Query psy8827
Match_columns 82
No_of_seqs 187 out of 1123
Neff 8.3
Searched_HMMs 46136
Date Fri Aug 16 20:12:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8827.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8827hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0614|consensus 99.7 5.5E-17 1.2E-21 116.2 3.0 76 1-76 215-290 (732)
2 KOG1113|consensus 99.6 7.1E-17 1.5E-21 110.5 0.4 77 1-77 183-259 (368)
3 TIGR03697 NtcA_cyano global ni 99.1 3.9E-10 8.4E-15 71.0 7.1 79 2-80 37-124 (193)
4 PLN03192 Voltage-dependent pot 99.1 3.9E-10 8.5E-15 84.8 8.0 69 2-70 440-508 (823)
5 PRK09392 ftrB transcriptional 99.1 7.5E-10 1.6E-14 72.0 7.7 79 2-80 73-158 (236)
6 PRK10402 DNA-binding transcrip 99.1 9.2E-10 2E-14 71.6 8.0 79 2-80 75-160 (226)
7 PF00027 cNMP_binding: Cyclic 99.0 3.2E-10 6.9E-15 63.0 4.0 48 2-49 43-90 (91)
8 PRK11753 DNA-binding transcrip 99.0 1.8E-09 3.9E-14 68.9 7.9 78 2-79 64-149 (211)
9 COG0664 Crp cAMP-binding prote 99.0 1.3E-09 2.8E-14 68.6 6.5 78 2-79 67-151 (214)
10 PRK13918 CRP/FNR family transc 98.7 4E-08 8.7E-13 62.3 6.2 78 2-80 52-130 (202)
11 cd00038 CAP_ED effector domain 98.6 6.9E-08 1.5E-12 54.8 4.5 51 2-52 61-111 (115)
12 PRK09391 fixK transcriptional 98.6 2.8E-07 6.1E-12 60.1 7.4 76 2-80 82-164 (230)
13 PRK11161 fumarate/nitrate redu 98.6 3.9E-07 8.5E-12 59.1 7.3 78 2-80 81-165 (235)
14 KOG0499|consensus 98.5 1.1E-07 2.4E-12 69.8 3.9 64 2-65 592-661 (815)
15 KOG0498|consensus 98.5 1.1E-07 2.4E-12 71.0 3.0 57 2-58 485-543 (727)
16 KOG1113|consensus 98.5 1.5E-07 3.3E-12 65.1 3.3 48 3-50 304-351 (368)
17 KOG0500|consensus 98.4 5.9E-07 1.3E-11 64.5 5.0 52 2-53 371-428 (536)
18 KOG0614|consensus 98.4 2.5E-07 5.5E-12 67.3 2.6 49 1-49 339-388 (732)
19 smart00100 cNMP Cyclic nucleot 98.3 2E-06 4.2E-11 48.8 5.5 52 2-53 61-114 (120)
20 PLN02868 acyl-CoA thioesterase 97.8 3.6E-05 7.8E-10 54.3 4.6 45 2-48 74-118 (413)
21 KOG2968|consensus 97.5 7.9E-05 1.7E-09 57.2 2.7 49 3-51 437-485 (1158)
22 KOG2968|consensus 97.4 0.00026 5.6E-09 54.5 4.1 53 1-53 551-603 (1158)
23 KOG2378|consensus 97.3 0.00023 5E-09 51.3 3.1 44 6-49 1-45 (573)
24 COG2905 Predicted signal-trans 97.2 0.0011 2.4E-08 48.9 5.4 50 2-51 70-119 (610)
25 KOG0501|consensus 94.8 0.0098 2.1E-07 44.7 0.5 50 1-50 609-660 (971)
26 PRK11832 putative DNA-binding 91.4 0.66 1.4E-05 30.5 5.0 46 5-50 66-111 (207)
27 PF04831 Popeye: Popeye protei 86.9 2.3 5E-05 26.7 4.8 35 18-52 89-123 (153)
28 cd06953 NR_LBD_DHR4_like The l 72.4 16 0.00034 23.7 5.2 32 47-78 34-65 (213)
29 cd06949 NR_LBD_ER Ligand bindi 72.0 19 0.0004 23.8 5.6 40 39-78 31-70 (235)
30 cd06929 NR_LBD_F1 Ligand-bindi 71.0 11 0.00024 23.1 4.1 28 50-77 12-39 (174)
31 cd06940 NR_LBD_REV_ERB The lig 70.9 18 0.00039 23.0 5.2 32 47-78 19-50 (189)
32 cd06942 NR_LBD_Sex_1_like The 70.0 14 0.00031 23.4 4.6 32 47-78 9-40 (191)
33 cd06941 NR_LBD_DmE78_like The 67.9 18 0.00039 22.9 4.7 30 49-78 11-40 (195)
34 cd06939 NR_LBD_ROR_like The li 67.0 27 0.00058 23.2 5.5 33 46-78 54-86 (241)
35 cd06936 NR_LBD_Fxr The ligand 65.6 25 0.00055 22.9 5.2 29 50-78 46-74 (221)
36 cd06933 NR_LBD_VDR The ligand 65.6 24 0.00053 23.3 5.1 35 44-78 41-75 (238)
37 cd06954 NR_LBD_LXR The ligand 64.7 27 0.00059 22.8 5.2 28 51-78 54-81 (236)
38 cd06946 NR_LBD_ERR The ligand 63.5 33 0.00072 22.1 5.4 32 47-78 34-65 (221)
39 COG3718 IolB Uncharacterized e 63.3 9.9 0.00021 25.8 2.9 35 5-39 64-111 (270)
40 cd06935 NR_LBD_TR The ligand b 62.3 29 0.00064 22.9 5.1 31 47-77 59-89 (243)
41 cd06938 NR_LBD_EcR The ligand 61.7 24 0.00052 23.1 4.5 28 51-78 50-77 (231)
42 cd06930 NR_LBD_F2 Ligand-bindi 61.5 25 0.00055 21.1 4.4 25 53-77 12-36 (165)
43 PF10330 Stb3: Putative Sin3 b 61.2 21 0.00045 20.6 3.6 36 39-74 9-45 (92)
44 cd06157 NR_LBD The ligand bind 59.2 28 0.0006 20.5 4.3 26 53-78 11-36 (168)
45 cd06944 NR_LBD_Ftz-F1_like The 58.7 37 0.0008 22.3 5.1 28 51-78 49-76 (237)
46 cd06932 NR_LBD_PPAR The ligand 58.3 41 0.0009 22.5 5.3 30 49-78 72-101 (259)
47 cd07072 NR_LBD_DHR38_like Liga 56.7 48 0.001 22.0 5.3 28 51-78 53-80 (239)
48 KOG2297|consensus 56.0 18 0.00039 25.8 3.3 66 4-76 79-149 (412)
49 cd07070 NR_LBD_SF-1 The ligand 54.4 41 0.00088 22.2 4.7 28 51-78 49-76 (237)
50 cd06937 NR_LBD_RAR The ligand 53.5 61 0.0013 21.3 5.4 30 49-78 47-76 (231)
51 cd06945 NR_LBD_Nurr1_like The 53.5 45 0.00099 22.0 4.8 29 50-78 51-79 (239)
52 cd06948 NR_LBD_COUP-TF Ligand 52.9 46 0.001 21.8 4.8 26 52-77 42-67 (236)
53 cd06943 NR_LBD_RXR_like The li 50.4 44 0.00096 21.2 4.3 27 51-77 41-67 (207)
54 smart00430 HOLI Ligand binding 50.1 21 0.00046 20.9 2.7 25 54-78 6-30 (163)
55 cd06934 NR_LBD_PXR_like The li 49.4 34 0.00074 22.4 3.7 28 51-78 46-73 (226)
56 cd07073 NR_LBD_AR Ligand bindi 49.0 60 0.0013 21.7 4.9 28 51-78 39-66 (246)
57 cd07068 NR_LBD_ER_like The lig 49.0 71 0.0015 20.6 5.5 28 51-78 38-65 (221)
58 cd07069 NR_LBD_Lrh-1 The ligan 48.6 57 0.0012 21.6 4.7 27 52-78 52-78 (241)
59 cd07076 NR_LBD_GR Ligand bindi 48.5 81 0.0018 21.2 5.5 36 43-78 31-66 (247)
60 cd07349 NR_LBD_SHP The ligand 47.3 62 0.0013 21.2 4.7 27 51-77 30-56 (222)
61 cd07348 NR_LBD_NGFI-B The liga 46.2 62 0.0013 21.5 4.6 28 51-78 52-79 (238)
62 cd07071 NR_LBD_Nurr1 The ligan 46.1 86 0.0019 20.8 5.5 28 51-78 52-79 (238)
63 cd07350 NR_LBD_Dax1 The ligand 46.1 68 0.0015 21.2 4.8 27 52-78 31-57 (232)
64 cd06951 NR_LBD_Dax1_like The l 45.4 70 0.0015 20.9 4.7 28 51-78 30-57 (222)
65 PF07943 PBP5_C: Penicillin-bi 45.0 45 0.00097 18.1 3.3 34 3-36 6-39 (91)
66 COG2933 Predicted SAM-dependen 44.8 93 0.002 21.9 5.3 49 33-81 44-92 (358)
67 cd06952 NR_LBD_TR2_like The li 44.7 59 0.0013 21.0 4.3 27 52-78 33-59 (222)
68 cd06947 NR_LBD_GR_Like Ligand 43.0 84 0.0018 21.0 4.8 28 51-78 39-66 (246)
69 cd06931 NR_LBD_HNF4_like The l 42.8 71 0.0015 20.5 4.4 25 54-78 46-70 (222)
70 cd06950 NR_LBD_Tlx_PNR_like Th 41.9 91 0.002 20.0 4.8 25 53-77 39-63 (206)
71 PF00104 Hormone_recep: Ligand 40.3 85 0.0018 19.0 5.6 27 52-78 29-55 (203)
72 cd07074 NR_LBD_PR Ligand bindi 39.6 1.1E+02 0.0025 20.5 5.1 33 46-78 34-66 (248)
73 PF05678 VQ: VQ motif; InterP 38.0 45 0.00098 15.2 2.5 20 30-49 4-23 (31)
74 cd07075 NR_LBD_MR Ligand bindi 36.3 1.2E+02 0.0025 20.4 4.7 29 50-78 38-66 (248)
75 PF01846 FF: FF domain; Inter 35.6 40 0.00088 16.4 2.0 39 38-76 3-46 (51)
76 COG1039 RnhC Ribonuclease HIII 30.6 21 0.00045 24.9 0.4 19 29-47 142-160 (297)
77 PF11626 Rap1_C: TRF2-interact 30.4 1E+02 0.0022 17.0 3.5 26 37-62 62-87 (87)
78 PF14037 YoqO: YoqO-like prote 30.2 30 0.00064 20.8 1.0 28 54-81 75-102 (117)
79 PF09823 DUF2357: Domain of un 27.4 92 0.002 20.1 3.1 61 2-62 2-63 (248)
80 cd08540 SAM_PNT-ERG Sterile al 26.1 37 0.00081 18.7 0.9 36 29-64 38-73 (75)
81 PRK12750 cpxP periplasmic repr 25.1 1.8E+02 0.004 18.3 4.0 43 36-78 103-146 (170)
82 KOG3179|consensus 24.9 20 0.00044 23.9 -0.3 33 4-36 135-179 (245)
83 PF02944 BESS: BESS motif; In 24.5 46 0.00099 15.4 0.9 16 61-76 10-25 (37)
84 KOG3542|consensus 23.9 83 0.0018 25.1 2.6 46 3-48 345-391 (1283)
85 COG1220 HslU ATP-dependent pro 23.1 1.2E+02 0.0026 22.2 3.1 42 31-72 331-372 (444)
86 PF02749 QRPTase_N: Quinolinat 23.1 64 0.0014 17.8 1.5 39 5-45 2-40 (88)
87 cd04467 S1_aIF5A S1_aIF5A: Arc 21.3 97 0.0021 16.1 1.9 25 20-44 3-27 (57)
88 PF10539 Dev_Cell_Death: Devel 21.1 2.1E+02 0.0046 17.5 3.8 30 19-48 78-107 (130)
89 PTZ00047 cytochrome c oxidase 21.0 2E+02 0.0044 18.3 3.6 40 4-48 120-159 (162)
90 smart00767 DCD DCD is a plant 20.8 1.5E+02 0.0033 18.2 2.9 32 18-49 77-108 (132)
91 PF12204 DUF3598: Domain of un 20.7 87 0.0019 21.0 2.0 25 3-27 93-118 (252)
92 cd08531 SAM_PNT-ERG_FLI-1 Ster 20.6 63 0.0014 17.7 1.1 21 28-48 37-57 (75)
93 COG1622 CyoA Heme/copper-type 20.6 2E+02 0.0043 19.4 3.7 42 5-51 185-226 (247)
94 cd08541 SAM_PNT-FLI-1 Sterile 20.2 62 0.0013 18.5 1.1 36 29-64 50-85 (91)
No 1
>KOG0614|consensus
Probab=99.65 E-value=5.5e-17 Score=116.19 Aligned_cols=76 Identities=29% Similarity=0.648 Sum_probs=71.5
Q ss_pred CcccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHHHHHHHHHHhhCccccCCCHHHHHH
Q psy8827 1 MHAYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKRKMYEKLIDAVPMLKSLQVMVFFL 76 (82)
Q Consensus 1 v~~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~ 76 (82)
++.+++|..|||+|++++++|+|||+|+++|++|.|+|+.|+.|++.....++.++.+||+++|+|++++++-...
T Consensus 215 l~~m~~gtvFGELAILynctRtAsV~alt~~~lWaidR~vFq~IM~~tg~~r~~~~~~fLrsv~~~q~l~Ee~L~K 290 (732)
T KOG0614|consen 215 LGKMGAGTVFGELAILYNCTRTASVRALTDVRLWAIDREVFQAIMMRTGLERHEQYMNFLRSVPLFQNLPEELLLK 290 (732)
T ss_pred eeccCCchhhhHHHHHhCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCCHHHHHH
Confidence 4678999999999999999999999999999999999999999999999999999999999999999999876543
No 2
>KOG1113|consensus
Probab=99.61 E-value=7.1e-17 Score=110.49 Aligned_cols=77 Identities=49% Similarity=0.846 Sum_probs=72.7
Q ss_pred CcccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHHHHHHHHHHhhCccccCCCHHHHHHH
Q psy8827 1 MHAYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKRKMYEKLIDAVPMLKSLQVMVFFLY 77 (82)
Q Consensus 1 v~~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~~ 77 (82)
+..++||++|||++|+++.||.|||+|.+++.+|.+++-.|++++......+++++..+++++|+++++...+|...
T Consensus 183 v~~~~~g~sFGElALmyn~PRaATv~a~t~~klWgldr~SFrrIi~~s~~kkrkMy~~~l~s~pil~~l~k~er~kv 259 (368)
T KOG1113|consen 183 VTTYSPGGSFGELALMYNPPRAATVVAKSLKKLWGLDRTSFRRIIMKSCIKKRKMYEPFLESVPILESLEKLERAKV 259 (368)
T ss_pred EeeeCCCCchhhhHhhhCCCcccceeeccccceEEEeeceeEEEeeccchhhhhhhhhhhhcchhhHHHHHHHHHhh
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999888653
No 3
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=99.11 E-value=3.9e-10 Score=71.00 Aligned_cols=79 Identities=11% Similarity=0.074 Sum_probs=60.7
Q ss_pred cccCCCCeeehhhhcCCCC--ceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHHHHHHH-------HHHhhCccccCCCHH
Q psy8827 2 HAYEDKGSFGELALLYNMP--RAATIKATSTGSLWAMDRKTFKQIVLKSAFKKRKMYE-------KLIDAVPMLKSLQVM 72 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~~~~--r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~~~~~~-------~~l~~~~~~~~l~~~ 72 (82)
..++||++||+.+++.+.+ +..+++|.++|+++.+++++|..++.+++........ .....+..+...+..
T Consensus 37 ~~~~~g~~~G~~~~~~~~~~~~~~~~~A~~~~~v~~i~~~~~~~l~~~~p~l~~~~~~~l~~~l~~~~~~~~~l~~~~~~ 116 (193)
T TIGR03697 37 ALLRENSVFGVLSLITGHRSDRFYHAVAFTRVELLAVPIEQVEKAIEEDPDLSMLLLQGLSSRILQTEMMIETLAHRDMG 116 (193)
T ss_pred EEccCCCEeeeeeeccCCCCccceEEEEecceEEEEeeHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHHHHHhCCHH
Confidence 5689999999999998875 5688999999999999999999999888766543333 233334455667788
Q ss_pred HHHHHHHh
Q psy8827 73 VFFLYLVC 80 (82)
Q Consensus 73 ~~~~~~~~ 80 (82)
+|++.+++
T Consensus 117 ~Rla~~L~ 124 (193)
T TIGR03697 117 SRLVSFLL 124 (193)
T ss_pred HHHHHHHH
Confidence 88776554
No 4
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=99.10 E-value=3.9e-10 Score=84.78 Aligned_cols=69 Identities=14% Similarity=0.212 Sum_probs=62.7
Q ss_pred cccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHHHHHHHHHHhhCccccCCC
Q psy8827 2 HAYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKRKMYEKLIDAVPMLKSLQ 70 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~~~~~~~~l~~~~~~~~l~ 70 (82)
+.+++||+|||++++.+.|+++|++|.++|+++.+++++|.+++++++........++++...-++.+.
T Consensus 440 ~~l~~Gd~FGE~~~l~~~p~~~t~ra~~~s~ll~l~~~~f~~ll~~~p~d~~~i~~~~l~~~~~l~~l~ 508 (823)
T PLN03192 440 GTLGCGDIFGEVGALCCRPQSFTFRTKTLSQLLRLKTSTLIEAMQTRQEDNVVILKNFLQHHKELHDLN 508 (823)
T ss_pred EEccCCCEecchHHhcCCCCCCeEEEcccEEEEEEEHHHHHHHHHHhhHHHHHHHHHHHHHhhhhcccc
Confidence 568999999999999999999999999999999999999999999999988888888888776666654
No 5
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=99.08 E-value=7.5e-10 Score=72.02 Aligned_cols=79 Identities=8% Similarity=0.050 Sum_probs=63.8
Q ss_pred cccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHHHHHH-------HHHHhhCccccCCCHHHH
Q psy8827 2 HAYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKRKMY-------EKLIDAVPMLKSLQVMVF 74 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~~~~~-------~~~l~~~~~~~~l~~~~~ 74 (82)
..+++|++||+.+++.+.|+.++++|.++|+++.+++++|.+++.+++....... ....+.+..+...+..+|
T Consensus 73 ~~~~~g~~~g~~~~~~~~~~~~~~~A~~~~~~~~i~~~~~~~l~~~~p~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~R 152 (236)
T PRK09392 73 AILRPVSTFILAAVVLDAPYLMSARTLTRSRVLMIPAELVREAMSEDPGFMRAVVFELAGCYRGLVKSLKNQKLRSSAER 152 (236)
T ss_pred EEeCCCchhhhHHHhCCCCCceEEEEcCceEEEEEeHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHH
Confidence 4678999999999999999999999999999999999999999988876654432 333444445566788888
Q ss_pred HHHHHh
Q psy8827 75 FLYLVC 80 (82)
Q Consensus 75 ~~~~~~ 80 (82)
++.++.
T Consensus 153 la~~Ll 158 (236)
T PRK09392 153 LANYLL 158 (236)
T ss_pred HHHHHH
Confidence 886654
No 6
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=99.08 E-value=9.2e-10 Score=71.56 Aligned_cols=79 Identities=15% Similarity=0.155 Sum_probs=60.2
Q ss_pred cccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHHHHHHHH-------HHhhCccccCCCHHHH
Q psy8827 2 HAYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKRKMYEK-------LIDAVPMLKSLQVMVF 74 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~~~~~~~-------~l~~~~~~~~l~~~~~ 74 (82)
..+.||++|||.+++.+.++++++.|.++|.++.+++++|..++..++......... ....+.....++..+|
T Consensus 75 ~~~~~g~~~G~~~~~~~~~~~~~~~A~~~~~i~~i~~~~~~~ll~~~p~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~R 154 (226)
T PRK10402 75 DFFAAPCFIGEIELIDKDHETKAVQAIEECWCLALPMKDCRPLLLNDALFLRKLCKFLSHKNYRNIVSLTQNQSFPLENR 154 (226)
T ss_pred eecCCCCeEEeehhhcCCCCCccEEEeccEEEEEEEHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHhccChHHHH
Confidence 467899999999999999999999999999999999999999998887554432222 2222222334577888
Q ss_pred HHHHHh
Q psy8827 75 FLYLVC 80 (82)
Q Consensus 75 ~~~~~~ 80 (82)
++.+++
T Consensus 155 la~~L~ 160 (226)
T PRK10402 155 LAAFIL 160 (226)
T ss_pred HHHHHH
Confidence 886654
No 7
>PF00027 cNMP_binding: Cyclic nucleotide-binding domain; InterPro: IPR000595 Proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues [, , ]. The best studied of these proteins is the prokaryotic catabolite gene activator (also known as the cAMP receptor protein) (gene crp) where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure. There are six invariant amino acids in this domain, three of which are glycine residues that are thought to be essential for maintenance of the structural integrity of the beta-barrel. cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain. The cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain. The cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section. Vertebrate cyclic nucleotide-gated ion-channels also contain this domain. Two such cations channels have been fully characterised, one is found in rod cells where it plays a role in visual signal transduction.; PDB: 1O7F_A 2BYV_E 3E97_A 3U10_A 2H6B_A 3SHR_A 2OZ6_A 1WGP_A 3LA2_A 3LA3_B ....
Probab=99.04 E-value=3.2e-10 Score=62.98 Aligned_cols=48 Identities=23% Similarity=0.360 Sum_probs=45.5
Q ss_pred cccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhH
Q psy8827 2 HAYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSA 49 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~ 49 (82)
..+++|++||+.+++.+.++..+++|.++|+++.+++++|.+++.++|
T Consensus 43 ~~~~~g~~~g~~~~~~~~~~~~~~~a~~~~~~~~i~~~~~~~~~~~~p 90 (91)
T PF00027_consen 43 FFLGPGDIFGEIELLTGKPSPFTVIALTDSEVLRIPREDFLQLLQQDP 90 (91)
T ss_dssp EEEETTEEESGHHHHHTSBBSSEEEESSSEEEEEEEHHHHHHHHHHSH
T ss_pred cceeeeccccceeecCCCccEEEEEEccCEEEEEEeHHHHHHHHHhCc
Confidence 467899999999999999999999999999999999999999998876
No 8
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=99.03 E-value=1.8e-09 Score=68.87 Aligned_cols=78 Identities=18% Similarity=0.146 Sum_probs=59.5
Q ss_pred cccCCCCeeehhhhcCCC-CceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHHHHH-------HHHHHhhCccccCCCHHH
Q psy8827 2 HAYEDKGSFGELALLYNM-PRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKRKM-------YEKLIDAVPMLKSLQVMV 73 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~~~-~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~~~~-------~~~~l~~~~~~~~l~~~~ 73 (82)
..+++|++||+.+++.+. +++++++|.++|+++.+++++|.+++..++...... .....+.+.-+...+..+
T Consensus 64 ~~~~~g~~~g~~~~~~~~~~~~~~~~a~~~~~v~~i~~~~~~~l~~~~p~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 143 (211)
T PRK11753 64 SYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMALSAQMARRLQNTSRKVGDLAFLDVTG 143 (211)
T ss_pred EEcCCCCEEeehhhccCCCCceEEEEEcCcEEEEEEcHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHhcChhh
Confidence 467999999999999865 688999999999999999999999998877654322 233334444456677778
Q ss_pred HHHHHH
Q psy8827 74 FFLYLV 79 (82)
Q Consensus 74 ~~~~~~ 79 (82)
|++..+
T Consensus 144 Rl~~~L 149 (211)
T PRK11753 144 RIAQTL 149 (211)
T ss_pred HHHHHH
Confidence 876543
No 9
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=99.01 E-value=1.3e-09 Score=68.60 Aligned_cols=78 Identities=22% Similarity=0.244 Sum_probs=56.2
Q ss_pred cccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHHHH-------HHHHHHhhCccccCCCHHHH
Q psy8827 2 HAYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKRK-------MYEKLIDAVPMLKSLQVMVF 74 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~~~-------~~~~~l~~~~~~~~l~~~~~ 74 (82)
..++|||+|||.+++.+.||+++++|.++|++|.+++++|..++.+.|...+. ........+......+..+|
T Consensus 67 ~~~~~g~~fg~~~l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~p~l~~~l~~~~~~~l~~~~~~~~~~~~~~~~~r 146 (214)
T COG0664 67 GFLGPGDFFGELALLGGDPRSASAVALTDVEVLEIPRKDFLELLAESPKLALALLRLLARRLRQALERLSLLARKDVEER 146 (214)
T ss_pred EEecCCchhhhHHHhcCCCccceEEEcceEEEEEecHHHHHHHHhhCcHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHH
Confidence 45789999999999999999999999999999999999999998773333222 22222333333344555666
Q ss_pred HHHHH
Q psy8827 75 FLYLV 79 (82)
Q Consensus 75 ~~~~~ 79 (82)
++..+
T Consensus 147 ~~~~l 151 (214)
T COG0664 147 LARFL 151 (214)
T ss_pred HHHHH
Confidence 55443
No 10
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=98.74 E-value=4e-08 Score=62.34 Aligned_cols=78 Identities=12% Similarity=0.024 Sum_probs=51.2
Q ss_pred cccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHH-HHHHHHHHhhCccccCCCHHHHHHHHHh
Q psy8827 2 HAYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKK-RKMYEKLIDAVPMLKSLQVMVFFLYLVC 80 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~-~~~~~~~l~~~~~~~~l~~~~~~~~~~~ 80 (82)
..++|||+|||.+++ +.+++.++.|.++|+++.++++.|..-+....... .+......+.+..+...+..+|++.+++
T Consensus 52 ~~~~~Gd~~G~~~~~-~~~~~~~~~A~~~~~v~~i~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~l~~~~~~~Rla~~Ll 130 (202)
T PRK13918 52 RYVRPGEYFGEEALA-GAERAYFAEAVTDSRIDVLNPALMSAEDNLVLTQHLVRTLARAYESIYRLVGQRLKNRIAAALL 130 (202)
T ss_pred EEecCCCeechHHhc-CCCCCceEEEcCceEEEEEEHHHcChhhHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHHHHH
Confidence 457999999998765 57899999999999999999887733221111111 1122233344444555677888886654
No 11
>cd00038 CAP_ED effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of
Probab=98.63 E-value=6.9e-08 Score=54.76 Aligned_cols=51 Identities=31% Similarity=0.423 Sum_probs=46.3
Q ss_pred cccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHH
Q psy8827 2 HAYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKK 52 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~ 52 (82)
..+.+|++||+.+++.+.++..+++|.++|.+|.+++++|..++.+.+...
T Consensus 61 ~~~~~g~~~g~~~~~~~~~~~~~~~a~~~~~~~~i~~~~~~~~~~~~~~~~ 111 (115)
T cd00038 61 GFLGPGDLFGELALLGNGPRSATVRALTDSELLVLPRSDFRRLLQEYPELA 111 (115)
T ss_pred EecCCccCcChHHHhcCCCCCceEEEcCceEEEEEeHHHHHHHHHHCcHhH
Confidence 457899999999999889999999999999999999999999998887543
No 12
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=98.61 E-value=2.8e-07 Score=60.12 Aligned_cols=76 Identities=13% Similarity=0.056 Sum_probs=57.4
Q ss_pred cccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHHHHHHHH-------HHhhCccccCCCHHHH
Q psy8827 2 HAYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKRKMYEK-------LIDAVPMLKSLQVMVF 74 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~~~~~~~-------~l~~~~~~~~l~~~~~ 74 (82)
..+.|||+||+. .+.+++.+++|+++|.++.++.++|.+++.+++...+..... ....+..+...+..+|
T Consensus 82 ~~~~~Gd~fG~~---~~~~~~~~~~A~~ds~v~~i~~~~f~~l~~~~p~l~~~l~~~l~~~l~~~~~~~~~l~~~~~~~R 158 (230)
T PRK09391 82 AFHLPGDVFGLE---SGSTHRFTAEAIVDTTVRLIKRRSLEQAAATDVDVARALLSLTAGGLRHAQDHMLLLGRKTAMER 158 (230)
T ss_pred EEecCCceeccc---CCCcCCeEEEEcCceEEEEEEHHHHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHH
Confidence 346899999974 466788999999999999999999999998887665433222 2334445666788888
Q ss_pred HHHHHh
Q psy8827 75 FLYLVC 80 (82)
Q Consensus 75 ~~~~~~ 80 (82)
++.++.
T Consensus 159 la~~Ll 164 (230)
T PRK09391 159 VAAFLL 164 (230)
T ss_pred HHHHHH
Confidence 886654
No 13
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=98.57 E-value=3.9e-07 Score=59.14 Aligned_cols=78 Identities=9% Similarity=-0.031 Sum_probs=56.9
Q ss_pred cccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHHHHH-------HHHHHhhCccccCCCHHHH
Q psy8827 2 HAYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKRKM-------YEKLIDAVPMLKSLQVMVF 74 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~~~~-------~~~~l~~~~~~~~l~~~~~ 74 (82)
..+.|||+||+.+++. .+.+.+++|.++++++.++++.|.+++.+++...... .......+..+...+..+|
T Consensus 81 ~~~~~gd~~g~~~~~~-~~~~~~~~a~~~~~i~~ip~~~f~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~R 159 (235)
T PRK11161 81 GFHLAGDLVGFDAIGS-GQHPSFAQALETSMVCEIPFETLDDLSGKMPKLRQQIMRLMSGEIKGDQEMILLLSKKNAEER 159 (235)
T ss_pred EeccCCceeccccccC-CCCcceEEEeccEEEEEEEHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHH
Confidence 3468999999987754 4556789999999999999999999998887654322 2223344445666788888
Q ss_pred HHHHHh
Q psy8827 75 FLYLVC 80 (82)
Q Consensus 75 ~~~~~~ 80 (82)
++.++.
T Consensus 160 la~~L~ 165 (235)
T PRK11161 160 LAAFIY 165 (235)
T ss_pred HHHHHH
Confidence 775543
No 14
>KOG0499|consensus
Probab=98.51 E-value=1.1e-07 Score=69.78 Aligned_cols=64 Identities=23% Similarity=0.363 Sum_probs=52.1
Q ss_pred cccCCCCeeehhhhcC---CCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHH---HHHHHHHHhhCcc
Q psy8827 2 HAYEDKGSFGELALLY---NMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKK---RKMYEKLIDAVPM 65 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~---~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~---~~~~~~~l~~~~~ 65 (82)
..|..|..|||++|+. +..|||+|+|.+.|.+++++++|++.++..+|..+ ++..+.++++-.-
T Consensus 592 ~tL~~GsVFGEISLLaigG~nRRTAnV~a~Gf~nLfvL~KkdLneil~~YP~sq~iLrkkAr~llk~nak 661 (815)
T KOG0499|consen 592 VTLKAGSVFGEISLLAIGGGNRRTANVVAHGFANLFVLDKKDLNEILVHYPDSQRILRKKARVLLKQNAK 661 (815)
T ss_pred EEecccceeeeeeeeeecCCCccchhhhhcccceeeEecHhHHHHHHHhCccHHHHHHHHHHHHHHhccc
Confidence 4688999999999984 56899999999999999999999999998776543 3455566665443
No 15
>KOG0498|consensus
Probab=98.46 E-value=1.1e-07 Score=71.02 Aligned_cols=57 Identities=18% Similarity=0.269 Sum_probs=51.0
Q ss_pred cccCCCCeee-hhhhcCC-CCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHHHHHHHH
Q psy8827 2 HAYEDKGSFG-ELALLYN-MPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKRKMYEK 58 (82)
Q Consensus 2 ~~l~~G~~FG-E~al~~~-~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~~~~~~~ 58 (82)
..|+|||+|| |+..... .|.++||+|.|.|++..|++++|..+++.++....++.+.
T Consensus 485 ~~L~~Gd~~GeEl~~~~~~~p~t~TVralt~~el~~L~~~dL~~V~~~f~~~~~~~l~~ 543 (727)
T KOG0498|consen 485 AILGPGDFFGEELLTWCLDLPQTRTVRALTYCELFRLSADDLKEVLQQFRRLGSKFLQH 543 (727)
T ss_pred EEecCCCccchHHHHHHhcCCCCceeehhhhhhHHhccHHHHHHHHHHhHHHHHHHHHh
Confidence 5799999999 9999988 8999999999999999999999999999988766666553
No 16
>KOG1113|consensus
Probab=98.46 E-value=1.5e-07 Score=65.10 Aligned_cols=48 Identities=33% Similarity=0.435 Sum_probs=45.0
Q ss_pred ccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHH
Q psy8827 3 AYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAF 50 (82)
Q Consensus 3 ~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~ 50 (82)
.+++||+|||++++.+.||.|||.|.++..|..++++.|++++.....
T Consensus 304 kl~~~dyfge~al~~~~pr~Atv~a~~~~kc~~~dk~~ferllgpc~d 351 (368)
T KOG1113|consen 304 KLKKGDYFGELALLKNLPRAATVVAKGRLKCAKLDKPRFERLLGPCQD 351 (368)
T ss_pred EechhhhcchHHHHhhchhhceeeccCCceeeeeChHHHHHHhhHHHH
Confidence 678999999999999999999999999999999999999999976654
No 17
>KOG0500|consensus
Probab=98.39 E-value=5.9e-07 Score=64.50 Aligned_cols=52 Identities=13% Similarity=0.319 Sum_probs=46.6
Q ss_pred cccCCCCeeehhhhcC------CCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHHH
Q psy8827 2 HAYEDKGSFGELALLY------NMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKR 53 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~------~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~~ 53 (82)
..+..|++|||++++. +..|+|+|++++.+.+.+++++|+-+.|.++|..+.
T Consensus 371 ~~L~~G~~FGEisIlni~g~~~gNRRtanvrSvGYSDlfvLskdDl~~aL~eYP~a~~ 428 (536)
T KOG0500|consen 371 VTLKAGSVFGEISILNIKGNKNGNRRTANVRSVGYSDLFVLSKDDLWEALSEYPDARK 428 (536)
T ss_pred EEecCCceeeeeEEEEEcCcccCCcceeeeeeeccceeeEeeHHHHHHHHHhCCHHHH
Confidence 4688999999999984 568999999999999999999999999999987643
No 18
>KOG0614|consensus
Probab=98.36 E-value=2.5e-07 Score=67.33 Aligned_cols=49 Identities=29% Similarity=0.379 Sum_probs=44.2
Q ss_pred CcccCCCCeeehhhhcCCCCceeEEEEcCc-EEEEEEcHHHHHHHHHhhH
Q psy8827 1 MHAYEDKGSFGELALLYNMPRAATIKATST-GSLWAMDRKTFKQIVLKSA 49 (82)
Q Consensus 1 v~~l~~G~~FGE~al~~~~~r~atv~a~~~-~~~~~l~~~~f~~ll~~~~ 49 (82)
++.++.||+|||-+|+....|+|+++|..+ +.|+.|+|+.|.+++....
T Consensus 339 lr~l~kGd~FGE~al~~edvRtAniia~~~gv~cl~lDresF~~liG~l~ 388 (732)
T KOG0614|consen 339 LRTLNKGDYFGERALLGEDVRTANIIAQAPGVECLTLDRESFKKLIGDLE 388 (732)
T ss_pred HhhccccchhhHHHhhccCccchhhhccCCCceEEEecHHHHHHhcccHH
Confidence 357899999999999999999999999988 9999999999999995443
No 19
>smart00100 cNMP Cyclic nucleotide-monophosphate binding domain. Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.
Probab=98.33 E-value=2e-06 Score=48.81 Aligned_cols=52 Identities=27% Similarity=0.254 Sum_probs=44.6
Q ss_pred cccCCCCeeehhhhc--CCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHHH
Q psy8827 2 HAYEDKGSFGELALL--YNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKR 53 (82)
Q Consensus 2 ~~l~~G~~FGE~al~--~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~~ 53 (82)
..+++|++||+.+++ ...+.+.++.+.++|.++.++.++|...+...+....
T Consensus 61 ~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~ 114 (120)
T smart00100 61 GILGPGDFFGELALLTNSRRAASATAVALELATLLRIDFRDFLQLLQENPQLLL 114 (120)
T ss_pred EeecCCceechhhhccCCCcccceEEEEEeeEEEEccCHHHHHHHHHHhHHHHH
Confidence 457899999999999 3467888999999999999999999999988876533
No 20
>PLN02868 acyl-CoA thioesterase family protein
Probab=97.80 E-value=3.6e-05 Score=54.35 Aligned_cols=45 Identities=18% Similarity=0.100 Sum_probs=39.7
Q ss_pred cccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhh
Q psy8827 2 HAYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKS 48 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~ 48 (82)
..+++|++||+. +.+.+++++++|.++|+++.++++.|+.+....
T Consensus 74 ~~l~~Gd~fG~~--l~~~~~~~~~~A~~d~~v~~ip~~~~~~~~~~~ 118 (413)
T PLN02868 74 FLLKRYDYFGYG--LSGSVHSADVVAVSELTCLVLPHEHCHLLSPKS 118 (413)
T ss_pred EEeCCCCEeehh--hCCCCcccEEEECCCEEEEEEcHHHHhhhcccc
Confidence 467999999985 688999999999999999999999999887433
No 21
>KOG2968|consensus
Probab=97.49 E-value=7.9e-05 Score=57.22 Aligned_cols=49 Identities=22% Similarity=0.257 Sum_probs=46.2
Q ss_pred ccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHH
Q psy8827 3 AYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFK 51 (82)
Q Consensus 3 ~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~ 51 (82)
..+||+.+|-++++.|.|-..+++|.++|.+..+++++|.+++.+++..
T Consensus 437 ~v~pG~ivgyla~lt~e~S~~tirArsdt~v~~isrs~l~~~~~~~p~I 485 (1158)
T KOG2968|consen 437 VVGPGEIVGYLAILTNEPSFITIRARSDTRVLFISRSDLERFLDAEPLI 485 (1158)
T ss_pred EecCCceechhhhhcCCcceEEEEEecceEEEEeeHHHHHHHHHhCceE
Confidence 5789999999999999999999999999999999999999999988743
No 22
>KOG2968|consensus
Probab=97.36 E-value=0.00026 Score=54.52 Aligned_cols=53 Identities=23% Similarity=0.283 Sum_probs=48.5
Q ss_pred CcccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHHH
Q psy8827 1 MHAYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKKR 53 (82)
Q Consensus 1 v~~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~~ 53 (82)
++.++.||.+|+...+.+.||..|+.|+.++++..|+..-|..+..++|..-.
T Consensus 551 ~~EygrGd~iG~~E~lt~~~R~tTv~AvRdSelariPe~l~~~ik~ryP~v~~ 603 (1158)
T KOG2968|consen 551 VGEYGRGDLIGEVEMLTKQPRATTVMAVRDSELARIPEGLLNFIKLRYPQVVT 603 (1158)
T ss_pred hhhccCcceeehhHHhhcCCccceEEEEeehhhhhccHHHHHHHHHhccHHHH
Confidence 46789999999999999999999999999999999999999999988886543
No 23
>KOG2378|consensus
Probab=97.30 E-value=0.00023 Score=51.28 Aligned_cols=44 Identities=32% Similarity=0.544 Sum_probs=38.8
Q ss_pred CCCeeehhhhcCCCCceeEEEE-cCcEEEEEEcHHHHHHHHHhhH
Q psy8827 6 DKGSFGELALLYNMPRAATIKA-TSTGSLWAMDRKTFKQIVLKSA 49 (82)
Q Consensus 6 ~G~~FGE~al~~~~~r~atv~a-~~~~~~~~l~~~~f~~ll~~~~ 49 (82)
.||-||.+++..+.||.||++. ..+|.++++++.+|.+|+.+..
T Consensus 1 eGddfgklalvnd~praativl~ed~~~fl~vDk~~Fn~I~~~vE 45 (573)
T KOG2378|consen 1 EGDDFGKLALVNDAPRAATIVLREDNCHFLRVDKHDFNRILHDVE 45 (573)
T ss_pred CCcccchhccccccccccceeeecCCCcceeecHHHHHHHHHhhh
Confidence 4999999999999999999775 4569999999999999996543
No 24
>COG2905 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]
Probab=97.16 E-value=0.0011 Score=48.86 Aligned_cols=50 Identities=12% Similarity=0.177 Sum_probs=44.6
Q ss_pred cccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHH
Q psy8827 2 HAYEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFK 51 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~ 51 (82)
..+..||.||-.+++.+.+-.-.+.|.+|+-++.|+++.|.++..+++..
T Consensus 70 ~~~~~gdlFg~~~l~~~~~~~~~~~aeedsl~y~lp~s~F~ql~~~n~~f 119 (610)
T COG2905 70 DRLAAGDLFGFSSLFTELNKQRYMAAEEDSLCYLLPKSVFMQLMEENPEF 119 (610)
T ss_pred eeeccCccccchhhcccCCCcceeEeeccceEEecCHHHHHHHHHhCcHH
Confidence 56889999999999999888888889999999999999999999776543
No 25
>KOG0501|consensus
Probab=94.79 E-value=0.0098 Score=44.67 Aligned_cols=50 Identities=16% Similarity=0.153 Sum_probs=40.6
Q ss_pred CcccCCCCeeehhhhcCCC--CceeEEEEcCcEEEEEEcHHHHHHHHHhhHH
Q psy8827 1 MHAYEDKGSFGELALLYNM--PRAATIKATSTGSLWAMDRKTFKQIVLKSAF 50 (82)
Q Consensus 1 v~~l~~G~~FGE~al~~~~--~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~ 50 (82)
|++|++||.||..-.-.+. ...|.|+|+|.|.+-.|.|+.+.+++.-+..
T Consensus 609 VAILGKGDVFGD~FWK~~t~~qs~ANVRALTYcDLH~IKrd~Ll~VLdFYtA 660 (971)
T KOG0501|consen 609 VAILGKGDVFGDEFWKENTLGQSAANVRALTYCDLHMIKRDKLLKVLDFYTA 660 (971)
T ss_pred EEEeecCccchhHHhhhhhhhhhhhhhhhhhhhhhhHHhHHHHHHHHHHHHH
Confidence 4789999999987555443 3457899999999999999999999976544
No 26
>PRK11832 putative DNA-binding transcriptional regulator; Provisional
Probab=91.41 E-value=0.66 Score=30.46 Aligned_cols=46 Identities=7% Similarity=0.008 Sum_probs=35.7
Q ss_pred CCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHH
Q psy8827 5 EDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAF 50 (82)
Q Consensus 5 ~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~ 50 (82)
...-.||=...+.+.......+|.++|+...++.++|.+++.+...
T Consensus 66 ~aP~IlGl~~~~~~~~~~~~l~ae~~c~~~~i~~~~~~~iie~~~L 111 (207)
T PRK11832 66 QAPYIMGLADGLMKNDIPYKLISEGNCTGYHLPAKQTITLIEQNQL 111 (207)
T ss_pred cCCeEeecccccCCCCceEEEEEcCccEEEEeeHHHHHHHHHHhch
Confidence 3445566655556666667899999999999999999999987653
No 27
>PF04831 Popeye: Popeye protein conserved region; InterPro: IPR006916 The Popeye (POP) family of proteins, is restricted to vertebrates and is preferentially expressed in developing and adult striated muscle. It is represented by a conserved region which includes three potential transmembrane domains []. The strong conservation of POP genes during evolution and their preferential expression in heart and skeletal muscle suggest that these novel proteins may have an important function in these tissues in vertebrates.; GO: 0016020 membrane
Probab=86.93 E-value=2.3 Score=26.70 Aligned_cols=35 Identities=17% Similarity=0.159 Sum_probs=29.7
Q ss_pred CCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHHH
Q psy8827 18 NMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFKK 52 (82)
Q Consensus 18 ~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~~ 52 (82)
++.-..|++|.++|+.+..+|+.+..++.+.+..+
T Consensus 89 ~~~FQVTitA~~~Cryl~W~R~kL~~~l~~~~~L~ 123 (153)
T PF04831_consen 89 DDKFQVTITAEEDCRYLCWPREKLYLLLAKDPFLA 123 (153)
T ss_pred CCeEEEEEEEcCCcEEEEEEHHHHHHHHhhCHHHH
Confidence 34557899999999999999999999998876543
No 28
>cd06953 NR_LBD_DHR4_like The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4. The ligand binding domain of Ecdysone-induced receptor DHR4: Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=72.36 E-value=16 Score=23.68 Aligned_cols=32 Identities=9% Similarity=0.008 Sum_probs=24.0
Q ss_pred hhHHHHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 47 KSAFKKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 47 ~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
+..........++.+++|.|..|+.+.++..+
T Consensus 34 ~la~~~l~~~I~waK~lp~F~~L~~~DQi~LL 65 (213)
T cd06953 34 RLGDELLFRQIQWTKKLPFFTELSIKDHTHLL 65 (213)
T ss_pred HHHHHHHHHHHHHHhcCCchhhCCHHHHHHHH
Confidence 33344456788999999999999987766543
No 29
>cd06949 NR_LBD_ER Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen). The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well conserved DNA binding domain (DBD), a variable N-terminal doma
Probab=72.03 E-value=19 Score=23.77 Aligned_cols=40 Identities=10% Similarity=0.046 Sum_probs=28.4
Q ss_pred HHHHHHHHhhHHHHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 39 KTFKQIVLKSAFKKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 39 ~~f~~ll~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.+.-..+.+..........++.+++|.|..|+.+.++..+
T Consensus 31 ~~~~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LL 70 (235)
T cd06949 31 ASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLL 70 (235)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHH
Confidence 3444444455555567888999999999999987766543
No 30
>cd06929 NR_LBD_F1 Ligand-binding domain of nuclear receptor family 1. Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=70.96 E-value=11 Score=23.09 Aligned_cols=28 Identities=7% Similarity=0.011 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHhhCccccCCCHHHHHHH
Q psy8827 50 FKKRKMYEKLIDAVPMLKSLQVMVFFLY 77 (82)
Q Consensus 50 ~~~~~~~~~~l~~~~~~~~l~~~~~~~~ 77 (82)
........++.+++|.|..|+.++++..
T Consensus 12 ~~~l~~~v~~ak~ip~F~~L~~~Dq~~L 39 (174)
T cd06929 12 TVAIRRVVEFAKRIPGFRELSQEDQIAL 39 (174)
T ss_pred HHHHHHHHhhccCCcCcccCChhHHHHH
Confidence 3445678899999999999999877654
No 31
>cd06940 NR_LBD_REV_ERB The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily. The ligand binding domain (LBD) of REV-ERB receptors: REV-ERBs are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. The LBD domain of REV-ERB is unusual in the nuclear receptor family by lacking the AF-2 region that is responsible for coactivator interaction. REV-ERBs act as constitutive repressors because of their inability to bind coactivators. REV-ERB receptors can bind to two classes of DNA response elements as either a monomer or heterodimer, indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target gene. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB. Like other members of
Probab=70.88 E-value=18 Score=22.97 Aligned_cols=32 Identities=13% Similarity=0.048 Sum_probs=24.6
Q ss_pred hhHHHHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 47 KSAFKKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 47 ~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
+..........++.+++|.|.+|+.+.++..+
T Consensus 19 ~~~~~~i~~~V~waK~iPgF~~L~~~DQi~LL 50 (189)
T cd06940 19 MSFTPAVREVVEFAKRIPGFRDLSQHDQVTLL 50 (189)
T ss_pred HHHHHHHHHHHHHHhcCCCcccCChhhHHHHH
Confidence 33344567889999999999999987766544
No 32
>cd06942 NR_LBD_Sex_1_like The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein. The ligand binding domain (LBD) of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein like: Sex-1 protein of C. elegans is a transcription factor belonging to the nuclear receptor superfamily. Sex-1 plays pivotal role in sex fate of C. elegans by regulating the transcription of the sex-determination gene xol-1, which specifies male (XO) fate when active and hermaphrodite (XX) fate when inactive. The Sex-1 protein directly represses xol-1 transcription by binding to its promoter. However, the active ligand for Sex-1 protein has not yet been identified. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Sex-1 like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=70.02 E-value=14 Score=23.36 Aligned_cols=32 Identities=9% Similarity=-0.002 Sum_probs=24.4
Q ss_pred hhHHHHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 47 KSAFKKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 47 ~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
+..........+|.+++|.|..|+.++++..+
T Consensus 9 ~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LL 40 (191)
T cd06942 9 HEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLL 40 (191)
T ss_pred HHHHHHHHHHHHHHhcCCCcccCChhHHHHHH
Confidence 33344557888999999999999988776543
No 33
>cd06941 NR_LBD_DmE78_like The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear receptor superfamily. The ligand binding domain (LBD) of Drosophila ecdysone-induced protein 78 (E78) like: Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. Two isoforms of E78, E78A and E78B, are expressed from two nested transcription units. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors ha
Probab=67.86 E-value=18 Score=22.86 Aligned_cols=30 Identities=10% Similarity=0.037 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 49 AFKKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 49 ~~~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.........++.+++|.|++|+.+.++..+
T Consensus 11 ~~~~l~~iI~waK~iP~F~~L~~~DQi~LL 40 (195)
T cd06941 11 LTPSVQRVVEFAKRIPGFCDLSQDDQLLLI 40 (195)
T ss_pred HHHHHHHHHHHHHcCCCcccCCHHHHHHHH
Confidence 334456788999999999999988776654
No 34
>cd06939 NR_LBD_ROR_like The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily. The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum, particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely r
Probab=66.99 E-value=27 Score=23.18 Aligned_cols=33 Identities=9% Similarity=0.036 Sum_probs=25.1
Q ss_pred HhhHHHHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 46 LKSAFKKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 46 ~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.+......+...+|.+++|.|..|+.+.++..|
T Consensus 54 ~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~LL 86 (241)
T cd06939 54 AEKITEAIQYVVEFAKRIPGFMELCQNDQIVLL 86 (241)
T ss_pred HHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHH
Confidence 333344567889999999999999987766544
No 35
>cd06936 NR_LBD_Fxr The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors. The ligand binding domain (LBD) of Farnesoid X receptor: Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. FXR is highly expressed in the liver, the intestine, the kidney, and the adrenals. FXR plays key roles in the regulation of bile acid, cholesterol, triglyceride, and glucose metabolism. Evidences show that it also regulates liver regeneration. Upon binding of ligands, such as bile acid, an endogenous ligand, FXRs bind to FXR response elements (FXREs) either as a monomer or as a heterodimer with retinoid X receptor (RXR), and regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. There are two FXR genes (FXRalpha and FXRbeta) in mammals. A single FXRalpha gene encodes four isoforms resulting from differential use of prom
Probab=65.63 E-value=25 Score=22.87 Aligned_cols=29 Identities=10% Similarity=0.130 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 50 FKKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 50 ~~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
........+|.+++|.|+.|+.++++..+
T Consensus 46 ~~~l~~~IefaK~iP~F~~L~~~DQi~LL 74 (221)
T cd06936 46 TSHVQVLVEFTKGLPGFETLDHEDQIALL 74 (221)
T ss_pred HHHHHHHHHHHhCCCchhhCChhHHHHHH
Confidence 34456788999999999999998776544
No 36
>cd06933 NR_LBD_VDR The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily. The ligand binding domain of vitamin D receptors (VDR): VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and
Probab=65.62 E-value=24 Score=23.27 Aligned_cols=35 Identities=9% Similarity=-0.010 Sum_probs=26.2
Q ss_pred HHHhhHHHHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 44 IVLKSAFKKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 44 ll~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.+.+..........+|.+++|.|..|+.+.++..|
T Consensus 41 ~l~~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~LL 75 (238)
T cd06933 41 HLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALL 75 (238)
T ss_pred HHHHHHHHHHHHHHHHHcCCCccccCChHHHHHHH
Confidence 33444445567889999999999999987776544
No 37
>cd06954 NR_LBD_LXR The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors. The ligand binding domain of Liver X receptors: Liver X receptors (LXRs) belong to a family of nuclear receptors of ligand-activated transcription factors. LXRs operate as cholesterol sensors which protect from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. Upon ligand binding a conformational change leads to recruitment of co-factors, which stimulates expression of target genes. Among the LXR target genes are several genes involved in cholesterol efflux from peripheral tissues such as the ATP-binding-cassette transporters ABCA1, ABCG1 and ApoE. There are two LXR isoforms in mammals, LXRalpha and LXRbeta. LXRalpha is expressed mainly in the liver, intestine, kidney, splee
Probab=64.69 E-value=27 Score=22.79 Aligned_cols=28 Identities=11% Similarity=0.008 Sum_probs=22.6
Q ss_pred HHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 51 KKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 51 ~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.......+|.+++|.|..|+.++++..+
T Consensus 54 ~~i~~~VefaK~lP~F~~L~~~DQi~LL 81 (236)
T cd06954 54 LSVQEIVDFAKQLPGFLTLTREDQIALL 81 (236)
T ss_pred HHHHHHHHHHcCCCCcccCChHHHHHHH
Confidence 3456788999999999999988776543
No 38
>cd06946 NR_LBD_ERR The ligand binding domain of estrogen receptor-related nuclear receptors. The ligand binding domain of estrogen receptor-related receptors (ERRs): The family of estrogen receptor-related receptors (ERRs), a subfamily of nuclear receptors, is closely related to the estrogen receptor (ER) family, but it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. There are three subtypes of ERRs: alpha, beta and gamma. ERRs bind at least two types of DNA sequence, the estrogen response element and another site, originally characterized as SF-1 (steroidogenic factor 1) response element. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-
Probab=63.49 E-value=33 Score=22.13 Aligned_cols=32 Identities=16% Similarity=0.053 Sum_probs=24.0
Q ss_pred hhHHHHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 47 KSAFKKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 47 ~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
+..........++.+++|.|+.|+.++++..+
T Consensus 34 ~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~LL 65 (221)
T cd06946 34 DLADRELVVIIGWAKHIPGFSSLSLNDQMSLL 65 (221)
T ss_pred HHHHHHHHHHHHHHHhCCCcccCCHHHHHHHH
Confidence 33334456788999999999999998776543
No 39
>COG3718 IolB Uncharacterized enzyme involved in inositol metabolism [Carbohydrate transport and metabolism]
Probab=63.29 E-value=9.9 Score=25.81 Aligned_cols=35 Identities=20% Similarity=0.314 Sum_probs=25.6
Q ss_pred CCCCeeehhh----hcCCCC---------ceeEEEEcCcEEEEEEcHH
Q psy8827 5 EDKGSFGELA----LLYNMP---------RAATIKATSTGSLWAMDRK 39 (82)
Q Consensus 5 ~~G~~FGE~a----l~~~~~---------r~atv~a~~~~~~~~l~~~ 39 (82)
..|+.||+++ .|.+.| +++++.|.+++++...+.-
T Consensus 64 ~~g~~f~~iG~R~SvFe~~p~~~vYvp~g~~~~vtA~t~~~vAvC~AP 111 (270)
T COG3718 64 AHGSTFGEIGTRMSVFERKPPDSVYVPAGSAFSVTATTDLEVAVCSAP 111 (270)
T ss_pred eccchHhhcccccccccCCCCCeEEecCCceEEEEeecceEEEEEeCC
Confidence 3577888775 666654 6789999999888776543
No 40
>cd06935 NR_LBD_TR The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors. The ligand binding domain (LBD) of thyroid hormone receptors: Thyroid hormone receptors are members of a superfamily of nuclear receptors. Thyroid hormone receptors (TR) mediate the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), a
Probab=62.31 E-value=29 Score=22.94 Aligned_cols=31 Identities=13% Similarity=0.091 Sum_probs=24.0
Q ss_pred hhHHHHHHHHHHHHhhCccccCCCHHHHHHH
Q psy8827 47 KSAFKKRKMYEKLIDAVPMLKSLQVMVFFLY 77 (82)
Q Consensus 47 ~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~~ 77 (82)
+..........+|.+++|.|.+|+.+.++..
T Consensus 59 ~~~~~~l~~iVefAK~iPgF~~L~~~DQi~L 89 (243)
T cd06935 59 KIITPAITRVVDFAKKLPMFTELPCEDQIIL 89 (243)
T ss_pred HHHHHHHHHHHHHHhcCCccccCChHHHHHH
Confidence 3334556788899999999999998776654
No 41
>cd06938 NR_LBD_EcR The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family. The ligand binding domain (LBD) of the ecdysone receptor: The ecdysone receptor (EcR) belongs to the superfamily of nuclear receptors (NRs) of ligand-dependent transcription factors. Ecdysone receptor is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. ECR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of ecdysone receptor are ecdysteroids#the endogenous steroidal hormones found in invertebrates. In addition, insecticide bisacylhydrazine used against pests has shown to act on EcR. EcR must be dimerised with a USP for high-affinity ligand binding to occur. The ligand binding triggers a conformational change in the C-terminal part of the EcR ligand-binding domain that leads to transcript
Probab=61.67 E-value=24 Score=23.06 Aligned_cols=28 Identities=11% Similarity=0.084 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 51 KKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 51 ~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.......+|.+++|.|..|+...++..+
T Consensus 50 ~~i~~iIefaK~lp~F~~L~~~DQi~LL 77 (231)
T cd06938 50 LTVQLIVEFAKRLPGFDKLSREDQITLL 77 (231)
T ss_pred HHHHHHHHHHhcCCccccCChhHHHHHH
Confidence 3456688999999999999987766543
No 42
>cd06930 NR_LBD_F2 Ligand-binding domain of nuclear receptor family 2. Ligand-binding domain (LBD) of nuclear receptor (NR) family 2: This is one of the major subfamily of nuclear receptors, including some well known nuclear receptors such as glucocorticoid receptor (GR), mineralocorticoid receptor (MR), estrogen receptor (ER), progesterone receptor (PR), and androgen receptor (AR), other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=61.54 E-value=25 Score=21.11 Aligned_cols=25 Identities=8% Similarity=0.010 Sum_probs=20.4
Q ss_pred HHHHHHHHhhCccccCCCHHHHHHH
Q psy8827 53 RKMYEKLIDAVPMLKSLQVMVFFLY 77 (82)
Q Consensus 53 ~~~~~~~l~~~~~~~~l~~~~~~~~ 77 (82)
.....++.+++|.|..|+.++++..
T Consensus 12 l~~~ie~ak~~p~F~~L~~~Dq~~L 36 (165)
T cd06930 12 LFKTVDWAKNLPAFRNLPLDDQLTL 36 (165)
T ss_pred HHHHHHHHHcCCccccCChHHHHHH
Confidence 3467789999999999999877654
No 43
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=61.23 E-value=21 Score=20.58 Aligned_cols=36 Identities=19% Similarity=0.235 Sum_probs=25.4
Q ss_pred HHHHHHHHhh-HHHHHHHHHHHHhhCccccCCCHHHH
Q psy8827 39 KTFKQIVLKS-AFKKRKMYEKLIDAVPMLKSLQVMVF 74 (82)
Q Consensus 39 ~~f~~ll~~~-~~~~~~~~~~~l~~~~~~~~l~~~~~ 74 (82)
..+-.+|..+ |..-|......-.++|-|+.+++...
T Consensus 9 ~~Lp~iLl~~GPLaIRhI~~~Lt~~vPgF~~ls~sKq 45 (92)
T PF10330_consen 9 YHLPEILLNHGPLAIRHITGYLTTSVPGFSDLSPSKQ 45 (92)
T ss_pred hhhHHHHHhcCcHHHHHHHHHHhccCCCcccCCHHHH
Confidence 3344455444 55556778888899999999998643
No 44
>cd06157 NR_LBD The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators. Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=59.19 E-value=28 Score=20.49 Aligned_cols=26 Identities=12% Similarity=0.184 Sum_probs=21.1
Q ss_pred HHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 53 RKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 53 ~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
......+.+++|.|+.|+.++++..+
T Consensus 11 ~~~~i~~~~~~~~f~~L~~~dq~~Ll 36 (168)
T cd06157 11 LLLIVEWAKSIPGFRELPLEDQIVLL 36 (168)
T ss_pred HHHHHHHHHcCCchhcCChHHHHHHH
Confidence 34677899999999999998876543
No 45
>cd06944 NR_LBD_Ftz-F1_like The ligand binding domain of FTZ-F1 like nuclear receptors. The ligand binding domain of FTZ-F1 like nuclear receptors: This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which required at several stages of development. Particularly, FTZ-F1 genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not
Probab=58.69 E-value=37 Score=22.32 Aligned_cols=28 Identities=14% Similarity=-0.006 Sum_probs=22.3
Q ss_pred HHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 51 KKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 51 ~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.......++.+++|.|+.|+.+.++..+
T Consensus 49 ~~l~~~VewaK~lp~F~~L~~~DQi~LL 76 (237)
T cd06944 49 QTLFSIVEWARNSVFFKELKVDDQMKLL 76 (237)
T ss_pred HHHHHHHHHHHhCCChhcCCHHHHHHHH
Confidence 3345688999999999999998776644
No 46
>cd06932 NR_LBD_PPAR The ligand binding domain of peroxisome proliferator-activated receptors. The ligand binding domain (LBD) of peroxisome proliferator-activated receptors (PPAR): Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response element located upstream of the peroxisome proliferator responsive genes and interacts with co-activators. There are three subtypes of peroxisome proliferator activated receptors, alpha, beta (or delta), and gamma, each with a distinct tissue distribution. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, P
Probab=58.27 E-value=41 Score=22.55 Aligned_cols=30 Identities=10% Similarity=0.202 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 49 AFKKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 49 ~~~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.....+...+|.+++|.|..|+.+.++..|
T Consensus 72 ~~~~i~~vVewAK~IPgF~~L~~~DQi~LL 101 (259)
T cd06932 72 SVETIRELTEFAKSLPGFRNLDLNDQVTLL 101 (259)
T ss_pred HHHHHHHHHHHHhcCCCcccCChhHHHHHH
Confidence 344567888999999999999987766544
No 47
>cd07072 NR_LBD_DHR38_like Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily. The ligand binding domain of nuclear receptor DHR38_like proteins: DHR38 is a member of the steroid receptor superfamily in Drosophila. DHR38 interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. At least four differentially expressed mRNA isoforms have been detected during development. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR38 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=56.67 E-value=48 Score=22.03 Aligned_cols=28 Identities=11% Similarity=0.093 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 51 KKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 51 ~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.......++.+++|.|..|+.+.++..|
T Consensus 53 ~~i~~iv~wAK~IPgF~~L~~~DQi~LL 80 (239)
T cd07072 53 SSIDVIKTFAEKIPGFPDLCKEDQELLF 80 (239)
T ss_pred HHHHHHHHHhccCCCccCCCHHHHHHHH
Confidence 4456788999999999999987766544
No 48
>KOG2297|consensus
Probab=56.03 E-value=18 Score=25.82 Aligned_cols=66 Identities=9% Similarity=0.074 Sum_probs=34.2
Q ss_pred cCCCCeeehhhhcCCCCce-eEEE-EcCcEEEEEEcHHHHHHHHHhhHHHHH---HHHHHHHhhCccccCCCHHHHHH
Q psy8827 4 YEDKGSFGELALLYNMPRA-ATIK-ATSTGSLWAMDRKTFKQIVLKSAFKKR---KMYEKLIDAVPMLKSLQVMVFFL 76 (82)
Q Consensus 4 l~~G~~FGE~al~~~~~r~-atv~-a~~~~~~~~l~~~~f~~ll~~~~~~~~---~~~~~~l~~~~~~~~l~~~~~~~ 76 (82)
+.||..-+. ++.+|| .+|. |.++-+...-....|++++.++..... .....+|. +++..++.+|..
T Consensus 79 ~~pg~~~sd----dge~~t~~cvfda~e~~E~i~~~~qvf~KliRRykyLeK~fE~e~~k~Ll---flk~F~e~Er~K 149 (412)
T KOG2297|consen 79 LQPGGVKSD----DGERHTSYCVFDAEEKREAIRNSVQVFQKLIRRYKYLEKNFENEMRKFLL---FLKLFEENERKK 149 (412)
T ss_pred cCCCCcccc----ccCccCceeEeecCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHccCHHHHHH
Confidence 445544433 334666 3443 334444455556778888887765432 23334443 445556666544
No 49
>cd07070 NR_LBD_SF-1 The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily. The ligand binding domain of nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a member of the nuclear hormone receptor superfamily, is an essential regulator of endocrine development and function and is considered a master regulator of reproduction. Most nuclear receptors function as homodimer or heterodimers, however SF-1 binds to its target genes as a monomer, recognizing the variations of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been determined as potential ligands of SF-1. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, SF-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=54.43 E-value=41 Score=22.18 Aligned_cols=28 Identities=14% Similarity=0.029 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 51 KKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 51 ~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.......++.+++|.|+.|+.+.++..+
T Consensus 49 ~~L~~~VeWaK~lP~F~~L~~~DQi~LL 76 (237)
T cd07070 49 QTFISIVDWARRCMVFKELEVADQMTLL 76 (237)
T ss_pred HHHHHHHHHHHhCCChhhCCHHHHHHHH
Confidence 3445688899999999999987776644
No 50
>cd06937 NR_LBD_RAR The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily. The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to
Probab=53.51 E-value=61 Score=21.26 Aligned_cols=30 Identities=13% Similarity=0.082 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 49 AFKKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 49 ~~~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.........++.+++|.|..|+.+.++..|
T Consensus 47 ~~~~l~~~V~wAK~iPgF~~L~~~DQi~LL 76 (231)
T cd06937 47 STKCIIKIVEFAKRLPGFTTLTIADQITLL 76 (231)
T ss_pred HHHHHHHHHHHHhcCCccccCCHHHHHHHH
Confidence 334456788999999999999987766544
No 51
>cd06945 NR_LBD_Nurr1_like The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily. The ligand binding domain of nuclear receptor Nurr1_like: This family of nuclear receptors, including Nurr1, Nerve growth factor-induced-B (NGFI-B) and DHR38 are involved in the embryo development. Nurr1 is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as
Probab=53.48 E-value=45 Score=22.02 Aligned_cols=29 Identities=17% Similarity=0.128 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 50 FKKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 50 ~~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
........++.+++|.|.+|+.+.++..|
T Consensus 51 ~~~l~~iv~wAK~IPgF~~L~~~DQi~LL 79 (239)
T cd06945 51 TGSVDVIRQWAEKIPGFKDLHREDQDLLL 79 (239)
T ss_pred HHHHHHHHHHHHhCCCcccCCHHHHHHHH
Confidence 33456788999999999999987776544
No 52
>cd06948 NR_LBD_COUP-TF Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member of the nuclear receptor family. The ligand binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs): COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. In mammals two isoforms named COUP-TFI and COUP-TFII have been identified. Both genes show an exceptional homology and overlapping expression patterns, suggesting that they may serve redundant functions. Although COUP-TF was originally characterized as a transcriptional activator of the chicken ovalbumin gene, COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone receptors, such as retinoic acid receptor (RAR), thyroid hormone
Probab=52.88 E-value=46 Score=21.82 Aligned_cols=26 Identities=15% Similarity=0.042 Sum_probs=21.1
Q ss_pred HHHHHHHHHhhCccccCCCHHHHHHH
Q psy8827 52 KRKMYEKLIDAVPMLKSLQVMVFFLY 77 (82)
Q Consensus 52 ~~~~~~~~l~~~~~~~~l~~~~~~~~ 77 (82)
......++.+++|.|..|+.+++++.
T Consensus 42 ~L~~~VewaK~lp~F~~L~~~DQi~L 67 (236)
T cd06948 42 LLFSAVEWARNIPFFPDLQVTDQVAL 67 (236)
T ss_pred HHHHHHHHHHhCcCcccCCHHHHHHH
Confidence 34568889999999999998777554
No 53
>cd06943 NR_LBD_RXR_like The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily. The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, func
Probab=50.39 E-value=44 Score=21.19 Aligned_cols=27 Identities=11% Similarity=0.096 Sum_probs=21.8
Q ss_pred HHHHHHHHHHhhCccccCCCHHHHHHH
Q psy8827 51 KKRKMYEKLIDAVPMLKSLQVMVFFLY 77 (82)
Q Consensus 51 ~~~~~~~~~l~~~~~~~~l~~~~~~~~ 77 (82)
........+.+++|.|+.|+.++++..
T Consensus 41 ~~l~~~Iewak~lp~F~~L~~~DQ~~L 67 (207)
T cd06943 41 KQLFQLVEWAKRIPHFSELPLDDQVIL 67 (207)
T ss_pred HHHHHHHHHHHhCchhhccChhhhHHH
Confidence 334578899999999999999877654
No 54
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=50.11 E-value=21 Score=20.89 Aligned_cols=25 Identities=12% Similarity=0.200 Sum_probs=20.3
Q ss_pred HHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 54 KMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 54 ~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.....+++++|.|+.|+.++++..+
T Consensus 6 ~~~~~~~~~~~~f~~L~~~dq~~Ll 30 (163)
T smart00430 6 LLAVEWAKTFPFFRELSQEDKLILL 30 (163)
T ss_pred HHHHHHHHhChhHhhCCHHHHHHHH
Confidence 3566788999999999998886654
No 55
>cd06934 NR_LBD_PXR_like The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor. The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of
Probab=49.43 E-value=34 Score=22.39 Aligned_cols=28 Identities=21% Similarity=0.191 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 51 KKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 51 ~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.......+|.+++|.|.+|+.+.++..|
T Consensus 46 ~~l~~iV~wAK~iPgF~~L~~~DQi~LL 73 (226)
T cd06934 46 YMIKQIIKFAKDLPYFRSLPIEDQISLL 73 (226)
T ss_pred HHHHHHHHHhcCCcccccCCcchHHHHH
Confidence 3456788999999999999987766544
No 56
>cd07073 NR_LBD_AR Ligand binding domain of the nuclear receptor androgen receptor, ligand activated transcription regulator. The ligand binding domain of the androgen receptor (AR): AR is a member of the nuclear receptor family. It is activated by binding either of the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for male primary sexual characteristics and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of an androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR-regulated genes and modulates their expression. Another mode of action is independent of their interactions with DNA. The receptors interact directly with signal transduction proteins in the cytoplasm, causing rapid changes in cell funct
Probab=48.98 E-value=60 Score=21.66 Aligned_cols=28 Identities=18% Similarity=0.172 Sum_probs=22.3
Q ss_pred HHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 51 KKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 51 ~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.......++.+++|.|.+|+-+.++..|
T Consensus 39 ~~L~~~VeWAK~iP~F~~L~~~DQi~LL 66 (246)
T cd07073 39 RQLVHVVKWAKALPGFRNLHVDDQMAVI 66 (246)
T ss_pred HHHHHHHHHHHcCCCccCCCHHHHHHHH
Confidence 3455788999999999999987766544
No 57
>cd07068 NR_LBD_ER_like The ligand binding domain of estrogen receptor and estrogen receptor-related receptors. The ligand binding domain of estrogen receptor (ER) and estrogen receptor-related receptors (ERRs): Estrogen receptors are a group of receptors which are activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. ERRs are closely related to the estrogen receptor (ER) family. But, it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signalin
Probab=48.96 E-value=71 Score=20.62 Aligned_cols=28 Identities=11% Similarity=0.067 Sum_probs=22.4
Q ss_pred HHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 51 KKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 51 ~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.......++.+++|.|+.|+.+.++..+
T Consensus 38 ~~l~~~vewaK~lp~F~~L~~~DQi~LL 65 (221)
T cd07068 38 RELVHIISWAKHIPGFSDLSLNDQMHLL 65 (221)
T ss_pred HHHHHHHHHHHhCCCcccCCHHHHHHHH
Confidence 3456788999999999999998776543
No 58
>cd07069 NR_LBD_Lrh-1 The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,. The ligand binding domain (LBD) of the liver receptor homolog-1 (LRH-1): LRH-1 belongs to nuclear hormone receptor superfamily, and is expressed mainly in the liver, intestine, exocrine pancreas, and ovary. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 binds DNA as a monomer, and is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. Recently, phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, LRH-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=48.63 E-value=57 Score=21.60 Aligned_cols=27 Identities=11% Similarity=-0.023 Sum_probs=22.0
Q ss_pred HHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 52 KRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 52 ~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
......++.+++|.|..|+.++++..|
T Consensus 52 ~L~~~VeWAK~iP~F~~L~~~DQi~LL 78 (241)
T cd07069 52 TLFSIVEWARSSIFFRELKVDDQMKLL 78 (241)
T ss_pred HHHHHHHHHhhCCCcccCCHHHHHHHH
Confidence 445778899999999999988776654
No 59
>cd07076 NR_LBD_GR Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor superfamily. The ligand binding domain of the glucocorticoid receptor (GR): GR is a ligand-activated transcription factor belonging to the nuclear receptor superfamily. It binds with high affinity to cortisol and other glucocorticoids. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. In the absence of hormone, the glucocorticoid receptor (GR) is complexes with a variety of heat shock proteins in the cytosol. The binding of the glucocorticoids results in release of the heat shock proteins and transforms it to its active state. One mechanism of action of GR is by direct activation of gene transcription. The activated form of GR forms dimers, translocates into the nucleus, and binds to specific hormone responsive elements, activating gene transcription
Probab=48.51 E-value=81 Score=21.17 Aligned_cols=36 Identities=14% Similarity=0.059 Sum_probs=25.7
Q ss_pred HHHHhhHHHHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 43 QIVLKSAFKKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 43 ~ll~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
..+.+......-...++.+++|.|.+|+-++++..|
T Consensus 31 ~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~LL 66 (247)
T cd07076 31 STLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLL 66 (247)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHH
Confidence 333444445556788999999999999987665544
No 60
>cd07349 NR_LBD_SHP The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the Small Heterodimer Partner (SHP): SHP is a member of the nuclear receptor superfamily. SHP has a ligand binding domain, but lacks the DNA binding domain, typical to almost all of the nuclear receptors. It functions as a transcriptional coregulator by directly interacting with other nuclear receptors through its AF-2 motif. The closest relative of SHP is DAX1 and they can form heterodimer. SHP is an orphan receptor, lacking an identified ligand.
Probab=47.27 E-value=62 Score=21.20 Aligned_cols=27 Identities=11% Similarity=0.020 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhhCccccCCCHHHHHHH
Q psy8827 51 KKRKMYEKLIDAVPMLKSLQVMVFFLY 77 (82)
Q Consensus 51 ~~~~~~~~~l~~~~~~~~l~~~~~~~~ 77 (82)
.......++.+++|.|..|+.++++..
T Consensus 30 ~~L~~~V~WAK~iP~F~~L~~~DQi~L 56 (222)
T cd07349 30 DVLVKTVAFMRNLPSFWQLPPQDQLLL 56 (222)
T ss_pred HHHHHHHHHHhcCCCcccCChHHHHHH
Confidence 345577889999999999998766544
No 61
>cd07348 NR_LBD_NGFI-B The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): NGFI-B is a member of the nuclear#steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of the embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LB
Probab=46.24 E-value=62 Score=21.50 Aligned_cols=28 Identities=14% Similarity=0.093 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 51 KKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 51 ~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.......++.+++|.|.+|+.+.++..|
T Consensus 52 ~~l~~iVewAK~iPgF~~L~~~DQi~LL 79 (238)
T cd07348 52 GSLEVIRKWAEKIPGFSDFCKEDQELLL 79 (238)
T ss_pred HHHHHHHHHHccCCCccCCChHHHHHHH
Confidence 3456788999999999999987766544
No 62
>cd07071 NR_LBD_Nurr1 The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of nuclear receptor Nurr1: Nurr1 belongs to the conserved family of nuclear receptors. It is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Nurr1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=46.12 E-value=86 Score=20.78 Aligned_cols=28 Identities=11% Similarity=0.093 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 51 KKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 51 ~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.......+|.+++|.|..|+.+.++..|
T Consensus 52 ~~i~~iVewAK~iPgF~~L~~~DQi~LL 79 (238)
T cd07071 52 GSMEIIRGWAEKIPGFTDLPKADQDLLF 79 (238)
T ss_pred HHHHHHHHHhccCCCccCCCHHHHHHHH
Confidence 3456788999999999999987766543
No 63
>cd07350 NR_LBD_Dax1 The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the DAX1 protein: DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) is a nuclear receptor with a typical ligand binding domain, but lacks the DNA binding domain. DAX1 plays an important role in the normal development of several hormone-producing tissues. Duplications of the region of the X chromosome containing DAX1 cause dosage sensitive sex reversal. DAX1 acts as a global repressor of many nuclear receptors, including SF-1, LRH-1, ERR, ER, AR and PR. DAX1 can form homodimer and heterodimerizes with its alternatively spliced isoform DAX1A and other nuclear receptors such as SHP, ERalpha and SF-1.
Probab=46.08 E-value=68 Score=21.19 Aligned_cols=27 Identities=11% Similarity=0.170 Sum_probs=21.2
Q ss_pred HHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 52 KRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 52 ~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
......++.+++|.|..|+.+.++..|
T Consensus 31 ~L~~~VeWAK~iP~F~~L~~~DQi~LL 57 (232)
T cd07350 31 VLVKTLRFVKGVPCFQELPLDDQLVLV 57 (232)
T ss_pred HHHHHHHHHHhCcCcccCChHHHHHHH
Confidence 345678899999999999987665543
No 64
>cd06951 NR_LBD_Dax1_like The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of DAX1-like proteins: This orphan nuclear receptor family includes DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) and the Small Heterodimer Partner (SHP). Both receptors have a typical ligand binding domain, but lack the DNA binding domain, typical to almost all of the nuclear receptors. They function as a transcriptional coregulator by directly interacting with other nuclear receptors. DAX1 and SHP can form heterodimers with each other, as well as with many other nuclear receptors. In addition, DAX1 can also form homodimers. DAX1 plays an important role in the normal development of several hormone-producing tissues. SHP has shown to regulate a variety of target genes.
Probab=45.40 E-value=70 Score=20.88 Aligned_cols=28 Identities=11% Similarity=0.034 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 51 KKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 51 ~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.......++.+++|.|.+|+.+.++..+
T Consensus 30 ~~L~~~V~wAK~iP~F~~L~~~DQi~LL 57 (222)
T cd06951 30 QVLLKTIRFVRNLPCFTYLPPDDQLRLL 57 (222)
T ss_pred HHHHHHHHHHHhCCCcccCChHHHHHHH
Confidence 3445678899999999999987765543
No 65
>PF07943 PBP5_C: Penicillin-binding protein 5, C-terminal domain; InterPro: IPR012907 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry contains proteins that are annotated as penicillin-binding protein 5 and 6. These belong to MEROPS peptidase family S11 (D-Ala-D-Ala carboxypeptidase A family, clan SE). Penicillin-binding protein 5 expressed by Escherichia coli functions as a D-alanyl-D-alanine carboxypeptidase. It is composed of two domains that are oriented at approximately right angles to each other. The N-terminal domain (IPR001967 from INTERPRO) is the catalytic domain. The C-terminal domain, this entry, is organised into a sandwich of two anti-parallel beta-sheets, and has a relatively hydrophobic surface as compared to the N-terminal domain. Its precise function is unknown; it may mediate interactions with other cell wall-synthesising enzymes, thus allowing the protein to be recruited to areas of active cell wall synthesis. It may also function as a linker domain that positions the active site in the catalytic domain closer to the peptidoglycan layer, to allow it to interact with cell wall peptides []. ; GO: 0009002 serine-type D-Ala-D-Ala carboxypeptidase activity, 0006508 proteolysis; PDB: 3A3J_A 3MFD_B 1XP4_D 3MZD_A 1NZU_A 1NJ4_A 1Z6F_A 3MZF_A 1NZO_A 3MZE_A ....
Probab=45.03 E-value=45 Score=18.06 Aligned_cols=34 Identities=3% Similarity=-0.043 Sum_probs=29.0
Q ss_pred ccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEE
Q psy8827 3 AYEDKGSFGELALLYNMPRAATIKATSTGSLWAM 36 (82)
Q Consensus 3 ~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l 36 (82)
.+..|+.++.+.+..+......+.+.++..++.-
T Consensus 6 l~~kg~~~~~~~v~~g~~~~v~l~~~~d~~~~~~ 39 (91)
T PF07943_consen 6 LLKKGQPVATVPVKKGKKKTVPLVAKEDIYITVP 39 (91)
T ss_dssp EE-TTCESEEEEEESCSSSEEEEEESSGEEEEEE
T ss_pred EeCCCCEEEEEEECCCCcCEEEEEECCCEEEEEE
Confidence 5678999999999999999999999999887763
No 66
>COG2933 Predicted SAM-dependent methyltransferase [General function prediction only]
Probab=44.85 E-value=93 Score=21.89 Aligned_cols=49 Identities=10% Similarity=0.057 Sum_probs=40.2
Q ss_pred EEEEcHHHHHHHHHhhHHHHHHHHHHHHhhCccccCCCHHHHHHHHHhh
Q psy8827 33 LWAMDRKTFKQIVLKSAFKKRKMYEKLIDAVPMLKSLQVMVFFLYLVCA 81 (82)
Q Consensus 33 ~~~l~~~~f~~ll~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~~~~~~ 81 (82)
+-+-+.++-.+++.+.+..+.-..++.+.--+.|+.|++.+|+.-++.+
T Consensus 44 feCyq~d~adrL~r~lpf~~lIFaRQ~~vv~~ll~~Lp~~dRIspiv~~ 92 (358)
T COG2933 44 FECYQPDDADRLIRELPFRRLIFARQWFVVGELLKDLPPEDRISPIVGM 92 (358)
T ss_pred EEEcCcccHHHHHHhCcHHHHHHHHHHHHhhhhhhcCCHHhcchHHHHH
Confidence 3344788899999998887777778888888999999999998877654
No 67
>cd06952 NR_LBD_TR2_like The ligand binding domain of the orphan nuclear receptors TR4 and TR2. The ligand binding domain of the TR4 and TR2 (human testicular receptor 4 and 2): TR4 and TR2 are orphan nuclear receptors. Several isoforms of TR4 and TR2 have been isolated in various tissues. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. The expression of TR2 is negatively regulated by androgen, retinoids, and radiation. The expression of both mouse TR2 and TR4 is up-regulated by neurocytokine ciliary neurotrophic factor (CNTF) in mouse. It has shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D
Probab=44.70 E-value=59 Score=20.95 Aligned_cols=27 Identities=7% Similarity=0.016 Sum_probs=21.4
Q ss_pred HHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 52 KRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 52 ~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.......+.+++|.|..|+.++++..+
T Consensus 33 ~l~~~v~wak~iP~F~~L~~~DQ~~LL 59 (222)
T cd06952 33 LLFLSIHWARSIPAFQALGAETQTSLV 59 (222)
T ss_pred HHHHHHHHHHhCCchhhCChHHHHHHH
Confidence 345788899999999999987765543
No 68
>cd06947 NR_LBD_GR_Like Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor. The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator prote
Probab=42.96 E-value=84 Score=20.99 Aligned_cols=28 Identities=14% Similarity=0.164 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 51 KKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 51 ~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.......++.+++|.|..|+.++++..|
T Consensus 39 ~~L~~~VeWAK~iPgF~~L~~~DQi~LL 66 (246)
T cd06947 39 RQLVSVVKWAKALPGFRNLHLDDQMTLI 66 (246)
T ss_pred HHHHHHHHHHHcCCCcccCCHHHHHHHH
Confidence 3445788999999999999987776543
No 69
>cd06931 NR_LBD_HNF4_like The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes. The ligand binding domain of hepatocyte nuclear factor 4 (HNF4) like proteins: HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal lig
Probab=42.81 E-value=71 Score=20.51 Aligned_cols=25 Identities=12% Similarity=0.069 Sum_probs=20.3
Q ss_pred HHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 54 KMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 54 ~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
....++.+.+|.|+.|+.++++..+
T Consensus 46 ~~~vewak~~p~F~~L~~~Dq~~Ll 70 (222)
T cd06931 46 LVLVEWAKYIPAFCELPLDDQVALL 70 (222)
T ss_pred HHHHHHHHhCCccccCChHHHHHHH
Confidence 3577788999999999998876543
No 70
>cd06950 NR_LBD_Tlx_PNR_like The ligand binding domain of Tailless-like proteins, orphan nuclear receptors. The ligand binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like family: This family includes photoreceptor cell-specific nuclear receptor (PNR), Tailless (TLX), and related receptors. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX and PNR have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge
Probab=41.85 E-value=91 Score=19.97 Aligned_cols=25 Identities=16% Similarity=0.177 Sum_probs=20.5
Q ss_pred HHHHHHHHhhCccccCCCHHHHHHH
Q psy8827 53 RKMYEKLIDAVPMLKSLQVMVFFLY 77 (82)
Q Consensus 53 ~~~~~~~l~~~~~~~~l~~~~~~~~ 77 (82)
.....++.+++|.|..|+.++++..
T Consensus 39 L~~~VewaK~ip~F~~L~~~DQi~L 63 (206)
T cd06950 39 LFMAVKWAKSIPAFSTLPFRDQLIL 63 (206)
T ss_pred HHHHHHHHHhCCccccCCHHHHHHH
Confidence 3467889999999999998877554
No 71
>PF00104 Hormone_recep: Ligand-binding domain of nuclear hormone receptor; InterPro: IPR000536 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences (IPR001628 from INTERPRO), connected via a linker region to a C-terminal ligand-binding domain. In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The ligand-binding domain acts in response to ligand binding, which caused a conformational change in the receptor to induce a response, thereby acting as a molecular switch to turn on transcriptional activity []. For example, after binding of the glucocorticoid receptor to the corticosteroid ligand, the receptor is induced to perform functions ranging from nuclear translocation, oligomerisation, cofactor/kinase/transcription factor association, and DNA binding []. The ligand-binding domain is a flexible unit, where the binding of a ligand stabilises its conformation, which in turn favours coactivator binding to modify receptor activity []; the coactivator can bind to the activator function 2 (AF2) site at the C-terminal end of the ligand-binding domain []. The binding of different ligands can alter the conformation of the ligand-binding domain, which ultimately affects the DNA-binding specificity of the DNA-binding domain. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components. This entry represents the C-terminal ligand-binding domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0003707 steroid hormone receptor activity, 0006355 regulation of transcription, DNA-dependent, 0043401 steroid hormone mediated signaling pathway, 0005634 nucleus; PDB: 3IXP_D 1R20_D 2R40_D 1R1K_D 1PDU_B 1OSH_A 3GD2_A 3DCT_A 3OMK_C 3FLI_A ....
Probab=40.31 E-value=85 Score=19.04 Aligned_cols=27 Identities=11% Similarity=0.149 Sum_probs=21.1
Q ss_pred HHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 52 KRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 52 ~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
.......+.+++|.|+.|+.+++...+
T Consensus 29 ~~~~~v~~~k~~p~f~~L~~~dk~~Ll 55 (203)
T PF00104_consen 29 ELRLIVDWAKSFPEFSELSMEDKIALL 55 (203)
T ss_dssp HHHHHHHHHHTSTTGGGS-HHHHHHHH
T ss_pred HHHHHHHHHHhCcCHHhhhhhhhhhHH
Confidence 345788899999999999998886644
No 72
>cd07074 NR_LBD_PR Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor. The ligand binding domain of the progesterone receptor (PR): PR is a member of the nuclear receptor superfamily of ligand dependent transcription factors, mediating the biological actions of progesterone. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. When no binding hormone is present the carboxyl terminal inhibits transcription. Binding to a hormone induces a structural change that removes the inhibitory action. After progesterone binds to the receptor, PR forms a dimer and the complex enters the nucleus where it interacts with the hormone response element (HRE) in the promoters of progesterone responsive genes and alters their transcription. In addition, rapid actions of PR that occur independent of transcription, have also been observed in several tissues
Probab=39.62 E-value=1.1e+02 Score=20.50 Aligned_cols=33 Identities=9% Similarity=0.049 Sum_probs=24.1
Q ss_pred HhhHHHHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 46 LKSAFKKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 46 ~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
-+......-...++.+++|.|.+|+.+.++..+
T Consensus 34 ~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~LL 66 (248)
T cd07074 34 NQLCERQLLSVVKWSKSLPGFRNLHIDDQITLI 66 (248)
T ss_pred HHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHH
Confidence 333344455778899999999999987766543
No 73
>PF05678 VQ: VQ motif; InterPro: IPR008889 This short motif is found in a variety of plant proteins. These proteins vary greatly in length and are mostly composed of low complexity regions. They all conserve a short motif FXhVQChTG, where X is any amino acid and h is a hydrophobic amino acid. The function of this motif is uncertain, however one protein in this family has been found to bind the SigA sigma factor Q9LDH1 from SWISSPROT. It would seem plausible that this motif is needed for this activity and that this whole family might be involved in modulating plastid sigma factors.
Probab=37.96 E-value=45 Score=15.19 Aligned_cols=20 Identities=15% Similarity=0.306 Sum_probs=16.2
Q ss_pred cEEEEEEcHHHHHHHHHhhH
Q psy8827 30 TGSLWAMDRKTFKQIVLKSA 49 (82)
Q Consensus 30 ~~~~~~l~~~~f~~ll~~~~ 49 (82)
+.+++..+..+|+.++++..
T Consensus 4 ~p~vi~~d~~~Fr~lVQ~LT 23 (31)
T PF05678_consen 4 PPTVIHTDPSNFRALVQRLT 23 (31)
T ss_pred CCEEEEeCHHHHHHHHHHhH
Confidence 45788899999999997653
No 74
>cd07075 NR_LBD_MR Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor superfamily. The ligand binding domain of the mineralocorticoid receptor (MR): MR, also called aldosterone receptor, is a member of nuclear receptor superfamily involved in the regulation of electrolyte and fluid balance. The receptor is activated by mineralocorticoids such as aldosterone and deoxycorticosterone as well as glucocorticoids, like cortisol and cortisone. Binding of its ligand results in its translocation to the cell nucleus, homodimerization and binding to hormone response elements (HREs) present in the promoter of MR controlled genes. This results in the recruitment of the coactivators and the transcription of the activated genes. MR is expressed in many tissues and its activation results in the expression of proteins regulating electrolyte and fluid balance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, MR h
Probab=36.30 E-value=1.2e+02 Score=20.43 Aligned_cols=29 Identities=14% Similarity=0.072 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHhhCccccCCCHHHHHHHH
Q psy8827 50 FKKRKMYEKLIDAVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 50 ~~~~~~~~~~l~~~~~~~~l~~~~~~~~~ 78 (82)
........++.+++|.|.+|+-++++..|
T Consensus 38 ~~~L~~iVeWAK~IPgF~~L~~~DQi~LL 66 (248)
T cd07075 38 GKQMIQVVKWAKVLPGFRNLPLEDQITLI 66 (248)
T ss_pred HHHHHHHHHHHHcCCCcccCCHHHHHHHH
Confidence 34456788999999999999987766544
No 75
>PF01846 FF: FF domain; InterPro: IPR002713 The FF domain may be involved in protein-protein interaction []. It often occurs as multiple copies and often accompanies WW domains IPR001202 from INTERPRO. PRP40 from yeast encodes a novel, essential splicing component that associates with the yeast U1 small nuclear ribonucleoprotein particle [].; PDB: 3HFH_B 2KIS_A 2DOD_A 2JUC_A 2LKS_A 1UZC_A 2KZG_A 2L9V_A 2DOF_A 2KFD_A ....
Probab=35.58 E-value=40 Score=16.38 Aligned_cols=39 Identities=13% Similarity=0.178 Sum_probs=26.0
Q ss_pred HHHHHHHHHhhH---HHHHHHHHHHHhhCccccCC--CHHHHHH
Q psy8827 38 RKTFKQIVLKSA---FKKRKMYEKLIDAVPMLKSL--QVMVFFL 76 (82)
Q Consensus 38 ~~~f~~ll~~~~---~~~~~~~~~~l~~~~~~~~l--~~~~~~~ 76 (82)
+++|..+|.++. ...+......+.+=|-+..+ ++.+|..
T Consensus 3 ~~~F~~lL~e~~i~~~s~W~~~~~~l~~dpry~~i~~~~~~R~~ 46 (51)
T PF01846_consen 3 REAFKELLKEHKITPYSSWEEVKPKLSKDPRYKAIGDSESERES 46 (51)
T ss_dssp HHHHHHHHHHTTS-TTSSHHHHHHHHTTSCHHHHSTSCHHHHHH
T ss_pred HHHHHHHHHhCCCCCCCcHHHHHHHHccCHHHHHhcCCHHHHHH
Confidence 578888887664 22355666677777777777 6666543
No 76
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=30.65 E-value=21 Score=24.87 Aligned_cols=19 Identities=21% Similarity=0.371 Sum_probs=13.0
Q ss_pred CcEEEEEEcHHHHHHHHHh
Q psy8827 29 STGSLWAMDRKTFKQIVLK 47 (82)
Q Consensus 29 ~~~~~~~l~~~~f~~ll~~ 47 (82)
-++.++.++.+.|..+..+
T Consensus 142 i~~~~l~l~p~kYNel~~k 160 (297)
T COG1039 142 IPHSVLTLDPKKYNELYKK 160 (297)
T ss_pred cCceEEEEChHHHHHHHHh
Confidence 3467777777777777654
No 77
>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=30.40 E-value=1e+02 Score=17.03 Aligned_cols=26 Identities=8% Similarity=0.305 Sum_probs=18.3
Q ss_pred cHHHHHHHHHhhHHHHHHHHHHHHhh
Q psy8827 37 DRKTFKQIVLKSAFKKRKMYEKLIDA 62 (82)
Q Consensus 37 ~~~~f~~ll~~~~~~~~~~~~~~l~~ 62 (82)
+.++++++..++...+......||++
T Consensus 62 ~~~~~~~L~~khG~~~i~~R~~FL~k 87 (87)
T PF11626_consen 62 DKDDIERLIKKHGEERIERRKEFLEK 87 (87)
T ss_dssp -HHHHHHHHHHH-HHHHHHHHHHHT-
T ss_pred CHHHHHHHHHHhCHHHHHHHHHHHhC
Confidence 77888888888877777777777753
No 78
>PF14037 YoqO: YoqO-like protein
Probab=30.19 E-value=30 Score=20.85 Aligned_cols=28 Identities=11% Similarity=0.304 Sum_probs=23.3
Q ss_pred HHHHHHHhhCccccCCCHHHHHHHHHhh
Q psy8827 54 KMYEKLIDAVPMLKSLQVMVFFLYLVCA 81 (82)
Q Consensus 54 ~~~~~~l~~~~~~~~l~~~~~~~~~~~~ 81 (82)
.+-+.+++++++|+.|.--.+..|++|-
T Consensus 75 ~~gq~~~~~~~if~Gw~~~akilyii~~ 102 (117)
T PF14037_consen 75 LEGQDQMEKHPIFQGWESIAKILYIIII 102 (117)
T ss_pred HHhHHHHHcCchHHHHHHHHHHHHHHHH
Confidence 3566789999999999999888888873
No 79
>PF09823 DUF2357: Domain of unknown function (DUF2357); InterPro: IPR018633 This entry was previously the N-terminal portion of DUF524 (IPR007505 from INTERPRO) before it was split into two. This domain has no known function. It is predicted to adopt an all beta secondary structure pattern followed by mainly alpha-helical structures [].
Probab=27.44 E-value=92 Score=20.15 Aligned_cols=61 Identities=7% Similarity=-0.000 Sum_probs=34.5
Q ss_pred cccCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEc-HHHHHHHHHhhHHHHHHHHHHHHhh
Q psy8827 2 HAYEDKGSFGELALLYNMPRAATIKATSTGSLWAMD-RKTFKQIVLKSAFKKRKMYEKLIDA 62 (82)
Q Consensus 2 ~~l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~-~~~f~~ll~~~~~~~~~~~~~~l~~ 62 (82)
+.+..|...|...+--...........-++.--.++ +++|+.++.+...........+++.
T Consensus 2 g~l~f~n~vG~~~l~v~~~~~~~~~~~~eV~p~Kl~y~~d~~~ml~dI~~~~~~l~~~~~~~ 63 (248)
T PF09823_consen 2 GSLNFGNYVGRSELEVRYDGKKEFRVPFEVFPTKLDYKEDYKAMLEDINEEYPGLAFDFLSK 63 (248)
T ss_pred ceEecCccceEEEEEEEECCceEEEEEEEEecCcCChHHHHHHHHHHHHHHHHHhHhhhccc
Confidence 467788888887774322111222222233334577 9999999988665544444444443
No 80
>cd08540 SAM_PNT-ERG Sterile alpha motif (SAM)/Pointed domain of ERG transcription factor. SAM Pointed domain of ERG subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. It may participate in formation of homodimers or heterodimers with ETS-2, Fli-1, ER81, and Pu-1. However, dimeric forms are inactive and SAM Pointed domain is not essential for dimerization, since ER81 and Pu-1 do not have it. In mouse, a regulator of this type binds the ESET histone H3-specific methyltransferase (human homolog is SETDB1), followed by modification of local chromatin structure through histone methylation. ERG regulators are involved in endothelial cell differentiation, bone morphogenesis and neural crest development. The Erg gene is a proto-oncogene. It is a target of chromosomal translocations resulting in fusions with new neighboring genes. Chimeric proteins were found in solid tumors such as myeloid leukemia or Ewing's sarcoma. Members of this subfamily are po
Probab=26.13 E-value=37 Score=18.65 Aligned_cols=36 Identities=11% Similarity=0.123 Sum_probs=21.1
Q ss_pred CcEEEEEEcHHHHHHHHHhhHHHHHHHHHHHHhhCc
Q psy8827 29 STGSLWAMDRKTFKQIVLKSAFKKRKMYEKLIDAVP 64 (82)
Q Consensus 29 ~~~~~~~l~~~~f~~ll~~~~~~~~~~~~~~l~~~~ 64 (82)
+--.++.+++++|.+........-.-.-.++|++-|
T Consensus 38 ~Gk~LC~LskedF~~~ap~~~GdiL~~HL~~Lr~~~ 73 (75)
T cd08540 38 DGKELCKMTKDDFQRLTPSYNADILLSHLHYLRETP 73 (75)
T ss_pred CHHHHHhCCHHHHHHHcCCCCchHHHHHHHHHHhCC
Confidence 445678899999998875443322223334454443
No 81
>PRK12750 cpxP periplasmic repressor CpxP; Reviewed
Probab=25.09 E-value=1.8e+02 Score=18.35 Aligned_cols=43 Identities=14% Similarity=0.093 Sum_probs=21.6
Q ss_pred EcHHHHHHHHHhhHHHHHHHHHHHHh-hCccccCCCHHHHHHHH
Q psy8827 36 MDRKTFKQIVLKSAFKKRKMYEKLID-AVPMLKSLQVMVFFLYL 78 (82)
Q Consensus 36 l~~~~f~~ll~~~~~~~~~~~~~~l~-~~~~~~~l~~~~~~~~~ 78 (82)
+|.+.++.+..+......+....+++ ....++-|+++||..|.
T Consensus 103 FDeaavral~~~~~~~~~e~~v~~~~~~~~~~~vLTpEQRak~~ 146 (170)
T PRK12750 103 FDEAAANDLAKQMVEKQVERRVKMLEKRHQMLSILTPEQKAKFQ 146 (170)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence 45555555543332222222222221 23458889999987653
No 82
>KOG3179|consensus
Probab=24.90 E-value=20 Score=23.93 Aligned_cols=33 Identities=21% Similarity=0.404 Sum_probs=18.5
Q ss_pred cCCCCeeehhh----hc-------CCCCceeEEEEcC-cEEEEEE
Q psy8827 4 YEDKGSFGELA----LL-------YNMPRAATIKATS-TGSLWAM 36 (82)
Q Consensus 4 l~~G~~FGE~a----l~-------~~~~r~atv~a~~-~~~~~~l 36 (82)
..||.+|||+. +. -+-|.+++..|-+ +|.+=..
T Consensus 135 ~~~~~yFG~~~~~l~IikcHqDevle~PE~a~llasSe~ceve~f 179 (245)
T KOG3179|consen 135 EKPEKYFGEIPKSLNIIKCHQDEVLELPEGAELLASSEKCEVEMF 179 (245)
T ss_pred ccchhhcccchhhhhHHhhcccceecCCchhhhhccccccceEEE
Confidence 46889999762 22 2346666665544 3443333
No 83
>PF02944 BESS: BESS motif; InterPro: IPR004210 The BESS domain has been named after the three proteins that originally defined the domain: BEAF (Boundary element associated factor 32) [], Suvar(3)7 [] and Stonewall []). The BESS domain is 40 amino acid residues long and is predicted to be composed of three alpha helices, as such it might be related to the myb/SANT HTH domain. The BESS domain directs a variety of protein-protein interactions, including interactions with itself, with Dorsal, and with a TBP-associated factor. It is found in a single copy in Drosophila proteins and is often associated with the MADF domain [, , ]. Proteins known to contain a BESS domain include: Drosophila Boundary element associated factor 32 (BEAF-32). Drosophila Suppressor of variegation protein 3-7 (Su(var)3-7), which could play a role in chromosome condensation. Drosophila Ravus, which is homologous to the C-terminal part of Su(var)3-7 []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation. Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3). It functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. ; GO: 0003677 DNA binding
Probab=24.53 E-value=46 Score=15.42 Aligned_cols=16 Identities=19% Similarity=0.187 Sum_probs=11.3
Q ss_pred hhCccccCCCHHHHHH
Q psy8827 61 DAVPMLKSLQVMVFFL 76 (82)
Q Consensus 61 ~~~~~~~~l~~~~~~~ 76 (82)
.-+|.++.|++.++..
T Consensus 10 Sl~p~~k~L~~~~k~~ 25 (37)
T PF02944_consen 10 SLLPHMKRLPPKQKLK 25 (37)
T ss_pred HhHHHHHhCCHHHHHH
Confidence 3358888888877643
No 84
>KOG3542|consensus
Probab=23.90 E-value=83 Score=25.11 Aligned_cols=46 Identities=9% Similarity=0.080 Sum_probs=31.0
Q ss_pred ccCCCCeeehhhhcCCCCceeEE-EEcCcEEEEEEcHHHHHHHHHhh
Q psy8827 3 AYEDKGSFGELALLYNMPRAATI-KATSTGSLWAMDRKTFKQIVLKS 48 (82)
Q Consensus 3 ~l~~G~~FGE~al~~~~~r~atv-~a~~~~~~~~l~~~~f~~ll~~~ 48 (82)
.+.-|++||--.-.+..-.-.-+ +-++||++..+...||-+|+...
T Consensus 345 ~l~mGnSFG~~PT~dkqym~G~mRTkVDDCqFVciaqqDycrIln~v 391 (1283)
T KOG3542|consen 345 ELKMGNSFGAEPTPDKQYMIGEMRTKVDDCQFVCIAQQDYCRILNTV 391 (1283)
T ss_pred EeecccccCCCCCcchhhhhhhhheecccceEEEeehhhHHHHHHHH
Confidence 35668888875544332221222 24789999999999999999544
No 85
>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=23.11 E-value=1.2e+02 Score=22.21 Aligned_cols=42 Identities=17% Similarity=0.174 Sum_probs=31.1
Q ss_pred EEEEEEcHHHHHHHHHhhHHHHHHHHHHHHhhCccccCCCHH
Q psy8827 31 GSLWAMDRKTFKQIVLKSAFKKRKMYEKLIDAVPMLKSLQVM 72 (82)
Q Consensus 31 ~~~~~l~~~~f~~ll~~~~~~~~~~~~~~l~~~~~~~~l~~~ 72 (82)
+++=.++.++|.++|.+....-.++|...++.-..--..+++
T Consensus 331 VEL~~Lt~~Df~rILtep~~sLikQY~aLlkTE~v~l~Ftdd 372 (444)
T COG1220 331 VELDALTKEDFERILTEPKASLIKQYKALLKTEGVELEFTDD 372 (444)
T ss_pred EEcccCCHHHHHHHHcCcchHHHHHHHHHHhhcCeeEEecHH
Confidence 577789999999999877666677888888765554444443
No 86
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=23.10 E-value=64 Score=17.80 Aligned_cols=39 Identities=21% Similarity=0.138 Sum_probs=24.6
Q ss_pred CCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHH
Q psy8827 5 EDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIV 45 (82)
Q Consensus 5 ~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll 45 (82)
+.||.-.+.-+..+.+-++++.|.+++.+..+ +.+..++
T Consensus 2 ~~gDlTt~~~~~~~~~~~a~i~are~gV~aG~--~~~~~i~ 40 (88)
T PF02749_consen 2 GRGDLTTEALIPPDKTGTATIIAREDGVLAGL--EEAEEIF 40 (88)
T ss_dssp TTG-HHHHHHSCTTSEEEEEEEESSSEEE-SH--HHHHHHH
T ss_pred cCCccCcccccCCCCEEEEEEEeCCCEEEECH--HHHHHHH
Confidence 34555555555566777889999999988755 4444444
No 87
>cd04467 S1_aIF5A S1_aIF5A: Archaeal translation Initiation Factor 5A (aIF5A), S1-like RNA-binding domain. aIF5A is a homolog of eukaryotic eIF5A. IF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is a post-translationally modified lysine and is essential for IF5A function. In yeast, eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the cold-shock domain which binds RNA. Moreover, IF5A prefers binding to the actively translating ribosome. This evidence suggests that IF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=21.33 E-value=97 Score=16.12 Aligned_cols=25 Identities=12% Similarity=0.225 Sum_probs=18.4
Q ss_pred CceeEEEEcCcEEEEEEcHHHHHHH
Q psy8827 20 PRAATIKATSTGSLWAMDRKTFKQI 44 (82)
Q Consensus 20 ~r~atv~a~~~~~~~~l~~~~f~~l 44 (82)
.|++.|++.+.-.+-.++-++|...
T Consensus 3 k~~aqVisi~g~~vQlMD~eTYeT~ 27 (57)
T cd04467 3 RKTGQVLSIMGDVVQLMDLETYETF 27 (57)
T ss_pred ceEEEEEEEcCCEEEEeccccceeE
Confidence 5788888888866666777777643
No 88
>PF10539 Dev_Cell_Death: Development and cell death domain; InterPro: IPR013989 The DCD (Development and Cell Death) domain is found in plant proteins involved in development and cell death. The DCD domain is an ~130 amino acid long stretch that contains several mostly invariable motifs. These include a FGLP and a LFL motif at the N terminus and a PAQV and a PLxE motif towards the C terminus of the domain. The DCD domain is present in proteins with different architectures. Some of these proteins contain additional recognizable motifs, like the KELCH repeats or the ParB domain []. Biological studies indicate a role of these proteins in phytohormone response, embryo development and programmed cell death by pathogens or ozone. The predicted secondary structure of the DCD domain is mostly composed of beta strands and confined by an alpha-helix at the N- and at the C terminus []. Proteins known to contain a DCD domain are listed below: Carrot B2 protein. Pea Gda-1 protein. Soybean N-rich protein (NRP).
Probab=21.07 E-value=2.1e+02 Score=17.48 Aligned_cols=30 Identities=13% Similarity=0.130 Sum_probs=26.7
Q ss_pred CCceeEEEEcCcEEEEEEcHHHHHHHHHhh
Q psy8827 19 MPRAATIKATSTGSLWAMDRKTFKQIVLKS 48 (82)
Q Consensus 19 ~~r~atv~a~~~~~~~~l~~~~f~~ll~~~ 48 (82)
.+.+|.|+-.....+.-|+.+.|+..+.++
T Consensus 78 ~~fPAQVrf~i~~~C~PL~E~~fk~aI~~N 107 (130)
T PF10539_consen 78 SPFPAQVRFRIRWDCPPLPESQFKPAIKDN 107 (130)
T ss_pred cccceEEEEEEeeeeecCCHHHHHHHHHHh
Confidence 588999999889999999999999999764
No 89
>PTZ00047 cytochrome c oxidase subunit II; Provisional
Probab=21.04 E-value=2e+02 Score=18.25 Aligned_cols=40 Identities=8% Similarity=0.023 Sum_probs=27.8
Q ss_pred cCCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhh
Q psy8827 4 YEDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKS 48 (82)
Q Consensus 4 l~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~ 48 (82)
-.+|.+.|.-+=+.|.-+.. -+..+.+++.++|..++.+.
T Consensus 120 ~~~G~y~gqCsElCG~gHs~-----M~~~V~vvs~~~F~~w~~~~ 159 (162)
T PTZ00047 120 LREGVFYGQCSEMCGTLHGF-----MPIVVEAVSPEAYAAHAKKY 159 (162)
T ss_pred CCCeEEEEEcchhcCcCccC-----ceEEEEEeCHHHHHHHHHHH
Confidence 35777777777777655532 23567788999999998654
No 90
>smart00767 DCD DCD is a plant specific domain in proteins involved in development and programmed cell death. The domain is shared by several proteins in the Arabidopsis and the rice genomes, which otherwise show a different protein architecture. Biological studies indicate a role of these proteins in phytohormone response, embryo development and programmed cell death by pathogens or ozone.
Probab=20.82 E-value=1.5e+02 Score=18.22 Aligned_cols=32 Identities=9% Similarity=0.134 Sum_probs=26.6
Q ss_pred CCCceeEEEEcCcEEEEEEcHHHHHHHHHhhH
Q psy8827 18 NMPRAATIKATSTGSLWAMDRKTFKQIVLKSA 49 (82)
Q Consensus 18 ~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~ 49 (82)
+.+.+|.|+-.....+.-|+.+.|+..+.++.
T Consensus 77 ~s~fPaQVrf~i~~~C~PL~E~~f~~aI~~nY 108 (132)
T smart00767 77 ESRFPAQVRFRIRKDCKPLPESEFRSAILENY 108 (132)
T ss_pred CCccCcEEEEEEeeeecCCCHHHHHHHHHHhC
Confidence 35689999999999999999999998876543
No 91
>PF12204 DUF3598: Domain of unknown function (DUF3598); InterPro: IPR022017 Proteins containing this domain are found in bacteria and eukaryotes and contain a barrel structure similar to that seen in the lipocalin superfamily. ; PDB: 2O62_B.
Probab=20.68 E-value=87 Score=21.01 Aligned_cols=25 Identities=24% Similarity=0.293 Sum_probs=16.7
Q ss_pred ccCCCCeee-hhhhcCCCCceeEEEE
Q psy8827 3 AYEDKGSFG-ELALLYNMPRAATIKA 27 (82)
Q Consensus 3 ~l~~G~~FG-E~al~~~~~r~atv~a 27 (82)
.+.|++.|| |+.++.+..|..-+..
T Consensus 93 ~l~p~~~f~~E~~l~~~d~R~r~v~~ 118 (252)
T PF12204_consen 93 QLAPFSYFGAELGLVHGDRRLRVVHI 118 (252)
T ss_dssp B-CTTC-SEEEEEEEETTEEEEEEEE
T ss_pred ccCCCCcccEEEEEEeCCccEEEEEE
Confidence 578888776 9999988666544444
No 92
>cd08531 SAM_PNT-ERG_FLI-1 Sterile alpha motif (SAM)/Pointed domain of ERG (Ets related gene) and FLI-1 (Friend leukemia integration 1) transcription factors. SAM Pointed domain of ERG/FLI-1 subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. The ERG and FLI regulators are involved in endothelial cell differentiation, bone morphogenesis and neural crest development. They are proto-oncogenes implicated in cancer development such as myeloid leukemia, Ewing's sarcoma and erythroleukemia. Members of this subfamily are potential targets for cancer therapy.
Probab=20.63 E-value=63 Score=17.71 Aligned_cols=21 Identities=14% Similarity=0.216 Sum_probs=15.3
Q ss_pred cCcEEEEEEcHHHHHHHHHhh
Q psy8827 28 TSTGSLWAMDRKTFKQIVLKS 48 (82)
Q Consensus 28 ~~~~~~~~l~~~~f~~ll~~~ 48 (82)
++--.++.+++++|.+.....
T Consensus 37 m~Gk~LC~lt~edF~~~~~~~ 57 (75)
T cd08531 37 IDGKELCKMTKEDFLRLTSAY 57 (75)
T ss_pred CChHHHHcCCHHHHHHHcCCC
Confidence 334567899999998887543
No 93
>COG1622 CyoA Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]
Probab=20.58 E-value=2e+02 Score=19.42 Aligned_cols=42 Identities=10% Similarity=-0.048 Sum_probs=28.0
Q ss_pred CCCCeeehhhhcCCCCceeEEEEcCcEEEEEEcHHHHHHHHHhhHHH
Q psy8827 5 EDKGSFGELALLYNMPRAATIKATSTGSLWAMDRKTFKQIVLKSAFK 51 (82)
Q Consensus 5 ~~G~~FGE~al~~~~~r~atv~a~~~~~~~~l~~~~f~~ll~~~~~~ 51 (82)
++|.+-|--+=+.|..++ .-+..+.+.++++|..++.+....
T Consensus 185 ~~G~Y~g~Cae~CG~gH~-----~M~~~v~vvs~~~f~~W~~~~~~~ 226 (247)
T COG1622 185 KPGTYRGICAEYCGPGHS-----FMRFKVIVVSQEDFDAWVAEVKAA 226 (247)
T ss_pred CCeEEEEEcHhhcCCCcc-----cceEEEEEEcHHHHHHHHHhhhhc
Confidence 456666665555554442 234688899999999999765443
No 94
>cd08541 SAM_PNT-FLI-1 Sterile alpha motif (SAM)/Pointed domain of friend leukemia integration 1 transcription activator. SAM Pointed domain of FLI-1 (Friend Leukemia Integration) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. The FLI-1 protein participates in regulation of cellular differentiation, proliferation, and survival. The Fli-1 gene was initially described in Friend virus-induced erythroleukemias as a site for virus integration. It is highly expressed in hematopoietic tissues and at lower level in lungs, heart, and ovaries. Fli-1 is a proto-oncogene implicated in Ewing's sarcoma and erythroleukemia. Members of this subfamily are potential targets for cancer therapy.
Probab=20.24 E-value=62 Score=18.54 Aligned_cols=36 Identities=8% Similarity=-0.004 Sum_probs=21.5
Q ss_pred CcEEEEEEcHHHHHHHHHhhHHHHHHHHHHHHhhCc
Q psy8827 29 STGSLWAMDRKTFKQIVLKSAFKKRKMYEKLIDAVP 64 (82)
Q Consensus 29 ~~~~~~~l~~~~f~~ll~~~~~~~~~~~~~~l~~~~ 64 (82)
+--.++.+++++|.++.......-.-.-.++|++.+
T Consensus 50 ~Gk~LC~LskedF~~~~p~~~gdiLw~HL~~Lr~~~ 85 (91)
T cd08541 50 DGKELCKMNKEDFLRATSLYNTEVLLSHLSYLRESS 85 (91)
T ss_pred CHHHHHhCCHHHHHHHcCCCccHHHHHHHHHHHhCc
Confidence 345678899999998765443333333334555543
Done!