Query 045860
Match_columns 160
No_of_seqs 142 out of 1367
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 06:15:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045860.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045860hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03194 putative disease resi 100.0 2.6E-43 5.6E-48 262.3 14.8 139 5-159 18-157 (187)
2 PLN03210 Resistant to P. syrin 100.0 2.9E-41 6.3E-46 310.4 16.8 155 1-159 1-156 (1153)
3 PF01582 TIR: TIR domain; Int 100.0 3E-29 6.5E-34 181.3 3.1 133 16-148 1-141 (141)
4 smart00255 TIR Toll - interleu 99.9 7.2E-26 1.6E-30 162.4 13.5 136 13-151 1-139 (140)
5 PF13676 TIR_2: TIR domain; PD 99.8 3.3E-20 7E-25 126.7 2.2 87 16-108 1-87 (102)
6 KOG3678 SARM protein (with ste 99.3 2.5E-11 5.4E-16 101.8 9.5 127 9-142 608-751 (832)
7 PF08937 DUF1863: MTH538 TIR-l 98.8 6.2E-09 1.3E-13 74.2 5.6 91 14-108 1-108 (130)
8 PF08357 SEFIR: SEFIR domain; 98.0 1E-05 2.2E-10 58.6 5.4 65 15-79 2-70 (150)
9 PF10137 TIR-like: Predicted n 97.3 0.00097 2.1E-08 47.3 6.8 78 15-95 1-91 (125)
10 PF13271 DUF4062: Domain of un 94.9 0.15 3.2E-06 33.2 6.3 66 15-82 1-67 (83)
11 COG4916 Uncharacterized protei 94.0 0.073 1.6E-06 42.2 3.7 95 9-107 173-273 (329)
12 PF05014 Nuc_deoxyrib_tr: Nucl 92.0 1.7 3.6E-05 29.7 7.9 80 27-110 13-100 (113)
13 cd00860 ThrRS_anticodon ThrRS 87.4 3.3 7.1E-05 26.4 6.2 59 14-78 2-61 (91)
14 COG4271 Predicted nucleotide-b 83.6 4.1 8.9E-05 31.3 5.7 86 15-106 84-185 (233)
15 PF14359 DUF4406: Domain of un 81.4 13 0.00029 24.7 7.1 64 30-95 18-85 (92)
16 cd00738 HGTP_anticodon HGTP an 80.5 7.6 0.00016 24.8 5.7 61 14-78 2-64 (94)
17 PF14258 DUF4350: Domain of un 79.6 10 0.00023 23.3 5.9 60 30-102 7-67 (70)
18 COG0400 Predicted esterase [Ge 76.5 12 0.00027 28.7 6.5 57 8-66 141-199 (207)
19 cd00858 GlyRS_anticodon GlyRS 75.0 16 0.00035 25.1 6.3 62 12-78 25-87 (121)
20 PF03129 HGTP_anticodon: Antic 74.1 13 0.00029 23.9 5.5 44 27-74 15-59 (94)
21 cd07373 2A5CPDO_A The alpha su 72.7 31 0.00068 27.4 8.2 77 27-106 90-173 (271)
22 COG4916 Uncharacterized protei 72.5 5.8 0.00013 31.7 3.8 98 12-111 5-107 (329)
23 PF08902 DUF1848: Domain of un 67.9 62 0.0013 26.0 9.6 132 14-157 48-198 (266)
24 cd02042 ParA ParA and ParB of 65.9 34 0.00074 22.3 6.9 63 16-78 3-72 (104)
25 PF10087 DUF2325: Uncharacteri 61.1 38 0.00083 22.3 5.6 45 30-76 12-57 (97)
26 cd00859 HisRS_anticodon HisRS 59.5 37 0.00079 21.0 5.2 34 15-49 3-36 (91)
27 TIGR00418 thrS threonyl-tRNA s 57.3 41 0.00089 29.5 6.7 61 12-77 469-529 (563)
28 cd00861 ProRS_anticodon_short 56.8 38 0.00082 21.6 5.0 47 28-78 18-64 (94)
29 PF02310 B12-binding: B12 bind 56.1 58 0.0013 21.7 8.1 75 30-112 17-92 (121)
30 KOG2792 Putative cytochrome C 55.9 19 0.00042 28.8 3.9 30 83-112 153-187 (280)
31 cd02426 Pol_gamma_b_Cterm C-te 53.8 12 0.00025 26.4 2.2 45 13-57 27-76 (128)
32 cd07363 45_DOPA_Dioxygenase Th 52.9 68 0.0015 25.1 6.7 76 27-106 80-157 (253)
33 PRK12325 prolyl-tRNA synthetas 52.9 55 0.0012 27.9 6.6 64 13-80 345-410 (439)
34 COG0125 Tmk Thymidylate kinase 52.6 1E+02 0.0022 23.6 8.1 97 16-114 4-141 (208)
35 TIGR02298 HpaD_Fe 3,4-dihydrox 48.8 1.4E+02 0.003 23.9 8.3 77 27-106 96-179 (282)
36 PRK09194 prolyl-tRNA synthetas 48.1 18 0.00038 32.0 2.9 46 11-56 466-513 (565)
37 PLN03194 putative disease resi 47.7 1.1E+02 0.0024 23.2 6.7 66 40-108 25-90 (187)
38 cd03364 TOPRIM_DnaG_primases T 46.3 29 0.00062 21.8 3.0 33 40-74 44-76 (79)
39 PF03709 OKR_DC_1_N: Orn/Lys/A 46.1 93 0.002 21.2 7.0 69 30-110 6-75 (115)
40 CHL00201 syh histidine-tRNA sy 45.7 65 0.0014 27.4 5.9 60 13-77 325-384 (430)
41 PF09419 PGP_phosphatase: Mito 45.3 75 0.0016 23.6 5.5 72 36-111 35-117 (168)
42 cd00862 ProRS_anticodon_zinc P 44.2 32 0.0007 26.0 3.5 46 12-57 9-60 (202)
43 COG1658 Small primase-like pro 43.3 51 0.0011 23.4 4.1 55 14-70 30-84 (127)
44 PRK13364 protocatechuate 4,5-d 43.0 1.7E+02 0.0038 23.4 9.1 122 27-156 98-239 (278)
45 PRK14938 Ser-tRNA(Thr) hydrola 41.7 1E+02 0.0023 26.1 6.3 57 13-74 274-331 (387)
46 cd01423 MGS_CPS_I_III Methylgl 41.7 43 0.00092 22.7 3.5 29 16-46 3-31 (116)
47 PF03720 UDPG_MGDP_dh_C: UDP-g 40.2 21 0.00046 24.0 1.8 55 22-76 11-75 (106)
48 PRK08661 prolyl-tRNA synthetas 40.2 82 0.0018 27.2 5.7 62 12-78 286-354 (477)
49 COG0683 LivK ABC-type branched 39.8 2E+02 0.0044 23.5 7.9 73 15-88 150-222 (366)
50 COG4088 Predicted nucleotide k 39.8 37 0.0008 26.7 3.1 113 28-147 16-152 (261)
51 PF12163 HobA: DNA replication 39.3 16 0.00036 27.5 1.2 74 28-107 3-79 (180)
52 PRK14799 thrS threonyl-tRNA sy 39.0 1.1E+02 0.0024 27.1 6.3 57 13-74 438-495 (545)
53 cd07371 2A5CPDO_AB The alpha a 38.4 2E+02 0.0043 22.7 11.0 77 27-106 87-170 (268)
54 KOG1016 Predicted DNA helicase 37.5 1.2E+02 0.0026 28.7 6.3 95 14-116 407-521 (1387)
55 PRK00413 thrS threonyl-tRNA sy 37.5 1.1E+02 0.0023 27.4 6.2 61 13-78 539-599 (638)
56 cd06340 PBP1_ABC_ligand_bindin 37.0 1.8E+02 0.0038 23.3 7.0 64 15-79 146-209 (347)
57 PLN02530 histidine-tRNA ligase 36.3 1.2E+02 0.0027 26.2 6.3 61 12-77 400-460 (487)
58 PRK03991 threonyl-tRNA synthet 36.0 1E+02 0.0022 27.7 5.8 60 13-78 499-559 (613)
59 PF03446 NAD_binding_2: NAD bi 35.3 36 0.00079 24.5 2.5 48 31-78 14-68 (163)
60 KOG1610 Corticosteroid 11-beta 35.2 50 0.0011 27.2 3.4 31 14-48 30-60 (322)
61 PRK12305 thrS threonyl-tRNA sy 34.9 1.4E+02 0.0031 26.2 6.5 61 13-78 476-536 (575)
62 PRK12444 threonyl-tRNA synthet 34.4 1.4E+02 0.003 26.8 6.4 62 12-77 540-601 (639)
63 TIGR00409 proS_fam_II prolyl-t 34.3 31 0.00067 30.6 2.3 46 13-58 473-520 (568)
64 PRK15057 UDP-glucose 6-dehydro 34.1 1.1E+02 0.0024 25.7 5.5 52 22-73 310-365 (388)
65 KOG1136 Predicted cleavage and 34.0 54 0.0012 27.6 3.4 44 64-107 191-241 (501)
66 cd06342 PBP1_ABC_LIVBP_like Ty 33.4 2.3E+02 0.0051 22.1 7.6 57 16-74 138-195 (334)
67 PRK05339 PEP synthetase regula 32.8 1.8E+02 0.0038 23.4 6.1 68 33-103 159-244 (269)
68 PRK10569 NAD(P)H-dependent FMN 32.0 1.9E+02 0.0041 21.6 6.0 82 29-113 19-113 (191)
69 COG1058 CinA Predicted nucleot 32.0 65 0.0014 25.7 3.5 43 30-77 23-68 (255)
70 TIGR00408 proS_fam_I prolyl-tR 31.5 1.4E+02 0.0031 25.7 5.8 63 12-78 281-348 (472)
71 TIGR00334 5S_RNA_mat_M5 ribonu 31.1 1.1E+02 0.0024 22.9 4.5 65 27-95 35-107 (174)
72 cd07367 CarBb CarBb is the B s 30.5 2.7E+02 0.0059 22.0 9.5 126 27-156 90-231 (268)
73 PF00350 Dynamin_N: Dynamin fa 30.0 1.9E+02 0.0041 20.2 5.5 45 59-106 120-165 (168)
74 cd01424 MGS_CPS_II Methylglyox 29.9 75 0.0016 21.2 3.2 30 15-46 2-31 (110)
75 PF09441 Abp2: ARS binding pro 29.7 25 0.00055 26.0 0.8 57 82-147 54-111 (175)
76 PRK10076 pyruvate formate lyas 29.5 2.2E+02 0.0048 21.7 6.1 34 16-49 42-75 (213)
77 PF12146 Hydrolase_4: Putative 29.4 86 0.0019 19.9 3.2 36 12-48 15-50 (79)
78 PF03618 Kinase-PPPase: Kinase 29.3 2.2E+02 0.0048 22.6 6.1 68 33-103 153-240 (255)
79 PF03437 BtpA: BtpA family; I 28.8 1.7E+02 0.0036 23.3 5.4 109 33-147 133-253 (254)
80 cd00154 Rab Rab family. Rab G 28.7 1.6E+02 0.0034 19.7 4.8 28 53-80 57-85 (159)
81 cd06335 PBP1_ABC_ligand_bindin 28.4 3E+02 0.0065 22.0 7.0 18 28-45 153-170 (347)
82 COG1180 PflA Pyruvate-formate 27.8 1.4E+02 0.0031 23.5 4.9 34 16-49 87-120 (260)
83 COG3340 PepE Peptidase E [Amin 27.7 2.4E+02 0.0052 22.1 5.8 70 14-88 34-104 (224)
84 PRK08306 dipicolinate synthase 27.4 81 0.0018 25.4 3.5 53 22-77 9-65 (296)
85 KOG0409 Predicted dehydrogenas 27.2 1.1E+02 0.0023 25.3 4.0 62 11-78 34-102 (327)
86 cd01857 HSR1_MMR1 HSR1/MMR1. 27.1 2.1E+02 0.0047 19.7 5.8 18 60-77 4-21 (141)
87 cd08584 PI-PLCc_GDPD_SF_unchar 26.8 1.2E+02 0.0027 23.0 4.1 45 43-91 126-170 (192)
88 COG0124 HisS Histidyl-tRNA syn 26.6 2.9E+02 0.0064 23.7 6.8 59 11-74 333-392 (429)
89 PF12913 SH3_6: SH3 domain of 26.5 21 0.00046 21.4 -0.1 16 15-30 28-43 (54)
90 cd00138 PLDc Phospholipase D. 26.5 2.4E+02 0.0051 19.9 7.0 30 52-81 17-46 (176)
91 cd06386 PBP1_NPR_C_like Ligand 26.0 2.7E+02 0.0058 22.9 6.5 39 30-69 157-195 (387)
92 PF09413 DUF2007: Domain of un 25.8 72 0.0016 19.2 2.3 22 30-51 12-33 (67)
93 PF07429 Glyco_transf_56: 4-al 25.6 76 0.0017 26.6 3.0 50 33-85 300-350 (360)
94 PF07894 DUF1669: Protein of u 25.1 3.7E+02 0.0081 21.8 7.5 77 42-133 121-197 (284)
95 COG2084 MmsB 3-hydroxyisobutyr 24.9 1.2E+02 0.0026 24.5 4.0 47 32-78 14-68 (286)
96 COG0276 HemH Protoheme ferro-l 24.7 4E+02 0.0087 22.0 7.4 76 30-108 75-161 (320)
97 cd01454 vWA_norD_type norD typ 24.7 2.6E+02 0.0057 19.9 6.5 44 68-111 103-154 (174)
98 COG1168 MalY Bifunctional PLP- 24.5 1.9E+02 0.0041 24.5 5.1 45 59-103 148-195 (388)
99 PF00875 DNA_photolyase: DNA p 24.2 2.7E+02 0.0058 19.8 6.9 89 30-126 55-146 (165)
100 PF13662 Toprim_4: Toprim doma 23.9 51 0.0011 20.7 1.4 33 35-69 40-74 (81)
101 cd04886 ACT_ThrD-II-like C-ter 23.7 1E+02 0.0023 17.9 2.8 32 12-45 41-72 (73)
102 cd07370 HPCD The Class III ext 23.5 3.8E+02 0.0081 21.2 7.8 77 27-106 94-176 (280)
103 PRK13762 tRNA-modifying enzyme 23.0 3.2E+02 0.0069 22.3 6.2 60 14-80 131-190 (322)
104 cd01241 PH_Akt Akt pleckstrin 22.8 83 0.0018 20.9 2.3 16 135-150 87-102 (102)
105 PF05818 TraT: Enterobacterial 22.6 1.2E+02 0.0025 23.6 3.4 37 11-47 19-56 (215)
106 PF10579 Rapsyn_N: Rapsyn N-te 22.6 59 0.0013 21.2 1.5 19 136-154 23-41 (80)
107 COG2077 Tpx Peroxiredoxin [Pos 22.5 64 0.0014 23.7 1.8 22 67-88 74-97 (158)
108 KOG1014 17 beta-hydroxysteroid 22.4 1.7E+02 0.0038 24.0 4.4 58 13-74 73-131 (312)
109 cd06379 PBP1_iGluR_NMDA_NR1 N- 22.3 3.3E+02 0.0071 22.1 6.2 14 29-42 170-183 (377)
110 TIGR03026 NDP-sugDHase nucleot 22.1 2.2E+02 0.0048 23.8 5.3 52 23-74 328-383 (411)
111 PF06309 Torsin: Torsin; Inte 21.8 3E+02 0.0065 19.5 6.0 60 16-75 54-127 (127)
112 PLN02908 threonyl-tRNA synthet 21.5 2.5E+02 0.0054 25.5 5.7 60 13-77 589-648 (686)
113 COG2861 Uncharacterized protei 21.4 4.2E+02 0.0092 21.1 6.6 70 28-102 138-210 (250)
114 COG3980 spsG Spore coat polysa 21.3 4.7E+02 0.01 21.5 6.6 62 12-77 157-219 (318)
115 cd07368 PhnC_Bs_like PhnC is a 21.2 4.3E+02 0.0092 21.0 9.9 78 27-106 95-186 (277)
116 PHA02456 zinc metallopeptidase 21.1 1.5E+02 0.0033 20.7 3.3 48 60-108 55-105 (141)
117 COG0415 PhrB Deoxyribodipyrimi 21.1 4.4E+02 0.0095 23.0 6.8 85 31-125 58-147 (461)
118 cd07949 PCA_45_Doxase_B_like_1 21.0 4.3E+02 0.0094 21.0 8.0 124 27-156 98-239 (276)
119 cd02067 B12-binding B12 bindin 20.7 2.7E+02 0.0058 18.5 7.6 46 31-81 17-62 (119)
120 cd06346 PBP1_ABC_ligand_bindin 20.6 4.1E+02 0.0088 20.8 6.3 26 28-54 152-177 (312)
121 cd06366 PBP1_GABAb_receptor Li 20.5 4.4E+02 0.0095 20.9 7.0 38 16-54 138-175 (350)
122 PF00762 Ferrochelatase: Ferro 20.5 2.9E+02 0.0063 22.5 5.5 12 69-80 116-127 (316)
123 PF01990 ATP-synt_F: ATP synth 20.4 2.6E+02 0.0056 18.1 4.8 47 33-82 9-55 (95)
124 cd07372 2A5CPDO_B The beta sub 20.2 4.7E+02 0.01 21.1 7.8 77 27-106 98-187 (294)
125 PF07283 TrbH: Conjugal transf 20.0 2E+02 0.0044 20.1 3.9 21 28-48 36-56 (121)
No 1
>PLN03194 putative disease resistance protein; Provisional
Probab=100.00 E-value=2.6e-43 Score=262.30 Aligned_cols=139 Identities=26% Similarity=0.471 Sum_probs=127.3
Q ss_pred CCCCCCCCcccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCCChh
Q 045860 5 SFQNISCGKYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYASSTW 84 (160)
Q Consensus 5 ss~~~~~~~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S~w 84 (160)
|++++....|||||||++.|+++.|++||+.+|+++||++|+|+.++.+|+.+.+.|.++|++|+++|+|||++|+.|.|
T Consensus 18 ~~~~~~~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S~W 97 (187)
T PLN03194 18 PSSSSSAKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYF 97 (187)
T ss_pred ccCCCCCCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccchh
Confidence 55566667899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhcCCceeeEEeccCchhhhcc-cchHHHHHHHHHHhhcCCHHHHHHHHHHHHHhhcccceeccC
Q 045860 85 CLDELLKITECKNREDQIFPIFYGVEPTVVRKQ-TASFGEAFAEHEEFFRDNIEKVQKWRHALKVVANISGWELKD 159 (160)
Q Consensus 85 c~~El~~~~~~~~~~~~iiPVf~~v~p~~v~~~-~~~f~~~f~~~~~~~~~~~~~~~~W~~al~~v~~~~g~~~~~ 159 (160)
|++||.+++++ +..||||||+|+|++||+| .|. .+++++++||.||++|++++|++++.
T Consensus 98 CLdEL~~I~e~---~~~ViPIFY~VdPsdVr~q~~~~-------------~~~e~v~~Wr~AL~~va~l~G~~~~~ 157 (187)
T PLN03194 98 CLHELALIMES---KKRVIPIFCDVKPSQLRVVDNGT-------------CPDEEIRRFNWALEEAKYTVGLTFDS 157 (187)
T ss_pred HHHHHHHHHHc---CCEEEEEEecCCHHHhhccccCC-------------CCHHHHHHHHHHHHHHhccccccCCC
Confidence 99999999986 4579999999999999997 321 23689999999999999999998753
No 2
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=100.00 E-value=2.9e-41 Score=310.44 Aligned_cols=155 Identities=43% Similarity=0.763 Sum_probs=145.2
Q ss_pred CCCCCCCCCCCCcccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCC
Q 045860 1 MATTSFQNISCGKYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYA 80 (160)
Q Consensus 1 ~~s~ss~~~~~~~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~ 80 (160)
|||+||++ +.++|||||||+|+|+|+.|++||+.+|.++||.+|.|+ ++.+|+.+..++.++|++|+++|||+|++|+
T Consensus 1 ~~~~~~~~-~~~~~~vf~sfrg~d~r~~f~~hl~~~l~~~~i~~f~d~-~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya 78 (1153)
T PLN03210 1 MASSSSSS-RNWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDN-EIERSQSLDPELKQAIRDSRIAVVVFSKNYA 78 (1153)
T ss_pred CCCCCCCC-CCCCCcEEeeCCCcccccCHHHHHHHHHHHCCCeEEccC-CccCCCcccHHHHHHHHhCeEEEEEecCCcc
Confidence 67766554 567899999999999999999999999999999999987 6999999999999999999999999999999
Q ss_pred CChhHHHHHHHHHHH-hhcCCceeeEEeccCchhhhcccchHHHHHHHHHHhhcCCHHHHHHHHHHHHHhhcccceeccC
Q 045860 81 SSTWCLDELLKITEC-KNREDQIFPIFYGVEPTVVRKQTASFGEAFAEHEEFFRDNIEKVQKWRHALKVVANISGWELKD 159 (160)
Q Consensus 81 ~S~wc~~El~~~~~~-~~~~~~iiPVf~~v~p~~v~~~~~~f~~~f~~~~~~~~~~~~~~~~W~~al~~v~~~~g~~~~~ 159 (160)
.|.||++||.++++| ++.+++||||||+|+|++||+|+|.||++|.++.+... ++++++||+||++|++++||++.+
T Consensus 79 ~s~wcl~el~~i~~~~~~~~~~v~pvfy~v~p~~v~~~~g~f~~~f~~~~~~~~--~~~~~~w~~al~~~~~~~g~~~~~ 156 (1153)
T PLN03210 79 SSSWCLNELLEIVRCKEELGQLVIPVFYGLDPSHVRKQTGDFGEAFEKTCQNKT--EDEKIQWKQALTDVANILGYHSQN 156 (1153)
T ss_pred cchHHHHHHHHHHHhhhhcCceEEEEEecccHHHHhhccchHHHHHHHHhcccc--hhHHHHHHHHHHHHhCcCceecCC
Confidence 999999999999999 88899999999999999999999999999999887653 689999999999999999999865
No 3
>PF01582 TIR: TIR domain; InterPro: IPR000157 In Drosophila melanogaster the Toll protein is involved in establishment of dorso-ventral polarity in the embryo. In addition, members of the Toll family play a key role in innate antibacterial and antifungal immunity in insects as well as in mammals. These proteins are type-I transmembrane receptors that share an intracellular 200 residue domain with the interleukin-1 receptor (IL-1R), the Toll/IL-1R homologous region (TIR). The similarity between Toll-like receptors (LTRs) and IL-1R is not restricted to sequence homology since these proteins also share a similar signalling pathway. They both induce the activation of a Rel type transcription factor via an adaptor protein and a protein kinase []. Interestingly, MyD88, a cytoplasmic adaptor protein found in mammals, contains a TIR domain associated to a DEATH domain (see IPR000488 from INTERPRO) [, , ]. Besides the mammalian and Drosophila melanogaster proteins, a TIR domain is also found in a number of plant proteins implicated in host defence []. As MyD88, these proteins are cytoplasmic. Site directed mutagenesis and deletion analysis have shown that the TIR domain is essential for Toll and IL-1R activities. Sequence analysis have revealed the presence of three highly conserved regions among the different members of the family: box 1 (FDAFISY), box 2 (GYKLC-RD-PG), and box 3 (a conserved W surrounded by basic residues). It has been proposed that boxes 1 and 2 are involved in the binding of proteins involved in signalling, whereas box 3 is primarily involved in directing localization of receptor, perhaps through interactions with cytoskeletal elements [].; GO: 0005515 protein binding, 0007165 signal transduction, 0005622 intracellular; PDB: 3J0A_A 2J67_B 3JRN_A 1FYV_A 1O77_D 1FYX_A 1FYW_A 3OZI_B 1T3G_B 2JS7_A ....
Probab=99.95 E-value=3e-29 Score=181.33 Aligned_cols=133 Identities=34% Similarity=0.570 Sum_probs=116.5
Q ss_pred EEEecccCCCcchHHHHHHHHHhcC--CcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCCChhHHHHHHHHH
Q 045860 16 AFLSFRGEDTRKGFIGYLYTALNNK--GIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYASSTWCLDELLKIT 93 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~--gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~ 93 (160)
|||||++.+.+..|+++|.++|+++ |+++|++++|+.+|..+.++|.++|++|+++|+|+|++|+.|.||+.|+..|+
T Consensus 1 vfisy~~~~d~~~~~~~L~~~Le~~~~g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~s~wc~~el~~a~ 80 (141)
T PF01582_consen 1 VFISYSGKDDREWFVSHLLPELEERPYGYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSRNYLSSEWCLFELQEAL 80 (141)
T ss_dssp EEEEE-GHHGHHHHHHCHHHHHHCTSSTS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESHHHHHHTHHHHHHHHHH
T ss_pred cEEEeCCCCcHHHHHHHHHHHHHhCCCCeEEEEechhhcccccccchhhHhhhhceeeEEEeecccccccchhhhhhhhh
Confidence 8999999333467899999999999 99999999999999999999999999999999999999999999999999999
Q ss_pred HH-hhc--CCceeeEEeccCchhhh-cccchHHHHHHHHHHhhcCC--HHHHHHHHHHHHH
Q 045860 94 EC-KNR--EDQIFPIFYGVEPTVVR-KQTASFGEAFAEHEEFFRDN--IEKVQKWRHALKV 148 (160)
Q Consensus 94 ~~-~~~--~~~iiPVf~~v~p~~v~-~~~~~f~~~f~~~~~~~~~~--~~~~~~W~~al~~ 148 (160)
++ ... ...|+|||+++.+++++ .+.+.|+..|..+......+ .+....|++++.+
T Consensus 81 ~~~~~~~~~~~Il~v~~~v~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~fW~~l~~~ 141 (141)
T PF01582_consen 81 ERLLEEGRDKLILPVFYDVSPSDVRPDQSLRFLLRFLTYLRWPDDDSREDRSWFWKKLRYH 141 (141)
T ss_dssp HHHHCSTCTTEEEEESSSS-CHHCHTHHHHHHHHHCTHCEETSSSGGGGGHHHHHHHHHHH
T ss_pred hhccccccccceeeEeccCChhhcChhhhHHHHHHhhhheeCCCCCCccHHHHHHHHHhcC
Confidence 99 443 48999999999999999 79999999998888776643 5688999998763
No 4
>smart00255 TIR Toll - interleukin 1 - resistance.
Probab=99.94 E-value=7.2e-26 Score=162.38 Aligned_cols=136 Identities=39% Similarity=0.674 Sum_probs=115.3
Q ss_pred cccEEEeccc-CCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCCChhHHHHHHH
Q 045860 13 KYDAFLSFRG-EDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYASSTWCLDELLK 91 (160)
Q Consensus 13 ~~dVFISy~~-~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S~wc~~El~~ 91 (160)
.|||||||++ ++....|+.+|...|...|+.+|.|+.. +|.....+|.++|++|+++|+|+|++|+.|.||..|+..
T Consensus 1 ~~dvFISys~~~~~~~~~v~~L~~~l~~~~~~v~~d~~~--~~~~~~~~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~ 78 (140)
T smart00255 1 EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFE--PGGGDLEEIDEAIEKSRIAIVVLSPNYAESEWCLDELVA 78 (140)
T ss_pred CCeEEEECCCCHHHHHHHHHHHHHHhhcCCcEEEecCcc--cccchHHHHHHHHHHCcEEEEEECcccccChhHHHHHHH
Confidence 4899999998 4555789999999999999999998743 343333499999999999999999999999999999999
Q ss_pred HHHH-h-hcCCceeeEEeccCchhhhcccchHHHHHHHHHHhhcCCHHHHHHHHHHHHHhhc
Q 045860 92 ITEC-K-NREDQIFPIFYGVEPTVVRKQTASFGEAFAEHEEFFRDNIEKVQKWRHALKVVAN 151 (160)
Q Consensus 92 ~~~~-~-~~~~~iiPVf~~v~p~~v~~~~~~f~~~f~~~~~~~~~~~~~~~~W~~al~~v~~ 151 (160)
++++ . ....+||||+++..|+.+..+.+.++..+...+..+.++..+ ..|+.++..+.+
T Consensus 79 a~~~~~~~~~~~iIPI~~~~~~~~~~~~~~~l~~~~~~~~~~w~~~~~~-~fW~~~~~~l~~ 139 (140)
T smart00255 79 ALENALEEGGLRVIPIFYEVIPSDVRKQPGKFRKVLKKNYLKWPEDEKE-RFWKKALYAVPS 139 (140)
T ss_pred HHHHHHHcCCCeEEEEEEecChHHHHhcccHHHHHHHHHHhhcCCchhH-HHHHHHHHHhcc
Confidence 9998 3 377899999999999999999999999998876666654444 789999988754
No 5
>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A.
Probab=99.79 E-value=3.3e-20 Score=126.68 Aligned_cols=87 Identities=33% Similarity=0.531 Sum_probs=76.0
Q ss_pred EEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCCChhHHHHHHHHHHH
Q 045860 16 AFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYASSTWCLDELLKITEC 95 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~~~ 95 (160)
|||||++.|. .++..|...|+++|+++|+|. ++.+|..+.++|.++|++|+.+|+++|++|..|+||..|+..|.+
T Consensus 1 VFIS~~~~D~--~~a~~l~~~L~~~g~~v~~d~-~~~~g~~~~~~i~~~i~~s~~~i~~~S~~~~~s~~~~~E~~~a~~- 76 (102)
T PF13676_consen 1 VFISYSSEDR--EFAERLAERLESAGIRVFLDR-DIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAWK- 76 (102)
T ss_dssp EEEEEEGGGC--CCHHHHHHHHHHTT--EE-GG-EE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHHC-
T ss_pred eEEEecCCcH--HHHHHHHHHHhhcCCEEEEEE-eCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHHH-
Confidence 8999999995 679999999999999999997 999999999999999999999999999999999999999999854
Q ss_pred hhcCCceeeEEec
Q 045860 96 KNREDQIFPIFYG 108 (160)
Q Consensus 96 ~~~~~~iiPVf~~ 108 (160)
.+++||||.++
T Consensus 77 --~~~~iipv~~~ 87 (102)
T PF13676_consen 77 --RGKPIIPVRLD 87 (102)
T ss_dssp --TSESEEEEECS
T ss_pred --CCCEEEEEEEC
Confidence 45689999975
No 6
>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]
Probab=99.27 E-value=2.5e-11 Score=101.83 Aligned_cols=127 Identities=26% Similarity=0.356 Sum_probs=98.9
Q ss_pred CCCCcccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCC-------
Q 045860 9 ISCGKYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYAS------- 81 (160)
Q Consensus 9 ~~~~~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~------- 81 (160)
+-++..||||||+..-. ...++.|.-.|+-+||+||+|.+.+..|.. .+.+.+.|..++.+|+|+||+.+.
T Consensus 608 ~~skq~DVFISYRRstG-nQLASLiKV~LQL~GyrVFIDVdKL~AGKF-dssLlkni~aAkhFiLVLtP~sLDr~lnD~n 685 (832)
T KOG3678|consen 608 MLSKQIDVFISYRRSTG-NQLASLIKVLLQLRGYRVFIDVDKLYAGKF-DSSLLKNIQAAKHFILVLTPNSLDRLLNDDN 685 (832)
T ss_pred cccCCcceEEEeecccc-HHHHHHHHHHHHhcCceEEEehhhhhcccc-cHHHHHHHHhhheeEEEeCcchHHHHhcccc
Confidence 45677899999987643 567888888999999999999988988865 578899999999999999999653
Q ss_pred -ChhHHHHHHHHHHHhhcCCceeeEEec---------cCchhhhcccchHHHHHHHHHHhhcCCHHHHHHH
Q 045860 82 -STWCLDELLKITECKNREDQIFPIFYG---------VEPTVVRKQTASFGEAFAEHEEFFRDNIEKVQKW 142 (160)
Q Consensus 82 -S~wc~~El~~~~~~~~~~~~iiPVf~~---------v~p~~v~~~~~~f~~~f~~~~~~~~~~~~~~~~W 142 (160)
-.|...|+.-+.++ ++.|||||-. +.|.|++..+..-|..|...++... .+++.++
T Consensus 686 CeDWVHKEl~~Afe~---~KNIiPI~D~aFE~Pt~ed~iPnDirmi~kyNGvKWvHdYQdA~--maKvvRF 751 (832)
T KOG3678|consen 686 CEDWVHKELKCAFEH---QKNIIPIFDTAFEFPTKEDQIPNDIRMITKYNGVKWVHDYQDAC--MAKVVRF 751 (832)
T ss_pred HHHHHHHHHHHHHHh---cCCeeeeecccccCCCchhcCcHHHHHHHhccCeeeehhhHHHH--HHHHHHH
Confidence 35777788877775 6789999843 7788888777655666666555433 4555555
No 7
>PF08937 DUF1863: MTH538 TIR-like domain (DUF1863); InterPro: IPR015032 This protein adopts the flavodoxin fold, that is, five parallel beta-strands and four helical segments. The structure is a three-layer sandwich with alpha-1 and alpha-4 on one side of the beta-sheet, and alpha-2 and alpha-3 on the other side. Probable role in signal transduction as a phosphorylation-independent conformational switch protein []. This domain is similar to the TIR domain [].; PDB: 3HYN_A.
Probab=98.84 E-value=6.2e-09 Score=74.18 Aligned_cols=91 Identities=20% Similarity=0.335 Sum_probs=49.3
Q ss_pred ccEEEecccCCCcchHHHHHHHHHhcC-------CcEE----------EEeCCCCCCCCCchHHHHHHHHhcceEEEEee
Q 045860 14 YDAFLSFRGEDTRKGFIGYLYTALNNK-------GIYV----------FRDDKQLEKGGSISPNLLKAIDESRISIIVLS 76 (160)
Q Consensus 14 ~dVFISy~~~D~~~~fv~~L~~~L~~~-------gi~v----------~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS 76 (160)
|.|||||++.|.. ..+..|...+... .+.. .-+..+......+...|.+.|..|+++||+++
T Consensus 1 ~~vFIS~~~~d~~-~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~I~~~i~~s~~~IVLig 79 (130)
T PF08937_consen 1 YKVFISYSHDDDD-WYYDQLKEWLENSYEIPRDKNFDFRFYDVSKWEPIRSRDDDSSSEYIKRKIRERIKNSSVTIVLIG 79 (130)
T ss_dssp ----------THH--HHHHHHHHHHH-------TTSS--BT---TTT---TTS---TTTTHHHHHHHHHHTEEEEEEE--
T ss_pred CCccccccccCcH-HHHHHHHHHhccccccccccccccCcccccccCcccCccccchHHHHHHHHHHHHhcCCEEEEEeC
Confidence 5799999998864 2466677777663 1211 11222223345788899999999999999999
Q ss_pred cCCCCChhHHHHHHHHHHHhhcCCceeeEEec
Q 045860 77 KNYASSTWCLDELLKITECKNREDQIFPIFYG 108 (160)
Q Consensus 77 ~~~~~S~wc~~El~~~~~~~~~~~~iiPVf~~ 108 (160)
++...|.|+.+|+..+++ .+..||.|.++
T Consensus 80 ~~T~~s~wV~~EI~~A~~---~~~~Ii~V~~~ 108 (130)
T PF08937_consen 80 PNTAKSKWVNWEIEYALK---KGKPIIGVYLP 108 (130)
T ss_dssp TT----HHHHHHHHHHTT---T---EEEEETT
T ss_pred CCcccCcHHHHHHHHHHH---CCCCEEEEECC
Confidence 999999999999999887 57788888764
No 8
>PF08357 SEFIR: SEFIR domain; InterPro: IPR013568 This domain is found in IL17 receptors (IL17Rs, e.g. Q60943 from SWISSPROT) and SEF proteins (e.g. Q8QHJ9 from SWISSPROT). The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (IPR000157 from INTERPRO), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways [].
Probab=98.04 E-value=1e-05 Score=58.62 Aligned_cols=65 Identities=23% Similarity=0.321 Sum_probs=52.9
Q ss_pred cEEEecccCCCcc-hHHHHHHHHHhcC-CcEEEEeCCCCCC--CCCchHHHHHHHHhcceEEEEeecCC
Q 045860 15 DAFLSFRGEDTRK-GFIGYLYTALNNK-GIYVFRDDKQLEK--GGSISPNLLKAIDESRISIIVLSKNY 79 (160)
Q Consensus 15 dVFISy~~~D~~~-~fv~~L~~~L~~~-gi~v~~d~~d~~~--G~~~~~~i~~~I~~S~~~ivvlS~~~ 79 (160)
-|||||+.....+ ..|..|...|++. |+.|.+|..+... +..+..=+.+.+++++.+|+|.||.+
T Consensus 2 kVfI~Ys~d~~~h~~~V~~la~~L~~~~g~~V~lD~~~~~~i~~~g~~~W~~~~~~~ad~Vliv~S~~~ 70 (150)
T PF08357_consen 2 KVFISYSHDSEEHKEWVLALAEFLRQNCGIDVILDQWELNEIARQGPPRWMERQIREADKVLIVCSPGY 70 (150)
T ss_pred eEEEEeCCCCHHHHHHHHHHHHHHHhccCCceeecHHhhcccccCCHHHHHHHHHhcCCEEEEEeccch
Confidence 4999998855432 4588899999999 9999999888743 55666677888999999999999543
No 9
>PF10137 TIR-like: Predicted nucleotide-binding protein containing TIR-like domain; InterPro: IPR019302 This entry represents a TIR-like domain found in a family of prokaryotic predicted nucleotide-binding proteins. Their exact function has not, as yet, been defined.
Probab=97.35 E-value=0.00097 Score=47.32 Aligned_cols=78 Identities=17% Similarity=0.126 Sum_probs=62.1
Q ss_pred cEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCC-------------C
Q 045860 15 DAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYA-------------S 81 (160)
Q Consensus 15 dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~-------------~ 81 (160)
.|||.|+ .|. ..+..+...|+..|+.+.+-......|..+.+.+.+.+.+++..|++++|+=. .
T Consensus 1 kVFIvhg-~~~--~~~~~v~~~L~~~~~ep~i~~~~~~~g~tiie~le~~~~~~~faIvl~TpDD~~~~~~~~~~~~~~a 77 (125)
T PF10137_consen 1 KVFIVHG-RDL--AAAEAVERFLEKLGLEPIIWHEQPNLGQTIIEKLEEAADSVDFAIVLFTPDDIGYSRGEEEDLQPRA 77 (125)
T ss_pred CEEEEeC-CCH--HHHHHHHHHHHhCCCceEEeecCCCCCCchHHHHHHHhccCCEEEEEEcccccccccCCcccccccc
Confidence 3899998 554 56788999999889877766656689999999999999999999999999611 1
Q ss_pred ChhHHHHHHHHHHH
Q 045860 82 STWCLDELLKITEC 95 (160)
Q Consensus 82 S~wc~~El~~~~~~ 95 (160)
......|+..++.+
T Consensus 78 R~NVifE~G~f~g~ 91 (125)
T PF10137_consen 78 RQNVIFELGLFIGK 91 (125)
T ss_pred ccceeehhhHHHhh
Confidence 23467788888875
No 10
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=94.89 E-value=0.15 Score=33.25 Aligned_cols=66 Identities=24% Similarity=0.215 Sum_probs=48.1
Q ss_pred cEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCC-CCCCchHHHHHHHHhcceEEEEeecCCCCC
Q 045860 15 DAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLE-KGGSISPNLLKAIDESRISIIVLSKNYASS 82 (160)
Q Consensus 15 dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~-~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S 82 (160)
.||||=.-.|.. .-...|...+.+.|+.+..-+. +. .+....+.+.+.|++|++.|.++-..|-..
T Consensus 1 rVFiSSt~~Dl~-~eR~~l~~~i~~~~~~~~~~e~-~~a~~~~~~~~cl~~v~~cDifI~ilG~rYG~~ 67 (83)
T PF13271_consen 1 RVFISSTFRDLK-EERDALIEAIRRLGCEPVGMEF-FPASDQSPLEICLKEVDECDIFILILGNRYGSV 67 (83)
T ss_pred CEEEecChhhHH-HHHHHHHHHHHHCCCeeeeeee-ecCCCCCHHHHHHHHHhhCCEEEEeeccccCCC
Confidence 389998777764 4467788889887765443321 32 345556778899999999999999998754
No 11
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=93.97 E-value=0.073 Score=42.21 Aligned_cols=95 Identities=22% Similarity=0.154 Sum_probs=65.3
Q ss_pred CCCCcccEEEecccCCCcchHHHHHHHHHhcC--CcEEEEeCC---CCCCCCCchHHHHHHH-HhcceEEEEeecCCCCC
Q 045860 9 ISCGKYDAFLSFRGEDTRKGFIGYLYTALNNK--GIYVFRDDK---QLEKGGSISPNLLKAI-DESRISIIVLSKNYASS 82 (160)
Q Consensus 9 ~~~~~~dVFISy~~~D~~~~fv~~L~~~L~~~--gi~v~~d~~---d~~~G~~~~~~i~~~I-~~S~~~ivvlS~~~~~S 82 (160)
...+.||+=+||.++-. +.|.++..+++.+ .+..|.|-. -+.+| ++.+.+...- .+|++.+|++..+|...
T Consensus 173 ~~~~~~DiG~SFaGEAR--~LVEqV~~E~~~~~~p~~~FYD~~~~~~L~~~-sL~~~L~~~Y~~rC~~~~VF~~~~Y~~K 249 (329)
T COG4916 173 SSEKPVDSGISFAGEAR--NLVEQVQTEHSGLDIPTRRFYDLLVAHPLYPG-SLVSTLDPGYDIRCVVTTVFNTGSYICK 249 (329)
T ss_pred ccccccceeeEeehhhh--hHHHHHHHhhhcccCCceeeeechhhccccCc-cHHHhcccccCceEEEEEEEeCCceEEe
Confidence 45678999999998863 7899999999955 466777641 12222 2222222222 26999999999999999
Q ss_pred hhHHHHHHHHHHHhhcCCceeeEEe
Q 045860 83 TWCLDELLKITECKNREDQIFPIFY 107 (160)
Q Consensus 83 ~wc~~El~~~~~~~~~~~~iiPVf~ 107 (160)
.||..|...+-.- ..-+.++||.|
T Consensus 250 ~~c~~E~~~~r~~-~~~d~~~rI~~ 273 (329)
T COG4916 250 STCHIEGLEGRLN-PILDTGFRIKY 273 (329)
T ss_pred eeeccchhhcccc-ccccccceEEE
Confidence 9999998765543 22235666665
No 12
>PF05014 Nuc_deoxyrib_tr: Nucleoside 2-deoxyribosyltransferase; InterPro: IPR007710 Nucleoside 2-deoxyribosyltransferase (2.4.2.6 from EC) catalyses the cleavage of the glycosidic bonds of 2-deoxyribonucleosides. Nucleoside 2-deoxyribosyltransferases can be divided into two groups based on their substrate specificity: class I enzymes are specific for the transfer of deoxyribose between two purines, while class II enzymes will transfer the deoxyribose between either purines or pyrimidines. The structure of the class I [] and class II [] enzymes are very similar. In class I enzymes, the purine base shields the active site from solvent, which the smaller pyrimidine base cannot do, while in class II enzymes the active site is shielded by a loop (residues 48-62). Both classes of enzymes are found in various Lactobacillus species and participate in nucleoside recycling in these microorganisms. This entry represents both classes of enzymes.; GO: 0050144 nucleoside deoxyribosyltransferase activity, 0070694 deoxyribonucleoside 5'-monophosphate N-glycosidase activity, 0009159 deoxyribonucleoside monophosphate catabolic process; PDB: 1S2L_A 1S2D_C 1S2I_A 1S3F_B 1S2G_C 2A0K_A 2F67_A 2F64_B 2F62_A 2F2T_A ....
Probab=91.99 E-value=1.7 Score=29.67 Aligned_cols=80 Identities=18% Similarity=0.120 Sum_probs=54.3
Q ss_pred chHHHHHHHHHhcCCcEEEEeCC-CCC---CCCCchHHH----HHHHHhcceEEEEeecCCCCChhHHHHHHHHHHHhhc
Q 045860 27 KGFIGYLYTALNNKGIYVFRDDK-QLE---KGGSISPNL----LKAIDESRISIIVLSKNYASSTWCLDELLKITECKNR 98 (160)
Q Consensus 27 ~~fv~~L~~~L~~~gi~v~~d~~-d~~---~G~~~~~~i----~~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~~~~~~ 98 (160)
...+..+...|++.|+.++.-.+ +.. .+..+..+| .++|++|+++|+++.+.- .+.-+..|+..|...
T Consensus 13 ~~~~~~~~~~L~~~g~~v~~P~~~~~~~~~~~~~~~~~i~~~d~~~i~~~D~via~l~~~~-~d~Gt~~ElG~A~al--- 88 (113)
T PF05014_consen 13 KARVERLREALEKNGFEVYSPQDNDENDEEDSQEWAREIFERDLEGIRECDIVIANLDGFR-PDSGTAFELGYAYAL--- 88 (113)
T ss_dssp HHHHHHHHHHHHTTTTEEEGGCTCSSS--TTSHHCHHHHHHHHHHHHHHSSEEEEEECSSS---HHHHHHHHHHHHT---
T ss_pred HHHHHHHHHHHHhCCCEEEeccccccccccccchHHHHHHHHHHHHHHHCCEEEEECCCCC-CCCcHHHHHHHHHHC---
Confidence 45688899999999998886542 221 122233333 568999999999988755 667788999999874
Q ss_pred CCceeeEEeccC
Q 045860 99 EDQIFPIFYGVE 110 (160)
Q Consensus 99 ~~~iiPVf~~v~ 110 (160)
+++|+-+.-+..
T Consensus 89 gkpv~~~~~d~~ 100 (113)
T PF05014_consen 89 GKPVILLTEDDR 100 (113)
T ss_dssp TSEEEEEECCCC
T ss_pred CCEEEEEEcCCc
Confidence 556655544433
No 13
>cd00860 ThrRS_anticodon ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=87.40 E-value=3.3 Score=26.45 Aligned_cols=59 Identities=10% Similarity=0.112 Sum_probs=37.6
Q ss_pred ccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHH-hcceEEEEeecC
Q 045860 14 YDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAID-ESRISIIVLSKN 78 (160)
Q Consensus 14 ~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~-~S~~~ivvlS~~ 78 (160)
++|+|...+.+. ...+..+...|++.|+++-+|.+. ..+...+..+-. +....|+ +.++
T Consensus 2 ~~v~ii~~~~~~-~~~a~~~~~~Lr~~g~~v~~d~~~----~~~~~~~~~a~~~g~~~~ii-ig~~ 61 (91)
T cd00860 2 VQVVVIPVTDEH-LDYAKEVAKKLSDAGIRVEVDLRN----EKLGKKIREAQLQKIPYILV-VGDK 61 (91)
T ss_pred eEEEEEeeCchH-HHHHHHHHHHHHHCCCEEEEECCC----CCHHHHHHHHHHcCCCEEEE-ECcc
Confidence 687777654433 345778999999999999998743 344455555543 3344444 4443
No 14
>COG4271 Predicted nucleotide-binding protein containing TIR -like domain [Transcription]
Probab=83.63 E-value=4.1 Score=31.29 Aligned_cols=86 Identities=16% Similarity=0.136 Sum_probs=59.2
Q ss_pred cEEEecccCCCcchHHHHHHHHHhcC-C-cEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCC-----C------
Q 045860 15 DAFLSFRGEDTRKGFIGYLYTALNNK-G-IYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYA-----S------ 81 (160)
Q Consensus 15 dVFISy~~~D~~~~fv~~L~~~L~~~-g-i~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~-----~------ 81 (160)
-|||-|+++- .+.....+|.+. . ..+|.|. -...|..+.+.+.+-|.+++..|++++|+=. .
T Consensus 84 kvFvv~ghd~----iArael~allrd~~l~~vi~d~-~~~~g~~ile~lek~i~~v~FAi~latPDDkgy~~~~~~~k~~ 158 (233)
T COG4271 84 KVFVVSGHDA----IARAELEALLRDWKLEPVILDG-LFSEGQTILESLEKYIAEVKFAIVLATPDDKGYRAVHSREKAF 158 (233)
T ss_pred eEEEEeccHH----HHHHHHHHHhhccccceEEecC-cccccHHHHHHHHHHhhhceEEEEEecCcccccccccchhhcc
Confidence 8999996543 455555666543 4 4566665 6778999999999999999999999999833 1
Q ss_pred ---ChhHHHHHHHHHHHhhcCCceeeEE
Q 045860 82 ---STWCLDELLKITECKNREDQIFPIF 106 (160)
Q Consensus 82 ---S~wc~~El~~~~~~~~~~~~iiPVf 106 (160)
......||...+.+ ..+.+|+.+.
T Consensus 159 praRqNVifELGm~mgr-LgRkrv~Il~ 185 (233)
T COG4271 159 PRARQNVIFELGMFMGR-LGRKRVMILM 185 (233)
T ss_pred ccccccchhhHhhHHhh-cccceEEEEe
Confidence 12356788777775 2234444443
No 15
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=81.38 E-value=13 Score=24.68 Aligned_cols=64 Identities=13% Similarity=0.066 Sum_probs=44.4
Q ss_pred HHHHHHHHhcCCcEEEEeCC-CCCCCCCchHHHH---HHHHhcceEEEEeecCCCCChhHHHHHHHHHHH
Q 045860 30 IGYLYTALNNKGIYVFRDDK-QLEKGGSISPNLL---KAIDESRISIIVLSKNYASSTWCLDELLKITEC 95 (160)
Q Consensus 30 v~~L~~~L~~~gi~v~~d~~-d~~~G~~~~~~i~---~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~~~ 95 (160)
.......|+.+|+.|.-=-. ....|.++.+-+. ..+..|+..++. |++-.|.-|+-|...|...
T Consensus 18 f~~~a~~L~~~G~~vvnPa~~~~~~~~~~~~ym~~~l~~L~~cD~i~~l--~gWe~S~GA~~E~~~A~~l 85 (92)
T PF14359_consen 18 FNAAAKRLRAKGYEVVNPAELGIPEGLSWEEYMRICLAMLSDCDAIYML--PGWENSRGARLEHELAKKL 85 (92)
T ss_pred HHHHHHHHHHCCCEEeCchhhCCCCCCCHHHHHHHHHHHHHhCCEEEEc--CCcccCcchHHHHHHHHHC
Confidence 45588899999976653221 2356666655443 445577755554 9999999999999988874
No 16
>cd00738 HGTP_anticodon HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b).
Probab=80.48 E-value=7.6 Score=24.80 Aligned_cols=61 Identities=20% Similarity=0.204 Sum_probs=38.0
Q ss_pred ccEEEecccCC--CcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecC
Q 045860 14 YDAFLSFRGED--TRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKN 78 (160)
Q Consensus 14 ~dVFISy~~~D--~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~ 78 (160)
++|+|...+.+ .....+..+...|++.|+.+-+|.. +..+...+..+-...-..++++.++
T Consensus 2 ~~v~ii~~~~~~~~~~~~a~~~~~~Lr~~g~~v~~~~~----~~~~~k~~~~a~~~g~~~~iiig~~ 64 (94)
T cd00738 2 IDVAIVPLTDPRVEAREYAQKLLNALLANGIRVLYDDR----ERKIGKKFREADLRGVPFAVVVGED 64 (94)
T ss_pred eEEEEEECCCCcHHHHHHHHHHHHHHHHCCCEEEecCC----CcCHhHHHHHHHhCCCCEEEEECCC
Confidence 57777654330 1235677899999999999999763 3455555555544333456666653
No 17
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=79.58 E-value=10 Score=23.29 Aligned_cols=60 Identities=20% Similarity=0.245 Sum_probs=37.2
Q ss_pred HHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCCChhHHHHHHHHHHH-hhcCCce
Q 045860 30 IGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYASSTWCLDELLKITEC-KNREDQI 102 (160)
Q Consensus 30 v~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~~~-~~~~~~i 102 (160)
..-++..|++.|+++-.... ..+.+...+.++++++|.+.-+. ..++....+. +.++..|
T Consensus 7 ~~a~~~~L~~~g~~v~~~~~-----------~~~~l~~~~~tll~i~~~~~~~~--~~~~~~l~~~v~~G~~lv 67 (70)
T PF14258_consen 7 TYALYQLLEEQGVKVERWRK-----------PYEALEADDGTLLVIGPDLRLSE--PEEAEALLEWVEAGNTLV 67 (70)
T ss_pred HHHHHHHHHHCCCeeEEecc-----------cHHHhCCCCCEEEEEeCCCCCCc--hHHHHHHHHHHHcCCEEE
Confidence 34588889999998864431 12244558889999999966554 3455544444 4344333
No 18
>COG0400 Predicted esterase [General function prediction only]
Probab=76.53 E-value=12 Score=28.66 Aligned_cols=57 Identities=25% Similarity=0.139 Sum_probs=43.5
Q ss_pred CCCCCcccEEEecccCCC--cchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHH
Q 045860 8 NISCGKYDAFLSFRGEDT--RKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAID 66 (160)
Q Consensus 8 ~~~~~~~dVFISy~~~D~--~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~ 66 (160)
.+.....-|||+|...|. ......+|.+.|++.|..|..... ..|..+..+-.+.+.
T Consensus 141 ~~~~~~~pill~hG~~Dpvvp~~~~~~l~~~l~~~g~~v~~~~~--~~GH~i~~e~~~~~~ 199 (207)
T COG0400 141 LPDLAGTPILLSHGTEDPVVPLALAEALAEYLTASGADVEVRWH--EGGHEIPPEELEAAR 199 (207)
T ss_pred ccccCCCeEEEeccCcCCccCHHHHHHHHHHHHHcCCCEEEEEe--cCCCcCCHHHHHHHH
Confidence 445667889999988886 445678899999999999998864 378888766555554
No 19
>cd00858 GlyRS_anticodon GlyRS Glycyl-anticodon binding domain. GlyRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=74.97 E-value=16 Score=25.09 Aligned_cols=62 Identities=15% Similarity=0.061 Sum_probs=39.2
Q ss_pred CcccEEEecccC-CCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecC
Q 045860 12 GKYDAFLSFRGE-DTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKN 78 (160)
Q Consensus 12 ~~~dVFISy~~~-D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~ 78 (160)
..++|||...++ +.....+..|...|+++|+++-+|.+ ..+...+..+-+.--..++++.++
T Consensus 25 ap~~v~Ii~~~~~~~~~~~a~~la~~LR~~gi~v~~d~~-----~sl~kqlk~A~k~g~~~~iiiG~~ 87 (121)
T cd00858 25 APIKVAVLPLVKRDELVEIAKEISEELRELGFSVKYDDS-----GSIGRRYARQDEIGTPFCVTVDFD 87 (121)
T ss_pred CCcEEEEEecCCcHHHHHHHHHHHHHHHHCCCEEEEeCC-----CCHHHHHHHhHhcCCCEEEEECcC
Confidence 357888877551 21234567799999999999999863 344455555544333345555554
No 20
>PF03129 HGTP_anticodon: Anticodon binding domain; InterPro: IPR004154 tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [] it is probably the anticodon binding domain [].; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding; PDB: 1KOG_B 1EVL_D 1EVK_B 1QF6_A 1FYF_B 2I4O_A 2I4M_A 2I4N_A 2I4L_A 1HC7_D ....
Probab=74.09 E-value=13 Score=23.91 Aligned_cols=44 Identities=25% Similarity=0.221 Sum_probs=31.2
Q ss_pred chHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHH-hcceEEEE
Q 045860 27 KGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAID-ESRISIIV 74 (160)
Q Consensus 27 ~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~-~S~~~ivv 74 (160)
..++.+|...|++.|+++.+|.. +..+...+..+-. +....|+|
T Consensus 15 ~~~a~~l~~~L~~~gi~v~~d~~----~~~~~k~~~~a~~~g~p~~iii 59 (94)
T PF03129_consen 15 IEYAQELANKLRKAGIRVELDDS----DKSLGKQIKYADKLGIPFIIII 59 (94)
T ss_dssp HHHHHHHHHHHHHTTSEEEEESS----SSTHHHHHHHHHHTTESEEEEE
T ss_pred HHHHHHHHHHHHHCCCEEEEECC----CCchhHHHHHHhhcCCeEEEEE
Confidence 35688899999999999999974 4455566666654 44444444
No 21
>cd07373 2A5CPDO_A The alpha subunit of the Class III extradiol dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol. 2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO) catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, which is an intermediate during p-chloronitrobenzene degradation. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. The active enzyme is probably a heterotetramer, composed of two alpha and two beta subunits. The alpha and beta subunits share significant sequence similarity and may have evolved by gene duplication. This model describes the alpha subunit, which does not contain a potential metal binding site and may not possess catalytic activity.
Probab=72.65 E-value=31 Score=27.37 Aligned_cols=77 Identities=16% Similarity=0.155 Sum_probs=55.2
Q ss_pred chHHHHHHHHHhcCCcEEE-EeCC--CCCCCCCchHHHHHHHH--hcceEEEEeecCCCCChhHHHHHHHHHHH--hhcC
Q 045860 27 KGFIGYLYTALNNKGIYVF-RDDK--QLEKGGSISPNLLKAID--ESRISIIVLSKNYASSTWCLDELLKITEC--KNRE 99 (160)
Q Consensus 27 ~~fv~~L~~~L~~~gi~v~-~d~~--d~~~G~~~~~~i~~~I~--~S~~~ivvlS~~~~~S~wc~~El~~~~~~--~~~~ 99 (160)
..++..|...|.+.|+.+- ++.. .+..|.-+. ..-+. ..++-||.+|.+...+....++|.+++.. +..+
T Consensus 90 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vP---L~~l~~~~~~iPvV~~s~~~~~~~~~~~~lG~al~~~l~~~~ 166 (271)
T cd07373 90 TALAEACVTACPEHGVHARGVDYDGFPIDTGTITA---CTLMGIGTEALPLVVASNNLYHSGEITEKLGAIAADAAKDQN 166 (271)
T ss_pred HHHHHHHHHHHHHCCCcEEEecCCCCCCcchhHHH---HHHHcccCCCCCEEEEEeCCCCCHHHHHHHHHHHHHHHHHcC
Confidence 4789999999999999886 6663 344553321 22332 46777888999887788888999999996 5555
Q ss_pred CceeeEE
Q 045860 100 DQIFPIF 106 (160)
Q Consensus 100 ~~iiPVf 106 (160)
.+|+.|-
T Consensus 167 ~rV~iIg 173 (271)
T cd07373 167 KRVAVVG 173 (271)
T ss_pred CeEEEEE
Confidence 6777664
No 22
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=72.49 E-value=5.8 Score=31.74 Aligned_cols=98 Identities=22% Similarity=0.407 Sum_probs=70.0
Q ss_pred CcccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCC--CCCCCchHHHHHHH-HhcceEEEEeecCCCCChhHHHH
Q 045860 12 GKYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQL--EKGGSISPNLLKAI-DESRISIIVLSKNYASSTWCLDE 88 (160)
Q Consensus 12 ~~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~--~~G~~~~~~i~~~I-~~S~~~ivvlS~~~~~S~wc~~E 88 (160)
.++.+=+||.+.|. ..++...+.|..+|+.++.|-.+= .-|..+.+-+.+-- +..-+++.++|.+|-.-.|-..|
T Consensus 5 ~~~~~a~~f~~~d~--~~~~~~~n~~~~~~v~~~y~~~~~a~~~~~~~~~~~~e~~q~~~~~~~~f~~~~~~r~~~~~~~ 82 (329)
T COG4916 5 VQFEIALSFAGEDR--EYVDRVANLLREAGVTVFYDIFEEANLWGKNLYDYLSEIYQDKALFTIMFISEHYSRKMWTNHE 82 (329)
T ss_pred hheeeeeeecCchH--HHHHHHHHHHHhhccEEEEeehhhhhhhhhHHHHHHHHHHhhhhHHHhhhhhccccCcCCCcHH
Confidence 35667789988885 678999999999999999874221 12333332222211 24566888999999999999999
Q ss_pred HHHHHHH--hhcCCceeeEEeccCc
Q 045860 89 LLKITEC--KNREDQIFPIFYGVEP 111 (160)
Q Consensus 89 l~~~~~~--~~~~~~iiPVf~~v~p 111 (160)
++..+.+ .+....++|-.++..|
T Consensus 83 ~~~~~a~~~~~~~~~~~~~~~~~~~ 107 (329)
T COG4916 83 RQAMQARAFQEHQEYILPARFDETP 107 (329)
T ss_pred HHHHHHHHhhhccEEehhhhhccCC
Confidence 9888876 5566688888887554
No 23
>PF08902 DUF1848: Domain of unknown function (DUF1848); InterPro: IPR014998 This group of proteins are functionally uncharacterised. The C terminus contains a cluster of cysteines that are similar to the iron-sulphur cluster found at the N terminus of IPR007197 from INTERPRO.
Probab=67.94 E-value=62 Score=25.96 Aligned_cols=132 Identities=20% Similarity=0.316 Sum_probs=77.4
Q ss_pred ccEEEecccCCCcchHHHHHHHHHhcCCcEEEEe------CCCCCCCCCchHHHHHHHHh------cceEE-----EEee
Q 045860 14 YDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRD------DKQLEKGGSISPNLLKAIDE------SRISI-----IVLS 76 (160)
Q Consensus 14 ~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d------~~d~~~G~~~~~~i~~~I~~------S~~~i-----vvlS 76 (160)
-|.++ |-.++.. .|..+| +.|+++|++.++. .++++|+-+-.+++.+.+.+ ...+| +++|
T Consensus 48 Vd~iV-FWTKnp~-P~l~~L-~~l~~~gy~~yfq~Tit~Y~~~lEp~vP~~~~~i~~f~~Ls~~iG~~rViWRYDPIil~ 124 (266)
T PF08902_consen 48 VDCIV-FWTKNPA-PFLPYL-DELDERGYPYYFQFTITGYGKDLEPNVPPKDERIETFRELSERIGPERVIWRYDPIILT 124 (266)
T ss_pred ceEEE-EecCCcH-HHHhhH-HHHHhCCCceEEEEEeCCCCccccCCCCCHHHHHHHHHHHHHHHCCCcEEEecCCEeEC
Confidence 34444 4455543 566544 7778889988876 56788886555544444332 22333 4566
Q ss_pred cCCCCChhHHHHHHHHHHH-hhcCCceeeEEeccCchhhhcccchHHHHHHHHHH-hhcCCHHHHHHHHHHHHHhhcccc
Q 045860 77 KNYASSTWCLDELLKITEC-KNREDQIFPIFYGVEPTVVRKQTASFGEAFAEHEE-FFRDNIEKVQKWRHALKVVANISG 154 (160)
Q Consensus 77 ~~~~~S~wc~~El~~~~~~-~~~~~~iiPVf~~v~p~~v~~~~~~f~~~f~~~~~-~~~~~~~~~~~W~~al~~v~~~~g 154 (160)
..|.- .|-+..+..+.+. .....+++-=|++..+.--++ +..+.- -..-+++....--..|.+++.-.|
T Consensus 125 ~~~~~-~~h~~~F~~la~~L~g~t~~~viSF~D~Y~k~~~~--------l~~~~~~~~~~~~~~~~~l~~~l~~ia~~~g 195 (266)
T PF08902_consen 125 DKYTV-DYHLEAFERLAEALAGYTDRCVISFLDLYRKVRRN--------LARLGFRIREPSEEEKRELAKRLAEIAKKYG 195 (266)
T ss_pred CCCCH-HHHHHHHHHHHHHHhccCCEEEEEeeeccHHHHHH--------HHhhcCCCCCCCHHHHHHHHHHHHHHHHHcC
Confidence 66444 6777777777777 666678888888874433222 111110 012235666667778888877777
Q ss_pred eec
Q 045860 155 WEL 157 (160)
Q Consensus 155 ~~~ 157 (160)
..+
T Consensus 196 ~~l 198 (266)
T PF08902_consen 196 MTL 198 (266)
T ss_pred CEE
Confidence 554
No 24
>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
Probab=65.94 E-value=34 Score=22.26 Aligned_cols=63 Identities=17% Similarity=0.128 Sum_probs=38.0
Q ss_pred EEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCC-------CCCCchHHHHHHHHhcceEEEEeecC
Q 045860 16 AFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLE-------KGGSISPNLLKAIDESRISIIVLSKN 78 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~-------~G~~~~~~i~~~I~~S~~~ivvlS~~ 78 (160)
+|.|..+.-.+-.++.+|...|.++|.++.+-+-|.. .+..+.......+..|+..|+++.+.
T Consensus 3 ~~~~~kgG~Gkst~~~~la~~~~~~~~~vl~~d~d~~~d~viiD~p~~~~~~~~~~l~~ad~viv~~~~~ 72 (104)
T cd02042 3 AVANQKGGVGKTTTAVNLAAALARRGKRVLLIDLDPQYDYIIIDTPPSLGLLTRNALAAADLVLIPVQPS 72 (104)
T ss_pred EEEeCCCCcCHHHHHHHHHHHHHhCCCcEEEEeCCCCCCEEEEeCcCCCCHHHHHHHHHCCEEEEeccCC
Confidence 3566655444345577799999988988777654433 11112233446666777777776665
No 25
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=61.07 E-value=38 Score=22.27 Aligned_cols=45 Identities=13% Similarity=0.194 Sum_probs=31.0
Q ss_pred HHHHHHHHhcCCcEEEEeCCCCCCCCC-chHHHHHHHHhcceEEEEee
Q 045860 30 IGYLYTALNNKGIYVFRDDKQLEKGGS-ISPNLLKAIDESRISIIVLS 76 (160)
Q Consensus 30 v~~L~~~L~~~gi~v~~d~~d~~~G~~-~~~~i~~~I~~S~~~ivvlS 76 (160)
...+...+++.|...-...+ ..|.. -...+...|.+++.+|++..
T Consensus 12 ~~~~~~~~~~~G~~~~~hg~--~~~~~~~~~~l~~~i~~aD~VIv~t~ 57 (97)
T PF10087_consen 12 ERRYKRILEKYGGKLIHHGR--DGGDEKKASRLPSKIKKADLVIVFTD 57 (97)
T ss_pred HHHHHHHHHHcCCEEEEEec--CCCCccchhHHHHhcCCCCEEEEEeC
Confidence 56788999999988766621 12222 22358889999999888743
No 26
>cd00859 HisRS_anticodon HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=59.51 E-value=37 Score=20.96 Aligned_cols=34 Identities=24% Similarity=0.128 Sum_probs=23.9
Q ss_pred cEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCC
Q 045860 15 DAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDK 49 (160)
Q Consensus 15 dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~ 49 (160)
||+|...+... ..-+-.+...|++.|+++.++..
T Consensus 3 ~v~i~~~~~~~-~~~a~~i~~~Lr~~g~~v~~~~~ 36 (91)
T cd00859 3 DVYVVPLGEGA-LSEALELAEQLRDAGIKAEIDYG 36 (91)
T ss_pred cEEEEEcChHH-HHHHHHHHHHHHHCCCEEEEecC
Confidence 67776544332 23366799999999999988753
No 27
>TIGR00418 thrS threonyl-tRNA synthetase. This model represents the threonyl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. Note that B. subtilis has closely related isozymes thrS and thrZ. The N-terminal regions are quite dissimilar between archaeal and eubacterial forms, while some eukaryotic forms are missing sequence there altogether..
Probab=57.35 E-value=41 Score=29.48 Aligned_cols=61 Identities=15% Similarity=0.170 Sum_probs=41.3
Q ss_pred CcccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeec
Q 045860 12 GKYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSK 77 (160)
Q Consensus 12 ~~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~ 77 (160)
...+|+|..-+++. ...+..|...|+++|++|-+|.+ +..+...+..+-..--..++|+.+
T Consensus 469 ~p~~v~vi~~~~~~-~~~a~~ia~~LR~~Gi~v~~d~~----~~sl~~q~k~A~~~g~~~~iiiG~ 529 (563)
T TIGR00418 469 APVQVVVIPVNERH-LDYAKKVAQKLKKAGIRVDVDDR----NERLGKKIREAQKQKIPYMLVVGD 529 (563)
T ss_pred CCceEEEEEccchH-HHHHHHHHHHHHHcCCEEEEECC----CCCHHHHHHHHHhcCCCEEEEEch
Confidence 45788887755443 35688899999999999999874 445666666664433334444444
No 28
>cd00861 ProRS_anticodon_short ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=56.83 E-value=38 Score=21.58 Aligned_cols=47 Identities=23% Similarity=0.204 Sum_probs=29.5
Q ss_pred hHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecC
Q 045860 28 GFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKN 78 (160)
Q Consensus 28 ~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~ 78 (160)
..+..|...|++.|+++.+|.+.- .+...+..+-..---.++++.++
T Consensus 18 ~~a~~la~~Lr~~g~~v~~d~~~~----~l~k~i~~a~~~g~~~~iiiG~~ 64 (94)
T cd00861 18 ELAEKLYAELQAAGVDVLLDDRNE----RPGVKFADADLIGIPYRIVVGKK 64 (94)
T ss_pred HHHHHHHHHHHHCCCEEEEECCCC----CcccchhHHHhcCCCEEEEECCc
Confidence 457789999999999999987533 33344455433323344444444
No 29
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=56.06 E-value=58 Score=21.72 Aligned_cols=75 Identities=23% Similarity=0.256 Sum_probs=47.4
Q ss_pred HHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCCChhHHHHHHHHHHH-hhcCCceeeEEec
Q 045860 30 IGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYASSTWCLDELLKITEC-KNREDQIFPIFYG 108 (160)
Q Consensus 30 v~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~~~-~~~~~~iiPVf~~ 108 (160)
...|...|++.|+.+-+-+-+... +++.+.+.+.+.-++.+|-.+.. ...++....+. ++.+..+.-|+-+
T Consensus 17 l~~la~~l~~~G~~v~~~d~~~~~-----~~l~~~~~~~~pd~V~iS~~~~~---~~~~~~~l~~~~k~~~p~~~iv~GG 88 (121)
T PF02310_consen 17 LLYLAAYLRKAGHEVDILDANVPP-----EELVEALRAERPDVVGISVSMTP---NLPEAKRLARAIKERNPNIPIVVGG 88 (121)
T ss_dssp HHHHHHHHHHTTBEEEEEESSB-H-----HHHHHHHHHTTCSEEEEEESSST---HHHHHHHHHHHHHTTCTTSEEEEEE
T ss_pred HHHHHHHHHHCCCeEEEECCCCCH-----HHHHHHHhcCCCcEEEEEccCcC---cHHHHHHHHHHHHhcCCCCEEEEEC
Confidence 556999999999998654323222 67888888888888888775444 34445545544 4444555555555
Q ss_pred cCch
Q 045860 109 VEPT 112 (160)
Q Consensus 109 v~p~ 112 (160)
..++
T Consensus 89 ~~~t 92 (121)
T PF02310_consen 89 PHAT 92 (121)
T ss_dssp SSSG
T ss_pred Cchh
Confidence 5543
No 30
>KOG2792 consensus Putative cytochrome C oxidase assembly protein [Energy production and conversion]
Probab=55.90 E-value=19 Score=28.78 Aligned_cols=30 Identities=30% Similarity=0.521 Sum_probs=22.4
Q ss_pred hhHHHHHHHHHHH-----hhcCCceeeEEeccCch
Q 045860 83 TWCLDELLKITEC-----KNREDQIFPIFYGVEPT 112 (160)
Q Consensus 83 ~wc~~El~~~~~~-----~~~~~~iiPVf~~v~p~ 112 (160)
.-|.+||.+.... ...+..++|||.-++|.
T Consensus 153 DICPdELeKm~~~Vd~i~~~~~~~~~PlFIsvDPe 187 (280)
T KOG2792|consen 153 DICPDELEKMSAVVDEIEAKPGLPPVPLFISVDPE 187 (280)
T ss_pred CcChHHHHHHHHHHHHHhccCCCCccceEEEeCcc
Confidence 3688998776664 34566778999999884
No 31
>cd02426 Pol_gamma_b_Cterm C-terminal domain of mitochondrial DNA polymerase gamma B subunit, which is required for processivity. Polymerase gamma replicates and repairs mitochondrial DNA. The c-terminal domain of its B subunit is strikingly similar to the anticodon-binding domain of glycyl tRNA synthetase.
Probab=53.78 E-value=12 Score=26.41 Aligned_cols=45 Identities=13% Similarity=0.172 Sum_probs=29.3
Q ss_pred cccEEEecc-c-CCCcchHHHHHHHHHhcCCcEEEEeCCCC---CCCCCc
Q 045860 13 KYDAFLSFR-G-EDTRKGFIGYLYTALNNKGIYVFRDDKQL---EKGGSI 57 (160)
Q Consensus 13 ~~dVFISy~-~-~D~~~~fv~~L~~~L~~~gi~v~~d~~d~---~~G~~~ 57 (160)
.|+|=|--- . .+.-...+..|+..|++.|+++.+|+++- .+|..+
T Consensus 27 P~qV~Iipi~~~~~~~~~~a~~l~~~L~~~gi~v~~D~r~~~~~~~G~k~ 76 (128)
T cd02426 27 PYKVAIDCGKGDTAELRDLCQGLKNELREAGLSVWPGYLETQHSSLEQLL 76 (128)
T ss_pred CeEEEEEeccCChHHHHHHHHHHHHHHHHcCCEEEeccCcccccCHHHHH
Confidence 466644422 1 12224567889999999999999998764 455443
No 32
>cd07363 45_DOPA_Dioxygenase The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine. This subfamily is composed of plant 4,5-DOPA Dioxygenase, the uncharacterized Escherichia coli protein Jw3007, and similar proteins. 4,5-DOPA Dioxygenase catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine (4,5-DOPA). The reaction results in the opening of the cyclic ring between carbons 4 and 5 and producing an unstable seco-DOPA that rearranges to betalamic acid. 4,5-DOPA Dioxygenase is a key enzyme in the biosynthetic pathway of the plant pigment betalain. Homologs of DODA are present not only in betalain-producing plants but also in bacteria and archaea. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated ca
Probab=52.93 E-value=68 Score=25.12 Aligned_cols=76 Identities=16% Similarity=0.119 Sum_probs=53.4
Q ss_pred chHHHHHHHHHhcCCcEEEEeC-CCCCCCCCchHHHHHHHHhcceEEEEeecCCCCChhHHHHHHHHHHH-hhcCCceee
Q 045860 27 KGFIGYLYTALNNKGIYVFRDD-KQLEKGGSISPNLLKAIDESRISIIVLSKNYASSTWCLDELLKITEC-KNREDQIFP 104 (160)
Q Consensus 27 ~~fv~~L~~~L~~~gi~v~~d~-~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~~~-~~~~~~iiP 104 (160)
..++.+|.+.|+++|+.+-... +.+.-|.-+. +.-...+.++-||.+|-+...+..-..+|.+++.. +. .+|+.
T Consensus 80 ~eLa~~i~~~l~~~gi~~~~~~~~~lDHG~~vP--L~~~~p~~~iPvV~isi~~~~~~~~~~~lG~aL~~l~~--~~v~i 155 (253)
T cd07363 80 PELAERVAELLKAAGIPARLDPERGLDHGAWVP--LKLMYPDADIPVVQLSLPASLDPAEHYALGRALAPLRD--EGVLI 155 (253)
T ss_pred HHHHHHHHHHHHhcCCCccccCCcCCcccHHHH--HHHHcCCCCCcEEEEEecCCCCHHHHHHHHHHHHhhhh--CCEEE
Confidence 4789999999999999877654 3444553321 22223346888999999888788888899999987 43 35555
Q ss_pred EE
Q 045860 105 IF 106 (160)
Q Consensus 105 Vf 106 (160)
|-
T Consensus 156 i~ 157 (253)
T cd07363 156 IG 157 (253)
T ss_pred Ee
Confidence 53
No 33
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=52.93 E-value=55 Score=27.91 Aligned_cols=64 Identities=17% Similarity=0.121 Sum_probs=40.0
Q ss_pred cccEEEeccc--CCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCC
Q 045860 13 KYDAFLSFRG--EDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYA 80 (160)
Q Consensus 13 ~~dVFISy~~--~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~ 80 (160)
.++|+|---. .+.....+..|...|++.|+++.+|+++-..| ..+..+-..---.++|+.++-+
T Consensus 345 P~qV~Iipi~~~~~~~~~~a~~i~~~L~~~Gi~v~~D~~~~~lg----~ki~~a~~~giP~~iiVG~~e~ 410 (439)
T PRK12325 345 PFKVGIINLKQGDEACDAACEKLYAALSAAGIDVLYDDTDERPG----AKFATMDLIGLPWQIIVGPKGL 410 (439)
T ss_pred CeEEEEEecCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHh----HHHHHHHHcCCCEEEEECCccc
Confidence 5789876542 22223567889999999999999998754444 3444443322234555565543
No 34
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=52.61 E-value=1e+02 Score=23.57 Aligned_cols=97 Identities=16% Similarity=0.256 Sum_probs=57.2
Q ss_pred EEEecccCCCc--chHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHh--------------------------
Q 045860 16 AFLSFRGEDTR--KGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDE-------------------------- 67 (160)
Q Consensus 16 VFISy~~~D~~--~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~-------------------------- 67 (160)
.||.+-|-|.. -..+..|...|+.+|++|.+-.. +.|.++.+.|.+.+..
T Consensus 4 ~fI~iEGiDGaGKTT~~~~L~~~l~~~g~~v~~trE--P~~~~ige~iR~~ll~~~~~~~~~~e~lLfaadR~~h~~~~i 81 (208)
T COG0125 4 MFIVIEGIDGAGKTTQAELLKERLEERGIKVVLTRE--PGGTPIGEKIRELLLNGEEKLSPKAEALLFAADRAQHLEEVI 81 (208)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeC--CCCChHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47888666542 34577799999999998877642 2222333222221111
Q ss_pred ---cceEEEEeecCCCCChhHHH--------HHHHHHHH--hhcCCceeeEEeccCchhh
Q 045860 68 ---SRISIIVLSKNYASSTWCLD--------ELLKITEC--KNREDQIFPIFYGVEPTVV 114 (160)
Q Consensus 68 ---S~~~ivvlS~~~~~S~wc~~--------El~~~~~~--~~~~~~iiPVf~~v~p~~v 114 (160)
-...-+|+++.|.-|.-+-+ ++...+.. ...-.+-+-+|++++|+.-
T Consensus 82 ~pal~~g~vVI~DRy~~Ss~AYQg~~~~~~~~~~~~l~~~~~~~~~PD~ti~Ldv~~e~a 141 (208)
T COG0125 82 KPALKEGKVVICDRYVDSSLAYQGGGRGLDLDWVLALNEFAPGGLKPDLTLYLDVPPEVA 141 (208)
T ss_pred HHhhcCCCEEEECCcccHHHHhhhhccCCCHHHHHHHHHhccCCCCCCEEEEEeCCHHHH
Confidence 11134788899998887755 33333333 2222456778889999774
No 35
>TIGR02298 HpaD_Fe 3,4-dihydroxyphenylacetate 2,3-dioxygenase. This enzyme catalyzes the ring-opening step in the degradation of 4-hydroxyphenylacetate.
Probab=48.79 E-value=1.4e+02 Score=23.91 Aligned_cols=77 Identities=6% Similarity=0.111 Sum_probs=52.5
Q ss_pred chHHHHHHHHHhcCCcEEEE---eCCCCCCCCCchHHHHHHH-HhcceEEEEeecC-CCCChhHHHHHHHHHHH--hhcC
Q 045860 27 KGFIGYLYTALNNKGIYVFR---DDKQLEKGGSISPNLLKAI-DESRISIIVLSKN-YASSTWCLDELLKITEC--KNRE 99 (160)
Q Consensus 27 ~~fv~~L~~~L~~~gi~v~~---d~~d~~~G~~~~~~i~~~I-~~S~~~ivvlS~~-~~~S~wc~~El~~~~~~--~~~~ 99 (160)
..++..|...+++.|+.+.. ..+.+..|.-+. ..-+ .+.++-||.+|.+ ...+..-..+|..++.. ++.+
T Consensus 96 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vP---L~~l~p~~~ipvV~is~~~~~~~~~~~~~lG~al~~~i~~~~ 172 (282)
T TIGR02298 96 PALGQLIADEAQEHGVKTLAHQVPSLGLEYGTLVP---MRYMNEDGHFKVVSIAAWCTVHDIEESRALGEAIRKAIEQSD 172 (282)
T ss_pred HHHHHHHHHHHHHCCCceeeccCCCCCCCeehHhH---HHHhCCCCCCcEEEEeecCCCCCHHHHHHHHHHHHHHHHhcC
Confidence 37899999999999998752 233445553322 2223 3467778888887 55577777899999988 5566
Q ss_pred CceeeEE
Q 045860 100 DQIFPIF 106 (160)
Q Consensus 100 ~~iiPVf 106 (160)
++|+.|-
T Consensus 173 ~rV~iIa 179 (282)
T TIGR02298 173 GRVAVLA 179 (282)
T ss_pred CCEEEEE
Confidence 6777663
No 36
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=48.08 E-value=18 Score=31.96 Aligned_cols=46 Identities=24% Similarity=0.356 Sum_probs=33.2
Q ss_pred CCcccEEEeccc-C-CCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCC
Q 045860 11 CGKYDAFLSFRG-E-DTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGS 56 (160)
Q Consensus 11 ~~~~dVFISy~~-~-D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~ 56 (160)
-..|+|+|.--. . +.....+..|+..|++.|+++.+|+++-.+|..
T Consensus 466 iaP~~v~Iv~~~~~~~~~~~~a~~i~~~L~~~gi~v~~Ddr~~~~g~k 513 (565)
T PRK09194 466 IAPFDVHIVPVNMKDEEVKELAEKLYAELQAAGIEVLLDDRKERPGVK 513 (565)
T ss_pred cCCceEEEEECCCCcHHHHHHHHHHHHHHhccCCeEEEECCCCCHHHH
Confidence 356899887643 2 222356788999999999999999976555533
No 37
>PLN03194 putative disease resistance protein; Provisional
Probab=47.68 E-value=1.1e+02 Score=23.22 Aligned_cols=66 Identities=14% Similarity=0.155 Sum_probs=46.2
Q ss_pred CCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCCChhHHHHHHHHHHHhhcCCceeeEEec
Q 045860 40 KGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYASSTWCLDELLKITECKNREDQIFPIFYG 108 (160)
Q Consensus 40 ~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~~~~~~~~~iiPVf~~ 108 (160)
+.+.||+.-+.-.....+..-+..++++..+.+++=........--..++..+++ .....|.||-.
T Consensus 25 ~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIe---eSri~IvVfS~ 90 (187)
T PLN03194 25 KPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIR---NCKVGVAVFSP 90 (187)
T ss_pred CCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHH---hCeEEEEEECC
Confidence 4789999876444445678889999999998888755445444444557777776 36677777743
No 38
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=46.32 E-value=29 Score=21.80 Aligned_cols=33 Identities=18% Similarity=0.215 Sum_probs=18.1
Q ss_pred CCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEE
Q 045860 40 KGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIV 74 (160)
Q Consensus 40 ~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivv 74 (160)
+.+-+|+|.. .+|......+.+.+......+-+
T Consensus 44 ~~vii~~D~D--~aG~~a~~~~~~~l~~~g~~~~~ 76 (79)
T cd03364 44 KEVILAFDGD--EAGQKAALRALELLLKLGLNVRV 76 (79)
T ss_pred CeEEEEECCC--HHHHHHHHHHHHHHHHCCCeEEE
Confidence 4666777753 35655555555555554444433
No 39
>PF03709 OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal domain; InterPro: IPR005308 This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure. Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, P43099 from SWISSPROT) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 106 Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].; GO: 0016831 carboxy-lyase activity; PDB: 3Q16_C 3N75_A 1C4K_A 1ORD_A 2VYC_D.
Probab=46.09 E-value=93 Score=21.15 Aligned_cols=69 Identities=25% Similarity=0.252 Sum_probs=41.6
Q ss_pred HHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHH-hcceEEEEeecCCCCChhHHHHHHHHHHHhhcCCceeeEEec
Q 045860 30 IGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAID-ESRISIIVLSKNYASSTWCLDELLKITECKNREDQIFPIFYG 108 (160)
Q Consensus 30 v~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~-~S~~~ivvlS~~~~~S~wc~~El~~~~~~~~~~~~iiPVf~~ 108 (160)
+..|..+|+++|+.+..-.. .++....++ .+++.-+|+|=+ ....-...++...+.. ...=||||+-
T Consensus 6 ~~~l~~~L~~~~~~vv~~~~--------~dd~~~~i~~~~~i~avvi~~d-~~~~~~~~~ll~~i~~---~~~~iPVFl~ 73 (115)
T PF03709_consen 6 SRELAEALEQRGREVVDADS--------TDDALAIIESFTDIAAVVISWD-GEEEDEAQELLDKIRE---RNFGIPVFLL 73 (115)
T ss_dssp HHHHHHHHHHTTTEEEEESS--------HHHHHHHHHCTTTEEEEEEECH-HHHHHHHHHHHHHHHH---HSTT-EEEEE
T ss_pred HHHHHHHHHHCCCEEEEeCC--------hHHHHHHHHhCCCeeEEEEEcc-cccchhHHHHHHHHHH---hCCCCCEEEE
Confidence 56799999999998775431 355666666 499999999876 1111122233322222 3345899875
Q ss_pred cC
Q 045860 109 VE 110 (160)
Q Consensus 109 v~ 110 (160)
.+
T Consensus 74 ~~ 75 (115)
T PF03709_consen 74 AE 75 (115)
T ss_dssp ES
T ss_pred ec
Confidence 54
No 40
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=45.68 E-value=65 Score=27.37 Aligned_cols=60 Identities=13% Similarity=0.118 Sum_probs=39.1
Q ss_pred cccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeec
Q 045860 13 KYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSK 77 (160)
Q Consensus 13 ~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~ 77 (160)
..||+|.+-+.+. ...+-.+...|+++|+++-++.. +..+...+..+-+..-..++|+.+
T Consensus 325 ~~~v~v~~~~~~~-~~~a~~ia~~LR~~Gi~veid~~----~~~l~k~~k~A~~~~~~~viiiG~ 384 (430)
T CHL00201 325 SIDVYIATQGLKA-QKKGWEIIQFLEKQNIKFELDLS----SSNFHKQIKQAGKKRAKACIILGD 384 (430)
T ss_pred CCCEEEEEcCHHH-HHHHHHHHHHHHhCCCeEEEeeC----CCCHHHHHHHHHHcCCCEEEEEec
Confidence 4689998754433 34577799999999999988753 344555666665543344555554
No 41
>PF09419 PGP_phosphatase: Mitochondrial PGP phosphatase; InterPro: IPR010021 This group of hypothetical proteins is a part of the IIIA subfamily of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterised members of this subfamily and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs [], all of which are found conserved here. This family consists of sequences from fungi, plants, cyanobacteria, Gram-positive bacteria and Deinococcus. There is presently no characterisation of any sequence in this family.
Probab=45.27 E-value=75 Score=23.57 Aligned_cols=72 Identities=24% Similarity=0.254 Sum_probs=44.4
Q ss_pred HHhcCCcEEEEeCC--CC-CCC-CCchHHHHHHHHhcce-----EEEEeecCCCCChhHHHHHHHHHHHhhcCCceeeEE
Q 045860 36 ALNNKGIYVFRDDK--QL-EKG-GSISPNLLKAIDESRI-----SIIVLSKNYASSTWCLDELLKITECKNREDQIFPIF 106 (160)
Q Consensus 36 ~L~~~gi~v~~d~~--d~-~~G-~~~~~~i~~~I~~S~~-----~ivvlS~~~~~S~wc~~El~~~~~~~~~~~~iiPVf 106 (160)
.|.+.||+..+-+. .+ .+. ..+.+++.+.+++++. -|+|+|.+--++.--..+-..+++. ..+ |||+
T Consensus 35 ~Lk~~Gik~li~DkDNTL~~~~~~~i~~~~~~~~~~l~~~~~~~~v~IvSNsaGs~~d~~~~~a~~~~~-~lg---Ipvl 110 (168)
T PF09419_consen 35 HLKKKGIKALIFDKDNTLTPPYEDEIPPEYAEWLNELKKQFGKDRVLIVSNSAGSSDDPDGERAEALEK-ALG---IPVL 110 (168)
T ss_pred hhhhcCceEEEEcCCCCCCCCCcCcCCHHHHHHHHHHHHHCCCCeEEEEECCCCcccCccHHHHHHHHH-hhC---CcEE
Confidence 48899998776432 23 233 5667888888887663 4899999876655333444444443 222 8887
Q ss_pred ec--cCc
Q 045860 107 YG--VEP 111 (160)
Q Consensus 107 ~~--v~p 111 (160)
.. -.|
T Consensus 111 ~h~~kKP 117 (168)
T PF09419_consen 111 RHRAKKP 117 (168)
T ss_pred EeCCCCC
Confidence 43 355
No 42
>cd00862 ProRS_anticodon_zinc ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only, and an additional C-terminal zinc-binding domain specific to this subfamily of aaRSs.
Probab=44.24 E-value=32 Score=26.03 Aligned_cols=46 Identities=20% Similarity=0.133 Sum_probs=32.3
Q ss_pred CcccEEEecccCCC-----cchHHHHHHHHHhcCCcEEEEeCCCC-CCCCCc
Q 045860 12 GKYDAFLSFRGEDT-----RKGFIGYLYTALNNKGIYVFRDDKQL-EKGGSI 57 (160)
Q Consensus 12 ~~~dVFISy~~~D~-----~~~fv~~L~~~L~~~gi~v~~d~~d~-~~G~~~ 57 (160)
..++|+|---.... -...+..|...|++.|+++-+|.++- .+|..+
T Consensus 9 AP~qVvIipi~~~~~~~~~~~~~a~~i~~~Lr~~Girv~~D~r~~~s~g~K~ 60 (202)
T cd00862 9 APIQVVIVPIGIKDEKREEVLEAADELAERLKAAGIRVHVDDRDNYTPGWKF 60 (202)
T ss_pred cCceEEEEEecCCccchHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHhHHH
Confidence 45788777533220 13467889999999999999998765 666554
No 43
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=43.30 E-value=51 Score=23.38 Aligned_cols=55 Identities=16% Similarity=0.193 Sum_probs=37.1
Q ss_pred ccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcce
Q 045860 14 YDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRI 70 (160)
Q Consensus 14 ~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~ 70 (160)
.++|+-..+.-....+.+.|..+++.+|+-++.|.. .+|+.+...+.+.+..+..
T Consensus 30 ~~~i~~~g~~i~~~~~ie~i~~~~~~k~VIILTD~D--~~Ge~Irk~l~~~l~~~~~ 84 (127)
T COG1658 30 AGVIITNGSAINSLETIELIKKAQKYKGVIILTDPD--RKGERIRKKLKEYLPGAKG 84 (127)
T ss_pred CceEEEcCCccchHHHHHHHHHhhccCCEEEEeCCC--cchHHHHHHHHHHhccccc
Confidence 456666554322235677788888888888888863 3788887777777766443
No 44
>PRK13364 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=42.99 E-value=1.7e+02 Score=23.41 Aligned_cols=122 Identities=12% Similarity=0.077 Sum_probs=67.6
Q ss_pred chHHHHHHHHHhcCCcEEEEe-CCCCCCCCCchHHHHHHHH-hc--ceEEEEeecCCCC----ChhHHHHHHHHHHH-hh
Q 045860 27 KGFIGYLYTALNNKGIYVFRD-DKQLEKGGSISPNLLKAID-ES--RISIIVLSKNYAS----STWCLDELLKITEC-KN 97 (160)
Q Consensus 27 ~~fv~~L~~~L~~~gi~v~~d-~~d~~~G~~~~~~i~~~I~-~S--~~~ivvlS~~~~~----S~wc~~El~~~~~~-~~ 97 (160)
..++.+|...|.+.|+.+... .+.+..|.-+. ..-+. .. .+-||-+|-|... +..-..+|..++.. ..
T Consensus 98 ~~lA~~i~~~l~~~gid~~~~~~~~lDHG~~vP---L~~l~~~~d~~~pvVpv~ln~~~~p~~~~~r~~~lG~al~~~i~ 174 (278)
T PRK13364 98 TELSWHIIESLVEEEFDITTCQEMLVDHAFTLP---LELFWPGRDYPVKVVPVCINTVQHPLPSARRCYKLGQAIGRAIA 174 (278)
T ss_pred HHHHHHHHHHHHHcCCCeecccCCCCCcchhhh---HHHhCcccCCCCCEEEEEeeccCCCCCCHHHHHHHHHHHHHHHH
Confidence 468899999999999987664 33455554332 22232 22 2334555544433 67777899999988 32
Q ss_pred ---cCCceeeEEec-------cCchhhhcccchHHHHHHHHHHhhcCCHHHHHHHH-HHHHHhhccccee
Q 045860 98 ---REDQIFPIFYG-------VEPTVVRKQTASFGEAFAEHEEFFRDNIEKVQKWR-HALKVVANISGWE 156 (160)
Q Consensus 98 ---~~~~iiPVf~~-------v~p~~v~~~~~~f~~~f~~~~~~~~~~~~~~~~W~-~al~~v~~~~g~~ 156 (160)
.+++|+.|--+ ..|..+ ....|=..|.+..++ +.+.+..|. +.+.+-++-.|++
T Consensus 175 ~~~~d~rV~iIaSG~LSH~l~~~p~G~--~~~~fD~~~l~~l~~---d~~~l~~~~~~e~~~~AG~~g~E 239 (278)
T PRK13364 175 SWPSDERVVVIGTGGLSHQLDGERAGF--INKDFDLQCMDSLVS---DPEWLTQYSNHELVELAGTQGVE 239 (278)
T ss_pred hcCCCCCEEEEEeCccccCCCCCCccc--CCHHHHHHHHHHHHh---CHHHHHcCCHHHHHHHcccccHH
Confidence 45677766422 122211 123455555555543 245555555 4555555555543
No 45
>PRK14938 Ser-tRNA(Thr) hydrolase; Provisional
Probab=41.70 E-value=1e+02 Score=26.09 Aligned_cols=57 Identities=23% Similarity=0.173 Sum_probs=38.2
Q ss_pred cccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHh-cceEEEE
Q 045860 13 KYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDE-SRISIIV 74 (160)
Q Consensus 13 ~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~-S~~~ivv 74 (160)
.++|+|-.-+++. ...+..|...|+++|+++.+|.+ +..+...+..+-+. ...+|+|
T Consensus 274 P~qV~IIpl~eel-~e~AlkLA~eLR~aGIrVeiDl~----srSLgKQiK~AdK~GaPfvIII 331 (387)
T PRK14938 274 PIQVRILPVKKDF-LDFSIQVAERLRKEGIRVNVDDL----DDSLGNKIRRAGTEWIPFVIII 331 (387)
T ss_pred cceEEEEEeChHH-HHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEE
Confidence 5687776655543 34577899999999999999863 44565666666543 4444444
No 46
>cd01423 MGS_CPS_I_III Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
Probab=41.68 E-value=43 Score=22.70 Aligned_cols=29 Identities=10% Similarity=0.096 Sum_probs=22.2
Q ss_pred EEEecccCCCcchHHHHHHHHHhcCCcEEEE
Q 045860 16 AFLSFRGEDTRKGFIGYLYTALNNKGIYVFR 46 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~gi~v~~ 46 (160)
||||.+..|. .. ...+...|.+.|++++-
T Consensus 3 vlisv~~~dk-~~-~~~~a~~l~~~G~~i~a 31 (116)
T cd01423 3 ILISIGSYSK-PE-LLPTAQKLSKLGYKLYA 31 (116)
T ss_pred EEEecCcccc-hh-HHHHHHHHHHCCCEEEE
Confidence 7999987764 23 55788888888998864
No 47
>PF03720 UDPG_MGDP_dh_C: UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; InterPro: IPR014027 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [, ]. The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin [], which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation []. In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence []. GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyses the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response [], while in A. vinelandii it is essential for the encystment process []. This entry represents the C-terminal substrate-binding domain of these enzymes. Structural studies indicate that this domain forms an incomplete dinucleotide binding fold [, ].; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 3GG2_D 1DLI_A 1DLJ_A 2Y0E_D 2Y0D_B 2Y0C_D 1MV8_B 1MUU_A 1MFZ_C 3TDK_B ....
Probab=40.24 E-value=21 Score=23.95 Aligned_cols=55 Identities=18% Similarity=0.236 Sum_probs=32.7
Q ss_pred cCCCcchHHHHHHHHHhcCCcEEEEeCCCCCC----------CCCchHHHHHHHHhcceEEEEee
Q 045860 22 GEDTRKGFIGYLYTALNNKGIYVFRDDKQLEK----------GGSISPNLLKAIDESRISIIVLS 76 (160)
Q Consensus 22 ~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~----------G~~~~~~i~~~I~~S~~~ivvlS 76 (160)
..|.|.+=+-.|...|.++|+.+.+.+--+.. +-...+.+.++++.++..|+...
T Consensus 11 ~~D~R~Sp~~~l~~~L~~~g~~V~~~DP~v~~~~~~~~~~~~~~~~~~~~~~~~~~~D~vvl~t~ 75 (106)
T PF03720_consen 11 TDDIRESPALELIEELKERGAEVSVYDPYVDEEEIKELGKLEGVEVCDDLEEALKGADAVVLATD 75 (106)
T ss_dssp SS--TT-HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHCHHHCEEEESSHHHHHTTESEEEESS-
T ss_pred CcccccCHHHHHHHHHHHCCCEEEEECCccChHHHHhhCCccceEEecCHHHHhcCCCEEEEEec
Confidence 36777777888999999999999887632221 11222345677777877666543
No 48
>PRK08661 prolyl-tRNA synthetase; Provisional
Probab=40.18 E-value=82 Score=27.25 Aligned_cols=62 Identities=15% Similarity=0.010 Sum_probs=37.8
Q ss_pred CcccEEEeccc-----CCCcchHHHHHHHHHhcCCcEEEEeC-CCCCCCCCchHHHHHHHH-hcceEEEEeecC
Q 045860 12 GKYDAFLSFRG-----EDTRKGFIGYLYTALNNKGIYVFRDD-KQLEKGGSISPNLLKAID-ESRISIIVLSKN 78 (160)
Q Consensus 12 ~~~dVFISy~~-----~D~~~~fv~~L~~~L~~~gi~v~~d~-~d~~~G~~~~~~i~~~I~-~S~~~ivvlS~~ 78 (160)
..++|+|---. .+.....+..|...|++.|+++.+|. ++..+| ..+..+-. +.. .++++.++
T Consensus 286 AP~qV~Iipi~~~~~~~~~~~~~a~~l~~~Lr~~GirV~lD~r~~~s~g----kK~~~ae~~GvP-~~IiIG~~ 354 (477)
T PRK08661 286 APIQVVIVPIFKKEEKKEEVLEYAKELAEELKKAGIRVKLDDRSDKTPG----WKFNEWELKGVP-LRIEIGPR 354 (477)
T ss_pred CCCeEEEEEecCCCcCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHH----HHHHHHHHCCCC-EEEEECcc
Confidence 35889877541 11123457889999999999999998 444444 34444432 333 44444544
No 49
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=39.78 E-value=2e+02 Score=23.46 Aligned_cols=73 Identities=12% Similarity=0.089 Sum_probs=42.1
Q ss_pred cEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCCChhHHHH
Q 045860 15 DAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYASSTWCLDE 88 (160)
Q Consensus 15 dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S~wc~~E 88 (160)
-|+|-+....-.+.+...+.+.|+.+|..+-.+. ...+++.-...+...|..+..-++++...+....-+..+
T Consensus 150 ~v~ii~~~~~yg~~~~~~~~~~l~~~G~~~~~~~-~~~~~~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~r~ 222 (366)
T COG0683 150 RVAIIGDDYAYGEGLADAFKAALKALGGEVVVEE-VYAPGDTDFSALVAKIKAAGPDAVLVGGYGPDAALFLRQ 222 (366)
T ss_pred EEEEEeCCCCcchhHHHHHHHHHHhCCCeEEEEE-eeCCCCCChHHHHHHHHhcCCCEEEECCCCccchHHHHH
Confidence 4555555544456677778888888888633322 455554334555666666666566666655554443333
No 50
>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=39.78 E-value=37 Score=26.70 Aligned_cols=113 Identities=19% Similarity=0.197 Sum_probs=55.7
Q ss_pred hHHHHHHHHHhcCCcEEEEeCCCCCCCC------Cch-------------HHHHHHHHhcceEEEEeecCCCCChhHHHH
Q 045860 28 GFIGYLYTALNNKGIYVFRDDKQLEKGG------SIS-------------PNLLKAIDESRISIIVLSKNYASSTWCLDE 88 (160)
Q Consensus 28 ~fv~~L~~~L~~~gi~v~~d~~d~~~G~------~~~-------------~~i~~~I~~S~~~ivvlS~~~~~S~wc~~E 88 (160)
.|+.+|.++|++++..+---..|...|- ++. ..|..+++ ...|+|=+-||-+| .+.+
T Consensus 16 tfakeLak~L~~~i~~vi~l~kdy~~~i~~DEslpi~ke~yres~~ks~~rlldSalk--n~~VIvDdtNYyks--mRrq 91 (261)
T COG4088 16 TFAKELAKELRQEIWRVIHLEKDYLRGILWDESLPILKEVYRESFLKSVERLLDSALK--NYLVIVDDTNYYKS--MRRQ 91 (261)
T ss_pred HHHHHHHHHHHHhhhhccccchhhhhheecccccchHHHHHHHHHHHHHHHHHHHHhc--ceEEEEecccHHHH--HHHH
Confidence 6899999999988654322211111111 111 11222333 55888888899887 3344
Q ss_pred HHHHHHHhhcCCceeeEEeccCchhhhc----ccchH-HHHHHHHHHhhcCCHHHHHHHHHHHH
Q 045860 89 LLKITECKNREDQIFPIFYGVEPTVVRK----QTASF-GEAFAEHEEFFRDNIEKVQKWRHALK 147 (160)
Q Consensus 89 l~~~~~~~~~~~~iiPVf~~v~p~~v~~----~~~~f-~~~f~~~~~~~~~~~~~~~~W~~al~ 147 (160)
|.-.. +.....--.|.+.+.++-... ....+ .+.+.+++.++.+ ++..-+|-.+|-
T Consensus 92 L~cea--k~~~tt~ciIyl~~plDtc~rrN~ergepip~Evl~qly~RfEe-Pn~~~rWDspll 152 (261)
T COG4088 92 LACEA--KERKTTWCIIYLRTPLDTCLRRNRERGEPIPEEVLRQLYDRFEE-PNPDRRWDSPLL 152 (261)
T ss_pred HHHHH--HhcCCceEEEEEccCHHHHHHhhccCCCCCCHHHHHHHHHhhcC-CCCCccccCceE
Confidence 43222 222223223333333333221 11122 3556667777754 666677765543
No 51
>PF12163 HobA: DNA replication regulator; InterPro: IPR021011 This family of proteins is found exclusively in epsilon-proteobacteria. Proteins in this family are approximately 180 amino acids in length. The crystal structure of HobA from Helicobacter pylori has been reported at 1.7A resolution; HobA represents a modified Rossmann fold consisting of a five-stranded parallel beta-sheet (beta1-5) flanked on one side by alpha-2, alpha-3 and alpha-6 helices and alpha-4 and alpha-5 on the other. The alpha-1 helix is extended away from and has minimal interaction with the globular part of the protein. Four monomers interact to form a tetrameric molecule. Four calcium atoms bind to the tetramer and these binding sites may have functional relevance. The closest structural homologue of HobA is a sugar isomerase (SIS) domain containing protein, the phosphoheptose isomerase from Pseudomonas aeruginosa. The SIS proteins share strong sequence homology with DiaA from Escherichia coli; yet, HobA and DiaA share no sequence homology []. HobA is a novel protein essential for initiation of H. pylori chromosome replication. It interacts specifically via DnaA with the oriC-DnaA complex. It is possible that HobA is essential for the correct formation and stabilisation of the orisome by facilitating the spatial positioning of DnaA at oriC [].; PDB: 2UVP_D 2WP0_A.
Probab=39.35 E-value=16 Score=27.45 Aligned_cols=74 Identities=15% Similarity=0.408 Sum_probs=39.1
Q ss_pred hHHHHHHHHHhcCC-cEEEEeCCCCCCCCCchHHHHHHHHh--cceEEEEeecCCCCChhHHHHHHHHHHHhhcCCceee
Q 045860 28 GFIGYLYTALNNKG-IYVFRDDKQLEKGGSISPNLLKAIDE--SRISIIVLSKNYASSTWCLDELLKITECKNREDQIFP 104 (160)
Q Consensus 28 ~fv~~L~~~L~~~g-i~v~~d~~d~~~G~~~~~~i~~~I~~--S~~~ivvlS~~~~~S~wc~~El~~~~~~~~~~~~iiP 104 (160)
.|..+..+.+++.| .-.|++++. -.|.+-+..+|+. -..+++|++.. ...|..+=+..-+......++++|
T Consensus 3 df~~Wtl~~iR~~~~~~sWlEe~R----~eW~pl~a~~l~~il~G~s~iliTD~--~R~WF~~Yil~~IN~~~~~RP~lP 76 (180)
T PF12163_consen 3 DFLQWTLETIREDGSFMSWLEERR----FEWTPLIASALSHILNGGSFILITDE--EREWFEEYILSNINNSHKNRPLLP 76 (180)
T ss_dssp EHHHHHHHHHHHHHHHHHCCCCT-----STHHHHHHHHHHHHHTT-EEEEEE-G--GGHHHHHHHHHHHS-SSTTS----
T ss_pred hHHHHHHHHHHccCCCccHHHHHh----hhhHHHHHHHHHHHhCCCeEEEEeCc--hhHHHHHHHHHhcCcccCCCCcce
Confidence 57788888888775 344887653 3555555555442 25566666665 456765444333332345678999
Q ss_pred EEe
Q 045860 105 IFY 107 (160)
Q Consensus 105 Vf~ 107 (160)
|+=
T Consensus 77 i~~ 79 (180)
T PF12163_consen 77 IFS 79 (180)
T ss_dssp EEE
T ss_pred EEe
Confidence 983
No 52
>PRK14799 thrS threonyl-tRNA synthetase; Provisional
Probab=38.95 E-value=1.1e+02 Score=27.13 Aligned_cols=57 Identities=14% Similarity=0.154 Sum_probs=38.5
Q ss_pred cccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHH-hcceEEEE
Q 045860 13 KYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAID-ESRISIIV 74 (160)
Q Consensus 13 ~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~-~S~~~ivv 74 (160)
..+|+|..-+++. ...+..|...|+++|+++-+|.+ +..+...+..+-. +...+|+|
T Consensus 438 P~qV~Iipi~e~~-~~~A~~Ia~~LR~~GirVelD~~----~~~lgkkir~A~k~gip~viII 495 (545)
T PRK14799 438 SVQVRVLPITDEV-NEYAEKVLNDMRKRRIRAEIDYA----GETLSKRIKNAYDQGVPYILIV 495 (545)
T ss_pred CceEEEEEcCHHH-HHHHHHHHHHHHhCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEE
Confidence 4688877654433 35688899999999999999874 4455566666543 34444444
No 53
>cd07371 2A5CPDO_AB The alpha and beta subunits of the Class III extradiol dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol. This subfamily contains both alpha and beta subunits of 2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO), which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, an intermediate during p-chloronitrobenzene degradation. 2A5CPDO is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. The active enzyme is probably a heterotetramer, composed of two alpha and two beta subunits. Alpha and beta subunits share significant sequence similarity and may have evolved by gene duplication.
Probab=38.41 E-value=2e+02 Score=22.73 Aligned_cols=77 Identities=10% Similarity=0.042 Sum_probs=50.5
Q ss_pred chHHHHHHHHHhcCCcEEEE-eC--CCCCCCCCchHHHHHHHH-hcceEEEEeecCC-CCChhHHHHHHHHHHH--hhcC
Q 045860 27 KGFIGYLYTALNNKGIYVFR-DD--KQLEKGGSISPNLLKAID-ESRISIIVLSKNY-ASSTWCLDELLKITEC--KNRE 99 (160)
Q Consensus 27 ~~fv~~L~~~L~~~gi~v~~-d~--~d~~~G~~~~~~i~~~I~-~S~~~ivvlS~~~-~~S~wc~~El~~~~~~--~~~~ 99 (160)
..++..|...|++.|+.+.. +. +.+..|.-+. ..-+. +.++-++++|-+. ..+..-..+|.+++.. +..+
T Consensus 87 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vP---L~~l~p~~~ipvV~vs~~~~~~~~~~~~~lG~al~~~l~~~~ 163 (268)
T cd07371 87 VELAEACVEEGRKAGLVTRMMRYPRFPIDTGTITA---LTLMRPGTDIPPVVISANNLYLSGEETEGEMDLAGKATRDAG 163 (268)
T ss_pred HHHHHHHHHHHHHCCCcEEEecCCCCCCCchhHHH---HHHhcCCCCCCeEEEEecCcCCCHHHHHHHHHHHHHHHHHcC
Confidence 47899999999999998875 22 2334453322 22233 3566677777443 3677778899999975 5555
Q ss_pred CceeeEE
Q 045860 100 DQIFPIF 106 (160)
Q Consensus 100 ~~iiPVf 106 (160)
++|+.|-
T Consensus 164 ~rv~iIg 170 (268)
T cd07371 164 KRVAVLG 170 (268)
T ss_pred CcEEEEE
Confidence 6777664
No 54
>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]
Probab=37.51 E-value=1.2e+02 Score=28.71 Aligned_cols=95 Identities=20% Similarity=0.331 Sum_probs=55.8
Q ss_pred ccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHH--hcceEEEEeecCCC-----CChhHH
Q 045860 14 YDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAID--ESRISIIVLSKNYA-----SSTWCL 86 (160)
Q Consensus 14 ~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~--~S~~~ivvlS~~~~-----~S~wc~ 86 (160)
.-+||--.++|.+..|.+.++.+|-+-|=.+.+.++. .+=.++..+|..++. ++|+-||+- .|. --.||+
T Consensus 407 ~~~~i~~d~eD~~qe~~~li~~AL~~PGPDlVICDEG-HrIKN~~A~iS~aLk~IrtrRRiVLT--GYPLQNNLlEYwCM 483 (1387)
T KOG1016|consen 407 SSGFIKDDSEDQRQEAYSLIRSALLEPGPDLVICDEG-HRIKNITAEISMALKAIRTRRRIVLT--GYPLQNNLLEYWCM 483 (1387)
T ss_pred CCcccCCchhhhHHHHHHHHHHHhcCCCCCeEEecCC-ceeccchHHHHHHHHHhhhceeEEEe--ccccccchHHHhhh
Confidence 4578888889998899999999999998766665521 111333445544444 233333331 221 124665
Q ss_pred ------------HHHHHHHHH-hhcCCceeeEEeccCchhhhc
Q 045860 87 ------------DELLKITEC-KNREDQIFPIFYGVEPTVVRK 116 (160)
Q Consensus 87 ------------~El~~~~~~-~~~~~~iiPVf~~v~p~~v~~ 116 (160)
.|+....++ .++|+. .+-+|.||+-
T Consensus 484 VDFVRP~yLGTR~eF~nmFErPI~NGQC-----vDStPdDvkl 521 (1387)
T KOG1016|consen 484 VDFVRPKYLGTRKEFINMFERPIKNGQC-----VDSTPDDVKL 521 (1387)
T ss_pred heeccccccchHHHHHHHhhccccCCcc-----ccCChhHHHH
Confidence 455555555 444443 3668899864
No 55
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=37.51 E-value=1.1e+02 Score=27.36 Aligned_cols=61 Identities=13% Similarity=0.087 Sum_probs=40.4
Q ss_pred cccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecC
Q 045860 13 KYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKN 78 (160)
Q Consensus 13 ~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~ 78 (160)
..||+|..-++.. ...+..|...|+++|+++-+|.+ +..+...+..|-..---.++|+.++
T Consensus 539 p~~v~Ii~~~~~~-~~~a~~i~~~Lr~~gi~v~~d~~----~~~l~kki~~A~~~g~~~~iiiG~~ 599 (638)
T PRK00413 539 PVQVVVLPITDKH-ADYAKEVAKKLKAAGIRVEVDLR----NEKIGYKIREAQLQKVPYMLVVGDK 599 (638)
T ss_pred cceEEEEEeChhH-HHHHHHHHHHHHhCCCEEEEECC----CCCHhHHHHHhhccCCCEEEEEcch
Confidence 4688887655433 35688899999999999999974 3455556666544333345555543
No 56
>cd06340 PBP1_ABC_ligand_binding_like_6 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=37.04 E-value=1.8e+02 Score=23.33 Aligned_cols=64 Identities=6% Similarity=0.020 Sum_probs=35.3
Q ss_pred cEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCC
Q 045860 15 DAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNY 79 (160)
Q Consensus 15 dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~ 79 (160)
.|.+-|...+-....+..+...+++.|+++-... .+.++..-...+...|..++.-++++.-..
T Consensus 146 ~v~~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~-~~~~~~~d~~~~i~~l~~~~~d~v~~~~~~ 209 (347)
T cd06340 146 TVALVHEDTEFGTSVAEAIKKFAKERGFEIVEDI-SYPANARDLTSEVLKLKAANPDAILPASYT 209 (347)
T ss_pred eEEEEecCchHhHHHHHHHHHHHHHcCCEEEEee-ccCCCCcchHHHHHHHHhcCCCEEEEcccc
Confidence 4555554333234456667778888888776443 455553323344555666555555555443
No 57
>PLN02530 histidine-tRNA ligase
Probab=36.26 E-value=1.2e+02 Score=26.16 Aligned_cols=61 Identities=15% Similarity=0.043 Sum_probs=40.1
Q ss_pred CcccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeec
Q 045860 12 GKYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSK 77 (160)
Q Consensus 12 ~~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~ 77 (160)
...||+|.+-+++. ...+-.+...|+++|+++-++..+ ..+...+..+-+.--..++++.+
T Consensus 400 ~~~dVlVi~~~~~~-~~~A~~ia~~LR~~Gi~vevd~~~----~~l~k~ik~A~k~g~~~iviiG~ 460 (487)
T PLN02530 400 HQVDDVVFALDEDL-QGAAAGVASRLREKGRSVDLVLEP----KKLKWVFKHAERIGAKRLVLVGA 460 (487)
T ss_pred CCCcEEEEEcChHH-HHHHHHHHHHHHHCCCeEEEecCC----CCHHHHHHHHHHCCCCEEEEEch
Confidence 44689998755443 345778999999999999887532 34555566665543334555554
No 58
>PRK03991 threonyl-tRNA synthetase; Validated
Probab=36.05 E-value=1e+02 Score=27.70 Aligned_cols=60 Identities=17% Similarity=0.127 Sum_probs=38.3
Q ss_pred cccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHH-hcceEEEEeecC
Q 045860 13 KYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAID-ESRISIIVLSKN 78 (160)
Q Consensus 13 ~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~-~S~~~ivvlS~~ 78 (160)
.++|+|.--+++. ...+..|...|++.|++|.+|+++- .+...+..+-. +... ++|+.++
T Consensus 499 P~qV~IIpi~e~~-~~~A~eIa~~Lr~~GirV~lDdr~~----slgkKir~A~~~GiP~-iIVIG~k 559 (613)
T PRK03991 499 PTQVRVIPVSERH-LDYAEEVADKLEAAGIRVDVDDRDE----SLGKKIRDAGKEWIPY-VVVIGDK 559 (613)
T ss_pred CceEEEEEeCHHH-HHHHHHHHHHHHhCCCEEEEECCCC----CHHHHHHHHHHcCCCE-EEEECcc
Confidence 4788777544332 4568889999999999999998643 44445555433 3333 4444433
No 59
>PF03446 NAD_binding_2: NAD binding domain of 6-phosphogluconate dehydrogenase; InterPro: IPR006115 6-Phosphogluconate dehydrogenase (1.1.1.44 from EC) (6PGD) is an oxidative carboxylase that catalyses the decarboxylating reduction of 6-phosphogluconate into ribulose 5-phosphate in the presence of NADP. This reaction is a component of the hexose mono-phosphate shunt and pentose phosphate pathways (PPP) [, ]. Prokaryotic and eukaryotic 6PGD are proteins of about 470 amino acids whose sequence are highly conserved []. The protein is a homodimer in which the monomers act independently []: each contains a large, mainly alpha-helical domain and a smaller beta-alpha-beta domain, containing a mixed parallel and anti-parallel 6-stranded beta sheet []. NADP is bound in a cleft in the small domain, the substrate binding in an adjacent pocket []. This family represents the NADP binding domain of 6-phosphogluconate dehydrogenase which adopts a Rossman fold. The C-terminal domain is described in IPR006114 from INTERPRO.; GO: 0004616 phosphogluconate dehydrogenase (decarboxylating) activity, 0006098 pentose-phosphate shunt, 0055114 oxidation-reduction process; PDB: 3AX6_D 3PDU_G 3Q3C_A 3OBB_A 4DLL_B 1PGP_A 1PGN_A 2PGD_A 1PGQ_A 1PGO_A ....
Probab=35.32 E-value=36 Score=24.51 Aligned_cols=48 Identities=17% Similarity=0.283 Sum_probs=34.1
Q ss_pred HHHHHHHhcCCcEEEEeCCCCC-------CCCCchHHHHHHHHhcceEEEEeecC
Q 045860 31 GYLYTALNNKGIYVFRDDKQLE-------KGGSISPNLLKAIDESRISIIVLSKN 78 (160)
Q Consensus 31 ~~L~~~L~~~gi~v~~d~~d~~-------~G~~~~~~i~~~I~~S~~~ivvlS~~ 78 (160)
..+...|.++|+.+...+++-. .|....+...+.++++++.+..+++.
T Consensus 14 ~~~a~~L~~~g~~v~~~d~~~~~~~~~~~~g~~~~~s~~e~~~~~dvvi~~v~~~ 68 (163)
T PF03446_consen 14 SAMARNLAKAGYEVTVYDRSPEKAEALAEAGAEVADSPAEAAEQADVVILCVPDD 68 (163)
T ss_dssp HHHHHHHHHTTTEEEEEESSHHHHHHHHHTTEEEESSHHHHHHHBSEEEE-SSSH
T ss_pred HHHHHHHHhcCCeEEeeccchhhhhhhHHhhhhhhhhhhhHhhcccceEeecccc
Confidence 4577888888999888765521 34445567788899999988887664
No 60
>KOG1610 consensus Corticosteroid 11-beta-dehydrogenase and related short chain-type dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism; General function prediction only]
Probab=35.23 E-value=50 Score=27.21 Aligned_cols=31 Identities=32% Similarity=0.496 Sum_probs=26.3
Q ss_pred ccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeC
Q 045860 14 YDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDD 48 (160)
Q Consensus 14 ~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~ 48 (160)
.-|||. ++|+ +|-..|+..|.++|++||.--
T Consensus 30 k~VlIT--GCDS--GfG~~LA~~L~~~Gf~V~Agc 60 (322)
T KOG1610|consen 30 KAVLIT--GCDS--GFGRLLAKKLDKKGFRVFAGC 60 (322)
T ss_pred cEEEEe--cCCc--HHHHHHHHHHHhcCCEEEEEe
Confidence 458884 8897 888999999999999998764
No 61
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=34.85 E-value=1.4e+02 Score=26.22 Aligned_cols=61 Identities=11% Similarity=0.138 Sum_probs=39.6
Q ss_pred cccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecC
Q 045860 13 KYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKN 78 (160)
Q Consensus 13 ~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~ 78 (160)
.++|+|.--+++. ...+..|...|++.||++-+|.+ +..+...+..|-..---.++|+.++
T Consensus 476 p~~v~Ii~~~~~~-~~~a~~i~~~Lr~~gi~v~~d~~----~~~l~kk~~~A~~~g~p~~iivG~~ 536 (575)
T PRK12305 476 PVQVVIIPVADAH-NEYAEEVAKKLRAAGIRVEVDTS----NERLNKKIRNAQKQKIPYMLVVGDK 536 (575)
T ss_pred CccEEEEEeChHH-HHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHhcCCCEEEEEech
Confidence 4688887644432 35578899999999999999875 3345556666644333344444443
No 62
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=34.44 E-value=1.4e+02 Score=26.76 Aligned_cols=62 Identities=13% Similarity=0.137 Sum_probs=40.4
Q ss_pred CcccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeec
Q 045860 12 GKYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSK 77 (160)
Q Consensus 12 ~~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~ 77 (160)
...+|+|-.-+++.....+..|...|+++|+++-+|.+ +..+...+..+-+.--..++++.+
T Consensus 540 ap~qV~Ii~~~~~~~~~~a~~la~~LR~~Gi~veid~~----~~sl~kq~k~A~k~g~~~~iiiG~ 601 (639)
T PRK12444 540 APVQVKVIPVSNAVHVQYADEVADKLAQAGIRVERDER----DEKLGYKIREAQMQKIPYVLVIGD 601 (639)
T ss_pred CCceEEEEEcccHHHHHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEEcc
Confidence 45788877655411235678899999999999999874 445556666664433334444444
No 63
>TIGR00409 proS_fam_II prolyl-tRNA synthetase, family II. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent groups. This group includes enzymes from Escherichia coli, Bacillus subtilis, Aquifex aeolicus, the spirochete Treponema pallidum, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae. The other group includes the Pro-specific domain of a human multifunctional tRNA ligase and the prolyl-tRNA synthetases from the Archaea, the Mycoplasmas, and the spirochete Borrelia burgdorferi.
Probab=34.35 E-value=31 Score=30.62 Aligned_cols=46 Identities=24% Similarity=0.403 Sum_probs=32.2
Q ss_pred cccEEEecc-cCC-CcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCch
Q 045860 13 KYDAFLSFR-GED-TRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSIS 58 (160)
Q Consensus 13 ~~dVFISy~-~~D-~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~ 58 (160)
.|+|=|.-- ..| .....+..|+..|++.|+++.+|+|+-.+|..+.
T Consensus 473 P~qV~Iip~~~~~~~~~~~a~~l~~~L~~~gi~v~~DDr~~~~G~K~~ 520 (568)
T TIGR00409 473 PYDVVIVVMNMKDEEQQQLAEELYSELLAQGVDVLLDDRNERAGVKFA 520 (568)
T ss_pred CeEEEEEEcCCChHHHHHHHHHHHHHHHhCCCEEEEECCCCCHHHHHH
Confidence 467755432 222 2235688899999999999999998766775543
No 64
>PRK15057 UDP-glucose 6-dehydrogenase; Provisional
Probab=34.13 E-value=1.1e+02 Score=25.66 Aligned_cols=52 Identities=13% Similarity=0.226 Sum_probs=37.4
Q ss_pred cCCCcchHHHHHHHHHhcCCcEEEEeCCCCCC----CCCchHHHHHHHHhcceEEE
Q 045860 22 GEDTRKGFIGYLYTALNNKGIYVFRDDKQLEK----GGSISPNLLKAIDESRISII 73 (160)
Q Consensus 22 ~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~----G~~~~~~i~~~I~~S~~~iv 73 (160)
..|.|.+=+-.|.+.|..+|..+..++--+.. +-.+.++..++++.|+..|+
T Consensus 310 t~D~R~Sp~~~i~~~L~~~G~~v~~~DP~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (388)
T PRK15057 310 SDNFRASSIQGIMKRIKAKGVEVIIYEPVMKEDSFFNSRLERDLATFKQQADVIIS 365 (388)
T ss_pred CCccccChHHHHHHHHHhCCCEEEEECCCCCchhhcCCeeeCCHHHHHHhCCEEEE
Confidence 35677776778999999999988887643322 33455667788888887776
No 65
>KOG1136 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]
Probab=33.96 E-value=54 Score=27.55 Aligned_cols=44 Identities=30% Similarity=0.621 Sum_probs=31.0
Q ss_pred HHHhcceEEEEeecCCC----CChhHHH-H-HHHHHHH-hhcCCceeeEEe
Q 045860 64 AIDESRISIIVLSKNYA----SSTWCLD-E-LLKITEC-KNREDQIFPIFY 107 (160)
Q Consensus 64 ~I~~S~~~ivvlS~~~~----~S~wc~~-E-l~~~~~~-~~~~~~iiPVf~ 107 (160)
.|..+|--+++--..|+ .|..|++ | |.+..+| .+.++.+||||-
T Consensus 191 ~id~~rpdlLIsESTYattiRdskr~rERdFLk~VhecVa~GGkvlIPvFA 241 (501)
T KOG1136|consen 191 WIDKCRPDLLISESTYATTIRDSKRCRERDFLKKVHECVARGGKVLIPVFA 241 (501)
T ss_pred hhccccCceEEeeccceeeeccccchhHHHHHHHHHHHHhcCCeEEEEeee
Confidence 46667777766555565 4778866 4 4555666 888999999995
No 66
>cd06342 PBP1_ABC_LIVBP_like Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup includes the type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup also includes a leucine-specific binding protein (or LivK), which is very similar in sequence and structure to leucine-isoleucine-valine binding protein (LIVBP). ABC-type active transport systems are transmembrane proteins that function in the transport of diverse sets of substrates across extra- and intracellular membranes, including carbohydrates, amino acids, inorganic ions, dipeptides and oligopeptides, metabolic products, lipids and sterols, and heme, to name a few.
Probab=33.35 E-value=2.3e+02 Score=22.09 Aligned_cols=57 Identities=16% Similarity=0.174 Sum_probs=31.5
Q ss_pred EEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCC-CchHHHHHHHHhcceEEEE
Q 045860 16 AFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGG-SISPNLLKAIDESRISIIV 74 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~-~~~~~i~~~I~~S~~~ivv 74 (160)
|.+-|...+-....+..+...|++.|+++-... .+.+|. .+. .+...|.++..-+++
T Consensus 138 v~~v~~~~~~g~~~~~~~~~~~~~~g~~v~~~~-~~~~~~~d~~-~~l~~i~~~~~~~vi 195 (334)
T cd06342 138 VAIIDDKTAYGQGLADEFKKALKAAGGKVVARE-GTTDGATDFS-AILTKIKAANPDAVF 195 (334)
T ss_pred EEEEeCCcchhhHHHHHHHHHHHHcCCEEEEEe-cCCCCCccHH-HHHHHHHhcCCCEEE
Confidence 545454444334556778888888888776543 355553 343 344455654443333
No 67
>PRK05339 PEP synthetase regulatory protein; Provisional
Probab=32.78 E-value=1.8e+02 Score=23.42 Aligned_cols=68 Identities=25% Similarity=0.278 Sum_probs=42.7
Q ss_pred HHHHHhcCCcEEEEeCCCCCCCCCchHHH-----------------HHHHHhcceEEEEeecCCCCChhHHHHHHHHHHH
Q 045860 33 LYTALNNKGIYVFRDDKQLEKGGSISPNL-----------------LKAIDESRISIIVLSKNYASSTWCLDELLKITEC 95 (160)
Q Consensus 33 L~~~L~~~gi~v~~d~~d~~~G~~~~~~i-----------------~~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~~~ 95 (160)
+.-.|..+||++.--. +.|+.++..++ ...|++.|.--+=. .+|++-.-|..|+..|-+.
T Consensus 159 lS~YLA~~G~KvAN~P--Lvpe~~lP~~L~~~~~~kivGLtIdp~rL~~IR~~Rl~~lg~-s~Ya~~~~i~~El~~A~~l 235 (269)
T PRK05339 159 TSLYLANKGIKAANYP--LVPEVPLPEELFPIDPKKIFGLTIDPERLIEIRKERLPNLGL-SRYASLEQCREELAEAERL 235 (269)
T ss_pred HHHHHHccCCceEeeC--CCCCCCCCHHHHhCCCCcEEEEeCCHHHHHHHHHHHhcccCc-CcCCCHHHHHHHHHHHHHH
Confidence 5566667888887553 44555554443 44455444422211 5689999999999999887
Q ss_pred -hhcCCcee
Q 045860 96 -KNREDQIF 103 (160)
Q Consensus 96 -~~~~~~ii 103 (160)
++.+-.+|
T Consensus 236 ~~k~~~pvI 244 (269)
T PRK05339 236 FRREGIPVI 244 (269)
T ss_pred HHHcCCCEE
Confidence 66554443
No 68
>PRK10569 NAD(P)H-dependent FMN reductase; Provisional
Probab=31.97 E-value=1.9e+02 Score=21.61 Aligned_cols=82 Identities=15% Similarity=0.191 Sum_probs=47.3
Q ss_pred HHHHHHHHHhcCCcEE-EEeCCCCCCC--------CCchHHHHHHHHhcceEEEEeecCCCCChhHHHHHHHHHHH----
Q 045860 29 FIGYLYTALNNKGIYV-FRDDKQLEKG--------GSISPNLLKAIDESRISIIVLSKNYASSTWCLDELLKITEC---- 95 (160)
Q Consensus 29 fv~~L~~~L~~~gi~v-~~d~~d~~~G--------~~~~~~i~~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~~~---- 95 (160)
.+..+...|.+.|..+ .+|-.++++. .+-...+.+.|++++. |++.||-|-.|-- --|..++++
T Consensus 19 l~~~~~~~l~~~g~ev~~idL~~l~~~~~~~~~~~~~~~~~~~~~i~~AD~-iIi~tP~Y~~s~p--g~LKn~iD~l~~~ 95 (191)
T PRK10569 19 LLEYAREWLNGLGVEVYHWNLQNFAPEDLLYARFDSPALKTFTEQLAQADG-LIVATPVYKASFS--GALKTLLDLLPER 95 (191)
T ss_pred HHHHHHHHHHhCCCEEEEEEccCCChHHHHhccCCCHHHHHHHHHHHHCCE-EEEECCccCCCCC--HHHHHHHHhCChh
Confidence 3555666777778766 4455555442 1223466778888885 5556999887642 123333332
Q ss_pred hhcCCceeeEEeccCchh
Q 045860 96 KNREDQIFPIFYGVEPTV 113 (160)
Q Consensus 96 ~~~~~~iiPVf~~v~p~~ 113 (160)
.-.++.++||-..-.+..
T Consensus 96 ~l~~K~v~iiat~G~~~~ 113 (191)
T PRK10569 96 ALEHKVVLPLATGGSVAH 113 (191)
T ss_pred hhCCCEEEEEEecCCchh
Confidence 234567777766544443
No 69
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=31.95 E-value=65 Score=25.67 Aligned_cols=43 Identities=16% Similarity=0.269 Sum_probs=27.4
Q ss_pred HHHHHHHHhcCCcEEEEeCCCCCCCCCc---hHHHHHHHHhcceEEEEeec
Q 045860 30 IGYLYTALNNKGIYVFRDDKQLEKGGSI---SPNLLKAIDESRISIIVLSK 77 (160)
Q Consensus 30 v~~L~~~L~~~gi~v~~d~~d~~~G~~~---~~~i~~~I~~S~~~ivvlS~ 77 (160)
+.+|.+.|...|+.+..-. ..||.. .+.+..++++++ ++|+|-
T Consensus 23 a~~la~~L~~~G~~v~~~~---~VgD~~~~I~~~l~~a~~r~D--~vI~tG 68 (255)
T COG1058 23 AAFLADELTELGVDLARIT---TVGDNPDRIVEALREASERAD--VVITTG 68 (255)
T ss_pred HHHHHHHHHhcCceEEEEE---ecCCCHHHHHHHHHHHHhCCC--EEEECC
Confidence 6789999999999988753 356553 334444455544 444443
No 70
>TIGR00408 proS_fam_I prolyl-tRNA synthetase, family I. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi. The other family includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae.
Probab=31.48 E-value=1.4e+02 Score=25.74 Aligned_cols=63 Identities=13% Similarity=0.077 Sum_probs=38.8
Q ss_pred CcccEEEec---ccC--CCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecC
Q 045860 12 GKYDAFLSF---RGE--DTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKN 78 (160)
Q Consensus 12 ~~~dVFISy---~~~--D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~ 78 (160)
..++|+|-- ... +.....+..|...|++.|+++.+|.++-.+| ..+..+-..---.++++.++
T Consensus 281 aP~qV~Iipi~~~~~~~~~~~~~A~~l~~~Lr~~girv~lD~r~~s~g----kk~k~Ae~~GvP~~IiIG~~ 348 (472)
T TIGR00408 281 APIQVVIIPIIFKKKENEKVMEAAREVRSRLKKAGFRVHIDDRDNRPG----RKFYQWEIKGIPLRIEVGPN 348 (472)
T ss_pred CcceEEEEEccCCCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHH----HHHHHHHHCCCCEEEEECcc
Confidence 458888874 221 1223568889999999999999998653444 44444433322344555554
No 71
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=31.07 E-value=1.1e+02 Score=22.91 Aligned_cols=65 Identities=15% Similarity=0.241 Sum_probs=44.4
Q ss_pred chHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCCC--------hhHHHHHHHHHHH
Q 045860 27 KGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYASS--------TWCLDELLKITEC 95 (160)
Q Consensus 27 ~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S--------~wc~~El~~~~~~ 95 (160)
......|..+.+.+|+-+|.|.+ .+|+.|...|.+.+-++..+-+ +..+... .-..+.+..|++.
T Consensus 35 ~~~i~~i~~~~~~rgVIIfTDpD--~~GekIRk~i~~~vp~~khafi--~~~~a~~~~~~iGVE~As~e~I~~AL~~ 107 (174)
T TIGR00334 35 DETINLIKKAQKKQGVIILTDPD--FPGEKIRKKIEQHLPGYENCFI--PKHLAKPNKKKIGVEEASVEAIIAALEN 107 (174)
T ss_pred HHHHHHHHHHhhcCCEEEEeCCC--CchHHHHHHHHHHCCCCeEEee--eHHhcCcCCCCcccCCCCHHHHHHHHHH
Confidence 34466788888889999999974 3899998888888877775443 4444321 1225566667665
No 72
>cd07367 CarBb CarBb is the B subunit of the Class III Extradiol ring-cleavage dioxygenase, 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBb is the B subunit of 2-aminophenol 1,6-dioxygenase (CarB), which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. It is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, it has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=30.50 E-value=2.7e+02 Score=21.98 Aligned_cols=126 Identities=15% Similarity=0.111 Sum_probs=70.8
Q ss_pred chHHHHHHHHHhcCCcEEEEeC-CCCCCCCCchHHHHHHHHhcceEEEEeecCCCC----ChhHHHHHHHHHHH--hh--
Q 045860 27 KGFIGYLYTALNNKGIYVFRDD-KQLEKGGSISPNLLKAIDESRISIIVLSKNYAS----STWCLDELLKITEC--KN-- 97 (160)
Q Consensus 27 ~~fv~~L~~~L~~~gi~v~~d~-~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~----S~wc~~El~~~~~~--~~-- 97 (160)
..++.+|...|.+.|+.+-.+. +.+..|.-+.=.... ...++-||-+|-|... +..-..+|..++.. +.
T Consensus 90 ~~LA~~i~~~l~~~g~~~~~~~~~~lDHG~~vPL~~l~--p~~~iPvV~isin~~~~p~~~~~~~~~lG~al~~~i~~~~ 167 (268)
T cd07367 90 REFARAFVRQAAEDGFDLAQAEELRPDHGVMVPLLFMG--PKLDIPVVPLIVNINTDPAPSPRRCWALGKVLAQYVEKRR 167 (268)
T ss_pred HHHHHHHHHHHHHcCCCeeeecCccCCcchhchHHHhC--CCCCCCEEEEEecccCCCCCCHHHHHHHHHHHHHHHHhcC
Confidence 4789999999999999776543 344455433222221 1356667767765443 56777899999988 44
Q ss_pred -cCCceeeEEeccCchhh-----hcccchHHHHHHHHHHhhcCCHHHHHHHH-HHHHHhhccccee
Q 045860 98 -REDQIFPIFYGVEPTVV-----RKQTASFGEAFAEHEEFFRDNIEKVQKWR-HALKVVANISGWE 156 (160)
Q Consensus 98 -~~~~iiPVf~~v~p~~v-----~~~~~~f~~~f~~~~~~~~~~~~~~~~W~-~al~~v~~~~g~~ 156 (160)
.+++|+.|--+.--=++ ......|-+.+.+..+.. +.+.+..+. ..+.+-++-.|++
T Consensus 168 ~~d~rV~iiaSGgLSH~l~~~~~~~~~~efD~~i~~~l~~g--d~~~L~~~~~~~~~~~ag~~g~e 231 (268)
T cd07367 168 PAGERVAVIAAGGLSHWLGVPRHGEVNEAFDRMFLDLLEGG--NGERLAGMGNDEILDQAGNGGLE 231 (268)
T ss_pred CCCCcEEEEEcccccCCCCCCcccccCHHHHHHHHHHHHcC--CHHHHHhCCHHHHHHhCcccchH
Confidence 66777766422111111 001134555555544432 355566665 4555555555544
No 73
>PF00350 Dynamin_N: Dynamin family; InterPro: IPR001401 Membrane transport between compartments in eukaryotic cells requires proteins that allow the budding and scission of nascent cargo vesicles from one compartment and their targeting and fusion with another. Dynamins are large GTPases that belong to a protein superfamily [] that, in eukaryotic cells, includes classical dynamins, dynamin-like proteins, OPA1, Mx proteins, mitofusins and guanylate-binding proteins/atlastins [, , , ], and are involved in the scission of a wide range of vesicles and organelles. They play a role in many processes including budding of transport vesicles, division of organelles, cytokinesis and pathogen resistance. The minimal distinguishing architectural features that are common to all dynamins and are distinct from other GTPases are the structure of the large GTPase domain (300 amino acids) and the presence of two additional domains; the middle domain and the GTPase effector domain (GED), which are involved in oligomerization and regulation of the GTPase activity. This entry represents the GTPase domain, containing the GTP-binding motifs that are needed for guanine-nucleotide binding and hydrolysis. The conservation of these motifs is absolute except for the the final motif in guanylate-binding proteins. The GTPase catalytic activity can be stimulated by oligomerisation of the protein, which is mediated by interactions between the GTPase domain, the middle domain and the GED.; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 1JWY_B 1JX2_B 3ZVR_A 2AKA_B 3L43_B 2X2F_D 2X2E_D 3SNH_A 3ZYS_D 3ZYC_D ....
Probab=29.95 E-value=1.9e+02 Score=20.23 Aligned_cols=45 Identities=7% Similarity=0.106 Sum_probs=30.2
Q ss_pred HHHHHHHHhcceEEEEeecCCCCChhHHHHHHHHHHH-hhcCCceeeEE
Q 045860 59 PNLLKAIDESRISIIVLSKNYASSTWCLDELLKITEC-KNREDQIFPIF 106 (160)
Q Consensus 59 ~~i~~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~~~-~~~~~~iiPVf 106 (160)
+.+.+.+..++..|+|++.+- .+...+.....+. .....+.+.|+
T Consensus 120 ~~~~~~~~~~d~vi~V~~~~~---~~~~~~~~~l~~~~~~~~~~~i~V~ 165 (168)
T PF00350_consen 120 EITEEYLPKADVVIFVVDANQ---DLTESDMEFLKQMLDPDKSRTIFVL 165 (168)
T ss_dssp HHHHHHHSTTEEEEEEEETTS---TGGGHHHHHHHHHHTTTCSSEEEEE
T ss_pred HHHHHhhccCCEEEEEeccCc---ccchHHHHHHHHHhcCCCCeEEEEE
Confidence 456778889999999997765 4455566655555 44555566554
No 74
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=29.91 E-value=75 Score=21.18 Aligned_cols=30 Identities=17% Similarity=0.158 Sum_probs=21.5
Q ss_pred cEEEecccCCCcchHHHHHHHHHhcCCcEEEE
Q 045860 15 DAFLSFRGEDTRKGFIGYLYTALNNKGIYVFR 46 (160)
Q Consensus 15 dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~ 46 (160)
.||+|.+..|. .-...+...|.+.|++++-
T Consensus 2 ~vl~s~~~~~k--~~~~~~~~~l~~~G~~l~a 31 (110)
T cd01424 2 TVFISVADRDK--PEAVEIAKRLAELGFKLVA 31 (110)
T ss_pred eEEEEEEcCcH--hHHHHHHHHHHHCCCEEEE
Confidence 37899877764 3345677888888888864
No 75
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=29.71 E-value=25 Score=26.03 Aligned_cols=57 Identities=23% Similarity=0.388 Sum_probs=33.2
Q ss_pred ChhHHHHHHHHHHH-hhcCCceeeEEeccCchhhhcccchHHHHHHHHHHhhcCCHHHHHHHHHHHH
Q 045860 82 STWCLDELLKITEC-KNREDQIFPIFYGVEPTVVRKQTASFGEAFAEHEEFFRDNIEKVQKWRHALK 147 (160)
Q Consensus 82 S~wc~~El~~~~~~-~~~~~~iiPVf~~v~p~~v~~~~~~f~~~f~~~~~~~~~~~~~~~~W~~al~ 147 (160)
|.|.++||..-++. +-+.=.=+-+.++|+|-++.+... -++..+. .-++.||+.|..
T Consensus 54 s~~~Lf~LI~k~~~keikTW~~La~~LGVepp~~ek~qS-----tQKvqQY----aVRLKRWM~aMH 111 (175)
T PF09441_consen 54 STFTLFELIRKLESKEIKTWAQLALELGVEPPDPEKGQS-----TQKVQQY----AVRLKRWMRAMH 111 (175)
T ss_pred hHHHHHHHHHHHhhhhHhHHHHHHHHhCCCCCCcccccc-----hHHHHHH----HHHHHHHHHHhh
Confidence 56778888766664 222223355667888888765321 2222221 356789998865
No 76
>PRK10076 pyruvate formate lyase II activase; Provisional
Probab=29.54 E-value=2.2e+02 Score=21.75 Aligned_cols=34 Identities=15% Similarity=-0.009 Sum_probs=25.0
Q ss_pred EEEecccCCCcchHHHHHHHHHhcCCcEEEEeCC
Q 045860 16 AFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDK 49 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~ 49 (160)
|=+|....-....|+..|...+++.|+++++|-.
T Consensus 42 Vt~SGGEPllq~~fl~~l~~~~k~~gi~~~leTn 75 (213)
T PRK10076 42 VTLSGGEVLMQAEFATRFLQRLRLWGVSCAIETA 75 (213)
T ss_pred EEEeCchHHcCHHHHHHHHHHHHHcCCCEEEECC
Confidence 3344443434567888999999999999999963
No 77
>PF12146 Hydrolase_4: Putative lysophospholipase; InterPro: IPR022742 This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins.
Probab=29.42 E-value=86 Score=19.87 Aligned_cols=36 Identities=22% Similarity=0.145 Sum_probs=26.9
Q ss_pred CcccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeC
Q 045860 12 GKYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDD 48 (160)
Q Consensus 12 ~~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~ 48 (160)
.+--|+|+|.-.+-. ..-.+|...|.++||.|+.-+
T Consensus 15 ~k~~v~i~HG~~eh~-~ry~~~a~~L~~~G~~V~~~D 50 (79)
T PF12146_consen 15 PKAVVVIVHGFGEHS-GRYAHLAEFLAEQGYAVFAYD 50 (79)
T ss_pred CCEEEEEeCCcHHHH-HHHHHHHHHHHhCCCEEEEEC
Confidence 456789998655432 235679999999999998865
No 78
>PF03618 Kinase-PPPase: Kinase/pyrophosphorylase; InterPro: IPR005177 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.; GO: 0005524 ATP binding, 0016772 transferase activity, transferring phosphorus-containing groups
Probab=29.34 E-value=2.2e+02 Score=22.63 Aligned_cols=68 Identities=21% Similarity=0.206 Sum_probs=43.3
Q ss_pred HHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEee-------------------cCCCCChhHHHHHHHHH
Q 045860 33 LYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLS-------------------KNYASSTWCLDELLKIT 93 (160)
Q Consensus 33 L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS-------------------~~~~~S~wc~~El~~~~ 93 (160)
|.-+|..+|+++---. +.|+.++.+++.+ +...+++-+.++ .+|+.-.-|..||..|-
T Consensus 153 lS~YLA~~G~KvAN~P--Lvpe~~lP~~L~~-~~~~ki~GLtidp~~L~~IR~~Rl~~lg~~~s~Ya~~~~i~~El~~A~ 229 (255)
T PF03618_consen 153 LSMYLANKGYKVANVP--LVPEVPLPEELFE-VDPKKIFGLTIDPERLIEIRRERLKSLGLDDSSYADLERIEEELEYAE 229 (255)
T ss_pred hhHHHHhcCcceeecC--cCCCCCCCHHHHh-CCCCcEEEEECCHHHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHH
Confidence 5556666888887543 5566666555543 233333333333 46888899999999998
Q ss_pred HH-hhcCCcee
Q 045860 94 EC-KNREDQIF 103 (160)
Q Consensus 94 ~~-~~~~~~ii 103 (160)
+. ++.+-.+|
T Consensus 230 ~l~~~~~~pvI 240 (255)
T PF03618_consen 230 RLFRKLGCPVI 240 (255)
T ss_pred HHHHHcCCCEE
Confidence 87 66664444
No 79
>PF03437 BtpA: BtpA family; InterPro: IPR005137 Photosystem I (PSI) is a large protein complex embedded within the photosynthetic thylakoid membrane. It consists of 11 subunits, ~100 chlorophyll a molecules, 2 phylloquinones, and 3 Fe4S4-clusters. The three dimensional structure of the PSI complex has been resolved at 2.5 A [], which allows the precise localisation of each cofactor. PSI together with photosystem II (PSII) catalyses the light-induced steps in oxygenic photosynthesis - a process found in cyanobacteria, eukaryotic algae (e.g. red algae, green algae) and higher plants. To date, three thylakoid proteins involved in the stable accumulation of PSI have been identified: BtpA [], Ycf3 [, ], and Ycf4 (IPR003359 from INTERPRO) []. Because translation of the psaA and psaB mRNAs encoding the two reaction centre polypeptides, of PSI and PSII respectively, is not affected in mutant strains lacking functional ycf3 and ycf4, the products of these two genes appear to act at a post-translational step of PSI biosynthesis. These gene products are therefore involved either in the stabilisation or in the assembly of the PSI complex. However, their exact roles remain unknown. The BtpA protein appears to act at the level of PSI stabilisation []. It is an extrinsic membrane protein located on the cytoplasmic side of the thylakoid membrane [, ]. Homologs of BtpA are found in the crenarchaeota and euryarchaeota, where their function remains unknown. The Ycf4 protein is firmly associated with the thylakoid membrane, presumably through a transmembrane domain []. Ycf4 co-fractionates with a protein complex larger than PSI upon sucrose density gradient centrifugation of solubilised thylakoids []. The Ycf3 protein is loosely associated with the thylakoid membrane and can be released from the membrane with sodium carbonate. This suggests that Ycf3 is not part of a stable complex and that it probably interacts transiently with its partners []. Ycf3 contains a number of tetratrico peptide repeats (TPR, IPR001440 from INTERPRO); TPR is a structural motif present in a wide range of proteins, which mediates protein-protein interactions.
Probab=28.84 E-value=1.7e+02 Score=23.28 Aligned_cols=109 Identities=14% Similarity=0.232 Sum_probs=63.8
Q ss_pred HHHHHhcCCcEEEEeCC---CCC-CCCCchHHHHHHHHhcceEEEEeecCCCCChhHHHHHHHHHHHhhcCCceeeEEe-
Q 045860 33 LYTALNNKGIYVFRDDK---QLE-KGGSISPNLLKAIDESRISIIVLSKNYASSTWCLDELLKITECKNREDQIFPIFY- 107 (160)
Q Consensus 33 L~~~L~~~gi~v~~d~~---d~~-~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~~~~~~~~~iiPVf~- 107 (160)
.+..|... ++++-|-. ... .+.++.+....+++.+..=-+++|-.-...+--..++..+-+. -. +|||.
T Consensus 133 ~R~~l~a~-v~ilaDV~~kh~~~l~~~~~~~~~~~a~~~~~aDaviVtG~~TG~~~~~~~l~~vr~~---~~--~PVlvG 206 (254)
T PF03437_consen 133 YRKRLGAD-VKILADVHVKHSSPLATRDLEEAAKDAVERGGADAVIVTGKATGEPPDPEKLKRVREA---VP--VPVLVG 206 (254)
T ss_pred HHHHcCCC-eEEEeeechhhcccCCCCCHHHHHHHHHHhcCCCEEEECCcccCCCCCHHHHHHHHhc---CC--CCEEEe
Confidence 44455555 88988842 111 2335555666777877776677777655544445555544432 22 99998
Q ss_pred -ccCchhhhcccch-----HHHHHHHHHH-hhcCCHHHHHHHHHHHH
Q 045860 108 -GVEPTVVRKQTAS-----FGEAFAEHEE-FFRDNIEKVQKWRHALK 147 (160)
Q Consensus 108 -~v~p~~v~~~~~~-----f~~~f~~~~~-~~~~~~~~~~~W~~al~ 147 (160)
+++++++.++... -|-.|++... .-+.|++++.++.+++.
T Consensus 207 SGvt~~Ni~~~l~~ADG~IVGS~~K~~G~~~n~VD~~Rv~~fm~~v~ 253 (254)
T PF03437_consen 207 SGVTPENIAEYLSYADGAIVGSYFKKDGKWENPVDPERVRRFMEAVK 253 (254)
T ss_pred cCCCHHHHHHHHHhCCEEEEeeeeeeCCEeCCcCCHHHHHHHHHHhh
Confidence 5999998775321 1223332222 11246889999888765
No 80
>cd00154 Rab Rab family. Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide di
Probab=28.69 E-value=1.6e+02 Score=19.71 Aligned_cols=28 Identities=11% Similarity=0.018 Sum_probs=19.7
Q ss_pred CCC-CchHHHHHHHHhcceEEEEeecCCC
Q 045860 53 KGG-SISPNLLKAIDESRISIIVLSKNYA 80 (160)
Q Consensus 53 ~G~-~~~~~i~~~I~~S~~~ivvlS~~~~ 80 (160)
+|. .+.......+++++..|+|++..-.
T Consensus 57 ~g~~~~~~~~~~~~~~~d~ii~v~d~~~~ 85 (159)
T cd00154 57 AGQERFRSITPSYYRGAHGAILVYDITNR 85 (159)
T ss_pred CChHHHHHHHHHHhcCCCEEEEEEECCCH
Confidence 453 3444556778899999999998653
No 81
>cd06335 PBP1_ABC_ligand_binding_like_2 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=28.40 E-value=3e+02 Score=21.95 Aligned_cols=18 Identities=22% Similarity=0.147 Sum_probs=10.3
Q ss_pred hHHHHHHHHHhcCCcEEE
Q 045860 28 GFIGYLYTALNNKGIYVF 45 (160)
Q Consensus 28 ~fv~~L~~~L~~~gi~v~ 45 (160)
..+..+...|++.|+.+-
T Consensus 153 ~~~~~~~~~~~~~G~~v~ 170 (347)
T cd06335 153 SNRKDLTAALAARGLKPV 170 (347)
T ss_pred hHHHHHHHHHHHcCCeeE
Confidence 445556666666666554
No 82
>COG1180 PflA Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=27.76 E-value=1.4e+02 Score=23.50 Aligned_cols=34 Identities=21% Similarity=0.135 Sum_probs=26.4
Q ss_pred EEEecccCCCcchHHHHHHHHHhcCCcEEEEeCC
Q 045860 16 AFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDK 49 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~ 49 (160)
|-+|+...-....|+..+..+.+++|+++.++-.
T Consensus 87 vt~SGGEP~~q~e~~~~~~~~ake~Gl~~~l~Tn 120 (260)
T COG1180 87 VTFSGGEPTLQAEFALDLLRAAKERGLHVALDTN 120 (260)
T ss_pred EEEECCcchhhHHHHHHHHHHHHHCCCcEEEEcC
Confidence 4556655545678899999999999999999854
No 83
>COG3340 PepE Peptidase E [Amino acid transport and metabolism]
Probab=27.69 E-value=2.4e+02 Score=22.06 Aligned_cols=70 Identities=17% Similarity=0.110 Sum_probs=46.0
Q ss_pred ccEEEecccCCCcc-hHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCCChhHHHH
Q 045860 14 YDAFLSFRGEDTRK-GFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYASSTWCLDE 88 (160)
Q Consensus 14 ~dVFISy~~~D~~~-~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S~wc~~E 88 (160)
-=+||=+.+.|..+ .++...+++|+..|..+- ++.....-.+.|.+-+.+.++..| =--|...=-|++.|
T Consensus 34 ~i~FIPtAs~~~~~~~Yv~k~~~~l~~lg~~v~----~L~l~~~~~~~Ie~~l~~~d~IyV-gGGNTF~LL~~lke 104 (224)
T COG3340 34 TIAFIPTASVDSEDDFYVEKVRNALAKLGLEVS----ELHLSKPPLAAIENKLMKADIIYV-GGGNTFNLLQELKE 104 (224)
T ss_pred eEEEEecCccccchHHHHHHHHHHHHHcCCeee----eeeccCCCHHHHHHhhhhccEEEE-CCchHHHHHHHHHH
Confidence 35699998877643 368889999999997654 455666666777777777876544 33333333344444
No 84
>PRK08306 dipicolinate synthase subunit A; Reviewed
Probab=27.38 E-value=81 Score=25.36 Aligned_cols=53 Identities=23% Similarity=0.213 Sum_probs=37.6
Q ss_pred cCCCcchHHHHHHHHHhcCCcEEEEe---CCCC-CCCCCchHHHHHHHHhcceEEEEeec
Q 045860 22 GEDTRKGFIGYLYTALNNKGIYVFRD---DKQL-EKGGSISPNLLKAIDESRISIIVLSK 77 (160)
Q Consensus 22 ~~D~~~~fv~~L~~~L~~~gi~v~~d---~~d~-~~G~~~~~~i~~~I~~S~~~ivvlS~ 77 (160)
+.|.|+ -.+.+.|.+.|+.|.+. +.+. ..|..+.+...+.+.++++.|.++.+
T Consensus 9 ggd~r~---~~~~~~l~~~G~~v~~~g~~~~~~~~~g~~~~~~~~~~~~~ad~ii~~~p~ 65 (296)
T PRK08306 9 GGDARQ---LELIRKLVELGAKVSLVGFDQLDHGFTGATKSSSLEEALSDVDVIILPVPG 65 (296)
T ss_pred cCcHHH---HHHHHHHHHCCCEEEEEeccccccccCCceeeccHHHHhccCCEEEECCcc
Confidence 566653 36889999999988863 2222 45666655556789999999998554
No 85
>KOG0409 consensus Predicted dehydrogenase [General function prediction only]
Probab=27.21 E-value=1.1e+02 Score=25.31 Aligned_cols=62 Identities=13% Similarity=0.196 Sum_probs=43.1
Q ss_pred CCcccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCC-------CCCCchHHHHHHHHhcceEEEEeecC
Q 045860 11 CGKYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLE-------KGGSISPNLLKAIDESRISIIVLSKN 78 (160)
Q Consensus 11 ~~~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~-------~G~~~~~~i~~~I~~S~~~ivvlS~~ 78 (160)
..+-=-||.-. - . =..+...|-+.|++|...++... .|....+.-.+-.+.|+++|.+++..
T Consensus 34 s~~~iGFIGLG-~-M----G~~M~~nLik~G~kVtV~dr~~~k~~~f~~~Ga~v~~sPaeVae~sDvvitmv~~~ 102 (327)
T KOG0409|consen 34 SKTRIGFIGLG-N-M----GSAMVSNLIKAGYKVTVYDRTKDKCKEFQEAGARVANSPAEVAEDSDVVITMVPNP 102 (327)
T ss_pred ccceeeEEeec-c-c----hHHHHHHHHHcCCEEEEEeCcHHHHHHHHHhchhhhCCHHHHHhhcCEEEEEcCCh
Confidence 34444477652 1 1 13577777888999999887765 36666566677889999999998765
No 86
>cd01857 HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with sequence NKXD) are relocated to the N terminus.
Probab=27.12 E-value=2.1e+02 Score=19.67 Aligned_cols=18 Identities=17% Similarity=0.447 Sum_probs=9.0
Q ss_pred HHHHHHHhcceEEEEeec
Q 045860 60 NLLKAIDESRISIIVLSK 77 (160)
Q Consensus 60 ~i~~~I~~S~~~ivvlS~ 77 (160)
++.++|++++..++|+.-
T Consensus 4 ~~~~~i~~aD~vl~ViD~ 21 (141)
T cd01857 4 QLWRVVERSDIVVQIVDA 21 (141)
T ss_pred HHHHHHhhCCEEEEEEEc
Confidence 344455555555555544
No 87
>cd08584 PI-PLCc_GDPD_SF_unchar2 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues.
Probab=26.82 E-value=1.2e+02 Score=23.03 Aligned_cols=45 Identities=16% Similarity=0.157 Sum_probs=31.8
Q ss_pred EEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCCChhHHHHHHH
Q 045860 43 YVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYASSTWCLDELLK 91 (160)
Q Consensus 43 ~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S~wc~~El~~ 91 (160)
-||+|.- -+..+..++.....++.+-|+++||.--.-. +..++..
T Consensus 126 ~VW~D~f---~~~~~~~~~~~~~~~~~~~~c~VSpELh~~~-~~~~~~~ 170 (192)
T cd08584 126 WVWIDSF---TSLWLDNDLILKLLKAGKKICLVSPELHGRD-HLAEWEA 170 (192)
T ss_pred EEEEecc---cccCCCHHHHHHHHHCCcEEEEECHHHcCCC-hHHHHHH
Confidence 3899862 3567777888888888999999999855433 3444443
No 88
>COG0124 HisS Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=26.60 E-value=2.9e+02 Score=23.72 Aligned_cols=59 Identities=24% Similarity=0.233 Sum_probs=40.4
Q ss_pred CCcccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHH-hcceEEEE
Q 045860 11 CGKYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAID-ESRISIIV 74 (160)
Q Consensus 11 ~~~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~-~S~~~ivv 74 (160)
....||||..-+++. ...+-.|...|++.|+.+-++-. +..+..++..|-+ .++.+|++
T Consensus 333 ~~~~~v~v~~~~~~~-~~~a~~la~~LR~~g~~~~~~~~----~r~~k~q~k~A~~~g~~~~vii 392 (429)
T COG0124 333 ETRVDVYVVPLGEDA-EPEALKLAQKLRAAGISVEVDYS----GRKLKKQFKYADKLGARFAVIL 392 (429)
T ss_pred CCCCCEEEEEcCchh-HHHHHHHHHHHHHcCCcEEEEec----cccHHHHHHHHHHCCCCEEEEE
Confidence 456799999877775 34577899999999999888763 2225555555554 35555554
No 89
>PF12913 SH3_6: SH3 domain of the SH3b1 type; PDB: 3M1U_B.
Probab=26.51 E-value=21 Score=21.43 Aligned_cols=16 Identities=13% Similarity=0.331 Sum_probs=12.6
Q ss_pred cEEEecccCCCcchHH
Q 045860 15 DAFLSFRGEDTRKGFI 30 (160)
Q Consensus 15 dVFISy~~~D~~~~fv 30 (160)
-|+|+|.+.|.+|.||
T Consensus 28 Pv~i~H~S~D~~W~fV 43 (54)
T PF12913_consen 28 PVYILHTSRDGAWAFV 43 (54)
T ss_dssp EEEEEEE-TTSSEEEE
T ss_pred CEEEEEECCCCCEEEE
Confidence 4899999999988765
No 90
>cd00138 PLDc Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of phospholipids to phosphatidic acid and a hydrophilic constituent. Phosphatidic acid is a compound that is heavily involved in signal transduction. The common features of the family members are that they can bind to a phosphodiester moiety, and that most of these enzymes are active as bi-lobed monomers or dimers.
Probab=26.46 E-value=2.4e+02 Score=19.95 Aligned_cols=30 Identities=30% Similarity=0.257 Sum_probs=21.4
Q ss_pred CCCCCchHHHHHHHHhcceEEEEeecCCCC
Q 045860 52 EKGGSISPNLLKAIDESRISIIVLSKNYAS 81 (160)
Q Consensus 52 ~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~ 81 (160)
..+..+.+.+.+.|.+++..|.+.+..|..
T Consensus 17 ~~~~~~~~~i~~~I~~A~~~I~i~~~~~~~ 46 (176)
T cd00138 17 VGGRSDLDALLEAISNAKKSIYIASFYLSP 46 (176)
T ss_pred cCcchHHHHHHHHHHhhheEEEEEEeEecc
Confidence 345666677778888888888888775553
No 91
>cd06386 PBP1_NPR_C_like Ligand-binding domain of type C natriuretic peptide receptor. Ligand-binding domain of type C natriuretic peptide receptor (NPR-C). NPR-C is found in atrial, mesentery, placenta, lung, kidney, venous tissue, aortic smooth muscle, and aortic endothelial cells. The affinity of NPR-C for natriuretic peptides is ANPCNPBNP. The extracellular domain of NPR-C is about 30% identical to NPR-A and NPR-B. However, unlike the cyclase-linked receptors, it contains only 37 intracellular amino acids and no guanylyl cyclase activity. Major function of NPR-C is to clear natriuretic peptides from the circulation or extracellular surroundings through constitutive receptor-mediated internalization and degradation.
Probab=26.03 E-value=2.7e+02 Score=22.86 Aligned_cols=39 Identities=13% Similarity=0.042 Sum_probs=21.2
Q ss_pred HHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcc
Q 045860 30 IGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESR 69 (160)
Q Consensus 30 v~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~ 69 (160)
...|...|+..|+.+-.... ...++.-...+.+.|+.+.
T Consensus 157 ~~~l~~~~~~~gi~v~~~~~-~~~~~~d~~~~l~~ik~~~ 195 (387)
T cd06386 157 LEGVHHVFQEEGYHMSIYPF-DETKDLDLDEIIRAIQASE 195 (387)
T ss_pred HHHHHHHHHhcCceEEEEec-CCCCcccHHHHHHHHHhcC
Confidence 56677888888877665432 1223322334555555444
No 92
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=25.79 E-value=72 Score=19.18 Aligned_cols=22 Identities=18% Similarity=0.363 Sum_probs=13.6
Q ss_pred HHHHHHHHhcCCcEEEEeCCCC
Q 045860 30 IGYLYTALNNKGIYVFRDDKQL 51 (160)
Q Consensus 30 v~~L~~~L~~~gi~v~~d~~d~ 51 (160)
+..+...|+++||.+++.+...
T Consensus 12 a~~i~~~L~~~gI~~~v~~~~~ 33 (67)
T PF09413_consen 12 AELIKGLLEENGIPAFVKNEHM 33 (67)
T ss_dssp HHHHHHHHHHTT--EE--S---
T ss_pred HHHHHHHHHhCCCcEEEECCcc
Confidence 6779999999999999976543
No 93
>PF07429 Glyco_transf_56: 4-alpha-L-fucosyltransferase glycosyl transferase group 56; InterPro: IPR009993 This family contains the bacterial enzyme 4-alpha-L-fucosyltransferase (Fuc4NAc transferase) (approximately 360 residues long). This catalyses the synthesis of Fuc4NAc-ManNAcA-GlcNAc-PP-Und (lipid III) as part of the biosynthetic pathway of enterobacterial common antigen (ECA), a polysaccharide comprised of the trisaccharide repeat unit Fuc4NAc-ManNAcA-GlcNAc [].; GO: 0008417 fucosyltransferase activity, 0009246 enterobacterial common antigen biosynthetic process, 0009276 Gram-negative-bacterium-type cell wall
Probab=25.61 E-value=76 Score=26.58 Aligned_cols=50 Identities=18% Similarity=0.387 Sum_probs=30.4
Q ss_pred HHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhc-ceEEEEeecCCCCChhH
Q 045860 33 LYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDES-RISIIVLSKNYASSTWC 85 (160)
Q Consensus 33 L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S-~~~ivvlS~~~~~S~wc 85 (160)
+...|.++|+.|+++.+++... . ..+..+.+... +..|.+++|+|.. .|.
T Consensus 300 ~~~~l~~~~ipVlf~~d~L~~~-~-v~ea~rql~~~dk~~iaFf~pny~~-~w~ 350 (360)
T PF07429_consen 300 FWQDLKEQGIPVLFYGDELDEA-L-VREAQRQLANVDKQQIAFFAPNYLQ-GWR 350 (360)
T ss_pred HHHHHHhCCCeEEeccccCCHH-H-HHHHHHHHhhCcccceeeeCCchHH-HHH
Confidence 5667778899888776554332 2 22333434433 3467799999887 453
No 94
>PF07894 DUF1669: Protein of unknown function (DUF1669); InterPro: IPR012461 This family is composed of sequences derived from hypothetical eukaryotic proteins of unknown function. Some members of this family are annotated as being potential phospholipases but no literature was found to support this.
Probab=25.11 E-value=3.7e+02 Score=21.79 Aligned_cols=77 Identities=13% Similarity=0.213 Sum_probs=47.8
Q ss_pred cEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCCChhHHHHHHHHHHHhhcCCceeeEEeccCchhhhcccchH
Q 045860 42 IYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYASSTWCLDELLKITECKNREDQIFPIFYGVEPTVVRKQTASF 121 (160)
Q Consensus 42 i~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~~~~~~~~~iiPVf~~v~p~~v~~~~~~f 121 (160)
+.++...-. ....+|.+.+.+.|++++.+|+|+-.-|..-. -..+|..|-. ++=+||+.=++...+.
T Consensus 121 ~~vy~qPp~-~~~p~IKE~vR~~I~~A~kVIAIVMD~FTD~d-If~DLleAa~-----kR~VpVYiLLD~~~~~------ 187 (284)
T PF07894_consen 121 ATVYFQPPK-DGQPHIKEVVRRMIQQAQKVIAIVMDVFTDVD-IFCDLLEAAN-----KRGVPVYILLDEQNLP------ 187 (284)
T ss_pred EEEEeCCCC-CCCCCHHHHHHHHHHHhcceeEEEeeccccHH-HHHHHHHHHH-----hcCCcEEEEechhcCh------
Confidence 566666521 34467888889999999999999988876633 2333444432 3345776555554433
Q ss_pred HHHHHHHHHhhc
Q 045860 122 GEAFAEHEEFFR 133 (160)
Q Consensus 122 ~~~f~~~~~~~~ 133 (160)
.|.+++++..
T Consensus 188 --~Fl~Mc~~~~ 197 (284)
T PF07894_consen 188 --HFLEMCEKLG 197 (284)
T ss_pred --HHHHHHHHCC
Confidence 3566666543
No 95
>COG2084 MmsB 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]
Probab=24.87 E-value=1.2e+02 Score=24.53 Aligned_cols=47 Identities=21% Similarity=0.273 Sum_probs=37.6
Q ss_pred HHHHHHhcCCcEEEEeCCCCCC--------CCCchHHHHHHHHhcceEEEEeecC
Q 045860 32 YLYTALNNKGIYVFRDDKQLEK--------GGSISPNLLKAIDESRISIIVLSKN 78 (160)
Q Consensus 32 ~L~~~L~~~gi~v~~d~~d~~~--------G~~~~~~i~~~I~~S~~~ivvlS~~ 78 (160)
-+...|.++|+.+...+|+..+ |........+++.++++.|..++..
T Consensus 14 pmA~~L~~aG~~v~v~~r~~~ka~~~~~~~Ga~~a~s~~eaa~~aDvVitmv~~~ 68 (286)
T COG2084 14 PMAANLLKAGHEVTVYNRTPEKAAELLAAAGATVAASPAEAAAEADVVITMLPDD 68 (286)
T ss_pred HHHHHHHHCCCEEEEEeCChhhhhHHHHHcCCcccCCHHHHHHhCCEEEEecCCH
Confidence 4778888999998888877554 6666667788999999999988765
No 96
>COG0276 HemH Protoheme ferro-lyase (ferrochelatase) [Coenzyme metabolism]
Probab=24.73 E-value=4e+02 Score=21.99 Aligned_cols=76 Identities=21% Similarity=0.322 Sum_probs=43.4
Q ss_pred HHHHHHHHhcC----CcEEEEeCCCCCCCCCchHHHHHHHHh---cceEEEEeecCCCCCh--hHHHHHHHHHHH-h-hc
Q 045860 30 IGYLYTALNNK----GIYVFRDDKQLEKGGSISPNLLKAIDE---SRISIIVLSKNYASST--WCLDELLKITEC-K-NR 98 (160)
Q Consensus 30 v~~L~~~L~~~----gi~v~~d~~d~~~G~~~~~~i~~~I~~---S~~~ivvlS~~~~~S~--wc~~El~~~~~~-~-~~ 98 (160)
...+..+|+++ .+.|++-.| -|.+..++....+.. .+++++.+.|.|..|. -..+++..+++. + ..
T Consensus 75 T~~q~~~L~~~L~~~~~~V~~amr---y~~P~i~~~v~~l~~~gv~~iv~~pLyPqyS~sTt~s~~~~~~~al~~~~~~~ 151 (320)
T COG0276 75 TRAQAAALEERLDLPDFKVYLAMR---YGPPFIEEAVEELKKDGVERIVVLPLYPQYSSSTTGSYVDELARALKELRGQP 151 (320)
T ss_pred HHHHHHHHHHHhCCCCccEEEeec---CCCCcHHHHHHHHHHcCCCeEEEEECCcccccccHHHHHHHHHHHHHhcCCCC
Confidence 34455555554 477777644 456666666666654 3457777788776554 345566666665 2 12
Q ss_pred CCceeeEEec
Q 045860 99 EDQIFPIFYG 108 (160)
Q Consensus 99 ~~~iiPVf~~ 108 (160)
....||-||+
T Consensus 152 ~i~~I~~~~~ 161 (320)
T COG0276 152 KISTIPDYYD 161 (320)
T ss_pred ceEEecCccC
Confidence 2355555554
No 97
>cd01454 vWA_norD_type norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial denitrification has been established as NO3- ------ NO2- ------ NO ------- N2O --------- N2. This reaction generally occurs under oxygen limiting conditions. Genetic and biochemical studies have shown that the first srep of the biochemical pathway is catalyzed by periplasmic nitrate reductases. This family is widely present in proteobacteria and firmicutes. This version of the domain is also present in some archaeal members. The function of the vWA domain in this sub-group is not known. Members of this subgroup have a conserved MIDAS motif.
Probab=24.71 E-value=2.6e+02 Score=19.89 Aligned_cols=44 Identities=14% Similarity=0.161 Sum_probs=26.8
Q ss_pred cceEEEEeecCCCCChh-------HHHHHHHHHHH-hhcCCceeeEEeccCc
Q 045860 68 SRISIIVLSKNYASSTW-------CLDELLKITEC-KNREDQIFPIFYGVEP 111 (160)
Q Consensus 68 S~~~ivvlS~~~~~S~w-------c~~El~~~~~~-~~~~~~iiPVf~~v~p 111 (160)
.+..|+++|....+... ...+...+... .+.+..++.|.++-..
T Consensus 103 ~~~~iiliTDG~~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~v~~igig~~~ 154 (174)
T cd01454 103 KRKILLVISDGEPNDLDYYEGNVFATEDALRAVIEARKLGIEVFGITIDRDA 154 (174)
T ss_pred cCcEEEEEeCCCcCcccccCcchhHHHHHHHHHHHHHhCCcEEEEEEecCcc
Confidence 46789999988776432 22333333443 5567788888876443
No 98
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=24.51 E-value=1.9e+02 Score=24.52 Aligned_cols=45 Identities=24% Similarity=0.326 Sum_probs=34.6
Q ss_pred HHHHHHHHhcc-eEEEEeecCC-CCChhHHHHHHHHHHH-hhcCCcee
Q 045860 59 PNLLKAIDESR-ISIIVLSKNY-ASSTWCLDELLKITEC-KNREDQIF 103 (160)
Q Consensus 59 ~~i~~~I~~S~-~~ivvlS~~~-~~S~wc~~El~~~~~~-~~~~~~ii 103 (160)
+.+.+++...+ ...++.+|+= ..+-|-.+||.++.+. .+.+-+||
T Consensus 148 ~~LE~~~~~~~vkl~iLCnPHNP~Grvwt~eeL~~i~elc~kh~v~VI 195 (388)
T COG1168 148 DALEKAFVDERVKLFILCNPHNPTGRVWTKEELRKIAELCLRHGVRVI 195 (388)
T ss_pred HHHHHHHhcCCccEEEEeCCCCCCCccccHHHHHHHHHHHHHcCCEEE
Confidence 57778888887 6777777774 4677999999999998 77665555
No 99
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=24.16 E-value=2.7e+02 Score=19.79 Aligned_cols=89 Identities=15% Similarity=0.137 Sum_probs=46.1
Q ss_pred HHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCCChhHHHHHHHHHHH-hhcCCceeeEE--
Q 045860 30 IGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYASSTWCLDELLKITEC-KNREDQIFPIF-- 106 (160)
Q Consensus 30 v~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~~~-~~~~~~iiPVf-- 106 (160)
+..|...|++.|+.+.+-. |+ ..+.+.+-+++..+..|++...|.... ... -..+.+. .+.+..+.-+-
T Consensus 55 L~~L~~~L~~~g~~L~v~~-----g~-~~~~l~~l~~~~~~~~V~~~~~~~~~~-~~r-d~~v~~~l~~~~i~~~~~~~~ 126 (165)
T PF00875_consen 55 LADLQESLRKLGIPLLVLR-----GD-PEEVLPELAKEYGATAVYFNEEYTPYE-RRR-DERVRKALKKHGIKVHTFDDH 126 (165)
T ss_dssp HHHHHHHHHHTTS-EEEEE-----SS-HHHHHHHHHHHHTESEEEEE---SHHH-HHH-HHHHHHHHHHTTSEEEEE--S
T ss_pred HHHHHHHHHhcCcceEEEe-----cc-hHHHHHHHHHhcCcCeeEeccccCHHH-HHH-HHHHHHHHHhcceEEEEECCc
Confidence 3457778888899887754 43 345566677788898999888876622 111 1112222 33333332211
Q ss_pred eccCchhhhcccchHHHHHH
Q 045860 107 YGVEPTVVRKQTASFGEAFA 126 (160)
Q Consensus 107 ~~v~p~~v~~~~~~f~~~f~ 126 (160)
+=+.|.++....|.....|.
T Consensus 127 ~L~~~~~i~~~~~~~~~vFt 146 (165)
T PF00875_consen 127 TLVPPDDIPKKDGEPYKVFT 146 (165)
T ss_dssp SSS-HHHCHSTTSSSHSSHH
T ss_pred EEEeccccccCCCCCcccHH
Confidence 11568888766665554443
No 100
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=23.88 E-value=51 Score=20.73 Aligned_cols=33 Identities=15% Similarity=0.229 Sum_probs=18.2
Q ss_pred HHHhc--CCcEEEEeCCCCCCCCCchHHHHHHHHhcc
Q 045860 35 TALNN--KGIYVFRDDKQLEKGGSISPNLLKAIDESR 69 (160)
Q Consensus 35 ~~L~~--~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~ 69 (160)
..+.. +.+-+++|... +|......+.+.+....
T Consensus 40 ~~~~~~~~~Vii~~D~D~--~G~~~a~~i~~~l~~~g 74 (81)
T PF13662_consen 40 EKLEKKVKEVIIAFDNDK--AGEKAAQKIAKKLLPLG 74 (81)
T ss_dssp HHHH---SEEEEEEESSH--HHHHHHHHHHHHHG---
T ss_pred HhhhccCceEEEEeCcCH--HHHHHHHHHHHHHHhhc
Confidence 44444 56778888642 67666666666554333
No 101
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.73 E-value=1e+02 Score=17.85 Aligned_cols=32 Identities=22% Similarity=0.276 Sum_probs=22.6
Q ss_pred CcccEEEecccCCCcchHHHHHHHHHhcCCcEEE
Q 045860 12 GKYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVF 45 (160)
Q Consensus 12 ~~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~ 45 (160)
..+.+++.....+. .-...+...|++.|+++.
T Consensus 41 ~~~~~~i~v~~~~~--~~l~~l~~~l~~~g~~~~ 72 (73)
T cd04886 41 GEVEVELTLETRGA--EHIEEIIAALREAGYDVR 72 (73)
T ss_pred ceEEEEEEEEeCCH--HHHHHHHHHHHHcCCEEe
Confidence 45667777766553 225789999999998774
No 102
>cd07370 HPCD The Class III extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase, catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate. 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase (HPCD) catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate (hpca), a central intermediate in the bacterial degradation of aromatic compounds. The enzyme incorporates both atoms of molecular oxygen into hpca, resulting in aromatic ring-opening to yield alpha-hydroxy-delta-carboxymethyl cis-muconic semialdehyde. HPCD is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon.
Probab=23.51 E-value=3.8e+02 Score=21.24 Aligned_cols=77 Identities=6% Similarity=0.112 Sum_probs=49.5
Q ss_pred chHHHHHHHHHhcCCcEEEEe---CCCCCCCCCchHHHHHHHH-hcceEEEEeecCCCCChhHHHHHHHHHHH--hhcCC
Q 045860 27 KGFIGYLYTALNNKGIYVFRD---DKQLEKGGSISPNLLKAID-ESRISIIVLSKNYASSTWCLDELLKITEC--KNRED 100 (160)
Q Consensus 27 ~~fv~~L~~~L~~~gi~v~~d---~~d~~~G~~~~~~i~~~I~-~S~~~ivvlS~~~~~S~wc~~El~~~~~~--~~~~~ 100 (160)
..++..|...+...|+.+-.. .+.+..|.-+. ...+. +.++-||.+|-+...+.--..+|..++.. ++.++
T Consensus 94 ~ela~~i~~~~~~~g~~~~~~~~~~~~lDhg~~vP---L~~l~p~~~~pvV~is~~~~~~~~~~~~lG~al~~~~~~~~~ 170 (280)
T cd07370 94 PELAHLIAEEATEHGVKTLAHEDPSLPLEYGTLVP---MRFMNEDDHFKVVSVAVWCTHDIEESRRLGEAIRRAIAASDR 170 (280)
T ss_pred HHHHHHHHHHHHHCCCCeeeecCCCCCCCeeHhhH---HHHhCCCCCceEEEEeecCCCCHHHHHHHHHHHHHHHHhcCC
Confidence 468899999999999875532 22233342211 12333 24777888888766677777899998887 44556
Q ss_pred ceeeEE
Q 045860 101 QIFPIF 106 (160)
Q Consensus 101 ~iiPVf 106 (160)
+|+.|-
T Consensus 171 ~v~iIa 176 (280)
T cd07370 171 RVALLA 176 (280)
T ss_pred CEEEEE
Confidence 666553
No 103
>PRK13762 tRNA-modifying enzyme; Provisional
Probab=23.03 E-value=3.2e+02 Score=22.32 Aligned_cols=60 Identities=20% Similarity=0.337 Sum_probs=41.1
Q ss_pred ccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCC
Q 045860 14 YDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYA 80 (160)
Q Consensus 14 ~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~ 80 (160)
-++-||..|+-+-+.+...|...+.++|++++++-. |.. .+..+.+ ......+.+|=+-.
T Consensus 131 ~~v~iSl~GEPlL~p~l~eli~~~k~~Gi~~~L~TN----G~~--~e~l~~L-~~~~d~i~VSLda~ 190 (322)
T PRK13762 131 KHVAISLSGEPTLYPYLPELIEEFHKRGFTTFLVTN----GTR--PDVLEKL-EEEPTQLYVSLDAP 190 (322)
T ss_pred CEEEEeCCccccchhhHHHHHHHHHHcCCCEEEECC----CCC--HHHHHHH-HhcCCEEEEEccCC
Confidence 468888888887667788899999999999999863 321 2344455 34445555666544
No 104
>cd01241 PH_Akt Akt pleckstrin homology (PH) domain. Akt pleckstrin homology (PH) domain. Akt (Protein Kinase B (PKB)) is a phosphatidylinositol 3'-kinase (PI3K)-dependent Ser/Thr kinase. The PH domain recruits Akt to the plasma membrane by binding to phosphoinositides (PtdIns-3,4-P2) and is required for activation. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=22.79 E-value=83 Score=20.87 Aligned_cols=16 Identities=38% Similarity=0.715 Sum_probs=13.4
Q ss_pred CHHHHHHHHHHHHHhh
Q 045860 135 NIEKVQKWRHALKVVA 150 (160)
Q Consensus 135 ~~~~~~~W~~al~~v~ 150 (160)
+++..+.|..||..|+
T Consensus 87 s~ee~~eWi~ai~~v~ 102 (102)
T cd01241 87 SPEEREEWIHAIQTVA 102 (102)
T ss_pred CHHHHHHHHHHHHhhC
Confidence 4788999999998774
No 105
>PF05818 TraT: Enterobacterial TraT complement resistance protein; InterPro: IPR008874 The traT gene is one of the F factor transfer genes and encodes an outer membrane protein which is involved in interactions between Escherichia coli and its surroundings []. The protein plays a role in preventing unproductive conjugation between bacteria carrying like plasmids.; GO: 0046999 regulation of conjugation, 0019867 outer membrane
Probab=22.58 E-value=1.2e+02 Score=23.60 Aligned_cols=37 Identities=22% Similarity=0.327 Sum_probs=26.7
Q ss_pred CCcccEEEeccc-CCCcchHHHHHHHHHhcCCcEEEEe
Q 045860 11 CGKYDAFLSFRG-EDTRKGFIGYLYTALNNKGIYVFRD 47 (160)
Q Consensus 11 ~~~~dVFISy~~-~D~~~~fv~~L~~~L~~~gi~v~~d 47 (160)
+.+--||++.+. .|..-.+-..|...|+.+||++--|
T Consensus 19 ~~~rtVyv~vrNTSd~~~~l~~~i~~~L~~kGY~vv~~ 56 (215)
T PF05818_consen 19 PSQRTVYVQVRNTSDKDINLESQIISALQAKGYQVVDD 56 (215)
T ss_pred cccceEEEEEecCCCCccchHHHHHHHHHHCCCEEecC
Confidence 345679999854 2322357778999999999988755
No 106
>PF10579 Rapsyn_N: Rapsyn N-terminal myristoylation and linker region; InterPro: IPR019568 Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane. Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane []. ; GO: 0008270 zinc ion binding, 0033130 acetylcholine receptor binding, 0007268 synaptic transmission, 0005856 cytoskeleton, 0030054 cell junction, 0045211 postsynaptic membrane
Probab=22.56 E-value=59 Score=21.17 Aligned_cols=19 Identities=32% Similarity=0.637 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHhhcccc
Q 045860 136 IEKVQKWRHALKVVANISG 154 (160)
Q Consensus 136 ~~~~~~W~~al~~v~~~~g 154 (160)
.+-+.+|+.||.++++-.+
T Consensus 23 ~~Al~~W~~aL~k~~~~~~ 41 (80)
T PF10579_consen 23 QQALQKWRKALEKITDRED 41 (80)
T ss_pred HHHHHHHHHHHhhcCChHH
Confidence 5679999999999988654
No 107
>COG2077 Tpx Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=22.47 E-value=64 Score=23.74 Aligned_cols=22 Identities=18% Similarity=0.449 Sum_probs=17.5
Q ss_pred hcceEEEEeecC--CCCChhHHHH
Q 045860 67 ESRISIIVLSKN--YASSTWCLDE 88 (160)
Q Consensus 67 ~S~~~ivvlS~~--~~~S~wc~~E 88 (160)
-....|.++|-+ |+.+.||..|
T Consensus 74 ~~~~~Vl~IS~DLPFAq~RfC~ae 97 (158)
T COG2077 74 LGNTVVLCISMDLPFAQKRFCGAE 97 (158)
T ss_pred cCCcEEEEEeCCChhHHhhhhhhc
Confidence 455778888888 8899999765
No 108
>KOG1014 consensus 17 beta-hydroxysteroid dehydrogenase type 3, HSD17B3 [Lipid transport and metabolism]
Probab=22.40 E-value=1.7e+02 Score=24.00 Aligned_cols=58 Identities=17% Similarity=0.279 Sum_probs=40.2
Q ss_pred cccEEEecccCCCcchHHHHHHHHHhcC-CcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEE
Q 045860 13 KYDAFLSFRGEDTRKGFIGYLYTALNNK-GIYVFRDDKQLEKGGSISPNLLKAIDESRISIIV 74 (160)
Q Consensus 13 ~~dVFISy~~~D~~~~fv~~L~~~L~~~-gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivv 74 (160)
.+.|+|-=|.++. .+.+.++++++ ++.+.+..-|+..|+...+.|.+.+.+-++.|+|
T Consensus 73 G~nvvLIsRt~~K----L~~v~kEI~~~~~vev~~i~~Dft~~~~~ye~i~~~l~~~~VgILV 131 (312)
T KOG1014|consen 73 GFNVVLISRTQEK----LEAVAKEIEEKYKVEVRIIAIDFTKGDEVYEKLLEKLAGLDVGILV 131 (312)
T ss_pred CCEEEEEeCCHHH----HHHHHHHHHHHhCcEEEEEEEecCCCchhHHHHHHHhcCCceEEEE
Confidence 4556665444442 46677777765 6777776667777877677788888888888877
No 109
>cd06379 PBP1_iGluR_NMDA_NR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore
Probab=22.32 E-value=3.3e+02 Score=22.08 Aligned_cols=14 Identities=21% Similarity=0.126 Sum_probs=7.6
Q ss_pred HHHHHHHHHhcCCc
Q 045860 29 FIGYLYTALNNKGI 42 (160)
Q Consensus 29 fv~~L~~~L~~~gi 42 (160)
.+..+...|++.|+
T Consensus 170 ~~~~~~~~~~~~g~ 183 (377)
T cd06379 170 AQKRFETLLEEREI 183 (377)
T ss_pred HHHHHHHHHHhcCC
Confidence 44455555555555
No 110
>TIGR03026 NDP-sugDHase nucleotide sugar dehydrogenase. All of these enzymes contain three Pfam domains, pfam03721, pfam00984, and pfam03720 for the N-terminal, central, and C-terminal regions respectively.
Probab=22.11 E-value=2.2e+02 Score=23.80 Aligned_cols=52 Identities=19% Similarity=0.201 Sum_probs=33.1
Q ss_pred CCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCC----chHHHHHHHHhcceEEEE
Q 045860 23 EDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGS----ISPNLLKAIDESRISIIV 74 (160)
Q Consensus 23 ~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~----~~~~i~~~I~~S~~~ivv 74 (160)
.|.|.+=+-.|...|.++|+.|..++--...... ..+.+.++++.++..|+.
T Consensus 328 ~d~r~sp~~~~~~~L~~~g~~v~~~DP~~~~~~~~~~~~~~~~~~~~~~ad~~v~~ 383 (411)
T TIGR03026 328 DDVRESPALDIIELLKEKGAKVKAYDPLVPEEEVKGLPLIDDLEEALKGADALVIL 383 (411)
T ss_pred CccccChHHHHHHHHHhCCCEEEEECCCCChhhhhhcccCCCHHHHHhCCCEEEEe
Confidence 5666666778999999999998887643222110 013445667777766665
No 111
>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins. Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor
Probab=21.79 E-value=3e+02 Score=19.47 Aligned_cols=60 Identities=18% Similarity=0.353 Sum_probs=35.9
Q ss_pred EEEeccc-CCCcchHHHH-HHHHHhcCC-----cEEEEeCCCCCCCCCc-------hHHHHHHHHhcceEEEEe
Q 045860 16 AFLSFRG-EDTRKGFIGY-LYTALNNKG-----IYVFRDDKQLEKGGSI-------SPNLLKAIDESRISIIVL 75 (160)
Q Consensus 16 VFISy~~-~D~~~~fv~~-L~~~L~~~g-----i~v~~d~~d~~~G~~~-------~~~i~~~I~~S~~~ivvl 75 (160)
.-+||.| .-+.++|+.. |..+|-..| +..|+-..+++....+ .+.|...+..|...++||
T Consensus 54 LVlSfHG~tGtGKn~v~~liA~~ly~~G~~S~~V~~f~~~~hFP~~~~v~~Yk~~L~~~I~~~v~~C~rslFIF 127 (127)
T PF06309_consen 54 LVLSFHGWTGTGKNFVSRLIAEHLYKSGMKSPFVHQFIATHHFPHNSNVDEYKEQLKSWIRGNVSRCPRSLFIF 127 (127)
T ss_pred EEEEeecCCCCcHHHHHHHHHHHHHhcccCCCceeeecccccCCCchHHHHHHHHHHHHHHHHHHhCCcCeeeC
Confidence 4466644 4456778777 777766554 4666666566544332 234555666777777764
No 112
>PLN02908 threonyl-tRNA synthetase
Probab=21.52 E-value=2.5e+02 Score=25.53 Aligned_cols=60 Identities=18% Similarity=0.181 Sum_probs=39.1
Q ss_pred cccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeec
Q 045860 13 KYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSK 77 (160)
Q Consensus 13 ~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~ 77 (160)
..+|+|..-+.+. ...+..+...|+++|++|-+|.. +..+...+..+-..--..++|+.+
T Consensus 589 p~qv~Vipv~~~~-~~~A~~va~~LR~~Gi~vevd~~----~~~l~kkir~A~~~g~~~viivG~ 648 (686)
T PLN02908 589 PRQAIVVPISEKS-QDYAEEVRAQLHAAGFYVDVDVT----DRKIQKKVREAQLAQYNYILVVGE 648 (686)
T ss_pred CceEEEEEECHHH-HHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEECc
Confidence 3588777655433 35688899999999999999863 556666666664432334444443
No 113
>COG2861 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.41 E-value=4.2e+02 Score=21.06 Aligned_cols=70 Identities=17% Similarity=0.265 Sum_probs=43.8
Q ss_pred hHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHh--cceEEEEeecCCCCChhHHHHHHHHHHH-hhcCCce
Q 045860 28 GFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDE--SRISIIVLSKNYASSTWCLDELLKITEC-KNREDQI 102 (160)
Q Consensus 28 ~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~--S~~~ivvlS~~~~~S~wc~~El~~~~~~-~~~~~~i 102 (160)
.....|..+|+++|+ .|+|+. ..|.+....|.+++.- -..-|++ .+-.+-.-...+|..+... +++|..|
T Consensus 138 ~aM~~~m~~Lk~r~l-~flDs~--T~a~S~a~~iAk~~gVp~~~rdvfL--D~e~~~~~V~kql~~~~~~Ark~G~ai 210 (250)
T COG2861 138 DAMEKLMEALKERGL-YFLDSG--TIANSLAGKIAKEIGVPVIKRDVFL--DDEDTEAAVLKQLDAAEKLARKNGSAI 210 (250)
T ss_pred HHHHHHHHHHHHCCe-EEEccc--ccccchhhhhHhhcCCceeeeeeee--cCcCCHHHHHHHHHHHHHHHHhcCceE
Confidence 346678899998887 677764 3566666667666543 3333333 4444555677777777777 6666543
No 114
>COG3980 spsG Spore coat polysaccharide biosynthesis protein, predicted glycosyltransferase [Cell envelope biogenesis, outer membrane]
Probab=21.30 E-value=4.7e+02 Score=21.53 Aligned_cols=62 Identities=16% Similarity=0.244 Sum_probs=39.2
Q ss_pred CcccEEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHh-cceEEEEeec
Q 045860 12 GKYDAFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDE-SRISIIVLSK 77 (160)
Q Consensus 12 ~~~dVFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~-S~~~ivvlS~ 77 (160)
..+||+|+..+.|.. ...-++..+|.+..+..-+-- ..+++...++....+. .++-+..-+.
T Consensus 157 ~~r~ilI~lGGsDpk-~lt~kvl~~L~~~~~nl~iV~---gs~~p~l~~l~k~~~~~~~i~~~~~~~ 219 (318)
T COG3980 157 PKRDILITLGGSDPK-NLTLKVLAELEQKNVNLHIVV---GSSNPTLKNLRKRAEKYPNINLYIDTN 219 (318)
T ss_pred chheEEEEccCCChh-hhHHHHHHHhhccCeeEEEEe---cCCCcchhHHHHHHhhCCCeeeEecch
Confidence 478999999999974 567789999988764333221 1345555566665554 4444444443
No 115
>cd07368 PhnC_Bs_like PhnC is a Class III Extradiol ring-cleavage dioxygenase involved in the polycyclic aromatic hydrocarbon (PAH) catabolic pathway. This subfamily is composed of Burkholderia sp. PhnC and similar poteins. PhnC is one of nine protein products encoded by the phn locus. These proteins are involved in the polycyclic aromatic hydrocarbon (PAH) catabolic pathway. PhnC is a member of the class III extradiol dioxygenase family, a group os enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B.
Probab=21.19 E-value=4.3e+02 Score=21.01 Aligned_cols=78 Identities=12% Similarity=0.131 Sum_probs=46.1
Q ss_pred chHHHHHHHHHhcCCcEEEEe-CCCCCCCCCchHHHHHHHHhc--------ceEEEE-eecCCCCChhHHHHHHHHHHH-
Q 045860 27 KGFIGYLYTALNNKGIYVFRD-DKQLEKGGSISPNLLKAIDES--------RISIIV-LSKNYASSTWCLDELLKITEC- 95 (160)
Q Consensus 27 ~~fv~~L~~~L~~~gi~v~~d-~~d~~~G~~~~~~i~~~I~~S--------~~~ivv-lS~~~~~S~wc~~El~~~~~~- 95 (160)
..++.+|...|.+.|+.+..+ ++.+..|.-+. +.-..... .+-|++ +|-...-+..-..+|..++..
T Consensus 95 ~eLA~~i~~~l~~~g~~~~~~~~~~lDHG~~vP--L~~l~~~~~~~~~~~p~VPV~~n~~~~p~~~~~~~~~lG~al~~a 172 (277)
T cd07368 95 EPLAHHIMQHGLEYGIDWAVARSFTVDHAATIP--IHLAVRPVRAKGKGMRAIPVYLATGVDPFITSWRAHELGRVIGAA 172 (277)
T ss_pred HHHHHHHHHHHHHcCCCEeeecCcCCCcchhcc--HHHHhCcccccCCCCCeEEEEEecccCCCCCHHHHHHHHHHHHHH
Confidence 378899999999999976554 44455664332 11112211 233333 333345666777899998887
Q ss_pred -h--hcCCceeeEE
Q 045860 96 -K--NREDQIFPIF 106 (160)
Q Consensus 96 -~--~~~~~iiPVf 106 (160)
+ ..+.+|+.|=
T Consensus 173 i~~~~~d~rVliIa 186 (277)
T cd07368 173 VEAWQGDERVAIIG 186 (277)
T ss_pred HHhcCCCCCEEEEE
Confidence 3 2356666553
No 116
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=21.12 E-value=1.5e+02 Score=20.72 Aligned_cols=48 Identities=21% Similarity=0.265 Sum_probs=32.6
Q ss_pred HHHHHHHhcceEEEEeecCCCCChhHHHHHHHHHHH---hhcCCceeeEEec
Q 045860 60 NLLKAIDESRISIIVLSKNYASSTWCLDELLKITEC---KNREDQIFPIFYG 108 (160)
Q Consensus 60 ~i~~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~~~---~~~~~~iiPVf~~ 108 (160)
.+...+..+-...+++.|+|.+ .-|.+-|..-+.. -..-..|.||-|-
T Consensus 55 ~L~~~LCG~~~~~i~IDP~~~~-KGC~~TL~HEL~H~WQ~RsYG~i~PITY~ 105 (141)
T PHA02456 55 ALPQDLCGQFVGWIEIDPDYAN-KGCRDTLAHELNHAWQFRTYGLVQPITYA 105 (141)
T ss_pred hcCcchhhcceeEEEECCcccc-cchHHHHHHHHHHHHhhhccceeeeeehh
Confidence 3445567788899999999998 4576655444433 2334578999763
No 117
>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]
Probab=21.09 E-value=4.4e+02 Score=22.97 Aligned_cols=85 Identities=15% Similarity=0.151 Sum_probs=52.4
Q ss_pred HHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCCChhHHHHHHHHHHH--hhcCCceeeEEec
Q 045860 31 GYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYASSTWCLDELLKITEC--KNREDQIFPIFYG 108 (160)
Q Consensus 31 ~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S~wc~~El~~~~~~--~~~~~~iiPVf~~ 108 (160)
..|...|.+.|+++++-. |+.. +.+.+-+++..+..|+....|. . +..+-..++.. ...+.. .-.|.+
T Consensus 58 ~~L~~~L~~~gi~L~v~~-----~~~~-~~l~~~~~~~~~~~v~~n~~~~--~-~~~~rD~al~~~l~~~gi~-~~~~~d 127 (461)
T COG0415 58 QALQQSLAELGIPLLVRE-----GDPE-QVLPELAKQLAATTVFWNRDYE--E-WERQRDAALAQPLTEVGIA-VHSFWD 127 (461)
T ss_pred HHHHHHHHHcCCceEEEe-----CCHH-HHHHHHHHHhCcceEEeeeeec--h-hHHHHHHHHHHHHHhcCce-EEEecc
Confidence 347788888999999875 4433 4566666766677777777772 2 33444444444 333333 333433
Q ss_pred ---cCchhhhcccchHHHHH
Q 045860 109 ---VEPTVVRKQTASFGEAF 125 (160)
Q Consensus 109 ---v~p~~v~~~~~~f~~~f 125 (160)
..|..++...|..-..|
T Consensus 128 ~~l~~p~~~~t~~~~~y~vf 147 (461)
T COG0415 128 ALLHEPGEVRTGSGEPYKVF 147 (461)
T ss_pred ccccCHhhccCCCCCCcccc
Confidence 67888888777554444
No 118
>cd07949 PCA_45_Doxase_B_like_1 The B subunit of unknown Class III extradiol dioxygenases with similarity to Protocatechuate 4,5-dioxygenase. This subfamily is composed of proteins of unknown function with similarity to the B subunit of Protocatechuate 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B.
Probab=21.04 E-value=4.3e+02 Score=21.04 Aligned_cols=124 Identities=13% Similarity=0.040 Sum_probs=65.7
Q ss_pred chHHHHHHHHHhcCCcEEEEe-CCCCCCCCCchHHHHHHHHh---cceEEEEeecCCCC----ChhHHHHHHHHHHH-hh
Q 045860 27 KGFIGYLYTALNNKGIYVFRD-DKQLEKGGSISPNLLKAIDE---SRISIIVLSKNYAS----STWCLDELLKITEC-KN 97 (160)
Q Consensus 27 ~~fv~~L~~~L~~~gi~v~~d-~~d~~~G~~~~~~i~~~I~~---S~~~ivvlS~~~~~----S~wc~~El~~~~~~-~~ 97 (160)
..++.+|...|.+.|+.+... ...+..|.-+. ..-+.. ..+-||-+|-+... +.....+|..++.. ..
T Consensus 98 ~~LA~~i~~~~~~~g~d~~~~~~~~lDHG~~vP---L~~l~~~~d~~~pvV~i~~n~~~~p~~~~~~~~~lG~al~~~i~ 174 (276)
T cd07949 98 PELSWHLIESLVEDEFDITTCQEMLVDHACTLP---MQLFWPGAEWPIKVVPVSINTVQHPLPSPKRCFKLGQAIGRAIE 174 (276)
T ss_pred HHHHHHHHHHHHHcCCCeeccCCCCCCcchhhH---HHHhcCccCCCCCEEEEEeccCCCCCCCHHHHHHHHHHHHHHHH
Confidence 478999999999999976654 34455554332 222222 23445555555333 66666799998887 32
Q ss_pred ---cCCceeeEEeccCchhhhc-----ccchHHHHHHHHHHhhcCCHHHHHHHH-HHHHHhhccccee
Q 045860 98 ---REDQIFPIFYGVEPTVVRK-----QTASFGEAFAEHEEFFRDNIEKVQKWR-HALKVVANISGWE 156 (160)
Q Consensus 98 ---~~~~iiPVf~~v~p~~v~~-----~~~~f~~~f~~~~~~~~~~~~~~~~W~-~al~~v~~~~g~~ 156 (160)
.+++|+.|--+.-.=.++. ....|-+.|.+..+. +.+.+..|. ..+.+-++-.|++
T Consensus 175 ~~~~d~rv~iiaSG~lSH~l~~~~~g~~~~~fD~~~~~~l~~---d~~~L~~~~~~~~~~~AG~~g~e 239 (276)
T cd07949 175 SYPEDLRVVVLGTGGLSHQLDGERAGFINKDFDRYCLDKMVD---NPEWLTKYSIEELVELAGTQGVE 239 (276)
T ss_pred hcCcCCCEEEEEeCccccCCCCCCcccchHHHHHHHHHHHhc---CHHHHHcCCHHHHHHHcccccHH
Confidence 3456766642211111111 112343444443331 355566665 5555555555544
No 119
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=20.74 E-value=2.7e+02 Score=18.53 Aligned_cols=46 Identities=20% Similarity=0.177 Sum_probs=31.7
Q ss_pred HHHHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCC
Q 045860 31 GYLYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYAS 81 (160)
Q Consensus 31 ~~L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~ 81 (160)
.-+...|+..|+.+..-.. .-+ .+++.+.+.+.+--++.+|-....
T Consensus 17 ~~~~~~l~~~G~~V~~lg~----~~~-~~~l~~~~~~~~pdvV~iS~~~~~ 62 (119)
T cd02067 17 NIVARALRDAGFEVIDLGV----DVP-PEEIVEAAKEEDADAIGLSGLLTT 62 (119)
T ss_pred HHHHHHHHHCCCEEEECCC----CCC-HHHHHHHHHHcCCCEEEEeccccc
Confidence 3477788899999954321 212 457888888888888888876333
No 120
>cd06346 PBP1_ABC_ligand_binding_like_11 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=20.55 E-value=4.1e+02 Score=20.77 Aligned_cols=26 Identities=23% Similarity=0.181 Sum_probs=12.9
Q ss_pred hHHHHHHHHHhcCCcEEEEeCCCCCCC
Q 045860 28 GFIGYLYTALNNKGIYVFRDDKQLEKG 54 (160)
Q Consensus 28 ~fv~~L~~~L~~~gi~v~~d~~d~~~G 54 (160)
..+..+...+++.|+++--.. .+.+|
T Consensus 152 ~~~~~~~~~~~~~G~~vv~~~-~~~~~ 177 (312)
T cd06346 152 GLADAFTKAFEALGGTVTNVV-AHEEG 177 (312)
T ss_pred HHHHHHHHHHHHcCCEEEEEE-eeCCC
Confidence 344455556666666554322 34444
No 121
>cd06366 PBP1_GABAb_receptor Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha_i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example.
Probab=20.53 E-value=4.4e+02 Score=20.88 Aligned_cols=38 Identities=18% Similarity=0.196 Sum_probs=20.5
Q ss_pred EEEecccCCCcchHHHHHHHHHhcCCcEEEEeCCCCCCC
Q 045860 16 AFLSFRGEDTRKGFIGYLYTALNNKGIYVFRDDKQLEKG 54 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~gi~v~~d~~d~~~G 54 (160)
|.+-|...+-.......+...|++.|+.+-... .+.+|
T Consensus 138 v~ii~~~~~~g~~~~~~~~~~~~~~g~~v~~~~-~~~~~ 175 (350)
T cd06366 138 VATIYEDDDYGSGGLPDLVDALQEAGIEISYRA-AFPPS 175 (350)
T ss_pred EEEEEEcCcccchhHHHHHHHHHHcCCEEEEEe-ccCCC
Confidence 444444333333456667777777777665443 34444
No 122
>PF00762 Ferrochelatase: Ferrochelatase; InterPro: IPR001015 Synonym(s): Protohaem ferro-lyase, Iron chelatase, etc. Ferrochelatase catalyses the last step in haem biosynthesis: the chelation of a ferrous ion to proto-porphyrin IX, to form protohaem [, ]. In eukaryotic cells, it binds to the mitochondrial inner membrane with its active site on the matrix side of the membrane. The X-ray structure of Bacillus subtilis and human ferrochelatase have been solved [, ]. The human enzyme exists as a homodimer. Each subunit contains one [2Fe-2S] cluster. The monomer is folded into two similar domains, each with a four-stranded parallel beta-sheet flanked by an alpha-helix in a beta-alpha-beta motif that is reminiscent of the fold found in the periplasmic binding proteins. The topological similarity between the domains suggests that they have arisen from a gene duplication event. However, significant differences exist between the two domains, including an N-terminal section (residues 80-130) that forms part of the active site pocket, and a C-terminal extension (residues 390-423) that is involved in coordination of the [2Fe-2S] cluster and in stabilisation of the homodimer. Ferrochelatase seems to have a structurally conserved core region that is common to the enzyme from bacteria, plants and mammals. Porphyrin binds in the identified cleft; this cleft also includes the metal-binding site of the enzyme. It is likely that the structure of the cleft region will have different conformations upon substrate binding and release [].; GO: 0004325 ferrochelatase activity, 0006783 heme biosynthetic process; PDB: 2QD3_B 2HRE_C 3HCN_B 2PNJ_A 2QD1_C 1HRK_A 2QD4_B 3AQI_B 2HRC_B 3HCO_B ....
Probab=20.51 E-value=2.9e+02 Score=22.49 Aligned_cols=12 Identities=33% Similarity=0.636 Sum_probs=4.9
Q ss_pred ceEEEEeecCCC
Q 045860 69 RISIIVLSKNYA 80 (160)
Q Consensus 69 ~~~ivvlS~~~~ 80 (160)
++.++.+.|.|.
T Consensus 116 ~ivvlPLyPqyS 127 (316)
T PF00762_consen 116 RIVVLPLYPQYS 127 (316)
T ss_dssp EEEEEESSSS--
T ss_pred eEEEEeCCCchh
Confidence 344445555554
No 123
>PF01990 ATP-synt_F: ATP synthase (F/14-kDa) subunit; InterPro: IPR008218 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit F found in the V1 complex of V-ATPases (both eukaryotic and bacterial), as well as in the A1 complex of A-ATPases. Subunit F is a 16 kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 2D00_E 3A5C_P 3J0J_H 3A5D_H 2OV6_A 2QAI_B 3AON_B 2I4R_A.
Probab=20.38 E-value=2.6e+02 Score=18.15 Aligned_cols=47 Identities=11% Similarity=0.192 Sum_probs=33.3
Q ss_pred HHHHHhcCCcEEEEeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCCCC
Q 045860 33 LYTALNNKGIYVFRDDKQLEKGGSISPNLLKAIDESRISIIVLSKNYASS 82 (160)
Q Consensus 33 L~~~L~~~gi~v~~d~~d~~~G~~~~~~i~~~I~~S~~~ivvlS~~~~~S 82 (160)
+..-|+-.|+..+.... ..+...+.+.+.+++.++.|++++.++...
T Consensus 9 ~v~gFrLaGv~~~~~~~---~~ee~~~~l~~l~~~~~~gIIii~e~~~~~ 55 (95)
T PF01990_consen 9 TVLGFRLAGVEGVYVNT---DPEEAEEALKELLKDEDVGIIIITEDLAEK 55 (95)
T ss_dssp HHHHHHHTTSEEEEESH---SHHHHHHHHHHHHHHTTEEEEEEEHHHHTT
T ss_pred HHHHHHHcCCCCccCCC---CHHHHHHHHHHHhcCCCccEEEeeHHHHHH
Confidence 45566777998887751 123445566667778999999999997774
No 124
>cd07372 2A5CPDO_B The beta subunit of the Class III extradiol dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol. 2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO), catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, which is an intermediate during p-chloronitrobenzene degradation. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. The active 2A5CPDO enzyme is probably a heterotetramer, composed of two alpha and two beta subunits. The alpha and beta subunits share significant sequence similarity and may have evolved by gene duplication. This model describes the beta subunit, which contains a putative metal binding site with two conserved histidines; these residues are equivalent to two out of three Fe(II) bindin
Probab=20.20 E-value=4.7e+02 Score=21.09 Aligned_cols=77 Identities=14% Similarity=0.097 Sum_probs=48.3
Q ss_pred chHHHHHHHHHhcCCcEEEE-eC--CCCCCCCCchHHHHHHHH-hcceEEEEeecCCC-------CChhHHHHHHHHHHH
Q 045860 27 KGFIGYLYTALNNKGIYVFR-DD--KQLEKGGSISPNLLKAID-ESRISIIVLSKNYA-------SSTWCLDELLKITEC 95 (160)
Q Consensus 27 ~~fv~~L~~~L~~~gi~v~~-d~--~d~~~G~~~~~~i~~~I~-~S~~~ivvlS~~~~-------~S~wc~~El~~~~~~ 95 (160)
..++..|...+.+.|+.+-. +. ..+..|.-+. ..-+. ..++-||.+|.+.+ .+..-..+|..++..
T Consensus 98 ~eLA~~i~~~~~~~Gi~~~~~~~~~~~LDHGt~vP---L~fl~p~~~~pvV~is~~~l~~~~~~~~~~~~~~~lG~ai~~ 174 (294)
T cd07372 98 VELAEACCEEGRKAGLVTKMMRNPRFRVDYGTITT---LHMIRPQWDIPVVGISANNTPYYLNTKEGLGEMDVLGKATRE 174 (294)
T ss_pred HHHHHHHHHHHHHCCCCeeeccCCCCCCCchHHHH---HHHhCCCCCCcEEEEecCcccccccccCCHHHHHHHHHHHHH
Confidence 47899999999999998764 22 2233442221 22233 36677888886643 234555678888877
Q ss_pred --hhcCCceeeEE
Q 045860 96 --KNREDQIFPIF 106 (160)
Q Consensus 96 --~~~~~~iiPVf 106 (160)
++.+.+|+.|-
T Consensus 175 al~~~~~RV~vIa 187 (294)
T cd07372 175 AIRKTGRRAVLLA 187 (294)
T ss_pred HHHhcCCeEEEEE
Confidence 55666777664
No 125
>PF07283 TrbH: Conjugal transfer protein TrbH; InterPro: IPR010837 This entry represents TrbH, a bacterial conjugal transfer protein approximately 150 residues long. TrbH contains a putative membrane lipoprotein lipid attachment site [].
Probab=20.02 E-value=2e+02 Score=20.13 Aligned_cols=21 Identities=43% Similarity=0.430 Sum_probs=19.0
Q ss_pred hHHHHHHHHHhcCCcEEEEeC
Q 045860 28 GFIGYLYTALNNKGIYVFRDD 48 (160)
Q Consensus 28 ~fv~~L~~~L~~~gi~v~~d~ 48 (160)
.|...|...|+.+||-|--++
T Consensus 36 ~Fg~aL~~~LR~~GYaV~e~~ 56 (121)
T PF07283_consen 36 PFGQALENALRAKGYAVIEDD 56 (121)
T ss_pred hHHHHHHHHHHhcCcEEEecC
Confidence 899999999999999888765
Done!