Query 031401
Match_columns 160
No_of_seqs 130 out of 1393
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 13:35:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031401.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031401hhsearch_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 3.1E-41 6.8E-46 251.2 14.7 139 4-158 17-156 (187)
2 PLN03210 Resistant to P. syrin 100.0 3.6E-39 7.9E-44 296.6 16.3 155 1-159 1-156 (1153)
3 PF01582 TIR: TIR domain; Int 99.9 1.4E-28 3E-33 177.9 3.6 132 16-148 1-141 (141)
4 smart00255 TIR Toll - interleu 99.9 3.2E-25 6.9E-30 159.0 13.6 136 13-151 1-139 (140)
5 PF13676 TIR_2: TIR domain; PD 99.8 3.7E-20 7.9E-25 126.4 1.9 87 16-108 1-87 (102)
6 KOG3678 SARM protein (with ste 99.3 5.9E-12 1.3E-16 105.6 9.3 126 10-142 609-751 (832)
7 PF08937 DUF1863: MTH538 TIR-l 98.8 6E-09 1.3E-13 74.3 5.8 92 14-109 1-109 (130)
8 PF08357 SEFIR: SEFIR domain; 98.0 1.3E-05 2.8E-10 58.0 5.9 65 15-79 2-70 (150)
9 PF10137 TIR-like: Predicted n 97.4 0.00086 1.9E-08 47.6 6.8 88 15-106 1-101 (125)
10 PF13271 DUF4062: Domain of un 95.5 0.072 1.6E-06 34.7 6.2 65 16-82 2-67 (83)
11 COG4916 Uncharacterized protei 94.7 0.047 1E-06 43.3 4.0 95 9-107 173-273 (329)
12 PF05014 Nuc_deoxyrib_tr: Nucl 93.6 1.6 3.4E-05 29.8 9.9 78 27-108 13-98 (113)
13 COG4271 Predicted nucleotide-b 86.5 2.6 5.5E-05 32.4 5.8 87 15-107 84-186 (233)
14 cd00860 ThrRS_anticodon ThrRS 84.7 5.4 0.00012 25.4 6.2 61 14-79 2-62 (91)
15 COG0400 Predicted esterase [Ge 80.6 8.8 0.00019 29.5 6.8 59 7-67 140-200 (207)
16 PF08902 DUF1848: Domain of un 75.4 40 0.00088 27.0 10.1 134 12-157 46-198 (266)
17 cd00738 HGTP_anticodon HGTP an 74.7 17 0.00037 23.1 6.1 62 14-79 2-65 (94)
18 PF03129 HGTP_anticodon: Antic 72.1 15 0.00033 23.6 5.4 47 27-77 15-61 (94)
19 cd00858 GlyRS_anticodon GlyRS 72.0 23 0.00049 24.3 6.5 65 11-80 24-89 (121)
20 cd07373 2A5CPDO_A The alpha su 71.3 35 0.00076 27.1 8.2 78 27-106 90-173 (271)
21 PF14359 DUF4406: Domain of un 71.3 27 0.00059 23.2 8.0 62 31-94 19-84 (92)
22 COG4916 Uncharacterized protei 67.8 7.8 0.00017 31.0 3.6 96 12-111 5-107 (329)
23 PF10087 DUF2325: Uncharacteri 64.7 32 0.00069 22.6 5.8 45 30-76 12-57 (97)
24 PF03358 FMN_red: NADPH-depend 57.5 63 0.0014 22.6 7.6 79 27-108 17-115 (152)
25 PF14258 DUF4350: Domain of un 53.6 49 0.0011 20.1 6.7 43 30-83 7-49 (70)
26 cd02042 ParA ParA and ParB of 53.1 61 0.0013 21.0 7.2 64 17-80 4-74 (104)
27 PF02310 B12-binding: B12 bind 52.6 67 0.0015 21.4 8.4 74 30-111 17-91 (121)
28 KOG2792 Putative cytochrome C 51.6 25 0.00055 28.2 3.9 29 84-112 154-187 (280)
29 cd00859 HisRS_anticodon HisRS 51.4 55 0.0012 20.1 5.5 59 14-77 2-60 (91)
30 cd02426 Pol_gamma_b_Cterm C-te 51.1 12 0.00026 26.3 2.0 31 27-57 43-76 (128)
31 TIGR00418 thrS threonyl-tRNA s 49.1 75 0.0016 27.9 7.0 63 11-78 468-530 (563)
32 COG0125 Tmk Thymidylate kinase 49.1 1.2E+02 0.0026 23.2 8.6 96 16-114 4-141 (208)
33 cd00861 ProRS_anticodon_short 49.0 67 0.0015 20.3 5.3 48 28-79 18-65 (94)
34 TIGR02298 HpaD_Fe 3,4-dihydrox 48.2 1.4E+02 0.0031 23.9 8.3 78 27-106 96-179 (282)
35 cd07363 45_DOPA_Dioxygenase Th 46.7 1.1E+02 0.0025 23.9 7.1 76 27-106 80-157 (253)
36 PLN03194 putative disease resi 46.3 99 0.0021 23.5 6.3 66 40-108 25-90 (187)
37 COG3286 Uncharacterized protei 45.4 1.2E+02 0.0026 23.3 6.5 51 100-154 146-198 (204)
38 PF09419 PGP_phosphatase: Mito 44.8 75 0.0016 23.6 5.4 69 36-108 35-112 (168)
39 COG1658 Small primase-like pro 44.1 51 0.0011 23.4 4.2 55 14-70 30-84 (127)
40 PRK12325 prolyl-tRNA synthetas 43.9 1.1E+02 0.0023 26.2 6.9 66 12-81 344-411 (439)
41 cd03364 TOPRIM_DnaG_primases T 43.1 40 0.00088 21.1 3.4 33 40-74 44-76 (79)
42 PF01990 ATP-synt_F: ATP synth 41.4 97 0.0021 20.2 5.1 55 33-92 9-63 (95)
43 COG4088 Predicted nucleotide k 41.3 45 0.00097 26.2 3.8 17 28-44 16-32 (261)
44 cd01423 MGS_CPS_I_III Methylgl 41.2 45 0.00098 22.6 3.6 29 16-46 3-31 (116)
45 PF03446 NAD_binding_2: NAD bi 40.9 26 0.00056 25.3 2.5 48 31-78 14-68 (163)
46 PRK10569 NAD(P)H-dependent FMN 40.6 1.5E+02 0.0033 22.1 7.3 82 28-112 18-112 (191)
47 CHL00201 syh histidine-tRNA sy 40.6 98 0.0021 26.3 6.2 61 12-77 324-384 (430)
48 KOG1016 Predicted DNA helicase 39.0 2E+02 0.0044 27.2 8.0 35 14-48 407-441 (1387)
49 PRK09194 prolyl-tRNA synthetas 38.7 31 0.00068 30.4 3.0 66 11-80 466-533 (565)
50 PLN02530 histidine-tRNA ligase 37.8 1.2E+02 0.0027 26.2 6.5 61 12-77 400-460 (487)
51 PF03720 UDPG_MGDP_dh_C: UDP-g 37.6 32 0.00069 23.1 2.3 55 22-76 11-75 (106)
52 PRK08661 prolyl-tRNA synthetas 37.5 1.1E+02 0.0023 26.5 6.1 64 11-78 285-354 (477)
53 cd00138 PLDc Phospholipase D. 36.0 1.3E+02 0.0028 21.4 5.5 29 52-80 17-45 (176)
54 cd01424 MGS_CPS_II Methylglyox 34.7 1.3E+02 0.0028 20.0 5.1 61 16-78 3-76 (110)
55 cd06340 PBP1_ABC_ligand_bindin 34.4 2.3E+02 0.005 22.7 7.3 64 15-79 146-209 (347)
56 PRK14938 Ser-tRNA(Thr) hydrola 34.4 1.8E+02 0.0039 24.7 6.6 61 12-77 273-333 (387)
57 cd00862 ProRS_anticodon_zinc P 33.9 63 0.0014 24.5 3.7 64 11-78 8-77 (202)
58 COG2130 Putative NADP-dependen 33.2 96 0.0021 25.7 4.7 61 13-82 196-257 (340)
59 COG0683 LivK ABC-type branched 33.0 2.7E+02 0.0059 22.7 7.9 71 15-86 150-220 (366)
60 KOG1136 Predicted cleavage and 32.6 62 0.0013 27.2 3.6 51 64-114 191-248 (501)
61 cd01243 PH_MRCK MRCK (myotonic 32.4 37 0.00081 23.9 2.0 18 135-152 104-121 (122)
62 PF01915 Glyco_hydro_3_C: Glyc 32.3 2.2E+02 0.0048 21.5 10.4 84 28-114 47-146 (227)
63 KOG1954 Endocytosis/signaling 31.3 1.9E+02 0.0042 24.8 6.3 75 50-127 164-239 (532)
64 COG1180 PflA Pyruvate-formate 30.8 1.1E+02 0.0024 24.1 4.7 39 16-54 87-125 (260)
65 PRK14799 thrS threonyl-tRNA sy 30.1 2.1E+02 0.0045 25.4 6.6 60 13-77 438-497 (545)
66 PRK00413 thrS threonyl-tRNA sy 30.0 2E+02 0.0043 25.6 6.7 61 13-78 539-599 (638)
67 TIGR00334 5S_RNA_mat_M5 ribonu 29.8 93 0.002 23.3 3.8 65 27-95 35-107 (174)
68 PRK03991 threonyl-tRNA synthet 29.4 1.3E+02 0.0028 27.0 5.4 62 12-78 498-559 (613)
69 KOG0409 Predicted dehydrogenas 29.3 93 0.002 25.7 4.0 48 31-78 48-102 (327)
70 PRK12305 thrS threonyl-tRNA sy 29.1 2.2E+02 0.0047 25.1 6.7 60 13-77 476-535 (575)
71 PRK15057 UDP-glucose 6-dehydro 28.7 1.3E+02 0.0029 25.2 5.1 51 23-73 311-365 (388)
72 COG2084 MmsB 3-hydroxyisobutyr 28.7 1E+02 0.0022 25.0 4.2 46 33-78 15-68 (286)
73 COG3613 Nucleoside 2-deoxyribo 28.6 2.5E+02 0.0055 21.0 6.4 77 29-108 21-107 (172)
74 PF12146 Hydrolase_4: Putative 27.8 95 0.0021 19.7 3.2 36 12-48 15-50 (79)
75 cd01857 HSR1_MMR1 HSR1/MMR1. 27.7 2E+02 0.0043 19.9 5.2 18 60-77 4-21 (141)
76 TIGR00409 proS_fam_II prolyl-t 27.4 39 0.00085 30.0 1.8 48 12-59 472-521 (568)
77 PRK12444 threonyl-tRNA synthet 27.2 2.6E+02 0.0056 25.1 6.9 64 11-78 539-602 (639)
78 cd06386 PBP1_NPR_C_like Ligand 26.7 2.4E+02 0.0051 23.2 6.2 42 30-72 157-198 (387)
79 cd07371 2A5CPDO_AB The alpha a 26.5 3.2E+02 0.007 21.5 11.8 78 27-106 87-170 (268)
80 cd00532 MGS-like MGS-like doma 26.4 1.9E+02 0.0041 19.4 4.8 61 16-78 2-77 (112)
81 KOG1610 Corticosteroid 11-beta 26.3 88 0.0019 25.8 3.4 31 14-48 30-60 (322)
82 cd06335 PBP1_ABC_ligand_bindin 26.3 3.4E+02 0.0073 21.7 7.3 31 15-45 140-170 (347)
83 COG1058 CinA Predicted nucleot 25.9 98 0.0021 24.7 3.6 42 30-76 23-67 (255)
84 PF08477 Miro: Miro-like prote 25.8 1.5E+02 0.0033 19.3 4.2 45 62-107 68-113 (119)
85 PF03437 BtpA: BtpA family; I 25.6 1.6E+02 0.0036 23.3 4.8 109 33-148 133-254 (254)
86 PF09441 Abp2: ARS binding pro 25.6 35 0.00075 25.3 0.9 57 82-147 54-111 (175)
87 cd06342 PBP1_ABC_LIVBP_like Ty 25.4 3.3E+02 0.0071 21.2 7.8 57 16-74 138-195 (334)
88 PRK07933 thymidylate kinase; V 25.0 2.6E+02 0.0056 21.1 5.7 30 17-46 2-33 (213)
89 PRK10628 LigB family dioxygena 24.6 3.4E+02 0.0073 21.5 6.4 75 18-95 62-136 (246)
90 PF15409 PH_8: Pleckstrin homo 24.6 69 0.0015 21.2 2.1 15 135-149 74-88 (89)
91 TIGR03567 FMN_reduc_SsuE FMN r 24.5 2.8E+02 0.006 20.0 6.1 78 28-108 17-107 (171)
92 cd00154 Rab Rab family. Rab G 24.5 2.1E+02 0.0045 19.1 4.8 29 53-81 57-86 (159)
93 PF08132 AdoMetDC_leader: S-ad 24.4 70 0.0015 18.8 1.9 24 3-26 10-33 (54)
94 PRK14495 putative molybdopteri 24.3 3.1E+02 0.0068 23.8 6.5 29 17-46 6-34 (452)
95 COG0431 Predicted flavoprotein 24.1 3E+02 0.0064 20.3 6.4 56 27-83 17-82 (184)
96 cd01241 PH_Akt Akt pleckstrin 24.0 75 0.0016 21.1 2.3 17 134-150 86-102 (102)
97 COG1168 MalY Bifunctional PLP- 23.6 1.8E+02 0.004 24.6 4.9 45 59-103 148-195 (388)
98 cd01266 PH_Gab Gab (Grb2-assoc 23.5 78 0.0017 21.2 2.4 17 134-150 92-108 (108)
99 cd07370 HPCD The Class III ext 23.3 3.8E+02 0.0083 21.2 7.9 78 27-106 94-176 (280)
100 PRK08155 acetolactate synthase 23.0 3E+02 0.0065 24.1 6.4 49 1-68 1-49 (564)
101 PF12913 SH3_6: SH3 domain of 23.0 19 0.00041 21.6 -0.7 16 15-30 28-43 (54)
102 PF00169 PH: PH domain; Inter 22.8 95 0.0021 19.3 2.6 17 134-150 87-103 (104)
103 PF00350 Dynamin_N: Dynamin fa 22.6 2.7E+02 0.0059 19.3 5.3 45 59-106 120-165 (168)
104 PRK13883 conjugal transfer pro 22.5 1.7E+02 0.0036 21.5 4.0 22 27-48 63-84 (151)
105 cd08584 PI-PLCc_GDPD_SF_unchar 22.5 1.4E+02 0.003 22.7 3.7 38 43-83 126-163 (192)
106 PF13662 Toprim_4: Toprim doma 22.2 66 0.0014 20.2 1.7 35 33-69 38-74 (81)
107 PF07283 TrbH: Conjugal transf 22.2 1.8E+02 0.0038 20.5 3.9 21 28-48 36-56 (121)
108 PF03709 OKR_DC_1_N: Orn/Lys/A 22.1 2.6E+02 0.0057 18.9 7.2 69 30-110 6-75 (115)
109 TIGR00408 proS_fam_I prolyl-tR 21.8 2.5E+02 0.0055 24.2 5.6 64 11-78 280-348 (472)
110 COG0710 AroD 3-dehydroquinate 21.8 4E+02 0.0086 20.9 6.7 82 29-115 80-163 (231)
111 cd06366 PBP1_GABAb_receptor Li 21.8 4.1E+02 0.0089 21.0 6.9 38 16-54 138-175 (350)
112 cd06346 PBP1_ABC_ligand_bindin 21.7 3.9E+02 0.0084 20.9 6.4 41 28-69 152-192 (312)
113 cd04886 ACT_ThrD-II-like C-ter 21.7 1.4E+02 0.003 17.3 3.0 33 11-45 40-72 (73)
114 COG3340 PepE Peptidase E [Amin 21.6 4E+02 0.0086 20.9 6.0 55 15-73 35-90 (224)
115 cd06379 PBP1_iGluR_NMDA_NR1 N- 21.5 4E+02 0.0087 21.5 6.6 13 30-42 171-183 (377)
116 PF02878 PGM_PMM_I: Phosphoglu 21.1 1.8E+02 0.0038 20.2 3.9 49 13-67 40-88 (137)
117 cd01260 PH_CNK Connector enhan 20.9 90 0.0019 20.1 2.2 16 134-149 81-96 (96)
118 PRK13762 tRNA-modifying enzyme 20.6 4.1E+02 0.0088 21.7 6.4 60 14-80 131-190 (322)
119 cd06328 PBP1_SBP_like_2 Peripl 20.4 4.4E+02 0.0095 20.9 6.8 54 15-70 138-192 (333)
120 PF05818 TraT: Enterobacterial 20.3 1.4E+02 0.0029 23.3 3.3 37 11-47 19-56 (215)
121 cd06361 PBP1_GPC6A_like Ligand 20.2 3.7E+02 0.008 22.4 6.2 20 27-46 186-205 (403)
122 smart00233 PH Pleckstrin homol 20.2 1.1E+02 0.0023 18.5 2.4 16 135-150 86-101 (102)
123 cd01867 Rab8_Rab10_Rab13_like 20.1 3.1E+02 0.0068 19.0 6.6 22 58-79 66-87 (167)
124 PF00875 DNA_photolyase: DNA p 20.0 2.7E+02 0.0059 19.8 4.8 47 30-82 55-101 (165)
No 1
>PLN03194 putative disease resistance protein; Provisional
Probab=100.00 E-value=3.1e-41 Score=251.16 Aligned_cols=139 Identities=25% Similarity=0.483 Sum_probs=127.4
Q ss_pred CCCCCCCCCcccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCcCCh
Q 031401 4 TSFQNVSHGEYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYASST 83 (160)
Q Consensus 4 ~sss~~~~~~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S~ 83 (160)
.|+|++....|||||||+++|++..|+.+|+.+|+++||++|+|+.++.+|+.+.++|.++|++|+++|+|+|++|+.|.
T Consensus 17 ~~~~~~~~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S~ 96 (187)
T PLN03194 17 YPSSSSSAKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESY 96 (187)
T ss_pred cccCCCCCCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccch
Confidence 45666667889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHhhcCCcceeEEeecCchhhhcc-cchHHHHHHHHHHhhccCHHHHHHHHHHHHHhhcccceeec
Q 031401 84 WCLDELLKIVECKNREDQIFPIFYEVEPTVVRKQ-TASFGEAFAKYEEFFRDNIEKVQKWRYALKVVANISGWELK 158 (160)
Q Consensus 84 wc~~El~~~~~~~~~~~~IiPI~~~~~p~~v~~~-~~~~~~~~~~~~~~~~~~~~~~~~w~~al~~~~~~~G~~~~ 158 (160)
||++||..++++ +..||||||+|+|++|+.| .+. .+++++++||+||+++++++|+.+.
T Consensus 97 WCLdEL~~I~e~---~~~ViPIFY~VdPsdVr~q~~~~-------------~~~e~v~~Wr~AL~~va~l~G~~~~ 156 (187)
T PLN03194 97 FCLHELALIMES---KKRVIPIFCDVKPSQLRVVDNGT-------------CPDEEIRRFNWALEEAKYTVGLTFD 156 (187)
T ss_pred hHHHHHHHHHHc---CCEEEEEEecCCHHHhhccccCC-------------CCHHHHHHHHHHHHHHhccccccCC
Confidence 999999999985 3579999999999999997 332 2368999999999999999999775
No 2
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=100.00 E-value=3.6e-39 Score=296.60 Aligned_cols=155 Identities=44% Similarity=0.774 Sum_probs=145.3
Q ss_pred CCCCCCCCCCCCcccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCc
Q 031401 1 MASTSFQNVSHGEYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYA 80 (160)
Q Consensus 1 m~s~sss~~~~~~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~ 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 67766555 578999999999999999999999999999999999987 6999999999999999999999999999999
Q ss_pred CChhHHHHHHHHHHH-hhcCCcceeEEeecCchhhhcccchHHHHHHHHHHhhccCHHHHHHHHHHHHHhhcccceeecC
Q 031401 81 SSTWCLDELLKIVEC-KNREDQIFPIFYEVEPTVVRKQTASFGEAFAKYEEFFRDNIEKVQKWRYALKVVANISGWELKD 159 (160)
Q Consensus 81 ~S~wc~~El~~~~~~-~~~~~~IiPI~~~~~p~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~al~~~~~~~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 88899999999999999999999999999999887654 689999999999999999998754
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=1.4e-28 Score=177.88 Aligned_cols=132 Identities=36% Similarity=0.636 Sum_probs=117.2
Q ss_pred EEEeccc-CCCchhHHHHHHHHHHcC--CceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCcCChhHHHHHHHH
Q 031401 16 AFLSFRG-EDTRKRFIGHLYTALNNK--GIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYASSTWCLDELLKI 92 (160)
Q Consensus 16 VFISy~~-~D~~~~fv~~L~~~L~~~--g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~ 92 (160)
|||||++ +| +..|+++|.++|++. |+++|++++|+.+|..+.++|.++|++|+++|+|+|++|+.|.||+.|+..|
T Consensus 1 vfisy~~~~d-~~~~~~~L~~~Le~~~~g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~s~wc~~el~~a 79 (141)
T PF01582_consen 1 VFISYSGKDD-REWFVSHLLPELEERPYGYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSRNYLSSEWCLFELQEA 79 (141)
T ss_dssp EEEEE-GHHG-HHHHHHCHHHHHHCTSSTS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESHHHHHHTHHHHHHHHH
T ss_pred cEEEeCCCCc-HHHHHHHHHHHHHhCCCCeEEEEechhhcccccccchhhHhhhhceeeEEEeecccccccchhhhhhhh
Confidence 8999999 55 467899999999999 9999999999999999999999999999999999999999999999999999
Q ss_pred HHH-hhc--CCcceeEEeecCchhhh-cccchHHHHHHHHHHhhccC--HHHHHHHHHHHHH
Q 031401 93 VEC-KNR--EDQIFPIFYEVEPTVVR-KQTASFGEAFAKYEEFFRDN--IEKVQKWRYALKV 148 (160)
Q Consensus 93 ~~~-~~~--~~~IiPI~~~~~p~~v~-~~~~~~~~~~~~~~~~~~~~--~~~~~~w~~al~~ 148 (160)
+++ ... ..+|+|+|+++.+++++ .+.+.|+..|..+.+....+ .+....|++++.+
T Consensus 80 ~~~~~~~~~~~~Il~v~~~v~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~fW~~l~~~ 141 (141)
T PF01582_consen 80 LERLLEEGRDKLILPVFYDVSPSDVRPDQSLRFLLRFLTYLRWPDDDSREDRSWFWKKLRYH 141 (141)
T ss_dssp HHHHHCSTCTTEEEEESSSS-CHHCHTHHHHHHHHHCTHCEETSSSGGGGGHHHHHHHHHHH
T ss_pred hhhccccccccceeeEeccCChhhcChhhhHHHHHHhhhheeCCCCCCccHHHHHHHHHhcC
Confidence 999 443 48999999999999999 69999999999988877654 5788999999763
No 4
>smart00255 TIR Toll - interleukin 1 - resistance.
Probab=99.93 E-value=3.2e-25 Score=159.03 Aligned_cols=136 Identities=41% Similarity=0.713 Sum_probs=114.1
Q ss_pred cccEEEecccC-CCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCcCChhHHHHHHH
Q 031401 13 EYDAFLSFRGE-DTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYASSTWCLDELLK 91 (160)
Q Consensus 13 ~yDVFISy~~~-D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~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 59999999993 444688999999999999999999653 344444499999999999999999999999999999999
Q ss_pred HHHH--hhcCCcceeEEeecCchhhhcccchHHHHHHHHHHhhccCHHHHHHHHHHHHHhhc
Q 031401 92 IVEC--KNREDQIFPIFYEVEPTVVRKQTASFGEAFAKYEEFFRDNIEKVQKWRYALKVVAN 151 (160)
Q Consensus 92 ~~~~--~~~~~~IiPI~~~~~p~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~al~~~~~ 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 3477899999999999999999999999998875555543333 789999988764
No 5
>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A.
Probab=99.78 E-value=3.7e-20 Score=126.42 Aligned_cols=87 Identities=33% Similarity=0.554 Sum_probs=76.0
Q ss_pred EEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCcCChhHHHHHHHHHHH
Q 031401 16 AFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYASSTWCLDELLKIVEC 95 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~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 579999999999999999997 999999999999999999999999999999999999999998854
Q ss_pred hhcCCcceeEEee
Q 031401 96 KNREDQIFPIFYE 108 (160)
Q Consensus 96 ~~~~~~IiPI~~~ 108 (160)
.++.||||.++
T Consensus 77 --~~~~iipv~~~ 87 (102)
T PF13676_consen 77 --RGKPIIPVRLD 87 (102)
T ss_dssp --TSESEEEEECS
T ss_pred --CCCEEEEEEEC
Confidence 45699999975
No 6
>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]
Probab=99.34 E-value=5.9e-12 Score=105.56 Aligned_cols=126 Identities=26% Similarity=0.376 Sum_probs=96.3
Q ss_pred CCCcccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCc----CC---
Q 031401 10 SHGEYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYA----SS--- 82 (160)
Q Consensus 10 ~~~~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~----~S--- 82 (160)
.++..||||||++... ...+..|.-.|+-+||+||+|...+..|. +.+.+.+.|..++.+|+|+||+.+ +.
T Consensus 609 ~skq~DVFISYRRstG-nQLASLiKV~LQL~GyrVFIDVdKL~AGK-FdssLlkni~aAkhFiLVLtP~sLDr~lnD~nC 686 (832)
T KOG3678|consen 609 LSKQIDVFISYRRSTG-NQLASLIKVLLQLRGYRVFIDVDKLYAGK-FDSSLLKNIQAAKHFILVLTPNSLDRLLNDDNC 686 (832)
T ss_pred ccCCcceEEEeecccc-HHHHHHHHHHHHhcCceEEEehhhhhccc-ccHHHHHHHHhhheeEEEeCcchHHHHhccccH
Confidence 4688999999988754 46788888889999999999999999987 568999999999999999999965 33
Q ss_pred -hhHHHHHHHHHHHhhcCCcceeEEee---------cCchhhhcccchHHHHHHHHHHhhccCHHHHHHH
Q 031401 83 -TWCLDELLKIVECKNREDQIFPIFYE---------VEPTVVRKQTASFGEAFAKYEEFFRDNIEKVQKW 142 (160)
Q Consensus 83 -~wc~~El~~~~~~~~~~~~IiPI~~~---------~~p~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~w 142 (160)
.|.-.|+..+++ ..+.|||||-. ..|.|++.....-|..|.+.++.-. ++++.++
T Consensus 687 eDWVHKEl~~Afe---~~KNIiPI~D~aFE~Pt~ed~iPnDirmi~kyNGvKWvHdYQdA~--maKvvRF 751 (832)
T KOG3678|consen 687 EDWVHKELKCAFE---HQKNIIPIFDTAFEFPTKEDQIPNDIRMITKYNGVKWVHDYQDAC--MAKVVRF 751 (832)
T ss_pred HHHHHHHHHHHHH---hcCCeeeeecccccCCCchhcCcHHHHHHHhccCeeeehhhHHHH--HHHHHHH
Confidence 455556555555 57799999833 6778887776666666666555433 3455444
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=98.85 E-value=6e-09 Score=74.26 Aligned_cols=92 Identities=21% Similarity=0.379 Sum_probs=49.5
Q ss_pred ccEEEecccCCCchhHHHHHHHHHHcC-------CceE-E---------eeCCCCCCCCCchHHHHHHHHhcceEEEEee
Q 031401 14 YDAFLSFRGEDTRKRFIGHLYTALNNK-------GIYV-F---------RDDKQLEKGGSISPNLLKTIEESRISIIVLS 76 (160)
Q Consensus 14 yDVFISy~~~D~~~~fv~~L~~~L~~~-------g~~v-~---------~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS 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 6899999999863 2567777777663 2221 1 1222223344788899999999999999999
Q ss_pred cCCcCChhHHHHHHHHHHHhhcCCcceeEEeec
Q 031401 77 KNYASSTWCLDELLKIVECKNREDQIFPIFYEV 109 (160)
Q Consensus 77 ~~~~~S~wc~~El~~~~~~~~~~~~IiPI~~~~ 109 (160)
++-..|.|+.+|+..++. .+..||.|.++.
T Consensus 80 ~~T~~s~wV~~EI~~A~~---~~~~Ii~V~~~~ 109 (130)
T PF08937_consen 80 PNTAKSKWVNWEIEYALK---KGKPIIGVYLPG 109 (130)
T ss_dssp TT----HHHHHHHHHHTT---T---EEEEETT-
T ss_pred CCcccCcHHHHHHHHHHH---CCCCEEEEECCC
Confidence 999999999999998887 577888887643
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=98.03 E-value=1.3e-05 Score=58.01 Aligned_cols=65 Identities=25% Similarity=0.352 Sum_probs=54.1
Q ss_pred cEEEecccCCCc-hhHHHHHHHHHHcC-CceEEeeCCCCCC--CCCchHHHHHHHHhcceEEEEeecCC
Q 031401 15 DAFLSFRGEDTR-KRFIGHLYTALNNK-GIYVFRDDKQLEK--GGSISPNLLKTIEESRISIIVLSKNY 79 (160)
Q Consensus 15 DVFISy~~~D~~-~~fv~~L~~~L~~~-g~~v~~d~~dl~~--G~~~~~~i~~~i~~S~~~I~vlS~~~ 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 499999995543 24588899999999 9999999988844 66777778889999999999999654
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=97.38 E-value=0.00086 Score=47.59 Aligned_cols=88 Identities=14% Similarity=0.154 Sum_probs=66.0
Q ss_pred cEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCc-------------C
Q 031401 15 DAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYA-------------S 81 (160)
Q Consensus 15 DVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~-------------~ 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 55778999999888888776667799999999999999999999999998511 2
Q ss_pred ChhHHHHHHHHHHHhhcCCcceeEE
Q 031401 82 STWCLDELLKIVECKNREDQIFPIF 106 (160)
Q Consensus 82 S~wc~~El~~~~~~~~~~~~IiPI~ 106 (160)
......|+..++.+ ..+.+++.+.
T Consensus 78 R~NVifE~G~f~g~-LGr~rv~~l~ 101 (125)
T PF10137_consen 78 RQNVIFELGLFIGK-LGRERVFILV 101 (125)
T ss_pred ccceeehhhHHHhh-cCcceEEEEE
Confidence 23456788877774 2334455444
No 10
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=95.48 E-value=0.072 Score=34.74 Aligned_cols=65 Identities=23% Similarity=0.222 Sum_probs=48.4
Q ss_pred EEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCC-CCCCchHHHHHHHHhcceEEEEeecCCcCC
Q 031401 16 AFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLE-KGGSISPNLLKTIEESRISIIVLSKNYASS 82 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~-~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S 82 (160)
||||=.-.|.. ...+.|...+.+.|+.+..-+. +. .+....+.+.+.|++|++.|.++-..|-..
T Consensus 2 VFiSSt~~Dl~-~eR~~l~~~i~~~~~~~~~~e~-~~a~~~~~~~~cl~~v~~cDifI~ilG~rYG~~ 67 (83)
T PF13271_consen 2 VFISSTFRDLK-EERDALIEAIRRLGCEPVGMEF-FPASDQSPLEICLKEVDECDIFILILGNRYGSV 67 (83)
T ss_pred EEEecChhhHH-HHHHHHHHHHHHCCCeeeeeee-ecCCCCCHHHHHHHHHhhCCEEEEeeccccCCC
Confidence 89998778864 4467788999887765544322 32 345556778899999999999999998754
No 11
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=94.67 E-value=0.047 Score=43.26 Aligned_cols=95 Identities=22% Similarity=0.176 Sum_probs=64.4
Q ss_pred CCCCcccEEEecccCCCchhHHHHHHHHHHcC--CceEEeeCCC---CCCCCCchHHHHHHH-HhcceEEEEeecCCcCC
Q 031401 9 VSHGEYDAFLSFRGEDTRKRFIGHLYTALNNK--GIYVFRDDKQ---LEKGGSISPNLLKTI-EESRISIIVLSKNYASS 82 (160)
Q Consensus 9 ~~~~~yDVFISy~~~D~~~~fv~~L~~~L~~~--g~~v~~d~~d---l~~G~~~~~~i~~~i-~~S~~~I~vlS~~~~~S 82 (160)
...+.||+=+||.++- ...|+.+..+++.. ....|+|-.- |-+| ++.+-+...- .+|++.++.+..+|...
T Consensus 173 ~~~~~~DiG~SFaGEA--R~LVEqV~~E~~~~~~p~~~FYD~~~~~~L~~~-sL~~~L~~~Y~~rC~~~~VF~~~~Y~~K 249 (329)
T COG4916 173 SSEKPVDSGISFAGEA--RNLVEQVQTEHSGLDIPTRRFYDLLVAHPLYPG-SLVSTLDPGYDIRCVVTTVFNTGSYICK 249 (329)
T ss_pred ccccccceeeEeehhh--hhHHHHHHHhhhcccCCceeeeechhhccccCc-cHHHhcccccCceEEEEEEEeCCceEEe
Confidence 3578899999999997 37799999999854 4555666421 2222 2322222222 37999999999999999
Q ss_pred hhHHHHHHHHHHHhhcCCcceeEEe
Q 031401 83 TWCLDELLKIVECKNREDQIFPIFY 107 (160)
Q Consensus 83 ~wc~~El~~~~~~~~~~~~IiPI~~ 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 9999998755442 22335566655
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=93.60 E-value=1.6 Score=29.83 Aligned_cols=78 Identities=18% Similarity=0.147 Sum_probs=52.9
Q ss_pred hhHHHHHHHHHHcCCceEEeeCC-CCC---CCCCchHHH----HHHHHhcceEEEEeecCCcCChhHHHHHHHHHHHhhc
Q 031401 27 KRFIGHLYTALNNKGIYVFRDDK-QLE---KGGSISPNL----LKTIEESRISIIVLSKNYASSTWCLDELLKIVECKNR 98 (160)
Q Consensus 27 ~~fv~~L~~~L~~~g~~v~~d~~-dl~---~G~~~~~~i----~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~~~~~~~ 98 (160)
..++..+.+.|+..|+.++.-.+ +.. .+..+..+| .++|++|+++|+++...- .+.-+..|+..|.. .
T Consensus 13 ~~~~~~~~~~L~~~g~~v~~P~~~~~~~~~~~~~~~~~i~~~d~~~i~~~D~via~l~~~~-~d~Gt~~ElG~A~a---l 88 (113)
T PF05014_consen 13 KARVERLREALEKNGFEVYSPQDNDENDEEDSQEWAREIFERDLEGIRECDIVIANLDGFR-PDSGTAFELGYAYA---L 88 (113)
T ss_dssp HHHHHHHHHHHHTTTTEEEGGCTCSSS--TTSHHCHHHHHHHHHHHHHHSSEEEEEECSSS---HHHHHHHHHHHH---T
T ss_pred HHHHHHHHHHHHhCCCEEEeccccccccccccchHHHHHHHHHHHHHHHCCEEEEECCCCC-CCCcHHHHHHHHHH---C
Confidence 45688899999999998887542 111 123333444 468999999999988755 66788999998887 3
Q ss_pred CCcceeEEee
Q 031401 99 EDQIFPIFYE 108 (160)
Q Consensus 99 ~~~IiPI~~~ 108 (160)
+++|+-+.-+
T Consensus 89 gkpv~~~~~d 98 (113)
T PF05014_consen 89 GKPVILLTED 98 (113)
T ss_dssp TSEEEEEECC
T ss_pred CCEEEEEEcC
Confidence 4455444333
No 13
>COG4271 Predicted nucleotide-binding protein containing TIR -like domain [Transcription]
Probab=86.50 E-value=2.6 Score=32.38 Aligned_cols=87 Identities=16% Similarity=0.163 Sum_probs=61.3
Q ss_pred cEEEecccCCCchhHHHHHHHHHHcC-Cc-eEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCc-----C------
Q 031401 15 DAFLSFRGEDTRKRFIGHLYTALNNK-GI-YVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYA-----S------ 81 (160)
Q Consensus 15 DVFISy~~~D~~~~fv~~L~~~L~~~-g~-~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~-----~------ 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 8999987653 466666677654 44 445554 6788999999999999999999999999833 1
Q ss_pred ---ChhHHHHHHHHHHHhhcCCcceeEEe
Q 031401 82 ---STWCLDELLKIVECKNREDQIFPIFY 107 (160)
Q Consensus 82 ---S~wc~~El~~~~~~~~~~~~IiPI~~ 107 (160)
......||...+.+ ..+.+|+.+..
T Consensus 159 praRqNVifELGm~mgr-LgRkrv~Il~k 186 (233)
T COG4271 159 PRARQNVIFELGMFMGR-LGRKRVMILMK 186 (233)
T ss_pred ccccccchhhHhhHHhh-cccceEEEEec
Confidence 22346677777764 34456655554
No 14
>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=84.70 E-value=5.4 Score=25.39 Aligned_cols=61 Identities=11% Similarity=0.123 Sum_probs=40.2
Q ss_pred ccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCC
Q 031401 14 YDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNY 79 (160)
Q Consensus 14 yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~ 79 (160)
++|+|...+.+. ...+..+...|++.|+++-+|.+. .++...+..+-..--..++++.++-
T Consensus 2 ~~v~ii~~~~~~-~~~a~~~~~~Lr~~g~~v~~d~~~----~~~~~~~~~a~~~g~~~~iiig~~e 62 (91)
T cd00860 2 VQVVVIPVTDEH-LDYAKEVAKKLSDAGIRVEVDLRN----EKLGKKIREAQLQKIPYILVVGDKE 62 (91)
T ss_pred eEEEEEeeCchH-HHHHHHHHHHHHHCCCEEEEECCC----CCHHHHHHHHHHcCCCEEEEECcch
Confidence 677777655443 345778999999999999998643 3455566666544444555555543
No 15
>COG0400 Predicted esterase [General function prediction only]
Probab=80.63 E-value=8.8 Score=29.47 Aligned_cols=59 Identities=22% Similarity=0.126 Sum_probs=45.5
Q ss_pred CCCCCCcccEEEecccCCC--chhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHh
Q 031401 7 QNVSHGEYDAFLSFRGEDT--RKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEE 67 (160)
Q Consensus 7 s~~~~~~yDVFISy~~~D~--~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~ 67 (160)
..+..+..-|||+|...|. ......+|.+.|+..|..|....- ..|..+..+-.+.+++
T Consensus 140 ~~~~~~~~pill~hG~~Dpvvp~~~~~~l~~~l~~~g~~v~~~~~--~~GH~i~~e~~~~~~~ 200 (207)
T COG0400 140 LLPDLAGTPILLSHGTEDPVVPLALAEALAEYLTASGADVEVRWH--EGGHEIPPEELEAARS 200 (207)
T ss_pred cccccCCCeEEEeccCcCCccCHHHHHHHHHHHHHcCCCEEEEEe--cCCCcCCHHHHHHHHH
Confidence 3446788999999999997 345578899999999999988753 4788887766665543
No 16
>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=75.42 E-value=40 Score=27.00 Aligned_cols=134 Identities=20% Similarity=0.311 Sum_probs=78.9
Q ss_pred CcccEEEecccCCCchhHHHHHHHHHHcCCceEEee------CCCCCCCCCchHHHHHHHHh------cceEE-----EE
Q 031401 12 GEYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRD------DKQLEKGGSISPNLLKTIEE------SRISI-----IV 74 (160)
Q Consensus 12 ~~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d------~~dl~~G~~~~~~i~~~i~~------S~~~I-----~v 74 (160)
...|.++ |-.++. ..|..+| +.|.+.||+.++. .++++|+-.-.+++.+.+.+ ..++| ++
T Consensus 46 ~~Vd~iV-FWTKnp-~P~l~~L-~~l~~~gy~~yfq~Tit~Y~~~lEp~vP~~~~~i~~f~~Ls~~iG~~rViWRYDPIi 122 (266)
T PF08902_consen 46 EDVDCIV-FWTKNP-APFLPYL-DELDERGYPYYFQFTITGYGKDLEPNVPPKDERIETFRELSERIGPERVIWRYDPII 122 (266)
T ss_pred hcceEEE-EecCCc-HHHHhhH-HHHHhCCCceEEEEEeCCCCccccCCCCCHHHHHHHHHHHHHHHCCCcEEEecCCEe
Confidence 3455555 556665 3566554 6777788888775 66788887655555544432 22233 45
Q ss_pred eecCCcCChhHHHHHHHHHHH-hhcCCcceeEEeecCchhhhcccchHHHHHHHHH-HhhccCHHHHHHHHHHHHHhhcc
Q 031401 75 LSKNYASSTWCLDELLKIVEC-KNREDQIFPIFYEVEPTVVRKQTASFGEAFAKYE-EFFRDNIEKVQKWRYALKVVANI 152 (160)
Q Consensus 75 lS~~~~~S~wc~~El~~~~~~-~~~~~~IiPI~~~~~p~~v~~~~~~~~~~~~~~~-~~~~~~~~~~~~w~~al~~~~~~ 152 (160)
+|..|-- .|-+..+..+.+. ....++++.=|++..+.--+.. .... .-...+++....--..|.+++.-
T Consensus 123 l~~~~~~-~~h~~~F~~la~~L~g~t~~~viSF~D~Y~k~~~~l--------~~~~~~~~~~~~~~~~~l~~~l~~ia~~ 193 (266)
T PF08902_consen 123 LTDKYTV-DYHLEAFERLAEALAGYTDRCVISFLDLYRKVRRNL--------ARLGFRIREPSEEEKRELAKRLAEIAKK 193 (266)
T ss_pred ECCCCCH-HHHHHHHHHHHHHHhccCCEEEEEeeeccHHHHHHH--------HhhcCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 6666444 6777777777776 6667788888888644322211 1111 01122356666677777777766
Q ss_pred cceee
Q 031401 153 SGWEL 157 (160)
Q Consensus 153 ~G~~~ 157 (160)
-|..+
T Consensus 194 ~g~~l 198 (266)
T PF08902_consen 194 YGMTL 198 (266)
T ss_pred cCCEE
Confidence 66543
No 17
>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=74.72 E-value=17 Score=23.06 Aligned_cols=62 Identities=18% Similarity=0.204 Sum_probs=39.5
Q ss_pred ccEEEecccCC--CchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCC
Q 031401 14 YDAFLSFRGED--TRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNY 79 (160)
Q Consensus 14 yDVFISy~~~D--~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~ 79 (160)
++|+|.....+ .....+..+...|...|+.+-+|.. +..+...+..+-...-..++++.++-
T Consensus 2 ~~v~ii~~~~~~~~~~~~a~~~~~~Lr~~g~~v~~~~~----~~~~~k~~~~a~~~g~~~~iiig~~e 65 (94)
T cd00738 2 IDVAIVPLTDPRVEAREYAQKLLNALLANGIRVLYDDR----ERKIGKKFREADLRGVPFAVVVGEDE 65 (94)
T ss_pred eEEEEEECCCCcHHHHHHHHHHHHHHHHCCCEEEecCC----CcCHhHHHHHHHhCCCCEEEEECCCh
Confidence 57777654431 1134577789999999999998763 34555566666544445677777643
No 18
>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=72.12 E-value=15 Score=23.62 Aligned_cols=47 Identities=21% Similarity=0.224 Sum_probs=32.9
Q ss_pred hhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeec
Q 031401 27 KRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSK 77 (160)
Q Consensus 27 ~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~ 77 (160)
..++..|...|.+.|+++.+|..+ ..+...+..+-..---.++++.+
T Consensus 15 ~~~a~~l~~~L~~~gi~v~~d~~~----~~~~k~~~~a~~~g~p~~iiiG~ 61 (94)
T PF03129_consen 15 IEYAQELANKLRKAGIRVELDDSD----KSLGKQIKYADKLGIPFIIIIGE 61 (94)
T ss_dssp HHHHHHHHHHHHHTTSEEEEESSS----STHHHHHHHHHHTTESEEEEEEH
T ss_pred HHHHHHHHHHHHHCCCEEEEECCC----CchhHHHHHHhhcCCeEEEEECc
Confidence 456888999999999999999744 44556667665544445555554
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=71.99 E-value=23 Score=24.32 Aligned_cols=65 Identities=14% Similarity=0.035 Sum_probs=42.6
Q ss_pred CCcccEEEecccCC-CchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCc
Q 031401 11 HGEYDAFLSFRGED-TRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYA 80 (160)
Q Consensus 11 ~~~yDVFISy~~~D-~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~ 80 (160)
-..+||||...+++ .....+..|...|...|+++-+|.+ ..+...+..+-+.--..++++.++-.
T Consensus 24 lap~~v~Ii~~~~~~~~~~~a~~la~~LR~~gi~v~~d~~-----~sl~kqlk~A~k~g~~~~iiiG~~e~ 89 (121)
T cd00858 24 LAPIKVAVLPLVKRDELVEIAKEISEELRELGFSVKYDDS-----GSIGRRYARQDEIGTPFCVTVDFDTL 89 (121)
T ss_pred cCCcEEEEEecCCcHHHHHHHHHHHHHHHHCCCEEEEeCC-----CCHHHHHHHhHhcCCCEEEEECcCch
Confidence 44688888876621 1234567799999999999999763 34555666665544446666665543
No 20
>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=71.31 E-value=35 Score=27.09 Aligned_cols=78 Identities=17% Similarity=0.143 Sum_probs=54.5
Q ss_pred hhHHHHHHHHHHcCCceEE-eeCC--CCCCCCCchHHHHHH-HHhcceEEEEeecCCcCChhHHHHHHHHHHH--hhcCC
Q 031401 27 KRFIGHLYTALNNKGIYVF-RDDK--QLEKGGSISPNLLKT-IEESRISIIVLSKNYASSTWCLDELLKIVEC--KNRED 100 (160)
Q Consensus 27 ~~fv~~L~~~L~~~g~~v~-~d~~--dl~~G~~~~~~i~~~-i~~S~~~I~vlS~~~~~S~wc~~El~~~~~~--~~~~~ 100 (160)
.+++..|...|.+.|+.+- ++.. .+..|.-.. +.-. -...++-|+.+|.+...+....+++-.++.+ +..++
T Consensus 90 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vP--L~~l~~~~~~iPvV~~s~~~~~~~~~~~~lG~al~~~l~~~~~ 167 (271)
T cd07373 90 TALAEACVTACPEHGVHARGVDYDGFPIDTGTITA--CTLMGIGTEALPLVVASNNLYHSGEITEKLGAIAADAAKDQNK 167 (271)
T ss_pred HHHHHHHHHHHHHCCCcEEEecCCCCCCcchhHHH--HHHHcccCCCCCEEEEEeCCCCCHHHHHHHHHHHHHHHHHcCC
Confidence 4778999999999999986 6663 355554332 2221 1246676778998887778888899998886 55567
Q ss_pred cceeEE
Q 031401 101 QIFPIF 106 (160)
Q Consensus 101 ~IiPI~ 106 (160)
+|+.|-
T Consensus 168 rV~iIg 173 (271)
T cd07373 168 RVAVVG 173 (271)
T ss_pred eEEEEE
Confidence 777664
No 21
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=71.28 E-value=27 Score=23.15 Aligned_cols=62 Identities=13% Similarity=0.049 Sum_probs=42.6
Q ss_pred HHHHHHHHcCCceEEeeCC-CCCCCCCchHHHH---HHHHhcceEEEEeecCCcCChhHHHHHHHHHH
Q 031401 31 GHLYTALNNKGIYVFRDDK-QLEKGGSISPNLL---KTIEESRISIIVLSKNYASSTWCLDELLKIVE 94 (160)
Q Consensus 31 ~~L~~~L~~~g~~v~~d~~-dl~~G~~~~~~i~---~~i~~S~~~I~vlS~~~~~S~wc~~El~~~~~ 94 (160)
......|+..|+.|.-=-. ....|..+..=+. ..+..|+.++ +=|.+-.|.-|+-|...|..
T Consensus 19 ~~~a~~L~~~G~~vvnPa~~~~~~~~~~~~ym~~~l~~L~~cD~i~--~l~gWe~S~GA~~E~~~A~~ 84 (92)
T PF14359_consen 19 NAAAKRLRAKGYEVVNPAELGIPEGLSWEEYMRICLAMLSDCDAIY--MLPGWENSRGARLEHELAKK 84 (92)
T ss_pred HHHHHHHHHCCCEEeCchhhCCCCCCCHHHHHHHHHHHHHhCCEEE--EcCCcccCcchHHHHHHHHH
Confidence 4578888889976643221 2356666554333 4566788543 34999999999999998876
No 22
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=67.83 E-value=7.8 Score=31.03 Aligned_cols=96 Identities=23% Similarity=0.463 Sum_probs=69.0
Q ss_pred CcccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHH---H--HhcceEEEEeecCCcCChhHH
Q 031401 12 GEYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKT---I--EESRISIIVLSKNYASSTWCL 86 (160)
Q Consensus 12 ~~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~---i--~~S~~~I~vlS~~~~~S~wc~ 86 (160)
-++.+=+||.++|. .+++...+-|..+|+.+++|-.+ ...-|.-+|..- | +..-.++...|.+|-.-.|..
T Consensus 5 ~~~~~a~~f~~~d~--~~~~~~~n~~~~~~v~~~y~~~~--~a~~~~~~~~~~~~e~~q~~~~~~~~f~~~~~~r~~~~~ 80 (329)
T COG4916 5 VQFEIALSFAGEDR--EYVDRVANLLREAGVTVFYDIFE--EANLWGKNLYDYLSEIYQDKALFTIMFISEHYSRKMWTN 80 (329)
T ss_pred hheeeeeeecCchH--HHHHHHHHHHHhhccEEEEeehh--hhhhhhhHHHHHHHHHHhhhhHHHhhhhhccccCcCCCc
Confidence 35667789999994 67888888899999999998543 222233333322 2 244557788899999999999
Q ss_pred HHHHHHHHH--hhcCCcceeEEeecCc
Q 031401 87 DELLKIVEC--KNREDQIFPIFYEVEP 111 (160)
Q Consensus 87 ~El~~~~~~--~~~~~~IiPI~~~~~p 111 (160)
.|++..+.+ .+....++|-.++..|
T Consensus 81 ~~~~~~~a~~~~~~~~~~~~~~~~~~~ 107 (329)
T COG4916 81 HERQAMQARAFQEHQEYILPARFDETP 107 (329)
T ss_pred HHHHHHHHHHhhhccEEehhhhhccCC
Confidence 999887776 5566688888876554
No 23
>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=64.66 E-value=32 Score=22.64 Aligned_cols=45 Identities=13% Similarity=0.220 Sum_probs=30.1
Q ss_pred HHHHHHHHHcCCceEEeeCCCCCCCCC-chHHHHHHHHhcceEEEEee
Q 031401 30 IGHLYTALNNKGIYVFRDDKQLEKGGS-ISPNLLKTIEESRISIIVLS 76 (160)
Q Consensus 30 v~~L~~~L~~~g~~v~~d~~dl~~G~~-~~~~i~~~i~~S~~~I~vlS 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 56788899999988766611 12221 12248889999998776654
No 24
>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1.5.1.29 from EC) reduces FMN and also reduces riboflavin and FAD, although more slowly. Members of this entry catalyse the reaction NAD(P)H + FMN = NAD(P)(+) + FMNH(2).; PDB: 3SVL_B 3GFS_F 3GFQ_A 1NNI_1 2GSW_B 3GFR_D 1T0I_B 3D7N_A 2R97_A 3B6K_A ....
Probab=57.46 E-value=63 Score=22.57 Aligned_cols=79 Identities=18% Similarity=0.167 Sum_probs=48.4
Q ss_pred hhHHHHHHHHHHcCCceE-EeeCCCCC-C-----------CCCchHHHHHHHHhcceEEEEeecCCcCChhHHHHHHHHH
Q 031401 27 KRFIGHLYTALNNKGIYV-FRDDKQLE-K-----------GGSISPNLLKTIEESRISIIVLSKNYASSTWCLDELLKIV 93 (160)
Q Consensus 27 ~~fv~~L~~~L~~~g~~v-~~d~~dl~-~-----------G~~~~~~i~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~~ 93 (160)
...++.+...|++.|+.+ .++-.+.. | -..-.+++.+.+.+++ .|++.||.|..+. .-.+..++
T Consensus 17 ~~l~~~~~~~l~~~g~e~~~i~l~~~~~p~~~~~~~~~~~~~d~~~~~~~~l~~aD-~iI~~sP~y~~~~--s~~lK~~l 93 (152)
T PF03358_consen 17 RKLAEAVAEQLEEAGAEVEVIDLADYPLPCCDGDFECPCYIPDDVQELYDKLKEAD-GIIFASPVYNGSV--SGQLKNFL 93 (152)
T ss_dssp HHHHHHHHHHHHHTTEEEEEEECTTSHCHHHHHHHHHTGCTSHHHHHHHHHHHHSS-EEEEEEEEBTTBE---HHHHHHH
T ss_pred HHHHHHHHHHHHHcCCEEEEEeccccchhhcccccccccCCcHHHHHHHhceecCC-eEEEeecEEcCcC--ChhhhHHH
Confidence 456788888888888766 34544431 1 1223356778888999 6778999998864 33455555
Q ss_pred HH-h------hcCCcceeEEee
Q 031401 94 EC-K------NREDQIFPIFYE 108 (160)
Q Consensus 94 ~~-~------~~~~~IiPI~~~ 108 (160)
++ . ..++.+.+|-..
T Consensus 94 D~~~~~~~~~~~~K~~~~i~~~ 115 (152)
T PF03358_consen 94 DRLSCWFRRALRGKPVAIIAVG 115 (152)
T ss_dssp HTHHHTHTTTTTTSEEEEEEEE
T ss_pred HHhccccccccCCCEEEEEEEe
Confidence 54 2 244555555443
No 25
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=53.57 E-value=49 Score=20.14 Aligned_cols=43 Identities=23% Similarity=0.298 Sum_probs=29.4
Q ss_pred HHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCcCCh
Q 031401 30 IGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYASST 83 (160)
Q Consensus 30 v~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S~ 83 (160)
...+...|++.|+.+--... ....+.....++++++|.+.-+.
T Consensus 7 ~~a~~~~L~~~g~~v~~~~~-----------~~~~l~~~~~tll~i~~~~~~~~ 49 (70)
T PF14258_consen 7 TYALYQLLEEQGVKVERWRK-----------PYEALEADDGTLLVIGPDLRLSE 49 (70)
T ss_pred HHHHHHHHHHCCCeeEEecc-----------cHHHhCCCCCEEEEEeCCCCCCc
Confidence 45688888999988854321 12244558889999999966553
No 26
>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=53.08 E-value=61 Score=21.01 Aligned_cols=64 Identities=14% Similarity=0.101 Sum_probs=37.2
Q ss_pred EEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCC-------CCCCchHHHHHHHHhcceEEEEeecCCc
Q 031401 17 FLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLE-------KGGSISPNLLKTIEESRISIIVLSKNYA 80 (160)
Q Consensus 17 FISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~-------~G~~~~~~i~~~i~~S~~~I~vlS~~~~ 80 (160)
|.+..+.-....++.+|...|.++|.++.+-+-|.. .+..+......++..|+..|+++.+...
T Consensus 4 ~~~~kgG~Gkst~~~~la~~~~~~~~~vl~~d~d~~~d~viiD~p~~~~~~~~~~l~~ad~viv~~~~~~~ 74 (104)
T cd02042 4 VANQKGGVGKTTTAVNLAAALARRGKRVLLIDLDPQYDYIIIDTPPSLGLLTRNALAAADLVLIPVQPSPL 74 (104)
T ss_pred EEeCCCCcCHHHHHHHHHHHHHhCCCcEEEEeCCCCCCEEEEeCcCCCCHHHHHHHHHCCEEEEeccCCHH
Confidence 555544333335567799999888988876544432 1111233444666777777766666543
No 27
>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=52.62 E-value=67 Score=21.41 Aligned_cols=74 Identities=18% Similarity=0.180 Sum_probs=46.9
Q ss_pred HHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCcCChhHHHHHHHHHHH-hhcCCcceeEEee
Q 031401 30 IGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYASSTWCLDELLKIVEC-KNREDQIFPIFYE 108 (160)
Q Consensus 30 v~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~~~~-~~~~~~IiPI~~~ 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 LLYLAAYLRKAGHEVDILDANVP-----PEELVEALRAERPDVVGISVSMTPN---LPEAKRLARAIKERNPNIPIVVGG 88 (121)
T ss_dssp HHHHHHHHHHTTBEEEEEESSB------HHHHHHHHHHTTCSEEEEEESSSTH---HHHHHHHHHHHHTTCTTSEEEEEE
T ss_pred HHHHHHHHHHCCCeEEEECCCCC-----HHHHHHHHhcCCCcEEEEEccCcCc---HHHHHHHHHHHHhcCCCCEEEEEC
Confidence 56689999999999854322322 2788888888888888888765443 3444444444 4444555555555
Q ss_pred cCc
Q 031401 109 VEP 111 (160)
Q Consensus 109 ~~p 111 (160)
..+
T Consensus 89 ~~~ 91 (121)
T PF02310_consen 89 PHA 91 (121)
T ss_dssp SSS
T ss_pred Cch
Confidence 444
No 28
>KOG2792 consensus Putative cytochrome C oxidase assembly protein [Energy production and conversion]
Probab=51.61 E-value=25 Score=28.15 Aligned_cols=29 Identities=31% Similarity=0.508 Sum_probs=20.5
Q ss_pred hHHHHHHHHHHH-----hhcCCcceeEEeecCch
Q 031401 84 WCLDELLKIVEC-----KNREDQIFPIFYEVEPT 112 (160)
Q Consensus 84 wc~~El~~~~~~-----~~~~~~IiPI~~~~~p~ 112 (160)
=|.+||.+.... ...+..++|||..++|.
T Consensus 154 ICPdELeKm~~~Vd~i~~~~~~~~~PlFIsvDPe 187 (280)
T KOG2792|consen 154 ICPDELEKMSAVVDEIEAKPGLPPVPLFISVDPE 187 (280)
T ss_pred cChHHHHHHHHHHHHHhccCCCCccceEEEeCcc
Confidence 477888765443 35666777999998883
No 29
>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=51.39 E-value=55 Score=20.08 Aligned_cols=59 Identities=15% Similarity=0.093 Sum_probs=34.1
Q ss_pred ccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeec
Q 031401 14 YDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSK 77 (160)
Q Consensus 14 yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~ 77 (160)
.||+|....... ..-+..+...|.+.|+++.++... ..+...+..+-...-..++++.+
T Consensus 2 ~~v~i~~~~~~~-~~~a~~i~~~Lr~~g~~v~~~~~~----~~~~~~~~~a~~~~~~~~i~i~~ 60 (91)
T cd00859 2 VDVYVVPLGEGA-LSEALELAEQLRDAGIKAEIDYGG----RKLKKQFKYADRSGARFAVILGE 60 (91)
T ss_pred CcEEEEEcChHH-HHHHHHHHHHHHHCCCEEEEecCC----CCHHHHHHHHHHcCCCEEEEEcH
Confidence 367776544432 233677899999999999887532 23444444443332234455554
No 30
>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=51.10 E-value=12 Score=26.29 Aligned_cols=31 Identities=13% Similarity=0.156 Sum_probs=24.2
Q ss_pred hhHHHHHHHHHHcCCceEEeeCCCC---CCCCCc
Q 031401 27 KRFIGHLYTALNNKGIYVFRDDKQL---EKGGSI 57 (160)
Q Consensus 27 ~~fv~~L~~~L~~~g~~v~~d~~dl---~~G~~~ 57 (160)
...+..|+..|+..|+.+++|.++- .+|..+
T Consensus 43 ~~~a~~l~~~L~~~gi~v~~D~r~~~~~~~G~k~ 76 (128)
T cd02426 43 RDLCQGLKNELREAGLSVWPGYLETQHSSLEQLL 76 (128)
T ss_pred HHHHHHHHHHHHHcCCEEEeccCcccccCHHHHH
Confidence 4557889999999999999998764 455544
No 31
>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=49.10 E-value=75 Score=27.86 Aligned_cols=63 Identities=13% Similarity=0.165 Sum_probs=43.6
Q ss_pred CCcccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecC
Q 031401 11 HGEYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKN 78 (160)
Q Consensus 11 ~~~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~ 78 (160)
....+|+|..-+++. ...+..|...|++.|++|-+|.+ +.++...+..|-..--..++|+.++
T Consensus 468 ~~p~~v~vi~~~~~~-~~~a~~ia~~LR~~Gi~v~~d~~----~~sl~~q~k~A~~~g~~~~iiiG~~ 530 (563)
T TIGR00418 468 LAPVQVVVIPVNERH-LDYAKKVAQKLKKAGIRVDVDDR----NERLGKKIREAQKQKIPYMLVVGDK 530 (563)
T ss_pred CCCceEEEEEccchH-HHHHHHHHHHHHHcCCEEEEECC----CCCHHHHHHHHHhcCCCEEEEEchh
Confidence 356788887765443 35688899999999999999864 4456667777655444456666543
No 32
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=49.09 E-value=1.2e+02 Score=23.24 Aligned_cols=96 Identities=19% Similarity=0.317 Sum_probs=56.4
Q ss_pred EEEecccCCCc--hhHHHHHHHHHHcCCceEEeeCCCCCCCC-CchHHHHHHHHh-------------------------
Q 031401 16 AFLSFRGEDTR--KRFIGHLYTALNNKGIYVFRDDKQLEKGG-SISPNLLKTIEE------------------------- 67 (160)
Q Consensus 16 VFISy~~~D~~--~~fv~~L~~~L~~~g~~v~~d~~dl~~G~-~~~~~i~~~i~~------------------------- 67 (160)
.||.+-+-|.. ...++.|...|+.+|+.|.+-. .||. .+...|.+.+.+
T Consensus 4 ~fI~iEGiDGaGKTT~~~~L~~~l~~~g~~v~~tr---EP~~~~ige~iR~~ll~~~~~~~~~~e~lLfaadR~~h~~~~ 80 (208)
T COG0125 4 MFIVIEGIDGAGKTTQAELLKERLEERGIKVVLTR---EPGGTPIGEKIRELLLNGEEKLSPKAEALLFAADRAQHLEEV 80 (208)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe---CCCCChHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888766653 3456779999999999887753 2443 222222221111
Q ss_pred ----cceEEEEeecCCcCChhHHH--------HHHHHHHH--hhcCCcceeEEeecCchhh
Q 031401 68 ----SRISIIVLSKNYASSTWCLD--------ELLKIVEC--KNREDQIFPIFYEVEPTVV 114 (160)
Q Consensus 68 ----S~~~I~vlS~~~~~S~wc~~--------El~~~~~~--~~~~~~IiPI~~~~~p~~v 114 (160)
-...-+|++..|.-|.-+-. ++...+.+ ...-.+=+.+|++++|+.-
T Consensus 81 i~pal~~g~vVI~DRy~~Ss~AYQg~~~~~~~~~~~~l~~~~~~~~~PD~ti~Ldv~~e~a 141 (208)
T COG0125 81 IKPALKEGKVVICDRYVDSSLAYQGGGRGLDLDWVLALNEFAPGGLKPDLTLYLDVPPEVA 141 (208)
T ss_pred HHHhhcCCCEEEECCcccHHHHhhhhccCCCHHHHHHHHHhccCCCCCCEEEEEeCCHHHH
Confidence 12234788888888876544 33333332 2222455667889998874
No 33
>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=49.03 E-value=67 Score=20.35 Aligned_cols=48 Identities=21% Similarity=0.209 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCC
Q 031401 28 RFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNY 79 (160)
Q Consensus 28 ~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~ 79 (160)
..+..|...|+..|+++.+|.+.- .+...+..+-..--..++++.++-
T Consensus 18 ~~a~~la~~Lr~~g~~v~~d~~~~----~l~k~i~~a~~~g~~~~iiiG~~e 65 (94)
T cd00861 18 ELAEKLYAELQAAGVDVLLDDRNE----RPGVKFADADLIGIPYRIVVGKKS 65 (94)
T ss_pred HHHHHHHHHHHHCCCEEEEECCCC----CcccchhHHHhcCCCEEEEECCch
Confidence 457789999999999999987543 444455555444444556665443
No 34
>TIGR02298 HpaD_Fe 3,4-dihydroxyphenylacetate 2,3-dioxygenase. This enzyme catalyzes the ring-opening step in the degradation of 4-hydroxyphenylacetate.
Probab=48.18 E-value=1.4e+02 Score=23.85 Aligned_cols=78 Identities=8% Similarity=0.071 Sum_probs=52.0
Q ss_pred hhHHHHHHHHHHcCCceEEe---eCCCCCCCCCchHHHHHHHHhcceEEEEeecC-CcCChhHHHHHHHHHHH--hhcCC
Q 031401 27 KRFIGHLYTALNNKGIYVFR---DDKQLEKGGSISPNLLKTIEESRISIIVLSKN-YASSTWCLDELLKIVEC--KNRED 100 (160)
Q Consensus 27 ~~fv~~L~~~L~~~g~~v~~---d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~-~~~S~wc~~El~~~~~~--~~~~~ 100 (160)
..++..|...+...|+.+.. ..+.+..|.-+. +.-.-.+.++-||-+|.+ ...+..-.+++-.++.. +..++
T Consensus 96 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vP--L~~l~p~~~ipvV~is~~~~~~~~~~~~~lG~al~~~i~~~~~ 173 (282)
T TIGR02298 96 PALGQLIADEAQEHGVKTLAHQVPSLGLEYGTLVP--MRYMNEDGHFKVVSIAAWCTVHDIEESRALGEAIRKAIEQSDG 173 (282)
T ss_pred HHHHHHHHHHHHHCCCceeeccCCCCCCCeehHhH--HHHhCCCCCCcEEEEeecCCCCCHHHHHHHHHHHHHHHHhcCC
Confidence 36899999999999998752 344455564332 222223456778888876 54567777888888887 44667
Q ss_pred cceeEE
Q 031401 101 QIFPIF 106 (160)
Q Consensus 101 ~IiPI~ 106 (160)
+|+.|-
T Consensus 174 rV~iIa 179 (282)
T TIGR02298 174 RVAVLA 179 (282)
T ss_pred CEEEEE
Confidence 777663
No 35
>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=46.67 E-value=1.1e+02 Score=23.86 Aligned_cols=76 Identities=16% Similarity=0.144 Sum_probs=53.6
Q ss_pred hhHHHHHHHHHHcCCceEEeeC-CCCCCCCCchHHHHHHHHhcceEEEEeecCCcCChhHHHHHHHHHHH-hhcCCccee
Q 031401 27 KRFIGHLYTALNNKGIYVFRDD-KQLEKGGSISPNLLKTIEESRISIIVLSKNYASSTWCLDELLKIVEC-KNREDQIFP 104 (160)
Q Consensus 27 ~~fv~~L~~~L~~~g~~v~~d~-~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~~~~-~~~~~~IiP 104 (160)
..++.+|.+.|...|+.+-.+. +.+..|.-+ -+.-...+.++-||.+|-+...+..-..++..++.. .. ++|+.
T Consensus 80 ~eLa~~i~~~l~~~gi~~~~~~~~~lDHG~~v--PL~~~~p~~~iPvV~isi~~~~~~~~~~~lG~aL~~l~~--~~v~i 155 (253)
T cd07363 80 PELAERVAELLKAAGIPARLDPERGLDHGAWV--PLKLMYPDADIPVVQLSLPASLDPAEHYALGRALAPLRD--EGVLI 155 (253)
T ss_pred HHHHHHHHHHHHhcCCCccccCCcCCcccHHH--HHHHHcCCCCCcEEEEEecCCCCHHHHHHHHHHHHhhhh--CCEEE
Confidence 4789999999999999887654 445555433 233333456788999998887778888899999986 42 35665
Q ss_pred EE
Q 031401 105 IF 106 (160)
Q Consensus 105 I~ 106 (160)
|-
T Consensus 156 i~ 157 (253)
T cd07363 156 IG 157 (253)
T ss_pred Ee
Confidence 54
No 36
>PLN03194 putative disease resistance protein; Provisional
Probab=46.32 E-value=99 Score=23.48 Aligned_cols=66 Identities=14% Similarity=0.180 Sum_probs=47.8
Q ss_pred CCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCcCChhHHHHHHHHHHHhhcCCcceeEEee
Q 031401 40 KGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYASSTWCLDELLKIVECKNREDQIFPIFYE 108 (160)
Q Consensus 40 ~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~~~~~~~~~~IiPI~~~ 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 4799999876555555688999999999998887765556666555667777776 35566777643
No 37
>COG3286 Uncharacterized protein conserved in archaea [Function unknown]
Probab=45.35 E-value=1.2e+02 Score=23.28 Aligned_cols=51 Identities=14% Similarity=0.188 Sum_probs=29.3
Q ss_pred CcceeE--EeecCchhhhcccchHHHHHHHHHHhhccCHHHHHHHHHHHHHhhcccc
Q 031401 100 DQIFPI--FYEVEPTVVRKQTASFGEAFAKYEEFFRDNIEKVQKWRYALKVVANISG 154 (160)
Q Consensus 100 ~~IiPI--~~~~~p~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~al~~~~~~~G 154 (160)
++|+|+ .++.+|+|+-...-.-| +....+... -+....|+++|..+++.-+
T Consensus 146 klVv~~S~~~~~~~dd~~eeave~G--ll~e~E~~~--~~~~~~~e~~L~~l~~~l~ 198 (204)
T COG3286 146 KLVVAVSIVYGLDPDDAAEEAVELG--LLEEGEDGL--RELIKNKERALETLLKALK 198 (204)
T ss_pred hhhhhhhhHhCCCHHHHHHHHHHhh--hhhccchhH--HHhhhhHHHHHHHHHHHhh
Confidence 355554 57899999866433222 111111100 2557789999999887663
No 38
>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=44.76 E-value=75 Score=23.58 Aligned_cols=69 Identities=23% Similarity=0.253 Sum_probs=43.7
Q ss_pred HHHcCCceEEeeCCC--C-CCC-CCchHHHHHHHHhcce-----EEEEeecCCcCChhHHHHHHHHHHHhhcCCcceeEE
Q 031401 36 ALNNKGIYVFRDDKQ--L-EKG-GSISPNLLKTIEESRI-----SIIVLSKNYASSTWCLDELLKIVECKNREDQIFPIF 106 (160)
Q Consensus 36 ~L~~~g~~v~~d~~d--l-~~G-~~~~~~i~~~i~~S~~-----~I~vlS~~~~~S~wc~~El~~~~~~~~~~~~IiPI~ 106 (160)
.|.+.||+..+-+.| | .+. ..+.+++.+.+++++. -|+|+|.+.-++.-...+-...+++. .+ |||+
T Consensus 35 ~Lk~~Gik~li~DkDNTL~~~~~~~i~~~~~~~~~~l~~~~~~~~v~IvSNsaGs~~d~~~~~a~~~~~~-lg---Ipvl 110 (168)
T PF09419_consen 35 HLKKKGIKALIFDKDNTLTPPYEDEIPPEYAEWLNELKKQFGKDRVLIVSNSAGSSDDPDGERAEALEKA-LG---IPVL 110 (168)
T ss_pred hhhhcCceEEEEcCCCCCCCCCcCcCCHHHHHHHHHHHHHCCCCeEEEEECCCCcccCccHHHHHHHHHh-hC---CcEE
Confidence 388889988663322 3 233 4577888888887774 38999999876654334444444431 11 8887
Q ss_pred ee
Q 031401 107 YE 108 (160)
Q Consensus 107 ~~ 108 (160)
..
T Consensus 111 ~h 112 (168)
T PF09419_consen 111 RH 112 (168)
T ss_pred Ee
Confidence 54
No 39
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=44.12 E-value=51 Score=23.37 Aligned_cols=55 Identities=16% Similarity=0.192 Sum_probs=38.2
Q ss_pred ccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcce
Q 031401 14 YDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRI 70 (160)
Q Consensus 14 yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~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 456666555322235677888888888998888873 4788888888887777443
No 40
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=43.90 E-value=1.1e+02 Score=26.18 Aligned_cols=66 Identities=17% Similarity=0.141 Sum_probs=41.9
Q ss_pred CcccEEEeccc--CCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCcC
Q 031401 12 GEYDAFLSFRG--EDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYAS 81 (160)
Q Consensus 12 ~~yDVFISy~~--~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~ 81 (160)
..++|+|---. .+.....+..|...|...|++|.+|.++-.+| ..+..+-..---.++|+.++-+.
T Consensus 344 aP~qV~Iipi~~~~~~~~~~a~~i~~~L~~~Gi~v~~D~~~~~lg----~ki~~a~~~giP~~iiVG~~e~~ 411 (439)
T PRK12325 344 APFKVGIINLKQGDEACDAACEKLYAALSAAGIDVLYDDTDERPG----AKFATMDLIGLPWQIIVGPKGLA 411 (439)
T ss_pred CCeEEEEEecCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHh----HHHHHHHHcCCCEEEEECCcccc
Confidence 34788876542 12224567889999999999999998765555 34444433333356666665443
No 41
>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=43.09 E-value=40 Score=21.10 Aligned_cols=33 Identities=18% Similarity=0.226 Sum_probs=19.6
Q ss_pred CCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEE
Q 031401 40 KGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIV 74 (160)
Q Consensus 40 ~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~v 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 5677777763 46666666666666554444443
No 42
>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=41.42 E-value=97 Score=20.23 Aligned_cols=55 Identities=15% Similarity=0.200 Sum_probs=38.2
Q ss_pred HHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCcCChhHHHHHHHH
Q 031401 33 LYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYASSTWCLDELLKI 92 (160)
Q Consensus 33 L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~ 92 (160)
+...|.-.|+..+... ...+.....+.+.+++..+.|++++.++... ...++...
T Consensus 9 ~v~gFrLaGv~~~~~~---~~~ee~~~~l~~l~~~~~~gIIii~e~~~~~--~~~~l~~~ 63 (95)
T PF01990_consen 9 TVLGFRLAGVEGVYVN---TDPEEAEEALKELLKDEDVGIIIITEDLAEK--IRDELDEY 63 (95)
T ss_dssp HHHHHHHTTSEEEEES---HSHHHHHHHHHHHHHHTTEEEEEEEHHHHTT--HHHHHHHH
T ss_pred HHHHHHHcCCCCccCC---CCHHHHHHHHHHHhcCCCccEEEeeHHHHHH--HHHHHHHH
Confidence 4566777899888875 1234455667777778999999999998885 34444433
No 43
>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=41.33 E-value=45 Score=26.24 Aligned_cols=17 Identities=24% Similarity=0.172 Sum_probs=13.8
Q ss_pred hHHHHHHHHHHcCCceE
Q 031401 28 RFIGHLYTALNNKGIYV 44 (160)
Q Consensus 28 ~fv~~L~~~L~~~g~~v 44 (160)
.|+.+|.+.|++++..+
T Consensus 16 tfakeLak~L~~~i~~v 32 (261)
T COG4088 16 TFAKELAKELRQEIWRV 32 (261)
T ss_pred HHHHHHHHHHHHhhhhc
Confidence 78999999999876443
No 44
>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=41.22 E-value=45 Score=22.56 Aligned_cols=29 Identities=10% Similarity=0.130 Sum_probs=22.4
Q ss_pred EEEecccCCCchhHHHHHHHHHHcCCceEEe
Q 031401 16 AFLSFRGEDTRKRFIGHLYTALNNKGIYVFR 46 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~g~~v~~ 46 (160)
||||.+..|.. . ...+...|...|++++-
T Consensus 3 vlisv~~~dk~-~-~~~~a~~l~~~G~~i~a 31 (116)
T cd01423 3 ILISIGSYSKP-E-LLPTAQKLSKLGYKLYA 31 (116)
T ss_pred EEEecCcccch-h-HHHHHHHHHHCCCEEEE
Confidence 79999888752 3 45788888888988864
No 45
>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=40.91 E-value=26 Score=25.30 Aligned_cols=48 Identities=17% Similarity=0.286 Sum_probs=34.2
Q ss_pred HHHHHHHHcCCceEEeeCCCC-------CCCCCchHHHHHHHHhcceEEEEeecC
Q 031401 31 GHLYTALNNKGIYVFRDDKQL-------EKGGSISPNLLKTIEESRISIIVLSKN 78 (160)
Q Consensus 31 ~~L~~~L~~~g~~v~~d~~dl-------~~G~~~~~~i~~~i~~S~~~I~vlS~~ 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 347778888899987776552 235556667788999999888877753
No 46
>PRK10569 NAD(P)H-dependent FMN reductase; Provisional
Probab=40.60 E-value=1.5e+02 Score=22.10 Aligned_cols=82 Identities=12% Similarity=0.165 Sum_probs=49.6
Q ss_pred hHHHHHHHHHHcCCceE-EeeCCCCCCCC--------CchHHHHHHHHhcceEEEEeecCCcCChhHHHHHHHHHHH---
Q 031401 28 RFIGHLYTALNNKGIYV-FRDDKQLEKGG--------SISPNLLKTIEESRISIIVLSKNYASSTWCLDELLKIVEC--- 95 (160)
Q Consensus 28 ~fv~~L~~~L~~~g~~v-~~d~~dl~~G~--------~~~~~i~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~~~~--- 95 (160)
..++.+.+.|.+.|..+ .+|-.++.+.+ .-..++.+.|.+++ .|++.||-|..|- .--+..+++.
T Consensus 18 ~l~~~~~~~l~~~g~ev~~idL~~l~~~~~~~~~~~~~~~~~~~~~i~~AD-~iIi~tP~Y~~s~--pg~LKn~iD~l~~ 94 (191)
T PRK10569 18 ALLEYAREWLNGLGVEVYHWNLQNFAPEDLLYARFDSPALKTFTEQLAQAD-GLIVATPVYKASF--SGALKTLLDLLPE 94 (191)
T ss_pred HHHHHHHHHHHhCCCEEEEEEccCCChHHHHhccCCCHHHHHHHHHHHHCC-EEEEECCccCCCC--CHHHHHHHHhCCh
Confidence 34566777777778776 45655655421 12346667888888 6788999998763 2223334433
Q ss_pred -hhcCCcceeEEeecCch
Q 031401 96 -KNREDQIFPIFYEVEPT 112 (160)
Q Consensus 96 -~~~~~~IiPI~~~~~p~ 112 (160)
.-.++.++||-....+.
T Consensus 95 ~~l~~K~v~iiat~G~~~ 112 (191)
T PRK10569 95 RALEHKVVLPLATGGSVA 112 (191)
T ss_pred hhhCCCEEEEEEecCCch
Confidence 23456777776554443
No 47
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=40.59 E-value=98 Score=26.27 Aligned_cols=61 Identities=11% Similarity=0.143 Sum_probs=40.4
Q ss_pred CcccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeec
Q 031401 12 GEYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSK 77 (160)
Q Consensus 12 ~~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~ 77 (160)
...||+|.+-+.+. ...+-.+...|.+.|+++-+|.. +..+...+..+-+..-..++|+.+
T Consensus 324 ~~~~v~v~~~~~~~-~~~a~~ia~~LR~~Gi~veid~~----~~~l~k~~k~A~~~~~~~viiiG~ 384 (430)
T CHL00201 324 QSIDVYIATQGLKA-QKKGWEIIQFLEKQNIKFELDLS----SSNFHKQIKQAGKKRAKACIILGD 384 (430)
T ss_pred CCCCEEEEEcCHHH-HHHHHHHHHHHHhCCCeEEEeeC----CCCHHHHHHHHHHcCCCEEEEEec
Confidence 44789998755433 34577799999999999988653 244555666665544445666665
No 48
>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]
Probab=39.04 E-value=2e+02 Score=27.25 Aligned_cols=35 Identities=23% Similarity=0.225 Sum_probs=29.4
Q ss_pred ccEEEecccCCCchhHHHHHHHHHHcCCceEEeeC
Q 031401 14 YDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDD 48 (160)
Q Consensus 14 yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~ 48 (160)
.-+||--.++|.+.+|.+.++.+|-+-|-.+.+.+
T Consensus 407 ~~~~i~~d~eD~~qe~~~li~~AL~~PGPDlVICD 441 (1387)
T KOG1016|consen 407 SSGFIKDDSEDQRQEAYSLIRSALLEPGPDLVICD 441 (1387)
T ss_pred CCcccCCchhhhHHHHHHHHHHHhcCCCCCeEEec
Confidence 45788888899888899999999999987776655
No 49
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=38.66 E-value=31 Score=30.42 Aligned_cols=66 Identities=21% Similarity=0.222 Sum_probs=41.8
Q ss_pred CCcccEEEeccc-CC-CchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCc
Q 031401 11 HGEYDAFLSFRG-ED-TRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYA 80 (160)
Q Consensus 11 ~~~yDVFISy~~-~D-~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~ 80 (160)
-..|+|+|.--. ++ .....+..|...|+..|+++.+|+++-.+|..+ ..+=..---.++++.++.+
T Consensus 466 iaP~~v~Iv~~~~~~~~~~~~a~~i~~~L~~~gi~v~~Ddr~~~~g~k~----~~ad~~GiP~~iiiG~~e~ 533 (565)
T PRK09194 466 IAPFDVHIVPVNMKDEEVKELAEKLYAELQAAGIEVLLDDRKERPGVKF----ADADLIGIPHRIVVGDRGL 533 (565)
T ss_pred cCCceEEEEECCCCcHHHHHHHHHHHHHHhccCCeEEEECCCCCHHHHH----HHHHhcCCCEEEEEcCccc
Confidence 456899887654 22 224567889999999999999999875555433 3332222224556665544
No 50
>PLN02530 histidine-tRNA ligase
Probab=37.83 E-value=1.2e+02 Score=26.19 Aligned_cols=61 Identities=11% Similarity=0.011 Sum_probs=41.6
Q ss_pred CcccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeec
Q 031401 12 GEYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSK 77 (160)
Q Consensus 12 ~~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~ 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 45789998755543 345778999999999999887533 34555666666544445666664
No 51
>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=37.60 E-value=32 Score=23.07 Aligned_cols=55 Identities=16% Similarity=0.244 Sum_probs=32.9
Q ss_pred cCCCchhHHHHHHHHHHcCCceEEeeCCCCCC----------CCCchHHHHHHHHhcceEEEEee
Q 031401 22 GEDTRKRFIGHLYTALNNKGIYVFRDDKQLEK----------GGSISPNLLKTIEESRISIIVLS 76 (160)
Q Consensus 22 ~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~----------G~~~~~~i~~~i~~S~~~I~vlS 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 35666666788999999999999887533321 22223456778888886665444
No 52
>PRK08661 prolyl-tRNA synthetase; Provisional
Probab=37.52 E-value=1.1e+02 Score=26.50 Aligned_cols=64 Identities=14% Similarity=0.032 Sum_probs=39.5
Q ss_pred CCcccEEEecccC-----CCchhHHHHHHHHHHcCCceEEeeC-CCCCCCCCchHHHHHHHHhcceEEEEeecC
Q 031401 11 HGEYDAFLSFRGE-----DTRKRFIGHLYTALNNKGIYVFRDD-KQLEKGGSISPNLLKTIEESRISIIVLSKN 78 (160)
Q Consensus 11 ~~~yDVFISy~~~-----D~~~~fv~~L~~~L~~~g~~v~~d~-~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~ 78 (160)
...++|+|---.. +.-...+..|...|+..|++|-+|. ++..+|. .+..+-..---.++++.++
T Consensus 285 iAP~qV~Iipi~~~~~~~~~~~~~a~~l~~~Lr~~GirV~lD~r~~~s~gk----K~~~ae~~GvP~~IiIG~~ 354 (477)
T PRK08661 285 IAPIQVVIVPIFKKEEKKEEVLEYAKELAEELKKAGIRVKLDDRSDKTPGW----KFNEWELKGVPLRIEIGPR 354 (477)
T ss_pred cCCCeEEEEEecCCCcCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHHH----HHHHHHHCCCCEEEEECcc
Confidence 3458888765421 1113457889999999999999998 4455553 4444433333355555555
No 53
>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=35.97 E-value=1.3e+02 Score=21.39 Aligned_cols=29 Identities=28% Similarity=0.237 Sum_probs=18.7
Q ss_pred CCCCCchHHHHHHHHhcceEEEEeecCCc
Q 031401 52 EKGGSISPNLLKTIEESRISIIVLSKNYA 80 (160)
Q Consensus 52 ~~G~~~~~~i~~~i~~S~~~I~vlS~~~~ 80 (160)
..+..+.+.+.+.|.+++..|.+.+..|.
T Consensus 17 ~~~~~~~~~i~~~I~~A~~~I~i~~~~~~ 45 (176)
T cd00138 17 VGGRSDLDALLEAISNAKKSIYIASFYLS 45 (176)
T ss_pred cCcchHHHHHHHHHHhhheEEEEEEeEec
Confidence 34455666667777777777777776544
No 54
>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=34.71 E-value=1.3e+02 Score=19.96 Aligned_cols=61 Identities=16% Similarity=0.307 Sum_probs=35.8
Q ss_pred EEEecccCCCchhHHHHHHHHHHcCCceEEeeC--------CCCC-----CCCCchHHHHHHHHhcceEEEEeecC
Q 031401 16 AFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDD--------KQLE-----KGGSISPNLLKTIEESRISIIVLSKN 78 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~--------~dl~-----~G~~~~~~i~~~i~~S~~~I~vlS~~ 78 (160)
|++|.+..|. .. ...+...|.+.||+++--. ..+. ....-..++.+.|.+-.+-++|-.|+
T Consensus 3 vl~s~~~~~k-~~-~~~~~~~l~~~G~~l~aT~gT~~~l~~~gi~~~~v~~~~~~~~~i~~~i~~~~id~vIn~~~ 76 (110)
T cd01424 3 VFISVADRDK-PE-AVEIAKRLAELGFKLVATEGTAKYLQEAGIPVEVVNKVSEGRPNIVDLIKNGEIQLVINTPS 76 (110)
T ss_pred EEEEEEcCcH-hH-HHHHHHHHHHCCCEEEEchHHHHHHHHcCCeEEEEeecCCCchhHHHHHHcCCeEEEEECCC
Confidence 7899888774 23 4467788888888886421 1111 00001245667777767666666554
No 55
>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=34.44 E-value=2.3e+02 Score=22.66 Aligned_cols=64 Identities=6% Similarity=0.030 Sum_probs=34.7
Q ss_pred cEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCC
Q 031401 15 DAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNY 79 (160)
Q Consensus 15 DVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~ 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 3555554333234456667778888888876433 455554323344445665555555554433
No 56
>PRK14938 Ser-tRNA(Thr) hydrolase; Provisional
Probab=34.35 E-value=1.8e+02 Score=24.69 Aligned_cols=61 Identities=18% Similarity=0.141 Sum_probs=40.6
Q ss_pred CcccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeec
Q 031401 12 GEYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSK 77 (160)
Q Consensus 12 ~~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~ 77 (160)
..++|+|..-+++. ...+..|...|++.|+++.+|.+ +..+...+..+-+.--..++++.+
T Consensus 273 AP~qV~IIpl~eel-~e~AlkLA~eLR~aGIrVeiDl~----srSLgKQiK~AdK~GaPfvIIIGe 333 (387)
T PRK14938 273 NPIQVRILPVKKDF-LDFSIQVAERLRKEGIRVNVDDL----DDSLGNKIRRAGTEWIPFVIIIGE 333 (387)
T ss_pred CcceEEEEEeChHH-HHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEECc
Confidence 45788776665543 34577899999999999999864 345666666665544444555543
No 57
>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=33.86 E-value=63 Score=24.46 Aligned_cols=64 Identities=16% Similarity=0.036 Sum_probs=39.3
Q ss_pred CCcccEEEecccCCC-----chhHHHHHHHHHHcCCceEEeeCCCC-CCCCCchHHHHHHHHhcceEEEEeecC
Q 031401 11 HGEYDAFLSFRGEDT-----RKRFIGHLYTALNNKGIYVFRDDKQL-EKGGSISPNLLKTIEESRISIIVLSKN 78 (160)
Q Consensus 11 ~~~yDVFISy~~~D~-----~~~fv~~L~~~L~~~g~~v~~d~~dl-~~G~~~~~~i~~~i~~S~~~I~vlS~~ 78 (160)
-..++|+|---..+. -...+..|...|...|+++-+|.++- .+|..+ ..+-..---.++++-++
T Consensus 8 iAP~qVvIipi~~~~~~~~~~~~~a~~i~~~Lr~~Girv~~D~r~~~s~g~K~----~~ae~~GvP~~I~IG~~ 77 (202)
T cd00862 8 VAPIQVVIVPIGIKDEKREEVLEAADELAERLKAAGIRVHVDDRDNYTPGWKF----NDWELKGVPLRIEIGPR 77 (202)
T ss_pred hcCceEEEEEecCCccchHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHhHHH----HHHHhCCCCEEEEECcc
Confidence 345778776543221 13457889999999999999998765 666544 33322222344555554
No 58
>COG2130 Putative NADP-dependent oxidoreductases [General function prediction only]
Probab=33.24 E-value=96 Score=25.67 Aligned_cols=61 Identities=28% Similarity=0.462 Sum_probs=39.2
Q ss_pred cccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHH-hcceEEEEeecCCcCC
Q 031401 13 EYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIE-ESRISIIVLSKNYASS 82 (160)
Q Consensus 13 ~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~-~S~~~I~vlS~~~~~S 82 (160)
.||+-|.|..+| |...|.++ .=+||.+++|. .|..+.+.....+. .+|+.++=.=..|...
T Consensus 196 GfD~~idyk~~d----~~~~L~~a-~P~GIDvyfeN----VGg~v~DAv~~~ln~~aRi~~CG~IS~YN~~ 257 (340)
T COG2130 196 GFDAGIDYKAED----FAQALKEA-CPKGIDVYFEN----VGGEVLDAVLPLLNLFARIPVCGAISQYNAP 257 (340)
T ss_pred CCceeeecCccc----HHHHHHHH-CCCCeEEEEEc----CCchHHHHHHHhhccccceeeeeehhhcCCC
Confidence 488888887775 33333222 22699999996 67777787777666 4555555454555543
No 59
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=32.98 E-value=2.7e+02 Score=22.70 Aligned_cols=71 Identities=11% Similarity=0.055 Sum_probs=42.4
Q ss_pred cEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCcCChhHH
Q 031401 15 DAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYASSTWCL 86 (160)
Q Consensus 15 DVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S~wc~ 86 (160)
-|+|-|....-...+.+.+.+.|+..|..+-. .....+++.-...+...|..+..-++++........-+.
T Consensus 150 ~v~ii~~~~~yg~~~~~~~~~~l~~~G~~~~~-~~~~~~~~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~ 220 (366)
T COG0683 150 RVAIIGDDYAYGEGLADAFKAALKALGGEVVV-EEVYAPGDTDFSALVAKIKAAGPDAVLVGGYGPDAALFL 220 (366)
T ss_pred EEEEEeCCCCcchhHHHHHHHHHHhCCCeEEE-EEeeCCCCCChHHHHHHHHhcCCCEEEECCCCccchHHH
Confidence 45565555544566677788888888886333 224555554355666666666666666665555443333
No 60
>KOG1136 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]
Probab=32.61 E-value=62 Score=27.22 Aligned_cols=51 Identities=24% Similarity=0.484 Sum_probs=36.1
Q ss_pred HHHhcceEEEEeecCCc----CChhHHH-HHHHHHH-H-hhcCCcceeEEeecCchhh
Q 031401 64 TIEESRISIIVLSKNYA----SSTWCLD-ELLKIVE-C-KNREDQIFPIFYEVEPTVV 114 (160)
Q Consensus 64 ~i~~S~~~I~vlS~~~~----~S~wc~~-El~~~~~-~-~~~~~~IiPI~~~~~p~~v 114 (160)
.|+.+|-.++|--..|+ .|..|++ |+..+.+ | ...++.+||||--....++
T Consensus 191 ~id~~rpdlLIsESTYattiRdskr~rERdFLk~VhecVa~GGkvlIPvFALGRAQEl 248 (501)
T KOG1136|consen 191 WIDKCRPDLLISESTYATTIRDSKRCRERDFLKKVHECVARGGKVLIPVFALGRAQEL 248 (501)
T ss_pred hhccccCceEEeeccceeeeccccchhHHHHHHHHHHHHhcCCeEEEEeeecchHHHH
Confidence 46778877777777777 4778876 6665554 5 7889999999965444444
No 61
>cd01243 PH_MRCK MRCK (myotonic dystrophy-related Cdc42-binding kinase) pleckstrin homology (PH) domain. MRCK (myotonic dystrophy-related Cdc42-binding kinase) pleckstrin homology (PH) domain. MRCK consists of a serine/threonine kinase domain, a cysteine rich (C1) region, a PH domain and a p21 binding motif. It has been shown to promote cytoskeletal reorganization, which affects many biological processes. The MRCK PH domain is responsible for its targeting to cell to cell junctions. 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=32.37 E-value=37 Score=23.93 Aligned_cols=18 Identities=33% Similarity=0.425 Sum_probs=14.7
Q ss_pred CHHHHHHHHHHHHHhhcc
Q 031401 135 NIEKVQKWRYALKVVANI 152 (160)
Q Consensus 135 ~~~~~~~w~~al~~~~~~ 152 (160)
++...+||..||.++..+
T Consensus 104 s~~eK~kWV~aL~~l~~~ 121 (122)
T cd01243 104 TEEEKSKWVGALSELHKI 121 (122)
T ss_pred CchHHHHHHHHHHHHHhh
Confidence 357789999999998765
No 62
>PF01915 Glyco_hydro_3_C: Glycosyl hydrolase family 3 C-terminal domain; InterPro: IPR002772 Glycoside hydrolase family 3 GH3 from CAZY comprises enzymes with a number of known activities; beta-glucosidase (3.2.1.21 from EC); beta-xylosidase (3.2.1.37 from EC); N-acetyl beta-glucosaminidase (3.2.1.52 from EC); glucan beta-1,3-glucosidase (3.2.1.58 from EC); cellodextrinase(3.2.1.74 from EC); exo-1,3-1,4-glucanase (3.2.1 from EC). These enzymes are two-domain globular proteins that are N-glycosylated at three sites []. This domain is often C-terminal to the glycoside hydrolase family 3, N-terminal domain IPR001764 from INTERPRO.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3LK6_D 3NVD_B 3BMX_B 3ABZ_D 3AC0_D 2X40_A 2X41_A 2X42_A 1J8V_A 1IEX_A ....
Probab=32.27 E-value=2.2e+02 Score=21.47 Aligned_cols=84 Identities=13% Similarity=0.183 Sum_probs=52.0
Q ss_pred hHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCC----------------cCChhHHHHHHH
Q 031401 28 RFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNY----------------ASSTWCLDELLK 91 (160)
Q Consensus 28 ~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~----------------~~S~wc~~El~~ 91 (160)
.+.+.|...+...++.+........ -.....+..+...+++.+|+++.+.+ +.-.++..|+..
T Consensus 47 t~~~~l~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~aD~vIv~~~~~~~e~~~~~~~~~~~~~~~~l~~~q~~li~ 125 (227)
T PF01915_consen 47 TPLDALKQRFGNAGVVVPEGGDAVD-DDEGIDEAVAAAKEADVVIVFVGRPSGEGNDNNTEGESDRSDLALPANQQELIK 125 (227)
T ss_dssp HHHHHHHHHHHTTSEEEECCCCCCC-CCSCHHHHHHHHHCSSEEEEEEETTSBCCCSS-EETTGSCSSTBCCCHHHHHHH
T ss_pred cHHhhhccccCCCceEEeeeccccc-cccchHHHHHHhhcCCEEEEeccccccccccccccccCCcccccchhhHHHHHH
Confidence 5567788888877777654332222 23344677888999999999988433 333467777777
Q ss_pred HHHHhhcCCcceeEEeecCchhh
Q 031401 92 IVECKNREDQIFPIFYEVEPTVV 114 (160)
Q Consensus 92 ~~~~~~~~~~IiPI~~~~~p~~v 114 (160)
.+.. .+..+|.|+....|-++
T Consensus 126 ~v~~--~~~~~Ivvv~~~~P~~l 146 (227)
T PF01915_consen 126 AVAA--AGKKVIVVVNSGNPYDL 146 (227)
T ss_dssp HHHH--HHSCEEEEEE-SSGGCG
T ss_pred HHHH--hcCCeEEEEecCCcccc
Confidence 6654 22455555555555555
No 63
>KOG1954 consensus Endocytosis/signaling protein EHD1 [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=31.34 E-value=1.9e+02 Score=24.84 Aligned_cols=75 Identities=15% Similarity=0.241 Sum_probs=51.7
Q ss_pred CCCCCCCchHHHHHHHHhcceEEEEeecCCcCChhHHHHHHHHHHH-hhcCCcceeEEeecCchhhhcccchHHHHHHH
Q 031401 50 QLEKGGSISPNLLKTIEESRISIIVLSKNYASSTWCLDELLKIVEC-KNREDQIFPIFYEVEPTVVRKQTASFGEAFAK 127 (160)
Q Consensus 50 dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~~~~-~~~~~~IiPI~~~~~p~~v~~~~~~~~~~~~~ 127 (160)
.+..|-.+...+.=-+++++++|+++-++-+. ...|+..++.. +...+.|=.|+-+.+.-+-.+.++.||...=.
T Consensus 164 risR~ydF~~v~~WFaeR~D~IiLlfD~hKLD---IsdEf~~vi~aLkG~EdkiRVVLNKADqVdtqqLmRVyGALmWs 239 (532)
T KOG1954|consen 164 RISRGYDFTGVLEWFAERVDRIILLFDAHKLD---ISDEFKRVIDALKGHEDKIRVVLNKADQVDTQQLMRVYGALMWS 239 (532)
T ss_pred cccccCChHHHHHHHHHhccEEEEEechhhcc---ccHHHHHHHHHhhCCcceeEEEeccccccCHHHHHHHHHHHHHh
Confidence 35566777777777899999999999999776 45688888888 65555655555444443444556677754433
No 64
>COG1180 PflA Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=30.79 E-value=1.1e+02 Score=24.13 Aligned_cols=39 Identities=18% Similarity=0.122 Sum_probs=27.7
Q ss_pred EEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCC
Q 031401 16 AFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKG 54 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G 54 (160)
|-+|+...-....|+..+..+.+++|+++++|-.-+.+.
T Consensus 87 vt~SGGEP~~q~e~~~~~~~~ake~Gl~~~l~TnG~~~~ 125 (260)
T COG1180 87 VTFSGGEPTLQAEFALDLLRAAKERGLHVALDTNGFLPP 125 (260)
T ss_pred EEEECCcchhhHHHHHHHHHHHHHCCCcEEEEcCCCCCH
Confidence 444444444457788889999999999999997654433
No 65
>PRK14799 thrS threonyl-tRNA synthetase; Provisional
Probab=30.12 E-value=2.1e+02 Score=25.42 Aligned_cols=60 Identities=10% Similarity=0.180 Sum_probs=39.5
Q ss_pred cccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeec
Q 031401 13 EYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSK 77 (160)
Q Consensus 13 ~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~ 77 (160)
..+|+|..-+++. ...+..|...|++.|+++-+|.+ +..+...+..|-..--..++|+.+
T Consensus 438 P~qV~Iipi~e~~-~~~A~~Ia~~LR~~GirVelD~~----~~~lgkkir~A~k~gip~viIIG~ 497 (545)
T PRK14799 438 SVQVRVLPITDEV-NEYAEKVLNDMRKRRIRAEIDYA----GETLSKRIKNAYDQGVPYILIVGK 497 (545)
T ss_pred CceEEEEEcCHHH-HHHHHHHHHHHHhCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEECh
Confidence 4688877655432 35688899999999999999874 344556666654433334555553
No 66
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=30.04 E-value=2e+02 Score=25.61 Aligned_cols=61 Identities=11% Similarity=0.099 Sum_probs=41.3
Q ss_pred cccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecC
Q 031401 13 EYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKN 78 (160)
Q Consensus 13 ~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~ 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 35688899999999999999874 3445556666655444456666653
No 67
>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=29.81 E-value=93 Score=23.34 Aligned_cols=65 Identities=14% Similarity=0.247 Sum_probs=44.7
Q ss_pred hhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCcCC--h------hHHHHHHHHHHH
Q 031401 27 KRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYASS--T------WCLDELLKIVEC 95 (160)
Q Consensus 27 ~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S--~------wc~~El~~~~~~ 95 (160)
......|..+.+.+|+-+|.|.. .+|..+...|.+.+-++... .+++.+... . =..+.+..|++.
T Consensus 35 ~~~i~~i~~~~~~rgVIIfTDpD--~~GekIRk~i~~~vp~~kha--fi~~~~a~~~~~~iGVE~As~e~I~~AL~~ 107 (174)
T TIGR00334 35 DETINLIKKAQKKQGVIILTDPD--FPGEKIRKKIEQHLPGYENC--FIPKHLAKPNKKKIGVEEASVEAIIAALEN 107 (174)
T ss_pred HHHHHHHHHHhhcCCEEEEeCCC--CchHHHHHHHHHHCCCCeEE--eeeHHhcCcCCCCcccCCCCHHHHHHHHHH
Confidence 34466788888889999999984 48999988888888877754 445444421 1 124566666664
No 68
>PRK03991 threonyl-tRNA synthetase; Validated
Probab=29.45 E-value=1.3e+02 Score=27.03 Aligned_cols=62 Identities=16% Similarity=0.136 Sum_probs=39.5
Q ss_pred CcccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecC
Q 031401 12 GEYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKN 78 (160)
Q Consensus 12 ~~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~ 78 (160)
..++|+|.--.++. ...+..|...|+..|++|.+|.++-..| ..+..+-..---.++|+.++
T Consensus 498 AP~qV~IIpi~e~~-~~~A~eIa~~Lr~~GirV~lDdr~~slg----kKir~A~~~GiP~iIVIG~k 559 (613)
T PRK03991 498 SPTQVRVIPVSERH-LDYAEEVADKLEAAGIRVDVDDRDESLG----KKIRDAGKEWIPYVVVIGDK 559 (613)
T ss_pred cCceEEEEEeCHHH-HHHHHHHHHHHHhCCCEEEEECCCCCHH----HHHHHHHHcCCCEEEEECcc
Confidence 34788776554332 4568889999999999999998654444 45555533333344555443
No 69
>KOG0409 consensus Predicted dehydrogenase [General function prediction only]
Probab=29.35 E-value=93 Score=25.66 Aligned_cols=48 Identities=17% Similarity=0.261 Sum_probs=37.7
Q ss_pred HHHHHHHHcCCceEEeeCCCCC-------CCCCchHHHHHHHHhcceEEEEeecC
Q 031401 31 GHLYTALNNKGIYVFRDDKQLE-------KGGSISPNLLKTIEESRISIIVLSKN 78 (160)
Q Consensus 31 ~~L~~~L~~~g~~v~~d~~dl~-------~G~~~~~~i~~~i~~S~~~I~vlS~~ 78 (160)
..+...|-+.|++|...+++.. .|....+.=.+-.+.|+++|.+++..
T Consensus 48 ~~M~~nLik~G~kVtV~dr~~~k~~~f~~~Ga~v~~sPaeVae~sDvvitmv~~~ 102 (327)
T KOG0409|consen 48 SAMVSNLIKAGYKVTVYDRTKDKCKEFQEAGARVANSPAEVAEDSDVVITMVPNP 102 (327)
T ss_pred HHHHHHHHHcCCEEEEEeCcHHHHHHHHHhchhhhCCHHHHHhhcCEEEEEcCCh
Confidence 3577888889999999888765 36666666667889999999998854
No 70
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=29.12 E-value=2.2e+02 Score=25.07 Aligned_cols=60 Identities=10% Similarity=0.155 Sum_probs=39.5
Q ss_pred cccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeec
Q 031401 13 EYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSK 77 (160)
Q Consensus 13 ~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~ 77 (160)
.++|+|.--+++. ...+..|...|.+.|+++-+|.++ ..+...+..|-..---.++|+.+
T Consensus 476 p~~v~Ii~~~~~~-~~~a~~i~~~Lr~~gi~v~~d~~~----~~l~kk~~~A~~~g~p~~iivG~ 535 (575)
T PRK12305 476 PVQVVIIPVADAH-NEYAEEVAKKLRAAGIRVEVDTSN----ERLNKKIRNAQKQKIPYMLVVGD 535 (575)
T ss_pred CccEEEEEeChHH-HHHHHHHHHHHHHCCCEEEEECCC----CCHHHHHHHHHhcCCCEEEEEec
Confidence 4688887554432 355788999999999999998753 34555666665543335555554
No 71
>PRK15057 UDP-glucose 6-dehydrogenase; Provisional
Probab=28.70 E-value=1.3e+02 Score=25.20 Aligned_cols=51 Identities=14% Similarity=0.246 Sum_probs=36.0
Q ss_pred CCCchhHHHHHHHHHHcCCceEEeeCCCCCC----CCCchHHHHHHHHhcceEEE
Q 031401 23 EDTRKRFIGHLYTALNNKGIYVFRDDKQLEK----GGSISPNLLKTIEESRISII 73 (160)
Q Consensus 23 ~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~----G~~~~~~i~~~i~~S~~~I~ 73 (160)
.|.|.+-+-.|.+.|..+|..|..++--+.. +..+.++...+++.++.+|+
T Consensus 311 ~D~R~Sp~~~i~~~L~~~G~~v~~~DP~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (388)
T PRK15057 311 DNFRASSIQGIMKRIKAKGVEVIIYEPVMKEDSFFNSRLERDLATFKQQADVIIS 365 (388)
T ss_pred CccccChHHHHHHHHHhCCCEEEEECCCCCchhhcCCeeeCCHHHHHHhCCEEEE
Confidence 4666666778999999999888766533322 34466777788888886654
No 72
>COG2084 MmsB 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]
Probab=28.68 E-value=1e+02 Score=24.97 Aligned_cols=46 Identities=20% Similarity=0.291 Sum_probs=37.6
Q ss_pred HHHHHHcCCceEEeeCCCCCC--------CCCchHHHHHHHHhcceEEEEeecC
Q 031401 33 LYTALNNKGIYVFRDDKQLEK--------GGSISPNLLKTIEESRISIIVLSKN 78 (160)
Q Consensus 33 L~~~L~~~g~~v~~d~~dl~~--------G~~~~~~i~~~i~~S~~~I~vlS~~ 78 (160)
+..+|.+.|+.+...+++..+ |........+++..++++|.+++..
T Consensus 15 mA~~L~~aG~~v~v~~r~~~ka~~~~~~~Ga~~a~s~~eaa~~aDvVitmv~~~ 68 (286)
T COG2084 15 MAANLLKAGHEVTVYNRTPEKAAELLAAAGATVAASPAEAAAEADVVITMLPDD 68 (286)
T ss_pred HHHHHHHCCCEEEEEeCChhhhhHHHHHcCCcccCCHHHHHHhCCEEEEecCCH
Confidence 678888999999888777554 6666677788999999999998865
No 73
>COG3613 Nucleoside 2-deoxyribosyltransferase [Nucleotide transport and metabolism]
Probab=28.61 E-value=2.5e+02 Score=21.00 Aligned_cols=77 Identities=14% Similarity=0.106 Sum_probs=50.4
Q ss_pred HHHHHHHHHHcCCceEEee--CCC----CCCC---CCchHHHHHHHHhcceEEEEeecCC-cCChhHHHHHHHHHHHhhc
Q 031401 29 FIGHLYTALNNKGIYVFRD--DKQ----LEKG---GSISPNLLKTIEESRISIIVLSKNY-ASSTWCLDELLKIVECKNR 98 (160)
Q Consensus 29 fv~~L~~~L~~~g~~v~~d--~~d----l~~G---~~~~~~i~~~i~~S~~~I~vlS~~~-~~S~wc~~El~~~~~~~~~ 98 (160)
-.+.|...|.+.|+.++.= .+. ..|+ ..+.+.-.+.|++|+++|.++.+-= ...+-..+|+..+.. .
T Consensus 21 ~~d~lkall~~~gf~~~~P~d~~~~~~~~~p~~~a~~i~e~d~~~i~~aD~vla~ld~fr~~~DsGTa~E~GYa~A---l 97 (172)
T COG3613 21 LRDELKALLLEAGFEVLSPFDEAEPIAETGPNETAEKIYEADIKLIDQADIVLANLDPFRPDPDSGTAFELGYAIA---L 97 (172)
T ss_pred HHHHHHHHHHHcCCeeeCcchhccCccccCccHHHHHHHHHHHHHHhhcCEEEEecCCCCCCCCCcchHHHHHHHH---c
Confidence 3667888888889888653 222 2221 1233344568999999999998754 223456789988887 4
Q ss_pred CCcceeEEee
Q 031401 99 EDQIFPIFYE 108 (160)
Q Consensus 99 ~~~IiPI~~~ 108 (160)
++.+++.+-+
T Consensus 98 gKPv~~~~~d 107 (172)
T COG3613 98 GKPVYAYRKD 107 (172)
T ss_pred CCceEEEeec
Confidence 6677776543
No 74
>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=27.80 E-value=95 Score=19.65 Aligned_cols=36 Identities=19% Similarity=0.133 Sum_probs=27.1
Q ss_pred CcccEEEecccCCCchhHHHHHHHHHHcCCceEEeeC
Q 031401 12 GEYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDD 48 (160)
Q Consensus 12 ~~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~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 467789998765543 346789999999999998754
No 75
>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=27.66 E-value=2e+02 Score=19.86 Aligned_cols=18 Identities=22% Similarity=0.462 Sum_probs=9.6
Q ss_pred HHHHHHHhcceEEEEeec
Q 031401 60 NLLKTIEESRISIIVLSK 77 (160)
Q Consensus 60 ~i~~~i~~S~~~I~vlS~ 77 (160)
++.+++++++.+++|+..
T Consensus 4 ~~~~~i~~aD~vl~ViD~ 21 (141)
T cd01857 4 QLWRVVERSDIVVQIVDA 21 (141)
T ss_pred HHHHHHhhCCEEEEEEEc
Confidence 445555555555555553
No 76
>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=27.39 E-value=39 Score=29.96 Aligned_cols=48 Identities=23% Similarity=0.424 Sum_probs=33.4
Q ss_pred CcccEEEecc-cCC-CchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchH
Q 031401 12 GEYDAFLSFR-GED-TRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISP 59 (160)
Q Consensus 12 ~~yDVFISy~-~~D-~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~ 59 (160)
..|+|-|.-- .+| .....+..|+..|+..|+.+.+|+|+-.+|..+.+
T Consensus 472 AP~qV~Iip~~~~~~~~~~~a~~l~~~L~~~gi~v~~DDr~~~~G~K~~d 521 (568)
T TIGR00409 472 APYDVVIVVMNMKDEEQQQLAEELYSELLAQGVDVLLDDRNERAGVKFAD 521 (568)
T ss_pred CCeEEEEEEcCCChHHHHHHHHHHHHHHHhCCCEEEEECCCCCHHHHHHh
Confidence 3467755432 222 22456888999999999999999998777765543
No 77
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=27.16 E-value=2.6e+02 Score=25.08 Aligned_cols=64 Identities=11% Similarity=0.153 Sum_probs=42.5
Q ss_pred CCcccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecC
Q 031401 11 HGEYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKN 78 (160)
Q Consensus 11 ~~~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~ 78 (160)
....+|+|..-+++.....+..|...|++.|+++-+|.+ +.++...+..|-..--..++++.++
T Consensus 539 ~ap~qV~Ii~~~~~~~~~~a~~la~~LR~~Gi~veid~~----~~sl~kq~k~A~k~g~~~~iiiG~~ 602 (639)
T PRK12444 539 LAPVQVKVIPVSNAVHVQYADEVADKLAQAGIRVERDER----DEKLGYKIREAQMQKIPYVLVIGDK 602 (639)
T ss_pred cCCceEEEEEcccHHHHHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEEcch
Confidence 346788877655411235678899999999999999864 3455566666655444456666553
No 78
>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=26.67 E-value=2.4e+02 Score=23.21 Aligned_cols=42 Identities=10% Similarity=0.049 Sum_probs=21.7
Q ss_pred HHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEE
Q 031401 30 IGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISI 72 (160)
Q Consensus 30 v~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I 72 (160)
...|...|+..|+.+..... ...++.-..++.+.|+++...|
T Consensus 157 ~~~l~~~~~~~gi~v~~~~~-~~~~~~d~~~~l~~ik~~~rvi 198 (387)
T cd06386 157 LEGVHHVFQEEGYHMSIYPF-DETKDLDLDEIIRAIQASERVV 198 (387)
T ss_pred HHHHHHHHHhcCceEEEEec-CCCCcccHHHHHHHHHhcCcEE
Confidence 55677777777877665432 1223322344455554444333
No 79
>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=26.50 E-value=3.2e+02 Score=21.51 Aligned_cols=78 Identities=10% Similarity=0.026 Sum_probs=50.2
Q ss_pred hhHHHHHHHHHHcCCceEEe---eCCCCCCCCCchHHHHHHHHhcceEEEEeecCC-cCChhHHHHHHHHHHH--hhcCC
Q 031401 27 KRFIGHLYTALNNKGIYVFR---DDKQLEKGGSISPNLLKTIEESRISIIVLSKNY-ASSTWCLDELLKIVEC--KNRED 100 (160)
Q Consensus 27 ~~fv~~L~~~L~~~g~~v~~---d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~-~~S~wc~~El~~~~~~--~~~~~ 100 (160)
.+++..|...|...|+.+.. ..+.+..|.-+. +.-.-.+.++-++.+|-+. ..+..-..++-.++.+ +..++
T Consensus 87 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vP--L~~l~p~~~ipvV~vs~~~~~~~~~~~~~lG~al~~~l~~~~~ 164 (268)
T cd07371 87 VELAEACVEEGRKAGLVTRMMRYPRFPIDTGTITA--LTLMRPGTDIPPVVISANNLYLSGEETEGEMDLAGKATRDAGK 164 (268)
T ss_pred HHHHHHHHHHHHHCCCcEEEecCCCCCCCchhHHH--HHHhcCCCCCCeEEEEecCcCCCHHHHHHHHHHHHHHHHHcCC
Confidence 47899999999999998875 233345554332 2222234566667776333 3567777889888865 55566
Q ss_pred cceeEE
Q 031401 101 QIFPIF 106 (160)
Q Consensus 101 ~IiPI~ 106 (160)
+|+.|-
T Consensus 165 rv~iIg 170 (268)
T cd07371 165 RVAVLG 170 (268)
T ss_pred cEEEEE
Confidence 777664
No 80
>cd00532 MGS-like MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site.
Probab=26.42 E-value=1.9e+02 Score=19.39 Aligned_cols=61 Identities=18% Similarity=0.297 Sum_probs=36.6
Q ss_pred EEEecccCCCchhHHHHHHHHHHcCCceEEeeC--------CCCC-----CCCC-chHHHHHHHHh-cceEEEEeecC
Q 031401 16 AFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDD--------KQLE-----KGGS-ISPNLLKTIEE-SRISIIVLSKN 78 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~--------~dl~-----~G~~-~~~~i~~~i~~-S~~~I~vlS~~ 78 (160)
||||-+..|.. . ...+...|...|+.++--. ..+. .+.. -.+++...|.+ -++-++|..|+
T Consensus 2 i~isv~d~~K~-~-~~~~a~~l~~~G~~i~AT~gTa~~L~~~Gi~~~~v~~~~~~g~~~i~~~i~~~g~idlVIn~~~ 77 (112)
T cd00532 2 VFLSVSDHVKA-M-LVDLAPKLSSDGFPLFATGGTSRVLADAGIPVRAVSKRHEDGEPTVDAAIAEKGKFDVVINLRD 77 (112)
T ss_pred EEEEEEcccHH-H-HHHHHHHHHHCCCEEEECcHHHHHHHHcCCceEEEEecCCCCCcHHHHHHhCCCCEEEEEEcCC
Confidence 68888877642 3 4467778887788775321 1110 1100 12567777877 78777777665
No 81
>KOG1610 consensus Corticosteroid 11-beta-dehydrogenase and related short chain-type dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism; General function prediction only]
Probab=26.30 E-value=88 Score=25.82 Aligned_cols=31 Identities=29% Similarity=0.376 Sum_probs=25.6
Q ss_pred ccEEEecccCCCchhHHHHHHHHHHcCCceEEeeC
Q 031401 14 YDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDD 48 (160)
Q Consensus 14 yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~ 48 (160)
.-||| .+.|+ +|-..|...|.++|++||---
T Consensus 30 k~VlI--TGCDS--GfG~~LA~~L~~~Gf~V~Agc 60 (322)
T KOG1610|consen 30 KAVLI--TGCDS--GFGRLLAKKLDKKGFRVFAGC 60 (322)
T ss_pred cEEEE--ecCCc--HHHHHHHHHHHhcCCEEEEEe
Confidence 45788 58886 788999999999999997654
No 82
>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=26.28 E-value=3.4e+02 Score=21.66 Aligned_cols=31 Identities=16% Similarity=0.119 Sum_probs=15.5
Q ss_pred cEEEecccCCCchhHHHHHHHHHHcCCceEE
Q 031401 15 DAFLSFRGEDTRKRFIGHLYTALNNKGIYVF 45 (160)
Q Consensus 15 DVFISy~~~D~~~~fv~~L~~~L~~~g~~v~ 45 (160)
.|.|-|...+-....+..+...|++.|+.+-
T Consensus 140 ~v~ii~~~~~~g~~~~~~~~~~~~~~G~~v~ 170 (347)
T cd06335 140 KVALLLDNTGWGRSNRKDLTAALAARGLKPV 170 (347)
T ss_pred eEEEEeccCchhhhHHHHHHHHHHHcCCeeE
Confidence 3444443332223445566666666666654
No 83
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=25.86 E-value=98 Score=24.66 Aligned_cols=42 Identities=19% Similarity=0.288 Sum_probs=28.0
Q ss_pred HHHHHHHHHcCCceEEeeCCCCCCCCC---chHHHHHHHHhcceEEEEee
Q 031401 30 IGHLYTALNNKGIYVFRDDKQLEKGGS---ISPNLLKTIEESRISIIVLS 76 (160)
Q Consensus 30 v~~L~~~L~~~g~~v~~d~~dl~~G~~---~~~~i~~~i~~S~~~I~vlS 76 (160)
+.+|.+.|...|+.+..-. ..|++ +.+.+..++++++ ++|+|
T Consensus 23 a~~la~~L~~~G~~v~~~~---~VgD~~~~I~~~l~~a~~r~D--~vI~t 67 (255)
T COG1058 23 AAFLADELTELGVDLARIT---TVGDNPDRIVEALREASERAD--VVITT 67 (255)
T ss_pred HHHHHHHHHhcCceEEEEE---ecCCCHHHHHHHHHHHHhCCC--EEEEC
Confidence 6789999999999997653 45655 3345555565644 44555
No 84
>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases. They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.
Probab=25.77 E-value=1.5e+02 Score=19.27 Aligned_cols=45 Identities=22% Similarity=0.319 Sum_probs=25.3
Q ss_pred HHHHHhcceEEEEeecCCcCChhHHHHHHHHHHH-hhcCCcceeEEe
Q 031401 62 LKTIEESRISIIVLSKNYASSTWCLDELLKIVEC-KNREDQIFPIFY 107 (160)
Q Consensus 62 ~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~~~~-~~~~~~IiPI~~ 107 (160)
...+..++.+|+|++..-..|-.-..++...+.. +..... +||++
T Consensus 68 ~~~~~~~d~~ilv~D~s~~~s~~~~~~~~~~l~~~~~~~~~-~piil 113 (119)
T PF08477_consen 68 QFFLKKADAVILVYDLSDPESLEYLSQLLKWLKNIRKRDKN-IPIIL 113 (119)
T ss_dssp HHHHHHSCEEEEEEECCGHHHHHHHHHHHHHHHHHHHHSSC-SEEEE
T ss_pred cchhhcCcEEEEEEcCCChHHHHHHHHHHHHHHHHHccCCC-CCEEE
Confidence 3459999999999986644433333334333444 322233 66554
No 85
>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=25.61 E-value=1.6e+02 Score=23.34 Aligned_cols=109 Identities=14% Similarity=0.220 Sum_probs=62.9
Q ss_pred HHHHHHcCCceEEeeCCCCC-----CCCCchHHHHHHHHhcceEEEEeecCCcCChhHHHHHHHHHHHhhcCCcceeEEe
Q 031401 33 LYTALNNKGIYVFRDDKQLE-----KGGSISPNLLKTIEESRISIIVLSKNYASSTWCLDELLKIVECKNREDQIFPIFY 107 (160)
Q Consensus 33 L~~~L~~~g~~v~~d~~dl~-----~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~~~~~~~~~~IiPI~~ 107 (160)
.+++|... +++|.|-. .+ .+.++.+....+++.+..=-+++|-.-...+=-..++..+-+ .-. +|||.
T Consensus 133 ~R~~l~a~-v~ilaDV~-~kh~~~l~~~~~~~~~~~a~~~~~aDaviVtG~~TG~~~~~~~l~~vr~---~~~--~PVlv 205 (254)
T PF03437_consen 133 YRKRLGAD-VKILADVH-VKHSSPLATRDLEEAAKDAVERGGADAVIVTGKATGEPPDPEKLKRVRE---AVP--VPVLV 205 (254)
T ss_pred HHHHcCCC-eEEEeeec-hhhcccCCCCCHHHHHHHHHHhcCCCEEEECCcccCCCCCHHHHHHHHh---cCC--CCEEE
Confidence 44445445 88888853 22 233455566667777777677777665544333444443332 222 99998
Q ss_pred --ecCchhhhcccch-----HHHHHHHHHHhhc-cCHHHHHHHHHHHHH
Q 031401 108 --EVEPTVVRKQTAS-----FGEAFAKYEEFFR-DNIEKVQKWRYALKV 148 (160)
Q Consensus 108 --~~~p~~v~~~~~~-----~~~~~~~~~~~~~-~~~~~~~~w~~al~~ 148 (160)
+++++++.++... -|-.|++...... -+++++++.++++++
T Consensus 206 GSGvt~~Ni~~~l~~ADG~IVGS~~K~~G~~~n~VD~~Rv~~fm~~v~~ 254 (254)
T PF03437_consen 206 GSGVTPENIAEYLSYADGAIVGSYFKKDGKWENPVDPERVRRFMEAVKK 254 (254)
T ss_pred ecCCCHHHHHHHHHhCCEEEEeeeeeeCCEeCCcCCHHHHHHHHHHhhC
Confidence 4899988765321 1333443333211 257889998888753
No 86
>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=25.57 E-value=35 Score=25.33 Aligned_cols=57 Identities=23% Similarity=0.373 Sum_probs=30.5
Q ss_pred ChhHHHHHHHHHHH-hhcCCcceeEEeecCchhhhcccchHHHHHHHHHHhhccCHHHHHHHHHHHH
Q 031401 82 STWCLDELLKIVEC-KNREDQIFPIFYEVEPTVVRKQTASFGEAFAKYEEFFRDNIEKVQKWRYALK 147 (160)
Q Consensus 82 S~wc~~El~~~~~~-~~~~~~IiPI~~~~~p~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~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 46777777666654 222223355667888887654211 1111111 145678888764
No 87
>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=25.41 E-value=3.3e+02 Score=21.23 Aligned_cols=57 Identities=14% Similarity=0.155 Sum_probs=31.1
Q ss_pred EEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCC-CchHHHHHHHHhcceEEEE
Q 031401 16 AFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGG-SISPNLLKTIEESRISIIV 74 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~-~~~~~i~~~i~~S~~~I~v 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 455553 343 444445554333333
No 88
>PRK07933 thymidylate kinase; Validated
Probab=25.01 E-value=2.6e+02 Score=21.14 Aligned_cols=30 Identities=23% Similarity=0.368 Sum_probs=22.2
Q ss_pred EEecccCCCc--hhHHHHHHHHHHcCCceEEe
Q 031401 17 FLSFRGEDTR--KRFIGHLYTALNNKGIYVFR 46 (160)
Q Consensus 17 FISy~~~D~~--~~fv~~L~~~L~~~g~~v~~ 46 (160)
||.+-+-|.. ...+..|.+.|+.+|+.|..
T Consensus 2 ~IviEG~dGsGKST~~~~L~~~L~~~g~~v~~ 33 (213)
T PRK07933 2 LIAIEGVDGAGKRTLTEALRAALEARGRSVAT 33 (213)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEE
Confidence 6777666653 34577899999999988765
No 89
>PRK10628 LigB family dioxygenase; Provisional
Probab=24.60 E-value=3.4e+02 Score=21.47 Aligned_cols=75 Identities=12% Similarity=0.119 Sum_probs=52.8
Q ss_pred EecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCcCChhHHHHHHHHHHH
Q 031401 18 LSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYASSTWCLDELLKIVEC 95 (160)
Q Consensus 18 ISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~~~~ 95 (160)
|.|.-.... ..+..+...|+..|+.+--..|.+..|.-. -+...--++++=|+-+|-....+.-...++..++..
T Consensus 62 ~~Ypa~G~p-~LA~~i~~ll~~~~~~~~~~~rGlDHG~Wv--pL~~m~P~adIPVvqlSl~~~~~~~~h~~lG~aL~~ 136 (246)
T PRK10628 62 THYPAPGSP-ALAQRLVELLAPVPVTLDKEAWGFDHGSWG--VLIKMYPDADIPMVQLSIDSTKPAAWHFEMGRKLAA 136 (246)
T ss_pred ecCCCCCCH-HHHHHHHHHhhhcCcccCCcccCcccchhh--hhhhhCCCCCCCeEEeecCCCCCHHHHHHHHHHHHh
Confidence 677555443 678889999998888321123667777533 344455578888999998887788788888888886
No 90
>PF15409 PH_8: Pleckstrin homology domain
Probab=24.59 E-value=69 Score=21.22 Aligned_cols=15 Identities=33% Similarity=0.561 Sum_probs=12.5
Q ss_pred CHHHHHHHHHHHHHh
Q 031401 135 NIEKVQKWRYALKVV 149 (160)
Q Consensus 135 ~~~~~~~w~~al~~~ 149 (160)
+++..+.|..||.++
T Consensus 74 s~~~f~~Wv~aL~~a 88 (89)
T PF15409_consen 74 SQEDFQRWVSALQKA 88 (89)
T ss_pred CHHHHHHHHHHHHhc
Confidence 368899999999875
No 91
>TIGR03567 FMN_reduc_SsuE FMN reductase, SsuE family. Members of this protein family use NAD(P)H to reduce FMN and regenerate FMNH2. Members include the homodimeric, NAD(P)H-dependent enzyme SsuE from Escherichia coli, which serves as a partner to an FMNH2-dependent alkanesulfonate monooxygenase. It is induced by sulfate starvation. The NADH-dependent enzyme MsuE from Pseudomonas aeruginosa is outside the scope of this model (see model TIGR03566).
Probab=24.51 E-value=2.8e+02 Score=20.04 Aligned_cols=78 Identities=17% Similarity=0.263 Sum_probs=44.4
Q ss_pred hHHHHHHHHHHcCCceE-EeeCCCCCCC--------CCchHHHHHHHHhcceEEEEeecCCcCChhHHHHHHHHHHH---
Q 031401 28 RFIGHLYTALNNKGIYV-FRDDKQLEKG--------GSISPNLLKTIEESRISIIVLSKNYASSTWCLDELLKIVEC--- 95 (160)
Q Consensus 28 ~fv~~L~~~L~~~g~~v-~~d~~dl~~G--------~~~~~~i~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~~~~--- 95 (160)
..+..+...|+..|..+ .+|-.+++.. ..-...+.+.|.+++ .|++.||.|..|- .--+..++++
T Consensus 17 ~l~~~~~~~l~~~~~~~~~idl~~l~~~~~~~~~~~~~~~~~l~~~i~~AD-~iI~~sP~Y~~si--p~~LK~~iD~~~~ 93 (171)
T TIGR03567 17 ALLRHVREALQEQGVEVDHLSVRDLPAEDLLFARFDSPAIKAATAQVAQAD-GVVVATPVYKASY--SGVLKALLDLLPQ 93 (171)
T ss_pred HHHHHHHHHHHHCCCeEEEEEecCCChHHhhhcCCCCHHHHHHHHHHHHCC-EEEEECCcccCCC--CHHHHHHHHhCCh
Confidence 34566777777767543 4444444321 112246667788888 6678999998774 2234444443
Q ss_pred -hhcCCcceeEEee
Q 031401 96 -KNREDQIFPIFYE 108 (160)
Q Consensus 96 -~~~~~~IiPI~~~ 108 (160)
...++.+.++-..
T Consensus 94 ~~l~~K~v~~~~~g 107 (171)
T TIGR03567 94 RALRGKVVLPIATG 107 (171)
T ss_pred hhhCCCEEEEEEcC
Confidence 2345566665443
No 92
>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=24.48 E-value=2.1e+02 Score=19.12 Aligned_cols=29 Identities=10% Similarity=0.031 Sum_probs=20.2
Q ss_pred CCC-CchHHHHHHHHhcceEEEEeecCCcC
Q 031401 53 KGG-SISPNLLKTIEESRISIIVLSKNYAS 81 (160)
Q Consensus 53 ~G~-~~~~~i~~~i~~S~~~I~vlS~~~~~ 81 (160)
||. .+.......+.+++.+|++++..-..
T Consensus 57 ~g~~~~~~~~~~~~~~~d~ii~v~d~~~~~ 86 (159)
T cd00154 57 AGQERFRSITPSYYRGAHGAILVYDITNRE 86 (159)
T ss_pred CChHHHHHHHHHHhcCCCEEEEEEECCCHH
Confidence 443 34445567788999999999986533
No 93
>PF08132 AdoMetDC_leader: S-adenosyl-l-methionine decarboxylase leader peptide; InterPro: IPR012511 This family consists of the S-adenosyl-l-methionine decarboxylase (AdoMetDC) leader peptides. AdoMetDC is a key regulatory enzyme in the biosynthesis of polyamines. All expressed plant AdoMetDC mRNA 5, leader sequences contain a highly conserved pair of overlapping upstream ORFs (uORFs) that overlap by one base. Sequences of the small uORFs are highly conserved between monocot, dicot and gymnosperm AdoMetDC mRNA species, suggesting a translational regulatory mechanism [].
Probab=24.41 E-value=70 Score=18.81 Aligned_cols=24 Identities=33% Similarity=0.314 Sum_probs=18.6
Q ss_pred CCCCCCCCCCcccEEEecccCCCc
Q 031401 3 STSFQNVSHGEYDAFLSFRGEDTR 26 (160)
Q Consensus 3 s~sss~~~~~~yDVFISy~~~D~~ 26 (160)
|+|+++...-.|.+=+.|+-+|.+
T Consensus 10 ssssss~~s~~yeaPLgYsIEDvR 33 (54)
T PF08132_consen 10 SSSSSSSNSLFYEAPLGYSIEDVR 33 (54)
T ss_pred ccccccccceEEeccccceeeecc
Confidence 456666667889999999988875
No 94
>PRK14495 putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/unknown domain fusion protein; Provisional
Probab=24.27 E-value=3.1e+02 Score=23.81 Aligned_cols=29 Identities=14% Similarity=0.366 Sum_probs=22.1
Q ss_pred EEecccCCCchhHHHHHHHHHHcCCceEEe
Q 031401 17 FLSFRGEDTRKRFIGHLYTALNNKGIYVFR 46 (160)
Q Consensus 17 FISy~~~D~~~~fv~~L~~~L~~~g~~v~~ 46 (160)
++.|++... -.++..|.+.|..+|++|..
T Consensus 6 IvG~sgSGK-TTLiekLI~~L~~rG~rVav 34 (452)
T PRK14495 6 IIGWKDAGK-TGLVERLVAAIAARGFSVST 34 (452)
T ss_pred EEecCCCCH-HHHHHHHHHHHHhCCCeEEE
Confidence 455544332 36789999999999999988
No 95
>COG0431 Predicted flavoprotein [General function prediction only]
Probab=24.14 E-value=3e+02 Score=20.29 Aligned_cols=56 Identities=20% Similarity=0.223 Sum_probs=33.8
Q ss_pred hhHHHHHHHHHHcCC-ceEEeeCCCCCCC------CCc---hHHHHHHHHhcceEEEEeecCCcCCh
Q 031401 27 KRFIGHLYTALNNKG-IYVFRDDKQLEKG------GSI---SPNLLKTIEESRISIIVLSKNYASST 83 (160)
Q Consensus 27 ~~fv~~L~~~L~~~g-~~v~~d~~dl~~G------~~~---~~~i~~~i~~S~~~I~vlS~~~~~S~ 83 (160)
..++.++...|+..+ +.+..+..+++.- +.. ...+.+.|..++ .+++.||.|..|-
T Consensus 17 ~~la~~~~~~l~~~~~~~~~~~~~~lP~~~~d~~~~~~p~~v~~~~~~i~~aD-~li~~tPeYn~s~ 82 (184)
T COG0431 17 RALAEAAAKLLPAGGEVEVEFDDLDLPLYNEDLEADGLPPAVQALREAIAAAD-GLIIATPEYNGSY 82 (184)
T ss_pred HHHHHHHHHhhcccCceEEEecccccCCCCcchhhccCCHHHHHHHHHHHhCC-EEEEECCccCCCC
Confidence 356777778887776 4444433222211 122 235567788888 5678899998763
No 96
>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=24.04 E-value=75 Score=21.09 Aligned_cols=17 Identities=29% Similarity=0.565 Sum_probs=13.7
Q ss_pred cCHHHHHHHHHHHHHhh
Q 031401 134 DNIEKVQKWRYALKVVA 150 (160)
Q Consensus 134 ~~~~~~~~w~~al~~~~ 150 (160)
++++..+.|..||..|+
T Consensus 86 ~s~ee~~eWi~ai~~v~ 102 (102)
T cd01241 86 ESPEEREEWIHAIQTVA 102 (102)
T ss_pred CCHHHHHHHHHHHHhhC
Confidence 34688999999998763
No 97
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=23.64 E-value=1.8e+02 Score=24.62 Aligned_cols=45 Identities=22% Similarity=0.314 Sum_probs=33.7
Q ss_pred HHHHHHHHhcc-eEEEEeecCCc-CChhHHHHHHHHHHH-hhcCCcce
Q 031401 59 PNLLKTIEESR-ISIIVLSKNYA-SSTWCLDELLKIVEC-KNREDQIF 103 (160)
Q Consensus 59 ~~i~~~i~~S~-~~I~vlS~~~~-~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 67888988887 66777777754 567999999999887 55554444
No 98
>cd01266 PH_Gab Gab (Grb2-associated binder) pleckstrin homology (PH) domain. Gab (Grb2-associated binder) pleckstrin homology (PH) domain. The Gab subfamily includes several Gab proteins, Drosophila DOS and C. elegans SOC-1. They are scaffolding adaptor proteins, which possess N-terminal PH domains and a C-terminus with proline-rich regions and multiple phosphorylation sites. Following activation of growth factor receptors, Gab proteins are tyrosine phosphorylated and activate PI3K, which generates 3-phosphoinositide lipids. By binding to these lipids via the PH domain, Gab proteins remain in proximity to the receptor, leading to further signaling. While not all Gab proteins depend on the PH domain for recruitment, it is required for Gab activity. 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 str
Probab=23.54 E-value=78 Score=21.15 Aligned_cols=17 Identities=18% Similarity=0.350 Sum_probs=14.1
Q ss_pred cCHHHHHHHHHHHHHhh
Q 031401 134 DNIEKVQKWRYALKVVA 150 (160)
Q Consensus 134 ~~~~~~~~w~~al~~~~ 150 (160)
++++..+.|..|+.+++
T Consensus 92 ~s~ee~~~Wi~~I~~~~ 108 (108)
T cd01266 92 KNEEEMTLWVNCICKLC 108 (108)
T ss_pred CCHHHHHHHHHHHHhhC
Confidence 45788999999998874
No 99
>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=23.25 E-value=3.8e+02 Score=21.21 Aligned_cols=78 Identities=8% Similarity=0.074 Sum_probs=48.3
Q ss_pred hhHHHHHHHHHHcCCceEEee---CCCCCCCCCchHHHHHHHHhcceEEEEeecCCcCChhHHHHHHHHHHH--hhcCCc
Q 031401 27 KRFIGHLYTALNNKGIYVFRD---DKQLEKGGSISPNLLKTIEESRISIIVLSKNYASSTWCLDELLKIVEC--KNREDQ 101 (160)
Q Consensus 27 ~~fv~~L~~~L~~~g~~v~~d---~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~~~~--~~~~~~ 101 (160)
..++.+|...+...|+.+... .+.+..|.-+ -+.-.-.+.++-||.+|-+...+.-...++..++.. +..+++
T Consensus 94 ~ela~~i~~~~~~~g~~~~~~~~~~~~lDhg~~v--PL~~l~p~~~~pvV~is~~~~~~~~~~~~lG~al~~~~~~~~~~ 171 (280)
T cd07370 94 PELAHLIAEEATEHGVKTLAHEDPSLPLEYGTLV--PMRFMNEDDHFKVVSVAVWCTHDIEESRRLGEAIRRAIAASDRR 171 (280)
T ss_pred HHHHHHHHHHHHHCCCCeeeecCCCCCCCeeHhh--HHHHhCCCCCceEEEEeecCCCCHHHHHHHHHHHHHHHHhcCCC
Confidence 367899999999999876532 2233344321 112222234667888887665666677788888887 445667
Q ss_pred ceeEE
Q 031401 102 IFPIF 106 (160)
Q Consensus 102 IiPI~ 106 (160)
|+.|-
T Consensus 172 v~iIa 176 (280)
T cd07370 172 VALLA 176 (280)
T ss_pred EEEEE
Confidence 76553
No 100
>PRK08155 acetolactate synthase catalytic subunit; Validated
Probab=23.04 E-value=3e+02 Score=24.07 Aligned_cols=49 Identities=22% Similarity=0.255 Sum_probs=29.1
Q ss_pred CCCCCCCCCCCCcccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhc
Q 031401 1 MASTSFQNVSHGEYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEES 68 (160)
Q Consensus 1 m~s~sss~~~~~~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S 68 (160)
|+|+.+++...+ - .-.+.|...|++.|++..+-. ||.... .+..++.++
T Consensus 1 ~~~~~~~~~~~~-----------~---~~~~~l~~~L~~~GV~~vFgv----pG~~~~-~l~dal~~~ 49 (564)
T PRK08155 1 MASSGTTSTRKR-----------F---TGAELIVRLLERQGIRIVTGI----PGGAIL-PLYDALSQS 49 (564)
T ss_pred CCCCCCCccCCc-----------c---cHHHHHHHHHHHcCCCEEEeC----CCcccH-HHHHHHhcc
Confidence 788776665443 1 225668888888887665532 665543 345555444
No 101
>PF12913 SH3_6: SH3 domain of the SH3b1 type; PDB: 3M1U_B.
Probab=22.99 E-value=19 Score=21.63 Aligned_cols=16 Identities=13% Similarity=0.308 Sum_probs=12.5
Q ss_pred cEEEecccCCCchhHH
Q 031401 15 DAFLSFRGEDTRKRFI 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 4899999999888765
No 102
>PF00169 PH: PH domain; InterPro: IPR001849 The pleckstrin homology (PH) domain is a domain of about 100 residues that occurs in a wide range of proteins involved in intracellular signalling or as constituents of the cytoskeleton [, , , , , , ]. The pleckstrin homology domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids. The 3D structure of several PH domains has been determined []. All known cases have a common structure consisting of two perpendicular anti-parallel beta sheets, followed by a C-terminal amphipathic helix. The loops connecting the beta-strands differ greatly in length, making the PH domain relatively difficult to detect. There are no totally invariant residues within the PH domain. Proteins reported to contain one more PH domains belong to the following families: Pleckstrin, the protein where this domain was first detected, is the major substrate of protein kinase C in platelets. Pleckstrin is one of the rare proteins to contains two PH domains. Ser/Thr protein kinases such as the Akt/Rac family, the beta-adrenergic receptor kinases, the mu isoform of PKC and the trypanosomal NrkA family. Tyrosine protein kinases belonging to the Btk/Itk/Tec subfamily. Insulin Receptor Substrate 1 (IRS-1). Regulators of small G-proteins like guanine nucleotide releasing factor GNRP (Ras-GRF) (which contains 2 PH domains), guanine nucleotide exchange proteins like vav, dbl, SoS and Saccharomyces cerevisiae CDC24, GTPase activating proteins like rasGAP and BEM2/IPL2, and the human break point cluster protein bcr. Cytoskeletal proteins such as dynamin (see IPR001401 from INTERPRO), Caenorhabditis elegans kinesin-like protein unc-104 (see IPR001752 from INTERPRO), spectrin beta-chain, syntrophin (2 PH domains) and S. cerevisiae nuclear migration protein NUM1. Mammalian phosphatidylinositol-specific phospholipase C (PI-PLC) (see IPR000909 from INTERPRO) isoforms gamma and delta. Isoform gamma contains two PH domains, the second one is split into two parts separated by about 400 residues. Oxysterol binding proteins OSBP, S. cerevisiae OSH1 and YHR073w. Mouse protein citron, a putative rho/rac effector that binds to the GTP-bound forms of rho and rac. Several S. cerevisiae proteins involved in cell cycle regulation and bud formation like BEM2, BEM3, BUD4 and the BEM1-binding proteins BOI2 (BEB1) and BOI1 (BOB1). C. elegans protein MIG-10. C. elegans hypothetical proteins C04D8.1, K06H7.4 and ZK632.12. S. cerevisiae hypothetical proteins YBR129c and YHR155w. ; GO: 0005515 protein binding; PDB: 1DYN_B 2DYN_B 3SNH_A 3ZYS_C 1X05_A 2I5F_A 1ZM0_B 1XX0_A 2I5C_C 3A8P_D ....
Probab=22.78 E-value=95 Score=19.26 Aligned_cols=17 Identities=18% Similarity=0.438 Sum_probs=13.9
Q ss_pred cCHHHHHHHHHHHHHhh
Q 031401 134 DNIEKVQKWRYALKVVA 150 (160)
Q Consensus 134 ~~~~~~~~w~~al~~~~ 150 (160)
++++....|.+||..+.
T Consensus 87 ~s~~~~~~W~~~i~~~~ 103 (104)
T PF00169_consen 87 ESEEERKRWIQAIQKAI 103 (104)
T ss_dssp SSHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHh
Confidence 35788999999998875
No 103
>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=22.62 E-value=2.7e+02 Score=19.35 Aligned_cols=45 Identities=7% Similarity=0.096 Sum_probs=28.5
Q ss_pred HHHHHHHHhcceEEEEeecCCcCChhHHHHHHHHHHH-hhcCCcceeEE
Q 031401 59 PNLLKTIEESRISIIVLSKNYASSTWCLDELLKIVEC-KNREDQIFPIF 106 (160)
Q Consensus 59 ~~i~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~~~~-~~~~~~IiPI~ 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 456678899999999997765 3344455555554 44445555554
No 104
>PRK13883 conjugal transfer protein TrbH; Provisional
Probab=22.54 E-value=1.7e+02 Score=21.46 Aligned_cols=22 Identities=27% Similarity=0.350 Sum_probs=15.9
Q ss_pred hhHHHHHHHHHHcCCceEEeeC
Q 031401 27 KRFIGHLYTALNNKGIYVFRDD 48 (160)
Q Consensus 27 ~~fv~~L~~~L~~~g~~v~~d~ 48 (160)
..|...|...|+++||-|--+.
T Consensus 63 D~Fg~aL~~aLR~~GYaV~e~~ 84 (151)
T PRK13883 63 DAFGQALVKALRDKGYALLEYN 84 (151)
T ss_pred cHHHHHHHHHHHHcCeEEEecC
Confidence 3677778888888887776544
No 105
>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=22.53 E-value=1.4e+02 Score=22.72 Aligned_cols=38 Identities=13% Similarity=0.182 Sum_probs=29.4
Q ss_pred eEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCcCCh
Q 031401 43 YVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYASST 83 (160)
Q Consensus 43 ~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S~ 83 (160)
-||+|.- .+..+..++.+...+..+-|+++||..-..+
T Consensus 126 ~VW~D~f---~~~~~~~~~~~~~~~~~~~~c~VSpELh~~~ 163 (192)
T cd08584 126 WVWIDSF---TSLWLDNDLILKLLKAGKKICLVSPELHGRD 163 (192)
T ss_pred EEEEecc---cccCCCHHHHHHHHHCCcEEEEECHHHcCCC
Confidence 4898863 3566777888888888999999999866544
No 106
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=22.21 E-value=66 Score=20.20 Aligned_cols=35 Identities=17% Similarity=0.250 Sum_probs=20.8
Q ss_pred HHHHHHc--CCceEEeeCCCCCCCCCchHHHHHHHHhcc
Q 031401 33 LYTALNN--KGIYVFRDDKQLEKGGSISPNLLKTIEESR 69 (160)
Q Consensus 33 L~~~L~~--~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~ 69 (160)
....+.. +.+-+|+|.. .+|......+.+.+....
T Consensus 38 ~~~~~~~~~~~Vii~~D~D--~~G~~~a~~i~~~l~~~g 74 (81)
T PF13662_consen 38 LREKLEKKVKEVIIAFDND--KAGEKAAQKIAKKLLPLG 74 (81)
T ss_dssp HHHHHH---SEEEEEEESS--HHHHHHHHHHHHHHG---
T ss_pred ChHhhhccCceEEEEeCcC--HHHHHHHHHHHHHHHhhc
Confidence 3345555 6788888874 378777777777665433
No 107
>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=22.20 E-value=1.8e+02 Score=20.46 Aligned_cols=21 Identities=43% Similarity=0.463 Sum_probs=19.1
Q ss_pred hHHHHHHHHHHcCCceEEeeC
Q 031401 28 RFIGHLYTALNNKGIYVFRDD 48 (160)
Q Consensus 28 ~fv~~L~~~L~~~g~~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 899999999999999998765
No 108
>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=22.10 E-value=2.6e+02 Score=18.88 Aligned_cols=69 Identities=25% Similarity=0.322 Sum_probs=41.1
Q ss_pred HHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHH-hcceEEEEeecCCcCChhHHHHHHHHHHHhhcCCcceeEEee
Q 031401 30 IGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIE-ESRISIIVLSKNYASSTWCLDELLKIVECKNREDQIFPIFYE 108 (160)
Q Consensus 30 v~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~-~S~~~I~vlS~~~~~S~wc~~El~~~~~~~~~~~~IiPI~~~ 108 (160)
+..|..+|+++|+.+..-.. .++....++ .+++..+|+|-+ ... ..+....++.-.....=||||+-
T Consensus 6 ~~~l~~~L~~~~~~vv~~~~--------~dd~~~~i~~~~~i~avvi~~d-~~~---~~~~~~ll~~i~~~~~~iPVFl~ 73 (115)
T PF03709_consen 6 SRELAEALEQRGREVVDADS--------TDDALAIIESFTDIAAVVISWD-GEE---EDEAQELLDKIRERNFGIPVFLL 73 (115)
T ss_dssp HHHHHHHHHHTTTEEEEESS--------HHHHHHHHHCTTTEEEEEEECH-HHH---HHHHHHHHHHHHHHSTT-EEEEE
T ss_pred HHHHHHHHHHCCCEEEEeCC--------hHHHHHHHHhCCCeeEEEEEcc-ccc---chhHHHHHHHHHHhCCCCCEEEE
Confidence 57799999999998865431 245555555 599999999977 111 12222233331123345899975
Q ss_pred cC
Q 031401 109 VE 110 (160)
Q Consensus 109 ~~ 110 (160)
..
T Consensus 74 ~~ 75 (115)
T PF03709_consen 74 AE 75 (115)
T ss_dssp ES
T ss_pred ec
Confidence 44
No 109
>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=21.83 E-value=2.5e+02 Score=24.22 Aligned_cols=64 Identities=13% Similarity=0.095 Sum_probs=40.6
Q ss_pred CCcccEEEec---ccCC--CchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecC
Q 031401 11 HGEYDAFLSF---RGED--TRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKN 78 (160)
Q Consensus 11 ~~~yDVFISy---~~~D--~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~ 78 (160)
-..++|+|-- ..++ .-...+..|...|++.|+++-+|.++-.+| ..+..+-..---.++++.++
T Consensus 280 iaP~qV~Iipi~~~~~~~~~~~~~A~~l~~~Lr~~girv~lD~r~~s~g----kk~k~Ae~~GvP~~IiIG~~ 348 (472)
T TIGR00408 280 VAPIQVVIIPIIFKKKENEKVMEAAREVRSRLKKAGFRVHIDDRDNRPG----RKFYQWEIKGIPLRIEVGPN 348 (472)
T ss_pred hCcceEEEEEccCCCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHH----HHHHHHHHCCCCEEEEECcc
Confidence 3458888874 2221 124567889999999999999998654444 45555544333455666655
No 110
>COG0710 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism]
Probab=21.82 E-value=4e+02 Score=20.89 Aligned_cols=82 Identities=15% Similarity=0.103 Sum_probs=44.8
Q ss_pred HHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCcCChhHHHHHHHHHHH-hhcC-CcceeEE
Q 031401 29 FIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYASSTWCLDELLKIVEC-KNRE-DQIFPIF 106 (160)
Q Consensus 29 fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S~wc~~El~~~~~~-~~~~-~~IiPI~ 106 (160)
....|....+.+| .-++|- ++..+.....++.+.-++-. +|+|-+-..+.+..+|+...+.+ ...+ +.+=.+.
T Consensus 80 ~i~ll~~la~~~~-~d~iDi-El~~~~~~~~~~~~~~~~~~---vI~SyH~F~~TP~~~~i~~~l~km~~~~aDivKiAv 154 (231)
T COG0710 80 YIELLKKLAELNG-PDYIDI-ELSSPEDDVKEIIKFAKKHG---VIVSYHDFEKTPPLEEIIERLDKMESLGADIVKIAV 154 (231)
T ss_pred HHHHHHHHHhhcC-CCEEEE-EccCcchhHHHHHhccccCC---EEEEeccCCCCCcHHHHHHHHHHHHhhCCCeEEEEe
Confidence 3455555555555 456665 23333222223332222222 89999999999999999988888 4333 4333333
Q ss_pred eecCchhhh
Q 031401 107 YEVEPTVVR 115 (160)
Q Consensus 107 ~~~~p~~v~ 115 (160)
.-.+..|+.
T Consensus 155 m~~~~~DvL 163 (231)
T COG0710 155 MPQSKEDVL 163 (231)
T ss_pred cCCCHHHHH
Confidence 333444443
No 111
>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=21.80 E-value=4.1e+02 Score=21.05 Aligned_cols=38 Identities=16% Similarity=0.157 Sum_probs=19.7
Q ss_pred EEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCC
Q 031401 16 AFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKG 54 (160)
Q Consensus 16 VFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~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 444444333223445667777777777665443 34444
No 112
>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=21.75 E-value=3.9e+02 Score=20.90 Aligned_cols=41 Identities=15% Similarity=0.037 Sum_probs=18.9
Q ss_pred hHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcc
Q 031401 28 RFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESR 69 (160)
Q Consensus 28 ~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~ 69 (160)
..+..+...|++.|+.+--.. .+.+|..=...+...|..++
T Consensus 152 ~~~~~~~~~~~~~G~~vv~~~-~~~~~~~d~~~~v~~l~~~~ 192 (312)
T cd06346 152 GLADAFTKAFEALGGTVTNVV-AHEEGKSSYSSEVAAAAAGG 192 (312)
T ss_pred HHHHHHHHHHHHcCCEEEEEE-eeCCCCCCHHHHHHHHHhcC
Confidence 334555666666666654322 34444322233334444333
No 113
>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=21.68 E-value=1.4e+02 Score=17.30 Aligned_cols=33 Identities=24% Similarity=0.323 Sum_probs=23.2
Q ss_pred CCcccEEEecccCCCchhHHHHHHHHHHcCCceEE
Q 031401 11 HGEYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVF 45 (160)
Q Consensus 11 ~~~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~ 45 (160)
...+.+++.....+.. . ...+...|+..|+.+.
T Consensus 40 ~~~~~~~i~v~~~~~~-~-l~~l~~~l~~~g~~~~ 72 (73)
T cd04886 40 LGEVEVELTLETRGAE-H-IEEIIAALREAGYDVR 72 (73)
T ss_pred CceEEEEEEEEeCCHH-H-HHHHHHHHHHcCCEEe
Confidence 3556677777665532 2 5789999999998874
No 114
>COG3340 PepE Peptidase E [Amino acid transport and metabolism]
Probab=21.58 E-value=4e+02 Score=20.85 Aligned_cols=55 Identities=16% Similarity=0.222 Sum_probs=40.0
Q ss_pred cEEEecccCCCch-hHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEE
Q 031401 15 DAFLSFRGEDTRK-RFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISII 73 (160)
Q Consensus 15 DVFISy~~~D~~~-~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~ 73 (160)
=+||=+++.|..+ .++...+++|+..|..+- ++.....-.+.|.+-+.+.+++.|
T Consensus 35 i~FIPtAs~~~~~~~Yv~k~~~~l~~lg~~v~----~L~l~~~~~~~Ie~~l~~~d~IyV 90 (224)
T COG3340 35 IAFIPTASVDSEDDFYVEKVRNALAKLGLEVS----ELHLSKPPLAAIENKLMKADIIYV 90 (224)
T ss_pred EEEEecCccccchHHHHHHHHHHHHHcCCeee----eeeccCCCHHHHHHhhhhccEEEE
Confidence 4699999888753 367889999999997663 355555556677777777886544
No 115
>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=21.48 E-value=4e+02 Score=21.54 Aligned_cols=13 Identities=23% Similarity=0.256 Sum_probs=6.5
Q ss_pred HHHHHHHHHcCCc
Q 031401 30 IGHLYTALNNKGI 42 (160)
Q Consensus 30 v~~L~~~L~~~g~ 42 (160)
+..+.+.|++.|+
T Consensus 171 ~~~~~~~~~~~g~ 183 (377)
T cd06379 171 QKRFETLLEEREI 183 (377)
T ss_pred HHHHHHHHHhcCC
Confidence 4445555555554
No 116
>PF02878 PGM_PMM_I: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I; InterPro: IPR005844 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain I found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 3I3W_B 1WQA_C 1KFQ_B 1KFI_A 2Z0F_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=21.07 E-value=1.8e+02 Score=20.21 Aligned_cols=49 Identities=14% Similarity=0.097 Sum_probs=28.0
Q ss_pred cccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHh
Q 031401 13 EYDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEE 67 (160)
Q Consensus 13 ~yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~ 67 (160)
..-|.|+|........+...+...|...|++|..-. ..-.+.+.-++..
T Consensus 40 ~~~VvVg~D~R~~s~~~~~~~~~~l~~~G~~V~~~g------~~~tP~~~~~~~~ 88 (137)
T PF02878_consen 40 GSRVVVGRDTRPSSPMLAKALAAGLRANGVDVIDIG------LVPTPALSFAIRQ 88 (137)
T ss_dssp SSEEEEEE-SSTTHHHHHHHHHHHHHHTTEEEEEEE------EB-HHHHHHHHHH
T ss_pred CCeEEEEEcccCCHHHHHHHHHHHHhhccccccccc------ccCcHHhhhhccc
Confidence 345677776665555666667777777777776432 2233455555554
No 117
>cd01260 PH_CNK Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. CNK is believed to regulate the activity and the subcellular localization of RAS activated RAF. CNK is composed of N-terminal SAM and PDZ domains along with a central or C-terminal PH domain. 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. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskelet
Probab=20.89 E-value=90 Score=20.10 Aligned_cols=16 Identities=13% Similarity=0.515 Sum_probs=12.7
Q ss_pred cCHHHHHHHHHHHHHh
Q 031401 134 DNIEKVQKWRYALKVV 149 (160)
Q Consensus 134 ~~~~~~~~w~~al~~~ 149 (160)
++++..++|..||..+
T Consensus 81 ~s~~e~~~Wi~ai~~~ 96 (96)
T cd01260 81 ETLDDLSQWVNHLITA 96 (96)
T ss_pred CCHHHHHHHHHHHHhC
Confidence 3468899999999753
No 118
>PRK13762 tRNA-modifying enzyme; Provisional
Probab=20.56 E-value=4.1e+02 Score=21.68 Aligned_cols=60 Identities=18% Similarity=0.321 Sum_probs=40.3
Q ss_pred ccEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCc
Q 031401 14 YDAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYA 80 (160)
Q Consensus 14 yDVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~ 80 (160)
-++-||..++-.-..+...|...+.++|++++++-.-.. .+..+.+ ......+.+|=+..
T Consensus 131 ~~v~iSl~GEPlL~p~l~eli~~~k~~Gi~~~L~TNG~~------~e~l~~L-~~~~d~i~VSLda~ 190 (322)
T PRK13762 131 KHVAISLSGEPTLYPYLPELIEEFHKRGFTTFLVTNGTR------PDVLEKL-EEEPTQLYVSLDAP 190 (322)
T ss_pred CEEEEeCCccccchhhHHHHHHHHHHcCCCEEEECCCCC------HHHHHHH-HhcCCEEEEEccCC
Confidence 367788777766555677888999999999999875422 3444555 34455566775544
No 119
>cd06328 PBP1_SBP_like_2 Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=20.44 E-value=4.4e+02 Score=20.88 Aligned_cols=54 Identities=7% Similarity=0.071 Sum_probs=31.9
Q ss_pred cEEEecccCCCchhHHHHHHHHHHcCCceEEeeCCCCCCCCC-chHHHHHHHHhcce
Q 031401 15 DAFLSFRGEDTRKRFIGHLYTALNNKGIYVFRDDKQLEKGGS-ISPNLLKTIEESRI 70 (160)
Q Consensus 15 DVFISy~~~D~~~~fv~~L~~~L~~~g~~v~~d~~dl~~G~~-~~~~i~~~i~~S~~ 70 (160)
.|.+.|...+-.......+...|++.|+.+-... .+.+|.. +... ...|..+..
T Consensus 138 ~v~~i~~~~~~g~~~~~~~~~~~~~~G~~vv~~~-~~~~~~~d~~~~-v~~l~~~~p 192 (333)
T cd06328 138 KIATLAQDYAFGRDGVAAFKAALEKLGAAIVTEE-YAPTDTTDFTPY-AQRLLDALK 192 (333)
T ss_pred eEEEEecCccccHHHHHHHHHHHHhCCCEEeeee-eCCCCCcchHHH-HHHHHhcCC
Confidence 4555555444445566778888888898886543 4566653 4444 444444443
No 120
>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=20.33 E-value=1.4e+02 Score=23.26 Aligned_cols=37 Identities=22% Similarity=0.372 Sum_probs=27.0
Q ss_pred CCcccEEEeccc-CCCchhHHHHHHHHHHcCCceEEee
Q 031401 11 HGEYDAFLSFRG-EDTRKRFIGHLYTALNNKGIYVFRD 47 (160)
Q Consensus 11 ~~~yDVFISy~~-~D~~~~fv~~L~~~L~~~g~~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 456679999864 2322356788999999999998654
No 121
>cd06361 PBP1_GPC6A_like Ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor. This family includes the ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor, and its fish homolog, the 5.24 chemoreceptor. GPRC6A is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses.
Probab=20.22 E-value=3.7e+02 Score=22.36 Aligned_cols=20 Identities=5% Similarity=0.159 Sum_probs=12.5
Q ss_pred hhHHHHHHHHHHcCCceEEe
Q 031401 27 KRFIGHLYTALNNKGIYVFR 46 (160)
Q Consensus 27 ~~fv~~L~~~L~~~g~~v~~ 46 (160)
...+..+..++++.|+.+-.
T Consensus 186 ~~~~~~f~~~~~~~GicIa~ 205 (403)
T cd06361 186 RSALETFIIQAEANGVCIAF 205 (403)
T ss_pred HHHHHHHHHHHHHCCeEEEE
Confidence 44566677777777765543
No 122
>smart00233 PH Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
Probab=20.19 E-value=1.1e+02 Score=18.53 Aligned_cols=16 Identities=25% Similarity=0.418 Sum_probs=13.3
Q ss_pred CHHHHHHHHHHHHHhh
Q 031401 135 NIEKVQKWRYALKVVA 150 (160)
Q Consensus 135 ~~~~~~~w~~al~~~~ 150 (160)
+++...+|..+|..+.
T Consensus 86 s~~~~~~W~~~i~~~~ 101 (102)
T smart00233 86 SEEEREEWVDALRKAI 101 (102)
T ss_pred CHHHHHHHHHHHHHhh
Confidence 4688999999998765
No 123
>cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2. Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. 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 dissociation inhi
Probab=20.09 E-value=3.1e+02 Score=19.05 Aligned_cols=22 Identities=9% Similarity=-0.141 Sum_probs=15.8
Q ss_pred hHHHHHHHHhcceEEEEeecCC
Q 031401 58 SPNLLKTIEESRISIIVLSKNY 79 (160)
Q Consensus 58 ~~~i~~~i~~S~~~I~vlS~~~ 79 (160)
.......+++++.+|++++-.-
T Consensus 66 ~~~~~~~~~~ad~~i~v~d~~~ 87 (167)
T cd01867 66 RTITTAYYRGAMGIILVYDITD 87 (167)
T ss_pred HHHHHHHhCCCCEEEEEEECcC
Confidence 3334456789999999998643
No 124
>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=20.01 E-value=2.7e+02 Score=19.77 Aligned_cols=47 Identities=17% Similarity=0.236 Sum_probs=31.0
Q ss_pred HHHHHHHHHcCCceEEeeCCCCCCCCCchHHHHHHHHhcceEEEEeecCCcCC
Q 031401 30 IGHLYTALNNKGIYVFRDDKQLEKGGSISPNLLKTIEESRISIIVLSKNYASS 82 (160)
Q Consensus 30 v~~L~~~L~~~g~~v~~d~~dl~~G~~~~~~i~~~i~~S~~~I~vlS~~~~~S 82 (160)
+..|...|++.|+.+.+-. |+ ..+.+.+-+++..+..|++...|...
T Consensus 55 L~~L~~~L~~~g~~L~v~~-----g~-~~~~l~~l~~~~~~~~V~~~~~~~~~ 101 (165)
T PF00875_consen 55 LADLQESLRKLGIPLLVLR-----GD-PEEVLPELAKEYGATAVYFNEEYTPY 101 (165)
T ss_dssp HHHHHHHHHHTTS-EEEEE-----SS-HHHHHHHHHHHHTESEEEEE---SHH
T ss_pred HHHHHHHHHhcCcceEEEe-----cc-hHHHHHHHHHhcCcCeeEeccccCHH
Confidence 4568888888999887654 33 34566667778888888888887763
Done!