Query 027649
Match_columns 220
No_of_seqs 131 out of 528
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 13:06:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027649.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027649hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13988 cell division topolog 100.0 1.1E-31 2.3E-36 209.5 11.0 94 85-191 2-95 (97)
2 PRK13991 cell division topolog 100.0 1.1E-29 2.4E-34 194.8 9.2 84 87-182 1-85 (87)
3 PRK13987 cell division topolog 100.0 9.6E-29 2.1E-33 190.9 8.2 86 87-185 1-90 (91)
4 TIGR01215 minE cell division t 100.0 2.5E-28 5.5E-33 184.3 8.8 81 87-180 1-81 (81)
5 PRK13989 cell division topolog 100.0 3.8E-28 8.2E-33 184.9 9.1 81 87-180 1-83 (84)
6 COG0851 MinE Septum formation 99.9 7E-27 1.5E-31 180.1 7.9 85 87-184 1-86 (88)
7 PRK00296 minE cell division to 99.9 1.8E-26 3.9E-31 176.2 8.8 82 87-181 1-83 (86)
8 PRK13990 cell division topolog 99.9 2.9E-24 6.3E-29 166.1 6.6 80 90-179 2-90 (90)
9 PF03776 MinE: Septum formatio 99.9 8.4E-25 1.8E-29 160.6 -2.2 68 111-180 1-70 (70)
10 TIGR03795 chp_BMA0021 conserve 71.4 8.5 0.00018 31.5 4.7 50 131-180 27-93 (114)
11 cd07072 NR_LBD_DHR38_like Liga 66.3 5.5 0.00012 35.3 2.8 42 110-152 140-182 (239)
12 cd06933 NR_LBD_VDR The ligand 64.9 6 0.00013 34.6 2.8 43 110-153 138-182 (238)
13 cd07071 NR_LBD_Nurr1 The ligan 64.5 5.8 0.00013 35.0 2.7 43 109-152 138-181 (238)
14 cd07348 NR_LBD_NGFI-B The liga 64.0 6 0.00013 35.0 2.7 32 121-152 149-181 (238)
15 cd06935 NR_LBD_TR The ligand b 57.9 9.4 0.0002 33.5 2.8 44 109-152 150-194 (243)
16 cd00491 4Oxalocrotonate_Tautom 56.3 29 0.00063 23.0 4.4 35 129-164 10-44 (58)
17 cd07349 NR_LBD_SHP The ligand 56.1 11 0.00024 32.9 2.9 42 110-153 130-174 (222)
18 cd06934 NR_LBD_PXR_like The li 55.9 11 0.00023 32.8 2.8 45 109-153 133-178 (226)
19 cd06939 NR_LBD_ROR_like The li 54.9 11 0.00025 33.1 2.8 45 109-153 145-190 (241)
20 PRK02220 4-oxalocrotonate taut 54.7 27 0.00057 23.7 4.1 37 128-165 10-46 (61)
21 cd06937 NR_LBD_RAR The ligand 54.4 11 0.00024 32.8 2.7 44 110-153 137-181 (231)
22 cd06940 NR_LBD_REV_ERB The lig 51.9 14 0.0003 31.1 2.8 45 109-153 110-155 (189)
23 PRK02289 4-oxalocrotonate taut 50.5 37 0.0008 23.5 4.3 36 128-164 10-45 (60)
24 cd06932 NR_LBD_PPAR The ligand 50.0 15 0.00032 32.8 2.7 44 110-153 163-207 (259)
25 TIGR00013 taut 4-oxalocrotonat 49.8 38 0.00081 23.0 4.2 36 129-165 11-46 (63)
26 COG1460 Uncharacterized protei 49.1 19 0.0004 29.7 3.0 31 117-151 83-113 (114)
27 cd06951 NR_LBD_Dax1_like The l 48.4 16 0.00035 31.7 2.7 45 109-153 132-176 (222)
28 PRK00745 4-oxalocrotonate taut 47.2 39 0.00085 22.9 4.0 36 129-165 11-46 (62)
29 cd01068 sensor_globin Globin d 45.6 77 0.0017 24.6 5.9 39 111-149 78-120 (147)
30 PF01361 Tautomerase: Tautomer 45.6 40 0.00087 22.8 3.8 35 129-164 10-44 (60)
31 cd06938 NR_LBD_EcR The ligand 44.7 20 0.00043 31.0 2.7 43 109-153 137-181 (231)
32 cd07073 NR_LBD_AR Ligand bindi 44.7 19 0.00041 32.1 2.6 32 121-152 139-173 (246)
33 cd07350 NR_LBD_Dax1 The ligand 44.7 21 0.00045 31.5 2.8 45 109-153 141-186 (232)
34 cd06941 NR_LBD_DmE78_like The 44.5 21 0.00045 29.8 2.7 44 109-152 100-144 (195)
35 cd06947 NR_LBD_GR_Like Ligand 42.6 21 0.00045 31.8 2.5 41 110-152 129-173 (246)
36 PRK00341 hypothetical protein; 42.4 34 0.00075 26.4 3.4 40 136-177 28-67 (91)
37 cd07076 NR_LBD_GR Ligand bindi 41.4 22 0.00049 31.9 2.6 33 121-153 139-174 (247)
38 PF04965 GPW_gp25: Gene 25-lik 40.4 73 0.0016 23.5 4.8 33 131-166 42-75 (99)
39 cd06945 NR_LBD_Nurr1_like The 39.6 24 0.00052 31.0 2.4 42 112-153 141-183 (239)
40 PF09581 Spore_III_AF: Stage I 37.6 2.3E+02 0.0049 23.4 7.8 66 115-181 65-132 (188)
41 PF03780 Asp23: Asp23 family; 37.3 44 0.00095 25.0 3.2 32 131-163 74-105 (108)
42 cd06952 NR_LBD_TR2_like The li 36.9 33 0.00072 29.2 2.8 43 110-152 128-171 (222)
43 cd07069 NR_LBD_Lrh-1 The ligan 35.6 33 0.00071 30.2 2.7 44 110-153 144-188 (241)
44 PF10850 DUF2653: Protein of u 34.3 56 0.0012 26.0 3.5 37 140-179 8-48 (91)
45 cd07075 NR_LBD_MR Ligand bindi 34.1 38 0.00082 30.5 2.8 31 122-152 140-173 (248)
46 PRK01964 4-oxalocrotonate taut 34.0 82 0.0018 21.7 4.0 37 129-166 11-47 (64)
47 cd06950 NR_LBD_Tlx_PNR_like Th 33.8 41 0.00089 28.6 2.9 44 109-152 124-168 (206)
48 PF06138 Chordopox_E11: Chordo 31.4 49 0.0011 27.9 2.8 47 117-164 13-61 (130)
49 PRK05697 flagellar basal body- 29.7 45 0.00098 27.5 2.4 39 115-153 80-120 (137)
50 PHA03001 putative virion core 28.8 79 0.0017 26.7 3.7 45 118-163 14-59 (132)
51 PRK11198 LysM domain/BON super 27.5 1E+02 0.0022 25.3 4.1 50 87-163 1-50 (147)
52 PF12143 PPO1_KFDV: Protein of 26.1 1.2E+02 0.0027 25.1 4.3 18 194-217 34-51 (130)
53 cd06954 NR_LBD_LXR The ligand 25.9 57 0.0012 28.1 2.5 29 125-153 158-187 (236)
54 PRK14981 DNA-directed RNA poly 25.6 79 0.0017 25.2 3.0 30 117-150 82-111 (112)
55 PRK07021 fliL flagellar basal 25.1 67 0.0015 26.6 2.7 39 114-152 104-144 (162)
56 PF11113 Phage_head_chap: Head 24.6 79 0.0017 23.2 2.6 20 194-220 19-38 (56)
57 PRK00907 hypothetical protein; 23.5 1.3E+02 0.0027 23.6 3.7 39 136-176 28-67 (92)
58 COG3413 Predicted DNA binding 22.7 1E+02 0.0022 26.3 3.4 57 72-151 155-212 (215)
59 cd07074 NR_LBD_PR Ligand bindi 21.5 82 0.0018 28.4 2.7 27 126-152 146-173 (248)
60 PF08776 VASP_tetra: VASP tetr 21.5 62 0.0013 22.3 1.4 15 135-149 20-34 (40)
61 PF14552 Tautomerase_2: Tautom 20.0 1.6E+02 0.0034 22.3 3.6 39 127-166 37-75 (82)
No 1
>PRK13988 cell division topological specificity factor MinE; Provisional
Probab=99.97 E-value=1.1e-31 Score=209.53 Aligned_cols=94 Identities=24% Similarity=0.433 Sum_probs=86.0
Q ss_pred HhHHHHHHHhhhhhhcCCCCCCCCCCcHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhccccccccCCcEEEEEee
Q 027649 85 INMSFFDRLNLAWKIVFPSPTTRRNSNARIAKQRLQMILFSDRCAVSDEAKRKIVNNIVHALSDFVEIESQDKVQLNVST 164 (220)
Q Consensus 85 ~~M~ffd~l~~aw~i~Fp~~~~kkksSa~IAKeRLKlILahDR~~~SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~ 164 (220)
.+|+||++||+ ++++|+++||+|||+||+|||++++|++|++||+||++||+|||+||+++ |+|++++
T Consensus 2 ~~~~~l~~lf~-----------~k~~Sa~~AK~RLk~iL~~dR~~~sp~~l~~mk~dIl~VIskYv~Id~~~-v~V~l~~ 69 (97)
T PRK13988 2 TLRDLLEKLFG-----------RQPASASTARERLQLVLAHDRADLSPELLEQMRKEILEVVARYVEIDPEE-GEVSLET 69 (97)
T ss_pred cHHHHHHHHhc-----------CCCCcHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHeeeCccc-eEEEEEe
Confidence 46899999985 56789999999999999999999999999999999999999999999996 9999999
Q ss_pred CCCCceEEEEEEeccCcCCCccccCCc
Q 027649 165 DTDLGTIYSVTVPVRRVKPEYLDSYDV 191 (220)
Q Consensus 165 d~d~~tvL~anIPVrrvK~~~~~~~e~ 191 (220)
+++. ++|+|||||+++|++++.+++.
T Consensus 70 ~~~~-~~L~~nIPi~~v~~~~~~~~~~ 95 (97)
T PRK13988 70 EDRM-TALVANLPIRRVKRGEIKFKES 95 (97)
T ss_pred CCCc-eEEEEEeeeeccccCCCCcCcc
Confidence 8874 7999999999999998876554
No 2
>PRK13991 cell division topological specificity factor MinE; Provisional
Probab=99.96 E-value=1.1e-29 Score=194.75 Aligned_cols=84 Identities=26% Similarity=0.495 Sum_probs=77.8
Q ss_pred HHHHHHHhhhhhhcCCCCCCCCCCcHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhccccc-cccCCcEEEEEeeC
Q 027649 87 MSFFDRLNLAWKIVFPSPTTRRNSNARIAKQRLQMILFSDRCAVSDEAKRKIVNNIVHALSDFVE-IESQDKVQLNVSTD 165 (220)
Q Consensus 87 M~ffd~l~~aw~i~Fp~~~~kkksSa~IAKeRLKlILahDR~~~SPd~Le~Lk~DILeVISKYVe-ID~e~kVeV~l~~d 165 (220)
|+||++||+ +++++||++||+|||+||+|||++++|++|++||+||++||+|||+ ||+++ |+|+++++
T Consensus 1 M~~l~~~f~----------~k~~~Sa~~AKeRLqliLahdR~~~~p~~l~~lk~eil~VIsKYv~~Id~~~-i~V~l~~~ 69 (87)
T PRK13991 1 MSFLDGLFG----------RKRDSSSELAKQRLLTVLVHDRVKLTPEMMEQMKADLAEVIKRYVPAIDAEA-IEVTLSRG 69 (87)
T ss_pred CChHHHhhc----------CCCCCcHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHhcccCccc-eEEEEEeC
Confidence 799999986 2456899999999999999999999999999999999999999999 99996 99999998
Q ss_pred CCCceEEEEEEeccCcC
Q 027649 166 TDLGTIYSVTVPVRRVK 182 (220)
Q Consensus 166 ~d~~tvL~anIPVrrvK 182 (220)
++ .++|++|||+++++
T Consensus 70 ~~-~~~Le~NIpl~~~~ 85 (87)
T PRK13991 70 EA-HDHLKADIPLRRTT 85 (87)
T ss_pred CC-ceEEEEEeEeeccc
Confidence 77 48999999999998
No 3
>PRK13987 cell division topological specificity factor MinE; Provisional
Probab=99.95 E-value=9.6e-29 Score=190.94 Aligned_cols=86 Identities=24% Similarity=0.575 Sum_probs=76.5
Q ss_pred HHHHHHHhhhhhhcCCCCCCCCCCcHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhccccccccCCcEEEEEeeCC
Q 027649 87 MSFFDRLNLAWKIVFPSPTTRRNSNARIAKQRLQMILFSDRCAVSDEAKRKIVNNIVHALSDFVEIESQDKVQLNVSTDT 166 (220)
Q Consensus 87 M~ffd~l~~aw~i~Fp~~~~kkksSa~IAKeRLKlILahDR~~~SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~d~ 166 (220)
|+||++|+ ++++||++||||||+||+|||++++|++|++||+||++||+|||+||+++ |+|++++++
T Consensus 1 M~~~~~f~------------~k~~Sa~~AKeRLq~iLa~dR~~~sp~~l~~lk~eIl~VI~kYv~Id~~~-v~i~l~~~~ 67 (91)
T PRK13987 1 MDLFKFFS------------KKPTSKDVAKERLKLILIHDRGDISPDVLEMIKEDILKVISKYVEIDNED-VDIKMTKSE 67 (91)
T ss_pred CchhHhhc------------CCCCcHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHheeeCccc-eEEEEEeCC
Confidence 67888653 35679999999999999999999999999999999999999999999996 999999865
Q ss_pred CC----ceEEEEEEeccCcCCCc
Q 027649 167 DL----GTIYSVTVPVRRVKPEY 185 (220)
Q Consensus 167 d~----~tvL~anIPVrrvK~~~ 185 (220)
+. .++|.||||++++|+.+
T Consensus 68 ~~~~~~~~aL~anIPi~~~~~~~ 90 (91)
T PRK13987 68 EIDEGMSPALIANIPIKKIKKKI 90 (91)
T ss_pred cccCCCcceEEEEccchHhhhcc
Confidence 42 26899999999999865
No 4
>TIGR01215 minE cell division topological specificity factor MinE. This protein is involved in the process of cell division. This protein prevents the proteins MinC and MinD to inhibit cell division at internal sites, but allows inhibiton at polar sites. This allows for correct cell division at the proper sites.
Probab=99.95 E-value=2.5e-28 Score=184.28 Aligned_cols=81 Identities=25% Similarity=0.516 Sum_probs=74.5
Q ss_pred HHHHHHHhhhhhhcCCCCCCCCCCcHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhccccccccCCcEEEEEeeCC
Q 027649 87 MSFFDRLNLAWKIVFPSPTTRRNSNARIAKQRLQMILFSDRCAVSDEAKRKIVNNIVHALSDFVEIESQDKVQLNVSTDT 166 (220)
Q Consensus 87 M~ffd~l~~aw~i~Fp~~~~kkksSa~IAKeRLKlILahDR~~~SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~d~ 166 (220)
|+||++|++ ++++||++||+|||+||+|||++++|+++++||+||++||+||++||+++ |+|++++++
T Consensus 1 M~l~~~f~~-----------~k~~Sa~~AKeRLq~iL~~dR~~~~p~~l~~mk~dil~VIskY~~id~~~-v~v~l~~~~ 68 (81)
T TIGR01215 1 MSLLEFFKS-----------RKKNSAEVAKDRLKLILAHDRAQLAPEYLEELRKEILEVISKYVEIDPEM-VEVSLESQG 68 (81)
T ss_pred CchHHHhhc-----------CCCCcHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHheecchHh-EEEEEEeCC
Confidence 789998874 45589999999999999999999999999999999999999999999995 999999987
Q ss_pred CCceEEEEEEeccC
Q 027649 167 DLGTIYSVTVPVRR 180 (220)
Q Consensus 167 d~~tvL~anIPVrr 180 (220)
+. ++|++|||+++
T Consensus 69 ~~-~~L~~nI~l~~ 81 (81)
T TIGR01215 69 DM-SVLEANITLPE 81 (81)
T ss_pred Ce-eEEEEEeEcCC
Confidence 74 89999999974
No 5
>PRK13989 cell division topological specificity factor MinE; Provisional
Probab=99.95 E-value=3.8e-28 Score=184.86 Aligned_cols=81 Identities=21% Similarity=0.393 Sum_probs=74.8
Q ss_pred HHHHHHHhhhhhhcCCCCCCCCCCcHHHHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHhccccccccCCcEEEEEee
Q 027649 87 MSFFDRLNLAWKIVFPSPTTRRNSNARIAKQRLQMILFSDRCA--VSDEAKRKIVNNIVHALSDFVEIESQDKVQLNVST 164 (220)
Q Consensus 87 M~ffd~l~~aw~i~Fp~~~~kkksSa~IAKeRLKlILahDR~~--~SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~ 164 (220)
|+||++|++ ++++||++||+|||+||+|||++ ++|+++++||+||++||+|||+||+++ |+|++++
T Consensus 1 M~l~~~f~~-----------~k~~Sa~vAKeRLqiiLa~dR~~~~~~p~~l~~lk~dil~VIsKYv~Id~~~-v~i~l~~ 68 (84)
T PRK13989 1 MSILSFLLG-----------EKKKTASVAKERLQIIIAHERVGGRQPPDYLPALQKELVAVISKYVKISPDD-IRVSLER 68 (84)
T ss_pred CchHHHhhc-----------CCCCcHHHHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHheeeCccc-eEEEEEe
Confidence 799999885 46789999999999999999987 899999999999999999999999996 9999999
Q ss_pred CCCCceEEEEEEeccC
Q 027649 165 DTDLGTIYSVTVPVRR 180 (220)
Q Consensus 165 d~d~~tvL~anIPVrr 180 (220)
+++ .++|++||+++.
T Consensus 69 ~~~-~~~Le~nI~Lp~ 83 (84)
T PRK13989 69 QDN-LEVLEVKIELPQ 83 (84)
T ss_pred CCC-eEEEEEEeECCC
Confidence 887 489999999874
No 6
>COG0851 MinE Septum formation topological specificity factor [Cell division and chromosome partitioning]
Probab=99.94 E-value=7e-27 Score=180.10 Aligned_cols=85 Identities=26% Similarity=0.477 Sum_probs=77.5
Q ss_pred HHHHHHHhhhhhhcCCCCCCCCCCcHHHHHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHHhccccccccCCcEEEEEeeC
Q 027649 87 MSFFDRLNLAWKIVFPSPTTRRNSNARIAKQRLQMILFSDR-CAVSDEAKRKIVNNIVHALSDFVEIESQDKVQLNVSTD 165 (220)
Q Consensus 87 M~ffd~l~~aw~i~Fp~~~~kkksSa~IAKeRLKlILahDR-~~~SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~d 165 (220)
|++|++|++ ++++||++||+|||+|||||| .+..|++++.||+||++||+|||+||++. |+|+++++
T Consensus 1 Msl~dff~~-----------r~~~Sa~~AkeRLQiilA~eR~~~~~pd~l~~Lr~eIl~VI~KYV~id~d~-v~v~~e~~ 68 (88)
T COG0851 1 MSLFDFFFS-----------RKKNSAETAKERLQLILAHERAAGLQPDYLEQLRKEILEVISKYVQIDPDK-VEVSLERD 68 (88)
T ss_pred CcHHHHHHh-----------cCCCcHHHHHHHHHHhhhhhhhcCCCcchHHHHHHHHHHHHHHHheeCccc-EEEEEcCC
Confidence 799999985 455999999999999999999 67799999999999999999999999995 99999998
Q ss_pred CCCceEEEEEEeccCcCCC
Q 027649 166 TDLGTIYSVTVPVRRVKPE 184 (220)
Q Consensus 166 ~d~~tvL~anIPVrrvK~~ 184 (220)
++ .++|++|||+++.+..
T Consensus 69 ~~-~s~Le~ni~lp~~~~~ 86 (88)
T COG0851 69 DR-ISILELNITLPEVSER 86 (88)
T ss_pred CC-eEEEEEeccccccccc
Confidence 86 4899999999988754
No 7
>PRK00296 minE cell division topological specificity factor MinE; Reviewed
Probab=99.93 E-value=1.8e-26 Score=176.19 Aligned_cols=82 Identities=24% Similarity=0.482 Sum_probs=74.1
Q ss_pred HHHHHHHhhhhhhcCCCCCCCCCCcHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhccccccccCCcEEEEEeeC
Q 027649 87 MSFFDRLNLAWKIVFPSPTTRRNSNARIAKQRLQMILFSDRCAV-SDEAKRKIVNNIVHALSDFVEIESQDKVQLNVSTD 165 (220)
Q Consensus 87 M~ffd~l~~aw~i~Fp~~~~kkksSa~IAKeRLKlILahDR~~~-SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~d 165 (220)
|+||++|++ ++++|+++||+|||+||+|||+++ +|+++++||+||++||+||++||+++ |+|+++++
T Consensus 1 M~l~~~f~~-----------kk~~Sa~~AKeRLq~iL~~dR~~~~~p~~l~~lk~dIl~VIsKY~~Id~~~-v~i~l~~~ 68 (86)
T PRK00296 1 MSLLDFFRS-----------RKKSTANVAKERLQIIVAHERSSRGEPDYLPQLRKEILEVIAKYVQIDPDK-VSVQLDKD 68 (86)
T ss_pred CchHHhhcc-----------CCCCcHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHheecChhh-EEEEEEeC
Confidence 789997763 446899999999999999999998 59999999999999999999999996 99999988
Q ss_pred CCCceEEEEEEeccCc
Q 027649 166 TDLGTIYSVTVPVRRV 181 (220)
Q Consensus 166 ~d~~tvL~anIPVrrv 181 (220)
++. ++|++||+++.-
T Consensus 69 ~~~-~~Le~nI~lp~~ 83 (86)
T PRK00296 69 GDI-STLELNVTLPEA 83 (86)
T ss_pred CCe-EEEEEEEEcCCc
Confidence 874 799999999873
No 8
>PRK13990 cell division topological specificity factor MinE; Provisional
Probab=99.90 E-value=2.9e-24 Score=166.06 Aligned_cols=80 Identities=20% Similarity=0.435 Sum_probs=68.4
Q ss_pred HHHHhhhhhhcCCCCCCCCCCcHHHHHHHHHHHHHhhCCC-------CCHHHHHHHHHHHHHHhccccccccCC--cEEE
Q 027649 90 FDRLNLAWKIVFPSPTTRRNSNARIAKQRLQMILFSDRCA-------VSDEAKRKIVNNIVHALSDFVEIESQD--KVQL 160 (220)
Q Consensus 90 fd~l~~aw~i~Fp~~~~kkksSa~IAKeRLKlILahDR~~-------~SPd~Le~Lk~DILeVISKYVeID~e~--kVeV 160 (220)
|++||+. | ++++||++||+|||+||+|||++ ++|++|++||+||++||+|||+||+++ +|+|
T Consensus 2 l~~lf~~----~-----~k~~Sa~vAKeRLqiiLaheR~~~~~~~~~~~pd~L~~lk~eIl~VI~KYv~Id~~~i~dV~v 72 (90)
T PRK13990 2 LAKLFGL----S-----KKQQSASVAKERLQIIVAHQRSELHPRSSKISSHLLAELKDEIIEVVKKYVALSEENIRDIDL 72 (90)
T ss_pred hhHhhCc----c-----cCCCcHHHHHHHhheeeeeecccCCcccccCCHHHHHHHHHHHHHHHHHheecChhccceEEE
Confidence 6677761 1 45689999999999999999986 467999999999999999999999996 2588
Q ss_pred EEeeCCCCceEEEEEEecc
Q 027649 161 NVSTDTDLGTIYSVTVPVR 179 (220)
Q Consensus 161 ~l~~d~d~~tvL~anIPVr 179 (220)
+++++++ .++|++|||+.
T Consensus 73 ~le~~~~-~~~LevnI~~~ 90 (90)
T PRK13990 73 KVEDSSK-NSTIEVNIPFN 90 (90)
T ss_pred EEecCCC-eEEEEEeeecC
Confidence 9988777 47999999974
No 9
>PF03776 MinE: Septum formation topological specificity factor MinE; InterPro: IPR005527 Cytokinesis needs to be regulated spatially in order to ensure that it occurs between the daughter genomes. In prokaryotes such as Escherichia coli, cytokinesis is initiated by FtsZ, a tubulin-like protein that assembles into a ring structure at the cell centre called the Z ring. A fundamental problem in prokaryotic cell biology is to understand how the midcell division site is identified. Two major negative regulatory systems are known to be involved in preventing Z-ring assembly at all sites except the midcell. One of these systems, called nucleoid occlusion, blocks Z-ring assembly in the area occupied by an unsegregated nucleoid until a critical stage in chromosome replication or segregation is reached. The other system consists of three proteins, MinC, MinD and MinE, which prevent assembly of Z rings in regions of the cell not covered by the nucleoid, such as the cell poles. MinC is an inhibitor of FtsZ polymerisation, resulting in the inhibition of Z ring assembly in the cell; MinD greatly enhances the inhibitory effects of MinC in vivo; and MinE antagonizes the effects of MinC and MinD []. MinE is a small bifunctional protein. The amino terminus of MinE is required to interact with MinD, while the carboxyl terminus is required for `topological specificity' - that is, the ability of MinE to antagonise MinCD inhibition of Z rings at the midcell position but not at the poles.; GO: 0032955 regulation of barrier septum formation, 0051301 cell division; PDB: 2KXO_A 3MCD_B 3KU7_A 3R9J_C 3R9I_E 1EV0_B.
Probab=99.88 E-value=8.4e-25 Score=160.62 Aligned_cols=68 Identities=32% Similarity=0.595 Sum_probs=58.9
Q ss_pred cHHHHHHHHHHHHHhhCCCCCH--HHHHHHHHHHHHHhccccccccCCcEEEEEeeCCCCceEEEEEEeccC
Q 027649 111 NARIAKQRLQMILFSDRCAVSD--EAKRKIVNNIVHALSDFVEIESQDKVQLNVSTDTDLGTIYSVTVPVRR 180 (220)
Q Consensus 111 Sa~IAKeRLKlILahDR~~~SP--d~Le~Lk~DILeVISKYVeID~e~kVeV~l~~d~d~~tvL~anIPVrr 180 (220)
||++||+|||+||+|||++++| ++|++||+||++||+||++|++++ |+|+++++++ .++|++|||+++
T Consensus 1 Sa~iAKeRLk~iL~~dR~~~~~~~~~l~~lk~eil~viskYv~i~~~~-v~v~l~~~~~-~~~L~~nIpl~~ 70 (70)
T PF03776_consen 1 SADIAKERLKLILAHDRGGLSPQPDYLEQLKKEILEVISKYVEIDEED-VEVQLERDDD-MSVLEANIPLPR 70 (70)
T ss_dssp HCHCSSCEEEEEEEEECCSC-CTTSSHHHHHHHHHHHHHHHS---CCC-EEEEEEECTT-EEEEEEEEEE--
T ss_pred ChHHHHHHHHHHHHHHccCCCCcHHHHHHHHHHHHHHHHhheecCccc-EEEEEEECCC-ceEEEEEEEcCC
Confidence 6899999999999999999998 999999999999999999999996 9999998877 589999999985
No 10
>TIGR03795 chp_BMA0021 conserved hypothetical protein, BMA_0021 family. Members of this protein family are found sparsely, mostly in members of the genus Burkholderia. Members often occur as tandem homologous genes, such as BMA_0021 and BMA_0022 in Burkholderia mallei ATCC 23344. The genes regularly are encoded near the so-called docking protein of TOMM (thiazole/oxazole-modified microcins) biosynthetic clusters, suggesting a role in bacteriocin biosynthesis. The function is unknown.
Probab=71.36 E-value=8.5 Score=31.51 Aligned_cols=50 Identities=18% Similarity=0.260 Sum_probs=38.6
Q ss_pred CHHHHHHHHHHHHHHhccccccccCCcEEEEEeeCCCC-----------------ceEEEEEEeccC
Q 027649 131 SDEAKRKIVNNIVHALSDFVEIESQDKVQLNVSTDTDL-----------------GTIYSVTVPVRR 180 (220)
Q Consensus 131 SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~d~d~-----------------~tvL~anIPVrr 180 (220)
+|++.++|.+|...+|++|+......+|+|++..+... ...+++.||..-
T Consensus 27 DpaFr~eLl~DPk~~L~e~Fgy~~P~~v~l~v~E~~~d~~~~~~~~~~~~~w~~~~n~i~l~iP~aP 93 (114)
T TIGR03795 27 SPEFKDELLADPVDALEKYFDYRCPWILDLKVTENSSDWTPYGWGAWTQGRWNLPVNRLTLGIPPAP 93 (114)
T ss_pred CHHHHHHHHHCHHHHHHHHhCCCCCCceEEEEEecCCCCCccccccccccCCccccCeEEEEcCCCC
Confidence 78999999999999999999987666788887654432 016888888643
No 11
>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=66.27 E-value=5.5 Score=35.29 Aligned_cols=42 Identities=17% Similarity=0.244 Sum_probs=33.0
Q ss_pred CcHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhcccccc
Q 027649 110 SNARIAKQRLQMILFSDRCAV-SDEAKRKIVNNIVHALSDFVEI 152 (220)
Q Consensus 110 sSa~IAKeRLKlILahDR~~~-SPd~Le~Lk~DILeVISKYVeI 152 (220)
...+.|==+ -++|..||.|+ .++.++++|+.+++++..|+.-
T Consensus 140 d~~E~a~Lk-AivLf~dr~gL~~~~~Ve~lQe~~~~aL~~yi~~ 182 (239)
T cd07072 140 DISAFACLC-ALTLITERHGLKEPHKVEQLQMKIISSLRDHVTY 182 (239)
T ss_pred CHHHHHHHH-HHHHhCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 445555333 25566899997 8999999999999999999874
No 12
>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=64.91 E-value=6 Score=34.62 Aligned_cols=43 Identities=14% Similarity=0.230 Sum_probs=31.9
Q ss_pred CcHHHHHHHHHHHHHh-hCCCC-CHHHHHHHHHHHHHHhccccccc
Q 027649 110 SNARIAKQRLQMILFS-DRCAV-SDEAKRKIVNNIVHALSDFVEIE 153 (220)
Q Consensus 110 sSa~IAKeRLKlILah-DR~~~-SPd~Le~Lk~DILeVISKYVeID 153 (220)
...+.|==. -++|.+ ||.|+ +++.++++|+.+++++..|++..
T Consensus 138 d~~E~alLk-AivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~ 182 (238)
T cd06933 138 HEEEHVLLM-AICILSPDRPGVQDHALIEAIQDRLSDTLQTYIRCR 182 (238)
T ss_pred CHHHHHHHH-HHHHHCCCCCCCcchHHHHHHHHHHHHHHHHHHHhc
Confidence 345555322 234444 99997 79999999999999999999743
No 13
>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=64.48 E-value=5.8 Score=35.03 Aligned_cols=43 Identities=16% Similarity=0.271 Sum_probs=34.2
Q ss_pred CCcHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhcccccc
Q 027649 109 NSNARIAKQRLQMILFSDRCAV-SDEAKRKIVNNIVHALSDFVEI 152 (220)
Q Consensus 109 ksSa~IAKeRLKlILahDR~~~-SPd~Le~Lk~DILeVISKYVeI 152 (220)
-...+.|==. -++|..||.|+ .++.++++|+.+..++..|+.-
T Consensus 138 ld~~E~alLk-AIvLf~D~~gL~~~~~Ve~lQe~~~~aL~~yi~~ 181 (238)
T cd07071 138 IDISAFSCIA-ALAMVTERHGLKEPKRVEELQNKIVNCLKDHVTF 181 (238)
T ss_pred CCHHHHHHHH-HHHHcCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3456776422 35667899998 7999999999999999999974
No 14
>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=64.03 E-value=6 Score=35.02 Aligned_cols=32 Identities=16% Similarity=0.407 Sum_probs=28.2
Q ss_pred HHHHhhCCCC-CHHHHHHHHHHHHHHhcccccc
Q 027649 121 MILFSDRCAV-SDEAKRKIVNNIVHALSDFVEI 152 (220)
Q Consensus 121 lILahDR~~~-SPd~Le~Lk~DILeVISKYVeI 152 (220)
++|..||.|+ .++.++++|+.+++++..|+.-
T Consensus 149 IvLf~Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~ 181 (238)
T cd07348 149 LVIITDRHGLKEPKRVEELQNRLISCLKEHVSG 181 (238)
T ss_pred HHHcCCCcCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 4556899997 7999999999999999999974
No 15
>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=57.91 E-value=9.4 Score=33.51 Aligned_cols=44 Identities=16% Similarity=0.290 Sum_probs=32.4
Q ss_pred CCcHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhcccccc
Q 027649 109 NSNARIAKQRLQMILFSDRCAV-SDEAKRKIVNNIVHALSDFVEI 152 (220)
Q Consensus 109 ksSa~IAKeRLKlILahDR~~~-SPd~Le~Lk~DILeVISKYVeI 152 (220)
-...+.|==.-=+++-.||.|+ .++.++++|+.+++++..|+.-
T Consensus 150 ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~ 194 (243)
T cd06935 150 LDDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAFEHYINY 194 (243)
T ss_pred CCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 3456666522223333499998 7999999999999999999873
No 16
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=56.26 E-value=29 Score=23.03 Aligned_cols=35 Identities=17% Similarity=0.398 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHHHHhccccccccCCcEEEEEee
Q 027649 129 AVSDEAKRKIVNNIVHALSDFVEIESQDKVQLNVST 164 (220)
Q Consensus 129 ~~SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~ 164 (220)
+.+++...+|-++|.+++.+++.+..++ +.|.+..
T Consensus 10 grt~eqk~~l~~~i~~~l~~~~g~~~~~-v~V~i~e 44 (58)
T cd00491 10 GRTDEQKRELIERVTEAVSEILGAPEAT-IVVIIDE 44 (58)
T ss_pred CCCHHHHHHHHHHHHHHHHHHhCcCccc-EEEEEEE
Confidence 4579999999999999999999999996 8888865
No 17
>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=56.11 E-value=11 Score=32.87 Aligned_cols=42 Identities=24% Similarity=0.252 Sum_probs=32.6
Q ss_pred CcHHHHHHHHH-HHHHh-hCCCC-CHHHHHHHHHHHHHHhccccccc
Q 027649 110 SNARIAKQRLQ-MILFS-DRCAV-SDEAKRKIVNNIVHALSDFVEIE 153 (220)
Q Consensus 110 sSa~IAKeRLK-lILah-DR~~~-SPd~Le~Lk~DILeVISKYVeID 153 (220)
...+.|= || +||.+ ||.++ .++.++.+++.+++++..|+.-.
T Consensus 130 d~~Eya~--LkaivLf~pd~~gl~~~~~V~~lqe~~~~aL~~~~~~~ 174 (222)
T cd07349 130 SPKEYAY--LKGTILFNPDVPGLTASSHVGHLQQEAQWALCEVLEPL 174 (222)
T ss_pred CHHHHHH--HHHHHHcCCCcccCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566664 44 45554 99988 78999999999999999998643
No 18
>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=55.91 E-value=11 Score=32.84 Aligned_cols=45 Identities=9% Similarity=0.202 Sum_probs=32.5
Q ss_pred CCcHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhccccccc
Q 027649 109 NSNARIAKQRLQMILFSDRCAV-SDEAKRKIVNNIVHALSDFVEIE 153 (220)
Q Consensus 109 ksSa~IAKeRLKlILahDR~~~-SPd~Le~Lk~DILeVISKYVeID 153 (220)
-...+.|==+==+++-.||.|+ .++.++++|+.+++++..|+.-.
T Consensus 133 ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~ 178 (226)
T cd06934 133 LQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQEKMALTLKSYIDSK 178 (226)
T ss_pred CCHHHHHHHHHHHHhCCCCcCCcChHHHHHHHHHHHHHHHHHHHHc
Confidence 3456666322223333499998 78999999999999999998743
No 19
>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=54.87 E-value=11 Score=33.09 Aligned_cols=45 Identities=18% Similarity=0.201 Sum_probs=35.0
Q ss_pred CCcHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhccccccc
Q 027649 109 NSNARIAKQRLQMILFSDRCAV-SDEAKRKIVNNIVHALSDFVEIE 153 (220)
Q Consensus 109 ksSa~IAKeRLKlILahDR~~~-SPd~Le~Lk~DILeVISKYVeID 153 (220)
-...+.|==+-=+++-.||.|+ .++.++++++.++.++..|+.-.
T Consensus 145 ld~~E~all~AivL~~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~ 190 (241)
T cd06939 145 LTEDEIALFSALVLISADRPGLQEKRKVEKLQQKIELALRHVLQKN 190 (241)
T ss_pred CCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3556776655444445699998 79999999999999999998743
No 20
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=54.65 E-value=27 Score=23.69 Aligned_cols=37 Identities=11% Similarity=0.217 Sum_probs=32.9
Q ss_pred CCCCHHHHHHHHHHHHHHhccccccccCCcEEEEEeeC
Q 027649 128 CAVSDEAKRKIVNNIVHALSDFVEIESQDKVQLNVSTD 165 (220)
Q Consensus 128 ~~~SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~d 165 (220)
.|.|++...+|-+.|-+++++.+.+.+++ |.|.+..-
T Consensus 10 ~Grs~eqk~~l~~~it~~l~~~~~~p~~~-v~V~i~e~ 46 (61)
T PRK02220 10 EGRTEEQLKALVKDVTAAVSKNTGAPAEH-IHVIINEM 46 (61)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHhCcChhh-EEEEEEEe
Confidence 35699999999999999999999999997 99888753
No 21
>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=54.39 E-value=11 Score=32.82 Aligned_cols=44 Identities=14% Similarity=0.232 Sum_probs=33.8
Q ss_pred CcHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhccccccc
Q 027649 110 SNARIAKQRLQMILFSDRCAV-SDEAKRKIVNNIVHALSDFVEIE 153 (220)
Q Consensus 110 sSa~IAKeRLKlILahDR~~~-SPd~Le~Lk~DILeVISKYVeID 153 (220)
...+.|==+-=+++-.||.++ .++.++++++.++.++..|+...
T Consensus 137 d~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~ 181 (231)
T cd06937 137 DDTEIGLLSAICLICGDRQDLEEPDRVEKLQEPLLEALKIYARKR 181 (231)
T ss_pred CHHHHHHHHHHHHcCCCCccCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 445666544434445699997 79999999999999999999854
No 22
>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=51.86 E-value=14 Score=31.12 Aligned_cols=45 Identities=11% Similarity=0.215 Sum_probs=35.4
Q ss_pred CCcHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhccccccc
Q 027649 109 NSNARIAKQRLQMILFSDRCAV-SDEAKRKIVNNIVHALSDFVEIE 153 (220)
Q Consensus 109 ksSa~IAKeRLKlILahDR~~~-SPd~Le~Lk~DILeVISKYVeID 153 (220)
-...+.|==+-=+++-.||.++ .++.++.+++.++.++.+|+.-.
T Consensus 110 ld~~E~a~LkAivLf~pd~~~L~~~~~Ve~lq~~~~~aL~~~~~~~ 155 (189)
T cd06940 110 LSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAKN 155 (189)
T ss_pred CCHHHHHHHHHHHHhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3556777655545555699987 89999999999999999998743
No 23
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=50.53 E-value=37 Score=23.51 Aligned_cols=36 Identities=11% Similarity=0.243 Sum_probs=32.4
Q ss_pred CCCCHHHHHHHHHHHHHHhccccccccCCcEEEEEee
Q 027649 128 CAVSDEAKRKIVNNIVHALSDFVEIESQDKVQLNVST 164 (220)
Q Consensus 128 ~~~SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~ 164 (220)
.|.|++...+|-++|-+++.+.+.+.++. |.|.+..
T Consensus 10 ~Grs~EqK~~L~~~it~a~~~~~~~p~~~-v~V~i~e 45 (60)
T PRK02289 10 EGRSQEQKNALAREVTEVVSRIAKAPKEA-IHVFIND 45 (60)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHhCcCcce-EEEEEEE
Confidence 36699999999999999999999999886 9998865
No 24
>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=50.04 E-value=15 Score=32.82 Aligned_cols=44 Identities=18% Similarity=0.255 Sum_probs=33.7
Q ss_pred CcHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhccccccc
Q 027649 110 SNARIAKQRLQMILFSDRCAV-SDEAKRKIVNNIVHALSDFVEIE 153 (220)
Q Consensus 110 sSa~IAKeRLKlILahDR~~~-SPd~Le~Lk~DILeVISKYVeID 153 (220)
...+.|==+-=+++-.||.|+ .+..++++|+.+++++..|+.-.
T Consensus 163 d~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~~i~~~ 207 (259)
T cd06932 163 TDSELALFCAVIILSPDRPGLINRKPVERIQEHVLQALELQLKKN 207 (259)
T ss_pred CHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHhhh
Confidence 445555544444455699997 89999999999999999998743
No 25
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=49.82 E-value=38 Score=23.02 Aligned_cols=36 Identities=14% Similarity=0.347 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHHHHhccccccccCCcEEEEEeeC
Q 027649 129 AVSDEAKRKIVNNIVHALSDFVEIESQDKVQLNVSTD 165 (220)
Q Consensus 129 ~~SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~d 165 (220)
+.+++....|-++|.+++++.+.+.+++ +.|.+..-
T Consensus 11 grt~eqK~~l~~~it~~l~~~lg~~~~~-v~V~i~e~ 46 (63)
T TIGR00013 11 GRTDEQKRQLIEGVTEAMAETLGANLES-IVVIIDEM 46 (63)
T ss_pred CCCHHHHHHHHHHHHHHHHHHhCCCccc-EEEEEEEc
Confidence 5689999999999999999999999997 88888653
No 26
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=49.09 E-value=19 Score=29.67 Aligned_cols=31 Identities=29% Similarity=0.469 Sum_probs=26.1
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHHHHHhccccc
Q 027649 117 QRLQMILFSDRCAVSDEAKRKIVNNIVHALSDFVE 151 (220)
Q Consensus 117 eRLKlILahDR~~~SPd~Le~Lk~DILeVISKYVe 151 (220)
+=|+.||+.+|...+++.++ .|+++|.||.+
T Consensus 83 ~ElRsIla~e~~~~s~E~l~----~Ildiv~Ky~~ 113 (114)
T COG1460 83 DELRSILAKERVMLSDEELD----KILDIVDKYRE 113 (114)
T ss_pred HHHHHHHHHccCCCCHHHHH----HHHHHHHHHhc
Confidence 56899999999999887665 58999999974
No 27
>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=48.39 E-value=16 Score=31.67 Aligned_cols=45 Identities=7% Similarity=-0.014 Sum_probs=35.3
Q ss_pred CCcHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhccccccc
Q 027649 109 NSNARIAKQRLQMILFSDRCAVSDEAKRKIVNNIVHALSDFVEIE 153 (220)
Q Consensus 109 ksSa~IAKeRLKlILahDR~~~SPd~Le~Lk~DILeVISKYVeID 153 (220)
-...+.|==+-=+++-.||.+++++.++++|+.++.++..|+...
T Consensus 132 ld~~Eya~LkAivLfnpD~~gl~~~~Ve~lQe~~~~aL~~yi~~~ 176 (222)
T cd06951 132 LDCKEYAYLKGAVLFTPVPPLLCPHYIEALQKEAQQALNEHTMMT 176 (222)
T ss_pred CCHHHHHHHHHHHHhCCCCCccCHHHHHHHHHHHHHHHHHHHHhh
Confidence 455677765544444559998899999999999999999999743
No 28
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=47.18 E-value=39 Score=22.92 Aligned_cols=36 Identities=19% Similarity=0.284 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHHHHhccccccccCCcEEEEEeeC
Q 027649 129 AVSDEAKRKIVNNIVHALSDFVEIESQDKVQLNVSTD 165 (220)
Q Consensus 129 ~~SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~d 165 (220)
+.+++....|-+.|-+++.++..+..++ +.|.+..-
T Consensus 11 grs~eqk~~l~~~it~~l~~~~~~p~~~-v~V~i~e~ 46 (62)
T PRK00745 11 GRTVEQKRKLVEEITRVTVETLGCPPES-VDIIITDV 46 (62)
T ss_pred CCCHHHHHHHHHHHHHHHHHHcCCChhH-EEEEEEEc
Confidence 5689999999999999999999999996 99888753
No 29
>cd01068 sensor_globin Globin domain present in Globin-Coupled-Sensors (GCS). These domains detect changes in intracellular concentrations of oxygen, carbon monoxyde, or nitrous oxide, which result in aerotaxis and/or gene regulation. One subgroup, the HemATs, are aerotactic heme sensors combining a globin with an MCP signaling domain, others function as gene regulators, by direct combination with DNA-binding domains, with domains modulating 2nd messengers, or with domains interacting with transcription factors or regulators.
Probab=45.57 E-value=77 Score=24.65 Aligned_cols=39 Identities=13% Similarity=0.146 Sum_probs=32.6
Q ss_pred cHHHHHHHHHHHHHhhCCCCCHHHH----HHHHHHHHHHhccc
Q 027649 111 NARIAKQRLQMILFSDRCAVSDEAK----RKIVNNIVHALSDF 149 (220)
Q Consensus 111 Sa~IAKeRLKlILahDR~~~SPd~L----e~Lk~DILeVISKY 149 (220)
.......|.++=.+|-|.|++|... ..+...|+++|.+-
T Consensus 78 d~~y~~~~~~iG~~H~~igl~~~~~~~~~~~~~~~l~~~l~~~ 120 (147)
T cd01068 78 DEAYIAQRVRIGEVHARIGLEPKWYLGGYAVLLELLIGALRES 120 (147)
T ss_pred CHHHHHHHHHHHHHHHHcCCCCcchHHHHHHHHHHHHHHHHHH
Confidence 3788999999999999999998777 57788888777543
No 30
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=45.56 E-value=40 Score=22.84 Aligned_cols=35 Identities=17% Similarity=0.368 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHHHHHhccccccccCCcEEEEEee
Q 027649 129 AVSDEAKRKIVNNIVHALSDFVEIESQDKVQLNVST 164 (220)
Q Consensus 129 ~~SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~ 164 (220)
+.+++.+.+|-++|-++++++..+..+. |.|-+..
T Consensus 10 g~~~e~K~~l~~~it~~~~~~lg~~~~~-i~V~i~E 44 (60)
T PF01361_consen 10 GRTAEQKRELAEAITDAVVEVLGIPPER-ISVVIEE 44 (60)
T ss_dssp TS-HHHHHHHHHHHHHHHHHHHTS-GGG-EEEEEEE
T ss_pred CCCHHHHHHHHHHHHHHHHHHhCcCCCe-EEEEEEE
Confidence 4488999999999999999999999886 9988875
No 31
>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=44.74 E-value=20 Score=30.99 Aligned_cols=43 Identities=30% Similarity=0.417 Sum_probs=33.3
Q ss_pred CCcHHHHHHHHH-HHHHhhCCCC-CHHHHHHHHHHHHHHhccccccc
Q 027649 109 NSNARIAKQRLQ-MILFSDRCAV-SDEAKRKIVNNIVHALSDFVEIE 153 (220)
Q Consensus 109 ksSa~IAKeRLK-lILahDR~~~-SPd~Le~Lk~DILeVISKYVeID 153 (220)
-...+.|= |+ ++|.+||.++ .++.++.+|+.+++++..|+.-.
T Consensus 137 ld~~E~~l--L~AI~Lf~d~~~L~~~~~Ve~~Q~~~~~aL~~y~~~~ 181 (231)
T cd06938 137 VDNAEYAL--LTAIVIFSDRPGLLQPKKVEKIQEIYLEALRAYVDNR 181 (231)
T ss_pred CCHHHHHH--HHHHHHccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 34466665 44 3456799887 68999999999999999999743
No 32
>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=44.69 E-value=19 Score=32.08 Aligned_cols=32 Identities=16% Similarity=0.273 Sum_probs=26.9
Q ss_pred HHHHh--hCCCC-CHHHHHHHHHHHHHHhcccccc
Q 027649 121 MILFS--DRCAV-SDEAKRKIVNNIVHALSDFVEI 152 (220)
Q Consensus 121 lILah--DR~~~-SPd~Le~Lk~DILeVISKYVeI 152 (220)
++|.+ |+.|+ +++.++.+|+.+..++.+|+.-
T Consensus 139 IiLfnp~d~~gL~~~~~Ve~lQe~~~~aL~~yi~~ 173 (246)
T cd07073 139 LLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIAC 173 (246)
T ss_pred HHHcCCCCcccccCHHHHHHHHHHHHHHHHHHHHh
Confidence 35666 67787 7999999999999999999864
No 33
>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=44.66 E-value=21 Score=31.48 Aligned_cols=45 Identities=13% Similarity=0.059 Sum_probs=34.4
Q ss_pred CCcHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhccccccc
Q 027649 109 NSNARIAKQRLQMILFSDRCAV-SDEAKRKIVNNIVHALSDFVEIE 153 (220)
Q Consensus 109 ksSa~IAKeRLKlILahDR~~~-SPd~Le~Lk~DILeVISKYVeID 153 (220)
-...+.|==+-=+++-.||.++ .++.++.+|+.+++++..|+...
T Consensus 141 ld~~E~a~LkAivLf~pD~~~L~~~~~Ve~lQe~~~~aL~~yi~~~ 186 (232)
T cd07350 141 ISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWEAQQALNEHVRMI 186 (232)
T ss_pred CCHHHHHHHHHHHHhCCCcccCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 4566777544434444599987 78999999999999999999853
No 34
>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=44.55 E-value=21 Score=29.80 Aligned_cols=44 Identities=18% Similarity=0.169 Sum_probs=34.3
Q ss_pred CCcHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhcccccc
Q 027649 109 NSNARIAKQRLQMILFSDRCAV-SDEAKRKIVNNIVHALSDFVEI 152 (220)
Q Consensus 109 ksSa~IAKeRLKlILahDR~~~-SPd~Le~Lk~DILeVISKYVeI 152 (220)
-...+.|==+-=+++..||.|+ .++.++.+++.++.++..|+.-
T Consensus 100 ld~~E~allkAi~Lf~pd~~gl~~~~~Ve~lq~~~~~aL~~~i~~ 144 (195)
T cd06941 100 LSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDRVLEALKVQVSR 144 (195)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 3556776655445555699987 7889999999999999999863
No 35
>cd06947 NR_LBD_GR_Like Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor. The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator prote
Probab=42.55 E-value=21 Score=31.78 Aligned_cols=41 Identities=15% Similarity=0.203 Sum_probs=31.7
Q ss_pred CcHHHHHHHHHHH-HHh--hCCCC-CHHHHHHHHHHHHHHhcccccc
Q 027649 110 SNARIAKQRLQMI-LFS--DRCAV-SDEAKRKIVNNIVHALSDFVEI 152 (220)
Q Consensus 110 sSa~IAKeRLKlI-Lah--DR~~~-SPd~Le~Lk~DILeVISKYVeI 152 (220)
...+.|= ||-| |.+ ||.|+ ++..++++|+.++.++..|+.-
T Consensus 129 d~~E~ac--LKAIvLfn~~d~~gL~~~~~Ve~lqe~i~~AL~~yi~~ 173 (246)
T cd06947 129 TYEEFLC--MKVLLLLSTIPKDGLKSQAAFDEMRMNYIKELRKAIVK 173 (246)
T ss_pred CHHHHHH--HHHHHHcCCCccccccCHHHHHHHHHHHHHHHHHHHHH
Confidence 4456554 5544 444 67787 7999999999999999999984
No 36
>PRK00341 hypothetical protein; Provisional
Probab=42.43 E-value=34 Score=26.39 Aligned_cols=40 Identities=8% Similarity=0.129 Sum_probs=28.1
Q ss_pred HHHHHHHHHHhccccccccCCcEEEEEeeCCCCceEEEEEEe
Q 027649 136 RKIVNNIVHALSDFVEIESQDKVQLNVSTDTDLGTIYSVTVP 177 (220)
Q Consensus 136 e~Lk~DILeVISKYVeID~e~kVeV~l~~d~d~~tvL~anIP 177 (220)
+.+++.|++++.+|.+++.+. +.++-+++|. ...+.++|-
T Consensus 28 ~~~~~~V~~iv~~~~~~~~~~-~~~k~Ss~Gk-Y~S~tv~i~ 67 (91)
T PRK00341 28 VGFKDLVIEILQKHADVDLST-LAERQSSNGK-YTTVQLHIV 67 (91)
T ss_pred hhHHHHHHHHHHHhCCCcccc-eeeccCCCCE-EEEEEEEEE
Confidence 567889999999999887774 7777776655 333444443
No 37
>cd07076 NR_LBD_GR Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor superfamily. The ligand binding domain of the glucocorticoid receptor (GR): GR is a ligand-activated transcription factor belonging to the nuclear receptor superfamily. It binds with high affinity to cortisol and other glucocorticoids. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. In the absence of hormone, the glucocorticoid receptor (GR) is complexes with a variety of heat shock proteins in the cytosol. The binding of the glucocorticoids results in release of the heat shock proteins and transforms it to its active state. One mechanism of action of GR is by direct activation of gene transcription. The activated form of GR forms dimers, translocates into the nucleus, and binds to specific hormone responsive elements, activating gene transcription
Probab=41.43 E-value=22 Score=31.87 Aligned_cols=33 Identities=18% Similarity=0.238 Sum_probs=27.5
Q ss_pred HHHHh--hCCCC-CHHHHHHHHHHHHHHhccccccc
Q 027649 121 MILFS--DRCAV-SDEAKRKIVNNIVHALSDFVEIE 153 (220)
Q Consensus 121 lILah--DR~~~-SPd~Le~Lk~DILeVISKYVeID 153 (220)
+||.+ ||.|+ +++..++||+.++.++.+|+.-.
T Consensus 139 IvLfnp~d~~GL~~~~~Ve~lqe~~~~aL~~yi~~~ 174 (247)
T cd07076 139 LLLLSTVPKDGLKSQELFDEIRMTYIKELGKAIVKR 174 (247)
T ss_pred HHhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 34444 88888 89999999999999999999843
No 38
>PF04965 GPW_gp25: Gene 25-like lysozyme; InterPro: IPR007048 The family of sequences represented by this entry include proteins from Bacteriophage T4 and related phage, which may be structural components of the outer wedge of the baseplate that has acidic lysozyme activity [, ]. They also include anti-adapter protein IraD, from bacteria, that inhibit RpoS proteolysis by regulating RssB activity [].; PDB: 2IA7_A.
Probab=40.36 E-value=73 Score=23.53 Aligned_cols=33 Identities=24% Similarity=0.356 Sum_probs=22.9
Q ss_pred CHHHHHHHHHHHHHHhccccccccCC-cEEEEEeeCC
Q 027649 131 SDEAKRKIVNNIVHALSDFVEIESQD-KVQLNVSTDT 166 (220)
Q Consensus 131 SPd~Le~Lk~DILeVISKYVeID~e~-kVeV~l~~d~ 166 (220)
+++....++.+|.++|.+|= +.- .++|++..++
T Consensus 42 ~~~~~~~i~~~I~~aI~~~E---PRl~~~~V~~~~~~ 75 (99)
T PF04965_consen 42 SPDTRQAIRREIREAIQRFE---PRLKVVSVEVEEDD 75 (99)
T ss_dssp -HHHHHHHHHHHHHHHHHH----TTEEEEEEEEE-TT
T ss_pred CHHHHHHHHHHHHHHHHHhC---CcEEEEEEEEEecC
Confidence 88999999999999999993 332 3556665533
No 39
>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=39.61 E-value=24 Score=30.97 Aligned_cols=42 Identities=17% Similarity=0.244 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhccccccc
Q 027649 112 ARIAKQRLQMILFSDRCAV-SDEAKRKIVNNIVHALSDFVEIE 153 (220)
Q Consensus 112 a~IAKeRLKlILahDR~~~-SPd~Le~Lk~DILeVISKYVeID 153 (220)
.+.|==+-=+++..||.|+ .++.++++|+.+++++..|+...
T Consensus 141 ~E~~~LkaivL~~pD~~gL~~~~~Ve~lQe~~~~aL~~y~~~~ 183 (239)
T cd06945 141 ISAFCCLALLLLITERHGLKEPKKVEELQNKIISCLRDHVTSN 183 (239)
T ss_pred HHHHHHHHHHHhCCCccccCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3444333333444599997 79999999999999999999854
No 40
>PF09581 Spore_III_AF: Stage III sporulation protein AF (Spore_III_AF); InterPro: IPR014245 This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.
Probab=37.55 E-value=2.3e+02 Score=23.41 Aligned_cols=66 Identities=18% Similarity=0.214 Sum_probs=42.0
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhccccccccCCcEEEEEeeCCCCc--eEEEEEEeccCc
Q 027649 115 AKQRLQMILFSDRCAVSDEAKRKIVNNIVHALSDFVEIESQDKVQLNVSTDTDLG--TIYSVTVPVRRV 181 (220)
Q Consensus 115 AKeRLKlILahDR~~~SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~d~d~~--tvL~anIPVrrv 181 (220)
-++..+-+=...+.....++-++|+++|-+.+..--.+.... |+|.+..+.+.. .+=.++|-+..-
T Consensus 65 i~~~~~~~~~~~~~~~~e~y~~~l~~~i~~~l~~~~g~~~~~-V~v~~~~~~~~~~~~I~~I~v~l~~~ 132 (188)
T PF09581_consen 65 IKQQGEELEASQRDQALEQYEEQLEKQIKALLEDKYGVEVVK-VEVEIDEDEESPDFEIKEIKVTLSEE 132 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCceEE-EEEEEEcCCCccccceeEEEEEEcCC
Confidence 344444444444444566788999999999999667777774 888888765321 244555555443
No 41
>PF03780 Asp23: Asp23 family; InterPro: IPR005531 This entry represents the alkaline shock protein 23 family. These small proteins are involved in alkaline pH tolerance of Staphylococcus aureus [,].
Probab=37.34 E-value=44 Score=25.01 Aligned_cols=32 Identities=22% Similarity=0.382 Sum_probs=28.6
Q ss_pred CHHHHHHHHHHHHHHhccccccccCCcEEEEEe
Q 027649 131 SDEAKRKIVNNIVHALSDFVEIESQDKVQLNVS 163 (220)
Q Consensus 131 SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~ 163 (220)
=|+..+++|+.|.+.|.++..++... |+|.+.
T Consensus 74 i~~v~~~iq~~V~~~v~~~tg~~v~~-V~V~V~ 105 (108)
T PF03780_consen 74 IPEVAEEIQEKVKEAVEEMTGIEVSE-VNVHVE 105 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCeeEE-EEEEEE
Confidence 38999999999999999999999985 888874
No 42
>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=36.95 E-value=33 Score=29.19 Aligned_cols=43 Identities=14% Similarity=0.176 Sum_probs=31.5
Q ss_pred CcHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhcccccc
Q 027649 110 SNARIAKQRLQMILFSDRCAV-SDEAKRKIVNNIVHALSDFVEI 152 (220)
Q Consensus 110 sSa~IAKeRLKlILahDR~~~-SPd~Le~Lk~DILeVISKYVeI 152 (220)
...+.|==+-=+++-.||.++ .++..+.||+.+++++..|+.-
T Consensus 128 d~~E~~~LkaiiLf~~d~~~l~~~~~v~~lq~~i~~aL~~y~~~ 171 (222)
T cd06952 128 DDHEYAYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYVGK 171 (222)
T ss_pred CHHHHHHHHHHHHhCCCCcCCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 445555433333334588887 7899999999999999999963
No 43
>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=35.56 E-value=33 Score=30.22 Aligned_cols=44 Identities=9% Similarity=0.104 Sum_probs=32.9
Q ss_pred CcHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhccccccc
Q 027649 110 SNARIAKQRLQMILFSDRCAV-SDEAKRKIVNNIVHALSDFVEIE 153 (220)
Q Consensus 110 sSa~IAKeRLKlILahDR~~~-SPd~Le~Lk~DILeVISKYVeID 153 (220)
...+.|==+-=+++-.|+.|+ .++.++.+++.++.++..|+...
T Consensus 144 d~~E~a~LKaivLfnpd~~gL~~~~~Ve~lQe~~~~aL~~yi~~~ 188 (241)
T cd07069 144 DQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCN 188 (241)
T ss_pred CHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 456666533333334599888 78999999999999999999853
No 44
>PF10850 DUF2653: Protein of unknown function (DUF2653); InterPro: IPR020516 This entry contains proteins with no known function.
Probab=34.35 E-value=56 Score=25.99 Aligned_cols=37 Identities=30% Similarity=0.518 Sum_probs=28.4
Q ss_pred HHHHHHhccccc----cccCCcEEEEEeeCCCCceEEEEEEecc
Q 027649 140 NNIVHALSDFVE----IESQDKVQLNVSTDTDLGTIYSVTVPVR 179 (220)
Q Consensus 140 ~DILeVISKYVe----ID~e~kVeV~l~~d~d~~tvL~anIPVr 179 (220)
.||+.+|+=|+. |.+++ |+|.+.=|++.| +.|.+-+.
T Consensus 8 qeIiNAvCl~~A~~~~i~P~d-VeVeL~yDdd~G--FsAEv~~n 48 (91)
T PF10850_consen 8 QEIINAVCLHIAERKGIQPED-VEVELMYDDDYG--FSAEVWVN 48 (91)
T ss_pred HHHHHHHHHHHHHhcCCCccc-EEEEEEEecCCC--eeEEEEEC
Confidence 688899888874 88997 999998887765 55655544
No 45
>cd07075 NR_LBD_MR Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor superfamily. The ligand binding domain of the mineralocorticoid receptor (MR): MR, also called aldosterone receptor, is a member of nuclear receptor superfamily involved in the regulation of electrolyte and fluid balance. The receptor is activated by mineralocorticoids such as aldosterone and deoxycorticosterone as well as glucocorticoids, like cortisol and cortisone. Binding of its ligand results in its translocation to the cell nucleus, homodimerization and binding to hormone response elements (HREs) present in the promoter of MR controlled genes. This results in the recruitment of the coactivators and the transcription of the activated genes. MR is expressed in many tissues and its activation results in the expression of proteins regulating electrolyte and fluid balance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, MR h
Probab=34.05 E-value=38 Score=30.45 Aligned_cols=31 Identities=23% Similarity=0.333 Sum_probs=26.1
Q ss_pred HHHh--hCCCC-CHHHHHHHHHHHHHHhcccccc
Q 027649 122 ILFS--DRCAV-SDEAKRKIVNNIVHALSDFVEI 152 (220)
Q Consensus 122 ILah--DR~~~-SPd~Le~Lk~DILeVISKYVeI 152 (220)
||.+ ||.|+ +++..+.||+.++.++.+|+.-
T Consensus 140 vLfn~d~~~gL~~~~~Ve~lqe~~~~aL~~yi~~ 173 (248)
T cd07075 140 LLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTK 173 (248)
T ss_pred HHhCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4444 47787 8999999999999999999983
No 46
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=33.96 E-value=82 Score=21.71 Aligned_cols=37 Identities=14% Similarity=0.322 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHHHhccccccccCCcEEEEEeeCC
Q 027649 129 AVSDEAKRKIVNNIVHALSDFVEIESQDKVQLNVSTDT 166 (220)
Q Consensus 129 ~~SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~d~ 166 (220)
+.+++...+|-+.|-+++.+.+.+.+++ +.|.+..-+
T Consensus 11 grt~eqk~~l~~~it~~l~~~lg~p~~~-v~V~i~e~~ 47 (64)
T PRK01964 11 GRPEEKIKNLIREVTEAISATLDVPKER-VRVIVNEVP 47 (64)
T ss_pred CCCHHHHHHHHHHHHHHHHHHhCcChhh-EEEEEEEcC
Confidence 5689999999999999999999999997 998887533
No 47
>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=33.81 E-value=41 Score=28.62 Aligned_cols=44 Identities=5% Similarity=0.071 Sum_probs=33.1
Q ss_pred CCcHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhcccccc
Q 027649 109 NSNARIAKQRLQMILFSDRCAV-SDEAKRKIVNNIVHALSDFVEI 152 (220)
Q Consensus 109 ksSa~IAKeRLKlILahDR~~~-SPd~Le~Lk~DILeVISKYVeI 152 (220)
-...+.|==+.=+++-.||.++ +++.++++|+.+++++.+|+.-
T Consensus 124 ld~~EyalLKai~L~npd~~~L~~~~~Ve~lq~~~~~aL~~y~~~ 168 (206)
T cd06950 124 VDATEFACLKAIVLFKPETRGLKDPAQVEALQDQAQLMLNKHIRT 168 (206)
T ss_pred CCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666544444445599888 6789999999999999999974
No 48
>PF06138 Chordopox_E11: Chordopoxvirus E11 protein; InterPro: IPR009201 This group represents a virion core protein, vaccinia E11L type.
Probab=31.42 E-value=49 Score=27.91 Aligned_cols=47 Identities=17% Similarity=0.390 Sum_probs=34.0
Q ss_pred HHHHHHHHhhCCCCCHH--HHHHHHHHHHHHhccccccccCCcEEEEEee
Q 027649 117 QRLQMILFSDRCAVSDE--AKRKIVNNIVHALSDFVEIESQDKVQLNVST 164 (220)
Q Consensus 117 eRLKlILahDR~~~SPd--~Le~Lk~DILeVISKYVeID~e~kVeV~l~~ 164 (220)
.|+|+....+-|.|.+. .+.+--+-.|++|+||+.+|..- .-+-+..
T Consensus 13 grvkl~~~~~~~~c~~~~~~~~~Av~~Fl~~L~kyI~veeSt-Fylvvrd 61 (130)
T PF06138_consen 13 GRVKLRYEEPDCKCARTGCEARRAVKHFLSVLKKYIDVEEST-FYLVVRD 61 (130)
T ss_pred ceeEEEEeCCCcccccccchHHHHHHHHHHHHHhhEEecccE-EEEEEec
Confidence 35666666666666554 45556677899999999999985 7777743
No 49
>PRK05697 flagellar basal body-associated protein FliL-like protein; Validated
Probab=29.68 E-value=45 Score=27.45 Aligned_cols=39 Identities=18% Similarity=0.234 Sum_probs=32.4
Q ss_pred HHHHHHHHHHhhCCC-C-CHHHHHHHHHHHHHHhccccccc
Q 027649 115 AKQRLQMILFSDRCA-V-SDEAKRKIVNNIVHALSDFVEIE 153 (220)
Q Consensus 115 AKeRLKlILahDR~~-~-SPd~Le~Lk~DILeVISKYVeID 153 (220)
-++||-++|.+-+.. + +++-.++||+||++.|.+-++-+
T Consensus 80 IRd~ii~lLs~~t~~eL~t~eGke~Lr~eil~~in~~L~~~ 120 (137)
T PRK05697 80 IRNALVELLGQQTEDKVKSLTGREEIRQECLKQVNELLEQE 120 (137)
T ss_pred HHHHHHHHHHcCCHHHhcCHHHHHHHHHHHHHHHHHHHhhc
Confidence 678888888877653 3 89999999999999999988743
No 50
>PHA03001 putative virion core protein; Provisional
Probab=28.75 E-value=79 Score=26.75 Aligned_cols=45 Identities=16% Similarity=0.343 Sum_probs=31.4
Q ss_pred HHHHHHHhhCCCCC-HHHHHHHHHHHHHHhccccccccCCcEEEEEe
Q 027649 118 RLQMILFSDRCAVS-DEAKRKIVNNIVHALSDFVEIESQDKVQLNVS 163 (220)
Q Consensus 118 RLKlILahDR~~~S-Pd~Le~Lk~DILeVISKYVeID~e~kVeV~l~ 163 (220)
|+|+....+-+.|. .-.+.+..+-.|++|.||+.+|..- .-+-+.
T Consensus 14 rvkl~~~~~~~~~~~~~~~~ka~~~fl~~L~kYi~v~eSt-Fylvvr 59 (132)
T PHA03001 14 RVKLAIENPDKVCATKAEMRKAINKFLELLKKYIHVDKST-FYLVVK 59 (132)
T ss_pred ceEEEEcCCCccccccchHHHHHHHHHHHHHhhEEecccE-EEEEEe
Confidence 45555544444332 3456677788899999999999995 777774
No 51
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=27.53 E-value=1e+02 Score=25.30 Aligned_cols=50 Identities=20% Similarity=0.311 Sum_probs=34.3
Q ss_pred HHHHHHHhhhhhhcCCCCCCCCCCcHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhccccccccCCcEEEEEe
Q 027649 87 MSFFDRLNLAWKIVFPSPTTRRNSNARIAKQRLQMILFSDRCAVSDEAKRKIVNNIVHALSDFVEIESQDKVQLNVS 163 (220)
Q Consensus 87 M~ffd~l~~aw~i~Fp~~~~kkksSa~IAKeRLKlILahDR~~~SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~ 163 (220)
||+|++..-+=+=+|.....+ | .-+.++..|++.|++ -.++..+ ++|.++
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~-------~------------------~~~~~~~~i~~~i~~-~~~~~~~-i~V~v~ 50 (147)
T PRK11198 1 MGLFSFVKEAGEKLFDAVTAQ-------A------------------DNEDAADALKEHISK-QGLGDAD-VNVQVE 50 (147)
T ss_pred CcHHHHHHHHHHHhcCCCCcc-------c------------------chHHHHHHHHHHHHh-cCCCcCC-ceEEEe
Confidence 788888877766677633211 1 127788888888888 5777775 877774
No 52
>PF12143 PPO1_KFDV: Protein of unknown function (DUF_B2219); InterPro: IPR022740 This domain represents the C terminus of polyphenol oxidases. This region is primarily found in eukaryotes, although a few bacterial members also exist. It is typically between 138 and 152 amino acids in length and the family is found in association with PF00264 from PFAM and PF12142 from PFAM. Many members are plant or plastid polyphenol oxidases, and there is a highly conserved KFDV sequence motif. ; GO: 0004097 catechol oxidase activity, 0055114 oxidation-reduction process
Probab=26.15 E-value=1.2e+02 Score=25.05 Aligned_cols=18 Identities=44% Similarity=0.700 Sum_probs=14.9
Q ss_pred eeeeeecCCCCccceeEEEEeeec
Q 027649 194 IANVEYKDTGETSGSVDVRFDFFV 217 (220)
Q Consensus 194 ~~~~~ykd~~~~~~~vdv~fdf~~ 217 (220)
|.+|+|++.. .|+||.||
T Consensus 34 IegIe~d~~~------~vkFDVfv 51 (130)
T PF12143_consen 34 IEGIEIDDDV------YVKFDVFV 51 (130)
T ss_pred EccEEecCCc------ceEEEEEE
Confidence 8899999876 48888886
No 53
>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=25.89 E-value=57 Score=28.07 Aligned_cols=29 Identities=24% Similarity=0.457 Sum_probs=25.5
Q ss_pred hhCCCC-CHHHHHHHHHHHHHHhccccccc
Q 027649 125 SDRCAV-SDEAKRKIVNNIVHALSDFVEIE 153 (220)
Q Consensus 125 hDR~~~-SPd~Le~Lk~DILeVISKYVeID 153 (220)
.||.++ .+..++.+|+.+..++..|+...
T Consensus 158 pd~~gL~~~~~V~~lQ~~~~~aL~~y~~~~ 187 (236)
T cd06954 158 ADRPNVQDHHRVERLQETYVEALHSYIKIK 187 (236)
T ss_pred CCcccCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 499887 67899999999999999999743
No 54
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=25.57 E-value=79 Score=25.15 Aligned_cols=30 Identities=20% Similarity=0.376 Sum_probs=23.5
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHHHHHhcccc
Q 027649 117 QRLQMILFSDRCAVSDEAKRKIVNNIVHALSDFV 150 (220)
Q Consensus 117 eRLKlILahDR~~~SPd~Le~Lk~DILeVISKYV 150 (220)
+=|+.|+.++|...+++-++ +|+++|++|.
T Consensus 82 dElrai~~~~~~~~~~e~l~----~ILd~l~k~~ 111 (112)
T PRK14981 82 DELRAIFAKERYTLSPEELD----EILDIVKKYR 111 (112)
T ss_pred HHHHHHHHHhccCCCHHHHH----HHHHHHHHhh
Confidence 45678999998888887775 5788888885
No 55
>PRK07021 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=25.10 E-value=67 Score=26.64 Aligned_cols=39 Identities=23% Similarity=0.359 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHhhCC-CC-CHHHHHHHHHHHHHHhcccccc
Q 027649 114 IAKQRLQMILFSDRC-AV-SDEAKRKIVNNIVHALSDFVEI 152 (220)
Q Consensus 114 IAKeRLKlILahDR~-~~-SPd~Le~Lk~DILeVISKYVeI 152 (220)
..|+++-++|.+-+. .+ +++-.++||+||++.|.+++.-
T Consensus 104 ~IRd~ii~~Ls~k~~~~L~~~eGk~~Lk~ei~~~in~~l~~ 144 (162)
T PRK07021 104 EVRSRLLLLLSRKHAAELATEEGKQKLAAEIKQTLSQPLVP 144 (162)
T ss_pred HHHHHHHHHHhcCCHHHhcCHHHHHHHHHHHHHHHHHHHhc
Confidence 367777777755544 23 7899999999999999999863
No 56
>PF11113 Phage_head_chap: Head assembly gene product; InterPro: IPR021049 This head assembly protein is also refereed to as gene product 40 (Gp40). A specific gp20-gp40 membrane insertion structure constitutes the T4 prohead assembly initiation complex [].
Probab=24.57 E-value=79 Score=23.17 Aligned_cols=20 Identities=35% Similarity=0.728 Sum_probs=13.9
Q ss_pred eeeeeecCCCCccceeEEEEeeecCCC
Q 027649 194 IANVEYKDTGETSGSVDVRFDFFVPDE 220 (220)
Q Consensus 194 ~~~~~ykd~~~~~~~vdv~fdf~~p~~ 220 (220)
|++++|+|.. +.+||-.|+|
T Consensus 19 i~~~~~~~G~-------l~vdfsT~~e 38 (56)
T PF11113_consen 19 ITELHYDDGK-------LKVDFSTPSE 38 (56)
T ss_pred EEEEEEcCCe-------EEEEEeCCCc
Confidence 7888888322 5677777765
No 57
>PRK00907 hypothetical protein; Provisional
Probab=23.49 E-value=1.3e+02 Score=23.60 Aligned_cols=39 Identities=8% Similarity=0.107 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhccccc-cccCCcEEEEEeeCCCCceEEEEEE
Q 027649 136 RKIVNNIVHALSDFVE-IESQDKVQLNVSTDTDLGTIYSVTV 176 (220)
Q Consensus 136 e~Lk~DILeVISKYVe-ID~e~kVeV~l~~d~d~~tvL~anI 176 (220)
+.+++.|++++.+|.. .+.. .++++-++.|.. ..+.+.|
T Consensus 28 ~~l~~~V~~vv~~h~p~~~~~-~i~~r~Ss~GkY-~Svtv~i 67 (92)
T PRK00907 28 RGLETELPRLLAATGVELLQE-RISWKHSSSGKY-VSVRIGF 67 (92)
T ss_pred hhHHHHHHHHHHHhCCCCCcC-cEEeccCCCCEE-EEEEEEE
Confidence 6788999999999985 4555 488888776652 3344444
No 58
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=22.70 E-value=1e+02 Score=26.28 Aligned_cols=57 Identities=21% Similarity=0.366 Sum_probs=44.2
Q ss_pred CcchhHHHHHHHHHhHHHHHHHhhhhhhcCCCCCCCCCCcHHHHHHHHHHHHHhhCCCCC-HHHHHHHHHHHHHHhcccc
Q 027649 72 PISHEVESFLLNAINMSFFDRLNLAWKIVFPSPTTRRNSNARIAKQRLQMILFSDRCAVS-DEAKRKIVNNIVHALSDFV 150 (220)
Q Consensus 72 ~~~~~~e~f~~~~~~M~ffd~l~~aw~i~Fp~~~~kkksSa~IAKeRLKlILahDR~~~S-Pd~Le~Lk~DILeVISKYV 150 (220)
..|.--...|..|..||+|| .| |+-+.+++||+ .|+| +.+.+-||+-.-+++..|+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd---------~P----R~~~l~dLA~~----------lGISkst~~ehLRrAe~Kl~~~~~ 211 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFD---------YP----RRVSLKDLAKE----------LGISKSTLSEHLRRAERKLIEAYF 211 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCC---------CC----ccCCHHHHHHH----------hCCCHHHHHHHHHHHHHHHHHHhh
Confidence 46667778999999999988 12 56678888875 6886 5677788888888888776
Q ss_pred c
Q 027649 151 E 151 (220)
Q Consensus 151 e 151 (220)
+
T Consensus 212 ~ 212 (215)
T COG3413 212 D 212 (215)
T ss_pred h
Confidence 4
No 59
>cd07074 NR_LBD_PR Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor. The ligand binding domain of the progesterone receptor (PR): PR is a member of the nuclear receptor superfamily of ligand dependent transcription factors, mediating the biological actions of progesterone. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. When no binding hormone is present the carboxyl terminal inhibits transcription. Binding to a hormone induces a structural change that removes the inhibitory action. After progesterone binds to the receptor, PR forms a dimer and the complex enters the nucleus where it interacts with the hormone response element (HRE) in the promoters of progesterone responsive genes and alters their transcription. In addition, rapid actions of PR that occur independent of transcription, have also been observed in several tissues
Probab=21.54 E-value=82 Score=28.39 Aligned_cols=27 Identities=7% Similarity=0.096 Sum_probs=19.8
Q ss_pred hCCCC-CHHHHHHHHHHHHHHhcccccc
Q 027649 126 DRCAV-SDEAKRKIVNNIVHALSDFVEI 152 (220)
Q Consensus 126 DR~~~-SPd~Le~Lk~DILeVISKYVeI 152 (220)
|+.|+ ++..++++|+.++.++.+|+..
T Consensus 146 d~~gL~~q~~Ve~lR~~y~~aL~~yi~~ 173 (248)
T cd07074 146 PLEGLRSQTQFDEMRSSYIRELIKAIGL 173 (248)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 66666 5777788888888888777653
No 60
>PF08776 VASP_tetra: VASP tetramerisation domain; InterPro: IPR014885 Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein. This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure []. ; PDB: 1USE_A 1USD_A.
Probab=21.46 E-value=62 Score=22.31 Aligned_cols=15 Identities=20% Similarity=0.341 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHhccc
Q 027649 135 KRKIVNNIVHALSDF 149 (220)
Q Consensus 135 Le~Lk~DILeVISKY 149 (220)
+.+||+||++++...
T Consensus 20 l~K~K~EIIeA~~~e 34 (40)
T PF08776_consen 20 LQKVKEEIIEAIRQE 34 (40)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 456666666666543
No 61
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=20.04 E-value=1.6e+02 Score=22.25 Aligned_cols=39 Identities=18% Similarity=0.311 Sum_probs=27.5
Q ss_pred CCCCCHHHHHHHHHHHHHHhccccccccCCcEEEEEeeCC
Q 027649 127 RCAVSDEAKRKIVNNIVHALSDFVEIESQDKVQLNVSTDT 166 (220)
Q Consensus 127 R~~~SPd~Le~Lk~DILeVISKYVeID~e~kVeV~l~~d~ 166 (220)
+.+-|.+...++=+.|.+-|..-..|.+++ |.|.+...+
T Consensus 37 ~~gRs~e~K~~ly~~l~~~L~~~~gi~p~D-v~I~l~e~~ 75 (82)
T PF14552_consen 37 GAGRSTEQKKALYRALAERLAEKLGIRPED-VMIVLVENP 75 (82)
T ss_dssp CS---HHHHHHHHHHHHHHHHHHH---GGG-EEEEEEEE-
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHcCCCHHH-EEEEEEECC
Confidence 346688999999999999999999999997 999987543
Done!