Query 046686
Match_columns 70
No_of_seqs 103 out of 155
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 03:26:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046686.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046686hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00625 tfb2 Transcription f 100.0 3.2E-30 6.9E-35 196.9 6.4 70 1-70 379-448 (448)
2 KOG3471 RNA polymerase II tran 100.0 2.9E-30 6.4E-35 196.3 4.9 70 1-70 394-463 (465)
3 COG5144 TFB2 RNA polymerase II 99.9 3.3E-25 7.2E-30 166.5 5.8 69 1-69 377-445 (447)
4 PF10566 Glyco_hydro_97: Glyco 81.5 3.5 7.7E-05 30.3 4.6 24 25-48 72-97 (273)
5 cd06568 GH20_SpHex_like A subg 76.6 2.9 6.3E-05 30.9 2.9 24 19-42 68-91 (329)
6 cd06569 GH20_Sm-chitobiase-lik 75.5 3.2 6.9E-05 32.1 3.0 24 19-42 90-113 (445)
7 cd02742 GH20_hexosaminidase Be 72.6 3.9 8.5E-05 29.6 2.7 25 18-42 64-88 (303)
8 cd06563 GH20_chitobiase-like T 72.6 3.6 7.7E-05 30.5 2.6 24 19-42 79-102 (357)
9 cd06564 GH20_DspB_LnbB-like Gl 72.4 4.3 9.3E-05 29.6 2.9 25 18-42 74-98 (326)
10 cd06562 GH20_HexA_HexB-like Be 72.2 3.8 8.2E-05 30.4 2.6 23 20-42 64-86 (348)
11 cd06570 GH20_chitobiase-like_1 72.2 4.5 9.8E-05 29.8 3.0 24 19-42 61-84 (311)
12 PF13496 DUF4120: Domain of un 69.9 4.3 9.2E-05 25.8 2.1 17 24-40 4-20 (95)
13 PF08671 SinI: Anti-repressor 68.9 8.8 0.00019 19.6 2.8 28 26-69 3-30 (30)
14 PF02244 Propep_M14: Carboxype 66.3 22 0.00047 20.1 6.2 46 23-68 6-55 (74)
15 cd06565 GH20_GcnA-like Glycosy 64.9 8.3 0.00018 28.0 3.1 23 20-42 54-76 (301)
16 PF00728 Glyco_hydro_20: Glyco 62.2 6.4 0.00014 28.2 2.1 21 22-42 69-89 (351)
17 COG4379 Mu-like prophage tail 56.2 19 0.0004 28.1 3.7 31 23-53 149-179 (386)
18 PF03102 NeuB: NeuB family; I 56.0 14 0.00031 26.4 3.0 24 23-46 53-76 (241)
19 cd07241 Glo_EDI_BRP_like_3 Thi 51.1 44 0.00096 19.3 4.2 38 21-58 77-120 (125)
20 cd07265 2_3_CTD_N N-terminal d 50.2 43 0.00092 19.8 4.1 38 21-58 68-112 (122)
21 cd01998 tRNA_Me_trans tRNA met 45.7 24 0.00052 26.2 2.9 37 29-68 170-207 (349)
22 cd07252 BphC1-RGP6_N_like N-te 44.4 54 0.0012 19.5 3.9 38 21-58 64-110 (120)
23 PF08727 P3A: Poliovirus 3A pr 41.3 15 0.00032 21.5 0.9 19 24-42 25-43 (57)
24 PLN02955 8-amino-7-oxononanoat 41.2 49 0.0011 26.2 4.1 55 9-64 250-304 (476)
25 cd07242 Glo_EDI_BRP_like_6 Thi 38.0 85 0.0019 18.4 4.3 37 22-58 76-121 (128)
26 COG1313 PflX Uncharacterized F 37.9 34 0.00073 26.3 2.6 20 21-40 310-329 (335)
27 PF10087 DUF2325: Uncharacteri 37.6 68 0.0015 19.2 3.6 34 11-44 46-80 (97)
28 cd08351 ChaP_like ChaP, an enz 37.2 85 0.0018 18.6 4.0 21 24-44 67-87 (123)
29 smart00702 P4Hc Prolyl 4-hydro 37.2 49 0.0011 21.4 3.1 24 16-39 3-26 (178)
30 cd07263 Glo_EDI_BRP_like_16 Th 36.1 83 0.0018 17.7 3.7 33 26-58 76-113 (119)
31 cd07238 Glo_EDI_BRP_like_5 Thi 35.3 52 0.0011 19.0 2.7 34 25-58 65-104 (112)
32 PF09286 Pro-kuma_activ: Pro-k 34.9 1.2E+02 0.0026 19.2 4.8 32 24-55 60-92 (143)
33 cd08357 Glo_EDI_BRP_like_18 Th 34.6 83 0.0018 18.2 3.6 35 25-59 75-119 (125)
34 PF13344 Hydrolase_6: Haloacid 34.6 41 0.00089 20.4 2.3 17 48-64 31-47 (101)
35 PRK00143 mnmA tRNA-specific 2- 34.1 38 0.00083 25.1 2.4 37 29-68 169-206 (346)
36 PRK09480 slmA division inhibit 33.7 15 0.00033 23.5 0.2 24 10-33 39-63 (194)
37 PF02836 Glyco_hydro_2_C: Glyc 33.4 41 0.00089 23.8 2.4 18 29-46 62-79 (298)
38 PRK11675 LexA regulated protei 32.9 46 0.001 20.9 2.3 18 23-40 57-74 (90)
39 PF09756 DDRGK: DDRGK domain; 32.6 23 0.0005 24.8 1.0 24 45-68 148-171 (188)
40 cd08345 Fosfomycin_RP Fosfomyc 32.3 86 0.0019 17.9 3.3 33 26-58 66-104 (113)
41 PF05954 Phage_GPD: Phage late 32.1 90 0.002 21.2 3.9 33 23-55 120-152 (292)
42 smart00348 IRF interferon regu 31.6 40 0.00086 21.5 1.9 17 38-54 15-31 (107)
43 cd08344 MhqB_like_N N-terminal 30.9 1E+02 0.0022 17.9 3.5 36 24-59 64-103 (112)
44 cd07233 Glyoxalase_I Glyoxalas 30.9 78 0.0017 18.2 3.0 33 26-58 79-116 (121)
45 cd08354 Glo_EDI_BRP_like_13 Th 30.3 95 0.0021 17.8 3.3 37 21-58 74-115 (122)
46 PRK00767 transcriptional regul 30.0 18 0.0004 23.2 0.1 26 11-36 39-65 (197)
47 PRK10668 DNA-binding transcrip 29.7 28 0.00061 22.9 1.0 25 11-35 41-66 (215)
48 PRK07534 methionine synthase I 29.5 1.1E+02 0.0024 22.8 4.2 32 14-45 145-176 (336)
49 COG1435 Tdk Thymidine kinase [ 28.9 1.1E+02 0.0024 21.9 3.9 35 14-48 83-119 (201)
50 PRK00464 nrdR transcriptional 28.8 45 0.00099 22.5 1.9 21 16-36 128-148 (154)
51 cd00531 NTF2_like Nuclear tran 28.8 62 0.0013 18.0 2.3 42 25-68 14-55 (124)
52 cd08362 BphC5-RrK37_N_like N-t 28.6 1.2E+02 0.0027 17.4 3.9 37 22-58 66-110 (120)
53 PLN00052 prolyl 4-hydroxylase; 28.5 57 0.0012 24.3 2.5 24 15-38 55-78 (310)
54 COG3525 Chb N-acetyl-beta-hexo 27.6 60 0.0013 27.4 2.7 25 18-42 338-362 (732)
55 TIGR00789 flhB_rel flhB C-term 27.2 47 0.001 20.2 1.6 19 29-47 30-48 (82)
56 COG2154 Pterin-4a-carbinolamin 26.9 85 0.0018 20.1 2.8 54 4-58 21-76 (101)
57 PF00464 SHMT: Serine hydroxym 26.7 94 0.002 24.0 3.5 29 20-48 178-206 (399)
58 PF15252 DUF4589: Domain of un 26.6 31 0.00067 25.1 0.8 17 7-23 130-146 (221)
59 KOG2230 Predicted beta-mannosi 26.5 28 0.0006 29.3 0.6 32 7-45 370-401 (867)
60 PRK11202 DNA-binding transcrip 26.1 40 0.00087 22.4 1.3 25 10-34 41-66 (203)
61 PF13707 RloB: RloB-like prote 26.1 1.2E+02 0.0026 19.6 3.6 23 24-46 75-98 (183)
62 PF01378 IgG_binding_B: B doma 26.1 1.1E+02 0.0024 17.7 2.9 25 30-54 28-54 (55)
63 TIGR03613 RutR pyrimidine util 26.0 22 0.00047 23.1 -0.1 28 10-37 37-65 (202)
64 cd07261 Glo_EDI_BRP_like_11 Th 25.7 1.4E+02 0.0031 17.1 4.8 43 16-58 61-108 (114)
65 cd08361 PpCmtC_N N-terminal do 25.5 1.3E+02 0.0029 18.0 3.5 39 21-59 66-113 (124)
66 COG4509 Uncharacterized protei 25.4 78 0.0017 23.3 2.7 29 13-41 178-206 (244)
67 PF02677 DUF208: Uncharacteriz 24.9 57 0.0012 22.7 1.8 27 15-41 136-162 (176)
68 TIGR03569 NeuB_NnaB N-acetylne 24.7 89 0.0019 23.4 3.0 24 23-46 73-96 (329)
69 PF13018 ESPR: Extended Signal 24.4 98 0.0021 14.8 2.2 16 40-55 6-21 (24)
70 PF00440 TetR_N: Bacterial reg 24.1 14 0.00029 19.4 -1.1 20 10-29 25-44 (47)
71 PF07845 DUF1636: Protein of u 24.0 65 0.0014 20.8 1.9 32 15-46 66-102 (116)
72 cd07244 FosA FosA, a Fosfomyci 23.9 1.6E+02 0.0034 17.4 3.5 34 25-58 67-103 (121)
73 PF03588 Leu_Phe_trans: Leucyl 23.8 87 0.0019 21.6 2.6 31 37-67 19-51 (173)
74 PF12696 TraG-D_C: TraM recogn 23.3 1.1E+02 0.0023 19.0 2.7 27 17-43 4-33 (128)
75 PF10662 PduV-EutP: Ethanolami 22.9 2.3E+02 0.0049 18.9 4.4 36 24-66 104-142 (143)
76 PF07409 GP46: Phage protein G 22.9 52 0.0011 21.3 1.3 28 2-43 45-72 (116)
77 cd07255 Glo_EDI_BRP_like_12 Th 22.8 1.7E+02 0.0036 16.9 4.0 37 22-58 72-112 (125)
78 TIGR02432 lysidine_TilS_N tRNA 22.6 1.1E+02 0.0023 19.9 2.8 19 29-47 154-172 (189)
79 PRK14996 TetR family transcrip 22.5 36 0.00078 22.1 0.5 22 10-31 37-59 (192)
80 PF12681 Glyoxalase_2: Glyoxal 22.0 1.6E+02 0.0035 16.5 3.3 33 26-58 65-103 (108)
81 COG0436 Aspartate/tyrosine/aro 21.8 1.3E+02 0.0028 22.6 3.4 30 24-53 181-210 (393)
82 PF11305 DUF3107: Protein of u 21.7 2E+02 0.0043 17.4 5.1 36 21-56 18-55 (74)
83 PF03614 Flag1_repress: Repres 21.7 70 0.0015 22.3 1.8 20 23-42 104-123 (165)
84 PF00128 Alpha-amylase: Alpha 21.4 92 0.002 20.9 2.3 24 20-43 46-69 (316)
85 PRK05569 flavodoxin; Provision 21.4 1.8E+02 0.0038 17.9 3.5 24 15-38 116-139 (141)
86 PRK09485 mmuM homocysteine met 21.3 1.9E+02 0.004 21.0 4.0 31 14-44 154-186 (304)
87 cd02407 PTH2_family Peptidyl-t 21.3 1.5E+02 0.0033 18.8 3.2 24 22-45 56-81 (115)
88 KOG1359 Glycine C-acetyltransf 20.7 2.1E+02 0.0045 22.5 4.2 50 8-58 193-242 (417)
89 smart00642 Aamy Alpha-amylase 20.5 1.7E+02 0.0037 19.4 3.4 25 21-45 65-89 (166)
90 PF01402 RHH_1: Ribbon-helix-h 20.4 94 0.002 15.3 1.7 17 24-40 7-23 (39)
91 COG2221 DsrA Dissimilatory sul 20.3 2.2E+02 0.0049 21.7 4.3 53 10-66 33-88 (317)
92 PF01408 GFO_IDH_MocA: Oxidore 20.1 1.4E+02 0.0031 17.5 2.8 23 22-44 96-118 (120)
No 1
>TIGR00625 tfb2 Transcription factor tfb2. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.96 E-value=3.2e-30 Score=196.89 Aligned_cols=70 Identities=30% Similarity=0.527 Sum_probs=68.9
Q ss_pred CcccccccCceeeeceEEecCCCCHHHHHHHHHHHHHcCeEEeeeCCcceEEEeccccHHHHHHHHhhcC
Q 046686 1 IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQNK 70 (70)
Q Consensus 1 IrLWe~ErnRi~~~~g~Ly~~F~s~~~fe~~~~yA~~~gvLlW~~~~kr~~~V~~~gh~~vr~f~k~~~~ 70 (70)
|||||+||||+++++||||++|+|++||+++++||+++|||+|+|++||+|||+++||++|++|||++++
T Consensus 379 i~lWe~e~~R~~~~~~~l~~~f~s~~~y~~~~~ya~~~~~l~w~~~~kr~~~V~~~gh~~v~~f~k~~~~ 448 (448)
T TIGR00625 379 IRLWELERDRLRFTEGVLYNDFLTQVDFELLLAYARELGVLVWENSAKRLFFITPAGHSDVKRFWKRQKH 448 (448)
T ss_pred HHHHHHHhcceEeecceeeeecCCHHHHHHHHHHHHHcCEEEEecCCceEEEEeccchHHHHHHHHhhcC
Confidence 7999999999999999999999999999999999999999999999999999999999999999999985
No 2
>KOG3471 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription; Replication, recombination and repair]
Probab=99.96 E-value=2.9e-30 Score=196.33 Aligned_cols=70 Identities=37% Similarity=0.574 Sum_probs=68.4
Q ss_pred CcccccccCceeeeceEEecCCCCHHHHHHHHHHHHHcCeEEeeeCCcceEEEeccccHHHHHHHHhhcC
Q 046686 1 IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQNK 70 (70)
Q Consensus 1 IrLWe~ErnRi~~~~g~Ly~~F~s~~~fe~~~~yA~~~gvLlW~~~~kr~~~V~~~gh~~vr~f~k~~~~ 70 (70)
|||||+||||+.++|||||++|+|..||+.+++||+++|+|+|+|+.||+|||+++||++|++|||+++|
T Consensus 394 IrLWElernR~~~~~g~LYs~Fls~~df~~l~eya~~~~vLvw~d~~kr~~vV~~~Ghs~Vk~f~Kr~~k 463 (465)
T KOG3471|consen 394 IRLWELERNRLRMTEGYLYSDFLSLSDFQLLLEYAREIGVLVWSDSDKRMFVVTKEGHSLVKRFWKRKSK 463 (465)
T ss_pred HHHHHHhhcceecccchhHHhhhhhhhHHHHHHHHHHcCeEEEecCcceEEEEecCccHHHHHHHHHhhc
Confidence 8999999999999999999999999999999999999999999999999999999999999999999764
No 3
>COG5144 TFB2 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription / DNA replication, recombination, and repair]
Probab=99.91 E-value=3.3e-25 Score=166.47 Aligned_cols=69 Identities=28% Similarity=0.423 Sum_probs=67.7
Q ss_pred CcccccccCceeeeceEEecCCCCHHHHHHHHHHHHHcCeEEeeeCCcceEEEeccccHHHHHHHHhhc
Q 046686 1 IRLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQN 69 (70)
Q Consensus 1 IrLWe~ErnRi~~~~g~Ly~~F~s~~~fe~~~~yA~~~gvLlW~~~~kr~~~V~~~gh~~vr~f~k~~~ 69 (70)
|+|||+||||+.++||+||+||.+.++|+.+++||++.|||+|+|+.||||||+.+||.+|++|+|++-
T Consensus 377 I~lWele~nRi~~~pG~LysdFlt~s~y~~~~eya~~~gvLvw~d~~Krmffi~~eG~s~v~~f~Kr~l 445 (447)
T COG5144 377 IVLWELERNRIFMVPGYLYSDFLTLSDYQKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSLVKEFVKRIL 445 (447)
T ss_pred eeeeeeccCcEEeecchHHhhhhchhhHHHHHHHHHhcCeEEeecccceEEEEEccCcHHHHHHHHHHh
Confidence 799999999999999999999999999999999999999999999999999999999999999999974
No 4
>PF10566 Glyco_hydro_97: Glycoside hydrolase 97 ; InterPro: IPR019563 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This is the 97th family of glycosidases, in this case bacterial. The central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, most probably form two additional non-catalytic domains with as yet unknown functions. The non-catalytic domains of glycosidases from the alpha-galactosidase and alpha-glucosidase superfamilies are also predominantly composed of beta-strands, and at least some of these domains are involved in oligomerisation and carbohydrate binding. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands []. ; PDB: 2JKP_A 2JKE_A 2D73_B 2ZQ0_B 2JKA_A 3A24_A.
Probab=81.51 E-value=3.5 Score=30.31 Aligned_cols=24 Identities=21% Similarity=0.343 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHcC--eEEeeeCCc
Q 046686 25 RDVFEAACDYARDRS--GLQWEDSKK 48 (70)
Q Consensus 25 ~~~fe~~~~yA~~~g--vLlW~~~~k 48 (70)
..+-..|++||++.| |+||-+...
T Consensus 72 ~~dl~elv~Ya~~KgVgi~lw~~~~~ 97 (273)
T PF10566_consen 72 DFDLPELVDYAKEKGVGIWLWYHSET 97 (273)
T ss_dssp T--HHHHHHHHHHTT-EEEEEEECCH
T ss_pred ccCHHHHHHHHHHcCCCEEEEEeCCc
Confidence 567889999999999 899988765
No 5
>cd06568 GH20_SpHex_like A subgroup of the Glycosyl hydrolase family 20 (GH20) catalytic domain found in proteins similar to the N-acetylhexosaminidase from Streptomyces plicatus (SpHex). SpHex catalyzes the hydrolysis of N-acetyl-beta-hexosaminides. An Asp residue within the active site plays a critical role in substrate-assisted catalysis by orienting the 2-acetamido group and stabilizing the transition state. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. Proteins belonging to this subgroup lack the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases.
Probab=76.61 E-value=2.9 Score=30.91 Aligned_cols=24 Identities=13% Similarity=0.216 Sum_probs=21.2
Q ss_pred ecCCCCHHHHHHHHHHHHHcCeEE
Q 046686 19 YDEFPSRDVFEAACDYARDRSGLQ 42 (70)
Q Consensus 19 y~~F~s~~~fe~~~~yA~~~gvLl 42 (70)
...|.|++|+..+++||++.||-|
T Consensus 68 ~~~~YT~~di~elv~yA~~rgI~v 91 (329)
T cd06568 68 PGGYYTQEDYKDIVAYAAERHITV 91 (329)
T ss_pred CCCcCCHHHHHHHHHHHHHcCCEE
Confidence 457899999999999999999943
No 6
>cd06569 GH20_Sm-chitobiase-like The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=75.47 E-value=3.2 Score=32.10 Aligned_cols=24 Identities=21% Similarity=0.145 Sum_probs=21.5
Q ss_pred ecCCCCHHHHHHHHHHHHHcCeEE
Q 046686 19 YDEFPSRDVFEAACDYARDRSGLQ 42 (70)
Q Consensus 19 y~~F~s~~~fe~~~~yA~~~gvLl 42 (70)
++.|.|++|+..+++||++.||-|
T Consensus 90 ~~g~YT~~di~eiv~yA~~rgI~V 113 (445)
T cd06569 90 GSGYYSRADYIEILKYAKARHIEV 113 (445)
T ss_pred cCCccCHHHHHHHHHHHHHcCCEE
Confidence 467899999999999999999855
No 7
>cd02742 GH20_hexosaminidase Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides. These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself.
Probab=72.59 E-value=3.9 Score=29.59 Aligned_cols=25 Identities=16% Similarity=0.074 Sum_probs=22.1
Q ss_pred EecCCCCHHHHHHHHHHHHHcCeEE
Q 046686 18 YYDEFPSRDVFEAACDYARDRSGLQ 42 (70)
Q Consensus 18 Ly~~F~s~~~fe~~~~yA~~~gvLl 42 (70)
-...|.|++|+..+++||++.||-+
T Consensus 64 ~~~~~yT~~di~elv~yA~~rgI~v 88 (303)
T cd02742 64 SPGGFYTYAQLKDIIEYAAARGIEV 88 (303)
T ss_pred CCCCeECHHHHHHHHHHHHHcCCEE
Confidence 4567899999999999999999965
No 8
>cd06563 GH20_chitobiase-like The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. This GH20 domain family includes an N-acetylglucosamidase (GlcNAcase A) from Pseudoalteromonas piscicida and an N-acetylhexosaminidase (SpHex) from Streptomyces plicatus. SpHex lacks the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=72.57 E-value=3.6 Score=30.52 Aligned_cols=24 Identities=21% Similarity=0.351 Sum_probs=21.0
Q ss_pred ecCCCCHHHHHHHHHHHHHcCeEE
Q 046686 19 YDEFPSRDVFEAACDYARDRSGLQ 42 (70)
Q Consensus 19 y~~F~s~~~fe~~~~yA~~~gvLl 42 (70)
+..|.|++|+..+++||++.||-|
T Consensus 79 ~~~~YT~~di~eiv~yA~~rgI~V 102 (357)
T cd06563 79 YGGFYTQEEIREIVAYAAERGITV 102 (357)
T ss_pred cCceECHHHHHHHHHHHHHcCCEE
Confidence 357889999999999999999943
No 9
>cd06564 GH20_DspB_LnbB-like Glycosyl hydrolase family 20 (GH20) catalytic domain of dispersin B (DspB), lacto-N-biosidase (LnbB) and related proteins. Dispersin B is a soluble beta-N-acetylglucosamidase found in bacteria that hydrolyzes the beta-1,6-linkages of PGA (poly-beta-(1,6)-N-acetylglucosamine), a major component of the extracellular polysaccharide matrix. Lacto-N-biosidase hydrolyzes lacto-N-biose (LNB) type I oligosaccharides at the nonreducing terminus to produce lacto-N-biose as part of the GNB/LNB (galacto-N-biose/lacto-N-biose I) degradation pathway. The lacto-N-biosidase from Bifidobacterium bifidum has this GH20 domain, a carbohydrate binding module 32, and a bacterial immunoglobulin-like domain 2, as well as a YSIRK signal peptide and a G5 membrane anchor at the N and C termini, respectively. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=72.40 E-value=4.3 Score=29.61 Aligned_cols=25 Identities=24% Similarity=0.367 Sum_probs=21.8
Q ss_pred EecCCCCHHHHHHHHHHHHHcCeEE
Q 046686 18 YYDEFPSRDVFEAACDYARDRSGLQ 42 (70)
Q Consensus 18 Ly~~F~s~~~fe~~~~yA~~~gvLl 42 (70)
-.+.|.|++|+..+++||++.||-+
T Consensus 74 ~~~~~YT~~di~eiv~yA~~rgI~v 98 (326)
T cd06564 74 ANDGYYTKEEFKELIAYAKDRGVNI 98 (326)
T ss_pred CCCCcccHHHHHHHHHHHHHcCCeE
Confidence 3567889999999999999999954
No 10
>cd06562 GH20_HexA_HexB-like Beta-N-acetylhexosaminidases catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides. The hexA and hexB genes encode the alpha- and beta-subunits of the two major beta-N-acetylhexosaminidase isoenzymes, N-acetyl-beta-D-hexosaminidase A (HexA) and beta-N-acetylhexosaminidase B (HexB). Both the alpha and the beta catalytic subunits have a TIM-barrel fold and belong to the glycosyl hydrolase family 20 (GH20). The HexA enzyme is a heterodimer containing one alpha and one beta subunit while the HexB enzyme is a homodimer containing two beta-subunits. Hexosaminidase mutations cause an inability to properly hydrolyze certain sphingolipids which accumulate in lysosomes within the brain, resulting in the lipid storage disorders Tay-Sachs and Sandhoff. Mutations in the alpha subunit cause in a deficiency in the HexA enzyme and result in
Probab=72.20 E-value=3.8 Score=30.37 Aligned_cols=23 Identities=22% Similarity=0.183 Sum_probs=20.4
Q ss_pred cCCCCHHHHHHHHHHHHHcCeEE
Q 046686 20 DEFPSRDVFEAACDYARDRSGLQ 42 (70)
Q Consensus 20 ~~F~s~~~fe~~~~yA~~~gvLl 42 (70)
+.|.|++|+..+++||++.||-+
T Consensus 64 ~~~YT~~di~eiv~yA~~rgI~v 86 (348)
T cd06562 64 SEVYTPEDVKEIVEYARLRGIRV 86 (348)
T ss_pred CceECHHHHHHHHHHHHHcCCEE
Confidence 46789999999999999999854
No 11
>cd06570 GH20_chitobiase-like_1 A functionally uncharacterized subgroup of the Glycosyl hydrolase family 20 (GH20) catalytic domain found in proteins similar to the chitobiase of Serratia marcescens, a beta-N-1,4-acetylhexosaminidase that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. This subgroup lacks the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=72.18 E-value=4.5 Score=29.82 Aligned_cols=24 Identities=21% Similarity=0.257 Sum_probs=21.1
Q ss_pred ecCCCCHHHHHHHHHHHHHcCeEE
Q 046686 19 YDEFPSRDVFEAACDYARDRSGLQ 42 (70)
Q Consensus 19 y~~F~s~~~fe~~~~yA~~~gvLl 42 (70)
+..|.|++|+..+++||++.||-+
T Consensus 61 ~~~~yT~~di~elv~yA~~rgI~v 84 (311)
T cd06570 61 DGLYYTQEQIREVVAYARDRGIRV 84 (311)
T ss_pred CCCccCHHHHHHHHHHHHHcCCEE
Confidence 456899999999999999999944
No 12
>PF13496 DUF4120: Domain of unknown function (DUF4120)
Probab=69.87 E-value=4.3 Score=25.85 Aligned_cols=17 Identities=12% Similarity=0.391 Sum_probs=14.7
Q ss_pred CHHHHHHHHHHHHHcCe
Q 046686 24 SRDVFEAACDYARDRSG 40 (70)
Q Consensus 24 s~~~fe~~~~yA~~~gv 40 (70)
-|+-|+.+++||+++|-
T Consensus 4 cqEhy~kvv~yA~sI~D 20 (95)
T PF13496_consen 4 CQEHYDKVVQYAESIGD 20 (95)
T ss_pred hHHHHHHHHHHHHHhcc
Confidence 36789999999999984
No 13
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=68.91 E-value=8.8 Score=19.56 Aligned_cols=28 Identities=21% Similarity=0.214 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHcCeEEeeeCCcceEEEeccccHHHHHHHHhhc
Q 046686 26 DVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQN 69 (70)
Q Consensus 26 ~~fe~~~~yA~~~gvLlW~~~~kr~~~V~~~gh~~vr~f~k~~~ 69 (70)
.|...+..-|++.|+- -++||+|++.+|
T Consensus 3 ~EW~~Li~eA~~~Gls----------------~eeir~FL~~~k 30 (30)
T PF08671_consen 3 EEWVELIKEAKESGLS----------------KEEIREFLEFNK 30 (30)
T ss_dssp HHHHHHHHHHHHTT------------------HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCC----------------HHHHHHHHHhCC
Confidence 4667788888888863 388999988764
No 14
>PF02244 Propep_M14: Carboxypeptidase activation peptide; InterPro: IPR003146 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The peptidases are synthesised as inactive molecules, zymogens, with propeptides that must be removed by proteolytic cleavage to activate the enzyme. Structural studies of carboxypeptidases A and B reveal the propeptide to exist as a globular domain, followed by an extended alpha-helix; this shields the catalytic site, without specifically binding to it, while the substrate-binding site is blocked by making specific contacts [, ]. Members of this propeptide family are found in the metallocarboxypeptidases: A1, A2 [], A3, A4, A5, A6, U, insect gut carboxypeptidase and B [], and and are associated with peptidases belonging to MEROPS peptidase family M14A. Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase.; GO: 0004180 carboxypeptidase activity, 0006508 proteolysis; PDB: 3D68_C 3D67_B 3D66_A 1PBA_A 3GLJ_A 1NSA_A 1KWM_A 2BOA_B 1PYT_A 1JQG_A ....
Probab=66.27 E-value=22 Score=20.08 Aligned_cols=46 Identities=13% Similarity=0.277 Sum_probs=38.2
Q ss_pred CCHHHHHHHHHHHHHcCeEEeeeCC---c-ceEEEeccccHHHHHHHHhh
Q 046686 23 PSRDVFEAACDYARDRSGLQWEDSK---K-MRLVVKAEIHIHIREFLRGQ 68 (70)
Q Consensus 23 ~s~~~fe~~~~yA~~~gvLlW~~~~---k-r~~~V~~~gh~~vr~f~k~~ 68 (70)
.|.+..+.+.+.....++-.|..+. . -.+.|+++....+.++++..
T Consensus 6 ~t~~q~~~L~~L~~~~~~dfW~~~~~~~~~~dv~V~p~~~~~f~~~L~~~ 55 (74)
T PF02244_consen 6 KTEEQLELLQELEQSNELDFWKEPSSVGRPVDVMVPPEKLEEFEELLKEH 55 (74)
T ss_dssp SSHHHHHHHHHHHHHSTEEEEESSSSTTSEEEEEEEGGGHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHhcccceeeecCCCCCCCeEEEEECHHHHHHHHHHHHHC
Confidence 4567789999999999999999887 2 36788898888899998864
No 15
>cd06565 GH20_GcnA-like Glycosyl hydrolase family 20 (GH20) catalytic domain of N-acetyl-beta-D-glucosaminidase (GcnA, also known as BhsA) and related proteins. GcnA is an exoglucosidase which cleaves N-acetyl-beta-D-galactosamine (NAG) and N-acetyl-beta-D-galactosamine residues from 4-methylumbelliferylated (4MU) substrates, as well as cleaving NAG from chito-oligosaccharides (i.e. NAG polymers). In contrast, sulfated forms of the substrate are unable to be cleaved and act instead as mild competitive inhibitors. Additionally, the enzyme is known to be poisoned by several first-row transition metals as well as by mercury. GcnA forms a homodimer with subunits comprised of three domains, an N-terminal zincin-like domain, this central catalytic GH20 domain, and a C-terminal alpha helical domain. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=64.92 E-value=8.3 Score=28.00 Aligned_cols=23 Identities=13% Similarity=0.036 Sum_probs=21.1
Q ss_pred cCCCCHHHHHHHHHHHHHcCeEE
Q 046686 20 DEFPSRDVFEAACDYARDRSGLQ 42 (70)
Q Consensus 20 ~~F~s~~~fe~~~~yA~~~gvLl 42 (70)
..+.|++|+..+.+||++.|+-|
T Consensus 54 ~~~yT~~ei~ei~~yA~~~gI~v 76 (301)
T cd06565 54 RGAYTKEEIREIDDYAAELGIEV 76 (301)
T ss_pred CCCcCHHHHHHHHHHHHHcCCEE
Confidence 67889999999999999999865
No 16
>PF00728 Glyco_hydro_20: Glycosyl hydrolase family 20, catalytic domain; InterPro: IPR015883 Glycoside hydrolase family 20 GH20 from CAZY comprises enzymes with several known activities; beta-hexosaminidase (3.2.1.52 from EC); lacto-N-biosidase (3.2.1.140 from EC). Carbonyl oxygen of the C-2 acetamido group of the substrate acts as the catalytic nucleophile/base in this family of enzymes. In the brain and other tissues, beta-hexosaminidase A degrades GM2 gangliosides; specifically, the enzyme hydrolyses terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides. There are 3 forms of beta-hexosaminidase: hexosaminidase A is a trimer, with one alpha, one beta-A and one beta-B chain; hexosaminidase B is a tetramer of two beta-A and two beta-B chains; and hexosaminidase S is a homodimer of alpha chains. The two beta chains are derived from the cleavage of a precursor. Mutations in the beta-chain lead to Sandhoff disease, a lysosomal storage disorder characterised by accumulation of GM2 ganglioside [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds; PDB: 3RPM_A 1C7T_A 1QBA_A 1QBB_A 1C7S_A 3RCN_A 2YL8_A 2YL6_A 2YLL_A 2YL5_C ....
Probab=62.21 E-value=6.4 Score=28.18 Aligned_cols=21 Identities=14% Similarity=0.284 Sum_probs=18.6
Q ss_pred CCCHHHHHHHHHHHHHcCeEE
Q 046686 22 FPSRDVFEAACDYARDRSGLQ 42 (70)
Q Consensus 22 F~s~~~fe~~~~yA~~~gvLl 42 (70)
+.|++|...+++||++.||-|
T Consensus 69 ~yT~~di~~lv~yA~~~gI~V 89 (351)
T PF00728_consen 69 YYTKEDIRELVAYAKERGIEV 89 (351)
T ss_dssp EBEHHHHHHHHHHHHHTT-EE
T ss_pred cCCHHHHHHHHHHHHHcCCce
Confidence 789999999999999999955
No 17
>COG4379 Mu-like prophage tail protein gpP [General function prediction only]
Probab=56.24 E-value=19 Score=28.08 Aligned_cols=31 Identities=23% Similarity=0.397 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHHHHcCeEEeeeCCcceEEE
Q 046686 23 PSRDVFEAACDYARDRSGLQWEDSKKMRLVV 53 (70)
Q Consensus 23 ~s~~~fe~~~~yA~~~gvLlW~~~~kr~~~V 53 (70)
++...+..+.++|+-.|+|.|.++..-.+|-
T Consensus 149 pGETa~daL~~iAr~~gll~~~e~DG~Lv~t 179 (386)
T COG4379 149 PGETAWDALTHIARHVGLLPWLEPDGTLVVT 179 (386)
T ss_pred CcchHHHHHHHHHhhcceeEEecCCceEEEe
Confidence 4567899999999999999998887755443
No 18
>PF03102 NeuB: NeuB family; InterPro: IPR013132 NeuB is the prokaryotic N-acetylneuraminic acid synthase (Neu5Ac). It catalyses the direct formation of Neu5Ac (the most common sialic acid) by condensation of phosphoenolpyruvate (PEP) and N-acetylmannosamine (ManNAc). This reaction has only been observed in prokaryotes; eukaryotes synthesise the 9-phosphate form, Neu5Ac-9-P, and utilise ManNAc-6-P instead of ManNAc. Such eukaryotic enzymes are not present in this family []. This family also contains SpsE spore coat polysaccharide biosynthesis proteins.; GO: 0016051 carbohydrate biosynthetic process; PDB: 3G8R_B 1XUU_A 1XUZ_A 3CM4_A 2ZDR_A 1VLI_A 2WQP_A.
Probab=56.02 E-value=14 Score=26.44 Aligned_cols=24 Identities=8% Similarity=0.117 Sum_probs=19.2
Q ss_pred CCHHHHHHHHHHHHHcCeEEeeeC
Q 046686 23 PSRDVFEAACDYARDRSGLQWEDS 46 (70)
Q Consensus 23 ~s~~~fe~~~~yA~~~gvLlW~~~ 46 (70)
.|.++|..+.+||+++|+..++.+
T Consensus 53 l~~e~~~~L~~~~~~~gi~f~stp 76 (241)
T PF03102_consen 53 LSEEQHKELFEYCKELGIDFFSTP 76 (241)
T ss_dssp S-HHHHHHHHHHHHHTT-EEEEEE
T ss_pred CCHHHHHHHHHHHHHcCCEEEECC
Confidence 578899999999999999887654
No 19
>cd07241 Glo_EDI_BRP_like_3 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=51.10 E-value=44 Score=19.25 Aligned_cols=38 Identities=11% Similarity=0.114 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHHHHHHHcCeEEeeeC-----Cc-ceEEEecccc
Q 046686 21 EFPSRDVFEAACDYARDRSGLQWEDS-----KK-MRLVVKAEIH 58 (70)
Q Consensus 21 ~F~s~~~fe~~~~yA~~~gvLlW~~~-----~k-r~~~V~~~gh 58 (70)
...|.++.+.+++.+++.|+-+...+ .. ..+|..++||
T Consensus 77 ~v~~~~~v~~~~~~l~~~g~~~~~~~~~~~~g~~~~~~~DPdG~ 120 (125)
T cd07241 77 SVGSKEAVDELTERLRADGYLIIGEPRTTGDGYYESVILDPEGN 120 (125)
T ss_pred ECCCHHHHHHHHHHHHHCCCEEEeCceecCCCeEEEEEECCCCC
Confidence 44567899999999999998666422 22 3456668876
No 20
>cd07265 2_3_CTD_N N-terminal domain of catechol 2,3-dioxygenase. This subfamily contains the N-terminal, non-catalytic, domain of catechol 2,3-dioxygenase. Catechol 2,3-dioxygenase (2,3-CTD, catechol:oxygen 2,3-oxidoreductase) catalyzes an extradiol cleavage of catechol to form 2-hydroxymuconate semialdehyde with the insertion of two atoms of oxygen. The enzyme is a homotetramer and contains catalytically essential Fe(II) . The reaction proceeds by an ordered bi-unit mechanism. First, catechol binds to the enzyme, this is then followed by the binding of dioxygen to form a tertiary complex, and then the aromatic ring is cleaved to produce 2-hydroxymuconate semialdehyde. Catechol 2,3-dioxygenase belongs to the type I extradiol dioxygenase family. The subunit comprises the N- and C-terminal domains of similar structure fold, resulting from an ancient gene duplication. The active site is located in a funnel-shaped space of the C-terminal domain. This subfamily represents the N-terminal do
Probab=50.17 E-value=43 Score=19.75 Aligned_cols=38 Identities=5% Similarity=-0.221 Sum_probs=27.6
Q ss_pred CCCCHHHHHHHHHHHHHcCeEEeeeC-------CcceEEEecccc
Q 046686 21 EFPSRDVFEAACDYARDRSGLQWEDS-------KKMRLVVKAEIH 58 (70)
Q Consensus 21 ~F~s~~~fe~~~~yA~~~gvLlW~~~-------~kr~~~V~~~gh 58 (70)
...|.++.+.+.+..++.|+-+...+ .+...|-.++||
T Consensus 68 ~v~~~~dv~~~~~~l~~~G~~~~~~~~~~~~~~~~~~~~~DPdG~ 112 (122)
T cd07265 68 KVLDDADLEKLEARLQAYGVAVERIPAGELPGVGRRVRFQLPSGH 112 (122)
T ss_pred EeCCHHHHHHHHHHHHHCCCcEEEcccCCCCCCceEEEEECCCCC
Confidence 45788899999999999999765422 234555567776
No 21
>cd01998 tRNA_Me_trans tRNA methyl transferase. This family represents tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs. This family of enzyme only presents in bacteria and eukaryote. The archaeal counterpart of this enzyme performs same function, but is completely unrelated in sequence.
Probab=45.70 E-value=24 Score=26.20 Aligned_cols=37 Identities=11% Similarity=0.093 Sum_probs=26.6
Q ss_pred HHHHHHHHHcCeEEeeeC-CcceEEEeccccHHHHHHHHhh
Q 046686 29 EAACDYARDRSGLQWEDS-KKMRLVVKAEIHIHIREFLRGQ 68 (70)
Q Consensus 29 e~~~~yA~~~gvLlW~~~-~kr~~~V~~~gh~~vr~f~k~~ 68 (70)
+.+++||+++|+.+|..+ +.-..||.. ...++|++.+
T Consensus 170 ~eVr~~A~~~gl~~~~k~~s~~iCFi~~---~~~~~fl~~~ 207 (349)
T cd01998 170 PEVREIAKELGLPVAKKKDSQGICFIGE---RNFRDFLKEY 207 (349)
T ss_pred HHHHHHHHHcCCCCCCCCCCCceEEecC---CCHHHHHHHh
Confidence 458999999999998654 445667754 3467777754
No 22
>cd07252 BphC1-RGP6_N_like N-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins. This subfamily contains the N-terminal, non-catalytic, domain of BphC1-RGP6 and similar proteins. BphC catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). This subfamily of BphCs belongs to the type I extradiol dioxygenase family, which require a metal in the active site in its catalytic mechanism. Polychlorinated biphenyl degrading bacteria demonstrate a multiplicity of 2,3-dihydroxybiphenyl 1,2-dioxygenases. For example, three types of BphC enzymes have been found in Rhodococcus globerulus (BphC1-RGP6 - BphC3-RGP6), all three enzymes are type I extradiol dioxygenases. BphC1-RGP6 has an internal duplication, it is a two-domain dioxygenase which forms octamers, and has Fe(II) at the catalytic site. Its N-
Probab=44.38 E-value=54 Score=19.48 Aligned_cols=38 Identities=13% Similarity=0.058 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHHHHHHHcCeEEeeeC---------CcceEEEecccc
Q 046686 21 EFPSRDVFEAACDYARDRSGLQWEDS---------KKMRLVVKAEIH 58 (70)
Q Consensus 21 ~F~s~~~fe~~~~yA~~~gvLlW~~~---------~kr~~~V~~~gh 58 (70)
...|.++.+.+++.+++.|+-+-..+ .+-..|..++||
T Consensus 64 ~v~~~~dl~~~~~~l~~~Gv~~~~~~~~~~~~~~~~~~~~~~DPdG~ 110 (120)
T cd07252 64 EVADEAALDALAARLRAAGVAVEEGSAELAAERGVEGLIRFADPDGN 110 (120)
T ss_pred EECCHHHHHHHHHHHHHcCCeEEEcCHHHHhhCCCcEEEEEECCCCC
Confidence 34667899999999999999664322 123566678886
No 23
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=41.32 E-value=15 Score=21.50 Aligned_cols=19 Identities=5% Similarity=0.025 Sum_probs=12.0
Q ss_pred CHHHHHHHHHHHHHcCeEE
Q 046686 24 SRDVFEAACDYARDRSGLQ 42 (70)
Q Consensus 24 s~~~fe~~~~yA~~~gvLl 42 (70)
+.-+=+.|++||++.|.++
T Consensus 25 ~SV~~~eV~~YC~~~GWIi 43 (57)
T PF08727_consen 25 RSVDSPEVREYCEEQGWII 43 (57)
T ss_dssp HHH--HHHHHHHHHHT--T
T ss_pred HhcCCHHHHHHHHHCCccc
Confidence 3344567999999999876
No 24
>PLN02955 8-amino-7-oxononanoate synthase
Probab=41.18 E-value=49 Score=26.18 Aligned_cols=55 Identities=15% Similarity=-0.027 Sum_probs=42.9
Q ss_pred CceeeeceEEecCCCCHHHHHHHHHHHHHcCeEEeeeCCcceEEEeccccHHHHHH
Q 046686 9 NKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREF 64 (70)
Q Consensus 9 nRi~~~~g~Ly~~F~s~~~fe~~~~yA~~~gvLlW~~~~kr~~~V~~~gh~~vr~f 64 (70)
.++-.+||+ |+.-.+....+.+++.|++.|++|--|++.-..++.+.|......|
T Consensus 250 ~~~Vv~EgV-~SmdGdiapL~eL~~L~~~~ga~LiVDEAH~~Gv~G~~G~G~~e~~ 304 (476)
T PLN02955 250 RKVVVTDSL-FSMDGDFAPMEELSQLRKKYGFLLVIDDAHGTFVCGENGGGVAEEF 304 (476)
T ss_pred ceEEEEeCC-CCCCCCcCCHHHHHHHHHHcCcEEEEcccccCceecCCCCcHHHHh
Confidence 357777776 6666666678888888999999999999999889888776655543
No 25
>cd07242 Glo_EDI_BRP_like_6 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=37.97 E-value=85 Score=18.39 Aligned_cols=37 Identities=11% Similarity=0.077 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHHHHcCeEEeeeCCc---------ceEEEecccc
Q 046686 22 FPSRDVFEAACDYARDRSGLQWEDSKK---------MRLVVKAEIH 58 (70)
Q Consensus 22 F~s~~~fe~~~~yA~~~gvLlW~~~~k---------r~~~V~~~gh 58 (70)
.++.++.+.+.+.+++.|+-+-..+.. ...|..++|+
T Consensus 76 v~~~~d~~~~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~DpdG~ 121 (128)
T cd07242 76 APSREAVDELYARLAKRGAEILYAPREPYAGGPGYYALFFEDPDGI 121 (128)
T ss_pred cCCHHHHHHHHHHHHHcCCeEecCCcccccCCCcEEEEEEECCCCc
Confidence 456789999999999999987764442 3344556664
No 26
>COG1313 PflX Uncharacterized Fe-S protein PflX, homolog of pyruvate formate lyase activating proteins [General function prediction only]
Probab=37.89 E-value=34 Score=26.27 Aligned_cols=20 Identities=25% Similarity=0.313 Sum_probs=18.0
Q ss_pred CCCCHHHHHHHHHHHHHcCe
Q 046686 21 EFPSRDVFEAACDYARDRSG 40 (70)
Q Consensus 21 ~F~s~~~fe~~~~yA~~~gv 40 (70)
-.+|.++|+.+.+||+.+|.
T Consensus 310 R~lt~eE~e~a~~~a~~~gl 329 (335)
T COG1313 310 RRLTREEYEKALEYAEKLGL 329 (335)
T ss_pred ccCCHHHHHHHHHHHHHcCC
Confidence 45899999999999999986
No 27
>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=37.60 E-value=68 Score=19.16 Aligned_cols=34 Identities=6% Similarity=-0.049 Sum_probs=26.4
Q ss_pred eeeeceE-EecCCCCHHHHHHHHHHHHHcCeEEee
Q 046686 11 DEMTRVH-YYDEFPSRDVFEAACDYARDRSGLQWE 44 (70)
Q Consensus 11 i~~~~g~-Ly~~F~s~~~fe~~~~yA~~~gvLlW~ 44 (70)
++-.+.+ +..+|-|-.....+.+.|++.|+.++-
T Consensus 46 i~~aD~VIv~t~~vsH~~~~~vk~~akk~~ip~~~ 80 (97)
T PF10087_consen 46 IKKADLVIVFTDYVSHNAMWKVKKAAKKYGIPIIY 80 (97)
T ss_pred cCCCCEEEEEeCCcChHHHHHHHHHHHHcCCcEEE
Confidence 3333444 567999999999999999999987653
No 28
>cd08351 ChaP_like ChaP, an enzyme involved in the biosynthesis of the antitumor agent chartreusin (cha); and similar proteins. ChaP is an enzyme involved in the biosynthesis of the potent antitumor agent chartreusin (cha). Cha is an aromatic polyketide glycoside produced by Streptomyces chartreusis. ChaP may play a role as a meta-cleavage dioxygenase in the oxidative rearrangement of the anthracyclic polyketide. ChaP belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.
Probab=37.18 E-value=85 Score=18.61 Aligned_cols=21 Identities=24% Similarity=0.390 Sum_probs=17.4
Q ss_pred CHHHHHHHHHHHHHcCeEEee
Q 046686 24 SRDVFEAACDYARDRSGLQWE 44 (70)
Q Consensus 24 s~~~fe~~~~yA~~~gvLlW~ 44 (70)
+.++.+.+.+.+++.|+-+..
T Consensus 67 ~~~dl~~~~~~l~~~G~~~~~ 87 (123)
T cd08351 67 SEEEFDRIFARIRERGIDYWA 87 (123)
T ss_pred CHHHHHHHHHHHHHcCCceec
Confidence 347899999999999997643
No 29
>smart00702 P4Hc Prolyl 4-hydroxylase alpha subunit homologues. Mammalian enzymes catalyse hydroxylation of collagen, for example. Prokaryotic enzymes might catalyse hydroxylation of antibiotic peptides. These are 2-oxoglutarate-dependent dioxygenases, requiring 2-oxoglutarate and dioxygen as cosubstrates and ferrous iron as a cofactor.
Probab=37.18 E-value=49 Score=21.44 Aligned_cols=24 Identities=17% Similarity=0.146 Sum_probs=21.6
Q ss_pred eEEecCCCCHHHHHHHHHHHHHcC
Q 046686 16 VHYYDEFPSRDVFEAACDYARDRS 39 (70)
Q Consensus 16 g~Ly~~F~s~~~fe~~~~yA~~~g 39 (70)
-+++.+|.|.++-+.+.+.|+..+
T Consensus 3 i~~~~~~ls~~ec~~li~~~~~~~ 26 (178)
T smart00702 3 VVVFHDFLSPAECQKLLEEAEPLG 26 (178)
T ss_pred EEEECCCCCHHHHHHHHHHhhhhc
Confidence 468899999999999999999876
No 30
>cd07263 Glo_EDI_BRP_like_16 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=36.07 E-value=83 Score=17.68 Aligned_cols=33 Identities=12% Similarity=0.094 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHcCeEEeeeC-----CcceEEEecccc
Q 046686 26 DVFEAACDYARDRSGLQWEDS-----KKMRLVVKAEIH 58 (70)
Q Consensus 26 ~~fe~~~~yA~~~gvLlW~~~-----~kr~~~V~~~gh 58 (70)
++++.+++.+++.|+-+-..+ .+...+..++|+
T Consensus 76 ~di~~~~~~l~~~g~~~~~~~~~~~~~~~~~~~DP~G~ 113 (119)
T cd07263 76 DDIDATYEELKARGVEFSEEPREMPYGTVAVFRDPDGN 113 (119)
T ss_pred hHHHHHHHHHHhCCCEEeeccccCCCceEEEEECCCCC
Confidence 679999999999998766444 233445556665
No 31
>cd07238 Glo_EDI_BRP_like_5 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The structure of this family is a that of a strand-swapped dimer.
Probab=35.32 E-value=52 Score=18.98 Aligned_cols=34 Identities=15% Similarity=-0.145 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHcCeEEeeeCC------cceEEEecccc
Q 046686 25 RDVFEAACDYARDRSGLQWEDSK------KMRLVVKAEIH 58 (70)
Q Consensus 25 ~~~fe~~~~yA~~~gvLlW~~~~------kr~~~V~~~gh 58 (70)
.++.+.+.+.+++.|+-+...+. +...|..++||
T Consensus 65 v~d~~~~~~~l~~~G~~~~~~~~~~~~g~~~~~~~DP~Gn 104 (112)
T cd07238 65 VDDVDAALARAVAAGFAIVYGPTDEPWGVRRFFVRDPFGK 104 (112)
T ss_pred eCCHHHHHHHHHhcCCeEecCCccCCCceEEEEEECCCCC
Confidence 35688999999999998776553 23345567776
No 32
>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.
Probab=34.94 E-value=1.2e+02 Score=19.19 Aligned_cols=32 Identities=13% Similarity=0.063 Sum_probs=23.6
Q ss_pred CHHHHHHHHHHHHHcCeEEee-eCCcceEEEec
Q 046686 24 SRDVFEAACDYARDRSGLQWE-DSKKMRLVVKA 55 (70)
Q Consensus 24 s~~~fe~~~~yA~~~gvLlW~-~~~kr~~~V~~ 55 (70)
+.++.+.+.+|.++.|+-... +.....+.|+.
T Consensus 60 ~~~~v~~V~~wL~~~G~~~~~~~~~~~~i~~~~ 92 (143)
T PF09286_consen 60 SPEDVAAVKSWLKSHGLTVVEVSANGDWITVSG 92 (143)
T ss_dssp -HHHHHHHHHHHHHCT-EEEEEETTTTEEEEEE
T ss_pred CHHHHHHHHHHHHHcCCceeEEeCCCCEEEEEE
Confidence 455678899999999998876 77777777753
No 33
>cd08357 Glo_EDI_BRP_like_18 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=34.65 E-value=83 Score=18.17 Aligned_cols=35 Identities=6% Similarity=-0.021 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHcCeEEeeeCC----------cceEEEeccccH
Q 046686 25 RDVFEAACDYARDRSGLQWEDSK----------KMRLVVKAEIHI 59 (70)
Q Consensus 25 ~~~fe~~~~yA~~~gvLlW~~~~----------kr~~~V~~~gh~ 59 (70)
.++.+.+.+.+++.|+-+-..+. +..+|..++||.
T Consensus 75 ~~dv~~~~~~l~~~g~~~~~~p~~~~~~~~~~~~~~~~~DPdG~~ 119 (125)
T cd08357 75 EEEFDALAERLEAAGVEFLIEPYTRFEGQPGEQETFFLKDPSGNA 119 (125)
T ss_pred HHHHHHHHHHHHHCCCcEecCcceeccCCcCceeEEEEECCCCCE
Confidence 48999999999999996543221 345566688873
No 34
>PF13344 Hydrolase_6: Haloacid dehalogenase-like hydrolase; PDB: 2HO4_B 1YV9_A 1WVI_B 3EPR_A 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A ....
Probab=34.59 E-value=41 Score=20.45 Aligned_cols=17 Identities=12% Similarity=0.106 Sum_probs=7.9
Q ss_pred cceEEEeccccHHHHHH
Q 046686 48 KMRLVVKAEIHIHIREF 64 (70)
Q Consensus 48 kr~~~V~~~gh~~vr~f 64 (70)
++.+|+|.+....-.++
T Consensus 31 ~~~~~lTNns~~s~~~~ 47 (101)
T PF13344_consen 31 KPVVFLTNNSSRSREEY 47 (101)
T ss_dssp SEEEEEES-SSS-HHHH
T ss_pred CCEEEEeCCCCCCHHHH
Confidence 55666665554333333
No 35
>PRK00143 mnmA tRNA-specific 2-thiouridylase MnmA; Reviewed
Probab=34.14 E-value=38 Score=25.14 Aligned_cols=37 Identities=11% Similarity=0.076 Sum_probs=26.4
Q ss_pred HHHHHHHHHcCeEEeeeCCcc-eEEEeccccHHHHHHHHhh
Q 046686 29 EAACDYARDRSGLQWEDSKKM-RLVVKAEIHIHIREFLRGQ 68 (70)
Q Consensus 29 e~~~~yA~~~gvLlW~~~~kr-~~~V~~~gh~~vr~f~k~~ 68 (70)
+.+++||++.|+-.|..+... .-|+.. ..+++|++..
T Consensus 169 ~eVr~~A~~~gl~~~~k~~s~~icf~~~---~~~~~fl~~~ 206 (346)
T PRK00143 169 PEVREIAEEAGLPVAKKKDSQGICFIGE---RDYRDFLKRY 206 (346)
T ss_pred HHHHHHHHHcCCCcCCCCCCCcccCCCc---hhHHHHHHHh
Confidence 468999999999888666654 445543 4678887753
No 36
>PRK09480 slmA division inhibitor protein; Provisional
Probab=33.66 E-value=15 Score=23.54 Aligned_cols=24 Identities=25% Similarity=0.534 Sum_probs=17.8
Q ss_pred ceeeeceEEecCCCCHHH-HHHHHH
Q 046686 10 KDEMTRVHYYDEFPSRDV-FEAACD 33 (70)
Q Consensus 10 Ri~~~~g~Ly~~F~s~~~-fe~~~~ 33 (70)
+...++|.+|.-|+|.++ |..+++
T Consensus 39 ~agvs~gt~Y~~F~~K~~L~~~v~~ 63 (194)
T PRK09480 39 RVGVSEAALYRHFPSKARMFEGLIE 63 (194)
T ss_pred HhCCCHhHHHHHCCCHHHHHHHHHH
Confidence 445678999999999876 555544
No 37
>PF02836 Glyco_hydro_2_C: Glycosyl hydrolases family 2, TIM barrel domain; InterPro: IPR006103 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities; beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. Beta-galactosidase from E. coli has a TIM-barrel-like core surrounded by four other largely beta domains [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3CMG_A 3FN9_C 1YQ2_A 3K4D_B 3LPG_B 3LPF_A 3K4A_B 3K46_B 3GM8_A 3DEC_A ....
Probab=33.45 E-value=41 Score=23.78 Aligned_cols=18 Identities=17% Similarity=0.311 Sum_probs=12.7
Q ss_pred HHHHHHHHHcCeEEeeeC
Q 046686 29 EAACDYARDRSGLQWEDS 46 (70)
Q Consensus 29 e~~~~yA~~~gvLlW~~~ 46 (70)
+...+.|.++|+|+|...
T Consensus 62 ~~~~~~cD~~GilV~~e~ 79 (298)
T PF02836_consen 62 PRFYDLCDELGILVWQEI 79 (298)
T ss_dssp HHHHHHHHHHT-EEEEE-
T ss_pred HHHHHHHhhcCCEEEEec
Confidence 345678999999999664
No 38
>PRK11675 LexA regulated protein; Provisional
Probab=32.89 E-value=46 Score=20.92 Aligned_cols=18 Identities=22% Similarity=0.242 Sum_probs=15.7
Q ss_pred CCHHHHHHHHHHHHHcCe
Q 046686 23 PSRDVFEAACDYARDRSG 40 (70)
Q Consensus 23 ~s~~~fe~~~~yA~~~gv 40 (70)
.+.+.|+.+.+||++.|+
T Consensus 57 ldedl~ekL~eyAe~~ni 74 (90)
T PRK11675 57 LNADLVDALNELAEARNI 74 (90)
T ss_pred ECHHHHHHHHHHHHHcCC
Confidence 367889999999999886
No 39
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=32.61 E-value=23 Score=24.79 Aligned_cols=24 Identities=13% Similarity=0.278 Sum_probs=4.2
Q ss_pred eCCcceEEEeccccHHHHHHHHhh
Q 046686 45 DSKKMRLVVKAEIHIHIREFLRGQ 68 (70)
Q Consensus 45 ~~~kr~~~V~~~gh~~vr~f~k~~ 68 (70)
|+..+.+.||++-.+.|..||+.+
T Consensus 148 DdrGkfIyIs~eE~~~va~fi~~r 171 (188)
T PF09756_consen 148 DDRGKFIYISEEEMEAVAKFIKQR 171 (188)
T ss_dssp -TT--EEE----------------
T ss_pred cCCCCeEEecHHHHHHHHHHHHHc
Confidence 667789999999999999999875
No 40
>cd08345 Fosfomycin_RP Fosfomycin resistant protein; inhibits the biological function of fosfomycin. This family contains three types of fosfomycin resistant protein. Fosfomycin inhibits the enzyme UDP-N-acetylglucosamine-3-enolpyruvyltransferase (MurA), which catalyzes the first committed step in bacterial cell wall biosynthesis. The three types of fosfomycin resistance proteins, employ different mechanisms to render fosfomycin [(1R,2S)-epoxypropylphosphonic acid] inactive. FosB catalyzes the addition of L-cysteine to the epoxide ring of fosfomycin. FosX catalyzes the addition of a water molecule to the C1 position of the antibiotic with inversion of configuration at C1. FosA catalyzes the addition of glutathione to the antibiotic fosfomycin, making it inactive. Catalytic activities of both FosX and FosA are Mn(II)-dependent, but FosB is activated by Mg(II). Fosfomycin resistant proteins are evolutionarily related to glyoxalase I and type I extradiol dioxygenases.
Probab=32.34 E-value=86 Score=17.87 Aligned_cols=33 Identities=6% Similarity=0.020 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHcCeEEeee------CCcceEEEecccc
Q 046686 26 DVFEAACDYARDRSGLQWED------SKKMRLVVKAEIH 58 (70)
Q Consensus 26 ~~fe~~~~yA~~~gvLlW~~------~~kr~~~V~~~gh 58 (70)
++.+.+.+.+++.|+-+... ..+...|..++|+
T Consensus 66 ~d~~~~~~~l~~~G~~~~~~~~~~~~~~~~~~~~DPdG~ 104 (113)
T cd08345 66 EEFDEYTERLKALGVEMKPERPRVQGEGRSIYFYDPDGH 104 (113)
T ss_pred HHHHHHHHHHHHcCCccCCCccccCCCceEEEEECCCCC
Confidence 68999999999999987643 1234445557775
No 41
>PF05954 Phage_GPD: Phage late control gene D protein (GPD); PDB: 2P5Z_X 3D37_A 1WRU_A 3CDD_E.
Probab=32.13 E-value=90 Score=21.24 Aligned_cols=33 Identities=12% Similarity=-0.025 Sum_probs=22.8
Q ss_pred CCHHHHHHHHHHHHHcCeEEeeeCCcceEEEec
Q 046686 23 PSRDVFEAACDYARDRSGLQWEDSKKMRLVVKA 55 (70)
Q Consensus 23 ~s~~~fe~~~~yA~~~gvLlW~~~~kr~~~V~~ 55 (70)
.+..||+-+..-|++.|+.+|-+.....+++..
T Consensus 120 ~~ESD~~Fl~Rla~~~G~~~~~~~~d~~lv~~~ 152 (292)
T PF05954_consen 120 YNESDWDFLQRLAEREGIWFYFDHDDGTLVFFD 152 (292)
T ss_dssp TT-BHHHHHHHHHHHTT-EEEEECETSEEEEES
T ss_pred cCchHHHHHHHHHHhcCcEEEEecCcceEEEec
Confidence 567899999999999999999544104455554
No 42
>smart00348 IRF interferon regulatory factor. interferon regulatory factor, also known as trytophan pentad repeat
Probab=31.63 E-value=40 Score=21.47 Aligned_cols=17 Identities=41% Similarity=0.794 Sum_probs=14.3
Q ss_pred cCeEEeeeCCcceEEEe
Q 046686 38 RSGLQWEDSKKMRLVVK 54 (70)
Q Consensus 38 ~gvLlW~~~~kr~~~V~ 54 (70)
...|.|.|++|++|-|.
T Consensus 15 ypGL~W~d~ekt~FrIP 31 (107)
T smart00348 15 YPGLCWEDEEKTRFRIP 31 (107)
T ss_pred CCCceEecCCCCEEEec
Confidence 34599999999999885
No 43
>cd08344 MhqB_like_N N-terminal domain of MhqB, a type I extradiol dioxygenase, and similar proteins. This subfamily contains the N-terminal, non-catalytic, domain of Burkholderia sp. NF100 MhqB and similar proteins. MhqB is a type I extradiol dioxygenase involved in the catabolism of methylhydroquinone, an intermediate in the degradation of fenitrothion. The purified enzyme has shown extradiol ring cleavage activity toward 3-methylcatechol. Fe2+ was suggested as a cofactor, the same as most other enzymes in the family. Burkholderia sp. NF100 MhqB is encoded on the plasmid pNF1. The type I family of extradiol dioxygenases contains two structurally homologous barrel-shaped domains at the N- and C-terminal. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism.
Probab=30.92 E-value=1e+02 Score=17.95 Aligned_cols=36 Identities=8% Similarity=-0.104 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHHHHcCeEEeeeC----CcceEEEeccccH
Q 046686 24 SRDVFEAACDYARDRSGLQWEDS----KKMRLVVKAEIHI 59 (70)
Q Consensus 24 s~~~fe~~~~yA~~~gvLlW~~~----~kr~~~V~~~gh~ 59 (70)
+.++++.+++.+++.|+-+...+ .....|..++||.
T Consensus 64 ~~~d~~~~~~~l~~~Gi~~~~~~~~~~~~~~~~~DP~Gn~ 103 (112)
T cd08344 64 FEDDFAAFARHLEAAGVALAAAPPGADPDGVWFRDPDGNL 103 (112)
T ss_pred EhhhHHHHHHHHHHcCCceecCCCcCCCCEEEEECCCCCE
Confidence 36889999999999999765432 1346667788873
No 44
>cd07233 Glyoxalase_I Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione. Glyoxalase I (also known as lactoylglutathione lyase; EC 4.4.1.5) is part of the glyoxalase system, a two-step system for detoxifying methylglyoxal, a side product of glycolysis. This system is responsible for the conversion of reactive, acyclic alpha-oxoaldehydes into the corresponding alpha-hydroxyacids and involves 2 enzymes, glyoxalase I and II. Glyoxalase I catalyses an intramolecular redox reaction of the hemithioacetal (formed from methylglyoxal and glutathione) to form the thioester, S-D-lactoylglutathione. This reaction involves the transfer of two hydrogen atoms from C1 to C2 of the methylglyoxal, and proceeds via an ene-diol intermediate. Glyoxalase I has a requirement for bound metal ions for catalysis. Eukaryotic glyoxalase I prefers the divalent cation zinc as cofactor, whereas Escherichia coil and other prokaryotic gly
Probab=30.90 E-value=78 Score=18.17 Aligned_cols=33 Identities=15% Similarity=0.053 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHcCeEEeeeCC----cc-eEEEecccc
Q 046686 26 DVFEAACDYARDRSGLQWEDSK----KM-RLVVKAEIH 58 (70)
Q Consensus 26 ~~fe~~~~yA~~~gvLlW~~~~----kr-~~~V~~~gh 58 (70)
.+++.+++.+++.|+-+-..+. .+ ..|..++||
T Consensus 79 ~did~~~~~l~~~G~~~~~~~~~~~~~~~~~~~DpdG~ 116 (121)
T cd07233 79 DDVYAACERLEEMGVEVTKPPGDGGMKGIAFIKDPDGY 116 (121)
T ss_pred CCHHHHHHHHHHCCCEEeeCCccCCCceEEEEECCCCC
Confidence 3488999999999996654433 33 355667776
No 45
>cd08354 Glo_EDI_BRP_like_13 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=30.25 E-value=95 Score=17.83 Aligned_cols=37 Identities=3% Similarity=-0.061 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHHHHHHHcCeEEeeeC-----CcceEEEecccc
Q 046686 21 EFPSRDVFEAACDYARDRSGLQWEDS-----KKMRLVVKAEIH 58 (70)
Q Consensus 21 ~F~s~~~fe~~~~yA~~~gvLlW~~~-----~kr~~~V~~~gh 58 (70)
.+.+ ++.+.+.+.+.+.|+-+-... .+.+.|..++|+
T Consensus 74 ~v~~-~dl~~~~~~l~~~g~~~~~~~~~~~~~~~~~~~DP~G~ 115 (122)
T cd08354 74 AIPA-EELAEWEAHLEAKGVAIESEVQWPRGGRSLYFRDPDGN 115 (122)
T ss_pred EcCH-HHHHHHHHHHHhcCCceeccccCCCCeeEEEEECCCCC
Confidence 4566 899999999999998543322 244555567775
No 46
>PRK00767 transcriptional regulator BetI; Validated
Probab=30.00 E-value=18 Score=23.20 Aligned_cols=26 Identities=15% Similarity=0.042 Sum_probs=19.4
Q ss_pred eeeeceEEecCCCCHHH-HHHHHHHHH
Q 046686 11 DEMTRVHYYDEFPSRDV-FEAACDYAR 36 (70)
Q Consensus 11 i~~~~g~Ly~~F~s~~~-fe~~~~yA~ 36 (70)
.-.+.|.||.-|+|.++ |..+.++..
T Consensus 39 aGvs~gslY~~F~~Ke~L~~~~l~~~~ 65 (197)
T PRK00767 39 AGVSTGIISHYFGGKDGLLEATMRHLL 65 (197)
T ss_pred hCCCHHHHHHHhCCHHHHHHHHHHHHH
Confidence 45678999999999877 666666543
No 47
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=29.73 E-value=28 Score=22.90 Aligned_cols=25 Identities=20% Similarity=0.304 Sum_probs=19.6
Q ss_pred eeeeceEEecCCCCHHH-HHHHHHHH
Q 046686 11 DEMTRVHYYDEFPSRDV-FEAACDYA 35 (70)
Q Consensus 11 i~~~~g~Ly~~F~s~~~-fe~~~~yA 35 (70)
.-.++|.||.-|+|.++ |..+++..
T Consensus 41 agvs~~tlY~~F~sKe~Ll~~v~~~~ 66 (215)
T PRK10668 41 AGVTRGAIYWHFKNKSDLFSEIWELS 66 (215)
T ss_pred hCCChHHHHHHCCCHHHHHHHHHHHH
Confidence 45678999999999877 77777553
No 48
>PRK07534 methionine synthase I; Validated
Probab=29.53 E-value=1.1e+02 Score=22.81 Aligned_cols=32 Identities=13% Similarity=0.081 Sum_probs=28.5
Q ss_pred eceEEecCCCCHHHHHHHHHHHHHcCeEEeee
Q 046686 14 TRVHYYDEFPSRDVFEAACDYARDRSGLQWED 45 (70)
Q Consensus 14 ~~g~Ly~~F~s~~~fe~~~~yA~~~gvLlW~~ 45 (70)
-+.+++.-|+|..|-..++..+++.|.-+|-+
T Consensus 145 vD~l~~ET~p~l~E~~a~~~~~~~~~~Pv~vS 176 (336)
T PRK07534 145 ADVLWVETISAPEEIRAAAEAAKLAGMPWCGT 176 (336)
T ss_pred CCEEEEeccCCHHHHHHHHHHHHHcCCeEEEE
Confidence 37789999999999999999999999888853
No 49
>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]
Probab=28.93 E-value=1.1e+02 Score=21.89 Aligned_cols=35 Identities=9% Similarity=-0.072 Sum_probs=30.0
Q ss_pred eceEEec--CCCCHHHHHHHHHHHHHcCeEEeeeCCc
Q 046686 14 TRVHYYD--EFPSRDVFEAACDYARDRSGLQWEDSKK 48 (70)
Q Consensus 14 ~~g~Ly~--~F~s~~~fe~~~~yA~~~gvLlW~~~~k 48 (70)
+++++.+ +|.+.+--+.+.+-|.++|+.++..--.
T Consensus 83 ~~~v~IDEaQF~~~~~v~~l~~lad~lgi~Vi~~GL~ 119 (201)
T COG1435 83 VDCVLIDEAQFFDEELVYVLNELADRLGIPVICYGLD 119 (201)
T ss_pred cCEEEEehhHhCCHHHHHHHHHHHhhcCCEEEEeccc
Confidence 5678887 8999999999999999999999976543
No 50
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=28.83 E-value=45 Score=22.55 Aligned_cols=21 Identities=24% Similarity=0.333 Sum_probs=17.0
Q ss_pred eEEecCCCCHHHHHHHHHHHH
Q 046686 16 VHYYDEFPSRDVFEAACDYAR 36 (70)
Q Consensus 16 g~Ly~~F~s~~~fe~~~~yA~ 36 (70)
+.+|++|.+.++|+..++-++
T Consensus 128 a~~~~~f~~~~~~~~~~~~~~ 148 (154)
T PRK00464 128 ASVYRSFKDVDDFEEEIEELA 148 (154)
T ss_pred hhhcCCCCCHHHHHHHHHHHH
Confidence 468999999999998776543
No 51
>cd00531 NTF2_like Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of divergent evolution wherein the proteins have many common structural details but diverge greatly in their function. For example, nuclear transport factor 2 (NTF2) mediates the nuclear import of RanGDP and binds to both RanGDP and FxFG repeat-containing nucleoporins while Ketosteroid isomerases catalyze the isomerization of delta-5-3-ketosteroid to delta-4-3-ketosteroid, by intramolecular transfer of the C4-beta proton to the C6-beta position. While the function of the beta sub-unit of the Ring hydroxylating dioxygenases is not known, Scytalone Dehydratases catalyzes two reactions in the biosynthetic pathway that produces fungal melanin. Members of the NTF2-like superfamily are widely distributed among bacteria, archaea
Probab=28.82 E-value=62 Score=18.05 Aligned_cols=42 Identities=12% Similarity=-0.046 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHcCeEEeeeCCcceEEEeccccHHHHHHHHhh
Q 046686 25 RDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIHIHIREFLRGQ 68 (70)
Q Consensus 25 ~~~fe~~~~yA~~~gvLlW~~~~kr~~~V~~~gh~~vr~f~k~~ 68 (70)
+.+.+.+..+..+-+++.+.... .+.....|++.|++|+...
T Consensus 14 ~~~~~~l~~~~~~d~~~~~~~~~--~~~~~~~g~~~i~~~~~~~ 55 (124)
T cd00531 14 AGDREWLALLYADDAYFEPPGGD--GLIYPDDGREAIEDRVRRL 55 (124)
T ss_pred CchHHHHHhhCcCcEEEEEccCC--EEEEcCChHHHHHHHHHhc
Confidence 45566666666666666654332 2334457899999998753
No 52
>cd08362 BphC5-RrK37_N_like N-terminal, non-catalytic, domain of BphC5 (2,3-dihydroxybiphenyl 1,2-dioxygenase) from Rhodococcus rhodochrous K37, and similar proteins. 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). The enzyme contains a N-terminal and a C-terminal domain of similar structure fold, resulting from an ancient gene duplication. BphC belongs to the type I extradiol dioxygenase family, which requires a metal in the active site for its catalytic activity. Polychlorinated biphenyl degrading bacteria demonstrate multiplicity of BphCs. Bacterium Rhodococcus rhodochrous K37 has eight genes encoding BphC enzymes. This family includes the N-terminal domain of BphC5-RrK37. The crystal structure of the protein from Novosphingobium aromaticivorans has a Mn(II)in the active site, although most proteins of type I extradiol dioxyge
Probab=28.55 E-value=1.2e+02 Score=17.38 Aligned_cols=37 Identities=14% Similarity=0.048 Sum_probs=25.9
Q ss_pred CCCHHHHHHHHHHHHHcCeEEeeeC--------CcceEEEecccc
Q 046686 22 FPSRDVFEAACDYARDRSGLQWEDS--------KKMRLVVKAEIH 58 (70)
Q Consensus 22 F~s~~~fe~~~~yA~~~gvLlW~~~--------~kr~~~V~~~gh 58 (70)
-.+.++.+.+.+.+++.|+-+-..+ .....|..++||
T Consensus 66 v~~~~~l~~~~~~l~~~G~~~~~~~~~~~~~~~~~~~~~~DP~G~ 110 (120)
T cd08362 66 VASRADVDALARQVAARGGTVLSEPGATDDPGGGYGFRFFDPDGR 110 (120)
T ss_pred eCCHHHHHHHHHHHHHcCCceecCCcccCCCCCceEEEEECCCCC
Confidence 3567899999999999999543222 223566678876
No 53
>PLN00052 prolyl 4-hydroxylase; Provisional
Probab=28.50 E-value=57 Score=24.30 Aligned_cols=24 Identities=21% Similarity=0.379 Sum_probs=21.2
Q ss_pred ceEEecCCCCHHHHHHHHHHHHHc
Q 046686 15 RVHYYDEFPSRDVFEAACDYARDR 38 (70)
Q Consensus 15 ~g~Ly~~F~s~~~fe~~~~yA~~~ 38 (70)
--++|.+|.|.+|-+.+.+.|+..
T Consensus 55 ~i~~~~nfLs~~Ecd~Li~la~~~ 78 (310)
T PLN00052 55 RIFVYKGFLSDAECDHLVKLAKKK 78 (310)
T ss_pred CEEEECCcCCHHHHHHHHHhcccc
Confidence 358999999999999999999864
No 54
>COG3525 Chb N-acetyl-beta-hexosaminidase [Carbohydrate transport and metabolism]
Probab=27.60 E-value=60 Score=27.38 Aligned_cols=25 Identities=20% Similarity=0.178 Sum_probs=22.9
Q ss_pred EecCCCCHHHHHHHHHHHHHcCeEE
Q 046686 18 YYDEFPSRDVFEAACDYARDRSGLQ 42 (70)
Q Consensus 18 Ly~~F~s~~~fe~~~~yA~~~gvLl 42 (70)
++..|-|+++...+++||.+.++.+
T Consensus 338 ~~ggfytqd~~relv~yAsar~Itv 362 (732)
T COG3525 338 RMGGFYTQDDIRELVAYASARQITV 362 (732)
T ss_pred cccCcccHHHHHHHHHHHhhcCcee
Confidence 5789999999999999999999876
No 55
>TIGR00789 flhB_rel flhB C-terminus-related protein. This model describes a short protein (80-93 residues) homologous to the C-terminus of the flagellar biosynthetic protein FlhB. It is found so far only in species that also have FlhB. In a phylogenetic tree based on alignment of both this family and the homologous region of FlhB and its homologs, the members of this family form a monophyletic set.
Probab=27.21 E-value=47 Score=20.17 Aligned_cols=19 Identities=21% Similarity=0.136 Sum_probs=16.7
Q ss_pred HHHHHHHHHcCeEEeeeCC
Q 046686 29 EAACDYARDRSGLQWEDSK 47 (70)
Q Consensus 29 e~~~~yA~~~gvLlW~~~~ 47 (70)
+.+++.|++.||.+.+|+.
T Consensus 30 ~~I~~~A~e~~VPi~~~~~ 48 (82)
T TIGR00789 30 ERIIEIAKKHGIPIVEDPD 48 (82)
T ss_pred HHHHHHHHHcCCCEEeCHH
Confidence 5689999999999999874
No 56
>COG2154 Pterin-4a-carbinolamine dehydratase [Coenzyme metabolism]
Probab=26.90 E-value=85 Score=20.06 Aligned_cols=54 Identities=20% Similarity=0.292 Sum_probs=39.4
Q ss_pred cccccCceeeeceEEecCCCCHHHHH-HHHHHHHHcCe-EEeeeCCcceEEEecccc
Q 046686 4 WESDLNKDEMTRVHYYDEFPSRDVFE-AACDYARDRSG-LQWEDSKKMRLVVKAEIH 58 (70)
Q Consensus 4 We~ErnRi~~~~g~Ly~~F~s~~~fe-~~~~yA~~~gv-LlW~~~~kr~~~V~~~gh 58 (70)
|++..++.+.+..|-|++|...-.|- .+...|+++|- .-|++.-+ .+.|+-.-|
T Consensus 21 W~l~~~~~~l~r~f~FknF~~a~~F~~~vA~~Ae~~~HHPdi~~~y~-~V~vtltTH 76 (101)
T COG2154 21 WELADDGAKLTRTFKFKNFKQAIAFVNRVAEIAEKLNHHPDIEVVYN-RVTVTLTTH 76 (101)
T ss_pred CEEecCcceEEEEEEcCCHHHHHHHHHHHHHHHHHhCCCCCeEEEee-eEEEEEEEc
Confidence 99999999999999999999888875 56778888875 44444444 344443333
No 57
>PF00464 SHMT: Serine hydroxymethyltransferase; InterPro: IPR001085 Synonym(s): Serine hydroxymethyltransferase, Serine aldolase, Threonine aldolase Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate (PLP) dependent enzyme and belongs to the aspartate aminotransferase superfamily (fold type I) []. The pyridoxal-P group is attached to a lysine residue around which the sequence is highly conserved in all forms of the enzyme []. The enzyme carries out interconversion of serine and glycine using PLP as the cofactor. SHMT catalyses the transfer of a hydroxymethyl group from N5, N10- methylene tetrahydrofolate to glycine, resulting in the formation of serine and tetrahydrofolate. Both eukaryotic and prokaryotic SHMT enzymes form tight obligate homodimers and the mammalian enzyme forms a homotetramer [, ]. PLP dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalysed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), D-amino acid superfamily (fold type IV) and glycogen phophorylase family (fold type V) [, ]. In vertebrates, glycine hydroxymethyltransferase exists in a cytoplasmic and a mitochondrial form whereas only one form is found in prokaryotes.; GO: 0004372 glycine hydroxymethyltransferase activity, 0006544 glycine metabolic process, 0006563 L-serine metabolic process; PDB: 3GBX_B 3H7F_A 1YJS_A 2VMW_A 2W7H_A 2W7E_A 2VMY_B 2W7L_A 2VMZ_A 2VMS_A ....
Probab=26.74 E-value=94 Score=24.03 Aligned_cols=29 Identities=14% Similarity=0.179 Sum_probs=20.2
Q ss_pred cCCCCHHHHHHHHHHHHHcCeEEeeeCCc
Q 046686 20 DEFPSRDVFEAACDYARDRSGLQWEDSKK 48 (70)
Q Consensus 20 ~~F~s~~~fe~~~~yA~~~gvLlW~~~~k 48 (70)
+.++-.-+|+.+++.|.+.|.+||-|-+.
T Consensus 178 S~y~~~~d~~~~reIad~vga~l~~D~sH 206 (399)
T PF00464_consen 178 SSYPRPIDFKRFREIADEVGAYLMADISH 206 (399)
T ss_dssp SSTSS---HHHHHHHHHHTT-EEEEE-TT
T ss_pred hhccCccCHHHHHHHHHhcCcEEEecccc
Confidence 34566789999999999999999988754
No 58
>PF15252 DUF4589: Domain of unknown function (DUF4589)
Probab=26.56 E-value=31 Score=25.07 Aligned_cols=17 Identities=6% Similarity=0.102 Sum_probs=14.7
Q ss_pred ccCceeeeceEEecCCC
Q 046686 7 DLNKDEMTRVHYYDEFP 23 (70)
Q Consensus 7 ErnRi~~~~g~Ly~~F~ 23 (70)
.|+|++|.+-|||..+=
T Consensus 130 tRERVRFSdKVlYHalC 146 (221)
T PF15252_consen 130 TRERVRFSDKVLYHALC 146 (221)
T ss_pred ccceeeccccceeeeee
Confidence 58999999999997654
No 59
>KOG2230 consensus Predicted beta-mannosidase [Carbohydrate transport and metabolism]
Probab=26.54 E-value=28 Score=29.31 Aligned_cols=32 Identities=28% Similarity=0.377 Sum_probs=22.8
Q ss_pred ccCceeeeceEEecCCCCHHHHHHHHHHHHHcCeEEeee
Q 046686 7 DLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWED 45 (70)
Q Consensus 7 ErnRi~~~~g~Ly~~F~s~~~fe~~~~yA~~~gvLlW~~ 45 (70)
-+|=++...|=.|. | +.| -.+|.++|+|+|.|
T Consensus 370 ~MN~lRVWGGGvYE---s-d~F---Y~lad~lGilVWQD 401 (867)
T KOG2230|consen 370 GMNMLRVWGGGVYE---S-DYF---YQLADSLGILVWQD 401 (867)
T ss_pred CcceEEEecCcccc---c-hhH---HHHhhhccceehhh
Confidence 45677777887774 2 222 35799999999976
No 60
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=26.14 E-value=40 Score=22.39 Aligned_cols=25 Identities=16% Similarity=0.224 Sum_probs=18.5
Q ss_pred ceeeeceEEecCCCCHHH-HHHHHHH
Q 046686 10 KDEMTRVHYYDEFPSRDV-FEAACDY 34 (70)
Q Consensus 10 Ri~~~~g~Ly~~F~s~~~-fe~~~~y 34 (70)
+...++|.+|.-|+|.++ |..+++.
T Consensus 41 ~Agvs~~t~Y~hF~sKe~L~~av~~~ 66 (203)
T PRK11202 41 EAGIAPTSFYRHFRDMDELGLTMVDE 66 (203)
T ss_pred HhCCCcchHHHHCCCHHHHHHHHHHH
Confidence 345789999999999877 5555443
No 61
>PF13707 RloB: RloB-like protein
Probab=26.13 E-value=1.2e+02 Score=19.63 Aligned_cols=23 Identities=17% Similarity=0.173 Sum_probs=19.4
Q ss_pred CHHHHHHHHHHHHHcCe-EEeeeC
Q 046686 24 SRDVFEAACDYARDRSG-LQWEDS 46 (70)
Q Consensus 24 s~~~fe~~~~yA~~~gv-LlW~~~ 46 (70)
..+.|+.+.+.|++.++ +.|+||
T Consensus 75 ~~~~~~~~~~~a~~~~i~l~~SnP 98 (183)
T PF13707_consen 75 EHEKLEEAIKKAKRNKINLAVSNP 98 (183)
T ss_pred cHHHHHHHHHhccccCeEEEEecC
Confidence 57789999999999888 777777
No 62
>PF01378 IgG_binding_B: B domain; InterPro: IPR000724 This domain is found as a tandem repeat in Streptococcal cell surface proteins, such as the IgG binding proteins G and MIG. These proteins are type I membrane proteins that bind to the constant Fc region of IgG with high affinity. The N terminus of MIG mediates binding to plasma proteinase inhibitor alpha 2-macroglobulin after complex formation with proteases.; GO: 0005618 cell wall; PDB: 1IGC_A 2IGH_A 2NMQ_A 1IGD_A 1PGX_A 2IGD_A 1QKZ_A 1GB4_A 1FCC_D 1FCL_A ....
Probab=26.06 E-value=1.1e+02 Score=17.67 Aligned_cols=25 Identities=28% Similarity=0.426 Sum_probs=18.4
Q ss_pred HHHHHHHHcCe-EEee-eCCcceEEEe
Q 046686 30 AACDYARDRSG-LQWE-DSKKMRLVVK 54 (70)
Q Consensus 30 ~~~~yA~~~gv-LlW~-~~~kr~~~V~ 54 (70)
.-.+||.+.|| ..|. |+....|+|+
T Consensus 28 ~F~~yan~ngv~gew~yd~at~tftvt 54 (55)
T PF01378_consen 28 AFRQYANDNGVDGEWSYDDATKTFTVT 54 (55)
T ss_dssp HHHHHHHHTTTTSEEEEETTTTEEEEE
T ss_pred HHHHHhccCCCCCccccccchhheecc
Confidence 45789999999 7785 4556677765
No 63
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=26.01 E-value=22 Score=23.12 Aligned_cols=28 Identities=21% Similarity=0.306 Sum_probs=21.7
Q ss_pred ceeeeceEEecCCCCHHH-HHHHHHHHHH
Q 046686 10 KDEMTRVHYYDEFPSRDV-FEAACDYARD 37 (70)
Q Consensus 10 Ri~~~~g~Ly~~F~s~~~-fe~~~~yA~~ 37 (70)
+...++|-+|.-|.|.++ |..++++.-+
T Consensus 37 ~agvs~~~lY~hF~sKe~L~~av~~~~~~ 65 (202)
T TIGR03613 37 LAGVSKTNLLYYFPSKDALYLAVLRQILD 65 (202)
T ss_pred HhCCCHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 456788999999999777 7777776543
No 64
>cd07261 Glo_EDI_BRP_like_11 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=25.68 E-value=1.4e+02 Score=17.08 Aligned_cols=43 Identities=5% Similarity=-0.090 Sum_probs=30.7
Q ss_pred eEEecCCCCHHHHHHHHHHHHHcCeEEeeeC-----CcceEEEecccc
Q 046686 16 VHYYDEFPSRDVFEAACDYARDRSGLQWEDS-----KKMRLVVKAEIH 58 (70)
Q Consensus 16 g~Ly~~F~s~~~fe~~~~yA~~~gvLlW~~~-----~kr~~~V~~~gh 58 (70)
..++=..+|.++.+.+.+.+.+.|+-+=..+ .....|..++||
T Consensus 61 ~~~~~~v~~~~~~~~~~~~~~~~g~~v~~~~~~~~~g~~~~~~DPdGn 108 (114)
T cd07261 61 SELAFMVDDGAAVDALYAEWQAKGVKIIQEPTEMDFGYTFVALDPDGH 108 (114)
T ss_pred eEEEEEcCCHHHHHHHHHHHHHCCCeEecCccccCCccEEEEECCCCC
Confidence 4555577888999999999999998554332 233555568877
No 65
>cd08361 PpCmtC_N N-terminal domain of 2,3-dihydroxy-p-cumate-3,4-dioxygenase (PpCmtC). This subfamily contains the N-terminal, non-catalytic, domain of PpCmtC. 2,3-dihydroxy-p-cumate-3,4-dioxygenase (CmtC of Pseudomonas putida F1) is a dioxygenase involved in the eight-step catabolism pathway of p-cymene. CmtC acts upon the reaction intermediate 2,3-dihydroxy-p-cumate, yielding 2-hydroxy-3-carboxy-6-oxo-7-methylocta-2,4-dienoate. The CmtC belongs to the type I family of extradiol dioxygenases. Fe2+ was suggested as a cofactor, same as other enzymes in the family. The type I family of extradiol dioxygenases contains two structurally homologous barrel-shaped domains at the N- and C-terminal. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism.
Probab=25.52 E-value=1.3e+02 Score=17.96 Aligned_cols=39 Identities=13% Similarity=0.049 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHHHHHHHcCeE-EeeeCC-------cc-eEEEeccccH
Q 046686 21 EFPSRDVFEAACDYARDRSGL-QWEDSK-------KM-RLVVKAEIHI 59 (70)
Q Consensus 21 ~F~s~~~fe~~~~yA~~~gvL-lW~~~~-------kr-~~~V~~~gh~ 59 (70)
.+.|.++.+.+.+..++.|+- .+..+. .+ ..|..++||.
T Consensus 66 ~v~~~~dv~~~~~~l~~~G~~~~~~~~~~~~~~~~~~~~~f~DPdG~~ 113 (124)
T cd08361 66 ELRDDDALESAATELEQYGHEVRRGTAEECELRKVKAFIAFRDPSGNS 113 (124)
T ss_pred EECCHHHHHHHHHHHHHcCCceEEcCHHHhhcCCcceEEEEECcCCCE
Confidence 468889999999999999984 442211 22 3456688773
No 66
>COG4509 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.44 E-value=78 Score=23.26 Aligned_cols=29 Identities=14% Similarity=0.084 Sum_probs=24.9
Q ss_pred eeceEEecCCCCHHHHHHHHHHHHHcCeE
Q 046686 13 MTRVHYYDEFPSRDVFEAACDYARDRSGL 41 (70)
Q Consensus 13 ~~~g~Ly~~F~s~~~fe~~~~yA~~~gvL 41 (70)
+.+-|+..+||+..||..-++.-+...|.
T Consensus 178 t~d~yi~tef~~d~dy~~fLne~KqkSV~ 206 (244)
T COG4509 178 TDDYYIETEFPVDIDYNEFLNEIKQKSVQ 206 (244)
T ss_pred ccceeeecCCCCchhHHHHHHHHHhhhee
Confidence 45678899999999999999999987764
No 67
>PF02677 DUF208: Uncharacterized BCR, COG1636; InterPro: IPR003828 This entry describes proteins of unknown function.
Probab=24.85 E-value=57 Score=22.69 Aligned_cols=27 Identities=11% Similarity=0.311 Sum_probs=23.7
Q ss_pred ceEEecCCCCHHHHHHHHHHHHHcCeE
Q 046686 15 RVHYYDEFPSRDVFEAACDYARDRSGL 41 (70)
Q Consensus 15 ~g~Ly~~F~s~~~fe~~~~yA~~~gvL 41 (70)
-.++|.||-...-|..-.+.+++.|..
T Consensus 136 v~f~~~DfRk~~g~~~~~~lske~glY 162 (176)
T PF02677_consen 136 VEFLYRDFRKKNGFQRSIELSKELGLY 162 (176)
T ss_pred CeEEeeccccCccHHHHHHHHHHhCCc
Confidence 358999999999999999999999864
No 68
>TIGR03569 NeuB_NnaB N-acetylneuraminate synthase. This family is a subset of the Pfam model pfam03102 and is believed to include only authentic NeuB N-acetylneuraminate (sialic acid) synthase enzymes. The majority of the genes identified by this model are observed adjacent to both the NeuA and NeuC genes which together effect the biosynthesis of CMP-N-acetylneuraminate from UDP-N-acetylglucosamine.
Probab=24.73 E-value=89 Score=23.45 Aligned_cols=24 Identities=8% Similarity=0.022 Sum_probs=19.9
Q ss_pred CCHHHHHHHHHHHHHcCeEEeeeC
Q 046686 23 PSRDVFEAACDYARDRSGLQWEDS 46 (70)
Q Consensus 23 ~s~~~fe~~~~yA~~~gvLlW~~~ 46 (70)
.+.++|+.+.+||++.|+...+.+
T Consensus 73 l~~e~~~~L~~~~~~~Gi~~~stp 96 (329)
T TIGR03569 73 LSEEDHRELKEYCESKGIEFLSTP 96 (329)
T ss_pred CCHHHHHHHHHHHHHhCCcEEEEe
Confidence 457889999999999999876544
No 69
>PF13018 ESPR: Extended Signal Peptide of Type V secretion system
Probab=24.44 E-value=98 Score=14.85 Aligned_cols=16 Identities=25% Similarity=0.541 Sum_probs=10.4
Q ss_pred eEEeeeCCcceEEEec
Q 046686 40 GLQWEDSKKMRLVVKA 55 (70)
Q Consensus 40 vLlW~~~~kr~~~V~~ 55 (70)
-++|+......++|++
T Consensus 6 r~iwn~~~~~~vvvsE 21 (24)
T PF13018_consen 6 RLIWNKARGTWVVVSE 21 (24)
T ss_pred EEEEECCCCeEEEEee
Confidence 3789766666666654
No 70
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=24.06 E-value=14 Score=19.43 Aligned_cols=20 Identities=25% Similarity=0.572 Sum_probs=15.7
Q ss_pred ceeeeceEEecCCCCHHHHH
Q 046686 10 KDEMTRVHYYDEFPSRDVFE 29 (70)
Q Consensus 10 Ri~~~~g~Ly~~F~s~~~fe 29 (70)
|...+.+.+|.-|+|.++.-
T Consensus 25 ~~gvs~~~~y~~f~~k~~l~ 44 (47)
T PF00440_consen 25 RAGVSKGSFYRYFPSKDDLL 44 (47)
T ss_dssp HHTSCHHHHHHHCSSHHHHH
T ss_pred HHccchhhHHHHcCCHHHHH
Confidence 45567888999999988753
No 71
>PF07845 DUF1636: Protein of unknown function (DUF1636); InterPro: IPR012863 The sequences featured in this family are derived from a number of hypothetical prokaryotic proteins. The region in question is approximately 130 amino acids long.
Probab=24.03 E-value=65 Score=20.79 Aligned_cols=32 Identities=9% Similarity=0.255 Sum_probs=24.7
Q ss_pred ceEEecCCCCHHHHHHHHHHHH-----HcCeEEeeeC
Q 046686 15 RVHYYDEFPSRDVFEAACDYAR-----DRSGLQWEDS 46 (70)
Q Consensus 15 ~g~Ly~~F~s~~~fe~~~~yA~-----~~gvLlW~~~ 46 (70)
-+|||-||.-.++=+.+++||+ +-|.+-|...
T Consensus 66 ~tYlfGdl~p~~~a~~il~~a~~Y~~s~dG~vp~~~r 102 (116)
T PF07845_consen 66 WTYLFGDLDPDEDAEDILAFAALYAASPDGLVPWRER 102 (116)
T ss_pred cEEEEecCCcccCHHHHHHHHHHHHhCCCCccccccC
Confidence 4799999998788888888776 4577777654
No 72
>cd07244 FosA FosA, a Fosfomycin resistance protein, catalyzes the addition of glutathione to the antibiotic fosfomycin, making it inactive. This subfamily family contains FosA, a fosfomycin resistant protein. Fosfomycin inhibits the enzyme UDP-N-acetylglucosamine-3-enolpyruvyltransferase (MurA), which catalyzes the first committed step in bacterial cell wall biosynthesis. FosA, catalyzes the addition of glutathione to the antibiotic fosfomycin, (1R,2S)-epoxypropylphosphonic acid, making it inactive. FosA is a Mn(II) dependent enzyme. It is evolutionarily related to glyoxalase I and type I extradiol dioxygenases.
Probab=23.91 E-value=1.6e+02 Score=17.38 Aligned_cols=34 Identities=12% Similarity=0.258 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHcCeEEeeeC---CcceEEEecccc
Q 046686 25 RDVFEAACDYARDRSGLQWEDS---KKMRLVVKAEIH 58 (70)
Q Consensus 25 ~~~fe~~~~yA~~~gvLlW~~~---~kr~~~V~~~gh 58 (70)
.++.+.+.+.+++.|+-++..+ .+...|..++|+
T Consensus 67 ~~dl~~~~~~l~~~G~~~~~~~~~~~~~~~f~DPdG~ 103 (121)
T cd07244 67 EEDFASLKEKLRQAGVKEWKENTSEGDSFYFLDPDGH 103 (121)
T ss_pred HHHHHHHHHHHHHcCCcccCCCCCCccEEEEECCCCC
Confidence 4789999999999999888543 244566667776
No 73
>PF03588 Leu_Phe_trans: Leucyl/phenylalanyl-tRNA protein transferase; InterPro: IPR004616 Leucyl/phenylalanyl-tRNA--protein transferase 2.3.2.6 from EC transfers a Leu or Phe to the amino end of certain proteins to enable degradation. The N-terminal residue controls the biological half-life of many proteins via the N-end rule pathway.; GO: 0008914 leucyltransferase activity, 0030163 protein catabolic process; PDB: 2Z3L_A 2Z3O_A 2Z3P_A 2DPT_B 2Z3M_B 2Z3N_B 2DPS_B 2Z3K_B 2CXA_A.
Probab=23.76 E-value=87 Score=21.62 Aligned_cols=31 Identities=23% Similarity=0.516 Sum_probs=17.2
Q ss_pred HcCeEEeeeCCcceEEEeccccHH--HHHHHHh
Q 046686 37 DRSGLQWEDSKKMRLVVKAEIHIH--IREFLRG 67 (70)
Q Consensus 37 ~~gvLlW~~~~kr~~~V~~~gh~~--vr~f~k~ 67 (70)
+-+-++|-++..|+++-..+-|-. +|..+|+
T Consensus 19 ~~~pilW~sp~pR~vl~~~~~hiskslrk~lr~ 51 (173)
T PF03588_consen 19 EGDPILWWSPDPRAVLPPDDFHISKSLRKFLRK 51 (173)
T ss_dssp TTS--EEE--SSEEEE-GGG----HHHHHHHHT
T ss_pred CCCceeeecCCCcEEEeccccccCHHHHHHhCC
Confidence 456789999999998887777755 7777775
No 74
>PF12696 TraG-D_C: TraM recognition site of TraD and TraG
Probab=23.33 E-value=1.1e+02 Score=18.97 Aligned_cols=27 Identities=19% Similarity=0.018 Sum_probs=21.9
Q ss_pred EEecCCCCH---HHHHHHHHHHHHcCeEEe
Q 046686 17 HYYDEFPSR---DVFEAACDYARDRSGLQW 43 (70)
Q Consensus 17 ~Ly~~F~s~---~~fe~~~~yA~~~gvLlW 43 (70)
++.++|++. ..++.+..-++..|+.+|
T Consensus 4 ~~lDE~~~~~~~~~l~~~~~~~r~~gi~~~ 33 (128)
T PF12696_consen 4 FILDEFGNLGPIPGLEDLLATGRSYGISFI 33 (128)
T ss_pred EEEEChhhcCCcHhHHHHHHHHhcCCCEEE
Confidence 567777764 579999999999999876
No 75
>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways. Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process
Probab=22.95 E-value=2.3e+02 Score=18.89 Aligned_cols=36 Identities=17% Similarity=0.199 Sum_probs=29.1
Q ss_pred CHHHHHHHHHHHHHcCeEEeeeCCcceEEEe---ccccHHHHHHHH
Q 046686 24 SRDVFEAACDYARDRSGLQWEDSKKMRLVVK---AEIHIHIREFLR 66 (70)
Q Consensus 24 s~~~fe~~~~yA~~~gvLlW~~~~kr~~~V~---~~gh~~vr~f~k 66 (70)
+.++-+.+..+-+..|+ +..|.|| .+|-+.+++|++
T Consensus 104 ~~~~i~~a~~~L~~aG~-------~~if~vS~~~~eGi~eL~~~L~ 142 (143)
T PF10662_consen 104 DDANIERAKKWLKNAGV-------KEIFEVSAVTGEGIEELKDYLE 142 (143)
T ss_pred chhhHHHHHHHHHHcCC-------CCeEEEECCCCcCHHHHHHHHh
Confidence 67889999999999998 2346664 789999999986
No 76
>PF07409 GP46: Phage protein GP46; InterPro: IPR010877 This entry is represented by Bacteriophage Mu, Gp46. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.88 E-value=52 Score=21.32 Aligned_cols=28 Identities=43% Similarity=0.633 Sum_probs=17.9
Q ss_pred cccccccCceeeeceEEecCCCCHHHHHHHHHHHHHcCeEEe
Q 046686 2 RLWESDLNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQW 43 (70)
Q Consensus 2 rLWe~ErnRi~~~~g~Ly~~F~s~~~fe~~~~yA~~~gvLlW 43 (70)
|||.++|.... .+.-..+.+||+| +|-|
T Consensus 45 RLwlL~R~K~t------------~~v~~~A~~ya~E--AL~w 72 (116)
T PF07409_consen 45 RLWLLRREKLT------------PRVRRRAEDYAEE--ALQW 72 (116)
T ss_pred ceeEEEeecch------------HHHHHHHHHHHHH--HHHH
Confidence 68888876543 3355677888876 4444
No 77
>cd07255 Glo_EDI_BRP_like_12 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=22.76 E-value=1.7e+02 Score=16.93 Aligned_cols=37 Identities=19% Similarity=0.044 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHHHHcCeEEeeeCC----cceEEEecccc
Q 046686 22 FPSRDVFEAACDYARDRSGLQWEDSK----KMRLVVKAEIH 58 (70)
Q Consensus 22 F~s~~~fe~~~~yA~~~gvLlW~~~~----kr~~~V~~~gh 58 (70)
..|.++.+.+++.+++.|+-+..-.. +...|-.++|+
T Consensus 72 v~~~~~v~~~~~~l~~~g~~~~~~~~~~~~~~~~~~DPdG~ 112 (125)
T cd07255 72 LPSRADLAAALRRLIELGIPLVGASDHLVSEALYLSDPEGN 112 (125)
T ss_pred CCCHHHHHHHHHHHHHcCCceeccccccceeEEEEECCCCC
Confidence 46788999999999999996643211 12334557765
No 78
>TIGR02432 lysidine_TilS_N tRNA(Ile)-lysidine synthetase, N-terminal domain. The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This family describes a protein domain found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain archictecture of this protein family is variable; some, including characterized proteins of E. coli and B. subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family ( pfam01171). It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer).
Probab=22.61 E-value=1.1e+02 Score=19.91 Aligned_cols=19 Identities=16% Similarity=0.258 Sum_probs=16.0
Q ss_pred HHHHHHHHHcCeEEeeeCC
Q 046686 29 EAACDYARDRSGLQWEDSK 47 (70)
Q Consensus 29 e~~~~yA~~~gvLlW~~~~ 47 (70)
+.+.+||++.|+-.|.++.
T Consensus 154 ~ei~~~~~~~~lp~~~~~~ 172 (189)
T TIGR02432 154 SEIEEYLKENGLPWFEDET 172 (189)
T ss_pred HHHHHHHHHcCCCeeeCCC
Confidence 3568999999999998875
No 79
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=22.51 E-value=36 Score=22.07 Aligned_cols=22 Identities=14% Similarity=0.073 Sum_probs=16.9
Q ss_pred ceeeeceEEecCCCCHHH-HHHH
Q 046686 10 KDEMTRVHYYDEFPSRDV-FEAA 31 (70)
Q Consensus 10 Ri~~~~g~Ly~~F~s~~~-fe~~ 31 (70)
+.-.+.|-||.-|+|.++ |..+
T Consensus 37 ~aGvsk~~lY~~F~sK~~L~~~~ 59 (192)
T PRK14996 37 EAQVAAGQVHHHFSSAGELKALA 59 (192)
T ss_pred HhCCCcHHHHHHcCCHHHHHHHH
Confidence 345688999999999888 4443
No 80
>PF12681 Glyoxalase_2: Glyoxalase-like domain; PDB: 3G12_B 1JIF_B 1JIE_B 1QTO_A 3OXH_A 2PJS_A 2RBB_A 3SK1_B 3SK2_B 3RRI_A ....
Probab=21.97 E-value=1.6e+02 Score=16.45 Aligned_cols=33 Identities=3% Similarity=0.035 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHcCeEEeee----C-C-cceEEEecccc
Q 046686 26 DVFEAACDYARDRSGLQWED----S-K-KMRLVVKAEIH 58 (70)
Q Consensus 26 ~~fe~~~~yA~~~gvLlW~~----~-~-kr~~~V~~~gh 58 (70)
++.+.+.+.+++.|+-+-.. + . +...|..++||
T Consensus 65 ~dv~~~~~~l~~~G~~~~~~~~~~~~g~~~~~~~DPdG~ 103 (108)
T PF12681_consen 65 EDVDALYERLKELGAEIVTEPRDDPWGQRSFYFIDPDGN 103 (108)
T ss_dssp SHHHHHHHHHHHTTSEEEEEEEEETTSEEEEEEE-TTS-
T ss_pred cCHHHHHHHHHHCCCeEeeCCEEcCCCeEEEEEECCCCC
Confidence 88999999999999875432 2 2 34556668876
No 81
>COG0436 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]
Probab=21.77 E-value=1.3e+02 Score=22.63 Aligned_cols=30 Identities=23% Similarity=0.272 Sum_probs=24.9
Q ss_pred CHHHHHHHHHHHHHcCeEEeeeCCcceEEE
Q 046686 24 SRDVFEAACDYARDRSGLQWEDSKKMRLVV 53 (70)
Q Consensus 24 s~~~fe~~~~yA~~~gvLlW~~~~kr~~~V 53 (70)
|.++++.++++|++.|+++=+|+.=.-|+-
T Consensus 181 ~~~~l~~i~~~a~~~~i~ii~DEiY~~l~y 210 (393)
T COG0436 181 SKEELKAIVELAREHDIIIISDEIYEELVY 210 (393)
T ss_pred CHHHHHHHHHHHHHcCeEEEEehhhhhccc
Confidence 689999999999999999888876555544
No 82
>PF11305 DUF3107: Protein of unknown function (DUF3107); InterPro: IPR021456 Some members in this family of proteins are annotated as ATP-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=21.69 E-value=2e+02 Score=17.37 Aligned_cols=36 Identities=33% Similarity=0.227 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHHHHHHHcC--eEEeeeCCcceEEEecc
Q 046686 21 EFPSRDVFEAACDYARDRS--GLQWEDSKKMRLVVKAE 56 (70)
Q Consensus 21 ~F~s~~~fe~~~~yA~~~g--vLlW~~~~kr~~~V~~~ 56 (70)
.=.|+++-...+.-|-.-| +|--.|++.|.++|..+
T Consensus 18 s~~s~dev~~~v~~Al~~~~~~l~LtD~kGr~~lVp~~ 55 (74)
T PF11305_consen 18 SDQSADEVEAAVTDALADGSGVLTLTDEKGRRVLVPAA 55 (74)
T ss_pred cCCCHHHHHHHHHHHHhCCCceEEEEeCCCCEEEEECC
Confidence 3357777777777776655 78889999999999764
No 83
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=21.66 E-value=70 Score=22.26 Aligned_cols=20 Identities=30% Similarity=0.409 Sum_probs=17.6
Q ss_pred CCHHHHHHHHHHHHHcCeEE
Q 046686 23 PSRDVFEAACDYARDRSGLQ 42 (70)
Q Consensus 23 ~s~~~fe~~~~yA~~~gvLl 42 (70)
||..||-++|++|-+.|+=+
T Consensus 104 psrrDFF~Icrka~qqg~sI 123 (165)
T PF03614_consen 104 PSRRDFFSICRKAHQQGKSI 123 (165)
T ss_pred CccchHHHHHHHHHHCCCeE
Confidence 88899999999999988743
No 84
>PF00128 Alpha-amylase: Alpha amylase, catalytic domain; InterPro: IPR006047 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Enzymes containing this domain, such as alpha-amylase, belong to family 13 (GH13 from CAZY) of the glycosyl hydrolases. The maltogenic alpha-amylase is an enzyme which catalyses hydrolysis of (1-4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive alpha-maltose residues from the non-reducing ends of the chains in the conversion of starch to maltose. Other enzymes include neopullulanase, which hydrolyses pullulan to panose, and cyclomaltodextrinase, which hydrolyses cyclodextrins. This entry represents the catalytic domain found in several protein members of this family. It has a structure consisting of an 8 stranded alpha/beta barrel that contains the active site, interrupted by a ~70 amino acid calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain []. More information about this protein can be found at Protein of the Month: alpha-Amylase [].; GO: 0003824 catalytic activity, 0043169 cation binding, 0005975 carbohydrate metabolic process; PDB: 3FAX_A 3FAW_A 2DH3_B 2DH2_A 1CIU_A 1A47_A 3BMW_A 3BMV_A 2FH8_A 2FH6_A ....
Probab=21.38 E-value=92 Score=20.86 Aligned_cols=24 Identities=21% Similarity=0.181 Sum_probs=20.6
Q ss_pred cCCCCHHHHHHHHHHHHHcCeEEe
Q 046686 20 DEFPSRDVFEAACDYARDRSGLQW 43 (70)
Q Consensus 20 ~~F~s~~~fe~~~~yA~~~gvLlW 43 (70)
..|-+.+||..+++-|.+.|+-|=
T Consensus 46 ~~~Gt~~d~~~Lv~~~h~~gi~Vi 69 (316)
T PF00128_consen 46 PRFGTMEDFKELVDAAHKRGIKVI 69 (316)
T ss_dssp TTTBHHHHHHHHHHHHHHTTCEEE
T ss_pred cccchhhhhhhhhhccccccceEE
Confidence 367889999999999999998654
No 85
>PRK05569 flavodoxin; Provisional
Probab=21.37 E-value=1.8e+02 Score=17.95 Aligned_cols=24 Identities=13% Similarity=0.192 Sum_probs=14.1
Q ss_pred ceEEecCCCCHHHHHHHHHHHHHc
Q 046686 15 RVHYYDEFPSRDVFEAACDYARDR 38 (70)
Q Consensus 15 ~g~Ly~~F~s~~~fe~~~~yA~~~ 38 (70)
.++-+..-|+.++.+.+.++++++
T Consensus 116 ~~~~~~~~p~~~~~~~~~~~g~~l 139 (141)
T PRK05569 116 GDLAVNESPNKEELNSAKELGKKL 139 (141)
T ss_pred eeEEEccCCCHHHHHHHHHHHHHH
Confidence 344445556666666666666654
No 86
>PRK09485 mmuM homocysteine methyltransferase; Provisional
Probab=21.34 E-value=1.9e+02 Score=21.02 Aligned_cols=31 Identities=16% Similarity=0.281 Sum_probs=26.7
Q ss_pred eceEEecCCCCHHHHHHHHHHHHHc--CeEEee
Q 046686 14 TRVHYYDEFPSRDVFEAACDYARDR--SGLQWE 44 (70)
Q Consensus 14 ~~g~Ly~~F~s~~~fe~~~~yA~~~--gvLlW~ 44 (70)
-+.+++.-|+|..|-..++..+++. +.-+|-
T Consensus 154 vD~i~~ET~~~~~E~~~~~~~~~~~~~~~pv~i 186 (304)
T PRK09485 154 ADLLACETIPNLDEAEALVELLKEEFPGVPAWL 186 (304)
T ss_pred CCEEEEeccCCHHHHHHHHHHHHHhcCCCcEEE
Confidence 4778999999999999999999966 676664
No 87
>cd02407 PTH2_family Peptidyl-tRNA hydrolase, type 2 (PTH2)_like . Peptidyl-tRNA hydrolase activity releases tRNA from the premature translation termination product peptidyl-tRNA. Two structurally different enzymes have been reported to encode such activity, Pth present in bacteria and eukaryotes and Pth2 present in archaea and eukaryotes.
Probab=21.34 E-value=1.5e+02 Score=18.84 Aligned_cols=24 Identities=17% Similarity=0.148 Sum_probs=18.9
Q ss_pred CCCHHHHHHHHHHHHHcCe--EEeee
Q 046686 22 FPSRDVFEAACDYARDRSG--LQWED 45 (70)
Q Consensus 22 F~s~~~fe~~~~yA~~~gv--LlW~~ 45 (70)
=+|.++...+.+-|++.|+ -+|.|
T Consensus 56 v~~~~~l~~l~~~a~~~gl~~~~v~D 81 (115)
T cd02407 56 VPSEEELLELAKKAKELGLPHSLIQD 81 (115)
T ss_pred CCCHHHHHHHHHHHHHcCCCeEEEEE
Confidence 3677889999999988775 57777
No 88
>KOG1359 consensus Glycine C-acetyltransferase/2-amino-3-ketobutyrate-CoA ligase [Amino acid transport and metabolism]
Probab=20.68 E-value=2.1e+02 Score=22.50 Aligned_cols=50 Identities=12% Similarity=-0.061 Sum_probs=38.0
Q ss_pred cCceeeeceEEecCCCCHHHHHHHHHHHHHcCeEEeeeCCcceEEEecccc
Q 046686 8 LNKDEMTRVHYYDEFPSRDVFEAACDYARDRSGLQWEDSKKMRLVVKAEIH 58 (70)
Q Consensus 8 rnRi~~~~g~Ly~~F~s~~~fe~~~~yA~~~gvLlW~~~~kr~~~V~~~gh 58 (70)
|-|+..|+|+. +-=-+-+--+.++..|+..|.||.-|+-.-+.|..+.|-
T Consensus 193 r~klv~TDg~F-SMDGdiaPl~ei~~La~kYgaLlfiDecHaTgf~G~tGr 242 (417)
T KOG1359|consen 193 RLKLVVTDGVF-SMDGDIAPLEEISQLAKKYGALLFIDECHATGFFGETGR 242 (417)
T ss_pred eEEEEEeccee-ccCCCcccHHHHHHHHHhcCcEEEEeecccceeecCCCC
Confidence 66788888863 322233445778999999999999999999999877654
No 89
>smart00642 Aamy Alpha-amylase domain.
Probab=20.47 E-value=1.7e+02 Score=19.38 Aligned_cols=25 Identities=24% Similarity=0.198 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHHHHHHHcCeEEeee
Q 046686 21 EFPSRDVFEAACDYARDRSGLQWED 45 (70)
Q Consensus 21 ~F~s~~~fe~~~~yA~~~gvLlW~~ 45 (70)
.|-+.++|..+++-|.+.|+-+--|
T Consensus 65 ~~Gt~~d~~~lv~~~h~~Gi~vilD 89 (166)
T smart00642 65 RFGTMEDFKELVDAAHARGIKVILD 89 (166)
T ss_pred ccCCHHHHHHHHHHHHHCCCEEEEE
Confidence 5678899999999999999976543
No 90
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=20.35 E-value=94 Score=15.28 Aligned_cols=17 Identities=12% Similarity=0.315 Sum_probs=13.9
Q ss_pred CHHHHHHHHHHHHHcCe
Q 046686 24 SRDVFEAACDYARDRSG 40 (70)
Q Consensus 24 s~~~fe~~~~yA~~~gv 40 (70)
+.+.++.+-++|++.|.
T Consensus 7 ~~~~~~~l~~~a~~~g~ 23 (39)
T PF01402_consen 7 PDELYERLDELAKELGR 23 (39)
T ss_dssp EHHHHHHHHHHHHHHTS
T ss_pred CHHHHHHHHHHHHHHCc
Confidence 46788999999998883
No 91
>COG2221 DsrA Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]
Probab=20.26 E-value=2.2e+02 Score=21.68 Aligned_cols=53 Identities=15% Similarity=0.168 Sum_probs=37.9
Q ss_pred ceeeeceEEecCCCCHHHHHHHHHHHHHcCe--EEeeeCCcceEE-EeccccHHHHHHHH
Q 046686 10 KDEMTRVHYYDEFPSRDVFEAACDYARDRSG--LQWEDSKKMRLV-VKAEIHIHIREFLR 66 (70)
Q Consensus 10 Ri~~~~g~Ly~~F~s~~~fe~~~~yA~~~gv--LlW~~~~kr~~~-V~~~gh~~vr~f~k 66 (70)
|+...+|. |.|.+.-..+++.|+..|. ..+.+...-.|. ++.+--+++.+-++
T Consensus 33 Rv~~ppgg----~l~~e~Lr~i~diAekyG~G~i~iT~rqg~ei~~i~~e~~~~v~~~L~ 88 (317)
T COG2221 33 RVRTPPGG----FLSAETLRKIADIAEKYGDGLIHITSRQGLEIPGISPEDADDVVEELR 88 (317)
T ss_pred EEecCCCC----ccCHHHHHHHHHHHHHhCCCeEEEEecCceEeccCCHHHHHHHHHHHH
Confidence 56666654 4588889999999999998 555555544444 67777777777765
No 92
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=20.11 E-value=1.4e+02 Score=17.50 Aligned_cols=23 Identities=9% Similarity=-0.038 Sum_probs=19.6
Q ss_pred CCCHHHHHHHHHHHHHcCeEEee
Q 046686 22 FPSRDVFEAACDYARDRSGLQWE 44 (70)
Q Consensus 22 F~s~~~fe~~~~yA~~~gvLlW~ 44 (70)
..|.++.+.+.+.|++.|+.++-
T Consensus 96 ~~~~~~~~~l~~~a~~~~~~~~V 118 (120)
T PF01408_consen 96 ALTLEEAEELVEAAKEKGVKVMV 118 (120)
T ss_dssp SSSHHHHHHHHHHHHHHTSCEEE
T ss_pred cCCHHHHHHHHHHHHHhCCEEEE
Confidence 45889999999999999988753
Done!