Query 015807
Match_columns 400
No_of_seqs 169 out of 1147
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 09:45:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015807.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015807hhsearch_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 1.6E-98 3E-103 726.2 31.4 288 78-400 6-295 (296)
2 TIGR00116 tsf translation elon 100.0 6.9E-97 2E-101 722.5 32.7 286 78-400 5-290 (290)
3 PRK09377 tsf elongation factor 100.0 6.6E-96 1E-100 715.6 32.9 284 78-399 6-289 (290)
4 PRK12332 tsf elongation factor 100.0 7.7E-69 1.7E-73 500.1 22.7 192 78-383 5-198 (198)
5 CHL00098 tsf elongation factor 100.0 1.4E-68 3E-73 498.7 22.0 195 78-386 2-199 (200)
6 PF00889 EF_TS: Elongation fac 100.0 1.5E-67 3.2E-72 499.8 22.1 221 129-382 1-221 (221)
7 KOG1071 Mitochondrial translat 100.0 2.7E-63 5.9E-68 481.9 15.6 272 76-386 45-335 (340)
8 KOG1071 Mitochondrial translat 98.6 2.8E-07 6E-12 91.4 10.2 134 238-399 103-237 (340)
9 PF00627 UBA: UBA/TS-N domain; 98.3 1.3E-06 2.9E-11 60.6 5.2 34 79-113 4-37 (37)
10 PRK06369 nac nascent polypepti 97.3 0.00041 8.9E-09 60.2 5.0 37 79-115 78-114 (115)
11 smart00165 UBA Ubiquitin assoc 97.2 0.0009 1.9E-08 45.9 4.9 34 79-113 3-36 (37)
12 TIGR00264 alpha-NAC-related pr 97.1 0.00069 1.5E-08 58.8 4.8 36 79-114 80-115 (116)
13 cd00194 UBA Ubiquitin Associat 97.0 0.0013 2.9E-08 45.2 4.9 35 79-114 3-37 (38)
14 CHL00098 tsf elongation factor 96.5 0.0047 1E-07 58.5 5.5 43 239-289 55-97 (200)
15 TIGR00116 tsf translation elon 96.3 0.024 5.2E-07 56.6 9.5 88 238-380 57-145 (290)
16 COG0264 Tsf Translation elonga 96.2 0.023 5E-07 56.6 8.6 92 239-382 59-151 (296)
17 PRK09377 tsf elongation factor 95.5 0.079 1.7E-06 53.0 9.4 88 238-380 58-146 (290)
18 PF14555 UBA_4: UBA-like domai 94.4 0.086 1.9E-06 37.6 4.6 36 79-114 2-37 (43)
19 PF03943 TAP_C: TAP C-terminal 93.1 0.075 1.6E-06 39.7 2.4 37 79-115 2-38 (51)
20 PRK12332 tsf elongation factor 92.9 0.15 3.2E-06 48.4 4.7 30 207-236 166-195 (198)
21 smart00804 TAP_C C-terminal do 92.3 0.45 9.7E-06 37.2 5.9 40 76-115 11-50 (63)
22 COG1308 EGD2 Transcription fac 91.8 0.32 7E-06 42.7 5.0 35 79-113 86-120 (122)
23 PF00889 EF_TS: Elongation fac 91.6 0.3 6.6E-06 46.9 5.2 87 239-380 3-90 (221)
24 PF02845 CUE: CUE domain; Int 86.6 2.1 4.6E-05 30.2 5.2 37 79-115 3-40 (42)
25 PF00542 Ribosomal_L12: Riboso 85.5 0.71 1.5E-05 36.5 2.6 27 77-103 13-39 (68)
26 PRK06771 hypothetical protein; 82.0 1.4 3E-05 37.1 3.0 23 78-100 69-91 (93)
27 smart00546 CUE Domain that may 79.4 6.4 0.00014 27.7 5.4 37 79-115 4-41 (43)
28 PF08938 HBS1_N: HBS1 N-termin 77.8 1 2.2E-05 36.4 0.8 46 79-124 30-78 (79)
29 PF06972 DUF1296: Protein of u 72.4 12 0.00025 29.1 5.4 38 78-115 6-44 (60)
30 COG4008 Predicted metal-bindin 69.4 12 0.00026 33.4 5.5 42 75-117 94-152 (153)
31 TIGR00855 L12 ribosomal protei 69.3 5.7 0.00012 35.3 3.5 29 77-105 71-99 (126)
32 PRK00157 rplL 50S ribosomal pr 64.7 7.9 0.00017 34.2 3.5 27 77-103 68-94 (123)
33 cd00387 Ribosomal_L7_L12 Ribos 64.1 9.7 0.00021 33.8 4.0 42 59-105 60-101 (127)
34 PF08285 DPM3: Dolichol-phosph 64.0 2.2 4.8E-05 35.7 -0.0 28 91-118 62-89 (91)
35 cd04772 HTH_TioE_rpt1 First He 63.1 12 0.00027 31.1 4.3 50 62-116 34-84 (99)
36 CHL00083 rpl12 ribosomal prote 61.1 14 0.0003 33.1 4.4 42 58-104 62-103 (131)
37 COG0222 RplL Ribosomal protein 61.0 9.3 0.0002 33.7 3.2 38 60-103 58-95 (124)
38 KOG0944 Ubiquitin-specific pro 51.8 14 0.0003 41.1 3.5 28 88-115 645-672 (763)
39 COG0789 SoxR Predicted transcr 50.4 15 0.00033 31.0 2.9 40 62-105 34-73 (124)
40 cd01106 HTH_TipAL-Mta Helix-Tu 50.1 28 0.0006 28.9 4.4 47 63-116 35-81 (103)
41 cd04773 HTH_TioE_rpt2 Second H 47.1 36 0.00077 28.8 4.6 51 62-116 34-86 (108)
42 cd01105 HTH_GlnR-like Helix-Tu 46.5 37 0.0008 27.6 4.4 50 63-117 36-85 (88)
43 PF07442 Ponericin: Ponericin; 44.6 20 0.00043 23.6 2.0 19 106-124 6-26 (29)
44 cd04780 HTH_MerR-like_sg5 Heli 44.2 25 0.00055 29.1 3.2 36 63-101 35-70 (95)
45 cd04763 HTH_MlrA-like Helix-Tu 40.4 26 0.00057 26.7 2.5 34 62-99 34-67 (68)
46 cd04788 HTH_NolA-AlbR Helix-Tu 40.3 44 0.00096 27.5 4.1 48 62-116 34-81 (96)
47 cd01107 HTH_BmrR Helix-Turn-He 38.9 46 0.001 28.0 4.0 49 62-116 35-83 (108)
48 PF11626 Rap1_C: TRF2-interact 38.9 58 0.0012 26.6 4.5 34 81-115 1-34 (87)
49 PF13411 MerR_1: MerR HTH fami 38.6 20 0.00043 27.1 1.6 34 64-101 35-68 (69)
50 smart00422 HTH_MERR helix_turn 36.3 37 0.00079 25.5 2.8 34 63-100 35-68 (70)
51 cd04765 HTH_MlrA-like_sg2 Heli 33.7 80 0.0017 26.3 4.6 51 62-115 34-87 (99)
52 PRK05441 murQ N-acetylmuramic 33.0 63 0.0014 32.4 4.6 34 83-116 241-274 (299)
53 cd00592 HTH_MerR-like Helix-Tu 32.8 85 0.0018 25.6 4.6 50 63-116 34-85 (100)
54 cd04787 HTH_HMRTR_unk Helix-Tu 32.7 85 0.0018 27.4 4.8 51 62-116 34-87 (133)
55 PF03474 DMA: DMRTA motif; In 32.1 42 0.00091 24.0 2.2 17 97-113 22-38 (39)
56 KOG4841 Dolichol-phosphate man 31.6 17 0.00038 30.3 0.2 29 90-118 65-93 (95)
57 cd04785 HTH_CadR-PbrR-like Hel 31.1 86 0.0019 27.1 4.6 50 62-115 34-86 (126)
58 cd04776 HTH_GnyR Helix-Turn-He 29.7 1E+02 0.0022 26.5 4.7 37 63-103 33-69 (118)
59 cd04768 HTH_BmrR-like Helix-Tu 29.4 82 0.0018 25.9 4.0 47 62-115 34-80 (96)
60 cd04770 HTH_HMRTR Helix-Turn-H 29.3 99 0.0021 26.3 4.6 50 62-115 34-86 (123)
61 cd07257 THT_oxygenase_C The C- 29.0 79 0.0017 27.7 4.1 52 104-156 76-130 (153)
62 KOG1715 Mitochondrial/chloropl 28.9 81 0.0018 29.9 4.2 27 76-102 131-157 (187)
63 KOG1364 Predicted ubiquitin re 28.8 1.1E+02 0.0023 31.7 5.4 42 78-119 7-49 (356)
64 cd07249 MMCE Methylmalonyl-CoA 28.3 1.1E+02 0.0024 24.6 4.6 45 104-149 81-127 (128)
65 PRK13752 putative transcriptio 28.2 88 0.0019 28.0 4.2 50 63-116 42-92 (144)
66 TIGR00274 N-acetylmuramic acid 27.5 88 0.0019 31.3 4.5 35 81-115 234-268 (291)
67 cd04764 HTH_MlrA-like_sg1 Heli 27.3 49 0.0011 25.0 2.1 34 62-99 33-66 (67)
68 PF02954 HTH_8: Bacterial regu 26.7 71 0.0015 22.3 2.7 18 96-113 11-28 (42)
69 CHL00102 rps20 ribosomal prote 26.5 70 0.0015 26.9 3.0 38 92-134 32-74 (93)
70 cd04784 HTH_CadR-PbrR Helix-Tu 26.5 1.2E+02 0.0026 26.1 4.7 49 62-114 34-85 (127)
71 KOG2561 Adaptor protein NUB1, 26.4 75 0.0016 34.2 3.8 36 89-124 314-349 (568)
72 cd08362 BphC5-RrK37_N_like N-t 26.2 84 0.0018 25.3 3.5 50 104-153 70-119 (120)
73 cd04766 HTH_HspR Helix-Turn-He 25.8 1.3E+02 0.0029 24.2 4.6 35 63-100 35-69 (91)
74 cd04786 HTH_MerR-like_sg7 Heli 24.9 1.4E+02 0.003 26.3 4.8 50 62-115 34-85 (131)
75 cd04783 HTH_MerR1 Helix-Turn-H 24.7 1.4E+02 0.0029 25.8 4.7 49 63-115 35-84 (126)
76 cd01282 HTH_MerR-like_sg3 Heli 24.7 1.3E+02 0.0028 25.4 4.5 50 63-116 34-89 (112)
77 TIGR02043 ZntR Zn(II)-responsi 24.5 1.5E+02 0.0032 25.9 4.9 51 62-116 35-89 (131)
78 cd04782 HTH_BltR Helix-Turn-He 24.1 1.4E+02 0.003 24.6 4.4 49 63-117 35-83 (97)
79 PF10178 DUF2372: Uncharacteri 23.3 2.4E+02 0.0052 23.5 5.6 32 275-306 44-80 (90)
80 cd04769 HTH_MerR2 Helix-Turn-H 23.2 1.5E+02 0.0034 25.1 4.7 50 63-116 34-87 (116)
81 TIGR02054 MerD mercuric resist 23.2 1.9E+02 0.0041 25.2 5.2 38 62-103 37-74 (120)
82 PF10607 CLTH: CTLH/CRA C-term 23.0 86 0.0019 27.1 3.1 22 93-116 6-27 (145)
83 smart00668 CTLH C-terminal to 22.9 64 0.0014 23.2 2.0 15 103-117 14-28 (58)
84 cd07265 2_3_CTD_N N-terminal d 22.9 92 0.002 25.4 3.2 48 104-153 73-121 (122)
85 PRK09514 zntR zinc-responsive 22.3 1.7E+02 0.0036 25.9 4.8 51 62-116 35-89 (140)
86 COG5207 UBP14 Isopeptidase T [ 21.8 32 0.0007 37.4 0.2 27 87-113 630-656 (749)
87 PRK00239 rpsT 30S ribosomal pr 21.7 88 0.0019 26.0 2.7 35 93-134 33-67 (88)
88 PRK09591 celC cellobiose phosp 21.2 95 0.0021 26.5 2.9 28 88-115 17-45 (104)
89 PF12651 RHH_3: Ribbon-helix-h 21.1 2.3E+02 0.005 20.2 4.5 29 76-114 12-40 (44)
90 cd01109 HTH_YyaN Helix-Turn-He 21.0 1.9E+02 0.0041 24.3 4.7 50 63-116 35-87 (113)
91 cd07237 BphC1-RGP6_C_like C-te 20.8 1.2E+02 0.0027 26.5 3.7 51 105-156 86-136 (154)
92 TIGR00823 EIIA-LAC phosphotran 20.7 1E+02 0.0022 26.1 3.0 28 88-115 14-42 (99)
93 cd07258 PpCmtC_C C-terminal do 20.4 1.2E+02 0.0025 26.5 3.4 54 104-158 68-121 (141)
94 cd04777 HTH_MerR-like_sg1 Heli 20.4 1.9E+02 0.0042 24.0 4.6 50 63-116 33-89 (107)
95 cd04790 HTH_Cfa-like_unk Helix 20.2 1.4E+02 0.0031 27.4 4.1 38 62-103 35-72 (172)
96 cd00215 PTS_IIA_lac PTS_IIA, P 20.1 1.1E+02 0.0023 25.9 2.9 28 88-115 12-40 (97)
97 KOG4530 Predicted flavoprotein 20.1 57 0.0012 30.5 1.4 94 209-304 67-168 (199)
No 1
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-98 Score=726.25 Aligned_cols=288 Identities=41% Similarity=0.597 Sum_probs=269.8
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHhchhhhhhhcccccCCceEEEEecCC--eEEEEEEeccccce
Q 015807 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNES--KAAVIELNCETDFV 155 (400)
Q Consensus 78 ~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~--~aalVElNCETDFV 155 (400)
+++||+||++||||||||||||+|++||||+|++|||++|+++|+||+||.|+||+|.++++++ .|+|||||||||||
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 6899999999999999999999999999999999999999999999999999999999999655 99999999999999
Q ss_pred ecchHHHHHHHHHHHHHHhhcCCCCCCCCCCCCChhhhhcccccCCCCCCCCCCcHHHHHHHHHHHhcceeeeeeeEEee
Q 015807 156 SRNEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLS 235 (400)
Q Consensus 156 ArN~~F~~la~~ia~~~l~~~~~~~~~~~~~~l~~e~l~~~~~~~~~~~~~~~~Tv~d~i~~~ia~iGENI~LrR~~~i~ 235 (400)
|||+.|+.|++.|++.++.+.+. +.+.+....+ .++.||++.+..++++|||||.|||+..+.
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 99999999999999999988653 3467765543 357899999999999999999999999998
Q ss_pred eCCCCeEEEEeccCCCCCCCcEEEEEEEeecCCCCCCchhhhHHHHHHHHHhhcCCcccCccCCCHHHHHHHHHHHHHHH
Q 015807 236 ASSPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQA 315 (400)
Q Consensus 236 ~~~~~~v~sYvH~~~~~~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~vle~Er~i~~~q~ 315 (400)
.+ ++.+++|+|++ |||||||.++++. ....++|+|||||||++|.||++++||++++++||+|+.+|+
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 HhcCCChHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEeeEEEEEeccccccccCCChhhh
Q 015807 316 ESTGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEVGEGIRRVEASNTDEP 395 (400)
Q Consensus 316 ~~~gKP~~iieKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~i~V~~F~R~~vGEgiek~~~~fa~Ev 395 (400)
..+|||++|++|||+|||+|||.|+|||+|+||+||++||+++|++. +++|.+|+||+|||||||++.|||+||
T Consensus 217 ~~~gKP~~i~eKiVeGr~~Kf~~E~~Ll~Q~fV~d~~~TV~~~lke~------~~~v~~FvR~evGegieK~~~dFa~EV 290 (296)
T COG0264 217 KAEGKPENIVEKIVEGRMNKFLAEVCLLEQPFVKDPKKTVEQLLKEA------NAKVTEFVRFEVGEGIEKKEEDFAAEV 290 (296)
T ss_pred HhcCChHHHHHHHHhHHHHHHHHHHhhccCceecCcchhHHHHHHhc------CceeeeeeeeeccCCceeccccHHHHH
Confidence 99999999999999999999999999999999999999999999996 589999999999999999999999999
Q ss_pred hhccC
Q 015807 396 VAQAA 400 (400)
Q Consensus 396 ~aq~~ 400 (400)
|+|+.
T Consensus 291 aa~~k 295 (296)
T COG0264 291 AAQMK 295 (296)
T ss_pred HHHhc
Confidence 99973
No 2
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=100.00 E-value=6.9e-97 Score=722.52 Aligned_cols=286 Identities=38% Similarity=0.571 Sum_probs=267.0
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHhchhhhhhhcccccCCceEEEEecCCeEEEEEEeccccceec
Q 015807 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFVSR 157 (400)
Q Consensus 78 ~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalVElNCETDFVAr 157 (400)
+++||+||++||+|||||||||+++|||+|+|++|||++|+++|+||+||.|+||+|+++++++.|+|||||||||||||
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 015807 158 NEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLSAS 237 (400)
Q Consensus 158 N~~F~~la~~ia~~~l~~~~~~~~~~~~~~l~~e~l~~~~~~~~~~~~~~~~Tv~d~i~~~ia~iGENI~LrR~~~i~~~ 237 (400)
|+.|++|+++|++.++.+... +.+++..+++ .++.|| |.+.++++++||||.|||+.++..+
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 9999999999999999999999865
Q ss_pred CCCeEEEEeccCCCCCCCcEEEEEEEeecCCCCCCchhhhHHHHHHHHHhhcCCcccCccCCCHHHHHHHHHHHHHHHHh
Q 015807 238 SPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQAES 317 (400)
Q Consensus 238 ~~~~v~sYvH~~~~~~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~vle~Er~i~~~q~~~ 317 (400)
++++++|+|++ ||||+||.+++..+ .++|++||||||||+|.||++++||++++++||+|+++|+..
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 89999999986421 269999999999999999999999999999999999999999
Q ss_pred cCCChHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEeeEEEEEeccccccccCCChhhhhh
Q 015807 318 TGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEVGEGIRRVEASNTDEPVA 397 (400)
Q Consensus 318 ~gKP~~iieKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~i~V~~F~R~~vGEgiek~~~~fa~Ev~a 397 (400)
+|||++|++||++|||+|||+|+|||+|+||+||++||+|||++. +++|++|+||+||||+|+++.|||+|||+
T Consensus 214 ~gKP~~i~eKIv~Grl~Kf~~E~~Ll~Q~fv~D~~~tV~~~l~~~------~~~v~~F~R~~vGegiek~~~~fa~eva~ 287 (290)
T TIGR00116 214 SGKPKEIAEKMVEGRMKKFLAEISLLGQKFVMDPSKTVGQFLKEK------NAKVTEFIRFEVGEGIEKKEEDFAAEVAA 287 (290)
T ss_pred cCCcHHHHHHHhhhHHHHHhhhceeeecccccCCccCHHHHHHHc------CCEEEEEEEEEecCCceeccccHHHHHHH
Confidence 999999999999999999999999999999999999999999995 38999999999999999999999999999
Q ss_pred ccC
Q 015807 398 QAA 400 (400)
Q Consensus 398 q~~ 400 (400)
|++
T Consensus 288 q~~ 290 (290)
T TIGR00116 288 QMK 290 (290)
T ss_pred hhC
Confidence 984
No 3
>PRK09377 tsf elongation factor Ts; Provisional
Probab=100.00 E-value=6.6e-96 Score=715.60 Aligned_cols=284 Identities=45% Similarity=0.624 Sum_probs=268.0
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHhchhhhhhhcccccCCceEEEEecCCeEEEEEEeccccceec
Q 015807 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFVSR 157 (400)
Q Consensus 78 ~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalVElNCETDFVAr 157 (400)
+++||+||++||+|||||||||+++|||+|+|++|||++|+++|+||+||.|+||+|++.++++.|+|||||||||||||
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 015807 158 NEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLSAS 237 (400)
Q Consensus 158 N~~F~~la~~ia~~~l~~~~~~~~~~~~~~l~~e~l~~~~~~~~~~~~~~~~Tv~d~i~~~ia~iGENI~LrR~~~i~~~ 237 (400)
|+.|++|+++|++.++.+... +.++++.+++ ++.||+|.+.++++++||||.|||+..+..+
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 3577776553 3679999999999999999999999999764
Q ss_pred CCCeEEEEeccCCCCCCCcEEEEEEEeecCCCCCCchhhhHHHHHHHHHhhcCCcccCccCCCHHHHHHHHHHHHHHHHh
Q 015807 238 SPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQAES 317 (400)
Q Consensus 238 ~~~~v~sYvH~~~~~~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~vle~Er~i~~~q~~~ 317 (400)
++++++|+|++ ||||+||.+++.+ .+++++||||||||+|.||++++||++++++||+|+++|+..
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 379999999999999999999999999999999999999999
Q ss_pred cCCChHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEeeEEEEEeccccccccCCChhhhhh
Q 015807 318 TGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEVGEGIRRVEASNTDEPVA 397 (400)
Q Consensus 318 ~gKP~~iieKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~i~V~~F~R~~vGEgiek~~~~fa~Ev~a 397 (400)
+|||++|+||||+|||+|||+|+|||+|+||+||++||+|||++. +++|++|+||+||||+|+++.|||+|||+
T Consensus 214 ~gKP~~i~eKIv~Grl~Kf~~e~~Ll~Q~fi~D~~~tV~~~l~~~------~i~v~~F~R~evGe~~e~~~~~fa~eva~ 287 (290)
T PRK09377 214 EGKPEEIVEKIVEGRLNKFLKEVVLLEQPFVKDPKKTVGQLLKEA------GAKVVGFVRFEVGEGIEKKEEDFAAEVAA 287 (290)
T ss_pred cCChHHHHHHHHhHHHHHHhhhceeccCcccCCCCcCHHHHHHHc------CCEEEEEEEEEecCcceecccchHHHHHh
Confidence 999999999999999999999999999999999999999999985 48999999999999999999999999999
Q ss_pred cc
Q 015807 398 QA 399 (400)
Q Consensus 398 q~ 399 (400)
|+
T Consensus 288 q~ 289 (290)
T PRK09377 288 QM 289 (290)
T ss_pred hc
Confidence 97
No 4
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=100.00 E-value=7.7e-69 Score=500.14 Aligned_cols=192 Identities=39% Similarity=0.660 Sum_probs=187.0
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHhchhhhhhhcccccCCceEEEEec--CCeEEEEEEeccccce
Q 015807 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQN--ESKAAVIELNCETDFV 155 (400)
Q Consensus 78 ~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~--~~~aalVElNCETDFV 155 (400)
+++||+||++||+|||||||||++++||+|+|++|||++|+++|+||++|.|+||+|+++++ ++.|+|||||||||||
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 7889999999999999
Q ss_pred ecchHHHHHHHHHHHHHHhhcCCCCCCCCCCCCChhhhhcccccCCCCCCCCCCcHHHHHHHHHHHhcceeeeeeeEEee
Q 015807 156 SRNEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLS 235 (400)
Q Consensus 156 ArN~~F~~la~~ia~~~l~~~~~~~~~~~~~~l~~e~l~~~~~~~~~~~~~~~~Tv~d~i~~~ia~iGENI~LrR~~~i~ 235 (400)
|||+.|++
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 015807 236 ASSPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQA 315 (400)
Q Consensus 236 ~~~~~~v~sYvH~~~~~~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~vle~Er~i~~~q~ 315 (400)
++++||||||||+|.||++++||++++++||+|+++|+
T Consensus 93 ------------------------------------------lak~iamhIaA~~P~~l~~~~v~~~~i~~E~~i~~~~~ 130 (198)
T PRK12332 93 ------------------------------------------LAKDIAMQIAAANPEYVSREDVPAEVIEKEKEIYRAQA 130 (198)
T ss_pred ------------------------------------------HHHHHHHHHHhhCCccCChhhCCHHHHHHHHHHHHHHH
Confidence 25899999999999999999999999999999999999
Q ss_pred HhcCCChHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEeeEEEEEeccc
Q 015807 316 ESTGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEVGEG 383 (400)
Q Consensus 316 ~~~gKP~~iieKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~i~V~~F~R~~vGEg 383 (400)
..+|||++|++||++|||+|||+|+||++|+|++|++.||+++|++..+.+|.+++|.+|+||++|||
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=1.4e-68 Score=498.74 Aligned_cols=195 Identities=33% Similarity=0.556 Sum_probs=188.3
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHhchhhhhhhcccccCCceEEEEe--cCCeEEEEEEeccccce
Q 015807 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQ--NESKAAVIELNCETDFV 155 (400)
Q Consensus 78 ~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~--~~~~aalVElNCETDFV 155 (400)
+++||+||++||+|||||||||++++||+|+|++|||++|+++|+||++|.|+||+|++++ +++.|+|||+|||||||
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 56789999999999999
Q ss_pred ecchHHHHHHHHHHHHHHhhcCCCCCCCCCCCCChhhhhcccccCCCCCCCCCCcHHHHHHHHHHHhcceeeeeeeEEee
Q 015807 156 SRNEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLS 235 (400)
Q Consensus 156 ArN~~F~~la~~ia~~~l~~~~~~~~~~~~~~l~~e~l~~~~~~~~~~~~~~~~Tv~d~i~~~ia~iGENI~LrR~~~i~ 235 (400)
|||+.|++
T Consensus 82 Arn~~F~~------------------------------------------------------------------------ 89 (200)
T CHL00098 82 ARREEFQK------------------------------------------------------------------------ 89 (200)
T ss_pred cccHHHHH------------------------------------------------------------------------
Confidence 99999952
Q ss_pred eCCCCeEEEEeccCCCCCCCcEEEEEEEeecCCCCCCchhhhHHHHHHHHHhhc-CCcccCccCCCHHHHHHHHHHHHHH
Q 015807 236 ASSPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQ-KPLFLTKELVSADALENEREILKSQ 314 (400)
Q Consensus 236 ~~~~~~v~sYvH~~~~~~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA~-~P~~ls~~~Vp~~vle~Er~i~~~q 314 (400)
++++|||||||| +|.||++++||++++++||+|+++|
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 157999999999 7999999999999999999999999
Q ss_pred HHhcCCChHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEeeEEEEEecccccc
Q 015807 315 AESTGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEVGEGIRR 386 (400)
Q Consensus 315 ~~~~gKP~~iieKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~i~V~~F~R~~vGEgiek 386 (400)
+..+|||++|++|||+|||+|||+|+|||+|+|++|+++||+++|++..+++|.+++|.+|+||+|||||||
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=1.5e-67 Score=499.76 Aligned_cols=221 Identities=46% Similarity=0.700 Sum_probs=193.8
Q ss_pred cCCceEEEEecCCeEEEEEEeccccceecchHHHHHHHHHHHHHHhhcCCCCCCCCCCCCChhhhhcccccCCCCCCCCC
Q 015807 129 ATEGLLALAQNESKAAVIELNCETDFVSRNEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGE 208 (400)
Q Consensus 129 a~EGlV~~~~~~~~aalVElNCETDFVArN~~F~~la~~ia~~~l~~~~~~~~~~~~~~l~~e~l~~~~~~~~~~~~~~~ 208 (400)
|+||+|+++++++.|+||||||||||||||+.|++|++.|+++++..... +++++..+++. +
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 68999999999999999999999999999999999999999999854322 45778777642 3
Q ss_pred CcHHHHHHHHHHHhcceeeeeeeEEeeeCCCCeEEEEeccCCCCCCCcEEEEEEEeecCCCCCCchhhhHHHHHHHHHhh
Q 015807 209 TTVQNAITEVAAIMGENVKLRRGFLLSASSPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVA 288 (400)
Q Consensus 209 ~Tv~d~i~~~ia~iGENI~LrR~~~i~~~~~~~v~sYvH~~~~~~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA 288 (400)
.||+|++.++++++||||.|||+.++.. +++++++|+|++ ||+|+||.++++.+. .+++||+|||||||
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 999999999976532 15899999999999
Q ss_pred cCCcccCccCCCHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHhhhhcCC
Q 015807 289 QKPLFLTKELVSADALENEREILKSQAESTGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGS 368 (400)
Q Consensus 289 ~~P~~ls~~~Vp~~vle~Er~i~~~q~~~~gKP~~iieKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~ 368 (400)
|+|.||++++||++++++||+++++|+..+|||++|++||++|||+|||+|+|||+|+||+|+++||+|||++.+++
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 99999999999999999999999999999999999999999999999999999999999999999999999999877
Q ss_pred CeEEeeEEEEEecc
Q 015807 369 PVKIGSFFRMEVGE 382 (400)
Q Consensus 369 ~i~V~~F~R~~vGE 382 (400)
++|++|+||+|||
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 8999999999997
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=2.7e-63 Score=481.91 Aligned_cols=272 Identities=33% Similarity=0.481 Sum_probs=216.8
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH----hchhhhhhhcccccCCceEEEEecCCeEEEEEEecc
Q 015807 76 EQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK----RGKVLASKKSSRTATEGLLALAQNESKAAVIELNCE 151 (400)
Q Consensus 76 ~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk----kG~akA~Kka~R~a~EGlV~~~~~~~~aalVElNCE 151 (400)
.++++||+||++|||||++|||||++||||++.|.+||+| .||.+|+|+++|+|+||+|++.+++++.||||||||
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 488899999999999999999999999999999999
Q ss_pred ccceecchHHHHHHHHHHHHHHhhcCC----CCCCC-----CCCCCChhhhhcccccCCCCCCCCCCcHHHHHHHHHHHh
Q 015807 152 TDFVSRNEIFQYLALALAKQALVAENV----SQPVS-----GLFPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIM 222 (400)
Q Consensus 152 TDFVArN~~F~~la~~ia~~~l~~~~~----~~~~~-----~~~~l~~e~l~~~~~~~~~~~~~~~~Tv~d~i~~~ia~i 222 (400)
|||||||+.||.|+..||...+.+... ..... ..++........+....+.+.-++..||+|.++.+|+++
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 999999999999999999998873211 00000 011111111222222223333344449999999999999
Q ss_pred cceeeeeeeEEeeeCCCCeEEEEeccCCCC------CCCcEEEEEEEeecCCCCCCchhhhHHHHHHHHHhhcCCcccCc
Q 015807 223 GENVKLRRGFLLSASSPGVVSTYLHTSPQS------GLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTK 296 (400)
Q Consensus 223 GENI~LrR~~~i~~~~~~~v~sYvH~~~~~------~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA~~P~~ls~ 296 (400)
||||++||+.++.++++..+++|.|+.+++ ..|++|+||+++..... .-..+.+++.||+||++|.|..+.
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 112456899999999999999877
Q ss_pred cCCCHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEeeEE
Q 015807 297 ELVSADALENEREILKSQAESTGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFF 376 (400)
Q Consensus 297 ~~Vp~~vle~Er~i~~~q~~~~gKP~~iieKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~i~V~~F~ 376 (400)
+.+ + .+|.. ++++|++||.|+|+.|+++||+++|+.. +.+|.+|+
T Consensus 282 e~~------------k------~e~~~-----------~~e~et~ll~q~~lld~~itv~~~l~~~------~~~V~Dfv 326 (340)
T KOG1071|consen 282 ESL------------K------DEPGQ-----------GAEAETALLSQPSLLDPSITVKEYLDPH------NVSVVDFV 326 (340)
T ss_pred ccc------------c------ccccc-----------cccchhhheecHhhcCchhhHHHHhccC------CcchHHHH
Confidence 111 1 12222 2589999999999999999999999954 68999999
Q ss_pred EEEecccccc
Q 015807 377 RMEVGEGIRR 386 (400)
Q Consensus 377 R~~vGEgiek 386 (400)
||+||| .|+
T Consensus 327 R~E~Ge-~e~ 335 (340)
T KOG1071|consen 327 RFEVGE-GER 335 (340)
T ss_pred HHHhcc-chh
Confidence 999999 443
No 8
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=98.58 E-value=2.8e-07 Score=91.36 Aligned_cols=134 Identities=19% Similarity=0.228 Sum_probs=108.7
Q ss_pred CCCeEEEEeccCCCCCCCcEEEEEEEeecCCCCC-CchhhhHHHHHHHHHhhcCCcccCccCCCHHHHHHHHHHHHHHHH
Q 015807 238 SPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSS-FDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQAE 316 (400)
Q Consensus 238 ~~~~v~sYvH~~~~~~~Gkig~LV~l~~~~~~~~-~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~vle~Er~i~~~q~~ 316 (400)
.+|.|+.|+|+ ||+ +||.++.+.+... .+..+.|..+|||.+.+. |.++. .....+.+|+++
T Consensus 103 ~eGlIgv~~~~------~r~-vlvElNCETDFVARn~~Fq~Lv~~iA~~~l~~-~~~~~---~~~s~~s~e~~l------ 165 (340)
T KOG1071|consen 103 KEGLIGVLQED------GRT-VLVELNCETDFVARNDIFQDLVDQIALSVLAH-CQTLK---TKHSSYSKEKEL------ 165 (340)
T ss_pred ccceeEEEEeC------CeE-EEEEeecccchhhccchHHHHHHHHHHHHHHh-hhhcc---cChhhhhhhhhc------
Confidence 37899999998 687 9999999877533 345678899999988773 33332 223444455443
Q ss_pred hcCCChHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEeeEEEEEeccccccccCCChhhhh
Q 015807 317 STGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEVGEGIRRVEASNTDEPV 396 (400)
Q Consensus 317 ~~gKP~~iieKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~i~V~~F~R~~vGEgiek~~~~fa~Ev~ 396 (400)
+| .|+..|-+.+.-|+.+++..|++.++++.|......+|.+++|.+|.+|..++|....--+|++++.
T Consensus 166 ---~~--------~~~g~kl~~~~~~l~~~~d~~gkvsl~d~l~~~i~~~GENvkvrR~~~~ka~~g~~l~~y~H~A~q~ 234 (340)
T KOG1071|consen 166 ---EM--------DGRGFKLSESLSLLPNLPDVEGKVSLKDQLALAIGKLGENVKVRRAACMKAPSGTYLGSYSHGAPQS 234 (340)
T ss_pred ---cc--------cchHHHhhHHHhhccCCCCcccceeHHHHHHHHHHHhccceEEeEEEEEecCCCceEEeeecCCCCC
Confidence 11 7888999999999999999999999999999999999999999999999999999999999999888
Q ss_pred hcc
Q 015807 397 AQA 399 (400)
Q Consensus 397 aq~ 399 (400)
+++
T Consensus 235 agt 237 (340)
T KOG1071|consen 235 AGT 237 (340)
T ss_pred ccc
Confidence 765
No 9
>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=98.31 E-value=1.3e-06 Score=60.57 Aligned_cols=34 Identities=26% Similarity=0.358 Sum_probs=32.1
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHH
Q 015807 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKEL 113 (400)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~L 113 (400)
+.|++|+++ |.+.-+|++||..++||++.|++||
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 10
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=97.27 E-value=0.00041 Score=60.18 Aligned_cols=37 Identities=24% Similarity=0.322 Sum_probs=35.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 015807 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (400)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (400)
++|+-++++||++..+|++||.+||||+-.|+-+|..
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 8999999999999999999999999999999999974
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=97.16 E-value=0.0009 Score=45.91 Aligned_cols=34 Identities=26% Similarity=0.216 Sum_probs=30.8
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHH
Q 015807 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKEL 113 (400)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~L 113 (400)
+.|.+|++. |.+--+|+.||..++||+++|++||
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 457777776 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=97.12 E-value=0.00069 Score=58.77 Aligned_cols=36 Identities=22% Similarity=0.386 Sum_probs=34.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHH
Q 015807 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELR 114 (400)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LR 114 (400)
++|+-++++||++..+||+||++||||+-.|+-+|.
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=97.05 E-value=0.0013 Score=45.24 Aligned_cols=35 Identities=23% Similarity=0.241 Sum_probs=31.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHH
Q 015807 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELR 114 (400)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LR 114 (400)
+.|.+|++ .|.+.-.|..||..++||+++|++||.
T Consensus 3 ~~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 3 EKLEQLLE-MGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 56778887 499999999999999999999999985
No 14
>CHL00098 tsf elongation factor Ts
Probab=96.47 E-value=0.0047 Score=58.51 Aligned_cols=43 Identities=26% Similarity=0.501 Sum_probs=34.5
Q ss_pred CCeEEEEeccCCCCCCCcEEEEEEEeecCCCCCCchhhhHHHHHHHHHhhc
Q 015807 239 PGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQ 289 (400)
Q Consensus 239 ~~~v~sYvH~~~~~~~Gkig~LV~l~~~~~~~~~~~~~~~ak~iAmHIaA~ 289 (400)
+|.+++|+|.+ |++|+||.++++.+... ..+.| +++|||||+.
T Consensus 55 eG~V~~yiH~~-----gk~gvlVeln~ETDfVA--rn~~F-~~la~~IAmh 97 (200)
T CHL00098 55 EGLIESYIHTG-----GKLGVLVEINCETDFVA--RREEF-QKLAKNIAMQ 97 (200)
T ss_pred cCeEEEEEecC-----CCEEEEEEEecCccccc--ccHHH-HHHHHHHHHH
Confidence 68999999986 89999999998754321 13467 9999999985
No 15
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=96.27 E-value=0.024 Score=56.62 Aligned_cols=88 Identities=18% Similarity=0.225 Sum_probs=66.6
Q ss_pred CCCeEEEEeccCCCCCCCcEEEEEEEeecCCCCC-CchhhhHHHHHHHHHhhcCCcccCccCCCHHHHHHHHHHHHHHHH
Q 015807 238 SPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSS-FDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQAE 316 (400)
Q Consensus 238 ~~~~v~sYvH~~~~~~~Gkig~LV~l~~~~~~~~-~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~vle~Er~i~~~q~~ 316 (400)
.+|.++.|++ |+.|+||.+.++.+... .+....|+++|+.++++.+|..+
T Consensus 57 ~EG~V~~~~~-------~~~~~ivElncETDFVArne~F~~l~~~ia~~~~~~~~~~~---------------------- 107 (290)
T TIGR00116 57 AEGVIVLKSD-------GNKAVIVEVNSETDFVAKNAGFKEFANKLLDELKANKITTL---------------------- 107 (290)
T ss_pred CCcEEEEEEc-------CCEEEEEEEecCCccccCChHHHHHHHHHHHHHHhcCCCCH----------------------
Confidence 3799999996 56899999999877643 23455789999999876544211
Q ss_pred hcCCChHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEeeEEEEEe
Q 015807 317 STGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEV 380 (400)
Q Consensus 317 ~~gKP~~iieKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~i~V~~F~R~~v 380 (400)
.-|+.+++ ++..|| |.+.+....+|.+|.|.+|.+|..
T Consensus 108 -----------------------e~l~~~~~--~~~~tv-d~i~~~~a~iGEnI~lrR~~~~~~ 145 (290)
T TIGR00116 108 -----------------------EELQAQEL--ENREKV-EYLAALAAKIGENINLRRVAVLEG 145 (290)
T ss_pred -----------------------HHHhhccc--cCCCcH-HHHHHHHHHhccceEEEEEEEEec
Confidence 02344555 345699 999999999999999999999975
No 16
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=96.16 E-value=0.023 Score=56.62 Aligned_cols=92 Identities=16% Similarity=0.307 Sum_probs=72.4
Q ss_pred CCeEEEEeccCCCCCCCcEEEEEEEeecCCCCC-CchhhhHHHHHHHHHhhcCCcccCccCCCHHHHHHHHHHHHHHHHh
Q 015807 239 PGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSS-FDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQAES 317 (400)
Q Consensus 239 ~~~v~sYvH~~~~~~~Gkig~LV~l~~~~~~~~-~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~vle~Er~i~~~q~~~ 317 (400)
.|.+..|+|+. |+.|+||.+.++.+... .+...+|+++|+.++...+|..+.. +.
T Consensus 59 EGli~~~~~~~-----~~~av~vEvN~ETDFVAkN~~F~~l~~~ia~~~l~~~~~~ve~--------------l~----- 114 (296)
T COG0264 59 EGLIAAKVDGD-----GKKAVLVEVNCETDFVAKNAEFQELANKIAKAALEKKPADVEE--------------LK----- 114 (296)
T ss_pred cceEEEEEcCC-----CcEEEEEEEeccccceeCChhHHHHHHHHHHHHHHhCcccHHH--------------HH-----
Confidence 78999999876 89999999998876533 2346689999999999988742210 00
Q ss_pred cCCChHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEeeEEEEEecc
Q 015807 318 TGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEVGE 382 (400)
Q Consensus 318 ~gKP~~iieKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~i~V~~F~R~~vGE 382 (400)
....+++.||.+.+.+....+|.++.+.+|.+|+.++
T Consensus 115 ----------------------------~~~~~~~~tv~e~~~~~~AkIGENi~lRR~~~~~~~~ 151 (296)
T COG0264 115 ----------------------------AAFEPGGKTVEEEIAALIAKIGENISLRRFAVLEAGD 151 (296)
T ss_pred ----------------------------hhhcccCccHHHHHHHHHHHhccceeEEEEEEeecCc
Confidence 0112447899999999999999999999999999876
No 17
>PRK09377 tsf elongation factor Ts; Provisional
Probab=95.51 E-value=0.079 Score=52.97 Aligned_cols=88 Identities=20% Similarity=0.334 Sum_probs=67.1
Q ss_pred CCCeEEEEeccCCCCCCCcEEEEEEEeecCCCCC-CchhhhHHHHHHHHHhhcCCcccCccCCCHHHHHHHHHHHHHHHH
Q 015807 238 SPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSS-FDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQAE 316 (400)
Q Consensus 238 ~~~~v~sYvH~~~~~~~Gkig~LV~l~~~~~~~~-~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~vle~Er~i~~~q~~ 316 (400)
.+|.|+.|+. |+.|+||.+.++.+... .+....|+++|+.+++...|..+
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 68999999999877643 23455789999999887655310
Q ss_pred hcCCChHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEeeEEEEEe
Q 015807 317 STGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEV 380 (400)
Q Consensus 317 ~~gKP~~iieKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~i~V~~F~R~~v 380 (400)
+ -|+.+++ ++.||++.+.+....+|.+|.|.+|.+|+.
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 467999999999999999999999999973
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=94.40 E-value=0.086 Score=37.65 Aligned_cols=36 Identities=28% Similarity=0.278 Sum_probs=31.2
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHH
Q 015807 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELR 114 (400)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LR 114 (400)
++|.++..-||+.--.|.+-|+.+|||++.|+..--
T Consensus 2 e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~ 37 (43)
T PF14555_consen 2 EKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYF 37 (43)
T ss_dssp HHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 579999999999999999999999999999998643
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=93.06 E-value=0.075 Score=39.66 Aligned_cols=37 Identities=24% Similarity=0.496 Sum_probs=32.9
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 015807 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (400)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (400)
++|.+|..+||.-.-=|.+-|++++||+++|+....+
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 6899999999999999999999999999999998764
No 20
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=92.87 E-value=0.15 Score=48.37 Aligned_cols=30 Identities=33% Similarity=0.390 Sum_probs=27.6
Q ss_pred CCCcHHHHHHHHHHHhcceeeeeeeEEeee
Q 015807 207 GETTVQNAITEVAAIMGENVKLRRGFLLSA 236 (400)
Q Consensus 207 ~~~Tv~d~i~~~ia~iGENI~LrR~~~i~~ 236 (400)
++.||+|.+.+.++++||||.|+||.++..
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 367999999999999999999999999865
No 21
>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=92.29 E-value=0.45 Score=37.17 Aligned_cols=40 Identities=30% Similarity=0.518 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 015807 76 EQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (400)
Q Consensus 76 ~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (400)
.+..+|.++-.+||.-.-=|.+.|+++|||++.|+....+
T Consensus 11 ~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~~ 50 (63)
T smart00804 11 EQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFTE 50 (63)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4468999999999999999999999999999999988654
No 22
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=91.78 E-value=0.32 Score=42.71 Aligned_cols=35 Identities=26% Similarity=0.276 Sum_probs=32.3
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHH
Q 015807 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKEL 113 (400)
Q Consensus 79 ~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~L 113 (400)
++|+-.=++||++--+.+|||+++|||+-.|+--|
T Consensus 86 eDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L 120 (122)
T COG1308 86 EDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKL 120 (122)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHh
Confidence 58888889999999999999999999999998765
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=91.57 E-value=0.3 Score=46.87 Aligned_cols=87 Identities=15% Similarity=0.253 Sum_probs=59.1
Q ss_pred CCeEEEEeccCCCCCCCcEEEEEEEeecCCCCC-CchhhhHHHHHHHHHhhcCCcccCccCCCHHHHHHHHHHHHHHHHh
Q 015807 239 PGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSS-FDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQAES 317 (400)
Q Consensus 239 ~~~v~sYvH~~~~~~~Gkig~LV~l~~~~~~~~-~~~~~~~ak~iAmHIaA~~P~~ls~~~Vp~~vle~Er~i~~~q~~~ 317 (400)
+|.++.|+++. .|+||.+.++.+... .+....|+++||..++...+..++
T Consensus 3 EG~V~~~v~~~-------~a~~vElncETDFVArn~~F~~l~~~ia~~~~~~~~~~~~---------------------- 53 (221)
T PF00889_consen 3 EGLVGIAVSGD-------KAAMVELNCETDFVARNEEFQNLAKEIADAALENKASDVE---------------------- 53 (221)
T ss_dssp EEEEEEEEETT-------EEEEEEEEESSHHHHTSHHHHHHHHHHHHHHHCTTEESHH----------------------
T ss_pred ceEEEEEEeCC-------cEEEEEEEccccceecCHHHHHHHHHHHHHHHHhCCCCHH----------------------
Confidence 68899999864 399999998765321 233457888888888732221110
Q ss_pred cCCChHHHHHHHHHHHhhhhhcccccccccccCCCCcHHHHHHHhhhhcCCCeEEeeEEEEEe
Q 015807 318 TGKSPMAIEKMVEGRLRKYYEEVVLMEQKFVMNDTLNIKTILDNLSKEVGSPVKIGSFFRMEV 380 (400)
Q Consensus 318 ~gKP~~iieKIveGrl~K~~~E~~LleQ~fi~D~~~tV~~~L~~~~k~~g~~i~V~~F~R~~v 380 (400)
.|+.+++- + .||+|.+.+....+|.++.|.+|.+|..
T Consensus 54 -----------------------~l~~~~~~--~-~tv~d~i~~~i~~igEnI~l~r~~~~~~ 90 (221)
T PF00889_consen 54 -----------------------ELLALPLA--S-KTVKDAIAELIAKIGENIQLRRAARISA 90 (221)
T ss_dssp -----------------------HHHHSB----S-SHHHHHHHHHHHHH-S-EEEEEEEEEE-
T ss_pred -----------------------HHHhcccc--c-ccHHHHHHHHHHHhCCCEEEeEEEEEec
Confidence 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=86.63 E-value=2.1 Score=30.18 Aligned_cols=37 Identities=24% Similarity=0.350 Sum_probs=31.5
Q ss_pred HHHHHHHHh-cCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 015807 79 NLIKQLREQ-TSAPMKDVKLALVDCDWDIEAALKELRK 115 (400)
Q Consensus 79 ~lIK~LR~~-Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (400)
+.|..|++. -+.+--.-+.+|.+++||+|.|++.|-+
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=85.54 E-value=0.71 Score=36.50 Aligned_cols=27 Identities=26% Similarity=0.375 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHhcC
Q 015807 77 QVNLIKQLREQTSAPMKDVKLALVDCD 103 (400)
Q Consensus 77 ~~~lIK~LR~~Tgagm~dCKkAL~e~n 103 (400)
.+..||.+|+.||.|++++|+..+...
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 469999999999999999999998874
No 26
>PRK06771 hypothetical protein; Provisional
Probab=82.04 E-value=1.4 Score=37.05 Aligned_cols=23 Identities=22% Similarity=0.270 Sum_probs=20.8
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHH
Q 015807 78 VNLIKQLREQTSAPMKDVKLALV 100 (400)
Q Consensus 78 ~~lIK~LR~~Tgagm~dCKkAL~ 100 (400)
++.||.+|+.||+|+.+.|++..
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=79.37 E-value=6.4 Score=27.72 Aligned_cols=37 Identities=16% Similarity=0.277 Sum_probs=31.8
Q ss_pred HHHHHHHHh-cCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 015807 79 NLIKQLREQ-TSAPMKDVKLALVDCDWDIEAALKELRK 115 (400)
Q Consensus 79 ~lIK~LR~~-Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (400)
+.|..|++. -+.+--.-+..|.+++||+|.|++.|-+
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=77.79 E-value=1 Score=36.40 Aligned_cols=46 Identities=30% Similarity=0.296 Sum_probs=34.3
Q ss_pred HHHHHHHHhcCCCH---HHHHHHHHhcCCCHHHHHHHHHHhchhhhhhh
Q 015807 79 NLIKQLREQTSAPM---KDVKLALVDCDWDIEAALKELRKRGKVLASKK 124 (400)
Q Consensus 79 ~lIK~LR~~Tgagm---~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kk 124 (400)
..+-++|+.-|... ..-+.||-.++.|+++|+.||+++-..+..|+
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 78999999999999999999998776655543
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=72.44 E-value=12 Score=29.14 Aligned_cols=38 Identities=16% Similarity=0.357 Sum_probs=34.5
Q ss_pred HHHHHHHHHhcCC-CHHHHHHHHHhcCCCHHHHHHHHHH
Q 015807 78 VNLIKQLREQTSA-PMKDVKLALVDCDWDIEAALKELRK 115 (400)
Q Consensus 78 ~~lIK~LR~~Tga-gm~dCKkAL~e~ngDiekAi~~LRk 115 (400)
-+.|..|++-||. +=-|-...|.+||.|-+.|.+-|--
T Consensus 6 rk~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~ 44 (60)
T PF06972_consen 6 RKTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLS 44 (60)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence 3789999999999 9999999999999999999988753
No 30
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=69.41 E-value=12 Score=33.40 Aligned_cols=42 Identities=31% Similarity=0.392 Sum_probs=33.7
Q ss_pred hHHHHHHHHHHHh-----------------cCCCHHHHHHHHHhcCCCHHHHHHHHHHhc
Q 015807 75 TEQVNLIKQLREQ-----------------TSAPMKDVKLALVDCDWDIEAALKELRKRG 117 (400)
Q Consensus 75 ~~~~~lIK~LR~~-----------------Tgagm~dCKkAL~e~ngDiekAi~~LRkkG 117 (400)
-++|++=|+|-+. .+.+--+.++||++++ |+.+|.++||.++
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
>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=69.25 E-value=5.7 Score=35.26 Aligned_cols=29 Identities=24% Similarity=0.235 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHhcCCC
Q 015807 77 QVNLIKQLREQTSAPMKDVKLALVDCDWD 105 (400)
Q Consensus 77 ~~~lIK~LR~~Tgagm~dCKkAL~e~ngD 105 (400)
.+..||.+|+-||.|+++.|+..+.+..-
T Consensus 71 Ki~vIK~vR~itgLgLkEAK~lVe~~P~~ 99 (126)
T TIGR00855 71 KIAVIKVVREITGLGLKEAKDLVEGAPKV 99 (126)
T ss_pred hhHHHHHHHHHcCCcHHHHHHHHHhCcHH
Confidence 35899999999999999999988877543
No 32
>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed
Probab=64.71 E-value=7.9 Score=34.22 Aligned_cols=27 Identities=26% Similarity=0.347 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHhcC
Q 015807 77 QVNLIKQLREQTSAPMKDVKLALVDCD 103 (400)
Q Consensus 77 ~~~lIK~LR~~Tgagm~dCKkAL~e~n 103 (400)
.+..||.+|+-||.|+++.|+..+.+.
T Consensus 68 Ki~vIK~vR~itgLgLkEAK~lVe~~P 94 (123)
T PRK00157 68 KIAVIKAVREITGLGLKEAKDLVEGAP 94 (123)
T ss_pred hHHHHHHHHHHhCCCHHHHHHHHHhCC
Confidence 368999999999999999999887764
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=64.15 E-value=9.7 Score=33.77 Aligned_cols=42 Identities=21% Similarity=0.343 Sum_probs=31.4
Q ss_pred ccceeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCC
Q 015807 59 SFALISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWD 105 (400)
Q Consensus 59 ~~~~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngD 105 (400)
.|.+....|... ..+..||.+|.-||.|+++.|+..+.+..-
T Consensus 60 ~F~V~L~~~~~~-----~Ki~vIK~VR~it~LgLkEAK~lVe~~P~~ 101 (127)
T cd00387 60 EFDVVLESFGAA-----KKIAVIKEVREITGLGLKEAKDLVESAPKV 101 (127)
T ss_pred eEEEEEeeCCch-----hhHHHHHHHHHHhCCChHHHHHHHHhCcHH
Confidence 345555555542 245899999999999999999988877543
No 34
>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=64.00 E-value=2.2 Score=35.65 Aligned_cols=28 Identities=29% Similarity=0.381 Sum_probs=26.1
Q ss_pred CHHHHHHHHHhcCCCHHHHHHHHHHhch
Q 015807 91 PMKDVKLALVDCDWDIEAALKELRKRGK 118 (400)
Q Consensus 91 gm~dCKkAL~e~ngDiekAi~~LRkkG~ 118 (400)
-+.||.+|=+|-..+|+.|.+-||+||.
T Consensus 62 tFnDcpeA~~eL~~eI~eAK~dLr~kGv 89 (91)
T PF08285_consen 62 TFNDCPEAAKELQKEIKEAKADLRKKGV 89 (91)
T ss_pred ccCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 3679999999999999999999999996
No 35
>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=63.05 E-value=12 Score=31.11 Aligned_cols=50 Identities=10% Similarity=0.025 Sum_probs=38.4
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhc-CCCHHHHHHHHHHh
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDC-DWDIEAALKELRKR 116 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~-ngDiekAi~~LRkk 116 (400)
...|.|+-.. ...+..|+.|| +|.||.+.|+-+... +||.+.+.+.|.++
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 3577887653 55678899998 599999998877665 48899888888764
No 36
>CHL00083 rpl12 ribosomal protein L12
Probab=61.10 E-value=14 Score=33.06 Aligned_cols=42 Identities=17% Similarity=0.273 Sum_probs=30.5
Q ss_pred CccceeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCC
Q 015807 58 SSFALISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDW 104 (400)
Q Consensus 58 ~~~~~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ng 104 (400)
+.|.+....|... ..+..||.+|+-||.|+++.|+..+.+.-
T Consensus 62 T~F~V~L~~~~~~-----~Ki~vIK~vr~it~lgLkeaK~lVe~~P~ 103 (131)
T CHL00083 62 TEFDVILEEVPAD-----KRIAVLKVVRSLTGLGLKEAKELVESLPK 103 (131)
T ss_pred ceeeEEEeecCCc-----chHHHHHHHHHHcCCCHHHHHHHHHhCCH
Confidence 3355556655322 23589999999999999999998876643
No 37
>COG0222 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]
Probab=61.01 E-value=9.3 Score=33.75 Aligned_cols=38 Identities=21% Similarity=0.350 Sum_probs=28.5
Q ss_pred cceeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC
Q 015807 60 FALISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD 103 (400)
Q Consensus 60 ~~~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n 103 (400)
|.+..+.+... .+..||..|+-||.|+++.|..-+.+.
T Consensus 58 fdVvL~~~g~k------KI~VIK~vR~itGLGLKEAKdlVe~aP 95 (124)
T COG0222 58 FDVVLKSAGGK------KIAVIKVVRELTGLGLKEAKDLVEGAP 95 (124)
T ss_pred eEEEecccCCc------chhHHHHHHHHhcccHHHHHHHHHhCc
Confidence 45566665333 358999999999999999998766653
No 38
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=51.81 E-value=14 Score=41.08 Aligned_cols=28 Identities=14% Similarity=0.058 Sum_probs=25.1
Q ss_pred cCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 015807 88 TSAPMKDVKLALVDCDWDIEAALKELRK 115 (400)
Q Consensus 88 Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (400)
-|-+--.|+|||.++|||+|.|++|+--
T Consensus 645 mGf~~~qa~~aL~~~n~nveravDWif~ 672 (763)
T KOG0944|consen 645 MGFSRNQAIKALKATNNNVERAVDWIFS 672 (763)
T ss_pred ecCcHHHHHHHHHhcCccHHHHHHHHHh
Confidence 4777789999999999999999999863
No 39
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=50.44 E-value=15 Score=30.98 Aligned_cols=40 Identities=20% Similarity=0.174 Sum_probs=33.4
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCC
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWD 105 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngD 105 (400)
...|.|+... ...+..|+.|| .+|.++.+||+.|...+-+
T Consensus 34 ~gyR~Ys~~d---l~~l~~I~~~r-~~G~~L~~I~~~l~~~~~~ 73 (124)
T COG0789 34 GGYRYYTPED---LELLQIIKTLR-ELGFSLAEIKELLDLLSAG 73 (124)
T ss_pred CCceecCHHH---HHHHHHHHHHH-HcCCCHHHHHHHHhccccc
Confidence 4678888774 55678899999 8999999999999998753
No 40
>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=50.12 E-value=28 Score=28.94 Aligned_cols=47 Identities=28% Similarity=0.367 Sum_probs=36.2
Q ss_pred eeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHh
Q 015807 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKR 116 (400)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkk 116 (400)
..|.|+-.. ...+..|+.||. .|.|+.++++-|...+ +...+.|..+
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 457787653 556788999998 7999999999998765 6666777654
No 41
>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=47.09 E-value=36 Score=28.78 Aligned_cols=51 Identities=18% Similarity=0.178 Sum_probs=37.9
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhc--CCCHHHHHHHHHHh
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDC--DWDIEAALKELRKR 116 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~--ngDiekAi~~LRkk 116 (400)
...|.|+... ...+..|+.||+ +|.|+.+.|..|... +++.+...+.|.++
T Consensus 34 ~g~R~Y~~~d---l~~l~~I~~lr~-~G~~l~~I~~~l~~~~~~~~~~~~~~~l~~~ 86 (108)
T cd04773 34 TGYRVYDPSD---VRDARLIHLLRR-GGYLLEQIATVVEQLRHAGGTEALAAALEQR 86 (108)
T ss_pred CCceeeCHHH---HHHHHHHHHHHH-CCCCHHHHHHHHHHhhcCCCHHHHHHHHHHH
Confidence 3567777653 456789999986 999999999999864 35566666666653
No 42
>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=46.54 E-value=37 Score=27.61 Aligned_cols=50 Identities=18% Similarity=0.167 Sum_probs=36.8
Q ss_pred eeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHhc
Q 015807 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRG 117 (400)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkkG 117 (400)
..|.|+... ...+..|+.||+ .|.++.++++-|..-+ +.+....-|-..|
T Consensus 36 g~R~Ys~~d---v~~l~~I~~Lr~-~G~sl~~i~~~l~~~~-~~~~~~~~~~~~~ 85 (88)
T cd01105 36 GQRKYSLAD---VDRLLVIKELLD-EGFTLAAAVEKLRRRR-VQAEVRRRLMKDG 85 (88)
T ss_pred CceecCHHH---HHHHHHHHHHHH-CCCCHHHHHHHHHHcc-CHHHHHHHHHHHh
Confidence 567888553 566889999998 9999999999998554 5555555554444
No 43
>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=44.59 E-value=20 Score=23.65 Aligned_cols=19 Identities=32% Similarity=0.351 Sum_probs=13.9
Q ss_pred HHHHHHHHHHh--chhhhhhh
Q 015807 106 IEAALKELRKR--GKVLASKK 124 (400)
Q Consensus 106 iekAi~~LRkk--G~akA~Kk 124 (400)
+.+|-+||+++ |+.+|+-+
T Consensus 6 ~k~~~~wlkkkgpgi~kaal~ 26 (29)
T PF07442_consen 6 LKKAGEWLKKKGPGILKAALK 26 (29)
T ss_pred HHHHHHHHHhcCchHHHHHHH
Confidence 56789999998 56666543
No 44
>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=44.21 E-value=25 Score=29.14 Aligned_cols=36 Identities=22% Similarity=0.435 Sum_probs=29.7
Q ss_pred eeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHh
Q 015807 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVD 101 (400)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e 101 (400)
..|.|+... ...+..|+.||+..|.++.++|+.|..
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 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=40.41 E-value=26 Score=26.66 Aligned_cols=34 Identities=24% Similarity=0.239 Sum_probs=27.6
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHH
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLAL 99 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL 99 (400)
...|.|+... ...+..|+.||+ .|.++-++|+-|
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 3557787664 566889999999 999999999876
No 46
>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=40.26 E-value=44 Score=27.53 Aligned_cols=48 Identities=21% Similarity=0.281 Sum_probs=35.0
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHh
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKR 116 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkk 116 (400)
...|.|+... ...+..|+.||+ +|.++.+.|+-|...+. ...++|+.+
T Consensus 34 ~gyR~Y~~~~---l~~l~~I~~lr~-~G~~l~eI~~~l~~~~~---~~~~~l~~~ 81 (96)
T cd04788 34 GGHRLYDRAD---IRRLHQIIALRR-LGFSLREIGRALDGPDF---DPLELLRRQ 81 (96)
T ss_pred CCceeeCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHhCCCh---hHHHHHHHH
Confidence 3468887653 566899999986 79999999998876442 445566543
No 47
>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=38.91 E-value=46 Score=27.99 Aligned_cols=49 Identities=29% Similarity=0.334 Sum_probs=36.6
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHh
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKR 116 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkk 116 (400)
...|.|+... ...+..|+.||. +|.++.+++.-+...+. +.....|..+
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 3567887654 556889999988 99999999987776553 6666666654
No 48
>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=38.85 E-value=58 Score=26.55 Aligned_cols=34 Identities=26% Similarity=0.107 Sum_probs=28.8
Q ss_pred HHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 015807 81 IKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (400)
Q Consensus 81 IK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (400)
|+. .+.+|...-.+-+||..|.||+..|..++..
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 7889999999999999999999999996654
No 49
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=38.60 E-value=20 Score=27.10 Aligned_cols=34 Identities=26% Similarity=0.481 Sum_probs=26.3
Q ss_pred eecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHh
Q 015807 64 SRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVD 101 (400)
Q Consensus 64 ~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e 101 (400)
.|.|+... ...+..|+.||+ .|.++.+.|+.|.+
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 37777664 566899999999 99999999998864
No 50
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=36.27 E-value=37 Score=25.53 Aligned_cols=34 Identities=29% Similarity=0.431 Sum_probs=27.0
Q ss_pred eeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHH
Q 015807 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALV 100 (400)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~ 100 (400)
..|.|+-.. ...+..|+.||+ .|.++.+++++|.
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 456677543 455789999998 9999999999885
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=33.73 E-value=80 Score=26.34 Aligned_cols=51 Identities=24% Similarity=0.154 Sum_probs=37.4
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCC---HHHHHHHHHH
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWD---IEAALKELRK 115 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngD---iekAi~~LRk 115 (400)
...|.|+... ...+..|+.|-+.+|.++.++|+-|...++. -+.+..-|++
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 3578888764 4556778887678999999999999987754 4555555653
No 52
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=33.01 E-value=63 Score=32.35 Aligned_cols=34 Identities=18% Similarity=0.174 Sum_probs=29.8
Q ss_pred HHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHh
Q 015807 83 QLREQTSAPMKDVKLALVDCDWDIEAALKELRKR 116 (400)
Q Consensus 83 ~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkk 116 (400)
=+.+.||+.--+|.++|++++|++..|+-.+...
T Consensus 241 i~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~~~~ 274 (299)
T PRK05441 241 IVMEATGVSREEAEAALEAADGSVKLAIVMILTG 274 (299)
T ss_pred HHHHHHCcCHHHHHHHHHHhCCCcHHHHHHHHhC
Confidence 3666799999999999999999999999987653
No 53
>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=32.84 E-value=85 Score=25.55 Aligned_cols=50 Identities=28% Similarity=0.401 Sum_probs=36.6
Q ss_pred eeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCC--HHHHHHHHHHh
Q 015807 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWD--IEAALKELRKR 116 (400)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngD--iekAi~~LRkk 116 (400)
..|.|+-.. ...+..|+.||. .|.++.+.++.|...+.+ .+...+.|..+
T Consensus 34 g~r~y~~~d---v~~l~~i~~l~~-~g~~~~~i~~~l~~~~~~~~~~~~~~~~~~~ 85 (100)
T cd00592 34 GYRLYSEED---LERLRLIRRLRE-LGLSLKEIRELLDARDEELSLAALLALLDEK 85 (100)
T ss_pred CCcccCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHhcccccchHHHHHHHHHHH
Confidence 456677553 556889999999 999999999999887654 34555555443
No 54
>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=32.66 E-value=85 Score=27.40 Aligned_cols=51 Identities=22% Similarity=0.257 Sum_probs=36.8
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC-CC--HHHHHHHHHHh
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD-WD--IEAALKELRKR 116 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n-gD--iekAi~~LRkk 116 (400)
...|.|+... ...+.+|+.|| .+|.++.+.|+-|...+ ++ .....++|+++
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 59999999999988654 22 23445666544
No 55
>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=32.11 E-value=42 Score=23.96 Aligned_cols=17 Identities=29% Similarity=0.606 Sum_probs=14.6
Q ss_pred HHHHhcCCCHHHHHHHH
Q 015807 97 LALVDCDWDIEAALKEL 113 (400)
Q Consensus 97 kAL~e~ngDiekAi~~L 113 (400)
-.|+-|+||+-+|+|.+
T Consensus 22 ~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 22 LILQRCNGDVVQAIEQF 38 (39)
T ss_pred HHHHHcCCcHHHHHHHh
Confidence 45889999999999964
No 56
>KOG4841 consensus Dolichol-phosphate mannosyltransferase, subunit 3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=31.60 E-value=17 Score=30.29 Aligned_cols=29 Identities=28% Similarity=0.384 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHhcCCCHHHHHHHHHHhch
Q 015807 90 APMKDVKLALVDCDWDIEAALKELRKRGK 118 (400)
Q Consensus 90 agm~dCKkAL~e~ngDiekAi~~LRkkG~ 118 (400)
|.+.||-+|-.|--+||.+|.+-||.||.
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 57
>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=31.06 E-value=86 Score=27.10 Aligned_cols=50 Identities=16% Similarity=0.171 Sum_probs=36.3
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC---CCHHHHHHHHHH
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD---WDIEAALKELRK 115 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n---gDiekAi~~LRk 115 (400)
...|.|+... ...+..|+.|| .+|.++.+.|+-|...+ .+.+.....|.+
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 255556666654
No 58
>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=29.65 E-value=1e+02 Score=26.50 Aligned_cols=37 Identities=16% Similarity=0.248 Sum_probs=30.5
Q ss_pred eeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC
Q 015807 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD 103 (400)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n 103 (400)
..|.|+... ...+..|+.||+ +|.|+.+.|+-|...+
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 59
>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=29.43 E-value=82 Score=25.92 Aligned_cols=47 Identities=21% Similarity=0.047 Sum_probs=34.6
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (400)
...|.|+... ...+..|+.||+ .|.++.+.|+.|...+. ...+.|.+
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 556889999988 69999999999976542 44445544
No 60
>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=29.32 E-value=99 Score=26.32 Aligned_cols=50 Identities=10% Similarity=0.079 Sum_probs=36.4
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCC---CHHHHHHHHHH
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDW---DIEAALKELRK 115 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ng---DiekAi~~LRk 115 (400)
...|.|+... ...+..|+.|| .+|.++.+.|.-|...+. +.+...+.|.+
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 55688999996 679999999999976542 34555566654
No 61
>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=28.96 E-value=79 Score=27.70 Aligned_cols=52 Identities=17% Similarity=0.110 Sum_probs=36.5
Q ss_pred CCHHHHH---HHHHHhchhhhhhhcccccCCceEEEEecCCeEEEEEEecccccee
Q 015807 104 WDIEAAL---KELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFVS 156 (400)
Q Consensus 104 gDiekAi---~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalVElNCETDFVA 156 (400)
.|++++. +.|+++|...... .+|....+.+.+++.+-.|-+|||-+|.|=|.
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 8899999864422 34444344566777777899999999987443
No 62
>KOG1715 consensus Mitochondrial/chloroplast ribosomal protein L12 [Translation, ribosomal structure and biogenesis]
Probab=28.85 E-value=81 Score=29.85 Aligned_cols=27 Identities=22% Similarity=0.383 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHhc
Q 015807 76 EQVNLIKQLREQTSAPMKDVKLALVDC 102 (400)
Q Consensus 76 ~~~~lIK~LR~~Tgagm~dCKkAL~e~ 102 (400)
+.++.||++|--||.|+.+.||=.+.+
T Consensus 131 ~KIkVIKEVR~~tgL~LkeAKklVE~a 157 (187)
T KOG1715|consen 131 SKIKVIKEVRALTGLGLKEAKKLVEKA 157 (187)
T ss_pred chhHHHHHHHHhccccHHHHHHHHHhc
Confidence 347899999999999999998755444
No 63
>KOG1364 consensus Predicted ubiquitin regulatory protein, contains UAS and UBX domains [Posttranslational modification, protein turnover, chaperones]
Probab=28.80 E-value=1.1e+02 Score=31.75 Aligned_cols=42 Identities=24% Similarity=0.367 Sum_probs=38.1
Q ss_pred HHHHHHHHHhcC-CCHHHHHHHHHhcCCCHHHHHHHHHHhchh
Q 015807 78 VNLIKQLREQTS-APMKDVKLALVDCDWDIEAALKELRKRGKV 119 (400)
Q Consensus 78 ~~lIK~LR~~Tg-agm~dCKkAL~e~ngDiekAi~~LRkkG~a 119 (400)
.+||++.+.-|+ --+-..++=|..++||++.|+.++++.|..
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 778888999999999999999999998763
No 64
>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=28.32 E-value=1.1e+02 Score=24.64 Aligned_cols=45 Identities=29% Similarity=0.339 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHhchhhhhhhcccccCCceEEEEecCCe--EEEEEEe
Q 015807 104 WDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESK--AAVIELN 149 (400)
Q Consensus 104 gDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~--aalVElN 149 (400)
.|++.+.+.|+++|...-. ...+....|.-....+... |.+|||.
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 4799999999999985432 2333456677666666555 9999984
No 65
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=28.19 E-value=88 Score=27.98 Aligned_cols=50 Identities=14% Similarity=0.167 Sum_probs=36.6
Q ss_pred eeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCC-HHHHHHHHHHh
Q 015807 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWD-IEAALKELRKR 116 (400)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngD-iekAi~~LRkk 116 (400)
..|.|+... ...+..|+.|| .+|.++.+.|+=|...++. -+...++|.++
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 35566677654
No 66
>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=27.46 E-value=88 Score=31.27 Aligned_cols=35 Identities=14% Similarity=0.250 Sum_probs=30.1
Q ss_pred HHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHH
Q 015807 81 IKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (400)
Q Consensus 81 IK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRk 115 (400)
+.=+.+-||++.-+|.++|.+++|++..|+-.+..
T Consensus 234 ~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~~~~ 268 (291)
T TIGR00274 234 VRIVRQATDCNKELAEQTLLAADQNVKLAIVMILS 268 (291)
T ss_pred HHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHHHHh
Confidence 33356679999999999999999999999997765
No 67
>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=27.31 E-value=49 Score=24.97 Aligned_cols=34 Identities=29% Similarity=0.370 Sum_probs=27.4
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHH
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLAL 99 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL 99 (400)
...|.|+.+. ...+..|+.||+ .|.++-+++.-|
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 566889999999 999999998876
No 68
>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=26.71 E-value=71 Score=22.32 Aligned_cols=18 Identities=28% Similarity=0.429 Sum_probs=15.2
Q ss_pred HHHHHhcCCCHHHHHHHH
Q 015807 96 KLALVDCDWDIEAALKEL 113 (400)
Q Consensus 96 KkAL~e~ngDiekAi~~L 113 (400)
..||..++||+.+|-+.|
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 69
>CHL00102 rps20 ribosomal protein S20
Probab=26.50 E-value=70 Score=26.92 Aligned_cols=38 Identities=16% Similarity=0.197 Sum_probs=26.9
Q ss_pred HHHHHHHHHh-----cCCCHHHHHHHHHHhchhhhhhhcccccCCceE
Q 015807 92 MKDVKLALVD-----CDWDIEAALKELRKRGKVLASKKSSRTATEGLL 134 (400)
Q Consensus 92 m~dCKkAL~e-----~ngDiekAi~~LRkkG~akA~Kka~R~a~EGlV 134 (400)
|..|.+|+++ ..||.+.|.++|.+ |.+.-|+.+.-|+|
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 24999999999985 55556666666665
No 70
>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=26.47 E-value=1.2e+02 Score=26.06 Aligned_cols=49 Identities=12% Similarity=0.133 Sum_probs=35.4
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC-C--CHHHHHHHHH
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD-W--DIEAALKELR 114 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n-g--DiekAi~~LR 114 (400)
...|.|+... ...+..|+.|| ..|.++.+.|+-|...+ + +.+.....|.
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 3455556655
No 71
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=26.40 E-value=75 Score=34.16 Aligned_cols=36 Identities=31% Similarity=0.487 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHHHhchhhhhhh
Q 015807 89 SAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKK 124 (400)
Q Consensus 89 gagm~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kk 124 (400)
|.--.|.|-||-.|+||+|-|++++.++-..+|.++
T Consensus 314 GfeesdaRlaLRsc~g~Vd~AvqfI~erre~laq~R 349 (568)
T KOG2561|consen 314 GFEESDARLALRSCNGDVDSAVQFIIERREKLAQKR 349 (568)
T ss_pred CCCchHHHHHHHhccccHHHHHHHHHHHHHHHHHHH
Confidence 555579999999999999999999988877777776
No 72
>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=26.24 E-value=84 Score=25.31 Aligned_cols=50 Identities=16% Similarity=0.309 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHhchhhhhhhcccccCCceEEEEecCCeEEEEEEecccc
Q 015807 104 WDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETD 153 (400)
Q Consensus 104 gDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalVElNCETD 153 (400)
.|+++..+.|++.|.........+....|-..+.+.+-.|..|||.|.|.
T Consensus 70 ~~l~~~~~~l~~~G~~~~~~~~~~~~~~~~~~~~~~DP~G~~iel~~~~~ 119 (120)
T cd08362 70 ADVDALARQVAARGGTVLSEPGATDDPGGGYGFRFFDPDGRLIEFSADVE 119 (120)
T ss_pred HHHHHHHHHHHHcCCceecCCcccCCCCCceEEEEECCCCCEEEEEeccc
Confidence 47889999999988854322111222223334556666789999998873
No 73
>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=25.84 E-value=1.3e+02 Score=24.24 Aligned_cols=35 Identities=23% Similarity=0.366 Sum_probs=29.1
Q ss_pred eeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHH
Q 015807 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALV 100 (400)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~ 100 (400)
..|.|+... ...+..|+.|++..|.++.+++..|.
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 457777664 45678999999999999999999996
No 74
>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=24.91 E-value=1.4e+02 Score=26.30 Aligned_cols=50 Identities=12% Similarity=0.283 Sum_probs=35.8
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC--CCHHHHHHHHHH
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD--WDIEAALKELRK 115 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n--gDiekAi~~LRk 115 (400)
...|.|+... ...+..|+.||+ .|.++.+.|+-|.... .+.+.....|.+
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 4568888653 556899999987 9999999999887543 345555555543
No 75
>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=24.74 E-value=1.4e+02 Score=25.76 Aligned_cols=49 Identities=14% Similarity=0.180 Sum_probs=37.0
Q ss_pred eeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC-CCHHHHHHHHHH
Q 015807 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD-WDIEAALKELRK 115 (400)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n-gDiekAi~~LRk 115 (400)
..|.|+... ...+..|+.|| .+|.++.+.|+-|.... ++.+...+.|..
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 478888664 55678999997 59999999999997654 356666666653
No 76
>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=24.69 E-value=1.3e+02 Score=25.44 Aligned_cols=50 Identities=18% Similarity=0.268 Sum_probs=36.0
Q ss_pred eeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC------CCHHHHHHHHHHh
Q 015807 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD------WDIEAALKELRKR 116 (400)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n------gDiekAi~~LRkk 116 (400)
..|.|+... ...+..|+.||+ +|.++.+.|.-|.... .....-.+.|.++
T Consensus 34 g~R~Y~~~~---~~~l~~I~~lr~-~G~sl~eI~~~l~~~~~~~~~~~~~~~~~~~l~~~ 89 (112)
T cd01282 34 GYRDYDEAA---VDRVRQIRRLLA-AGLTLEEIREFLPCLRGGEPTFRPCPDLLAVLRRE 89 (112)
T ss_pred CCeecCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHHHhhCCCccCCccHHHHHHHHHH
Confidence 568888653 556889999985 9999999999887543 2345556666543
No 77
>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=24.47 E-value=1.5e+02 Score=25.90 Aligned_cols=51 Identities=12% Similarity=0.151 Sum_probs=36.6
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhc----CCCHHHHHHHHHHh
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDC----DWDIEAALKELRKR 116 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~----ngDiekAi~~LRkk 116 (400)
...|.|+... ...+..|+.||+ .|.++.+.|+-|... +.+.+...+.|.++
T Consensus 35 ~gyR~Y~~~~---l~~l~~I~~lr~-~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~ 89 (131)
T TIGR02043 35 SGYRLYTDED---QKRLRFILKAKE-LGFTLDEIKELLSIKLDATEHSCAEVKAIVDAK 89 (131)
T ss_pred CCceecCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHH
Confidence 4578888653 556899999986 899999999988743 23455656666543
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=24.10 E-value=1.4e+02 Score=24.61 Aligned_cols=49 Identities=22% Similarity=0.305 Sum_probs=36.6
Q ss_pred eeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHHHhc
Q 015807 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRG 117 (400)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LRkkG 117 (400)
..|.|+... ...+..|+.||+ .|.++.+.|.-|.. .+.+...+.|.++-
T Consensus 35 gyR~Y~~~~---~~~l~~I~~lr~-~G~~l~eI~~~l~~--~~~~~~~~~l~~~~ 83 (97)
T cd04782 35 GYRYYTLEQ---FEQLDIILLLKE-LGISLKEIKDYLDN--RNPDELIELLKKQE 83 (97)
T ss_pred CCccCCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHhc--CCHHHHHHHHHHHH
Confidence 467777653 456789999986 69999999988764 36777777776543
No 79
>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=23.33 E-value=2.4e+02 Score=23.51 Aligned_cols=32 Identities=25% Similarity=0.270 Sum_probs=17.7
Q ss_pred hhhHHHHHHHHH---hhcCCc--ccCccCCCHHHHHH
Q 015807 275 LKRVGSELAMHI---VAQKPL--FLTKELVSADALEN 306 (400)
Q Consensus 275 ~~~~ak~iAmHI---aA~~P~--~ls~~~Vp~~vle~ 306 (400)
+.-.||+|+-|| ...+|. .|.-.+.+.+.+..
T Consensus 44 l~v~Ar~L~~~i~~~~~~r~lllalgLkd~s~e~lk~ 80 (90)
T PF10178_consen 44 LHVYARQLIEFISQEGSNRPLLLALGLKDHSPETLKA 80 (90)
T ss_dssp HHHHHHHHHHHHHHHTTT-EEEEEEE-SS--HHHHHH
T ss_pred HHHHHHHHHHHHhccCCCCcEEEEEeccCCCHHHHHH
Confidence 445799999999 445555 34445555555443
No 80
>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=23.20 E-value=1.5e+02 Score=25.06 Aligned_cols=50 Identities=16% Similarity=0.212 Sum_probs=37.3
Q ss_pred eeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcCC----CHHHHHHHHHHh
Q 015807 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDW----DIEAALKELRKR 116 (400)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~ng----DiekAi~~LRkk 116 (400)
..|.|+... ...+..|+.||+ .|.|+.+-|.-|...+. ..+...+.|.++
T Consensus 34 ~yR~Y~~~d---~~~l~~I~~lr~-~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~ 87 (116)
T cd04769 34 NYRVYDAQH---VECLRFIKEARQ-LGFTLAELKAIFAGHEGRAVLPWPHLQQALEDK 87 (116)
T ss_pred CceeeCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHhccccCCcCcHHHHHHHHHHH
Confidence 678888664 556889999987 99999999998887653 345555666543
No 81
>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=23.19 E-value=1.9e+02 Score=25.21 Aligned_cols=38 Identities=11% Similarity=0.107 Sum_probs=30.3
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD 103 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n 103 (400)
...|.|+... ...+.+|+.||. +|.|+.++|.-|...+
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 4578888764 556889999998 9999999998776544
No 82
>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=23.03 E-value=86 Score=27.08 Aligned_cols=22 Identities=27% Similarity=0.447 Sum_probs=17.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHh
Q 015807 93 KDVKLALVDCDWDIEAALKELRKR 116 (400)
Q Consensus 93 ~dCKkAL~e~ngDiekAi~~LRkk 116 (400)
...++++ -+||++.|++|+.+.
T Consensus 6 ~~I~~~I--~~g~i~~Ai~w~~~~ 27 (145)
T PF10607_consen 6 KKIRQAI--LNGDIDPAIEWLNEN 27 (145)
T ss_pred HHHHHHH--HcCCHHHHHHHHHHc
Confidence 3556777 689999999999863
No 83
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=22.87 E-value=64 Score=23.24 Aligned_cols=15 Identities=27% Similarity=0.136 Sum_probs=13.0
Q ss_pred CCCHHHHHHHHHHhc
Q 015807 103 DWDIEAALKELRKRG 117 (400)
Q Consensus 103 ngDiekAi~~LRkkG 117 (400)
+||++.|++|+.+..
T Consensus 14 ~g~~~~a~~~~~~~~ 28 (58)
T smart00668 14 KGDWDEALEWLSSLK 28 (58)
T ss_pred cCCHHHHHHHHHHcC
Confidence 799999999998654
No 84
>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=22.86 E-value=92 Score=25.43 Aligned_cols=48 Identities=15% Similarity=0.165 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHhchhhhhhhcccccC-CceEEEEecCCeEEEEEEecccc
Q 015807 104 WDIEAALKELRKRGKVLASKKSSRTAT-EGLLALAQNESKAAVIELNCETD 153 (400)
Q Consensus 104 gDiekAi~~LRkkG~akA~Kka~R~a~-EGlV~~~~~~~~aalVElNCETD 153 (400)
-|++++.+.|+++|+.--.. ..+... -|. .+++.+-.|-++|+.|+.|
T Consensus 73 ~dv~~~~~~l~~~G~~~~~~-~~~~~~~~~~-~~~~~DPdG~~iE~~~~~~ 121 (122)
T cd07265 73 ADLEKLEARLQAYGVAVERI-PAGELPGVGR-RVRFQLPSGHTMELYADKE 121 (122)
T ss_pred HHHHHHHHHHHHCCCcEEEc-ccCCCCCCce-EEEEECCCCCEEEEEEecc
Confidence 48999999999999753211 111111 122 4566666788999999876
No 85
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=22.29 E-value=1.7e+02 Score=25.94 Aligned_cols=51 Identities=8% Similarity=0.147 Sum_probs=37.4
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhc----CCCHHHHHHHHHHh
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDC----DWDIEAALKELRKR 116 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~----ngDiekAi~~LRkk 116 (400)
...|.|+... ...+..|+.||+ +|.++.+.+.-|... +.+.+...+.|.++
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 556889999986 699999999988643 33566667777654
No 86
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=21.77 E-value=32 Score=37.42 Aligned_cols=27 Identities=15% Similarity=0.042 Sum_probs=24.2
Q ss_pred hcCCCHHHHHHHHHhcCCCHHHHHHHH
Q 015807 87 QTSAPMKDVKLALVDCDWDIEAALKEL 113 (400)
Q Consensus 87 ~Tgagm~dCKkAL~e~ngDiekAi~~L 113 (400)
.-|.....|+|||.+.|+|++.+++|.
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 368888999999999999999999885
No 87
>PRK00239 rpsT 30S ribosomal protein S20; Reviewed
Probab=21.71 E-value=88 Score=25.99 Aligned_cols=35 Identities=34% Similarity=0.458 Sum_probs=22.0
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhchhhhhhhcccccCCceE
Q 015807 93 KDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLL 134 (400)
Q Consensus 93 ~dCKkAL~e~ngDiekAi~~LRkkG~akA~Kka~R~a~EGlV 134 (400)
..+..|+++ ||.|.|.++|.+ +.+.-|+.+.-|+|
T Consensus 33 Kk~~~ai~~--~~~~~a~~~~~~-----a~s~iDka~~Kgii 67 (88)
T PRK00239 33 KKVEAAIAA--GDKEAAEEALKA-----AQSKIDKAASKGVI 67 (88)
T ss_pred HHHHHHHHc--CCHHHHHHHHHH-----HHHHHHHHHHCCCc
Confidence 345556554 899999999985 44444444444544
No 88
>PRK09591 celC cellobiose phosphotransferase system IIA component; Reviewed
Probab=21.21 E-value=95 Score=26.52 Aligned_cols=28 Identities=14% Similarity=0.192 Sum_probs=23.1
Q ss_pred cCCCHHHHHHHHHhcC-CCHHHHHHHHHH
Q 015807 88 TSAPMKDVKLALVDCD-WDIEAALKELRK 115 (400)
Q Consensus 88 Tgagm~dCKkAL~e~n-gDiekAi~~LRk 115 (400)
.|-.=..|.+||..+. ||+++|.+.|++
T Consensus 17 aG~Ars~~~eAl~~ak~gdf~~A~~~l~e 45 (104)
T PRK09591 17 SGNARTEVHEAFAAMREGNFDLAEQKLNQ 45 (104)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 4555567889999885 999999999985
No 89
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=21.10 E-value=2.3e+02 Score=20.23 Aligned_cols=29 Identities=28% Similarity=0.444 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHhcCCCHHHHHHHHH
Q 015807 76 EQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELR 114 (400)
Q Consensus 76 ~~~~lIK~LR~~Tgagm~dCKkAL~e~ngDiekAi~~LR 114 (400)
+.++.+++|=++||.|+.+- +++|++.+-
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 90
>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=21.00 E-value=1.9e+02 Score=24.31 Aligned_cols=50 Identities=28% Similarity=0.296 Sum_probs=36.3
Q ss_pred eeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC-C--CHHHHHHHHHHh
Q 015807 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD-W--DIEAALKELRKR 116 (400)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n-g--DiekAi~~LRkk 116 (400)
..|.|+... ...+..|+.||+ .|.|+.+.|+-|.... | +.+...++|..+
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 556889999985 8999999999887532 3 356667777654
No 91
>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=20.80 E-value=1.2e+02 Score=26.47 Aligned_cols=51 Identities=22% Similarity=0.291 Sum_probs=37.0
Q ss_pred CHHHHHHHHHHhchhhhhhhcccccCCceEEEEecCCeEEEEEEecccccee
Q 015807 105 DIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFVS 156 (400)
Q Consensus 105 DiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalVElNCETDFVA 156 (400)
|++.+.+.|+++|..-... .+|....|...+++.+-.|.+||+.|.++-+.
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 4567888888888754321 23444556677888888899999999998884
No 92
>TIGR00823 EIIA-LAC phosphotransferase system enzyme II, lactose-specific, factor III. operon. While the Lac permeases consist of two polypeptide chains (IIA and IICB), the Chb permease of E. coli consists of three (IIA, IIB and IIC). In B. subtilis, a PTS permease similar to the Chb permease of E. coli is believed to transport lichenan (a b-1,3;1,4 glucan) degradation products, oligosaccharides of 2-4 glucose units. This model is specific for the IIA subunit of the Lac PTS family.
Probab=20.73 E-value=1e+02 Score=26.07 Aligned_cols=28 Identities=14% Similarity=0.032 Sum_probs=22.8
Q ss_pred cCCCHHHHHHHHHhcC-CCHHHHHHHHHH
Q 015807 88 TSAPMKDVKLALVDCD-WDIEAALKELRK 115 (400)
Q Consensus 88 Tgagm~dCKkAL~e~n-gDiekAi~~LRk 115 (400)
.|-.=..|-+||..+. ||+++|.+.|++
T Consensus 14 aG~Ars~~~eAl~~a~~gdfe~A~~~l~e 42 (99)
T TIGR00823 14 AGDARSKALEALKAAKAGDFAKARALVEQ 42 (99)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 4445567889999885 999999999985
No 93
>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=20.41 E-value=1.2e+02 Score=26.48 Aligned_cols=54 Identities=11% Similarity=0.099 Sum_probs=38.3
Q ss_pred CCHHHHHHHHHHhchhhhhhhcccccCCceEEEEecCCeEEEEEEeccccceecc
Q 015807 104 WDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFVSRN 158 (400)
Q Consensus 104 gDiekAi~~LRkkG~akA~Kka~R~a~EGlV~~~~~~~~aalVElNCETDFVArN 158 (400)
-|++++.+.|++.|+... .-.+|....+...+++.+-.|.+||+.|+.+..+..
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 367888999999887432 113444434556667777789999999999887653
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=20.38 E-value=1.9e+02 Score=24.00 Aligned_cols=50 Identities=10% Similarity=0.136 Sum_probs=35.0
Q ss_pred eeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC--C-----CHHHHHHHHHHh
Q 015807 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD--W-----DIEAALKELRKR 116 (400)
Q Consensus 63 ~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n--g-----DiekAi~~LRkk 116 (400)
..|.|+... ...+..|+.||+ +|.++.+.|.-|...+ | +.+...++|.++
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 456889999998 7999999999887543 2 234456667654
No 95
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, 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 domain
Probab=20.20 E-value=1.4e+02 Score=27.39 Aligned_cols=38 Identities=16% Similarity=0.249 Sum_probs=29.7
Q ss_pred eeeecccCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHhcC
Q 015807 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD 103 (400)
Q Consensus 62 ~~~r~~ss~~~~~~~~~~lIK~LR~~Tgagm~dCKkAL~e~n 103 (400)
...|.|+... ...+..|+.||+ .|.++.+||.-|...+
T Consensus 35 ~gyR~Y~~~d---l~rL~~I~~lr~-~G~sL~eI~~ll~~~~ 72 (172)
T cd04790 35 SNYRLYGERD---LERLEQICAYRS-AGVSLEDIRSLLQQPG 72 (172)
T ss_pred CCCccCCHHH---HHHHHHHHHHHH-cCCCHHHHHHHHhcCC
Confidence 4578888653 455789999975 9999999999887654
No 96
>cd00215 PTS_IIA_lac PTS_IIA, PTS system, lactose/cellobiose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. This family of proteins normally function as a homotrimer, stabilized by a centrally located metal ion. Separation into subunits is thought to occur after phosphorylation.
Probab=20.10 E-value=1.1e+02 Score=25.90 Aligned_cols=28 Identities=18% Similarity=0.071 Sum_probs=22.6
Q ss_pred cCCCHHHHHHHHHhcC-CCHHHHHHHHHH
Q 015807 88 TSAPMKDVKLALVDCD-WDIEAALKELRK 115 (400)
Q Consensus 88 Tgagm~dCKkAL~e~n-gDiekAi~~LRk 115 (400)
.|-.=..|-+||.++. ||+++|.+.|++
T Consensus 12 aG~Ars~~~eAl~~a~~g~fe~A~~~l~e 40 (97)
T cd00215 12 AGNARSKALEALKAAKEGDFAEAEELLEE 40 (97)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 3444567889999884 999999999986
No 97
>KOG4530 consensus Predicted flavoprotein [General function prediction only]
Probab=20.09 E-value=57 Score=30.49 Aligned_cols=94 Identities=18% Similarity=0.189 Sum_probs=58.5
Q ss_pred CcHHHHHHHHHHHhcceeeeeeeEEeeeCCCCeEEEEec---cCC----CCCCCcEEEEEEEeecCCCCCCchhhhHHHH
Q 015807 209 TTVQNAITEVAAIMGENVKLRRGFLLSASSPGVVSTYLH---TSP----QSGLGRIAGLLSLEVEDGSSSFDPLKRVGSE 281 (400)
Q Consensus 209 ~Tv~d~i~~~ia~iGENI~LrR~~~i~~~~~~~v~sYvH---~~~----~~~~Gkig~LV~l~~~~~~~~~~~~~~~ak~ 281 (400)
++|.+.-...+-..+-+|.=.-...|.+| .+-.+|-- |.. ++-.||=+.+|++-+-......+.+++++.-
T Consensus 67 ~~vd~y~~~~t~aw~~ki~~aD~ivFvtP--qYN~gypA~LKNAlD~lyheW~gKPalivSyGGhGGg~c~~qL~~v~~f 144 (199)
T KOG4530|consen 67 KSVDEYYPPVTEAWRQKILEADSIVFVTP--QYNFGYPAPLKNALDWLYHEWAGKPALIVSYGGHGGGRCQYQLRQVGVF 144 (199)
T ss_pred ccccccCcHHHHHHHHHHhhcceEEEecc--cccCCCchHHHHHHHHhhhhhcCCceEEEEecCCCCchHHHHHHHHHhh
Confidence 34555555555556666654444445443 23333421 110 2335899999999775444445678899999
Q ss_pred HHHHHhhcCCcc-cCccCCCHHHH
Q 015807 282 LAMHIVAQKPLF-LTKELVSADAL 304 (400)
Q Consensus 282 iAmHIaA~~P~~-ls~~~Vp~~vl 304 (400)
|-||++-..|.+ |....+|+.++
T Consensus 145 Lkm~vai~~P~~Tlp~~~~pq~~v 168 (199)
T KOG4530|consen 145 LKMHVAINKPEFTLPAFQPPQKFV 168 (199)
T ss_pred heeeeeccCcccccccccCchhcc
Confidence 999999999985 66677777654
Done!