDs are distinct from the ubiquitous bacterial DSDs coded by the dsdA gene, mammalian L-serine dehydratases (LSD) and mammalian serine racemase (SerRac), which are fold type II PLP-dependent enzymes. At present, the enzymatic and biochemical properties
Probab=98.44 E-value=3.2e-06 Score=76.19 Aligned_cols=140 Identities=14% Similarity=0.121 Sum_probs=96.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHH-HHHHcCCcccccccHHHHHHHHhcCC-CCceEE--
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIR-QVYEAGHRCFGENYVQEIVEKAAQLP-DDLEWH-- 108 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~-~a~~~G~r~FGENrvQEl~~K~~~L~-~~i~WH-- 108 (185)
.+.|..|++.+++... +..+++.+..|++....|. ...++|..-|+-..+.|+..=. ... +++-+.
T Consensus 10 l~~l~~N~~~m~~~~~---------~~~~~l~~h~Kt~~~~~i~~~~~~~G~~g~~vas~~Ea~~l~-~~G~~~il~~~~ 79 (382)
T cd06818 10 ASALAHNLAWMQAFAA---------AHGVKLAPHGKTTMAPQLFRRQLEAGAWGITVATVAQARVAL-AFGVRRVLLANQ 79 (382)
T ss_pred HHHHHHHHHHHHHHHh---------hcCcEEEeecchhhhHHHHHHHHHcCCCEEEEeEHHHHHHHH-HcCCCeEEEecC
Confidence 4556677777665542 2358999999999987764 4456899999999999987532 221 233222
Q ss_pred EEecccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc-------------cC
Q 029918 109 FIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI-------------KC 175 (185)
Q Consensus 109 fIG~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~-------------~~ 175 (185)
.+|.-.-.-+..+++..+...+.=.|||++.++.|++.+.+.+ ++++|+|+||+ ...+.|+. .+
T Consensus 80 ~~~~~~~~~l~~l~~~~~~~~i~~~vds~~~l~~L~~~a~~~g-~~~~v~i~vn~--g~~R~G~~~~~~~~~l~~~i~~~ 156 (382)
T cd06818 80 LVGKANLRRLAALLAADPDFEFFCLVDSVDNVRALAAFFAALE-RPLNVLIELGV--PGGRTGVRTEAEALALADAIAAS 156 (382)
T ss_pred cCChHHHHHHHHhhhcCCCCCEEEEECCHHHHHHHHHHHHhcC-CceEEEEEECC--CCCCCCCCCHHHHHHHHHHHHcC
Confidence 1233322334445521123445568999999999999998765 68999999998 47788873 48
Q ss_pred CcccccccCC
Q 029918 176 SWSHSCLLMI 185 (185)
Q Consensus 176 ~~l~l~g~m~ 185 (185)
|+|+|.|||+
T Consensus 157 ~~l~l~Gi~~ 166 (382)
T cd06818 157 PALRLAGVEG 166 (382)
T ss_pred CCceEeEEEe
Confidence 9999999985
No 20
>cd06826 PLPDE_III_AR2 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme, Alanine Racemase 2. This subfamily is composed of bacterial alanine racemases (EC 5.1.1.1) with similarity to Yersinia pestis and Vibrio cholerae alanine racemase (AR) 2. ARs catalyze the interconversion between L- and D-alanine, an essential component of the peptidoglycan layer of bacterial cell walls. These proteins are similar to other bacterial ARs and are fold type III PLP-dependent enzymes containing contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Probab=98.31 E-value=1.4e-05 Score=71.73 Aligned_cols=135 Identities=13% Similarity=0.199 Sum_probs=98.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecC----CCHHHHH-HHHHcCCcccccccHHHHHHHHhc-CCCCce
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKT----KPVSVIR-QVYEAGHRCFGENYVQEIVEKAAQ-LPDDLE 106 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt----~p~e~I~-~a~~~G~r~FGENrvQEl~~K~~~-L~~~i~ 106 (185)
.+.|..|++.+++.+ ++..++++|.|. |....|. .++++|++.||-..+.|+..=.+. ++.++
T Consensus 8 l~al~~N~~~i~~~~----------~~~~~i~~vvKAnAYGhG~~~va~~l~~~g~~~f~Vas~~Ea~~lr~~Gi~~~i- 76 (365)
T cd06826 8 TGAFENNIKLLKKLL----------GGNTKLCAVMKADAYGHGIALVMPSIIAQNIPCVGITSNEEARVVREAGFTGKI- 76 (365)
T ss_pred HHHHHHHHHHHHHhC----------CCCCEEEEEEEeccccccHHHHHHHHHHCCCCEEEEccHHHHHHHHhcCCCCCE-
Confidence 345566666665543 235699999999 8888776 556889999999999999754443 22233
Q ss_pred EEEEecccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc-------------
Q 029918 107 WHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI------------- 173 (185)
Q Consensus 107 WHfIG~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~------------- 173 (185)
.=| |..-...++.++ . .++.-+|||+.-++.|++.+.+.+ ++.+|.|.||+.| -++.||.
T Consensus 77 lvl-~~~~~~e~~~~i---~-~~i~~~v~s~~~l~~l~~~a~~~~-~~~~v~LkvDt~G-m~R~Gi~~~~~~~~~~~~~~ 149 (365)
T cd06826 77 LRV-RTATPSEIEDAL---A-YNIEELIGSLDQAEQIDSLAKRHG-KTLPVHLALNSGG-MSRNGLELSTAQGKEDAVAI 149 (365)
T ss_pred EEE-eCCCHHHHHHHH---H-cCCEEEECCHHHHHHHHHHHHHcC-CceEEEEEECCCC-CCCCCCCcchhhHHHHHHHH
Confidence 333 666667788887 2 356688999999999999887665 6899999999832 2777763
Q ss_pred -cCCcccccccCC
Q 029918 174 -KCSWSHSCLLMI 185 (185)
Q Consensus 174 -~~~~l~l~g~m~ 185 (185)
.+++|++.|+||
T Consensus 150 ~~~~~l~l~Gi~t 162 (365)
T cd06826 150 ATLPNLKIVGIMT 162 (365)
T ss_pred HHCCCCcEEEEEE
Confidence 268999999986
No 21
>cd06843 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE. This subfamily is composed of PvsE from Vibrio parahaemolyticus and similar proteins. PvsE is a vibrioferrin biosynthesis protein which is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. It has been suggested that PvsE may be involved in the biosynthesis of the polycarboxylate siderophore vibrioferrin. It may catalyze the decarboxylation of serine to yield ethanolamine. PvsE may require homodimer formation and the presence of the PLP cofactor for activity.
Probab=98.15 E-value=6.9e-05 Score=66.95 Aligned_cols=138 Identities=18% Similarity=0.152 Sum_probs=98.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHHcCCcccccccHHHHHHHHhcCCCCceEEEEec
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGN 112 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~~i~WHfIG~ 112 (185)
.+.|.+|++.+++.. |..+++.++.|+-|...|..++..|...|.=.-..|+..=....+ +-+-.|-|+
T Consensus 9 ~~~l~~N~~~l~~~~----------~~~~~i~yavKaN~~~~vl~~l~~~g~g~dvaS~~E~~~~~~~~~-~~~I~~~gp 77 (377)
T cd06843 9 LAALRAHARALRASL----------PPGCELFYAIKANSDPPILRALAPHVDGFEVASGGEIAHVRAAVP-DAPLIFGGP 77 (377)
T ss_pred HHHHHHHHHHHHHhc----------CCCCeEEEEeccCCCHHHHHHHHHcCCcEEEeCHHHHHHHHhcCC-CCeEEEeCC
Confidence 345566666555432 346889999999999999888877778888888888875443333 234467788
Q ss_pred ccccc-hHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCC------------CCCcccccc------
Q 029918 113 LQSNK-VKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTS------------GEEYGECFI------ 173 (185)
Q Consensus 113 LQsNK-vk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis------------~E~sKsG~~------ 173 (185)
.-+.+ ++.++. ..+..| +|||+.-+++|++.+.+.+ .+++|+|.||++ ++++|.|+.
T Consensus 78 ~k~~~~l~~a~~--~gi~~i-~vds~~el~~l~~~a~~~~-~~~~v~lRi~~~~~~~~~~~~~~~~~~srfG~~~~~~~~ 153 (377)
T cd06843 78 GKTDSELAQALA--QGVERI-HVESELELRRLNAVARRAG-RTAPVLLRVNLALPDLPSSTLTMGGQPTPFGIDEADLPD 153 (377)
T ss_pred CCCHHHHHHHHH--cCCCEE-EeCCHHHHHHHHHHHHHcC-CCceEEEEECCCCCCCCCcceecCCCCCCCCcCHHHHHH
Confidence 55554 566652 234444 5999999999999887654 578999999984 455788973
Q ss_pred ------cCCcccccccCC
Q 029918 174 ------KCSWSHSCLLMI 185 (185)
Q Consensus 174 ------~~~~l~l~g~m~ 185 (185)
.++++.+.|||+
T Consensus 154 ~~~~~~~~~~l~~~Glh~ 171 (377)
T cd06843 154 ALELLRDLPNIRLRGFHF 171 (377)
T ss_pred HHHHHHhCCCccEEEEEE
Confidence 478899999874
No 22
>cd06827 PLPDE_III_AR_proteobact Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases. This subfamily is composed mainly of proteobacterial alanine racemases (EC 5.1.1.1), fold type III PLP-dependent enzymes that catalyze the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. hese proteins are similar to other bacterial ARs and are fold type III PLP-dependent enzymes containing contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Probab=98.13 E-value=4.3e-05 Score=68.63 Aligned_cols=131 Identities=17% Similarity=0.220 Sum_probs=97.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecC----CCHHHHHHHHHcCCcccccccHHHHHHHHhc-CCCCceE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKT----KPVSVIRQVYEAGHRCFGENYVQEIVEKAAQ-LPDDLEW 107 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt----~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~-L~~~i~W 107 (185)
.+.|..|++.+++.+ ++ ++|++|.|. |....|..++.. ++.||=..+.|+..=.+. ++.+| .
T Consensus 8 l~~l~~N~~~l~~~~----------~~-~~l~~vvKanaYGhG~~~ia~~l~~-~~~f~Vas~~Ea~~lr~~G~~~~i-l 74 (354)
T cd06827 8 LAALRHNLRLVRELA----------PN-SKILAVVKANAYGHGLVRVAKALAD-ADGFAVACIEEALALREAGITKPI-L 74 (354)
T ss_pred HHHHHHHHHHHHhhC----------CC-CeEEEEEeeccccCCHHHHHHHHHc-CCEEEEccHHHHHHHHhCCCCCCE-E
Confidence 345666666665543 22 789999999 777778777666 999999999998754443 22233 4
Q ss_pred EEEecccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc------------cC
Q 029918 108 HFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI------------KC 175 (185)
Q Consensus 108 HfIG~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~------------~~ 175 (185)
=|-|+.....++.++ ..++.=+|||++-++.|++.+ .+ .+.+|.|.||++ -++.|+. .+
T Consensus 75 vl~~~~~~~~~~~~~----~~~l~~~v~s~~~l~~l~~~~--~~-~~~~v~l~vDtG--m~R~Gi~~~e~~~~~~~i~~~ 145 (354)
T cd06827 75 LLEGFFSADELPLAA----EYNLWTVVHSEEQLEWLEQAA--LS-KPLNVWLKLDSG--MHRLGFSPEEYAAAYQRLKAS 145 (354)
T ss_pred EEECCCCHHHHHHHH----HcCCEEEECCHHHHHHHHHhc--CC-CCeEEEEEeeCC--cCCCCCCHHHHHHHHHHHHhC
Confidence 455666667777766 246788999999999998876 23 578999999987 5888872 47
Q ss_pred CcccccccCC
Q 029918 176 SWSHSCLLMI 185 (185)
Q Consensus 176 ~~l~l~g~m~ 185 (185)
++|.+.|+||
T Consensus 146 ~~l~l~Gi~t 155 (354)
T cd06827 146 PNVASIVLMT 155 (354)
T ss_pred CCceEEEEEe
Confidence 9999999986
No 23
>cd06839 PLPDE_III_Btrk_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase. This subfamily is composed of Bacillus circulans BtrK decarboxylase and similar proteins. These proteins are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases, eukaryotic ornithine decarboxylases and diaminopimelate decarboxylases. BtrK is presumed to function as a PLP-dependent decarboxylase involved in the biosynthesis of the aminoglycoside antibiotic butirosin. Homodimer formation and the presence of the PLP cofactor may be required for catalytic activity.
Probab=98.09 E-value=6.8e-05 Score=66.57 Aligned_cols=138 Identities=12% Similarity=0.040 Sum_probs=98.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHHcCCcccccccHHHHHHHHhcCCCCceEEEEec
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGN 112 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~~i~WHfIG~ 112 (185)
.+.|.+|++.+++.+ |..+++..+.|+-+...|..++..+...|.=.-..|+..=...--++-+-.|.|+
T Consensus 14 ~~~l~~n~~~l~~~~----------~~~~~~~yavKan~~~~v~~~l~~~g~g~~vaS~~E~~~~~~~G~~~~~I~~~~~ 83 (382)
T cd06839 14 RDRVRERYAALRAAL----------PPAIEIYYSLKANPNPALVAHLRQLGDGAEVASAGELALALEAGVPPEKILFAGP 83 (382)
T ss_pred HHHHHHHHHHHHHhc----------CCCcEEEEEeccCCCHHHHHHHHHcCCCEEEeCHHHHHHHHHcCCCHHHEEEeCC
Confidence 455666776665443 3358999999999998888877554478888888888744332111123467788
Q ss_pred c-cccchHHHhhcCCCcc-EEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeC-----------CCCCcccccc------
Q 029918 113 L-QSNKVKPLLAGVPNLA-MVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNT-----------SGEEYGECFI------ 173 (185)
Q Consensus 113 L-QsNKvk~~~~~~~~~~-~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNi-----------s~E~sKsG~~------ 173 (185)
. ...-++.++ .. . ..=+|||++-++.|.+.+.+.+ .+++|+|+||. +++.+|.|+.
T Consensus 84 ~k~~~~l~~a~---~~-g~~~i~vds~~el~~l~~~a~~~~-~~~~v~lRin~~~~~~~~g~~~~~~~sKfG~~~~~~~~ 158 (382)
T cd06839 84 GKSDAELRRAI---EA-GIGTINVESLEELERIDALAEEHG-VVARVALRINPDFELKGSGMKMGGGPSQFGIDVEELPA 158 (382)
T ss_pred CCCHHHHHHHH---HC-CCCEEEECCHHHHHHHHHHHHhcC-CCCeEEEEECCCCCCCCCccccCCCCCCcCCCHHHHHH
Confidence 5 555566666 22 3 3449999999999999887654 57899999996 4567899973
Q ss_pred ------cCCcccccccCC
Q 029918 174 ------KCSWSHSCLLMI 185 (185)
Q Consensus 174 ------~~~~l~l~g~m~ 185 (185)
.++++++.|||.
T Consensus 159 ~~~~~~~~~~l~l~Glh~ 176 (382)
T cd06839 159 VLARIAALPNLRFVGLHI 176 (382)
T ss_pred HHHHHHhCCCCcEEEEEE
Confidence 468899999873
No 24
>cd06810 PLPDE_III_ODC_DapDC_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Ornithine and Diaminopimelate Decarboxylases, and Related Enzymes. This family includes eukaryotic ornithine decarboxylase (ODC, EC 4.1.1.17), diaminopimelate decarboxylase (DapDC, EC 4.1.1.20), plant and prokaryotic biosynthetic arginine decarboxylase (ADC, EC 4.1.1.19), carboxynorspermidine decarboxylase (CANSDC), and ODC-like enzymes from diverse bacterial species. These proteins are fold type III PLP-dependent enzymes that catalyze essential steps in the biosynthesis of polyamine and lysine. ODC and ADC participate in alternative pathways of the biosynthesis of putrescine, which is the precursor of aliphatic polyamines in many organisms. ODC catalyzes the direct synthesis of putrescine from L-ornithine, while ADC converts L-arginine to agmatine, which is hydrolysed to putrescine by agmatinase in a pathway that exists only in plants and bacteria. DapDC converts meso-2,6-diaminoheptanedioate to
Probab=98.06 E-value=7.6e-05 Score=65.81 Aligned_cols=135 Identities=18% Similarity=0.200 Sum_probs=96.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHH-HcCCcccccccHHHHHHHHhcCCCCceEEEEec
Q 029918 34 GVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVY-EAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGN 112 (185)
Q Consensus 34 ~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~-~~G~r~FGENrvQEl~~K~~~L~~~i~WHfIG~ 112 (185)
+.+..|++.+++.+ + ..+++..+.|+.+...|..++ +.|. .|.=....|+..=.+.-.+.-.-.|=|+
T Consensus 9 ~~l~~n~~~l~~~~-------~---~~~~i~~avKan~~~~i~~~l~~~G~-g~~vas~~E~~~~~~~G~~~~~iv~~gp 77 (368)
T cd06810 9 DIIRAHYAALKEAL-------P---SGVKLFYAVKANPNPHVLRTLAEAGT-GFDVASKGELALALAAGVPPERIIFTGP 77 (368)
T ss_pred HHHHHHHHHHHHhC-------C---CCCeEEEEEccCCCHHHHHHHHHcCC-cEEEeCHHHHHHHHHcCCCHHHEEEcCC
Confidence 44556666665544 2 468999999999988776655 6788 9999999998654433211123456687
Q ss_pred ccc-cchHHHhhcCCCcc-EEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCC-----------CCCcccccc------
Q 029918 113 LQS-NKVKPLLAGVPNLA-MVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTS-----------GEEYGECFI------ 173 (185)
Q Consensus 113 LQs-NKvk~~~~~~~~~~-~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis-----------~E~sKsG~~------ 173 (185)
.-+ ..++.++. . . .+=+|||++.+++|++.+.+.+ ++++|+|+||++ ++.+|.|+.
T Consensus 78 ~~~~~~l~~~~~---~-~~~~~~vds~~el~~l~~~~~~~~-~~~~v~lrin~g~~~~~~~~~~~~~~srfGi~~~e~~~ 152 (368)
T cd06810 78 AKSVSEIEAALA---S-GVDHIVVDSLDELERLNELAKKLG-PKARILLRVNPDVSAGTHKISTGGLKSKFGLSLSEARA 152 (368)
T ss_pred CCCHHHHHHHHH---C-CCCEEEeCCHHHHHHHHHHHHHhC-CCCeEEEEECCCCCCCcccCccCCCCCCcCCCHHHHHH
Confidence 644 56777772 2 3 5678999999999999887654 578999999987 356899973
Q ss_pred ------cCCcccccccCC
Q 029918 174 ------KCSWSHSCLLMI 185 (185)
Q Consensus 174 ------~~~~l~l~g~m~ 185 (185)
.++ +.+.|||+
T Consensus 153 ~~~~~~~~~-l~l~Gl~~ 169 (368)
T cd06810 153 ALERAKELD-LRLVGLHF 169 (368)
T ss_pred HHHHHHhCC-CcEEEEEE
Confidence 356 89999984
No 25
>cd06828 PLPDE_III_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase. Diaminopimelate decarboxylase (DapDC, EC 4.1.1.20) participates in the last step of lysine biosynthesis. It converts meso-2,6-diaminoheptanedioate to L-lysine. It is a fold type III PLP-dependent enzyme that contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. DapDC exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Probab=97.97 E-value=0.00025 Score=62.62 Aligned_cols=139 Identities=17% Similarity=0.079 Sum_probs=98.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHH-HcCCcccccccHHHHHHHHhcCCCCceEEEEe
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVY-EAGHRCFGENYVQEIVEKAAQLPDDLEWHFIG 111 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~-~~G~r~FGENrvQEl~~K~~~L~~~i~WHfIG 111 (185)
.+.|.+|++.+++.+ +. ..+++..+.|+-|...|..++ ++| ..|.=.-..|+..=...-.+.-+-.|-|
T Consensus 10 ~~~l~~n~~~l~~~~-------~~--~~~~~~yavKaN~~~~v~~~l~~~G-~g~~vaS~~E~~~~~~~G~~~~~I~~~~ 79 (373)
T cd06828 10 EATIRENYRRLKEAF-------SG--PGFKICYAVKANSNLAILKLLAEEG-LGADVVSGGELYRALKAGFPPERIVFTG 79 (373)
T ss_pred HHHHHHHHHHHHHhh-------CC--CCcEEEEEehhCCCHHHHHHHHHcC-CcEEEeCHHHHHHHHHcCCCcccEEEeC
Confidence 344556666555443 21 469999999999987766655 668 7888888888764433221112356778
Q ss_pred cc-cccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeC------------CCCCcccccc-----
Q 029918 112 NL-QSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNT------------SGEEYGECFI----- 173 (185)
Q Consensus 112 ~L-QsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNi------------s~E~sKsG~~----- 173 (185)
+. ....++.++ ..-..+=+|||+.-+++|++.+.+.+ .+.+|+|+||. +++.+|.|+.
T Consensus 80 p~k~~~~l~~a~---~~g~~~~~ids~~el~~l~~~a~~~~-~~~~v~lRv~~~~~~~~~~~~~~g~~~srfGi~~~e~~ 155 (373)
T cd06828 80 NGKSDEELELAL---ELGILRINVDSLSELERLGEIAPELG-KGAPVALRVNPGVDAGTHPYISTGGKDSKFGIPLEQAL 155 (373)
T ss_pred CCCCHHHHHHHH---HcCCeEEEECCHHHHHHHHHHHHhcC-CCCeEEEEECCCCCCCCCCCeecCCCCCCCCCCHHHHH
Confidence 75 556677777 22226678999999999999987654 57899999985 4456898973
Q ss_pred -------cCCcccccccCC
Q 029918 174 -------KCSWSHSCLLMI 185 (185)
Q Consensus 174 -------~~~~l~l~g~m~ 185 (185)
.|+++.+.|+|+
T Consensus 156 ~~~~~~~~~~~l~l~Gi~~ 174 (373)
T cd06828 156 EAYRRAKELPGLKLVGLHC 174 (373)
T ss_pred HHHHHHHhCCCCcEEEEEE
Confidence 479999999974
No 26
>TIGR01048 lysA diaminopimelate decarboxylase. This family consists of diaminopimelate decarboxylase, an enzyme which catalyzes the conversion of diaminopimelic acid into lysine during the last step of lysine biosynthesis.
Probab=97.91 E-value=0.00034 Score=63.12 Aligned_cols=138 Identities=17% Similarity=0.154 Sum_probs=96.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHH-HcCCcccccccHHHHHHHHhc-CCCCceEEEE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVY-EAGHRCFGENYVQEIVEKAAQ-LPDDLEWHFI 110 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~-~~G~r~FGENrvQEl~~K~~~-L~~~i~WHfI 110 (185)
.+.|.+|++.+++.+ +.. .+++..+.|+-|...|..++ +.|. .|.=.-..|+..=... ++++ +--|-
T Consensus 32 ~~~l~~n~~~l~~~~-------~~~--~~~i~yavKaN~~~~vl~~l~~~G~-g~dvaS~~E~~~~~~~G~~~~-~I~~~ 100 (417)
T TIGR01048 32 EETIRERFRAYKEAF-------GGA--YSLVCYAVKANSNLALLRLLAELGS-GFDVVSGGELYRALAAGFPPE-KIVFN 100 (417)
T ss_pred HHHHHHHHHHHHHhh-------CCC--CceEEEEehhCCCHHHHHHHHHcCC-cEEEeCHHHHHHHHHcCCCcc-eEEEe
Confidence 566677777666544 211 58999999999987766654 6785 7888888887643332 2321 34566
Q ss_pred ec-ccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCC------------CCCcccccc----
Q 029918 111 GN-LQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTS------------GEEYGECFI---- 173 (185)
Q Consensus 111 G~-LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis------------~E~sKsG~~---- 173 (185)
|+ .-...++.++. ..+.. =+|||++.+++|++.+.+.+ .+++|+|+||.+ ++.+|.|+.
T Consensus 101 gp~k~~~~l~~a~~--~gi~~-i~iDs~~el~~l~~~a~~~~-~~~~v~lRIn~~~~~~~~~~~~~g~~~srfGi~~~~~ 176 (417)
T TIGR01048 101 GNGKSRAELERALE--LGIRC-INVDSESELELLNEIAPELG-KKARVSLRVNPGVDAKTHPYISTGLEDSKFGIDVEEA 176 (417)
T ss_pred CCCCCHHHHHHHHH--cCCCE-EEeCCHHHHHHHHHHHHhcC-CCceEEEEECCCCCCCCCCCeecCCCCCCCCCCHHHH
Confidence 76 35666777773 22322 48999999999999887654 578999999953 566899973
Q ss_pred --------cCCcccccccCC
Q 029918 174 --------KCSWSHSCLLMI 185 (185)
Q Consensus 174 --------~~~~l~l~g~m~ 185 (185)
.++++.+.|||+
T Consensus 177 ~~~~~~~~~~~~l~l~Glh~ 196 (417)
T TIGR01048 177 LEAYLYALQLPHLELVGIHC 196 (417)
T ss_pred HHHHHHHHhCCCCCEEEEEE
Confidence 578899999863
No 27
>cd06825 PLPDE_III_VanT Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, VanT and similar proteins. This subfamily is composed of Enterococcus gallinarum VanT and similar proteins. VanT is a membrane-bound serine racemase (EC 5.1.1.18) that is essential for vancomycin resistance in Enterococcus gallinarum. It converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. The C-terminal region of this protein contains a PLP-binding TIM-barrel domain followed by beta-sandwich domain, which is homologous to the fold type III PLP-dependent enzyme, bacterial alanine racemase (AR). AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. On the basis of this similarity, it has been suggested that dimer formation of VanT is required for its catalytic activity, and that it catalyzes the racemization of serine in a mechanistically similar manner to that of alanine by
Probab=97.79 E-value=0.00045 Score=62.34 Aligned_cols=130 Identities=14% Similarity=0.171 Sum_probs=92.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecC----CCHHHHHHHH-HcCCcccccccHHHHHHHHhc-CCCCce
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKT----KPVSVIRQVY-EAGHRCFGENYVQEIVEKAAQ-LPDDLE 106 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt----~p~e~I~~a~-~~G~r~FGENrvQEl~~K~~~-L~~~i~ 106 (185)
.+.|..|++.+++++ +..++|+||.|. |....|..++ ++|++.||--++.|+..=.+. +..+|-
T Consensus 8 l~al~~N~~~i~~~~----------~~~~~i~~VVKanAYGhG~~~va~~l~~~G~~~faVa~~~EA~~Lr~~Gi~~~Il 77 (368)
T cd06825 8 LSALEHNVKEIKRLL----------PSTCKLMAVVKANAYGHGDVEVARVLEQIGIDFFAVATIDEGIRLREAGIKGEIL 77 (368)
T ss_pred HHHHHHHHHHHHHhC----------CCCCeEEEEEeccccCCCHHHHHHHHHHcCCCEEEEccHHHHHHHHhcCCCCCEE
Confidence 345566666665554 224799999999 9987776654 689999999999999764432 222331
Q ss_pred EEEEecccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc-----------cC
Q 029918 107 WHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI-----------KC 175 (185)
Q Consensus 107 WHfIG~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~-----------~~ 175 (185)
..|..-...+..++ ..+++-+|+|+.-++.|++.+ ++++|.|.|+++- ...||. .+
T Consensus 78 --vl~~~~~~~~~~~~----~~~l~~~i~~~~~l~~l~~~~-----~~~~vhlkvDtGm--~R~G~~~~~~~~~~~~~~~ 144 (368)
T cd06825 78 --ILGYTPPVRAKELK----KYSLTQTLISEAYAEELSKYA-----VNIKVHLKVDTGM--HRLGESPEDIDSILAIYRL 144 (368)
T ss_pred --EEcCCCHHHHHHHH----HcCCEEEECCHHHHHHHHhcC-----CCceEEEEeeCCC--CCCCCCHHHHHHHHHHHhC
Confidence 23655445567666 246778899999999998754 4689999999853 344542 48
Q ss_pred CcccccccCC
Q 029918 176 SWSHSCLLMI 185 (185)
Q Consensus 176 ~~l~l~g~m~ 185 (185)
|+|.+.|+||
T Consensus 145 ~~l~~~Gi~t 154 (368)
T cd06825 145 KNLKVSGIFS 154 (368)
T ss_pred CCCcEEEEEC
Confidence 9999999986
No 28
>cd06817 PLPDE_III_DSD Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Eukaryotic D-Serine Dehydratase. This subfamily is composed of chicken D-serine dehydratase (DSD, EC 4.3.1.18) and similar eukaryotic proteins. Chicken DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. It is a fold type III PLP-dependent enzyme with similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as dimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Experimental data suggest that chicken DSD also exists as dimers. Sequence comparison and biochemical experiments show that chicken DSD is distinct from the ubiquitous bacterial DSDs coded by dsdA gene, mammalian L-serine dehydratases (LSD) and mammalian serine racemase (SerRac), which are fold type II PL
Probab=97.76 E-value=0.00032 Score=64.06 Aligned_cols=141 Identities=14% Similarity=0.057 Sum_probs=100.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHH-HHHcCC--cccccccHHHHHHHHhcC-CCCceEE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQ-VYEAGH--RCFGENYVQEIVEKAAQL-PDDLEWH 108 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~-a~~~G~--r~FGENrvQEl~~K~~~L-~~~i~WH 108 (185)
.+.+..|++.++++... ..++|.++.|+|...+|.. ++++|. ..|+=-.+.|+..=...- ..+|+-=
T Consensus 13 l~al~~Ni~~m~~~~~~---------~~~~l~phvKaHg~~~ia~~~~~~Ga~~~~~~Vatl~EA~~lr~~G~~~~I~di 83 (389)
T cd06817 13 RAKFKRNCERMLQRAKA---------LGVKFRPHVKTHKTLEGTRLQLGEGRPSRGIVVSTLAEAEFLLPLGEEGRVDDI 83 (389)
T ss_pred HHHHHHHHHHHHHHHHH---------cCCceeeeecCcCCHHHHHHHhhCCCCccCEEEecHHHHHHHHHhccccccccE
Confidence 56677777777665531 2479999999999988876 457798 999999999998654321 1123323
Q ss_pred EEe-cccccchHHHhhcCCCcc-EEEecCcHHHHHHHHHH-HHhcCCCCccEEEEEeCCCCCccccc-------------
Q 029918 109 FIG-NLQSNKVKPLLAGVPNLA-MVESVDNEKIAGRLNRM-VETMGRKPLKVLVQVNTSGEEYGECF------------- 172 (185)
Q Consensus 109 fIG-~LQsNKvk~~~~~~~~~~-~IhSVDs~kLA~~L~k~-a~~~~~~~l~VLIQVNis~E~sKsG~------------- 172 (185)
++| ++...+++.++..-..++ +.-.|||..-++.|++. +...+ .+++|+|+||++.-- .|+
T Consensus 84 lla~~~~~~~~~~l~~l~~~~~~i~~~Vds~~~l~~l~~~~a~~~g-~~~~V~lkvDtGm~R--~Gv~~~~~~~~~l~~~ 160 (389)
T cd06817 84 LYGLPVPPSKLPRLAELSKKLGHLRVMVDNPEQLDFLEQFQPLKSG-KKWSVFIKVDCGTHR--AGVPPESEDAKELIQK 160 (389)
T ss_pred EEECCCCHHHHHHHHHHHhhcCceEEEECCHHHHHHHHHHHhhccC-CceEEEEEEcCCCCc--CCCCCChHHHHHHHHH
Confidence 567 567788888873101123 77899999999999987 65554 689999999994321 222
Q ss_pred -cc-CCcccccccCC
Q 029918 173 -IK-CSWSHSCLLMI 185 (185)
Q Consensus 173 -~~-~~~l~l~g~m~ 185 (185)
.. +++|+|.|+|+
T Consensus 161 i~~~~~~L~l~Gi~t 175 (389)
T cd06817 161 LEKASEAVELFGFYS 175 (389)
T ss_pred HHhhCCCcEEEEEEE
Confidence 34 89999999986
No 29
>PRK11930 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional
Probab=97.72 E-value=0.00073 Score=66.57 Aligned_cols=134 Identities=8% Similarity=0.108 Sum_probs=91.2
Q ss_pred HHHHHHHHHHHHHHcCCCCCCeEEEEeecCCC-----HHHHHHHHHcCCcccccccHHHHHHHHhc-CCCCceEEEEecc
Q 029918 40 LRSVIQRVHQAAERSSRPPDRIRIVAVSKTKP-----VSVIRQVYEAGHRCFGENYVQEIVEKAAQ-LPDDLEWHFIGNL 113 (185)
Q Consensus 40 l~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p-----~e~I~~a~~~G~r~FGENrvQEl~~K~~~-L~~~i~WHfIG~L 113 (185)
+..++..++...+.++ ..++++||.|--- .+-.+.++++|++.||-.++.|+..=.+. ++.+| ...|+.
T Consensus 466 l~al~~N~~~i~~~~~---~~~k~~aVvKa~aYGhG~~~va~~l~~~G~~~f~Va~l~Ea~~lr~~g~~~~I--lvl~~~ 540 (822)
T PRK11930 466 LNAIVHNLNYYRSKLK---PETKIMCMVKAFAYGSGSYEIAKLLQEHRVDYLAVAYADEGVSLRKAGITLPI--MVMNPE 540 (822)
T ss_pred HHHHHHHHHHHHhhCC---CCCEEEEEEeeccccCCHHHHHHHHHHCCCCEEEEeeHHHHHHHHhcCCCCCE--EEEeCC
Confidence 4445555544444333 3579999999754 44445556889999999999998744332 22232 334665
Q ss_pred cccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCccccc------------ccCCccccc
Q 029918 114 QSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECF------------IKCSWSHSC 181 (185)
Q Consensus 114 QsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~------------~~~~~l~l~ 181 (185)
..-+..++ . .++.-+|+|+.-++.|++.+.+.+.++++|.|.|+++- ...|| ..+|++.+.
T Consensus 541 -~~~~~~~~---~-~~l~~~i~s~~~l~~l~~~~~~~~~~~~~v~l~vDtGm--~R~G~~~~~~~~~~~~i~~~~~l~~~ 613 (822)
T PRK11930 541 -PTSFDTII---D-YKLEPEIYSFRLLDAFIKAAQKKGITGYPIHIKIDTGM--HRLGFEPEDIPELARRLKKQPALKVR 613 (822)
T ss_pred -HHHHHHHH---H-cCCEEEECCHHHHHHHHHHHHHcCCCceEEEEEeeCCC--CCCCCChHHHHHHHHHHHhCCCCcEE
Confidence 34466666 2 56778899999999999888765325789999999853 34454 258999999
Q ss_pred ccCC
Q 029918 182 LLMI 185 (185)
Q Consensus 182 g~m~ 185 (185)
|+||
T Consensus 614 Gi~t 617 (822)
T PRK11930 614 SVFS 617 (822)
T ss_pred EEEC
Confidence 9986
No 30
>cd06814 PLPDE_III_DSD_D-TA_like_3 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 3. This subfamily is composed of uncharacterized bacterial proteins with similarity to eukaryotic D-serine dehydratases (DSD) and D-threonine aldolases (D-TA). DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. DSD and D-TA are fold type III PLP-dependent enzymes, similar to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on their similarity to AR, it is possible mem
Probab=97.68 E-value=0.00086 Score=60.96 Aligned_cols=137 Identities=12% Similarity=0.128 Sum_probs=95.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHH-H-HcCCcccccccHHHHHHHHhcCC-CCceEEE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQV-Y-EAGHRCFGENYVQEIVEKAAQLP-DDLEWHF 109 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a-~-~~G~r~FGENrvQEl~~K~~~L~-~~i~WHf 109 (185)
.+.+..|++.+++++ + ..++|.+|.|++-...+... + ++|.+.|+=..+.|+..=..... .+| +
T Consensus 16 l~al~~Ni~~m~~~~-------~---~g~~lrphvKa~ky~~~~~~~l~~~Ga~g~~vat~~Eae~l~~~~~~~dI---L 82 (379)
T cd06814 16 KDRLDHNIDLLREHL-------A---GSLAYRIVAKSLPSPPLLRHIMKRAGTRRLMVFHQPFLNAVAKAFPDADI---L 82 (379)
T ss_pred HHHHHHHHHHHHHhh-------C---CCCcEEEEeccccCHHHHHHHHhhCCCCEEEEecHHHHHHHHhcCCCcCe---E
Confidence 556667777666554 2 35899999999998655444 4 68999999999999987444332 255 4
Q ss_pred Ee-cccccchHHHhhcCC------CccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCccccc----------
Q 029918 110 IG-NLQSNKVKPLLAGVP------NLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECF---------- 172 (185)
Q Consensus 110 IG-~LQsNKvk~~~~~~~------~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~---------- 172 (185)
+| ++...++..+++... ..++.=+|||..-++.|++.+.+.+ .+++|+|+||++-- ..||
T Consensus 83 l~~p~~~~~~~r~~~~l~~~~~~~~~~l~~~Vds~e~l~~l~~~a~~~g-~~l~V~lkVDtGm~--R~Gv~~~~~~~~l~ 159 (379)
T cd06814 83 LGKPMPVAAAARFYRQLTGSAFRPARQLQWLIDTPERLAQYRALARSLG-LTLRINLELDVGLH--RGGFADPQTLPKAL 159 (379)
T ss_pred EeCCCCcHHHHHHHhhccccccchhcCEEEEECCHHHHHHHHHHHHHcC-CceEEEEEeCCCCC--CCCCCCHHHHHHHH
Confidence 77 555666655531001 2346678999999999999887654 68999999998532 2333
Q ss_pred ---ccCCcccccccCC
Q 029918 173 ---IKCSWSHSCLLMI 185 (185)
Q Consensus 173 ---~~~~~l~l~g~m~ 185 (185)
..+++|++.|+|+
T Consensus 160 ~~i~~~~~l~~~Gi~t 175 (379)
T cd06814 160 TAIDAPPRLRFSGLMG 175 (379)
T ss_pred HHHHhCCCceEEEEEE
Confidence 2478999999985
No 31
>cd06812 PLPDE_III_DSD_D-TA_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 1. This subfamily is composed of uncharacterized bacterial proteins with similarity to eukaryotic D-serine dehydratases (DSD) and D-threonine aldolases (D-TA). DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. DSD and D-TA are fold type III PLP-dependent enzymes, similar to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on their similarity to AR, it is possible mem
Probab=97.62 E-value=0.001 Score=59.16 Aligned_cols=138 Identities=13% Similarity=0.096 Sum_probs=93.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHH-HHHHcCCcccccccHHHHHHHHhcCCCCceEEEEe
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIR-QVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIG 111 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~-~a~~~G~r~FGENrvQEl~~K~~~L~~~i~WHfIG 111 (185)
.+.+..|++.+++... +..+++.++.|+.+...|. .+.++|..-|+=..+.|+..=... .+..-+++
T Consensus 13 ~~~l~~Ni~~~~~~~~---------~~~~~l~~~vKa~~~~~i~~~~~~~G~~~~~vas~~Ea~~~~~a---G~~~il~~ 80 (374)
T cd06812 13 EARMDRNIARLRQRLS---------RLGVRLRPHLKTAKSLEVARRLLAAGASPATVSTLKEAEAFAEA---GYRDILYA 80 (374)
T ss_pred HHHHHHHHHHHHHHHH---------HcCCceeeEecccCCHHHHHHHHhCCCCcEEEccHHHHHHHHHc---CCCeeEEe
Confidence 5667778877776652 1257899999999976554 455789988999999998753322 12222222
Q ss_pred -cccccchHHHhhcCC-CccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc-------------cCC
Q 029918 112 -NLQSNKVKPLLAGVP-NLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI-------------KCS 176 (185)
Q Consensus 112 -~LQsNKvk~~~~~~~-~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~-------------~~~ 176 (185)
++-..|+..++.... ...+.=.|||+.-++.|++.+.+.+ .+++|+|.||++. .+.|+. ..+
T Consensus 81 ~~~~~~~~~~~~~l~~~~~~~~~~vds~~~l~~l~~~a~~~~-~~~~V~l~vd~G~--~R~Gv~~~~~~~~~l~~~i~~~ 157 (374)
T cd06812 81 VGIAPAKLPRVLALRRQGVNLTILLDSVEQAQAVAAFSRQHG-VRFPVLIEIDCDG--HRGGIAPDSDALLEIARILHDG 157 (374)
T ss_pred CCCCHHHHHHHHHHHhcCCceEEEECCHHHHHHHHHHHHHcC-CceEEEEEeCCCC--CcCCCCCCcHHHHHHHHHHhcC
Confidence 133456666552001 1334568999999999999887665 6899999999853 456652 126
Q ss_pred cccccccCC
Q 029918 177 WSHSCLLMI 185 (185)
Q Consensus 177 ~l~l~g~m~ 185 (185)
+|+|.|+|+
T Consensus 158 ~l~l~Gi~~ 166 (374)
T cd06812 158 GAELRGVLT 166 (374)
T ss_pred CceEEEEEc
Confidence 899999984
No 32
>PRK03646 dadX alanine racemase; Reviewed
Probab=97.53 E-value=0.0019 Score=58.23 Aligned_cols=130 Identities=15% Similarity=0.131 Sum_probs=95.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecC----CCHHHHHHHHHcCCcccccccHHHHHHHHhc-CCCCc-e
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKT----KPVSVIRQVYEAGHRCFGENYVQEIVEKAAQ-LPDDL-E 106 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt----~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~-L~~~i-~ 106 (185)
.+.|..|++.+++.+ + .++++||.|. |....|..++. +++.||-.++.|+..=.+. +..+| -
T Consensus 10 l~al~~N~~~i~~~~----------~-~~~i~aVVKanAYGhG~~~va~~l~-~~~~faVa~l~Ea~~LR~~Gi~~~Ilv 77 (355)
T PRK03646 10 LQALKQNLSIVREAA----------P-GARVWSVVKANAYGHGIERIWSALG-ATDGFAVLNLEEAITLRERGWKGPILM 77 (355)
T ss_pred HHHHHHHHHHHHHhC----------C-CCeEEEEEeeccccCCHHHHHHHHh-cCCEEEEeeHHHHHHHHhcCCCCCEEE
Confidence 456677777776553 2 3789999999 99999988875 4999999999999764432 22233 2
Q ss_pred EEEEecccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCccccc------------cc
Q 029918 107 WHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECF------------IK 174 (185)
Q Consensus 107 WHfIG~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~------------~~ 174 (185)
|. |......+..++ ..++.-+|+|..-++.|++.+ .+ ++++|.|.|+++- +..|| ..
T Consensus 78 l~--~~~~~~~~~~~~----~~~l~~~i~s~~~l~~l~~~~--~~-~~~~vhLkvDTGM--~R~G~~~~e~~~~~~~i~~ 146 (355)
T PRK03646 78 LE--GFFHAQDLELYD----QHRLTTCVHSNWQLKALQNAR--LK-APLDIYLKVNSGM--NRLGFQPERVQTVWQQLRA 146 (355)
T ss_pred Ee--CCCCHHHHHHHH----HCCCEEEECCHHHHHHHHHhc--cC-CCeEEEEEeeCCC--CCCCCCHHHHHHHHHHHHh
Confidence 33 554556677766 357889999999999998865 23 5789999999853 44455 24
Q ss_pred CCcccccccCC
Q 029918 175 CSWSHSCLLMI 185 (185)
Q Consensus 175 ~~~l~l~g~m~ 185 (185)
+++|.+.|+||
T Consensus 147 ~~~l~~~Gi~s 157 (355)
T PRK03646 147 MGNVGEMTLMS 157 (355)
T ss_pred CCCCEEEEEEc
Confidence 78999999986
No 33
>cd06813 PLPDE_III_DSD_D-TA_like_2 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 2. This subfamily is composed of uncharacterized bacterial proteins with similarity to eukaryotic D-serine dehydratases (DSD) and D-threonine aldolases (D-TA). DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. DSD and D-TA are fold type III PLP-dependent enzymes, similar to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on their similarity to AR, it is possible mem
Probab=97.44 E-value=0.0025 Score=57.74 Aligned_cols=136 Identities=15% Similarity=0.062 Sum_probs=91.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHH-HHH-cCCcccccccHHHHHHHHhcCCCCceEEEE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQ-VYE-AGHRCFGENYVQEIVEKAAQLPDDLEWHFI 110 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~-a~~-~G~r~FGENrvQEl~~K~~~L~~~i~WHfI 110 (185)
.+.+..|++.++++. + .++|.+++|+++.-.|.. +.+ .|+..|+=-.+.|+..=...-..+|- +-
T Consensus 18 ldal~~N~~~l~~~~-------~----~~~ir~~vKa~~~~~ll~~~l~~~G~~g~~vas~~Ea~~l~~aG~~~IL--l~ 84 (388)
T cd06813 18 LDALDANAADLVRRA-------G----GKPIRVASKSVRCRALLRRVLAAPGFQGVMAFTLAEALWLARQGFDDIL--VA 84 (388)
T ss_pred HHHHHHHHHHHHHHc-------C----CCcEEEEeccccCHHHHHHHHhhcCCceEEEecHHHHHHHHHcCCCeEE--Ee
Confidence 556667776665442 1 357999999999987653 455 59999999999998654332223433 33
Q ss_pred ecc-cccchHHHhhcCCC----ccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCC---------Ccccc-----
Q 029918 111 GNL-QSNKVKPLLAGVPN----LAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGE---------EYGEC----- 171 (185)
Q Consensus 111 G~L-QsNKvk~~~~~~~~----~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E---------~sKsG----- 171 (185)
++. -..++..++ .. ..+.-.|||..-++.|+..+.+.+ .+++|+|.||++-- -++.+
T Consensus 85 ~p~~~~~~l~~~~---~~~~~~~~i~~~Vds~~~l~~l~~~a~~~~-~~~~V~l~IDtGm~R~G~~~G~~Rs~~~~~~~~ 160 (388)
T cd06813 85 YPSVDRAALRELA---ADPKLGATITLMVDSVEHLDLLDAVAAPMR-VEVRVCIDIDASLRFGGLHFGVRRSPLHTPAQA 160 (388)
T ss_pred CCCCCHHHHHHHH---hhhccCCeEEEEEcCHHHHHHHHHHHHhcC-CceEEEEEECCCccccccccCcCCCCCCCHHHH
Confidence 354 335577776 32 245677999999999988876554 68999999999421 11111
Q ss_pred ------cccCCcccccccCC
Q 029918 172 ------FIKCSWSHSCLLMI 185 (185)
Q Consensus 172 ------~~~~~~l~l~g~m~ 185 (185)
+..+++|+|.|+|+
T Consensus 161 ~~l~~~i~~~~~l~l~Gi~t 180 (388)
T cd06813 161 LALAKAIAARPGLRLVGLMG 180 (388)
T ss_pred HHHHHHHhcCCCcEEEEEEE
Confidence 13589999999995
No 34
>cd06842 PLPDE_III_Y4yA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Y4yA. This subfamily is composed of the hypothetical Rhizobium sp. protein Y4yA and similar uncharacterized bacterial proteins. These proteins are homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarboxylases.
Probab=97.44 E-value=0.0033 Score=57.61 Aligned_cols=139 Identities=11% Similarity=0.033 Sum_probs=100.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHH-HcCCcccccccHHHHHHHHhc-CCCCceEEEE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVY-EAGHRCFGENYVQEIVEKAAQ-LPDDLEWHFI 110 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~-~~G~r~FGENrvQEl~~K~~~-L~~~i~WHfI 110 (185)
.+.|..|++.+++.... . +..+++..+.|+.|...|..++ +.|. .|.=....|+..=... .+++ +-+|-
T Consensus 17 ~~~l~~N~~~l~~~~~~----~---~~~~~~~yavKaN~~~~il~~l~~~G~-g~dvaS~~E~~~~~~~G~~~~-~I~~~ 87 (423)
T cd06842 17 PQTFRENIAALRAVLDR----H---GVDGRVYFARKANKSLALVRAAAAAGI-GVDVASLAELRQALAAGVRGD-RIVAT 87 (423)
T ss_pred HHHHHHHHHHHHHHHHH----h---CCCeEEEEEeccCCCHHHHHHHHHcCC-CEEECCHHHHHHHHHCCCCCC-eEEEE
Confidence 66777888877665532 2 3368999999999987776654 6787 8999999998654332 2222 23777
Q ss_pred ecccccc-hHHHhhcCCCccEEEecCcHHHHHHHHHHHHh-cCCCCccEEEEEeCCC--CCcccccc------------c
Q 029918 111 GNLQSNK-VKPLLAGVPNLAMVESVDNEKIAGRLNRMVET-MGRKPLKVLVQVNTSG--EEYGECFI------------K 174 (185)
Q Consensus 111 G~LQsNK-vk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~-~~~~~l~VLIQVNis~--E~sKsG~~------------~ 174 (185)
|+.-+.. ++.++. ..+.=+|||+.-++.|.+.+.. .+ .+.+|+|.||++. ..+|.|+. .
T Consensus 88 g~~k~~~~i~~a~~----~gi~i~vDs~~el~~l~~~a~~~~~-~~~~v~lRIn~~~~~~~sRfGi~~~e~~~~~~~i~~ 162 (423)
T cd06842 88 GPAKTDEFLWLAVR----HGATIAVDSLDELDRLLALARGYTT-GPARVLLRLSPFPASLPSRFGMPAAEVRTALERLAQ 162 (423)
T ss_pred CCCCCHHHHHHHHh----CCCEEEECCHHHHHHHHHHHHhcCC-CCCEEEEEEeCCCCCCCCCCCCCHHHHHHHHHHHHh
Confidence 9987766 565552 2334699999999999988875 43 5789999999965 46899972 2
Q ss_pred C-CcccccccCC
Q 029918 175 C-SWSHSCLLMI 185 (185)
Q Consensus 175 ~-~~l~l~g~m~ 185 (185)
+ +++.+.||++
T Consensus 163 ~~~~l~l~Glh~ 174 (423)
T cd06842 163 LRERVRLVGFHF 174 (423)
T ss_pred cCCCCeEEEEEE
Confidence 4 8999999873
No 35
>PLN02537 diaminopimelate decarboxylase
Probab=97.23 E-value=0.0076 Score=54.66 Aligned_cols=137 Identities=13% Similarity=-0.020 Sum_probs=93.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHH-HcCCcccccccHHHHHHHHh-cCCCCceEEEE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVY-EAGHRCFGENYVQEIVEKAA-QLPDDLEWHFI 110 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~-~~G~r~FGENrvQEl~~K~~-~L~~~i~WHfI 110 (185)
.+.+.+|++.+++.+. ...+++..+.|+.|...|..++ ++|...+.-+.. |+.--.. -++++ .--|.
T Consensus 25 ~~~l~~N~~~~~~~~~---------~~~~~i~yavKaN~~~~il~~l~~~G~~~~~~S~~-E~~~al~~G~~~~-~ii~~ 93 (410)
T PLN02537 25 KPQITRNYEAYKEALE---------GLRSIIGYAIKANNNLKILEHLRELGCGAVLVSGN-ELRLALRAGFDPT-RCIFN 93 (410)
T ss_pred HHHHHHHHHHHHHHhc---------cCCceEEEEehhcCCHHHHHHHHHcCCCEEEeCHH-HHHHHHHcCCCcc-eEEEE
Confidence 6677777777765541 1257899999999987777665 678888888774 4433222 23332 23666
Q ss_pred ecccccc-hHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCC------------CCCcccccc----
Q 029918 111 GNLQSNK-VKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTS------------GEEYGECFI---- 173 (185)
Q Consensus 111 G~LQsNK-vk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis------------~E~sKsG~~---- 173 (185)
|+.-+.. ++.++. ..+.-+|||+.-+++|.+.+.+.+ .+++|+|-||.. ...+|.|+.
T Consensus 94 g~~k~~~~l~~a~~----~gv~i~ids~~el~~l~~~a~~~~-~~~~v~lRvnp~~~~~~~~~i~tG~~~sRfGi~~~~~ 168 (410)
T PLN02537 94 GNGKLLEDLVLAAQ----EGVFVNVDSEFDLENIVEAARIAG-KKVNVLLRINPDVDPQVHPYVATGNKNSKFGIRNEKL 168 (410)
T ss_pred CCCCCHHHHHHHHH----CCCEEEECCHHHHHHHHHHHHhcC-CCceEEEEECCCCCCCCCCccccCCCCCCCCCCHHHH
Confidence 7765544 444442 233459999999999999887664 578999999943 345888973
Q ss_pred --------cCC-cccccccCC
Q 029918 174 --------KCS-WSHSCLLMI 185 (185)
Q Consensus 174 --------~~~-~l~l~g~m~ 185 (185)
..+ +|++.|+++
T Consensus 169 ~~~~~~~~~~~~~l~l~Glh~ 189 (410)
T PLN02537 169 QWFLDAVKAHPNELKLVGAHC 189 (410)
T ss_pred HHHHHHHHhCCCCCcEEEEEe
Confidence 356 899999874
No 36
>TIGR03099 dCO2ase_PEP1 pyridoxal-dependent decarboxylase, exosortase system type 1 associated. The sequences in this family contain the pyridoxal binding domain (pfam02784) and C-terminal sheet domain (pfam00278) of a family of Pyridoxal-dependent decarboxylases. Characterized enzymes in this family decarboxylate substrates such as ornithine, diaminopimelate and arginine. The genes of the family modeled here, with the exception of those observed in certain Burkholderia species, are all found in the context of exopolysaccharide biosynthesis loci containing the exosortase/PEP-CTERM protein sorting system. More specifically, these are characteristic of the type 1 exosortase system represented by the Genome Property GenProp0652. The substrate of these enzymes may be a precursor of the carrier or linker which is hypothesized to release the PEP-CTERM protein from the exosortase enzyme. These enzymes are apparently most closely related to the diaminopimelate decarboxylase modeled by TIGR01048
Probab=96.87 E-value=0.025 Score=50.86 Aligned_cols=124 Identities=17% Similarity=0.227 Sum_probs=90.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHHcCCcccccccHHHHHHHHhc-CCCCceEEEEe
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQ-LPDDLEWHFIG 111 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~-L~~~i~WHfIG 111 (185)
.+.|.+|++.+++.+ |..+++..+.|+-|...|..++..|...|.=.-..|+..=... .+.+ +-.|-|
T Consensus 32 ~~~l~~n~~~l~~~~----------~~~~~i~yavKaN~~~~vl~~l~~~g~g~dvaS~~E~~~~~~~G~~~~-~I~~~g 100 (398)
T TIGR03099 32 RGLVSERVAALRKAL----------PEELAIHYAVKANPMPALLAHMAPLVDGFDVASAGELAVALDTGYDPG-CISFAG 100 (398)
T ss_pred HHHHHHHHHHHHHhc----------cccCcEEEEeccCCCHHHHHHHHHcCCcEEEeCHHHHHHHHHcCCChh-HEEEeC
Confidence 666777777776543 3358999999999999999888888888988888888743332 2221 356778
Q ss_pred cc-cccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCC-----------CCCccccc
Q 029918 112 NL-QSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTS-----------GEEYGECF 172 (185)
Q Consensus 112 ~L-QsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis-----------~E~sKsG~ 172 (185)
+. ...-++.++. ..++=+|||+.-++.|.+.+.+.+ .+.+|+|.||.+ +..+|.|+
T Consensus 101 p~k~~~~l~~a~~----~gv~i~vDs~~el~~l~~~a~~~~-~~~~v~LRin~~~~~~~~~~~~~~~~srFGi 168 (398)
T TIGR03099 101 PGKTDAELRRALA----AGVLINVESLRELNRLAALSEALG-LRARVAVRVNPDFELKGSGMKMGGGAKQFGI 168 (398)
T ss_pred CCCCHHHHHHHHh----CCCEEEECCHHHHHHHHHHHHhcC-CCCcEEEEECCCCCCCCcccccCCCCCcCCC
Confidence 85 5555777662 234568999999999999887654 468999999973 23488887
No 37
>cd06841 PLPDE_III_MccE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme MccE. This subfamily is composed of uncharacterized proteins with similarity to Escherichia coli MccE, a hypothetical protein that is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Most members of this subfamily share the same domain architecture as ODC and DapDC. A few members, including Escherichia coli MccE, contain an additional acetyltransferase domain at the C-terminus.
Probab=96.81 E-value=0.032 Score=49.97 Aligned_cols=139 Identities=15% Similarity=0.101 Sum_probs=95.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHH-HcCCcccccccHHHHHHHHhc-CCCCceEEEE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVY-EAGHRCFGENYVQEIVEKAAQ-LPDDLEWHFI 110 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~-~~G~r~FGENrvQEl~~K~~~-L~~~i~WHfI 110 (185)
.+.|.+|++.+++.+.+ ....+++..+.|.-|...|..++ +.|+..+-= -..|+..=... +++ -.-.|-
T Consensus 14 ~~~l~~n~~~l~~~~~~-------~~~~~~i~yavKaN~~~~vl~~l~~~g~~~dva-S~~E~~~~~~~G~~~-~~Ii~~ 84 (379)
T cd06841 14 EDALRENYRELLGAFKK-------RYPNVVIAYSYKTNYLPAICKILHEEGGYAEVV-SAMEYELALKLGVPG-KRIIFN 84 (379)
T ss_pred HHHHHHHHHHHHHHHhh-------cCCCeEEEEEehhcccHHHHHHHHHcCCeEEEe-CHHHHHHHHHcCCCh-HHEEEE
Confidence 56677788777665532 11348999999999998777665 678777644 45777543332 222 234667
Q ss_pred ecccc-cchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCC---Ccccccc-------------
Q 029918 111 GNLQS-NKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGE---EYGECFI------------- 173 (185)
Q Consensus 111 G~LQs-NKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E---~sKsG~~------------- 173 (185)
|+.-+ .-++.++. + .++=+|||+.-++.|.+.+.+.+ ++.+|+|-||+... .+|.|+.
T Consensus 85 g~~k~~~~l~~a~~---~-g~~i~ids~~el~~l~~~~~~~~-~~~~v~lRv~~~~g~~~~~rfGi~~~e~~~~~~~~~~ 159 (379)
T cd06841 85 GPYKSKEELEKALE---E-GALINIDSFDELERILEIAKELG-RVAKVGIRLNMNYGNNVWSRFGFDIEENGEALAALKK 159 (379)
T ss_pred CCCCCHHHHHHHHH---C-CCEEEECCHHHHHHHHHHHHhcC-CcceEEEEECCCCCCCCCCCCCCchhhhHHHHHHHHH
Confidence 88765 55777662 2 34568999999999999887654 57899999998544 6898973
Q ss_pred --cCCcccccccCC
Q 029918 174 --KCSWSHSCLLMI 185 (185)
Q Consensus 174 --~~~~l~l~g~m~ 185 (185)
.++++.+.|+++
T Consensus 160 ~~~~~~l~~~Glh~ 173 (379)
T cd06841 160 IQESKNLSLVGLHC 173 (379)
T ss_pred hhcCCCeeEEEEEe
Confidence 136788888763
No 38
>COG3457 Predicted amino acid racemase [Amino acid transport and metabolism]
Probab=96.72 E-value=0.044 Score=50.05 Aligned_cols=116 Identities=16% Similarity=0.162 Sum_probs=84.3
Q ss_pred CeEEEEeecCC--CHHHHHHHHHcCCcccccccHHHHHHHHhcCCCCceEEEEecccccchHHHhhcCCCccEEEecCcH
Q 029918 60 RIRIVAVSKTK--PVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNE 137 (185)
Q Consensus 60 ~V~LvAVSKt~--p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~~i~WHfIG~LQsNKvk~~~~~~~~~~~IhSVDs~ 137 (185)
.|.|.+|||-. .+.-.+.+..+|+...+|.|..++..=.+.=. .+-.|+.-.==.--+..++ ..+| |=++.++
T Consensus 28 gI~~~~vtK~~~g~~~iae~l~~~Gi~~iaesr~~n~~~lr~~g~-~~~~~Llr~P~~sei~~vv---~~~D-vs~~sel 102 (353)
T COG3457 28 GIELYGVTKQFGGDPFIAEALLALGIEGIAESRIDNAIRLREAGC-TIPGHLLRSPCMSEIEDVV---RKVD-VSTVSEL 102 (353)
T ss_pred CCEEEEEEeeccCChHHHHHHHhcCcceeeehhHHHHHHHHHcCC-CcCceEeecccHHHHHHHH---HhcC-eEEEecH
Confidence 59999999976 45556666778999999999999975443311 2223443211123466677 6788 6688999
Q ss_pred HHHHHHHHHHHhcCCCCccEEEEEeCCCCCccccc---------------ccCCccccccc
Q 029918 138 KIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECF---------------IKCSWSHSCLL 183 (185)
Q Consensus 138 kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~---------------~~~~~l~l~g~ 183 (185)
.-|.+|+..|.+.| +..+||+=|-.++ =.-|. .+||++++.|+
T Consensus 103 ~~arqlse~A~~~G-k~h~VlLmVd~~D--lreG~~~~~~~~l~~~V~eI~~lkGi~~vGl 160 (353)
T COG3457 103 DTARQLSEAAVRMG-KVHDVLLMVDYGD--LREGQWGFLIEDLEETVEEIQQLKGIHLVGL 160 (353)
T ss_pred HHHHHHHHHHHHhC-cceeEEEEEEccc--ccCcchhhHHHHHHHHHHHHhcCCCceEEee
Confidence 99999999999887 6889999999876 22221 36999999998
No 39
>cd00622 PLPDE_III_ODC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase. This subfamily is composed mainly of eukaryotic ornithine decarboxylases (ODC, EC 4.1.1.17) and ODC-like enzymes from prokaryotes represented by Vibrio vulnificus LysineOrnithine decarboxylase. These are fold type III PLP-dependent enzymes that differ from most bacterial ODCs which are fold type I PLP-dependent enzymes. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. Members of this subfamily contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity. Also members of this su
Probab=95.47 E-value=0.33 Score=42.96 Aligned_cols=133 Identities=13% Similarity=0.069 Sum_probs=87.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHH-HcCCcccccccHHHHHHHHhcCCCCceEEEEe
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVY-EAGHRCFGENYVQEIVEKAAQLPDDLEWHFIG 111 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~-~~G~r~FGENrvQEl~~K~~~L~~~i~WHfIG 111 (185)
.+.+.+|++.+++.+ | .+++.++.|+-+...|..++ +.|+ .|+=.-..|+..=...-.+.-.-.|-|
T Consensus 9 ~~~l~~N~~~~~~~~----------~-~~~~~~avKAN~~~~v~~~l~~~G~-g~~vaS~~E~~~~~~~G~~~~~i~~~~ 76 (362)
T cd00622 9 LGDVVRKYRRWKKAL----------P-RVRPFYAVKCNPDPAVLRTLAALGA-GFDCASKGEIELVLGLGVSPERIIFAN 76 (362)
T ss_pred HHHHHHHHHHHHHHC----------C-CCeEEEEeccCCCHHHHHHHHHcCC-CeEecCHHHHHHHHHcCCCcceEEEcC
Confidence 455666776665543 2 36899999999988876665 6788 999999999875433322223457778
Q ss_pred cc-cccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCC------cccccc---------cC
Q 029918 112 NL-QSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEE------YGECFI---------KC 175 (185)
Q Consensus 112 ~L-QsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~------sKsG~~---------~~ 175 (185)
+. -...++.++. ..+..+ .+||+.-++.|.+.+. ..++.|-||+...- +|.|+. .+
T Consensus 77 ~~k~~~~l~~a~~--~gi~~~-~~ds~~el~~l~~~~~-----~~~v~vri~~~~~~~~~~~~sRfGi~~~~~~~~~~~~ 148 (362)
T cd00622 77 PCKSISDIRYAAE--LGVRLF-TFDSEDELEKIAKHAP-----GAKLLLRIATDDSGALCPLSRKFGADPEEARELLRRA 148 (362)
T ss_pred CCCCHHHHHHHHH--cCCCEE-EECCHHHHHHHHHHCC-----CCEEEEEEeeCCCCCCCcccCCCCCCHHHHHHHHHHH
Confidence 76 6666888773 234433 3799999999987652 24667777664332 378873 11
Q ss_pred --CcccccccCC
Q 029918 176 --SWSHSCLLMI 185 (185)
Q Consensus 176 --~~l~l~g~m~ 185 (185)
.++.+.|+++
T Consensus 149 ~~~~~~~~Glh~ 160 (362)
T cd00622 149 KELGLNVVGVSF 160 (362)
T ss_pred HHcCCEEEEEEE
Confidence 3678888763
No 40
>COG0787 Alr Alanine racemase [Cell envelope biogenesis, outer membrane]
Probab=95.46 E-value=0.39 Score=44.18 Aligned_cols=134 Identities=16% Similarity=0.126 Sum_probs=93.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeec----CCCHHHHHH-HHHcCCcccccccHHHHHHHHhcCCCC-ce
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSK----TKPVSVIRQ-VYEAGHRCFGENYVQEIVEKAAQLPDD-LE 106 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSK----t~p~e~I~~-a~~~G~r~FGENrvQEl~~K~~~L~~~-i~ 106 (185)
...|+.|++.+++.. ++ .+|+||-| .|.+..|.. ++++|++.||=-.++|+.+=-+...++ .-
T Consensus 11 l~Al~~N~~~i~~~~----------~~-~~~~AVVKAnAYGhG~~~va~~l~~~g~~~f~VA~l~EAi~LR~~gi~~~~I 79 (360)
T COG0787 11 LGALRHNLRALRELA----------GP-AKLMAVVKANAYGHGAVRVAKALLDAGADGFGVASLEEAIELREAGITGAPI 79 (360)
T ss_pred HHHHHHHHHHHHHhC----------CC-cEEEEEEeccccCCCHHHHHHHHHHcCCCEEEECcHHHHHHHHHcCCCCCCE
Confidence 556677777766654 22 89999999 477766654 567899999999999998876655442 11
Q ss_pred EEEEecccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc------------c
Q 029918 107 WHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI------------K 174 (185)
Q Consensus 107 WHfIG~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~------------~ 174 (185)
.=|-|-.-..=...++ ..++.-+|.|++-++.+.+.+... ++++|-|.|+++ =+..||. .
T Consensus 80 lvL~g~~~~~~~~~~~----~~~l~~~v~s~~ql~~l~~~~~~~--~~l~vhLkiDTG--M~RlG~~~~e~~~~~~~~~~ 151 (360)
T COG0787 80 LVLEGFFPAEELELAA----AYNLTPVVNSLEQLEALKNAALKN--KPLKVHLKIDTG--MNRLGLRPEEAVALAIDLIA 151 (360)
T ss_pred EEEcCcCChhhHHHHH----HcCCeEEECCHHHHHHHHHhhhhc--CceEEEEEECCC--CCcCCCChHHHHHHHHHHhh
Confidence 2222233333333343 345677888888888888877653 489999999986 5666763 5
Q ss_pred CCcccccccCC
Q 029918 175 CSWSHSCLLMI 185 (185)
Q Consensus 175 ~~~l~l~g~m~ 185 (185)
++++.+.|+|+
T Consensus 152 ~~~~~~~gi~S 162 (360)
T COG0787 152 LKNLDLEGIFS 162 (360)
T ss_pred ccCCceEEEEc
Confidence 77778888886
No 41
>COG3616 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]
Probab=91.13 E-value=4.3 Score=37.57 Aligned_cols=135 Identities=16% Similarity=0.207 Sum_probs=85.9
Q ss_pred HHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHH-HHHcCCcccccc--cHHHHHHHHhcCCCCceEEE-Eeccccc
Q 029918 41 RSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQ-VYEAGHRCFGEN--YVQEIVEKAAQLPDDLEWHF-IGNLQSN 116 (185)
Q Consensus 41 ~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~-a~~~G~r~FGEN--rvQEl~~K~~~L~~~i~WHf-IG~LQsN 116 (185)
+.+..+|...-+.+++. .++|=++-||+....+.. .+++|- +|=. -+.|+.-.+..==++|-|=. ++....-
T Consensus 26 dr~~~Ni~r~qa~~~~~--g~~lrph~KT~k~~~la~~ql~aGa--~git~~tl~eae~~a~aGi~dIl~a~p~~~~~~~ 101 (368)
T COG3616 26 DRLDGNIDRMQARADDH--GVRLRPHVKTHKCPELARIQLDAGA--WGITCATLGEAEVFADAGIDDILLAYPLPGRAAL 101 (368)
T ss_pred HHHhhhHHHHHHhcccc--CceeecccccccCHHHHHHHHhcCC--ceeEeechHHHHHHHccCccceEEecCCCchhHH
Confidence 44444444444444443 588888999998765544 556776 4433 46777666554223555555 4444443
Q ss_pred c-hHHHhhcCCCcc-EEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCccccc-------------ccCCccccc
Q 029918 117 K-VKPLLAGVPNLA-MVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECF-------------IKCSWSHSC 181 (185)
Q Consensus 117 K-vk~~~~~~~~~~-~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~-------------~~~~~l~l~ 181 (185)
. ...+. ..++ +.=-+||..-++.|...+...+ +|++||||+.++.- .+|+ ..-+.|+|.
T Consensus 102 ~~L~~l~---~~~~~~~~~iDs~~~~~~l~~~~~~~~-~pl~v~iE~D~G~~--R~Gv~t~~~~~~La~~~~~~~~l~~~ 175 (368)
T COG3616 102 AALAELL---ADPPRISVLIDSVEQLDALAALARDAG-KPLRVLIEIDSGLH--RSGVRTPEVAEALAAEIAAAPGLRLA 175 (368)
T ss_pred HHHHHhc---CCCCceEEEeCCHHHHHHHHHHHHhcC-CCeeEEEEeCCCCC--ccCcCChHHHHHHHHhhhhccceEEe
Confidence 4 33333 3344 5556888888888988887665 79999999998432 3454 248999999
Q ss_pred ccCC
Q 029918 182 LLMI 185 (185)
Q Consensus 182 g~m~ 185 (185)
|+|+
T Consensus 176 Gv~~ 179 (368)
T COG3616 176 GVMT 179 (368)
T ss_pred eeec
Confidence 9996
No 42
>TIGR03619 F420_Rv2161c probable F420-dependent oxidoreductase, Rv2161c family. Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea 34H, Rhodopseudomonas palustris HaA2, and others. Partial phylogenetic profiling identifies protein subfamilies, within the larger family called luciferase-like monooxygenanases (pfam00296), that appear only in F420-positive genomes and are likely to be F420-dependent. This model describes a domain found in a distinctive subset of bacterial luciferase homologs, found only in F420-biosynthesizing members of the Actinobacteria.
Probab=89.75 E-value=0.68 Score=39.55 Aligned_cols=49 Identities=18% Similarity=0.308 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCCeEEEEee------cCCCHHHHHHHHHcCCccc
Q 029918 38 TALRSVIQRVHQAAERSSRPPDRIRIVAVS------KTKPVSVIRQVYEAGHRCF 86 (185)
Q Consensus 38 ~nl~~V~~rI~~a~~~~gR~p~~V~LvAVS------Kt~p~e~I~~a~~~G~r~F 86 (185)
+.+....+.+.++|+++||+|.++++.+.. -..-++.+....++|+++|
T Consensus 188 ~~~~~~~~~~~~~~~~~Gr~~~~~~~~~~~~~~~g~~~~~~~~l~~~~~~G~~~~ 242 (246)
T TIGR03619 188 DRLAAAVARLRDLAAAAGRDPDAVEVVLVRTDPDGDADADAEDLAAYADLGVTRL 242 (246)
T ss_pred HHHHHHHHHHHHHHHHcCCCccceeEEeeccccCCCHHHHHHHHHHHHHcCCcEE
Confidence 345677888899999999999999888772 2333556666667788765
No 43
>PRK11165 diaminopimelate decarboxylase; Provisional
Probab=82.01 E-value=17 Score=33.40 Aligned_cols=113 Identities=14% Similarity=0.106 Sum_probs=73.9
Q ss_pred EEEEeecCCCHHHHHHHH-HcCCcccccccHHHHHHHHh-cCCCCc---eEEEEecc-cccchHHHhhcCCCccEEEecC
Q 029918 62 RIVAVSKTKPVSVIRQVY-EAGHRCFGENYVQEIVEKAA-QLPDDL---EWHFIGNL-QSNKVKPLLAGVPNLAMVESVD 135 (185)
Q Consensus 62 ~LvAVSKt~p~e~I~~a~-~~G~r~FGENrvQEl~~K~~-~L~~~i---~WHfIG~L-QsNKvk~~~~~~~~~~~IhSVD 135 (185)
++--..|+.|...|.... +.|+ -|==.-..|+..=.. -+++++ +-.|-|+. -..+++.++. ..+ .| +||
T Consensus 48 ~i~yavKan~~~~il~~~~~~G~-g~dvaS~~E~~~a~~~G~~~~~~~~~Ii~~gp~k~~~~l~~a~~--~gv-~i-~vD 122 (420)
T PRK11165 48 VIRFAQKACSNIHILRLMREQGV-KVDAVSLGEIERALAAGYKPGTEPDEIVFTADVIDRATLARVVE--LKI-PV-NAG 122 (420)
T ss_pred cceEEehhCCCHHHHHHHHHcCC-CEEEeCHHHHHHHHHcCCCCCCCCCeEEEeCCCCCHHHHHHHHH--CCC-EE-EEC
Confidence 466788999987776655 5675 454445555543222 133322 45777887 4456888873 223 34 699
Q ss_pred cHHHHHHHHHHHHhcCCCCccEEEEEeCC------------CCCcccccc-----------cCCcccccccC
Q 029918 136 NEKIAGRLNRMVETMGRKPLKVLVQVNTS------------GEEYGECFI-----------KCSWSHSCLLM 184 (185)
Q Consensus 136 s~kLA~~L~k~a~~~~~~~l~VLIQVNis------------~E~sKsG~~-----------~~~~l~l~g~m 184 (185)
|+.-++.|++.+. ..+|+|.||.. +..+|.|+. .-++|.|.||+
T Consensus 123 s~~el~~i~~~~~-----~~~v~lRvn~~~~~~~~~~~~~~~~~sKFGi~~~~~~~~~~~~~~~~l~l~GlH 189 (420)
T PRK11165 123 SIDMLDQLGQVSP-----GHRVWLRINPGFGHGHSQKTNTGGENSKHGIWHEDLPAALAVIQRYGLKLVGIH 189 (420)
T ss_pred CHHHHHHHHHhcC-----CCcEEEEECCCCCCCCCCceecCCCCCCCCCCHHHHHHHHHHHHhCCCcEEEEE
Confidence 9999999998764 25899999963 346888962 24578888876
No 44
>TIGR01047 nspC carboxynorspermidine decarboxylase. This protein is related to diaminopimelate decarboxylase. It is the last enzyme in norspermidine biosynthesis by an unusual pathway shown in Vibrio alginolyticus.
Probab=81.38 E-value=42 Score=30.46 Aligned_cols=123 Identities=11% Similarity=0.054 Sum_probs=76.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHH-cCCcccccccHHHHHHHHhcCCCCceEEEEe
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYE-AGHRCFGENYVQEIVEKAAQLPDDLEWHFIG 111 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~-~G~r~FGENrvQEl~~K~~~L~~~i~WHfIG 111 (185)
.+.|.+|+..+++... +..+++.-+.|.-|...|...+. +|. -|-=.-..|+..=...+++++ +|-|
T Consensus 10 ~~~i~~~~~~l~~~~~---------~~~~~i~YAvKAN~~~~il~~l~~~g~-G~D~aS~gEl~~al~a~~~~~--i~~~ 77 (380)
T TIGR01047 10 EEKLRKNLEILEHVQQ---------QSGAKVLLALKGFAFWGVFPILREYLD-GCTASGLWEAKLAKEEFGKEI--HVYS 77 (380)
T ss_pred HHHHHHHHHHHHHHHh---------hcCCEEEEEEcccCChHHHHHHHHHCC-cccccCHHHHHHHHHHCCCcE--EEEC
Confidence 4455666666544431 22578999999999877666554 343 222333344433222355444 6668
Q ss_pred cccccc-hHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCC------------CCCccccc
Q 029918 112 NLQSNK-VKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTS------------GEEYGECF 172 (185)
Q Consensus 112 ~LQsNK-vk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis------------~E~sKsG~ 172 (185)
+--+.. ++.++ .. ..+=+|||+.-+++|.+.+.+.+ ...+|+|=||.. +..||.|+
T Consensus 78 ~~k~~~el~~a~---~~-g~~i~idS~~el~~l~~~a~~~~-~~~~i~lRinp~~~~~~~~~~~~~~~~sKFGi 146 (380)
T TIGR01047 78 PAYSEEDVPEII---PL-ADHIIFNSLAQWARYRHLVEGKN-SAVKLGLRINPEYSEVGTDLYNPCGQFSRLGV 146 (380)
T ss_pred CCCCHHHHHHHH---Hc-CCEEEECCHHHHHHHHHHHHhcC-CCceEEEEECCCCCCCCcccccCCCCCCCCCC
Confidence 866544 44444 33 23558999999999999886544 456999999974 34688887
No 45
>COG0019 LysA Diaminopimelate decarboxylase [Amino acid transport and metabolism]
Probab=80.68 E-value=36 Score=31.57 Aligned_cols=134 Identities=14% Similarity=0.126 Sum_probs=87.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHH---cCCcccccccHHHHHHHHhcCCCCceEEE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYE---AGHRCFGENYVQEIVEKAAQLPDDLEWHF 109 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~---~G~r~FGENrvQEl~~K~~~L~~~i~WHf 109 (185)
.+.|.+|+..+..-.. . ...++.-+.|-.|...|..++. .|...-..+=+.-+.+- -.|++ +-||
T Consensus 34 ~~~l~~~~~~~~~a~~-------~--~~~~i~yAvKAn~~~~il~~l~~~g~g~Dv~S~gEl~~al~a--G~~~~-~I~f 101 (394)
T COG0019 34 EATLRRNARELKSAFP-------G--SGAKVFYAVKANSNPAILRLLAEEGSGFDVASLGELELALAA--GFPPE-RIVF 101 (394)
T ss_pred HHHHHHHHHHHHHHhc-------c--CCceEEEEEcCCCCHHHHHHHHHhCCCceecCHHHHHHHHHc--CCChh-hEEE
Confidence 5666666666655442 1 1578999999999999988886 35555444333332221 24433 6788
Q ss_pred Eecccccc-hHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCC------------CCCcccccc---
Q 029918 110 IGNLQSNK-VKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTS------------GEEYGECFI--- 173 (185)
Q Consensus 110 IG~LQsNK-vk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis------------~E~sKsG~~--- 173 (185)
=|+-=+.. +..++ +.-.-.=+|||+.-.++|++.+... +.+|++=||.. ++.||.|+.
T Consensus 102 ~g~~ks~~ei~~a~---e~gi~~i~vdS~~El~~l~~~a~~~---~~~v~lRInP~~~~~th~~~~tg~~~sKFG~~~~~ 175 (394)
T COG0019 102 SGPAKSEEEIAFAL---ELGIKLINVDSEEELERLSAIAPGL---VARVSLRINPGVSAGTHEYIATGGKSSKFGISPEE 175 (394)
T ss_pred CCCCCCHHHHHHHH---HcCCcEEEeCCHHHHHHHHHhcccc---CceEEEEECCCCCCccCccccCCccccccCCCHHH
Confidence 88866655 45555 2222234799999999999887632 57899999864 455788873
Q ss_pred ---------cCCcccccccC
Q 029918 174 ---------KCSWSHSCLLM 184 (185)
Q Consensus 174 ---------~~~~l~l~g~m 184 (185)
+.+++.+.||+
T Consensus 176 a~~~~~~~~~~~~l~~~Glh 195 (394)
T COG0019 176 ALDVLERAAKLLGLELVGLH 195 (394)
T ss_pred HHHHHHHHHhcCCCceEEEE
Confidence 35678888775
No 46
>cd06836 PLPDE_III_ODC_DapDC_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Uncharacterized Proteins with similarity to Ornithine and Diaminopimelate Decarboxylases. This subfamily contains uncharacterized proteins with similarity to ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarbo
Probab=79.60 E-value=47 Score=29.97 Aligned_cols=108 Identities=14% Similarity=0.159 Sum_probs=68.1
Q ss_pred CeEEEEeecCCCHHHHHHHHH-cCCcccccccHHHHHHHHhc-CCCCceEEEEecccccc-hHHHhhcCCCccEEEecCc
Q 029918 60 RIRIVAVSKTKPVSVIRQVYE-AGHRCFGENYVQEIVEKAAQ-LPDDLEWHFIGNLQSNK-VKPLLAGVPNLAMVESVDN 136 (185)
Q Consensus 60 ~V~LvAVSKt~p~e~I~~a~~-~G~r~FGENrvQEl~~K~~~-L~~~i~WHfIG~LQsNK-vk~~~~~~~~~~~IhSVDs 136 (185)
.+++.-..|.-|...|..++. .|. .|==.-..|+..=... ++++ +-.|-|+.=+.. ++.+++ ..+ .| .+||
T Consensus 27 ~~~~~yAvKaN~~~~il~~l~~~G~-g~DvaS~~El~~al~~G~~~~-~Ii~~gp~K~~~~L~~ai~--~gv-~i-~iDS 100 (379)
T cd06836 27 PVLHTFAVKANPLVPVLRLLAEAGA-GAEVASPGELELALAAGFPPE-RIVFDSPAKTRAELREALE--LGV-AI-NIDN 100 (379)
T ss_pred CcEEEEEEecCCCHHHHHHHHHcCC-cEEEcCHHHHHHHHHcCCChh-hEEEeCCCCCHHHHHHHHH--CCC-EE-EECC
Confidence 578888899999888777664 443 2212223333222222 3332 457888876655 555552 223 56 6999
Q ss_pred HHHHHHHHHHHHhcCCCCccEEEEEeCC------------CCCcccccc
Q 029918 137 EKIAGRLNRMVETMGRKPLKVLVQVNTS------------GEEYGECFI 173 (185)
Q Consensus 137 ~kLA~~L~k~a~~~~~~~l~VLIQVNis------------~E~sKsG~~ 173 (185)
+.-.++|.+.+.+......+|+|-||.. +..||.|+.
T Consensus 101 ~~El~~i~~~a~~~~~~~~~v~lRvnp~~~~~~~~~~~~~~~~skFG~~ 149 (379)
T cd06836 101 FQELERIDALVAEFKEASSRIGLRVNPQVGAGKIGALSTATATSKFGVA 149 (379)
T ss_pred HHHHHHHHHHHHHhcCCCceEEEEECCCCCCCCccccccCCCCCCCCcC
Confidence 9999999998865122457999999963 346888874
No 47
>PF02784 Orn_Arg_deC_N: Pyridoxal-dependent decarboxylase, pyridoxal binding domain; InterPro: IPR022644 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region [].; GO: 0003824 catalytic activity; PDB: 2OO0_A 2ON3_A 1D7K_B 3VAB_A 2J66_A 3C5Q_A 2QGH_A 1TWI_B 1TUF_A 3N2O_A ....
Probab=78.99 E-value=37 Score=28.46 Aligned_cols=111 Identities=20% Similarity=0.296 Sum_probs=65.0
Q ss_pred HHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHH-HcCCcccccccHHHHHHHHhc-CCCCceEEEEecccccc-
Q 029918 41 RSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVY-EAGHRCFGENYVQEIVEKAAQ-LPDDLEWHFIGNLQSNK- 117 (185)
Q Consensus 41 ~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~-~~G~r~FGENrvQEl~~K~~~-L~~~i~WHfIG~LQsNK- 117 (185)
..+++++.++.++.. |..+++.-..|.-|...|...+ +.|+ .|==.-..|+.-=... ++ +=+-+|-|+.=+..
T Consensus 3 ~~~~~~~~~~~~~~~--~~~~~i~yA~KaN~~~~vl~~l~~~g~-g~dv~S~~El~~a~~~g~~-~~~Ii~~gp~k~~~~ 78 (251)
T PF02784_consen 3 DRIIERIRAAWKAFL--PYNVKIFYAVKANPNPAVLKILAEEGC-GFDVASPGELELALKAGFP-PDRIIFTGPGKSDEE 78 (251)
T ss_dssp HHHHHHHHHHHHHHT--TT-EEEEEEGGGS--HHHHHHHHHTTC-EEEESSHHHHHHHHHTTTT-GGGEEEECSS--HHH
T ss_pred HHHHHHHHHHHHhcC--CCCcEEEEEECcCCCHHHHHHHHHcCC-ceEEecccchHHHHhhhcc-ccceeEecCcccHHH
Confidence 345566666665554 3379999999999987776655 4553 2222234444322222 22 23568889965554
Q ss_pred hHHHhhcCC-CccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCC
Q 029918 118 VKPLLAGVP-NLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTS 164 (185)
Q Consensus 118 vk~~~~~~~-~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis 164 (185)
++.++ . ....| +|||+.-.+.|.+.+.. .+|+|=||.+
T Consensus 79 l~~a~---~~~~~~i-~vDs~~el~~l~~~~~~-----~~v~lRin~~ 117 (251)
T PF02784_consen 79 LEEAI---ENGVATI-NVDSLEELERLAELAPE-----ARVGLRINPG 117 (251)
T ss_dssp HHHHH---HHTESEE-EESSHHHHHHHHHHHCT-----HEEEEEBE-S
T ss_pred HHHHH---hCCceEE-EeCCHHHHHHHhccCCC-----ceeeEEEeec
Confidence 44445 3 33344 79999999999988742 2889988876
No 48
>TIGR03856 F420_MSMEG_2906 probable F420-dependent oxidoreductase, MSMEG_2906 family. This model describes a small family of enzymes in the bacterial luciferase-like monooxygenase family, which includes F420-dependent enzymes such as N5,N10-methylenetetrahydromethanopterin reductase as well as FMN-dependent enzymes. All members of this family are from species that produce coenzyme F420; SIMBAL analysis suggests that members of this family bind F420 rather than FMN.
Probab=76.87 E-value=6.3 Score=33.95 Aligned_cols=46 Identities=15% Similarity=0.097 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHHcCCcc
Q 029918 38 TALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRC 85 (185)
Q Consensus 38 ~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~~G~r~ 85 (185)
+.+....+.+.+.|+++||+|+++++..-. ..++.+....++|++.
T Consensus 181 ~~~~~~~~~l~~~a~~~Grd~~~i~~~~~~--~~~~~~~~~~~~G~~~ 226 (249)
T TIGR03856 181 ETYRRKSQILDRHCADVGRDPATIERSVSW--PGLDSADAYVAAGVTL 226 (249)
T ss_pred HHHHHHHHHHHHHHHHcCCChhHeEEEecC--CCHHHHHHHHHcCCcE
Confidence 346677888999999999999999887754 3478888888888873
No 49
>TIGR02356 adenyl_thiF thiazole biosynthesis adenylyltransferase ThiF, E. coli subfamily. Members of the HesA/MoeB/ThiF family of proteins (pfam00899) include a number of members encoded in the midst of thiamine biosynthetic operons. This mix of known and putative ThiF proteins shows a deep split in phylogenetic trees, with the Escherichia. coli ThiF and the E. coli MoeB proteins seemingly more closely related than E. coli ThiF and Campylobacter (for example) ThiF. This model represents the more widely distributed clade of ThiF proteins such found in E. coli.
Probab=75.06 E-value=12 Score=31.04 Aligned_cols=67 Identities=15% Similarity=0.251 Sum_probs=50.2
Q ss_pred CCcccccccHHHHHHHHhcCCCCceEEEEe-cccccchHHHhhcCCCcc-EEEecCcHHHHHHHHHHHHhcC
Q 029918 82 GHRCFGENYVQEIVEKAAQLPDDLEWHFIG-NLQSNKVKPLLAGVPNLA-MVESVDNEKIAGRLNRMVETMG 151 (185)
Q Consensus 82 G~r~FGENrvQEl~~K~~~L~~~i~WHfIG-~LQsNKvk~~~~~~~~~~-~IhSVDs~kLA~~L~k~a~~~~ 151 (185)
...+.|.++++.+.++...+.+.++|..+. .+....+..++ ..+| +|-++|+.+....|++.|.+.+
T Consensus 68 ~~~diG~~Ka~~~~~~l~~~np~v~i~~~~~~i~~~~~~~~~---~~~D~Vi~~~d~~~~r~~l~~~~~~~~ 136 (202)
T TIGR02356 68 TEEDVGRPKVEVAAQRLRELNSDIQVTALKERVTAENLELLI---NNVDLVLDCTDNFATRYLINDACVALG 136 (202)
T ss_pred ChhhCCChHHHHHHHHHHHhCCCCEEEEehhcCCHHHHHHHH---hCCCEEEECCCCHHHHHHHHHHHHHcC
Confidence 345779999999999999987777776553 34433345555 4555 5789999999999999998764
No 50
>cd06830 PLPDE_III_ADC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase. This subfamily includes plants and biosynthetic prokaryotic arginine decarboxylases (ADC, EC 4.1.1.19). ADC is involved in the biosynthesis of putrescine, which is the precursor of aliphatic polyamines in many organisms. It catalyzes the decarboxylation of L-arginine to agmatine, which is then hydrolyzed to putrescine by agmatinase. ADC is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC), which are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. Homodimer formation and the presence of both PLP and Mg2+ cofactors may be required for catalytic activity. Prokaryotic ADCs (biodegradative), which are fold type I PLP-dependent enzymes, are not included in this family.
Probab=74.58 E-value=69 Score=29.30 Aligned_cols=145 Identities=10% Similarity=0.055 Sum_probs=86.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHH-HcCC---cccccccHHHHHHHHhc-CCCCceE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVY-EAGH---RCFGENYVQEIVEKAAQ-LPDDLEW 107 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~-~~G~---r~FGENrvQEl~~K~~~-L~~~i~W 107 (185)
.+.|.+|+..+++-+..+..+.|=. ..+++.-..|.-|...|..++ +.|+ ..|==.-..|+.-=... .+++ +.
T Consensus 12 ~~~i~~~~~~l~~af~~~~~~~~~~-~~~~~~YAvKAN~~~~vl~~l~~~G~~~~~g~DvaS~~El~~al~~G~~~~-~i 89 (409)
T cd06830 12 PDILRHRIERLNAAFAKAIEEYGYK-GKYQGVYPIKVNQQREVVEEIVKAGKRYNIGLEAGSKPELLAALALLKTPD-AL 89 (409)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCcC-CceEEEEEeecCCHHHHHHHHHHcCCccceeEEeCCHHHHHHHHhcCCCCC-CE
Confidence 5678888888877775554443322 368899999999997776655 5674 23322334444322221 2233 33
Q ss_pred EEEecccccchHHHhh-cCCC----ccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCC-----------CCcccc
Q 029918 108 HFIGNLQSNKVKPLLA-GVPN----LAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSG-----------EEYGEC 171 (185)
Q Consensus 108 HfIG~LQsNKvk~~~~-~~~~----~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~-----------E~sKsG 171 (185)
.|-++ .|-..-++ .+.. ..++=++||+.-++.|.+.+.+.+ .+.+|+|=||... ..+|.|
T Consensus 90 i~~~g---~K~~~~l~~a~~~~~~g~~v~i~vDs~~EL~~l~~~a~~~~-~~~~v~lRinp~~~~~~~~~~~~~~~sKFG 165 (409)
T cd06830 90 IICNG---YKDDEYIELALLARKLGHNVIIVIEKLSELDLILELAKKLG-VKPLLGVRIKLASKGSGKWQESGGDRSKFG 165 (409)
T ss_pred EEECC---cCCHHHHHHHHhcCcCCceEEEEECCHHHHHHHHHHHHHcC-CCceEEEEEccCCCCCcceeccCCCCCCCC
Confidence 44444 23333221 0011 123448999999999999887654 4679999999753 347888
Q ss_pred cc------------cC-Cccccccc
Q 029918 172 FI------------KC-SWSHSCLL 183 (185)
Q Consensus 172 ~~------------~~-~~l~l~g~ 183 (185)
+. .+ +++++.||
T Consensus 166 i~~~~~~~~~~~~~~~~~~l~l~Gl 190 (409)
T cd06830 166 LTASEILEVVEKLKEAGMLDRLKLL 190 (409)
T ss_pred CCHHHHHHHHHHHHhcCcCCeEEEE
Confidence 62 23 46777776
No 51
>cd01483 E1_enzyme_family Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS.
Probab=73.88 E-value=17 Score=27.84 Aligned_cols=66 Identities=14% Similarity=0.319 Sum_probs=48.5
Q ss_pred CcccccccHHHHHHHHhcCCCCceEEEEe-cccccchHHHhhcCCCcc-EEEecCcHHHHHHHHHHHHhcC
Q 029918 83 HRCFGENYVQEIVEKAAQLPDDLEWHFIG-NLQSNKVKPLLAGVPNLA-MVESVDNEKIAGRLNRMVETMG 151 (185)
Q Consensus 83 ~r~FGENrvQEl~~K~~~L~~~i~WHfIG-~LQsNKvk~~~~~~~~~~-~IhSVDs~kLA~~L~k~a~~~~ 151 (185)
..+.|.++++.+.++...+.+.++|..+- .+........+ ..++ +|-+.|+.+.-..|++.|.+.+
T Consensus 47 ~~~vG~~Ka~~~~~~l~~~~p~v~i~~~~~~~~~~~~~~~~---~~~diVi~~~d~~~~~~~l~~~~~~~~ 114 (143)
T cd01483 47 QADIGKPKAEVAARRLNELNPGVNVTAVPEGISEDNLDDFL---DGVDLVIDAIDNIAVRRALNRACKELG 114 (143)
T ss_pred hhHCCChHHHHHHHHHHHHCCCcEEEEEeeecChhhHHHHh---cCCCEEEECCCCHHHHHHHHHHHHHcC
Confidence 46789999999999999987666666552 34433233444 3455 6889999999999999998754
No 52
>cd06829 PLPDE_III_CANSDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase. Carboxynorspermidine decarboxylase (CANSDC) catalyzes the decarboxylation of carboxynorspermidine, the last step in the biosynthesis of norspermidine. It is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC), which are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. Based on this similarity, CANSDC may require homodimer formation and the presence of the PLP cofactor for its catalytic activity.
Probab=72.43 E-value=70 Score=28.42 Aligned_cols=102 Identities=8% Similarity=-0.053 Sum_probs=65.1
Q ss_pred CCeEEEEeecCCCHHHHHHHHH-cC--CcccccccHHHHHHHHhcCCCCceEEEEecccccc-hHHHhhcCCCccEEEec
Q 029918 59 DRIRIVAVSKTKPVSVIRQVYE-AG--HRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQSNK-VKPLLAGVPNLAMVESV 134 (185)
Q Consensus 59 ~~V~LvAVSKt~p~e~I~~a~~-~G--~r~FGENrvQEl~~K~~~L~~~i~WHfIG~LQsNK-vk~~~~~~~~~~~IhSV 134 (185)
..+++.-+.|.-|...|...+. +| ...--.+-+.-+. ...+. +..+-|+--+.. ++.++ .... .=++
T Consensus 25 ~~~~i~YAvKaN~~~~il~~l~~~G~g~DvaS~~El~~a~---~~~~~--~~i~~~~~k~~~el~~a~---~~~~-~~~~ 95 (346)
T cd06829 25 SGAKILLALKAFSMWSVFPLIREYLDGTTASSLFEARLGR---EEFGG--EVHTYSPAYRDDEIDEIL---RLAD-HIIF 95 (346)
T ss_pred cCCEEEEEEhhcCCHHHHHHHHHhCCccEecCHHHHHHHH---HHCCC--ceEEECCCCCHHHHHHHH---HcCC-EEEE
Confidence 3678999999999988777664 44 3332322233222 12333 555558866543 33345 3322 4489
Q ss_pred CcHHHHHHHHHHHHhcCCCCccEEEEEeCCC------------CCccccc
Q 029918 135 DNEKIAGRLNRMVETMGRKPLKVLVQVNTSG------------EEYGECF 172 (185)
Q Consensus 135 Ds~kLA~~L~k~a~~~~~~~l~VLIQVNis~------------E~sKsG~ 172 (185)
||+.-.++|.+.+.+ .+.+|+|-||.+. ..+|.|+
T Consensus 96 Ds~~EL~~l~~~~~~---~~~~v~lRvnp~~~~~~~~~~~~~~~~sKFG~ 142 (346)
T cd06829 96 NSLSQLERFKDRAKA---AGISVGLRINPEYSEVETDLYDPCAPGSRLGV 142 (346)
T ss_pred CCHHHHHHHHHHHhc---cCCeEEEEECCCCCCCCCceecCCCCCCCCCC
Confidence 999999999998763 3569999999753 3678886
No 53
>cd01487 E1_ThiF_like E1_ThiF_like. Member of superfamily of activating enzymes (E1) of the ubiquitin-like proteins. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like substrate, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of the substrate. The exact function of this family is unknown.
Probab=68.92 E-value=22 Score=28.75 Aligned_cols=87 Identities=18% Similarity=0.248 Sum_probs=59.8
Q ss_pred CCeEEEEeecCCCHHHHHHHHHcCCcccccccHHHHHHHHhcCCCCceEE-EEecccccchHHHhhcCCCcc-EEEecCc
Q 029918 59 DRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWH-FIGNLQSNKVKPLLAGVPNLA-MVESVDN 136 (185)
Q Consensus 59 ~~V~LvAVSKt~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~~i~WH-fIG~LQsNKvk~~~~~~~~~~-~IhSVDs 136 (185)
..++|+=.-+.-+..--+..| ...+.|.++++.+..++..+.+.+++. +-..+....+..++ ..+| +|.++|+
T Consensus 24 g~i~lvD~D~v~~sNl~Rq~~--~~~~vg~~Ka~~~~~~l~~lnp~v~i~~~~~~~~~~~~~~~l---~~~DlVi~~~d~ 98 (174)
T cd01487 24 GNLKLVDFDVVEPSNLNRQQY--FLSQIGEPKVEALKENLREINPFVKIEAINIKIDENNLEGLF---GDCDIVVEAFDN 98 (174)
T ss_pred CeEEEEeCCEEcCcchhcccc--cHhhCCChHHHHHHHHHHHHCCCCEEEEEEeecChhhHHHHh---cCCCEEEECCCC
Confidence 356766655533333333332 345789999999999999986666654 34566666666777 5676 5788999
Q ss_pred HHHHHHHHHHHHhc
Q 029918 137 EKIAGRLNRMVETM 150 (185)
Q Consensus 137 ~kLA~~L~k~a~~~ 150 (185)
...-..+++.+.+.
T Consensus 99 ~~~r~~i~~~~~~~ 112 (174)
T cd01487 99 AETKAMLAESLLGN 112 (174)
T ss_pred HHHHHHHHHHHHHH
Confidence 99988888877654
No 54
>cd01485 E1-1_like Ubiquitin activating enzyme (E1), repeat 1-like. E1, a highly conserved small protein present universally in eukaryotic cells, is part of cascade to attach ubiquitin (Ub) covalently to substrate proteins. This cascade consists of activating (E1), conjugating (E2), and/or ligating (E3) enzymes and then targets them for degradation by the 26S proteasome. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and ubiquitin's C-terminus. The E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. A set of novel molecules with a structural similarity to Ub, called Ub-like proteins (Ubls), have similar conjugation cascades. In contrast to ubiquitin-E1, which is a single-chain protein with a weakly conserved two-fold repeat, many of the Ubls-E1are a heterodimer where each subunit corresponds to one half of a single-chain E1. This CD represents the family homol
Probab=62.29 E-value=33 Score=28.33 Aligned_cols=65 Identities=11% Similarity=0.195 Sum_probs=49.3
Q ss_pred cccccccHHHHHHHHhcCCCCceEEEEe-ccc--ccchHHHhhcCCCccE-EEecCcHHHHHHHHHHHHhcC
Q 029918 84 RCFGENYVQEIVEKAAQLPDDLEWHFIG-NLQ--SNKVKPLLAGVPNLAM-VESVDNEKIAGRLNRMVETMG 151 (185)
Q Consensus 84 r~FGENrvQEl~~K~~~L~~~i~WHfIG-~LQ--sNKvk~~~~~~~~~~~-IhSVDs~kLA~~L~k~a~~~~ 151 (185)
.+.|.++++.+.++...+.++++.+.+- .+. .+...... ..+++ |-+.|+......|++.|.+.+
T Consensus 70 ~~iG~~Ka~~~~~~L~~lNp~v~i~~~~~~~~~~~~~~~~~~---~~~dvVi~~~d~~~~~~~ln~~c~~~~ 138 (198)
T cd01485 70 SNSGMNRAAASYEFLQELNPNVKLSIVEEDSLSNDSNIEEYL---QKFTLVIATEENYERTAKVNDVCRKHH 138 (198)
T ss_pred hhcCchHHHHHHHHHHHHCCCCEEEEEecccccchhhHHHHH---hCCCEEEECCCCHHHHHHHHHHHHHcC
Confidence 6789999999999999997777766653 333 23455566 56764 778899999999999998764
No 55
>cd06831 PLPDE_III_ODC_like_AZI Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase-like Antizyme Inhibitor. Antizyme inhibitor (AZI) is homologous to the fold type III PLP-dependent enzyme ODC but does not retain any decarboxylase activity. Like ODC, AZI is presumed to exist as a homodimer. Antizyme is a regulatory protein that binds directly to the ODC monomer to block its active site, leading to its degradation by the 26S proteasome. AZI binds to Antizyme with a higher affinity than ODC, preventing the formation of the Antizyme-ODC complex. Thus, AZI blocks the ability of Antizyme to promote ODC degradation, which leads to increased ODC enzymatic activity and polyamine levels. AZI also prevents the degradation of other proteins regulated by Antizyme, such as cyclin D1.
Probab=60.57 E-value=1.4e+02 Score=27.41 Aligned_cols=119 Identities=11% Similarity=0.098 Sum_probs=73.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHH-cCCcccccccHHHHHHHH-hcCCCCceEEEE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYE-AGHRCFGENYVQEIVEKA-AQLPDDLEWHFI 110 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~-~G~r~FGENrvQEl~~K~-~~L~~~i~WHfI 110 (185)
.+.|.+++..+++.+ | .+++.=..|.-|...|..++. .|. -|==.-..|+..=. .-+++ =+-.|-
T Consensus 20 ~~~i~~~~~~l~~~l----------p-~~~~~YAvKaN~~~~il~~l~~~G~-g~DvaS~gEl~~al~~G~~~-~~Iif~ 86 (394)
T cd06831 20 LGKIVKKHSQWQTVM----------A-QIKPFYTVRCNSTPAVLEILAALGT-GFACSSKNEMALVQELGVSP-ENIIYT 86 (394)
T ss_pred HHHHHHHHHHHHHHC----------C-CCeEEeeeccCCCHHHHHHHHHcCC-CeEeCCHHHHHHHHhcCCCc-CCEEEe
Confidence 555666666665554 3 578888999999988777665 442 23222233332211 12332 246888
Q ss_pred ecccccc-hHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCC------Cccccc
Q 029918 111 GNLQSNK-VKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGE------EYGECF 172 (185)
Q Consensus 111 G~LQsNK-vk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E------~sKsG~ 172 (185)
|+.=+.+ ++.+++ ..+..| ++||+.-+++|.+.+. ..+|+|-||.... .+|.|+
T Consensus 87 gp~K~~~~l~~a~~--~Gv~~i-~vDS~~El~~i~~~~~-----~~~v~lRi~~~~~~~~~~~~~KFGi 147 (394)
T cd06831 87 NPCKQASQIKYAAK--VGVNIM-TCDNEIELKKIARNHP-----NAKLLLHIATEDNIGGEEMNMKFGT 147 (394)
T ss_pred CCCCCHHHHHHHHH--CCCCEE-EECCHHHHHHHHHhCC-----CCcEEEEEeccCCCCCCccCCCCCC
Confidence 9875555 666662 223334 8999999999987542 3578888887533 268886
No 56
>TIGR02355 moeB molybdopterin synthase sulfurylase MoeB. This model describes the molybdopterin biosynthesis protein MoeB in E. coli and related species. The enzyme covalently modifies the molybdopterin synthase MoaD by sulfurylation. This enzyme is closely related to ThiF, a thiamine biosynthesis enzyme that modifies ThiS by an analogous adenylation. Both MoeB and ThiF belong to the HesA/MoeB/ThiF family (pfam00899).
Probab=58.32 E-value=36 Score=29.09 Aligned_cols=65 Identities=17% Similarity=0.257 Sum_probs=49.1
Q ss_pred cccccccHHHHHHHHhcCCCCceEEE-EecccccchHHHhhcCCCcc-EEEecCcHHHHHHHHHHHHhcC
Q 029918 84 RCFGENYVQEIVEKAAQLPDDLEWHF-IGNLQSNKVKPLLAGVPNLA-MVESVDNEKIAGRLNRMVETMG 151 (185)
Q Consensus 84 r~FGENrvQEl~~K~~~L~~~i~WHf-IG~LQsNKvk~~~~~~~~~~-~IhSVDs~kLA~~L~k~a~~~~ 151 (185)
.+.|.++++.+.++...+.+++.-.. -..+....+..++ ..+| +|.+.|+......|++.|.+.+
T Consensus 73 ~diG~~Ka~~a~~~l~~inp~v~i~~~~~~i~~~~~~~~~---~~~DlVvd~~D~~~~r~~ln~~~~~~~ 139 (240)
T TIGR02355 73 ANIGQPKVESAKDALTQINPHIAINPINAKLDDAELAALI---AEHDIVVDCTDNVEVRNQLNRQCFAAK 139 (240)
T ss_pred hhCCCcHHHHHHHHHHHHCCCcEEEEEeccCCHHHHHHHh---hcCCEEEEcCCCHHHHHHHHHHHHHcC
Confidence 47899999999999998866544333 3466655566666 4566 5789999999999999998764
No 57
>PRK05690 molybdopterin biosynthesis protein MoeB; Provisional
Probab=54.81 E-value=38 Score=28.96 Aligned_cols=66 Identities=15% Similarity=0.241 Sum_probs=49.6
Q ss_pred CcccccccHHHHHHHHhcCCCCceE-EEEecccccchHHHhhcCCCcc-EEEecCcHHHHHHHHHHHHhcC
Q 029918 83 HRCFGENYVQEIVEKAAQLPDDLEW-HFIGNLQSNKVKPLLAGVPNLA-MVESVDNEKIAGRLNRMVETMG 151 (185)
Q Consensus 83 ~r~FGENrvQEl~~K~~~L~~~i~W-HfIG~LQsNKvk~~~~~~~~~~-~IhSVDs~kLA~~L~k~a~~~~ 151 (185)
..+.|.++++.+.++...+.++++- -+-..++...+..++ ..+| +|.+.|+.+....|++.|.+.+
T Consensus 80 ~~dvG~~Ka~~a~~~l~~lnp~v~i~~~~~~i~~~~~~~~~---~~~DiVi~~~D~~~~r~~ln~~~~~~~ 147 (245)
T PRK05690 80 DATIGQPKVESARAALARINPHIAIETINARLDDDELAALI---AGHDLVLDCTDNVATRNQLNRACFAAK 147 (245)
T ss_pred hhhCCChHHHHHHHHHHHHCCCCEEEEEeccCCHHHHHHHH---hcCCEEEecCCCHHHHHHHHHHHHHhC
Confidence 3578999999999999988655432 234566665566666 5566 5789999999999999998753
No 58
>cd00757 ThiF_MoeB_HesA_family ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD and ThiS, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS. MoeB, as the MPT synthase (MoaE/MoaD complex) sulfurase, is involved in the biosynthesis of the molybdenum cofactor, a derivative of the tricyclic pterin, molybdopterin (MPT). ThiF catalyzes the adenylation of ThiS, as part of the biosynthesis pathway of thiamin pyrophosphate (vitamin B1).
Probab=53.52 E-value=49 Score=27.66 Aligned_cols=65 Identities=15% Similarity=0.240 Sum_probs=47.3
Q ss_pred cccccccHHHHHHHHhcCCCCceEEEEe-cccccchHHHhhcCCCcc-EEEecCcHHHHHHHHHHHHhcC
Q 029918 84 RCFGENYVQEIVEKAAQLPDDLEWHFIG-NLQSNKVKPLLAGVPNLA-MVESVDNEKIAGRLNRMVETMG 151 (185)
Q Consensus 84 r~FGENrvQEl~~K~~~L~~~i~WHfIG-~LQsNKvk~~~~~~~~~~-~IhSVDs~kLA~~L~k~a~~~~ 151 (185)
.+.|.++++.+.++...+.+++++..+- .+-...+..++ ..+| +|-++|+.+.-..|++.|.+.+
T Consensus 70 ~diG~~Ka~~~~~~l~~~np~~~i~~~~~~i~~~~~~~~~---~~~DvVi~~~d~~~~r~~l~~~~~~~~ 136 (228)
T cd00757 70 ADVGQPKAEAAAERLRAINPDVEIEAYNERLDAENAEELI---AGYDLVLDCTDNFATRYLINDACVKLG 136 (228)
T ss_pred hhCCChHHHHHHHHHHHhCCCCEEEEecceeCHHHHHHHH---hCCCEEEEcCCCHHHHHHHHHHHHHcC
Confidence 3689999999999999986655554442 33233455566 4455 5789999999999999998764
No 59
>cd01492 Aos1_SUMO Ubiquitin activating enzyme (E1) subunit Aos1. Aos1 is part of the heterodimeric activating enzyme (E1), specific for the SUMO family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. The E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by SUMO family of ubiquitin-like proteins (Ublps) is involved in cell division, nuclear transport, the stress response and signal transduction. Aos1 contains part of the adenylation domain.
Probab=52.51 E-value=69 Score=26.44 Aligned_cols=65 Identities=12% Similarity=0.234 Sum_probs=47.6
Q ss_pred CcccccccHHHHHHHHhcCCCCceEEEE-ecccccchHHHhhcCCCccE-EEecCcHHHHHHHHHHHHhcC
Q 029918 83 HRCFGENYVQEIVEKAAQLPDDLEWHFI-GNLQSNKVKPLLAGVPNLAM-VESVDNEKIAGRLNRMVETMG 151 (185)
Q Consensus 83 ~r~FGENrvQEl~~K~~~L~~~i~WHfI-G~LQsNKvk~~~~~~~~~~~-IhSVDs~kLA~~L~k~a~~~~ 151 (185)
..+.|.++++-+.++...+.++++.+.+ ..+. ....... ..+++ |-+.|+.+....|++.|.+.+
T Consensus 69 ~~diG~~Ka~a~~~~L~~lNp~v~i~~~~~~~~-~~~~~~~---~~~dvVi~~~~~~~~~~~ln~~c~~~~ 135 (197)
T cd01492 69 AEDLGQNRAEASLERLRALNPRVKVSVDTDDIS-EKPEEFF---SQFDVVVATELSRAELVKINELCRKLG 135 (197)
T ss_pred HHHcCchHHHHHHHHHHHHCCCCEEEEEecCcc-ccHHHHH---hCCCEEEECCCCHHHHHHHHHHHHHcC
Confidence 3577999999999999999776555443 3333 2344555 46775 668899999999999998764
No 60
>PRK08644 thiamine biosynthesis protein ThiF; Provisional
Probab=51.20 E-value=59 Score=27.24 Aligned_cols=87 Identities=18% Similarity=0.252 Sum_probs=57.4
Q ss_pred CCeEEEEeecCCCHHHHHHHHHcCCcccccccHHHHHHHHhcCCCCceEEEE-ecccccchHHHhhcCCCcc-EEEecCc
Q 029918 59 DRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFI-GNLQSNKVKPLLAGVPNLA-MVESVDN 136 (185)
Q Consensus 59 ~~V~LvAVSKt~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~~i~WHfI-G~LQsNKvk~~~~~~~~~~-~IhSVDs 136 (185)
..++|+=-.+--+..--+..| ...+.|.+++..+..++..+.+++++..+ ..+....+..++ ..+| +|..+|+
T Consensus 53 g~i~lvD~D~ve~sNL~Rq~~--~~~dvG~~Ka~~a~~~l~~lnp~v~v~~~~~~i~~~~~~~~~---~~~DvVI~a~D~ 127 (212)
T PRK08644 53 GNLKLVDFDVVEPSNLNRQQY--FISQIGMPKVEALKENLLEINPFVEIEAHNEKIDEDNIEELF---KDCDIVVEAFDN 127 (212)
T ss_pred CeEEEEeCCEeccccccccEe--ehhhCCChHHHHHHHHHHHHCCCCEEEEEeeecCHHHHHHHH---cCCCEEEECCCC
Confidence 345655544433333222222 23468999999999999988666766543 456665565666 5677 4678899
Q ss_pred HHHHHHHHHHHHhc
Q 029918 137 EKIAGRLNRMVETM 150 (185)
Q Consensus 137 ~kLA~~L~k~a~~~ 150 (185)
...-..+++.|.+.
T Consensus 128 ~~~r~~l~~~~~~~ 141 (212)
T PRK08644 128 AETKAMLVETVLEH 141 (212)
T ss_pred HHHHHHHHHHHHHh
Confidence 99888898888765
No 61
>TIGR02354 thiF_fam2 thiamine biosynthesis protein ThiF, family 2. Members of the HesA/MoeB/ThiF family of proteins (pfam00899) include a number of members encoded in the midst of thiamine biosynthetic operons. This mix of known and putative ThiF proteins shows a deep split in phylogenetic trees, with one the E. coli ThiF and the E. coli MoeB proteins seemingly more closely related than E. coli ThiF and Campylobacter (for example) ThiF. This model represents the divergent clade of putative ThiF proteins such found in Campylobacter.
Probab=48.55 E-value=79 Score=26.28 Aligned_cols=97 Identities=15% Similarity=0.197 Sum_probs=61.5
Q ss_pred HHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHHcCCcccccccHHHHHHHHhcCCCCceEEEE-ecccccchHHHhhcC
Q 029918 47 VHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFI-GNLQSNKVKPLLAGV 125 (185)
Q Consensus 47 I~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~~i~WHfI-G~LQsNKvk~~~~~~ 125 (185)
|...+.++|- ..++|+=-..--+..--+.. .+..++|.++++.+.++...+.+.+.+..+ ..+....+..++
T Consensus 36 ia~~La~~Gv--g~i~lvD~D~ve~sNL~Rq~--~~~~~iG~~Ka~~~~~~l~~inp~~~i~~~~~~i~~~~~~~~~--- 108 (200)
T TIGR02354 36 VAINLARAGI--GKLILVDFDVVEPSNLNRQQ--YKASQVGEPKTEALKENISEINPYTEIEAYDEKITEENIDKFF--- 108 (200)
T ss_pred HHHHHHHcCC--CEEEEECCCEEccccccccc--CChhhCCCHHHHHHHHHHHHHCCCCEEEEeeeeCCHhHHHHHh---
Confidence 3344445553 34666544433333322222 244678999999999999988666666633 566666677777
Q ss_pred CCcc-EEEecCcHHHHHHHHHHHHhc
Q 029918 126 PNLA-MVESVDNEKIAGRLNRMVETM 150 (185)
Q Consensus 126 ~~~~-~IhSVDs~kLA~~L~k~a~~~ 150 (185)
..+| +|..+|+...-..|.+.+...
T Consensus 109 ~~~DlVi~a~Dn~~~k~~l~~~~~~~ 134 (200)
T TIGR02354 109 KDADIVCEAFDNAEAKAMLVNAVLEK 134 (200)
T ss_pred cCCCEEEECCCCHHHHHHHHHHHHHH
Confidence 5676 477889999887877776543
No 62
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=48.38 E-value=17 Score=25.39 Aligned_cols=28 Identities=18% Similarity=0.343 Sum_probs=24.9
Q ss_pred CCeEEEEeecCCCHHHHHHHHHcCCccc
Q 029918 59 DRIRIVAVSKTKPVSVIRQVYEAGHRCF 86 (185)
Q Consensus 59 ~~V~LvAVSKt~p~e~I~~a~~~G~r~F 86 (185)
..+.+|.+|.....+.+..++++|...|
T Consensus 70 ~~~~ii~~t~~~~~~~~~~~~~~g~~~~ 97 (112)
T PF00072_consen 70 PSIPIIVVTDEDDSDEVQEALRAGADDY 97 (112)
T ss_dssp TTSEEEEEESSTSHHHHHHHHHTTESEE
T ss_pred ccccEEEecCCCCHHHHHHHHHCCCCEE
Confidence 5789999999999999999999998754
No 63
>COG1210 GalU UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]
Probab=48.25 E-value=23 Score=32.06 Aligned_cols=114 Identities=17% Similarity=0.219 Sum_probs=67.4
Q ss_pred CeEEEEeecCCCHHH------------HHHHHHcCCcccc---------------cccH----------HHHHHHHhcCC
Q 029918 60 RIRIVAVSKTKPVSV------------IRQVYEAGHRCFG---------------ENYV----------QEIVEKAAQLP 102 (185)
Q Consensus 60 ~V~LvAVSKt~p~e~------------I~~a~~~G~r~FG---------------ENrv----------QEl~~K~~~L~ 102 (185)
.-|++.+||+.|-|. +.+|+++|+.++. -++- .++.++...+|
T Consensus 15 GTRfLPATKaiPKEMLPIvdKP~IqYiVeEa~~aGIe~i~iVTgr~K~~IeDhFD~s~ELE~~L~~~~K~~~L~~v~~i~ 94 (291)
T COG1210 15 GTRFLPATKAIPKEMLPIVDKPLIQYIVEEAVAAGIEEILIVTGRGKRAIEDHFDTSYELENTLEKRGKRELLEEVRSIP 94 (291)
T ss_pred ccccccccccCchhhccccCchhHHHHHHHHHHcCCCEEEEEecCCcchHHHhCcCcHHHHHHHHHhCHHHHHHHHHhcc
Confidence 358899999999874 5789999998653 2221 13444455566
Q ss_pred CCceEEEEeccccc-------chHHHhhcCCCccEE---EecC--cHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCccc
Q 029918 103 DDLEWHFIGNLQSN-------KVKPLLAGVPNLAMV---ESVD--NEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGE 170 (185)
Q Consensus 103 ~~i~WHfIG~LQsN-------Kvk~~~~~~~~~~~I---hSVD--s~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKs 170 (185)
+.+.-|||-+=.-. -++.+++. +.|.++ +=++ ..-|++.++.+.+ .+. --|.+|=.-..+.+|+
T Consensus 95 ~~~~i~~vRQ~e~~GLGhAVl~A~~~vg~-EpFaVlL~Ddl~~~~~~~l~qmi~~ye~-~g~--svi~v~ev~~e~v~kY 170 (291)
T COG1210 95 PLVTISFVRQKEPLGLGHAVLCAKPFVGD-EPFAVLLPDDLVDSEKPCLKQMIELYEE-TGG--SVIGVEEVPPEDVSKY 170 (291)
T ss_pred cCceEEEEecCCCCcchhHHHhhhhhcCC-CceEEEeCCeeecCCchHHHHHHHHHHH-hCC--cEEEEEECCHHHCccc
Confidence 77889998654433 23445532 223322 1123 3445555555544 443 2466666667788999
Q ss_pred ccccCCc
Q 029918 171 CFIKCSW 177 (185)
Q Consensus 171 G~~~~~~ 177 (185)
|+..|-.
T Consensus 171 Gvi~~g~ 177 (291)
T COG1210 171 GVIDPGE 177 (291)
T ss_pred ceEecCc
Confidence 9877443
No 64
>PRK05600 thiamine biosynthesis protein ThiF; Validated
Probab=47.86 E-value=55 Score=29.92 Aligned_cols=67 Identities=16% Similarity=0.228 Sum_probs=52.1
Q ss_pred CCcccccccHHHHHHHHhcCCCCceEEEE-ecccccchHHHhhcCCCcc-EEEecCcHHHHHHHHHHHHhcC
Q 029918 82 GHRCFGENYVQEIVEKAAQLPDDLEWHFI-GNLQSNKVKPLLAGVPNLA-MVESVDNEKIAGRLNRMVETMG 151 (185)
Q Consensus 82 G~r~FGENrvQEl~~K~~~L~~~i~WHfI-G~LQsNKvk~~~~~~~~~~-~IhSVDs~kLA~~L~k~a~~~~ 151 (185)
+-.++|.+++.-+.+++..+.++++|..+ ..+...-+..++ ..+| +|...|+++.-..|++.|.+.+
T Consensus 88 ~~~diG~~Ka~~~~~~l~~~np~v~i~~~~~~i~~~~~~~~~---~~~DlVid~~Dn~~~r~~in~~~~~~~ 156 (370)
T PRK05600 88 GASDVGRPKVEVAAERLKEIQPDIRVNALRERLTAENAVELL---NGVDLVLDGSDSFATKFLVADAAEITG 156 (370)
T ss_pred ChhHCCCHHHHHHHHHHHHHCCCCeeEEeeeecCHHHHHHHH---hCCCEEEECCCCHHHHHHHHHHHHHcC
Confidence 34578999999999999999777887766 466555566666 5566 4778999999889999998764
No 65
>PLN02439 arginine decarboxylase
Probab=44.75 E-value=3.1e+02 Score=26.80 Aligned_cols=137 Identities=17% Similarity=0.092 Sum_probs=81.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHH-HHcCCc-ccc--cccHHHHHHHHhcC-CCCceEE
Q 029918 34 GVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQV-YEAGHR-CFG--ENYVQEIVEKAAQL-PDDLEWH 108 (185)
Q Consensus 34 ~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a-~~~G~r-~FG--ENrvQEl~~K~~~L-~~~i~WH 108 (185)
+.|.+|+..+.+-...+..+.+ .+...+.+=..|.-|-..|.+. .++|.. .+| -.-..|+..=.... +.+...-
T Consensus 7 d~l~~ri~~L~~aF~~ai~~~~-y~~~~~~~YavKaN~~~~Vl~~l~~~G~~~~~GlEa~S~~EL~~al~~~~~~~~~~i 85 (559)
T PLN02439 7 DVLKNRLESLQSAFDYAIQSQG-YNSHYQGVFPVKCNQDRFLVEDIVKFGSPFRFGLEAGSKPELLLAMSCLCKGSPDAF 85 (559)
T ss_pred HHHHHHHHHHHHHHHHHHHhcc-cCCCeEEEEEeecCCCHHHHHHHHHcCCccCceeEEeCHHHHHHHHHcCCCCCCCeE
Confidence 4577888888887766655544 3456899999999887666555 456743 133 23344554433332 1112233
Q ss_pred EEecccccc--hHHHhhc-CCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeC-----------CCCCccccc
Q 029918 109 FIGNLQSNK--VKPLLAG-VPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNT-----------SGEEYGECF 172 (185)
Q Consensus 109 fIG~LQsNK--vk~~~~~-~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNi-----------s~E~sKsG~ 172 (185)
++|+=-+.+ ++.++.. .-.+.++=.|||+.-.+.|...+.+.+ .+.+|.|=||. +++.+|+|+
T Consensus 86 i~~NG~Kd~e~i~~Al~~~~lG~~~~IviDs~~EL~~I~~~a~~l~-~~p~IglRi~~~~~~~~~~~~tgg~~sKFGl 162 (559)
T PLN02439 86 LICNGYKDAEYVSLALLARKLGLNTVIVLEQEEELDLVIEASQRLG-VRPVIGVRAKLRTKHSGHFGSTSGEKGKFGL 162 (559)
T ss_pred EECCCCCCHHHHHHHHHhhhCCCCeEEEECCHHHHHHHHHHHHHcC-CCceEEEEEecCCCCCCCccccCCCCCCCCC
Confidence 466653332 2222100 001233448899999999998887665 34578888764 567889997
No 66
>PF00899 ThiF: ThiF family; InterPro: IPR000594 Ubiquitin-activating enzyme (E1 enzyme) [, ] activates ubiquitin by first adenylating with ATP its C-terminal glycine residue and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thiolester and free AMP. Later the ubiquitin moiety is transferred to a cysteine residue on one of the many forms of ubiquitin- conjugating enzymes (E2). The family of ubiquitin-activating enzymes shares in its catalytic domain significant similarity with a large family of NAD/FAD-binding proteins. This domain is based on the common NAD/FAD-binding fold and finds members of several families, including UBA ubiquitin activating enzymes; the hesA/moeB/thiF family; NADH peroxidases; the LDH family; sarcosin oxidase; phytoene dehydrogenases; alanine dehydrogenases; hydroxyacyl-CoA dehydrogenases and many other NAD/FAD dependent dehydrogenases and oxidases.; GO: 0003824 catalytic activity; PDB: 1ZKM_D 1ZUD_3 1ZFN_D 1R4M_G 2NVU_A 1R4N_C 3DBR_A 3DBH_C 3DBL_G 1YOV_A ....
Probab=40.03 E-value=1.3e+02 Score=22.78 Aligned_cols=65 Identities=20% Similarity=0.334 Sum_probs=47.9
Q ss_pred cccccccHHHHHHHHhcCCCCceEEEE-ecccccchHHHhhcCCCcc-EEEecCcHHHHHHHHHHHHhcC
Q 029918 84 RCFGENYVQEIVEKAAQLPDDLEWHFI-GNLQSNKVKPLLAGVPNLA-MVESVDNEKIAGRLNRMVETMG 151 (185)
Q Consensus 84 r~FGENrvQEl~~K~~~L~~~i~WHfI-G~LQsNKvk~~~~~~~~~~-~IhSVDs~kLA~~L~k~a~~~~ 151 (185)
.++|++++.-+.+++..+.+.+++.-+ -.+.......++ ..++ +|.++|+.+.-..|++.|.+.+
T Consensus 51 ~~vG~~Ka~~~~~~l~~~np~~~v~~~~~~~~~~~~~~~~---~~~d~vi~~~d~~~~~~~l~~~~~~~~ 117 (135)
T PF00899_consen 51 EDVGKNKAEAAKERLQEINPDVEVEAIPEKIDEENIEELL---KDYDIVIDCVDSLAARLLLNEICREYG 117 (135)
T ss_dssp GGTTSBHHHHHHHHHHHHSTTSEEEEEESHCSHHHHHHHH---HTSSEEEEESSSHHHHHHHHHHHHHTT
T ss_pred ccchhHHHHHHHHHHHHhcCceeeeeeecccccccccccc---cCCCEEEEecCCHHHHHHHHHHHHHcC
Confidence 367999999999999988555554433 444455566666 3444 6889999999999999998764
No 67
>PRK05354 arginine decarboxylase; Provisional
Probab=39.39 E-value=4e+02 Score=26.52 Aligned_cols=134 Identities=14% Similarity=0.101 Sum_probs=83.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHH-HHHcCCcc-ccc--ccHHHHHHHHhcC-CCCceE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQ-VYEAGHRC-FGE--NYVQEIVEKAAQL-PDDLEW 107 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~-a~~~G~r~-FGE--NrvQEl~~K~~~L-~~~i~W 107 (185)
.+.|.+|+..+++-...+..+.|-. ...+++-..|.-|-..|.+ +.++|.+. +|= .-.-|+..=.... +++...
T Consensus 71 ~~~L~~ri~~L~~aF~~a~~~~~y~-g~~~~~YAiKaN~~~~Vl~~l~~~G~~~~~GlEv~S~~EL~~AL~~g~~~~~lI 149 (634)
T PRK05354 71 PDILQDRVRSLNAAFKKAIEEYGYQ-GDYRGVYPIKVNQQRRVVEEIVASGKPYNLGLEAGSKPELMAVLALAGDPGALI 149 (634)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhccC-CCceEEEEeccCChHHHHHHHHHcCCCCceeEEECCHHHHHHHHHcCCCCCcEE
Confidence 6778888998888887777766644 4689999999988866655 55678542 342 2234443333222 222223
Q ss_pred EEEecccccc----hHHHhhcCC-CccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCC-----------CCCcccc
Q 029918 108 HFIGNLQSNK----VKPLLAGVP-NLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTS-----------GEEYGEC 171 (185)
Q Consensus 108 HfIG~LQsNK----vk~~~~~~~-~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis-----------~E~sKsG 171 (185)
.+=| .| ++.++.... ...++=.|||+.-.+.|.+.+.+.+ ....|.|=||.+ |+.||.|
T Consensus 150 i~NG----~Kd~e~I~~Al~~~~lG~~v~ivIDs~~EL~~I~~~a~~~~-~~p~IglRi~~~~~~~g~~~~tgG~~SKFG 224 (634)
T PRK05354 150 VCNG----YKDREYIRLALIGRKLGHKVFIVIEKLSELELILEEAKELG-VKPRLGVRARLASQGSGKWQSSGGEKSKFG 224 (634)
T ss_pred EcCC----CCCHHHHHHHHHhHhcCCCEEEEECCHHHHHHHHHHHHhcC-CCCeEEEEEecCCCCCCCcccCCCCCCCCC
Confidence 3434 34 333320000 1235568999999999998887665 456888988764 6778999
Q ss_pred c
Q 029918 172 F 172 (185)
Q Consensus 172 ~ 172 (185)
+
T Consensus 225 l 225 (634)
T PRK05354 225 L 225 (634)
T ss_pred C
Confidence 7
No 68
>PRK07878 molybdopterin biosynthesis-like protein MoeZ; Validated
Probab=38.08 E-value=1.2e+02 Score=27.75 Aligned_cols=67 Identities=13% Similarity=0.140 Sum_probs=50.0
Q ss_pred CCcccccccHHHHHHHHhcCCCCceEE-EEecccccchHHHhhcCCCcc-EEEecCcHHHHHHHHHHHHhcC
Q 029918 82 GHRCFGENYVQEIVEKAAQLPDDLEWH-FIGNLQSNKVKPLLAGVPNLA-MVESVDNEKIAGRLNRMVETMG 151 (185)
Q Consensus 82 G~r~FGENrvQEl~~K~~~L~~~i~WH-fIG~LQsNKvk~~~~~~~~~~-~IhSVDs~kLA~~L~k~a~~~~ 151 (185)
+..+.|.++++-+.++...+.++++-. +-+.+...-+..++ ..+| +|-+.|+...-..||+.|.+.+
T Consensus 89 ~~~diG~~Ka~~a~~~l~~~np~v~i~~~~~~i~~~~~~~~~---~~~D~Vvd~~d~~~~r~~ln~~~~~~~ 157 (392)
T PRK07878 89 GQSDVGRSKAQSARDSIVEINPLVNVRLHEFRLDPSNAVELF---SQYDLILDGTDNFATRYLVNDAAVLAG 157 (392)
T ss_pred ChhcCCChHHHHHHHHHHHhCCCcEEEEEeccCChhHHHHHH---hcCCEEEECCCCHHHHHHHHHHHHHcC
Confidence 446789999999999999986654432 33566665566677 5666 4778999999889999998754
No 69
>PRK08762 molybdopterin biosynthesis protein MoeB; Validated
Probab=37.69 E-value=1.2e+02 Score=27.44 Aligned_cols=88 Identities=20% Similarity=0.268 Sum_probs=59.9
Q ss_pred CeEEEEeecCCCHHHHHHHHHcCCc------------------------ccccccHHHHHHHHhcCCCCceEEEE-eccc
Q 029918 60 RIRIVAVSKTKPVSVIRQVYEAGHR------------------------CFGENYVQEIVEKAAQLPDDLEWHFI-GNLQ 114 (185)
Q Consensus 60 ~V~LvAVSKt~p~e~I~~a~~~G~r------------------------~FGENrvQEl~~K~~~L~~~i~WHfI-G~LQ 114 (185)
.|-++++ -......+..+..+|+. ++|.++++.+.+++..+.+++.+..+ ..+.
T Consensus 137 ~VlvvG~-GG~Gs~ia~~La~~Gvg~i~lvD~d~v~~sNl~Rq~l~~~~diG~~Ka~~~~~~l~~~np~v~v~~~~~~~~ 215 (376)
T PRK08762 137 RVLLIGA-GGLGSPAALYLAAAGVGTLGIVDHDVVDRSNLQRQILHTEDRVGQPKVDSAAQRLAALNPDVQVEAVQERVT 215 (376)
T ss_pred cEEEECC-CHHHHHHHHHHHHcCCCeEEEEeCCEecchhhccccccchhhCCCcHHHHHHHHHHHHCCCCEEEEEeccCC
Confidence 3555544 24455556666667763 57899999999999888655554333 4444
Q ss_pred ccchHHHhhcCCCcc-EEEecCcHHHHHHHHHHHHhcC
Q 029918 115 SNKVKPLLAGVPNLA-MVESVDNEKIAGRLNRMVETMG 151 (185)
Q Consensus 115 sNKvk~~~~~~~~~~-~IhSVDs~kLA~~L~k~a~~~~ 151 (185)
...+..++ ..+| +|...|+...-..|++.|.+.+
T Consensus 216 ~~~~~~~~---~~~D~Vv~~~d~~~~r~~ln~~~~~~~ 250 (376)
T PRK08762 216 SDNVEALL---QDVDVVVDGADNFPTRYLLNDACVKLG 250 (376)
T ss_pred hHHHHHHH---hCCCEEEECCCCHHHHHHHHHHHHHcC
Confidence 44556666 4455 5789999987778999998764
No 70
>TIGR03854 F420_MSMEG_3544 probable F420-dependent oxidoreductase, MSMEG_3544 family. Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea 34H, Rhodopseudomonas palustris HaA2, and others. Partial phylogenetic profiling identifies protein subfamilies, within the larger family called luciferase-like monooxygenanases (pfam00296), that appear only in F420-positive genomes and are likely to be F420-dependent. This model describes a small family, closely related to other such families in the putative F420-binding region, exemplified by MSMEG_3544 in Mycobacterium smegmatis.
Probab=31.14 E-value=1.2e+02 Score=26.54 Aligned_cols=24 Identities=17% Similarity=0.133 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCeE
Q 029918 39 ALRSVIQRVHQAAERSSRPPDRIR 62 (185)
Q Consensus 39 nl~~V~~rI~~a~~~~gR~p~~V~ 62 (185)
.+....+.+.++|.++||++..+.
T Consensus 186 ~~~~~~~~~r~~a~~~Gr~~~~~~ 209 (290)
T TIGR03854 186 EARAGRRTIEAAAAAAGREIEPDH 209 (290)
T ss_pred HHHHHHHHHHHHHHHcCCCCCcce
Confidence 356677788888999999876543
No 71
>TIGR01273 speA arginine decarboxylase, biosynthetic. A distinct biodegradative form is also pyridoxal phosphate-dependent but is not similar in sequence.
Probab=31.07 E-value=5.4e+02 Score=25.55 Aligned_cols=134 Identities=12% Similarity=0.068 Sum_probs=85.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHH-HHcCCcc-ccc--ccHHHHHHHHhcC-CCCceE
Q 029918 33 DGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQV-YEAGHRC-FGE--NYVQEIVEKAAQL-PDDLEW 107 (185)
Q Consensus 33 ~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a-~~~G~r~-FGE--NrvQEl~~K~~~L-~~~i~W 107 (185)
.+.|.++++.+++-...+..+.+- +...+++-..|.-|-..|.+. .+.|... +|= .-.-|+..=.... +++...
T Consensus 64 ~~iL~~~i~~l~~aF~~a~~~~~Y-~g~~~~~YavKaN~~~~Vl~~l~~~G~~~~~GlEv~S~~EL~~Al~~g~~p~~~I 142 (624)
T TIGR01273 64 PDILQHRIRSLNDAFANAIEEYQY-AGHYQGVYPIKVNQHRSVVEDIVAFGKGLNYGLEAGSKPELLAAMAYATKPGAPI 142 (624)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcc-CCCeeEEEEeccCCcHHHHHHHHHcCCCCceEEEECCHHHHHHHHHcCCCCCCEE
Confidence 566788899988888777666554 347899999999888666555 4677432 443 2234443333322 234556
Q ss_pred EEEecccccchHHHhh-cCC----CccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCC-----------CCCcccc
Q 029918 108 HFIGNLQSNKVKPLLA-GVP----NLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTS-----------GEEYGEC 171 (185)
Q Consensus 108 HfIG~LQsNKvk~~~~-~~~----~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis-----------~E~sKsG 171 (185)
.+=| .|-+..++ ++. ...++=.|||+.-.+.|.+.+.+.+ .+..|.|=||.+ |+.+|.|
T Consensus 143 i~NG----~K~~e~I~~Al~~~~lG~~v~IvIDs~~EL~~I~~~a~~~~-~~~~IglRvnl~~~~~g~~~~tgg~~SKFG 217 (624)
T TIGR01273 143 VCNG----YKDREYIELALIGRKLGHNVFIVIEKLSELDLVIEEAKKLG-VKPKLGLRARLASKGSGKWASSGGEKSKFG 217 (624)
T ss_pred EeCC----CCCHHHHHHHHHhhhcCCCeEEEECCHHHHHHHHHHHHhcC-CCceEEEEEecCCCCCCCcccCCCCCCCCC
Confidence 7767 34433221 000 1244568999999999998887665 466899999853 4668888
Q ss_pred c
Q 029918 172 F 172 (185)
Q Consensus 172 ~ 172 (185)
+
T Consensus 218 l 218 (624)
T TIGR01273 218 L 218 (624)
T ss_pred C
Confidence 6
No 72
>PF10498 IFT57: Intra-flagellar transport protein 57 ; InterPro: IPR019530 Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated []. This protein is known as Huntington-interacting protein-1 in humans.
Probab=30.51 E-value=99 Score=28.51 Aligned_cols=20 Identities=35% Similarity=0.385 Sum_probs=15.8
Q ss_pred HHHHhhhhhhHHHHHHhhhc
Q 029918 8 EERKRRENHINEQVEAETMA 27 (185)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~m~ 27 (185)
|.-..||.|||.|+|.+.--
T Consensus 255 ekI~sREk~iN~qle~l~~e 274 (359)
T PF10498_consen 255 EKIESREKYINNQLEPLIQE 274 (359)
T ss_pred HHHHHHHHHHHHHhHHHHHH
Confidence 45578999999999987633
No 73
>cd01489 Uba2_SUMO Ubiquitin activating enzyme (E1) subunit UBA2. UBA2 is part of the heterodimeric activating enzyme (E1), specific for the SUMO family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. The E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by SUMO family of ubiquitin-like proteins (Ublps) is involved in cell division, nuclear transport, the stress response and signal transduction. UBA2 contains both the nucleotide-binding motif involved in adenylation and the catalytic cysteine involved in the thioester intermediate and Ublp transfer to E2.
Probab=28.50 E-value=3.5e+02 Score=24.40 Aligned_cols=67 Identities=12% Similarity=0.163 Sum_probs=48.4
Q ss_pred CCcccccccHHHHHHHHhcCCCCceEEEE-eccccc-chHHHhhcCCCcc-EEEecCcHHHHHHHHHHHHhcC
Q 029918 82 GHRCFGENYVQEIVEKAAQLPDDLEWHFI-GNLQSN-KVKPLLAGVPNLA-MVESVDNEKIAGRLNRMVETMG 151 (185)
Q Consensus 82 G~r~FGENrvQEl~~K~~~L~~~i~WHfI-G~LQsN-Kvk~~~~~~~~~~-~IhSVDs~kLA~~L~k~a~~~~ 151 (185)
+..+.|.++++-+.++...+.+++..... +.+..+ .....+ ..++ +|-++|+.+.-..|++.|...+
T Consensus 46 ~~~dVGk~Kaevaa~~l~~lNp~v~V~~~~~~i~~~~~~~~f~---~~~DvVv~a~Dn~~ar~~in~~c~~~~ 115 (312)
T cd01489 46 RKKHVGKSKAQVAKEAVLSFNPNVKIVAYHANIKDPDFNVEFF---KQFDLVFNALDNLAARRHVNKMCLAAD 115 (312)
T ss_pred ChhHcCcHHHHHHHHHHHHHCCCCeEEEEeccCCCccchHHHH---hcCCEEEECCCCHHHHHHHHHHHHHCC
Confidence 34567999999999999998665555433 566653 233455 4566 5788999998888999998653
No 74
>cd01573 modD_like ModD; Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase) present in some modABC operons in bacteria, which are involved in molybdate transport. In general, QPRTases are part of the de novo synthesis pathway of NAD in both prokaryotes and eukaryotes. They catalyse the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide.
Probab=28.31 E-value=1.9e+02 Score=25.39 Aligned_cols=72 Identities=14% Similarity=0.135 Sum_probs=51.6
Q ss_pred EEEeecCCCHHHHHHHHHcCCccccc-----ccHHHHHHHHhcCCCCceEEEEecccccchHHHhhcCCCccEEEecCcH
Q 029918 63 IVAVSKTKPVSVIRQVYEAGHRCFGE-----NYVQEIVEKAAQLPDDLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNE 137 (185)
Q Consensus 63 LvAVSKt~p~e~I~~a~~~G~r~FGE-----NrvQEl~~K~~~L~~~i~WHfIG~LQsNKvk~~~~~~~~~~~IhSVDs~ 137 (185)
.|.|| .++.+++.+|.++|...++= --+.++.......++++..=.||.+--+.+..+++ -.++.| ++.++
T Consensus 185 ~IgVe-v~t~eea~~A~~~gaD~I~ld~~~p~~l~~~~~~~~~~~~~i~i~AsGGI~~~ni~~~~~--~Gvd~I-~vsai 260 (272)
T cd01573 185 KIVVE-VDSLEEALAAAEAGADILQLDKFSPEELAELVPKLRSLAPPVLLAAAGGINIENAAAYAA--AGADIL-VTSAP 260 (272)
T ss_pred eEEEE-cCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHhccCCCceEEEECCCCHHHHHHHHH--cCCcEE-EEChh
Confidence 57888 67889999999998876542 12344554444333357889999998888888874 458888 88876
Q ss_pred H
Q 029918 138 K 138 (185)
Q Consensus 138 k 138 (185)
-
T Consensus 261 ~ 261 (272)
T cd01573 261 Y 261 (272)
T ss_pred h
Confidence 4
No 75
>PRK08223 hypothetical protein; Validated
Probab=27.77 E-value=2.2e+02 Score=25.52 Aligned_cols=67 Identities=12% Similarity=0.170 Sum_probs=49.0
Q ss_pred CCcccccccHHHHHHHHhcCCCCceEEEE-ecccccchHHHhhcCCCccE-EEecCcH--HHHHHHHHHHHhcC
Q 029918 82 GHRCFGENYVQEIVEKAAQLPDDLEWHFI-GNLQSNKVKPLLAGVPNLAM-VESVDNE--KIAGRLNRMVETMG 151 (185)
Q Consensus 82 G~r~FGENrvQEl~~K~~~L~~~i~WHfI-G~LQsNKvk~~~~~~~~~~~-IhSVDs~--kLA~~L~k~a~~~~ 151 (185)
...+.|.++++-+.++...+.+.++-+-+ ..|...-+..++ ..+|+ |...|++ ..-..|++.|.+.+
T Consensus 74 ~~~diG~~Kve~a~~~l~~iNP~v~V~~~~~~l~~~n~~~ll---~~~DlVvD~~D~~~~~~r~~ln~~c~~~~ 144 (287)
T PRK08223 74 MMSTLGRPKAEVLAEMVRDINPELEIRAFPEGIGKENADAFL---DGVDVYVDGLDFFEFDARRLVFAACQQRG 144 (287)
T ss_pred ChhHCCCcHHHHHHHHHHHHCCCCEEEEEecccCccCHHHHH---hCCCEEEECCCCCcHHHHHHHHHHHHHcC
Confidence 45578999999999999999766555433 466666677777 56664 6778865 56677899988754
No 76
>cd06840 PLPDE_III_Bif_AspK_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bifunctional Aspartate Kinase/Diaminopimelate Decarboxylase. Bifunctional aspartate kinase/diaminopimelate decarboxylase (AspK/DapDC, EC 4.1.1.20/EC 2.7.2.4) typically exists in bacteria. These proteins contain an N-terminal AspK region and a C-terminal DapDC region, which contains a PLP-binding TIM-barrel domain followed by beta-sandwich domain, characteristic of fold type III PLP-dependent enzymes. Members of this subfamily have not been fully characterized. Based on their sequence, these proteins may catalyze both reactions catalyzed by AspK and DapDC. AspK catalyzes the phosphorylation of L-aspartate to produce 4-phospho-L-aspartate while DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine.
Probab=26.23 E-value=4.8e+02 Score=23.41 Aligned_cols=101 Identities=18% Similarity=0.158 Sum_probs=62.1
Q ss_pred eEEEEeecCCCHHHHHHHH-HcCCcccccccHHHHHHHHhc---CCCCceEEEEecccccc-hHHHhhcCCCccEEEecC
Q 029918 61 IRIVAVSKTKPVSVIRQVY-EAGHRCFGENYVQEIVEKAAQ---LPDDLEWHFIGNLQSNK-VKPLLAGVPNLAMVESVD 135 (185)
Q Consensus 61 V~LvAVSKt~p~e~I~~a~-~~G~r~FGENrvQEl~~K~~~---L~~~i~WHfIG~LQsNK-vk~~~~~~~~~~~IhSVD 135 (185)
+++.-..|.-|...|..++ ++|. .|==.-..|+.-=... .++ =+--|-|+.=+.. ++.+++ ..+ .| ++|
T Consensus 36 ~~~~yAvKaN~~~~vl~~l~~~G~-g~dvaS~~El~~al~~~~G~~~-~~Iif~gp~K~~~~l~~a~~--~gv-~i-~~D 109 (368)
T cd06840 36 DSLFYAIKANPHPDVLRTLEEAGL-GFECVSIGELDLVLKLFPDLDP-RRVLFTPNFAARSEYEQALE--LGV-NV-TVD 109 (368)
T ss_pred CeEEEEeccCCCHHHHHHHHHcCC-eEEEcCHHHHHHHHHcccCCCc-ceEEEcCCCCCHHHHHHHHH--CCC-EE-EEC
Confidence 4788899999887766655 4553 2322233344332222 322 2345668775543 666662 223 45 899
Q ss_pred cHHHHHHHHHHHHhcCCCCccEEEEEeCC------------CCCccccc
Q 029918 136 NEKIAGRLNRMVETMGRKPLKVLVQVNTS------------GEEYGECF 172 (185)
Q Consensus 136 s~kLA~~L~k~a~~~~~~~l~VLIQVNis------------~E~sKsG~ 172 (185)
|+.-.++|.+.+. ..+|+|-||.. +..+|.|+
T Consensus 110 s~~El~~i~~~~~-----~~~v~lRi~~~~~~~~~~~~~~~~~~skFG~ 153 (368)
T cd06840 110 NLHPLREWPELFR-----GREVILRIDPGQGEGHHKHVRTGGPESKFGL 153 (368)
T ss_pred CHHHHHHHHHhcc-----cCCEEEEECCCCCCCCCCceecCCCCCCCCC
Confidence 9998888877653 35899999975 24588886
No 77
>PLN00064 photosystem II protein Psb27; Provisional
Probab=25.89 E-value=3.1e+02 Score=23.03 Aligned_cols=65 Identities=18% Similarity=0.203 Sum_probs=46.2
Q ss_pred hHHHHHHhhhcccccChHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHHc--CCc-cccccc
Q 029918 17 INEQVEAETMAASAATDGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEA--GHR-CFGENY 90 (185)
Q Consensus 17 ~~~~~~~~~m~~~~~~~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~~--G~r-~FGENr 90 (185)
|+.--++..|... .+...+...+.++.|..-..+.-|.+ .|+..-+.-++..|+.+ |+- .||-||
T Consensus 74 i~~lr~tI~L~~d---dp~~a~a~aeaR~~iNdyvSrYRr~~------~v~Gl~SFttMyTALNaLAGHY~Sfgpnr 141 (166)
T PLN00064 74 IGKVRSTINMDKT---DPNVADAVAELRETSNSWVAKYRREK------ALLGRPSFRDMYSALNAVSGHYISFGPTA 141 (166)
T ss_pred HHHHHHHHcCCCC---CccHHHHHHHHHHHHHHHHHHhcCCC------cccCcccHHHHHHHHHHHHHHhhccCCCC
Confidence 4444455555443 33445666778888888888887775 36777889999999984 866 899888
No 78
>PRK07411 hypothetical protein; Validated
Probab=25.68 E-value=2.4e+02 Score=25.91 Aligned_cols=67 Identities=13% Similarity=0.168 Sum_probs=50.0
Q ss_pred CCcccccccHHHHHHHHhcCCCCceEEEE-ecccccchHHHhhcCCCcc-EEEecCcHHHHHHHHHHHHhcC
Q 029918 82 GHRCFGENYVQEIVEKAAQLPDDLEWHFI-GNLQSNKVKPLLAGVPNLA-MVESVDNEKIAGRLNRMVETMG 151 (185)
Q Consensus 82 G~r~FGENrvQEl~~K~~~L~~~i~WHfI-G~LQsNKvk~~~~~~~~~~-~IhSVDs~kLA~~L~k~a~~~~ 151 (185)
+..++|.+++.-+.++...+.+.++-..+ ..+....+..++ ..+| +|...|+.+.-..|++.|.+.+
T Consensus 85 ~~~dvG~~Ka~~a~~~l~~~np~v~v~~~~~~~~~~~~~~~~---~~~D~Vvd~~d~~~~r~~ln~~~~~~~ 153 (390)
T PRK07411 85 GTSWVGKPKIESAKNRILEINPYCQVDLYETRLSSENALDIL---APYDVVVDGTDNFPTRYLVNDACVLLN 153 (390)
T ss_pred ChHHCCCcHHHHHHHHHHHHCCCCeEEEEecccCHHhHHHHH---hCCCEEEECCCCHHHHHHHHHHHHHcC
Confidence 34578999999999999988665544433 456665666677 4566 5788999999999999997654
No 79
>TIGR03044 PS_II_psb27 photosystem II protein Psb27. Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single model families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins.
Probab=24.26 E-value=3.4e+02 Score=22.00 Aligned_cols=72 Identities=19% Similarity=0.297 Sum_probs=48.5
Q ss_pred hHHHHHHhhhcccccChHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHHc--CC-ccccccc--H
Q 029918 17 INEQVEAETMAASAATDGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEA--GH-RCFGENY--V 91 (185)
Q Consensus 17 ~~~~~~~~~m~~~~~~~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~~--G~-r~FGENr--v 91 (185)
|+.-.++..|+.. .+...+...+.++.|.+-..+.-|.| .|++..+.-+++.|+.+ |+ ..|| || .
T Consensus 45 i~tlr~~i~lpkd---~p~~~~a~~~ar~~indyvsrYRr~~------~v~g~~SFttm~TALNsLAGHY~sy~-~rPlP 114 (135)
T TIGR03044 45 IQTLREAIDLPDD---DPNKSEAQAEARQLINDYISRYRRRP------RVNGLSSFTTMQTALNSLAGHYKSYA-NRPLP 114 (135)
T ss_pred HHHHHHHHcCCCC---CccHHHHHHHHHHHHHHHHHHhcCCC------CcCCcccHHHHHHHHHHHHHHhccCC-CCCCC
Confidence 4444556665443 33445556677788888888887776 37788999999999984 64 4678 88 4
Q ss_pred HHHHHHH
Q 029918 92 QEIVEKA 98 (185)
Q Consensus 92 QEl~~K~ 98 (185)
+++.+..
T Consensus 115 eklk~Rl 121 (135)
T TIGR03044 115 EKLKERL 121 (135)
T ss_pred HHHHHHH
Confidence 5554443
No 80
>TIGR03857 F420_MSMEG_2249 probable F420-dependent oxidoreductase, MSMEG_2249 family. Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea 34H, Rhodopseudomonas palustris HaA2, and others. Partial phylogenetic profiling identifies protein subfamilies, within the larger family called luciferase-like monooxygenanases (pfam00296), that appear only in F420-positive genomes and are likely to be F420-dependent. This model describes a distinctive subfamily, found only in F420-biosynthesizing members of the Actinobacteria of the bacterial luciferase-like monooxygenase (LLM) superfamily.
Probab=23.52 E-value=1.2e+02 Score=27.03 Aligned_cols=27 Identities=33% Similarity=0.507 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCeEEEE
Q 029918 39 ALRSVIQRVHQAAERSSRPPDRIRIVA 65 (185)
Q Consensus 39 nl~~V~~rI~~a~~~~gR~p~~V~LvA 65 (185)
.+......+.+++.++||+|.++++++
T Consensus 184 ~~~~~~~~~~~~a~~~Gr~~~~~~v~~ 210 (329)
T TIGR03857 184 AVARSVAIVRRAAEAAGRDPASVRVYA 210 (329)
T ss_pred HHHHHHHHHHHHHHHcCCChhhceEEE
Confidence 356677888899999999988766544
No 81
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=23.43 E-value=2.5e+02 Score=22.81 Aligned_cols=57 Identities=21% Similarity=0.220 Sum_probs=31.6
Q ss_pred chhhHHHHHhhhhhhHHHHHHhhhcccccChHHHHHHHHHHHHHHHHHHHHcCCCCCCeEE
Q 029918 3 NQEHEEERKRRENHINEQVEAETMAASAATDGVAATALRSVIQRVHQAAERSSRPPDRIRI 63 (185)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~i~~nl~~V~~rI~~a~~~~gR~p~~V~L 63 (185)
+|.||-|.++. .++.|||++.-..+.+ ..=.+.|....+++...+..+++.|..+.+
T Consensus 74 ~Qk~eLE~~k~--~L~qqv~~L~~e~s~~--~~E~da~k~k~e~l~~~~~~~~~~~~~pS~ 130 (135)
T KOG4196|consen 74 QQKHELEKEKA--ELQQQVEKLKEENSRL--RRELDAYKSKYEALQNSAVSVGASPVSPSS 130 (135)
T ss_pred HHHHHHHHHHH--HHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHhhhhhccCCCCCCcc
Confidence 35555555543 4678888887554432 111245555556655555545666655543
No 82
>PRK05597 molybdopterin biosynthesis protein MoeB; Validated
Probab=23.06 E-value=2.8e+02 Score=25.09 Aligned_cols=65 Identities=14% Similarity=0.115 Sum_probs=46.2
Q ss_pred cccccccHHHHHHHHhcCCCCceEEEE-ecccccchHHHhhcCCCcc-EEEecCcHHHHHHHHHHHHhcC
Q 029918 84 RCFGENYVQEIVEKAAQLPDDLEWHFI-GNLQSNKVKPLLAGVPNLA-MVESVDNEKIAGRLNRMVETMG 151 (185)
Q Consensus 84 r~FGENrvQEl~~K~~~L~~~i~WHfI-G~LQsNKvk~~~~~~~~~~-~IhSVDs~kLA~~L~k~a~~~~ 151 (185)
.+.|-++++.+.++..++.++++-..+ ..+...-+..++ ..+| +|-+.|+...-..|+..|.+.+
T Consensus 77 ~diG~~Ka~~a~~~l~~~np~v~v~~~~~~i~~~~~~~~~---~~~DvVvd~~d~~~~r~~~n~~c~~~~ 143 (355)
T PRK05597 77 AGVGQPKAESAREAMLALNPDVKVTVSVRRLTWSNALDEL---RDADVILDGSDNFDTRHLASWAAARLG 143 (355)
T ss_pred hHCCChHHHHHHHHHHHHCCCcEEEEEEeecCHHHHHHHH---hCCCEEEECCCCHHHHHHHHHHHHHcC
Confidence 477999999999999999665443322 344433344556 4566 5888999988888999998754
No 83
>COG0205 PfkA 6-phosphofructokinase [Carbohydrate transport and metabolism]
Probab=20.96 E-value=75 Score=29.28 Aligned_cols=32 Identities=19% Similarity=0.178 Sum_probs=21.4
Q ss_pred ccccHHHHHHHHhcCCCCceEEEEecccccch
Q 029918 87 GENYVQEIVEKAAQLPDDLEWHFIGNLQSNKV 118 (185)
Q Consensus 87 GENrvQEl~~K~~~L~~~i~WHfIG~LQsNKv 118 (185)
|....+...+......-+++||+.||+|+-=.
T Consensus 237 ~~~~~~~i~~~~~~~~~~~r~t~LGhiqRgg~ 268 (347)
T COG0205 237 GAELLAAIEELLALGDFETRVTVLGHIQRGGT 268 (347)
T ss_pred hhhHHHHHHHHhhhcccceEEEeccccccCCC
Confidence 66666665555443213789999999998643
No 84
>TIGR03860 FMN_nitrolo FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family. This model represents a distinctive clade, in which all characterized members are FMN-binding, within the larger family of luciferase-like monooxygenases (LLM), among which there are both FMN- and F420-binding enzymes. A well-characterized member is nitrilotriacetate monooxygenase from Aminobacter aminovorans (Chelatobacter heintzii), where nitrilotriacetate is a chelating agent used in detergents.
Probab=20.69 E-value=1.1e+02 Score=28.34 Aligned_cols=26 Identities=19% Similarity=0.434 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCeEEE
Q 029918 39 ALRSVIQRVHQAAERSSRPPDRIRIV 64 (185)
Q Consensus 39 nl~~V~~rI~~a~~~~gR~p~~V~Lv 64 (185)
.+....+.+.++|.++||+|++++++
T Consensus 240 ~~~~~~~~~r~~a~~~GR~p~~~~v~ 265 (422)
T TIGR03860 240 DAQAFYADIKARAAAAGRDPDDVKIL 265 (422)
T ss_pred HHHHHHHHHHHHHHHhCCChhhccee
Confidence 45667778888999999999888764
No 85
>PLN00035 histone H4; Provisional
Probab=20.09 E-value=3.9e+02 Score=20.57 Aligned_cols=40 Identities=23% Similarity=0.260 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHH-cCCccccc
Q 029918 38 TALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYE-AGHRCFGE 88 (185)
Q Consensus 38 ~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~-~G~r~FGE 88 (185)
+.++.|.......+.-++| ||..+++|..|+. .|...+|-
T Consensus 61 ~~l~~I~~dav~ya~HA~R-----------KTV~~~DV~~Alkr~g~~lyGf 101 (103)
T PLN00035 61 IFLENVIRDAVTYTEHARR-----------KTVTAMDVVYALKRQGRTLYGF 101 (103)
T ss_pred HHHHHHHHHHHHHHHhcCC-----------CcCcHHHHHHHHHHcCCcCCCC
Confidence 3344444444455566666 6788999988876 57776663
Done!