Query 016590
Match_columns 386
No_of_seqs 167 out of 1161
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 08:13:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016590.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016590hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0264 Tsf Translation elonga 100.0 2E-93 4.3E-98 687.4 30.1 274 78-386 6-281 (296)
2 TIGR00116 tsf translation elon 100.0 8.5E-92 1.8E-96 683.3 31.0 272 78-386 5-276 (290)
3 PRK09377 tsf elongation factor 100.0 3.7E-91 8E-96 678.8 31.3 271 78-386 6-276 (290)
4 PRK12332 tsf elongation factor 100.0 3E-69 6.5E-74 500.4 21.3 192 78-383 5-198 (198)
5 CHL00098 tsf elongation factor 100.0 5.1E-69 1.1E-73 499.1 20.8 195 78-386 2-199 (200)
6 PF00889 EF_TS: Elongation fac 100.0 5.8E-68 1.3E-72 500.0 21.7 221 129-382 1-221 (221)
7 KOG1071 Mitochondrial translat 100.0 6.5E-64 1.4E-68 483.9 14.5 270 76-383 45-333 (340)
8 PF00627 UBA: UBA/TS-N domain; 98.3 9.3E-07 2E-11 61.0 5.2 34 79-113 4-37 (37)
9 KOG1071 Mitochondrial translat 98.3 4E-06 8.6E-11 82.9 10.0 119 238-384 103-222 (340)
10 PRK06369 nac nascent polypepti 97.4 0.00029 6.2E-09 60.8 5.1 37 79-115 78-114 (115)
11 smart00165 UBA Ubiquitin assoc 97.2 0.00064 1.4E-08 46.4 4.9 34 79-113 3-36 (37)
12 TIGR00264 alpha-NAC-related pr 97.2 0.00046 1E-08 59.5 4.8 36 79-114 80-115 (116)
13 cd00194 UBA Ubiquitin Associat 97.2 0.00093 2E-08 45.8 4.9 35 79-114 3-37 (38)
14 COG0264 Tsf Translation elonga 96.4 0.014 3E-07 57.8 8.5 92 239-382 59-151 (296)
15 TIGR00116 tsf translation elon 96.4 0.019 4.1E-07 57.0 9.4 88 238-380 57-145 (290)
16 CHL00098 tsf elongation factor 96.4 0.0059 1.3E-07 57.5 5.4 44 238-289 54-97 (200)
17 PRK09377 tsf elongation factor 95.7 0.063 1.4E-06 53.4 9.4 88 238-380 58-146 (290)
18 PF14555 UBA_4: UBA-like domai 94.8 0.063 1.4E-06 38.1 4.6 37 79-115 2-38 (43)
19 PF03943 TAP_C: TAP C-terminal 93.5 0.059 1.3E-06 40.0 2.4 37 79-115 2-38 (51)
20 smart00804 TAP_C C-terminal do 93.1 0.31 6.8E-06 37.8 5.9 40 76-115 11-50 (63)
21 PRK12332 tsf elongation factor 93.0 0.14 3E-06 48.3 4.7 30 207-236 166-195 (198)
22 COG1308 EGD2 Transcription fac 92.4 0.25 5.5E-06 43.1 5.0 36 79-114 86-121 (122)
23 PF00889 EF_TS: Elongation fac 91.9 0.32 6.9E-06 46.5 5.7 87 239-380 3-90 (221)
24 PF02845 CUE: CUE domain; Int 87.9 1.6 3.5E-05 30.6 5.2 37 79-115 3-40 (42)
25 PF00542 Ribosomal_L12: Riboso 85.8 0.67 1.5E-05 36.4 2.5 27 77-103 13-39 (68)
26 PRK06771 hypothetical protein; 82.1 1.5 3.2E-05 36.7 3.2 23 78-100 69-91 (93)
27 smart00546 CUE Domain that may 81.6 4.9 0.00011 28.1 5.3 37 79-115 4-41 (43)
28 PF08938 HBS1_N: HBS1 N-termin 81.1 0.78 1.7E-05 36.8 1.2 46 79-124 30-78 (79)
29 PF06972 DUF1296: Protein of u 77.4 6 0.00013 30.5 4.9 36 79-114 7-43 (60)
30 COG4008 Predicted metal-bindin 72.5 9.4 0.0002 33.8 5.5 42 75-117 94-152 (153)
31 PRK00157 rplL 50S ribosomal pr 69.7 6.9 0.00015 34.4 4.1 26 78-103 69-94 (123)
32 TIGR00855 L12 ribosomal protei 69.7 5.5 0.00012 35.2 3.5 28 78-105 72-99 (126)
33 cd00387 Ribosomal_L7_L12 Ribos 68.7 9.5 0.00021 33.6 4.8 29 77-105 73-101 (127)
34 cd04772 HTH_TioE_rpt1 First He 62.4 12 0.00026 31.0 4.1 50 62-116 34-84 (99)
35 CHL00083 rpl12 ribosomal prote 61.5 9.9 0.00021 33.8 3.6 27 78-104 77-103 (131)
36 COG0222 RplL Ribosomal protein 61.4 9.1 0.0002 33.6 3.2 38 60-103 58-95 (124)
37 PF08285 DPM3: Dolichol-phosph 61.0 3 6.5E-05 34.7 0.2 29 91-119 62-90 (91)
38 COG0789 SoxR Predicted transcr 51.3 14 0.00031 31.0 2.8 41 62-106 34-74 (124)
39 cd01106 HTH_TipAL-Mta Helix-Tu 50.5 25 0.00055 29.0 4.1 47 63-116 35-81 (103)
40 KOG0944 Ubiquitin-specific pro 50.2 15 0.00033 40.6 3.4 28 88-115 645-672 (763)
41 cd01105 HTH_GlnR-like Helix-Tu 48.5 32 0.00069 27.8 4.3 51 63-118 36-86 (88)
42 cd04773 HTH_TioE_rpt2 Second H 47.3 33 0.00071 28.8 4.4 50 62-115 34-85 (108)
43 cd04780 HTH_MerR-like_sg5 Heli 44.6 24 0.00052 29.1 3.1 36 63-101 35-70 (95)
44 PF11626 Rap1_C: TRF2-interact 43.6 44 0.00095 27.1 4.4 34 81-115 1-34 (87)
45 cd04763 HTH_MlrA-like Helix-Tu 41.9 24 0.00053 26.7 2.5 34 62-99 34-67 (68)
46 PF03474 DMA: DMRTA motif; In 40.5 26 0.00056 24.9 2.2 17 97-113 22-38 (39)
47 cd04788 HTH_NolA-AlbR Helix-Tu 39.4 43 0.00093 27.4 3.8 47 62-115 34-80 (96)
48 cd07257 THT_oxygenase_C The C- 39.2 58 0.0012 28.4 4.9 52 104-156 76-130 (153)
49 PF13411 MerR_1: MerR HTH fami 38.0 19 0.00042 27.0 1.4 34 64-101 35-68 (69)
50 cd01107 HTH_BmrR Helix-Turn-He 37.6 48 0.001 27.7 3.9 49 62-116 35-83 (108)
51 cd04765 HTH_MlrA-like_sg2 Heli 37.3 63 0.0014 26.8 4.5 51 62-115 34-87 (99)
52 smart00422 HTH_MERR helix_turn 36.0 35 0.00077 25.5 2.6 34 63-100 35-68 (70)
53 cd07249 MMCE Methylmalonyl-CoA 35.2 94 0.002 24.9 5.3 45 104-149 81-127 (128)
54 KOG1364 Predicted ubiquitin re 34.3 76 0.0017 32.6 5.3 42 78-119 7-49 (356)
55 cd08362 BphC5-RrK37_N_like N-t 33.8 68 0.0015 25.7 4.2 50 104-153 70-119 (120)
56 cd00592 HTH_MerR-like Helix-Tu 33.5 78 0.0017 25.6 4.5 48 63-114 34-83 (100)
57 PRK05441 murQ N-acetylmuramic 33.5 52 0.0011 32.7 4.1 32 84-115 242-273 (299)
58 cd04787 HTH_HMRTR_unk Helix-Tu 32.0 82 0.0018 27.3 4.6 51 62-116 34-87 (133)
59 cd04785 HTH_CadR-PbrR-like Hel 30.5 85 0.0018 27.0 4.4 50 62-115 34-86 (126)
60 KOG4841 Dolichol-phosphate man 29.7 21 0.00044 29.7 0.4 29 90-118 65-93 (95)
61 cd04770 HTH_HMRTR Helix-Turn-H 29.3 94 0.002 26.3 4.5 50 62-115 34-86 (123)
62 cd04764 HTH_MlrA-like_sg1 Heli 29.2 42 0.00091 25.2 2.0 34 62-99 33-66 (67)
63 cd07265 2_3_CTD_N N-terminal d 29.1 78 0.0017 25.7 3.8 49 104-153 73-121 (122)
64 cd04768 HTH_BmrR-like Helix-Tu 29.0 78 0.0017 25.9 3.7 47 62-115 34-80 (96)
65 cd04776 HTH_GnyR Helix-Turn-He 28.9 1E+02 0.0022 26.3 4.6 37 63-103 33-69 (118)
66 cd07258 PpCmtC_C C-terminal do 28.9 87 0.0019 27.1 4.3 54 104-158 68-121 (141)
67 KOG1715 Mitochondrial/chloropl 27.9 86 0.0019 29.5 4.1 27 76-102 131-157 (187)
68 cd07237 BphC1-RGP6_C_like C-te 27.5 94 0.002 27.1 4.2 51 105-156 86-136 (154)
69 TIGR00274 N-acetylmuramic acid 27.2 69 0.0015 31.8 3.7 32 84-115 237-268 (291)
70 PF07442 Ponericin: Ponericin; 27.0 46 0.001 21.8 1.6 18 106-123 6-25 (29)
71 PF02954 HTH_8: Bacterial regu 26.9 71 0.0015 22.2 2.7 18 96-113 11-28 (42)
72 PRK13752 putative transcriptio 26.8 90 0.002 27.8 4.0 50 63-116 42-92 (144)
73 PF10607 CLTH: CTLH/CRA C-term 26.5 68 0.0015 27.6 3.1 21 93-115 6-26 (145)
74 KOG0944 Ubiquitin-specific pro 26.2 62 0.0013 36.1 3.3 35 80-115 574-609 (763)
75 cd08353 Glo_EDI_BRP_like_7 Thi 25.7 1.1E+02 0.0024 25.5 4.3 44 104-149 96-139 (142)
76 cd04784 HTH_CadR-PbrR Helix-Tu 25.6 1.2E+02 0.0026 25.9 4.5 49 62-114 34-85 (127)
77 smart00668 CTLH C-terminal to 25.6 54 0.0012 23.5 2.0 15 103-117 14-28 (58)
78 cd04782 HTH_BltR Helix-Turn-He 25.0 1.3E+02 0.0027 24.7 4.3 48 63-116 35-82 (97)
79 cd04786 HTH_MerR-like_sg7 Heli 24.9 1.3E+02 0.0028 26.3 4.5 50 62-115 34-85 (131)
80 cd04766 HTH_HspR Helix-Turn-He 24.8 1.3E+02 0.0029 24.1 4.4 35 63-100 35-69 (91)
81 TIGR02043 ZntR Zn(II)-responsi 24.3 1.4E+02 0.003 25.9 4.7 50 62-115 35-88 (131)
82 PF10178 DUF2372: Uncharacteri 24.0 2.4E+02 0.0052 23.4 5.7 36 274-309 43-83 (90)
83 cd01282 HTH_MerR-like_sg3 Heli 24.0 1.3E+02 0.0028 25.4 4.3 49 63-115 34-88 (112)
84 cd04783 HTH_MerR1 Helix-Turn-H 24.0 1.3E+02 0.0029 25.7 4.5 49 63-115 35-84 (126)
85 CHL00102 rps20 ribosomal prote 23.2 73 0.0016 26.6 2.5 38 92-134 32-74 (93)
86 TIGR02054 MerD mercuric resist 23.1 1.8E+02 0.004 25.1 5.1 38 62-103 37-74 (120)
87 KOG2561 Adaptor protein NUB1, 23.0 64 0.0014 34.4 2.6 36 89-124 314-349 (568)
88 PF12651 RHH_3: Ribbon-helix-h 22.8 1.9E+02 0.0042 20.5 4.3 29 76-114 12-40 (44)
89 COG1437 CyaB Adenylate cyclase 22.5 63 0.0014 30.2 2.2 81 90-170 69-156 (178)
90 PRK09514 zntR zinc-responsive 22.1 1.6E+02 0.0034 25.9 4.6 51 62-116 35-89 (140)
91 cd05007 SIS_Etherase N-acetylm 22.1 49 0.0011 32.1 1.5 29 82-110 227-255 (257)
92 PRK12570 N-acetylmuramic acid- 21.4 1.1E+02 0.0024 30.4 3.9 34 82-115 236-269 (296)
93 cd08352 Glo_EDI_BRP_like_1 Thi 21.3 1.6E+02 0.0035 23.2 4.3 43 104-148 81-123 (125)
94 cd04777 HTH_MerR-like_sg1 Heli 21.3 1.7E+02 0.0037 24.2 4.5 50 63-116 33-89 (107)
95 cd04769 HTH_MerR2 Helix-Turn-H 21.2 1.7E+02 0.0036 24.7 4.5 49 63-115 34-86 (116)
96 COG5207 UBP14 Isopeptidase T [ 21.1 34 0.00073 37.1 0.2 27 87-113 630-656 (749)
97 PF13986 DUF4224: Domain of un 20.8 1.4E+02 0.0029 21.8 3.2 32 82-126 6-37 (47)
98 cd01109 HTH_YyaN Helix-Turn-He 20.7 1.9E+02 0.004 24.2 4.6 50 63-116 35-87 (113)
99 TIGR03213 23dbph12diox 2,3-dih 20.1 1.6E+02 0.0035 28.2 4.6 49 105-155 219-267 (286)
100 cd08345 Fosfomycin_RP Fosfomyc 20.1 1.7E+02 0.0037 23.0 4.2 47 104-152 66-112 (113)
101 cd08347 PcpA_C_like C-terminal 20.1 1E+02 0.0022 27.2 3.1 59 104-166 77-135 (157)
No 1
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-93 Score=687.38 Aligned_cols=274 Identities=42% Similarity=0.621 Sum_probs=256.4
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHcccccccccccccccCCcEEEEecCC--eEEEEEEeccccce
Q 016590 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNES--KAAVIELNCETDFV 155 (386)
Q Consensus 78 ~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~--~aalvElNCETDFV 155 (386)
+++||+||++||||||||||||+|++||+|+|++|||++|+++|+||+||.|+||+|+++++++ +|+|||||||||||
T Consensus 6 a~~VKeLRe~TgAGMmdCKkAL~E~~Gd~EkAie~LR~kG~akA~KKa~R~AaEGli~~~~~~~~~~av~vEvN~ETDFV 85 (296)
T COG0264 6 AALVKELREKTGAGMMDCKKALEEANGDIEKAIEWLREKGIAKAAKKAGRIAAEGLIAAKVDGDGKKAVLVEVNCETDFV 85 (296)
T ss_pred HHHHHHHHHHhCCcHHHHHHHHHHcCCCHHHHHHHHHHhchHhhhhhcCcchhcceEEEEEcCCCcEEEEEEEeccccce
Confidence 6899999999999999999999999999999999999999999999999999999999999555 99999999999999
Q ss_pred ecchHHHHHHHHHHHHHHhhcCCCCCCCCCCCCChhhhhccccCCCCCCCCCCCcHHHHHHHHHHHhcceeeeeeeEEee
Q 016590 156 SRNEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLS 235 (386)
Q Consensus 156 ArN~~F~~la~~ia~~~l~~~~~~~~~~~~~~l~~e~l~~~~~~~~~~~~~~~~Tv~d~i~~~ia~iGENI~LrR~~~~~ 235 (386)
|||+.|+.|++.|++.++.+... +.+.+....+ +++.||++.+..++++|||||.|||+..+.
T Consensus 86 AkN~~F~~l~~~ia~~~l~~~~~----------~ve~l~~~~~-------~~~~tv~e~~~~~~AkIGENi~lRR~~~~~ 148 (296)
T COG0264 86 AKNAEFQELANKIAKAALEKKPA----------DVEELKAAFE-------PGGKTVEEEIAALIAKIGENISLRRFAVLE 148 (296)
T ss_pred eCChhHHHHHHHHHHHHHHhCcc----------cHHHHHhhhc-------ccCccHHHHHHHHHHHhccceeEEEEEEee
Confidence 99999999999999999988753 3467765543 357899999999999999999999999998
Q ss_pred eCCCCeEEEEecCCCCCCCCcEEEEEEEeecCCCCCCchhhhHHHHHHHHhhhcCCcccccCCCCHHHHHHHHHHHHHHH
Q 016590 236 ASSPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQA 315 (386)
Q Consensus 236 ~~~~~~v~sY~H~~~~~~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~~le~Er~i~~~q~ 315 (386)
.+ ++.+++|+|++ |||||||.++++. ....++|+|||||||++|.||+.++||++++++||+|+.+|+
T Consensus 149 ~~-~~~v~~Y~H~~-----griGVlv~~~~~~------~~~~~ak~iAMHiAA~~P~~ls~~dV~~e~v~~Er~i~~~~~ 216 (296)
T COG0264 149 AG-DGVVGSYLHGN-----GRIGVLVALKGGA------ADEELAKDIAMHIAAMNPQYLSREDVPAEVVEKEREIFLAQL 216 (296)
T ss_pred cC-cccEEEEEeCC-----CcEEEEEEEeccc------hHHHHHHHHHHHHHhcCCccCChhhCCHHHHHHHHHHHHHHH
Confidence 75 36899999997 9999999998751 245899999999999999999999999999999999999999
Q ss_pred HhcCCChHHHHHHHHhhhhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEEeEEEEEecccccC
Q 016590 316 ESTGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEVGEGIRR 386 (386)
Q Consensus 316 ~~~gKP~~i~eKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~v~V~~F~R~~vGEgiek 386 (386)
..+|||++|++|||+|||+|||.|+|||+|+||+||++||+|+|++. +++|.+|+||+|||||||
T Consensus 217 ~~~gKP~~i~eKiVeGr~~Kf~~E~~Ll~Q~fV~d~~~TV~~~lke~------~~~v~~FvR~evGegieK 281 (296)
T COG0264 217 KAEGKPENIVEKIVEGRMNKFLAEVCLLEQPFVKDPKKTVEQLLKEA------NAKVTEFVRFEVGEGIEK 281 (296)
T ss_pred HhcCChHHHHHHHHhHHHHHHHHHHhhccCceecCcchhHHHHHHhc------CceeeeeeeeeccCCcee
Confidence 99999999999999999999999999999999999999999999986 589999999999999987
No 2
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=100.00 E-value=8.5e-92 Score=683.32 Aligned_cols=272 Identities=38% Similarity=0.593 Sum_probs=253.2
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHcccccccccccccccCCcEEEEecCCeEEEEEEeccccceec
Q 016590 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFVSR 157 (386)
Q Consensus 78 ~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalvElNCETDFVAr 157 (386)
+++||+||++||+|||||||||+++|||+|+|++|||++|+++|+||+||.|+||+|+++++++.|+|||||||||||||
T Consensus 5 a~~IK~LRe~Tgagm~dCKkAL~e~~gDiekAi~~LRkkG~akA~Kk~~R~a~EG~V~~~~~~~~~~ivElncETDFVAr 84 (290)
T TIGR00116 5 AQLVKELRERTGAGMMDCKKALTEANGDFEKAIKNLRESGIAKAAKKADRVAAEGVIVLKSDGNKAVIVEVNSETDFVAK 84 (290)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHhchhHHHHhcccccCCcEEEEEEcCCEEEEEEEecCCccccC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHHhhcCCCCCCCCCCCCChhhhhccccCCCCCCCCCCCcHHHHHHHHHHHhcceeeeeeeEEeeeC
Q 016590 158 NEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLSAS 237 (386)
Q Consensus 158 N~~F~~la~~ia~~~l~~~~~~~~~~~~~~l~~e~l~~~~~~~~~~~~~~~~Tv~d~i~~~ia~iGENI~LrR~~~~~~~ 237 (386)
|+.|++|++.|++.++.+... +.+++..+++ .++.|| |.+.++++++||||.|||+.++..+
T Consensus 85 ne~F~~l~~~ia~~~~~~~~~----------~~e~l~~~~~-------~~~~tv-d~i~~~~a~iGEnI~lrR~~~~~~~ 146 (290)
T TIGR00116 85 NAGFKEFANKLLDELKANKIT----------TLEELQAQEL-------ENREKV-EYLAALAAKIGENINLRRVAVLEGD 146 (290)
T ss_pred ChHHHHHHHHHHHHHHhcCCC----------CHHHHhhccc-------cCCCcH-HHHHHHHHHhccceEEEEEEEEecC
Confidence 999999999999999876543 3467766543 246799 9999999999999999999999875
Q ss_pred CCCeEEEEecCCCCCCCCcEEEEEEEeecCCCCCCchhhhHHHHHHHHhhhcCCcccccCCCCHHHHHHHHHHHHHHHHh
Q 016590 238 SPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQAES 317 (386)
Q Consensus 238 ~~~~v~sY~H~~~~~~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~~le~Er~i~~~q~~~ 317 (386)
++++++|+|++ ||||+||.+++..+ .++|++||||||||+|.||++++||++++++||+|+++|+..
T Consensus 147 -~~~v~~Y~H~~-----gkigvlv~~~~~~~-------~~~ak~iAmhIaA~~P~~l~~~~vp~~vie~Erei~~~~~~~ 213 (290)
T TIGR00116 147 -SNVIGSYLHAG-----ARIGVLVALKGKAD-------EELAKHIAMHVAASKPQFIDPDDVSAEVVKKERQIQTDQAEL 213 (290)
T ss_pred -CCcEEEEEcCC-----CcEEEEEEEecCch-------HHHHHHHHHHHHhcCCccCchhhCCHHHHHHHHHHHHHHHHh
Confidence 47999999986 99999999986432 268999999999999999999999999999999999999999
Q ss_pred cCCChHHHHHHHHhhhhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEEeEEEEEecccccC
Q 016590 318 TGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEVGEGIRR 386 (386)
Q Consensus 318 ~gKP~~i~eKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~v~V~~F~R~~vGEgiek 386 (386)
+|||++|+|||++|||+|||+|+|||+|+||+||++||+|||++. +++|++|+||+||||+||
T Consensus 214 ~gKP~~i~eKIv~Grl~Kf~~E~~Ll~Q~fv~D~~~tV~~~l~~~------~~~v~~F~R~~vGegiek 276 (290)
T TIGR00116 214 SGKPKEIAEKMVEGRMKKFLAEISLLGQKFVMDPSKTVGQFLKEK------NAKVTEFIRFEVGEGIEK 276 (290)
T ss_pred cCCcHHHHHHHhhhHHHHHhhhceeeecccccCCccCHHHHHHHc------CCEEEEEEEEEecCCcee
Confidence 999999999999999999999999999999999999999999985 389999999999999975
No 3
>PRK09377 tsf elongation factor Ts; Provisional
Probab=100.00 E-value=3.7e-91 Score=678.82 Aligned_cols=271 Identities=46% Similarity=0.647 Sum_probs=254.5
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHcccccccccccccccCCcEEEEecCCeEEEEEEeccccceec
Q 016590 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFVSR 157 (386)
Q Consensus 78 ~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalvElNCETDFVAr 157 (386)
+++||+||++||+|||||||||+++|||+|+|++|||++|+++|+||+||.|+||+|+++++++.|+|||||||||||||
T Consensus 6 ~~~IK~LR~~Tgagm~dCKkAL~e~~gD~ekAi~~Lrk~G~akA~Kk~~R~a~EG~I~~~~~~~~~~~vElncETDFVAr 85 (290)
T PRK09377 6 AALVKELRERTGAGMMDCKKALTEADGDIEKAIEWLRKKGLAKAAKKAGRVAAEGLVAAKVDGNKGVLVEVNSETDFVAK 85 (290)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHhchhhHHHhcCccccceEEEEEeCCCEEEEEEEecCCccccC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHHhhcCCCCCCCCCCCCChhhhhccccCCCCCCCCCCCcHHHHHHHHHHHhcceeeeeeeEEeeeC
Q 016590 158 NEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLSAS 237 (386)
Q Consensus 158 N~~F~~la~~ia~~~l~~~~~~~~~~~~~~l~~e~l~~~~~~~~~~~~~~~~Tv~d~i~~~ia~iGENI~LrR~~~~~~~ 237 (386)
|+.|++|+++|++.++.+... +.+++..+++ ++.||+|.+.++++++||||.|||+..+..+
T Consensus 86 ne~F~~l~~~i~~~~l~~~~~----------~~e~ll~~~~--------~g~tv~d~i~~~~~~iGEnI~l~R~~~~~~~ 147 (290)
T PRK09377 86 NEDFQALANEVAEAALAAKPA----------DVEALLALKL--------DGGTVEEARTELIAKIGENISLRRFARLEKD 147 (290)
T ss_pred ChHHHHHHHHHHHHHHhcCCC----------CHHHHHhccc--------cCCcHHHHHHHHHHHhcCceEEEEEEEEeec
Confidence 999999999999999986543 3577776653 3679999999999999999999999999764
Q ss_pred CCCeEEEEecCCCCCCCCcEEEEEEEeecCCCCCCchhhhHHHHHHHHhhhcCCcccccCCCCHHHHHHHHHHHHHHHHh
Q 016590 238 SPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQAES 317 (386)
Q Consensus 238 ~~~~v~sY~H~~~~~~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~~le~Er~i~~~q~~~ 317 (386)
++++++|+|++ ||||+||.+++.+ .++||+||||||||+|.||++++||++++++||+|+++|++.
T Consensus 148 -~~~i~~Y~H~~-----gkigvlV~~~~~~--------~~~ak~iAMhIaA~~P~~l~~~~vp~~~i~~E~~i~~~~~~~ 213 (290)
T PRK09377 148 -GGVVGSYLHGG-----GRIGVLVALEGGD--------EELAKDIAMHIAAMNPEYLSREDVPAEVVEKEREIAKEQAKE 213 (290)
T ss_pred -CCEEEEEEcCC-----CcEEEEEEEccCc--------HHHHHHHHHHHHhcCCccCChhhCCHHHHHHHHHHHHHHHHh
Confidence 78999999986 9999999998642 269999999999999999999999999999999999999999
Q ss_pred cCCChHHHHHHHHhhhhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEEeEEEEEecccccC
Q 016590 318 TGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEVGEGIRR 386 (386)
Q Consensus 318 ~gKP~~i~eKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~v~V~~F~R~~vGEgiek 386 (386)
+|||++|+|||++|||+|||+|+|||+|+||+||++||+|||++. +++|++|+||+||||+|+
T Consensus 214 ~gKP~~i~eKIv~Grl~Kf~~e~~Ll~Q~fi~D~~~tV~~~l~~~------~i~v~~F~R~evGe~~e~ 276 (290)
T PRK09377 214 EGKPEEIVEKIVEGRLNKFLKEVVLLEQPFVKDPKKTVGQLLKEA------GAKVVGFVRFEVGEGIEK 276 (290)
T ss_pred cCChHHHHHHHHhHHHHHHhhhceeccCcccCCCCcCHHHHHHHc------CCEEEEEEEEEecCccee
Confidence 999999999999999999999999999999999999999999985 489999999999999875
No 4
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=100.00 E-value=3e-69 Score=500.42 Aligned_cols=192 Identities=39% Similarity=0.660 Sum_probs=187.3
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHcccccccccccccccCCcEEEEec--CCeEEEEEEeccccce
Q 016590 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQN--ESKAAVIELNCETDFV 155 (386)
Q Consensus 78 ~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~--~~~aalvElNCETDFV 155 (386)
+++||+||++||+|||||||||++++||+|+|++|||++|+++|+||++|.|+||+|+++++ +++|+|||||||||||
T Consensus 5 a~~ik~LR~~tga~~~~ck~AL~~~~gd~~~A~~~lr~~g~~~a~kk~~r~~~eG~i~~~i~~~~~~~~lve~n~ETDFV 84 (198)
T PRK12332 5 AKLVKELREKTGAGMMDCKKALEEANGDMEKAIEWLREKGLAKAAKKAGRVAAEGLVGSYIHTGGRIGVLVELNCETDFV 84 (198)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHhhhhHHHHhccccccCceEEEEEecCCCEEEEEEEeccCCcc
Confidence 58999999999999999999999999999999999999999999999999999999999995 7899999999999999
Q ss_pred ecchHHHHHHHHHHHHHHhhcCCCCCCCCCCCCChhhhhccccCCCCCCCCCCCcHHHHHHHHHHHhcceeeeeeeEEee
Q 016590 156 SRNEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLS 235 (386)
Q Consensus 156 ArN~~F~~la~~ia~~~l~~~~~~~~~~~~~~l~~e~l~~~~~~~~~~~~~~~~Tv~d~i~~~ia~iGENI~LrR~~~~~ 235 (386)
|||+.|++
T Consensus 85 a~n~~F~~------------------------------------------------------------------------ 92 (198)
T PRK12332 85 ARTEEFKE------------------------------------------------------------------------ 92 (198)
T ss_pred ccCHHHHH------------------------------------------------------------------------
Confidence 99999975
Q ss_pred eCCCCeEEEEecCCCCCCCCcEEEEEEEeecCCCCCCchhhhHHHHHHHHhhhcCCcccccCCCCHHHHHHHHHHHHHHH
Q 016590 236 ASSPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQA 315 (386)
Q Consensus 236 ~~~~~~v~sY~H~~~~~~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~~le~Er~i~~~q~ 315 (386)
+|++||||||||+|.||+.++||++++++||+|+++|+
T Consensus 93 ------------------------------------------lak~iamhIaA~~P~~l~~~~v~~~~i~~E~~i~~~~~ 130 (198)
T PRK12332 93 ------------------------------------------LAKDIAMQIAAANPEYVSREDVPAEVIEKEKEIYRAQA 130 (198)
T ss_pred ------------------------------------------HHHHHHHHHHhhCCccCChhhCCHHHHHHHHHHHHHHH
Confidence 26899999999999999999999999999999999999
Q ss_pred HhcCCChHHHHHHHHhhhhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEEeEEEEEeccc
Q 016590 316 ESTGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEVGEG 383 (386)
Q Consensus 316 ~~~gKP~~i~eKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~v~V~~F~R~~vGEg 383 (386)
..+|||++|+|||++|||+|||+|+||++|+|++|++.||+++|++..+.+|.+++|.+|+||+||||
T Consensus 131 ~~~gKP~~i~ekiv~Grl~K~~~E~~Ll~Q~fv~d~~~TV~e~l~e~~a~iGEnI~V~rF~R~evGeg 198 (198)
T PRK12332 131 LNEGKPENIVEKIVEGRIEKFYKEVCLLEQPFIKDPSKTVEDLIKEAIAKIGENIVVRRFARFELGEG 198 (198)
T ss_pred HhcCCcHHHHHHHHhHHHHHHHhhhhhhcCcccCCCCccHHHHHHHHHHHhCCCeEEEEEEEEEcCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999996
No 5
>CHL00098 tsf elongation factor Ts
Probab=100.00 E-value=5.1e-69 Score=499.11 Aligned_cols=195 Identities=33% Similarity=0.556 Sum_probs=188.6
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHcccccccccccccccCCcEEEEe--cCCeEEEEEEeccccce
Q 016590 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQ--NESKAAVIELNCETDFV 155 (386)
Q Consensus 78 ~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~--~~~~aalvElNCETDFV 155 (386)
+++||+||++||+|||||||||++++||+|+|++|||++|+++|+||++|.|+||+|++++ +++.|||||+|||||||
T Consensus 2 a~~ik~LR~~Tgag~~dck~AL~e~~gd~~~A~~~Lr~~g~~~a~kk~~r~~~eG~V~~yiH~~gk~gvlVeln~ETDfV 81 (200)
T CHL00098 2 AELVKELRDKTGAGMMDCKKALQEANGDFEKALESLRQKGLASANKKSTRITTEGLIESYIHTGGKLGVLVEINCETDFV 81 (200)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHhhhhHHHHhhccccccCeEEEEEecCCCEEEEEEEecCcccc
Confidence 4899999999999999999999999999999999999999999999999999999999998 57889999999999999
Q ss_pred ecchHHHHHHHHHHHHHHhhcCCCCCCCCCCCCChhhhhccccCCCCCCCCCCCcHHHHHHHHHHHhcceeeeeeeEEee
Q 016590 156 SRNEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLS 235 (386)
Q Consensus 156 ArN~~F~~la~~ia~~~l~~~~~~~~~~~~~~l~~e~l~~~~~~~~~~~~~~~~Tv~d~i~~~ia~iGENI~LrR~~~~~ 235 (386)
|||+.|++
T Consensus 82 Arn~~F~~------------------------------------------------------------------------ 89 (200)
T CHL00098 82 ARREEFQK------------------------------------------------------------------------ 89 (200)
T ss_pred cccHHHHH------------------------------------------------------------------------
Confidence 99999953
Q ss_pred eCCCCeEEEEecCCCCCCCCcEEEEEEEeecCCCCCCchhhhHHHHHHHHhhhc-CCcccccCCCCHHHHHHHHHHHHHH
Q 016590 236 ASSPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQ-KPLFLTKELVSADALENEREILKSQ 314 (386)
Q Consensus 236 ~~~~~~v~sY~H~~~~~~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA~-~P~~ls~~~Vp~~~le~Er~i~~~q 314 (386)
+|++|||||||| +|.||++++||++++++||+|+++|
T Consensus 90 ------------------------------------------la~~IAmhiaA~p~p~~l~~~~vp~~~i~~E~~i~~~~ 127 (200)
T CHL00098 90 ------------------------------------------LAKNIAMQIAACPNVKYVSLEDIPEEIINLEKKIESEK 127 (200)
T ss_pred ------------------------------------------HHHHHHHHHHcCCCCeEecHHHCCHHHHHHHHHHHHHH
Confidence 158999999999 7999999999999999999999999
Q ss_pred HHhcCCChHHHHHHHHhhhhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEEeEEEEEecccccC
Q 016590 315 AESTGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEVGEGIRR 386 (386)
Q Consensus 315 ~~~~gKP~~i~eKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~v~V~~F~R~~vGEgiek 386 (386)
+..+|||++|++|||+|||+|||+|+||++|+|++|+++||+++|++..+++|.+++|.+|+||+||||+||
T Consensus 128 ~~~~gKp~~i~ekiv~Grl~k~~~e~~LLeQ~fv~D~~~TV~~~l~e~~akiGeni~V~rF~R~~vGegiek 199 (200)
T CHL00098 128 DDLQNKPEEIKEKIVEGRIKKRLKELSLLDQPFIRDQSITVEELIKQNIAKLGENIQIRRFARFTLGEGEEK 199 (200)
T ss_pred HHhcCCcHHHHHHHHhhHHHHHHHHhhhhcCcccCCCCccHHHHHHHHHHhcCCCcEEEEEEEEEecCCccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999987
No 6
>PF00889 EF_TS: Elongation factor TS; InterPro: IPR014039 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the C-terminal dimerisation domain found primarily in EF-Tu (EF1A) proteins from bacteria, mitochondria and chloroplasts. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005622 intracellular; PDB: 1XB2_B 3AVU_A 3AVW_A 3AGQ_A 3AGP_A 3AVT_A 3AVY_A 3AVX_A 3AVV_A 1TFE_A ....
Probab=100.00 E-value=5.8e-68 Score=500.05 Aligned_cols=221 Identities=46% Similarity=0.700 Sum_probs=194.0
Q ss_pred ccCCcEEEEecCCeEEEEEEeccccceecchHHHHHHHHHHHHHHhhcCCCCCCCCCCCCChhhhhccccCCCCCCCCCC
Q 016590 129 ATEGLLALAQNESKAAVIELNCETDFVSRNEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGE 208 (386)
Q Consensus 129 a~EGlV~~~~~~~~aalvElNCETDFVArN~~F~~la~~ia~~~l~~~~~~~~~~~~~~l~~e~l~~~~~~~~~~~~~~~ 208 (386)
|+||+|+++++++.|+||||||||||||||+.|++|++.|+++++..... +++++..+++. +
T Consensus 1 a~EG~V~~~v~~~~a~~vElncETDFVArn~~F~~l~~~ia~~~~~~~~~----------~~~~l~~~~~~--------~ 62 (221)
T PF00889_consen 1 AAEGLVGIAVSGDKAAMVELNCETDFVARNEEFQNLAKEIADAALENKAS----------DVEELLALPLA--------S 62 (221)
T ss_dssp --EEEEEEEEETTEEEEEEEEESSHHHHTSHHHHHHHHHHHHHHHCTTEE----------SHHHHHHSB----------S
T ss_pred CCceEEEEEEeCCcEEEEEEEccccceecCHHHHHHHHHHHHHHHHhCCC----------CHHHHHhcccc--------c
Confidence 68999999999999999999999999999999999999999999854332 45778777642 3
Q ss_pred CcHHHHHHHHHHHhcceeeeeeeEEeeeCCCCeEEEEecCCCCCCCCcEEEEEEEeecCCCCCCchhhhHHHHHHHHhhh
Q 016590 209 TTVQNAITEVAAIMGENVKLRRGFLLSASSPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVA 288 (386)
Q Consensus 209 ~Tv~d~i~~~ia~iGENI~LrR~~~~~~~~~~~v~sY~H~~~~~~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA 288 (386)
.||+|++.++++++||||.|||+..+.. +++++++|+|++ ||+|+||.++++.+. .+++||+|||||||
T Consensus 63 ~tv~d~i~~~i~~igEnI~l~r~~~~~~-~~~~v~~Y~H~~-----gkig~lV~~~~~~~~-----~~~~ak~iAmhIaA 131 (221)
T PF00889_consen 63 KTVKDAIAELIAKIGENIQLRRAARISA-PNGFVGSYVHNN-----GKIGVLVALEGDNDS-----AKEFAKDIAMHIAA 131 (221)
T ss_dssp SHHHHHHHHHHHHH-S-EEEEEEEEEE--TTSEEEEEEET------TTEEEEEEEET-SHG-----GHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHhCCCEEEeEEEEEec-cCCEEEEEECCC-----CcEEEEEEEEcCcch-----HHHHHHHHHHHHhh
Confidence 7999999999999999999999999998 489999999997 999999999976542 15899999999999
Q ss_pred cCCcccccCCCCHHHHHHHHHHHHHHHHhcCCChHHHHHHHHhhhhhhhhcccccccccccCCCCcHHHHHHHhhhhcCC
Q 016590 289 QKPLFLTKELVSADALENEREILKSQAESTGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGS 368 (386)
Q Consensus 289 ~~P~~ls~~~Vp~~~le~Er~i~~~q~~~~gKP~~i~eKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~ 368 (386)
|+|.||++++||++++++||+++++|+..+|||++|++||++|||+|||+|+|||+|+||+|+++||+|||++.+++
T Consensus 132 ~~P~~l~~~~vp~~~~~~E~~i~~~~~~~~gKpe~i~ekIv~Gkl~k~~~e~~Ll~Q~fv~D~~~tV~~~l~~~~~~--- 208 (221)
T PF00889_consen 132 MNPKYLSEEDVPAEVLEKEKEIAKEQAKAEGKPENIIEKIVEGKLKKFYKENCLLEQPFVKDPKKTVKQYLKEVGKE--- 208 (221)
T ss_dssp H--SBSSCTGS-CCHHHHHHHHHHHHHHTTTS-HHHHHHHHHHHHHHHHHHCBTCCSBETTETTSBHHHHHHCTTHH---
T ss_pred hCccccCcccCCHHHHHHHHHHHHHHhhccCCcHHHHHHHhhhhHhheehheeecCCCccCCCCccHHHHHHhcCCC---
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999887
Q ss_pred CeEEEeEEEEEecc
Q 016590 369 PVKIGSFFRMEVGE 382 (386)
Q Consensus 369 ~v~V~~F~R~~vGE 382 (386)
++|++|+||+|||
T Consensus 209 -i~v~~F~R~~vGE 221 (221)
T PF00889_consen 209 -IKVVGFVRFEVGE 221 (221)
T ss_dssp --EEEEEEEEETTT
T ss_pred -cEEEEEEEEecCC
Confidence 8999999999998
No 7
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.5e-64 Score=483.90 Aligned_cols=270 Identities=33% Similarity=0.488 Sum_probs=217.0
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH----cccccccccccccccCCcEEEEecCCeEEEEEEecc
Q 016590 76 EQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK----RGKVLASKKSSRTATEGLLALAQNESKAAVIELNCE 151 (386)
Q Consensus 76 ~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk----kG~akA~Kka~R~a~EGlV~~~~~~~~aalvElNCE 151 (386)
.++++||+||++|||||++|||||++||||+..|.+||+| .||.+|+|+++|+|+||+|++.+++++.||||||||
T Consensus 45 ~~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~~L~k~aqk~g~~~A~K~~sR~t~eGlIgv~~~~~r~vlvElNCE 124 (340)
T KOG1071|consen 45 SSKALLKKLREKTGASMVNCKKALEECGGDLVLAEEWLHKKAQKEGWSKAAKKASRTTKEGLIGVLQEDGRTVLVELNCE 124 (340)
T ss_pred ccHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHHHHHHHHHHhhhhHHhhhcccccccceeEEEEeCCeEEEEEeecc
Confidence 4579999999999999999999999999999999999996 588899999999999999999999999999999999
Q ss_pred ccceecchHHHHHHHHHHHHHHhhcCC----CCCCC-----CCCCCChhhhhccccCCCCCCCCCCCcHHHHHHHHHHHh
Q 016590 152 TDFVSRNEIFQYLALALAKQALVAENV----SQPVS-----GLFPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIM 222 (386)
Q Consensus 152 TDFVArN~~F~~la~~ia~~~l~~~~~----~~~~~-----~~~~l~~e~l~~~~~~~~~~~~~~~~Tv~d~i~~~ia~i 222 (386)
|||||||+.||.||..||...+.+... ..... ..++..+.....+....+.+.-++..||+|.++.+|+++
T Consensus 125 TDFVARn~~Fq~Lv~~iA~~~l~~~~~~~~~~s~~s~e~~l~~~~~g~kl~~~~~~l~~~~d~~gkvsl~d~l~~~i~~~ 204 (340)
T KOG1071|consen 125 TDFVARNDIFQDLVDQIALSVLAHCQTLKTKHSSYSKEKELEMDGRGFKLSESLSLLPNLPDVEGKVSLKDQLALAIGKL 204 (340)
T ss_pred cchhhccchHHHHHHHHHHHHHHhhhhcccChhhhhhhhhccccchHHHhhHHHhhccCCCCcccceeHHHHHHHHHHHh
Confidence 999999999999999999999873221 00000 011111112222222223333344559999999999999
Q ss_pred cceeeeeeeEEeeeCCCCeEEEEecCCCCC------CCCcEEEEEEEeecCCCCCCchhhhHHHHHHHHhhhcCCccccc
Q 016590 223 GENVKLRRGFLLSASSPGVVSTYLHTSPQS------GLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTK 296 (386)
Q Consensus 223 GENI~LrR~~~~~~~~~~~v~sY~H~~~~~------~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA~~P~~ls~ 296 (386)
||||++||+.++.++++..+++|.|+.+++ ..|++|+||+++..... .-..+.+++.||+||++|.|..+.
T Consensus 205 GENvkvrR~~~~ka~~g~~l~~y~H~A~q~agt~~l~~g~~~alvAi~~~~s~--~~~~~~~~~~i~q~ivgm~p~s~~- 281 (340)
T KOG1071|consen 205 GENVKVRRAACMKAPSGTYLGSYSHGAPQSAGTHKLPLGEYGALVAINSVSSQ--LTSLEDVAKQICQHIVGMSPESVG- 281 (340)
T ss_pred ccceEEeEEEEEecCCCceEEeeecCCCCCccccccccccchhhhhhhhccch--hhhHHHHHHHHHHHhhccChhhhc-
Confidence 999999999999998888999999988631 26899999999765432 112456899999999999999887
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcCCChHHHHHHHHhhhhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEEeEE
Q 016590 297 ELVSADALENEREILKSQAESTGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFF 376 (386)
Q Consensus 297 ~~Vp~~~le~Er~i~~~q~~~~gKP~~i~eKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~v~V~~F~ 376 (386)
+.++ .+|.. ++++|++||.|+|+.|+++||+++++.. +++|.+|+
T Consensus 282 e~~k------------------~e~~~-----------~~e~et~ll~q~~lld~~itv~~~l~~~------~~~V~Dfv 326 (340)
T KOG1071|consen 282 ESLK------------------DEPGQ-----------GAEAETALLSQPSLLDPSITVKEYLDPH------NVSVVDFV 326 (340)
T ss_pred cccc------------------ccccc-----------cccchhhheecHhhcCchhhHHHHhccC------CcchHHHH
Confidence 2111 12222 2588999999999999999999999843 68999999
Q ss_pred EEEeccc
Q 016590 377 RMEVGEG 383 (386)
Q Consensus 377 R~~vGEg 383 (386)
||+|||+
T Consensus 327 R~E~Ge~ 333 (340)
T KOG1071|consen 327 RFEVGEG 333 (340)
T ss_pred HHHhccc
Confidence 9999993
No 8
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=98.35 E-value=9.3e-07 Score=61.01 Aligned_cols=34 Identities=26% Similarity=0.358 Sum_probs=32.2
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHH
Q 016590 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKEL 113 (386)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~L 113 (386)
+.|++|+++ |.+.-+|++||..++||++.|++||
T Consensus 4 ~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 4 EKVQQLMEM-GFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 789999999 9999999999999999999999998
No 9
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=98.29 E-value=4e-06 Score=82.90 Aligned_cols=119 Identities=20% Similarity=0.276 Sum_probs=95.0
Q ss_pred CCCeEEEEecCCCCCCCCcEEEEEEEeecCCCCC-CchhhhHHHHHHHHhhhcCCcccccCCCCHHHHHHHHHHHHHHHH
Q 016590 238 SPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSS-FDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQAE 316 (386)
Q Consensus 238 ~~~~v~sY~H~~~~~~~Gkig~LV~l~~~~~~~~-~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~~le~Er~i~~~q~~ 316 (386)
.+|.|+.|+|+ ||+ +||.++.+++... .+..+.+.++|||.+.+. |.++.. ....+.+|+++
T Consensus 103 ~eGlIgv~~~~------~r~-vlvElNCETDFVARn~~Fq~Lv~~iA~~~l~~-~~~~~~---~~s~~s~e~~l------ 165 (340)
T KOG1071|consen 103 KEGLIGVLQED------GRT-VLVELNCETDFVARNDIFQDLVDQIALSVLAH-CQTLKT---KHSSYSKEKEL------ 165 (340)
T ss_pred ccceeEEEEeC------CeE-EEEEeecccchhhccchHHHHHHHHHHHHHHh-hhhccc---Chhhhhhhhhc------
Confidence 37899999997 687 9999999887532 345678899999988773 333322 23344444443
Q ss_pred hcCCChHHHHHHHHhhhhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEEeEEEEEecccc
Q 016590 317 STGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEVGEGI 384 (386)
Q Consensus 317 ~~gKP~~i~eKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~v~V~~F~R~~vGEgi 384 (386)
+| .|+..|.+.+.-|+.|++..|++.+|++.|......+|.|++|.+|.+|..++|.
T Consensus 166 ---~~--------~~~g~kl~~~~~~l~~~~d~~gkvsl~d~l~~~i~~~GENvkvrR~~~~ka~~g~ 222 (340)
T KOG1071|consen 166 ---EM--------DGRGFKLSESLSLLPNLPDVEGKVSLKDQLALAIGKLGENVKVRRAACMKAPSGT 222 (340)
T ss_pred ---cc--------cchHHHhhHHHhhccCCCCcccceeHHHHHHHHHHHhccceEEeEEEEEecCCCc
Confidence 22 6888999999999999999999999999999999999999999999999999874
No 10
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=97.36 E-value=0.00029 Score=60.80 Aligned_cols=37 Identities=24% Similarity=0.322 Sum_probs=35.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 016590 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (386)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (386)
++|+-++++||++..+|++||++||||+-.|+-+|.+
T Consensus 78 edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L~~ 114 (115)
T PRK06369 78 EDIELVAEQTGVSEEEARKALEEANGDLAEAILKLSS 114 (115)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHHhc
Confidence 8999999999999999999999999999999999975
No 11
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=97.25 E-value=0.00064 Score=46.40 Aligned_cols=34 Identities=26% Similarity=0.216 Sum_probs=30.9
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHH
Q 016590 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKEL 113 (386)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~L 113 (386)
+.|.+|++. |.+--+|+.||..++||+++|++||
T Consensus 3 ~~v~~L~~m-Gf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 3 EKIDQLLEM-GFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHHc-CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 467777776 9999999999999999999999998
No 12
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=97.23 E-value=0.00046 Score=59.51 Aligned_cols=36 Identities=22% Similarity=0.386 Sum_probs=34.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHH
Q 016590 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELR 114 (386)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LR 114 (386)
++|+-++++||++..+||+||++||||+-.|+-+|.
T Consensus 80 eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~~L~ 115 (116)
T TIGR00264 80 DDIELVMKQCNVSKEEARRALEECGGDLAEAIMKLE 115 (116)
T ss_pred HHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHhh
Confidence 789999999999999999999999999999999885
No 13
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=97.15 E-value=0.00093 Score=45.79 Aligned_cols=35 Identities=23% Similarity=0.237 Sum_probs=31.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHH
Q 016590 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELR 114 (386)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LR 114 (386)
+.|.+|++. |.+.-.|..||..++||+++|++||.
T Consensus 3 ~~v~~L~~m-Gf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 3 EKLEQLLEM-GFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHHc-CCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 567788874 99999999999999999999999985
No 14
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=96.40 E-value=0.014 Score=57.81 Aligned_cols=92 Identities=15% Similarity=0.290 Sum_probs=72.9
Q ss_pred CCeEEEEecCCCCCCCCcEEEEEEEeecCCCCC-CchhhhHHHHHHHHhhhcCCcccccCCCCHHHHHHHHHHHHHHHHh
Q 016590 239 PGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSS-FDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQAES 317 (386)
Q Consensus 239 ~~~v~sY~H~~~~~~~Gkig~LV~l~~~~~~~~-~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~~le~Er~i~~~q~~~ 317 (386)
.|.+..|+|++ |+.|+||.+.++++... .+....|+++|+.++...+|..+..
T Consensus 59 EGli~~~~~~~-----~~~av~vEvN~ETDFVAkN~~F~~l~~~ia~~~l~~~~~~ve~--------------------- 112 (296)
T COG0264 59 EGLIAAKVDGD-----GKKAVLVEVNCETDFVAKNAEFQELANKIAKAALEKKPADVEE--------------------- 112 (296)
T ss_pred cceEEEEEcCC-----CcEEEEEEEeccccceeCChhHHHHHHHHHHHHHHhCcccHHH---------------------
Confidence 78999999876 89999999999887532 3446789999999999987732210
Q ss_pred cCCChHHHHHHHHhhhhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEEeEEEEEecc
Q 016590 318 TGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEVGE 382 (386)
Q Consensus 318 ~gKP~~i~eKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~v~V~~F~R~~vGE 382 (386)
|. ....+++.||.+.+.+....+|.++.+.+|.+|+.+.
T Consensus 113 ------------------------l~--~~~~~~~~tv~e~~~~~~AkIGENi~lRR~~~~~~~~ 151 (296)
T COG0264 113 ------------------------LK--AAFEPGGKTVEEEIAALIAKIGENISLRRFAVLEAGD 151 (296)
T ss_pred ------------------------HH--hhhcccCccHHHHHHHHHHHhccceeEEEEEEeecCc
Confidence 00 1122458899999999999999999999999999876
No 15
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=96.38 E-value=0.019 Score=57.03 Aligned_cols=88 Identities=18% Similarity=0.230 Sum_probs=67.1
Q ss_pred CCCeEEEEecCCCCCCCCcEEEEEEEeecCCCCC-CchhhhHHHHHHHHhhhcCCcccccCCCCHHHHHHHHHHHHHHHH
Q 016590 238 SPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSS-FDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQAE 316 (386)
Q Consensus 238 ~~~~v~sY~H~~~~~~~Gkig~LV~l~~~~~~~~-~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~~le~Er~i~~~q~~ 316 (386)
..|.++.|++ |+.|+||.+.++++... .+....|+++|+.++++.+|..+
T Consensus 57 ~EG~V~~~~~-------~~~~~ivElncETDFVArne~F~~l~~~ia~~~~~~~~~~~---------------------- 107 (290)
T TIGR00116 57 AEGVIVLKSD-------GNKAVIVEVNSETDFVAKNAGFKEFANKLLDELKANKITTL---------------------- 107 (290)
T ss_pred CCcEEEEEEc-------CCEEEEEEEecCCccccCChHHHHHHHHHHHHHHhcCCCCH----------------------
Confidence 3789999996 56899999999887643 34456789999999876544210
Q ss_pred hcCCChHHHHHHHHhhhhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEEeEEEEEe
Q 016590 317 STGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEV 380 (386)
Q Consensus 317 ~~gKP~~i~eKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~v~V~~F~R~~v 380 (386)
+ -|+.+++ ++..|| |.+.+....+|.++.|.+|.+|..
T Consensus 108 -----e------------------~l~~~~~--~~~~tv-d~i~~~~a~iGEnI~lrR~~~~~~ 145 (290)
T TIGR00116 108 -----E------------------ELQAQEL--ENREKV-EYLAALAAKIGENINLRRVAVLEG 145 (290)
T ss_pred -----H------------------HHhhccc--cCCCcH-HHHHHHHHHhccceEEEEEEEEec
Confidence 0 2334555 356799 999999999999999999999975
No 16
>CHL00098 tsf elongation factor Ts
Probab=96.35 E-value=0.0059 Score=57.54 Aligned_cols=44 Identities=25% Similarity=0.501 Sum_probs=34.7
Q ss_pred CCCeEEEEecCCCCCCCCcEEEEEEEeecCCCCCCchhhhHHHHHHHHhhhc
Q 016590 238 SPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQ 289 (386)
Q Consensus 238 ~~~~v~sY~H~~~~~~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA~ 289 (386)
.+|.+++|+|.+ |++|+||.++++++... ..+.| +++|||||+.
T Consensus 54 ~eG~V~~yiH~~-----gk~gvlVeln~ETDfVA--rn~~F-~~la~~IAmh 97 (200)
T CHL00098 54 TEGLIESYIHTG-----GKLGVLVEINCETDFVA--RREEF-QKLAKNIAMQ 97 (200)
T ss_pred ccCeEEEEEecC-----CCEEEEEEEecCccccc--ccHHH-HHHHHHHHHH
Confidence 368999999986 89999999998765321 22467 9999999985
No 17
>PRK09377 tsf elongation factor Ts; Provisional
Probab=95.67 E-value=0.063 Score=53.40 Aligned_cols=88 Identities=20% Similarity=0.334 Sum_probs=67.5
Q ss_pred CCCeEEEEecCCCCCCCCcEEEEEEEeecCCCCC-CchhhhHHHHHHHHhhhcCCcccccCCCCHHHHHHHHHHHHHHHH
Q 016590 238 SPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSS-FDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQAE 316 (386)
Q Consensus 238 ~~~~v~sY~H~~~~~~~Gkig~LV~l~~~~~~~~-~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~~le~Er~i~~~q~~ 316 (386)
..|.++.|+. |+.|+||.+.++++... .+....|+++|+.++++..|..+
T Consensus 58 ~EG~I~~~~~-------~~~~~~vElncETDFVArne~F~~l~~~i~~~~l~~~~~~~---------------------- 108 (290)
T PRK09377 58 AEGLVAAKVD-------GNKGVLVEVNSETDFVAKNEDFQALANEVAEAALAAKPADV---------------------- 108 (290)
T ss_pred cceEEEEEeC-------CCEEEEEEEecCCccccCChHHHHHHHHHHHHHHhcCCCCH----------------------
Confidence 3788888763 68999999999887643 33456789999999887655310
Q ss_pred hcCCChHHHHHHHHhhhhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEEeEEEEEe
Q 016590 317 STGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEV 380 (386)
Q Consensus 317 ~~gKP~~i~eKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~v~V~~F~R~~v 380 (386)
+ -|+.+++ ++.||++.+.+....+|.++.|.+|.+|+.
T Consensus 109 -----e------------------~ll~~~~---~g~tv~d~i~~~~~~iGEnI~l~R~~~~~~ 146 (290)
T PRK09377 109 -----E------------------ALLALKL---DGGTVEEARTELIAKIGENISLRRFARLEK 146 (290)
T ss_pred -----H------------------HHHhccc---cCCcHHHHHHHHHHHhcCceEEEEEEEEee
Confidence 0 1344555 467999999999999999999999999974
No 18
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=94.76 E-value=0.063 Score=38.10 Aligned_cols=37 Identities=27% Similarity=0.275 Sum_probs=31.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 016590 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (386)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (386)
++|.++..-||+.--.|.+-|+.+|||++.|+..--.
T Consensus 2 e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~ 38 (43)
T PF14555_consen 2 EKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFD 38 (43)
T ss_dssp HHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 5799999999999999999999999999999986443
No 19
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=93.48 E-value=0.059 Score=40.01 Aligned_cols=37 Identities=24% Similarity=0.496 Sum_probs=33.1
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 016590 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (386)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (386)
++|.+|..+||.-.-=|.+-|++++||++.|+....+
T Consensus 2 ~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~~ 38 (51)
T PF03943_consen 2 EMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNFEE 38 (51)
T ss_dssp HHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 6899999999999999999999999999999998875
No 20
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=93.05 E-value=0.31 Score=37.82 Aligned_cols=40 Identities=30% Similarity=0.518 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 016590 76 EQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (386)
Q Consensus 76 ~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (386)
.+..+|.++-.+||.-.-=|.+.|+++|||++.|+....+
T Consensus 11 ~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~~ 50 (63)
T smart00804 11 EQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFTE 50 (63)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4468999999999999999999999999999999998654
No 21
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=93.02 E-value=0.14 Score=48.30 Aligned_cols=30 Identities=33% Similarity=0.390 Sum_probs=27.7
Q ss_pred CCCcHHHHHHHHHHHhcceeeeeeeEEeee
Q 016590 207 GETTVQNAITEVAAIMGENVKLRRGFLLSA 236 (386)
Q Consensus 207 ~~~Tv~d~i~~~ia~iGENI~LrR~~~~~~ 236 (386)
++.||+|.+.+.++++||||.|+||.++..
T Consensus 166 ~~~TV~e~l~e~~a~iGEnI~V~rF~R~ev 195 (198)
T PRK12332 166 PSKTVEDLIKEAIAKIGENIVVRRFARFEL 195 (198)
T ss_pred CCccHHHHHHHHHHHhCCCeEEEEEEEEEc
Confidence 467999999999999999999999999865
No 22
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=92.36 E-value=0.25 Score=43.11 Aligned_cols=36 Identities=25% Similarity=0.267 Sum_probs=32.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHH
Q 016590 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELR 114 (386)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LR 114 (386)
++|+-.=++||++--+.+|||+++|||+-.||--|-
T Consensus 86 eDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~ 121 (122)
T COG1308 86 EDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLT 121 (122)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhc
Confidence 578888899999999999999999999999987663
No 23
>PF00889 EF_TS: Elongation factor TS; InterPro: IPR014039 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the C-terminal dimerisation domain found primarily in EF-Tu (EF1A) proteins from bacteria, mitochondria and chloroplasts. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005622 intracellular; PDB: 1XB2_B 3AVU_A 3AVW_A 3AGQ_A 3AGP_A 3AVT_A 3AVY_A 3AVX_A 3AVV_A 1TFE_A ....
Probab=91.93 E-value=0.32 Score=46.46 Aligned_cols=87 Identities=15% Similarity=0.252 Sum_probs=59.5
Q ss_pred CCeEEEEecCCCCCCCCcEEEEEEEeecCCCCC-CchhhhHHHHHHHHhhhcCCcccccCCCCHHHHHHHHHHHHHHHHh
Q 016590 239 PGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSS-FDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQAES 317 (386)
Q Consensus 239 ~~~v~sY~H~~~~~~~Gkig~LV~l~~~~~~~~-~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~~le~Er~i~~~q~~~ 317 (386)
.|.++.|+++. .|+||.+..+++... .+....|+++||..++...+..+
T Consensus 3 EG~V~~~v~~~-------~a~~vElncETDFVArn~~F~~l~~~ia~~~~~~~~~~~----------------------- 52 (221)
T PF00889_consen 3 EGLVGIAVSGD-------KAAMVELNCETDFVARNEEFQNLAKEIADAALENKASDV----------------------- 52 (221)
T ss_dssp EEEEEEEEETT-------EEEEEEEEESSHHHHTSHHHHHHHHHHHHHHHCTTEESH-----------------------
T ss_pred ceEEEEEEeCC-------cEEEEEEEccccceecCHHHHHHHHHHHHHHHHhCCCCH-----------------------
Confidence 68899999864 399999999876421 23455788888888873222111
Q ss_pred cCCChHHHHHHHHhhhhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEEeEEEEEe
Q 016590 318 TGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEV 380 (386)
Q Consensus 318 ~gKP~~i~eKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~v~V~~F~R~~v 380 (386)
+ .|+.+++- + .||+|.+.+....+|.++.|.+|.+|..
T Consensus 53 ----~------------------~l~~~~~~--~-~tv~d~i~~~i~~igEnI~l~r~~~~~~ 90 (221)
T PF00889_consen 53 ----E------------------ELLALPLA--S-KTVKDAIAELIAKIGENIQLRRAARISA 90 (221)
T ss_dssp ----H------------------HHHHSB----S-SHHHHHHHHHHHHH-S-EEEEEEEEEE-
T ss_pred ----H------------------HHHhcccc--c-ccHHHHHHHHHHHhCCCEEEeEEEEEec
Confidence 0 22333332 2 8999999999999999999999999998
No 24
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=87.86 E-value=1.6 Score=30.56 Aligned_cols=37 Identities=24% Similarity=0.350 Sum_probs=31.4
Q ss_pred HHHHHHHHh-cCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 016590 79 NLIKQLREQ-TSAPMKDVKLALVDCDWDIEAALKELRK 115 (386)
Q Consensus 79 ~lIK~LR~~-Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (386)
+.|..|++. -+.+--.-+.+|.+++||+|.|++.|-+
T Consensus 3 ~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 578888888 5689999999999999999999998753
No 25
>PF00542 Ribosomal_L12: Ribosomal protein L7/L12 C-terminal domain; InterPro: IPR013823 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the C-terminal domain of the large subunit ribosomal proteins, known as the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain []. The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post translational modification of the addition of an acetyl group to the N terminus of L7.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1DD4_B 1DD3_A 1RQU_B 2GYA_5 2GYC_5 1RQS_A 1RQV_A 1CTF_A 2XUX_L.
Probab=85.78 E-value=0.67 Score=36.41 Aligned_cols=27 Identities=26% Similarity=0.375 Sum_probs=21.5
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHhcC
Q 016590 77 QVNLIKQLREQTSAPMKDVKLALVDCD 103 (386)
Q Consensus 77 ~~~lIK~LR~~Tgagm~dCKkAL~e~n 103 (386)
.++.||.+|+.||.|++++|+..+...
T Consensus 13 ki~vIK~vR~~tgl~L~eAK~~vd~~p 39 (68)
T PF00542_consen 13 KIKVIKEVREITGLGLKEAKKLVDSLP 39 (68)
T ss_dssp HHHHHHHHHHHC---HHHHHHHHCTTT
T ss_pred hHHHHHHHHHHhCCcHHHHHHHHHhCC
Confidence 468999999999999999999998874
No 26
>PRK06771 hypothetical protein; Provisional
Probab=82.14 E-value=1.5 Score=36.72 Aligned_cols=23 Identities=22% Similarity=0.270 Sum_probs=20.8
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHH
Q 016590 78 VNLIKQLREQTSAPMKDVKLALV 100 (386)
Q Consensus 78 ~~lIK~LR~~Tgagm~dCKkAL~ 100 (386)
++.||.+|+.||+|+.+.|++..
T Consensus 69 i~AIK~~Re~tG~~L~eAK~yVD 91 (93)
T PRK06771 69 VTAVKRVREAFGFSLLEAKQYVD 91 (93)
T ss_pred hHHHHHHHHHcCCCHHHHHHHHh
Confidence 58999999999999999998754
No 27
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=81.56 E-value=4.9 Score=28.15 Aligned_cols=37 Identities=16% Similarity=0.277 Sum_probs=31.8
Q ss_pred HHHHHHHHh-cCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 016590 79 NLIKQLREQ-TSAPMKDVKLALVDCDWDIEAALKELRK 115 (386)
Q Consensus 79 ~lIK~LR~~-Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (386)
+.|..|++. -+.+--.-+..|.+++||+|.|++.|-+
T Consensus 4 ~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~ 41 (43)
T smart00546 4 EALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLE 41 (43)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 578888888 5688889999999999999999988753
No 28
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=81.12 E-value=0.78 Score=36.80 Aligned_cols=46 Identities=30% Similarity=0.296 Sum_probs=34.4
Q ss_pred HHHHHHHHhcCCCH---HHHHHHHHhcCCCHHHHHHHHHHccccccccc
Q 016590 79 NLIKQLREQTSAPM---KDVKLALVDCDWDIEAALKELRKRGKVLASKK 124 (386)
Q Consensus 79 ~lIK~LR~~Tgagm---~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kk 124 (386)
..+-++|+.-|... ..-+.||-.++.|+++|+.||+++-..+..|+
T Consensus 30 ~~l~~vr~~Lg~~~~~e~~i~eal~~~~fDvekAl~~Ll~~~~~~~~~~ 78 (79)
T PF08938_consen 30 SCLPQVREVLGDYVPPEEQIKEALWHYYFDVEKALDYLLSKFKKKKPKK 78 (79)
T ss_dssp HHCCCHHHHCCCCC--CCHHHHHHHHTTT-CCHHHHHHHHCCHSSS---
T ss_pred HHHHHHHHHHcccCCCHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCC
Confidence 34566788877644 78899999999999999999998877665553
No 29
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=77.42 E-value=6 Score=30.50 Aligned_cols=36 Identities=17% Similarity=0.394 Sum_probs=33.5
Q ss_pred HHHHHHHHhcCC-CHHHHHHHHHhcCCCHHHHHHHHH
Q 016590 79 NLIKQLREQTSA-PMKDVKLALVDCDWDIEAALKELR 114 (386)
Q Consensus 79 ~lIK~LR~~Tga-gm~dCKkAL~e~ngDiekAi~~LR 114 (386)
++|..|++-||. +=-|-...|.+||.|-+.|.+-|-
T Consensus 7 k~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL 43 (60)
T PF06972_consen 7 KTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLL 43 (60)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHH
Confidence 789999999999 999999999999999999998874
No 30
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=72.49 E-value=9.4 Score=33.83 Aligned_cols=42 Identities=31% Similarity=0.392 Sum_probs=33.7
Q ss_pred hHHHHHHHHHHHh-----------------cCCCHHHHHHHHHhcCCCHHHHHHHHHHcc
Q 016590 75 TEQVNLIKQLREQ-----------------TSAPMKDVKLALVDCDWDIEAALKELRKRG 117 (386)
Q Consensus 75 ~~~~~lIK~LR~~-----------------Tgagm~dCKkAL~e~ngDiekAi~~LRkkG 117 (386)
-+.|++=|+|-+. .+.+--+.++||+++| |+..|+++||.++
T Consensus 94 ~EYM~lKkqLae~il~~s~~~~e~v~v~a~a~v~~eeAr~aleeag-Dl~~A~k~l~~~~ 152 (153)
T COG4008 94 EEYMELKKQLAEYILGHSEPPVEEVEVLADAFVTPEEAREALEEAG-DLRTAMKILRMKS 152 (153)
T ss_pred HHHHHHHHHHHHHHhccCCCcHHHHHHHHHhcCCHHHHHHHHHHcC-CHHHHHHHHHHhc
Confidence 4667777777542 3467778999999999 9999999999876
No 31
>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed
Probab=69.70 E-value=6.9 Score=34.40 Aligned_cols=26 Identities=27% Similarity=0.341 Sum_probs=23.5
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhcC
Q 016590 78 VNLIKQLREQTSAPMKDVKLALVDCD 103 (386)
Q Consensus 78 ~~lIK~LR~~Tgagm~dCKkAL~e~n 103 (386)
+..||.+|+-||.|+++.|+..+.+.
T Consensus 69 i~vIK~vR~itgLgLkEAK~lVe~~P 94 (123)
T PRK00157 69 IAVIKAVREITGLGLKEAKDLVEGAP 94 (123)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHhCC
Confidence 58999999999999999999887764
No 32
>TIGR00855 L12 ribosomal protein L7/L12. THis model resembles Pfam model pfam00542 but matches the full length of prokaryotic and organellar proteins rather than just the C-terminus.
Probab=69.68 E-value=5.5 Score=35.16 Aligned_cols=28 Identities=25% Similarity=0.226 Sum_probs=24.6
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhcCCC
Q 016590 78 VNLIKQLREQTSAPMKDVKLALVDCDWD 105 (386)
Q Consensus 78 ~~lIK~LR~~Tgagm~dCKkAL~e~ngD 105 (386)
+..||.+|+.||.|+++.|+..+.+..-
T Consensus 72 i~vIK~vR~itgLgLkEAK~lVe~~P~~ 99 (126)
T TIGR00855 72 IAVIKVVREITGLGLKEAKDLVEGAPKV 99 (126)
T ss_pred hHHHHHHHHHcCCcHHHHHHHHHhCcHH
Confidence 5899999999999999999998877543
No 33
>cd00387 Ribosomal_L7_L12 Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and
Probab=68.66 E-value=9.5 Score=33.62 Aligned_cols=29 Identities=24% Similarity=0.276 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHhcCCC
Q 016590 77 QVNLIKQLREQTSAPMKDVKLALVDCDWD 105 (386)
Q Consensus 77 ~~~lIK~LR~~Tgagm~dCKkAL~e~ngD 105 (386)
-+..||.+|.-||.|+++.|+..+.+..-
T Consensus 73 Ki~vIK~VR~it~LgLkEAK~lVe~~P~~ 101 (127)
T cd00387 73 KIAVIKEVREITGLGLKEAKDLVESAPKV 101 (127)
T ss_pred hHHHHHHHHHHhCCChHHHHHHHHhCcHH
Confidence 35899999999999999999998887543
No 34
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=62.45 E-value=12 Score=31.00 Aligned_cols=50 Identities=10% Similarity=0.025 Sum_probs=38.1
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhc-CCCHHHHHHHHHHc
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDC-DWDIEAALKELRKR 116 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~-ngDiekAi~~LRkk 116 (386)
...|.|+-.. ...+..|+.|| +|.||.+.|+-+... +||.+.+.+.|.++
T Consensus 34 ~g~R~Y~~~~---v~~l~~I~~l~--~g~~l~~i~~~~~~~~~~~~~~~~~ll~~~ 84 (99)
T cd04772 34 NGYRIYTDKH---IAALRAYRALL--PGYGYRVAQRIMRAVHAGIVASALALVDAA 84 (99)
T ss_pred CCCeecCHHH---HHHHHHHHHHh--hCCCHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence 3577787653 55678899998 599999998877665 48899888888753
No 35
>CHL00083 rpl12 ribosomal protein L12
Probab=61.52 E-value=9.9 Score=33.77 Aligned_cols=27 Identities=19% Similarity=0.212 Sum_probs=23.8
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhcCC
Q 016590 78 VNLIKQLREQTSAPMKDVKLALVDCDW 104 (386)
Q Consensus 78 ~~lIK~LR~~Tgagm~dCKkAL~e~ng 104 (386)
+..||.+|+-||.|+++.|+..+...-
T Consensus 77 i~vIK~vr~it~lgLkeaK~lVe~~P~ 103 (131)
T CHL00083 77 IAVLKVVRSLTGLGLKEAKELVESLPK 103 (131)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCH
Confidence 589999999999999999998877643
No 36
>COG0222 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]
Probab=61.40 E-value=9.1 Score=33.62 Aligned_cols=38 Identities=21% Similarity=0.334 Sum_probs=28.2
Q ss_pred cceeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC
Q 016590 60 FALISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD 103 (386)
Q Consensus 60 ~~~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n 103 (386)
|.+..+.+..++ +..||..|+-||.|+++.|..-+.+.
T Consensus 58 fdVvL~~~g~kK------I~VIK~vR~itGLGLKEAKdlVe~aP 95 (124)
T COG0222 58 FDVVLKSAGGKK------IAVIKVVRELTGLGLKEAKDLVEGAP 95 (124)
T ss_pred eEEEecccCCcc------hhHHHHHHHHhcccHHHHHHHHHhCc
Confidence 445555553333 48999999999999999998766653
No 37
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=60.97 E-value=3 Score=34.69 Aligned_cols=29 Identities=28% Similarity=0.335 Sum_probs=26.5
Q ss_pred CHHHHHHHHHhcCCCHHHHHHHHHHcccc
Q 016590 91 PMKDVKLALVDCDWDIEAALKELRKRGKV 119 (386)
Q Consensus 91 gm~dCKkAL~e~ngDiekAi~~LRkkG~a 119 (386)
-+-||.+|=+|--.+++.|.+-||+||..
T Consensus 62 tFnDcpeA~~eL~~eI~eAK~dLr~kGv~ 90 (91)
T PF08285_consen 62 TFNDCPEAAKELQKEIKEAKADLRKKGVD 90 (91)
T ss_pred ccCCCHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 46799999999999999999999999963
No 38
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=51.31 E-value=14 Score=31.00 Aligned_cols=41 Identities=20% Similarity=0.148 Sum_probs=33.7
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCCH
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDI 106 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDi 106 (386)
...|.|+... ...+..|+.|| .+|.++.+||+.|...+-+-
T Consensus 34 ~gyR~Ys~~d---l~~l~~I~~~r-~~G~~L~~I~~~l~~~~~~~ 74 (124)
T COG0789 34 GGYRYYTPED---LELLQIIKTLR-ELGFSLAEIKELLDLLSAGE 74 (124)
T ss_pred CCceecCHHH---HHHHHHHHHHH-HcCCCHHHHHHHHhcccccc
Confidence 4678888764 56678899999 89999999999999988533
No 39
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=50.46 E-value=25 Score=29.02 Aligned_cols=47 Identities=28% Similarity=0.367 Sum_probs=35.7
Q ss_pred eeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHc
Q 016590 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKR 116 (386)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkk 116 (386)
..|.|+-.. ...+..|+.||+ .|.|+.++++.|...+ +...+.|..+
T Consensus 35 g~R~y~~~d---i~~l~~i~~lr~-~g~~l~~i~~~~~~~~---~~~~~~l~~~ 81 (103)
T cd01106 35 GYRLYTEED---LERLQQILFLKE-LGFSLKEIKELLKDPS---EDLLEALREQ 81 (103)
T ss_pred CceeeCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHHcCc---HHHHHHHHHH
Confidence 457777653 556788999998 7999999999998766 6666666543
No 40
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=50.25 E-value=15 Score=40.57 Aligned_cols=28 Identities=14% Similarity=0.058 Sum_probs=25.0
Q ss_pred cCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 016590 88 TSAPMKDVKLALVDCDWDIEAALKELRK 115 (386)
Q Consensus 88 Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (386)
-|-+--.|+|||.++|||++.|++|+--
T Consensus 645 mGf~~~qa~~aL~~~n~nveravDWif~ 672 (763)
T KOG0944|consen 645 MGFSRNQAIKALKATNNNVERAVDWIFS 672 (763)
T ss_pred ecCcHHHHHHHHHhcCccHHHHHHHHHh
Confidence 4677788999999999999999999874
No 41
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=48.49 E-value=32 Score=27.80 Aligned_cols=51 Identities=18% Similarity=0.150 Sum_probs=37.6
Q ss_pred eeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHccc
Q 016590 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGK 118 (386)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkkG~ 118 (386)
..|.|+... ...+..|+.||+ .|.++.++++-|..-+ +.+....-|-..|.
T Consensus 36 g~R~Ys~~d---v~~l~~I~~Lr~-~G~sl~~i~~~l~~~~-~~~~~~~~~~~~~~ 86 (88)
T cd01105 36 GQRKYSLAD---VDRLLVIKELLD-EGFTLAAAVEKLRRRR-VQAEVRRRLMKDGL 86 (88)
T ss_pred CceecCHHH---HHHHHHHHHHHH-CCCCHHHHHHHHHHcc-CHHHHHHHHHHHhc
Confidence 567788553 566889999998 9999999999998555 55555555554443
No 42
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=47.33 E-value=33 Score=28.83 Aligned_cols=50 Identities=16% Similarity=0.150 Sum_probs=37.2
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhc--CCCHHHHHHHHHH
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDC--DWDIEAALKELRK 115 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~--ngDiekAi~~LRk 115 (386)
...|.|+... ...+..|+.||+ .|.|+.+.+..|... +++.+...+.|.+
T Consensus 34 ~g~R~Y~~~d---l~~l~~I~~lr~-~G~~l~~I~~~l~~~~~~~~~~~~~~~l~~ 85 (108)
T cd04773 34 TGYRVYDPSD---VRDARLIHLLRR-GGYLLEQIATVVEQLRHAGGTEALAAALEQ 85 (108)
T ss_pred CCceeeCHHH---HHHHHHHHHHHH-CCCCHHHHHHHHHHhhcCCCHHHHHHHHHH
Confidence 3467777653 456789999986 999999999999865 3556666666654
No 43
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=44.59 E-value=24 Score=29.11 Aligned_cols=36 Identities=22% Similarity=0.435 Sum_probs=29.6
Q ss_pred eeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHh
Q 016590 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVD 101 (386)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e 101 (386)
..|.|+... ...+..|+.||+..|.++.++|+.|..
T Consensus 35 g~r~Y~~~d---v~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 35 NQAEYSEAH---VERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred CCeecCHHH---HHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 346776553 566899999999999999999999987
No 44
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=43.63 E-value=44 Score=27.09 Aligned_cols=34 Identities=26% Similarity=0.107 Sum_probs=28.8
Q ss_pred HHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 016590 81 IKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (386)
Q Consensus 81 IK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (386)
|++ .+.+|...-.+=.||..|.||+..|..++..
T Consensus 1 i~~-~~~~g~~~~~v~~aL~~tSgd~~~a~~~vl~ 34 (87)
T PF11626_consen 1 IKH-YEELGYSREFVTHALYATSGDPELARRFVLN 34 (87)
T ss_dssp -HH-HHHHTB-HHHHHHHHHHTTTBHHHHHHHHHH
T ss_pred Cch-HHHhCCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 456 7889999999999999999999999997654
No 45
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=41.85 E-value=24 Score=26.68 Aligned_cols=34 Identities=24% Similarity=0.239 Sum_probs=27.5
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHH
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLAL 99 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL 99 (386)
...|.|+... ...+..|+.||+ .|.++-++|+-|
T Consensus 34 ~g~R~yt~~d---i~~l~~i~~l~~-~g~~l~~i~~~l 67 (68)
T cd04763 34 GGHRLFNDAD---IDRILEIKRWID-NGVQVSKVKKLL 67 (68)
T ss_pred CCCcccCHHH---HHHHHHHHHHHH-cCCCHHHHHHHh
Confidence 4557787664 566789999999 999999999876
No 46
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=40.45 E-value=26 Score=24.86 Aligned_cols=17 Identities=29% Similarity=0.606 Sum_probs=14.6
Q ss_pred HHHHhcCCCHHHHHHHH
Q 016590 97 LALVDCDWDIEAALKEL 113 (386)
Q Consensus 97 kAL~e~ngDiekAi~~L 113 (386)
-.|+-|+||+-+|||.+
T Consensus 22 ~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 22 LILQRCNGDVVQAIEQF 38 (39)
T ss_pred HHHHHcCCcHHHHHHHh
Confidence 46889999999999974
No 47
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=39.42 E-value=43 Score=27.45 Aligned_cols=47 Identities=21% Similarity=0.276 Sum_probs=34.2
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (386)
...|.|+... ...+..|+.||+ +|.++.+.++-|...+. ...++|+.
T Consensus 34 ~gyR~Y~~~~---l~~l~~I~~lr~-~G~~l~eI~~~l~~~~~---~~~~~l~~ 80 (96)
T cd04788 34 GGHRLYDRAD---IRRLHQIIALRR-LGFSLREIGRALDGPDF---DPLELLRR 80 (96)
T ss_pred CCceeeCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHhCCCh---hHHHHHHH
Confidence 3468887653 566899999986 79999999998876542 34555554
No 48
>cd07257 THT_oxygenase_C The C-terminal domain of 2,4,5-Trihydroxytoluene (THT) oxygenase, which is an extradiol dioxygenease in the 2,4-dinitrotoluene (DNT) degradation pathway. This subfamily contains the C-terminal, catalytic, domain of THT oxygenase. THT oxygenase is an extradiol dioxygenase in the 2,4-dinitrotoluene (DNT) degradation pathway. It catalyzes the conversion of 2,4,5-trihydroxytoluene to an unstable ring fission product, 2,4-dihydroxy-5-methyl-6-oxo-2,4-hexadienoic acid. The native protein was determined to be a dimer by gel filtration. The enzyme belongs to the type I family of extradiol dioxygenases which contains two structurally homologous barrel-shaped domains at the N- and C-terminus of each monomer. The active-site metal is located in the C-terminal barrel. Fe(II) is required for its catalytic activity.
Probab=39.16 E-value=58 Score=28.42 Aligned_cols=52 Identities=17% Similarity=0.110 Sum_probs=37.5
Q ss_pred CCHHHHH---HHHHHcccccccccccccccCCcEEEEecCCeEEEEEEecccccee
Q 016590 104 WDIEAAL---KELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFVS 156 (386)
Q Consensus 104 gDiekAi---~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalvElNCETDFVA 156 (386)
.|++++. +.|+++|...... .+|....+.+.+++.+-.|-+|||-+|.|=|.
T Consensus 76 ~die~~~~~~~~L~~~Gv~v~~~-~g~~~~g~~~~~y~~DPdG~~iEl~~~~~~~~ 130 (153)
T cd07257 76 HDFDAQGLGHDYLREKGYEHVWG-VGRHILGSQIFDYWFDPWGFIVEHYTDGDLVN 130 (153)
T ss_pred CCHHHHHHHHHHHHHCCCcEeec-CCccCCCCCEEEEEECCCCCEEEEEcCceeEc
Confidence 4788876 8899999865432 34544445567788777899999999987443
No 49
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=37.96 E-value=19 Score=26.99 Aligned_cols=34 Identities=26% Similarity=0.481 Sum_probs=26.1
Q ss_pred eccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHh
Q 016590 64 SRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVD 101 (386)
Q Consensus 64 ~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e 101 (386)
.|.|+... ...+..|+.||+ .|.++.+.++.|.+
T Consensus 35 ~r~y~~~d---v~~l~~i~~l~~-~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 35 YRYYSEED---VERLREIKELRK-QGMSLEEIKKLLKQ 68 (69)
T ss_dssp SEEE-HHH---HHHHHHHHHHHH-TTTHHHHHHHHH--
T ss_pred eeeccHHH---HHHHHHHHHHHH-CcCCHHHHHHHHcc
Confidence 47777653 566899999999 99999999998864
No 50
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=37.56 E-value=48 Score=27.74 Aligned_cols=49 Identities=29% Similarity=0.334 Sum_probs=36.1
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHc
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKR 116 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkk 116 (386)
...|.|+... ...+..|+.||+ +|.++.+++.-+...+. +.....|..+
T Consensus 35 ngyR~Y~~~~---i~~l~~I~~lr~-~G~sl~~i~~l~~~~~~--~~~~~~l~~~ 83 (108)
T cd01107 35 TGYRYYSAEQ---LERLNRIKYLRD-LGFPLEEIKEILDADND--DELRKLLREK 83 (108)
T ss_pred CCccccCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHhcCCH--HHHHHHHHHH
Confidence 3567777654 556789999988 99999999987776553 6666666543
No 51
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=37.27 E-value=63 Score=26.80 Aligned_cols=51 Identities=24% Similarity=0.154 Sum_probs=37.5
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCC---HHHHHHHHHH
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWD---IEAALKELRK 115 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngD---iekAi~~LRk 115 (386)
...|.|+... ...+..|+.|-+.+|.++.++|+-|...++. -+.|..-|++
T Consensus 34 ~g~R~Yt~~d---i~~l~~I~~llr~~G~~l~~i~~~l~~~~~~~~~~~~~~~~~~~ 87 (99)
T cd04765 34 GGRRYYRPKD---VELLLLIKHLLYEKGYTIEGAKQALKEDGAAAIREEEAEERLPS 87 (99)
T ss_pred CCCeeeCHHH---HHHHHHHHHHHHHCCCCHHHHHHHHHhccccccchhhHHHHHHH
Confidence 3577888764 4556778887678999999999999988754 4556665653
No 52
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=36.05 E-value=35 Score=25.46 Aligned_cols=34 Identities=29% Similarity=0.431 Sum_probs=26.9
Q ss_pred eeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHH
Q 016590 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALV 100 (386)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~ 100 (386)
..|.|+-.. ...+..|+.||+ .|.++.+++++|.
T Consensus 35 g~r~y~~~d---l~~l~~i~~lr~-~g~~~~~i~~~l~ 68 (70)
T smart00422 35 GYRLYSDED---LERLRFIKRLKE-LGFSLEEIKELLE 68 (70)
T ss_pred CCEecCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHh
Confidence 456676543 455789999998 9999999999885
No 53
>cd07249 MMCE Methylmalonyl-CoA epimerase (MMCE). MMCE, also called methylmalonyl-CoA racemase (EC 5.1.99.1) interconverts (2R)-methylmalonyl-CoA and (2S)-methylmalonyl-CoA. MMCE has been found in bacteria, archaea, and in animals. In eukaryotes, MMCE is an essential enzyme in a pathway that converts propionyl-CoA to succinyl-CoA, and is important in the breakdown of odd-chain length fatty acids, branched-chain amino acids, and other metabolites. In bacteria, MMCE participates in the reverse pathway for propionate fermentation, glyoxylate regeneration, and the biosynthesis of polyketide antibiotics. MMCE is closely related to glyoxalase I and type I extradiol dioxygenases.
Probab=35.23 E-value=94 Score=24.91 Aligned_cols=45 Identities=29% Similarity=0.339 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHcccccccccccccccCCcEEEEecCCe--EEEEEEe
Q 016590 104 WDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESK--AAVIELN 149 (386)
Q Consensus 104 gDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~--aalvElN 149 (386)
.|++.+.+.|+++|..--. ...+....|.-....+..- |.+|||.
T Consensus 81 ~d~~~~~~~l~~~G~~~~~-~~~~~~~~g~~~~~~d~~~~~g~~iE~~ 127 (128)
T cd07249 81 DDIDAALARLKAQGVRLLQ-EGPRIGAGGKRVAFLHPKDTGGVLIELV 127 (128)
T ss_pred CCHHHHHHHHHHCCCeeec-cCCCccCCCCEEEEEecCCCceEEEEec
Confidence 4799999999999986433 2333556677666666555 9999984
No 54
>KOG1364 consensus Predicted ubiquitin regulatory protein, contains UAS and UBX domains [Posttranslational modification, protein turnover, chaperones]
Probab=34.27 E-value=76 Score=32.63 Aligned_cols=42 Identities=24% Similarity=0.367 Sum_probs=38.2
Q ss_pred HHHHHHHHHhcC-CCHHHHHHHHHhcCCCHHHHHHHHHHcccc
Q 016590 78 VNLIKQLREQTS-APMKDVKLALVDCDWDIEAALKELRKRGKV 119 (386)
Q Consensus 78 ~~lIK~LR~~Tg-agm~dCKkAL~e~ngDiekAi~~LRkkG~a 119 (386)
.+||++.+.-|+ ..+-..++=|..++||++.||.++++.|..
T Consensus 7 ~~lv~~fl~It~~~t~e~A~q~L~~~~~~le~ai~Lffe~~~~ 49 (356)
T KOG1364|consen 7 RALVSKFLAITVQQTVEIATQYLSAADWDLEAAINLFFEHGGF 49 (356)
T ss_pred HHHHHHHHHHhccccHHHHHHHHHhcCCcHHHHHHHHHHhccc
Confidence 489999999999 788889999999999999999999998763
No 55
>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=33.76 E-value=68 Score=25.72 Aligned_cols=50 Identities=16% Similarity=0.309 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHcccccccccccccccCCcEEEEecCCeEEEEEEecccc
Q 016590 104 WDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETD 153 (386)
Q Consensus 104 gDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalvElNCETD 153 (386)
.|+++..+.|++.|.........+....|-..+.+.+--|..|||.|.|.
T Consensus 70 ~~l~~~~~~l~~~G~~~~~~~~~~~~~~~~~~~~~~DP~G~~iel~~~~~ 119 (120)
T cd08362 70 ADVDALARQVAARGGTVLSEPGATDDPGGGYGFRFFDPDGRLIEFSADVE 119 (120)
T ss_pred HHHHHHHHHHHHcCCceecCCcccCCCCCceEEEEECCCCCEEEEEeccc
Confidence 47889999999999864432111222223334556667789999999873
No 56
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=33.53 E-value=78 Score=25.61 Aligned_cols=48 Identities=29% Similarity=0.391 Sum_probs=35.5
Q ss_pred eeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCC--HHHHHHHHH
Q 016590 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWD--IEAALKELR 114 (386)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngD--iekAi~~LR 114 (386)
..|.|+-.. ...+..|+.||. .|.++.+.++.|...+.+ .+...+.|.
T Consensus 34 g~r~y~~~d---v~~l~~i~~l~~-~g~~~~~i~~~l~~~~~~~~~~~~~~~~~ 83 (100)
T cd00592 34 GYRLYSEED---LERLRLIRRLRE-LGLSLKEIRELLDARDEELSLAALLALLD 83 (100)
T ss_pred CCcccCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHhcccccchHHHHHHHHH
Confidence 456677553 556789999999 999999999999887654 344444444
No 57
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=33.49 E-value=52 Score=32.73 Aligned_cols=32 Identities=19% Similarity=0.214 Sum_probs=28.9
Q ss_pred HHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 016590 84 LREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (386)
Q Consensus 84 LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (386)
+.+.||++--+|.++|++++|++..|+-.+..
T Consensus 242 ~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~~~ 273 (299)
T PRK05441 242 VMEATGVSREEAEAALEAADGSVKLAIVMILT 273 (299)
T ss_pred HHHHHCcCHHHHHHHHHHhCCCcHHHHHHHHh
Confidence 56679999999999999999999999998764
No 58
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=31.95 E-value=82 Score=27.33 Aligned_cols=51 Identities=22% Similarity=0.257 Sum_probs=36.4
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC-CC--HHHHHHHHHHc
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD-WD--IEAALKELRKR 116 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n-gD--iekAi~~LRkk 116 (386)
...|.|+... ...+.+|+.|| .+|.++.+.|+-|...+ ++ .....++|+++
T Consensus 34 ~gyR~Y~~~~---~~~l~~I~~lr-~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~ 87 (133)
T cd04787 34 NGYRLYSEKD---LSRLRFILSAR-QLGFSLKDIKEILSHADQGESPCPMVRRLIEQR 87 (133)
T ss_pred CCeeeCCHHH---HHHHHHHHHHH-HcCCCHHHHHHHHhhhccCCCcHHHHHHHHHHH
Confidence 3468888764 56689999998 49999999999988654 22 23445566543
No 59
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=30.50 E-value=85 Score=26.96 Aligned_cols=50 Identities=16% Similarity=0.171 Sum_probs=36.0
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC---CCHHHHHHHHHH
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD---WDIEAALKELRK 115 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n---gDiekAi~~LRk 115 (386)
...|.|+... ...+..|+.|| .+|.++.+.|+-|...+ .+.+.....|.+
T Consensus 34 ~g~R~Y~~~~---l~~l~~I~~lr-~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~ 86 (126)
T cd04785 34 GGYRLYGAAH---VERLRFIRRAR-DLGFSLEEIRALLALSDRPDRSCAEADAIARA 86 (126)
T ss_pred CCccccCHHH---HHHHHHHHHHH-HCCCCHHHHHHHHhhhhcCCCCHHHHHHHHHH
Confidence 3568888664 55688999998 89999999999887543 245555665543
No 60
>KOG4841 consensus Dolichol-phosphate mannosyltransferase, subunit 3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=29.71 E-value=21 Score=29.69 Aligned_cols=29 Identities=28% Similarity=0.384 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHhcCCCHHHHHHHHHHccc
Q 016590 90 APMKDVKLALVDCDWDIEAALKELRKRGK 118 (386)
Q Consensus 90 agm~dCKkAL~e~ngDiekAi~~LRkkG~ 118 (386)
|.+-||-+|-.|--+||.+|.+-|+.||.
T Consensus 65 ATfnDc~eA~veL~~~IkEAr~~L~rkg~ 93 (95)
T KOG4841|consen 65 ATFNDCEEAAVELQSQIKEARADLARKGL 93 (95)
T ss_pred eccCCcHHHHHHHHHHHHHHHHHHHHccC
Confidence 45789999999999999999999999986
No 61
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=29.33 E-value=94 Score=26.29 Aligned_cols=50 Identities=10% Similarity=0.079 Sum_probs=36.1
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCC---CHHHHHHHHHH
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDW---DIEAALKELRK 115 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ng---DiekAi~~LRk 115 (386)
...|.|+... ...+..|+.|| .+|.++.+.|.-|...+. +.+...+.|.+
T Consensus 34 ~gyR~Y~~~~---i~~l~~I~~lr-~~G~sl~eI~~~l~~~~~~~~~~~~~~~~l~~ 86 (123)
T cd04770 34 NGYRLYGEAD---LARLRFIRRAQ-ALGFSLAEIRELLSLRDDGAAPCAEVRALLEE 86 (123)
T ss_pred CCCccCCHHH---HHHHHHHHHHH-HCCCCHHHHHHHHHhhhcCCCCHHHHHHHHHH
Confidence 3578888664 56688999996 679999999999986542 34555555543
No 62
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=29.24 E-value=42 Score=25.20 Aligned_cols=34 Identities=29% Similarity=0.370 Sum_probs=27.4
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHH
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLAL 99 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL 99 (386)
...|.|+.+. ...+..|+.||+ .|.++-+++.-|
T Consensus 33 ~g~R~y~~~~---l~~l~~i~~l~~-~g~~l~~i~~~l 66 (67)
T cd04764 33 NGRRYYTDED---IELLKKIKTLLE-KGLSIKEIKEIL 66 (67)
T ss_pred CCceeeCHHH---HHHHHHHHHHHH-CCCCHHHHHHHh
Confidence 3557787664 566789999999 999999998876
No 63
>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=29.11 E-value=78 Score=25.73 Aligned_cols=49 Identities=12% Similarity=0.072 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHcccccccccccccccCCcEEEEecCCeEEEEEEecccc
Q 016590 104 WDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETD 153 (386)
Q Consensus 104 gDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalvElNCETD 153 (386)
.|++++.+.|+++|..--.. ..+....+--.+++.+--|-++|+.|+.|
T Consensus 73 ~dv~~~~~~l~~~G~~~~~~-~~~~~~~~~~~~~~~DPdG~~iE~~~~~~ 121 (122)
T cd07265 73 ADLEKLEARLQAYGVAVERI-PAGELPGVGRRVRFQLPSGHTMELYADKE 121 (122)
T ss_pred HHHHHHHHHHHHCCCcEEEc-ccCCCCCCceEEEEECCCCCEEEEEEecc
Confidence 48999999999999753221 11111111124566777889999999876
No 64
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=28.98 E-value=78 Score=25.90 Aligned_cols=47 Identities=21% Similarity=0.047 Sum_probs=34.2
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (386)
...|.|+... ...+..|+.||+ .|.++.+.|+.|...+. ...+.|.+
T Consensus 34 ~gyR~Y~~~~---l~~l~~I~~lr~-~G~~l~~I~~~l~~~~~---~~~~~l~~ 80 (96)
T cd04768 34 NGYRYYSYAQ---LYQLQFILFLRE-LGFSLAEIKELLDTEME---ELTAMLLE 80 (96)
T ss_pred CCeeeCCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHhcCcH---HHHHHHHH
Confidence 3578888764 556789999988 69999999999976543 34444443
No 65
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.91 E-value=1e+02 Score=26.33 Aligned_cols=37 Identities=16% Similarity=0.248 Sum_probs=30.4
Q ss_pred eeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC
Q 016590 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD 103 (386)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n 103 (386)
..|.|+... ...+..|+.||+ +|.++.+.|+-|....
T Consensus 33 gyR~Y~~~~---l~~l~~I~~lr~-~G~~L~~I~~~l~~~~ 69 (118)
T cd04776 33 QTRVYSRRD---RARLKLILRGKR-LGFSLEEIRELLDLYD 69 (118)
T ss_pred CccccCHHH---HHHHHHHHHHHH-CCCCHHHHHHHHHhhc
Confidence 578888764 566889999997 8999999999998753
No 66
>cd07258 PpCmtC_C C-terminal domain of 2,3-dihydroxy-p-cumate-3,4-dioxygenase (PpCmtC). This subfamily contains the C-terminal, 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 for 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=28.91 E-value=87 Score=27.12 Aligned_cols=54 Identities=11% Similarity=0.099 Sum_probs=39.4
Q ss_pred CCHHHHHHHHHHcccccccccccccccCCcEEEEecCCeEEEEEEeccccceecc
Q 016590 104 WDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFVSRN 158 (386)
Q Consensus 104 gDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalvElNCETDFVArN 158 (386)
-|++++.+.|++.|+... .-.+|....+...+++.+-.|.+||+.|+.+..+..
T Consensus 68 ~~v~~~~~~l~~~G~~~~-~~p~~~~~~~~~~~y~~DPdG~~iE~~~~~~~~~~~ 121 (141)
T cd07258 68 DDIGKALYRIKAHDVKVV-FGPGRHPPSDSIFFYFLDPDGITVEYSFGMEEFAEH 121 (141)
T ss_pred HHHHHHHHHHHHCCCcEE-eCCceECCCCCEEEEEECCCCCEEEEEeCcceeccc
Confidence 367889999999997532 123454444556678888889999999999887653
No 67
>KOG1715 consensus Mitochondrial/chloroplast ribosomal protein L12 [Translation, ribosomal structure and biogenesis]
Probab=27.93 E-value=86 Score=29.53 Aligned_cols=27 Identities=22% Similarity=0.383 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHhc
Q 016590 76 EQVNLIKQLREQTSAPMKDVKLALVDC 102 (386)
Q Consensus 76 ~~~~lIK~LR~~Tgagm~dCKkAL~e~ 102 (386)
+-++.||++|--||.|+.+.||=.+.+
T Consensus 131 ~KIkVIKEVR~~tgL~LkeAKklVE~a 157 (187)
T KOG1715|consen 131 SKIKVIKEVRALTGLGLKEAKKLVEKA 157 (187)
T ss_pred chhHHHHHHHHhccccHHHHHHHHHhc
Confidence 347899999999999999998755544
No 68
>cd07237 BphC1-RGP6_C_like C-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 C-terminal, 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 BphCs. 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 C-terminal repeat is represented in thi
Probab=27.52 E-value=94 Score=27.10 Aligned_cols=51 Identities=22% Similarity=0.291 Sum_probs=37.9
Q ss_pred CHHHHHHHHHHcccccccccccccccCCcEEEEecCCeEEEEEEecccccee
Q 016590 105 DIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFVS 156 (386)
Q Consensus 105 DiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalvElNCETDFVA 156 (386)
|++.+.+.|+++|..-... .+|....|...+++.+-.|.+||+.|.++-+.
T Consensus 86 ~l~~~~~~L~~~G~~v~~~-~~~~~~~~~~~~y~~DPdG~~iEl~~~~~~~~ 136 (154)
T cd07237 86 DVGRAYDRVRARGIPIAMT-LGRHTNDRMLSFYVRTPSGFAIEYGWGGRTVD 136 (154)
T ss_pred HHHHHHHHHHHcCCceecc-CCccCCCCcEEEEEECCCCcEEEeccCceEcc
Confidence 4667888899988754322 24444556777888888899999999998884
No 69
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=27.20 E-value=69 Score=31.84 Aligned_cols=32 Identities=16% Similarity=0.233 Sum_probs=28.8
Q ss_pred HHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 016590 84 LREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (386)
Q Consensus 84 LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (386)
+.+.||++.-+|.++|.+++|++..|+-.+..
T Consensus 237 ~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~~~~ 268 (291)
T TIGR00274 237 VRQATDCNKELAEQTLLAADQNVKLAIVMILS 268 (291)
T ss_pred HHHHhCcCHHHHHHHHHHhCCCcHHHHHHHHh
Confidence 56679999999999999999999999997764
No 70
>PF07442 Ponericin: Ponericin; InterPro: IPR010002 This family contains a number of ponericin peptides (approximately 30 residues long) from the venom of the predatory ant Pachycondyla goeldii (Ponerine ant). These peptides exhibit antibacterial and insecticidal properties, and may adopt an amphipathic alpha-helical structure in polar environments such as cell membranes [].; GO: 0005576 extracellular region
Probab=27.00 E-value=46 Score=21.84 Aligned_cols=18 Identities=28% Similarity=0.311 Sum_probs=13.1
Q ss_pred HHHHHHHHHHc--ccccccc
Q 016590 106 IEAALKELRKR--GKVLASK 123 (386)
Q Consensus 106 iekAi~~LRkk--G~akA~K 123 (386)
+.+|-+||+++ |+.+|+-
T Consensus 6 ~k~~~~wlkkkgpgi~kaal 25 (29)
T PF07442_consen 6 LKKAGEWLKKKGPGILKAAL 25 (29)
T ss_pred HHHHHHHHHhcCchHHHHHH
Confidence 56889999998 4556543
No 71
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=26.89 E-value=71 Score=22.19 Aligned_cols=18 Identities=28% Similarity=0.429 Sum_probs=15.2
Q ss_pred HHHHHhcCCCHHHHHHHH
Q 016590 96 KLALVDCDWDIEAALKEL 113 (386)
Q Consensus 96 KkAL~e~ngDiekAi~~L 113 (386)
..||..++||+.+|-+.|
T Consensus 11 ~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 11 RQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHhCCCHHHHHHHH
Confidence 579999999999998887
No 72
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=26.82 E-value=90 Score=27.76 Aligned_cols=50 Identities=14% Similarity=0.167 Sum_probs=36.2
Q ss_pred eeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCC-HHHHHHHHHHc
Q 016590 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWD-IEAALKELRKR 116 (386)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngD-iekAi~~LRkk 116 (386)
..|.|+... ...+..|+.|| .+|.++.+.|.=|...++. -+...++|.++
T Consensus 42 gyR~Y~~~~---l~rl~~I~~lr-~~G~sL~eI~~ll~~~~~~~~~~~~~ll~~k 92 (144)
T PRK13752 42 SIRRYGEAD---VTRVRFVKSAQ-RLGFSLDEIAELLRLEDGTHCEEASSLAEHK 92 (144)
T ss_pred CCeecCHHH---HHHHHHHHHHH-HcCCCHHHHHHHHhccCCCCHHHHHHHHHHH
Confidence 368888764 56689999999 8999999999877544432 35566666543
No 73
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=26.53 E-value=68 Score=27.57 Aligned_cols=21 Identities=29% Similarity=0.463 Sum_probs=17.2
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHH
Q 016590 93 KDVKLALVDCDWDIEAALKELRK 115 (386)
Q Consensus 93 ~dCKkAL~e~ngDiekAi~~LRk 115 (386)
...++++ -+||++.|++|+.+
T Consensus 6 ~~I~~~I--~~g~i~~Ai~w~~~ 26 (145)
T PF10607_consen 6 KKIRQAI--LNGDIDPAIEWLNE 26 (145)
T ss_pred HHHHHHH--HcCCHHHHHHHHHH
Confidence 3556777 68999999999986
No 74
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=26.16 E-value=62 Score=36.07 Aligned_cols=35 Identities=31% Similarity=0.242 Sum_probs=30.5
Q ss_pred HHHHHHHhcCCCHHHHHHHHHhc-CCCHHHHHHHHHH
Q 016590 80 LIKQLREQTSAPMKDVKLALVDC-DWDIEAALKELRK 115 (386)
Q Consensus 80 lIK~LR~~Tgagm~dCKkAL~e~-ngDiekAi~~LRk 115 (386)
.|.||=+ .|.|+-+|++||=-+ |.|.|.|..||-+
T Consensus 574 ~i~qL~~-MGFp~eac~rAly~tgN~~aEaA~NWl~~ 609 (763)
T KOG0944|consen 574 VISQLVE-MGFPEEACRRALYYTGNSGAEAASNWLME 609 (763)
T ss_pred HHHHHHH-cCCCHHHHHHHHhhhcCccHHHHHHHHHH
Confidence 5666654 599999999999999 8999999999986
No 75
>cd08353 Glo_EDI_BRP_like_7 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 structures of this family demonstrate domain swapping, which is shared by glyoxalase I and antibiotic resistance proteins.
Probab=25.66 E-value=1.1e+02 Score=25.49 Aligned_cols=44 Identities=25% Similarity=0.248 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHcccccccccccccccCCcEEEEecCCeEEEEEEe
Q 016590 104 WDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELN 149 (386)
Q Consensus 104 gDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalvElN 149 (386)
.|++++.+.|+++|....... .....|.-.+++.+..|.+|||-
T Consensus 96 ~d~d~~~~~l~~~G~~~~~~~--~~~~~~~r~~~~~DPdG~~iEl~ 139 (142)
T cd08353 96 DDIDARVARLRKHGAELVGEV--VQYENSYRLCYIRGPEGILIELA 139 (142)
T ss_pred CCHHHHHHHHHHCCCceeCCc--eecCCCeEEEEEECCCCCEEEee
Confidence 489999999999998765432 22334555566667788888873
No 76
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=25.59 E-value=1.2e+02 Score=25.92 Aligned_cols=49 Identities=12% Similarity=0.133 Sum_probs=35.0
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC-C--CHHHHHHHHH
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD-W--DIEAALKELR 114 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n-g--DiekAi~~LR 114 (386)
...|.|+... ...+..|+.|| ..|.++.+.|+-|...+ + +.+.....|.
T Consensus 34 ~gyR~Y~~~~---l~~l~~I~~lr-~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~ 85 (127)
T cd04784 34 NNYRLYDEEH---LERLLFIRRCR-SLDMSLDEIRTLLQLQDDPEASCAEVNALID 85 (127)
T ss_pred CCCeecCHHH---HHHHHHHHHHH-HcCCCHHHHHHHHHhhhcCCCcHHHHHHHHH
Confidence 3568888764 55678999998 56999999999887543 2 3455555554
No 77
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=25.56 E-value=54 Score=23.52 Aligned_cols=15 Identities=27% Similarity=0.136 Sum_probs=12.9
Q ss_pred CCCHHHHHHHHHHcc
Q 016590 103 DWDIEAALKELRKRG 117 (386)
Q Consensus 103 ngDiekAi~~LRkkG 117 (386)
.||++.|++|+.+..
T Consensus 14 ~g~~~~a~~~~~~~~ 28 (58)
T smart00668 14 KGDWDEALEWLSSLK 28 (58)
T ss_pred cCCHHHHHHHHHHcC
Confidence 799999999998654
No 78
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=24.96 E-value=1.3e+02 Score=24.71 Aligned_cols=48 Identities=23% Similarity=0.317 Sum_probs=35.9
Q ss_pred eeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHc
Q 016590 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKR 116 (386)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkk 116 (386)
..|.|+... ...+..|+.||+ .|.++.+.|.-|.. .+.+...+.|.++
T Consensus 35 gyR~Y~~~~---~~~l~~I~~lr~-~G~~l~eI~~~l~~--~~~~~~~~~l~~~ 82 (97)
T cd04782 35 GYRYYTLEQ---FEQLDIILLLKE-LGISLKEIKDYLDN--RNPDELIELLKKQ 82 (97)
T ss_pred CCccCCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHhc--CCHHHHHHHHHHH
Confidence 467777653 556789999986 69999999988764 3677777777654
No 79
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=24.88 E-value=1.3e+02 Score=26.32 Aligned_cols=50 Identities=12% Similarity=0.283 Sum_probs=35.5
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC--CCHHHHHHHHHH
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD--WDIEAALKELRK 115 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n--gDiekAi~~LRk 115 (386)
...|.|+... ...+..|+.||+ .|.++.+.|+-|.... .+.+...+.|.+
T Consensus 34 ~gyR~Y~~~~---v~~l~~I~~lr~-~GfsL~eI~~ll~~~~~~~~~~~~~~~l~~ 85 (131)
T cd04786 34 NGYRDYPPET---VWVLEIISSAQQ-AGFSLDEIRQLLPADASNWQHDELLAALER 85 (131)
T ss_pred CCCeecCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHhcccCCCCHHHHHHHHHH
Confidence 4567887653 566899999987 9999999999887543 344555555543
No 80
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=24.79 E-value=1.3e+02 Score=24.13 Aligned_cols=35 Identities=23% Similarity=0.366 Sum_probs=29.0
Q ss_pred eeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHH
Q 016590 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALV 100 (386)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~ 100 (386)
..|.|+... ...+..|+.|++..|.++.+++..|.
T Consensus 35 g~R~y~~~d---v~~l~~i~~L~~d~g~~l~~i~~~l~ 69 (91)
T cd04766 35 GTRRYSERD---IERLRRIQRLTQELGVNLAGVKRILE 69 (91)
T ss_pred CCeeECHHH---HHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 456777654 45578999999999999999999996
No 81
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=24.30 E-value=1.4e+02 Score=25.91 Aligned_cols=50 Identities=12% Similarity=0.136 Sum_probs=35.9
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhc----CCCHHHHHHHHHH
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDC----DWDIEAALKELRK 115 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~----ngDiekAi~~LRk 115 (386)
...|.|+... ...+..|+.||+ .|.++.+.|.-|... +.+.+...+.|.+
T Consensus 35 ~gyR~Y~~~~---l~~l~~I~~lr~-~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~ 88 (131)
T TIGR02043 35 SGYRLYTDED---QKRLRFILKAKE-LGFTLDEIKELLSIKLDATEHSCAEVKAIVDA 88 (131)
T ss_pred CCceecCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHHhhccCCCCCHHHHHHHHHH
Confidence 4568888653 556889999986 899999999988743 2345555565554
No 82
>PF10178 DUF2372: Uncharacterised conserved protein (DUF2372); InterPro: IPR018788 Proteasome assembly chaperone 3 (PSMG3) promotes assembly of the 20S proteasome []. It may cooperate with PSMG1-PSMG2 heterodimers to orchestrate the correct assembly of proteasomes.; PDB: 2Z5E_A.
Probab=24.04 E-value=2.4e+02 Score=23.37 Aligned_cols=36 Identities=25% Similarity=0.249 Sum_probs=19.5
Q ss_pred hhhhHHHHHHHHh---hhcCCcc--cccCCCCHHHHHHHHH
Q 016590 274 PLKRVGSELAMHI---VAQKPLF--LTKELVSADALENERE 309 (386)
Q Consensus 274 ~~~~~ak~iAmHI---aA~~P~~--ls~~~Vp~~~le~Er~ 309 (386)
.+.-.||+|+-|| ...+|.- |.-.+.+.+.+..-.+
T Consensus 43 ~l~v~Ar~L~~~i~~~~~~r~lllalgLkd~s~e~lk~i~~ 83 (90)
T PF10178_consen 43 LLHVYARQLIEFISQEGSNRPLLLALGLKDHSPETLKAIVE 83 (90)
T ss_dssp HHHHHHHHHHHHHHHHTTT-EEEEEEE-SS--HHHHHHHHH
T ss_pred HHHHHHHHHHHHHhccCCCCcEEEEEeccCCCHHHHHHHHH
Confidence 3456799999999 4455553 4445555555444333
No 83
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.03 E-value=1.3e+02 Score=25.36 Aligned_cols=49 Identities=18% Similarity=0.270 Sum_probs=35.2
Q ss_pred eeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC------CCHHHHHHHHHH
Q 016590 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD------WDIEAALKELRK 115 (386)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n------gDiekAi~~LRk 115 (386)
..|.|+... ...+..|+.||+ +|.++.+.|.-|.... .....-.+.|.+
T Consensus 34 g~R~Y~~~~---~~~l~~I~~lr~-~G~sl~eI~~~l~~~~~~~~~~~~~~~~~~~l~~ 88 (112)
T cd01282 34 GYRDYDEAA---VDRVRQIRRLLA-AGLTLEEIREFLPCLRGGEPTFRPCPDLLAVLRR 88 (112)
T ss_pred CCeecCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHHHhhCCCccCCccHHHHHHHHH
Confidence 468887653 556889999985 9999999999887643 234455566654
No 84
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=23.99 E-value=1.3e+02 Score=25.65 Aligned_cols=49 Identities=14% Similarity=0.180 Sum_probs=36.6
Q ss_pred eeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC-CCHHHHHHHHHH
Q 016590 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD-WDIEAALKELRK 115 (386)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n-gDiekAi~~LRk 115 (386)
..|.|+... ...+..|+.|| .+|.++.+.|+-|.... ++.+.....|..
T Consensus 35 gyR~Y~~~~---l~~l~~I~~lr-~~G~sL~eI~~~l~~~~~~~~~~~~~~l~~ 84 (126)
T cd04783 35 GYRRYPEET---VTRLRFIKRAQ-ELGFTLDEIAELLELDDGTDCSEARELAEQ 84 (126)
T ss_pred CCeecCHHH---HHHHHHHHHHH-HcCCCHHHHHHHHhcccCCCHHHHHHHHHH
Confidence 467887664 55678999997 59999999999997664 356666666653
No 85
>CHL00102 rps20 ribosomal protein S20
Probab=23.21 E-value=73 Score=26.64 Aligned_cols=38 Identities=16% Similarity=0.197 Sum_probs=26.3
Q ss_pred HHHHHHHHHh-----cCCCHHHHHHHHHHcccccccccccccccCCcE
Q 016590 92 MKDVKLALVD-----CDWDIEAALKELRKRGKVLASKKSSRTATEGLL 134 (386)
Q Consensus 92 m~dCKkAL~e-----~ngDiekAi~~LRkkG~akA~Kka~R~a~EGlV 134 (386)
|-.|.+|+++ ..||.+.|.++|.+ |.+.-|+.+.-|+|
T Consensus 32 iKk~~~ai~~~~~~~~~~d~~~a~~~l~~-----a~s~iDkaa~KGvi 74 (93)
T CHL00102 32 IKKYLKNLEDYKTSPNSNNKKKVQETLSS-----VYSKIDKAVKKGVF 74 (93)
T ss_pred HHHHHHHHHhhcccCCcccHHHHHHHHHH-----HHHHHHHHHHcCCc
Confidence 5567777776 23899999999985 55555555555554
No 86
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=23.14 E-value=1.8e+02 Score=25.11 Aligned_cols=38 Identities=11% Similarity=0.107 Sum_probs=30.2
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD 103 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n 103 (386)
...|.|+... ...+.+|+.||. +|.|+.++|.-|...+
T Consensus 37 ~gyR~Y~~~~---l~rL~~I~~lr~-~G~~L~eI~~ll~~~~ 74 (120)
T TIGR02054 37 SGYGIFDDAS---LQRLRFVRAAFE-AGIGLGELARLCRALD 74 (120)
T ss_pred CCCeeCCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHHhhc
Confidence 4578888664 556889999998 9999999998776544
No 87
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=23.02 E-value=64 Score=34.44 Aligned_cols=36 Identities=31% Similarity=0.487 Sum_probs=31.0
Q ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHHHccccccccc
Q 016590 89 SAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKK 124 (386)
Q Consensus 89 gagm~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kk 124 (386)
|.--.|.|-||-.|+||+|-|++++.++-..+|.++
T Consensus 314 GfeesdaRlaLRsc~g~Vd~AvqfI~erre~laq~R 349 (568)
T KOG2561|consen 314 GFEESDARLALRSCNGDVDSAVQFIIERREKLAQKR 349 (568)
T ss_pred CCCchHHHHHHHhccccHHHHHHHHHHHHHHHHHHH
Confidence 555579999999999999999999988777777766
No 88
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=22.80 E-value=1.9e+02 Score=20.52 Aligned_cols=29 Identities=28% Similarity=0.444 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHH
Q 016590 76 EQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELR 114 (386)
Q Consensus 76 ~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LR 114 (386)
+.++.+++|=++||.|+.+- +++|++.+-
T Consensus 12 el~~~L~~ls~~t~i~~S~L----------l~eAle~~l 40 (44)
T PF12651_consen 12 ELYEKLKELSEETGIPKSKL----------LREALEDYL 40 (44)
T ss_pred HHHHHHHHHHHHHCCCHHHH----------HHHHHHHHH
Confidence 56788999999999999875 677777653
No 89
>COG1437 CyaB Adenylate cyclase, class 2 (thermophilic) [Nucleotide transport and metabolism]
Probab=22.50 E-value=63 Score=30.20 Aligned_cols=81 Identities=15% Similarity=0.111 Sum_probs=53.5
Q ss_pred CCHHHHHHHHHhc---CCCHHHHHHHHHHccccccc--ccccccccCCcEEEEecC--CeEEEEEEeccccceecchHHH
Q 016590 90 APMKDVKLALVDC---DWDIEAALKELRKRGKVLAS--KKSSRTATEGLLALAQNE--SKAAVIELNCETDFVSRNEIFQ 162 (386)
Q Consensus 90 agm~dCKkAL~e~---ngDiekAi~~LRkkG~akA~--Kka~R~a~EGlV~~~~~~--~~aalvElNCETDFVArN~~F~ 162 (386)
..|-.|.|+..|. ..|+++|.++|++-|...+. ||..+.=.-|-+.+.+|. +-|-.+||-++||+-.-=+.=.
T Consensus 69 p~ld~~~k~r~E~E~~v~D~~~~~~il~~LGF~~~~~VkK~R~iY~~~~~~i~lD~VegLG~F~EIE~~~~d~~e~~~~~ 148 (178)
T COG1437 69 PKLDRESKTREEIEIEVSDVEKALEILKRLGFKEVAVVKKTREIYKVGNVTIELDAVEGLGDFLEIEVMVDDENEIDGAK 148 (178)
T ss_pred ccccccccceeeEEEEeCCHHHHHHHHHHcCCceeeEEEEEEEEEeeCCEEEEEecccCCcccEEEEEecCCchhhHHHH
Confidence 3455677777776 37999999999999987653 333344344446666653 5799999999999754433333
Q ss_pred HHHHHHHH
Q 016590 163 YLALALAK 170 (386)
Q Consensus 163 ~la~~ia~ 170 (386)
.-+.+++.
T Consensus 149 ~~~~~i~~ 156 (178)
T COG1437 149 EEIEEIAR 156 (178)
T ss_pred HHHHHHHH
Confidence 33444443
No 90
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=22.12 E-value=1.6e+02 Score=25.94 Aligned_cols=51 Identities=8% Similarity=0.147 Sum_probs=37.0
Q ss_pred eeeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhc----CCCHHHHHHHHHHc
Q 016590 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDC----DWDIEAALKELRKR 116 (386)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~----ngDiekAi~~LRkk 116 (386)
...|.|+... ...+..|+.||+ +|.++.+.+.-|... +.+.+...+.|.++
T Consensus 35 ~gyR~Y~~~~---l~~l~~I~~lr~-~G~sL~eI~~~l~~~~~~~~~~~~~~~~~l~~~ 89 (140)
T PRK09514 35 GGYRLYTEQD---LQRLRFIRRAKQ-LGFTLEEIRELLSIRLDPEHHTCQEVKGIVDEK 89 (140)
T ss_pred CCCeeeCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHHhcccCCcCCHHHHHHHHHHH
Confidence 3568888664 556789999986 699999999988643 23566666666643
No 91
>cd05007 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.
Probab=22.09 E-value=49 Score=32.11 Aligned_cols=29 Identities=21% Similarity=0.302 Sum_probs=25.1
Q ss_pred HHHHHhcCCCHHHHHHHHHhcCCCHHHHH
Q 016590 82 KQLREQTSAPMKDVKLALVDCDWDIEAAL 110 (386)
Q Consensus 82 K~LR~~Tgagm~dCKkAL~e~ngDiekAi 110 (386)
.=+.+.||++--+|.++|.+++|++..|+
T Consensus 227 ~i~~~~~~~~~~~a~~~l~~~~~~~k~a~ 255 (257)
T cd05007 227 RIVMEATGVSRDEAEAALEQAGGDVKTAI 255 (257)
T ss_pred HHHHHHHCcCHHHHHHHHHHhCCCceeee
Confidence 33567799999999999999999998876
No 92
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=21.41 E-value=1.1e+02 Score=30.40 Aligned_cols=34 Identities=18% Similarity=0.223 Sum_probs=29.1
Q ss_pred HHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 016590 82 KQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (386)
Q Consensus 82 K~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (386)
.=+.+-||++.-+|.++|.+++|++..|+-.+..
T Consensus 236 ~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~~~~ 269 (296)
T PRK12570 236 RIVMQATGCSEDEAKELLKESDNDVKLAILMILT 269 (296)
T ss_pred HHHHHHHCcCHHHHHHHHHHhCCccHHHHHHHHh
Confidence 3355669999999999999999999999987654
No 93
>cd08352 Glo_EDI_BRP_like_1 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=21.32 E-value=1.6e+02 Score=23.20 Aligned_cols=43 Identities=26% Similarity=0.232 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHcccccccccccccccCCcEEEEecCCeEEEEEE
Q 016590 104 WDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIEL 148 (386)
Q Consensus 104 gDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalvEl 148 (386)
.|++.+.+.|++.|...... .+....|.-..+..+..|.++||
T Consensus 81 ~d~~~~~~~l~~~G~~~~~~--~~~~~~~~~~~~~~DP~G~~iEl 123 (125)
T cd08352 81 EDIEAAVKHLKAKGVEVEPI--RVDEFTGKRFTFFYDPDGLPLEL 123 (125)
T ss_pred CCHHHHHHHHHHcCCccccc--cccCCCceEEEEEECCCCCEEEe
Confidence 57999999999999865432 23344565556666667888887
No 94
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.25 E-value=1.7e+02 Score=24.17 Aligned_cols=50 Identities=10% Similarity=0.136 Sum_probs=34.8
Q ss_pred eeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC--C-----CHHHHHHHHHHc
Q 016590 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD--W-----DIEAALKELRKR 116 (386)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n--g-----DiekAi~~LRkk 116 (386)
..|.|+... ...+..|+.||+ +|.++.+.|.-|...+ + +.+...++|.++
T Consensus 33 g~r~Y~~~~---~~~l~~I~~lr~-~G~sL~eI~~~l~~~~~~~~~~~~~~~~~~~~l~~~ 89 (107)
T cd04777 33 GQYFFDEKC---QDDLEFILELKG-LGFSLIEIQKIFSYKRLTKSRTHEDQDYYKSFLKNK 89 (107)
T ss_pred CccccCHHH---HHHHHHHHHHHH-CCCCHHHHHHHHHhcccccccchhhHHHHHHHHHHH
Confidence 356676653 556889999998 7999999999887643 2 234456666643
No 95
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.20 E-value=1.7e+02 Score=24.70 Aligned_cols=49 Identities=16% Similarity=0.198 Sum_probs=36.3
Q ss_pred eeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCC----CHHHHHHHHHH
Q 016590 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDW----DIEAALKELRK 115 (386)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ng----DiekAi~~LRk 115 (386)
..|.|+... ...+..|+.||+ .|.++.+-|.-|...+. +.+...+.|.+
T Consensus 34 ~yR~Y~~~d---~~~l~~I~~lr~-~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~ 86 (116)
T cd04769 34 NYRVYDAQH---VECLRFIKEARQ-LGFTLAELKAIFAGHEGRAVLPWPHLQQALED 86 (116)
T ss_pred CceeeCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHhccccCCcCcHHHHHHHHHH
Confidence 568887664 556789999987 99999999998887653 34555555553
No 96
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=21.10 E-value=34 Score=37.07 Aligned_cols=27 Identities=15% Similarity=0.042 Sum_probs=24.1
Q ss_pred hcCCCHHHHHHHHHhcCCCHHHHHHHH
Q 016590 87 QTSAPMKDVKLALVDCDWDIEAALKEL 113 (386)
Q Consensus 87 ~Tgagm~dCKkAL~e~ngDiekAi~~L 113 (386)
+-|.....|+|||.+.|+|++.+++|.
T Consensus 630 e~Gln~n~~Rkal~~~n~d~~r~V~w~ 656 (749)
T COG5207 630 ENGLNPNLCRKALMDMNTDSKRRVVWC 656 (749)
T ss_pred HcCCCHHHHHHHHHHccCCchheEEEE
Confidence 367888999999999999999998885
No 97
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=20.78 E-value=1.4e+02 Score=21.76 Aligned_cols=32 Identities=19% Similarity=0.284 Sum_probs=22.7
Q ss_pred HHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHccccccccccc
Q 016590 82 KQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSS 126 (386)
Q Consensus 82 K~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kka~ 126 (386)
.+|++.||+. .-.+-++||++.|+---....|
T Consensus 6 ~El~elTG~k-------------~~~~Q~~~L~~~Gi~~~~~~~G 37 (47)
T PF13986_consen 6 EELQELTGYK-------------RPSKQIRWLRRNGIPFVVRADG 37 (47)
T ss_pred HHHHHHHCCC-------------CHHHHHHHHHHCCCeeEECCCC
Confidence 3788889976 4556689999999865444333
No 98
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.72 E-value=1.9e+02 Score=24.22 Aligned_cols=50 Identities=28% Similarity=0.296 Sum_probs=35.9
Q ss_pred eeccccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC-C--CHHHHHHHHHHc
Q 016590 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD-W--DIEAALKELRKR 116 (386)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n-g--DiekAi~~LRkk 116 (386)
..|.|+... ...+..|+.||+ .|.|+.+.|+-|.... + +.+...++|..+
T Consensus 35 gyR~Y~~~~---l~~l~~I~~lr~-~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~ 87 (113)
T cd01109 35 GIRDFTEED---LEWLEFIKCLRN-TGMSIKDIKEYAELRREGDSTIPERLELLEEH 87 (113)
T ss_pred CCccCCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHHHHccCCccHHHHHHHHHHH
Confidence 457777653 566889999985 8999999999887542 3 356666777643
No 99
>TIGR03213 23dbph12diox 2,3-dihydroxybiphenyl 1,2-dioxygenase. Members of this protein family all have activity as 2,3-dihydroxybiphenyl 1,2-dioxygenase, the third enzyme of a pathway for biphenyl degradation. Many of the extradiol ring-cleaving dioxygenases, to which these proteins belong, act on a range of related substrates. Note that some members of this family may be found operons for toluene or naphthalene degradation, where other activities of the same enzyme may be more significant; the trusted cutoff for this model is set relatively high to exclude most such instances.
Probab=20.14 E-value=1.6e+02 Score=28.24 Aligned_cols=49 Identities=14% Similarity=0.264 Sum_probs=37.2
Q ss_pred CHHHHHHHHHHcccccccccccccccCCcEEEEecCCeEEEEEEeccccce
Q 016590 105 DIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFV 155 (386)
Q Consensus 105 DiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalvElNCETDFV 155 (386)
+++++.+.|+++|+ . ....+|...-|-..+++.+-.|.++|+.|.=+.+
T Consensus 219 ~v~~~~~~l~~~G~-~-~~~~~r~~~~~~~~~y~~DP~G~~iE~~~~~~~~ 267 (286)
T TIGR03213 219 DVGLALDRVDADGI-V-ASTLGRHTNDHMVSFYVATPSGWLVEYGWGARVV 267 (286)
T ss_pred HHHHHHHHHHHCCC-E-EecCCcCCCCCeEEEEEECCCCcEEEeecCcEEe
Confidence 45559999999998 3 3345676666777888888889999999975544
No 100
>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=20.14 E-value=1.7e+02 Score=23.00 Aligned_cols=47 Identities=17% Similarity=0.282 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHcccccccccccccccCCcEEEEecCCeEEEEEEeccc
Q 016590 104 WDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCET 152 (386)
Q Consensus 104 gDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalvElNCET 152 (386)
-|++.+.+.|+++|...-.. ..+....|. .+.+.+-.|..+||.|.|
T Consensus 66 ~d~~~~~~~l~~~G~~~~~~-~~~~~~~~~-~~~~~DPdG~~iEi~~~~ 112 (113)
T cd08345 66 EEFDEYTERLKALGVEMKPE-RPRVQGEGR-SIYFYDPDGHLLELHAGT 112 (113)
T ss_pred HHHHHHHHHHHHcCCccCCC-ccccCCCce-EEEEECCCCCEEEEEeCc
Confidence 47899999999999864321 112222343 344555678999999976
No 101
>cd08347 PcpA_C_like C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins. The C-terminal domain of Sphingobium chlorophenolicum (formerly Sphingomonas chlorophenolica) 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins. PcpA is a key enzyme in the pentachlorophenol (PCP) degradation pathway, catalyzing the conversion of 2,6-dichloro-p-hydroquinone to 2-chloromaleylacetate. This domain 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=20.13 E-value=1e+02 Score=27.18 Aligned_cols=59 Identities=17% Similarity=0.094 Sum_probs=40.3
Q ss_pred CCHHHHHHHHHHcccccccccccccccCCcEEEEecCCeEEEEEEeccccceecchHHHHHHH
Q 016590 104 WDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFVSRNEIFQYLAL 166 (386)
Q Consensus 104 gDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalvElNCETDFVArN~~F~~la~ 166 (386)
.|++.+.+.|+++|+... .-.++ .+.-.++..+-.|.+||+.|.++...=.+.|-.|..
T Consensus 77 ~dvd~~~~~L~~~Gv~~~-~~~~~---~~~~s~yf~DPdG~~iEl~~~~~~~~~~~~~~~~~~ 135 (157)
T cd08347 77 EELEAWKERLEALGLPVS-GIVDR---FYFKSLYFREPGGILFEIATDGPGFTVDEPLEELGE 135 (157)
T ss_pred HHHHHHHHHHHHCCCCcc-ccccc---ccEEEEEEECCCCcEEEEEECCCCccccCChhHcCC
Confidence 468999999999998532 11112 222356677778999999999987766666655543
Done!