Query 043319
Match_columns 164
No_of_seqs 157 out of 1253
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 03:51:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043319.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043319hhsearch_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 1.3E-44 2.9E-49 275.7 12.9 138 7-162 17-156 (187)
2 PLN03210 Resistant to P. syrin 100.0 1.7E-43 3.6E-48 332.0 14.6 151 11-163 6-156 (1153)
3 PF01582 TIR: TIR domain; Int 99.9 3.6E-28 7.8E-33 179.1 1.9 132 20-151 1-140 (141)
4 smart00255 TIR Toll - interleu 99.9 4E-26 8.7E-31 166.6 12.6 137 17-155 1-139 (140)
5 PF13676 TIR_2: TIR domain; PD 99.8 1.5E-19 3.3E-24 125.7 4.8 87 20-112 1-87 (102)
6 KOG3678 SARM protein (with ste 99.2 3.8E-11 8.2E-16 103.2 8.0 105 12-122 607-729 (832)
7 PF08937 DUF1863: MTH538 TIR-l 98.7 4.2E-08 9E-13 71.3 5.7 89 18-111 1-107 (130)
8 PF08357 SEFIR: SEFIR domain; 98.0 4.1E-05 8.8E-10 56.5 8.0 64 19-82 2-70 (150)
9 PF10137 TIR-like: Predicted n 97.3 0.001 2.2E-08 48.3 6.1 96 19-119 1-112 (125)
10 PF13271 DUF4062: Domain of un 95.6 0.04 8.7E-07 36.8 5.5 66 19-85 1-67 (83)
11 COG4916 Uncharacterized protei 91.7 0.26 5.7E-06 40.0 4.0 101 13-119 173-282 (329)
12 COG4271 Predicted nucleotide-b 91.2 0.92 2E-05 35.6 6.4 96 19-120 84-199 (233)
13 PF05014 Nuc_deoxyrib_tr: Nucl 90.6 2.4 5.2E-05 29.5 7.7 67 31-98 13-88 (113)
14 PF14258 DUF4350: Domain of un 85.4 5.3 0.00011 25.2 6.3 61 35-107 8-68 (70)
15 PF14359 DUF4406: Domain of un 80.9 13 0.00029 25.2 7.1 63 34-98 18-85 (92)
16 cd00860 ThrRS_anticodon ThrRS 80.4 7.1 0.00015 25.3 5.6 60 18-81 2-61 (91)
17 PF03129 HGTP_anticodon: Antic 73.8 8.9 0.00019 25.3 4.6 48 31-81 15-62 (94)
18 cd00738 HGTP_anticodon HGTP an 73.7 13 0.00029 24.1 5.5 60 18-81 2-64 (94)
19 COG0400 Predicted esterase [Ge 68.7 17 0.00036 28.5 5.7 56 13-69 142-199 (207)
20 cd00858 GlyRS_anticodon GlyRS 67.9 16 0.00036 25.6 5.1 61 17-82 26-88 (121)
21 cd02426 Pol_gamma_b_Cterm C-te 67.1 5.8 0.00013 28.5 2.7 32 31-62 43-78 (128)
22 KOG2534 DNA polymerase IV (fam 58.0 81 0.0018 26.7 8.0 66 15-80 187-255 (353)
23 PF03720 UDPG_MGDP_dh_C: UDP-g 58.0 13 0.00028 25.6 3.0 56 26-81 11-77 (106)
24 COG1658 Small primase-like pro 56.3 24 0.00053 25.6 4.3 56 17-73 29-84 (127)
25 cd07363 45_DOPA_Dioxygenase Th 53.6 67 0.0015 25.7 6.9 68 31-100 80-149 (253)
26 PLN02924 thymidylate kinase 53.3 45 0.00098 26.1 5.8 45 1-49 2-48 (220)
27 cd02042 ParA ParA and ParB of 51.6 67 0.0015 21.2 5.8 64 20-83 3-74 (104)
28 cd01424 MGS_CPS_II Methylglyox 51.1 40 0.00087 23.0 4.6 31 19-51 2-32 (110)
29 cd00861 ProRS_anticodon_short 50.5 39 0.00084 21.9 4.4 49 31-82 17-65 (94)
30 PF09837 DUF2064: Uncharacteri 49.1 93 0.002 22.0 7.4 85 15-109 8-95 (122)
31 PF09441 Abp2: ARS binding pro 47.8 9.6 0.00021 28.9 1.0 57 85-151 54-111 (175)
32 KOG1136 Predicted cleavage and 46.7 27 0.00059 29.9 3.6 45 67-111 191-241 (501)
33 TIGR00418 thrS threonyl-tRNA s 46.0 50 0.0011 29.5 5.5 61 16-80 469-529 (563)
34 TIGR00334 5S_RNA_mat_M5 ribonu 45.4 50 0.0011 25.3 4.6 44 31-75 35-78 (174)
35 PF02310 B12-binding: B12 bind 43.3 1E+02 0.0022 20.9 6.2 60 33-100 16-76 (121)
36 PRK12325 prolyl-tRNA synthetas 42.4 33 0.00072 29.8 3.7 63 17-83 345-410 (439)
37 cd00859 HisRS_anticodon HisRS 41.4 88 0.0019 19.5 4.9 58 19-80 3-60 (91)
38 cd07373 2A5CPDO_A The alpha su 41.0 1.9E+02 0.0041 23.3 7.9 76 31-109 90-172 (271)
39 PF10087 DUF2325: Uncharacteri 39.7 1.1E+02 0.0024 20.4 5.3 58 33-91 11-69 (97)
40 PF08902 DUF1848: Domain of un 38.2 2E+02 0.0044 23.6 7.4 127 24-161 53-198 (266)
41 COG0710 AroD 3-dehydroquinate 38.0 1.2E+02 0.0027 24.2 6.1 67 32-103 79-146 (231)
42 cd06342 PBP1_ABC_LIVBP_like Ty 37.8 1.6E+02 0.0034 23.5 6.9 57 20-77 138-195 (334)
43 PRK09194 prolyl-tRNA synthetas 37.3 27 0.00058 31.4 2.4 64 16-83 467-533 (565)
44 cd06371 PBP1_sensory_GC_DEF_li 37.0 1.6E+02 0.0035 24.6 7.0 53 32-84 147-202 (382)
45 cd06340 PBP1_ABC_ligand_bindin 36.3 1.4E+02 0.0031 24.3 6.5 63 19-82 146-209 (347)
46 cd01423 MGS_CPS_I_III Methylgl 35.8 49 0.0011 22.8 3.1 30 20-51 3-32 (116)
47 cd03364 TOPRIM_DnaG_primases T 34.4 46 0.001 21.3 2.7 31 44-75 44-74 (79)
48 PRK14938 Ser-tRNA(Thr) hydrola 34.2 1E+02 0.0022 26.7 5.3 59 17-79 274-332 (387)
49 cd00862 ProRS_anticodon_zinc P 33.7 43 0.00094 25.9 2.8 47 17-63 10-63 (202)
50 PLN03194 putative disease resi 33.6 1.8E+02 0.0038 22.6 6.1 64 43-110 24-88 (187)
51 COG0683 LivK ABC-type branched 33.3 2.2E+02 0.0047 23.7 7.2 74 19-92 150-223 (366)
52 COG2130 Putative NADP-dependen 31.8 1.1E+02 0.0024 25.8 5.0 60 17-84 196-256 (340)
53 PRK08350 hypothetical protein; 31.7 47 0.001 28.2 2.8 33 15-47 279-311 (341)
54 PF09419 PGP_phosphatase: Mito 31.5 97 0.0021 23.5 4.3 68 40-112 35-112 (168)
55 PF01113 DapB_N: Dihydrodipico 31.3 1.1E+02 0.0024 21.4 4.5 29 18-50 68-96 (124)
56 KOG2792 Putative cytochrome C 31.1 52 0.0011 27.0 2.9 31 86-116 153-187 (280)
57 COG1168 MalY Bifunctional PLP- 30.8 1.2E+02 0.0025 26.3 5.0 46 62-107 148-195 (388)
58 cd01241 PH_Akt Akt pleckstrin 30.8 46 0.00099 22.6 2.2 17 138-154 86-102 (102)
59 PF07894 DUF1669: Protein of u 30.5 3.1E+02 0.0068 22.7 7.8 82 46-142 121-202 (284)
60 CHL00201 syh histidine-tRNA sy 30.4 1.1E+02 0.0024 26.5 5.0 60 17-80 325-384 (430)
61 PF01990 ATP-synt_F: ATP synth 30.4 1.5E+02 0.0032 19.8 4.7 46 38-85 10-55 (95)
62 COG4916 Uncharacterized protei 30.2 65 0.0014 26.5 3.3 97 16-115 5-107 (329)
63 cd06335 PBP1_ABC_ligand_bindin 30.1 2.2E+02 0.0047 23.2 6.6 54 19-73 140-194 (347)
64 PRK03991 threonyl-tRNA synthet 29.9 64 0.0014 29.5 3.6 43 17-60 499-542 (613)
65 PF01976 DUF116: Protein of un 29.8 1.7E+02 0.0036 21.9 5.3 66 33-112 74-139 (158)
66 PRK14799 thrS threonyl-tRNA sy 29.7 1.2E+02 0.0026 27.4 5.2 60 17-80 438-497 (545)
67 cd00532 MGS-like MGS-like doma 29.6 1.9E+02 0.0041 19.8 5.5 60 20-81 2-77 (112)
68 cd08584 PI-PLCc_GDPD_SF_unchar 29.4 1.2E+02 0.0026 23.6 4.6 36 48-85 127-162 (192)
69 KOG0095 GTPase Rab30, small G 29.4 2.2E+02 0.0047 21.7 5.8 60 71-132 80-141 (213)
70 PF03437 BtpA: BtpA family; I 29.3 2.3E+02 0.005 22.9 6.4 109 36-151 132-253 (254)
71 PRK08661 prolyl-tRNA synthetas 29.2 67 0.0015 28.3 3.5 46 17-62 287-339 (477)
72 cd06366 PBP1_GABAb_receptor Li 29.1 2.6E+02 0.0056 22.6 6.9 51 20-71 138-191 (350)
73 TIGR00409 proS_fam_II prolyl-t 29.0 43 0.00092 30.3 2.3 33 31-63 489-522 (568)
74 PRK15057 UDP-glucose 6-dehydro 28.4 1.1E+02 0.0024 26.2 4.6 55 22-76 304-365 (388)
75 cd06379 PBP1_iGluR_NMDA_NR1 N- 28.1 2E+02 0.0043 23.8 6.1 41 32-73 169-214 (377)
76 PRK12305 thrS threonyl-tRNA sy 27.5 1.4E+02 0.003 26.8 5.3 60 17-80 476-535 (575)
77 cd01857 HSR1_MMR1 HSR1/MMR1. 27.4 1.7E+02 0.0037 20.6 4.9 18 64-81 5-22 (141)
78 TIGR00640 acid_CoA_mut_C methy 27.2 2.4E+02 0.0052 20.2 8.9 86 20-112 5-90 (132)
79 PRK00413 thrS threonyl-tRNA sy 27.1 1.4E+02 0.0031 27.0 5.4 60 17-80 539-598 (638)
80 PHA02456 zinc metallopeptidase 27.0 86 0.0019 22.5 3.1 47 63-112 55-105 (141)
81 cd02951 SoxW SoxW family; SoxW 26.4 2.2E+02 0.0047 19.4 5.6 31 61-93 3-34 (125)
82 PRK02551 flavoprotein NrdI; Pr 26.3 2.8E+02 0.006 20.7 8.2 119 20-154 7-150 (154)
83 cd04142 RRP22 RRP22 subfamily. 26.1 2.9E+02 0.0063 20.8 7.3 54 64-120 74-130 (198)
84 COG1058 CinA Predicted nucleot 26.0 91 0.002 25.3 3.5 43 32-76 21-66 (255)
85 PHA00407 phage lambda Rz1-like 25.7 43 0.00094 22.2 1.3 22 140-161 25-51 (84)
86 cd06361 PBP1_GPC6A_like Ligand 25.6 2.2E+02 0.0047 24.2 6.0 28 30-57 185-212 (403)
87 TIGR03026 NDP-sugDHase nucleot 25.4 1.4E+02 0.0031 25.4 4.8 57 22-78 321-384 (411)
88 PF15409 PH_8: Pleckstrin homo 25.1 62 0.0013 21.9 2.1 16 138-153 73-88 (89)
89 cd00138 PLDc Phospholipase D. 24.7 1.4E+02 0.0029 21.7 4.1 38 32-69 21-64 (176)
90 PF09886 DUF2113: Uncharacteri 24.5 2.7E+02 0.0059 21.6 5.7 54 28-98 128-184 (188)
91 cd06328 PBP1_SBP_like_2 Peripl 24.0 2.5E+02 0.0055 22.7 5.9 54 19-73 138-192 (333)
92 PF03358 FMN_red: NADPH-depend 23.9 2.7E+02 0.0058 19.6 6.4 78 31-111 17-114 (152)
93 PF00350 Dynamin_N: Dynamin fa 23.6 2.4E+02 0.0052 20.0 5.2 46 62-110 120-165 (168)
94 cd06352 PBP1_NPR_GC_like Ligan 23.3 1.6E+02 0.0036 24.2 4.7 41 31-72 152-195 (389)
95 cd06327 PBP1_SBP_like_1 Peripl 23.3 3.2E+02 0.007 21.9 6.4 52 20-72 138-190 (334)
96 PF03618 Kinase-PPPase: Kinase 23.3 3.1E+02 0.0066 22.3 6.1 27 80-106 213-239 (255)
97 COG0415 PhrB Deoxyribodipyrimi 23.3 3E+02 0.0066 24.4 6.4 88 35-131 58-149 (461)
98 cd01266 PH_Gab Gab (Grb2-assoc 23.3 76 0.0016 21.7 2.3 17 138-154 92-108 (108)
99 PF13289 SIR2_2: SIR2-like dom 23.2 1.9E+02 0.0041 20.0 4.5 12 33-44 76-87 (143)
100 PF03709 OKR_DC_1_N: Orn/Lys/A 23.1 2.6E+02 0.0057 19.3 7.3 71 33-115 5-76 (115)
101 cd06346 PBP1_ABC_ligand_bindin 22.9 2.4E+02 0.0052 22.5 5.5 43 31-73 151-193 (312)
102 PRK13883 conjugal transfer pro 22.9 97 0.0021 23.2 2.9 26 28-53 60-85 (151)
103 PLN02530 histidine-tRNA ligase 22.8 2E+02 0.0044 25.3 5.3 61 16-80 400-460 (487)
104 PRK12444 threonyl-tRNA synthet 22.3 2E+02 0.0044 26.2 5.4 61 17-80 541-601 (639)
105 PF12146 Hydrolase_4: Putative 22.2 1.1E+02 0.0024 19.8 2.8 36 16-52 15-50 (79)
106 PF02337 Gag_p10: Retroviral G 21.8 73 0.0016 21.7 1.9 21 32-52 9-29 (90)
107 PF00875 DNA_photolyase: DNA p 21.7 3.2E+02 0.0069 19.8 5.9 92 34-132 55-148 (165)
108 TIGR00177 molyb_syn molybdenum 21.7 1.4E+02 0.003 21.5 3.5 46 32-77 27-73 (144)
109 PF00113 Enolase_C: Enolase, C 21.7 92 0.002 25.8 2.8 32 17-48 228-259 (295)
110 PF08477 Miro: Miro-like prote 21.6 2.5E+02 0.0054 18.5 4.8 46 65-111 68-113 (119)
111 smart00233 PH Pleckstrin homol 21.2 96 0.0021 19.1 2.4 16 139-154 86-101 (102)
112 cd01251 PH_centaurin_alpha Cen 21.1 1.1E+02 0.0023 20.8 2.6 19 138-156 84-102 (103)
113 cd02986 DLP Dim1 family, Dim1- 20.9 2.1E+02 0.0045 20.3 4.1 50 65-121 6-60 (114)
114 cd01238 PH_Tec Tec pleckstrin 20.7 83 0.0018 21.5 2.1 16 138-153 91-106 (106)
115 PRK07933 thymidylate kinase; V 20.7 2.2E+02 0.0048 21.9 4.7 31 21-51 2-34 (213)
116 cd06547 GH85_ENGase Endo-beta- 20.6 2.6E+02 0.0056 23.6 5.3 62 20-83 176-245 (339)
117 PF13662 Toprim_4: Toprim doma 20.0 72 0.0016 20.4 1.6 32 39-71 40-73 (81)
No 1
>PLN03194 putative disease resistance protein; Provisional
Probab=100.00 E-value=1.3e-44 Score=275.70 Aligned_cols=138 Identities=36% Similarity=0.616 Sum_probs=125.9
Q ss_pred CCCcCCCCCceecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCC-cCCcccchHHHHHhhhcCCeEEEEeecCccCc
Q 043319 7 KPCVEKSGVHKYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQ-LNRGDEISESLVNAIEASDISVIVFSESYASS 85 (164)
Q Consensus 7 ~~~~~~s~~~~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~-~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S 85 (164)
+|+++ +....|||||||+++|+|+.|++||+.+|+++||++|+|+. +++|+.+.++|.+||++|+++|+|||++|++|
T Consensus 17 ~~~~~-~~~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S 95 (187)
T PLN03194 17 YPSSS-SSAKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCES 95 (187)
T ss_pred cccCC-CCCCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccc
Confidence 34444 45788999999999999999999999999999999999998 99999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHhhhhhcceeeeEEEeeCCcccccc-cCchHHHHHHHHHHhcCChHHHHHHHHHHHHhhcccceeec
Q 043319 86 RWCLDELVKILDCKKEYAQIVIPVFYRVDPSDVRNR-TGSFGDSFSKLAERLKVNTEELRSWRNALKEAATLSGFHSL 162 (164)
Q Consensus 86 ~wc~~El~~~~~~~~~~~~~iiPVfy~v~p~~v~~~-~g~f~~~f~~~~~~~~~~~~~~~~W~~Al~~v~~~~G~~~~ 162 (164)
.||++||+.|+++. ..||||||+|+|+|||+| .|. .+.+++++||.||++|++++|++++
T Consensus 96 ~WCLdEL~~I~e~~----~~ViPIFY~VdPsdVr~q~~~~-------------~~~e~v~~Wr~AL~~va~l~G~~~~ 156 (187)
T PLN03194 96 YFCLHELALIMESK----KRVIPIFCDVKPSQLRVVDNGT-------------CPDEEIRRFNWALEEAKYTVGLTFD 156 (187)
T ss_pred hhHHHHHHHHHHcC----CEEEEEEecCCHHHhhccccCC-------------CCHHHHHHHHHHHHHHhccccccCC
Confidence 99999999999863 489999999999999997 432 2478999999999999999999875
No 2
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=100.00 E-value=1.7e-43 Score=332.03 Aligned_cols=151 Identities=45% Similarity=0.806 Sum_probs=142.9
Q ss_pred CCCCCceecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHH
Q 043319 11 EKSGVHKYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESYASSRWCLD 90 (164)
Q Consensus 11 ~~s~~~~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~ 90 (164)
+.+..++|||||||||+|+|+.|++||+.+|.++||++|.|+++++|+.+.+++.+||++|+++|||||++|++|.||++
T Consensus 6 ~~~~~~~~~vf~sfrg~d~r~~f~~hl~~~l~~~~i~~f~d~~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya~s~wcl~ 85 (1153)
T PLN03210 6 SSSRNWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDNEIERSQSLDPELKQAIRDSRIAVVVFSKNYASSSWCLN 85 (1153)
T ss_pred CCCCCCCCcEEeeCCCcccccCHHHHHHHHHHHCCCeEEccCCccCCCcccHHHHHHHHhCeEEEEEecCCcccchHHHH
Confidence 33357999999999999999999999999999999999998889999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhhhcceeeeEEEeeCCcccccccCchHHHHHHHHHHhcCChHHHHHHHHHHHHhhcccceeecC
Q 043319 91 ELVKILDCKKEYAQIVIPVFYRVDPSDVRNRTGSFGDSFSKLAERLKVNTEELRSWRNALKEAATLSGFHSLN 163 (164)
Q Consensus 91 El~~~~~~~~~~~~~iiPVfy~v~p~~v~~~~g~f~~~f~~~~~~~~~~~~~~~~W~~Al~~v~~~~G~~~~~ 163 (164)
||++|++|+++.+++||||||+|+|+|||+|+|.||++|.++++.. +++++++||.||++|++++|+++.+
T Consensus 86 el~~i~~~~~~~~~~v~pvfy~v~p~~v~~~~g~f~~~f~~~~~~~--~~~~~~~w~~al~~~~~~~g~~~~~ 156 (1153)
T PLN03210 86 ELLEIVRCKEELGQLVIPVFYGLDPSHVRKQTGDFGEAFEKTCQNK--TEDEKIQWKQALTDVANILGYHSQN 156 (1153)
T ss_pred HHHHHHHhhhhcCceEEEEEecccHHHHhhccchHHHHHHHHhccc--chhHHHHHHHHHHHHhCcCceecCC
Confidence 9999999999999999999999999999999999999999988653 4789999999999999999999753
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=99.94 E-value=3.6e-28 Score=179.13 Aligned_cols=132 Identities=32% Similarity=0.560 Sum_probs=115.5
Q ss_pred EEEecccCcCcccHHHHHHHHHhcC--CeeeeecCC-cCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHH
Q 043319 20 VFVSFRGEDTQDNFTSHLYSTLCRQ--NIQTFIDDQ-LNRGDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKIL 96 (164)
Q Consensus 20 VFISy~~~D~~~~f~~~L~~~L~~~--gi~vf~d~~-~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~ 96 (164)
|||||++.+.+..|+.+|..+|+++ |+++|++++ +.+|..+.+++.++|++|+++|+|+|++|+.|.||+.||..++
T Consensus 1 vfisy~~~~d~~~~~~~L~~~Le~~~~g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~s~wc~~el~~a~ 80 (141)
T PF01582_consen 1 VFISYSGKDDREWFVSHLLPELEERPYGYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSRNYLSSEWCLFELQEAL 80 (141)
T ss_dssp EEEEE-GHHGHHHHHHCHHHHHHCTSSTS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESHHHHHHTHHHHHHHHHH
T ss_pred cEEEeCCCCcHHHHHHHHHHHHHhCCCCeEEEEechhhcccccccchhhHhhhhceeeEEEeecccccccchhhhhhhhh
Confidence 8999999433578999999999999 999999998 9999999999999999999999999999999999999999999
Q ss_pred Hhhhhh--cceeeeEEEeeCCcccc-cccCchHHHHHHHHHHhcCC--hHHHHHHHHHHH
Q 043319 97 DCKKEY--AQIVIPVFYRVDPSDVR-NRTGSFGDSFSKLAERLKVN--TEELRSWRNALK 151 (164)
Q Consensus 97 ~~~~~~--~~~iiPVfy~v~p~~v~-~~~g~f~~~f~~~~~~~~~~--~~~~~~W~~Al~ 151 (164)
++..+. ..+|+||||++.+++++ .+.+.|+..|.........+ .+....|++++.
T Consensus 81 ~~~~~~~~~~~Il~v~~~v~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~fW~~l~~ 140 (141)
T PF01582_consen 81 ERLLEEGRDKLILPVFYDVSPSDVRPDQSLRFLLRFLTYLRWPDDDSREDRSWFWKKLRY 140 (141)
T ss_dssp HHHHCSTCTTEEEEESSSS-CHHCHTHHHHHHHHHCTHCEETSSSGGGGGHHHHHHHHHH
T ss_pred hhccccccccceeeEeccCChhhcChhhhHHHHHHhhhheeCCCCCCccHHHHHHHHHhc
Confidence 997654 48999999999999999 78999999988777655443 578999999875
No 4
>smart00255 TIR Toll - interleukin 1 - resistance.
Probab=99.94 E-value=4e-26 Score=166.63 Aligned_cols=137 Identities=41% Similarity=0.692 Sum_probs=115.9
Q ss_pred eecEEEeccc-CcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHH
Q 043319 17 KYDVFVSFRG-EDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKI 95 (164)
Q Consensus 17 ~ydVFISy~~-~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~ 95 (164)
+|||||||++ ++....|+.+|...|...|+.+|.|+....|.... +|.++|++|+++|+|+||+|+.|.||..|+..+
T Consensus 1 ~~dvFISys~~~~~~~~~v~~L~~~l~~~~~~v~~d~~~~~~~~~~-~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~a 79 (140)
T smart00255 1 EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFEPGGGDLE-EIDEAIEKSRIAIVVLSPNYAESEWCLDELVAA 79 (140)
T ss_pred CCeEEEECCCCHHHHHHHHHHHHHHhhcCCcEEEecCcccccchHH-HHHHHHHHCcEEEEEECcccccChhHHHHHHHH
Confidence 5999999999 44557899999999999999999998633333333 999999999999999999999999999999999
Q ss_pred HHhhhh-hcceeeeEEEeeCCcccccccCchHHHHHHHHHHhcCChHHHHHHHHHHHHhhc
Q 043319 96 LDCKKE-YAQIVIPVFYRVDPSDVRNRTGSFGDSFSKLAERLKVNTEELRSWRNALKEAAT 155 (164)
Q Consensus 96 ~~~~~~-~~~~iiPVfy~v~p~~v~~~~g~f~~~f~~~~~~~~~~~~~~~~W~~Al~~v~~ 155 (164)
+++..+ ...+||||+++..|+++.++.+.++..+......+..+..+ +.|+.++..+.+
T Consensus 80 ~~~~~~~~~~~iIPI~~~~~~~~~~~~~~~l~~~~~~~~~~w~~~~~~-~fW~~~~~~l~~ 139 (140)
T smart00255 80 LENALEEGGLRVIPIFYEVIPSDVRKQPGKFRKVLKKNYLKWPEDEKE-RFWKKALYAVPS 139 (140)
T ss_pred HHHHHHcCCCeEEEEEEecChHHHHhcccHHHHHHHHHHhhcCCchhH-HHHHHHHHHhcc
Confidence 987654 66899999999889899999999999998875565544444 789999988764
No 5
>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A.
Probab=99.78 E-value=1.5e-19 Score=125.68 Aligned_cols=87 Identities=32% Similarity=0.563 Sum_probs=75.0
Q ss_pred EEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHhh
Q 043319 20 VFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKILDCK 99 (164)
Q Consensus 20 VFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~ 99 (164)
|||||+++|. .++..|...|++.|+++|+|.++.+|+.+.+.|.++|++|+..|+++|++|..|+||..|+..+.+
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--EFAERLAERLESAGIRVFLDRDIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAWK-- 76 (102)
T ss_dssp EEEEEEGGGC--CCHHHHHHHHHHTT--EE-GGEE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHHC--
T ss_pred eEEEecCCcH--HHHHHHHHHHhhcCCEEEEEEeCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHHH--
Confidence 8999999994 699999999999999999997799999999999999999999999999999999999999999844
Q ss_pred hhhcceeeeEEEe
Q 043319 100 KEYAQIVIPVFYR 112 (164)
Q Consensus 100 ~~~~~~iiPVfy~ 112 (164)
.+..||||.++
T Consensus 77 --~~~~iipv~~~ 87 (102)
T PF13676_consen 77 --RGKPIIPVRLD 87 (102)
T ss_dssp --TSESEEEEECS
T ss_pred --CCCEEEEEEEC
Confidence 34589999953
No 6
>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]
Probab=99.21 E-value=3.8e-11 Score=103.15 Aligned_cols=105 Identities=26% Similarity=0.413 Sum_probs=83.9
Q ss_pred CCCCceecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCC-cCCcccchHHHHHhhhcCCeEEEEeecCccC----c-
Q 043319 12 KSGVHKYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQ-LNRGDEISESLVNAIEASDISVIVFSESYAS----S- 85 (164)
Q Consensus 12 ~s~~~~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~-~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~----S- 85 (164)
-+.+++.||||||++.. ...+++-|...|+-+|++||+|-+ +..|+ +.+.+.+.|..++.+|+|++||.+. .
T Consensus 607 a~~skq~DVFISYRRst-GnQLASLiKV~LQL~GyrVFIDVdKL~AGK-FdssLlkni~aAkhFiLVLtP~sLDr~lnD~ 684 (832)
T KOG3678|consen 607 AMLSKQIDVFISYRRST-GNQLASLIKVLLQLRGYRVFIDVDKLYAGK-FDSSLLKNIQAAKHFILVLTPNSLDRLLNDD 684 (832)
T ss_pred ccccCCcceEEEeeccc-cHHHHHHHHHHHHhcCceEEEehhhhhccc-ccHHHHHHHHhhheeEEEeCcchHHHHhccc
Confidence 34578899999998764 467999999999999999999999 88886 5668899999999999999999763 3
Q ss_pred ---hhHHHHHHHHHHhhhhhcceeeeEEEe---------eCCccccccc
Q 043319 86 ---RWCLDELVKILDCKKEYAQIVIPVFYR---------VDPSDVRNRT 122 (164)
Q Consensus 86 ---~wc~~El~~~~~~~~~~~~~iiPVfy~---------v~p~~v~~~~ 122 (164)
+|.-.||..++++ +..|||||-. +.|.|++..+
T Consensus 685 nCeDWVHKEl~~Afe~----~KNIiPI~D~aFE~Pt~ed~iPnDirmi~ 729 (832)
T KOG3678|consen 685 NCEDWVHKELKCAFEH----QKNIIPIFDTAFEFPTKEDQIPNDIRMIT 729 (832)
T ss_pred cHHHHHHHHHHHHHHh----cCCeeeeecccccCCCchhcCcHHHHHHH
Confidence 4555666666665 4489999842 5677777543
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=98.68 E-value=4.2e-08 Score=71.33 Aligned_cols=89 Identities=21% Similarity=0.374 Sum_probs=47.3
Q ss_pred ecEEEecccCcCcccHHHHHHHHHhcC-------Ceee-e---------ecCC-cCCcccchHHHHHhhhcCCeEEEEee
Q 043319 18 YDVFVSFRGEDTQDNFTSHLYSTLCRQ-------NIQT-F---------IDDQ-LNRGDEISESLVNAIEASDISVIVFS 79 (164)
Q Consensus 18 ydVFISy~~~D~~~~f~~~L~~~L~~~-------gi~v-f---------~d~~-~~~G~~~~~~i~~aI~~S~~~Ivv~S 79 (164)
|+|||||++.|.. ..+..|...+... .+.. | .+.. ....+.+...|.++|++|.++||+++
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 5799999998852 3677777777652 2211 1 1111 22334678899999999999999999
Q ss_pred cCccCchhHHHHHHHHHHhhhhhcceeeeEEE
Q 043319 80 ESYASSRWCLDELVKILDCKKEYAQIVIPVFY 111 (164)
Q Consensus 80 ~~y~~S~wc~~El~~~~~~~~~~~~~iiPVfy 111 (164)
++...|.|+..|+..+++. +..||-|.+
T Consensus 80 ~~T~~s~wV~~EI~~A~~~----~~~Ii~V~~ 107 (130)
T PF08937_consen 80 PNTAKSKWVNWEIEYALKK----GKPIIGVYL 107 (130)
T ss_dssp TT----HHHHHHHHHHTTT-------EEEEET
T ss_pred CCcccCcHHHHHHHHHHHC----CCCEEEEEC
Confidence 9999999999999988763 557777765
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=97.99 E-value=4.1e-05 Score=56.46 Aligned_cols=64 Identities=23% Similarity=0.366 Sum_probs=51.6
Q ss_pred cEEEecccCcCc-ccHHHHHHHHHhcC-CeeeeecCC-cC--CcccchHHHHHhhhcCCeEEEEeecCc
Q 043319 19 DVFVSFRGEDTQ-DNFTSHLYSTLCRQ-NIQTFIDDQ-LN--RGDEISESLVNAIEASDISVIVFSESY 82 (164)
Q Consensus 19 dVFISy~~~D~~-~~f~~~L~~~L~~~-gi~vf~d~~-~~--~G~~~~~~i~~aI~~S~~~Ivv~S~~y 82 (164)
.|||||++.... ...|..|...|++. |+.|.+|.- .. ++..+..=+.+.+++++.+|+|+||.+
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 499999985443 36799999999999 999999986 53 355666667778999999999999554
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=97.25 E-value=0.001 Score=48.32 Aligned_cols=96 Identities=21% Similarity=0.237 Sum_probs=69.0
Q ss_pred cEEEecccCcCcccHHHHHHHHHhcCCeeeeecCC-cCCcccchHHHHHhhhcCCeEEEEeecCc-------------cC
Q 043319 19 DVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQ-LNRGDEISESLVNAIEASDISVIVFSESY-------------AS 84 (164)
Q Consensus 19 dVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~-~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y-------------~~ 84 (164)
.|||.|+ .|. ..+..+...|+..|+.+..-.. ...|..+.+.+.+.+.+++.+|++++|+= ..
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 4899998 443 6888999999988887666555 78999999999999999999999999852 22
Q ss_pred chhHHHHHHHHHHhhhhhcceeeeEEE-ee-CCcccc
Q 043319 85 SRWCLDELVKILDCKKEYAQIVIPVFY-RV-DPSDVR 119 (164)
Q Consensus 85 S~wc~~El~~~~~~~~~~~~~iiPVfy-~v-~p~~v~ 119 (164)
-+..+.|+..++.+. +..+++-+.- ++ .|||+.
T Consensus 78 R~NVifE~G~f~g~L--Gr~rv~~l~~~~v~~PSDl~ 112 (125)
T PF10137_consen 78 RQNVIFELGLFIGKL--GRERVFILVKGGVELPSDLS 112 (125)
T ss_pred ccceeehhhHHHhhc--CcceEEEEEcCCccCCcccC
Confidence 345677888877642 2234444432 12 356654
No 10
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=95.63 E-value=0.04 Score=36.77 Aligned_cols=66 Identities=17% Similarity=0.224 Sum_probs=49.0
Q ss_pred cEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCc-CCcccchHHHHHhhhcCCeEEEEeecCccCc
Q 043319 19 DVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQL-NRGDEISESLVNAIEASDISVIVFSESYASS 85 (164)
Q Consensus 19 dVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~-~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S 85 (164)
.||||-.-.|- +.--..|.+.+.+.|.....-+.+ ..+....+.+.+.|++|++.|.++...|-..
T Consensus 1 rVFiSSt~~Dl-~~eR~~l~~~i~~~~~~~~~~e~~~a~~~~~~~~cl~~v~~cDifI~ilG~rYG~~ 67 (83)
T PF13271_consen 1 RVFISSTFRDL-KEERDALIEAIRRLGCEPVGMEFFPASDQSPLEICLKEVDECDIFILILGNRYGSV 67 (83)
T ss_pred CEEEecChhhH-HHHHHHHHHHHHHCCCeeeeeeeecCCCCCHHHHHHHHHhhCCEEEEeeccccCCC
Confidence 38999877775 345677888888877655443332 3355666788899999999999999998764
No 11
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=91.69 E-value=0.26 Score=40.04 Aligned_cols=101 Identities=18% Similarity=0.153 Sum_probs=69.3
Q ss_pred CCCceecEEEecccCcCcccHHHHHHHHHhc--CCeeeeecCC----cCCcccchHHHHHhhh--cCCeEEEEeecCccC
Q 043319 13 SGVHKYDVFVSFRGEDTQDNFTSHLYSTLCR--QNIQTFIDDQ----LNRGDEISESLVNAIE--ASDISVIVFSESYAS 84 (164)
Q Consensus 13 s~~~~ydVFISy~~~D~~~~f~~~L~~~L~~--~gi~vf~d~~----~~~G~~~~~~i~~aI~--~S~~~Ivv~S~~y~~ 84 (164)
+..+.||+=|||.|+- | ..++....+++. .-+..|+|-. +-+|. +. .++.-+- .|++.+|....+|..
T Consensus 173 ~~~~~~DiG~SFaGEA-R-~LVEqV~~E~~~~~~p~~~FYD~~~~~~L~~~s-L~-~~L~~~Y~~rC~~~~VF~~~~Y~~ 248 (329)
T COG4916 173 SSEKPVDSGISFAGEA-R-NLVEQVQTEHSGLDIPTRRFYDLLVAHPLYPGS-LV-STLDPGYDIRCVVTTVFNTGSYIC 248 (329)
T ss_pred ccccccceeeEeehhh-h-hHHHHHHHhhhcccCCceeeeechhhccccCcc-HH-HhcccccCceEEEEEEEeCCceEE
Confidence 4678899999999875 3 799999999984 3467788865 33443 22 2333322 588899999999999
Q ss_pred chhHHHHHHHHHHhhhhhcceeeeEEE-eeCCcccc
Q 043319 85 SRWCLDELVKILDCKKEYAQIVIPVFY-RVDPSDVR 119 (164)
Q Consensus 85 S~wc~~El~~~~~~~~~~~~~iiPVfy-~v~p~~v~ 119 (164)
-.||.-|...+.+... -..+.||.| ++.-+-+.
T Consensus 249 K~~c~~E~~~~r~~~~--~d~~~rI~~~~~d~~a~d 282 (329)
T COG4916 249 KSTCHIEGLEGRLNPI--LDTGFRIKYLYADNIAID 282 (329)
T ss_pred eeeeccchhhcccccc--ccccceEEEEecCCcccc
Confidence 9999999877644321 235666665 44444443
No 12
>COG4271 Predicted nucleotide-binding protein containing TIR -like domain [Transcription]
Probab=91.17 E-value=0.92 Score=35.57 Aligned_cols=96 Identities=20% Similarity=0.221 Sum_probs=66.0
Q ss_pred cEEEecccCcCcccHHHHHHHHHhc-CC-eeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCcc-------------
Q 043319 19 DVFVSFRGEDTQDNFTSHLYSTLCR-QN-IQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESYA------------- 83 (164)
Q Consensus 19 dVFISy~~~D~~~~f~~~L~~~L~~-~g-i~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~------------- 83 (164)
.|||-|+++ ..+.....+|.+ .. ..+|.|.-+..|+.+.+.+.+-|.+++.+|++.+|+=.
T Consensus 84 kvFvv~ghd----~iArael~allrd~~l~~vi~d~~~~~g~~ile~lek~i~~v~FAi~latPDDkgy~~~~~~~k~~p 159 (233)
T COG4271 84 KVFVVSGHD----AIARAELEALLRDWKLEPVILDGLFSEGQTILESLEKYIAEVKFAIVLATPDDKGYRAVHSREKAFP 159 (233)
T ss_pred eEEEEeccH----HHHHHHHHHHhhccccceEEecCcccccHHHHHHHHHHhhhceEEEEEecCcccccccccchhhccc
Confidence 999999764 366666666653 33 56677766889999999999999999999999999843
Q ss_pred -CchhHHHHHHHHHHhhhhhcceeeeEEE---ee-CCccccc
Q 043319 84 -SSRWCLDELVKILDCKKEYAQIVIPVFY---RV-DPSDVRN 120 (164)
Q Consensus 84 -~S~wc~~El~~~~~~~~~~~~~iiPVfy---~v-~p~~v~~ 120 (164)
.-.....||...+-+. ++.+|+-+.- +| -|||+..
T Consensus 160 raRqNVifELGm~mgrL--gRkrv~Il~k~~envelPSDi~G 199 (233)
T COG4271 160 RARQNVIFELGMFMGRL--GRKRVMILMKRDENVELPSDIAG 199 (233)
T ss_pred cccccchhhHhhHHhhc--ccceEEEEecccccccCccccCc
Confidence 2334667887776642 2334443322 12 4777754
No 13
>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=90.56 E-value=2.4 Score=29.46 Aligned_cols=67 Identities=16% Similarity=0.110 Sum_probs=49.2
Q ss_pred ccHHHHHHHHHhcCCeeeeecCC--cC---Cccc----chHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHh
Q 043319 31 DNFTSHLYSTLCRQNIQTFIDDQ--LN---RGDE----ISESLVNAIEASDISVIVFSESYASSRWCLDELVKILDC 98 (164)
Q Consensus 31 ~~f~~~L~~~L~~~gi~vf~d~~--~~---~G~~----~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~ 98 (164)
..+...+.+.|++.|+.++...+ .. .+.. +-+.-.++|++|+++|+++...- .+.=+.-|+..+...
T Consensus 13 ~~~~~~~~~~L~~~g~~v~~P~~~~~~~~~~~~~~~~~i~~~d~~~i~~~D~via~l~~~~-~d~Gt~~ElG~A~al 88 (113)
T PF05014_consen 13 KARVERLREALEKNGFEVYSPQDNDENDEEDSQEWAREIFERDLEGIRECDIVIANLDGFR-PDSGTAFELGYAYAL 88 (113)
T ss_dssp HHHHHHHHHHHHTTTTEEEGGCTCSSS--TTSHHCHHHHHHHHHHHHHHSSEEEEEECSSS---HHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHhCCCEEEeccccccccccccchHHHHHHHHHHHHHHHCCEEEEECCCCC-CCCcHHHHHHHHHHC
Confidence 56889999999999999988764 21 1222 33344568999999999998765 556688899998764
No 14
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=85.44 E-value=5.3 Score=25.21 Aligned_cols=61 Identities=21% Similarity=0.221 Sum_probs=37.3
Q ss_pred HHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHhhhhhcceee
Q 043319 35 SHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKILDCKKEYAQIVI 107 (164)
Q Consensus 35 ~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~ii 107 (164)
.-|++.|++.|+.|-.... ..+++....-.+++++|.+.-+. -.++..+.+..+.++..||
T Consensus 8 ~a~~~~L~~~g~~v~~~~~----------~~~~l~~~~~tll~i~~~~~~~~--~~~~~~l~~~v~~G~~lvl 68 (70)
T PF14258_consen 8 YALYQLLEEQGVKVERWRK----------PYEALEADDGTLLVIGPDLRLSE--PEEAEALLEWVEAGNTLVL 68 (70)
T ss_pred HHHHHHHHHCCCeeEEecc----------cHHHhCCCCCEEEEEeCCCCCCc--hHHHHHHHHHHHcCCEEEE
Confidence 4567788888988855432 12344557889999999966553 2444444444445555544
No 15
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=80.93 E-value=13 Score=25.23 Aligned_cols=63 Identities=13% Similarity=0.037 Sum_probs=42.7
Q ss_pred HHHHHHHHhcCCeeeeecCCc--CCcccchHHH---HHhhhcCCeEEEEeecCccCchhHHHHHHHHHHh
Q 043319 34 TSHLYSTLCRQNIQTFIDDQL--NRGDEISESL---VNAIEASDISVIVFSESYASSRWCLDELVKILDC 98 (164)
Q Consensus 34 ~~~L~~~L~~~gi~vf~d~~~--~~G~~~~~~i---~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~ 98 (164)
.....+.|+..|..|.---.+ ..|..+.+-+ ...|.+|+..++ =|++-+|.=|.-|...+...
T Consensus 18 f~~~a~~L~~~G~~vvnPa~~~~~~~~~~~~ym~~~l~~L~~cD~i~~--l~gWe~S~GA~~E~~~A~~l 85 (92)
T PF14359_consen 18 FNAAAKRLRAKGYEVVNPAELGIPEGLSWEEYMRICLAMLSDCDAIYM--LPGWENSRGARLEHELAKKL 85 (92)
T ss_pred HHHHHHHHHHCCCEEeCchhhCCCCCCCHHHHHHHHHHHHHhCCEEEE--cCCcccCcchHHHHHHHHHC
Confidence 345778889999766543333 5555544433 345667885444 49999999999999888653
No 16
>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=80.44 E-value=7.1 Score=25.29 Aligned_cols=60 Identities=12% Similarity=0.172 Sum_probs=38.0
Q ss_pred ecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecC
Q 043319 18 YDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSES 81 (164)
Q Consensus 18 ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~ 81 (164)
++|+|...+++. ...+..+...|++.|+++-+|.. +..+...+..|-+.---.++++.++
T Consensus 2 ~~v~ii~~~~~~-~~~a~~~~~~Lr~~g~~v~~d~~---~~~~~~~~~~a~~~g~~~~iiig~~ 61 (91)
T cd00860 2 VQVVVIPVTDEH-LDYAKEVAKKLSDAGIRVEVDLR---NEKLGKKIREAQLQKIPYILVVGDK 61 (91)
T ss_pred eEEEEEeeCchH-HHHHHHHHHHHHHCCCEEEEECC---CCCHHHHHHHHHHcCCCEEEEECcc
Confidence 677777655433 45788899999999999998764 2344445555544333344444443
No 17
>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=73.82 E-value=8.9 Score=25.28 Aligned_cols=48 Identities=17% Similarity=0.246 Sum_probs=32.0
Q ss_pred ccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecC
Q 043319 31 DNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSES 81 (164)
Q Consensus 31 ~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~ 81 (164)
..++.+|...|.+.|+++.+|.. +..+...+..|-..=--.++|+.++
T Consensus 15 ~~~a~~l~~~L~~~gi~v~~d~~---~~~~~k~~~~a~~~g~p~~iiiG~~ 62 (94)
T PF03129_consen 15 IEYAQELANKLRKAGIRVELDDS---DKSLGKQIKYADKLGIPFIIIIGEK 62 (94)
T ss_dssp HHHHHHHHHHHHHTTSEEEEESS---SSTHHHHHHHHHHTTESEEEEEEHH
T ss_pred HHHHHHHHHHHHHCCCEEEEECC---CCchhHHHHHHhhcCCeEEEEECch
Confidence 46889999999999999999874 3344445555544333344555443
No 18
>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=73.69 E-value=13 Score=24.06 Aligned_cols=60 Identities=18% Similarity=0.245 Sum_probs=38.4
Q ss_pred ecEEEecccC---cCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecC
Q 043319 18 YDVFVSFRGE---DTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSES 81 (164)
Q Consensus 18 ydVFISy~~~---D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~ 81 (164)
++|+|-..+. . ....+..+...|++.|+.+-+|.. +..+...+..+-+.---.++++.++
T Consensus 2 ~~v~ii~~~~~~~~-~~~~a~~~~~~Lr~~g~~v~~~~~---~~~~~k~~~~a~~~g~~~~iiig~~ 64 (94)
T cd00738 2 IDVAIVPLTDPRVE-AREYAQKLLNALLANGIRVLYDDR---ERKIGKKFREADLRGVPFAVVVGED 64 (94)
T ss_pred eEEEEEECCCCcHH-HHHHHHHHHHHHHHCCCEEEecCC---CcCHhHHHHHHHhCCCCEEEEECCC
Confidence 5666665433 2 235778899999999999998764 3455555555544444566666653
No 19
>COG0400 Predicted esterase [General function prediction only]
Probab=68.74 E-value=17 Score=28.52 Aligned_cols=56 Identities=16% Similarity=0.137 Sum_probs=43.4
Q ss_pred CCCceecEEEecccCcC--cccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhh
Q 043319 13 SGVHKYDVFVSFRGEDT--QDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIE 69 (164)
Q Consensus 13 s~~~~ydVFISy~~~D~--~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~ 69 (164)
......-|||+|-..|. ......+|.+.|+..|..|.... ...|-.+.++-.++++
T Consensus 142 ~~~~~~pill~hG~~Dpvvp~~~~~~l~~~l~~~g~~v~~~~-~~~GH~i~~e~~~~~~ 199 (207)
T COG0400 142 PDLAGTPILLSHGTEDPVVPLALAEALAEYLTASGADVEVRW-HEGGHEIPPEELEAAR 199 (207)
T ss_pred cccCCCeEEEeccCcCCccCHHHHHHHHHHHHHcCCCEEEEE-ecCCCcCCHHHHHHHH
Confidence 35678899999988886 35688999999999999998866 4577777766555544
No 20
>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=67.89 E-value=16 Score=25.55 Aligned_cols=61 Identities=11% Similarity=0.016 Sum_probs=41.2
Q ss_pred eecEEEeccc--CcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCc
Q 043319 17 KYDVFVSFRG--EDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESY 82 (164)
Q Consensus 17 ~ydVFISy~~--~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y 82 (164)
.+||||-.-+ .+ ....+..|...|++.|++|-+|.. ..+..++..|-+.---.++++.++-
T Consensus 26 p~~v~Ii~~~~~~~-~~~~a~~la~~LR~~gi~v~~d~~----~sl~kqlk~A~k~g~~~~iiiG~~e 88 (121)
T cd00858 26 PIKVAVLPLVKRDE-LVEIAKEISEELRELGFSVKYDDS----GSIGRRYARQDEIGTPFCVTVDFDT 88 (121)
T ss_pred CcEEEEEecCCcHH-HHHHHHHHHHHHHHCCCEEEEeCC----CCHHHHHHHhHhcCCCEEEEECcCc
Confidence 5788887765 32 245778899999999999998763 3555566666554444566666553
No 21
>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=67.07 E-value=5.8 Score=28.55 Aligned_cols=32 Identities=6% Similarity=0.067 Sum_probs=25.9
Q ss_pred ccHHHHHHHHHhcCCeeeeecCC-c---CCcccchH
Q 043319 31 DNFTSHLYSTLCRQNIQTFIDDQ-L---NRGDEISE 62 (164)
Q Consensus 31 ~~f~~~L~~~L~~~gi~vf~d~~-~---~~G~~~~~ 62 (164)
...+..|+..|++.|++|+.|++ - .+|..+.+
T Consensus 43 ~~~a~~l~~~L~~~gi~v~~D~r~~~~~~~G~k~~~ 78 (128)
T cd02426 43 RDLCQGLKNELREAGLSVWPGYLETQHSSLEQLLDK 78 (128)
T ss_pred HHHHHHHHHHHHHcCCEEEeccCcccccCHHHHHHh
Confidence 56889999999999999999887 3 56666543
No 22
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=58.00 E-value=81 Score=26.69 Aligned_cols=66 Identities=14% Similarity=0.137 Sum_probs=42.6
Q ss_pred CceecEEEecccC-cCcccHHHHHHHHHhcCCeeeeecCCcCCcc-cchHHHHHhhhcCC-eEEEEeec
Q 043319 15 VHKYDVFVSFRGE-DTQDNFTSHLYSTLCRQNIQTFIDDQLNRGD-EISESLVNAIEASD-ISVIVFSE 80 (164)
Q Consensus 15 ~~~ydVFISy~~~-D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~-~~~~~i~~aI~~S~-~~Ivv~S~ 80 (164)
+-..|+-|++.+. ++.......|+..|++.|+..|.++...-|+ .....+..++..-. ...|+..|
T Consensus 187 ggDvD~LithP~~~s~~~~~~~~l~~~le~~g~il~~~~~~S~~Ek~~l~~~~s~~~~~~~~mgv~~LP 255 (353)
T KOG2534|consen 187 GGDVDFLITHPGSTSTEAKLLQLLMILLEKKGLLLYYDQLHSCGEKLRLPSRKSALDHFKKFMGVFRLP 255 (353)
T ss_pred CCCeeEEEeCCCCCchhhhHHHHHHHHHHhcCeEEEEeeeccccccccccchhhhHhhhhhEEEEEEcC
Confidence 3467888888644 2245677899999999999999988733333 33344445544433 45555556
No 23
>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=57.98 E-value=13 Score=25.57 Aligned_cols=56 Identities=18% Similarity=0.318 Sum_probs=34.9
Q ss_pred cCcCcccHHHHHHHHHhcCCeeeeecCC-cCC----------cccchHHHHHhhhcCCeEEEEeecC
Q 043319 26 GEDTQDNFTSHLYSTLCRQNIQTFIDDQ-LNR----------GDEISESLVNAIEASDISVIVFSES 81 (164)
Q Consensus 26 ~~D~~~~f~~~L~~~L~~~gi~vf~d~~-~~~----------G~~~~~~i~~aI~~S~~~Ivv~S~~ 81 (164)
..|.|.+=+-.|.+.|.++|+.|...+- +.. |-.+.+.+.++++.++..|+.-..+
T Consensus 11 ~~D~R~Sp~~~l~~~L~~~g~~V~~~DP~v~~~~~~~~~~~~~~~~~~~~~~~~~~~D~vvl~t~h~ 77 (106)
T PF03720_consen 11 TDDIRESPALELIEELKERGAEVSVYDPYVDEEEIKELGKLEGVEVCDDLEEALKGADAVVLATDHD 77 (106)
T ss_dssp SS--TT-HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHCHHHCEEEESSHHHHHTTESEEEESS--G
T ss_pred CcccccCHHHHHHHHHHHCCCEEEEECCccChHHHHhhCCccceEEecCHHHHhcCCCEEEEEecCH
Confidence 3578889999999999999999877654 221 2223345678888888877765533
No 24
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=56.31 E-value=24 Score=25.58 Aligned_cols=56 Identities=9% Similarity=0.096 Sum_probs=40.3
Q ss_pred eecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCe
Q 043319 17 KYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDI 73 (164)
Q Consensus 17 ~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~ 73 (164)
..++|+-..+.-....+++.|..++..+|+-++.|-+ .+|+.+...+.+.+.++.-
T Consensus 29 ~~~~i~~~g~~i~~~~~ie~i~~~~~~k~VIILTD~D-~~Ge~Irk~l~~~l~~~~~ 84 (127)
T COG1658 29 DAGVIITNGSAINSLETIELIKKAQKYKGVIILTDPD-RKGERIRKKLKEYLPGAKG 84 (127)
T ss_pred CCceEEEcCCccchHHHHHHHHHhhccCCEEEEeCCC-cchHHHHHHHHHHhccccc
Confidence 3566776655322246888888888899999988875 6788888888887777443
No 25
>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=53.59 E-value=67 Score=25.65 Aligned_cols=68 Identities=18% Similarity=0.139 Sum_probs=48.2
Q ss_pred ccHHHHHHHHHhcCCeeeeecCC--cCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHhhh
Q 043319 31 DNFTSHLYSTLCRQNIQTFIDDQ--LNRGDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKILDCKK 100 (164)
Q Consensus 31 ~~f~~~L~~~L~~~gi~vf~d~~--~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~ 100 (164)
..++.+|.+.|.+.|+.+-.+.+ +--|--+. +.-...+.++=||.+|-+...+..-..+|.+++...+
T Consensus 80 ~eLa~~i~~~l~~~gi~~~~~~~~~lDHG~~vP--L~~~~p~~~iPvV~isi~~~~~~~~~~~lG~aL~~l~ 149 (253)
T cd07363 80 PELAERVAELLKAAGIPARLDPERGLDHGAWVP--LKLMYPDADIPVVQLSLPASLDPAEHYALGRALAPLR 149 (253)
T ss_pred HHHHHHHHHHHHhcCCCccccCCcCCcccHHHH--HHHHcCCCCCcEEEEEecCCCCHHHHHHHHHHHHhhh
Confidence 46999999999999998876543 44443333 2222345678899999888767777779999887654
No 26
>PLN02924 thymidylate kinase
Probab=53.33 E-value=45 Score=26.14 Aligned_cols=45 Identities=18% Similarity=0.144 Sum_probs=35.5
Q ss_pred CCCCCCCCCcCCCCCceecEEEecccCcCc--ccHHHHHHHHHhcCCeeee
Q 043319 1 MSMKAQKPCVEKSGVHKYDVFVSFRGEDTQ--DNFTSHLYSTLCRQNIQTF 49 (164)
Q Consensus 1 ~~~~~~~~~~~~s~~~~ydVFISy~~~D~~--~~f~~~L~~~L~~~gi~vf 49 (164)
.+|.+.||+.+...+. ||.+-|-|.. ..-+..|.+.|+.+|+.+-
T Consensus 2 ~~~~~~~~~~~~~~g~----~IviEGiDGsGKsTq~~~L~~~l~~~g~~v~ 48 (220)
T PLN02924 2 FSMGMETESSVESRGA----LIVLEGLDRSGKSTQCAKLVSFLKGLGVAAE 48 (220)
T ss_pred CccccCCCCCcCCCCe----EEEEECCCCCCHHHHHHHHHHHHHhcCCCce
Confidence 3688888888876654 9999887752 4688999999999998864
No 27
>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=51.57 E-value=67 Score=21.21 Aligned_cols=64 Identities=17% Similarity=0.177 Sum_probs=39.3
Q ss_pred EEEecccCcCcccHHHHHHHHHhcCCeeeeecCC-cC-------CcccchHHHHHhhhcCCeEEEEeecCcc
Q 043319 20 VFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQ-LN-------RGDEISESLVNAIEASDISVIVFSESYA 83 (164)
Q Consensus 20 VFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~-~~-------~G~~~~~~i~~aI~~S~~~Ivv~S~~y~ 83 (164)
+|.|..+.-.+..++.+|...|.++|.++..-+. .. -+-.+.+....++..|+..|+++.++..
T Consensus 3 ~~~~~kgG~Gkst~~~~la~~~~~~~~~vl~~d~d~~~d~viiD~p~~~~~~~~~~l~~ad~viv~~~~~~~ 74 (104)
T cd02042 3 AVANQKGGVGKTTTAVNLAAALARRGKRVLLIDLDPQYDYIIIDTPPSLGLLTRNALAAADLVLIPVQPSPL 74 (104)
T ss_pred EEEeCCCCcCHHHHHHHHHHHHHhCCCcEEEEeCCCCCCEEEEeCcCCCCHHHHHHHHHCCEEEEeccCCHH
Confidence 3666665544456789999999988887765431 11 1112233444667777777777766544
No 28
>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=51.12 E-value=40 Score=23.01 Aligned_cols=31 Identities=16% Similarity=0.221 Sum_probs=21.9
Q ss_pred cEEEecccCcCcccHHHHHHHHHhcCCeeeeec
Q 043319 19 DVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFID 51 (164)
Q Consensus 19 dVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d 51 (164)
.||+|.+..|. .-...+.+.|.+.|++++--
T Consensus 2 ~vl~s~~~~~k--~~~~~~~~~l~~~G~~l~aT 32 (110)
T cd01424 2 TVFISVADRDK--PEAVEIAKRLAELGFKLVAT 32 (110)
T ss_pred eEEEEEEcCcH--hHHHHHHHHHHHCCCEEEEc
Confidence 37899987763 34457777777888888653
No 29
>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=50.53 E-value=39 Score=21.93 Aligned_cols=49 Identities=16% Similarity=0.241 Sum_probs=31.2
Q ss_pred ccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCc
Q 043319 31 DNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESY 82 (164)
Q Consensus 31 ~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y 82 (164)
...+..|...|++.|++|.+|.+ +..+...+..|-+.---.++++.++-
T Consensus 17 ~~~a~~la~~Lr~~g~~v~~d~~---~~~l~k~i~~a~~~g~~~~iiiG~~e 65 (94)
T cd00861 17 QELAEKLYAELQAAGVDVLLDDR---NERPGVKFADADLIGIPYRIVVGKKS 65 (94)
T ss_pred HHHHHHHHHHHHHCCCEEEEECC---CCCcccchhHHHhcCCCEEEEECCch
Confidence 35788899999999999999875 22344444455443333455555443
No 30
>PF09837 DUF2064: Uncharacterized protein conserved in bacteria (DUF2064); InterPro: IPR018641 This entry contains proteins that have no known function. ; PDB: 3CGX_A.
Probab=49.11 E-value=93 Score=22.03 Aligned_cols=85 Identities=14% Similarity=0.272 Sum_probs=43.7
Q ss_pred CceecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcC---CeEEEEeecCccCchhHHHH
Q 043319 15 VHKYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEAS---DISVIVFSESYASSRWCLDE 91 (164)
Q Consensus 15 ~~~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S---~~~Ivv~S~~y~~S~wc~~E 91 (164)
...+|++|.|...+.. .....+ ....++.++. ++|..+.+.+.++++.. .-.|+++.-+... -+...
T Consensus 8 ~~~~~~~l~~~~~~~~-~~~~~~---~~~~~~~~~~----Q~g~dLG~Rm~~a~~~~~~g~~~vvliGsD~P~--l~~~~ 77 (122)
T PF09837_consen 8 ADGADVVLAYTPDGDH-AAFRQL---WLPSGFSFFP----QQGGDLGERMANAFQQAARGYEPVVLIGSDCPD--LTPDD 77 (122)
T ss_dssp TSSSEEEEEE----TT-HHHHHH---HH-TTSEEEE------SSSHHHHHHHHHHHHHTT-SEEEEE-SS-TT----HHH
T ss_pred CCCcCEEEEEcCCccH-HHHhcc---ccCCCCEEee----cCCCCHHHHHHHHHHHHHcCCCcEEEEcCCCCC--CCHHH
Confidence 4568999999877643 333222 3344555554 45666766666666654 3367777766665 34556
Q ss_pred HHHHHHhhhhhcceeeeE
Q 043319 92 LVKILDCKKEYAQIVIPV 109 (164)
Q Consensus 92 l~~~~~~~~~~~~~iiPV 109 (164)
|..+.+..+....++-|-
T Consensus 78 l~~A~~~L~~~d~VlgPa 95 (122)
T PF09837_consen 78 LEQAFEALQRHDVVLGPA 95 (122)
T ss_dssp HHHHHHHTTT-SEEEEEB
T ss_pred HHHHHHHhccCCEEEeec
Confidence 677766655555566563
No 31
>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=47.77 E-value=9.6 Score=28.86 Aligned_cols=57 Identities=21% Similarity=0.393 Sum_probs=34.5
Q ss_pred chhHHHHHHHHHHhhhhhcceeeeEEEeeCCccccc-ccCchHHHHHHHHHHhcCChHHHHHHHHHHH
Q 043319 85 SRWCLDELVKILDCKKEYAQIVIPVFYRVDPSDVRN-RTGSFGDSFSKLAERLKVNTEELRSWRNALK 151 (164)
Q Consensus 85 S~wc~~El~~~~~~~~~~~~~iiPVfy~v~p~~v~~-~~g~f~~~f~~~~~~~~~~~~~~~~W~~Al~ 151 (164)
|.|.+.||..-++..+.+.=.=+-+.++|+|-++.+ |+. ++...+.-++++|+.|+.
T Consensus 54 s~~~Lf~LI~k~~~keikTW~~La~~LGVepp~~ek~qSt----------QKvqQYaVRLKRWM~aMH 111 (175)
T PF09441_consen 54 STFTLFELIRKLESKEIKTWAQLALELGVEPPDPEKGQST----------QKVQQYAVRLKRWMRAMH 111 (175)
T ss_pred hHHHHHHHHHHHhhhhHhHHHHHHHHhCCCCCCcccccch----------HHHHHHHHHHHHHHHHhh
Confidence 568888887766654433333345567899888764 321 111123457789999875
No 32
>KOG1136 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]
Probab=46.72 E-value=27 Score=29.91 Aligned_cols=45 Identities=24% Similarity=0.550 Sum_probs=33.6
Q ss_pred hhhcCCeEEEEeecCcc----CchhHHH-HHHHH-HHhhhhhcceeeeEEE
Q 043319 67 AIEASDISVIVFSESYA----SSRWCLD-ELVKI-LDCKKEYAQIVIPVFY 111 (164)
Q Consensus 67 aI~~S~~~Ivv~S~~y~----~S~wc~~-El~~~-~~~~~~~~~~iiPVfy 111 (164)
.|..++--++|--..|+ .|..|++ |+.+. .+|-..++.++||||-
T Consensus 191 ~id~~rpdlLIsESTYattiRdskr~rERdFLk~VhecVa~GGkvlIPvFA 241 (501)
T KOG1136|consen 191 WIDKCRPDLLISESTYATTIRDSKRCRERDFLKKVHECVARGGKVLIPVFA 241 (501)
T ss_pred hhccccCceEEeeccceeeeccccchhHHHHHHHHHHHHhcCCeEEEEeee
Confidence 46677777777666776 4888977 66554 6677778999999995
No 33
>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=45.98 E-value=50 Score=29.48 Aligned_cols=61 Identities=15% Similarity=0.213 Sum_probs=41.9
Q ss_pred ceecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeec
Q 043319 16 HKYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSE 80 (164)
Q Consensus 16 ~~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~ 80 (164)
...||+|-.-+++. ...+..|.+.|++.|++|-+|.. +..+...+..|-+.---.++|+.+
T Consensus 469 ~p~~v~vi~~~~~~-~~~a~~ia~~LR~~Gi~v~~d~~---~~sl~~q~k~A~~~g~~~~iiiG~ 529 (563)
T TIGR00418 469 APVQVVVIPVNERH-LDYAKKVAQKLKKAGIRVDVDDR---NERLGKKIREAQKQKIPYMLVVGD 529 (563)
T ss_pred CCceEEEEEccchH-HHHHHHHHHHHHHcCCEEEEECC---CCCHHHHHHHHHhcCCCEEEEEch
Confidence 34778877655443 46889999999999999999864 445666666665544445555554
No 34
>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=45.36 E-value=50 Score=25.32 Aligned_cols=44 Identities=11% Similarity=0.191 Sum_probs=36.7
Q ss_pred ccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEE
Q 043319 31 DNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISV 75 (164)
Q Consensus 31 ~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~I 75 (164)
......|..+.+.+|+-+|.|.+ .+|+.|...|.+.+.++..+-
T Consensus 35 ~~~i~~i~~~~~~rgVIIfTDpD-~~GekIRk~i~~~vp~~khaf 78 (174)
T TIGR00334 35 DETINLIKKAQKKQGVIILTDPD-FPGEKIRKKIEQHLPGYENCF 78 (174)
T ss_pred HHHHHHHHHHhhcCCEEEEeCCC-CchHHHHHHHHHHCCCCeEEe
Confidence 45678888889999999999986 689999999988888777543
No 35
>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=43.34 E-value=1e+02 Score=20.86 Aligned_cols=60 Identities=25% Similarity=0.181 Sum_probs=37.9
Q ss_pred HHHHHHHHHhcCCeeeee-cCCcCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHhhh
Q 043319 33 FTSHLYSTLCRQNIQTFI-DDQLNRGDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKILDCKK 100 (164)
Q Consensus 33 f~~~L~~~L~~~gi~vf~-d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~ 100 (164)
=+..|...|++.|+.|-+ |-...+ +++.+.+.+.+.-++.+|-.+.. ...++..+.+..+
T Consensus 16 Gl~~la~~l~~~G~~v~~~d~~~~~-----~~l~~~~~~~~pd~V~iS~~~~~---~~~~~~~l~~~~k 76 (121)
T PF02310_consen 16 GLLYLAAYLRKAGHEVDILDANVPP-----EELVEALRAERPDVVGISVSMTP---NLPEAKRLARAIK 76 (121)
T ss_dssp HHHHHHHHHHHTTBEEEEEESSB-H-----HHHHHHHHHTTCSEEEEEESSST---HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCeEEEECCCCCH-----HHHHHHHhcCCCcEEEEEccCcC---cHHHHHHHHHHHH
Confidence 346788899999998854 433222 57778888777777778765443 3444544444433
No 36
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=42.40 E-value=33 Score=29.82 Aligned_cols=63 Identities=16% Similarity=0.142 Sum_probs=39.5
Q ss_pred eecEEEeccc--CcCcccHHHHHHHHHhcCCeeeeecCC-cCCcccchHHHHHhhhcCCeEEEEeecCcc
Q 043319 17 KYDVFVSFRG--EDTQDNFTSHLYSTLCRQNIQTFIDDQ-LNRGDEISESLVNAIEASDISVIVFSESYA 83 (164)
Q Consensus 17 ~ydVFISy~~--~D~~~~f~~~L~~~L~~~gi~vf~d~~-~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~ 83 (164)
.++|+|---. .+.....+..|...|++.|++|.+|++ -..|..+. .+-..---.++|+.++-.
T Consensus 345 P~qV~Iipi~~~~~~~~~~a~~i~~~L~~~Gi~v~~D~~~~~lg~ki~----~a~~~giP~~iiVG~~e~ 410 (439)
T PRK12325 345 PFKVGIINLKQGDEACDAACEKLYAALSAAGIDVLYDDTDERPGAKFA----TMDLIGLPWQIIVGPKGL 410 (439)
T ss_pred CeEEEEEecCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHhHHHH----HHHHcCCCEEEEECCccc
Confidence 3688776432 222346889999999999999999986 55555443 332222235556665544
No 37
>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=41.36 E-value=88 Score=19.49 Aligned_cols=58 Identities=22% Similarity=0.239 Sum_probs=33.4
Q ss_pred cEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeec
Q 043319 19 DVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSE 80 (164)
Q Consensus 19 dVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~ 80 (164)
||+|-..+.+. ..-+-.+...|++.|++|.++.. +..+...+..+-..--..++++.+
T Consensus 3 ~v~i~~~~~~~-~~~a~~i~~~Lr~~g~~v~~~~~---~~~~~~~~~~a~~~~~~~~i~i~~ 60 (91)
T cd00859 3 DVYVVPLGEGA-LSEALELAEQLRDAGIKAEIDYG---GRKLKKQFKYADRSGARFAVILGE 60 (91)
T ss_pred cEEEEEcChHH-HHHHHHHHHHHHHCCCEEEEecC---CCCHHHHHHHHHHcCCCEEEEEcH
Confidence 67776544432 24577888999999999988653 123333444443332234455544
No 38
>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=41.00 E-value=1.9e+02 Score=23.30 Aligned_cols=76 Identities=13% Similarity=0.145 Sum_probs=50.6
Q ss_pred ccHHHHHHHHHhcCCeeee-ecCC---cCCcccchHHHHHhh--hcCCeEEEEeecCccCchhHHHHHHHHHHh-hhhhc
Q 043319 31 DNFTSHLYSTLCRQNIQTF-IDDQ---LNRGDEISESLVNAI--EASDISVIVFSESYASSRWCLDELVKILDC-KKEYA 103 (164)
Q Consensus 31 ~~f~~~L~~~L~~~gi~vf-~d~~---~~~G~~~~~~i~~aI--~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~-~~~~~ 103 (164)
..++..|.+.|.+.|+.+- .+.. +--|--+. +.-+ ...++-||.+|.+...+.....+|.+++.. .++.+
T Consensus 90 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vP---L~~l~~~~~~iPvV~~s~~~~~~~~~~~~lG~al~~~l~~~~ 166 (271)
T cd07373 90 TALAEACVTACPEHGVHARGVDYDGFPIDTGTITA---CTLMGIGTEALPLVVASNNLYHSGEITEKLGAIAADAAKDQN 166 (271)
T ss_pred HHHHHHHHHHHHHCCCcEEEecCCCCCCcchhHHH---HHHHcccCCCCCEEEEEeCCCCCHHHHHHHHHHHHHHHHHcC
Confidence 4699999999999999885 5553 23333222 1223 246677888998886677777899998885 44444
Q ss_pred ceeeeE
Q 043319 104 QIVIPV 109 (164)
Q Consensus 104 ~~iiPV 109 (164)
.+|+-|
T Consensus 167 ~rV~iI 172 (271)
T cd07373 167 KRVAVV 172 (271)
T ss_pred CeEEEE
Confidence 566644
No 39
>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=39.74 E-value=1.1e+02 Score=20.41 Aligned_cols=58 Identities=12% Similarity=0.172 Sum_probs=36.5
Q ss_pred HHHHHHHHHhcCCeeeeecCCcCCcc-cchHHHHHhhhcCCeEEEEeecCccCchhHHHH
Q 043319 33 FTSHLYSTLCRQNIQTFIDDQLNRGD-EISESLVNAIEASDISVIVFSESYASSRWCLDE 91 (164)
Q Consensus 33 f~~~L~~~L~~~gi~vf~d~~~~~G~-~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~E 91 (164)
....+.+.+++.|...-.. .-..|. .-...+...|.++++.|++.+----+..|...+
T Consensus 11 ~~~~~~~~~~~~G~~~~~h-g~~~~~~~~~~~l~~~i~~aD~VIv~t~~vsH~~~~~vk~ 69 (97)
T PF10087_consen 11 RERRYKRILEKYGGKLIHH-GRDGGDEKKASRLPSKIKKADLVIVFTDYVSHNAMWKVKK 69 (97)
T ss_pred cHHHHHHHHHHcCCEEEEE-ecCCCCccchhHHHHhcCCCCEEEEEeCCcChHHHHHHHH
Confidence 5667888899999876554 111121 122247788999999988876555555444333
No 40
>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=38.21 E-value=2e+02 Score=23.55 Aligned_cols=127 Identities=17% Similarity=0.268 Sum_probs=72.3
Q ss_pred cccCcCcccHHHHHHHHHhcCCeeeeecC-------CcCCcccchHHHHHhhh-------cCCeEE----EEeecCccCc
Q 043319 24 FRGEDTQDNFTSHLYSTLCRQNIQTFIDD-------QLNRGDEISESLVNAIE-------ASDISV----IVFSESYASS 85 (164)
Q Consensus 24 y~~~D~~~~f~~~L~~~L~~~gi~vf~d~-------~~~~G~~~~~~i~~aI~-------~S~~~I----vv~S~~y~~S 85 (164)
|-.++. ..|..+| ..|.+.|++.++.- +++|+-+-.+++.+.++ .-++.. +++|..|.-
T Consensus 53 FWTKnp-~P~l~~L-~~l~~~gy~~yfq~Tit~Y~~~lEp~vP~~~~~i~~f~~Ls~~iG~~rViWRYDPIil~~~~~~- 129 (266)
T PF08902_consen 53 FWTKNP-APFLPYL-DELDERGYPYYFQFTITGYGKDLEPNVPPKDERIETFRELSERIGPERVIWRYDPIILTDKYTV- 129 (266)
T ss_pred EecCCc-HHHHhhH-HHHHhCCCceEEEEEeCCCCccccCCCCCHHHHHHHHHHHHHHHCCCcEEEecCCEeECCCCCH-
Confidence 545554 3677777 67778888877652 26666543333333322 233321 456666544
Q ss_pred hhHHHHHHHHHHhhhhhcceeeeEEEeeCCcccccccCchHHHHHHHHHHh-cCChHHHHHHHHHHHHhhcccceee
Q 043319 86 RWCLDELVKILDCKKEYAQIVIPVFYRVDPSDVRNRTGSFGDSFSKLAERL-KVNTEELRSWRNALKEAATLSGFHS 161 (164)
Q Consensus 86 ~wc~~El~~~~~~~~~~~~~iiPVfy~v~p~~v~~~~g~f~~~f~~~~~~~-~~~~~~~~~W~~Al~~v~~~~G~~~ 161 (164)
.|-++.+..+.+.......+++-=|++..+.--++. ..+.-.. ..+++....--..|.++|...|..+
T Consensus 130 ~~h~~~F~~la~~L~g~t~~~viSF~D~Y~k~~~~l--------~~~~~~~~~~~~~~~~~l~~~l~~ia~~~g~~l 198 (266)
T PF08902_consen 130 DYHLEAFERLAEALAGYTDRCVISFLDLYRKVRRNL--------ARLGFRIREPSEEEKRELAKRLAEIAKKYGMTL 198 (266)
T ss_pred HHHHHHHHHHHHHHhccCCEEEEEeeeccHHHHHHH--------HhhcCCCCCCCHHHHHHHHHHHHHHHHHcCCEE
Confidence 677777777777666556666666766644322221 1111001 2245666677788888888888765
No 41
>COG0710 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism]
Probab=38.04 E-value=1.2e+02 Score=24.18 Aligned_cols=67 Identities=13% Similarity=0.190 Sum_probs=43.3
Q ss_pred cHHHHHHHHHhcCCeeeeecCC-cCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHhhhhhc
Q 043319 32 NFTSHLYSTLCRQNIQTFIDDQ-LNRGDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKILDCKKEYA 103 (164)
Q Consensus 32 ~f~~~L~~~L~~~gi~vf~d~~-~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~ 103 (164)
.....|.+..+.+| ..++|-+ ..+++.+ .++...-++-. +|+|-+...+.+..+|+..++..+...+
T Consensus 79 ~~i~ll~~la~~~~-~d~iDiEl~~~~~~~-~~~~~~~~~~~---vI~SyH~F~~TP~~~~i~~~l~km~~~~ 146 (231)
T COG0710 79 EYIELLKKLAELNG-PDYIDIELSSPEDDV-KEIIKFAKKHG---VIVSYHDFEKTPPLEEIIERLDKMESLG 146 (231)
T ss_pred HHHHHHHHHHhhcC-CCEEEEEccCcchhH-HHHHhccccCC---EEEEeccCCCCCcHHHHHHHHHHHHhhC
Confidence 46666666666666 5677766 3333322 23333223333 8899999999999999999988875544
No 42
>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=37.81 E-value=1.6e+02 Score=23.50 Aligned_cols=57 Identities=11% Similarity=0.156 Sum_probs=32.7
Q ss_pred EEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCc-ccchHHHHHhhhcCCeEEEE
Q 043319 20 VFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRG-DEISESLVNAIEASDISVIV 77 (164)
Q Consensus 20 VFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G-~~~~~~i~~aI~~S~~~Ivv 77 (164)
|.+-|...+-....+..|.+.|++.|+++-....+.+| ..+. .+...|+++..-+|+
T Consensus 138 v~~v~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~~d~~-~~l~~i~~~~~~~vi 195 (334)
T cd06342 138 VAIIDDKTAYGQGLADEFKKALKAAGGKVVAREGTTDGATDFS-AILTKIKAANPDAVF 195 (334)
T ss_pred EEEEeCCcchhhHHHHHHHHHHHHcCCEEEEEecCCCCCccHH-HHHHHHHhcCCCEEE
Confidence 44445433333456778888888889887765555555 3444 344556654433333
No 43
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=37.34 E-value=27 Score=31.43 Aligned_cols=64 Identities=17% Similarity=0.298 Sum_probs=40.9
Q ss_pred ceecEEEeccc--CcCcccHHHHHHHHHhcCCeeeeecCC-cCCcccchHHHHHhhhcCCeEEEEeecCcc
Q 043319 16 HKYDVFVSFRG--EDTQDNFTSHLYSTLCRQNIQTFIDDQ-LNRGDEISESLVNAIEASDISVIVFSESYA 83 (164)
Q Consensus 16 ~~ydVFISy~~--~D~~~~f~~~L~~~L~~~gi~vf~d~~-~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~ 83 (164)
-.|+|+|---. .+.....+..|+..|++.|+++.+|++ -.+|..+.+.- ..+.. .++++.++..
T Consensus 467 aP~~v~Iv~~~~~~~~~~~~a~~i~~~L~~~gi~v~~Ddr~~~~g~k~~~ad---~~GiP-~~iiiG~~e~ 533 (565)
T PRK09194 467 APFDVHIVPVNMKDEEVKELAEKLYAELQAAGIEVLLDDRKERPGVKFADAD---LIGIP-HRIVVGDRGL 533 (565)
T ss_pred CCceEEEEECCCCcHHHHHHHHHHHHHHhccCCeEEEECCCCCHHHHHHHHH---hcCCC-EEEEEcCccc
Confidence 34888887543 222346889999999999999999987 56666554322 22223 3455555533
No 44
>cd06371 PBP1_sensory_GC_DEF_like Ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. This group includes the ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. They share a similar topology with an N-terminal extracellular ligand-binding domain, a single transmembrane domain, and a C-terminal cytosolic region that contains kinase-like and catalytic domains. GC-D is specifically expressed in a subpopulation of olfactory sensory neurons. GC-E and GC-F are colocalized within the same photoreceptor cells of the retina and have important roles in phototransduction. Unlike the other family members, GC-E and GC-F have no known extracellular ligands. Instead, they are activated under low calcium conditions by guanylyl cyclase activating proteins called GCAPs. GC-D expressing neurons have been implicated in pheromone detection and GC-D is phyloge
Probab=37.05 E-value=1.6e+02 Score=24.59 Aligned_cols=53 Identities=6% Similarity=0.145 Sum_probs=31.2
Q ss_pred cHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcC---CeEEEEeecCccC
Q 043319 32 NFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEAS---DISVIVFSESYAS 84 (164)
Q Consensus 32 ~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S---~~~Ivv~S~~y~~ 84 (164)
.....|.+.|++.|+.+-....+.+++.--..+.+.|+.. ++.|+.....+..
T Consensus 147 ~~~~~l~~~l~~~gi~v~~~~~~~~~~~d~~~~L~~lk~~~~~~viv~~~~~~~~~ 202 (382)
T cd06371 147 ETAQKLASALRAHGLPVGLVTSMGPDEKGAREALKKVRSADRVRVVIMCMHSVLIG 202 (382)
T ss_pred HHHHHHHHHHHHCCCcEEEEEEecCCHHHHHHHHHHHhcCCCcEEEEEEeeccccC
Confidence 4677888888888987665444554543233555666653 4455444444543
No 45
>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=36.32 E-value=1.4e+02 Score=24.27 Aligned_cols=63 Identities=10% Similarity=0.068 Sum_probs=36.1
Q ss_pred cEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcc-cchHHHHHhhhcCCeEEEEeecCc
Q 043319 19 DVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGD-EISESLVNAIEASDISVIVFSESY 82 (164)
Q Consensus 19 dVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~-~~~~~i~~aI~~S~~~Ivv~S~~y 82 (164)
.|.+-|...+-....+..+...+++.|+.|-....+.++. .+. .+...|+.++.-+|++.-..
T Consensus 146 ~v~~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~d~~-~~i~~l~~~~~d~v~~~~~~ 209 (347)
T cd06340 146 TVALVHEDTEFGTSVAEAIKKFAKERGFEIVEDISYPANARDLT-SEVLKLKAANPDAILPASYT 209 (347)
T ss_pred eEEEEecCchHhHHHHHHHHHHHHHcCCEEEEeeccCCCCcchH-HHHHHHHhcCCCEEEEcccc
Confidence 3555553322224567777788888898887655555554 444 34455666555555554333
No 46
>cd01423 MGS_CPS_I_III Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
Probab=35.82 E-value=49 Score=22.84 Aligned_cols=30 Identities=7% Similarity=0.064 Sum_probs=22.6
Q ss_pred EEEecccCcCcccHHHHHHHHHhcCCeeeeec
Q 043319 20 VFVSFRGEDTQDNFTSHLYSTLCRQNIQTFID 51 (164)
Q Consensus 20 VFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d 51 (164)
||||.+..|. .-...+.+.|...|++++--
T Consensus 3 vlisv~~~dk--~~~~~~a~~l~~~G~~i~aT 32 (116)
T cd01423 3 ILISIGSYSK--PELLPTAQKLSKLGYKLYAT 32 (116)
T ss_pred EEEecCcccc--hhHHHHHHHHHHCCCEEEEc
Confidence 7999987763 34557778888889988753
No 47
>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=34.40 E-value=46 Score=21.27 Aligned_cols=31 Identities=10% Similarity=0.195 Sum_probs=17.3
Q ss_pred CCeeeeecCCcCCcccchHHHHHhhhcCCeEE
Q 043319 44 QNIQTFIDDQLNRGDEISESLVNAIEASDISV 75 (164)
Q Consensus 44 ~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~I 75 (164)
+.+-+|+|.+ .+|......+.+.+..-...+
T Consensus 44 ~~vii~~D~D-~aG~~a~~~~~~~l~~~g~~~ 74 (79)
T cd03364 44 KEVILAFDGD-EAGQKAALRALELLLKLGLNV 74 (79)
T ss_pred CeEEEEECCC-HHHHHHHHHHHHHHHHCCCeE
Confidence 4566677765 556655555555555444333
No 48
>PRK14938 Ser-tRNA(Thr) hydrolase; Provisional
Probab=34.17 E-value=1e+02 Score=26.68 Aligned_cols=59 Identities=19% Similarity=0.175 Sum_probs=38.7
Q ss_pred eecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEee
Q 043319 17 KYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFS 79 (164)
Q Consensus 17 ~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S 79 (164)
.++|+|-.-+++. ...+..|...|++.|+++.+|.. +..+..++..|-+.---.++++.
T Consensus 274 P~qV~IIpl~eel-~e~AlkLA~eLR~aGIrVeiDl~---srSLgKQiK~AdK~GaPfvIIIG 332 (387)
T PRK14938 274 PIQVRILPVKKDF-LDFSIQVAERLRKEGIRVNVDDL---DDSLGNKIRRAGTEWIPFVIIIG 332 (387)
T ss_pred cceEEEEEeChHH-HHHHHHHHHHHHHCCCEEEEECC---CCCHHHHHHHHHHcCCCEEEEEC
Confidence 4677776655443 35788999999999999999874 34555566666544333444444
No 49
>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=33.71 E-value=43 Score=25.86 Aligned_cols=47 Identities=17% Similarity=0.147 Sum_probs=33.2
Q ss_pred eecEEEecccCc-----CcccHHHHHHHHHhcCCeeeeecCC-c-CCcccchHH
Q 043319 17 KYDVFVSFRGED-----TQDNFTSHLYSTLCRQNIQTFIDDQ-L-NRGDEISES 63 (164)
Q Consensus 17 ~ydVFISy~~~D-----~~~~f~~~L~~~L~~~gi~vf~d~~-~-~~G~~~~~~ 63 (164)
.++|+|---+.+ .-...+..|...|...||++.+|.+ - .+|..+...
T Consensus 10 P~qVvIipi~~~~~~~~~~~~~a~~i~~~Lr~~Girv~~D~r~~~s~g~K~~~a 63 (202)
T cd00862 10 PIQVVIVPIGIKDEKREEVLEAADELAERLKAAGIRVHVDDRDNYTPGWKFNDW 63 (202)
T ss_pred CceEEEEEecCCccchHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHhHHHHHH
Confidence 367776643322 0235789999999999999999886 4 788776543
No 50
>PLN03194 putative disease resistance protein; Provisional
Probab=33.64 E-value=1.8e+02 Score=22.61 Aligned_cols=64 Identities=11% Similarity=0.257 Sum_probs=44.7
Q ss_pred cCCeeeeecCC-cCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHhhhhhcceeeeEE
Q 043319 43 RQNIQTFIDDQ-LNRGDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKILDCKKEYAQIVIPVF 110 (164)
Q Consensus 43 ~~gi~vf~d~~-~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf 110 (164)
++.+.||+.-+ -.-...+...+.++++...+.+++-.......+--..+|..+++. ....|.||
T Consensus 24 ~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIee----Sri~IvVf 88 (187)
T PLN03194 24 AKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRN----CKVGVAVF 88 (187)
T ss_pred CCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHh----CeEEEEEE
Confidence 45788999765 333346788899999999988887665565555445566666654 44888887
No 51
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=33.28 E-value=2.2e+02 Score=23.67 Aligned_cols=74 Identities=12% Similarity=0.103 Sum_probs=46.0
Q ss_pred cEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHH
Q 043319 19 DVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESYASSRWCLDEL 92 (164)
Q Consensus 19 dVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El 92 (164)
.|+|-|+...-...+...+.+.|+..|.++-.+....|++.--..+...|..+..-+|++........-..+++
T Consensus 150 ~v~ii~~~~~yg~~~~~~~~~~l~~~G~~~~~~~~~~~~~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~r~~ 223 (366)
T COG0683 150 RVAIIGDDYAYGEGLADAFKAALKALGGEVVVEEVYAPGDTDFSALVAKIKAAGPDAVLVGGYGPDAALFLRQA 223 (366)
T ss_pred EEEEEeCCCCcchhHHHHHHHHHHhCCCeEEEEEeeCCCCCChHHHHHHHHhcCCCEEEECCCCccchHHHHHH
Confidence 46666654444467888999999999997444344555553344566667766666666666655544444443
No 52
>COG2130 Putative NADP-dependent oxidoreductases [General function prediction only]
Probab=31.82 E-value=1.1e+02 Score=25.82 Aligned_cols=60 Identities=18% Similarity=0.406 Sum_probs=39.2
Q ss_pred eecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhc-CCeEEEEeecCccC
Q 043319 17 KYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEA-SDISVIVFSESYAS 84 (164)
Q Consensus 17 ~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~-S~~~Ivv~S~~y~~ 84 (164)
.+|+-|.|+.+| |...|.++-- +||.+++|. .|..+.+.....+.. .|+.++=.=..|.+
T Consensus 196 GfD~~idyk~~d----~~~~L~~a~P-~GIDvyfeN---VGg~v~DAv~~~ln~~aRi~~CG~IS~YN~ 256 (340)
T COG2130 196 GFDAGIDYKAED----FAQALKEACP-KGIDVYFEN---VGGEVLDAVLPLLNLFARIPVCGAISQYNA 256 (340)
T ss_pred CCceeeecCccc----HHHHHHHHCC-CCeEEEEEc---CCchHHHHHHHhhccccceeeeeehhhcCC
Confidence 589999997654 6666654443 899999987 466666666666654 55544434444544
No 53
>PRK08350 hypothetical protein; Provisional
Probab=31.75 E-value=47 Score=28.19 Aligned_cols=33 Identities=12% Similarity=0.076 Sum_probs=28.4
Q ss_pred CceecEEEecccCcCcccHHHHHHHHHhcCCee
Q 043319 15 VHKYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQ 47 (164)
Q Consensus 15 ~~~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~ 47 (164)
...|-+.+|||+-++.+.|+.+|.-+|...-|+
T Consensus 279 ~~g~~~vvSHRSGETeD~~IAdLaVa~~agqIK 311 (341)
T PRK08350 279 SERITPILAEAKYESADEALPHLAVGLRCPAML 311 (341)
T ss_pred HcCCeEEeecCCCCCcchhHHHHHHHhCCCccc
Confidence 345889999999888899999999999877776
No 54
>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=31.49 E-value=97 Score=23.47 Aligned_cols=68 Identities=26% Similarity=0.282 Sum_probs=41.3
Q ss_pred HHhcCCeeeee-cCC--c-CCc-ccchHHHHHhhhcCCe-----EEEEeecCccCchhHHHHHHHHHHhhhhhcceeeeE
Q 043319 40 TLCRQNIQTFI-DDQ--L-NRG-DEISESLVNAIEASDI-----SVIVFSESYASSRWCLDELVKILDCKKEYAQIVIPV 109 (164)
Q Consensus 40 ~L~~~gi~vf~-d~~--~-~~G-~~~~~~i~~aI~~S~~-----~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~iiPV 109 (164)
.|.+.||+..+ |.+ + .+. ..+.+++.+.+++++. .|+|+|.+--+++---.+-...++.. .=|||
T Consensus 35 ~Lk~~Gik~li~DkDNTL~~~~~~~i~~~~~~~~~~l~~~~~~~~v~IvSNsaGs~~d~~~~~a~~~~~~-----lgIpv 109 (168)
T PF09419_consen 35 HLKKKGIKALIFDKDNTLTPPYEDEIPPEYAEWLNELKKQFGKDRVLIVSNSAGSSDDPDGERAEALEKA-----LGIPV 109 (168)
T ss_pred hhhhcCceEEEEcCCCCCCCCCcCcCCHHHHHHHHHHHHHCCCCeEEEEECCCCcccCccHHHHHHHHHh-----hCCcE
Confidence 38999998544 554 4 455 3567788888877663 48999998766552222333333321 22888
Q ss_pred EEe
Q 043319 110 FYR 112 (164)
Q Consensus 110 fy~ 112 (164)
+..
T Consensus 110 l~h 112 (168)
T PF09419_consen 110 LRH 112 (168)
T ss_pred EEe
Confidence 743
No 55
>PF01113 DapB_N: Dihydrodipicolinate reductase, N-terminus; InterPro: IPR000846 Dihydrodipicolinate reductase catalyzes the second step in the biosynthesis of diaminopimelic acid and lysine, the NAD or NADP-dependent reduction of 2,3-dihydrodipicolinate into 2,3,4,5-tetrahydrodipicolinate [, , ]. In Escherichia coli and Mycobacterium tuberculosis, dihydrodipicolinate reductase has equal specificity for NADH and NADPH, however in Thermotoga maritima there it has a greater affinity for NADPH []. In addition, the enzyme is inhibited by high concentrations of its substrate, which consequently acts as a feedback control on the lysine biosynthesis pathway. In T. maritima, the enzyme also lacks N-terminal and C-terminal loops which are present in enzyme of the former two organisms. This entry represents the N-terminal domain of dihydrodipicolinate reductase which binds the dinucleotide NAD(P)H.; GO: 0008839 dihydrodipicolinate reductase activity, 0009089 lysine biosynthetic process via diaminopimelate, 0055114 oxidation-reduction process; PDB: 3QY9_D 1VM6_C 1ARZ_A 1DIH_A 1DRW_A 1DRV_A 1DRU_A 2DAP_A 1DAP_B 3DAP_A ....
Probab=31.31 E-value=1.1e+02 Score=21.38 Aligned_cols=29 Identities=24% Similarity=0.329 Sum_probs=11.8
Q ss_pred ecEEEecccCcCcccHHHHHHHHHhcCCeeeee
Q 043319 18 YDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFI 50 (164)
Q Consensus 18 ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~ 50 (164)
.||-|-|+..+ ....++..+++. |+++-.
T Consensus 68 ~DVvIDfT~p~---~~~~~~~~~~~~-g~~~Vi 96 (124)
T PF01113_consen 68 ADVVIDFTNPD---AVYDNLEYALKH-GVPLVI 96 (124)
T ss_dssp -SEEEEES-HH---HHHHHHHHHHHH-T-EEEE
T ss_pred CCEEEEcCChH---HhHHHHHHHHhC-CCCEEE
Confidence 56666665433 233344333333 444443
No 56
>KOG2792 consensus Putative cytochrome C oxidase assembly protein [Energy production and conversion]
Probab=31.06 E-value=52 Score=27.01 Aligned_cols=31 Identities=32% Similarity=0.506 Sum_probs=21.5
Q ss_pred hhHHHHHHHHHHh---hh-hhcceeeeEEEeeCCc
Q 043319 86 RWCLDELVKILDC---KK-EYAQIVIPVFYRVDPS 116 (164)
Q Consensus 86 ~wc~~El~~~~~~---~~-~~~~~iiPVfy~v~p~ 116 (164)
+=|-+||.+.... .+ ..+..++|||.-|+|.
T Consensus 153 DICPdELeKm~~~Vd~i~~~~~~~~~PlFIsvDPe 187 (280)
T KOG2792|consen 153 DICPDELEKMSAVVDEIEAKPGLPPVPLFISVDPE 187 (280)
T ss_pred CcChHHHHHHHHHHHHHhccCCCCccceEEEeCcc
Confidence 3588888775443 22 2456777999999994
No 57
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=30.81 E-value=1.2e+02 Score=26.33 Aligned_cols=46 Identities=22% Similarity=0.222 Sum_probs=34.6
Q ss_pred HHHHHhhhcCC-eEEEEeecCcc-CchhHHHHHHHHHHhhhhhcceee
Q 043319 62 ESLVNAIEASD-ISVIVFSESYA-SSRWCLDELVKILDCKKEYAQIVI 107 (164)
Q Consensus 62 ~~i~~aI~~S~-~~Ivv~S~~y~-~S~wc~~El~~~~~~~~~~~~~ii 107 (164)
+.+.+++.+.+ ++.++.+|+=. ..-|..+||.++.+...+.+-+||
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 47777888887 67777887755 688999999999886655555554
No 58
>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=30.76 E-value=46 Score=22.64 Aligned_cols=17 Identities=29% Similarity=0.526 Sum_probs=14.2
Q ss_pred CChHHHHHHHHHHHHhh
Q 043319 138 VNTEELRSWRNALKEAA 154 (164)
Q Consensus 138 ~~~~~~~~W~~Al~~v~ 154 (164)
++++..++|..||..|.
T Consensus 86 ~s~ee~~eWi~ai~~v~ 102 (102)
T cd01241 86 ESPEEREEWIHAIQTVA 102 (102)
T ss_pred CCHHHHHHHHHHHHhhC
Confidence 45789999999998874
No 59
>PF07894 DUF1669: Protein of unknown function (DUF1669); InterPro: IPR012461 This family is composed of sequences derived from hypothetical eukaryotic proteins of unknown function. Some members of this family are annotated as being potential phospholipases but no literature was found to support this.
Probab=30.53 E-value=3.1e+02 Score=22.68 Aligned_cols=82 Identities=15% Similarity=0.323 Sum_probs=50.6
Q ss_pred eeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHhhhhhcceeeeEEEeeCCcccccccCch
Q 043319 46 IQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKILDCKKEYAQIVIPVFYRVDPSDVRNRTGSF 125 (164)
Q Consensus 46 i~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~iiPVfy~v~p~~v~~~~g~f 125 (164)
+.|+...-....-+|.+.+.+.|++++..|.|+-.-|-.-+- +.+|..|.. .+=+||++=++...+
T Consensus 121 ~~vy~qPp~~~~p~IKE~vR~~I~~A~kVIAIVMD~FTD~dI-f~DLleAa~------kR~VpVYiLLD~~~~------- 186 (284)
T PF07894_consen 121 ATVYFQPPKDGQPHIKEVVRRMIQQAQKVIAIVMDVFTDVDI-FCDLLEAAN------KRGVPVYILLDEQNL------- 186 (284)
T ss_pred EEEEeCCCCCCCCCHHHHHHHHHHHhcceeEEEeeccccHHH-HHHHHHHHH------hcCCcEEEEechhcC-------
Confidence 445553322233467778888999999999998877776432 333444332 244588766555555
Q ss_pred HHHHHHHHHHhcCChHH
Q 043319 126 GDSFSKLAERLKVNTEE 142 (164)
Q Consensus 126 ~~~f~~~~~~~~~~~~~ 142 (164)
..|.+++++...+...
T Consensus 187 -~~Fl~Mc~~~~v~~~~ 202 (284)
T PF07894_consen 187 -PHFLEMCEKLGVNLQH 202 (284)
T ss_pred -hHHHHHHHHCCCChhh
Confidence 4678888877654433
No 60
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=30.39 E-value=1.1e+02 Score=26.48 Aligned_cols=60 Identities=17% Similarity=0.246 Sum_probs=39.6
Q ss_pred eecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeec
Q 043319 17 KYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSE 80 (164)
Q Consensus 17 ~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~ 80 (164)
..||+|.+-+.+. ...+-.+.+.|+++|++|-+|.. +..+...+..|-+.--..++|+.+
T Consensus 325 ~~~v~v~~~~~~~-~~~a~~ia~~LR~~Gi~veid~~---~~~l~k~~k~A~~~~~~~viiiG~ 384 (430)
T CHL00201 325 SIDVYIATQGLKA-QKKGWEIIQFLEKQNIKFELDLS---SSNFHKQIKQAGKKRAKACIILGD 384 (430)
T ss_pred CCCEEEEEcCHHH-HHHHHHHHHHHHhCCCeEEEeeC---CCCHHHHHHHHHHcCCCEEEEEec
Confidence 3689998754432 35677889999999999887542 344555666665544445566655
No 61
>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=30.39 E-value=1.5e+02 Score=19.78 Aligned_cols=46 Identities=15% Similarity=0.281 Sum_probs=32.7
Q ss_pred HHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCccCc
Q 043319 38 YSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESYASS 85 (164)
Q Consensus 38 ~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S 85 (164)
..-++-.|+..+... ...+...+.+.+.+++.++.|++++.++...
T Consensus 10 v~gFrLaGv~~~~~~--~~~ee~~~~l~~l~~~~~~gIIii~e~~~~~ 55 (95)
T PF01990_consen 10 VLGFRLAGVEGVYVN--TDPEEAEEALKELLKDEDVGIIIITEDLAEK 55 (95)
T ss_dssp HHHHHHTTSEEEEES--HSHHHHHHHHHHHHHHTTEEEEEEEHHHHTT
T ss_pred HHHHHHcCCCCccCC--CCHHHHHHHHHHHhcCCCccEEEeeHHHHHH
Confidence 345666788887754 1234455566667778999999999998874
No 62
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=30.18 E-value=65 Score=26.54 Aligned_cols=97 Identities=19% Similarity=0.377 Sum_probs=67.2
Q ss_pred ceecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCC---cCCcccchHHHHHhhh--cCCeEEEEeecCccCchhHHH
Q 043319 16 HKYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQ---LNRGDEISESLVNAIE--ASDISVIVFSESYASSRWCLD 90 (164)
Q Consensus 16 ~~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~---~~~G~~~~~~i~~aI~--~S~~~Ivv~S~~y~~S~wc~~ 90 (164)
-++.+=+||.+.|. .+++..-.-|...|+.+|+|-. -.-|..+-+ ++..|. ..-+++...|.+|-.-.|...
T Consensus 5 ~~~~~a~~f~~~d~--~~~~~~~n~~~~~~v~~~y~~~~~a~~~~~~~~~-~~~e~~q~~~~~~~~f~~~~~~r~~~~~~ 81 (329)
T COG4916 5 VQFEIALSFAGEDR--EYVDRVANLLREAGVTVFYDIFEEANLWGKNLYD-YLSEIYQDKALFTIMFISEHYSRKMWTNH 81 (329)
T ss_pred hheeeeeeecCchH--HHHHHHHHHHHhhccEEEEeehhhhhhhhhHHHH-HHHHHHhhhhHHHhhhhhccccCcCCCcH
Confidence 35667789998884 6888888899999999998752 223333331 222233 345567888999999999999
Q ss_pred HHHHHHHhh-hhhcceeeeEEEeeCC
Q 043319 91 ELVKILDCK-KEYAQIVIPVFYRVDP 115 (164)
Q Consensus 91 El~~~~~~~-~~~~~~iiPVfy~v~p 115 (164)
|+....... .+....++|-.++..|
T Consensus 82 ~~~~~~a~~~~~~~~~~~~~~~~~~~ 107 (329)
T COG4916 82 ERQAMQARAFQEHQEYILPARFDETP 107 (329)
T ss_pred HHHHHHHHHhhhccEEehhhhhccCC
Confidence 998876643 4455688888876543
No 63
>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=30.07 E-value=2.2e+02 Score=23.21 Aligned_cols=54 Identities=13% Similarity=0.182 Sum_probs=27.8
Q ss_pred cEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcc-cchHHHHHhhhcCCe
Q 043319 19 DVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGD-EISESLVNAIEASDI 73 (164)
Q Consensus 19 dVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~-~~~~~i~~aI~~S~~ 73 (164)
.|.|-|...+-....+..+.+.|++.|+.+-....+.++. .+.. ....|+++..
T Consensus 140 ~v~ii~~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~~~d~s~-~i~~i~~~~~ 194 (347)
T cd06335 140 KVALLLDNTGWGRSNRKDLTAALAARGLKPVAVEWFNWGDKDMTA-QLLRAKAAGA 194 (347)
T ss_pred eEEEEeccCchhhhHHHHHHHHHHHcCCeeEEEeeecCCCccHHH-HHHHHHhCCC
Confidence 3444443322234566777777777787765444444443 3443 3344444443
No 64
>PRK03991 threonyl-tRNA synthetase; Validated
Probab=29.93 E-value=64 Score=29.54 Aligned_cols=43 Identities=21% Similarity=0.217 Sum_probs=31.2
Q ss_pred eecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCC-cCCcccc
Q 043319 17 KYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQ-LNRGDEI 60 (164)
Q Consensus 17 ~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~-~~~G~~~ 60 (164)
.++|+|---+++ ....+..|.+.|++.|++|.+|++ -..|..+
T Consensus 499 P~qV~IIpi~e~-~~~~A~eIa~~Lr~~GirV~lDdr~~slgkKi 542 (613)
T PRK03991 499 PTQVRVIPVSER-HLDYAEEVADKLEAAGIRVDVDDRDESLGKKI 542 (613)
T ss_pred CceEEEEEeCHH-HHHHHHHHHHHHHhCCCEEEEECCCCCHHHHH
Confidence 368777654433 346899999999999999999886 4444433
No 65
>PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein.
Probab=29.79 E-value=1.7e+02 Score=21.87 Aligned_cols=66 Identities=14% Similarity=0.169 Sum_probs=40.4
Q ss_pred HHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHhhhhhcceeeeEEEe
Q 043319 33 FTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKILDCKKEYAQIVIPVFYR 112 (164)
Q Consensus 33 f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~iiPVfy~ 112 (164)
=+..|.+..++.|++|++- +|..+.-.+....+ -+..|.| =|..+|...++.....+..++-|+.+
T Consensus 74 ~Ig~l~~lae~~g~~v~i~----~Ggt~ar~~ik~~~-p~~iigV---------AC~~dL~~g~~~~~~~~ip~~gV~l~ 139 (158)
T PF01976_consen 74 DIGDLKKLAEKYGYKVYIA----TGGTLARKIIKEYR-PKAIIGV---------ACERDLISGIQDLKPLGIPVQGVLLD 139 (158)
T ss_pred chhHHHHHHHHcCCEEEEE----cChHHHHHHHHHhC-CCEEEEE---------echHHHHHHHHHHhhcCCCeeEEEeC
Confidence 3567888888999999983 34433323222222 1223333 29999999887765555677777664
No 66
>PRK14799 thrS threonyl-tRNA synthetase; Provisional
Probab=29.67 E-value=1.2e+02 Score=27.43 Aligned_cols=60 Identities=15% Similarity=0.295 Sum_probs=38.8
Q ss_pred eecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeec
Q 043319 17 KYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSE 80 (164)
Q Consensus 17 ~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~ 80 (164)
..+|+|-.-+++. ...+..+.+.|++.|++|-+|.+ +..+...+..|-..---.++|+.+
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 3578776654432 46788999999999999999874 344555565654433334444543
No 67
>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=29.57 E-value=1.9e+02 Score=19.81 Aligned_cols=60 Identities=17% Similarity=0.238 Sum_probs=35.7
Q ss_pred EEEecccCcCcccHHHHHHHHHhcCCeeeeecCC---------c-----CCccc-chHHHHHhhhc-CCeEEEEeecC
Q 043319 20 VFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQ---------L-----NRGDE-ISESLVNAIEA-SDISVIVFSES 81 (164)
Q Consensus 20 VFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~---------~-----~~G~~-~~~~i~~aI~~-S~~~Ivv~S~~ 81 (164)
||||-+..|. .-...+...|.+.|+.++--.. + ..+.. -.+++.+.|++ -.+-+||..|+
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 VFLSVSDHVK--AMLVDLAPKLSSDGFPLFATGGTSRVLADAGIPVRAVSKRHEDGEPTVDAAIAEKGKFDVVINLRD 77 (112)
T ss_pred EEEEEEcccH--HHHHHHHHHHHHCCCEEEECcHHHHHHHHcCCceEEEEecCCCCCcHHHHHHhCCCCEEEEEEcCC
Confidence 6888876663 3444666777777877754321 0 01100 12467777877 78877777665
No 68
>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=29.44 E-value=1.2e+02 Score=23.56 Aligned_cols=36 Identities=11% Similarity=0.179 Sum_probs=28.1
Q ss_pred eeecCCcCCcccchHHHHHhhhcCCeEEEEeecCccCc
Q 043319 48 TFIDDQLNRGDEISESLVNAIEASDISVIVFSESYASS 85 (164)
Q Consensus 48 vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S 85 (164)
||+|. + -+..+..++...+.+..+-|+++||.-..-
T Consensus 127 VW~D~-f-~~~~~~~~~~~~~~~~~~~~c~VSpELh~~ 162 (192)
T cd08584 127 VWIDS-F-TSLWLDNDLILKLLKAGKKICLVSPELHGR 162 (192)
T ss_pred EEEec-c-cccCCCHHHHHHHHHCCcEEEEECHHHcCC
Confidence 78876 2 346677788888888899999999987653
No 69
>KOG0095 consensus GTPase Rab30, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.41 E-value=2.2e+02 Score=21.69 Aligned_cols=60 Identities=22% Similarity=0.385 Sum_probs=38.8
Q ss_pred CCeEEEEeecCccCchhHHHHHHHHHHhhhhhcceeeeEEE--eeCCcccccccCchHHHHHHH
Q 043319 71 SDISVIVFSESYASSRWCLDELVKILDCKKEYAQIVIPVFY--RVDPSDVRNRTGSFGDSFSKL 132 (164)
Q Consensus 71 S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~iiPVfy--~v~p~~v~~~~g~f~~~f~~~ 132 (164)
+...|++..-....|--|+-|...-++... ...|+-|+. +++..|=|+....-|+.|.+.
T Consensus 80 ahalilvydiscqpsfdclpewlreie~ya--n~kvlkilvgnk~d~~drrevp~qigeefs~~ 141 (213)
T KOG0095|consen 80 AHALILVYDISCQPSFDCLPEWLREIEQYA--NNKVLKILVGNKIDLADRREVPQQIGEEFSEA 141 (213)
T ss_pred cceEEEEEecccCcchhhhHHHHHHHHHHh--hcceEEEeeccccchhhhhhhhHHHHHHHHHh
Confidence 445666777777778889888766555432 457888887 455555554444456667654
No 70
>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=29.32 E-value=2.3e+02 Score=22.95 Aligned_cols=109 Identities=17% Similarity=0.284 Sum_probs=60.5
Q ss_pred HHHHHHhcCCeeeeecCCc-----CCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHhhhhhcceeeeEE
Q 043319 36 HLYSTLCRQNIQTFIDDQL-----NRGDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKILDCKKEYAQIVIPVF 110 (164)
Q Consensus 36 ~L~~~L~~~gi~vf~d~~~-----~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf 110 (164)
..++.|... +++|-|-.. ..+.++.+....+++.+..=-+++|-.-...+=-++++..+.+. - . +|||
T Consensus 132 r~R~~l~a~-v~ilaDV~~kh~~~l~~~~~~~~~~~a~~~~~aDaviVtG~~TG~~~~~~~l~~vr~~----~-~-~PVl 204 (254)
T PF03437_consen 132 RYRKRLGAD-VKILADVHVKHSSPLATRDLEEAAKDAVERGGADAVIVTGKATGEPPDPEKLKRVREA----V-P-VPVL 204 (254)
T ss_pred HHHHHcCCC-eEEEeeechhhcccCCCCCHHHHHHHHHHhcCCCEEEECCcccCCCCCHHHHHHHHhc----C-C-CCEE
Confidence 334555556 999988542 23445666666677766665555565444333334455443322 1 2 9999
Q ss_pred E--eeCCcccccccC-----chHHHHHHHHH-HhcCChHHHHHHHHHHH
Q 043319 111 Y--RVDPSDVRNRTG-----SFGDSFSKLAE-RLKVNTEELRSWRNALK 151 (164)
Q Consensus 111 y--~v~p~~v~~~~g-----~f~~~f~~~~~-~~~~~~~~~~~W~~Al~ 151 (164)
. ++.++++.++.. .-|-.|.+... .-+.|.+++++..+++.
T Consensus 205 vGSGvt~~Ni~~~l~~ADG~IVGS~~K~~G~~~n~VD~~Rv~~fm~~v~ 253 (254)
T PF03437_consen 205 VGSGVTPENIAEYLSYADGAIVGSYFKKDGKWENPVDPERVRRFMEAVK 253 (254)
T ss_pred EecCCCHHHHHHHHHhCCEEEEeeeeeeCCEeCCcCCHHHHHHHHHHhh
Confidence 9 588888765411 11122222111 11357899999988765
No 71
>PRK08661 prolyl-tRNA synthetase; Provisional
Probab=29.24 E-value=67 Score=28.28 Aligned_cols=46 Identities=17% Similarity=0.186 Sum_probs=32.2
Q ss_pred eecEEEeccc-----CcCcccHHHHHHHHHhcCCeeeeecC-C-cCCcccchH
Q 043319 17 KYDVFVSFRG-----EDTQDNFTSHLYSTLCRQNIQTFIDD-Q-LNRGDEISE 62 (164)
Q Consensus 17 ~ydVFISy~~-----~D~~~~f~~~L~~~L~~~gi~vf~d~-~-~~~G~~~~~ 62 (164)
.++|+|---. .+.-...+..|.+.|++.|++|.+|. + ..+|..+.+
T Consensus 287 P~qV~Iipi~~~~~~~~~~~~~a~~l~~~Lr~~GirV~lD~r~~~s~gkK~~~ 339 (477)
T PRK08661 287 PIQVVIVPIFKKEEKKEEVLEYAKELAEELKKAGIRVKLDDRSDKTPGWKFNE 339 (477)
T ss_pred CCeEEEEEecCCCcCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHH
Confidence 4778776431 12224578999999999999999998 4 666665543
No 72
>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=29.07 E-value=2.6e+02 Score=22.61 Aligned_cols=51 Identities=14% Similarity=0.232 Sum_probs=30.8
Q ss_pred EEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCc---ccchHHHHHhhhcC
Q 043319 20 VFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRG---DEISESLVNAIEAS 71 (164)
Q Consensus 20 VFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G---~~~~~~i~~aI~~S 71 (164)
|.+-|...+-....+..+.+.|++.|+.+-....+.+| ..+.+. ...|+.+
T Consensus 138 v~ii~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~~~~d~~~~-l~~i~~~ 191 (350)
T cd06366 138 VATIYEDDDYGSGGLPDLVDALQEAGIEISYRAAFPPSANDDDITDA-LKKLKEK 191 (350)
T ss_pred EEEEEEcCcccchhHHHHHHHHHHcCCEEEEEeccCCCCChhHHHHH-HHHHhcC
Confidence 44445433333457788888999999887666556665 244433 4455543
No 73
>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=29.02 E-value=43 Score=30.32 Aligned_cols=33 Identities=27% Similarity=0.528 Sum_probs=27.9
Q ss_pred ccHHHHHHHHHhcCCeeeeecCC-cCCcccchHH
Q 043319 31 DNFTSHLYSTLCRQNIQTFIDDQ-LNRGDEISES 63 (164)
Q Consensus 31 ~~f~~~L~~~L~~~gi~vf~d~~-~~~G~~~~~~ 63 (164)
...+..|++.|+..|++|.+|++ ..+|..+.+.
T Consensus 489 ~~~a~~l~~~L~~~gi~v~~DDr~~~~G~K~~da 522 (568)
T TIGR00409 489 QQLAEELYSELLAQGVDVLLDDRNERAGVKFADS 522 (568)
T ss_pred HHHHHHHHHHHHhCCCEEEEECCCCCHHHHHHhh
Confidence 46889999999999999999998 7778776543
No 74
>PRK15057 UDP-glucose 6-dehydrogenase; Provisional
Probab=28.37 E-value=1.1e+02 Score=26.20 Aligned_cols=55 Identities=5% Similarity=0.229 Sum_probs=39.8
Q ss_pred Eecc--cCcCcccHHHHHHHHHhcCCeeeeecCC-cCC----cccchHHHHHhhhcCCeEEE
Q 043319 22 VSFR--GEDTQDNFTSHLYSTLCRQNIQTFIDDQ-LNR----GDEISESLVNAIEASDISVI 76 (164)
Q Consensus 22 ISy~--~~D~~~~f~~~L~~~L~~~gi~vf~d~~-~~~----G~~~~~~i~~aI~~S~~~Iv 76 (164)
++|. ..|.|.+=+-.|.+.|..+|..|-..+- +.. |-.+.++..+++++++..|+
T Consensus 304 lafK~~t~D~R~Sp~~~i~~~L~~~G~~v~~~DP~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (388)
T PRK15057 304 LIMKSGSDNFRASSIQGIMKRIKAKGVEVIIYEPVMKEDSFFNSRLERDLATFKQQADVIIS 365 (388)
T ss_pred ceeCCCCCccccChHHHHHHHHHhCCCEEEEECCCCCchhhcCCeeeCCHHHHHHhCCEEEE
Confidence 4564 3478888899999999999988766554 322 34456677788888888766
No 75
>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=28.13 E-value=2e+02 Score=23.76 Aligned_cols=41 Identities=12% Similarity=0.155 Sum_probs=21.3
Q ss_pred cHHHHHHHHHhcCCe----eeeecCCcCCcc-cchHHHHHhhhcCCe
Q 043319 32 NFTSHLYSTLCRQNI----QTFIDDQLNRGD-EISESLVNAIEASDI 73 (164)
Q Consensus 32 ~f~~~L~~~L~~~gi----~vf~d~~~~~G~-~~~~~i~~aI~~S~~ 73 (164)
..+..+.+.|++.|+ .+-....+.+|+ .+. .+.+.|+.++.
T Consensus 169 ~~~~~~~~~~~~~g~~~~~~v~~~~~~~~~~~d~~-~~l~~ik~~~~ 214 (377)
T cd06379 169 AAQKRFETLLEEREIEFKIKVEKVVEFEPGEKNVT-SLLQEAKELTS 214 (377)
T ss_pred HHHHHHHHHHHhcCCccceeeeEEEecCCchhhHH-HHHHHHhhcCC
Confidence 466677777777777 433333344443 333 33444554333
No 76
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=27.54 E-value=1.4e+02 Score=26.76 Aligned_cols=60 Identities=12% Similarity=0.215 Sum_probs=38.7
Q ss_pred eecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeec
Q 043319 17 KYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSE 80 (164)
Q Consensus 17 ~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~ 80 (164)
.+||+|---+++. ...+..|.+.|++.||+|-+|.+ +..+...+..|-+.---.++|+.+
T Consensus 476 p~~v~Ii~~~~~~-~~~a~~i~~~Lr~~gi~v~~d~~---~~~l~kk~~~A~~~g~p~~iivG~ 535 (575)
T PRK12305 476 PVQVVIIPVADAH-NEYAEEVAKKLRAAGIRVEVDTS---NERLNKKIRNAQKQKIPYMLVVGD 535 (575)
T ss_pred CccEEEEEeChHH-HHHHHHHHHHHHHCCCEEEEECC---CCCHHHHHHHHHhcCCCEEEEEec
Confidence 3578886644432 45788999999999999999875 334444555554443334555554
No 77
>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=27.38 E-value=1.7e+02 Score=20.56 Aligned_cols=18 Identities=33% Similarity=0.423 Sum_probs=9.3
Q ss_pred HHHhhhcCCeEEEEeecC
Q 043319 64 LVNAIEASDISVIVFSES 81 (164)
Q Consensus 64 i~~aI~~S~~~Ivv~S~~ 81 (164)
+.++|++++++++|++-.
T Consensus 5 ~~~~i~~aD~vl~ViD~~ 22 (141)
T cd01857 5 LWRVVERSDIVVQIVDAR 22 (141)
T ss_pred HHHHHhhCCEEEEEEEcc
Confidence 444555555555555543
No 78
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=27.20 E-value=2.4e+02 Score=20.22 Aligned_cols=86 Identities=13% Similarity=0.093 Sum_probs=50.6
Q ss_pred EEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHhh
Q 043319 20 VFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKILDCK 99 (164)
Q Consensus 20 VFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~ 99 (164)
|+|.=-+.|..+.=+.-+...|+..|+.|..-. ++.-.+++.++..+.+.-++++|--.... +..+..+++..
T Consensus 5 v~~a~~g~D~Hd~g~~iv~~~l~~~GfeVi~lg----~~~s~e~~v~aa~e~~adii~iSsl~~~~---~~~~~~~~~~L 77 (132)
T TIGR00640 5 ILVAKMGQDGHDRGAKVIATAYADLGFDVDVGP----LFQTPEEIARQAVEADVHVVGVSSLAGGH---LTLVPALRKEL 77 (132)
T ss_pred EEEEeeCCCccHHHHHHHHHHHHhCCcEEEECC----CCCCHHHHHHHHHHcCCCEEEEcCchhhh---HHHHHHHHHHH
Confidence 455444455432233445566888999987633 23334567777788888888887766553 33344444444
Q ss_pred hhhcceeeeEEEe
Q 043319 100 KEYAQIVIPVFYR 112 (164)
Q Consensus 100 ~~~~~~iiPVfy~ 112 (164)
++.+..-+||+..
T Consensus 78 ~~~g~~~i~vivG 90 (132)
T TIGR00640 78 DKLGRPDILVVVG 90 (132)
T ss_pred HhcCCCCCEEEEe
Confidence 3434445778875
No 79
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=27.08 E-value=1.4e+02 Score=27.01 Aligned_cols=60 Identities=13% Similarity=0.137 Sum_probs=39.6
Q ss_pred eecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeec
Q 043319 17 KYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSE 80 (164)
Q Consensus 17 ~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~ 80 (164)
..||+|-.-++.. ...+..|.+.|++.|++|-+|.+ +..+...+..|-+.---.++|+.+
T Consensus 539 p~~v~Ii~~~~~~-~~~a~~i~~~Lr~~gi~v~~d~~---~~~l~kki~~A~~~g~~~~iiiG~ 598 (638)
T PRK00413 539 PVQVVVLPITDKH-ADYAKEVAKKLKAAGIRVEVDLR---NEKIGYKIREAQLQKVPYMLVVGD 598 (638)
T ss_pred cceEEEEEeChhH-HHHHHHHHHHHHhCCCEEEEECC---CCCHhHHHHHhhccCCCEEEEEcc
Confidence 3578877654432 46788999999999999999874 344555555554443345555654
No 80
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=26.98 E-value=86 Score=22.47 Aligned_cols=47 Identities=23% Similarity=0.339 Sum_probs=32.9
Q ss_pred HHHHhhhcCCeEEEEeecCccCchhHHH----HHHHHHHhhhhhcceeeeEEEe
Q 043319 63 SLVNAIEASDISVIVFSESYASSRWCLD----ELVKILDCKKEYAQIVIPVFYR 112 (164)
Q Consensus 63 ~i~~aI~~S~~~Ivv~S~~y~~S~wc~~----El~~~~~~~~~~~~~iiPVfy~ 112 (164)
.+...+..+-+.-+++.|||.+- -|.+ ||..+.+.+ .-..|.||-|-
T Consensus 55 ~L~~~LCG~~~~~i~IDP~~~~K-GC~~TL~HEL~H~WQ~R--sYG~i~PITY~ 105 (141)
T PHA02456 55 ALPQDLCGQFVGWIEIDPDYANK-GCRDTLAHELNHAWQFR--TYGLVQPITYA 105 (141)
T ss_pred hcCcchhhcceeEEEECCccccc-chHHHHHHHHHHHHhhh--ccceeeeeehh
Confidence 34445677889999999999984 4765 566666543 23589999884
No 81
>cd02951 SoxW SoxW family; SoxW is a bacterial periplasmic TRX, containing a redox active CXXC motif, encoded by a genetic locus (sox operon) involved in thiosulfate oxidation. Sulfur bacteria oxidize sulfur compounds to provide reducing equivalents for carbon dioxide fixation during autotrophic growth and the respiratory electron transport chain. It is unclear what the role of SoxW is, since it has been found to be dispensable in the oxidation of thiosulfate to sulfate. SoxW is specifically kept in the reduced state by SoxV, which is essential in thiosulfate oxidation.
Probab=26.39 E-value=2.2e+02 Score=19.45 Aligned_cols=31 Identities=19% Similarity=0.251 Sum_probs=20.5
Q ss_pred hHHHHHhhhcC-CeEEEEeecCccCchhHHHHHH
Q 043319 61 SESLVNAIEAS-DISVIVFSESYASSRWCLDELV 93 (164)
Q Consensus 61 ~~~i~~aI~~S-~~~Ivv~S~~y~~S~wc~~El~ 93 (164)
.+++.+++++- +..++.|....+ .+|.....
T Consensus 3 ~~~~~~a~~~~~k~vlv~f~a~wC--~~C~~~~~ 34 (125)
T cd02951 3 YEDLAEAAADGKKPLLLLFSQPGC--PYCDKLKR 34 (125)
T ss_pred HHHHHHHHHcCCCcEEEEEeCCCC--HHHHHHHH
Confidence 34677888888 777777765554 46765443
No 82
>PRK02551 flavoprotein NrdI; Provisional
Probab=26.26 E-value=2.8e+02 Score=20.68 Aligned_cols=119 Identities=16% Similarity=0.266 Sum_probs=61.3
Q ss_pred EEEecccCcCcccHHHHHHHHHhcC--CeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCc-cCc--------hhH
Q 043319 20 VFVSFRGEDTQDNFTSHLYSTLCRQ--NIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESY-ASS--------RWC 88 (164)
Q Consensus 20 VFISy~~~D~~~~f~~~L~~~L~~~--gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y-~~S--------~wc 88 (164)
+|+|-++.- +.|+..|...+.++ ++.... +...+.+.++-. .+. ..--.+++.|.| -.. .|.
T Consensus 7 ~Y~S~TGNt--~rFv~kL~~~~~~~~~~~~~~~---i~~~~~i~~~~~-~~~-~~~p~vli~pTY~~gG~~~~~~~~~~v 79 (154)
T PRK02551 7 VYISLSGNT--RSFVKRLSDYLATQHKDIEVNP---INIKDLIHETTD-FFP-ETEPFVAFLPTYLEGGNGIDNGDVEIL 79 (154)
T ss_pred EEEeCChhH--HHHHHHHhcHHhhcccccccee---cccccccCcccc-ccc-cCCCEEEEEeeecCCCCCcccCccccc
Confidence 578876653 47999998666442 333321 222222211100 011 122345667788 222 466
Q ss_pred HHHHHHHHHhhhhhcceeeeEEEeeCCcccccccCchHHHHHHHHHHh--------------cCChHHHHHHHHHHHHhh
Q 043319 89 LDELVKILDCKKEYAQIVIPVFYRVDPSDVRNRTGSFGDSFSKLAERL--------------KVNTEELRSWRNALKEAA 154 (164)
Q Consensus 89 ~~El~~~~~~~~~~~~~iiPVfy~v~p~~v~~~~g~f~~~f~~~~~~~--------------~~~~~~~~~W~~Al~~v~ 154 (164)
.+.+...+..... ...+.=|+ -..+.+||+.|+...... .-+.+.+++-+..|.+..
T Consensus 80 p~~v~dFL~~~~N-~~~~~gVi--------gsGNrNfg~~F~~aa~~ia~~~~vP~L~~fEl~GT~~Dv~~v~~~~~~~~ 150 (154)
T PRK02551 80 TTPLGDFIAYHDN-AKRCLGII--------GSGNRNFNNQYCLTAKQYAKRFGFPMLADFELRGTPSDIERIAAIIAELY 150 (154)
T ss_pred hHHHHHHHcchhh-hhheEEEE--------eecccHHHHHHHHHHHHHHHHcCCCEEEEeeccCCHHHHHHHHHHHHHHH
Confidence 6666666543222 33444444 123457999999765542 234667777776666543
No 83
>cd04142 RRP22 RRP22 subfamily. RRP22 (Ras-related protein on chromosome 22) subfamily consists of proteins that inhibit cell growth and promote caspase-independent cell death. Unlike most Ras proteins, RRP22 is down-regulated in many human tumor cells due to promoter methylation. RRP22 localizes to the nucleolus in a GTP-dependent manner, suggesting a novel function in modulating transport of nucleolar components. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Like most Ras family proteins, RRP22 is farnesylated.
Probab=26.09 E-value=2.9e+02 Score=20.81 Aligned_cols=54 Identities=11% Similarity=0.052 Sum_probs=31.6
Q ss_pred HHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHhhhhh---cceeeeEEEeeCCccccc
Q 043319 64 LVNAIEASDISVIVFSESYASSRWCLDELVKILDCKKEY---AQIVIPVFYRVDPSDVRN 120 (164)
Q Consensus 64 i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~---~~~iiPVfy~v~p~~v~~ 120 (164)
...+++.++++|+|++.+ +..-++++...++..... ...-+||+.=....|+..
T Consensus 74 ~~~~~~~ad~iilv~D~~---~~~S~~~~~~~~~~i~~~~~~~~~~~piiivgNK~Dl~~ 130 (198)
T cd04142 74 RFRGLRNSRAFILVYDIC---SPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQQR 130 (198)
T ss_pred HHhhhccCCEEEEEEECC---CHHHHHHHHHHHHHHHHhcccCCCCCCEEEEEECccccc
Confidence 445688999999999976 344444444443332111 123367777556666643
No 84
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=25.97 E-value=91 Score=25.35 Aligned_cols=43 Identities=23% Similarity=0.253 Sum_probs=28.5
Q ss_pred cHHHHHHHHHhcCCeeeeecCCcCCcc---cchHHHHHhhhcCCeEEE
Q 043319 32 NFTSHLYSTLCRQNIQTFIDDQLNRGD---EISESLVNAIEASDISVI 76 (164)
Q Consensus 32 ~f~~~L~~~L~~~gi~vf~d~~~~~G~---~~~~~i~~aI~~S~~~Iv 76 (164)
.=+.+|.+.|...|+.+..-.- .|| .|.+.+..+++.+++.|+
T Consensus 21 tNa~~la~~L~~~G~~v~~~~~--VgD~~~~I~~~l~~a~~r~D~vI~ 66 (255)
T COG1058 21 TNAAFLADELTELGVDLARITT--VGDNPDRIVEALREASERADVVIT 66 (255)
T ss_pred chHHHHHHHHHhcCceEEEEEe--cCCCHHHHHHHHHHHHhCCCEEEE
Confidence 3467899999999999877542 344 345566666667555443
No 85
>PHA00407 phage lambda Rz1-like protein
Probab=25.69 E-value=43 Score=22.18 Aligned_cols=22 Identities=45% Similarity=0.679 Sum_probs=17.1
Q ss_pred hHHHHHHHHHHH-----Hhhcccceee
Q 043319 140 TEELRSWRNALK-----EAATLSGFHS 161 (164)
Q Consensus 140 ~~~~~~W~~Al~-----~v~~~~G~~~ 161 (164)
..+.++|+.||- -|+.++|+.+
T Consensus 25 kktl~rwkaaLIGlllicv~tISGCaS 51 (84)
T PHA00407 25 KKTLRRWKAALIGLLLICVATISGCAS 51 (84)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHhhhhh
Confidence 577889999974 5778888755
No 86
>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=25.60 E-value=2.2e+02 Score=24.17 Aligned_cols=28 Identities=4% Similarity=-0.060 Sum_probs=18.7
Q ss_pred cccHHHHHHHHHhcCCeeeeecCCcCCc
Q 043319 30 QDNFTSHLYSTLCRQNIQTFIDDQLNRG 57 (164)
Q Consensus 30 ~~~f~~~L~~~L~~~gi~vf~d~~~~~G 57 (164)
....+..|.+++++.|+.+-....+.++
T Consensus 185 G~~~~~~f~~~~~~~GicIa~~e~~~~~ 212 (403)
T cd06361 185 GRSALETFIIQAEANGVCIAFKEILPAS 212 (403)
T ss_pred HHHHHHHHHHHHHHCCeEEEEEEEecCc
Confidence 3467788888888888776544434443
No 87
>TIGR03026 NDP-sugDHase nucleotide sugar dehydrogenase. All of these enzymes contain three Pfam domains, pfam03721, pfam00984, and pfam03720 for the N-terminal, central, and C-terminal regions respectively.
Probab=25.43 E-value=1.4e+02 Score=25.40 Aligned_cols=57 Identities=16% Similarity=0.275 Sum_probs=38.8
Q ss_pred Eeccc--CcCcccHHHHHHHHHhcCCeeeeecCC-cCCccc----chHHHHHhhhcCCeEEEEe
Q 043319 22 VSFRG--EDTQDNFTSHLYSTLCRQNIQTFIDDQ-LNRGDE----ISESLVNAIEASDISVIVF 78 (164)
Q Consensus 22 ISy~~--~D~~~~f~~~L~~~L~~~gi~vf~d~~-~~~G~~----~~~~i~~aI~~S~~~Ivv~ 78 (164)
++|.. .|.|.+=+-.|.+.|.++|..|...+- ...... ..+.+.+++++++..|+.-
T Consensus 321 lafK~~t~d~r~sp~~~~~~~L~~~g~~v~~~DP~~~~~~~~~~~~~~~~~~~~~~ad~~v~~t 384 (411)
T TIGR03026 321 LAFKPNTDDVRESPALDIIELLKEKGAKVKAYDPLVPEEEVKGLPLIDDLEEALKGADALVILT 384 (411)
T ss_pred eEecCCCCccccChHHHHHHHHHhCCCEEEEECCCCChhhhhhcccCCCHHHHHhCCCEEEEec
Confidence 46653 477888889999999999998877665 322211 1235567788888777654
No 88
>PF15409 PH_8: Pleckstrin homology domain
Probab=25.14 E-value=62 Score=21.93 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=13.3
Q ss_pred CChHHHHHHHHHHHHh
Q 043319 138 VNTEELRSWRNALKEA 153 (164)
Q Consensus 138 ~~~~~~~~W~~Al~~v 153 (164)
.+++..+.|..||..+
T Consensus 73 ~s~~~f~~Wv~aL~~a 88 (89)
T PF15409_consen 73 KSQEDFQRWVSALQKA 88 (89)
T ss_pred CCHHHHHHHHHHHHhc
Confidence 3578999999999864
No 89
>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=24.75 E-value=1.4e+02 Score=21.65 Aligned_cols=38 Identities=18% Similarity=0.254 Sum_probs=17.9
Q ss_pred cHHHHHHHHHhcCCeeeeecCC-cCC-----cccchHHHHHhhh
Q 043319 32 NFTSHLYSTLCRQNIQTFIDDQ-LNR-----GDEISESLVNAIE 69 (164)
Q Consensus 32 ~f~~~L~~~L~~~gi~vf~d~~-~~~-----G~~~~~~i~~aI~ 69 (164)
.+...+.+.+.+..-.+++-.- +.+ +..+.+.|.++.+
T Consensus 21 ~~~~~i~~~I~~A~~~I~i~~~~~~~~~~~~~~~l~~~L~~a~~ 64 (176)
T cd00138 21 SDLDALLEAISNAKKSIYIASFYLSPLITEYGPVILDALLAAAR 64 (176)
T ss_pred hHHHHHHHHHHhhheEEEEEEeEecccccccchHHHHHHHHHHH
Confidence 3445555555544434443333 333 4445555555554
No 90
>PF09886 DUF2113: Uncharacterized protein conserved in archaea (DUF2113); InterPro: IPR016762 There is currently no experimental data for members of this group or their homologues. Based on distant sequence similarity, they may be tentatively predicted to be nucleic acid-binding proteins, they are also likely to be linked to methanogenesis or a process closely connected to it.
Probab=24.49 E-value=2.7e+02 Score=21.58 Aligned_cols=54 Identities=15% Similarity=0.318 Sum_probs=39.4
Q ss_pred cCcccHHHHHHHHHhc---CCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHh
Q 043319 28 DTQDNFTSHLYSTLCR---QNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKILDC 98 (164)
Q Consensus 28 D~~~~f~~~L~~~L~~---~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~ 98 (164)
|.++.|...|+.++.+ .|++|-.+. -.-..+++|-|++-..-+|- +|.....+.
T Consensus 128 Dp~~~l~~~v~da~~RI~PEGFRVr~~~----------------~~~~~f~~vASE~~i~~ewi-~~a~e~~~e 184 (188)
T PF09886_consen 128 DPSEDLKKKVYDAMFRIAPEGFRVRRHY----------------YEGNSFAFVASEETIKDEWI-EEAKEMIEE 184 (188)
T ss_pred CcHHHHHHHHHHHHHHhCCCccEEeecc----------------ccCCeEEEEECCCCCCHHHH-HHHHHHHHH
Confidence 5567899999999987 588876643 12345788999999999997 555554443
No 91
>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=23.97 E-value=2.5e+02 Score=22.69 Aligned_cols=54 Identities=2% Similarity=-0.081 Sum_probs=34.6
Q ss_pred cEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCccc-chHHHHHhhhcCCe
Q 043319 19 DVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDE-ISESLVNAIEASDI 73 (164)
Q Consensus 19 dVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~-~~~~i~~aI~~S~~ 73 (164)
.|.+-|...+-...+...+.+.|++.|+++-......+|.. +...+ ..|+.+..
T Consensus 138 ~v~~i~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~d~~~~v-~~l~~~~p 192 (333)
T cd06328 138 KIATLAQDYAFGRDGVAAFKAALEKLGAAIVTEEYAPTDTTDFTPYA-QRLLDALK 192 (333)
T ss_pred eEEEEecCccccHHHHHHHHHHHHhCCCEEeeeeeCCCCCcchHHHH-HHHHhcCC
Confidence 45555644443356778888999999999887665667753 55444 45554443
No 92
>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=23.86 E-value=2.7e+02 Score=19.64 Aligned_cols=78 Identities=15% Similarity=0.108 Sum_probs=43.8
Q ss_pred ccHHHHHHHHHhcCCeeeee-c-CCc-CC-----------cccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHH
Q 043319 31 DNFTSHLYSTLCRQNIQTFI-D-DQL-NR-----------GDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKIL 96 (164)
Q Consensus 31 ~~f~~~L~~~L~~~gi~vf~-d-~~~-~~-----------G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~ 96 (164)
...+..+.+.|++.|+.+-+ + .+. .| -..-.+++.+.+.+++. |++.||.|..+-= -.|..++
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 RKLAEAVAEQLEEAGAEVEVIDLADYPLPCCDGDFECPCYIPDDVQELYDKLKEADG-IIFASPVYNGSVS--GQLKNFL 93 (152)
T ss_dssp HHHHHHHHHHHHHTTEEEEEEECTTSHCHHHHHHHHHTGCTSHHHHHHHHHHHHSSE-EEEEEEEBTTBE---HHHHHHH
T ss_pred HHHHHHHHHHHHHcCCEEEEEeccccchhhcccccccccCCcHHHHHHHhceecCCe-EEEeecEEcCcCC--hhhhHHH
Confidence 35788888999888866522 1 111 11 01122466778888885 5668899886422 2344444
Q ss_pred Hhh------hhhcceeeeEEE
Q 043319 97 DCK------KEYAQIVIPVFY 111 (164)
Q Consensus 97 ~~~------~~~~~~iiPVfy 111 (164)
++. .-.+..+.+|-.
T Consensus 94 D~~~~~~~~~~~~K~~~~i~~ 114 (152)
T PF03358_consen 94 DRLSCWFRRALRGKPVAIIAV 114 (152)
T ss_dssp HTHHHTHTTTTTTSEEEEEEE
T ss_pred HHhccccccccCCCEEEEEEE
Confidence 433 113456666543
No 93
>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=23.62 E-value=2.4e+02 Score=19.99 Aligned_cols=46 Identities=11% Similarity=0.073 Sum_probs=28.2
Q ss_pred HHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHhhhhhcceeeeEE
Q 043319 62 ESLVNAIEASDISVIVFSESYASSRWCLDELVKILDCKKEYAQIVIPVF 110 (164)
Q Consensus 62 ~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf 110 (164)
.-+.+.+..+++.|+|++.+-. |...+...+.+..+....+.+-|+
T Consensus 120 ~~~~~~~~~~d~vi~V~~~~~~---~~~~~~~~l~~~~~~~~~~~i~V~ 165 (168)
T PF00350_consen 120 EITEEYLPKADVVIFVVDANQD---LTESDMEFLKQMLDPDKSRTIFVL 165 (168)
T ss_dssp HHHHHHHSTTEEEEEEEETTST---GGGHHHHHHHHHHTTTCSSEEEEE
T ss_pred HHHHHhhccCCEEEEEeccCcc---cchHHHHHHHHHhcCCCCeEEEEE
Confidence 4466678899999999976653 343455555554444444555543
No 94
>cd06352 PBP1_NPR_GC_like Ligand-binding domain of membrane guanylyl-cyclase receptors. Ligand-binding domain of membrane guanylyl-cyclase receptors. Membrane guanylyl cyclases (GC) have a single membrane-spanning region and are activated by endogenous and exogenous peptides. This family can be divided into three major subfamilies: the natriuretic peptide receptors (NPRs), sensory organ-specific membrane GCs, and the enterotoxin/guanylin receptors. The binding of peptide ligands to the receptor results in the activation of the cytosolic catalytic domain. Three types of NPRs have been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/ GC-B, and NPR-C. In addition, two of the GCs, GC-D and GC-G, appear to be pseudogenes in humans. Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are produced in the heart, and both bind to the NPR-A. NPR-C, also termed the clearance receptor, binds each of the natriuretic peptides and can alter circulating levels of these peptides. The l
Probab=23.34 E-value=1.6e+02 Score=24.19 Aligned_cols=41 Identities=15% Similarity=0.044 Sum_probs=25.7
Q ss_pred ccHHHHHHHHHhcCCeeeeecCCcCCc---ccchHHHHHhhhcCC
Q 043319 31 DNFTSHLYSTLCRQNIQTFIDDQLNRG---DEISESLVNAIEASD 72 (164)
Q Consensus 31 ~~f~~~L~~~L~~~gi~vf~d~~~~~G---~~~~~~i~~aI~~S~ 72 (164)
...+..+.++|++.|+.+-....+.++ ..+...+ +.|+.+.
T Consensus 152 ~~~~~~~~~~~~~~G~~v~~~~~~~~~~~~~d~~~~l-~~i~~~~ 195 (389)
T cd06352 152 FFTLEALEAALREFNLTVSHVVFMEDNSGAEDLLEIL-QDIKRRS 195 (389)
T ss_pred HHHHHHHHHHHHhcCCeEEEEEEecCCccchhHHHHH-HHhhhcc
Confidence 456778888888888877655445554 3454444 4455554
No 95
>cd06327 PBP1_SBP_like_1 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Solute binding proteins are the primary specific receptors that initiate uptake of a broad range of solutes, including amino acids, peptides and inorganic ions. The members are predicted to have a similar function to an active transport system for short chain amides and urea by sequence comparison and phylogenetic analysis. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus may also be involved in transport of amino acids.
Probab=23.34 E-value=3.2e+02 Score=21.88 Aligned_cols=52 Identities=12% Similarity=0.022 Sum_probs=29.5
Q ss_pred EEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcc-cchHHHHHhhhcCC
Q 043319 20 VFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGD-EISESLVNAIEASD 72 (164)
Q Consensus 20 VFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~-~~~~~i~~aI~~S~ 72 (164)
|.|-+...+-...++..+...|++.|+.+-....+..+. .+...+.+ +.+++
T Consensus 138 v~~i~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~d~~~~v~~-l~~~~ 190 (334)
T cd06327 138 WFFLTADYAFGHSLERDARKVVKANGGKVVGSVRHPLGTSDFSSYLLQ-AQASG 190 (334)
T ss_pred EEEEecchHHhHHHHHHHHHHHHhcCCEEcCcccCCCCCccHHHHHHH-HHhCC
Confidence 344443322224577888888888998886655544443 45544444 44433
No 96
>PF03618 Kinase-PPPase: Kinase/pyrophosphorylase; InterPro: IPR005177 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.; GO: 0005524 ATP binding, 0016772 transferase activity, transferring phosphorus-containing groups
Probab=23.31 E-value=3.1e+02 Score=22.31 Aligned_cols=27 Identities=22% Similarity=0.080 Sum_probs=20.6
Q ss_pred cCccCchhHHHHHHHHHHhhhhhccee
Q 043319 80 ESYASSRWCLDELVKILDCKKEYAQIV 106 (164)
Q Consensus 80 ~~y~~S~wc~~El~~~~~~~~~~~~~i 106 (164)
.+|++-+-|.+||..+-+..++.+-.+
T Consensus 213 s~Ya~~~~i~~El~~A~~l~~~~~~pv 239 (255)
T PF03618_consen 213 SSYADLERIEEELEYAERLFRKLGCPV 239 (255)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHcCCCE
Confidence 579999999999999887766544333
No 97
>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]
Probab=23.27 E-value=3e+02 Score=24.40 Aligned_cols=88 Identities=19% Similarity=0.324 Sum_probs=51.1
Q ss_pred HHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHh-hhhhcceeeeEEE--
Q 043319 35 SHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKILDC-KKEYAQIVIPVFY-- 111 (164)
Q Consensus 35 ~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~-~~~~~~~iiPVfy-- 111 (164)
..|.+.|.+.|+.+++-. |+.. +.+.+-+++..+..|+....|. .| ..+-..++.. ..+.+..+. .|.
T Consensus 58 ~~L~~~L~~~gi~L~v~~----~~~~-~~l~~~~~~~~~~~v~~n~~~~--~~-~~~rD~al~~~l~~~gi~~~-~~~d~ 128 (461)
T COG0415 58 QALQQSLAELGIPLLVRE----GDPE-QVLPELAKQLAATTVFWNRDYE--EW-ERQRDAALAQPLTEVGIAVH-SFWDA 128 (461)
T ss_pred HHHHHHHHHcCCceEEEe----CCHH-HHHHHHHHHhCcceEEeeeeec--hh-HHHHHHHHHHHHHhcCceEE-Eeccc
Confidence 457888999999998854 4432 2455556666677777888883 23 2333333333 222333333 343
Q ss_pred -eeCCcccccccCchHHHHHH
Q 043319 112 -RVDPSDVRNRTGSFGDSFSK 131 (164)
Q Consensus 112 -~v~p~~v~~~~g~f~~~f~~ 131 (164)
-..|.+|+.+.|..=+.|..
T Consensus 129 ~l~~p~~~~t~~~~~y~vfT~ 149 (461)
T COG0415 129 LLHEPGEVRTGSGEPYKVFTP 149 (461)
T ss_pred cccCHhhccCCCCCCccccch
Confidence 36788898877755444443
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=23.26 E-value=76 Score=21.66 Aligned_cols=17 Identities=29% Similarity=0.524 Sum_probs=14.5
Q ss_pred CChHHHHHHHHHHHHhh
Q 043319 138 VNTEELRSWRNALKEAA 154 (164)
Q Consensus 138 ~~~~~~~~W~~Al~~v~ 154 (164)
++++..+.|..|+.+|+
T Consensus 92 ~s~ee~~~Wi~~I~~~~ 108 (108)
T cd01266 92 KNEEEMTLWVNCICKLC 108 (108)
T ss_pred CCHHHHHHHHHHHHhhC
Confidence 46889999999998874
No 99
>PF13289 SIR2_2: SIR2-like domain
Probab=23.22 E-value=1.9e+02 Score=19.95 Aligned_cols=12 Identities=33% Similarity=0.393 Sum_probs=5.8
Q ss_pred HHHHHHHHHhcC
Q 043319 33 FTSHLYSTLCRQ 44 (164)
Q Consensus 33 f~~~L~~~L~~~ 44 (164)
+-..|...|..+
T Consensus 76 ~~~~l~~~l~~~ 87 (143)
T PF13289_consen 76 FPNFLRSLLRSK 87 (143)
T ss_pred HHHHHHHHHcCC
Confidence 445555555333
No 100
>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=23.06 E-value=2.6e+02 Score=19.27 Aligned_cols=71 Identities=24% Similarity=0.304 Sum_probs=42.8
Q ss_pred HHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhh-cCCeEEEEeecCccCchhHHHHHHHHHHhhhhhcceeeeEEE
Q 043319 33 FTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIE-ASDISVIVFSESYASSRWCLDELVKILDCKKEYAQIVIPVFY 111 (164)
Q Consensus 33 f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~-~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~iiPVfy 111 (164)
....|..+|++.|+.|..-.. .+.....++ .+++.-+|+|=+ ... .++...+++..+ ....=||||+
T Consensus 5 ~~~~l~~~L~~~~~~vv~~~~-------~dd~~~~i~~~~~i~avvi~~d-~~~---~~~~~~ll~~i~-~~~~~iPVFl 72 (115)
T PF03709_consen 5 ASRELAEALEQRGREVVDADS-------TDDALAIIESFTDIAAVVISWD-GEE---EDEAQELLDKIR-ERNFGIPVFL 72 (115)
T ss_dssp HHHHHHHHHHHTTTEEEEESS-------HHHHHHHHHCTTTEEEEEEECH-HHH---HHHHHHHHHHHH-HHSTT-EEEE
T ss_pred HHHHHHHHHHHCCCEEEEeCC-------hHHHHHHHHhCCCeeEEEEEcc-ccc---chhHHHHHHHHH-HhCCCCCEEE
Confidence 567899999999998876442 233445555 489999999866 111 122223333322 2346689998
Q ss_pred eeCC
Q 043319 112 RVDP 115 (164)
Q Consensus 112 ~v~p 115 (164)
-.+.
T Consensus 73 ~~~~ 76 (115)
T PF03709_consen 73 LAER 76 (115)
T ss_dssp EESC
T ss_pred EecC
Confidence 6663
No 101
>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=22.90 E-value=2.4e+02 Score=22.49 Aligned_cols=43 Identities=12% Similarity=-0.075 Sum_probs=24.3
Q ss_pred ccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCe
Q 043319 31 DNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDI 73 (164)
Q Consensus 31 ~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~ 73 (164)
...+..+...+++.|+.+-....+.+|..=-..+...|+.++.
T Consensus 151 ~~~~~~~~~~~~~~G~~vv~~~~~~~~~~d~~~~v~~l~~~~p 193 (312)
T cd06346 151 VGLADAFTKAFEALGGTVTNVVAHEEGKSSYSSEVAAAAAGGP 193 (312)
T ss_pred hHHHHHHHHHHHHcCCEEEEEEeeCCCCCCHHHHHHHHHhcCC
Confidence 3456667777777887766544455664322234455554443
No 102
>PRK13883 conjugal transfer protein TrbH; Provisional
Probab=22.85 E-value=97 Score=23.17 Aligned_cols=26 Identities=19% Similarity=0.189 Sum_probs=18.4
Q ss_pred cCcccHHHHHHHHHhcCCeeeeecCC
Q 043319 28 DTQDNFTSHLYSTLCRQNIQTFIDDQ 53 (164)
Q Consensus 28 D~~~~f~~~L~~~L~~~gi~vf~d~~ 53 (164)
|+.+.|...|..+|+++|+-|--++.
T Consensus 60 ~~~D~Fg~aL~~aLR~~GYaV~e~~~ 85 (151)
T PRK13883 60 PTPDAFGQALVKALRDKGYALLEYNP 85 (151)
T ss_pred CCCcHHHHHHHHHHHHcCeEEEecCC
Confidence 33346888888888888887776554
No 103
>PLN02530 histidine-tRNA ligase
Probab=22.79 E-value=2e+02 Score=25.34 Aligned_cols=61 Identities=13% Similarity=0.062 Sum_probs=41.0
Q ss_pred ceecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeec
Q 043319 16 HKYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSE 80 (164)
Q Consensus 16 ~~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~ 80 (164)
...||+|.+-+++. ...+-.+.+.|+++|++|-++-. +..+...+..|-+.--..|+++.+
T Consensus 400 ~~~dVlVi~~~~~~-~~~A~~ia~~LR~~Gi~vevd~~---~~~l~k~ik~A~k~g~~~iviiG~ 460 (487)
T PLN02530 400 HQVDDVVFALDEDL-QGAAAGVASRLREKGRSVDLVLE---PKKLKWVFKHAERIGAKRLVLVGA 460 (487)
T ss_pred CCCcEEEEEcChHH-HHHHHHHHHHHHHCCCeEEEecC---CCCHHHHHHHHHHCCCCEEEEEch
Confidence 34689998755443 35778899999999999977643 234555666666554455666654
No 104
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=22.34 E-value=2e+02 Score=26.19 Aligned_cols=61 Identities=13% Similarity=0.146 Sum_probs=40.4
Q ss_pred eecEEEecccCcCcccHHHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeec
Q 043319 17 KYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSE 80 (164)
Q Consensus 17 ~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~ 80 (164)
..+|+|-.-+++.....+..|...|++.|++|-+|.. +..+...+..|-+.---.++|+.+
T Consensus 541 p~qV~Ii~~~~~~~~~~a~~la~~LR~~Gi~veid~~---~~sl~kq~k~A~k~g~~~~iiiG~ 601 (639)
T PRK12444 541 PVQVKVIPVSNAVHVQYADEVADKLAQAGIRVERDER---DEKLGYKIREAQMQKIPYVLVIGD 601 (639)
T ss_pred CceEEEEEcccHHHHHHHHHHHHHHHHCCCEEEEECC---CCCHHHHHHHHHHcCCCEEEEEcc
Confidence 4677776655411246788999999999999999874 345555666665544445555554
No 105
>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=22.22 E-value=1.1e+02 Score=19.80 Aligned_cols=36 Identities=22% Similarity=0.148 Sum_probs=26.7
Q ss_pred ceecEEEecccCcCcccHHHHHHHHHhcCCeeeeecC
Q 043319 16 HKYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQTFIDD 52 (164)
Q Consensus 16 ~~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~vf~d~ 52 (164)
.+--|+|+|.-.+- ...-.+|.+.|.++|+.|+.-+
T Consensus 15 ~k~~v~i~HG~~eh-~~ry~~~a~~L~~~G~~V~~~D 50 (79)
T PF12146_consen 15 PKAVVVIVHGFGEH-SGRYAHLAEFLAEQGYAVFAYD 50 (79)
T ss_pred CCEEEEEeCCcHHH-HHHHHHHHHHHHhCCCEEEEEC
Confidence 45678999964443 2355788899999999998755
No 106
>PF02337 Gag_p10: Retroviral GAG p10 protein; InterPro: IPR003322 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from beta-retroviruses such as Mason-Pfizer monkey virus (MPMV) (Simian Mason-Pfizer virus) and Mouse mammary tumor virus (MMTV) [, ]. This entry also identifies matrix proteins from several eukaryotic endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome [].; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 2F77_X 2F76_X.
Probab=21.81 E-value=73 Score=21.69 Aligned_cols=21 Identities=29% Similarity=0.245 Sum_probs=14.8
Q ss_pred cHHHHHHHHHhcCCeeeeecC
Q 043319 32 NFTSHLYSTLCRQNIQTFIDD 52 (164)
Q Consensus 32 ~f~~~L~~~L~~~gi~vf~d~ 52 (164)
.|+..|...|+.+|++|-..+
T Consensus 9 ~fv~~Lk~lLk~rGi~v~~~~ 29 (90)
T PF02337_consen 9 PFVSILKHLLKERGIRVKKKD 29 (90)
T ss_dssp HHHHHHHHHHHCCT----HHH
T ss_pred HHHHHHHHHHHHcCeeecHHH
Confidence 699999999999999886543
No 107
>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=21.75 E-value=3.2e+02 Score=19.77 Aligned_cols=92 Identities=20% Similarity=0.237 Sum_probs=45.4
Q ss_pred HHHHHHHHhcCCeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCccCchhHHHHHHHHHHhhhhhcceeeeEE--E
Q 043319 34 TSHLYSTLCRQNIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESYASSRWCLDELVKILDCKKEYAQIVIPVF--Y 111 (164)
Q Consensus 34 ~~~L~~~L~~~gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf--y 111 (164)
+..|...|++.|+...+-. |+ ..+.+.+-+++..+..|++...|....-=.+ ..+.+...+.+..+.-+- +
T Consensus 55 L~~L~~~L~~~g~~L~v~~----g~-~~~~l~~l~~~~~~~~V~~~~~~~~~~~~rd--~~v~~~l~~~~i~~~~~~~~~ 127 (165)
T PF00875_consen 55 LADLQESLRKLGIPLLVLR----GD-PEEVLPELAKEYGATAVYFNEEYTPYERRRD--ERVRKALKKHGIKVHTFDDHT 127 (165)
T ss_dssp HHHHHHHHHHTTS-EEEEE----SS-HHHHHHHHHHHHTESEEEEE---SHHHHHHH--HHHHHHHHHTTSEEEEE--SS
T ss_pred HHHHHHHHHhcCcceEEEe----cc-hHHHHHHHHHhcCcCeeEeccccCHHHHHHH--HHHHHHHHhcceEEEEECCcE
Confidence 3567788888998876632 33 3335555677788888989988876322111 111121122122221110 0
Q ss_pred eeCCcccccccCchHHHHHHH
Q 043319 112 RVDPSDVRNRTGSFGDSFSKL 132 (164)
Q Consensus 112 ~v~p~~v~~~~g~f~~~f~~~ 132 (164)
=+.|.++....|..-..|...
T Consensus 128 L~~~~~i~~~~~~~~~vFtpf 148 (165)
T PF00875_consen 128 LVPPDDIPKKDGEPYKVFTPF 148 (165)
T ss_dssp SS-HHHCHSTTSSSHSSHHHH
T ss_pred EEeccccccCCCCCcccHHHH
Confidence 145777876666555555433
No 108
>TIGR00177 molyb_syn molybdenum cofactor synthesis domain. The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by this model. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine receptors and GABA receptors, rather than a protein of molybdenum cofactor biosynthesis.
Probab=21.69 E-value=1.4e+02 Score=21.50 Aligned_cols=46 Identities=17% Similarity=0.160 Sum_probs=27.3
Q ss_pred cHHHHHHHHHhcCCeeeeecCCcCCc-ccchHHHHHhhhcCCeEEEE
Q 043319 32 NFTSHLYSTLCRQNIQTFIDDQLNRG-DEISESLVNAIEASDISVIV 77 (164)
Q Consensus 32 ~f~~~L~~~L~~~gi~vf~d~~~~~G-~~~~~~i~~aI~~S~~~Ivv 77 (164)
.....|.+.|++.|+.+..-.-+... +.+.+.+.++++++++.|..
T Consensus 27 ~n~~~l~~~l~~~G~~v~~~~~v~Dd~~~i~~~l~~~~~~~DliItt 73 (144)
T TIGR00177 27 SNGPLLAALLEEAGFNVSRLGIVPDDPEEIREILRKAVDEADVVLTT 73 (144)
T ss_pred CcHHHHHHHHHHCCCeEEEEeecCCCHHHHHHHHHHHHhCCCEEEEC
Confidence 45567888899999876653321111 23455566666666665554
No 109
>PF00113 Enolase_C: Enolase, C-terminal TIM barrel domain; InterPro: IPR020810 Enolase (2-phospho-D-glycerate hydrolase) is an essential glycolytic enzyme that catalyses the interconversion of 2-phosphoglycerate and phosphoenolpyruvate [, ]. In vertebrates, there are 3 different, tissue-specific isoenzymes, designated alpha, beta and gamma. Alpha is present in most tissues, beta is localised in muscle tissue, and gamma is found only in nervous tissue. The functional enzyme exists as a dimer of any 2 isoforms. In immature organs and in adult liver, it is usually an alpha homodimer, in adult skeletal muscle, a beta homodimer, and in adult neurons, a gamma homodimer. In developing muscle, it is usually an alpha/beta heterodimer, and in the developing nervous system, an alpha/gamma heterodimer []. The tissue specific forms display minor kinetic differences. Tau-crystallin, one of the major lens proteins in some fish, reptiles and birds, has been shown [] to be evolutionary related to enolase. Neuron-specific enolase is released in a variety of neurological diseases, such as multiple sclerosis and after seizures or acute stroke. Several tumour cells have also been found positive for neuron-specific enolase. Beta-enolase deficiency is associated with glycogenosis type XIII defect.; GO: 0000287 magnesium ion binding, 0004634 phosphopyruvate hydratase activity, 0006096 glycolysis, 0000015 phosphopyruvate hydratase complex; PDB: 2FYM_D 3H8A_C 1E9I_D 3TQP_B 2PU1_A 1OEP_A 2PA6_A 1PDY_A 1PDZ_A 3UJ2_E ....
Probab=21.68 E-value=92 Score=25.84 Aligned_cols=32 Identities=34% Similarity=0.472 Sum_probs=19.9
Q ss_pred eecEEEecccCcCcccHHHHHHHHHhcCCeee
Q 043319 17 KYDVFVSFRGEDTQDNFTSHLYSTLCRQNIQT 48 (164)
Q Consensus 17 ~ydVFISy~~~D~~~~f~~~L~~~L~~~gi~v 48 (164)
.|.+.+|||+.++...|+.+|.-.|...-|++
T Consensus 228 g~~~vvS~rsgEteD~~iadLaVg~~a~~iK~ 259 (295)
T PF00113_consen 228 GWGVVVSHRSGETEDTFIADLAVGLGAGQIKT 259 (295)
T ss_dssp T-EEEEE--SS--S--HHHHHHHHTT-SEEEE
T ss_pred CceeeccCCCCCcCchhHHHHHhccCcCeEec
Confidence 47899999988888899999999997765554
No 110
>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=21.61 E-value=2.5e+02 Score=18.50 Aligned_cols=46 Identities=22% Similarity=0.278 Sum_probs=24.8
Q ss_pred HHhhhcCCeEEEEeecCccCchhHHHHHHHHHHhhhhhcceeeeEEE
Q 043319 65 VNAIEASDISVIVFSESYASSRWCLDELVKILDCKKEYAQIVIPVFY 111 (164)
Q Consensus 65 ~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~iiPVfy 111 (164)
...+..++..|+|++..-..|-.=+.++..-+...+..... +||++
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 34589999999999866443322222333223333222223 77665
No 111
>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=21.16 E-value=96 Score=19.10 Aligned_cols=16 Identities=38% Similarity=0.682 Sum_probs=13.7
Q ss_pred ChHHHHHHHHHHHHhh
Q 043319 139 NTEELRSWRNALKEAA 154 (164)
Q Consensus 139 ~~~~~~~W~~Al~~v~ 154 (164)
+++..++|..||..+.
T Consensus 86 s~~~~~~W~~~i~~~~ 101 (102)
T smart00233 86 SEEEREEWVDALRKAI 101 (102)
T ss_pred CHHHHHHHHHHHHHhh
Confidence 5789999999998765
No 112
>cd01251 PH_centaurin_alpha Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha is a phophatidlyinositide binding protein consisting of an N-terminal ArfGAP domain and two PH domains. In response to growth factor activation, PI3K phosphorylates phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 1 is recruited to the plasma membrane following growth factor stimulation by specific binding of its PH domain to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 2 is constitutively bound to the plasma membrane since it binds phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate with equal affinity. 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 specifici
Probab=21.07 E-value=1.1e+02 Score=20.85 Aligned_cols=19 Identities=16% Similarity=0.389 Sum_probs=15.6
Q ss_pred CChHHHHHHHHHHHHhhcc
Q 043319 138 VNTEELRSWRNALKEAATL 156 (164)
Q Consensus 138 ~~~~~~~~W~~Al~~v~~~ 156 (164)
.+++..+.|.+||..|-+.
T Consensus 84 ~s~~e~~~Wi~ai~~v~~~ 102 (103)
T cd01251 84 ETEQDRREWIAAFQNVLSR 102 (103)
T ss_pred CCHHHHHHHHHHHHHHhcC
Confidence 4588899999999988654
No 113
>cd02986 DLP Dim1 family, Dim1-like protein (DLP) subfamily; DLP is a novel protein which shares 38% sequence identity to Dim1. Like Dim1, it is also implicated in pre-mRNA splicing and cell cycle progression. DLP is located in the nucleus and has been shown to interact with the U5 small nuclear ribonucleoprotein particle (snRNP)-specific 102kD protein (or Prp6). Dim1 protein, also known as U5 snRNP-specific 15kD protein is a component of U5 snRNP, which pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5] tri-snRNP complex required for pre-mRNA splicing. Dim1 adopts a thioredoxin fold but does not contain the redox active CXXC motif.
Probab=20.86 E-value=2.1e+02 Score=20.28 Aligned_cols=50 Identities=24% Similarity=0.234 Sum_probs=26.1
Q ss_pred HHhhh--cCCeEEEEeecCccCchhHH--HHHHHHHHhhhh-hcceeeeEEEeeCCcccccc
Q 043319 65 VNAIE--ASDISVIVFSESYASSRWCL--DELVKILDCKKE-YAQIVIPVFYRVDPSDVRNR 121 (164)
Q Consensus 65 ~~aI~--~S~~~Ivv~S~~y~~S~wc~--~El~~~~~~~~~-~~~~iiPVfy~v~p~~v~~~ 121 (164)
.++|. +.+..|+-|+. +||. ..+..+++.... .... -+||.|+.+++...
T Consensus 6 d~~i~~~~~klVVVdF~a-----~WC~pCk~mdp~l~ela~~~~~~--~~f~kVDVDev~dv 60 (114)
T cd02986 6 DQAIKSTAEKVLVLRFGR-----DEDAVCLQLDDILSKTSHDLSKM--ASIYLVDVDKVPVY 60 (114)
T ss_pred HHHHHhcCCCEEEEEEeC-----CCChhHHHHHHHHHHHHHHccCc--eEEEEEeccccHHH
Confidence 34444 45556665655 4553 255555554322 2222 56777777776543
No 114
>cd01238 PH_Tec Tec pleckstrin homology (PH) domain. Tec pleckstrin homology (PH) domain. Proteins in the Tec family of cytoplasmic protein tyrosine kinases that includes Bruton's tyrosine kinase (BTK), BMX, IL2-inducible T-cell kinase (Itk) and Tec. These proteins generally have an N-terminal PH domain, followed by a Tek homology (TH) domain, a SH3 domain, a SH2 domain and a kinase domain. Tec PH domains tether these proteins to membranes following the activation of PI3K and its subsequent phosphorylation of phosphoinositides. The importance of PH domain membrane anchoring is confirmed by the discovery of a mutation of a critical arginine residue in the BTK PH domain, which causes X-linked agammaglobulinemia (XLA) in humans and a related disorder is mice. 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 dis
Probab=20.70 E-value=83 Score=21.51 Aligned_cols=16 Identities=31% Similarity=0.495 Sum_probs=13.2
Q ss_pred CChHHHHHHHHHHHHh
Q 043319 138 VNTEELRSWRNALKEA 153 (164)
Q Consensus 138 ~~~~~~~~W~~Al~~v 153 (164)
.+++..++|..||.+|
T Consensus 91 ~s~~er~~WI~ai~~~ 106 (106)
T cd01238 91 PTEELRKRWIKALKQV 106 (106)
T ss_pred CCHHHHHHHHHHHHhC
Confidence 3578889999999875
No 115
>PRK07933 thymidylate kinase; Validated
Probab=20.67 E-value=2.2e+02 Score=21.94 Aligned_cols=31 Identities=16% Similarity=0.184 Sum_probs=23.0
Q ss_pred EEecccCcCc--ccHHHHHHHHHhcCCeeeeec
Q 043319 21 FVSFRGEDTQ--DNFTSHLYSTLCRQNIQTFID 51 (164)
Q Consensus 21 FISy~~~D~~--~~f~~~L~~~L~~~gi~vf~d 51 (164)
||.+-|-|.. ...+..|.+.|+.+|++|..-
T Consensus 2 ~IviEG~dGsGKST~~~~L~~~L~~~g~~v~~~ 34 (213)
T PRK07933 2 LIAIEGVDGAGKRTLTEALRAALEARGRSVATL 34 (213)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence 7777666642 468889999999998877643
No 116
>cd06547 GH85_ENGase Endo-beta-N-acetylglucosaminidase (ENGase) hydrolyzes the N-N'-diacetylchitobiosyl core of N-glycosylproteins. The beta-1,4-glycosyl bond located between two N-acetylglucosamine residues is hydrolyzed such that N-acetylglucosamine 1 remains with the protein and N-acetylglucosamine 2 forms the reducing end of the released glycan. ENGase is a key enzyme in the processing of free oligosaccharides in the cytosol of eukaryotes. Oligosaccharides formed in the lumen of the endoplasmic reticulum are transported into the cytosol where they are catabolized by cytosolic ENGases and other enzymes, possibly to maximize the reutilization of the component sugars. ENGases have an eight-stranded alpha/beta barrel topology and are classified as a family 85 glycosyl hydrolase (GH85) domain. The GH85 ENGases are sequence-similar to the family 18 glycosyl hydrolases, also known as GH18 chitinases. An ENGase-like protein is also found in bacteria and is included in this alignment mod
Probab=20.56 E-value=2.6e+02 Score=23.56 Aligned_cols=62 Identities=16% Similarity=0.330 Sum_probs=37.4
Q ss_pred EEEecccCcCcccHHHH--HHHHHhcC------CeeeeecCCcCCcccchHHHHHhhhcCCeEEEEeecCcc
Q 043319 20 VFVSFRGEDTQDNFTSH--LYSTLCRQ------NIQTFIDDQLNRGDEISESLVNAIEASDISVIVFSESYA 83 (164)
Q Consensus 20 VFISy~~~D~~~~f~~~--L~~~L~~~------gi~vf~d~~~~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~ 83 (164)
+|+.|...+. ..... +.+.+.+. ||.||-.....+|..........+++-.++|.+++|...
T Consensus 176 ~FlNY~W~~~--~l~~s~~~a~~~g~~~~dvy~GiDv~grg~~~~~~~~~~~~~~~~~~~~~Svalfap~W~ 245 (339)
T cd06547 176 IFLNYWWTEE--SLERSVQLAEGLGRSPYDVYVGVDVWGRGTKGGGGWNSDKALDEIKKAGLSVALFAPGWT 245 (339)
T ss_pred eeEecCCCcc--hHHHHHHHHHHcCCCHhHEEEEEEEEcCCcccCCCCchhhhhhhhcccCeEEEEEcCcch
Confidence 7999988763 23322 33444443 556664332223333345666788899999999988743
No 117
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=20.01 E-value=72 Score=20.44 Aligned_cols=32 Identities=9% Similarity=0.291 Sum_probs=19.1
Q ss_pred HHHhc--CCeeeeecCCcCCcccchHHHHHhhhcC
Q 043319 39 STLCR--QNIQTFIDDQLNRGDEISESLVNAIEAS 71 (164)
Q Consensus 39 ~~L~~--~gi~vf~d~~~~~G~~~~~~i~~aI~~S 71 (164)
..+.. +.+-+++|.+ .+|+.....+.+.+...
T Consensus 40 ~~~~~~~~~Vii~~D~D-~~G~~~a~~i~~~l~~~ 73 (81)
T PF13662_consen 40 EKLEKKVKEVIIAFDND-KAGEKAAQKIAKKLLPL 73 (81)
T ss_dssp HHHH---SEEEEEEESS-HHHHHHHHHHHHHHG--
T ss_pred HhhhccCceEEEEeCcC-HHHHHHHHHHHHHHHhh
Confidence 34444 6677788775 47777777776655433
Done!