Query psy8804
Match_columns 114
No_of_seqs 158 out of 593
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 19:41:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8804.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8804hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3542|consensus 99.5 3.7E-14 8.1E-19 122.7 5.1 95 1-95 28-123 (1283)
2 PRK09392 ftrB transcriptional 99.4 5.8E-13 1.3E-17 99.9 8.4 88 9-96 6-106 (236)
3 PLN02868 acyl-CoA thioesterase 99.3 6.9E-12 1.5E-16 102.5 9.6 89 6-95 4-104 (413)
4 smart00100 cNMP Cyclic nucleot 99.2 1E-10 2.2E-15 75.7 8.1 65 17-81 1-75 (120)
5 KOG1113|consensus 99.2 6.7E-11 1.5E-15 95.8 7.8 81 2-82 114-199 (368)
6 PLN03192 Voltage-dependent pot 99.1 1.8E-10 3.8E-15 101.1 9.0 87 10-96 374-473 (823)
7 COG0664 Crp cAMP-binding prote 99.1 2.7E-10 5.8E-15 81.9 7.1 85 12-96 2-100 (214)
8 KOG0614|consensus 99.1 1.2E-10 2.6E-15 99.0 6.0 89 3-91 265-377 (732)
9 PRK11161 fumarate/nitrate redu 99.1 3.3E-10 7.2E-15 84.7 7.8 84 12-95 15-112 (235)
10 PRK11753 DNA-binding transcrip 99.1 4.6E-10 1E-14 82.3 8.4 77 19-95 6-97 (211)
11 cd00038 CAP_ED effector domain 99.1 5.5E-10 1.2E-14 72.1 7.4 79 17-95 1-93 (115)
12 PRK10402 DNA-binding transcrip 98.9 4.3E-09 9.3E-14 79.0 5.9 69 27-95 25-107 (226)
13 PRK13918 CRP/FNR family transc 98.7 2.2E-08 4.8E-13 73.0 6.1 64 32-95 5-83 (202)
14 PF00027 cNMP_binding: Cyclic 98.7 2.3E-08 5E-13 63.1 3.6 60 36-95 2-75 (91)
15 KOG0498|consensus 98.6 8E-08 1.7E-12 84.3 7.2 68 9-76 418-494 (727)
16 KOG0614|consensus 98.6 4.2E-08 9.2E-13 83.8 4.4 82 4-85 148-234 (732)
17 PRK09391 fixK transcriptional 98.5 2E-07 4.3E-12 70.3 5.9 67 29-95 34-111 (230)
18 COG2905 Predicted signal-trans 98.5 3.2E-07 6.9E-12 78.5 7.0 77 6-82 3-85 (610)
19 KOG0500|consensus 98.4 4.9E-07 1.1E-11 76.3 6.7 76 7-82 304-386 (536)
20 KOG3542|consensus 98.4 2.7E-07 5.9E-12 80.9 4.6 75 2-76 273-353 (1283)
21 TIGR03697 NtcA_cyano global ni 98.3 1.1E-06 2.4E-11 63.3 5.2 56 41-96 1-72 (193)
22 KOG1113|consensus 98.2 1E-06 2.2E-11 71.8 3.4 73 10-82 240-318 (368)
23 KOG0499|consensus 97.9 1.2E-05 2.6E-10 69.7 4.8 74 9-82 526-607 (815)
24 KOG2968|consensus 96.1 0.0042 9.1E-08 56.3 2.6 57 26-82 501-567 (1158)
25 KOG0501|consensus 96.0 0.01 2.3E-07 52.1 4.6 68 10-77 548-620 (971)
26 PF04831 Popeye: Popeye protei 92.8 0.69 1.5E-05 34.0 7.0 60 17-76 9-77 (153)
27 KOG2968|consensus 92.8 0.076 1.6E-06 48.6 2.4 68 7-77 92-169 (1158)
28 PF10330 Stb3: Putative Sin3 b 76.9 6.1 0.00013 26.7 4.3 43 5-47 23-66 (92)
29 TIGR02451 anti_sig_ChrR anti-s 76.4 9.5 0.00021 28.9 5.8 62 32-93 128-198 (215)
30 PF07883 Cupin_2: Cupin domain 75.3 7.7 0.00017 23.0 4.2 30 36-65 3-33 (71)
31 PF12973 Cupin_7: ChrR Cupin-l 72.0 17 0.00037 23.3 5.5 41 32-72 25-65 (91)
32 PRK11832 putative DNA-binding 69.3 12 0.00025 28.7 4.8 40 26-65 15-55 (207)
33 KOG2378|consensus 64.8 0.39 8.5E-06 41.1 -4.3 59 2-60 376-435 (573)
34 COG3718 IolB Uncharacterized e 62.3 20 0.00043 28.5 4.9 56 34-93 32-93 (270)
35 cd06929 NR_LBD_F1 Ligand-bindi 59.6 10 0.00022 26.8 2.8 31 3-33 13-43 (174)
36 cd06942 NR_LBD_Sex_1_like The 48.6 21 0.00045 26.1 3.0 30 3-32 13-42 (191)
37 cd06940 NR_LBD_REV_ERB The lig 47.3 26 0.00056 25.7 3.3 33 3-35 23-55 (189)
38 cd06938 NR_LBD_EcR The ligand 44.3 29 0.00063 26.2 3.3 30 4-33 51-80 (231)
39 cd06930 NR_LBD_F2 Ligand-bindi 43.9 36 0.00078 23.5 3.5 30 3-32 10-39 (165)
40 cd06952 NR_LBD_TR2_like The li 43.3 31 0.00066 25.7 3.2 33 3-35 32-64 (222)
41 PF05899 Cupin_3: Protein of u 41.6 53 0.0012 20.4 3.7 14 52-65 26-39 (74)
42 TIGR00090 iojap_ybeB iojap-lik 40.0 21 0.00046 23.8 1.7 54 19-74 36-90 (99)
43 cd06954 NR_LBD_LXR The ligand 39.5 41 0.00089 25.3 3.4 30 5-34 56-85 (236)
44 cd06157 NR_LBD The ligand bind 39.4 45 0.00097 22.4 3.3 31 3-33 9-39 (168)
45 smart00430 HOLI Ligand binding 39.1 35 0.00076 22.8 2.7 29 3-31 3-31 (163)
46 cd00165 S4 S4/Hsp/ tRNA synthe 36.3 55 0.0012 18.4 3.0 10 100-109 58-67 (70)
47 PF00352 TBP: Transcription fa 35.4 85 0.0019 20.0 4.0 42 25-66 20-64 (86)
48 cd06941 NR_LBD_DmE78_like The 35.3 55 0.0012 23.8 3.4 31 3-33 13-43 (195)
49 cd06936 NR_LBD_Fxr The ligand 35.3 49 0.0011 24.9 3.2 30 4-33 48-77 (221)
50 cd07072 NR_LBD_DHR38_like Liga 35.3 53 0.0012 25.3 3.5 31 4-34 54-84 (239)
51 PF10014 2OG-Fe_Oxy_2: 2OG-Fe 34.6 1.1E+02 0.0024 22.7 5.1 57 52-108 124-184 (195)
52 cd07068 NR_LBD_ER_like The lig 33.7 65 0.0014 24.0 3.7 30 3-32 38-67 (221)
53 cd06935 NR_LBD_TR The ligand b 33.6 54 0.0012 25.1 3.3 32 4-35 64-95 (243)
54 cd06939 NR_LBD_ROR_like The li 33.1 59 0.0013 24.9 3.4 31 4-34 60-90 (241)
55 PRK11538 ribosome-associated p 32.9 30 0.00065 23.5 1.6 54 19-74 41-95 (105)
56 cd06943 NR_LBD_RXR_like The li 32.3 49 0.0011 24.2 2.8 31 4-34 42-72 (207)
57 cd06946 NR_LBD_ERR The ligand 32.3 66 0.0014 23.9 3.5 31 3-33 38-68 (221)
58 TIGR03037 anthran_nbaC 3-hydro 32.1 1.2E+02 0.0027 22.3 4.8 19 45-64 43-61 (159)
59 cd06932 NR_LBD_PPAR The ligand 31.9 54 0.0012 25.4 3.1 32 3-34 74-105 (259)
60 CHL00133 psbV photosystem II c 31.6 57 0.0012 24.1 3.0 21 15-35 127-147 (163)
61 PF05726 Pirin_C: Pirin C-term 31.4 85 0.0018 20.7 3.6 32 37-68 5-37 (104)
62 cd06953 NR_LBD_DHR4_like The l 31.0 64 0.0014 24.1 3.2 31 4-34 39-69 (213)
63 cd06945 NR_LBD_Nurr1_like The 30.0 73 0.0016 24.3 3.5 30 4-33 53-82 (239)
64 COG1096 Predicted RNA-binding 29.3 45 0.00097 25.3 2.1 42 65-106 4-45 (188)
65 cd06949 NR_LBD_ER Ligand bindi 28.8 77 0.0017 24.1 3.4 31 4-34 44-74 (235)
66 cd07070 NR_LBD_SF-1 The ligand 28.8 72 0.0016 24.3 3.2 30 5-34 51-80 (237)
67 cd06931 NR_LBD_HNF4_like The l 27.7 82 0.0018 23.3 3.3 30 3-32 43-72 (222)
68 COG1917 Uncharacterized conser 26.8 1.2E+02 0.0026 20.4 3.8 42 34-75 46-92 (131)
69 PF14525 AraC_binding_2: AraC- 26.8 1.7E+02 0.0037 19.7 4.6 24 42-65 44-69 (172)
70 PRK03511 minC septum formation 26.7 2.2E+02 0.0049 21.7 5.7 32 36-67 127-165 (228)
71 PRK13290 ectC L-ectoine syntha 26.4 2.2E+02 0.0048 19.6 5.2 31 35-65 39-69 (125)
72 cd06951 NR_LBD_Dax1_like The l 26.2 90 0.0019 23.5 3.3 30 4-33 31-60 (222)
73 PRK07963 fliN flagellar motor 26.0 1.1E+02 0.0024 21.9 3.6 43 34-76 77-119 (137)
74 cd07348 NR_LBD_NGFI-B The liga 25.9 92 0.002 23.9 3.4 31 4-34 53-83 (238)
75 cd06937 NR_LBD_RAR The ligand 25.6 97 0.0021 23.5 3.4 31 4-34 50-80 (231)
76 cd07073 NR_LBD_AR Ligand bindi 25.5 1E+02 0.0022 23.8 3.6 30 4-33 40-69 (246)
77 cd06933 NR_LBD_VDR The ligand 25.2 93 0.002 23.7 3.3 31 4-34 49-79 (238)
78 cd07071 NR_LBD_Nurr1 The ligan 24.9 1.1E+02 0.0023 23.6 3.5 31 4-34 53-83 (238)
79 cd07350 NR_LBD_Dax1 The ligand 24.9 96 0.0021 23.7 3.3 29 5-33 32-60 (232)
80 PF07697 7TMR-HDED: 7TM-HD ext 24.8 52 0.0011 23.9 1.8 31 21-51 174-206 (222)
81 PF13128 DUF3954: Protein of u 24.8 1.1E+02 0.0024 18.4 2.8 24 51-77 9-32 (50)
82 COG5458 Uncharacterized conser 24.5 1.1E+02 0.0025 21.9 3.3 56 42-109 43-106 (144)
83 PF11149 DUF2924: Protein of u 24.3 1.6E+02 0.0035 21.2 4.1 52 17-69 48-112 (136)
84 COG0850 MinC Septum formation 24.1 2.4E+02 0.0051 21.6 5.3 33 35-67 116-155 (219)
85 KOG3212|consensus 23.4 72 0.0016 24.5 2.3 74 19-96 105-182 (208)
86 PRK07721 fliI flagellum-specif 23.3 3E+02 0.0064 23.3 6.2 69 8-76 267-346 (438)
87 PRK00394 transcription factor; 23.3 1.6E+02 0.0035 21.7 4.2 41 26-66 18-61 (179)
88 cd06944 NR_LBD_Ftz-F1_like The 23.3 1.1E+02 0.0024 23.1 3.4 31 4-34 50-80 (237)
89 cd06948 NR_LBD_COUP-TF Ligand 23.1 1.1E+02 0.0024 23.1 3.3 29 5-33 43-71 (236)
90 TIGR01222 minC septum site-det 23.0 2.5E+02 0.0055 21.1 5.3 34 34-67 115-155 (217)
91 PRK06789 flagellar motor switc 22.7 1.6E+02 0.0036 18.9 3.6 43 35-77 25-67 (74)
92 cd04518 TBP_archaea archaeal T 22.5 1.9E+02 0.0041 21.3 4.4 42 25-66 18-62 (174)
93 PF00104 Hormone_recep: Ligand 22.2 1.1E+02 0.0023 21.3 3.0 29 4-32 29-57 (203)
94 cd07069 NR_LBD_Lrh-1 The ligan 22.2 1.2E+02 0.0026 23.2 3.4 30 4-33 52-81 (241)
95 cd07349 NR_LBD_SHP The ligand 21.8 1.3E+02 0.0027 22.9 3.4 29 5-33 32-60 (222)
96 PF07742 BTG: BTG family; Int 21.6 2.2E+02 0.0048 19.7 4.3 38 19-57 79-116 (118)
97 PF14299 PP2: Phloem protein 2 21.5 1.1E+02 0.0024 21.7 2.9 39 69-107 27-74 (154)
98 cd06934 NR_LBD_PXR_like The li 21.2 1.1E+02 0.0024 23.1 2.9 31 4-34 47-77 (226)
99 KOG4353|consensus 20.8 1.1E+02 0.0023 22.2 2.6 14 54-67 90-103 (139)
100 smart00835 Cupin_1 Cupin. This 20.7 2.9E+02 0.0063 18.9 5.6 32 34-65 33-65 (146)
101 cd06950 NR_LBD_Tlx_PNR_like Th 20.7 1.2E+02 0.0026 22.4 3.1 30 4-33 38-67 (206)
102 PHA00672 hypothetical protein 20.6 1.2E+02 0.0025 22.0 2.8 33 32-65 48-80 (152)
103 KOG1448|consensus 20.2 1.3E+02 0.0028 24.7 3.2 53 13-65 2-64 (316)
104 COG0662 {ManC} Mannose-6-phosp 20.1 2.2E+02 0.0049 19.3 4.1 29 37-65 42-71 (127)
No 1
>KOG3542|consensus
Probab=99.47 E-value=3.7e-14 Score=122.74 Aligned_cols=95 Identities=34% Similarity=0.606 Sum_probs=87.3
Q ss_pred ChhhHHHHHHHhhCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEeCcccCCCCcceeecc
Q psy8804 1 MADDLQIIYYGLHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFIDGSMFLPQSRNFVFNV 80 (114)
Q Consensus 1 ~~ed~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~g~~~~p~~~fg~~~~ 80 (114)
+++|+...++.|+++..|++|-...|+.+|+.+++++++...++|+.||.+.+|||+++|+|.|.|.+++|.++||..+-
T Consensus 28 t~~~~rN~~~~lh~ld~~snl~~~~lk~l~~~aryer~~g~~ilf~~~~var~wyillsgsv~v~gqi~mp~~~fgkr~g 107 (1283)
T KOG3542|consen 28 TPDDIRNVYEQLHQLDTFSNLFIGPLKALCKTARYERHPGQYILFRDGDVARSWYILLSGSVFVEGQIYMPYGCFGKRTG 107 (1283)
T ss_pred ChhhhhhHHHHHhhhhhhhhhhhhhHHHhhhhhhhhcCCCceEEecccchhhheeeeeccceEeecceecCccccccccc
Confidence 36788889999999999999999999999999999999999999999999999999999999999999999999995432
Q ss_pred c-CceeeeeecCcccc
Q psy8804 81 F-SPVFGLILNPSVSM 95 (114)
Q Consensus 81 ~-~~~~~~~~~~~~~~ 95 (114)
- ..|.||+|.++|.+
T Consensus 108 ~~r~~nclllq~semi 123 (1283)
T KOG3542|consen 108 QNRTHNCLLLQESEMI 123 (1283)
T ss_pred cccccceeeeccccee
Confidence 2 38999999999954
No 2
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=99.43 E-value=5.8e-13 Score=99.89 Aligned_cols=88 Identities=20% Similarity=0.244 Sum_probs=76.8
Q ss_pred HHHhhCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEe----C-----cccCCCCcceeec
Q psy8804 9 YYGLHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFID----G-----SMFLPQSRNFVFN 79 (114)
Q Consensus 9 ~~~Lr~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~----g-----~~~~p~~~fg~~~ 79 (114)
.+.|+.+++|++|++++++.|+..+..++|++|++|+++||+++.+|+|++|.|++. | ....||+.||+.+
T Consensus 6 ~~~l~~~~~f~~L~~~~~~~l~~~~~~~~~~~ge~l~~~g~~~~~~~~v~~G~v~~~~~~~~~~~~i~~~~~g~~~g~~~ 85 (236)
T PRK09392 6 LIRLRNLPLFADMADATFERLMRGAFLQRFPPGTMLITEGEPADFLFVVLDGLVELSASSQDRETTLAILRPVSTFILAA 85 (236)
T ss_pred HHHHhcCccccCCCHHHHHHHHhhcceeecCCCCEEEeCCCccceEEEEEeCEEEEEEcCCCceEEEEEeCCCchhhhHH
Confidence 468999999999999999999999999999999999999999999999999999973 3 2555999999887
Q ss_pred ccC----ceeeeeecCccccc
Q psy8804 80 VFS----PVFGLILNPSVSMA 96 (114)
Q Consensus 80 ~~~----~~~~~~~~~~~~~~ 96 (114)
.+. ++.+.++++++++.
T Consensus 86 ~~~~~~~~~~~~A~~~~~~~~ 106 (236)
T PRK09392 86 VVLDAPYLMSARTLTRSRVLM 106 (236)
T ss_pred HhCCCCCceEEEEcCceEEEE
Confidence 765 55678888888654
No 3
>PLN02868 acyl-CoA thioesterase family protein
Probab=99.33 E-value=6.9e-12 Score=102.50 Aligned_cols=89 Identities=12% Similarity=0.071 Sum_probs=74.1
Q ss_pred HHHHHHhhCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEe-----C----cccCCCCcce
Q psy8804 6 QIIYYGLHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFID-----G----SMFLPQSRNF 76 (114)
Q Consensus 6 e~i~~~Lr~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~-----g----~~~~p~~~fg 76 (114)
+.+...|+++++|++|+++++++|+..+..++|++|++||++||+.+.+|+|++|+|++. | ....||+.||
T Consensus 4 ~~~~~~L~~~~~F~~L~~~~l~~l~~~~~~~~~~~Ge~I~~~Gd~~~~lyiI~~G~V~v~~~~~~ge~~l~~l~~Gd~fG 83 (413)
T PLN02868 4 ESVVEFLGSVPLLQRLPSSSLKKIAEVVVPKRYGKGEYVVREGEPGDGLYFIWKGEAEVSGPAEEESRPEFLLKRYDYFG 83 (413)
T ss_pred HHHHHHHhcCcccccCCHHHHHHHHHhceEEEECCCCEEEeCCCcCceEEEEEeCEEEEEEECCCCcEEEEEeCCCCEee
Confidence 456788999999999999999999999999999999999999999999999999999973 2 2445999999
Q ss_pred eecccC---ceeeeeecCcccc
Q psy8804 77 VFNVFS---PVFGLILNPSVSM 95 (114)
Q Consensus 77 ~~~~~~---~~~~~~~~~~~~~ 95 (114)
+. ..+ ++.+.++++++++
T Consensus 84 ~~-l~~~~~~~~~~A~~d~~v~ 104 (413)
T PLN02868 84 YG-LSGSVHSADVVAVSELTCL 104 (413)
T ss_pred hh-hCCCCcccEEEECCCEEEE
Confidence 74 222 4556666666543
No 4
>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=99.21 E-value=1e-10 Score=75.67 Aligned_cols=65 Identities=25% Similarity=0.364 Sum_probs=58.4
Q ss_pred CCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEe-----C-----cccCCCCcceeeccc
Q psy8804 17 ALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFID-----G-----SMFLPQSRNFVFNVF 81 (114)
Q Consensus 17 lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~-----g-----~~~~p~~~fg~~~~~ 81 (114)
+|++++++.++.++.....+.|++|++|+++||+.+++|+|++|.+++. | ....||..||+...+
T Consensus 1 ~f~~l~~~~~~~l~~~~~~~~~~~g~~l~~~g~~~~~~y~v~~G~v~~~~~~~~g~~~~~~~~~~g~~~g~~~~~ 75 (120)
T smart00100 1 LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIILSGEVRVYKVLEDGREQILGILGPGDFFGELALL 75 (120)
T ss_pred CcCCCCHHHHHHHHHhceEEEeCCCCEEEeCCCcCCcEEEEEeeEEEEEEECCCCceEEEEeecCCceechhhhc
Confidence 5899999999999999999999999999999999999999999999963 2 244599999988777
No 5
>KOG1113|consensus
Probab=99.19 E-value=6.7e-11 Score=95.84 Aligned_cols=81 Identities=12% Similarity=0.181 Sum_probs=74.0
Q ss_pred hhhHHHHHHHhhCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEe--C---cccCCCCcce
Q psy8804 2 ADDLQIIYYGLHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFID--G---SMFLPQSRNF 76 (114)
Q Consensus 2 ~ed~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~--g---~~~~p~~~fg 76 (114)
+++.+-+.+.+++.-+|++|+++++.++...+..+++++|+.|..|||.|+.||+|-+|++.|+ | ....||++||
T Consensus 114 ~e~~~~L~~a~r~~~LF~~Ld~eq~~~v~dam~~~~v~~G~~Vi~qGdeGd~fYvI~kGt~dVyv~~~~v~~~~~g~sFG 193 (368)
T KOG1113|consen 114 DETRRRLEEAFRKNLLFANLDDEQLSQVLDAMFEKRVKAGETVIKQGDEGDNFYVIDKGTFDVYVNGTYVTTYSPGGSFG 193 (368)
T ss_pred HHHHHHHHHHHHhccccccCCHHHHHHHHHhhceeeecCCcEEEecCCcCCcEEEEecceEEEEECCeEEeeeCCCCchh
Confidence 4677778899999999999999999999999999999999999999999999999999999986 3 3556999999
Q ss_pred eecccC
Q psy8804 77 VFNVFS 82 (114)
Q Consensus 77 ~~~~~~ 82 (114)
|++...
T Consensus 194 ElALmy 199 (368)
T KOG1113|consen 194 ELALMY 199 (368)
T ss_pred hhHhhh
Confidence 988776
No 6
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=99.14 E-value=1.8e-10 Score=101.14 Aligned_cols=87 Identities=13% Similarity=-0.019 Sum_probs=77.5
Q ss_pred HHhhCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEe----C-----cccCCCCcceeecc
Q psy8804 10 YGLHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFID----G-----SMFLPQSRNFVFNV 80 (114)
Q Consensus 10 ~~Lr~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~----g-----~~~~p~~~fg~~~~ 80 (114)
+.++++++|++++++.+.+|+..+..+.|++|+.||.|||.++.+|+|++|+|++. | +...||+.||+...
T Consensus 374 ~~l~~~~lF~~~s~~~l~~L~~~~~~~~~~pge~I~~qge~~~~lY~I~~G~V~i~~~~~~~e~~l~~l~~Gd~FGE~~~ 453 (823)
T PLN03192 374 PVVEKVYLFKGVSREILLLLVTKMKAEYIPPREDVIMQNEAPDDVYIVVSGEVEIIDSEGEKERVVGTLGCGDIFGEVGA 453 (823)
T ss_pred HHHhhCcchhcCCHHHHHHHHHhhheeeeCCCCEEEECCCCCceEEEEEecEEEEEEecCCcceeeEEccCCCEecchHH
Confidence 46899999999999999999999999999999999999999999999999999973 2 24459999999988
Q ss_pred cC----ceeeeeecCccccc
Q psy8804 81 FS----PVFGLILNPSVSMA 96 (114)
Q Consensus 81 ~~----~~~~~~~~~~~~~~ 96 (114)
|. |..+.+.+.++|+.
T Consensus 454 l~~~p~~~t~ra~~~s~ll~ 473 (823)
T PLN03192 454 LCCRPQSFTFRTKTLSQLLR 473 (823)
T ss_pred hcCCCCCCeEEEcccEEEEE
Confidence 86 77888889988764
No 7
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=99.11 E-value=2.7e-10 Score=81.85 Aligned_cols=85 Identities=21% Similarity=0.249 Sum_probs=72.5
Q ss_pred hhCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEe-----Cc-----ccCCCCcceeeccc
Q psy8804 12 LHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFID-----GS-----MFLPQSRNFVFNVF 81 (114)
Q Consensus 12 Lr~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~-----g~-----~~~p~~~fg~~~~~ 81 (114)
++..+.|..++++.+..++.....+++++|++||+|||+++++|+|++|.|++. |+ ...||+.||+.+.+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~g~~~~~~y~v~~G~v~~~~~~~~G~~~~~~~~~~g~~fg~~~l~ 81 (214)
T COG0664 2 LKENPLLNLLPSELLELLALKLEVRKLPKGEVLFTEGEEADSLYIILSGIVKLYANTEDGREIILGFLGPGDFFGELALL 81 (214)
T ss_pred cccccccccCCHHHHHHHhhhceeEeeCCCCEEEcCCCcCceEEEEEEeEEEEEEECCCCcEEEEEEecCCchhhhHHHh
Confidence 456678888899999998889999999999999999999999999999999963 32 46699999999888
Q ss_pred C----ceeeeeecCccccc
Q psy8804 82 S----PVFGLILNPSVSMA 96 (114)
Q Consensus 82 ~----~~~~~~~~~~~~~~ 96 (114)
. +..+.++++++++.
T Consensus 82 ~~~~~~~~~~a~~~~~~~~ 100 (214)
T COG0664 82 GGDPRSASAVALTDVEVLE 100 (214)
T ss_pred cCCCccceEEEcceEEEEE
Confidence 5 66788888877653
No 8
>KOG0614|consensus
Probab=99.11 E-value=1.2e-10 Score=99.03 Aligned_cols=89 Identities=16% Similarity=0.185 Sum_probs=76.7
Q ss_pred hhHHHHHHHhhCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEeC-----------cccCC
Q psy8804 3 DDLQIIYYGLHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFIDG-----------SMFLP 71 (114)
Q Consensus 3 ed~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~g-----------~~~~p 71 (114)
+..+..+++||.+|+|.+|+++-|..++.+.....|.+|+.|++||+.|+.||||-.|+|+|.- +....
T Consensus 265 ~r~~~~~~fLrsv~~~q~l~Ee~L~KiaD~le~~~Yd~g~yIirqge~G~~ffii~~G~V~vtq~~e~~~q~~~lr~l~k 344 (732)
T KOG0614|consen 265 ERHEQYMNFLRSVPLFQNLPEELLLKIADVLEEEYYDAGEYIIRQGEKGDTFFIISKGTVKVTQQDEGSTQPQELRTLNK 344 (732)
T ss_pred HHHHHHHHHHHhhhhhccCCHHHHHHHHHHHHHHhhcCCceEEeecCCCCeEEEEecceEEEeecCCCCCchhHHhhccc
Confidence 3455667999999999999999999999999999999999999999999999999999999852 23347
Q ss_pred CCcceeecccC------------c-eeeeeecC
Q psy8804 72 QSRNFVFNVFS------------P-VFGLILNP 91 (114)
Q Consensus 72 ~~~fg~~~~~~------------~-~~~~~~~~ 91 (114)
|++|||.+.+. | .+|++|+-
T Consensus 345 Gd~FGE~al~~edvRtAniia~~~gv~cl~lDr 377 (732)
T KOG0614|consen 345 GDYFGERALLGEDVRTANIIAQAPGVECLTLDR 377 (732)
T ss_pred cchhhHHHhhccCccchhhhccCCCceEEEecH
Confidence 88999877766 3 57888765
No 9
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=99.10 E-value=3.3e-10 Score=84.74 Aligned_cols=84 Identities=20% Similarity=0.212 Sum_probs=67.7
Q ss_pred hhCCCCCCCCCHHHHHHHHhhcc-eeEecCCCEEEecCCCCCeEEEEEeeeEEEe-----Cc-----ccCCCCcceeecc
Q psy8804 12 LHGLEALAPYRDSVLRSLCRVVR-YERHQANDVLYYTGELSTSWYILLSGSVFID-----GS-----MFLPQSRNFVFNV 80 (114)
Q Consensus 12 Lr~v~lF~~L~~~~l~~La~~~~-~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~-----g~-----~~~p~~~fg~~~~ 80 (114)
+++.+.|..|++++++.|...+. .+.|++|++||++||+.+++|+|++|.|++. |+ ...||+.||....
T Consensus 15 ~~~~~~~~~l~~~~l~~L~~~~~~~~~~~kge~l~~~Gd~~~~ly~v~~G~v~~~~~~~~G~e~i~~~~~~gd~~g~~~~ 94 (235)
T PRK11161 15 ISQLCIPFTLNEHELDQLDNIIERKKPIQKGQTLFKAGDELKSLYAIRSGTIKSYTITEQGDEQITGFHLAGDLVGFDAI 94 (235)
T ss_pred ccccccccCCCHHHHHHHHHhhhhceeecCCCEeECCCCCcceEEEEeeceEEEEEECCCCCEEEEEeccCCceeccccc
Confidence 66777777899999999999875 5689999999999999999999999999963 43 3459999997655
Q ss_pred cC---ceeeeeecCcccc
Q psy8804 81 FS---PVFGLILNPSVSM 95 (114)
Q Consensus 81 ~~---~~~~~~~~~~~~~ 95 (114)
+. +..+.++++++++
T Consensus 95 ~~~~~~~~~~a~~~~~i~ 112 (235)
T PRK11161 95 GSGQHPSFAQALETSMVC 112 (235)
T ss_pred cCCCCcceEEEeccEEEE
Confidence 53 4556677776654
No 10
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=99.10 E-value=4.6e-10 Score=82.28 Aligned_cols=77 Identities=17% Similarity=0.186 Sum_probs=65.6
Q ss_pred CCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEe-----Cc-----ccCCCCcceeecccC-----c
Q psy8804 19 APYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFID-----GS-----MFLPQSRNFVFNVFS-----P 83 (114)
Q Consensus 19 ~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~-----g~-----~~~p~~~fg~~~~~~-----~ 83 (114)
+.+++++++.+++.+..+.|++|++||++||+.+.+|+|++|.|++. |+ ...||+.||+...|. +
T Consensus 6 ~~~~~~~~~~l~~~~~~~~~~kg~~l~~~g~~~~~~y~V~~G~v~~~~~~~~g~~~~~~~~~~g~~~g~~~~~~~~~~~~ 85 (211)
T PRK11753 6 KPQTDPTLEWFLSHCHIHKYPAKSTLIHAGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERS 85 (211)
T ss_pred CCCCHHHHHHHHhhCeEEEeCCCCEEEeCCCCCCeEEEEEeCEEEEEEECCCCCEEEEEEcCCCCEEeehhhccCCCCce
Confidence 57899999999999999999999999999999999999999999963 43 456999999988776 2
Q ss_pred eeeeeecCcccc
Q psy8804 84 VFGLILNPSVSM 95 (114)
Q Consensus 84 ~~~~~~~~~~~~ 95 (114)
+.+.++++++++
T Consensus 86 ~~~~a~~~~~v~ 97 (211)
T PRK11753 86 AWVRAKTACEVA 97 (211)
T ss_pred EEEEEcCcEEEE
Confidence 355677777755
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=99.09 E-value=5.5e-10 Score=72.08 Aligned_cols=79 Identities=24% Similarity=0.284 Sum_probs=64.2
Q ss_pred CCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEe-----C-----cccCCCCcceeecccC----
Q psy8804 17 ALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFID-----G-----SMFLPQSRNFVFNVFS---- 82 (114)
Q Consensus 17 lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~-----g-----~~~~p~~~fg~~~~~~---- 82 (114)
+|+.|+++.++.++..+..+.+++|++|+.+|++.+++|+|++|.|++. | ....+|+.+|....+.
T Consensus 1 ~f~~l~~~~~~~l~~~~~~~~~~~g~~l~~~~~~~~~~~~i~~G~v~~~~~~~~g~~~~~~~~~~g~~~g~~~~~~~~~~ 80 (115)
T cd00038 1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLFGELALLGNGPR 80 (115)
T ss_pred CcccCCHHHHHHHHhhceeeeeCCCCEEEcCCCCCCeEEEEEeCEEEEEEECCCCcEEEEEecCCccCcChHHHhcCCCC
Confidence 5899999999999999999999999999999999999999999999973 2 2344899999876653
Q ss_pred ceeeeeecCcccc
Q psy8804 83 PVFGLILNPSVSM 95 (114)
Q Consensus 83 ~~~~~~~~~~~~~ 95 (114)
+....++++++++
T Consensus 81 ~~~~~a~~~~~~~ 93 (115)
T cd00038 81 SATVRALTDSELL 93 (115)
T ss_pred CceEEEcCceEEE
Confidence 3344555665543
No 12
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=98.87 E-value=4.3e-09 Score=79.04 Aligned_cols=69 Identities=9% Similarity=0.083 Sum_probs=57.8
Q ss_pred HHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEE-----eCc-----ccCCCCcceeecccC----ceeeeeecCc
Q psy8804 27 RSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFI-----DGS-----MFLPQSRNFVFNVFS----PVFGLILNPS 92 (114)
Q Consensus 27 ~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI-----~g~-----~~~p~~~fg~~~~~~----~~~~~~~~~~ 92 (114)
..|++.+..++|++|++||.+||+.+.+|+|++|.|++ +|+ ...||+.||+.++|. ++.+.+++++
T Consensus 25 ~~i~~~~~~~~~~kge~l~~~G~~~~~~y~V~~G~v~v~~~~~~G~e~~~~~~~~g~~~G~~~~~~~~~~~~~~~A~~~~ 104 (226)
T PRK10402 25 FDVSADTELFHFLAREYIVQEGQQPSYLFYLTRGRAKLYATLANGKVSLIDFFAAPCFIGEIELIDKDHETKAVQAIEEC 104 (226)
T ss_pred HHHHhhhhheeeCCCCEEEcCCCCCceEEEEEeCEEEEEEECCCCCEeeeeecCCCCeEEeehhhcCCCCCccEEEeccE
Confidence 35777889999999999999999999999999999996 343 455999999988775 5667888887
Q ss_pred ccc
Q psy8804 93 VSM 95 (114)
Q Consensus 93 ~~~ 95 (114)
+++
T Consensus 105 ~i~ 107 (226)
T PRK10402 105 WCL 107 (226)
T ss_pred EEE
Confidence 754
No 13
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=98.75 E-value=2.2e-08 Score=73.00 Aligned_cols=64 Identities=22% Similarity=0.169 Sum_probs=51.2
Q ss_pred hcceeEecCCCEEEecCC--CCCeEEEEEeeeEEE-----eCc-----ccCCCCcceeecccC---ceeeeeecCcccc
Q psy8804 32 VVRYERHQANDVLYYTGE--LSTSWYILLSGSVFI-----DGS-----MFLPQSRNFVFNVFS---PVFGLILNPSVSM 95 (114)
Q Consensus 32 ~~~~~~~~~G~~If~qGd--~~~~~yiIlsG~VkI-----~g~-----~~~p~~~fg~~~~~~---~~~~~~~~~~~~~ 95 (114)
.....+|++|++||+||| +++++|+|++|.|++ +|+ ...||+.||+...+. +..+.++++++++
T Consensus 5 ~~~~~~~~kg~~l~~~Gd~~~~~~~y~I~~G~vr~~~~~~~G~e~~l~~~~~Gd~~G~~~~~~~~~~~~~~A~~~~~v~ 83 (202)
T PRK13918 5 VVDTVTYRPGAVILYPGVPGPSDMLYRVRSGLVRLHTVDDEGNALTLRYVRPGEYFGEEALAGAERAYFAEAVTDSRID 83 (202)
T ss_pred ccceeEecCCCEEEcCCCCCCCCeEEEEEeeEEEEEEECCCCCEEEEEEecCCCeechHHhcCCCCCceEEEcCceEEE
Confidence 456789999999999999 779999999999996 343 456999999876654 5567788877753
No 14
>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=98.67 E-value=2.3e-08 Score=63.10 Aligned_cols=60 Identities=23% Similarity=0.386 Sum_probs=46.7
Q ss_pred eEecCCCEEEecCCCCCeEEEEEeeeEEEe-----Cc-----ccCCCCcceeecccC----ceeeeeecCcccc
Q psy8804 36 ERHQANDVLYYTGELSTSWYILLSGSVFID-----GS-----MFLPQSRNFVFNVFS----PVFGLILNPSVSM 95 (114)
Q Consensus 36 ~~~~~G~~If~qGd~~~~~yiIlsG~VkI~-----g~-----~~~p~~~fg~~~~~~----~~~~~~~~~~~~~ 95 (114)
++|++|++|+++|++.+++|+|++|.+++. |+ ...||+.||..+.+. +..+.++++++++
T Consensus 2 ~~~~~g~~i~~~g~~~~~~~~i~~G~v~~~~~~~~~~~~~~~~~~~g~~~g~~~~~~~~~~~~~~~a~~~~~~~ 75 (91)
T PF00027_consen 2 KTYKKGEVIYRQGDPCDHIYIILSGEVKVSSINEDGKEQIIFFLGPGDIFGEIELLTGKPSPFTVIALTDSEVL 75 (91)
T ss_dssp EEESTTEEEEETTSBESEEEEEEESEEEEEEETTTSEEEEEEEEETTEEESGHHHHHTSBBSSEEEESSSEEEE
T ss_pred eEECCCCEEEeCCCcCCEEEEEEECceEEEeceecceeeeecceeeeccccceeecCCCccEEEEEEccCEEEE
Confidence 689999999999999999999999999962 22 445999999766665 3455566665543
No 15
>KOG0498|consensus
Probab=98.63 E-value=8e-08 Score=84.29 Aligned_cols=68 Identities=19% Similarity=0.260 Sum_probs=61.8
Q ss_pred HHHhhCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEe---C------cccCCCCcce
Q psy8804 9 YYGLHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFID---G------SMFLPQSRNF 76 (114)
Q Consensus 9 ~~~Lr~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~---g------~~~~p~~~fg 76 (114)
.+.++++|+|+++++.-|+.||...+.+.|++|++|++|||+.+.+|+|.+|++.+. | ....||+.||
T Consensus 418 ~~lv~~vpLF~~md~~~L~al~~rlk~~~f~pge~iireGd~v~~myFI~rG~le~~~~~~g~~~~~~~L~~Gd~~G 494 (727)
T KOG0498|consen 418 LDLVRKVPLFAGMDDGLLDALCSRLKPEYFTPGEYIIREGDPVTDMYFIVRGSLESITTDGGGFFVVAILGPGDFFG 494 (727)
T ss_pred HHHHhhCchhhcCCHHHHHHHHHHhhhhccCCCCeEEecCCccceeEEEEeeeEEEEEccCCceEEEEEecCCCccc
Confidence 468899999999999999999999999999999999999999999999999999963 1 2344999999
No 16
>KOG0614|consensus
Probab=98.60 E-value=4.2e-08 Score=83.78 Aligned_cols=82 Identities=13% Similarity=0.124 Sum_probs=73.9
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEe--Cc---ccCCCCcceee
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFID--GS---MFLPQSRNFVF 78 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~--g~---~~~p~~~fg~~ 78 (114)
.-+.|.+.++...++++|.+.+++++..++....|++|+.|++|||+|+.+|++.+|++.|. |+ .+.||..|||+
T Consensus 148 ~k~lI~dAi~~NdFLknLd~~Qi~e~v~~Myp~~~~~gs~IIrege~Gs~~yV~aeG~~~V~~~g~ll~~m~~gtvFGEL 227 (732)
T KOG0614|consen 148 AKQLIRDAIQKNDFLKNLDASQIKELVDCMYPVEYRAGSWIIREGEPGSHLYVSAEGELQVSREGKLLGKMGAGTVFGEL 227 (732)
T ss_pred HHHHHHHHHHhhHHHHhhhHHHHHHHHHhhCcccccCCcEEEecCCCCceEEEeecceEEEeeCCeeeeccCCchhhhHH
Confidence 34668889999999999999999999999999999999999999999999999999999985 43 45599999999
Q ss_pred cccCcee
Q psy8804 79 NVFSPVF 85 (114)
Q Consensus 79 ~~~~~~~ 85 (114)
|.+--|.
T Consensus 228 AILynct 234 (732)
T KOG0614|consen 228 AILYNCT 234 (732)
T ss_pred HHHhCCc
Confidence 9998663
No 17
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=98.53 E-value=2e-07 Score=70.34 Aligned_cols=67 Identities=16% Similarity=0.040 Sum_probs=53.0
Q ss_pred HHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEe-----Cc-----ccCCCCcceeeccc-CceeeeeecCcccc
Q psy8804 29 LCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFID-----GS-----MFLPQSRNFVFNVF-SPVFGLILNPSVSM 95 (114)
Q Consensus 29 La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~-----g~-----~~~p~~~fg~~~~~-~~~~~~~~~~~~~~ 95 (114)
++..+..++|++|++||++||+++++|+|++|.|++. |+ ...||+.||...-. .+..+.++++++++
T Consensus 34 ~~~~~~~~~~~kge~l~~~Gd~~~~ly~I~~G~vkl~~~~~~G~e~i~~~~~~Gd~fG~~~~~~~~~~~~A~~ds~v~ 111 (230)
T PRK09391 34 AGLVASEFSYKKGEEIYGEGEPADYVYQVESGAVRTYRLLSDGRRQIGAFHLPGDVFGLESGSTHRFTAEAIVDTTVR 111 (230)
T ss_pred ccceeeeEEECCCCEEECCCCCCCeEEEEEeCEEEEEEECCCCcEEEEEEecCCceecccCCCcCCeEEEEcCceEEE
Confidence 5667788999999999999999999999999999962 43 34599999864321 25677888887755
No 18
>COG2905 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]
Probab=98.50 E-value=3.2e-07 Score=78.50 Aligned_cols=77 Identities=13% Similarity=0.152 Sum_probs=67.5
Q ss_pred HHHHHHhhCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEe---Cc---ccCCCCcceeec
Q psy8804 6 QIIYYGLHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFID---GS---MFLPQSRNFVFN 79 (114)
Q Consensus 6 e~i~~~Lr~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~---g~---~~~p~~~fg~~~ 79 (114)
..+.++|+++|.|+.|+++++.+|.....++.|++|++|..-|.|-.++|+|++|.|.+. |+ ...-|+.||-.+
T Consensus 3 ~~~~~Fl~~~pPF~~L~~eel~~L~~~l~v~yy~kge~ii~~~~p~~~l~vi~kG~vev~~~~g~v~~~~~~gdlFg~~~ 82 (610)
T COG2905 3 DEPDQFLQQHPPFSQLPAEELEQLMGALEVKYYRKGEIIIYAGSPVHYLYVIRKGVVEVRSDGGEVLDRLAAGDLFGFSS 82 (610)
T ss_pred CCHHHHHhcCCCcccCCHHHHHHHHhhhccccccCCCeeecCCCCcceeEEEEeceeeEEcCCCeeeeeeccCccccchh
Confidence 345789999999999999999999999999999999999999999999999999999963 33 555888998655
Q ss_pred ccC
Q psy8804 80 VFS 82 (114)
Q Consensus 80 ~~~ 82 (114)
+|.
T Consensus 83 l~~ 85 (610)
T COG2905 83 LFT 85 (610)
T ss_pred hcc
Confidence 554
No 19
>KOG0500|consensus
Probab=98.44 E-value=4.9e-07 Score=76.31 Aligned_cols=76 Identities=14% Similarity=0.229 Sum_probs=66.9
Q ss_pred HHHHHhhCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEE---eCcc----cCCCCcceeec
Q psy8804 7 IIYYGLHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFI---DGSM----FLPQSRNFVFN 79 (114)
Q Consensus 7 ~i~~~Lr~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI---~g~~----~~p~~~fg~~~ 79 (114)
...+.|+++++|+...+.-|.+|.-..+..-|.||++|++.||.|..+|||..|++.| +|.. ..-|..|||++
T Consensus 304 vh~dTLkkV~iF~~ce~~lL~elVLklk~qvfSPgDyICrKGdvgkEMyIVk~G~L~Vv~dDg~t~~~~L~~G~~FGEis 383 (536)
T KOG0500|consen 304 VHLDTLKKVRIFQDCEAGLLVELVLKLKPQVFSPGDYICRKGDVGKEMYIVKEGKLAVVADDGVTVFVTLKAGSVFGEIS 383 (536)
T ss_pred HHHHHHHhhhHHHhcchhHHHHHHHHhcceeeCCCCeEEecCcccceEEEEEccEEEEEecCCcEEEEEecCCceeeeeE
Confidence 3578999999999999999999999999999999999999999999999999999996 3532 23899999877
Q ss_pred ccC
Q psy8804 80 VFS 82 (114)
Q Consensus 80 ~~~ 82 (114)
.+.
T Consensus 384 Iln 386 (536)
T KOG0500|consen 384 ILN 386 (536)
T ss_pred EEE
Confidence 665
No 20
>KOG3542|consensus
Probab=98.41 E-value=2.7e-07 Score=80.87 Aligned_cols=75 Identities=28% Similarity=0.371 Sum_probs=67.4
Q ss_pred hhhHHHHHHHhhCCCCCCCCCHHHHHHHHhhcceeEe-cCCCEEEecCCCCCeEEEEEeeeEEEe---Cc--ccCCCCcc
Q psy8804 2 ADDLQIIYYGLHGLEALAPYRDSVLRSLCRVVRYERH-QANDVLYYTGELSTSWYILLSGSVFID---GS--MFLPQSRN 75 (114)
Q Consensus 2 ~ed~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~~~~~-~~G~~If~qGd~~~~~yiIlsG~VkI~---g~--~~~p~~~f 75 (114)
.||++.+.++++++|.|++|+-...++||..+.+.-+ .+|.+|...|++-++||+|+.|.|.|. |+ ...=|.+|
T Consensus 273 ddDieqLLeFMhqlpAFAnmtMSvrReLC~vMvFaVVe~AGtivL~dgeeLDSWsVIlNG~VEv~~PdGk~e~l~mGnSF 352 (1283)
T KOG3542|consen 273 DDDIEQLLEFMHQLPAFANMTMSVRRELCLVMVFAVVEDAGTIVLADGEELDSWSVILNGCVEVVKPDGKREELKMGNSF 352 (1283)
T ss_pred hHHHHHHHHHHHhchHhhcccHHHHHHHHHHHHHHHHhhcCeEEecCCcccceeEEEecceEEEecCCCceEEeeccccc
Confidence 4899999999999999999999999999999999877 799999999999999999999999983 54 33367788
Q ss_pred e
Q psy8804 76 F 76 (114)
Q Consensus 76 g 76 (114)
|
T Consensus 353 G 353 (1283)
T KOG3542|consen 353 G 353 (1283)
T ss_pred C
Confidence 7
No 21
>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=98.31 E-value=1.1e-06 Score=63.33 Aligned_cols=56 Identities=16% Similarity=0.320 Sum_probs=45.4
Q ss_pred CCEEEecCCCCCeEEEEEeeeEEE-----eCc-----ccCCCCcceeecccCc------eeeeeecCccccc
Q psy8804 41 NDVLYYTGELSTSWYILLSGSVFI-----DGS-----MFLPQSRNFVFNVFSP------VFGLILNPSVSMA 96 (114)
Q Consensus 41 G~~If~qGd~~~~~yiIlsG~VkI-----~g~-----~~~p~~~fg~~~~~~~------~~~~~~~~~~~~~ 96 (114)
|++||++||+.+++|+|++|.|++ +|+ ...||+.||+.+.+.. .++.++++++++.
T Consensus 1 g~~l~~~g~~~~~~~~i~~G~v~~~~~~~~G~e~~l~~~~~g~~~G~~~~~~~~~~~~~~~~~A~~~~~v~~ 72 (193)
T TIGR03697 1 GKTIFFPGDPAEKVYFLRRGAVKLSRVYESGEEITVALLRENSVFGVLSLITGHRSDRFYHAVAFTRVELLA 72 (193)
T ss_pred CCceecCCCCCCcEEEEEecEEEEEEeCCCCcEeeeEEccCCCEeeeeeeccCCCCccceEEEEecceEEEE
Confidence 789999999999999999999996 243 4569999999887752 4577888877653
No 22
>KOG1113|consensus
Probab=98.21 E-value=1e-06 Score=71.79 Aligned_cols=73 Identities=10% Similarity=0.075 Sum_probs=66.5
Q ss_pred HHhhCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEeCc------ccCCCCcceeecccC
Q psy8804 10 YGLHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFIDGS------MFLPQSRNFVFNVFS 82 (114)
Q Consensus 10 ~~Lr~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~g~------~~~p~~~fg~~~~~~ 82 (114)
++|+.+|+++.|...+...++.......|++|+.|..||++|+.||+|.+|.|.+..+ ...+++.||+.+++.
T Consensus 240 ~~l~s~pil~~l~k~er~kv~dal~~k~y~~G~~Vi~qg~~ge~f~~i~eGEvdv~~~~~~v~vkl~~~dyfge~al~~ 318 (368)
T KOG1113|consen 240 PFLESVPILESLEKLERAKVADALGTKSYKDGERVIVQGDQGEHFYIIEEGEVDVLKKRDGVEVKLKKGDYFGELALLK 318 (368)
T ss_pred hhhhcchhhHHHHHHHHHhhhcccceeeccCCceEEeccCCcceEEEecccccchhhccCCeEEEechhhhcchHHHHh
Confidence 4899999999999999999999999999999999999999999999999999997532 456899999888776
No 23
>KOG0499|consensus
Probab=97.94 E-value=1.2e-05 Score=69.72 Aligned_cols=74 Identities=18% Similarity=0.219 Sum_probs=65.0
Q ss_pred HHHhhCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEeC----cc----cCCCCcceeecc
Q psy8804 9 YYGLHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFIDG----SM----FLPQSRNFVFNV 80 (114)
Q Consensus 9 ~~~Lr~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~g----~~----~~p~~~fg~~~~ 80 (114)
+..|.++.+|++.+.+.++.+.-..+-..|-+|+.|++.||.|..+|||..|.|+|-| +. ...|..|||.+.
T Consensus 526 y~~lSKVqLFq~Cdr~mirDmllrLRsV~yLPgDfVCkKGeiGkEMYIIk~GqvQVlGGp~~~~Vl~tL~~GsVFGEISL 605 (815)
T KOG0499|consen 526 YSILSKVQLFQGCDRQMIRDMLLRLRSVLYLPGDFVCKKGEIGKEMYIIKHGQVQVLGGPDGTKVLVTLKAGSVFGEISL 605 (815)
T ss_pred hhhhhHHHHhhhhHHHHHHHHHHHhhceeecCCceeeecccccceeEEeecceEEEecCCCCCEEEEEecccceeeeeee
Confidence 4678889999999999999998888889999999999999999999999999999854 33 338999998776
Q ss_pred cC
Q psy8804 81 FS 82 (114)
Q Consensus 81 ~~ 82 (114)
+.
T Consensus 606 La 607 (815)
T KOG0499|consen 606 LA 607 (815)
T ss_pred ee
Confidence 65
No 24
>KOG2968|consensus
Probab=96.05 E-value=0.0042 Score=56.35 Aligned_cols=57 Identities=23% Similarity=0.325 Sum_probs=42.1
Q ss_pred HHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEE--e---Ccc-----cCCCCcceeecccC
Q psy8804 26 LRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFI--D---GSM-----FLPQSRNFVFNVFS 82 (114)
Q Consensus 26 l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI--~---g~~-----~~p~~~fg~~~~~~ 82 (114)
++.+--.....++.+|+++|+|||.+++.|+|++|+++- . |+. +..|+.+|++.++.
T Consensus 501 lr~~D~AldWv~l~~g~alyrqgD~Sd~iyvVl~GRlRsv~~~~~~k~~i~~EygrGd~iG~~E~lt 567 (1158)
T KOG2968|consen 501 LRKLDFALDWVRLEPGQALYRQGDSSDSIYVVLNGRLRSVIRQSGGKKEIVGEYGRGDLIGEVEMLT 567 (1158)
T ss_pred HhhhhhhcceEEeccccHHHhcCCccCcEEEEecCeehhhhhccCccchhhhhccCcceeehhHHhh
Confidence 344445557788999999999999999999999999992 1 222 24666777655554
No 25
>KOG0501|consensus
Probab=95.99 E-value=0.01 Score=52.10 Aligned_cols=68 Identities=21% Similarity=0.198 Sum_probs=58.8
Q ss_pred HHhhCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEE-eC----cccCCCCccee
Q psy8804 10 YGLHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFI-DG----SMFLPQSRNFV 77 (114)
Q Consensus 10 ~~Lr~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI-~g----~~~~p~~~fg~ 77 (114)
...+.+|.|+--++.=|+.||-.-...+-.+|+.|++.||.-+++++|++|+..| +. .+...|+.||+
T Consensus 548 KVFnEHpaFRLASDGCLRaLAm~f~~~H~APGDLlYHtGESvDaLcFvVsGSLEVIQDDEVVAILGKGDVFGD 620 (971)
T KOG0501|consen 548 KVFNEHPAFRLASDGCLRALAMEFQTNHCAPGDLLYHTGESVDALCFVVSGSLEVIQDDEVVAILGKGDVFGD 620 (971)
T ss_pred hhhccCcceeeccchhHHHHHHHHHhccCCCcceeeecCCccceEEEEEecceEEeecCcEEEEeecCccchh
Confidence 3567899999999999999999888888899999999999999999999999995 22 24458888883
No 26
>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=92.78 E-value=0.69 Score=33.98 Aligned_cols=60 Identities=12% Similarity=0.160 Sum_probs=47.5
Q ss_pred CCC--CCCHHHHHHHHhh-cceeEecCCCEEEecCCC-CCeEEEEEeeeEEEe--C---cccCCCCcce
Q psy8804 17 ALA--PYRDSVLRSLCRV-VRYERHQANDVLYYTGEL-STSWYILLSGSVFID--G---SMFLPQSRNF 76 (114)
Q Consensus 17 lF~--~L~~~~l~~La~~-~~~~~~~~G~~If~qGd~-~~~~yiIlsG~VkI~--g---~~~~p~~~fg 76 (114)
+|+ +.+..+.++|+.+ +.+..+++|+.-.-||.. .+.+-+++||+++|. | +...|-+.-+
T Consensus 9 lF~Pl~Vs~~~Fk~iv~~~~~i~~L~~~~~YAvE~~T~~drLSlLLsGr~~Vs~~g~fLH~I~p~qFlD 77 (153)
T PF04831_consen 9 LFQPLKVSRQQFKKIVGCCCEIRTLKKGETYAVEGKTPIDRLSLLLSGRMRVSCDGRFLHYIYPYQFLD 77 (153)
T ss_pred hccCcCCCHHHHHHHHhhhceEEEecCCceeeecCCcccceEeEEEcCcEEEEECCEeeEeeccccccc
Confidence 455 6689999999888 788999999999999985 599999999999985 4 2344555544
No 27
>KOG2968|consensus
Probab=92.76 E-value=0.076 Score=48.56 Aligned_cols=68 Identities=25% Similarity=0.371 Sum_probs=52.1
Q ss_pred HHHHHhhCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEEEeeeEEEe-----C-----cccCCCCcce
Q psy8804 7 IIYYGLHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFID-----G-----SMFLPQSRNF 76 (114)
Q Consensus 7 ~i~~~Lr~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~-----g-----~~~~p~~~fg 76 (114)
.|...|+.+.+| .....-+|++.....++.+|++||+.|++.+..|++.+|.++|+ | +.+.||+.|-
T Consensus 92 eil~~L~~i~~~---EkP~fl~L~rh~~t~~l~~Gd~i~~~~~~dd~i~vv~sg~l~v~~~~~~g~~~llk~V~~G~~~t 168 (1158)
T KOG2968|consen 92 EILYMLSAIRIL---EKPVFLELDRHIETLSLDAGDYIFKPGESDDSIYVVISGELTVHIRNGDGKEYLLKTVPPGGSFT 168 (1158)
T ss_pred HHHHHHHHhHhh---ccceeeeechhhhhhcccCCceeccCCCCCceEEEEeccceEEEecCCCCceeeEeeccCCCchH
Confidence 345667766676 22233446788899999999999999999999999999999974 2 3555887775
Q ss_pred e
Q psy8804 77 V 77 (114)
Q Consensus 77 ~ 77 (114)
+
T Consensus 169 S 169 (1158)
T KOG2968|consen 169 S 169 (1158)
T ss_pred h
Confidence 3
No 28
>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=76.92 E-value=6.1 Score=26.73 Aligned_cols=43 Identities=16% Similarity=0.127 Sum_probs=29.9
Q ss_pred HHHHHHHh-hCCCCCCCCCHHHHHHHHhhcceeEecCCCEEEec
Q psy8804 5 LQIIYYGL-HGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYT 47 (114)
Q Consensus 5 ~e~i~~~L-r~v~lF~~L~~~~l~~La~~~~~~~~~~G~~If~q 47 (114)
|..|+..| ..+|-|+.|+++-.|+|.-.+...-=..|+++|..
T Consensus 23 IRhI~~~Lt~~vPgF~~ls~sKqRRLi~~ALE~gd~~~~VvFEK 66 (92)
T PF10330_consen 23 IRHITGYLTTSVPGFSDLSPSKQRRLIMAALEGGDKDGDVVFEK 66 (92)
T ss_pred HHHHHHHHhccCCCcccCCHHHHHHHHHHHHhcCCCCCCEEEEE
Confidence 34455544 48999999999999998666555333556666654
No 29
>TIGR02451 anti_sig_ChrR anti-sigma factor, putative, ChrR family. The member of this family from Rhodobacter sphaeroides has been shown both to form a complex with sigma(E) and to negatively regulate tetrapyrrole biosynthesis. This protein likely contains (at least) two distinct functional domains; several smaller homologs (excluded by the model) show homology only to the C-terminal, including a motif PxHxHxGxE.
Probab=76.41 E-value=9.5 Score=28.92 Aligned_cols=62 Identities=13% Similarity=0.021 Sum_probs=42.0
Q ss_pred hcceeEecCCCEEEecCCCCCeEEEEEeeeEEEeCcccCCC-------CcceeecccC--ceeeeeecCcc
Q psy8804 32 VVRYERHQANDVLYYTGELSTSWYILLSGSVFIDGSMFLPQ-------SRNFVFNVFS--PVFGLILNPSV 93 (114)
Q Consensus 32 ~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~g~~~~p~-------~~fg~~~~~~--~~~~~~~~~~~ 93 (114)
.+...++++|..+-.....+..+.+||+|+..-.+..+.+| +..=...... +|=|+++...-
T Consensus 128 ~v~Ll~i~pG~~~p~H~H~G~E~tlVLeG~f~de~g~y~~Gd~i~~p~~~~H~p~a~~~~~Cicl~v~dap 198 (215)
T TIGR02451 128 RVRLLYIEAGQSIPQHTHKGFELTLVLHGAFSDETGVYGVGDFEEADGSVQHQPRTVSGGDCLCLAVLDAP 198 (215)
T ss_pred EEEEEEECCCCccCCCcCCCcEEEEEEEEEEEcCCCccCCCeEEECCCCCCcCcccCCCCCeEEEEEecCC
Confidence 44677889999999999999999999999987443333333 2222333332 47787776654
No 30
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=75.33 E-value=7.7 Score=22.96 Aligned_cols=30 Identities=10% Similarity=0.109 Sum_probs=23.3
Q ss_pred eEecCCCEEEecCCCCC-eEEEEEeeeEEEe
Q psy8804 36 ERHQANDVLYYTGELST-SWYILLSGSVFID 65 (114)
Q Consensus 36 ~~~~~G~~If~qGd~~~-~~yiIlsG~VkI~ 65 (114)
.++++|...=..-.+.. .++++++|++.+.
T Consensus 3 ~~~~pG~~~~~h~H~~~~e~~~vl~G~~~~~ 33 (71)
T PF07883_consen 3 VTLPPGGSIPPHRHPGEDEFFYVLSGEGTLT 33 (71)
T ss_dssp EEEETTEEEEEEEESSEEEEEEEEESEEEEE
T ss_pred EEECCCCCCCCEECCCCCEEEEEEECCEEEE
Confidence 46778877666666666 8999999999974
No 31
>PF12973 Cupin_7: ChrR Cupin-like domain; PDB: 3O14_B 2Z2S_F 2Q1Z_B 3EBR_A.
Probab=72.00 E-value=17 Score=23.34 Aligned_cols=41 Identities=12% Similarity=0.022 Sum_probs=30.6
Q ss_pred hcceeEecCCCEEEecCCCCCeEEEEEeeeEEEeCcccCCC
Q psy8804 32 VVRYERHQANDVLYYTGELSTSWYILLSGSVFIDGSMFLPQ 72 (114)
Q Consensus 32 ~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~g~~~~p~ 72 (114)
.+...++++|..+=...-.+....+||+|+.......+.+|
T Consensus 25 ~~~L~r~~pG~~~p~H~H~g~ee~~VLeG~~~d~~~~~~~G 65 (91)
T PF12973_consen 25 RVSLLRLEPGASLPRHRHPGGEEILVLEGELSDGDGRYGAG 65 (91)
T ss_dssp EEEEEEE-TTEEEEEEEESS-EEEEEEECEEEETTCEEETT
T ss_pred EEEEEEECCCCCcCccCCCCcEEEEEEEEEEEECCccCCCC
Confidence 45678899999998888888899999999999764444333
No 32
>PRK11832 putative DNA-binding transcriptional regulator; Provisional
Probab=69.32 E-value=12 Score=28.73 Aligned_cols=40 Identities=10% Similarity=0.177 Sum_probs=31.8
Q ss_pred HHHHHhhcceeEecCCCEE-EecCCCCCeEEEEEeeeEEEe
Q psy8804 26 LRSLCRVVRYERHQANDVL-YYTGELSTSWYILLSGSVFID 65 (114)
Q Consensus 26 l~~La~~~~~~~~~~G~~I-f~qGd~~~~~yiIlsG~VkI~ 65 (114)
.+.|...+....+++|..+ +.+.......|++++|.|.+.
T Consensus 15 ~~~L~~~g~~~~~~~~~~~i~~~~~~~~~~~ll~~G~vsir 55 (207)
T PRK11832 15 DKCLSRYGTRFEFNNEKQVIFSSDVNNEDTFVILEGVISLR 55 (207)
T ss_pred HHHhhccCCeEecCCCcEEeccccCCCceEEEEEeceEEEE
Confidence 3456778888999999996 665555578999999999984
No 33
>KOG2378|consensus
Probab=64.80 E-value=0.39 Score=41.14 Aligned_cols=59 Identities=14% Similarity=0.215 Sum_probs=51.1
Q ss_pred hhhHHHHHHHhhCCCCCCCCCHHHHHHHH-hhcceeEecCCCEEEecCCCCCeEEEEEee
Q psy8804 2 ADDLQIIYYGLHGLEALAPYRDSVLRSLC-RVVRYERHQANDVLYYTGELSTSWYILLSG 60 (114)
Q Consensus 2 ~ed~e~i~~~Lr~v~lF~~L~~~~l~~La-~~~~~~~~~~G~~If~qGd~~~~~yiIlsG 60 (114)
..+++.+...++.+..+...+---..+++ .+..+++|-++..+|++|+..++||.|+-|
T Consensus 376 tanleLl~~R~neVq~wv~tei~lc~ql~kr~qllkkfiKiaal~ke~~~l~sffAV~~G 435 (573)
T KOG2378|consen 376 TANLELLLRRFNEVQHWVATEILLCQQLGKRCQLLKKFIKIAALCKEGENLNSFFAVVMG 435 (573)
T ss_pred chhHHHHHHHHhhchhhhhchhhhhcchhHHHHHHHHHHHHHHHHHhhccccchHHHhhc
Confidence 35778888888888888888888888888 666678999999999999999999999999
No 34
>COG3718 IolB Uncharacterized enzyme involved in inositol metabolism [Carbohydrate transport and metabolism]
Probab=62.29 E-value=20 Score=28.47 Aligned_cols=56 Identities=16% Similarity=0.116 Sum_probs=37.3
Q ss_pred ceeEecCCCEEEecCCCCCeEEEEEeeeEEEeCcccCCCCcce----eecccC--ceeeeeecCcc
Q psy8804 34 RYERHQANDVLYYTGELSTSWYILLSGSVFIDGSMFLPQSRNF----VFNVFS--PVFGLILNPSV 93 (114)
Q Consensus 34 ~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~g~~~~p~~~fg----~~~~~~--~~~~~~~~~~~ 93 (114)
+..++++|+.+-.+-..-+...++++|++.|. ..|..|+ ..++|+ |-+|+-|...+
T Consensus 32 ~~~~L~~Ges~~~~~~~~E~clV~v~Gk~~vs----~~g~~f~~iG~R~SvFe~~p~~~vYvp~g~ 93 (270)
T COG3718 32 RLLRLAAGESATEETGDRERCLVLVTGKATVS----AHGSTFGEIGTRMSVFERKPPDSVYVPAGS 93 (270)
T ss_pred EEEEccCCCcccccCCCceEEEEEEeeeEEEe----eccchHhhcccccccccCCCCCeEEecCCc
Confidence 34577899988777777788889999999985 2233333 334555 55665555544
No 35
>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=59.56 E-value=10 Score=26.75 Aligned_cols=31 Identities=3% Similarity=-0.120 Sum_probs=25.9
Q ss_pred hhHHHHHHHhhCCCCCCCCCHHHHHHHHhhc
Q psy8804 3 DDLQIIYYGLHGLEALAPYRDSVLRSLCRVV 33 (114)
Q Consensus 3 ed~e~i~~~Lr~v~lF~~L~~~~l~~La~~~ 33 (114)
.++..+.++.|++|.|+.|+.+++..|.+.+
T Consensus 13 ~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~~ 43 (174)
T cd06929 13 VAIRRVVEFAKRIPGFRELSQEDQIALLKGG 43 (174)
T ss_pred HHHHHHHhhccCCcCcccCChhHHHHHHHhc
Confidence 4667788999999999999999988875543
No 36
>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=48.57 E-value=21 Score=26.10 Aligned_cols=30 Identities=10% Similarity=0.000 Sum_probs=25.0
Q ss_pred hhHHHHHHHhhCCCCCCCCCHHHHHHHHhh
Q psy8804 3 DDLQIIYYGLHGLEALAPYRDSVLRSLCRV 32 (114)
Q Consensus 3 ed~e~i~~~Lr~v~lF~~L~~~~l~~La~~ 32 (114)
..++.+.++.|++|.|..|+.+++..|.+.
T Consensus 13 ~~i~~~IefaK~iPgF~~L~~~DQi~LLk~ 42 (191)
T cd06942 13 MHIQEIVQFVKSIPGFNQLSGEDRAQLLKG 42 (191)
T ss_pred HHHHHHHHHHhcCCCcccCChhHHHHHHHH
Confidence 457778899999999999999998876543
No 37
>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=47.28 E-value=26 Score=25.73 Aligned_cols=33 Identities=3% Similarity=-0.018 Sum_probs=26.7
Q ss_pred hhHHHHHHHhhCCCCCCCCCHHHHHHHHhhcce
Q psy8804 3 DDLQIIYYGLHGLEALAPYRDSVLRSLCRVVRY 35 (114)
Q Consensus 3 ed~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~~ 35 (114)
..+..+.++.|++|.|+.|+.+++-.|.+.+..
T Consensus 23 ~~i~~~V~waK~iPgF~~L~~~DQi~LLk~~w~ 55 (189)
T cd06940 23 PAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTF 55 (189)
T ss_pred HHHHHHHHHHhcCCCcccCChhhHHHHHHHhhH
Confidence 356778899999999999999998887655543
No 38
>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=44.34 E-value=29 Score=26.19 Aligned_cols=30 Identities=13% Similarity=0.062 Sum_probs=24.1
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVV 33 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~ 33 (114)
.++.+.++.|++|.|+.|+.+++-.|.+.+
T Consensus 51 ~i~~iIefaK~lp~F~~L~~~DQi~LLK~~ 80 (231)
T cd06938 51 TVQLIVEFAKRLPGFDKLSREDQITLLKAC 80 (231)
T ss_pred HHHHHHHHHhcCCccccCChhHHHHHHHHH
Confidence 355678999999999999999887765443
No 39
>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=43.92 E-value=36 Score=23.49 Aligned_cols=30 Identities=13% Similarity=-0.153 Sum_probs=24.6
Q ss_pred hhHHHHHHHhhCCCCCCCCCHHHHHHHHhh
Q psy8804 3 DDLQIIYYGLHGLEALAPYRDSVLRSLCRV 32 (114)
Q Consensus 3 ed~e~i~~~Lr~v~lF~~L~~~~l~~La~~ 32 (114)
.++..+.++.|++|.|..|+.++...|.+.
T Consensus 10 ~~l~~~ie~ak~~p~F~~L~~~Dq~~Llk~ 39 (165)
T cd06930 10 RVLFKTVDWAKNLPAFRNLPLDDQLTLLQN 39 (165)
T ss_pred HHHHHHHHHHHcCCccccCChHHHHHHHHH
Confidence 345567899999999999999998887555
No 40
>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=43.34 E-value=31 Score=25.72 Aligned_cols=33 Identities=15% Similarity=0.015 Sum_probs=26.5
Q ss_pred hhHHHHHHHhhCCCCCCCCCHHHHHHHHhhcce
Q psy8804 3 DDLQIIYYGLHGLEALAPYRDSVLRSLCRVVRY 35 (114)
Q Consensus 3 ed~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~~ 35 (114)
.++..+.++.+++|.|+.|+.+++..|.+.+..
T Consensus 32 ~~l~~~v~wak~iP~F~~L~~~DQ~~LLk~~w~ 64 (222)
T cd06952 32 RLLFLSIHWARSIPAFQALGAETQTSLVRACWP 64 (222)
T ss_pred HHHHHHHHHHHhCCchhhCChHHHHHHHHHHhH
Confidence 456778899999999999999998876555433
No 41
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=41.57 E-value=53 Score=20.43 Aligned_cols=14 Identities=29% Similarity=0.624 Sum_probs=12.4
Q ss_pred CeEEEEEeeeEEEe
Q psy8804 52 TSWYILLSGSVFID 65 (114)
Q Consensus 52 ~~~yiIlsG~VkI~ 65 (114)
+.+..|++|+|.|.
T Consensus 26 ~E~~~vleG~v~it 39 (74)
T PF05899_consen 26 DEFFYVLEGEVTIT 39 (74)
T ss_dssp EEEEEEEEEEEEEE
T ss_pred CEEEEEEEeEEEEE
Confidence 77889999999985
No 42
>TIGR00090 iojap_ybeB iojap-like ribosome-associated protein. This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown.
Probab=39.97 E-value=21 Score=23.81 Aligned_cols=54 Identities=20% Similarity=0.322 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHhhcceeEecCCC-EEEecCCCCCeEEEEEeeeEEEeCcccCCCCc
Q psy8804 19 APYRDSVLRSLCRVVRYERHQAND-VLYYTGELSTSWYILLSGSVFIDGSMFLPQSR 74 (114)
Q Consensus 19 ~~L~~~~l~~La~~~~~~~~~~G~-~If~qGd~~~~~yiIlsG~VkI~g~~~~p~~~ 74 (114)
.+.++.+.+.++......--+.|. ..-.+|...+.|.++--|.|-|+ ++.|..+
T Consensus 36 Tg~S~rh~~aia~~v~~~~k~~~~~~~~~EG~~~~~WillD~g~ivVH--if~~e~R 90 (99)
T TIGR00090 36 SGTSSRHVKAIADNVEEELKEAGLKPLGVEGLEEGDWVLVDLGDVVVH--IFQPEAR 90 (99)
T ss_pred EeCCHHHHHHHHHHHHHHHHHcCCCcccccCCCCCCEEEEECCCEEEE--eCChHHh
Confidence 356777777776654432223333 34688999999999999999997 7766544
No 43
>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=39.47 E-value=41 Score=25.32 Aligned_cols=30 Identities=13% Similarity=-0.020 Sum_probs=24.4
Q ss_pred HHHHHHHhhCCCCCCCCCHHHHHHHHhhcc
Q psy8804 5 LQIIYYGLHGLEALAPYRDSVLRSLCRVVR 34 (114)
Q Consensus 5 ~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~ 34 (114)
+..+.++.|++|.|..|+.+++-.|.+.+.
T Consensus 56 i~~~VefaK~lP~F~~L~~~DQi~LLK~~~ 85 (236)
T cd06954 56 VQEIVDFAKQLPGFLTLTREDQIALLKAST 85 (236)
T ss_pred HHHHHHHHcCCCCcccCChHHHHHHHHHhH
Confidence 456789999999999999999887655443
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=39.45 E-value=45 Score=22.43 Aligned_cols=31 Identities=13% Similarity=0.013 Sum_probs=24.6
Q ss_pred hhHHHHHHHhhCCCCCCCCCHHHHHHHHhhc
Q psy8804 3 DDLQIIYYGLHGLEALAPYRDSVLRSLCRVV 33 (114)
Q Consensus 3 ed~e~i~~~Lr~v~lF~~L~~~~l~~La~~~ 33 (114)
.++..+.+++++.|.|+.|+.++...|.+..
T Consensus 9 ~~~~~~i~~~~~~~~f~~L~~~dq~~Llk~~ 39 (168)
T cd06157 9 RDLLLIVEWAKSIPGFRELPLEDQIVLLKSF 39 (168)
T ss_pred HHHHHHHHHHHcCCchhcCChHHHHHHHHHH
Confidence 3556678999999999999999977765543
No 45
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=39.11 E-value=35 Score=22.85 Aligned_cols=29 Identities=10% Similarity=-0.038 Sum_probs=24.9
Q ss_pred hhHHHHHHHhhCCCCCCCCCHHHHHHHHh
Q psy8804 3 DDLQIIYYGLHGLEALAPYRDSVLRSLCR 31 (114)
Q Consensus 3 ed~e~i~~~Lr~v~lF~~L~~~~l~~La~ 31 (114)
.++..+.++++..|.|+.|+.++...|.+
T Consensus 3 ~~~~~~~~~~~~~~~f~~L~~~dq~~Llk 31 (163)
T smart00430 3 RDLLLAVEWAKTFPFFRELSQEDKLILLK 31 (163)
T ss_pred hHHHHHHHHHHhChhHhhCCHHHHHHHHH
Confidence 45677889999999999999999888765
No 46
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=36.35 E-value=55 Score=18.42 Aligned_cols=10 Identities=0% Similarity=0.388 Sum_probs=6.9
Q ss_pred eeeecCCccc
Q psy8804 100 STLWDPGSMF 109 (114)
Q Consensus 100 ~~~~~~~~~~ 109 (114)
.+.|+|+.+.
T Consensus 58 ~i~~ed~~~l 67 (70)
T cd00165 58 DIVYEDKKLL 67 (70)
T ss_pred ceeeccCCEE
Confidence 7778877543
No 47
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=35.42 E-value=85 Score=20.02 Aligned_cols=42 Identities=19% Similarity=0.302 Sum_probs=31.2
Q ss_pred HHHHHHhhcceeEecCC---CEEEecCCCCCeEEEEEeeeEEEeC
Q psy8804 25 VLRSLCRVVRYERHQAN---DVLYYTGELSTSWYILLSGSVFIDG 66 (114)
Q Consensus 25 ~l~~La~~~~~~~~~~G---~~If~qGd~~~~~yiIlsG~VkI~g 66 (114)
.|++|+.......|++. -++++-.++.-.+.|--+|++-|.|
T Consensus 20 dL~~la~~~~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itG 64 (86)
T PF00352_consen 20 DLEELAEELENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITG 64 (86)
T ss_dssp -HHHHHHHSTTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEE
T ss_pred CHHHHHhhccCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEe
Confidence 35556555566677664 4689988888888888999999986
No 48
>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=35.34 E-value=55 Score=23.83 Aligned_cols=31 Identities=6% Similarity=-0.064 Sum_probs=24.9
Q ss_pred hhHHHHHHHhhCCCCCCCCCHHHHHHHHhhc
Q psy8804 3 DDLQIIYYGLHGLEALAPYRDSVLRSLCRVV 33 (114)
Q Consensus 3 ed~e~i~~~Lr~v~lF~~L~~~~l~~La~~~ 33 (114)
..+..+.++-|++|.|+.|+.+++-.|.+.+
T Consensus 13 ~~l~~iI~waK~iP~F~~L~~~DQi~LLk~~ 43 (195)
T cd06941 13 PSVQRVVEFAKRIPGFCDLSQDDQLLLIKAG 43 (195)
T ss_pred HHHHHHHHHHHcCCCcccCCHHHHHHHHHHH
Confidence 3566788999999999999999887765443
No 49
>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=35.33 E-value=49 Score=24.90 Aligned_cols=30 Identities=13% Similarity=0.104 Sum_probs=24.3
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVV 33 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~ 33 (114)
++..+.++.|++|.|+.|+.+++-.|.+.+
T Consensus 48 ~l~~~IefaK~iP~F~~L~~~DQi~LLk~~ 77 (221)
T cd06936 48 HVQVLVEFTKGLPGFETLDHEDQIALLKGS 77 (221)
T ss_pred HHHHHHHHHhCCCchhhCChhHHHHHHHHh
Confidence 456678999999999999999887765443
No 50
>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=35.25 E-value=53 Score=25.27 Aligned_cols=31 Identities=6% Similarity=0.008 Sum_probs=25.0
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhcc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVVR 34 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~ 34 (114)
.++.+.++-|++|.|+.|+.+++-.|.+.+.
T Consensus 54 ~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w 84 (239)
T cd07072 54 SIDVIKTFAEKIPGFPDLCKEDQELLFQSAS 84 (239)
T ss_pred HHHHHHHHhccCCCccCCCHHHHHHHHHHhH
Confidence 4566789999999999999999877655443
No 51
>PF10014 2OG-Fe_Oxy_2: 2OG-Fe dioxygenase; InterPro: IPR018724 Members of this family of hypothetical bacterial proteins have no known function. Some are described as putative biofilm formation or putative agglutination proteins. ; PDB: 3PL0_B.
Probab=34.63 E-value=1.1e+02 Score=22.66 Aligned_cols=57 Identities=16% Similarity=0.043 Sum_probs=36.9
Q ss_pred CeEEEEEeeeEEEeCccc----CCCCcceeecccCceeeeeecCccccceeeeeeecCCcc
Q psy8804 52 TSWYILLSGSVFIDGSMF----LPQSRNFVFNVFSPVFGLILNPSVSMAAKVSTLWDPGSM 108 (114)
Q Consensus 52 ~~~yiIlsG~VkI~g~~~----~p~~~fg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 108 (114)
+...+.+=++-.|.|... .++.........+|.++++++..+++-.++.|+=.+++-
T Consensus 124 d~v~~~li~r~Ni~GG~s~i~~~~~~~~~~~~l~~p~d~l~~~D~~~~H~vtpI~~~~~~~ 184 (195)
T PF10014_consen 124 DFVFIHLINRHNIEGGESQIYDNDKEILFFFTLLEPGDTLLVDDRRVWHYVTPIRPVDPSR 184 (195)
T ss_dssp SEEEEEEEEEESEEE--EEEEETTSSEEEEE---STTEEEEEETTTEEEEE--EEES-TT-
T ss_pred CEEEEEEEcCCCccCceEEEEeCCCCcceEEEecCCCCEEEEeCCcceECCCceecCCCCC
Confidence 455666777777765221 255566678888899999999999999999998887763
No 52
>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=33.70 E-value=65 Score=24.02 Aligned_cols=30 Identities=10% Similarity=-0.035 Sum_probs=24.5
Q ss_pred hhHHHHHHHhhCCCCCCCCCHHHHHHHHhh
Q psy8804 3 DDLQIIYYGLHGLEALAPYRDSVLRSLCRV 32 (114)
Q Consensus 3 ed~e~i~~~Lr~v~lF~~L~~~~l~~La~~ 32 (114)
.++..+.++.|++|.|+.|+.+++..|.+.
T Consensus 38 ~~l~~~vewaK~lp~F~~L~~~DQi~LLk~ 67 (221)
T cd07068 38 RELVHIISWAKHIPGFSDLSLNDQMHLLQS 67 (221)
T ss_pred HHHHHHHHHHHhCCCcccCCHHHHHHHHHH
Confidence 345567899999999999999998886544
No 53
>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=33.62 E-value=54 Score=25.07 Aligned_cols=32 Identities=6% Similarity=-0.162 Sum_probs=25.1
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhcce
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVVRY 35 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~~ 35 (114)
.+..+.++-|++|.|+.|+.+++-.|.+.+..
T Consensus 64 ~l~~iVefAK~iPgF~~L~~~DQi~LLk~~~~ 95 (243)
T cd06935 64 AITRVVDFAKKLPMFTELPCEDQIILLKGCCM 95 (243)
T ss_pred HHHHHHHHHhcCCccccCChHHHHHHHHHhHH
Confidence 35567899999999999999998876555433
No 54
>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=33.11 E-value=59 Score=24.90 Aligned_cols=31 Identities=6% Similarity=-0.061 Sum_probs=24.8
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhcc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVVR 34 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~ 34 (114)
.++.+.++-|++|-|..|+.+++-.|.+.+.
T Consensus 60 ~i~~vVefAK~IPgF~~L~~~DQi~LLk~~~ 90 (241)
T cd06939 60 AIQYVVEFAKRIPGFMELCQNDQIVLLKAGS 90 (241)
T ss_pred HHHHHHHHHhcCCCcccCCHHHHHHHHHHhH
Confidence 4667889999999999999998877654433
No 55
>PRK11538 ribosome-associated protein; Provisional
Probab=32.86 E-value=30 Score=23.54 Aligned_cols=54 Identities=22% Similarity=0.274 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHhhcceeEecCC-CEEEecCCCCCeEEEEEeeeEEEeCcccCCCCc
Q psy8804 19 APYRDSVLRSLCRVVRYERHQAN-DVLYYTGELSTSWYILLSGSVFIDGSMFLPQSR 74 (114)
Q Consensus 19 ~~L~~~~l~~La~~~~~~~~~~G-~~If~qGd~~~~~yiIlsG~VkI~g~~~~p~~~ 74 (114)
.+-+..+.+.|+......--+.| ...-.+|.....|.++--|.|-|+ ++.|..+
T Consensus 41 tg~S~rh~~aia~~v~~~~k~~~~~~~~~eG~~~~~WillD~g~ivVH--if~~e~R 95 (105)
T PRK11538 41 TGTSSRHVMSIADHVVQESRAAGLLPLGVEGENAADWIVVDLGDVIVH--VMQEESR 95 (105)
T ss_pred EeCCHHHHHHHHHHHHHHHHHcCCCCCcccCCCCCCEEEEeCCCEEEE--cCCHHHH
Confidence 35677778877766543222333 345678999999999999999997 7777654
No 56
>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=32.34 E-value=49 Score=24.18 Aligned_cols=31 Identities=10% Similarity=-0.130 Sum_probs=25.1
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhcc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVVR 34 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~ 34 (114)
++..+.++.|++|.|..|+.+++-.|.+.+.
T Consensus 42 ~l~~~Iewak~lp~F~~L~~~DQ~~LLk~~~ 72 (207)
T cd06943 42 QLFQLVEWAKRIPHFSELPLDDQVILLRAGW 72 (207)
T ss_pred HHHHHHHHHHhCchhhccChhhhHHHHHHHH
Confidence 4566789999999999999999888755543
No 57
>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=32.33 E-value=66 Score=23.92 Aligned_cols=31 Identities=13% Similarity=0.039 Sum_probs=24.6
Q ss_pred hhHHHHHHHhhCCCCCCCCCHHHHHHHHhhc
Q psy8804 3 DDLQIIYYGLHGLEALAPYRDSVLRSLCRVV 33 (114)
Q Consensus 3 ed~e~i~~~Lr~v~lF~~L~~~~l~~La~~~ 33 (114)
.++..+.++.|++|.|+.|+.+++-.|.+.+
T Consensus 38 ~~l~~~Ve~aK~lp~F~~L~~~DQi~LLk~~ 68 (221)
T cd06946 38 RELVVIIGWAKHIPGFSSLSLNDQMSLLQSA 68 (221)
T ss_pred HHHHHHHHHHHhCCCcccCCHHHHHHHHHHH
Confidence 3456678999999999999999987764443
No 58
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=32.07 E-value=1.2e+02 Score=22.28 Aligned_cols=19 Identities=11% Similarity=0.538 Sum_probs=15.4
Q ss_pred EecCCCCCeEEEEEeeeEEE
Q psy8804 45 YYTGELSTSWYILLSGSVFI 64 (114)
Q Consensus 45 f~qGd~~~~~yiIlsG~VkI 64 (114)
++. ++++-||.+++|++.|
T Consensus 43 ~H~-~~tdE~FyqleG~~~l 61 (159)
T TIGR03037 43 FHD-DPGEEFFYQLKGEMYL 61 (159)
T ss_pred ccc-CCCceEEEEEcceEEE
Confidence 555 3489999999999987
No 59
>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=31.88 E-value=54 Score=25.43 Aligned_cols=32 Identities=6% Similarity=-0.081 Sum_probs=25.5
Q ss_pred hhHHHHHHHhhCCCCCCCCCHHHHHHHHhhcc
Q psy8804 3 DDLQIIYYGLHGLEALAPYRDSVLRSLCRVVR 34 (114)
Q Consensus 3 ed~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~ 34 (114)
+.++.+.++-|++|.|..|+.+++-.|.+.+.
T Consensus 74 ~~i~~vVewAK~IPgF~~L~~~DQi~LLk~~~ 105 (259)
T cd06932 74 ETIRELTEFAKSLPGFRNLDLNDQVTLLKYGV 105 (259)
T ss_pred HHHHHHHHHHhcCCCcccCChhHHHHHHHHhh
Confidence 45677889999999999999998877654443
No 60
>CHL00133 psbV photosystem II cytochrome c550; Validated
Probab=31.61 E-value=57 Score=24.12 Aligned_cols=21 Identities=10% Similarity=0.161 Sum_probs=18.0
Q ss_pred CCCCCCCCHHHHHHHHhhcce
Q psy8804 15 LEALAPYRDSVLRSLCRVVRY 35 (114)
Q Consensus 15 v~lF~~L~~~~l~~La~~~~~ 35 (114)
+|.|..|++++++.++.....
T Consensus 127 MPa~~~LsdeEL~aVAaYIl~ 147 (163)
T CHL00133 127 FPKMRSLTDEDLYAIAGHILL 147 (163)
T ss_pred CCCCCCCCHHHHHHHHHHHHh
Confidence 677889999999999988654
No 61
>PF05726 Pirin_C: Pirin C-terminal cupin domain; InterPro: IPR008778 This entry represents C-terminal domain of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localised within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures []. Pirin is composed of two structurally similar domains arranged face to face. The N-terminal domain additionally features four beta-strands, and the C-terminal domain also includes four additional -strands and a short alpha-helix. Although the two domains are similar, the C-terminal domain of Pirin differs from the N-terminal domain as it does not contain a metal binding site and its sequence does not contain the conserved metal-coordinating residues []. Pirin is confirmed to be a member of the cupin superfamily on the basis of primary sequence and structural similarity. The presence of a metal binding site in the N-terminal beta-barrel of Pirin, may be significant in its role in regulating NFI DNA replication and NF-kappaB transcription factor activity []. Pirin structure has been found to closely resemble members of the cupin superfamily. Pirin contains the two characteristic sequences of the cupin superfamily, namely PG-(X)5-HXH-(X)4-E-(X)6-G and G-(X)5-PXG-(X)2-H-(X)3-N separated by a variable stretch of 15-50 amino acids. These motifs are best conserved in the N-terminal where the conserved histidine and glutamic acid residues correspond to the metal-coordinating residues. The C-terminal domain motifs lack the metal binding residues normally associated with the cupin fold []. Pirin was identified to be a metal-binding protein [], and was found that the metal-binding residues of Pirins are highly conserved across mammals, plants, fungi, and prokaryotic organisms. Pirin acts as a cofactor for the transcription factor NFI, the regulatory mechanism of which is generally believed to require the assistance of a metal ion []. Structural data supports the hypothesis that the bound iron of Pirin may participate in this transcriptional regulation by enhancing and stabilising the formation of the p50,Bcl3,DNA complex []. Metals have been implicated directly or indirectly in the NF-kappaB family of transcription factors that control expression of a number of early response genes associated with inflammatory responses, cell growth, cell cycle progression, and neoplastic transformation []. However, most metal-dependent transcription factors are DNA-binding proteins that bind to specific sequences when the metal binds to the protein. Pirin, on the other hand, appears to function differently and bind to the transcription factor DNA complex [].; PDB: 1J1L_A 3ACL_A 2P17_A.
Probab=31.44 E-value=85 Score=20.67 Aligned_cols=32 Identities=16% Similarity=0.226 Sum_probs=21.0
Q ss_pred EecCCCEEEec-CCCCCeEEEEEeeeEEEeCcc
Q psy8804 37 RHQANDVLYYT-GELSTSWYILLSGSVFIDGSM 68 (114)
Q Consensus 37 ~~~~G~~If~q-Gd~~~~~yiIlsG~VkI~g~~ 68 (114)
++++|..+-.. -...+.+..+++|++.|.|..
T Consensus 5 ~l~~g~~~~~~~~~~~~~~iyv~~G~~~v~~~~ 37 (104)
T PF05726_consen 5 KLEPGASFTLPLPPGHNAFIYVLEGSVEVGGEE 37 (104)
T ss_dssp EE-TT-EEEEEEETT-EEEEEEEESEEEETTTT
T ss_pred EECCCCEEEeecCCCCEEEEEEEECcEEECCCc
Confidence 45666665544 344578888899999998765
No 62
>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=30.98 E-value=64 Score=24.08 Aligned_cols=31 Identities=10% Similarity=-0.232 Sum_probs=24.7
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhcc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVVR 34 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~ 34 (114)
.+..+.++.|++|.|..|+.+++-.|.+.+.
T Consensus 39 ~l~~~I~waK~lp~F~~L~~~DQi~LLk~~w 69 (213)
T cd06953 39 LLFRQIQWTKKLPFFTELSIKDHTHLLTTKW 69 (213)
T ss_pred HHHHHHHHHhcCCchhhCCHHHHHHHHHHHH
Confidence 3556789999999999999999887655443
No 63
>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=30.00 E-value=73 Score=24.31 Aligned_cols=30 Identities=7% Similarity=0.005 Sum_probs=24.4
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVV 33 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~ 33 (114)
.+..+.++-|++|-|+.|+.+++-.|.+.+
T Consensus 53 ~l~~iv~wAK~IPgF~~L~~~DQi~LLk~~ 82 (239)
T cd06945 53 SVDVIRQWAEKIPGFKDLHREDQDLLLESA 82 (239)
T ss_pred HHHHHHHHHHhCCCcccCCHHHHHHHHHHH
Confidence 456678999999999999999987765443
No 64
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=29.32 E-value=45 Score=25.35 Aligned_cols=42 Identities=24% Similarity=0.218 Sum_probs=35.0
Q ss_pred eCcccCCCCcceeecccCceeeeeecCccccceeeeeeecCC
Q psy8804 65 DGSMFLPQSRNFVFNVFSPVFGLILNPSVSMAAKVSTLWDPG 106 (114)
Q Consensus 65 ~g~~~~p~~~fg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 106 (114)
.|++++||+.-+...-|.|-+....+...++.|++.+.+.|.
T Consensus 4 ~g~~v~PGd~~a~~EE~~~G~gt~~~~g~i~Aa~~G~~~~d~ 45 (188)
T COG1096 4 DGTFVLPGDVLAVIEEFLPGEGTYEEGGEIRAAATGVVRRDD 45 (188)
T ss_pred cCcEEcCcceeeeeeeeecCCCeEeECCEEEEeecccEEEcc
Confidence 467889999999888888998888889999999988776553
No 65
>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=28.81 E-value=77 Score=24.10 Aligned_cols=31 Identities=6% Similarity=-0.092 Sum_probs=24.6
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhcc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVVR 34 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~ 34 (114)
.+..+.++.|++|.|..|+.+++-.|.+.+.
T Consensus 44 ~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w 74 (235)
T cd06949 44 ELVHMINWAKKIPGFVDLSLHDQVHLLESAW 74 (235)
T ss_pred HHHHHHHHHHhCCCcccCCHHHHHHHHHHhH
Confidence 4566789999999999999999877654443
No 66
>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=28.80 E-value=72 Score=24.28 Aligned_cols=30 Identities=7% Similarity=-0.168 Sum_probs=23.9
Q ss_pred HHHHHHHhhCCCCCCCCCHHHHHHHHhhcc
Q psy8804 5 LQIIYYGLHGLEALAPYRDSVLRSLCRVVR 34 (114)
Q Consensus 5 ~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~ 34 (114)
+-.+.++.|++|.|+.|+.+++-.|.+.+.
T Consensus 51 L~~~VeWaK~lP~F~~L~~~DQi~LLk~~w 80 (237)
T cd07070 51 FISIVDWARRCMVFKELEVADQMTLLQNCW 80 (237)
T ss_pred HHHHHHHHHhCCChhhCCHHHHHHHHHHHH
Confidence 445678999999999999999887655443
No 67
>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=27.74 E-value=82 Score=23.30 Aligned_cols=30 Identities=13% Similarity=0.024 Sum_probs=24.1
Q ss_pred hhHHHHHHHhhCCCCCCCCCHHHHHHHHhh
Q psy8804 3 DDLQIIYYGLHGLEALAPYRDSVLRSLCRV 32 (114)
Q Consensus 3 ed~e~i~~~Lr~v~lF~~L~~~~l~~La~~ 32 (114)
.++..+.++.+.+|.|+.|+.++...|.+.
T Consensus 43 ~~l~~~vewak~~p~F~~L~~~Dq~~Llk~ 72 (222)
T cd06931 43 QQLLVLVEWAKYIPAFCELPLDDQVALLRA 72 (222)
T ss_pred HHHHHHHHHHHhCCccccCChHHHHHHHHH
Confidence 355667899999999999999998776444
No 68
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=26.82 E-value=1.2e+02 Score=20.36 Aligned_cols=42 Identities=10% Similarity=0.068 Sum_probs=30.5
Q ss_pred ceeEecCCCEEEecCCC-CCeEEEEEeeeEEEe--C--cccCCCCcc
Q psy8804 34 RYERHQANDVLYYTGEL-STSWYILLSGSVFID--G--SMFLPQSRN 75 (114)
Q Consensus 34 ~~~~~~~G~~If~qGd~-~~~~yiIlsG~VkI~--g--~~~~p~~~f 75 (114)
..-.+++|..+=..--+ ++...++++|+++++ | ....+|+.+
T Consensus 46 ~~v~~~~G~~~~~H~hp~~~~~~~Vl~G~~~~~~~g~~~~l~~Gd~i 92 (131)
T COG1917 46 VLVTFEPGAVIPWHTHPLGEQTIYVLEGEGTVQLEGEKKELKAGDVI 92 (131)
T ss_pred EEEEECCCcccccccCCCcceEEEEEecEEEEEecCCceEecCCCEE
Confidence 34567888888888887 778999999999975 3 233355553
No 69
>PF14525 AraC_binding_2: AraC-binding-like domain
Probab=26.80 E-value=1.7e+02 Score=19.66 Aligned_cols=24 Identities=21% Similarity=0.289 Sum_probs=14.5
Q ss_pred CEEEecCCCCCeEEEE--EeeeEEEe
Q psy8804 42 DVLYYTGELSTSWYIL--LSGSVFID 65 (114)
Q Consensus 42 ~~If~qGd~~~~~yiI--lsG~VkI~ 65 (114)
++.++.....++++++ ++|+..+.
T Consensus 44 ~~~vr~~~~~~~~~l~~~~~G~~~~~ 69 (172)
T PF14525_consen 44 QRRVRSDAPDDHYLLVLPLSGSARIE 69 (172)
T ss_pred CEEEECCCCCCEEEEEEEccCCEEEE
Confidence 4555555545555444 78888864
No 70
>PRK03511 minC septum formation inhibitor; Reviewed
Probab=26.74 E-value=2.2e+02 Score=21.75 Aligned_cols=32 Identities=13% Similarity=0.266 Sum_probs=21.7
Q ss_pred eEecCCCEEEec-C------CCCCeEEEEEeeeEEEeCc
Q psy8804 36 ERHQANDVLYYT-G------ELSTSWYILLSGSVFIDGS 67 (114)
Q Consensus 36 ~~~~~G~~If~q-G------d~~~~~yiIlsG~VkI~g~ 67 (114)
+.+..|+.|+.+ | +....--++-.|.|-|+|.
T Consensus 127 ~~vRSGQ~i~a~~gdlvVlG~Vn~GAEViA~GnI~V~G~ 165 (228)
T PRK03511 127 TPVRSGQRIYAPQCDLIVTSHVSAGAELIADGNIHVYGM 165 (228)
T ss_pred CCccCCCEEEecCCCEEEEccCCCCCEEEeCCCEEEEEE
Confidence 445668888876 3 4566667777777777763
No 71
>PRK13290 ectC L-ectoine synthase; Reviewed
Probab=26.37 E-value=2.2e+02 Score=19.62 Aligned_cols=31 Identities=6% Similarity=-0.163 Sum_probs=19.7
Q ss_pred eeEecCCCEEEecCCCCCeEEEEEeeeEEEe
Q psy8804 35 YERHQANDVLYYTGELSTSWYILLSGSVFID 65 (114)
Q Consensus 35 ~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~ 65 (114)
.-.+++|+.+-..-.....++.|++|+..+.
T Consensus 39 ~~~l~pG~~~~~h~h~~~E~~yVL~G~~~~~ 69 (125)
T PRK13290 39 ETTIYAGTETHLHYKNHLEAVYCIEGEGEVE 69 (125)
T ss_pred EEEECCCCcccceeCCCEEEEEEEeCEEEEE
Confidence 3467888655332222235899999999864
No 72
>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=26.20 E-value=90 Score=23.54 Aligned_cols=30 Identities=13% Similarity=-0.091 Sum_probs=23.9
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVV 33 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~ 33 (114)
.+..+.++-|++|.|+.|+.+++-.|.+.+
T Consensus 31 ~L~~~V~wAK~iP~F~~L~~~DQi~LLk~~ 60 (222)
T cd06951 31 VLLKTIRFVRNLPCFTYLPPDDQLRLLRRS 60 (222)
T ss_pred HHHHHHHHHHhCCCcccCChHHHHHHHHHH
Confidence 456678999999999999999886654443
No 73
>PRK07963 fliN flagellar motor switch protein FliN; Validated
Probab=25.97 E-value=1.1e+02 Score=21.90 Aligned_cols=43 Identities=16% Similarity=0.220 Sum_probs=36.1
Q ss_pred ceeEecCCCEEEecCCCCCeEEEEEeeeEEEeCcccCCCCcce
Q psy8804 34 RYERHQANDVLYYTGELSTSWYILLSGSVFIDGSMFLPQSRNF 76 (114)
Q Consensus 34 ~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~g~~~~p~~~fg 76 (114)
.+..+++|++|--+...++.+-+.+.|..+..|....-++.+|
T Consensus 77 dLL~L~~GDVI~Ld~~~~epv~V~Vng~~if~GevGvv~~k~A 119 (137)
T PRK07963 77 ELLRLTQGSVVALDGLAGEPLDILINGYLIAQGEVVVVADKYG 119 (137)
T ss_pred HHhCCCCCCEEEeCCCCCCCEEEEECCEEEEEEEEEEECCEEE
Confidence 3456788999999988889999999999998887777777766
No 74
>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=25.94 E-value=92 Score=23.92 Aligned_cols=31 Identities=10% Similarity=0.055 Sum_probs=24.5
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhcc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVVR 34 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~ 34 (114)
.+..+.++-|++|.|.+|+.+++-.|.+.+.
T Consensus 53 ~l~~iVewAK~iPgF~~L~~~DQi~LLk~~w 83 (238)
T cd07348 53 SLEVIRKWAEKIPGFSDFCKEDQELLLESAF 83 (238)
T ss_pred HHHHHHHHHccCCCccCCChHHHHHHHHHHH
Confidence 4566789999999999999998877654443
No 75
>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=25.61 E-value=97 Score=23.47 Aligned_cols=31 Identities=10% Similarity=-0.098 Sum_probs=24.5
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhcc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVVR 34 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~ 34 (114)
.+..+.++-|++|.|+.|+.+++-.|.+.+.
T Consensus 50 ~l~~~V~wAK~iPgF~~L~~~DQi~LLk~~w 80 (231)
T cd06937 50 CIIKIVEFAKRLPGFTTLTIADQITLLKAAC 80 (231)
T ss_pred HHHHHHHHHhcCCccccCCHHHHHHHHHHHH
Confidence 3556789999999999999998877654443
No 76
>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=25.53 E-value=1e+02 Score=23.76 Aligned_cols=30 Identities=7% Similarity=-0.056 Sum_probs=23.7
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVV 33 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~ 33 (114)
.+..+.++-|++|.|++|+-+++-.|.+.+
T Consensus 40 ~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~ 69 (246)
T cd07073 40 QLVHVVKWAKALPGFRNLHVDDQMAVIQYS 69 (246)
T ss_pred HHHHHHHHHHcCCCccCCCHHHHHHHHHHH
Confidence 455678999999999999988877764443
No 77
>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=25.23 E-value=93 Score=23.69 Aligned_cols=31 Identities=6% Similarity=-0.073 Sum_probs=24.7
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhcc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVVR 34 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~ 34 (114)
.++.+.++-|++|.|..|+.+++-.|.+.+.
T Consensus 49 ~l~~iI~wAK~iPgF~~L~~~DQi~LLk~~~ 79 (238)
T cd06933 49 SIQKVIGFAKMIPGFRDLTAEDQIALLKSSA 79 (238)
T ss_pred HHHHHHHHHcCCCccccCChHHHHHHHHHhH
Confidence 4566789999999999999998877655444
No 78
>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=24.95 E-value=1.1e+02 Score=23.57 Aligned_cols=31 Identities=10% Similarity=-0.005 Sum_probs=24.8
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhcc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVVR 34 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~ 34 (114)
.++.+.++-|++|.|..|+.+++-.|.+.+.
T Consensus 53 ~i~~iVewAK~iPgF~~L~~~DQi~LLk~~~ 83 (238)
T cd07071 53 SMEIIRGWAEKIPGFTDLPKADQDLLFESAF 83 (238)
T ss_pred HHHHHHHHhccCCCccCCCHHHHHHHHHHHH
Confidence 4566789999999999999998877655443
No 79
>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=24.88 E-value=96 Score=23.69 Aligned_cols=29 Identities=14% Similarity=0.008 Sum_probs=23.1
Q ss_pred HHHHHHHhhCCCCCCCCCHHHHHHHHhhc
Q psy8804 5 LQIIYYGLHGLEALAPYRDSVLRSLCRVV 33 (114)
Q Consensus 5 ~e~i~~~Lr~v~lF~~L~~~~l~~La~~~ 33 (114)
+..+.++.|++|.|..|+-+++-.|.+.+
T Consensus 32 L~~~VeWAK~iP~F~~L~~~DQi~LLk~~ 60 (232)
T cd07350 32 LVKTLRFVKGVPCFQELPLDDQLVLVRSC 60 (232)
T ss_pred HHHHHHHHHhCcCcccCChHHHHHHHHHh
Confidence 44567899999999999999887764443
No 80
>PF07697 7TMR-HDED: 7TM-HD extracellular; InterPro: IPR011624 This entry represents the extracellular domain of the 7TM-HD (7TM Receptors with HD hydrolase) protein family []. These proteins are known or predicted, to posses metal-dependent phospohydrolase activity.
Probab=24.81 E-value=52 Score=23.87 Aligned_cols=31 Identities=16% Similarity=0.164 Sum_probs=21.2
Q ss_pred CCHHHHHHHHhhcceeE--ecCCCEEEecCCCC
Q psy8804 21 YRDSVLRSLCRVVRYER--HQANDVLYYTGELS 51 (114)
Q Consensus 21 L~~~~l~~La~~~~~~~--~~~G~~If~qGd~~ 51 (114)
.+...+++..+...... +++|++|.++||.-
T Consensus 174 ~T~~~~~~a~~~V~pv~~~V~~Ge~IV~kGe~V 206 (222)
T PF07697_consen 174 ATEKAREEALASVSPVRGMVKKGEVIVRKGEIV 206 (222)
T ss_pred HHHHHHHHHHhcCCchHhhccCCCEEecCCcEe
Confidence 34455555555555555 79999999999864
No 81
>PF13128 DUF3954: Protein of unknown function (DUF3954)
Probab=24.75 E-value=1.1e+02 Score=18.41 Aligned_cols=24 Identities=25% Similarity=0.236 Sum_probs=17.9
Q ss_pred CCeEEEEEeeeEEEeCcccCCCCccee
Q psy8804 51 STSWYILLSGSVFIDGSMFLPQSRNFV 77 (114)
Q Consensus 51 ~~~~yiIlsG~VkI~g~~~~p~~~fg~ 77 (114)
.+..|++..|+|.. .--|...||+
T Consensus 9 ~ngiYiV~~G~v~~---i~pP~sGfGe 32 (50)
T PF13128_consen 9 ENGIYIVKDGEVTF---IEPPESGFGE 32 (50)
T ss_pred CCeEEEEECCeEEE---cCCCCCCcce
Confidence 47899999999985 3346666886
No 82
>COG5458 Uncharacterized conserved protein [Function unknown]
Probab=24.55 E-value=1.1e+02 Score=21.89 Aligned_cols=56 Identities=20% Similarity=0.209 Sum_probs=32.2
Q ss_pred CEEEecCC---CCCeEEEEEeeeEEEe-----CcccCCCCcceeecccCceeeeeecCccccceeeeeeecCCccc
Q psy8804 42 DVLYYTGE---LSTSWYILLSGSVFID-----GSMFLPQSRNFVFNVFSPVFGLILNPSVSMAAKVSTLWDPGSMF 109 (114)
Q Consensus 42 ~~If~qGd---~~~~~yiIlsG~VkI~-----g~~~~p~~~fg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 109 (114)
.++=+..| .|.++|-|+.|.|+-- .+.+.-++. .+-|+ ++|+|. ++.+.|++--+|
T Consensus 43 RMvPkR~~Ell~GgSLYwViKG~VqcRQ~ll~Ir~ftd~eg------igRC~-l~L~P~-----vi~t~pqPrRaF 106 (144)
T COG5458 43 RMVPKRIDELLDGGSLYWVIKGQVQCRQKLLDIRTFTDGEG------IGRCH-LTLDPE-----VIRTEPQPRRAF 106 (144)
T ss_pred cccchhHHHHhcCCeEEEEEeceeehhhhceeeeeccCCCc------cceeE-EeeCCc-----ceecCCCccccc
Confidence 33444444 4889999999999842 233333333 33344 566663 345556666655
No 83
>PF11149 DUF2924: Protein of unknown function (DUF2924); InterPro: IPR021322 This entry is represented by Bacteriophage WO, Gp30. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This bacterial family of proteins has no known function.
Probab=24.35 E-value=1.6e+02 Score=21.16 Aligned_cols=52 Identities=15% Similarity=0.144 Sum_probs=35.0
Q ss_pred CCCCCCHHHHHHHHhhcce------------eEecCCCEEEec-CCCCCeEEEEEeeeEEEeCccc
Q psy8804 17 ALAPYRDSVLRSLCRVVRY------------ERHQANDVLYYT-GELSTSWYILLSGSVFIDGSMF 69 (114)
Q Consensus 17 lF~~L~~~~l~~La~~~~~------------~~~~~G~~If~q-Gd~~~~~yiIlsG~VkI~g~~~ 69 (114)
.|.+|+++..+.|...+.. ....+|..|.++ +.....+.++-+| ..-+|+.+
T Consensus 48 a~GgL~~~~~~rL~~la~~~~~~~~~~~~~~~~~~pGt~LvREw~G~~h~V~V~~dG-fey~Gr~y 112 (136)
T PF11149_consen 48 AFGGLSEETRRRLDALAEELEKRKRAKRRDDRRPAPGTRLVREWNGREHEVTVLEDG-FEYQGRRY 112 (136)
T ss_pred HHCCCCHHHHHHHHHHHhccccccccCCCcccCCCCCcEEEEEECCEEEEEEEeCCC-EEECCccc
Confidence 6789999998887665544 334678889888 5555555555666 65555443
No 84
>COG0850 MinC Septum formation inhibitor [Cell division and chromosome partitioning]
Probab=24.12 E-value=2.4e+02 Score=21.64 Aligned_cols=33 Identities=15% Similarity=0.350 Sum_probs=23.1
Q ss_pred eeEecCCCEEEecC-------CCCCeEEEEEeeeEEEeCc
Q psy8804 35 YERHQANDVLYYTG-------ELSTSWYILLSGSVFIDGS 67 (114)
Q Consensus 35 ~~~~~~G~~If~qG-------d~~~~~yiIlsG~VkI~g~ 67 (114)
.+....|+.|+..| |...+--|+-.|.|-|+|.
T Consensus 116 ~~~VRSGQ~Iy~~~gDlivlG~VnpGAeIiA~GnI~VyG~ 155 (219)
T COG0850 116 ETPVRSGQRIYAPGGDLIVLGDVNPGAEIIADGNIHVYGK 155 (219)
T ss_pred EeeccCCCEEEeeCCCEEEEccCCCCCEEEeCCcEEEEEE
Confidence 34557788555554 5666777888888888874
No 85
>KOG3212|consensus
Probab=23.44 E-value=72 Score=24.53 Aligned_cols=74 Identities=12% Similarity=0.296 Sum_probs=47.5
Q ss_pred CCCCHHHHHHHHhhcce----eEecCCCEEEecCCCCCeEEEEEeeeEEEeCcccCCCCcceeecccCceeeeeecCccc
Q psy8804 19 APYRDSVLRSLCRVVRY----ERHQANDVLYYTGELSTSWYILLSGSVFIDGSMFLPQSRNFVFNVFSPVFGLILNPSVS 94 (114)
Q Consensus 19 ~~L~~~~l~~La~~~~~----~~~~~G~~If~qGd~~~~~yiIlsG~VkI~g~~~~p~~~fg~~~~~~~~~~~~~~~~~~ 94 (114)
++-+.-++..+|...+. .+-+...-+-.+|+..+.||++-=|++.|+ .+.|-++ +-.-++.+++.-=+..++
T Consensus 105 Sgrs~rhl~aiAe~lv~m~Kik~~kgd~hvriegk~s~dW~v~D~g~~vvH--~mseeaR--e~YdLEsLWa~~S~ddr~ 180 (208)
T KOG3212|consen 105 SGRSDRHLRAIAEALVYMAKIKSQKGDKHVRIEGKQSSDWIVIDYGKFVVH--AMSEEAR--EYYDLESLWAAESSDDRT 180 (208)
T ss_pred ecCchHHHHHHHHHHHHHHHHhhcCCCcccccccccCCCeEEEEeceEEEE--ecCHHHh--hhccHHHHhcccCcCchh
Confidence 56677777777665443 122223345678999999999999999997 6666666 444466666544444444
Q ss_pred cc
Q psy8804 95 MA 96 (114)
Q Consensus 95 ~~ 96 (114)
-|
T Consensus 181 sd 182 (208)
T KOG3212|consen 181 SD 182 (208)
T ss_pred hc
Confidence 33
No 86
>PRK07721 fliI flagellum-specific ATP synthase; Validated
Probab=23.34 E-value=3e+02 Score=23.28 Aligned_cols=69 Identities=13% Similarity=0.152 Sum_probs=46.8
Q ss_pred HHHHhhCCCCCCCCCHHHHHHHHhhcceeEe-cCCC-----EEEecCC-----CCCeEEEEEeeeEEEeCcccCCCCcce
Q psy8804 8 IYYGLHGLEALAPYRDSVLRSLCRVVRYERH-QAND-----VLYYTGE-----LSTSWYILLSGSVFIDGSMFLPQSRNF 76 (114)
Q Consensus 8 i~~~Lr~v~lF~~L~~~~l~~La~~~~~~~~-~~G~-----~If~qGd-----~~~~~yiIlsG~VkI~g~~~~p~~~fg 76 (114)
|.-.+...|-.+++++.....+.+......- +.|. +|.-.|+ .++.+..+..|.+..+++....|.++.
T Consensus 267 isl~~ge~P~~~G~dp~~~~~l~~ller~~~~~~GsIT~~~TVlv~~hdm~e~i~d~v~~i~dG~Ivls~~la~~g~~PA 346 (438)
T PRK07721 267 IGLAVGEPPTTKGYTPSVFAILPKLLERTGTNASGSITAFYTVLVDGDDMNEPIADTVRGILDGHFVLDRQLANKGQYPA 346 (438)
T ss_pred HHHhcCCCCccccCCHHHHHHHHHHHHHhcCCCCCCeeeEEEEEEECCCCCchhhhhEEEecCEEEEEeccHHHCCCCCc
Confidence 3335668899999999999887665443222 4673 4444444 467889999999998876655555543
No 87
>PRK00394 transcription factor; Reviewed
Probab=23.31 E-value=1.6e+02 Score=21.73 Aligned_cols=41 Identities=17% Similarity=0.250 Sum_probs=31.0
Q ss_pred HHHHHhhcceeEecCC---CEEEecCCCCCeEEEEEeeeEEEeC
Q psy8804 26 LRSLCRVVRYERHQAN---DVLYYTGELSTSWYILLSGSVFIDG 66 (114)
Q Consensus 26 l~~La~~~~~~~~~~G---~~If~qGd~~~~~yiIlsG~VkI~g 66 (114)
|+.|+....--.|++. -.+++-.+|.-..-|-.+|++.+.|
T Consensus 18 L~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIf~sGKiv~tG 61 (179)
T PRK00394 18 LEKVAEDLPNAEYNPEQFPGLVYRLEDPKIAALIFRSGKVVCTG 61 (179)
T ss_pred HHHHHhhCCCceeCcccCceEEEEecCCceEEEEEcCCcEEEEc
Confidence 4555544445567664 4899999999888888999999987
No 88
>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=23.28 E-value=1.1e+02 Score=23.12 Aligned_cols=31 Identities=10% Similarity=-0.160 Sum_probs=24.2
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhcc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVVR 34 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~ 34 (114)
.+..+.++.|++|.|+.|+-+++-.|.+.+.
T Consensus 50 ~l~~~VewaK~lp~F~~L~~~DQi~LLk~~w 80 (237)
T cd06944 50 TLFSIVEWARNSVFFKELKVDDQMKLLQNCW 80 (237)
T ss_pred HHHHHHHHHHhCCChhcCCHHHHHHHHHHHh
Confidence 3445679999999999999999887655443
No 89
>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=23.15 E-value=1.1e+02 Score=23.12 Aligned_cols=29 Identities=10% Similarity=-0.054 Sum_probs=23.9
Q ss_pred HHHHHHHhhCCCCCCCCCHHHHHHHHhhc
Q psy8804 5 LQIIYYGLHGLEALAPYRDSVLRSLCRVV 33 (114)
Q Consensus 5 ~e~i~~~Lr~v~lF~~L~~~~l~~La~~~ 33 (114)
+-.+.++.|++|.|..|+.+++-.|.+.+
T Consensus 43 L~~~VewaK~lp~F~~L~~~DQi~LLk~~ 71 (236)
T cd06948 43 LFSAVEWARNIPFFPDLQVTDQVALLRLS 71 (236)
T ss_pred HHHHHHHHHhCcCcccCCHHHHHHHHHHh
Confidence 44467899999999999999988776665
No 90
>TIGR01222 minC septum site-determining protein MinC. The minC protein assists in correct placement of the septum for cell division by inhibiting septum formation at other sites. Homologs from Deinocoocus, Synechocystis PCC 6803, and Helicobacter pylori do not hit the full length of the model and score between the trusted and noise cutoffs.
Probab=22.99 E-value=2.5e+02 Score=21.05 Aligned_cols=34 Identities=15% Similarity=0.317 Sum_probs=25.4
Q ss_pred ceeEecCCCEEEec-------CCCCCeEEEEEeeeEEEeCc
Q psy8804 34 RYERHQANDVLYYT-------GELSTSWYILLSGSVFIDGS 67 (114)
Q Consensus 34 ~~~~~~~G~~If~q-------Gd~~~~~yiIlsG~VkI~g~ 67 (114)
..+.+..|+.|+.+ |+-...--++-.|.|-|+|+
T Consensus 115 i~~~vRSGQ~i~~~~gDliilG~Vn~GAeViA~GnI~V~G~ 155 (217)
T TIGR01222 115 IKTPVRSGQQIYAKHGDLIVLGNVNAGAEVLADGNIHVYGK 155 (217)
T ss_pred EeCcccCCCEEEecCCCEEEECCCCCCCEEEeCCCEEEEEE
Confidence 33456789999998 45667777888888888874
No 91
>PRK06789 flagellar motor switch protein; Validated
Probab=22.65 E-value=1.6e+02 Score=18.88 Aligned_cols=43 Identities=7% Similarity=0.133 Sum_probs=36.6
Q ss_pred eeEecCCCEEEecCCCCCeEEEEEeeeEEEeCcccCCCCccee
Q psy8804 35 YERHQANDVLYYTGELSTSWYILLSGSVFIDGSMFLPQSRNFV 77 (114)
Q Consensus 35 ~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~g~~~~p~~~fg~ 77 (114)
..++.+|++|--+...++-.=+.+.|+.--.|..+.-++.||-
T Consensus 25 ll~L~~Gsvi~Ldk~~~epvdI~vNg~lia~GEvVvv~~~fGV 67 (74)
T PRK06789 25 LLHITKGTLYRLENSTKNTVRLMLENEEIGTGKILTKNGKMYV 67 (74)
T ss_pred HhcCCCCCEEEeCCcCCCCEEEEECCEEEeEEeEEEECCEEEE
Confidence 3467899999999999999999999999888888887778773
No 92
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=22.51 E-value=1.9e+02 Score=21.28 Aligned_cols=42 Identities=14% Similarity=0.224 Sum_probs=31.7
Q ss_pred HHHHHHhhcceeEecCCC---EEEecCCCCCeEEEEEeeeEEEeC
Q psy8804 25 VLRSLCRVVRYERHQAND---VLYYTGELSTSWYILLSGSVFIDG 66 (114)
Q Consensus 25 ~l~~La~~~~~~~~~~G~---~If~qGd~~~~~yiIlsG~VkI~g 66 (114)
+|+.|+....--.|.+.. .+++-.+|.-..-|--||++.+.|
T Consensus 18 dL~~la~~~~n~eY~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~tG 62 (174)
T cd04518 18 DLEKVAAELPNAEYNPDQFPGLVYRLEDPKIAALIFRSGKMVCTG 62 (174)
T ss_pred cHHHHHhhCCCcEECCCcCcEEEEEccCCcEEEEEECCCeEEEEc
Confidence 355565555556676643 889999998888888999999987
No 93
>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=22.20 E-value=1.1e+02 Score=21.26 Aligned_cols=29 Identities=10% Similarity=0.070 Sum_probs=23.4
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhh
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRV 32 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~ 32 (114)
++..+.++.+..|-|+.|+.++...|.+.
T Consensus 29 ~~~~~v~~~k~~p~f~~L~~~dk~~Llk~ 57 (203)
T PF00104_consen 29 ELRLIVDWAKSFPEFSELSMEDKIALLKS 57 (203)
T ss_dssp HHHHHHHHHHTSTTGGGS-HHHHHHHHHH
T ss_pred HHHHHHHHHHhCcCHHhhhhhhhhhHHhh
Confidence 45567889999999999999999887664
No 94
>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=22.20 E-value=1.2e+02 Score=23.21 Aligned_cols=30 Identities=10% Similarity=-0.159 Sum_probs=24.0
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVV 33 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~ 33 (114)
.+..+.++-|++|.|..|+-+++-.|.+.+
T Consensus 52 ~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~ 81 (241)
T cd07069 52 TLFSIVEWARSSIFFRELKVDDQMKLLQNC 81 (241)
T ss_pred HHHHHHHHHhhCCCcccCCHHHHHHHHHHH
Confidence 455678999999999999999887765443
No 95
>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=21.80 E-value=1.3e+02 Score=22.86 Aligned_cols=29 Identities=10% Similarity=-0.118 Sum_probs=22.7
Q ss_pred HHHHHHHhhCCCCCCCCCHHHHHHHHhhc
Q psy8804 5 LQIIYYGLHGLEALAPYRDSVLRSLCRVV 33 (114)
Q Consensus 5 ~e~i~~~Lr~v~lF~~L~~~~l~~La~~~ 33 (114)
+..+.++-|++|.|+.|+-+++-.|.+.+
T Consensus 32 L~~~V~WAK~iP~F~~L~~~DQi~LLk~~ 60 (222)
T cd07349 32 LVKTVAFMRNLPSFWQLPPQDQLLLLQNC 60 (222)
T ss_pred HHHHHHHHhcCCCcccCChHHHHHHHHHc
Confidence 44567899999999999999877654443
No 96
>PF07742 BTG: BTG family; InterPro: IPR002087 Anti-proliferative proteins have been shown to include mammalian and avian protein BTG1 (which appears to be involved in negative regulation of cell proliferation) and rat/mouse NGF-inducible protein PC3/TIS21 (BTG2) [, , ]. These proteins have from 158 to 363 amino acid residues, that are highly similar and include 3 conserved cysteine residues. BTG2 seems to have a signal sequence; while the other proteins may lack such a domain. The sequence of the N-terminal half of these proteins is well conserved.; PDB: 3DJU_B 3E9V_A 2Z15_D 2D5R_B 3DJN_B.
Probab=21.60 E-value=2.2e+02 Score=19.68 Aligned_cols=38 Identities=26% Similarity=0.163 Sum_probs=24.9
Q ss_pred CCCCHHHHHHHHhhcceeEecCCCEEEecCCCCCeEEEE
Q psy8804 19 APYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYIL 57 (114)
Q Consensus 19 ~~L~~~~l~~La~~~~~~~~~~G~~If~qGd~~~~~yiI 57 (114)
++++.+++..+.-.-......+|++-++-||.+ .+.+.
T Consensus 79 sgl~~~~l~~~LP~eltlWvDPgeVs~R~ge~g-~~~v~ 116 (118)
T PF07742_consen 79 SGLSYEDLRSLLPRELTLWVDPGEVSYRIGEKG-SICVL 116 (118)
T ss_dssp TT--HHHHHHHS-TTEEEEEETTEEEEEESTTS--EEEE
T ss_pred hCCCHHHHHHhcchhcEEEECCCEEEEEEcCCC-ceEEe
Confidence 467777776654444455779999999999999 55543
No 97
>PF14299 PP2: Phloem protein 2
Probab=21.46 E-value=1.1e+02 Score=21.75 Aligned_cols=39 Identities=18% Similarity=0.121 Sum_probs=30.8
Q ss_pred cCCCCcceeecccC---------ceeeeeecCccccceeeeeeecCCc
Q psy8804 69 FLPQSRNFVFNVFS---------PVFGLILNPSVSMAAKVSTLWDPGS 107 (114)
Q Consensus 69 ~~p~~~fg~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~ 107 (114)
..|..+|.++|.|. ...|.+|+|.-.|+|...+...+++
T Consensus 27 ~~~~srf~evAeL~~V~WLeI~G~i~~~~Lsp~t~Y~vy~v~kl~~~~ 74 (154)
T PF14299_consen 27 PLPDSRFSEVAELLQVCWLEIRGKINTRMLSPGTTYAVYFVFKLKDDA 74 (154)
T ss_pred cCCcccceeeeEEEEEEEEEEEEEEEceEcCCCCEEEEEEEEEecCCC
Confidence 34888898888877 4467889999999999888887763
No 98
>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=21.19 E-value=1.1e+02 Score=23.11 Aligned_cols=31 Identities=13% Similarity=-0.098 Sum_probs=24.3
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhcc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVVR 34 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~~ 34 (114)
.++.+.++-|++|.|..|+-+++-.|.+.+.
T Consensus 47 ~l~~iV~wAK~iPgF~~L~~~DQi~LLk~~~ 77 (226)
T cd06934 47 MIKQIIKFAKDLPYFRSLPIEDQISLLKGAT 77 (226)
T ss_pred HHHHHHHHhcCCcccccCCcchHHHHHHHhH
Confidence 3556789999999999999988777654443
No 99
>KOG4353|consensus
Probab=20.84 E-value=1.1e+02 Score=22.15 Aligned_cols=14 Identities=36% Similarity=0.660 Sum_probs=12.1
Q ss_pred EEEEEeeeEEEeCc
Q psy8804 54 WYILLSGSVFIDGS 67 (114)
Q Consensus 54 ~yiIlsG~VkI~g~ 67 (114)
+-|+.+|+|+.+|.
T Consensus 90 vLvvvsGtVkFdG~ 103 (139)
T KOG4353|consen 90 VLVVVSGTVKFDGN 103 (139)
T ss_pred EEEEEeeeEEEcCC
Confidence 67779999999985
No 100
>smart00835 Cupin_1 Cupin. This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant.
Probab=20.72 E-value=2.9e+02 Score=18.92 Aligned_cols=32 Identities=9% Similarity=-0.007 Sum_probs=22.8
Q ss_pred ceeEecCCCEEEecCCC-CCeEEEEEeeeEEEe
Q psy8804 34 RYERHQANDVLYYTGEL-STSWYILLSGSVFID 65 (114)
Q Consensus 34 ~~~~~~~G~~If~qGd~-~~~~yiIlsG~VkI~ 65 (114)
....+++|...-.+-.+ +..++.|++|+..+.
T Consensus 33 ~~~~i~pg~~~~~h~H~~~~e~~~Vl~G~~~~~ 65 (146)
T smart00835 33 ARVNLEPGGMLPPHYHPRATELLYVVRGEGRVG 65 (146)
T ss_pred EEEEecCCcCcCCeeCCCCCEEEEEEeCeEEEE
Confidence 44566788776555433 678999999998863
No 101
>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=20.69 E-value=1.2e+02 Score=22.39 Aligned_cols=30 Identities=10% Similarity=-0.158 Sum_probs=23.3
Q ss_pred hHHHHHHHhhCCCCCCCCCHHHHHHHHhhc
Q psy8804 4 DLQIIYYGLHGLEALAPYRDSVLRSLCRVV 33 (114)
Q Consensus 4 d~e~i~~~Lr~v~lF~~L~~~~l~~La~~~ 33 (114)
.+..+.++-|++|.|..|+.+++-.|.+.+
T Consensus 38 ~L~~~VewaK~ip~F~~L~~~DQi~LLk~~ 67 (206)
T cd06950 38 LLFMAVKWAKSIPAFSTLPFRDQLILLEES 67 (206)
T ss_pred HHHHHHHHHHhCCccccCCHHHHHHHHHHH
Confidence 445567899999999999999886654443
No 102
>PHA00672 hypothetical protein
Probab=20.58 E-value=1.2e+02 Score=22.04 Aligned_cols=33 Identities=18% Similarity=0.033 Sum_probs=26.1
Q ss_pred hcceeEecCCCEEEecCCCCCeEEEEEeeeEEEe
Q psy8804 32 VVRYERHQANDVLYYTGELSTSWYILLSGSVFID 65 (114)
Q Consensus 32 ~~~~~~~~~G~~If~qGd~~~~~yiIlsG~VkI~ 65 (114)
.++..+.|+|..|--.=-.-+.+ |+.+|.+.|+
T Consensus 48 YARei~IPkGt~LtG~~hkf~~~-ii~sG~itV~ 80 (152)
T PHA00672 48 YARTIRIPAGVALTGALIKVSTV-LIFSGHATVF 80 (152)
T ss_pred eEEEEeccCceeeeeeeeEeeEE-EEecccEEEE
Confidence 45666779999888777777888 9999998864
No 103
>KOG1448|consensus
Probab=20.18 E-value=1.3e+02 Score=24.69 Aligned_cols=53 Identities=19% Similarity=0.252 Sum_probs=38.9
Q ss_pred hCCCCCCCCCHHHHHH-HHhh-------cceeEecCCCEEEecCC--CCCeEEEEEeeeEEEe
Q psy8804 13 HGLEALAPYRDSVLRS-LCRV-------VRYERHQANDVLYYTGE--LSTSWYILLSGSVFID 65 (114)
Q Consensus 13 r~v~lF~~L~~~~l~~-La~~-------~~~~~~~~G~~If~qGd--~~~~~yiIlsG~VkI~ 65 (114)
+++++|.+.+..+|.+ +|.. ...++|.-|++-+.=|+ .+...|++.+|+=.++
T Consensus 2 ~~i~lf~g~shp~La~~I~~~lgi~l~~v~~kkf~nge~~v~i~esvR~~dV~iiqsgsg~in 64 (316)
T KOG1448|consen 2 KNIKLFSGDSHPELAERIAARLGIELGKVNLKKFSNGETSVQIGESVRGEDVYIIQSGSGPIN 64 (316)
T ss_pred CceEEEcCCCCHHHHHHHHHHhCCCcceeeeEEccCCcEEEecccccccCcEEEeccCCCcch
Confidence 4677899888888776 4433 35678888997776665 4788999998887653
No 104
>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=20.08 E-value=2.2e+02 Score=19.26 Aligned_cols=29 Identities=7% Similarity=0.110 Sum_probs=18.8
Q ss_pred EecCCCEE-EecCCCCCeEEEEEeeeEEEe
Q psy8804 37 RHQANDVL-YYTGELSTSWYILLSGSVFID 65 (114)
Q Consensus 37 ~~~~G~~I-f~qGd~~~~~yiIlsG~VkI~ 65 (114)
.+++|+-+ +.--...+-+|+|++|..++.
T Consensus 42 ~v~pg~~~~~~~H~~~dE~~~Vl~G~g~v~ 71 (127)
T COG0662 42 LVKPGEEISLHHHHHRDEHWYVLEGTGKVT 71 (127)
T ss_pred EECCCcccCcccccCcceEEEEEeeEEEEE
Confidence 34454443 333333589999999999975
Done!