Query 020628
Match_columns 323
No_of_seqs 175 out of 1716
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 03:54:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020628.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020628hhsearch_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 4.6E-64 1E-68 470.8 24.4 212 78-318 6-219 (296)
2 TIGR00116 tsf translation elon 100.0 2.8E-63 6.1E-68 470.5 25.0 210 78-318 5-214 (290)
3 PRK09377 tsf elongation factor 100.0 5.3E-63 1.2E-67 468.6 24.9 209 78-318 6-214 (290)
4 KOG1071 Mitochondrial translat 100.0 5.2E-51 1.1E-55 383.7 17.7 220 72-295 42-281 (340)
5 PRK12332 tsf elongation factor 100.0 1.5E-49 3.2E-54 358.9 17.3 157 78-237 5-196 (198)
6 CHL00098 tsf elongation factor 100.0 3.1E-48 6.7E-53 350.5 16.0 159 78-238 2-195 (200)
7 PF00889 EF_TS: Elongation fac 100.0 3.2E-41 6.8E-46 309.9 16.1 161 129-318 1-161 (221)
8 PF00889 EF_TS: Elongation fac 99.6 1.6E-15 3.4E-20 139.8 10.5 120 104-236 63-219 (221)
9 PRK12332 tsf elongation factor 99.6 1.5E-15 3.2E-20 137.7 9.0 77 237-318 56-133 (198)
10 TIGR00116 tsf translation elon 99.6 7.7E-15 1.7E-19 140.0 13.6 116 104-237 119-271 (290)
11 CHL00098 tsf elongation factor 99.6 1.4E-15 3.1E-20 137.9 8.0 77 237-318 53-131 (200)
12 PRK09377 tsf elongation factor 99.6 2.1E-14 4.6E-19 137.0 12.1 117 103-237 118-271 (290)
13 COG0264 Tsf Translation elonga 99.6 5.7E-14 1.2E-18 133.0 14.0 118 103-236 121-275 (296)
14 PF00627 UBA: UBA/TS-N domain; 98.4 8.9E-07 1.9E-11 59.3 5.2 34 79-113 4-37 (37)
15 PRK06369 nac nascent polypepti 97.5 0.00017 3.7E-09 60.3 5.0 37 79-115 78-114 (115)
16 TIGR00264 alpha-NAC-related pr 97.4 0.00026 5.6E-09 59.2 4.8 36 79-114 80-115 (116)
17 smart00165 UBA Ubiquitin assoc 97.3 0.00059 1.3E-08 45.2 4.8 34 79-113 3-36 (37)
18 cd00194 UBA Ubiquitin Associat 97.2 0.00084 1.8E-08 44.6 4.8 35 79-114 3-37 (38)
19 KOG1071 Mitochondrial translat 95.7 0.024 5.2E-07 55.0 6.2 45 237-288 102-147 (340)
20 PF14555 UBA_4: UBA-like domai 95.3 0.037 8.1E-07 38.1 4.6 37 79-115 2-38 (43)
21 PF03943 TAP_C: TAP C-terminal 94.4 0.031 6.7E-07 40.2 2.3 37 79-115 2-38 (51)
22 COG1308 EGD2 Transcription fac 93.8 0.12 2.5E-06 43.8 5.0 36 79-114 86-121 (122)
23 smart00804 TAP_C C-terminal do 93.6 0.24 5.1E-06 37.3 5.8 40 76-115 11-50 (63)
24 PF00542 Ribosomal_L12: Riboso 90.4 0.22 4.9E-06 37.9 2.4 28 77-104 13-40 (68)
25 PF02845 CUE: CUE domain; Int 88.2 1.5 3.4E-05 29.7 5.2 37 79-115 3-40 (42)
26 PRK06771 hypothetical protein; 86.5 0.76 1.7E-05 37.2 3.2 23 78-100 69-91 (93)
27 PF06972 DUF1296: Protein of u 81.3 5.3 0.00011 29.8 5.5 38 78-115 6-44 (60)
28 TIGR00855 L12 ribosomal protei 80.6 3.2 6.8E-05 35.5 4.7 30 77-106 71-100 (126)
29 PF08938 HBS1_N: HBS1 N-termin 79.4 0.95 2.1E-05 35.2 1.1 45 80-124 31-78 (79)
30 smart00546 CUE Domain that may 79.1 6.5 0.00014 26.6 5.1 37 79-115 4-41 (43)
31 PRK00157 rplL 50S ribosomal pr 78.8 3.7 8.1E-05 34.9 4.6 28 77-104 68-95 (123)
32 cd00387 Ribosomal_L7_L12 Ribos 75.1 6.1 0.00013 33.7 4.9 30 77-106 73-102 (127)
33 PF08285 DPM3: Dolichol-phosph 75.0 1.1 2.3E-05 36.2 0.3 28 92-119 63-90 (91)
34 CHL00083 rpl12 ribosomal prote 73.8 6.4 0.00014 33.8 4.8 30 77-106 76-105 (131)
35 COG0222 RplL Ribosomal protein 71.6 6.1 0.00013 33.5 4.0 26 78-103 70-95 (124)
36 COG4008 Predicted metal-bindin 70.5 11 0.00024 32.4 5.3 28 89-117 125-152 (153)
37 PF12651 RHH_3: Ribbon-helix-h 64.9 15 0.00032 25.4 4.3 39 65-115 3-41 (44)
38 cd04772 HTH_TioE_rpt1 First He 62.3 15 0.00032 29.6 4.4 53 62-119 34-87 (99)
39 cd01105 HTH_GlnR-like Helix-Tu 60.1 18 0.0004 28.3 4.6 51 63-118 36-86 (88)
40 COG0789 SoxR Predicted transcr 53.8 16 0.00034 29.8 3.4 40 62-105 34-73 (124)
41 cd01106 HTH_TipAL-Mta Helix-Tu 51.9 28 0.00061 27.8 4.5 48 63-117 35-82 (103)
42 KOG0944 Ubiquitin-specific pro 50.6 15 0.00033 39.4 3.4 28 88-115 645-672 (763)
43 cd04773 HTH_TioE_rpt2 Second H 50.2 32 0.0007 27.9 4.7 51 63-117 35-87 (108)
44 KOG4841 Dolichol-phosphate man 48.8 7.2 0.00016 31.2 0.6 30 90-119 65-94 (95)
45 cd04780 HTH_MerR-like_sg5 Heli 46.6 48 0.001 26.4 5.0 48 64-114 36-84 (95)
46 PF11626 Rap1_C: TRF2-interact 44.5 44 0.00096 26.2 4.5 34 81-115 1-34 (87)
47 cd04763 HTH_MlrA-like Helix-Tu 44.4 24 0.00053 25.8 2.8 34 62-99 34-67 (68)
48 PF03474 DMA: DMRTA motif; In 44.3 21 0.00045 24.4 2.2 17 97-113 22-38 (39)
49 cd04788 HTH_NolA-AlbR Helix-Tu 44.0 40 0.00087 26.7 4.2 48 62-116 34-81 (96)
50 cd01107 HTH_BmrR Helix-Turn-He 43.2 39 0.00084 27.4 4.1 52 63-120 36-87 (108)
51 PF13411 MerR_1: MerR HTH fami 42.0 19 0.00041 26.2 1.9 34 64-101 35-68 (69)
52 KOG1364 Predicted ubiquitin re 40.0 52 0.0011 32.8 5.0 43 78-120 7-50 (356)
53 PRK05441 murQ N-acetylmuramic 39.6 37 0.00081 32.8 4.0 32 84-115 242-273 (299)
54 KOG1715 Mitochondrial/chloropl 38.8 46 0.00099 30.3 4.1 26 77-102 132-157 (187)
55 cd04765 HTH_MlrA-like_sg2 Heli 37.7 69 0.0015 25.7 4.7 51 62-115 34-87 (99)
56 cd00592 HTH_MerR-like Helix-Tu 37.7 66 0.0014 25.2 4.6 51 63-117 34-86 (100)
57 cd04770 HTH_HMRTR Helix-Turn-H 37.5 71 0.0015 26.2 4.9 51 62-116 34-87 (123)
58 cd04766 HTH_HspR Helix-Turn-He 37.1 73 0.0016 24.8 4.7 35 63-100 35-69 (91)
59 cd04785 HTH_CadR-PbrR-like Hel 36.5 73 0.0016 26.5 4.9 51 62-116 34-87 (126)
60 cd04787 HTH_HMRTR_unk Helix-Tu 34.7 79 0.0017 26.5 4.8 50 63-116 35-87 (133)
61 cd04776 HTH_GnyR Helix-Turn-He 34.1 92 0.002 25.7 5.0 50 63-116 33-88 (118)
62 cd04764 HTH_MlrA-like_sg1 Heli 33.9 35 0.00076 24.8 2.3 34 62-99 33-66 (67)
63 smart00422 HTH_MERR helix_turn 33.6 56 0.0012 23.5 3.3 34 63-100 35-68 (70)
64 KOG2561 Adaptor protein NUB1, 33.5 38 0.00083 35.0 3.1 36 89-124 314-349 (568)
65 cd04768 HTH_BmrR-like Helix-Tu 33.2 76 0.0016 25.1 4.2 47 62-115 34-80 (96)
66 TIGR00274 N-acetylmuramic acid 31.1 61 0.0013 31.2 4.0 32 84-115 237-268 (291)
67 PF02954 HTH_8: Bacterial regu 30.4 57 0.0012 21.9 2.6 19 95-113 10-28 (42)
68 cd04784 HTH_CadR-PbrR Helix-Tu 30.3 1.1E+02 0.0023 25.4 4.8 50 62-115 34-86 (127)
69 PRK13752 putative transcriptio 30.0 88 0.0019 26.9 4.4 50 63-116 42-92 (144)
70 cd07257 THT_oxygenase_C The C- 29.9 90 0.002 26.3 4.5 51 104-155 76-129 (153)
71 TIGR02043 ZntR Zn(II)-responsi 28.7 1.2E+02 0.0026 25.5 4.9 52 62-117 35-90 (131)
72 cd04786 HTH_MerR-like_sg7 Heli 28.3 1.2E+02 0.0026 25.6 4.9 51 62-116 34-86 (131)
73 PF00216 Bac_DNA_binding: Bact 28.1 70 0.0015 24.4 3.2 30 78-107 4-33 (90)
74 cd01282 HTH_MerR-like_sg3 Heli 27.5 1.2E+02 0.0026 24.7 4.6 50 63-116 34-89 (112)
75 cd01109 HTH_YyaN Helix-Turn-He 27.2 1.5E+02 0.0032 24.0 5.1 51 63-117 35-88 (113)
76 cd04782 HTH_BltR Helix-Turn-He 27.0 1.3E+02 0.0029 23.7 4.7 51 63-119 35-85 (97)
77 TIGR02054 MerD mercuric resist 26.5 1.5E+02 0.0032 24.9 5.0 38 62-103 37-74 (120)
78 PF10607 CLTH: CTLH/CRA C-term 26.3 70 0.0015 26.6 3.1 22 93-116 6-27 (145)
79 cd04783 HTH_MerR1 Helix-Turn-H 26.2 1.4E+02 0.0029 24.8 4.8 50 63-116 35-85 (126)
80 PRK12570 N-acetylmuramic acid- 26.2 82 0.0018 30.4 3.9 33 83-115 237-269 (296)
81 cd05007 SIS_Etherase N-acetylm 25.9 37 0.00081 31.9 1.5 29 82-110 227-255 (257)
82 PRK09514 zntR zinc-responsive 25.2 1.5E+02 0.0032 25.3 4.9 52 62-117 35-90 (140)
83 cd07249 MMCE Methylmalonyl-CoA 25.1 1.6E+02 0.0034 22.8 4.8 45 104-149 81-127 (128)
84 PRK04358 hypothetical protein; 25.0 1.2E+02 0.0026 28.3 4.5 53 63-116 84-149 (217)
85 PF13986 DUF4224: Domain of un 24.8 96 0.0021 21.8 3.0 33 82-127 6-38 (47)
86 cd08347 PcpA_C_like C-terminal 24.8 63 0.0014 27.6 2.6 57 104-164 77-133 (157)
87 smart00668 CTLH C-terminal to 24.6 57 0.0012 22.6 1.9 16 103-118 14-29 (58)
88 TIGR02047 CadR-PbrR Cd(II)/Pb( 24.5 1.7E+02 0.0037 24.4 5.1 50 62-115 34-86 (127)
89 COG1437 CyaB Adenylate cyclase 24.4 1.1E+02 0.0023 27.8 3.9 65 92-156 71-142 (178)
90 PF03765 CRAL_TRIO_N: CRAL/TRI 24.3 73 0.0016 22.3 2.4 20 96-115 35-54 (55)
91 cd08362 BphC5-RrK37_N_like N-t 24.3 1.2E+02 0.0026 23.5 3.9 50 104-153 70-119 (120)
92 KOG3763 mRNA export factor TAP 23.9 1.4E+02 0.0029 31.8 5.1 38 78-115 536-573 (585)
93 PRK09591 celC cellobiose phosp 23.4 83 0.0018 25.8 2.9 30 86-115 15-45 (104)
94 cd00215 PTS_IIA_lac PTS_IIA, P 23.2 75 0.0016 25.8 2.6 30 87-116 11-41 (97)
95 cd04777 HTH_MerR-like_sg1 Heli 23.0 1.9E+02 0.0041 23.1 5.0 50 64-117 34-90 (107)
96 TIGR00823 EIIA-LAC phosphotran 22.8 90 0.002 25.4 3.0 30 86-115 12-42 (99)
97 cd04769 HTH_MerR2 Helix-Turn-H 22.6 1.8E+02 0.0039 23.7 4.8 50 63-116 34-87 (116)
98 PF07442 Ponericin: Ponericin; 22.4 65 0.0014 20.4 1.5 13 106-118 6-18 (29)
99 cd00591 HU_IHF Integration hos 22.3 1.1E+02 0.0023 23.3 3.2 28 79-106 4-31 (87)
100 PF10178 DUF2372: Uncharacteri 21.7 2.5E+02 0.0055 22.4 5.3 40 274-313 43-87 (90)
101 cd01108 HTH_CueR Helix-Turn-He 21.5 2E+02 0.0044 23.8 5.0 52 62-117 34-88 (127)
102 cd04790 HTH_Cfa-like_unk Helix 20.9 1.4E+02 0.003 26.4 4.1 39 62-104 35-73 (172)
103 cd07237 BphC1-RGP6_C_like C-te 20.9 1.4E+02 0.0031 25.1 4.0 50 105-155 86-135 (154)
104 TIGR02044 CueR Cu(I)-responsiv 20.2 2.2E+02 0.0049 23.5 5.0 51 62-116 34-87 (127)
105 PHA01735 hypothetical protein 20.0 51 0.0011 25.4 0.9 18 101-118 30-47 (76)
No 1
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.6e-64 Score=470.78 Aligned_cols=212 Identities=42% Similarity=0.575 Sum_probs=192.0
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHHhchhhhcccccccccCCceEEEec--CCeEEEEEEecCCchh
Q 020628 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQN--ESKAAVIELNCETDFV 155 (323)
Q Consensus 78 ~~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk~G~a~A~Kr~~R~a~EGlV~~yv~--~~~avlVElncETDFV 155 (323)
+++||+||++||+|||||||||+|++||+|+|++|||++|+++|.||++|+++||+|..+++ +++|+|||||||||||
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 67999999999999999999999999999999999999999999999999999999999995 5599999999999999
Q ss_pred hhcHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHhcccccCCCCCCCCcccHHHHHHHHHHhhccceEEeEEEEee
Q 020628 156 SRNEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLS 235 (323)
Q Consensus 156 Arn~~F~~Lak~IA~~iaa~~~~~p~~~~~~~v~~e~l~~~~~lldq~~id~~~TV~d~i~e~ia~~GEnI~L~Rf~r~~ 235 (323)
|+|+.|+.|+++|+.+++...+. +.|.+... +++++.||++.+..+++++||||.|||+..++
T Consensus 86 AkN~~F~~l~~~ia~~~l~~~~~----------~ve~l~~~-------~~~~~~tv~e~~~~~~AkIGENi~lRR~~~~~ 148 (296)
T COG0264 86 AKNAEFQELANKIAKAALEKKPA----------DVEELKAA-------FEPGGKTVEEEIAALIAKIGENISLRRFAVLE 148 (296)
T ss_pred eCChhHHHHHHHHHHHHHHhCcc----------cHHHHHhh-------hcccCccHHHHHHHHHHHhccceeEEEEEEee
Confidence 99999999999999999988732 23555432 23457899999999999999999999999998
Q ss_pred ecCCCeeEEEecCCCCCCCCcEEEEEEEeecCCCCCCchhHHHHHHHHHHHhhcCCcccCcCCCCHHHHHHHHHHHHHhh
Q 020628 236 ASSPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQD 315 (323)
Q Consensus 236 ~~~~~~v~~Y~H~~~~~~~Grig~LV~l~~~~~~~~~~~~~~la~~IAmHIvA~~P~~ls~~~Vp~~vle~Er~i~~~qa 315 (323)
..+ +.+++|+|++ ||||+||.+++.+ ...++|++|||||||++|+||++++||++++++||+|+.+|+
T Consensus 149 ~~~-~~v~~Y~H~~-----griGVlv~~~~~~------~~~~~ak~iAMHiAA~~P~~ls~~dV~~e~v~~Er~i~~~~~ 216 (296)
T COG0264 149 AGD-GVVGSYLHGN-----GRIGVLVALKGGA------ADEELAKDIAMHIAAMNPQYLSREDVPAEVVEKEREIFLAQL 216 (296)
T ss_pred cCc-ccEEEEEeCC-----CcEEEEEEEeccc------hHHHHHHHHHHHHHhcCCccCChhhCCHHHHHHHHHHHHHHH
Confidence 544 7899999998 9999999999751 246899999999999999999999999999999999999977
Q ss_pred cCc
Q 020628 316 MHP 318 (323)
Q Consensus 316 ~~~ 318 (323)
+.+
T Consensus 217 ~~~ 219 (296)
T COG0264 217 KAE 219 (296)
T ss_pred Hhc
Confidence 654
No 2
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=100.00 E-value=2.8e-63 Score=470.47 Aligned_cols=210 Identities=35% Similarity=0.521 Sum_probs=189.4
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHHhchhhhcccccccccCCceEEEecCCeEEEEEEecCCchhhh
Q 020628 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFVSR 157 (323)
Q Consensus 78 ~~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk~G~a~A~Kr~~R~a~EGlV~~yv~~~~avlVElncETDFVAr 157 (323)
+++||+||++||+|||||||||+++|||+|+|++|||++|+++|.||++|.++||+|+++++++.|+|||||||||||||
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 56999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHhcccccCCCCCCCCcccHHHHHHHHHHhhccceEEeEEEEeeec
Q 020628 158 NEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLSAS 237 (323)
Q Consensus 158 n~~F~~Lak~IA~~iaa~~~~~p~~~~~~~v~~e~l~~~~~lldq~~id~~~TV~d~i~e~ia~~GEnI~L~Rf~r~~~~ 237 (323)
|+.|++|+++|+++++...+. +.+.+... ++ +++.|| |.+.++++++||||+|+||.++..
T Consensus 85 ne~F~~l~~~ia~~~~~~~~~----------~~e~l~~~------~~-~~~~tv-d~i~~~~a~iGEnI~lrR~~~~~~- 145 (290)
T TIGR00116 85 NAGFKEFANKLLDELKANKIT----------TLEELQAQ------EL-ENREKV-EYLAALAAKIGENINLRRVAVLEG- 145 (290)
T ss_pred ChHHHHHHHHHHHHHHhcCCC----------CHHHHhhc------cc-cCCCcH-HHHHHHHHHhccceEEEEEEEEec-
Confidence 999999999999999876422 23444432 22 345799 999999999999999999999985
Q ss_pred CCCeeEEEecCCCCCCCCcEEEEEEEeecCCCCCCchhHHHHHHHHHHHhhcCCcccCcCCCCHHHHHHHHHHHHHhhcC
Q 020628 238 SPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQDMH 317 (323)
Q Consensus 238 ~~~~v~~Y~H~~~~~~~Grig~LV~l~~~~~~~~~~~~~~la~~IAmHIvA~~P~~ls~~~Vp~~vle~Er~i~~~qa~~ 317 (323)
+++++++|+|++ ||||+||.+++..+ .++|++||||||||+|.||++++||++++++||+|+++|++.
T Consensus 146 ~~~~v~~Y~H~~-----gkigvlv~~~~~~~-------~~~ak~iAmhIaA~~P~~l~~~~vp~~vie~Erei~~~~~~~ 213 (290)
T TIGR00116 146 DSNVIGSYLHAG-----ARIGVLVALKGKAD-------EELAKHIAMHVAASKPQFIDPDDVSAEVVKKERQIQTDQAEL 213 (290)
T ss_pred CCCcEEEEEcCC-----CcEEEEEEEecCch-------HHHHHHHHHHHHhcCCccCchhhCCHHHHHHHHHHHHHHHHh
Confidence 447999999986 99999999986432 369999999999999999999999999999999999999876
Q ss_pred c
Q 020628 318 P 318 (323)
Q Consensus 318 ~ 318 (323)
+
T Consensus 214 ~ 214 (290)
T TIGR00116 214 S 214 (290)
T ss_pred c
Confidence 4
No 3
>PRK09377 tsf elongation factor Ts; Provisional
Probab=100.00 E-value=5.3e-63 Score=468.55 Aligned_cols=209 Identities=46% Similarity=0.609 Sum_probs=191.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHHhchhhhcccccccccCCceEEEecCCeEEEEEEecCCchhhh
Q 020628 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFVSR 157 (323)
Q Consensus 78 ~~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk~G~a~A~Kr~~R~a~EGlV~~yv~~~~avlVElncETDFVAr 157 (323)
+++||+||++||+|||||||||+++|||+|+|++|||++|+++|.||++|.++||+|+++++++.|+|||||||||||||
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 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHhcccccCCCCCCCCcccHHHHHHHHHHhhccceEEeEEEEeeec
Q 020628 158 NEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGETTVQNAITEVAAIMGENVKLRRGFLLSAS 237 (323)
Q Consensus 158 n~~F~~Lak~IA~~iaa~~~~~p~~~~~~~v~~e~l~~~~~lldq~~id~~~TV~d~i~e~ia~~GEnI~L~Rf~r~~~~ 237 (323)
|+.|++|+++|+.++++..+. +.+.+...++ ++.||+|.+.++++++||||+|+||.+++.
T Consensus 86 ne~F~~l~~~i~~~~l~~~~~----------~~e~ll~~~~--------~g~tv~d~i~~~~~~iGEnI~l~R~~~~~~- 146 (290)
T PRK09377 86 NEDFQALANEVAEAALAAKPA----------DVEALLALKL--------DGGTVEEARTELIAKIGENISLRRFARLEK- 146 (290)
T ss_pred ChHHHHHHHHHHHHHHhcCCC----------CHHHHHhccc--------cCCcHHHHHHHHHHHhcCceEEEEEEEEee-
Confidence 999999999999999886532 3355544332 367999999999999999999999999985
Q ss_pred CCCeeEEEecCCCCCCCCcEEEEEEEeecCCCCCCchhHHHHHHHHHHHhhcCCcccCcCCCCHHHHHHHHHHHHHhhcC
Q 020628 238 SPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQDMH 317 (323)
Q Consensus 238 ~~~~v~~Y~H~~~~~~~Grig~LV~l~~~~~~~~~~~~~~la~~IAmHIvA~~P~~ls~~~Vp~~vle~Er~i~~~qa~~ 317 (323)
+++.+++|+|++ ||||+||.+++.+ .++|++|||||||++|.||++++||++++++||+|+++|++.
T Consensus 147 ~~~~i~~Y~H~~-----gkigvlV~~~~~~--------~~~ak~iAMhIaA~~P~~l~~~~vp~~~i~~E~~i~~~~~~~ 213 (290)
T PRK09377 147 DGGVVGSYLHGG-----GRIGVLVALEGGD--------EELAKDIAMHIAAMNPEYLSREDVPAEVVEKEREIAKEQAKE 213 (290)
T ss_pred cCCEEEEEEcCC-----CcEEEEEEEccCc--------HHHHHHHHHHHHhcCCccCChhhCCHHHHHHHHHHHHHHHHh
Confidence 678999999986 9999999998642 379999999999999999999999999999999999999875
Q ss_pred c
Q 020628 318 P 318 (323)
Q Consensus 318 ~ 318 (323)
+
T Consensus 214 ~ 214 (290)
T PRK09377 214 E 214 (290)
T ss_pred c
Confidence 4
No 4
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.2e-51 Score=383.72 Aligned_cols=220 Identities=32% Similarity=0.456 Sum_probs=179.2
Q ss_pred CcchHHHHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHH----hchhhhcccccccccCCceEEEecCCeEEEEE
Q 020628 72 PAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK----RGKVLASKKSSRTATEGLLALAQNESKAAVIE 147 (323)
Q Consensus 72 p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk----~G~a~A~Kr~~R~a~EGlV~~yv~~~~avlVE 147 (323)
|+ ..++++||+||++||+||++|||||++||||++.|.+||+| .||.+|.|+++|.|+||+|++++++++.||||
T Consensus 42 ~s-~~~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~~L~k~aqk~g~~~A~K~~sR~t~eGlIgv~~~~~r~vlvE 120 (340)
T KOG1071|consen 42 PS-ASSKALLKKLREKTGASMVNCKKALEECGGDLVLAEEWLHKKAQKEGWSKAAKKASRTTKEGLIGVLQEDGRTVLVE 120 (340)
T ss_pred cc-cccHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHHHHHHHHHHhhhhHHhhhcccccccceeEEEEeCCeEEEEE
Confidence 54 24588999999999999999999999999999999999996 47778999999999999999999999889999
Q ss_pred EecCCchhhhcHHHHHHHHHHHHHHHHhc---CCCCCCCC-CCCCC-----HHHHhcccccCCCCCC-CCcccHHHHHHH
Q 020628 148 LNCETDFVSRNEIFQYLALALAKQALVAE---NVSQPVSG-LFPVG-----PEYLEGLKLNLDHPKI-GGETTVQNAITE 217 (323)
Q Consensus 148 lncETDFVArn~~F~~Lak~IA~~iaa~~---~~~p~~~~-~~~v~-----~e~l~~~~~lldq~~i-d~~~TV~d~i~e 217 (323)
|||||||||||+.|+.|+.+||+..++.. ...+...+ ...+. ....+ ..-++.+++. +++.|++|.|..
T Consensus 121 lNCETDFVARn~~Fq~Lv~~iA~~~l~~~~~~~~~~s~~s~e~~l~~~~~g~kl~~-~~~~l~~~~d~~gkvsl~d~l~~ 199 (340)
T KOG1071|consen 121 LNCETDFVARNDIFQDLVDQIALSVLAHCQTLKTKHSSYSKEKELEMDGRGFKLSE-SLSLLPNLPDVEGKVSLKDQLAL 199 (340)
T ss_pred eecccchhhccchHHHHHHHHHHHHHHhhhhcccChhhhhhhhhccccchHHHhhH-HHhhccCCCCcccceeHHHHHHH
Confidence 99999999999999999999999999832 11121111 11111 11111 1123445555 777799999999
Q ss_pred HHHhhccceEEeEEEEeeecCCCeeEEEecCCCCC------CCCcEEEEEEEeecCCCCCCchhHHHHHHHHHHHhhcCC
Q 020628 218 VAAIMGENVKLRRGFLLSASSPGVVSTYLHTSPQS------GLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVAQKP 291 (323)
Q Consensus 218 ~ia~~GEnI~L~Rf~r~~~~~~~~v~~Y~H~~~~~------~~Grig~LV~l~~~~~~~~~~~~~~la~~IAmHIvA~~P 291 (323)
.|+++||||+++|+.+|.++++..+++|.|+.+++ .+|++|+||+++...+. .-..+.+++.|+.||++|.|
T Consensus 200 ~i~~~GENvkvrR~~~~ka~~g~~l~~y~H~A~q~agt~~l~~g~~~alvAi~~~~s~--~~~~~~~~~~i~q~ivgm~p 277 (340)
T KOG1071|consen 200 AIGKLGENVKVRRAACMKAPSGTYLGSYSHGAPQSAGTHKLPLGEYGALVAINSVSSQ--LTSLEDVAKQICQHIVGMSP 277 (340)
T ss_pred HHHHhccceEEeEEEEEecCCCceEEeeecCCCCCccccccccccchhhhhhhhccch--hhhHHHHHHHHHHHhhccCh
Confidence 99999999999999999999999999999988631 27899999999865431 12245799999999999999
Q ss_pred cccC
Q 020628 292 LFLT 295 (323)
Q Consensus 292 ~~ls 295 (323)
..+.
T Consensus 278 ~s~~ 281 (340)
T KOG1071|consen 278 ESVG 281 (340)
T ss_pred hhhc
Confidence 9888
No 5
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=100.00 E-value=1.5e-49 Score=358.87 Aligned_cols=157 Identities=38% Similarity=0.474 Sum_probs=149.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHHhchhhhcccccccccCCceEEEec--CCeEEEEEEecCCchh
Q 020628 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQN--ESKAAVIELNCETDFV 155 (323)
Q Consensus 78 ~~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk~G~a~A~Kr~~R~a~EGlV~~yv~--~~~avlVElncETDFV 155 (323)
+++||+||++||+|||||||||.+++||+|+|++|||++|+++|.||++|.++||+|++|+| ++.|+|||||||||||
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 57999999999999999999999999999999999999999999999999999999999998 7889999999999999
Q ss_pred hhcHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHhccc--------------------------------ccCCCC
Q 020628 156 SRNEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLK--------------------------------LNLDHP 203 (323)
Q Consensus 156 Arn~~F~~Lak~IA~~iaa~~~~~p~~~~~~~v~~e~l~~~~--------------------------------~lldq~ 203 (323)
|||+.|++|+++|||||++++ |.|++.++||++.++++. ||++|+
T Consensus 85 a~n~~F~~lak~iamhIaA~~---P~~l~~~~v~~~~i~~E~~i~~~~~~~~gKP~~i~ekiv~Grl~K~~~E~~Ll~Q~ 161 (198)
T PRK12332 85 ARTEEFKELAKDIAMQIAAAN---PEYVSREDVPAEVIEKEKEIYRAQALNEGKPENIVEKIVEGRIEKFYKEVCLLEQP 161 (198)
T ss_pred ccCHHHHHHHHHHHHHHHhhC---CccCChhhCCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHhHHHHHHHhhhhhhcCc
Confidence 999999999999999999997 789999999998876652 889999
Q ss_pred CC-CCcccHHHHHHHHHHhhccceEEeEEEEeeec
Q 020628 204 KI-GGETTVQNAITEVAAIMGENVKLRRGFLLSAS 237 (323)
Q Consensus 204 ~i-d~~~TV~d~i~e~ia~~GEnI~L~Rf~r~~~~ 237 (323)
|+ |++.||+|.|.+.++++||||+|+||.||++.
T Consensus 162 fv~d~~~TV~e~l~e~~a~iGEnI~V~rF~R~evG 196 (198)
T PRK12332 162 FIKDPSKTVEDLIKEAIAKIGENIVVRRFARFELG 196 (198)
T ss_pred ccCCCCccHHHHHHHHHHHhCCCeEEEEEEEEEcC
Confidence 98 77889999999999999999999999999864
No 6
>CHL00098 tsf elongation factor Ts
Probab=100.00 E-value=3.1e-48 Score=350.47 Aligned_cols=159 Identities=37% Similarity=0.475 Sum_probs=150.4
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHHhchhhhcccccccccCCceEEEec--CCeEEEEEEecCCchh
Q 020628 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSRTATEGLLALAQN--ESKAAVIELNCETDFV 155 (323)
Q Consensus 78 ~~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk~G~a~A~Kr~~R~a~EGlV~~yv~--~~~avlVElncETDFV 155 (323)
+++||+||++||+||||||+||.+++||+|+|++|||++|+++|.||++|.+++|+|++|+| ++.|||||+|||||||
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 46999999999999999999999999999999999999999999999999999999999997 6789999999999999
Q ss_pred hhcHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHhccc--------------------------------ccCCCC
Q 020628 156 SRNEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLK--------------------------------LNLDHP 203 (323)
Q Consensus 156 Arn~~F~~Lak~IA~~iaa~~~~~p~~~~~~~v~~e~l~~~~--------------------------------~lldq~ 203 (323)
|||+.|++|+++|||||+++ ++|.|++.++||++.+++++ ||++|+
T Consensus 82 Arn~~F~~la~~IAmhiaA~--p~p~~l~~~~vp~~~i~~E~~i~~~~~~~~gKp~~i~ekiv~Grl~k~~~e~~LLeQ~ 159 (200)
T CHL00098 82 ARREEFQKLAKNIAMQIAAC--PNVKYVSLEDIPEEIINLEKKIESEKDDLQNKPEEIKEKIVEGRIKKRLKELSLLDQP 159 (200)
T ss_pred cccHHHHHHHHHHHHHHHcC--CCCeEecHHHCCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHhhHHHHHHHHhhhhcCc
Confidence 99999999999999999998 23789999999999887664 899999
Q ss_pred CC-CCcccHHHHHHHHHHhhccceEEeEEEEeeecC
Q 020628 204 KI-GGETTVQNAITEVAAIMGENVKLRRGFLLSASS 238 (323)
Q Consensus 204 ~i-d~~~TV~d~i~e~ia~~GEnI~L~Rf~r~~~~~ 238 (323)
|+ |++.||++.|.+.++++||||+|+||.||++.+
T Consensus 160 fv~D~~~TV~~~l~e~~akiGeni~V~rF~R~~vGe 195 (200)
T CHL00098 160 FIRDQSITVEELIKQNIAKLGENIQIRRFARFTLGE 195 (200)
T ss_pred ccCCCCccHHHHHHHHHHhcCCCcEEEEEEEEEecC
Confidence 99 889999999999999999999999999999754
No 7
>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=3.2e-41 Score=309.86 Aligned_cols=161 Identities=45% Similarity=0.661 Sum_probs=134.3
Q ss_pred ccCCceEEEecCCeEEEEEEecCCchhhhcHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHhcccccCCCCCCCCc
Q 020628 129 ATEGLLALAQNESKAAVIELNCETDFVSRNEIFQYLALALAKQALVAENVSQPVSGLFPVGPEYLEGLKLNLDHPKIGGE 208 (323)
Q Consensus 129 a~EGlV~~yv~~~~avlVElncETDFVArn~~F~~Lak~IA~~iaa~~~~~p~~~~~~~v~~e~l~~~~~lldq~~id~~ 208 (323)
|+||+|+++++++.|+||||||||||||||+.|++|+++|+.+++.... .+.+.+...++ + +
T Consensus 1 a~EG~V~~~v~~~~a~~vElncETDFVArn~~F~~l~~~ia~~~~~~~~----------~~~~~l~~~~~-------~-~ 62 (221)
T PF00889_consen 1 AAEGLVGIAVSGDKAAMVELNCETDFVARNEEFQNLAKEIADAALENKA----------SDVEELLALPL-------A-S 62 (221)
T ss_dssp --EEEEEEEEETTEEEEEEEEESSHHHHTSHHHHHHHHHHHHHHHCTTE----------ESHHHHHHSB----------S
T ss_pred CCceEEEEEEeCCcEEEEEEEccccceecCHHHHHHHHHHHHHHHHhCC----------CCHHHHHhccc-------c-c
Confidence 5799999999999999999999999999999999999999999984331 13456654443 2 3
Q ss_pred ccHHHHHHHHHHhhccceEEeEEEEeeecCCCeeEEEecCCCCCCCCcEEEEEEEeecCCCCCCchhHHHHHHHHHHHhh
Q 020628 209 TTVQNAITEVAAIMGENVKLRRGFLLSASSPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSSFDPLKRVGSELAMHIVA 288 (323)
Q Consensus 209 ~TV~d~i~e~ia~~GEnI~L~Rf~r~~~~~~~~v~~Y~H~~~~~~~Grig~LV~l~~~~~~~~~~~~~~la~~IAmHIvA 288 (323)
.||+|.+.++++++||||+|+|+.+++. +++++++|+|++ ||+|+||.++++.+.. +++|++|||||||
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-----GKIGVLVALEGDNDSA-----KEFAKDIAMHIAA 131 (221)
T ss_dssp SHHHHHHHHHHHHH-S-EEEEEEEEEE--TTSEEEEEEET------TTEEEEEEEET-SHGG-----HHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHhCCCEEEeEEEEEec-cCCEEEEEECCC-----CcEEEEEEEEcCcchH-----HHHHHHHHHHHhh
Confidence 7999999999999999999999999996 889999999998 9999999999866421 6899999999999
Q ss_pred cCCcccCcCCCCHHHHHHHHHHHHHhhcCc
Q 020628 289 QKPLFLTKELVSADALENEREILKSQDMHP 318 (323)
Q Consensus 289 ~~P~~ls~~~Vp~~vle~Er~i~~~qa~~~ 318 (323)
|+|.||++++||++++++||+|+++|++.+
T Consensus 132 ~~P~~l~~~~vp~~~~~~E~~i~~~~~~~~ 161 (221)
T PF00889_consen 132 MNPKYLSEEDVPAEVLEKEKEIAKEQAKAE 161 (221)
T ss_dssp H--SBSSCTGS-CCHHHHHHHHHHHHHHTT
T ss_pred hCccccCcccCCHHHHHHHHHHHHHHhhcc
Confidence 999999999999999999999999999864
No 8
>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=99.62 E-value=1.6e-15 Score=139.76 Aligned_cols=120 Identities=19% Similarity=0.243 Sum_probs=96.7
Q ss_pred CcHHHHHHHHH-Hhchhhhccccccccc-CCceEEEec--CCeEEEEEEecCCchhhhcHHHHHHHHHHHHHHHHhcCCC
Q 020628 104 WDIEAALKELR-KRGKVLASKKSSRTAT-EGLLALAQN--ESKAAVIELNCETDFVSRNEIFQYLALALAKQALVAENVS 179 (323)
Q Consensus 104 gDiekAi~~Lr-k~G~a~A~Kr~~R~a~-EGlV~~yv~--~~~avlVElncETDFVArn~~F~~Lak~IA~~iaa~~~~~ 179 (323)
..+..++..+. +.|+++..+|+.+... +|.++.|+| |++|+||+++++++.. ..++++|||||++++
T Consensus 63 ~tv~d~i~~~i~~igEnI~l~r~~~~~~~~~~v~~Y~H~~gkig~lV~~~~~~~~~------~~~ak~iAmhIaA~~--- 133 (221)
T PF00889_consen 63 KTVKDAIAELIAKIGENIQLRRAARISAPNGFVGSYVHNNGKIGVLVALEGDNDSA------KEFAKDIAMHIAAMN--- 133 (221)
T ss_dssp SHHHHHHHHHHHHH-S-EEEEEEEEEE-TTSEEEEEEET-TTEEEEEEEET-SHGG------HHHHHHHHHHHHHH----
T ss_pred ccHHHHHHHHHHHhCCCEEEeEEEEEeccCCEEEEEECCCCcEEEEEEEEcCcchH------HHHHHHHHHHHhhhC---
Confidence 66777777776 7899999999999874 899999999 5789999999998876 789999999999998
Q ss_pred CCCCCCCCCCHHHHhccc--------------------------------ccCCCCCC-CCcccHHHHHHHHHHhhccce
Q 020628 180 QPVSGLFPVGPEYLEGLK--------------------------------LNLDHPKI-GGETTVQNAITEVAAIMGENV 226 (323)
Q Consensus 180 p~~~~~~~v~~e~l~~~~--------------------------------~lldq~~i-d~~~TV~d~i~e~ia~~GEnI 226 (323)
|.+++.+++|++.+++++ |||+|+|+ |+++||+|.|.+ .|.+|
T Consensus 134 P~~l~~~~vp~~~~~~E~~i~~~~~~~~gKpe~i~ekIv~Gkl~k~~~e~~Ll~Q~fv~D~~~tV~~~l~~----~~~~i 209 (221)
T PF00889_consen 134 PKYLSEEDVPAEVLEKEKEIAKEQAKAEGKPENIIEKIVEGKLKKFYKENCLLEQPFVKDPKKTVKQYLKE----VGKEI 209 (221)
T ss_dssp -SBSSCTGS-CCHHHHHHHHHHHHHHTTTS-HHHHHHHHHHHHHHHHHHCBTCCSBETTETTSBHHHHHHC----TTHH-
T ss_pred ccccCcccCCHHHHHHHHHHHHHHhhccCCcHHHHHHHhhhhHhheehheeecCCCccCCCCccHHHHHHh----cCCCc
Confidence 789999999998887553 89999999 889999995554 54448
Q ss_pred EEeEEEEeee
Q 020628 227 KLRRGFLLSA 236 (323)
Q Consensus 227 ~L~Rf~r~~~ 236 (323)
+|.+|.||++
T Consensus 210 ~v~~F~R~~v 219 (221)
T PF00889_consen 210 KVVGFVRFEV 219 (221)
T ss_dssp EEEEEEEEET
T ss_pred EEEEEEEEec
Confidence 9999999986
No 9
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=99.61 E-value=1.5e-15 Score=137.70 Aligned_cols=77 Identities=32% Similarity=0.620 Sum_probs=70.0
Q ss_pred cCCCeeEEEecCCCCCCCCcEEEEEEEeecCCCCC-CchhHHHHHHHHHHHhhcCCcccCcCCCCHHHHHHHHHHHHHhh
Q 020628 237 SSPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSSS-FDPLKRVGSELAMHIVAQKPLFLTKELVSADALENEREILKSQD 315 (323)
Q Consensus 237 ~~~~~v~~Y~H~~~~~~~Grig~LV~l~~~~~~~~-~~~~~~la~~IAmHIvA~~P~~ls~~~Vp~~vle~Er~i~~~qa 315 (323)
..+|.+++|+|.+ |+.|+||+|++++++.. .+.+..||++|||||||++|.||++++||++++++||+|+++|+
T Consensus 56 ~~eG~i~~~i~~~-----~~~~~lve~n~ETDFVa~n~~F~~lak~iamhIaA~~P~~l~~~~v~~~~i~~E~~i~~~~~ 130 (198)
T PRK12332 56 AAEGLVGSYIHTG-----GRIGVLVELNCETDFVARTEEFKELAKDIAMQIAAANPEYVSREDVPAEVIEKEKEIYRAQA 130 (198)
T ss_pred ccCceEEEEEecC-----CCEEEEEEEeccCCccccCHHHHHHHHHHHHHHHhhCCccCChhhCCHHHHHHHHHHHHHHH
Confidence 4579999999986 89999999999999843 55677899999999999999999999999999999999999998
Q ss_pred cCc
Q 020628 316 MHP 318 (323)
Q Consensus 316 ~~~ 318 (323)
+.+
T Consensus 131 ~~~ 133 (198)
T PRK12332 131 LNE 133 (198)
T ss_pred Hhc
Confidence 864
No 10
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=99.61 E-value=7.7e-15 Score=139.96 Aligned_cols=116 Identities=15% Similarity=0.123 Sum_probs=99.2
Q ss_pred CcHHHHHHHHH-Hhchhhhccccccccc-CCceEEEec--CCeEEEEEEecCCchhhhcHHHHHHHHHHHHHHHHhcCCC
Q 020628 104 WDIEAALKELR-KRGKVLASKKSSRTAT-EGLLALAQN--ESKAAVIELNCETDFVSRNEIFQYLALALAKQALVAENVS 179 (323)
Q Consensus 104 gDiekAi~~Lr-k~G~a~A~Kr~~R~a~-EGlV~~yv~--~~~avlVElncETDFVArn~~F~~Lak~IA~~iaa~~~~~ 179 (323)
..+ +++..+. +.|+++..+|+.+... +|.|+.|+| |++|+||+++|++|. .|+++|||||++++
T Consensus 119 ~tv-d~i~~~~a~iGEnI~lrR~~~~~~~~~~v~~Y~H~~gkigvlv~~~~~~~~--------~~ak~iAmhIaA~~--- 186 (290)
T TIGR00116 119 EKV-EYLAALAAKIGENINLRRVAVLEGDSNVIGSYLHAGARIGVLVALKGKADE--------ELAKHIAMHVAASK--- 186 (290)
T ss_pred CcH-HHHHHHHHHhccceEEEEEEEEecCCCcEEEEEcCCCcEEEEEEEecCchH--------HHHHHHHHHHHhcC---
Confidence 367 5555555 7899999999999875 479999999 578999999997662 58999999999998
Q ss_pred CCCCCCCCCCHHHHhccc--------------------------------ccCCCCCC-CCcccHHHHHHHHHHhhccce
Q 020628 180 QPVSGLFPVGPEYLEGLK--------------------------------LNLDHPKI-GGETTVQNAITEVAAIMGENV 226 (323)
Q Consensus 180 p~~~~~~~v~~e~l~~~~--------------------------------~lldq~~i-d~~~TV~d~i~e~ia~~GEnI 226 (323)
|.|++.+++|++.+++++ |||+|||+ |++.||.|.+.+ .++
T Consensus 187 P~~l~~~~vp~~vie~Erei~~~~~~~~gKP~~i~eKIv~Grl~Kf~~E~~Ll~Q~fv~D~~~tV~~~l~~------~~~ 260 (290)
T TIGR00116 187 PQFIDPDDVSAEVVKKERQIQTDQAELSGKPKEIAEKMVEGRMKKFLAEISLLGQKFVMDPSKTVGQFLKE------KNA 260 (290)
T ss_pred CccCchhhCCHHHHHHHHHHHHHHHHhcCCcHHHHHHHhhhHHHHHhhhceeeecccccCCccCHHHHHHH------cCC
Confidence 889999999998887663 89999999 999999997777 459
Q ss_pred EEeEEEEeeec
Q 020628 227 KLRRGFLLSAS 237 (323)
Q Consensus 227 ~L~Rf~r~~~~ 237 (323)
+|.+|+||++.
T Consensus 261 ~v~~F~R~~vG 271 (290)
T TIGR00116 261 KVTEFIRFEVG 271 (290)
T ss_pred EEEEEEEEEec
Confidence 99999999974
No 11
>CHL00098 tsf elongation factor Ts
Probab=99.60 E-value=1.4e-15 Score=137.91 Aligned_cols=77 Identities=19% Similarity=0.427 Sum_probs=68.5
Q ss_pred cCCCeeEEEecCCCCCCCCcEEEEEEEeecCCC-CCCchhHHHHHHHHHHHhhc-CCcccCcCCCCHHHHHHHHHHHHHh
Q 020628 237 SSPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGS-SSFDPLKRVGSELAMHIVAQ-KPLFLTKELVSADALENEREILKSQ 314 (323)
Q Consensus 237 ~~~~~v~~Y~H~~~~~~~Grig~LV~l~~~~~~-~~~~~~~~la~~IAmHIvA~-~P~~ls~~~Vp~~vle~Er~i~~~q 314 (323)
..+|.+++|+|.+ |++|+||++++++++ +..+.+.++|++|||||||+ +|.||++++||++++++||+|+++|
T Consensus 53 ~~eG~V~~yiH~~-----gk~gvlVeln~ETDfVArn~~F~~la~~IAmhiaA~p~p~~l~~~~vp~~~i~~E~~i~~~~ 127 (200)
T CHL00098 53 TTEGLIESYIHTG-----GKLGVLVEINCETDFVARREEFQKLAKNIAMQIAACPNVKYVSLEDIPEEIINLEKKIESEK 127 (200)
T ss_pred cccCeEEEEEecC-----CCEEEEEEEecCcccccccHHHHHHHHHHHHHHHcCCCCeEecHHHCCHHHHHHHHHHHHHH
Confidence 3568999999986 899999999998775 23456789999999999999 7999999999999999999999999
Q ss_pred hcCc
Q 020628 315 DMHP 318 (323)
Q Consensus 315 a~~~ 318 (323)
++.+
T Consensus 128 ~~~~ 131 (200)
T CHL00098 128 DDLQ 131 (200)
T ss_pred HHhc
Confidence 9864
No 12
>PRK09377 tsf elongation factor Ts; Provisional
Probab=99.56 E-value=2.1e-14 Score=136.95 Aligned_cols=117 Identities=18% Similarity=0.178 Sum_probs=101.3
Q ss_pred CCcHHHHHHHHH-Hhchhhhcccccccc-cCCceEEEec--CCeEEEEEEecCCchhhhcHHHHHHHHHHHHHHHHhcCC
Q 020628 103 DWDIEAALKELR-KRGKVLASKKSSRTA-TEGLLALAQN--ESKAAVIELNCETDFVSRNEIFQYLALALAKQALVAENV 178 (323)
Q Consensus 103 ~gDiekAi~~Lr-k~G~a~A~Kr~~R~a-~EGlV~~yv~--~~~avlVElncETDFVArn~~F~~Lak~IA~~iaa~~~~ 178 (323)
+..+...+..+. +.|+++..+|+.+.. .+|.|+.|+| |++||||+++|+++ +|+++|||||++++
T Consensus 118 g~tv~d~i~~~~~~iGEnI~l~R~~~~~~~~~~i~~Y~H~~gkigvlV~~~~~~~---------~~ak~iAMhIaA~~-- 186 (290)
T PRK09377 118 GGTVEEARTELIAKIGENISLRRFARLEKDGGVVGSYLHGGGRIGVLVALEGGDE---------ELAKDIAMHIAAMN-- 186 (290)
T ss_pred CCcHHHHHHHHHHHhcCceEEEEEEEEeecCCEEEEEEcCCCcEEEEEEEccCcH---------HHHHHHHHHHHhcC--
Confidence 557888888887 789999999998886 4789999999 57899999999743 58999999999998
Q ss_pred CCCCCCCCCCCHHHHhccc--------------------------------ccCCCCCC-CCcccHHHHHHHHHHhhccc
Q 020628 179 SQPVSGLFPVGPEYLEGLK--------------------------------LNLDHPKI-GGETTVQNAITEVAAIMGEN 225 (323)
Q Consensus 179 ~p~~~~~~~v~~e~l~~~~--------------------------------~lldq~~i-d~~~TV~d~i~e~ia~~GEn 225 (323)
|.|++.+++|++.+++++ |||+|+|+ |++.||.+.|.+ .+
T Consensus 187 -P~~l~~~~vp~~~i~~E~~i~~~~~~~~gKP~~i~eKIv~Grl~Kf~~e~~Ll~Q~fi~D~~~tV~~~l~~------~~ 259 (290)
T PRK09377 187 -PEYLSREDVPAEVVEKEREIAKEQAKEEGKPEEIVEKIVEGRLNKFLKEVVLLEQPFVKDPKKTVGQLLKE------AG 259 (290)
T ss_pred -CccCChhhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHhHHHHHHhhhceeccCcccCCCCcCHHHHHHH------cC
Confidence 789999999988876552 89999999 999999997776 56
Q ss_pred eEEeEEEEeeec
Q 020628 226 VKLRRGFLLSAS 237 (323)
Q Consensus 226 I~L~Rf~r~~~~ 237 (323)
++|.+|+||++.
T Consensus 260 i~v~~F~R~evG 271 (290)
T PRK09377 260 AKVVGFVRFEVG 271 (290)
T ss_pred CEEEEEEEEEec
Confidence 999999999974
No 13
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=99.56 E-value=5.7e-14 Score=132.97 Aligned_cols=118 Identities=16% Similarity=0.160 Sum_probs=102.2
Q ss_pred CCcHHHHHHHHH-Hhchhhhcccccccc-cCCceEEEecC--CeEEEEEEecCCchhhhcHHHHHHHHHHHHHHHHhcCC
Q 020628 103 DWDIEAALKELR-KRGKVLASKKSSRTA-TEGLLALAQNE--SKAAVIELNCETDFVSRNEIFQYLALALAKQALVAENV 178 (323)
Q Consensus 103 ~gDiekAi~~Lr-k~G~a~A~Kr~~R~a-~EGlV~~yv~~--~~avlVElncETDFVArn~~F~~Lak~IA~~iaa~~~~ 178 (323)
+-.++.++..|. +.|+++-.+|+.+.. .+|.|++|+|+ ++||||++.+. | ....++++||||+++++
T Consensus 121 ~~tv~e~~~~~~AkIGENi~lRR~~~~~~~~~~v~~Y~H~~griGVlv~~~~~-~------~~~~~ak~iAMHiAA~~-- 191 (296)
T COG0264 121 GKTVEEEIAALIAKIGENISLRRFAVLEAGDGVVGSYLHGNGRIGVLVALKGG-A------ADEELAKDIAMHIAAMN-- 191 (296)
T ss_pred CccHHHHHHHHHHHhccceeEEEEEEeecCcccEEEEEeCCCcEEEEEEEecc-c------hHHHHHHHHHHHHHhcC--
Confidence 445777777776 789999999998877 45799999995 57999999997 3 45789999999999997
Q ss_pred CCCCCCCCCCCHHHHhccc--------------------------------ccCCCCCC-CCcccHHHHHHHHHHhhccc
Q 020628 179 SQPVSGLFPVGPEYLEGLK--------------------------------LNLDHPKI-GGETTVQNAITEVAAIMGEN 225 (323)
Q Consensus 179 ~p~~~~~~~v~~e~l~~~~--------------------------------~lldq~~i-d~~~TV~d~i~e~ia~~GEn 225 (323)
|.|++.++||++.+++++ |||+|||+ |+++||++.|.+. +
T Consensus 192 -P~~ls~~dV~~e~v~~Er~i~~~~~~~~gKP~~i~eKiVeGr~~Kf~~E~~Ll~Q~fV~d~~~TV~~~lke~------~ 264 (296)
T COG0264 192 -PQYLSREDVPAEVVEKEREIFLAQLKAEGKPENIVEKIVEGRMNKFLAEVCLLEQPFVKDPKKTVEQLLKEA------N 264 (296)
T ss_pred -CccCChhhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHhHHHHHHHHHHhhccCceecCcchhHHHHHHhc------C
Confidence 899999999999988764 89999999 9999999977774 7
Q ss_pred eEEeEEEEeee
Q 020628 226 VKLRRGFLLSA 236 (323)
Q Consensus 226 I~L~Rf~r~~~ 236 (323)
+++.+|+||++
T Consensus 265 ~~v~~FvR~ev 275 (296)
T COG0264 265 AKVTEFVRFEV 275 (296)
T ss_pred ceeeeeeeeec
Confidence 99999999996
No 14
>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=98.36 E-value=8.9e-07 Score=59.28 Aligned_cols=34 Identities=26% Similarity=0.358 Sum_probs=31.9
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHH
Q 020628 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKEL 113 (323)
Q Consensus 79 ~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~L 113 (323)
+.|++|+++ |.+-.+|++||..++||++.|++||
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 589999999 9999999999999999999999998
No 15
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=97.48 E-value=0.00017 Score=60.31 Aligned_cols=37 Identities=24% Similarity=0.322 Sum_probs=35.3
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHH
Q 020628 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 79 ~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk 115 (323)
++|+.++++||++..+|++||.++|||+-.|+-+|.+
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 6899999999999999999999999999999999874
No 16
>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=97.38 E-value=0.00026 Score=59.24 Aligned_cols=36 Identities=22% Similarity=0.386 Sum_probs=34.4
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHH
Q 020628 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELR 114 (323)
Q Consensus 79 ~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lr 114 (323)
++|+.++++||++..+||+||+++|||+-.|+-+|.
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 689999999999999999999999999999999885
No 17
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=97.27 E-value=0.00059 Score=45.17 Aligned_cols=34 Identities=26% Similarity=0.216 Sum_probs=30.7
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHH
Q 020628 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKEL 113 (323)
Q Consensus 79 ~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~L 113 (323)
+.|.+|++. |.+--+|+.||..++||+++|++||
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 357778776 8999999999999999999999998
No 18
>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=97.19 E-value=0.00084 Score=44.63 Aligned_cols=35 Identities=23% Similarity=0.241 Sum_probs=31.5
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHH
Q 020628 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELR 114 (323)
Q Consensus 79 ~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lr 114 (323)
+.|.+|++ .|.+-.+|..||..++||+++|++||.
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 36788887 499999999999999999999999985
No 19
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=95.68 E-value=0.024 Score=55.03 Aligned_cols=45 Identities=20% Similarity=0.355 Sum_probs=39.8
Q ss_pred cCCCeeEEEecCCCCCCCCcEEEEEEEeecCCCC-CCchhHHHHHHHHHHHhh
Q 020628 237 SSPGVVSTYLHTSPQSGLGRIAGLLSLEVEDGSS-SFDPLKRVGSELAMHIVA 288 (323)
Q Consensus 237 ~~~~~v~~Y~H~~~~~~~Grig~LV~l~~~~~~~-~~~~~~~la~~IAmHIvA 288 (323)
..+|.|+.|.|+ ||+ +||+|+|++++. +.+.++.|.++|||.+.+
T Consensus 102 t~eGlIgv~~~~------~r~-vlvElNCETDFVARn~~Fq~Lv~~iA~~~l~ 147 (340)
T KOG1071|consen 102 TKEGLIGVLQED------GRT-VLVELNCETDFVARNDIFQDLVDQIALSVLA 147 (340)
T ss_pred cccceeEEEEeC------CeE-EEEEeecccchhhccchHHHHHHHHHHHHHH
Confidence 357899999998 688 999999999984 477899999999999988
No 20
>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=95.32 E-value=0.037 Score=38.07 Aligned_cols=37 Identities=27% Similarity=0.275 Sum_probs=31.8
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHH
Q 020628 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 79 ~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk 115 (323)
++|.++..-||+.--.|++-|+.+|||++.|+..--.
T Consensus 2 e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~ 38 (43)
T PF14555_consen 2 EKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFD 38 (43)
T ss_dssp HHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4799999999999999999999999999999987544
No 21
>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=94.41 E-value=0.031 Score=40.18 Aligned_cols=37 Identities=24% Similarity=0.496 Sum_probs=32.9
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHH
Q 020628 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 79 ~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk 115 (323)
++|.+|..+||.-.-=|.+-|++++||++.|+....+
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 5899999999999999999999999999999999874
No 22
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=93.85 E-value=0.12 Score=43.80 Aligned_cols=36 Identities=25% Similarity=0.267 Sum_probs=33.0
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHH
Q 020628 79 NLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELR 114 (323)
Q Consensus 79 ~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lr 114 (323)
++||-.=++||++--+.+|||+++|||+-.||--|-
T Consensus 86 eDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~ 121 (122)
T COG1308 86 EDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLT 121 (122)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhc
Confidence 589999999999999999999999999999987663
No 23
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=93.63 E-value=0.24 Score=37.27 Aligned_cols=40 Identities=30% Similarity=0.518 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHH
Q 020628 76 EQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 76 ~~~~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk 115 (323)
.+..+|.++-.+||.-.-=|.+.|+++|||++.|+....+
T Consensus 11 ~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~~ 50 (63)
T smart00804 11 EQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFTE 50 (63)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3467999999999999999999999999999999998764
No 24
>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=90.37 E-value=0.22 Score=37.87 Aligned_cols=28 Identities=25% Similarity=0.321 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhcCC
Q 020628 77 QVNLIKQLREQTSAPMKDVKLALVDCDW 104 (323)
Q Consensus 77 ~~~lIK~LR~~Tga~~~dCKkAL~e~~g 104 (323)
.++.||.+|+.||.|++++|+..+....
T Consensus 13 ki~vIK~vR~~tgl~L~eAK~~vd~~p~ 40 (68)
T PF00542_consen 13 KIKVIKEVREITGLGLKEAKKLVDSLPK 40 (68)
T ss_dssp HHHHHHHHHHHC---HHHHHHHHCTTTE
T ss_pred hHHHHHHHHHHhCCcHHHHHHHHHhCCH
Confidence 4789999999999999999999988743
No 25
>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=88.23 E-value=1.5 Score=29.68 Aligned_cols=37 Identities=24% Similarity=0.328 Sum_probs=31.0
Q ss_pred HHHHHHHHHcC-CCHHHHHHHHHhcCCcHHHHHHHHHH
Q 020628 79 NLIKQLREQTS-APMKDVKLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 79 ~lIK~LR~~Tg-a~~~dCKkAL~e~~gDiekAi~~Lrk 115 (323)
+.|++|++.-. .+--.-+.+|.+++||+|.|++.|-+
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 46888888865 78889999999999999999998854
No 26
>PRK06771 hypothetical protein; Provisional
Probab=86.53 E-value=0.76 Score=37.17 Aligned_cols=23 Identities=22% Similarity=0.270 Sum_probs=20.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHH
Q 020628 78 VNLIKQLREQTSAPMKDVKLALV 100 (323)
Q Consensus 78 ~~lIK~LR~~Tga~~~dCKkAL~ 100 (323)
++.||.+|+.||+|+.+.|+...
T Consensus 69 i~AIK~~Re~tG~~L~eAK~yVD 91 (93)
T PRK06771 69 VTAVKRVREAFGFSLLEAKQYVD 91 (93)
T ss_pred hHHHHHHHHHcCCCHHHHHHHHh
Confidence 57899999999999999999764
No 27
>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=81.30 E-value=5.3 Score=29.78 Aligned_cols=38 Identities=16% Similarity=0.357 Sum_probs=34.5
Q ss_pred HHHHHHHHHHcCC-CHHHHHHHHHhcCCcHHHHHHHHHH
Q 020628 78 VNLIKQLREQTSA-PMKDVKLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 78 ~~lIK~LR~~Tga-~~~dCKkAL~e~~gDiekAi~~Lrk 115 (323)
-..|.-|++-||. +=-|-...|.+||.|-++|.+-|--
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 4689999999999 9999999999999999999988853
No 28
>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=80.56 E-value=3.2 Score=35.49 Aligned_cols=30 Identities=23% Similarity=0.258 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhcCCcH
Q 020628 77 QVNLIKQLREQTSAPMKDVKLALVDCDWDI 106 (323)
Q Consensus 77 ~~~lIK~LR~~Tga~~~dCKkAL~e~~gDi 106 (323)
.+..||.+|+-||.|+++.|+..+.+...+
T Consensus 71 Ki~vIK~vR~itgLgLkEAK~lVe~~P~~i 100 (126)
T TIGR00855 71 KIAVIKVVREITGLGLKEAKDLVEGAPKVL 100 (126)
T ss_pred hhHHHHHHHHHcCCcHHHHHHHHHhCcHHH
Confidence 367999999999999999999888775443
No 29
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=79.36 E-value=0.95 Score=35.17 Aligned_cols=45 Identities=31% Similarity=0.296 Sum_probs=33.9
Q ss_pred HHHHHHHHcCCCH---HHHHHHHHhcCCcHHHHHHHHHHhchhhhccc
Q 020628 80 LIKQLREQTSAPM---KDVKLALVDCDWDIEAALKELRKRGKVLASKK 124 (323)
Q Consensus 80 lIK~LR~~Tga~~---~dCKkAL~e~~gDiekAi~~Lrk~G~a~A~Kr 124 (323)
.+-++|+.-|... .+-++||-.++.|+++|+.||+++..+...|+
T Consensus 31 ~l~~vr~~Lg~~~~~e~~i~eal~~~~fDvekAl~~Ll~~~~~~~~~~ 78 (79)
T PF08938_consen 31 CLPQVREVLGDYVPPEEQIKEALWHYYFDVEKALDYLLSKFKKKKPKK 78 (79)
T ss_dssp HCCCHHHHCCCCC--CCHHHHHHHHTTT-CCHHHHHHHHCCHSSS---
T ss_pred HHHHHHHHHcccCCCHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCC
Confidence 4556788888644 68999999999999999999998776665543
No 30
>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=79.13 E-value=6.5 Score=26.63 Aligned_cols=37 Identities=16% Similarity=0.252 Sum_probs=30.6
Q ss_pred HHHHHHHHHcC-CCHHHHHHHHHhcCCcHHHHHHHHHH
Q 020628 79 NLIKQLREQTS-APMKDVKLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 79 ~lIK~LR~~Tg-a~~~dCKkAL~e~~gDiekAi~~Lrk 115 (323)
+.|+.|++.-- .+--..+..|.+++||+|.|++.|-+
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 46778887754 77788999999999999999988753
No 31
>PRK00157 rplL 50S ribosomal protein L7/L12; Reviewed
Probab=78.79 E-value=3.7 Score=34.92 Aligned_cols=28 Identities=25% Similarity=0.293 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhcCC
Q 020628 77 QVNLIKQLREQTSAPMKDVKLALVDCDW 104 (323)
Q Consensus 77 ~~~lIK~LR~~Tga~~~dCKkAL~e~~g 104 (323)
.+..||.+|+-||.|+++.|+..+....
T Consensus 68 Ki~vIK~vR~itgLgLkEAK~lVe~~P~ 95 (123)
T PRK00157 68 KIAVIKAVREITGLGLKEAKDLVEGAPK 95 (123)
T ss_pred hHHHHHHHHHHhCCCHHHHHHHHHhCCH
Confidence 3779999999999999999998877643
No 32
>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=75.06 E-value=6.1 Score=33.74 Aligned_cols=30 Identities=23% Similarity=0.298 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhcCCcH
Q 020628 77 QVNLIKQLREQTSAPMKDVKLALVDCDWDI 106 (323)
Q Consensus 77 ~~~lIK~LR~~Tga~~~dCKkAL~e~~gDi 106 (323)
.+..||.+|.-||.|+++.|+..+.+..-+
T Consensus 73 Ki~vIK~VR~it~LgLkEAK~lVe~~P~~i 102 (127)
T cd00387 73 KIAVIKEVREITGLGLKEAKDLVESAPKVL 102 (127)
T ss_pred hHHHHHHHHHHhCCChHHHHHHHHhCcHHH
Confidence 478999999999999999999888775443
No 33
>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=74.98 E-value=1.1 Score=36.19 Aligned_cols=28 Identities=29% Similarity=0.346 Sum_probs=25.9
Q ss_pred HHHHHHHHHhcCCcHHHHHHHHHHhchh
Q 020628 92 MKDVKLALVDCDWDIEAALKELRKRGKV 119 (323)
Q Consensus 92 ~~dCKkAL~e~~gDiekAi~~Lrk~G~a 119 (323)
+.||.+|=+|-..+|++|.+.||+||..
T Consensus 63 FnDcpeA~~eL~~eI~eAK~dLr~kGv~ 90 (91)
T PF08285_consen 63 FNDCPEAAKELQKEIKEAKADLRKKGVD 90 (91)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 5599999999999999999999999964
No 34
>CHL00083 rpl12 ribosomal protein L12
Probab=73.84 E-value=6.4 Score=33.84 Aligned_cols=30 Identities=20% Similarity=0.252 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhcCCcH
Q 020628 77 QVNLIKQLREQTSAPMKDVKLALVDCDWDI 106 (323)
Q Consensus 77 ~~~lIK~LR~~Tga~~~dCKkAL~e~~gDi 106 (323)
.+..||.+|+-||.|+++.|+..+...-.+
T Consensus 76 Ki~vIK~vr~it~lgLkeaK~lVe~~P~~i 105 (131)
T CHL00083 76 RIAVLKVVRSLTGLGLKEAKELVESLPKTI 105 (131)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHHHhCCHHH
Confidence 377999999999999999999887765433
No 35
>COG0222 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]
Probab=71.57 E-value=6.1 Score=33.55 Aligned_cols=26 Identities=27% Similarity=0.328 Sum_probs=22.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcC
Q 020628 78 VNLIKQLREQTSAPMKDVKLALVDCD 103 (323)
Q Consensus 78 ~~lIK~LR~~Tga~~~dCKkAL~e~~ 103 (323)
+..||..|+-||.|+++.|...+.+.
T Consensus 70 I~VIK~vR~itGLGLKEAKdlVe~aP 95 (124)
T COG0222 70 IAVIKVVRELTGLGLKEAKDLVEGAP 95 (124)
T ss_pred hhHHHHHHHHhcccHHHHHHHHHhCc
Confidence 66899999999999999998776663
No 36
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=70.47 E-value=11 Score=32.39 Aligned_cols=28 Identities=25% Similarity=0.374 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHhcCCcHHHHHHHHHHhc
Q 020628 89 SAPMKDVKLALVDCDWDIEAALKELRKRG 117 (323)
Q Consensus 89 ga~~~dCKkAL~e~~gDiekAi~~Lrk~G 117 (323)
+.+--+.++||+++| |+..|+++||.++
T Consensus 125 ~v~~eeAr~aleeag-Dl~~A~k~l~~~~ 152 (153)
T COG4008 125 FVTPEEAREALEEAG-DLRTAMKILRMKS 152 (153)
T ss_pred cCCHHHHHHHHHHcC-CHHHHHHHHHHhc
Confidence 377789999999999 9999999999876
No 37
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=64.85 E-value=15 Score=25.41 Aligned_cols=39 Identities=23% Similarity=0.382 Sum_probs=28.5
Q ss_pred hhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHH
Q 020628 65 RNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 65 r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk 115 (323)
+.|+...|. +.++.+++|=++||.|+.+- +++|++.+-+
T Consensus 3 ~r~t~~l~~--el~~~L~~ls~~t~i~~S~L----------l~eAle~~l~ 41 (44)
T PF12651_consen 3 KRFTFSLDK--ELYEKLKELSEETGIPKSKL----------LREALEDYLE 41 (44)
T ss_pred eEEEEecCH--HHHHHHHHHHHHHCCCHHHH----------HHHHHHHHHH
Confidence 345554453 66788999999999999875 6777777654
No 38
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=62.25 E-value=15 Score=29.56 Aligned_cols=53 Identities=9% Similarity=0.028 Sum_probs=38.8
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcC-CcHHHHHHHHHHhchh
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD-WDIEAALKELRKRGKV 119 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~-gDiekAi~~Lrk~G~a 119 (323)
.-.|.|+-. ....+..|+.|| +|.||.+.|+-+.... ||.+++.+.|.++-..
T Consensus 34 ~g~R~Y~~~---~v~~l~~I~~l~--~g~~l~~i~~~~~~~~~~~~~~~~~ll~~~~~~ 87 (99)
T cd04772 34 NGYRIYTDK---HIAALRAYRALL--PGYGYRVAQRIMRAVHAGIVASALALVDAAHAL 87 (99)
T ss_pred CCCeecCHH---HHHHHHHHHHHh--hCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence 356777754 245577888887 5999999988777654 8899888888765433
No 39
>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=60.13 E-value=18 Score=28.27 Aligned_cols=51 Identities=18% Similarity=0.150 Sum_probs=37.7
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHHhch
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGK 118 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk~G~ 118 (323)
-.|.|+.. ....+..|+.||+ .|.++.++++-|.+-+ +.+....-|...|.
T Consensus 36 g~R~Ys~~---dv~~l~~I~~Lr~-~G~sl~~i~~~l~~~~-~~~~~~~~~~~~~~ 86 (88)
T cd01105 36 GQRKYSLA---DVDRLLVIKELLD-EGFTLAAAVEKLRRRR-VQAEVRRRLMKDGL 86 (88)
T ss_pred CceecCHH---HHHHHHHHHHHHH-CCCCHHHHHHHHHHcc-CHHHHHHHHHHHhc
Confidence 56778854 2455788999998 9999999999998554 56666666655553
No 40
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=53.78 E-value=16 Score=29.76 Aligned_cols=40 Identities=20% Similarity=0.174 Sum_probs=32.1
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcCCc
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWD 105 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~gD 105 (323)
...|.|+... .+.+..|+.|| .+|.++.+||+.|...+.+
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 4567888661 45577899998 8999999999999998753
No 41
>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=51.85 E-value=28 Score=27.83 Aligned_cols=48 Identities=27% Similarity=0.352 Sum_probs=35.4
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHHhc
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRG 117 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk~G 117 (323)
-.|.|+-. ....+..|+.||+ .|.|+.++++-|...+ ++..+.|.++-
T Consensus 35 g~R~y~~~---di~~l~~i~~lr~-~g~~l~~i~~~~~~~~---~~~~~~l~~~~ 82 (103)
T cd01106 35 GYRLYTEE---DLERLQQILFLKE-LGFSLKEIKELLKDPS---EDLLEALREQK 82 (103)
T ss_pred CceeeCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHHcCc---HHHHHHHHHHH
Confidence 35667754 2455778999998 7999999999998766 66666666443
No 42
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=50.64 E-value=15 Score=39.41 Aligned_cols=28 Identities=14% Similarity=0.058 Sum_probs=24.2
Q ss_pred cCCCHHHHHHHHHhcCCcHHHHHHHHHH
Q 020628 88 TSAPMKDVKLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 88 Tga~~~dCKkAL~e~~gDiekAi~~Lrk 115 (323)
-|-+--.|++||.++|||+|.|++|+--
T Consensus 645 mGf~~~qa~~aL~~~n~nveravDWif~ 672 (763)
T KOG0944|consen 645 MGFSRNQAIKALKATNNNVERAVDWIFS 672 (763)
T ss_pred ecCcHHHHHHHHHhcCccHHHHHHHHHh
Confidence 3556668999999999999999999873
No 43
>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=50.20 E-value=32 Score=27.95 Aligned_cols=51 Identities=18% Similarity=0.180 Sum_probs=37.0
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhc--CCcHHHHHHHHHHhc
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDC--DWDIEAALKELRKRG 117 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~--~gDiekAi~~Lrk~G 117 (323)
-.|.|+.. ....+..|+.||+ +|.|+.+.|+.|... +++.+...+.|.++-
T Consensus 35 g~R~Y~~~---dl~~l~~I~~lr~-~G~~l~~I~~~l~~~~~~~~~~~~~~~l~~~~ 87 (108)
T cd04773 35 GYRVYDPS---DVRDARLIHLLRR-GGYLLEQIATVVEQLRHAGGTEALAAALEQRR 87 (108)
T ss_pred CceeeCHH---HHHHHHHHHHHHH-CCCCHHHHHHHHHHhhcCCCHHHHHHHHHHHH
Confidence 45677754 2455788999986 999999999999865 355666666666543
No 44
>KOG4841 consensus Dolichol-phosphate mannosyltransferase, subunit 3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=48.82 E-value=7.2 Score=31.23 Aligned_cols=30 Identities=27% Similarity=0.349 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHhcCCcHHHHHHHHHHhchh
Q 020628 90 APMKDVKLALVDCDWDIEAALKELRKRGKV 119 (323)
Q Consensus 90 a~~~dCKkAL~e~~gDiekAi~~Lrk~G~a 119 (323)
|.+.||-+|-.|--+||.+|.+.|+.||..
T Consensus 65 ATfnDc~eA~veL~~~IkEAr~~L~rkg~r 94 (95)
T KOG4841|consen 65 ATFNDCEEAAVELQSQIKEARADLARKGLR 94 (95)
T ss_pred eccCCcHHHHHHHHHHHHHHHHHHHHccCC
Confidence 457799999999999999999999999853
No 45
>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=46.56 E-value=48 Score=26.43 Aligned_cols=48 Identities=23% Similarity=0.414 Sum_probs=33.9
Q ss_pred hhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhc-CCcHHHHHHHHH
Q 020628 64 SRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDC-DWDIEAALKELR 114 (323)
Q Consensus 64 ~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~-~gDiekAi~~Lr 114 (323)
.|.|+.. ....+..|+.||+..|.++.++|+.|... +..+..=.+.|.
T Consensus 36 ~r~Y~~~---dv~~l~~I~~L~~~~G~~l~~I~~~l~~~~~~~~~~~~~~~~ 84 (95)
T cd04780 36 QAEYSEA---HVERLRLIRALQQEGGLPISQIKEVLDAIADASLPSTLLALA 84 (95)
T ss_pred CeecCHH---HHHHHHHHHHHHHHcCCCHHHHHHHHHhcCcccHHHHHHHHH
Confidence 3667654 25568899999999999999999999872 233444444443
No 46
>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=44.52 E-value=44 Score=26.19 Aligned_cols=34 Identities=26% Similarity=0.107 Sum_probs=28.5
Q ss_pred HHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHH
Q 020628 81 IKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 81 IK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk 115 (323)
|++ .+++|.+.-.+-+||..|.||+..|...+..
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 566 7889999999999999999999999996653
No 47
>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=44.41 E-value=24 Score=25.80 Aligned_cols=34 Identities=24% Similarity=0.239 Sum_probs=26.9
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHH
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLAL 99 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL 99 (323)
.-.|.|+.. .+..+..|+.||+ .|.++.++|+-|
T Consensus 34 ~g~R~yt~~---di~~l~~i~~l~~-~g~~l~~i~~~l 67 (68)
T cd04763 34 GGHRLFNDA---DIDRILEIKRWID-NGVQVSKVKKLL 67 (68)
T ss_pred CCCcccCHH---HHHHHHHHHHHHH-cCCCHHHHHHHh
Confidence 345778765 2556788999999 999999999876
No 48
>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=44.28 E-value=21 Score=24.44 Aligned_cols=17 Identities=29% Similarity=0.606 Sum_probs=14.6
Q ss_pred HHHHhcCCcHHHHHHHH
Q 020628 97 LALVDCDWDIEAALKEL 113 (323)
Q Consensus 97 kAL~e~~gDiekAi~~L 113 (323)
-.|+.|+||+-+|||.+
T Consensus 22 ~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 22 LILQRCNGDVVQAIEQF 38 (39)
T ss_pred HHHHHcCCcHHHHHHHh
Confidence 45889999999999964
No 49
>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=44.03 E-value=40 Score=26.73 Aligned_cols=48 Identities=21% Similarity=0.281 Sum_probs=34.2
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHHh
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKR 116 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk~ 116 (323)
.-.|.|+.. ....+..|+.||+ +|.|+.+.|+-|...+. ...++|.++
T Consensus 34 ~gyR~Y~~~---~l~~l~~I~~lr~-~G~~l~eI~~~l~~~~~---~~~~~l~~~ 81 (96)
T cd04788 34 GGHRLYDRA---DIRRLHQIIALRR-LGFSLREIGRALDGPDF---DPLELLRRQ 81 (96)
T ss_pred CCceeeCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHhCCCh---hHHHHHHHH
Confidence 345778754 2556889999986 79999999999876542 445555544
No 50
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=43.16 E-value=39 Score=27.41 Aligned_cols=52 Identities=29% Similarity=0.306 Sum_probs=36.9
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHHhchhh
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVL 120 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk~G~a~ 120 (323)
--|.|+.. ....+..|+.||+ +|.|+.+++.-+...+. ++....|..+-...
T Consensus 36 gyR~Y~~~---~i~~l~~I~~lr~-~G~sl~~i~~l~~~~~~--~~~~~~l~~~~~~l 87 (108)
T cd01107 36 GYRYYSAE---QLERLNRIKYLRD-LGFPLEEIKEILDADND--DELRKLLREKLAEL 87 (108)
T ss_pred CccccCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHhcCCH--HHHHHHHHHHHHHH
Confidence 45677754 2455789999988 99999999987776553 66666666544433
No 51
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=42.00 E-value=19 Score=26.18 Aligned_cols=34 Identities=26% Similarity=0.481 Sum_probs=25.6
Q ss_pred hhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHh
Q 020628 64 SRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVD 101 (323)
Q Consensus 64 ~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e 101 (323)
.|.|+.. ....+..|+.||+ .|.++.+.|+.|.+
T Consensus 35 ~r~y~~~---dv~~l~~i~~l~~-~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 35 YRYYSEE---DVERLREIKELRK-QGMSLEEIKKLLKQ 68 (69)
T ss_dssp SEEE-HH---HHHHHHHHHHHHH-TTTHHHHHHHHH--
T ss_pred eeeccHH---HHHHHHHHHHHHH-CcCCHHHHHHHHcc
Confidence 3677755 2556889999999 99999999998864
No 52
>KOG1364 consensus Predicted ubiquitin regulatory protein, contains UAS and UBX domains [Posttranslational modification, protein turnover, chaperones]
Probab=39.99 E-value=52 Score=32.78 Aligned_cols=43 Identities=23% Similarity=0.349 Sum_probs=38.4
Q ss_pred HHHHHHHHHHcC-CCHHHHHHHHHhcCCcHHHHHHHHHHhchhh
Q 020628 78 VNLIKQLREQTS-APMKDVKLALVDCDWDIEAALKELRKRGKVL 120 (323)
Q Consensus 78 ~~lIK~LR~~Tg-a~~~dCKkAL~e~~gDiekAi~~Lrk~G~a~ 120 (323)
.+||++.+.-|+ ..+-..++=|..++||++.||.++++.|...
T Consensus 7 ~~lv~~fl~It~~~t~e~A~q~L~~~~~~le~ai~Lffe~~~~~ 50 (356)
T KOG1364|consen 7 RALVSKFLAITVQQTVEIATQYLSAADWDLEAAINLFFEHGGFT 50 (356)
T ss_pred HHHHHHHHHHhccccHHHHHHHHHhcCCcHHHHHHHHHHhcccc
Confidence 469999999999 7777899999999999999999999988643
No 53
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=39.62 E-value=37 Score=32.75 Aligned_cols=32 Identities=19% Similarity=0.214 Sum_probs=28.9
Q ss_pred HHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHH
Q 020628 84 LREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 84 LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk 115 (323)
+.+.||++--+|.++|++++|++..|+-.+..
T Consensus 242 ~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~~~ 273 (299)
T PRK05441 242 VMEATGVSREEAEAALEAADGSVKLAIVMILT 273 (299)
T ss_pred HHHHHCcCHHHHHHHHHHhCCCcHHHHHHHHh
Confidence 56679999999999999999999999998764
No 54
>KOG1715 consensus Mitochondrial/chloroplast ribosomal protein L12 [Translation, ribosomal structure and biogenesis]
Probab=38.84 E-value=46 Score=30.31 Aligned_cols=26 Identities=23% Similarity=0.395 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhc
Q 020628 77 QVNLIKQLREQTSAPMKDVKLALVDC 102 (323)
Q Consensus 77 ~~~lIK~LR~~Tga~~~dCKkAL~e~ 102 (323)
.+..||++|--||.|+.+.|+=.+.+
T Consensus 132 KIkVIKEVR~~tgL~LkeAKklVE~a 157 (187)
T KOG1715|consen 132 KIKVIKEVRALTGLGLKEAKKLVEKA 157 (187)
T ss_pred hhHHHHHHHHhccccHHHHHHHHHhc
Confidence 47899999999999999998755443
No 55
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=37.75 E-value=69 Score=25.73 Aligned_cols=51 Identities=24% Similarity=0.154 Sum_probs=36.4
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcCCc---HHHHHHHHHH
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWD---IEAALKELRK 115 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~gD---iekAi~~Lrk 115 (323)
.-.|.|+.. ....+..|+.|-+..|.++.++|+-|...++. -+.++.-|.+
T Consensus 34 ~g~R~Yt~~---di~~l~~I~~llr~~G~~l~~i~~~l~~~~~~~~~~~~~~~~~~~ 87 (99)
T cd04765 34 GGRRYYRPK---DVELLLLIKHLLYEKGYTIEGAKQALKEDGAAAIREEEAEERLPS 87 (99)
T ss_pred CCCeeeCHH---HHHHHHHHHHHHHHCCCCHHHHHHHHHhccccccchhhHHHHHHH
Confidence 346778865 13446677776678999999999999987754 5556666653
No 56
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=37.70 E-value=66 Score=25.22 Aligned_cols=51 Identities=27% Similarity=0.365 Sum_probs=36.8
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcCCc--HHHHHHHHHHhc
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWD--IEAALKELRKRG 117 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~gD--iekAi~~Lrk~G 117 (323)
..|.|+-. .+..+..|+.||. .|.|+.+.++.|...+.+ .+...+.|..+.
T Consensus 34 g~r~y~~~---dv~~l~~i~~l~~-~g~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~ 86 (100)
T cd00592 34 GYRLYSEE---DLERLRLIRRLRE-LGLSLKEIRELLDARDEELSLAALLALLDEKL 86 (100)
T ss_pred CCcccCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHhcccccchHHHHHHHHHHHH
Confidence 45667754 1455789999999 999999999999887654 445555555443
No 57
>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=37.48 E-value=71 Score=26.20 Aligned_cols=51 Identities=10% Similarity=0.095 Sum_probs=35.9
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcCC---cHHHHHHHHHHh
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDW---DIEAALKELRKR 116 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~g---DiekAi~~Lrk~ 116 (323)
.--|.|+.. ....+..|+.|| .+|.|+.+.|+-|...+. +.+.....|.++
T Consensus 34 ~gyR~Y~~~---~i~~l~~I~~lr-~~G~sl~eI~~~l~~~~~~~~~~~~~~~~l~~~ 87 (123)
T cd04770 34 NGYRLYGEA---DLARLRFIRRAQ-ALGFSLAEIRELLSLRDDGAAPCAEVRALLEEK 87 (123)
T ss_pred CCCccCCHH---HHHHHHHHHHHH-HCCCCHHHHHHHHHhhhcCCCCHHHHHHHHHHH
Confidence 345778865 255688999996 679999999999986542 345555666543
No 58
>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=37.10 E-value=73 Score=24.82 Aligned_cols=35 Identities=23% Similarity=0.366 Sum_probs=28.1
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHH
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALV 100 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~ 100 (323)
-.|.|+.. ....+..|+.|++..|.|+.+++..|.
T Consensus 35 g~R~y~~~---dv~~l~~i~~L~~d~g~~l~~i~~~l~ 69 (91)
T cd04766 35 GTRRYSER---DIERLRRIQRLTQELGVNLAGVKRILE 69 (91)
T ss_pred CCeeECHH---HHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 34667755 244578999999999999999999996
No 59
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=36.46 E-value=73 Score=26.49 Aligned_cols=51 Identities=16% Similarity=0.171 Sum_probs=35.8
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcC---CcHHHHHHHHHHh
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD---WDIEAALKELRKR 116 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~---gDiekAi~~Lrk~ 116 (323)
...|.|+.. ....+..|+.|| .+|.|+.+.|+-|.... .+.++....|.++
T Consensus 34 ~g~R~Y~~~---~l~~l~~I~~lr-~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~ 87 (126)
T cd04785 34 GGYRLYGAA---HVERLRFIRRAR-DLGFSLEEIRALLALSDRPDRSCAEADAIARAH 87 (126)
T ss_pred CCccccCHH---HHHHHHHHHHHH-HCCCCHHHHHHHHhhhhcCCCCHHHHHHHHHHH
Confidence 345778865 245578899997 89999999999887543 2555666666543
No 60
>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=34.73 E-value=79 Score=26.54 Aligned_cols=50 Identities=22% Similarity=0.282 Sum_probs=35.0
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcC-Cc--HHHHHHHHHHh
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD-WD--IEAALKELRKR 116 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~-gD--iekAi~~Lrk~ 116 (323)
--|.|+.. ....+..|+.|| .+|.++.+.|+-|...+ ++ .....++|.++
T Consensus 35 gyR~Y~~~---~~~~l~~I~~lr-~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~ 87 (133)
T cd04787 35 GYRLYSEK---DLSRLRFILSAR-QLGFSLKDIKEILSHADQGESPCPMVRRLIEQR 87 (133)
T ss_pred CeeeCCHH---HHHHHHHHHHHH-HcCCCHHHHHHHHhhhccCCCcHHHHHHHHHHH
Confidence 45778865 255688999998 59999999999988654 22 23445566544
No 61
>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=34.12 E-value=92 Score=25.74 Aligned_cols=50 Identities=20% Similarity=0.303 Sum_probs=34.9
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcC-Cc-----HHHHHHHHHHh
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD-WD-----IEAALKELRKR 116 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~-gD-----iekAi~~Lrk~ 116 (323)
--|.|+.. ....+..|+.||+ +|.|+.+.|+-|.... |+ +++.++.|.++
T Consensus 33 gyR~Y~~~---~l~~l~~I~~lr~-~G~~L~~I~~~l~~~~~~~~~~~~~~~~~~~l~~~ 88 (118)
T cd04776 33 QTRVYSRR---DRARLKLILRGKR-LGFSLEEIRELLDLYDPPGGNRKQLEKMLEKIEKR 88 (118)
T ss_pred CccccCHH---HHHHHHHHHHHHH-CCCCHHHHHHHHHhhccCCchHHHHHHHHHHHHHH
Confidence 45778765 2456788999997 8999999999998653 22 34455555543
No 62
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=33.95 E-value=35 Score=24.81 Aligned_cols=34 Identities=29% Similarity=0.370 Sum_probs=26.9
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHH
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLAL 99 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL 99 (323)
.-.|.|+.+ ....+..|+.||+ .|.++.++|+-|
T Consensus 33 ~g~R~y~~~---~l~~l~~i~~l~~-~g~~l~~i~~~l 66 (67)
T cd04764 33 NGRRYYTDE---DIELLKKIKTLLE-KGLSIKEIKEIL 66 (67)
T ss_pred CCceeeCHH---HHHHHHHHHHHHH-CCCCHHHHHHHh
Confidence 455778765 2556789999999 999999999876
No 63
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=33.62 E-value=56 Score=23.54 Aligned_cols=34 Identities=29% Similarity=0.431 Sum_probs=26.3
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHH
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALV 100 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~ 100 (323)
-.|.|+-. ....+..|+.||+ .|.++.++++.|.
T Consensus 35 g~r~y~~~---dl~~l~~i~~lr~-~g~~~~~i~~~l~ 68 (70)
T smart00422 35 GYRLYSDE---DLERLRFIKRLKE-LGFSLEEIKELLE 68 (70)
T ss_pred CCEecCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHh
Confidence 45667744 1445778999998 9999999999885
No 64
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=33.49 E-value=38 Score=34.99 Aligned_cols=36 Identities=31% Similarity=0.487 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHhcCCcHHHHHHHHHHhchhhhccc
Q 020628 89 SAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKK 124 (323)
Q Consensus 89 ga~~~dCKkAL~e~~gDiekAi~~Lrk~G~a~A~Kr 124 (323)
|.--.|.|-||-.|+||+|-|++++.++-+.+|.+|
T Consensus 314 GfeesdaRlaLRsc~g~Vd~AvqfI~erre~laq~R 349 (568)
T KOG2561|consen 314 GFEESDARLALRSCNGDVDSAVQFIIERREKLAQKR 349 (568)
T ss_pred CCCchHHHHHHHhccccHHHHHHHHHHHHHHHHHHH
Confidence 333459999999999999999999999988888777
No 65
>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=33.21 E-value=76 Score=25.12 Aligned_cols=47 Identities=21% Similarity=0.047 Sum_probs=33.4
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHH
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk 115 (323)
.-.|.|+.. ....+..|+.||+ .|.|+.+.|+.|...+. ...+.|.+
T Consensus 34 ~gyR~Y~~~---~l~~l~~I~~lr~-~G~~l~~I~~~l~~~~~---~~~~~l~~ 80 (96)
T cd04768 34 NGYRYYSYA---QLYQLQFILFLRE-LGFSLAEIKELLDTEME---ELTAMLLE 80 (96)
T ss_pred CCeeeCCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHhcCcH---HHHHHHHH
Confidence 355778865 2455789999988 69999999999986543 44444443
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=31.14 E-value=61 Score=31.23 Aligned_cols=32 Identities=16% Similarity=0.233 Sum_probs=28.7
Q ss_pred HHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHH
Q 020628 84 LREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 84 LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk 115 (323)
+.+-||++--+|.++|.+++|++.-|+-.+..
T Consensus 237 ~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~~~~ 268 (291)
T TIGR00274 237 VRQATDCNKELAEQTLLAADQNVKLAIVMILS 268 (291)
T ss_pred HHHHhCcCHHHHHHHHHHhCCCcHHHHHHHHh
Confidence 55669999999999999999999999997764
No 67
>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=30.41 E-value=57 Score=21.90 Aligned_cols=19 Identities=26% Similarity=0.461 Sum_probs=15.6
Q ss_pred HHHHHHhcCCcHHHHHHHH
Q 020628 95 VKLALVDCDWDIEAALKEL 113 (323)
Q Consensus 95 CKkAL~e~~gDiekAi~~L 113 (323)
-.+||..++||+.+|-+.|
T Consensus 10 i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 10 IRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHhCCCHHHHHHHH
Confidence 3589999999999998877
No 68
>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=30.28 E-value=1.1e+02 Score=25.44 Aligned_cols=50 Identities=12% Similarity=0.138 Sum_probs=34.5
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcC-C--cHHHHHHHHHH
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD-W--DIEAALKELRK 115 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~-g--DiekAi~~Lrk 115 (323)
..-|.|+.. ....+..|+.|| ..|.|+.+.|+-|...+ + +.+.....|.+
T Consensus 34 ~gyR~Y~~~---~l~~l~~I~~lr-~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~ 86 (127)
T cd04784 34 NNYRLYDEE---HLERLLFIRRCR-SLDMSLDEIRTLLQLQDDPEASCAEVNALIDE 86 (127)
T ss_pred CCCeecCHH---HHHHHHHHHHHH-HcCCCHHHHHHHHHhhhcCCCcHHHHHHHHHH
Confidence 345778865 245577899997 56999999999887543 2 34555565553
No 69
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=29.99 E-value=88 Score=26.94 Aligned_cols=50 Identities=14% Similarity=0.167 Sum_probs=35.1
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcCCc-HHHHHHHHHHh
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWD-IEAALKELRKR 116 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~gD-iekAi~~Lrk~ 116 (323)
--|.|+.. ....+..|+.|| .+|.|+.+.|+=|...++. -+...++|.++
T Consensus 42 gyR~Y~~~---~l~rl~~I~~lr-~~G~sL~eI~~ll~~~~~~~~~~~~~ll~~k 92 (144)
T PRK13752 42 SIRRYGEA---DVTRVRFVKSAQ-RLGFSLDEIAELLRLEDGTHCEEASSLAEHK 92 (144)
T ss_pred CCeecCHH---HHHHHHHHHHHH-HcCCCHHHHHHHHhccCCCCHHHHHHHHHHH
Confidence 35778865 245688999999 8999999999877644432 35566666544
No 70
>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=29.94 E-value=90 Score=26.33 Aligned_cols=51 Identities=18% Similarity=0.106 Sum_probs=35.3
Q ss_pred CcHHHHH---HHHHHhchhhhcccccccccCCceEEEecCCeEEEEEEecCCchh
Q 020628 104 WDIEAAL---KELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFV 155 (323)
Q Consensus 104 gDiekAi---~~Lrk~G~a~A~Kr~~R~a~EGlV~~yv~~~~avlVElncETDFV 155 (323)
.|++++. +.|+++|...... -+|....+.+..|...--|-+|||-++.+-+
T Consensus 76 ~die~~~~~~~~L~~~Gv~v~~~-~g~~~~g~~~~~y~~DPdG~~iEl~~~~~~~ 129 (153)
T cd07257 76 HDFDAQGLGHDYLREKGYEHVWG-VGRHILGSQIFDYWFDPWGFIVEHYTDGDLV 129 (153)
T ss_pred CCHHHHHHHHHHHHHCCCcEeec-CCccCCCCCEEEEEECCCCCEEEEEcCceeE
Confidence 4788876 8899999876532 2333333456778876678899999987744
No 71
>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=28.72 E-value=1.2e+02 Score=25.48 Aligned_cols=52 Identities=12% Similarity=0.120 Sum_probs=36.3
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhc----CCcHHHHHHHHHHhc
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDC----DWDIEAALKELRKRG 117 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~----~gDiekAi~~Lrk~G 117 (323)
.-.|.|+.. ....+..|+.||+ .|.|+.+.|+-|... +.+.+...+.|.++-
T Consensus 35 ~gyR~Y~~~---~l~~l~~I~~lr~-~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~~ 90 (131)
T TIGR02043 35 SGYRLYTDE---DQKRLRFILKAKE-LGFTLDEIKELLSIKLDATEHSCAEVKAIVDAKL 90 (131)
T ss_pred CCceecCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHHhhccCCCCCHHHHHHHHHHHH
Confidence 456778754 2455789999985 899999999988743 234556666665443
No 72
>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=28.26 E-value=1.2e+02 Score=25.62 Aligned_cols=51 Identities=12% Similarity=0.295 Sum_probs=35.3
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcC--CcHHHHHHHHHHh
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD--WDIEAALKELRKR 116 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~--gDiekAi~~Lrk~ 116 (323)
..-|.|+.. ....+..|+.||+ .|.++.+.|+-|.... .+.+.....|.++
T Consensus 34 ~gyR~Y~~~---~v~~l~~I~~lr~-~GfsL~eI~~ll~~~~~~~~~~~~~~~l~~k 86 (131)
T cd04786 34 NGYRDYPPE---TVWVLEIISSAQQ-AGFSLDEIRQLLPADASNWQHDELLAALERK 86 (131)
T ss_pred CCCeecCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHhcccCCCCHHHHHHHHHHH
Confidence 345777754 2455789999987 9999999999887542 3455555555543
No 73
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=28.12 E-value=70 Score=24.43 Aligned_cols=30 Identities=33% Similarity=0.259 Sum_probs=24.7
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCcHH
Q 020628 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIE 107 (323)
Q Consensus 78 ~~lIK~LR~~Tga~~~dCKkAL~e~~gDie 107 (323)
-++|+.+.++||.+-.||++.|.+.-.-+.
T Consensus 4 ~eli~~ia~~~~~s~~~v~~vl~~~~~~i~ 33 (90)
T PF00216_consen 4 KELIKRIAEKTGLSKKDVEAVLDALFDVIK 33 (90)
T ss_dssp HHHHHHHHHHHTSSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHHH
Confidence 469999999999999999999987544333
No 74
>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=27.47 E-value=1.2e+02 Score=24.68 Aligned_cols=50 Identities=18% Similarity=0.268 Sum_probs=34.9
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcC------CcHHHHHHHHHHh
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD------WDIEAALKELRKR 116 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~------gDiekAi~~Lrk~ 116 (323)
-.|.|+.. ....+..|+.||+ +|.|+.+.|.-|.... .+..+-.+.|.++
T Consensus 34 g~R~Y~~~---~~~~l~~I~~lr~-~G~sl~eI~~~l~~~~~~~~~~~~~~~~~~~l~~~ 89 (112)
T cd01282 34 GYRDYDEA---AVDRVRQIRRLLA-AGLTLEEIREFLPCLRGGEPTFRPCPDLLAVLRRE 89 (112)
T ss_pred CCeecCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHHHhhCCCccCCccHHHHHHHHHH
Confidence 45778754 2455889999985 9999999999887543 2345555666544
No 75
>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=27.17 E-value=1.5e+02 Score=24.05 Aligned_cols=51 Identities=27% Similarity=0.288 Sum_probs=35.9
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcC---CcHHHHHHHHHHhc
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD---WDIEAALKELRKRG 117 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~---gDiekAi~~Lrk~G 117 (323)
.-|.|+.. ..+.+..|+.||+ .|.|+.+.|+-|.... .+.+...+.|.++-
T Consensus 35 gyR~Y~~~---~l~~l~~I~~lr~-~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~ 88 (113)
T cd01109 35 GIRDFTEE---DLEWLEFIKCLRN-TGMSIKDIKEYAELRREGDSTIPERLELLEEHR 88 (113)
T ss_pred CCccCCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHHHHccCCccHHHHHHHHHHHH
Confidence 45677754 2556888999985 8999999999887532 33566677776543
No 76
>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=26.99 E-value=1.3e+02 Score=23.72 Aligned_cols=51 Identities=24% Similarity=0.302 Sum_probs=36.5
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHHhchh
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKV 119 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk~G~a 119 (323)
-.|.|+.. ....+..|+.||+ .|.|+.+.|.-|.. .+.+...+.|.++-..
T Consensus 35 gyR~Y~~~---~~~~l~~I~~lr~-~G~~l~eI~~~l~~--~~~~~~~~~l~~~~~~ 85 (97)
T cd04782 35 GYRYYTLE---QFEQLDIILLLKE-LGISLKEIKDYLDN--RNPDELIELLKKQEKE 85 (97)
T ss_pred CCccCCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHhc--CCHHHHHHHHHHHHHH
Confidence 45777755 2455778999986 69999999998864 3667777777755433
No 77
>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=26.53 E-value=1.5e+02 Score=24.90 Aligned_cols=38 Identities=11% Similarity=0.107 Sum_probs=29.0
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcC
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD 103 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~ 103 (323)
.-.|.|+.. ....+.+|+.||+ +|.|+.++|.-|...+
T Consensus 37 ~gyR~Y~~~---~l~rL~~I~~lr~-~G~~L~eI~~ll~~~~ 74 (120)
T TIGR02054 37 SGYGIFDDA---SLQRLRFVRAAFE-AGIGLGELARLCRALD 74 (120)
T ss_pred CCCeeCCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHHhhc
Confidence 456778765 2455788999998 9999999998776543
No 78
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=26.30 E-value=70 Score=26.65 Aligned_cols=22 Identities=27% Similarity=0.447 Sum_probs=17.4
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHHh
Q 020628 93 KDVKLALVDCDWDIEAALKELRKR 116 (323)
Q Consensus 93 ~dCKkAL~e~~gDiekAi~~Lrk~ 116 (323)
.+.+++| -+||++.|++|+.+.
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 679999999999864
No 79
>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=26.23 E-value=1.4e+02 Score=24.78 Aligned_cols=50 Identities=14% Similarity=0.194 Sum_probs=35.9
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcC-CcHHHHHHHHHHh
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD-WDIEAALKELRKR 116 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~-gDiekAi~~Lrk~ 116 (323)
.-|.|+.. ....+..|+.|| .+|.|+.+.|+-|.... ++.++....|.++
T Consensus 35 gyR~Y~~~---~l~~l~~I~~lr-~~G~sL~eI~~~l~~~~~~~~~~~~~~l~~~ 85 (126)
T cd04783 35 GYRRYPEE---TVTRLRFIKRAQ-ELGFTLDEIAELLELDDGTDCSEARELAEQK 85 (126)
T ss_pred CCeecCHH---HHHHHHHHHHHH-HcCCCHHHHHHHHhcccCCCHHHHHHHHHHH
Confidence 45777755 245577899997 59999999999997664 3566666666543
No 80
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=26.16 E-value=82 Score=30.41 Aligned_cols=33 Identities=18% Similarity=0.202 Sum_probs=28.7
Q ss_pred HHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHH
Q 020628 83 QLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 83 ~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk 115 (323)
=+.+-||++.-+|.++|.+++|++.-|+-.+..
T Consensus 237 i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~~~~ 269 (296)
T PRK12570 237 IVMQATGCSEDEAKELLKESDNDVKLAILMILT 269 (296)
T ss_pred HHHHHHCcCHHHHHHHHHHhCCccHHHHHHHHh
Confidence 355669999999999999999999999987664
No 81
>cd05007 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.
Probab=25.88 E-value=37 Score=31.93 Aligned_cols=29 Identities=21% Similarity=0.302 Sum_probs=25.1
Q ss_pred HHHHHHcCCCHHHHHHHHHhcCCcHHHHH
Q 020628 82 KQLREQTSAPMKDVKLALVDCDWDIEAAL 110 (323)
Q Consensus 82 K~LR~~Tga~~~dCKkAL~e~~gDiekAi 110 (323)
.=+.+-||++--+|.++|.+++|++..|+
T Consensus 227 ~i~~~~~~~~~~~a~~~l~~~~~~~k~a~ 255 (257)
T cd05007 227 RIVMEATGVSRDEAEAALEQAGGDVKTAI 255 (257)
T ss_pred HHHHHHHCcCHHHHHHHHHHhCCCceeee
Confidence 33566799999999999999999998876
No 82
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=25.23 E-value=1.5e+02 Score=25.26 Aligned_cols=52 Identities=8% Similarity=0.116 Sum_probs=36.5
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhc----CCcHHHHHHHHHHhc
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDC----DWDIEAALKELRKRG 117 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~----~gDiekAi~~Lrk~G 117 (323)
.-.|.|+.. ....+..|+.||+ +|.|+.+.++-|... +.+.+...+.|.++-
T Consensus 35 ~gyR~Y~~~---~l~~l~~I~~lr~-~G~sL~eI~~~l~~~~~~~~~~~~~~~~~l~~~~ 90 (140)
T PRK09514 35 GGYRLYTEQ---DLQRLRFIRRAKQ-LGFTLEEIRELLSIRLDPEHHTCQEVKGIVDEKL 90 (140)
T ss_pred CCCeeeCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHHhcccCCcCCHHHHHHHHHHHH
Confidence 345778765 2455788999986 799999999988643 235666666666543
No 83
>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=25.13 E-value=1.6e+02 Score=22.84 Aligned_cols=45 Identities=29% Similarity=0.339 Sum_probs=31.3
Q ss_pred CcHHHHHHHHHHhchhhhcccccccccCCceEEEecCCe--EEEEEEe
Q 020628 104 WDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESK--AAVIELN 149 (323)
Q Consensus 104 gDiekAi~~Lrk~G~a~A~Kr~~R~a~EGlV~~yv~~~~--avlVEln 149 (323)
.|++++.+.|++.|...-.. -.+....|.-..+.+..- |.+|||.
T Consensus 81 ~d~~~~~~~l~~~G~~~~~~-~~~~~~~g~~~~~~d~~~~~g~~iE~~ 127 (128)
T cd07249 81 DDIDAALARLKAQGVRLLQE-GPRIGAGGKRVAFLHPKDTGGVLIELV 127 (128)
T ss_pred CCHHHHHHHHHHCCCeeecc-CCCccCCCCEEEEEecCCCceEEEEec
Confidence 47999999999999875432 222345677666776544 8899873
No 84
>PRK04358 hypothetical protein; Provisional
Probab=25.03 E-value=1.2e+02 Score=28.33 Aligned_cols=53 Identities=15% Similarity=0.251 Sum_probs=43.1
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcC-------------CcHHHHHHHHHHh
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD-------------WDIEAALKELRKR 116 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~-------------gDiekAi~~Lrk~ 116 (323)
+.++|....|+ .-.-+.|..+|+|-+-|+--.=+|.-++. .++.+-|.+||++
T Consensus 84 sP~ry~v~IPA-~i~ye~I~~mR~RInkGLRVAEeavrea~~~~~~~~~~~~~~~~v~~~I~~lRek 149 (217)
T PRK04358 84 SPNRYEIKIPA-EIFYEYIEDMRERINKGLRVAEEAVREAALECYDLSKEEIEREVVGKIISKLREK 149 (217)
T ss_pred CCCceeeeccH-HHHHHHHHHHHHHHhcchHHHHHHHHHHHhhhccccccchhhhhHHHHHHHHHHH
Confidence 56677777787 44478999999999999998888888865 6788899999965
No 85
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=24.84 E-value=96 Score=21.76 Aligned_cols=33 Identities=21% Similarity=0.323 Sum_probs=23.7
Q ss_pred HHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHHhchhhhcccccc
Q 020628 82 KQLREQTSAPMKDVKLALVDCDWDIEAALKELRKRGKVLASKKSSR 127 (323)
Q Consensus 82 K~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk~G~a~A~Kr~~R 127 (323)
.+|++-||+. .-.+-++||++.|+.--.+..+|
T Consensus 6 ~El~elTG~k-------------~~~~Q~~~L~~~Gi~~~~~~~G~ 38 (47)
T PF13986_consen 6 EELQELTGYK-------------RPSKQIRWLRRNGIPFVVRADGR 38 (47)
T ss_pred HHHHHHHCCC-------------CHHHHHHHHHHCCCeeEECCCCC
Confidence 3677888876 45667899999998766554443
No 86
>cd08347 PcpA_C_like C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins. The C-terminal domain of Sphingobium chlorophenolicum (formerly Sphingomonas chlorophenolica) 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins. PcpA is a key enzyme in the pentachlorophenol (PCP) degradation pathway, catalyzing the conversion of 2,6-dichloro-p-hydroquinone to 2-chloromaleylacetate. This domain belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.
Probab=24.78 E-value=63 Score=27.65 Aligned_cols=57 Identities=16% Similarity=0.091 Sum_probs=37.2
Q ss_pred CcHHHHHHHHHHhchhhhcccccccccCCceEEEecCCeEEEEEEecCCchhhhcHHHHHH
Q 020628 104 WDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFVSRNEIFQYL 164 (323)
Q Consensus 104 gDiekAi~~Lrk~G~a~A~Kr~~R~a~EGlV~~yv~~~~avlVElncETDFVArn~~F~~L 164 (323)
.|++.+.+.|++.|..... -....+.-..|...--|.+||+.+.++...-.+.|..|
T Consensus 77 ~dvd~~~~~L~~~Gv~~~~----~~~~~~~~s~yf~DPdG~~iEl~~~~~~~~~~~~~~~~ 133 (157)
T cd08347 77 EELEAWKERLEALGLPVSG----IVDRFYFKSLYFREPGGILFEIATDGPGFTVDEPLEEL 133 (157)
T ss_pred HHHHHHHHHHHHCCCCccc----ccccccEEEEEEECCCCcEEEEEECCCCccccCChhHc
Confidence 5689999999999975421 11122334567766678899999998765444434333
No 87
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=24.59 E-value=57 Score=22.60 Aligned_cols=16 Identities=25% Similarity=0.115 Sum_probs=13.3
Q ss_pred CCcHHHHHHHHHHhch
Q 020628 103 DWDIEAALKELRKRGK 118 (323)
Q Consensus 103 ~gDiekAi~~Lrk~G~ 118 (323)
+||+++|++|+.+...
T Consensus 14 ~g~~~~a~~~~~~~~~ 29 (58)
T smart00668 14 KGDWDEALEWLSSLKP 29 (58)
T ss_pred cCCHHHHHHHHHHcCH
Confidence 6999999999986543
No 88
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal 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-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=24.55 E-value=1.7e+02 Score=24.38 Aligned_cols=50 Identities=14% Similarity=0.128 Sum_probs=34.2
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcC---CcHHHHHHHHHH
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD---WDIEAALKELRK 115 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~---gDiekAi~~Lrk 115 (323)
.-.|.|+.. ....+..|+.||+ +|.|+.+.|+-|...+ .+.+...+.|.+
T Consensus 34 ~gyR~Y~~~---~l~~l~~I~~lr~-lG~sL~eI~~~l~~~~~~~~~~~~~~~~l~~ 86 (127)
T TIGR02047 34 NNYRVYTVG---HVERLAFIRNCRT-LDMSLAEIRQLLRYQDKPEKSCSDVNALLDE 86 (127)
T ss_pred CCCCcCCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHHhhhCCCCCHHHHHHHHHH
Confidence 456778755 2455789999974 9999999999886432 234555555553
No 89
>COG1437 CyaB Adenylate cyclase, class 2 (thermophilic) [Nucleotide transport and metabolism]
Probab=24.38 E-value=1.1e+02 Score=27.83 Aligned_cols=65 Identities=17% Similarity=0.193 Sum_probs=43.2
Q ss_pred HHHHHHHHHhcC---CcHHHHHHHHHHhchhhhcc--cccccccCCceEEEec--CCeEEEEEEecCCchhh
Q 020628 92 MKDVKLALVDCD---WDIEAALKELRKRGKVLASK--KSSRTATEGLLALAQN--ESKAAVIELNCETDFVS 156 (323)
Q Consensus 92 ~~dCKkAL~e~~---gDiekAi~~Lrk~G~a~A~K--r~~R~a~EGlV~~yv~--~~~avlVElncETDFVA 156 (323)
|-.|.|+..|.. .|+++|.++|++-|-..+.. |--+.=.-|-+-+.+| .+.|-.+||-+++|+-.
T Consensus 71 ld~~~k~r~E~E~~v~D~~~~~~il~~LGF~~~~~VkK~R~iY~~~~~~i~lD~VegLG~F~EIE~~~~d~~ 142 (178)
T COG1437 71 LDRESKTREEIEIEVSDVEKALEILKRLGFKEVAVVKKTREIYKVGNVTIELDAVEGLGDFLEIEVMVDDEN 142 (178)
T ss_pred ccccccceeeEEEEeCCHHHHHHHHHHcCCceeeEEEEEEEEEeeCCEEEEEecccCCcccEEEEEecCCch
Confidence 334556666653 79999999999998876532 2222212333555555 45799999999999753
No 90
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=24.31 E-value=73 Score=22.32 Aligned_cols=20 Identities=35% Similarity=0.393 Sum_probs=14.5
Q ss_pred HHHHHhcCCcHHHHHHHHHH
Q 020628 96 KLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 96 KkAL~e~~gDiekAi~~Lrk 115 (323)
-+=|.+.+||+++|.+.|++
T Consensus 35 lRFLRARkf~v~~A~~mL~~ 54 (55)
T PF03765_consen 35 LRFLRARKFDVEKAFKMLKK 54 (55)
T ss_dssp HHHHHHTTT-HHHHHHHHHH
T ss_pred HHHHHHccCCHHHHHHHHHh
Confidence 34455678999999999875
No 91
>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=24.27 E-value=1.2e+02 Score=23.52 Aligned_cols=50 Identities=16% Similarity=0.309 Sum_probs=31.4
Q ss_pred CcHHHHHHHHHHhchhhhcccccccccCCceEEEecCCeEEEEEEecCCc
Q 020628 104 WDIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETD 153 (323)
Q Consensus 104 gDiekAi~~Lrk~G~a~A~Kr~~R~a~EGlV~~yv~~~~avlVElncETD 153 (323)
.|+++..+.|++.|.......-.+....|-...++..--|..|||.|.+.
T Consensus 70 ~~l~~~~~~l~~~G~~~~~~~~~~~~~~~~~~~~~~DP~G~~iel~~~~~ 119 (120)
T cd08362 70 ADVDALARQVAARGGTVLSEPGATDDPGGGYGFRFFDPDGRLIEFSADVE 119 (120)
T ss_pred HHHHHHHHHHHHcCCceecCCcccCCCCCceEEEEECCCCCEEEEEeccc
Confidence 47899999999999875432111222223334566655677889888753
No 92
>KOG3763 consensus mRNA export factor TAP/MEX67 [RNA processing and modification]
Probab=23.93 E-value=1.4e+02 Score=31.84 Aligned_cols=38 Identities=24% Similarity=0.325 Sum_probs=32.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcCCcHHHHHHHHHH
Q 020628 78 VNLIKQLREQTSAPMKDVKLALVDCDWDIEAALKELRK 115 (323)
Q Consensus 78 ~~lIK~LR~~Tga~~~dCKkAL~e~~gDiekAi~~Lrk 115 (323)
-++|+++-++||.-.-=.-+-|+++|||+|-|++...+
T Consensus 536 ~e~l~~~~~~tGln~~~s~~c~e~~nWdy~~A~k~F~~ 573 (585)
T KOG3763|consen 536 DEKLLKFQEETGLNSEWSTMCLEQNNWDYERALKLFIE 573 (585)
T ss_pred HHHHHHHHHHhcCChHHHHHHHHHccCCHHHHHHHHHH
Confidence 46899999999987777778899999999999987753
No 93
>PRK09591 celC cellobiose phosphotransferase system IIA component; Reviewed
Probab=23.41 E-value=83 Score=25.84 Aligned_cols=30 Identities=13% Similarity=0.162 Sum_probs=24.1
Q ss_pred HHcCCCHHHHHHHHHhcC-CcHHHHHHHHHH
Q 020628 86 EQTSAPMKDVKLALVDCD-WDIEAALKELRK 115 (323)
Q Consensus 86 ~~Tga~~~dCKkAL~e~~-gDiekAi~~Lrk 115 (323)
--.|-.=..|.+||.+.. ||+++|.+.|.+
T Consensus 15 ~~aG~Ars~~~eAl~~ak~gdf~~A~~~l~e 45 (104)
T PRK09591 15 LHSGNARTEVHEAFAAMREGNFDLAEQKLNQ 45 (104)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 345555568899999985 999999999985
No 94
>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=23.24 E-value=75 Score=25.76 Aligned_cols=30 Identities=17% Similarity=0.073 Sum_probs=23.4
Q ss_pred HcCCCHHHHHHHHHhcC-CcHHHHHHHHHHh
Q 020628 87 QTSAPMKDVKLALVDCD-WDIEAALKELRKR 116 (323)
Q Consensus 87 ~Tga~~~dCKkAL~e~~-gDiekAi~~Lrk~ 116 (323)
-.|-.=..|-+||.+.. ||+++|.+.|++-
T Consensus 11 ~aG~Ars~~~eAl~~a~~g~fe~A~~~l~ea 41 (97)
T cd00215 11 HAGNARSKALEALKAAKEGDFAEAEELLEEA 41 (97)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 34445567889999885 9999999999853
No 95
>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=22.95 E-value=1.9e+02 Score=23.11 Aligned_cols=50 Identities=10% Similarity=0.159 Sum_probs=34.1
Q ss_pred hhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcC--C-----cHHHHHHHHHHhc
Q 020628 64 SRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD--W-----DIEAALKELRKRG 117 (323)
Q Consensus 64 ~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~--g-----DiekAi~~Lrk~G 117 (323)
.|.|+.. ..+.+..|+.||+ +|.|+.+.|+-|...+ + +.+...++|.++-
T Consensus 34 ~r~Y~~~---~~~~l~~I~~lr~-~G~sL~eI~~~l~~~~~~~~~~~~~~~~~~~~l~~~~ 90 (107)
T cd04777 34 QYFFDEK---CQDDLEFILELKG-LGFSLIEIQKIFSYKRLTKSRTHEDQDYYKSFLKNKK 90 (107)
T ss_pred ccccCHH---HHHHHHHHHHHHH-CCCCHHHHHHHHHhcccccccchhhHHHHHHHHHHHH
Confidence 4567654 1455788999987 7999999999887542 2 2344566666543
No 96
>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=22.78 E-value=90 Score=25.38 Aligned_cols=30 Identities=13% Similarity=0.011 Sum_probs=23.8
Q ss_pred HHcCCCHHHHHHHHHhcC-CcHHHHHHHHHH
Q 020628 86 EQTSAPMKDVKLALVDCD-WDIEAALKELRK 115 (323)
Q Consensus 86 ~~Tga~~~dCKkAL~e~~-gDiekAi~~Lrk 115 (323)
-..|-.=..|-+||.+.. ||+++|.+.|.+
T Consensus 12 ~~aG~Ars~~~eAl~~a~~gdfe~A~~~l~e 42 (99)
T TIGR00823 12 AYAGDARSKALEALKAAKAGDFAKARALVEQ 42 (99)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 344555567889999985 999999999985
No 97
>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=22.63 E-value=1.8e+02 Score=23.73 Aligned_cols=50 Identities=16% Similarity=0.212 Sum_probs=35.1
Q ss_pred hhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcCC----cHHHHHHHHHHh
Q 020628 63 ISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDW----DIEAALKELRKR 116 (323)
Q Consensus 63 ~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~g----DiekAi~~Lrk~ 116 (323)
--|.|+.. ....+..|+.||+ .|.|+.+-|.-|...+. +.+...+.|.++
T Consensus 34 ~yR~Y~~~---d~~~l~~I~~lr~-~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~ 87 (116)
T cd04769 34 NYRVYDAQ---HVECLRFIKEARQ-LGFTLAELKAIFAGHEGRAVLPWPHLQQALEDK 87 (116)
T ss_pred CceeeCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHhccccCCcCcHHHHHHHHHHH
Confidence 45677754 2455778999987 99999999998887652 345555555543
No 98
>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=22.39 E-value=65 Score=20.39 Aligned_cols=13 Identities=31% Similarity=0.440 Sum_probs=10.4
Q ss_pred HHHHHHHHHHhch
Q 020628 106 IEAALKELRKRGK 118 (323)
Q Consensus 106 iekAi~~Lrk~G~ 118 (323)
+.+|-+||+++|-
T Consensus 6 ~k~~~~wlkkkgp 18 (29)
T PF07442_consen 6 LKKAGEWLKKKGP 18 (29)
T ss_pred HHHHHHHHHhcCc
Confidence 5678999999863
No 99
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=22.29 E-value=1.1e+02 Score=23.26 Aligned_cols=28 Identities=29% Similarity=0.216 Sum_probs=23.6
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCcH
Q 020628 79 NLIKQLREQTSAPMKDVKLALVDCDWDI 106 (323)
Q Consensus 79 ~lIK~LR~~Tga~~~dCKkAL~e~~gDi 106 (323)
++++.|-++||.+..||++.|.....-+
T Consensus 4 ~l~~~ia~~~~~~~~~v~~vl~~~~~~i 31 (87)
T cd00591 4 ELIEAIAEKTGLSKKDAEAAVDAFLDVI 31 (87)
T ss_pred HHHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 5899999999999999999988754433
No 100
>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=21.66 E-value=2.5e+02 Score=22.42 Aligned_cols=40 Identities=23% Similarity=0.262 Sum_probs=25.0
Q ss_pred hhHHHHHHHHHHH---hhcCCc--ccCcCCCCHHHHHHHHHHHHH
Q 020628 274 PLKRVGSELAMHI---VAQKPL--FLTKELVSADALENEREILKS 313 (323)
Q Consensus 274 ~~~~la~~IAmHI---vA~~P~--~ls~~~Vp~~vle~Er~i~~~ 313 (323)
.+.-.|++|+-|| ...+|. .|.-.+.+.+.++.=.+.+++
T Consensus 43 ~l~v~Ar~L~~~i~~~~~~r~lllalgLkd~s~e~lk~i~~~i~~ 87 (90)
T PF10178_consen 43 LLHVYARQLIEFISQEGSNRPLLLALGLKDHSPETLKAIVEVIRE 87 (90)
T ss_dssp HHHHHHHHHHHHHHHHTTT-EEEEEEE-SS--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhccCCCCcEEEEEeccCCCHHHHHHHHHHHHH
Confidence 3456799999999 444555 455667888887776666654
No 101
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins 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 winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion 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=21.47 E-value=2e+02 Score=23.83 Aligned_cols=52 Identities=10% Similarity=0.078 Sum_probs=36.2
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcC---CcHHHHHHHHHHhc
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCD---WDIEAALKELRKRG 117 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~---gDiekAi~~Lrk~G 117 (323)
.-.|.|+.. ....+..|+.|| .+|.|+.+.|+-|.... .+.+.....|.++-
T Consensus 34 ~g~R~Y~~~---~~~~l~~I~~lr-~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~ 88 (127)
T cd01108 34 NGYRVYNQR---DIEELRFIRRAR-DLGFSLEEIRELLALWRDPSRASADVKALALEHI 88 (127)
T ss_pred CCceecCHH---HHHHHHHHHHHH-HcCCCHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 356778765 245578899998 49999999999886432 34566666666543
No 102
>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=20.91 E-value=1.4e+02 Score=26.38 Aligned_cols=39 Identities=15% Similarity=0.199 Sum_probs=29.2
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhcCC
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDCDW 104 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~~g 104 (323)
.--|.|+.. ....+..|+.||+ .|.|+.+||.-|...+.
T Consensus 35 ~gyR~Y~~~---dl~rL~~I~~lr~-~G~sL~eI~~ll~~~~~ 73 (172)
T cd04790 35 SNYRLYGER---DLERLEQICAYRS-AGVSLEDIRSLLQQPGD 73 (172)
T ss_pred CCCccCCHH---HHHHHHHHHHHHH-cCCCHHHHHHHHhcCCh
Confidence 455778755 1445778999965 99999999998876553
No 103
>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=20.87 E-value=1.4e+02 Score=25.12 Aligned_cols=50 Identities=22% Similarity=0.294 Sum_probs=36.3
Q ss_pred cHHHHHHHHHHhchhhhcccccccccCCceEEEecCCeEEEEEEecCCchh
Q 020628 105 DIEAALKELRKRGKVLASKKSSRTATEGLLALAQNESKAAVIELNCETDFV 155 (323)
Q Consensus 105 DiekAi~~Lrk~G~a~A~Kr~~R~a~EGlV~~yv~~~~avlVElncETDFV 155 (323)
|++++.+.|+++|...... .++....|....|+..--|.++|+.++++-+
T Consensus 86 ~l~~~~~~L~~~G~~v~~~-~~~~~~~~~~~~y~~DPdG~~iEl~~~~~~~ 135 (154)
T cd07237 86 DVGRAYDRVRARGIPIAMT-LGRHTNDRMLSFYVRTPSGFAIEYGWGGRTV 135 (154)
T ss_pred HHHHHHHHHHHcCCceecc-CCccCCCCcEEEEEECCCCcEEEeccCceEc
Confidence 5667888899998765432 2333345677888877778899999998876
No 104
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper 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-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=20.18 E-value=2.2e+02 Score=23.53 Aligned_cols=51 Identities=16% Similarity=0.152 Sum_probs=34.6
Q ss_pred hhhhhhccCCCcchHHHHHHHHHHHHcCCCHHHHHHHHHhc---CCcHHHHHHHHHHh
Q 020628 62 LISRNFSDQAPAATEQVNLIKQLREQTSAPMKDVKLALVDC---DWDIEAALKELRKR 116 (323)
Q Consensus 62 ~~~r~~ss~~p~~~~~~~lIK~LR~~Tga~~~dCKkAL~e~---~gDiekAi~~Lrk~ 116 (323)
.-.|.|+.. ....+..|+.|| .+|.|+.+.|+=|... +.+.+.....|.++
T Consensus 34 ~gyR~Y~~~---~l~~l~~I~~lr-~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~ 87 (127)
T TIGR02044 34 GGYRTYTQQ---HLDELRLISRAR-QVGFSLEECKELLNLWNDPNRTSADVKARTLEK 87 (127)
T ss_pred CCCeecCHH---HHHHHHHHHHHH-HCCCCHHHHHHHHHhhccCCCCHHHHHHHHHHH
Confidence 456778865 245577899998 6999999999988642 23445555555433
No 105
>PHA01735 hypothetical protein
Probab=20.04 E-value=51 Score=25.43 Aligned_cols=18 Identities=22% Similarity=0.152 Sum_probs=14.2
Q ss_pred hcCCcHHHHHHHHHHhch
Q 020628 101 DCDWDIEAALKELRKRGK 118 (323)
Q Consensus 101 e~~gDiekAi~~Lrk~G~ 118 (323)
++--|+..|++||+.+++
T Consensus 30 ATtaDL~AA~d~Lk~NdI 47 (76)
T PHA01735 30 ATTADLRAACDWLKSNDI 47 (76)
T ss_pred ccHHHHHHHHHHHHHCCC
Confidence 455799999999997664
Done!