Query psy17538
Match_columns 164
No_of_seqs 116 out of 408
Neff 7.4
Searched_HMMs 46136
Date Sat Aug 17 01:05:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17538.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17538hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd09248 BRO1_Rhophilin_1 Prote 100.0 1.3E-48 2.8E-53 329.5 17.1 149 4-164 1-151 (384)
2 cd09244 BRO1_Rhophilin Protein 100.0 1.7E-48 3.7E-53 327.3 17.2 149 4-164 1-151 (350)
3 cd09240 BRO1_Alix Protein-inte 100.0 2.3E-47 5E-52 321.0 17.9 162 2-164 1-164 (346)
4 cd09249 BRO1_Rhophilin_2 Prote 100.0 2.4E-47 5.2E-52 321.6 16.8 149 4-164 1-151 (385)
5 cd09239 BRO1_HD-PTP_like Prote 100.0 1.2E-46 2.6E-51 318.0 16.9 150 3-164 7-159 (361)
6 cd09241 BRO1_ScRim20-like Prot 100.0 2.9E-45 6.3E-50 309.2 17.7 151 3-164 1-151 (355)
7 cd09242 BRO1_ScBro1_like Prote 100.0 3.1E-45 6.7E-50 308.4 17.4 150 4-164 1-152 (348)
8 cd09246 BRO1_Alix_like_1 Prote 100.0 1.2E-44 2.6E-49 305.2 17.6 151 4-164 1-156 (353)
9 PF03097 BRO1: BRO1-like domai 100.0 9.6E-41 2.1E-45 282.6 13.5 151 3-164 1-152 (377)
10 cd09034 BRO1_Alix_like Protein 100.0 1.2E-37 2.6E-42 261.1 15.8 151 4-164 1-157 (345)
11 KOG2220|consensus 100.0 9.7E-33 2.1E-37 249.1 15.8 152 1-162 1-154 (714)
12 cd09243 BRO1_Brox_like Protein 99.9 3.3E-24 7.1E-29 180.8 15.0 143 4-164 2-157 (353)
13 cd09245 BRO1_UmRIM23-like Prot 99.9 1.4E-22 3E-27 174.1 14.8 102 62-164 57-179 (413)
14 cd09247 BRO1_Alix_like_2 Prote 99.8 5.4E-19 1.2E-23 149.0 9.7 96 64-164 59-156 (346)
15 KOG2220|consensus 98.1 4.7E-06 1E-10 76.5 6.7 147 3-163 102-250 (714)
16 KOG2002|consensus 80.0 4.4 9.5E-05 38.9 5.8 45 120-164 751-798 (1018)
17 smart00671 SEL1 Sel1-like repe 73.4 8.7 0.00019 20.4 3.8 31 121-156 3-33 (36)
18 PF06552 TOM20_plant: Plant sp 73.0 12 0.00025 29.3 5.6 41 115-160 65-105 (186)
19 PF02071 NSF: Aromatic-di-Alan 70.1 1.9 4.1E-05 18.7 0.4 12 147-158 1-12 (12)
20 PF00515 TPR_1: Tetratricopept 69.9 9.2 0.0002 20.2 3.3 28 119-155 1-28 (34)
21 PF13424 TPR_12: Tetratricopep 69.0 14 0.0003 23.3 4.6 34 117-159 44-77 (78)
22 PF07719 TPR_2: Tetratricopept 67.9 14 0.00031 19.1 3.8 30 119-157 1-30 (34)
23 cd05525 Bromo_ASH1 Bromodomain 67.2 32 0.00068 24.1 6.4 66 3-75 28-104 (106)
24 PF13176 TPR_7: Tetratricopept 58.8 19 0.00041 19.6 3.3 27 122-157 2-28 (36)
25 PF08238 Sel1: Sel1 repeat; I 58.0 28 0.00061 18.7 4.8 17 140-156 20-36 (39)
26 PF13181 TPR_8: Tetratricopept 56.1 18 0.0004 18.8 2.9 28 119-155 1-28 (34)
27 PF13414 TPR_11: TPR repeat; P 53.2 26 0.00056 21.4 3.6 30 118-155 36-65 (69)
28 cd02682 MIT_AAA_Arch MIT: doma 51.6 40 0.00087 22.3 4.4 38 123-162 3-40 (75)
29 cd05522 Bromo_Rsc1_2_II Bromod 50.1 83 0.0018 21.7 6.1 58 12-75 45-103 (104)
30 PF13374 TPR_10: Tetratricopep 44.5 50 0.0011 17.6 3.8 33 119-160 2-34 (42)
31 cd05503 Bromo_BAZ2A_B_like Bro 38.6 1.2E+02 0.0027 20.5 5.8 30 13-46 39-68 (97)
32 COG4957 Predicted transcriptio 38.2 44 0.00096 24.9 3.2 32 6-40 65-105 (148)
33 PF05402 PqqD: Coenzyme PQQ sy 35.2 1E+02 0.0023 18.9 4.4 29 20-51 34-63 (68)
34 cd05505 Bromo_WSTF_like Bromod 35.1 1.5E+02 0.0032 20.3 6.1 57 13-75 39-96 (97)
35 cd05529 Bromo_WDR9_I_like Brom 34.6 1.7E+02 0.0038 21.0 6.4 30 13-46 67-96 (128)
36 PF14823 Sirohm_synth_C: Siroh 34.5 1E+02 0.0022 20.0 4.2 23 36-58 1-23 (70)
37 cd05517 Bromo_polybromo_II Bro 33.1 1.6E+02 0.0036 20.2 5.6 42 3-48 26-76 (103)
38 PF12358 DUF3644: Protein of u 31.1 81 0.0018 20.5 3.4 31 20-53 46-76 (77)
39 PF08631 SPO22: Meiosis protei 29.0 96 0.0021 25.1 4.2 41 111-159 27-67 (278)
40 COG1528 Ftn Ferritin-like prot 28.7 2.3E+02 0.0051 21.7 5.9 45 117-164 12-64 (167)
41 cd06936 NR_LBD_Fxr The ligand 27.8 91 0.002 24.5 3.8 33 17-52 165-197 (221)
42 KOG4061|consensus 27.4 68 0.0015 25.1 2.8 37 18-54 138-179 (217)
43 PF07426 Dynactin_p22: Dynacti 26.8 1.3E+02 0.0028 23.1 4.3 59 21-82 109-167 (174)
44 cd06929 NR_LBD_F1 Ligand-bindi 26.7 1.1E+02 0.0024 22.5 3.9 34 17-53 134-167 (174)
45 cd02681 MIT_calpain7_1 MIT: do 26.2 1.7E+02 0.0036 19.3 4.2 35 124-160 4-38 (76)
46 PF11569 Homez: Homeodomain le 24.9 54 0.0012 20.5 1.6 29 10-46 3-31 (56)
47 cd06937 NR_LBD_RAR The ligand 24.9 99 0.0021 24.5 3.5 33 17-52 170-202 (231)
48 smart00526 H15 Domain in histo 24.2 1.2E+02 0.0026 18.9 3.2 20 19-41 27-46 (66)
49 cd06941 NR_LBD_DmE78_like The 24.2 1.1E+02 0.0023 23.4 3.5 32 17-51 134-165 (195)
50 cd05497 Bromo_Brdt_I_like Brom 23.9 2.5E+02 0.0055 19.4 5.3 30 13-46 46-75 (107)
51 PF09205 DUF1955: Domain of un 23.6 27 0.00059 26.3 0.1 33 119-151 120-158 (161)
52 cd06932 NR_LBD_PPAR The ligand 23.3 1.1E+02 0.0024 24.8 3.6 33 17-52 196-228 (259)
53 cd06940 NR_LBD_REV_ERB The lig 22.8 1.2E+02 0.0027 23.1 3.6 32 17-51 144-175 (189)
54 cd05509 Bromo_gcn5_like Bromod 22.8 2.5E+02 0.0054 18.9 5.8 30 13-46 40-69 (101)
55 cd06953 NR_LBD_DHR4_like The l 22.4 1.4E+02 0.0029 23.3 3.8 33 17-52 163-195 (213)
56 cd06942 NR_LBD_Sex_1_like The 22.3 1.5E+02 0.0033 22.5 4.0 34 17-53 135-168 (191)
57 cd05513 Bromo_brd7_like Bromod 22.1 1.4E+02 0.003 20.5 3.4 30 13-46 40-69 (98)
58 PF00439 Bromodomain: Bromodom 21.9 1.4E+02 0.0031 18.9 3.4 31 12-46 34-64 (84)
59 cd07070 NR_LBD_SF-1 The ligand 21.7 1.3E+02 0.0027 24.0 3.5 33 17-52 175-207 (237)
60 cd06954 NR_LBD_LXR The ligand 21.4 1.2E+02 0.0027 23.8 3.5 34 17-53 176-209 (236)
61 cd06938 NR_LBD_EcR The ligand 21.4 1.3E+02 0.0028 23.7 3.5 34 17-52 170-203 (231)
62 cd05520 Bromo_polybromo_III Br 21.3 1.4E+02 0.003 20.6 3.3 40 3-46 26-74 (103)
63 PF12063 DUF3543: Domain of un 21.1 1.8E+02 0.0039 23.4 4.4 49 112-163 153-201 (238)
64 cd05507 Bromo_brd8_like Bromod 21.1 1.6E+02 0.0034 20.3 3.6 31 13-47 42-72 (104)
65 KOG2150|consensus 20.6 2.1E+02 0.0046 26.2 5.0 46 38-83 46-91 (575)
66 cd06935 NR_LBD_TR The ligand b 20.1 1.4E+02 0.003 23.8 3.5 33 17-52 184-216 (243)
No 1
>cd09248 BRO1_Rhophilin_1 Protein-interacting Bro1-like domain of RhoA-binding protein Rhophilin-1. This subfamily contains the Bro1-like domain of the RhoA-binding protein, Rhophilin-1. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding protein Rhophilin-2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Rhophilin-1 binds both GDP- and GTP-bound RhoA. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. In addition to this Bro1-like domain, Rhophilin-1 contains an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. The Drosophila knockout of the Rhophilin-1 is embryonic lethal, suggesting an essential role i
Probab=100.00 E-value=1.3e-48 Score=329.45 Aligned_cols=149 Identities=30% Similarity=0.547 Sum_probs=141.1
Q ss_pred CCCCCCCCCCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHHHHhHhccC
Q psy17538 4 FLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHESSLEVIYSYYDHLVSLESKIF 83 (164)
Q Consensus 4 ~l~iPlK~t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~~~~~~~~~~~~l~~Yy~qL~~l~~rfp 83 (164)
||+||+|+|.+|||.+||++||.++|+ ++|+.|++||.+|++||+++. .+..++++++.|.+||+||+.|+.|||
T Consensus 1 mi~lplK~T~~vDl~~pL~~yI~~~Y~---q~~~~y~~dl~~l~~LR~~~~--~~~~~~sgle~L~~YY~qL~~Le~RFp 75 (384)
T cd09248 1 MIPLGLKETKELDLPTPLKELISEHFG---EDGTSYEAEIRELEDLRQAMR--TPSRSEAGLELLMAYYNQLCFLDARFF 75 (384)
T ss_pred CCCCCCCcCCcCChHHHHHHHHHHHcC---CCHHHHHHHHHHHHHHHHHhc--CCCCChhHHHHHHHHHHHHHHHHhcCC
Confidence 899999999999999999999999999 889999999999999999854 567789999999999999999999999
Q ss_pred CCC--CccceeeccccccCCCCCCcccceecchhhhHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHHHh
Q psy17538 84 PAT--VNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYL 161 (164)
Q Consensus 84 ~~~--~~i~F~W~ds~~~~~~~~~~~~~~~~~l~fE~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~~l 161 (164)
+++ ++|+|+|+|+|+. .++++.++.|||+||||||||+|||+|+.++|.++||+|+||++||+|||||+||
T Consensus 76 ~~~~~~~v~FtW~Daf~~-------~~~~q~sl~FEKasVLFNigAL~Sqlaa~~~r~t~eGlK~A~~~FQ~AAG~F~~L 148 (384)
T cd09248 76 PPAKSLGLFFHWYDSLTG-------VPAQQRALAFEKGSVLFNIGALHTQIGARQDRSCTEGTRRAIDAFQRAAGAFSLL 148 (384)
T ss_pred CCcccccceeeeeccCCC-------CccccccHHHHHHHHHHhHHHHHHHHHhhccCCChHHHHHHHHHHHHHHHHHHHH
Confidence 864 7899999999983 5789999999999999999999999999999999999999999999999999999
Q ss_pred hcC
Q psy17538 162 KST 164 (164)
Q Consensus 162 ~e~ 164 (164)
+|+
T Consensus 149 ~e~ 151 (384)
T cd09248 149 REN 151 (384)
T ss_pred HHH
Confidence 985
No 2
>cd09244 BRO1_Rhophilin Protein-interacting Bro1-like domain of RhoA-binding protein Rhophilin and related domains. This family contains the Bro1-like domain of RhoA-binding proteins, Rhophilin-1 and -2, and related domains. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Rhophilin-1 and -2 bind both GDP- and GTP-bound RhoA. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. In addition to this Bro1-like domain, Rhophilin-1 and -2, contain an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. Their PDZ domains have limited homology. Rhophilin-1 and -2 have different ac
Probab=100.00 E-value=1.7e-48 Score=327.32 Aligned_cols=149 Identities=31% Similarity=0.627 Sum_probs=141.9
Q ss_pred CCCCCCCCCCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHHHHhHhccC
Q psy17538 4 FLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHESSLEVIYSYYDHLVSLESKIF 83 (164)
Q Consensus 4 ~l~iPlK~t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~~~~~~~~~~~~l~~Yy~qL~~l~~rfp 83 (164)
||+||+|+|.+|||.+||++||.++|+ ++|+.|++||.+|++||++++ .+..++++++.|.+||+||+.|+.|||
T Consensus 1 mi~l~lK~T~~vd~~~~L~~yI~~~Y~---e~~~~y~~~l~~l~~LR~~~~--~~~~~~~g~~~L~~YY~qL~~le~RFp 75 (350)
T cd09244 1 MIPLGLKETKEIDFMEPFKDFILEHYS---EDPSLYEDEIADFTDLRQAMR--TPSRDEAGIELLFEYYNQLYFVERRFF 75 (350)
T ss_pred CCCCCCCcCCcCChHHHHHHHHHHHcC---CCHHHHHHHHHHHHHHHHHhh--CCCCChhHHHHHHHHHHHHHHHHhcCC
Confidence 899999999999999999999999999 889999999999999999987 567789999999999999999999998
Q ss_pred CCC--CccceeeccccccCCCCCCcccceecchhhhHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHHHh
Q psy17538 84 PAT--VNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYL 161 (164)
Q Consensus 84 ~~~--~~i~F~W~ds~~~~~~~~~~~~~~~~~l~fE~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~~l 161 (164)
+++ ++|.|+|+|+|++ .+++++++.||||||||||||+|||+|+.++|.+++|+|+||++||+|||+|+||
T Consensus 76 ~~~~~~~v~F~W~Ds~~~-------~~~~q~sl~fEkasVLFNigAl~Sq~aa~~~r~~~eglK~A~~~Fq~AAG~F~~l 148 (350)
T cd09244 76 PPDRSLGIYFHWYDSLTG-------VPSVQRSVAFEKASVLFNIGALYTQIGAKQDRTTEEGIEAAVDAFQRAAGAFNYL 148 (350)
T ss_pred CccccccceeeeecccCC-------CccccccHHHHHHHHHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHH
Confidence 764 8899999999983 5789999999999999999999999999999999999999999999999999999
Q ss_pred hcC
Q psy17538 162 KST 164 (164)
Q Consensus 162 ~e~ 164 (164)
+||
T Consensus 149 ~e~ 151 (350)
T cd09244 149 REN 151 (350)
T ss_pred HHh
Confidence 985
No 3
>cd09240 BRO1_Alix Protein-interacting, N-terminal, Bro1-like domain of mammalian Alix and related domains. This family contains the N-terminal, Bro1-like domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), also called apoptosis-linked gene-2 interacting protein 1 (AIP1). It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also f
Probab=100.00 E-value=2.3e-47 Score=321.03 Aligned_cols=162 Identities=53% Similarity=0.864 Sum_probs=150.7
Q ss_pred CCCCCCCCCCCCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHHHHhHhc
Q psy17538 2 AEFLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHESSLEVIYSYYDHLVSLESK 81 (164)
Q Consensus 2 ~~~l~iPlK~t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~~~~~~~~~~~~l~~Yy~qL~~l~~r 81 (164)
++||+||+|+|.+|||.+||++||.++|+++ ++|+.|++||++|++||+++++..++.++++++.+.+||+||..|+.|
T Consensus 1 ~~~l~iplK~t~~vd~~~~l~~~I~~~y~~~-~~~~~~~~~l~~l~~lR~~~~~~~~~~~~~~~~~l~~Yy~qL~~l~~r 79 (346)
T cd09240 1 ASFISVPLKKSSEVDLVKPLEKFIKNTYSSG-EEQADYKEAIKELNKLRNNAVCRPLDKHESSLELLLRYYDQLCAIEPK 79 (346)
T ss_pred CCeeeccCcCCCcCChHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHHHHHHhhcCCCCcchhHHHHHHHHHHHHHHHHhc
Confidence 4799999999999999999999999999965 689999999999999999997555567789999999999999999999
Q ss_pred cCCCC--CccceeeccccccCCCCCCcccceecchhhhHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHH
Q psy17538 82 IFPAT--VNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFN 159 (164)
Q Consensus 82 fp~~~--~~i~F~W~ds~~~~~~~~~~~~~~~~~l~fE~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~ 159 (164)
||.++ ++|+|+|+|+|+++++++++.++++.++.||++||||||||++|++|+.++|.++||+|+||++||+|||+|+
T Consensus 80 fp~~~~~~~v~F~W~d~~~~~~~~~~~~~~~~~~l~fEka~vlfNiaal~s~la~~~~~~~~eglK~A~~~fq~AAG~F~ 159 (346)
T cd09240 80 FPFSESQIQVTFTWKDAFDKGSLFGGSKKLALSSLGYEKVCVLFNIAALQSQIAAEQNLDTDEGLKLAAKLFQQAAGIFN 159 (346)
T ss_pred CCCCcccccceeeeecccccccccCCCcccccccHHHHHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHH
Confidence 99865 8899999999998777766677899999999999999999999999999999999999999999999999999
Q ss_pred HhhcC
Q psy17538 160 YLKST 164 (164)
Q Consensus 160 ~l~e~ 164 (164)
||+|+
T Consensus 160 ~l~e~ 164 (346)
T cd09240 160 HLKET 164 (346)
T ss_pred HHHHh
Confidence 99985
No 4
>cd09249 BRO1_Rhophilin_2 Protein-interacting Bro1-like domain of RhoA-binding protein Rhophilin-2. This subfamily contains the Bro1-like domain of RhoA-binding protein, Rhophilin-2. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding protein Rhophilin-1, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Rhophilin-2, binds both GDP- and GTP-bound RhoA. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. In addition to this Bro1-like domain, Rhophilin-2 contains an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. Roles for Rhophilin-2 may include limiting stress fiber formation or increasing the turnover of F-
Probab=100.00 E-value=2.4e-47 Score=321.58 Aligned_cols=149 Identities=33% Similarity=0.578 Sum_probs=141.0
Q ss_pred CCCCCCCCCCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHHHHhHhccC
Q psy17538 4 FLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHESSLEVIYSYYDHLVSLESKIF 83 (164)
Q Consensus 4 ~l~iPlK~t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~~~~~~~~~~~~l~~Yy~qL~~l~~rfp 83 (164)
||+||+|+|.+|||.+||++||.++|+ ++|+.|++||.+|++||+++ +.+..++++++.|.+||+||+.|+.|||
T Consensus 1 ~i~lplK~T~~VD~~~pL~~yI~~~Y~---q~~~~y~~dl~~l~~LR~~~--~~~~~~~sg~e~L~~YY~qL~~Le~RFp 75 (385)
T cd09249 1 LIPLGLKETKDVDFSVPLKDFILEHYS---EDGSEYEDEIADLMDLRQAC--RTPSRDEAGVELLMSYFSQLGFLENRFF 75 (385)
T ss_pred CCCCCCCcCCccChHHHHHHHHHHHcC---CCHHHHHHHHHHHHHHHHHh--cCCCCChhHHHHHHHHHHHHHHHHhhCC
Confidence 799999999999999999999999999 88999999999999999985 3667889999999999999999999999
Q ss_pred CCC--CccceeeccccccCCCCCCcccceecchhhhHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHHHh
Q psy17538 84 PAT--VNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYL 161 (164)
Q Consensus 84 ~~~--~~i~F~W~ds~~~~~~~~~~~~~~~~~l~fE~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~~l 161 (164)
+++ ++|+|+|+|+|++ .++++.++.||++||||||||+|||+|+.++|.+++|+|+||.+||+|||+|+||
T Consensus 76 ~~~~~~~v~FtW~Dsf~~-------~~~~q~sl~fEkasVLFNigAl~Sqlaa~~~r~t~eGlK~A~~~FQ~AAG~F~~L 148 (385)
T cd09249 76 PPTRQMGILFTWYDSFTG-------VPVSQQNLLLEKASILFNIGALYTQIGTRCNRQTQAGLESAVDAFQRAAGVLNYL 148 (385)
T ss_pred CCcccccceeeeeccCCC-------CccccccHHHHHHHHHHhHHHHHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHH
Confidence 754 8899999999982 5789999999999999999999999999999999999999999999999999999
Q ss_pred hcC
Q psy17538 162 KST 164 (164)
Q Consensus 162 ~e~ 164 (164)
+|+
T Consensus 149 ~e~ 151 (385)
T cd09249 149 KET 151 (385)
T ss_pred HHh
Confidence 985
No 5
>cd09239 BRO1_HD-PTP_like Protein-interacting, N-terminal, Bro1-like domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains. This family contains the N-terminal, Bro1-like domain of mammalian His-Domain type N23 protein tyrosine phosphatase (HD-PTP) and related domains. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. HD-PTP participates in cell migration and endosomal trafficking. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-l
Probab=100.00 E-value=1.2e-46 Score=318.04 Aligned_cols=150 Identities=29% Similarity=0.476 Sum_probs=141.7
Q ss_pred CCCCCCCCCCCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHHHHhHhcc
Q psy17538 3 EFLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHESSLEVIYSYYDHLVSLESKI 82 (164)
Q Consensus 3 ~~l~iPlK~t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~~~~~~~~~~~~l~~Yy~qL~~l~~rf 82 (164)
|||+||+|+|.+|||.+||++||.++|+ ++|+.|++||++|++||++++ .+..++++++.|.+||+||+.|+.||
T Consensus 7 p~l~iplK~t~~vd~~~~L~~~I~~~y~---~~~~~~~~~l~~l~~LR~~~~--~~~~~~~~~~~l~~Yy~qL~~l~~rf 81 (361)
T cd09239 7 PMLWLQLKSSGEFTFQPALKKYILENYG---EDPELYSEELKSLEQLRQEAV--NPPRDFEGCSVLKRYYGQLHLLQSRF 81 (361)
T ss_pred CccccCCCCCCCCchHHHHHHHHHHHhC---CCHHHHHHHHHHHHHHHHHhc--cCCCChHHHHHHHHHHHHHHHHHhcC
Confidence 8999999999999999999999999999 889999999999999999987 45667899999999999999999999
Q ss_pred CCCC---CccceeeccccccCCCCCCcccceecchhhhHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHH
Q psy17538 83 FPAT---VNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFN 159 (164)
Q Consensus 83 p~~~---~~i~F~W~ds~~~~~~~~~~~~~~~~~l~fE~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~ 159 (164)
|++. ++|+|+|+|+|++ .++++.++.||++||||||||+|||+|+.++|.++||+|+||++||+|||+|+
T Consensus 82 p~~~~~~~~v~F~W~d~~~~-------~~~~~~~l~fEka~vlfNigal~sq~a~~~~r~~~~glK~A~~~fq~AAG~F~ 154 (361)
T cd09239 82 PMGAGQEAAVPFTWTDIFSG-------SEVTHEDIKFEEASVLYNIGALHSQLGASDKRDSEEGMKVACTHFQCAAWAFA 154 (361)
T ss_pred CCCccccccceeeeecccCC-------CchhhhhHHHHHHHHHHHHHHHHHHHHHhccCCChHHHHHHHHHHHHHHHHHH
Confidence 9863 6899999999973 57789999999999999999999999999999999999999999999999999
Q ss_pred HhhcC
Q psy17538 160 YLKST 164 (164)
Q Consensus 160 ~l~e~ 164 (164)
||+|+
T Consensus 155 ~l~e~ 159 (361)
T cd09239 155 YLREH 159 (361)
T ss_pred HHHHh
Confidence 99985
No 6
>cd09241 BRO1_ScRim20-like Protein-interacting, N-terminal, Bro1-like domain of Saccharomyces cerevisiae Rim20 and related proteins. This family contains the N-terminal, Bro1-like domain of Saccharomyces cerevisiae Rim20 (also known as PalA) and related proteins. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Saccharomyces cerevisiae Bro1, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Rim20 and Rim23 participate in the response to the external pH via the Rim101 pathway. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind comp
Probab=100.00 E-value=2.9e-45 Score=309.21 Aligned_cols=151 Identities=31% Similarity=0.503 Sum_probs=142.1
Q ss_pred CCCCCCCCCCCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHHHHhHhcc
Q psy17538 3 EFLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHESSLEVIYSYYDHLVSLESKI 82 (164)
Q Consensus 3 ~~l~iPlK~t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~~~~~~~~~~~~l~~Yy~qL~~l~~rf 82 (164)
+||+||+|+|.+|||.+||++||.++|+ ++|+.|++||++|++||++++ .+.+++++++.+.+||.||+.|+.||
T Consensus 1 ~~l~ip~K~t~~vd~~~~l~~~I~~~y~---~~~~~~~~dl~~l~~lR~~~~--~~~~~~~~~~~l~~Yy~~L~~l~~rf 75 (355)
T cd09241 1 NLLSIPFKRTLPVDLKDALRNYISNHYF---QTPSSFEDDLAEIDKLRNDAI--NPEPSVNGLSLLKEYYAQLVVLSKKF 75 (355)
T ss_pred CcCccCCCcCCcCCHHHHHHHHHHHhcC---CCHHHHHHHHHHHHHHHHHhh--CCCCChhHHHHHHHHHHHHHHHHhcC
Confidence 6899999999999999999999999999 889999999999999999997 44779999999999999999999999
Q ss_pred CCCCCccceeeccccccCCCCCCcccceecchhhhHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHHHhh
Q psy17538 83 FPATVNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYLK 162 (164)
Q Consensus 83 p~~~~~i~F~W~ds~~~~~~~~~~~~~~~~~l~fE~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~~l~ 162 (164)
| +.+|+|+|+|+|++++ ..++++.++.||++|||||+||+|||+|..++|.+++|+|+||++||+|||+|+||+
T Consensus 76 p--~~~i~F~W~d~~~~~~----~~~~~~~~l~fEka~VLfNigal~sq~a~~~~~~~~~glK~A~~~fq~AAG~F~~l~ 149 (355)
T cd09241 76 P--DDQLEFTWYPTLGYKS----SGPVSLSSLKFERANILYNLGALYSQLALSENRYTDEGLKRACSYFQASAGCFEYIL 149 (355)
T ss_pred C--CcCCceeeecccCCCC----CCceeeccHHHHHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHH
Confidence 9 6889999999998631 257899999999999999999999999999999999999999999999999999999
Q ss_pred cC
Q psy17538 163 ST 164 (164)
Q Consensus 163 e~ 164 (164)
|+
T Consensus 150 ~~ 151 (355)
T cd09241 150 QH 151 (355)
T ss_pred Hh
Confidence 85
No 7
>cd09242 BRO1_ScBro1_like Protein-interacting, N-terminal, Bro1-like domain of Saccharomyces cerevisiae Bro1 and related proteins. This family contains the N-terminal, Bro1-like domain of Saccharomyces cerevisiae Bro1 and related proteins. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Saccharomyces cerevisiae Rim20 (also known as PalA), Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Bro1 participates in endosomal trafficking. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: Snf7 in the
Probab=100.00 E-value=3.1e-45 Score=308.35 Aligned_cols=150 Identities=32% Similarity=0.521 Sum_probs=141.8
Q ss_pred CCCCCCCCCCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHHHHhHhccC
Q psy17538 4 FLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHESSLEVIYSYYDHLVSLESKIF 83 (164)
Q Consensus 4 ~l~iPlK~t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~~~~~~~~~~~~l~~Yy~qL~~l~~rfp 83 (164)
||+||+|+|.+|||.+||++||.++|+ ++|+.|++||++|++||++++ .+..++++++.+.+||+||+.|+.|||
T Consensus 1 ~l~lplK~t~~vd~~~~L~~~I~~~y~---~~~~~~~~~l~~l~~lR~~~~--~~~~~~~~~~~l~~Yy~qL~~l~~rfp 75 (348)
T cd09242 1 LISLPLKDTEEVDWKKPLSSYLKRSYG---SSTFYYEEEIAEFDRLRQDAN--GVLADETGRDLLYKYYGQLELLELRFP 75 (348)
T ss_pred CCCCCCCcCCccChHHHHHHHHHHHcC---CCHHHHHHHHHHHHHHHHHhc--CCCCCHHHHHHHHHHHHHHHHHHhhcC
Confidence 799999999999999999999999999 889999999999999999997 345589999999999999999999999
Q ss_pred CCC--CccceeeccccccCCCCCCcccceecchhhhHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHHHh
Q psy17538 84 PAT--VNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYL 161 (164)
Q Consensus 84 ~~~--~~i~F~W~ds~~~~~~~~~~~~~~~~~l~fE~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~~l 161 (164)
+++ .+|+|+|+|+|++ +.++++.++.||++|||||+|++||++|..++|.+++|+|+||++||+|||+|+||
T Consensus 76 ~~~~~~~v~F~W~d~~~~------~~~~~~~sl~fEka~VLfNiaal~s~~A~~~~~~~~~~~K~A~~~fq~AAG~f~~l 149 (348)
T cd09242 76 FNNKELKVDFTWYDAFYK------SKKVKQHSLAFEKASVLFNIGALLSQLAAEKYREDEDDLKEAITNLQQAAGCFQYI 149 (348)
T ss_pred CCCccccceeeeeecCCC------CCceeecchHHHHHHHHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHH
Confidence 864 8899999999984 36889999999999999999999999999999999999999999999999999999
Q ss_pred hcC
Q psy17538 162 KST 164 (164)
Q Consensus 162 ~e~ 164 (164)
+|+
T Consensus 150 ~e~ 152 (348)
T cd09242 150 NEN 152 (348)
T ss_pred HHh
Confidence 975
No 8
>cd09246 BRO1_Alix_like_1 Protein-interacting, N-terminal, Bro1-like domain of an Uncharacterized family of the BRO1_Alix_like superfamily. This domain family is comprised of uncharacterized proteins. It belongs to the BRO1_Alix_like superfamily which includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20 and Rim23 interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP and Bro
Probab=100.00 E-value=1.2e-44 Score=305.23 Aligned_cols=151 Identities=30% Similarity=0.524 Sum_probs=139.5
Q ss_pred CCCCCCCCCCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhhccC-CChhhHHHHHHHHHHHHHhHhcc
Q psy17538 4 FLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFE-KHESSLEVIYSYYDHLVSLESKI 82 (164)
Q Consensus 4 ~l~iPlK~t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~~~~-~~~~~~~~l~~Yy~qL~~l~~rf 82 (164)
||+||+|+|.+|||.+||++||.++|++ ++|+.|++||.+|++||++++ .+. .++++++.+.+||+||+.|+.||
T Consensus 1 ~l~ip~K~t~~vd~~~~L~~~I~~~y~~--~~~~~~~~~l~~l~~LR~~~~--~~~~~~~~~~~~l~~Yy~~L~~l~~rf 76 (353)
T cd09246 1 MLSIHRKKTETVDLVSPLRAYISETYSE--REAQDAEDDLAELQQLRSEVR--TLQEKHAASRELLLRYYRALCAVESRF 76 (353)
T ss_pred CCCCCCCcccccchHhHHHHHHHHHcCC--cCHHHHHHHHHHHHHHHHHhh--cCCCCChhHHHHHHHHHHHHHHHHccC
Confidence 7999999999999999999999999994 358999999999999999987 333 35789999999999999999999
Q ss_pred CCCC----CccceeeccccccCCCCCCcccceecchhhhHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHH
Q psy17538 83 FPAT----VNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIF 158 (164)
Q Consensus 83 p~~~----~~i~F~W~ds~~~~~~~~~~~~~~~~~l~fE~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f 158 (164)
|+++ .+|+|+|+|+|++ +.++++.++.||++|||||+||+|||+|+.++|.+++|+|+||++||+|||+|
T Consensus 77 p~~~~~~~~~v~F~W~d~~~~------~~~~~~~sl~fEka~vlfNiaal~s~~a~~~~~~~~~glK~A~~~fq~AAG~F 150 (353)
T cd09246 77 PISEESGHARVSFSWYDAFRP------HRKATQANVHFEKAAVLFNLGALSSQLGLQQDRTTAEGIKQACHAFQAAAGAF 150 (353)
T ss_pred CCCcccccccceeEeeccCCC------CcceeecchHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHH
Confidence 9863 6899999999984 36889999999999999999999999999999999999999999999999999
Q ss_pred HHhhcC
Q psy17538 159 NYLKST 164 (164)
Q Consensus 159 ~~l~e~ 164 (164)
+||+|+
T Consensus 151 ~~l~e~ 156 (353)
T cd09246 151 AHLRDK 156 (353)
T ss_pred HHHHHh
Confidence 999975
No 9
>PF03097 BRO1: BRO1-like domain; InterPro: IPR004328 The BRO1 domain has about 390 residues and occurs in a number of eukaryotic proteins such as yeast BRO1 and human PDCD6IP/Alix that are involved in protein targeting to the vacuole or lysosome. The BRO1 domain of fungal and mammalian proteins binds with multivesicular body components (ESCRT-III proteins) such as yeast Snf7 and mammalian CHMP4b, and can function to target BRO1 domain-containing proteins to endosomes [, , ]. The BRO1 domain has a boomerang shape composed of 14 alpha-helices and 3 beta-sheets. It contains a TPR-like substructure in the central part []. The C terminus is less conserved. This domain is found in a number of signal transduction proteins. The Saccharomyces cerevisiae protein Bro1p is required for sorting endocytic cargo to the lumen of multivesicular bodies (MVBs). Alix appears to be the mammalian orthologue of Bro1p []. Alix is also involved in the ESCRT pathway, which facilitates membrane fission events during enveloped virus budding, multivesicular body formation, and cytokinesis. To promote HIV budding and cytokinesis, the ALIX protein must bind and recruit CHMP4 subunits of the ESCRT-III complex. The Bro1 domain of ALIX binds specifically to C-terminal residues of the human CHMP4 proteins [, ]. Likewise, the Homo sapiens Brox protein has a Bro1 domain. CHMP4 proteins are components of endosomal sorting complex required for transport III, via their Bro1 domains and to play roles in sorting of ubiquitinated cargoes []. Alix also binds to the nucleocapsid (NC) domain of HIV-1 Gag. Alix and the Bro1 domain can be specifically packaged into viral particles via the NC []. Myopic is the Drosophila homologue of the Bro1-domain tyrosine phosphatase HD-PTP, and it promotes the epidermal growth factor receptor (EGFR) signalling []. The Caenorhabditis elegans Bro1-domain protein, ALX-1, interacts with LIN-12/Notch. The EGO-2 protein also contains a Bro1 domain. Notch-type signalling mediates numerous inductive events during development [].; PDB: 2VSV_A 1ZB1_A 3UM3_A 3ULY_A 3R9M_A 3ZXP_A 3UM2_A 3UM0_A 3UM1_D 3RAU_B ....
Probab=100.00 E-value=9.6e-41 Score=282.58 Aligned_cols=151 Identities=42% Similarity=0.667 Sum_probs=128.7
Q ss_pred CCCCCCCCCCCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhhcc-CCChhhHHHHHHHHHHHHHhHhc
Q psy17538 3 EFLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVF-EKHESSLEVIYSYYDHLVSLESK 81 (164)
Q Consensus 3 ~~l~iPlK~t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~~~-~~~~~~~~~l~~Yy~qL~~l~~r 81 (164)
|||+||+|+|.++||.++|++||.++|+ ++|+.|+++|+++++||++++ .+ ++++++++.+.+||.||..|+.|
T Consensus 1 ~~~~lplK~t~~vd~~~~l~~~i~~~y~---~~~~~~~~~l~~l~~lR~~~~--~~~~~~~~~~~~l~~Y~~~L~~l~~~ 75 (377)
T PF03097_consen 1 PMLSLPLKKTKEVDLKKPLKKYISSHYG---EDPDSFDEDLKELDKLRQDAR--NPQSPSESGLKLLEEYYPQLESLEKR 75 (377)
T ss_dssp ---------BEEE-CHHHHHHHHHHHCS---SCCHCCHHHHHHHHHHHHHHH--TSS-SSHHHHHHHHHHHHHHHHHCCC
T ss_pred CcCCCCCCCCCCCCHHHHHHHHHHHHhC---CCHHHHHHHHHHHHHHHHHHh--ccCCCchhHHHHHHHHHHHHHHHHHh
Confidence 7999999999999999999999999998 889999999999999999997 44 78899999999999999999999
Q ss_pred cCCCCCccceeeccccccCCCCCCcccceecchhhhHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHHHh
Q psy17538 82 IFPATVNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYL 161 (164)
Q Consensus 82 fp~~~~~i~F~W~ds~~~~~~~~~~~~~~~~~l~fE~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~~l 161 (164)
||...++|.|+|+|+|.+ +.+++++++.||++|||||+|++|+++|+.++|.+++|+|+|+++||+|||+|+||
T Consensus 76 ~p~~~~~i~F~W~d~~~~------~~~~~~~~~~fE~a~vL~N~aa~~s~~a~~~~~~~~~~~k~A~~~fq~AAg~f~~l 149 (377)
T PF03097_consen 76 FPSDQIQISFTWSDSLST------GKPVSQSSLAFEKACVLFNIAALYSQLAASQNRSTDEGLKEACNYFQRAAGIFQYL 149 (377)
T ss_dssp SCSSCCTT-EEEE-TTST------TSEEEESSHHHHHHHHHHHHHHHHHHHHHHS-TTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred cccccceeeEeeeccccC------CCcccchhhHHHHHHHHHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHHHHHHH
Confidence 995447899999999964 36899999999999999999999999999999999999999999999999999999
Q ss_pred hcC
Q psy17538 162 KST 164 (164)
Q Consensus 162 ~e~ 164 (164)
+++
T Consensus 150 ~~~ 152 (377)
T PF03097_consen 150 REN 152 (377)
T ss_dssp HHH
T ss_pred HHh
Confidence 873
No 10
>cd09034 BRO1_Alix_like Protein-interacting Bro1-like domain of mammalian Alix and related domains. This superfamily includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and Rhophilin-2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Brox, Bro1 and Rim20 interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to
Probab=100.00 E-value=1.2e-37 Score=261.11 Aligned_cols=151 Identities=35% Similarity=0.560 Sum_probs=135.5
Q ss_pred CCCCCCCCCCCCCchHHHHHHHHhhCCCCcc-cHHHHHHHHHHHHHHHHHHhhhccC--CChhhHHHHHHHHHHHHHhHh
Q psy17538 4 FLAVPLKKPTDVDIIKPLKNLIALQFPNDNE-KLDILNEKLNLFSKLRTAAVWKVFE--KHESSLEVIYSYYDHLVSLES 80 (164)
Q Consensus 4 ~l~iPlK~t~~~d~~~~l~~~I~~~y~~~~~-~~~~~~~dl~~l~~LR~~~~~~~~~--~~~~~~~~l~~Yy~qL~~l~~ 80 (164)
||++|+|+|.++||..+|++||.++|+ + +++.|+++|+++++||++++....+ ..+++++.|.+||.+|..|+.
T Consensus 1 ~i~~plk~t~~vd~~~~l~~~i~~~~~---~~~~~~~~~~l~~~~~lR~~~~~~~~~~~~~~~~~~~l~~Y~~~L~~l~~ 77 (345)
T cd09034 1 FIGLPLKKTKEVDVKVPLSKFIPKNYG---ELEATAVEDLIEKLSKLRNNIVTEQNNDTTCENLLEALKEYLPYLLGLEK 77 (345)
T ss_pred CCCCCCCCCceeeechhhHHHhhHhhC---cccchhhHHHHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHHHHHHHHh
Confidence 689999999999999999999999999 5 7899999999999999998733212 138899999999999999999
Q ss_pred ccCCCC--CccceeeccccccCCCCCCcccceecchhhhHHHHHHHHHHHHHHHHHhCCCCC-hhhHHHHHHHHHHHHHH
Q psy17538 81 KIFPAT--VNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAALQSAIAQAQSLDT-DEGLKLAAKMLQSSAGI 157 (164)
Q Consensus 81 rfp~~~--~~i~F~W~ds~~~~~~~~~~~~~~~~~l~fE~a~vLfNiaa~~s~~a~~~~~~~-~~~~K~A~~~fq~AAg~ 157 (164)
|||.+. .+++|+|+|+|++ +++... ++.||++|||||+|++||++|..+++.+ ++|+|.||++||+|||+
T Consensus 78 ~~~~~~~~~~i~F~W~d~~~~------~~~~~~-~l~fE~~~vLfn~aa~~s~~a~~~~~~~~~~~~k~A~~~fq~AAG~ 150 (345)
T cd09034 78 KLPFQKLRDNVEFTWTDSFDT------KKESAT-SLRYELLSILFNLAALASQLANEKLITGSEEDLKQAIKSLQKAAGY 150 (345)
T ss_pred cCCcccccccceeEeecccCC------Ccchhh-hHHHHHHHHHHHHHHHHHHHHHhccCCCchHHHHHHHHHHHHHHHH
Confidence 999643 7899999999985 244445 9999999999999999999999999988 89999999999999999
Q ss_pred HHHhhcC
Q psy17538 158 FNYLKST 164 (164)
Q Consensus 158 f~~l~e~ 164 (164)
|+||+++
T Consensus 151 F~~l~~~ 157 (345)
T cd09034 151 FEYLKEH 157 (345)
T ss_pred HHHHHHh
Confidence 9999874
No 11
>KOG2220|consensus
Probab=100.00 E-value=9.7e-33 Score=249.13 Aligned_cols=152 Identities=43% Similarity=0.664 Sum_probs=138.9
Q ss_pred CCCC-CCCCCCCCCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHHHHhH
Q psy17538 1 MAEF-LAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHESSLEVIYSYYDHLVSLE 79 (164)
Q Consensus 1 m~~~-l~iPlK~t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~~~~~~~~~~~~l~~Yy~qL~~l~ 79 (164)
|..+ +++|+|+|.++||.+||.+||...|+ +.+....++++++.+||..++ ....+.++.+.+.+||.||+.|+
T Consensus 1 M~~~~~~~~lK~t~e~d~~~~l~~~i~~~y~---~~~~~~~~~i~~~~~lR~~a~--~~~~~~~~~~~l~~yy~qL~~l~ 75 (714)
T KOG2220|consen 1 METLPLPIPLKKTSEVDFLKPLSKLIQLSYG---ESQENRNDAIEKLEKLRNNAN--GVPKPSEGLEVLKRYYGQLCYLE 75 (714)
T ss_pred CCccccCcccccCCccchhhhHHHHHHHhcC---CchhhHHHHHHHHHHHHhccc--cCCcchhhhHHHHHHHHHHHHHH
Confidence 7766 99999999999999999999999999 666666799999999999997 33467889999999999999999
Q ss_pred hccCCCCCccc-eeeccccccCCCCCCcccceecchhhhHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHH
Q psy17538 80 SKIFPATVNIP-FRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIF 158 (164)
Q Consensus 80 ~rfp~~~~~i~-F~W~ds~~~~~~~~~~~~~~~~~l~fE~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f 158 (164)
.|||+++.+++ |+|+|+|.++ ..++++.+|.||++|||||||++|+++|+.++|.+.+|+|.||++||.|||||
T Consensus 76 ~r~p~~~~~~~~F~W~d~~~~~-----~~~~~~~~L~fEka~vLfni~~l~s~iaa~~~~~~~d~~k~a~~~fq~aagaf 150 (714)
T KOG2220|consen 76 SRFPMSENEIEEFTWKDAFDSG-----AKKVTQISLGFEKACVLFNIAALYSQIAAHQSRETVDGYKAAIAHFQAAAGAF 150 (714)
T ss_pred HhcCcccccccceeeeecccCC-----ccceeeccchhhHHHHHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHHHH
Confidence 99999764444 9999999862 37899999999999999999999999999999999999999999999999999
Q ss_pred HHhh
Q psy17538 159 NYLK 162 (164)
Q Consensus 159 ~~l~ 162 (164)
.|++
T Consensus 151 ~~l~ 154 (714)
T KOG2220|consen 151 RYLS 154 (714)
T ss_pred Hhhc
Confidence 9998
No 12
>cd09243 BRO1_Brox_like Protein-interacting Bro1-like domain of human Brox1 and related proteins. This family contains the Bro1-like domain of a single-domain protein, human Brox, and related domains. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: CHMP4 in the case of Brox. Human Brox can bind to human immunodeficiency virus type 1 (
Probab=99.92 E-value=3.3e-24 Score=180.76 Aligned_cols=143 Identities=20% Similarity=0.229 Sum_probs=111.3
Q ss_pred CCCCCCCCCCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhh--ccCCC-hhhHHHHHHHHHHHHHhHh
Q psy17538 4 FLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWK--VFEKH-ESSLEVIYSYYDHLVSLES 80 (164)
Q Consensus 4 ~l~iPlK~t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~--~~~~~-~~~~~~l~~Yy~qL~~l~~ 80 (164)
|=+.|||.|.+++|. ++ .... + ....+-+.++..-|..++.. ++..+ .+....+.+|...|.+|..
T Consensus 2 ~~r~~~k~t~~~~f~--~~----~~~~----~-~~~~~~~~~~~~~r~~l~~~~~~~~~~~~~~~~a~~~Yl~ll~g~~~ 70 (353)
T cd09243 2 FHRNPLKATAPVKFD--LK----GVAT----T-PAASKLCSDLRTARARLLELLSDPSNDVDTVKTAFNAYLSLLQGFIL 70 (353)
T ss_pred CCCCccccccccccc--cc----cccC----C-hhHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence 346899999999995 22 2222 2 26778889999999988754 33334 3467899999999999975
Q ss_pred ccCC--CC----CccceeeccccccCCCCCCcccceecchhhhHHHHHHHHHHHHHHHHHhC----CCCChhhHHHHHHH
Q psy17538 81 KIFP--AT----VNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAALQSAIAQAQ----SLDTDEGLKLAAKM 150 (164)
Q Consensus 81 rfp~--~~----~~i~F~W~ds~~~~~~~~~~~~~~~~~l~fE~a~vLfNiaa~~s~~a~~~----~~~~~~~~K~A~~~ 150 (164)
-..- ++ -.|.|+|+|+|.+ +.++++.++.||++|||||||++|+++|+.. ++ ++||+|+||++
T Consensus 71 ~~d~~~~~~~l~~~v~F~W~dsl~~------~~~~~q~sl~fEk~sVLfNigal~s~~As~~~~~~~~-s~e~~K~A~~~ 143 (353)
T cd09243 71 ALDGKTQESKLRYLINFKWTDSLLG------NEPSVQQDAIFELASMLFNVALWYTKHASKLAGKEDI-TEDEAKDVHKS 143 (353)
T ss_pred cccccCCccccceeeeEEEECCCCC------CCceeeccHHHHHHHHHHHHHHHHHHHHHHHhccCCC-CcHHHHHHHHH
Confidence 3211 11 5799999999963 3688999999999999999999998876554 34 44999999999
Q ss_pred HHHHHHHHHHhhcC
Q psy17538 151 LQSSAGIFNYLKST 164 (164)
Q Consensus 151 fq~AAg~f~~l~e~ 164 (164)
||+|||+|+||+|+
T Consensus 144 fq~AAG~F~~l~e~ 157 (353)
T cd09243 144 LRTAAGIFQFVKEN 157 (353)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999985
No 13
>cd09245 BRO1_UmRIM23-like Protein-interacting, Bro1-like domain of Ustilago maydis Rim23 (PalC), and related domains. This family contains the Bro1-like domain of Ustilago maydis Rim23 (also known as PalC), and related proteins. It belongs to the BRO1_Alix_like superfamily which includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23 interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Rim20 and Rim23 participate in the response to the external pH via the Rim101 pathway. Through its Bro1-like domain, Rim23 allows the interaction between the endosomal and plasma membrane complexes. Bro1-like domains are boomerang-shape, and part of the domain is a tetratricop
Probab=99.89 E-value=1.4e-22 Score=174.09 Aligned_cols=102 Identities=25% Similarity=0.381 Sum_probs=88.7
Q ss_pred hhhHHHHHHHHHHHHHhHhccCCCC----CccceeeccccccCCCCCCcccceecchhhhHHHHHHHHHHHHHHHHHhC-
Q psy17538 62 ESSLEVIYSYYDHLVSLESKIFPAT----VNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAALQSAIAQAQ- 136 (164)
Q Consensus 62 ~~~~~~l~~Yy~qL~~l~~rfp~~~----~~i~F~W~ds~~~~~~~~~~~~~~~~~l~fE~a~vLfNiaa~~s~~a~~~- 136 (164)
.+.++.|.+||.+|..|+.+||.++ ..|.|+|+|+|..++ ..++..+++.++.||+++||||+|++||++|...
T Consensus 57 ~~~~~aL~~Ylp~L~~l~~~~~~~~~~l~~~i~F~W~~tl~~~~-~~~~~~~~~~sl~fE~a~VLfnla~l~S~~A~~~l 135 (413)
T cd09245 57 LTVVKALEEYLPYLLAIDACLSHDELILKSEPTFEWRTTLSSTS-GRESPRLPLPGLHYELAFVLLTYAYALSNLARSIL 135 (413)
T ss_pred HHHHHHHHHHHHHHHHHHccCCcchhcccccceeEeecccccCC-CCCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5688999999999999999999753 469999999998543 1222458999999999999999999999999983
Q ss_pred --------C--------CCChhhHHHHHHHHHHHHHHHHHhhcC
Q psy17538 137 --------S--------LDTDEGLKLAAKMLQSSAGIFNYLKST 164 (164)
Q Consensus 137 --------~--------~~~~~~~K~A~~~fq~AAg~f~~l~e~ 164 (164)
+ +.++||+|.||++||+|||||+||+++
T Consensus 136 ~~~~~~~~~~~is~~~~~~~~e~lK~A~~~l~~AAGvf~~L~~~ 179 (413)
T cd09245 136 APLGAYETDRSISDASRKQRDERLKAATKLLCKAAGIFDYLATR 179 (413)
T ss_pred cccccccccccccccccccchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 2 677999999999999999999999874
No 14
>cd09247 BRO1_Alix_like_2 Protein-interacting Bro1-like domain of an Uncharacterized family of the BRO1_Alix_like superfamily. This domain family is comprised of uncharacterized proteins. It belongs to the BRO1_Alix_like superfamily which includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20 and Rim23 interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP and Bro1 function in
Probab=99.78 E-value=5.4e-19 Score=148.99 Aligned_cols=96 Identities=26% Similarity=0.331 Sum_probs=75.5
Q ss_pred hHHHHHHHHHHHHHhHhccCC--CCCccceeeccccccCCCCCCcccceecchhhhHHHHHHHHHHHHHHHHHhCCCCCh
Q psy17538 64 SLEVIYSYYDHLVSLESKIFP--ATVNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAALQSAIAQAQSLDTD 141 (164)
Q Consensus 64 ~~~~l~~Yy~qL~~l~~rfp~--~~~~i~F~W~ds~~~~~~~~~~~~~~~~~l~fE~a~vLfNiaa~~s~~a~~~~~~~~ 141 (164)
.+..|..|...|..+..++-. -..+++|+|+|+|++. .++..+++.++.||++|||||+|++||++|..+.+.
T Consensus 59 yl~~L~~~~~~L~~~~~~~~~~~l~~~i~F~W~~~l~~~---~~~~~~~~~sl~fE~~~vLfn~aa~~s~~A~~~~~~-- 133 (346)
T cd09247 59 YLPYLEGYLPALENLVNHRDKVQLNEQLSFRWTSGLGSS---KGPKAFQSDSLRFELGMVLFLYGAALRERASEVLPT-- 133 (346)
T ss_pred HHHHHHHHHHhhccCCccchHHhhcccCceeeecccCCC---CCCceeeccchHHHHHHHHHHHHHHHHHHHHHhccH--
Confidence 455566666666666655410 0268999999999841 012456788999999999999999999999987664
Q ss_pred hhHHHHHHHHHHHHHHHHHhhcC
Q psy17538 142 EGLKLAAKMLQSSAGIFNYLKST 164 (164)
Q Consensus 142 ~~~K~A~~~fq~AAg~f~~l~e~ 164 (164)
||+|.||++||+|||||+||+++
T Consensus 134 e~~K~A~~~l~~AAG~f~~l~~~ 156 (346)
T cd09247 134 EDFKEAATHLRRAAGVFEFLAHD 156 (346)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 89999999999999999999874
No 15
>KOG2220|consensus
Probab=98.15 E-value=4.7e-06 Score=76.49 Aligned_cols=147 Identities=19% Similarity=0.160 Sum_probs=109.1
Q ss_pred CCCCCCCCCCCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHHHHhHhc-
Q psy17538 3 EFLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHESSLEVIYSYYDHLVSLESK- 81 (164)
Q Consensus 3 ~~l~iPlK~t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~~~~~~~~~~~~l~~Yy~qL~~l~~r- 81 (164)
+|+++.++++..+++..+|...|.-++.. ++++.|+..+..|+..|.... .+..+.-+.+.+.. +.++.....+
T Consensus 102 ~~~~L~fEka~vLfni~~l~s~iaa~~~~--~~~d~~k~a~~~fq~aagaf~--~l~~~~~~~~~~~d-~~~~~l~~~~~ 176 (714)
T KOG2220|consen 102 TQISLGFEKACVLFNIAALYSQIAAHQSR--ETVDGYKAAIAHFQAAAGAFR--YLSRDALGVEPLVD-LSSLTLVFLRF 176 (714)
T ss_pred eeccchhhHHHHHHHHHHHHHHHHHHhcc--CchHHHHHHHHHHHHHHHHHH--hhcHHhcCcccccc-cCHHHHHHHHH
Confidence 58889999999999999999999999984 467899999999999887654 22222333333444 2333322222
Q ss_pred cCCCC-CccceeeccccccCCCCCCcccceecchhhhHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHHH
Q psy17538 82 IFPAT-VNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNY 160 (164)
Q Consensus 82 fp~~~-~~i~F~W~ds~~~~~~~~~~~~~~~~~l~fE~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~~ 160 (164)
++... -.+-| +++..+ .+-.+--..+++.+++||.+|++.++++..+|.+.+++..+.--++.++|++.|
T Consensus 177 l~~AqAQec~f--~ks~~d-------~~~~~~iaKis~q~~~fy~~Al~~~~~~~~~~~~~~w~~~~~~k~~~~~~v~~~ 247 (714)
T KOG2220|consen 177 LMLAQAQECFF--YKSLTD-------NPKPSIIAKLSAQVVLFYEEALKAQIGARADRITKEWLTLVAAKFARFAGVAYY 247 (714)
T ss_pred hhHHhhchhee--ehhhcC-------CcchHHHHHHHHHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHHHHHHH
Confidence 23212 22233 777763 344566677999999999999999999999999999999999999999999998
Q ss_pred hhc
Q psy17538 161 LKS 163 (164)
Q Consensus 161 l~e 163 (164)
+..
T Consensus 248 ~~~ 250 (714)
T KOG2220|consen 248 YQS 250 (714)
T ss_pred HHH
Confidence 764
No 16
>KOG2002|consensus
Probab=80.01 E-value=4.4 Score=38.87 Aligned_cols=45 Identities=27% Similarity=0.295 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHhC---CCCChhhHHHHHHHHHHHHHHHHHhhcC
Q psy17538 120 CVLFNIAALQSAIAQAQ---SLDTDEGLKLAAKMLQSSAGIFNYLKST 164 (164)
Q Consensus 120 ~vLfNiaa~~s~~a~~~---~~~~~~~~K~A~~~fq~AAg~f~~l~e~ 164 (164)
.|+||+|.++.++|... .+.+.+.+..|..-+..|--+|++|+++
T Consensus 751 ~v~FN~a~v~kkla~s~lr~~k~t~eev~~a~~~le~a~r~F~~ls~~ 798 (1018)
T KOG2002|consen 751 SVKFNLALVLKKLAESILRLEKRTLEEVLEAVKELEEARRLFTELSKN 798 (1018)
T ss_pred hHHhHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 49999999999999885 5678899999999999999999999864
No 17
>smart00671 SEL1 Sel1-like repeats. These represent a subfamily of TPR (tetratricopeptide repeat) sequences.
Probab=73.45 E-value=8.7 Score=20.38 Aligned_cols=31 Identities=16% Similarity=0.281 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHH
Q psy17538 121 VLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAG 156 (164)
Q Consensus 121 vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg 156 (164)
.+|++|.+|. .......+.++|..+|++||-
T Consensus 3 a~~~lg~~~~-----~G~g~~~d~~~A~~~~~~Aa~ 33 (36)
T smart00671 3 AQYNLGQMYE-----YGLGVKKDLEKALEYYKKAAE 33 (36)
T ss_pred HHHHHHHHHH-----cCCCCCcCHHHHHHHHHHHHH
Confidence 4577777762 222456678999999999984
No 18
>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins. Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.
Probab=73.02 E-value=12 Score=29.29 Aligned_cols=41 Identities=10% Similarity=0.067 Sum_probs=27.3
Q ss_pred hhhHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHHH
Q psy17538 115 AWERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNY 160 (164)
Q Consensus 115 ~fE~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~~ 160 (164)
.-.+.-.++|+|.+|+-+|--... -.+|-.+|++|..+|+-
T Consensus 65 ~P~~hdAlw~lGnA~ts~A~l~~d-----~~~A~~~F~kA~~~Fqk 105 (186)
T PF06552_consen 65 NPNKHDALWCLGNAYTSLAFLTPD-----TAEAEEYFEKATEYFQK 105 (186)
T ss_dssp -TT-HHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHH
T ss_pred CCchHHHHHHHHHHHHHHHhhcCC-----hHHHHHHHHHHHHHHHH
Confidence 335567889999999999976533 35666777777777753
No 19
>PF02071 NSF: Aromatic-di-Alanine (AdAR) repeat ; InterPro: IPR000744 Regulated exocytosis of neurotransmitters and hormones, as well as intracellular traffic, requires fusion of two lipid bilayers. SNARE proteins are thought to form a protein bridge, the SNARE complex, between an incoming vesicle and the acceptor compartment. SNARE proteins contribute to the specificity of membrane fusion, implying that the mechanisms by which SNAREs are targeted to subcellular compartments are important for specific docking and fusion of vesicles. This mechanism involves a family of conserved proteins, members of which appear to function at all sites of constitutive and regulated secretion in eukaryotes []. Among them are 2 types of cytosolic protein, NSF (N-ethyl-maleimide-sensitive protein) and the SNAPs (alpha-, beta- and gamma-soluble NSF attachment proteins). The yeast vesicular fusion protein, sec17, a cytoplasmic peripheral membrane protein involved in vesicular transport between the endoplasmic reticulum and the golgi apparatus, shows a high degree of sequence similarity to the alpha-SNAP family. SNAP-25 and its non-neuronal homologue Syndet/SNAP-23 are synthesized as soluble proteins in the cytosol. Both SNAP-25 and Syndet/SNAP-23 are palmitoylated at cysteine residues clustered in a loop between two N- and C-terminal coils and palmitoylation is essential for membrane binding and plasma membrane targeting. The C-terminal and the N-terminal helices of SNAP-25, are each targeted to the plasma membrane by two distinct cysteine-rich domains and appear to regulate the availability of SNAP to form complexes with SNARE [].; GO: 0006886 intracellular protein transport
Probab=70.07 E-value=1.9 Score=18.69 Aligned_cols=12 Identities=25% Similarity=0.346 Sum_probs=8.8
Q ss_pred HHHHHHHHHHHH
Q psy17538 147 AAKMLQSSAGIF 158 (164)
Q Consensus 147 A~~~fq~AAg~f 158 (164)
|.+++++||-||
T Consensus 1 A~~~y~~Aa~~y 12 (12)
T PF02071_consen 1 AIKCYEKAAECY 12 (12)
T ss_pred CcHHHHHHHhhC
Confidence 457888888765
No 20
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=69.86 E-value=9.2 Score=20.17 Aligned_cols=28 Identities=11% Similarity=0.116 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHH
Q psy17538 119 VCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSA 155 (164)
Q Consensus 119 a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AA 155 (164)
|-++||+|.+|..++ ...+|..+|++|-
T Consensus 1 a~~~~~~g~~~~~~~---------~~~~A~~~~~~al 28 (34)
T PF00515_consen 1 AEAYYNLGNAYFQLG---------DYEEALEYYQRAL 28 (34)
T ss_dssp HHHHHHHHHHHHHTT----------HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhC---------CchHHHHHHHHHH
Confidence 457888888886553 3678888888874
No 21
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=68.95 E-value=14 Score=23.31 Aligned_cols=34 Identities=18% Similarity=0.216 Sum_probs=27.8
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHH
Q psy17538 117 ERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFN 159 (164)
Q Consensus 117 E~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~ 159 (164)
+.+.+++|+|.+|...| ...+|..+|++|.-+++
T Consensus 44 ~~a~~~~~lg~~~~~~g---------~~~~A~~~~~~al~i~~ 77 (78)
T PF13424_consen 44 DTANTLNNLGECYYRLG---------DYEEALEYYQKALDIFE 77 (78)
T ss_dssp HHHHHHHHHHHHHHHTT---------HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHcC---------CHHHHHHHHHHHHhhhc
Confidence 66899999999996653 36899999999988775
No 22
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=67.94 E-value=14 Score=19.13 Aligned_cols=30 Identities=3% Similarity=0.099 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHH
Q psy17538 119 VCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGI 157 (164)
Q Consensus 119 a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~ 157 (164)
|-++|++|.+|.+.+ ..++|..+|++|.-+
T Consensus 1 a~~~~~lg~~~~~~~---------~~~~A~~~~~~al~l 30 (34)
T PF07719_consen 1 AEAWYYLGQAYYQLG---------NYEEAIEYFEKALEL 30 (34)
T ss_dssp HHHHHHHHHHHHHTT----------HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhC---------CHHHHHHHHHHHHHH
Confidence 346778888775543 368999999988643
No 23
>cd05525 Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=67.21 E-value=32 Score=24.10 Aligned_cols=66 Identities=17% Similarity=0.224 Sum_probs=39.0
Q ss_pred CCCCCCCCCC---------CCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhhccCCChh--hHHHHHHH
Q psy17538 3 EFLAVPLKKP---------TDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHES--SLEVIYSY 71 (164)
Q Consensus 3 ~~l~iPlK~t---------~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~~~~~~~~--~~~~l~~Y 71 (164)
||+.+|-|.. .|+||.. +++=|.+... .++++|..|+..+- .+....+. .-+.. ....|.++
T Consensus 28 ~F~~lp~k~~~pdYy~~I~~P~dL~t-I~~kl~~~~Y---~s~~ef~~D~~l~f--~Na~~yn~-~~S~i~~~A~~L~~~ 100 (106)
T cd05525 28 PFINLPSKKKNPDYYERITDPVDLST-IEKQILTGYY---KTPEAFDSDMLKVF--RNAEKYYG-RKSPIGRDVCRLRKA 100 (106)
T ss_pred hhccCCCcccCCchhhhCCCCcCHHH-HHHHHcCCCC---CCHHHHHHHHHHHH--HHHHHHCC-CCCHHHHHHHHHHHH
Confidence 5777777633 5788876 5555555433 36789999998762 22222232 22322 44677777
Q ss_pred HHHH
Q psy17538 72 YDHL 75 (164)
Q Consensus 72 y~qL 75 (164)
|.|.
T Consensus 101 f~~~ 104 (106)
T cd05525 101 YYQA 104 (106)
T ss_pred HHHc
Confidence 7664
No 24
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=58.79 E-value=19 Score=19.63 Aligned_cols=27 Identities=11% Similarity=0.180 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHH
Q psy17538 122 LFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGI 157 (164)
Q Consensus 122 LfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~ 157 (164)
+.|+|.+|.+.|- ..+|..+|++|..+
T Consensus 2 l~~Lg~~~~~~g~---------~~~Ai~~y~~aL~l 28 (36)
T PF13176_consen 2 LNNLGRIYRQQGD---------YEKAIEYYEQALAL 28 (36)
T ss_dssp HHHHHHHHHHCT----------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCC---------HHHHHHHHHHHHHh
Confidence 5678888866543 57899999998754
No 25
>PF08238 Sel1: Sel1 repeat; InterPro: IPR006597 Sel1-like repeats are tetratricopeptide repeat sequences originally identified in a Caenorhabditis elegans receptor molecule which is a key negative regulator of the Notch pathway []. Mammalian homologues have since been identified although these mainly pancreatic proteins have yet to have a function assigned.; PDB: 2XM6_A 3RJV_A 1OUV_A 1KLX_A.
Probab=58.04 E-value=28 Score=18.68 Aligned_cols=17 Identities=18% Similarity=0.130 Sum_probs=14.3
Q ss_pred ChhhHHHHHHHHHHHHH
Q psy17538 140 TDEGLKLAAKMLQSSAG 156 (164)
Q Consensus 140 ~~~~~K~A~~~fq~AAg 156 (164)
...+.++|..+|++||-
T Consensus 20 ~~~d~~~A~~~~~~Aa~ 36 (39)
T PF08238_consen 20 VPKDYEKAFKWYEKAAE 36 (39)
T ss_dssp SCHHHHHHHHHHHHHHH
T ss_pred ccccccchHHHHHHHHH
Confidence 45579999999999984
No 26
>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A ....
Probab=56.06 E-value=18 Score=18.83 Aligned_cols=28 Identities=7% Similarity=0.214 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHH
Q psy17538 119 VCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSA 155 (164)
Q Consensus 119 a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AA 155 (164)
|.+++++|.+|.+++ ...+|..+|++|-
T Consensus 1 a~~~~~lg~~y~~~~---------~~~~A~~~~~~a~ 28 (34)
T PF13181_consen 1 AEAYYNLGKIYEQLG---------DYEEALEYFEKAL 28 (34)
T ss_dssp -HHHHHHHHHHHHTT---------SHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcC---------CHHHHHHHHHHHH
Confidence 467888898887653 3577777887764
No 27
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=53.16 E-value=26 Score=21.37 Aligned_cols=30 Identities=7% Similarity=0.117 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHH
Q psy17538 118 RVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSA 155 (164)
Q Consensus 118 ~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AA 155 (164)
-+.+++|+|.+|...+ +..++|..+|++|.
T Consensus 36 ~~~~~~~~g~~~~~~~--------~~~~~A~~~~~~al 65 (69)
T PF13414_consen 36 NAEAYYNLGLAYMKLG--------KDYEEAIEDFEKAL 65 (69)
T ss_dssp HHHHHHHHHHHHHHTT--------THHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHhC--------ccHHHHHHHHHHHH
Confidence 3558999999997775 24678888888774
No 28
>cd02682 MIT_AAA_Arch MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in mostly archaebacterial AAA-ATPases. The molecular function of the MIT domain is unclear.
Probab=51.59 E-value=40 Score=22.33 Aligned_cols=38 Identities=8% Similarity=-0.018 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHHHhh
Q psy17538 123 FNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYLK 162 (164)
Q Consensus 123 fNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~~l~ 162 (164)
=+.|.-+.+.|..++. .....+|..++|.|++.+..+.
T Consensus 3 ~~~A~~~a~~AVe~D~--~gr~~eAi~~Y~~aIe~L~q~~ 40 (75)
T cd02682 3 EEMARKYAINAVKAEK--EGNAEDAITNYKKAIEVLSQIV 40 (75)
T ss_pred HHHHHHHHHHHHHHHh--cCCHHHHHHHHHHHHHHHHHHH
Confidence 3567777888888753 3357899999999999886653
No 29
>cd05522 Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=50.12 E-value=83 Score=21.75 Aligned_cols=58 Identities=12% Similarity=0.139 Sum_probs=32.5
Q ss_pred CCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhhccCCC-hhhHHHHHHHHHHH
Q psy17538 12 PTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKH-ESSLEVIYSYYDHL 75 (164)
Q Consensus 12 t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~~~~~~-~~~~~~l~~Yy~qL 75 (164)
..|+||.+ +++=|.+... .+++.|.+|+..+-. +....+.++.. ......+.+|+..|
T Consensus 45 ~~Pmdl~t-I~~kl~~~~Y---~s~~~f~~D~~li~~--Na~~yn~~~s~i~~~A~~l~~~f~~l 103 (104)
T cd05522 45 SNPISLDD-IKKKVKRRKY---KSFDQFLNDLNLMFE--NAKLYNENDSQEYKDAVLLEKEARLL 103 (104)
T ss_pred CCCcCHHH-HHHHHccCCC---CCHHHHHHHHHHHHH--HHHHHCCCCCHHHHHHHHHHHHHHHh
Confidence 45788876 5555555433 467889999987632 22222322211 22446777777654
No 30
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=44.52 E-value=50 Score=17.59 Aligned_cols=33 Identities=21% Similarity=0.157 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHHH
Q psy17538 119 VCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNY 160 (164)
Q Consensus 119 a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~~ 160 (164)
|..+.|+|.+|...| ...+|..++++|.-+.+-
T Consensus 2 a~~~~~la~~~~~~g---------~~~~A~~~~~~al~~~~~ 34 (42)
T PF13374_consen 2 ASALNNLANAYRAQG---------RYEEALELLEEALEIRER 34 (42)
T ss_dssp HHHHHHHHHHHHHCT----------HHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHhhh---------hcchhhHHHHHHHHHHHH
Confidence 567888888886542 367888888888766543
No 31
>cd05503 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=38.59 E-value=1.2e+02 Score=20.46 Aligned_cols=30 Identities=13% Similarity=0.231 Sum_probs=20.4
Q ss_pred CCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHH
Q psy17538 13 TDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLF 46 (164)
Q Consensus 13 ~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l 46 (164)
.|+||.+ +++=|.+... ..+++|..|+..+
T Consensus 39 ~PmdL~t-I~~kl~~~~Y---~s~~ef~~D~~li 68 (97)
T cd05503 39 KPMDFST-IREKLESGQY---KTLEEFAEDVRLV 68 (97)
T ss_pred CCCCHHH-HHHHHccCCC---CCHHHHHHHHHHH
Confidence 5789876 4555544433 3678999999866
No 32
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=38.25 E-value=44 Score=24.85 Aligned_cols=32 Identities=34% Similarity=0.444 Sum_probs=23.5
Q ss_pred CCCCCCCCCCCch---------HHHHHHHHhhCCCCcccHHHHH
Q psy17538 6 AVPLKKPTDVDII---------KPLKNLIALQFPNDNEKLDILN 40 (164)
Q Consensus 6 ~iPlK~t~~~d~~---------~~l~~~I~~~y~~~~~~~~~~~ 40 (164)
++|.|++...|+. +.||+++..+|+ -.|++|+
T Consensus 65 AV~~kKSVtpD~IicLEDGkkfKSLKRHL~t~~g---mTPd~YR 105 (148)
T COG4957 65 AVPIKKSVTPDYIICLEDGKKFKSLKRHLTTHYG---LTPDEYR 105 (148)
T ss_pred CCCcccccCCCeEEEeccCcchHHHHHHHhcccC---CCHHHHH
Confidence 5677877766643 458999999999 5677774
No 33
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=35.18 E-value=1e+02 Score=18.92 Aligned_cols=29 Identities=17% Similarity=0.316 Sum_probs=18.7
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHHHHH-HHHHH
Q psy17538 20 PLKNLIALQFPNDNEKLDILNEKLNLF-SKLRT 51 (164)
Q Consensus 20 ~l~~~I~~~y~~~~~~~~~~~~dl~~l-~~LR~ 51 (164)
.+-+.+.++|+ .+++...+|+..+ ..|++
T Consensus 34 ei~~~l~~~y~---~~~~~~~~dv~~fl~~L~~ 63 (68)
T PF05402_consen 34 EIVDALAEEYD---VDPEEAEEDVEEFLEQLRE 63 (68)
T ss_dssp HHHHHHHHHTT-----HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcC---CCHHHHHHHHHHHHHHHHH
Confidence 36677778887 6677778777654 56654
No 34
>cd05505 Bromo_WSTF_like Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=35.13 E-value=1.5e+02 Score=20.27 Aligned_cols=57 Identities=9% Similarity=0.002 Sum_probs=31.1
Q ss_pred CCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhhccCCC-hhhHHHHHHHHHHH
Q psy17538 13 TDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKH-ESSLEVIYSYYDHL 75 (164)
Q Consensus 13 ~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~~~~~~-~~~~~~l~~Yy~qL 75 (164)
.|+||.+ +++=|.+... .++++|..|+..+-.- ....+.++.. -.....|.+||..+
T Consensus 39 ~PmDL~t-I~~kl~~~~Y---~s~~ef~~D~~li~~N--a~~yN~~~s~i~~~a~~le~~f~~~ 96 (97)
T cd05505 39 NPMDLQT-MQTKCSCGSY---SSVQEFLDDMKLVFSN--AEKYYENGSYVLSCMRKTEQCCVNL 96 (97)
T ss_pred CcCCHHH-HHHHHcCCCC---CCHHHHHHHHHHHHHH--HHHHCCCCCHHHHHHHHHHHHHHHh
Confidence 5788876 5555555433 3578998888866322 2222222211 12346677776543
No 35
>cd05529 Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=34.59 E-value=1.7e+02 Score=20.97 Aligned_cols=30 Identities=13% Similarity=0.357 Sum_probs=20.4
Q ss_pred CCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHH
Q psy17538 13 TDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLF 46 (164)
Q Consensus 13 ~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l 46 (164)
.|+||.. +++=|.+.+. .+.+.|..|+..+
T Consensus 67 ~PmdL~t-I~~kl~~~~Y---~s~~~f~~Dv~Li 96 (128)
T cd05529 67 VPMDLET-IRSRLENRYY---RSLEALRHDVRLI 96 (128)
T ss_pred CCCCHHH-HHHHHhcCCC---CCHHHHHHHHHHH
Confidence 5788876 5555555444 3577898888866
No 36
>PF14823 Sirohm_synth_C: Sirohaem biosynthesis protein C-terminal; PDB: 1KYQ_B.
Probab=34.47 E-value=1e+02 Score=20.02 Aligned_cols=23 Identities=17% Similarity=0.033 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcc
Q psy17538 36 LDILNEKLNLFSKLRTAAVWKVF 58 (164)
Q Consensus 36 ~~~~~~dl~~l~~LR~~~~~~~~ 58 (164)
|....++|+.+-.||..+....+
T Consensus 1 p~~~g~AIe~vG~LR~~LR~~ap 23 (70)
T PF14823_consen 1 PKNLGEAIENVGELRSRLREVAP 23 (70)
T ss_dssp ---HHHHHHHHHHHHHHHHHHS-
T ss_pred CccHHHHHHHHHHHHHHHHhcCC
Confidence 34677889999999999974433
No 37
>cd05517 Bromo_polybromo_II Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=33.11 E-value=1.6e+02 Score=20.24 Aligned_cols=42 Identities=19% Similarity=0.339 Sum_probs=27.9
Q ss_pred CCCCCCCCCC---------CCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHHH
Q psy17538 3 EFLAVPLKKP---------TDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSK 48 (164)
Q Consensus 3 ~~l~iPlK~t---------~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~ 48 (164)
+|+.+|-|.. .|+||.. +++=|.+.+. .++++|..|+..+-.
T Consensus 26 ~F~~lp~~~~~pdYy~vI~~PmdL~t-I~~kl~~~~Y---~s~~~f~~D~~lm~~ 76 (103)
T cd05517 26 LFQKLPSKVLYPDYYAVIKEPIDLKT-IAQRIQSGYY---KSIEDMEKDLDLMVK 76 (103)
T ss_pred HHhcCCCCCCCCCHHHHcCCCcCHHH-HHHHHCcCCC---CCHHHHHHHHHHHHH
Confidence 3556665543 4789976 6666666555 467899999987644
No 38
>PF12358 DUF3644: Protein of unknown function (DUF3644) ; InterPro: IPR022104 This domain family is found in bacteria, and is typically between 65 and 80 amino acids in length.
Probab=31.13 E-value=81 Score=20.53 Aligned_cols=31 Identities=19% Similarity=0.374 Sum_probs=24.1
Q ss_pred HHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHH
Q psy17538 20 PLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAA 53 (164)
Q Consensus 20 ~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~ 53 (164)
.|+.+|...|. ..++....-|+.|-.+|+++
T Consensus 46 ~L~~~l~~~~~---~~~~~vr~NL~~LielR~~~ 76 (77)
T PF12358_consen 46 SLRKCLKKYFT---NENDPVRKNLEFLIELRNTI 76 (77)
T ss_pred hHHHHHHHhcc---CCChHHHHHHHHHHHHHHcc
Confidence 37777888776 45667888999999999864
No 39
>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []. It is also involved in sporulation [].
Probab=29.03 E-value=96 Score=25.10 Aligned_cols=41 Identities=24% Similarity=0.161 Sum_probs=30.5
Q ss_pred ecchhhhHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHH
Q psy17538 111 VCSLAWERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFN 159 (164)
Q Consensus 111 ~~~l~fE~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~ 159 (164)
.++..-|.|.++||+|--..... +....|+..+|+|--+++
T Consensus 27 ~~~~~~~La~~~yn~G~~l~~~~--------~~~~~a~~wL~~a~~~l~ 67 (278)
T PF08631_consen 27 DPDMAEELARVCYNIGKSLLSKK--------DKYEEAVKWLQRAYDILE 67 (278)
T ss_pred CcHHHHHHHHHHHHHHHHHHHcC--------CChHHHHHHHHHHHHHHH
Confidence 34456699999999998664443 457888888888877764
No 40
>COG1528 Ftn Ferritin-like protein [Inorganic ion transport and metabolism]
Probab=28.67 E-value=2.3e+02 Score=21.71 Aligned_cols=45 Identities=31% Similarity=0.338 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHH--------HHHHHHHHHhhcC
Q psy17538 117 ERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKML--------QSSAGIFNYLKST 164 (164)
Q Consensus 117 E~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~f--------q~AAg~f~~l~e~ 164 (164)
|+.+-=|+.|-+|.++|+.++. .|++.+.+.| ..|-=+|+|++++
T Consensus 12 ~Q~N~E~yas~lYl~maa~~~~---~~l~G~A~f~~~qa~EE~~H~~k~~~yl~~~ 64 (167)
T COG1528 12 EQMNLEFYASNLYLQMAAWCSS---ESLPGFAKFLRAQAQEELTHAMKLFNYLNER 64 (167)
T ss_pred HHHHHHHHHHHHHHHHHHHHhh---cCChhHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5566667778888888888863 4444444444 4566688888763
No 41
>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=27.83 E-value=91 Score=24.50 Aligned_cols=33 Identities=24% Similarity=0.349 Sum_probs=28.3
Q ss_pred chHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHH
Q psy17538 17 IIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTA 52 (164)
Q Consensus 17 ~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~ 52 (164)
+..+|..|+..+|. ..|..|.+-|..|-.||.-
T Consensus 165 ~~~aL~~y~~~~~p---~~p~rf~~LL~~L~~LR~l 197 (221)
T cd06936 165 LLDLLQKFCKLYHP---EDPQHFACLLGRLTELRTL 197 (221)
T ss_pred HHHHHHHHHHhhCC---CchhHHHHHHHHhHHHHHH
Confidence 45789999999888 6788999999999999974
No 42
>KOG4061|consensus
Probab=27.38 E-value=68 Score=25.14 Aligned_cols=37 Identities=14% Similarity=0.315 Sum_probs=24.6
Q ss_pred hHHHHHHHHhhCCCC-----cccHHHHHHHHHHHHHHHHHHh
Q psy17538 18 IKPLKNLIALQFPND-----NEKLDILNEKLNLFSKLRTAAV 54 (164)
Q Consensus 18 ~~~l~~~I~~~y~~~-----~~~~~~~~~dl~~l~~LR~~~~ 54 (164)
..++...|-.||.+- +++|+.+++-++.+.+.|++=.
T Consensus 138 T~AVEtvIg~HYNdQlr~l~~~~pe~~kell~~i~~fRDeEl 179 (217)
T KOG4061|consen 138 TEAVETVIGGHYNDQLRELAEDDPEEHKELLSTITKFRDEEL 179 (217)
T ss_pred HHHHHHHHHHhhhHHHHHHHHhCcHhHHHHHHHHHHHhHHHH
Confidence 456677888888742 2456677777777777776543
No 43
>PF07426 Dynactin_p22: Dynactin subunit p22; InterPro: IPR009991 This family contains p22, the smallest subunit of dynactin, a complex that binds to cytoplasmic dynein and is a required activator for cytoplasmic dynein-mediated vesicular transport. Dynactin localises to the cleavage furrow and to the midbodies of dividing cells, suggesting that it may function in cytokinesis [].
Probab=26.80 E-value=1.3e+02 Score=23.09 Aligned_cols=59 Identities=17% Similarity=0.196 Sum_probs=30.7
Q ss_pred HHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHHHHhHhcc
Q psy17538 21 LKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKHESSLEVIYSYYDHLVSLESKI 82 (164)
Q Consensus 21 l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~~~~~~~~~~~~~~~l~~Yy~qL~~l~~rf 82 (164)
|+.++.+.+- ++...+.+.|+.|...--.--......+......+.+|-.....++..|
T Consensus 109 L~pvL~se~i---~~vp~~~~kL~~L~~~~~~Q~e~~~~ls~~~~~Ll~~YN~ii~~lSk~F 167 (174)
T PF07426_consen 109 LEPVLDSESI---RNVPELCDKLQKLSQIHLEQQEESEELSEEVQELLQQYNKIILLLSKQF 167 (174)
T ss_pred hhhhcCcHHH---hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555444 3344455555544433211111112334556677888888888887776
No 44
>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=26.67 E-value=1.1e+02 Score=22.47 Aligned_cols=34 Identities=18% Similarity=0.458 Sum_probs=27.2
Q ss_pred chHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHH
Q psy17538 17 IIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAA 53 (164)
Q Consensus 17 ~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~ 53 (164)
+..+|.+|+..+|+ +.|..|.+-+..+..||.-.
T Consensus 134 ~~~aL~~y~~~~~~---~~~~Rf~~Ll~~l~~lr~l~ 167 (174)
T cd06929 134 LLEALQRYLKVNHP---DAPQMFAKLLKKLTELRTLN 167 (174)
T ss_pred HHHHHHHHHHhcCC---CChhHHHHHHHHhHHHHHHH
Confidence 45678888888888 67888998888888888654
No 45
>cd02681 MIT_calpain7_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear.
Probab=26.20 E-value=1.7e+02 Score=19.29 Aligned_cols=35 Identities=14% Similarity=0.101 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHHH
Q psy17538 124 NIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNY 160 (164)
Q Consensus 124 Niaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~~ 160 (164)
+-|.-+.+.|...+. .....+|..+++.|...|..
T Consensus 4 ~~Ai~~a~~Ave~D~--~g~y~eA~~~Y~~aie~l~~ 38 (76)
T cd02681 4 RDAVQFARLAVQRDQ--EGRYSEAVFYYKEAAQLLIY 38 (76)
T ss_pred HHHHHHHHHHHHHHH--ccCHHHHHHHHHHHHHHHHH
Confidence 446667777777753 33578888888888888866
No 46
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=24.88 E-value=54 Score=20.54 Aligned_cols=29 Identities=24% Similarity=0.362 Sum_probs=12.0
Q ss_pred CCCCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHH
Q psy17538 10 KKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLF 46 (164)
Q Consensus 10 K~t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l 46 (164)
+.+.++|+ +||.+|-.+|-. ..+.||..|
T Consensus 3 ~~~~~~d~-~pL~~Yy~~h~~-------L~E~DL~~L 31 (56)
T PF11569_consen 3 ASGKPVDI-QPLEDYYLKHKQ-------LQEEDLDEL 31 (56)
T ss_dssp ---------HHHHHHHHHT-----------TTHHHHH
T ss_pred CCCCCcch-HHHHHHHHHcCC-------ccHhhHHHH
Confidence 34567777 679999887533 455666643
No 47
>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=24.85 E-value=99 Score=24.49 Aligned_cols=33 Identities=21% Similarity=0.339 Sum_probs=27.7
Q ss_pred chHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHH
Q psy17538 17 IIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTA 52 (164)
Q Consensus 17 ~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~ 52 (164)
+..+|+.||..+|. ..|..|.+-|-.|-.||.-
T Consensus 170 ~~~aL~~yi~~~~p---~~p~rf~kLLl~Lp~LR~l 202 (231)
T cd06937 170 LLEALKIYARKRRP---DKPHMFPKMLMKITDLRSI 202 (231)
T ss_pred HHHHHHHHHHhhCC---CcccHHHHHHHHhHHHHHH
Confidence 45678999999988 6688999999999999963
No 48
>smart00526 H15 Domain in histone families 1 and 5.
Probab=24.23 E-value=1.2e+02 Score=18.88 Aligned_cols=20 Identities=10% Similarity=0.205 Sum_probs=14.2
Q ss_pred HHHHHHHHhhCCCCcccHHHHHH
Q psy17538 19 KPLKNLIALQFPNDNEKLDILNE 41 (164)
Q Consensus 19 ~~l~~~I~~~y~~~~~~~~~~~~ 41 (164)
..+++||..+|. .++..+..
T Consensus 27 ~aI~kyi~~~~~---~~~~~~~~ 46 (66)
T smart00526 27 QAIKKYIEANYK---VLPNNFRS 46 (66)
T ss_pred HHHHHHHHHhCC---CChHHHHH
Confidence 569999999988 44544433
No 49
>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=24.20 E-value=1.1e+02 Score=23.36 Aligned_cols=32 Identities=19% Similarity=0.354 Sum_probs=26.4
Q ss_pred chHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHH
Q psy17538 17 IIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRT 51 (164)
Q Consensus 17 ~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~ 51 (164)
+..+|..||..+|. +.|..|..-+..+-.||.
T Consensus 134 ~~~aL~~~i~~~~p---~~~~rf~~Ll~~Lp~Lr~ 165 (195)
T cd06941 134 VLEALKVQVSRNRP---AEAQLFASLLMKIPELRS 165 (195)
T ss_pred HHHHHHHHHHhhCC---CcccHHHHHHHHhHHHHH
Confidence 34678899998888 678899999999989986
No 50
>cd05497 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=23.86 E-value=2.5e+02 Score=19.41 Aligned_cols=30 Identities=13% Similarity=0.113 Sum_probs=19.7
Q ss_pred CCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHH
Q psy17538 13 TDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLF 46 (164)
Q Consensus 13 ~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l 46 (164)
.|+||.. +++=|.+.+. ..+++|..|+..+
T Consensus 46 ~PmDL~t-I~~kL~~~~Y---~s~~ef~~D~~li 75 (107)
T cd05497 46 TPMDLGT-IKKRLENNYY---WSASECIQDFNTM 75 (107)
T ss_pred CcccHHH-HHHHHcCCCC---CCHHHHHHHHHHH
Confidence 4678876 4444455444 3577899998866
No 51
>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus. Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.
Probab=23.62 E-value=27 Score=26.26 Aligned_cols=33 Identities=21% Similarity=0.272 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHhC------CCCChhhHHHHHHHH
Q psy17538 119 VCVLFNIAALQSAIAQAQ------SLDTDEGLKLAAKML 151 (164)
Q Consensus 119 a~vLfNiaa~~s~~a~~~------~~~~~~~~K~A~~~f 151 (164)
+.+|+-||.+|-.+|..- .++.+.|+|+||..-
T Consensus 120 p~~L~kia~Ay~klg~~r~~~ell~~ACekG~kEAC~nI 158 (161)
T PF09205_consen 120 PEFLVKIANAYKKLGNTREANELLKEACEKGLKEACRNI 158 (161)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-HHHHHHH
T ss_pred HHHHHHHHHHHHHhcchhhHHHHHHHHHHhchHHHHHHh
Confidence 578899999998888763 345677888888753
No 52
>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=23.34 E-value=1.1e+02 Score=24.78 Aligned_cols=33 Identities=15% Similarity=0.335 Sum_probs=28.0
Q ss_pred chHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHH
Q psy17538 17 IIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTA 52 (164)
Q Consensus 17 ~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~ 52 (164)
+..+|+.||..+|. +.|..|..-|..|-.||.-
T Consensus 196 ~~~aL~~~i~~~~p---~~~~rf~kLLl~L~~LRsl 228 (259)
T cd06932 196 VLQALELQLKKNHP---DSPQLFAKLLQKMVDLRQL 228 (259)
T ss_pred HHHHHHHHHhhhCC---CcccHHHHHHHHHHHHHHH
Confidence 46688999999987 6788999999999999964
No 53
>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=22.84 E-value=1.2e+02 Score=23.09 Aligned_cols=32 Identities=34% Similarity=0.546 Sum_probs=26.0
Q ss_pred chHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHH
Q psy17538 17 IIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRT 51 (164)
Q Consensus 17 ~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~ 51 (164)
+..+|+.||..+|. +.|..|..-+..|-.||.
T Consensus 144 ~~~aL~~~~~~~~p---~~~~rf~kLL~~L~~LR~ 175 (189)
T cd06940 144 LIRALRTLIAKNHP---NEPSIFTKLLLKLPDLRT 175 (189)
T ss_pred HHHHHHHHHHHhCC---CCccHHHHHHHHHHHHHH
Confidence 45678889988887 567788888888888886
No 54
>cd05509 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=22.83 E-value=2.5e+02 Score=18.91 Aligned_cols=30 Identities=13% Similarity=0.254 Sum_probs=20.6
Q ss_pred CCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHH
Q psy17538 13 TDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLF 46 (164)
Q Consensus 13 ~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l 46 (164)
.|+||.. +++-|.+.+. .++++|..|+..+
T Consensus 40 ~PmdL~t-I~~kl~~~~Y---~s~~~f~~Dv~li 69 (101)
T cd05509 40 KPMDLST-MEEKLENGYY---VTLEEFVADLKLI 69 (101)
T ss_pred CCCCHHH-HHHHHhcCCC---CCHHHHHHHHHHH
Confidence 4688876 5555555444 3678999998866
No 55
>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=22.44 E-value=1.4e+02 Score=23.31 Aligned_cols=33 Identities=18% Similarity=0.415 Sum_probs=27.3
Q ss_pred chHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHH
Q psy17538 17 IIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTA 52 (164)
Q Consensus 17 ~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~ 52 (164)
+..+|.+|+..+|. ..|..|.+-+..+..||.-
T Consensus 163 ~~~aL~~y~~~~~~---~~p~Rf~~LL~~L~~Lr~l 195 (213)
T cd06953 163 YWYVLQDFTELNYP---NQPNRFSDLLSCLPEIRAA 195 (213)
T ss_pred HHHHHHHHHHHhCC---CcchHHHHHHHHhHHHHHH
Confidence 45678999998886 6788999999999999874
No 56
>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=22.30 E-value=1.5e+02 Score=22.50 Aligned_cols=34 Identities=15% Similarity=0.277 Sum_probs=27.6
Q ss_pred chHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHH
Q psy17538 17 IIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAA 53 (164)
Q Consensus 17 ~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~ 53 (164)
+...|..|+..+|. ..+..|.+-+..+..||...
T Consensus 135 l~~~L~~~~~~~~~---~~~~rf~kLL~~l~~Lr~~~ 168 (191)
T cd06942 135 LFQFLKSVLFKDGE---DTEQRLQKLFDILNRLRNMN 168 (191)
T ss_pred HHHHHHHHHHhcCC---ChHHHHHHHHHHHHHHHHHH
Confidence 45678888888888 66789999999999999754
No 57
>cd05513 Bromo_brd7_like Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=22.10 E-value=1.4e+02 Score=20.51 Aligned_cols=30 Identities=13% Similarity=0.247 Sum_probs=20.2
Q ss_pred CCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHH
Q psy17538 13 TDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLF 46 (164)
Q Consensus 13 ~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l 46 (164)
.|+||.+ +++=|.+... .++++|.+|+..+
T Consensus 40 ~PmDL~t-I~~kl~~~~Y---~s~~~f~~D~~li 69 (98)
T cd05513 40 HPMDFST-MKEKIKNNDY---QSIEEFKDDFKLM 69 (98)
T ss_pred CccCHHH-HHHHHhCCCC---CCHHHHHHHHHHH
Confidence 4678876 5555555444 3678999999866
No 58
>PF00439 Bromodomain: Bromodomain; InterPro: IPR001487 Bromodomains are found in a variety of mammalian, invertebrate and yeast DNA-binding proteins []. Bromodomains can interact with acetylated lysine []. In some proteins, the classical bromodomain has diverged to such an extent that parts of the region are either missing or contain an insertion (e.g., mammalian protein HRX, Caenorhabditis elegans hypothetical protein ZK783.4, yeast protein YTA7). The bromodomain may occur as a single copy, or in duplicate. The precise function of the domain is unclear, but it may be involved in protein-protein interactions and may play a role in assembly or activity of multi-component complexes involved in transcriptional activation [].; GO: 0005515 protein binding; PDB: 3P1C_A 4A9K_B 3SVH_A 3P1E_B 3P1F_A 1JSP_B 2L85_A 3P1D_B 3DWY_B 2D82_A ....
Probab=21.93 E-value=1.4e+02 Score=18.92 Aligned_cols=31 Identities=13% Similarity=0.236 Sum_probs=18.2
Q ss_pred CCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHH
Q psy17538 12 PTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLF 46 (164)
Q Consensus 12 t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l 46 (164)
..|+||..--++.-...|. +++.|..|+..+
T Consensus 34 ~~P~dL~~I~~kl~~~~Y~----s~~~f~~Dv~~i 64 (84)
T PF00439_consen 34 KNPMDLSTIRKKLENGKYK----SIEEFEADVRLI 64 (84)
T ss_dssp SSS--HHHHHHHHHTTSSS----SHHHHHHHHHHH
T ss_pred hhccchhhhhHHhhccchh----hHHHHHHHHHHH
Confidence 3578887644444444455 577898888755
No 59
>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=21.68 E-value=1.3e+02 Score=24.00 Aligned_cols=33 Identities=15% Similarity=0.164 Sum_probs=27.9
Q ss_pred chHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHH
Q psy17538 17 IIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTA 52 (164)
Q Consensus 17 ~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~ 52 (164)
+..+|..||..+|. ..|..|.+-|-.|-.||.-
T Consensus 175 ~~~aL~~y~~~~~p---~~~~Rf~kLLl~Lp~LRsi 207 (237)
T cd07070 175 ANAALLDYTLCHYP---HCGDKFQQLLLRLVEVRAL 207 (237)
T ss_pred HHHHHHHHHHhcCC---CcchHHHHHHHHhHHHHHh
Confidence 45789999999998 6678999999999999963
No 60
>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=21.44 E-value=1.2e+02 Score=23.77 Aligned_cols=34 Identities=21% Similarity=0.302 Sum_probs=28.3
Q ss_pred chHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHHH
Q psy17538 17 IIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAA 53 (164)
Q Consensus 17 ~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~~ 53 (164)
+..+|..|+..+|. +.|..|..-|..|-.||.-.
T Consensus 176 ~~~aL~~y~~~~~p---~~~~rf~klL~~L~~Lr~l~ 209 (236)
T cd06954 176 YVEALHSYIKIKRP---SDRLMFPRMLMKLVSLRTLS 209 (236)
T ss_pred HHHHHHHHHHhcCC---CcccHHHHHHHHHHHHHHHH
Confidence 56789999999998 56778999999999999743
No 61
>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=21.40 E-value=1.3e+02 Score=23.71 Aligned_cols=34 Identities=21% Similarity=0.380 Sum_probs=27.5
Q ss_pred chHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHH
Q psy17538 17 IIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTA 52 (164)
Q Consensus 17 ~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~ 52 (164)
+...|..|+..+|.. +.|..|.+-|..+..||.-
T Consensus 170 ~~~aL~~y~~~~~~~--~~~~rf~kLL~~L~~Lr~l 203 (231)
T cd06938 170 YLEALRAYVDNRRPP--SQRVIFAKLLSILTELRTL 203 (231)
T ss_pred HHHHHHHHHHHhCCC--CcccHHHHHHHHHHHHHHH
Confidence 457789999999873 2678999999999999964
No 62
>cd05520 Bromo_polybromo_III Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.
Probab=21.25 E-value=1.4e+02 Score=20.64 Aligned_cols=40 Identities=25% Similarity=0.420 Sum_probs=25.1
Q ss_pred CCCCCCCCC---------CCCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHH
Q psy17538 3 EFLAVPLKK---------PTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLF 46 (164)
Q Consensus 3 ~~l~iPlK~---------t~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l 46 (164)
+|+.+|-+. +.|+||.. +++=|.+... .++++|..|+..+
T Consensus 26 pF~~~p~~~~~PdYy~iI~~PmdL~t-I~~kl~~~~Y---~s~~~f~~D~~lm 74 (103)
T cd05520 26 PFLKLPSKRKYPDYYQEIKNPISLQQ-IRTKLKNGEY---ETLEELEADLNLM 74 (103)
T ss_pred hhhcCCCcccCCCHHHHcCCCcCHHH-HHHHHccCCC---CCHHHHHHHHHHH
Confidence 466666543 35789977 4444444433 4677898888866
No 63
>PF12063 DUF3543: Domain of unknown function (DUF3543); InterPro: IPR022708 This domain belonging to serine/threonine-protein kinases is functionally uncharacterised. This domain is found in eukaryotes. It is typically between 217 to 291 amino acids in length and is found associated with PF00069 from PFAM. This domain has a single completely conserved residue A that may be functionally important. ; GO: 0004674 protein serine/threonine kinase activity
Probab=21.13 E-value=1.8e+02 Score=23.39 Aligned_cols=49 Identities=16% Similarity=0.208 Sum_probs=37.9
Q ss_pred cchhhhHHHHHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHHHHHhhc
Q psy17538 112 CSLAWERVCVLFNIAALQSAIAQAQSLDTDEGLKLAAKMLQSSAGIFNYLKS 163 (164)
Q Consensus 112 ~~l~fE~a~vLfNiaa~~s~~a~~~~~~~~~~~K~A~~~fq~AAg~f~~l~e 163 (164)
..+.-|| +||+-|.-.++.|+-... ..+.+..+...|+.|.++++.|.+
T Consensus 153 ~~itAek--LiYdrALemsr~AA~~El-~g~~~~~ce~~Y~tA~~lLe~Ll~ 201 (238)
T PF12063_consen 153 SGITAEK--LIYDRALEMSRTAAVDEL-FGENLEGCEQRYETAIWLLEALLD 201 (238)
T ss_pred cccCHHH--HHHHHHHHHHHHHHHHHH-hCcCHhHHHHHHHHHHHHHHHHHh
Confidence 3455566 689999999998887643 334678899999999999998865
No 64
>cd05507 Bromo_brd8_like Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=21.11 E-value=1.6e+02 Score=20.28 Aligned_cols=31 Identities=13% Similarity=0.076 Sum_probs=21.3
Q ss_pred CCCCchHHHHHHHHhhCCCCcccHHHHHHHHHHHH
Q psy17538 13 TDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFS 47 (164)
Q Consensus 13 ~~~d~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~ 47 (164)
.|+||.. +++=|.+... ..+++|..|+..+-
T Consensus 42 ~PmDL~t-I~~kl~~~~Y---~s~~ef~~D~~li~ 72 (104)
T cd05507 42 RPMDLST-IKKNIENGTI---RSTAEFQRDVLLMF 72 (104)
T ss_pred CCcCHHH-HHHHHhcCCC---CCHHHHHHHHHHHH
Confidence 5788876 5555665444 35788999998663
No 65
>KOG2150|consensus
Probab=20.65 E-value=2.1e+02 Score=26.20 Aligned_cols=46 Identities=7% Similarity=-0.011 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHHHHhHhccC
Q psy17538 38 ILNEKLNLFSKLRTAAVWKVFEKHESSLEVIYSYYDHLVSLESKIF 83 (164)
Q Consensus 38 ~~~~dl~~l~~LR~~~~~~~~~~~~~~~~~l~~Yy~qL~~l~~rfp 83 (164)
+...+|++|++||+++-.=....+.-..+.|..|=..++.-..||-
T Consensus 46 DLKkEIKKLQRlRdQIKtW~ss~dIKDK~~L~d~RrlIE~~MErfK 91 (575)
T KOG2150|consen 46 DLKKEIKKLQRLRDQIKTWQSSSDIKDKDSLLDNRRLIEQRMERFK 91 (575)
T ss_pred HHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHH
Confidence 3445667999999998411113333456888888888887777775
No 66
>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=20.06 E-value=1.4e+02 Score=23.81 Aligned_cols=33 Identities=12% Similarity=0.119 Sum_probs=27.3
Q ss_pred chHHHHHHHHhhCCCCcccHHHHHHHHHHHHHHHHH
Q psy17538 17 IIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTA 52 (164)
Q Consensus 17 ~~~~l~~~I~~~y~~~~~~~~~~~~dl~~l~~LR~~ 52 (164)
+..+|+.||..+|. +.|..|.+-|..|-.||.-
T Consensus 184 ~~~aL~~yi~~~~p---~~~~rf~kLL~~L~~LR~i 216 (243)
T cd06935 184 FLLAFEHYINYRKH---HVPHFWPKLLMKVTDLRMI 216 (243)
T ss_pred HHHHHHHHHHhhCC---CCccHHHHHHHHHHHHHHH
Confidence 45678999998887 5678899999999999974
Done!