Query 048296
Match_columns 167
No_of_seqs 112 out of 1388
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 08:16:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048296.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048296hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0014 MADS box transcription 100.0 1.8E-34 3.9E-39 219.6 3.7 153 9-161 1-176 (195)
2 cd00265 MADS_MEF2_like MEF2 (m 100.0 7.5E-33 1.6E-37 181.0 2.7 69 10-78 1-73 (77)
3 smart00432 MADS MADS domain. 100.0 6.4E-31 1.4E-35 162.7 3.3 58 10-67 1-58 (59)
4 cd00266 MADS_SRF_like SRF-like 100.0 1.4E-30 3.1E-35 172.7 3.5 70 10-79 1-75 (83)
5 cd00120 MADS MADS: MCM1, Agamo 100.0 1.7E-30 3.7E-35 160.9 2.6 58 10-67 1-58 (59)
6 PF00319 SRF-TF: SRF-type tran 99.9 3.2E-29 7E-34 150.3 -1.8 51 17-67 1-51 (51)
7 KOG0015 Regulator of arginine 99.8 8.7E-21 1.9E-25 148.9 4.1 78 1-78 54-144 (338)
8 COG5068 ARG80 Regulator of arg 99.4 2.4E-13 5.2E-18 111.5 2.3 60 8-67 80-139 (412)
9 PF01486 K-box: K-box region; 98.3 2.3E-07 5E-12 63.5 1.9 67 95-164 14-80 (100)
10 PF06698 DUF1192: Protein of u 87.6 1.5 3.3E-05 26.9 4.2 47 121-167 12-58 (59)
11 PF10584 Proteasome_A_N: Prote 73.8 0.94 2E-05 22.4 -0.2 12 53-64 5-16 (23)
12 PF10491 Nrf1_DNA-bind: NLS-bi 57.9 13 0.00027 28.7 3.1 37 40-76 45-88 (214)
13 PF09151 DUF1936: Domain of un 52.1 20 0.00043 19.0 2.3 20 43-62 3-22 (36)
14 COG4917 EutP Ethanolamine util 51.1 11 0.00023 27.2 1.7 25 43-67 59-83 (148)
15 PF09941 DUF2173: Uncharacteri 49.1 17 0.00036 25.1 2.3 26 40-66 3-28 (108)
16 PF14263 DUF4354: Domain of un 46.4 14 0.0003 26.2 1.6 44 19-67 41-84 (124)
17 PF04161 Arv1: Arv1-like famil 45.9 6.7 0.00014 30.1 -0.0 36 43-78 2-42 (208)
18 KOG0184 20S proteasome, regula 43.4 14 0.00031 28.8 1.4 22 44-65 3-24 (254)
19 PHA02109 hypothetical protein 42.6 1.4E+02 0.0031 22.5 6.5 11 68-78 139-149 (233)
20 PF01502 PRA-CH: Phosphoribosy 40.6 16 0.00034 23.6 1.1 37 25-61 18-63 (75)
21 PF04945 YHS: YHS domain; Int 38.2 32 0.00069 19.5 2.1 33 46-78 5-41 (47)
22 PF13540 RCC1_2: Regulator of 38.2 30 0.00064 17.7 1.8 23 44-67 3-25 (30)
23 KOG0278 Serine/threonine kinas 37.6 19 0.00042 28.9 1.4 25 37-67 262-286 (334)
24 TIGR01916 F420_cofE F420-0:gam 36.8 30 0.00066 27.4 2.3 27 41-67 133-159 (243)
25 COG0139 HisI Phosphoribosyl-AM 33.8 35 0.00075 23.7 2.0 39 24-62 49-96 (111)
26 PF09158 MotCF: Bacteriophage 33.5 30 0.00065 23.7 1.6 49 13-76 19-72 (103)
27 PRK04098 sec-independent trans 33.5 7.7 0.00017 28.7 -1.3 27 50-76 14-42 (158)
28 PF07106 TBPIP: Tat binding pr 33.4 55 0.0012 24.0 3.2 35 124-158 103-137 (169)
29 PF09278 MerR-DNA-bind: MerR, 33.1 96 0.0021 18.4 3.8 24 135-158 34-57 (65)
30 PF00383 dCMP_cyt_deam_1: Cyti 32.2 38 0.00082 22.2 2.0 32 36-67 7-42 (102)
31 PF08796 DUF1797: Protein of u 32.1 44 0.00096 21.0 2.1 19 47-65 24-42 (67)
32 PF13252 DUF4043: Protein of u 32.0 24 0.00053 29.3 1.2 29 39-67 270-300 (341)
33 PF11629 Mst1_SARAH: C termina 31.4 95 0.0021 18.2 3.2 22 125-146 3-24 (49)
34 PF11460 DUF3007: Protein of u 30.2 37 0.00081 23.3 1.6 20 124-143 84-103 (104)
35 PRK13293 F420-0--gamma-glutamy 30.0 45 0.00097 26.5 2.3 27 41-67 134-160 (245)
36 PF03250 Tropomodulin: Tropomo 29.8 52 0.0011 24.0 2.4 22 124-145 18-39 (147)
37 KOG0183 20S proteasome, regula 29.3 38 0.00082 26.4 1.7 17 49-65 4-20 (249)
38 PF13186 SPASM: Iron-sulfur cl 28.7 51 0.0011 19.2 2.0 21 47-67 1-21 (64)
39 cd01284 Riboflavin_deaminase-r 28.3 61 0.0013 22.4 2.5 31 37-67 1-37 (115)
40 cd01854 YjeQ_engC YjeQ/EngC. 28.1 75 0.0016 25.5 3.4 52 18-75 52-103 (287)
41 PF06937 EURL: EURL protein; 28.0 1.4E+02 0.003 24.1 4.7 41 122-162 211-251 (285)
42 COG4831 Roadblock/LC7 domain [ 27.9 53 0.0011 22.3 2.0 29 38-67 3-31 (109)
43 PF08432 Vfa1: AAA-ATPase Vps4 27.2 44 0.00096 25.1 1.8 14 47-60 11-24 (182)
44 PF03937 Sdh5: Flavinator of s 25.1 74 0.0016 20.1 2.3 24 120-143 22-45 (74)
45 KOG4252 GTP-binding protein [S 25.0 45 0.00098 25.5 1.5 15 47-61 91-105 (246)
46 PF07676 PD40: WD40-like Beta 25.0 90 0.0019 16.4 2.4 18 50-67 10-27 (39)
47 PF06020 Roughex: Drosophila r 25.0 35 0.00075 27.8 0.9 16 44-59 183-198 (334)
48 KOG1123 RNA polymerase II tran 24.9 51 0.0011 29.4 1.9 25 53-77 546-588 (776)
49 COG5000 NtrY Signal transducti 23.9 55 0.0012 29.6 2.0 23 44-66 374-396 (712)
50 PF06296 DUF1044: Protein of u 23.7 1.4E+02 0.0029 21.0 3.6 35 126-160 81-115 (120)
51 PF11232 Med25: Mediator compl 23.4 74 0.0016 23.4 2.3 18 45-62 109-126 (152)
52 PRK00977 exodeoxyribonuclease 21.6 2E+02 0.0044 18.5 3.9 34 128-161 29-69 (80)
53 PF03670 UPF0184: Uncharacteri 21.4 2.1E+02 0.0046 18.8 3.9 29 131-159 34-62 (83)
54 PF03785 Peptidase_C25_C: Pept 21.3 46 0.00099 21.8 0.7 27 39-65 15-41 (81)
55 PF15079 DUF4546: Domain of un 20.7 76 0.0017 23.8 1.9 38 126-163 75-112 (205)
56 PF06780 Erp_C: Erp protein C- 20.6 1.9E+02 0.0042 21.0 3.9 37 118-155 54-90 (146)
57 KOG3154 Uncharacterized conser 20.5 61 0.0013 25.5 1.4 27 48-74 75-103 (263)
58 cd00187 TOP4c DNA Topoisomeras 20.4 1.6E+02 0.0035 25.5 4.1 60 15-77 257-328 (445)
59 cd00468 HIT_like HIT family: H 20.2 1.4E+02 0.0031 18.4 3.0 26 125-150 30-55 (86)
60 PF13082 DUF3931: Protein of u 20.1 61 0.0013 19.3 1.1 37 13-49 7-45 (66)
61 PF12018 DUF3508: Domain of un 20.1 1.4E+02 0.003 24.0 3.5 42 27-78 210-252 (281)
No 1
>KOG0014 consensus MADS box transcription factor [Transcription]
Probab=100.00 E-value=1.8e-34 Score=219.63 Aligned_cols=153 Identities=39% Similarity=0.546 Sum_probs=107.5
Q ss_pred CCcceeEEEeeccCCcceeeeeccccccccchhhhhcccccceEEEEEcCCCceeeccc------hhhhhhhhhhhhhhc
Q 048296 9 TGRKKIEIKRIENNSSRKVAFSKRRKGMFKKASELCRLCDTEIAIIVFSPKGRLYSFGD------HVIDKFIEDEIVSDI 82 (167)
Q Consensus 9 mgR~ki~i~~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~v~va~ivfsp~~k~~~~~~------~Vi~ry~~~~~~~~~ 82 (167)
|||+||+|++|+|+++|+|||+|||.||||||+||||||||+||+|||||+|++|.||+ .|+++|...+.....
T Consensus 1 M~R~ki~i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~ 80 (195)
T KOG0014|consen 1 MGRGKIEIKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPSGKLYEFGSSDESVDAVVDRFLNLTEPSRK 80 (195)
T ss_pred CCCCccceeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCCCCccccCCcchhHHHHHHHHHhhhhhhhc
Confidence 89999999999999999999999999999999999999999999999999999999987 899999887664433
Q ss_pred ccCcchhhhhhh--cCccccc--------------cCcccchhhhhhhhhhhHHHHHhhhhcccCH-HHHHHHHHHHHHH
Q 048296 83 HSSSSSKEAIKE--NDCVTEL--------------TGEEKSEEEDMHKEQTELEFWWEQSIEDLNM-EELEKYKSCLEEL 145 (167)
Q Consensus 83 ~~~~~~~~~~~e--l~~l~~~--------------l~~~k~~~~~l~~~~~~~~~~~~~~l~~Ls~-~eL~~L~~~Le~~ 145 (167)
........++.. +..+... ........+.+...........+.++.+++. .+|..++..++..
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~l~~~~~l~~~~~~l~~~ 160 (195)
T KOG0014|consen 81 KKRVNLESFLRNKKLTELVEEEEKEELKLQLKKSLESSLKVDPEDLELLELEQRKLTGEDLQSLSSLNELNSLESQLESS 160 (195)
T ss_pred ccccchhhHhhhhhhhcccchhhhhhccchhhhhhhhhhhcchhhhhhhHHHHHHHhccccccCCHHHHhcchhhHHHHh
Confidence 222222222110 1111100 0111111111111001134566788888988 8999999999998
Q ss_pred hhhhhHHHHHHHHHHh
Q 048296 146 RSNVAMKVEEMVMRRT 161 (167)
Q Consensus 146 l~~v~~R~~~L~~~~~ 161 (167)
+..++......+.+++
T Consensus 161 ~~~~~~~~~~~~~~~~ 176 (195)
T KOG0014|consen 161 LHNSRSSKSKPLSDSN 176 (195)
T ss_pred hcCCCCCCCcCCcchh
Confidence 8877776655555443
No 2
>cd00265 MADS_MEF2_like MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I subgroup mainly in position of the alpha helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.97 E-value=7.5e-33 Score=181.05 Aligned_cols=69 Identities=54% Similarity=0.956 Sum_probs=66.2
Q ss_pred CcceeEEEeeccCCcceeeeeccccccccchhhhhcccccceEEEEEcCCCceeeccc----hhhhhhhhhhh
Q 048296 10 GRKKIEIKRIENNSSRKVAFSKRRKGMFKKASELCRLCDTEIAIIVFSPKGRLYSFGD----HVIDKFIEDEI 78 (167)
Q Consensus 10 gR~ki~i~~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~v~va~ivfsp~~k~~~~~~----~Vi~ry~~~~~ 78 (167)
||+||+|++|+|+.+|++||+||+.||||||+||||||||+||+|||||+|++|.|++ +|++||...+.
T Consensus 1 gr~ki~i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s~s~~~vl~ry~~~~~ 73 (77)
T cd00265 1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPSMEKIIERYQKTSG 73 (77)
T ss_pred CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCCCHHHHHHHHHhccc
Confidence 8999999999999999999999999999999999999999999999999999999987 99999988654
No 3
>smart00432 MADS MADS domain.
Probab=99.96 E-value=6.4e-31 Score=162.70 Aligned_cols=58 Identities=67% Similarity=1.154 Sum_probs=56.6
Q ss_pred CcceeEEEeeccCCcceeeeeccccccccchhhhhcccccceEEEEEcCCCceeeccc
Q 048296 10 GRKKIEIKRIENNSSRKVAFSKRRKGMFKKASELCRLCDTEIAIIVFSPKGRLYSFGD 67 (167)
Q Consensus 10 gR~ki~i~~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~v~va~ivfsp~~k~~~~~~ 67 (167)
||+||+|++|+|+++|++||+||+.||||||+||||||||+||+|||||+|++|.|++
T Consensus 1 gR~Ki~i~~I~~~~~R~~tf~kRk~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~ 58 (59)
T smart00432 1 GRRKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPTGKLYEFAS 58 (59)
T ss_pred CCCcceeEEeeCcchhhhhhHhhhhhHHHHHHHHhhccCCeEEEEEECCCCCeeeccC
Confidence 8999999999999999999999999999999999999999999999999999999875
No 4
>cd00266 MADS_SRF_like SRF-like/Type I subfamily of MADS (MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero- and homo-dimers. Differs from the MEF-like/Type II subgroup mainly in position of the alpha 2 helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.96 E-value=1.4e-30 Score=172.66 Aligned_cols=70 Identities=59% Similarity=0.931 Sum_probs=65.6
Q ss_pred CcceeEEEeeccCCcceeeeeccccccccchhhhhcccccceEEEEEcCCCceeeccc-----hhhhhhhhhhhh
Q 048296 10 GRKKIEIKRIENNSSRKVAFSKRRKGMFKKASELCRLCDTEIAIIVFSPKGRLYSFGD-----HVIDKFIEDEIV 79 (167)
Q Consensus 10 gR~ki~i~~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~v~va~ivfsp~~k~~~~~~-----~Vi~ry~~~~~~ 79 (167)
||+||+|++|+|+.+|++||+||+.||||||+||||||||+||+|||||+|+++.|++ +++++|...+..
T Consensus 1 gr~Ki~i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~~~~~~~l~~~~~~~~~ 75 (83)
T cd00266 1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSSEVEGVISRFEVLSAL 75 (83)
T ss_pred CCccceeEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCcHHHHHHHHHHhhcCHh
Confidence 7999999999999999999999999999999999999999999999999999888876 789999886663
No 5
>cd00120 MADS MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers. Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.96 E-value=1.7e-30 Score=160.92 Aligned_cols=58 Identities=71% Similarity=1.130 Sum_probs=56.6
Q ss_pred CcceeEEEeeccCCcceeeeeccccccccchhhhhcccccceEEEEEcCCCceeeccc
Q 048296 10 GRKKIEIKRIENNSSRKVAFSKRRKGMFKKASELCRLCDTEIAIIVFSPKGRLYSFGD 67 (167)
Q Consensus 10 gR~ki~i~~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~v~va~ivfsp~~k~~~~~~ 67 (167)
||+||+|++|+|+.+|++||+||+.||||||+||||||||+||+|||||+|+++.|++
T Consensus 1 gr~Ki~i~~I~~~~~R~~tf~kR~~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~ 58 (59)
T cd00120 1 GRGKIEIKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPSGKLYEFWS 58 (59)
T ss_pred CCccceeEEeeCcchhhhhHHHHhchHHHhhhhheeccCCcEEEEEECCCCCcccccC
Confidence 7999999999999999999999999999999999999999999999999999999975
No 6
>PF00319 SRF-TF: SRF-type transcription factor (DNA-binding and dimerisation domain); InterPro: IPR002100 Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box [], that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. In SRF, the MADS box has been shown to be involved in DNA-binding and dimerisation []. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit. The DNA wraps around the coiled coil allowing the basic N-termini of the helices to fit into the DNA major groove. The chain extending from the helix N-termini reaches over the DNA backbone and penetrates into the minor groove. A 4-stranded, anti-parallel beta-sheet packs against the coiled-coil face opposite the DNA and is the central element of the dimerisation interface. The MADS-box domain is commonly found associated with K-box region see IPR002487 from INTERPRO ; GO: 0003677 DNA binding, 0046983 protein dimerization activity; PDB: 1MNM_B 1N6J_A 1TQE_S 3MU6_D 3P57_I 1EGW_A 1C7U_B 3KOV_A 1HBX_A 1K6O_C ....
Probab=99.94 E-value=3.2e-29 Score=150.32 Aligned_cols=51 Identities=67% Similarity=1.121 Sum_probs=46.8
Q ss_pred EeeccCCcceeeeeccccccccchhhhhcccccceEEEEEcCCCceeeccc
Q 048296 17 KRIENNSSRKVAFSKRRKGMFKKASELCRLCDTEIAIIVFSPKGRLYSFGD 67 (167)
Q Consensus 17 ~~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~v~va~ivfsp~~k~~~~~~ 67 (167)
++|+|++.|++||+||+.||||||+||||||||+||+|||||+|++|+|++
T Consensus 1 K~I~n~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~~iv~~~~g~~~~f~s 51 (51)
T PF00319_consen 1 KRIENKSRRKVTFSKRKKGLFKKASELSTLCGVDVALIVFSPDGKLYTFPS 51 (51)
T ss_dssp S--SSHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEEETTSEEEEEES
T ss_pred CCccchhHhHhHHHHHHhhhhhccceeeeecCCeEEEEEECCCCCEEEecC
Confidence 579999999999999999999999999999999999999999999999986
No 7
>KOG0015 consensus Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.81 E-value=8.7e-21 Score=148.87 Aligned_cols=78 Identities=37% Similarity=0.556 Sum_probs=71.0
Q ss_pred CCCCCCCCCCcceeEEEeeccCCcceeeeeccccccccchhhhhcccccceEEEEEcCCCceeeccc-------------
Q 048296 1 MPKKKPKGTGRKKIEIKRIENNSSRKVAFSKRRKGMFKKASELCRLCDTEIAIIVFSPKGRLYSFGD------------- 67 (167)
Q Consensus 1 ~~~~~~~~mgR~ki~i~~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~v~va~ivfsp~~k~~~~~~------------- 67 (167)
|..++|++.||+||+|.||+|...|.+||+|||.||||||+|||||+|.+|-++|.|.+|-||+|..
T Consensus 54 ~~~~~k~~~gr~kik~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaTpKLep~i~s~~Gk 133 (338)
T KOG0015|consen 54 QKDGGKKTTGRVKIKMEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATPKLEPMITSDEGK 133 (338)
T ss_pred ccCCCccccceeeccchhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEeccccccccccchhhH
Confidence 3456888899999999999999999999999999999999999999999999999999999999976
Q ss_pred hhhhhhhhhhh
Q 048296 68 HVIDKFIEDEI 78 (167)
Q Consensus 68 ~Vi~ry~~~~~ 78 (167)
.+|...++.+.
T Consensus 134 ~lIq~cLn~pd 144 (338)
T KOG0015|consen 134 ALIQACLNAPD 144 (338)
T ss_pred HHHHHHhcCCC
Confidence 67777776655
No 8
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.36 E-value=2.4e-13 Score=111.50 Aligned_cols=60 Identities=40% Similarity=0.568 Sum_probs=58.5
Q ss_pred CCCcceeEEEeeccCCcceeeeeccccccccchhhhhcccccceEEEEEcCCCceeeccc
Q 048296 8 GTGRKKIEIKRIENNSSRKVAFSKRRKGMFKKASELCRLCDTEIAIIVFSPKGRLYSFGD 67 (167)
Q Consensus 8 ~mgR~ki~i~~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~v~va~ivfsp~~k~~~~~~ 67 (167)
+|||+|+.|.+|+|+.+|.+||+||+.||+|||.||++|.|.+|.++|.|.+|.++.|..
T Consensus 80 ~~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~t 139 (412)
T COG5068 80 SVTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTT 139 (412)
T ss_pred ccccccCCcccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecC
Confidence 689999999999999999999999999999999999999999999999999999999976
No 9
>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development. The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=98.34 E-value=2.3e-07 Score=63.45 Aligned_cols=67 Identities=19% Similarity=0.344 Sum_probs=56.0
Q ss_pred cCccccccCcccchhhhhhhhhhhHHHHHhhhhcccCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhhhh
Q 048296 95 NDCVTELTGEEKSEEEDMHKEQTELEFWWEQSIEDLNMEELEKYKSCLEELRSNVAMKVEEMVMRRTCEK 164 (167)
Q Consensus 95 l~~l~~~l~~~k~~~~~l~~~~~~~~~~~~~~l~~Ls~~eL~~L~~~Le~~l~~v~~R~~~L~~~~~~~~ 164 (167)
++.+..++..++..++.++ ...+++.|++|++||++||..|+..|+..+..|+.|+.+++.+++...
T Consensus 14 ~e~~~~e~~~L~~~~~~L~---~~~R~~~GedL~~Ls~~eL~~LE~~Le~aL~~VR~rK~~~l~~~i~~l 80 (100)
T PF01486_consen 14 HEELQQEIAKLRKENESLQ---KELRHLMGEDLESLSLKELQQLEQQLESALKRVRSRKDQLLMEQIEEL 80 (100)
T ss_pred HHHHHHHHHHHHHHHHHHH---HHHhccccccccccchHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 4445556666666777776 344778899999999999999999999999999999999999998764
No 10
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=87.63 E-value=1.5 Score=26.93 Aligned_cols=47 Identities=17% Similarity=0.205 Sum_probs=31.6
Q ss_pred HHHhhhhcccCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhhhhccC
Q 048296 121 FWWEQSIEDLNMEELEKYKSCLEELRSNVAMKVEEMVMRRTCEKDFL 167 (167)
Q Consensus 121 ~~~~~~l~~Ls~~eL~~L~~~Le~~l~~v~~R~~~L~~~~~~~~~~~ 167 (167)
+..|.+|+.||++||.+--..|+.-..+++.-+..-.........||
T Consensus 12 ~~ig~dLs~lSv~EL~~RIa~L~aEI~R~~~~~~~K~a~r~AAealF 58 (59)
T PF06698_consen 12 HEIGEDLSLLSVEELEERIALLEAEIARLEAAIAKKSASRAAAEALF 58 (59)
T ss_pred cccCCCchhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34678999999999998888877766666555554444433333333
No 11
>PF10584 Proteasome_A_N: Proteasome subunit A N-terminal signature; InterPro: IPR000426 The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). This family contains the alpha subunit sequences which range from 210 to 290 amino acids. These sequences are classified as non-peptidase homologues in MEROPS peptidase family T1 (clan PB(T)). ; GO: 0004175 endopeptidase activity, 0006511 ubiquitin-dependent protein catabolic process, 0019773 proteasome core complex, alpha-subunit complex; PDB: 3H4P_M 1IRU_O 3UN4_U 1FNT_A 3OEV_G 3OEU_U 3SDK_U 3DY3_G 3MG7_G 3L5Q_C ....
Probab=73.79 E-value=0.94 Score=22.39 Aligned_cols=12 Identities=58% Similarity=1.146 Sum_probs=9.1
Q ss_pred EEEEcCCCceee
Q 048296 53 IIVFSPKGRLYS 64 (167)
Q Consensus 53 ~ivfsp~~k~~~ 64 (167)
+.+|||+|+++.
T Consensus 5 ~t~FSp~Grl~Q 16 (23)
T PF10584_consen 5 ITTFSPDGRLFQ 16 (23)
T ss_dssp TTSBBTTSSBHH
T ss_pred ceeECCCCeEEe
Confidence 357999998753
No 12
>PF10491 Nrf1_DNA-bind: NLS-binding and DNA-binding and dimerisation domains of Nrf1; InterPro: IPR019525 Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila []. In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human []. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, Q8C4C0 from SWISSPROT, there is also an NLS domain at 88-116, and a DNA binding and dimerisation domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity [].
Probab=57.87 E-value=13 Score=28.73 Aligned_cols=37 Identities=14% Similarity=0.268 Sum_probs=29.8
Q ss_pred hhhhhcccccceEEEEEcCCC---ceeeccc----hhhhhhhhh
Q 048296 40 ASELCRLCDTEIAIIVFSPKG---RLYSFGD----HVIDKFIED 76 (167)
Q Consensus 40 a~ELs~LC~v~va~ivfsp~~---k~~~~~~----~Vi~ry~~~ 76 (167)
..|++|-+|-.|+|+|.+|+. .--.||. .|+..|...
T Consensus 45 ~de~~trvGqqavvl~~~p~kp~~~f~vfGa~pL~~vv~~~~~~ 88 (214)
T PF10491_consen 45 IDEYTTRVGQQAVVLCCTPSKPNPVFKVFGAAPLENVVRNLKPV 88 (214)
T ss_pred HHHHHHhhhceeEEEEecCCCCCCceeeecchhHHHHHHHHHHH
Confidence 479999999999999999985 3445676 888888654
No 13
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=52.12 E-value=20 Score=19.01 Aligned_cols=20 Identities=30% Similarity=0.702 Sum_probs=15.2
Q ss_pred hhcccccceEEEEEcCCCce
Q 048296 43 LCRLCDTEIAIIVFSPKGRL 62 (167)
Q Consensus 43 Ls~LC~v~va~ivfsp~~k~ 62 (167)
|+--|||-|-+-||...|..
T Consensus 3 lcpkcgvgvl~pvy~~kgei 22 (36)
T PF09151_consen 3 LCPKCGVGVLEPVYNQKGEI 22 (36)
T ss_dssp B-TTTSSSBEEEEE-TTS-E
T ss_pred cCCccCceEEEEeecCCCcE
Confidence 66779999999999999954
No 14
>COG4917 EutP Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=51.15 E-value=11 Score=27.16 Aligned_cols=25 Identities=20% Similarity=0.292 Sum_probs=22.0
Q ss_pred hhcccccceEEEEEcCCCceeeccc
Q 048296 43 LCRLCDTEIAIIVFSPKGRLYSFGD 67 (167)
Q Consensus 43 Ls~LC~v~va~ivfsp~~k~~~~~~ 67 (167)
+.++|||+|-++|-+.+.+...|++
T Consensus 59 ~tt~~dadvi~~v~~and~~s~f~p 83 (148)
T COG4917 59 ITTLQDADVIIYVHAANDPESRFPP 83 (148)
T ss_pred HHHhhccceeeeeecccCccccCCc
Confidence 6789999999999999988777776
No 15
>PF09941 DUF2173: Uncharacterized conserved protein (DUF2173); InterPro: IPR018685 This family of various hypothetical prokaryotic proteins has no known function.
Probab=49.11 E-value=17 Score=25.14 Aligned_cols=26 Identities=27% Similarity=0.335 Sum_probs=21.5
Q ss_pred hhhhhcccccceEEEEEcCCCceeecc
Q 048296 40 ASELCRLCDTEIAIIVFSPKGRLYSFG 66 (167)
Q Consensus 40 a~ELs~LC~v~va~ivfsp~~k~~~~~ 66 (167)
-.+|-.|-||-+| ..||++|++..|-
T Consensus 3 l~~Lm~lpGv~AA-g~Fs~~G~l~e~~ 28 (108)
T PF09941_consen 3 LDKLMKLPGVVAA-GEFSDDGKLVEYK 28 (108)
T ss_pred HHHhhcCCCeEEE-EEECCCCeEEeee
Confidence 4678888888666 8999999998874
No 16
>PF14263 DUF4354: Domain of unknown function (DUF4354); PDB: 3NRF_B 3SB3_A.
Probab=46.37 E-value=14 Score=26.19 Aligned_cols=44 Identities=18% Similarity=0.435 Sum_probs=30.7
Q ss_pred eccCCcceeeeeccccccccchhhhhcccccceEEEEEcCCCceeeccc
Q 048296 19 IENNSSRKVAFSKRRKGMFKKASELCRLCDTEIAIIVFSPKGRLYSFGD 67 (167)
Q Consensus 19 I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~v~va~ivfsp~~k~~~~~~ 67 (167)
|.++.....||.=.-..+-.+.-+|+.+| ++.|+|.|+-|-.-.
T Consensus 41 v~~k~~ytktF~V~vaN~s~~~idLsk~C-----f~a~~~~gk~f~ldT 84 (124)
T PF14263_consen 41 VGGKSFYTKTFDVTVANLSDKDIDLSKMC-----FKAYSPDGKEFKLDT 84 (124)
T ss_dssp ETTEEEEEEEEEEEEEE-SSS-EE-TT-E-----EEEEETTS-EEEEEE
T ss_pred ecCccceEEEEEEEEecCCCCccccccch-----hhhccccCCEEEecc
Confidence 44566677788888888999999999986 999999998765544
No 17
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=45.94 E-value=6.7 Score=30.13 Aligned_cols=36 Identities=31% Similarity=0.554 Sum_probs=29.2
Q ss_pred hhcccccceE--EEEEcCCC-ceeeccc--hhhhhhhhhhh
Q 048296 43 LCRLCDTEIA--IIVFSPKG-RLYSFGD--HVIDKFIEDEI 78 (167)
Q Consensus 43 Ls~LC~v~va--~ivfsp~~-k~~~~~~--~Vi~ry~~~~~ 78 (167)
.||-||.+|- -..|||++ ++-.++. .+.|+|-+.+.
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~vaDkYiE~d~ 42 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVADKYIEYDN 42 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccCCcccceecccc
Confidence 3788999975 46899998 7888877 99999987665
No 18
>KOG0184 consensus 20S proteasome, regulatory subunit alpha type PSMA3/PRE10 [Posttranslational modification, protein turnover, chaperones]
Probab=43.43 E-value=14 Score=28.82 Aligned_cols=22 Identities=23% Similarity=0.468 Sum_probs=18.6
Q ss_pred hcccccceEEEEEcCCCceeec
Q 048296 44 CRLCDTEIAIIVFSPKGRLYSF 65 (167)
Q Consensus 44 s~LC~v~va~ivfsp~~k~~~~ 65 (167)
||-+|-+.|.-+|||+|.+|.-
T Consensus 3 sIGtGyDls~s~fSpdGrvfQv 24 (254)
T KOG0184|consen 3 SIGTGYDLSASTFSPDGRVFQV 24 (254)
T ss_pred cccccccccceeeCCCCceehH
Confidence 5677889999999999988764
No 19
>PHA02109 hypothetical protein
Probab=42.58 E-value=1.4e+02 Score=22.50 Aligned_cols=11 Identities=18% Similarity=0.096 Sum_probs=8.7
Q ss_pred hhhhhhhhhhh
Q 048296 68 HVIDKFIEDEI 78 (167)
Q Consensus 68 ~Vi~ry~~~~~ 78 (167)
+|+.||.+...
T Consensus 139 ~VL~R~R~~~~ 149 (233)
T PHA02109 139 AVLTRTRRIET 149 (233)
T ss_pred hhhhhhhhhhh
Confidence 89999987554
No 20
>PF01502 PRA-CH: Phosphoribosyl-AMP cyclohydrolase; InterPro: IPR002496 Phosphoribosyl-AMP cyclohydrolase 3.5.4.19 from EC catalyses the third step in the histidine biosynthetic pathway: 5-phosphoribosyl-AMP + H2O = 5-(5-phospho-D-ribosylaminoformimino)-1-(5-phospho-ribosyl) imidazole-4-carboxamide It requires Zn2+ ions for activity [].; GO: 0004635 phosphoribosyl-AMP cyclohydrolase activity, 0000105 histidine biosynthetic process; PDB: 1ZPS_B.
Probab=40.58 E-value=16 Score=23.58 Aligned_cols=37 Identities=22% Similarity=0.432 Sum_probs=27.8
Q ss_pred ceeeeeccccccccc---------hhhhhcccccceEEEEEcCCCc
Q 048296 25 RKVAFSKRRKGMFKK---------ASELCRLCDTEIAIIVFSPKGR 61 (167)
Q Consensus 25 R~~tf~KRr~gL~KK---------a~ELs~LC~v~va~ivfsp~~k 61 (167)
+..-||+-|++|+.| +.|+.+-||-++-++..-|.|.
T Consensus 18 ~~~y~SRSR~~lW~KGetSG~~q~v~~i~~DCD~D~ll~~V~~~G~ 63 (75)
T PF01502_consen 18 RATYYSRSRNRLWRKGETSGNTQKVVEIRLDCDGDALLFKVEQVGP 63 (75)
T ss_dssp B-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-
T ss_pred cEEEEEccCCcEeeEECCCCCEEEEEEEEecCCCCeEEEEEEeCCC
Confidence 444568888888666 5689999999999999988885
No 21
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=38.21 E-value=32 Score=19.52 Aligned_cols=33 Identities=24% Similarity=0.426 Sum_probs=23.1
Q ss_pred ccccce---EEEEEcCCCceeeccc-hhhhhhhhhhh
Q 048296 46 LCDTEI---AIIVFSPKGRLYSFGD-HVIDKFIEDEI 78 (167)
Q Consensus 46 LC~v~v---a~ivfsp~~k~~~~~~-~Vi~ry~~~~~ 78 (167)
-||..| +-.-..=+|+.|.|.| .=.+.|...|.
T Consensus 5 vcg~~v~~~~~~~~~y~G~~Y~FCS~~C~~~F~~~Pe 41 (47)
T PF04945_consen 5 VCGMKVPGNAAYSVEYNGRTYYFCSEGCKEKFEANPE 41 (47)
T ss_dssp GGG-BE-----EEEEETTEEEEESSHHHHHHHHCSHH
T ss_pred CCCCEEccCccEEEEECCEEEEEcCHHHHHHHHHCHH
Confidence 377777 6666677899999999 77888876543
No 22
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=38.16 E-value=30 Score=17.71 Aligned_cols=23 Identities=22% Similarity=0.442 Sum_probs=15.1
Q ss_pred hcccccceEEEEEcCCCceeeccc
Q 048296 44 CRLCDTEIAIIVFSPKGRLYSFGD 67 (167)
Q Consensus 44 s~LC~v~va~ivfsp~~k~~~~~~ 67 (167)
+|-||..-.+++. .+|++|.||.
T Consensus 3 ~ia~G~~ht~al~-~~g~v~~wG~ 25 (30)
T PF13540_consen 3 QIACGGYHTCALT-SDGEVYCWGD 25 (30)
T ss_dssp EEEEESSEEEEEE--TTEEEEEE-
T ss_pred EEEecCCEEEEEE-cCCCEEEEcC
Confidence 3557766665555 5789999985
No 23
>KOG0278 consensus Serine/threonine kinase receptor-associated protein [Lipid transport and metabolism]
Probab=37.60 E-value=19 Score=28.93 Aligned_cols=25 Identities=36% Similarity=0.643 Sum_probs=18.5
Q ss_pred ccchhhhhcccccceEEEEEcCCCceeeccc
Q 048296 37 FKKASELCRLCDTEIAIIVFSPKGRLYSFGD 67 (167)
Q Consensus 37 ~KKa~ELs~LC~v~va~ivfsp~~k~~~~~~ 67 (167)
+.|-.-=.|+| |-|||+|.+|..||
T Consensus 262 ~nkgh~gpVhc------VrFSPdGE~yAsGS 286 (334)
T KOG0278|consen 262 YNKGHFGPVHC------VRFSPDGELYASGS 286 (334)
T ss_pred cccCCCCceEE------EEECCCCceeeccC
Confidence 33444344555 89999999999998
No 24
>TIGR01916 F420_cofE F420-0:gamma-glutamyl ligase. This model represents an enzyme of coenzyme F(420) biosynthesis, as catalyzed by MJ0768 of Methanococcus jannaschii and by the N-terminal half of FbiB of Mycobacterium bovis strain BCG. Note that only two glutamates are ligated in M. jannaschii, but five to six in the Mycobacterium lineage. In M. jannaschii, CofE catalyzes the GTP-dependent addition of two L-glutamates.
Probab=36.75 E-value=30 Score=27.39 Aligned_cols=27 Identities=22% Similarity=0.470 Sum_probs=23.5
Q ss_pred hhhhcccccceEEEEEcCCCceeeccc
Q 048296 41 SELCRLCDTEIAIIVFSPKGRLYSFGD 67 (167)
Q Consensus 41 ~ELs~LC~v~va~ivfsp~~k~~~~~~ 67 (167)
.+|--.+|++|+|||+.+.|.+|--|.
T Consensus 133 ~~l~~~~g~~v~VIItDt~gr~~R~G~ 159 (243)
T TIGR01916 133 RGLRELTGVDVGVIITDTNGRPFREGQ 159 (243)
T ss_pred HHHHHHHCCCEEEEEECCCCCccccCC
Confidence 356667999999999999999998887
No 25
>COG0139 HisI Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]
Probab=33.82 E-value=35 Score=23.68 Aligned_cols=39 Identities=18% Similarity=0.366 Sum_probs=29.0
Q ss_pred cceeeeeccccccccc---------hhhhhcccccceEEEEEcCCCce
Q 048296 24 SRKVAFSKRRKGMFKK---------ASELCRLCDTEIAIIVFSPKGRL 62 (167)
Q Consensus 24 ~R~~tf~KRr~gL~KK---------a~ELs~LC~v~va~ivfsp~~k~ 62 (167)
.+..-||+-|+-|++| +.|+.+=||.++-+++..|.|.+
T Consensus 49 g~~~y~SRSR~~lW~KGetSG~~q~v~~i~~DCD~Dall~~V~q~gg~ 96 (111)
T COG0139 49 GEAHYYSRSRQELWTKGETSGHTQKVVEIRLDCDGDALLLLVEQIGGP 96 (111)
T ss_pred CeEEEEEcchhhheccccccCceEEEEEEEcCCCCCEEEEEEEeCCCC
Confidence 3444457777756554 67899999999999999996643
No 26
>PF09158 MotCF: Bacteriophage T4 MotA, C-terminal; InterPro: IPR015241 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the C-terminal domain of MotA factors, which adopts a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. It contains a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end [].; PDB: 1KAF_B.
Probab=33.55 E-value=30 Score=23.65 Aligned_cols=49 Identities=37% Similarity=0.571 Sum_probs=31.4
Q ss_pred eeEEEee-ccCCcceeeeeccccccccchhhhhcccccceEEEEEcCCCceeeccc----hhhhhhhhh
Q 048296 13 KIEIKRI-ENNSSRKVAFSKRRKGMFKKASELCRLCDTEIAIIVFSPKGRLYSFGD----HVIDKFIED 76 (167)
Q Consensus 13 ki~i~~I-~n~~~R~~tf~KRr~gL~KKa~ELs~LC~v~va~ivfsp~~k~~~~~~----~Vi~ry~~~ 76 (167)
+|+++-+ +|.++=.++|.||..|+-+ +=...+|..--||- .++..|.+.
T Consensus 19 ~ie~K~~~~~RSN~~i~f~KRt~Girq---------------fEi~n~G~~RI~gYk~se~~~~~f~sl 72 (103)
T PF09158_consen 19 KIEVKEIVIDRSNYEIRFKKRTKGIRQ---------------FEIRNKGEFRIFGYKMSEEIIKKFTSL 72 (103)
T ss_dssp T--EEEEEEETTEEEEEEEEEETTEEE---------------EEEETTSEEEEEEES--HHHHHHHHHT
T ss_pred ceeeeeeEeeccceEEeeecccCceeE---------------EEEecCCcEEEEEEcCCHHHHHHHHhc
Confidence 3667666 7888899999999999832 22234565444443 777777553
No 27
>PRK04098 sec-independent translocase; Provisional
Probab=33.51 E-value=7.7 Score=28.66 Aligned_cols=27 Identities=19% Similarity=0.249 Sum_probs=15.4
Q ss_pred ceEEEEEcCCCceeeccc--hhhhhhhhh
Q 048296 50 EIAIIVFSPKGRLYSFGD--HVIDKFIED 76 (167)
Q Consensus 50 ~va~ivfsp~~k~~~~~~--~Vi~ry~~~ 76 (167)
=||+|||+|.-=|..-.. ..+..|+..
T Consensus 14 vVaLlvfGP~KLP~~~r~lGk~ir~~K~~ 42 (158)
T PRK04098 14 VVAIIFLGPDKLPQAMVDIAKFFKAVKKT 42 (158)
T ss_pred HHHHhhcCchHHHHHHHHHHHHHHHHHHH
Confidence 478899999853322222 455555543
No 28
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=33.35 E-value=55 Score=23.98 Aligned_cols=35 Identities=23% Similarity=0.159 Sum_probs=22.9
Q ss_pred hhhhcccCHHHHHHHHHHHHHHhhhhhHHHHHHHH
Q 048296 124 EQSIEDLNMEELEKYKSCLEELRSNVAMKVEEMVM 158 (167)
Q Consensus 124 ~~~l~~Ls~~eL~~L~~~Le~~l~~v~~R~~~L~~ 158 (167)
..-...++.+||......|..-...+..|+..|-.
T Consensus 103 ~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~ 137 (169)
T PF07106_consen 103 ASLSSEPTNEELREEIEELEEEIEELEEKLEKLRS 137 (169)
T ss_pred HHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 33445567777777777777777777777766654
No 29
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=33.06 E-value=96 Score=18.44 Aligned_cols=24 Identities=17% Similarity=0.243 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHH
Q 048296 135 LEKYKSCLEELRSNVAMKVEEMVM 158 (167)
Q Consensus 135 L~~L~~~Le~~l~~v~~R~~~L~~ 158 (167)
..+....+...+..|.++++.|..
T Consensus 34 ~~~~~~~l~~~~~~i~~~i~~L~~ 57 (65)
T PF09278_consen 34 CADRRALLEEKLEEIEEQIAELQA 57 (65)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344446778888888888877753
No 30
>PF00383 dCMP_cyt_deam_1: Cytidine and deoxycytidylate deaminase zinc-binding region; InterPro: IPR002125 Cytidine deaminase (3.5.4.5 from EC) (cytidine aminohydrolase) catalyzes the hydrolysis of cytidine into uridine and ammonia while deoxycytidylate deaminase (3.5.4.12 from EC) (dCMP deaminase) hydrolyzes dCMP into dUMP. Both enzymes are known to bind zinc and to require it for their catalytic activity [, ]. These two enzymes do not share any sequence similarity with the exception of a region that contains three conserved histidine and cysteine residues which are thought to be involved in the binding of the catalytic zinc ion. Such a region is also found in other proteins [, ]: Yeast cytosine deaminase (3.5.4.1 from EC) (gene FCY1) which transforms cytosine into uracil. Mammalian apolipoprotein B mRNA editing protein, responsible for the postranscriptional editing of a CAA codon into a UAA (stop) codon in the APOB mRNA. Riboflavin biosynthesis protein ribG, which converts 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate. Bacillus cereus blasticidin-S deaminase (3.5.4.23 from EC), which catalyzes the deamination of the cytosine moiety of the antibiotics blasticidin S, cytomycin and acetylblasticidin S. Bacillus subtilis protein comEB. This protein is required for the binding and uptake of transforming DNA. B. subtilis hypothetical protein yaaJ. Escherichia coli hypothetical protein yfhC. Yeast hypothetical protein YJL035c. ; GO: 0008270 zinc ion binding, 0016787 hydrolase activity; PDB: 3MPZ_C 3R2N_C 1WKQ_A 1TIY_B 2B3J_C 2O7P_B 2OBC_A 2G6V_B 2D30_B 2D5N_B ....
Probab=32.16 E-value=38 Score=22.18 Aligned_cols=32 Identities=19% Similarity=0.463 Sum_probs=22.8
Q ss_pred cccchhhhhccc----ccceEEEEEcCCCceeeccc
Q 048296 36 MFKKASELCRLC----DTEIAIIVFSPKGRLYSFGD 67 (167)
Q Consensus 36 L~KKa~ELs~LC----~v~va~ivfsp~~k~~~~~~ 67 (167)
+++.|.+++... +.+|+.++++|+|++...|.
T Consensus 7 ~m~~a~~~a~~s~~~~~~~vgaviv~~~~~~i~~g~ 42 (102)
T PF00383_consen 7 FMRIAIELAKRSRPCGNFPVGAVIVDPDGKIIATGY 42 (102)
T ss_dssp HHHHHHHHHHTHBTTTSSSEEEEEEETTTEEEEEEE
T ss_pred HHHHHHHHHHhccccCCCCEEEEEEeccCccEEEEe
Confidence 455555655555 88999999999887655554
No 31
>PF08796 DUF1797: Protein of unknown function (DUF1797); InterPro: IPR014904 The function of this protein is unknown. It forms a central anti-parallel beta sheet with flanking alpha helical regions. ; PDB: 2FFG_B.
Probab=32.07 E-value=44 Score=21.01 Aligned_cols=19 Identities=5% Similarity=0.329 Sum_probs=15.6
Q ss_pred cccceEEEEEcCCCceeec
Q 048296 47 CDTEIAIIVFSPKGRLYSF 65 (167)
Q Consensus 47 C~v~va~ivfsp~~k~~~~ 65 (167)
-|+++|-|.|.|....|..
T Consensus 24 ~G~~~c~V~y~~~t~~F~l 42 (67)
T PF08796_consen 24 EGVEVCTVTYDQETETFEL 42 (67)
T ss_dssp TTEEEEEEEEETTTTEEEE
T ss_pred CCEEEEEEEEECCCCeEEE
Confidence 5899999999998766554
No 32
>PF13252 DUF4043: Protein of unknown function (DUF4043)
Probab=31.95 E-value=24 Score=29.34 Aligned_cols=29 Identities=17% Similarity=0.241 Sum_probs=21.8
Q ss_pred chhhhhcccccceEEEEEcC--CCceeeccc
Q 048296 39 KASELCRLCDTEIAIIVFSP--KGRLYSFGD 67 (167)
Q Consensus 39 Ka~ELs~LC~v~va~ivfsp--~~k~~~~~~ 67 (167)
.+-.-+.|||+.++++.|+. +|-.|.|..
T Consensus 270 ~~v~ralLlGaQA~~~A~G~~~~~~~~~w~E 300 (341)
T PF13252_consen 270 VAVARALLLGAQALVIAFGKSGSGMRFFWVE 300 (341)
T ss_pred cceeeeeeechhheeeeeeccCCCcccccch
Confidence 34456789999999999998 445666643
No 33
>PF11629 Mst1_SARAH: C terminal SARAH domain of Mst1; InterPro: IPR024205 The SARAH (Sav/Rassf/Hpo) domain is found at the C terminus in three classes of eukaryotic tumour suppressors that give the domain its name. In the Sav (Salvador) and Hpo (Hippo) families, the SARAH domain mediates signal transduction from Hpo via the Sav scaffolding protein to the downstream component Wts (Warts); the phosphorylation of Wts by Hpo triggers cell cycle arrest and apoptosis by down-regulating cyclin E, Diap 1 and other targets []. The SARAH domain is also involved in dimerisation, as in the human Hpo orthologue, Mst1, which homodimerises via its C-terminal SARAH domain. The SARAH domain is found associated with other domains, such as protein kinase domains, WW/rsp5/WWP domain (IPR001202 from INTERPRO), C1 domain (IPR002219 from INTERPRO), LIM domain (IPR001781 from INTERPRO), or the Ras-associating (RA) domain (IPR000159 from INTERPRO).; GO: 0004674 protein serine/threonine kinase activity; PDB: 2JO8_A.
Probab=31.35 E-value=95 Score=18.25 Aligned_cols=22 Identities=23% Similarity=0.252 Sum_probs=14.5
Q ss_pred hhhcccCHHHHHHHHHHHHHHh
Q 048296 125 QSIEDLNMEELEKYKSCLEELR 146 (167)
Q Consensus 125 ~~l~~Ls~~eL~~L~~~Le~~l 146 (167)
+.|..+|.+||.+....|+.-+
T Consensus 3 ~fLk~ls~~eL~~rl~~LD~~M 24 (49)
T PF11629_consen 3 EFLKFLSYEELQQRLASLDPEM 24 (49)
T ss_dssp GGGGGS-HHHHHHHHHHHHHHH
T ss_pred HHHhhCCHHHHHHHHHhCCHHH
Confidence 3467888999887777665443
No 34
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=30.24 E-value=37 Score=23.26 Aligned_cols=20 Identities=35% Similarity=0.584 Sum_probs=16.8
Q ss_pred hhhhcccCHHHHHHHHHHHH
Q 048296 124 EQSIEDLNMEELEKYKSCLE 143 (167)
Q Consensus 124 ~~~l~~Ls~~eL~~L~~~Le 143 (167)
...++.||++|+..|...++
T Consensus 84 qkRle~l~~eE~~~L~~eie 103 (104)
T PF11460_consen 84 QKRLEELSPEELEALQAEIE 103 (104)
T ss_pred HHHHHhCCHHHHHHHHHHhc
Confidence 35678999999999988776
No 35
>PRK13293 F420-0--gamma-glutamyl ligase; Reviewed
Probab=29.98 E-value=45 Score=26.48 Aligned_cols=27 Identities=22% Similarity=0.455 Sum_probs=23.4
Q ss_pred hhhhcccccceEEEEEcCCCceeeccc
Q 048296 41 SELCRLCDTEIAIIVFSPKGRLYSFGD 67 (167)
Q Consensus 41 ~ELs~LC~v~va~ivfsp~~k~~~~~~ 67 (167)
.+|--.||++|+|||....|.+|-.|.
T Consensus 134 ~~l~~~~g~~v~VIItDt~gr~~R~G~ 160 (245)
T PRK13293 134 EGLEELTGKKVGVIITDTNGRPFRKGQ 160 (245)
T ss_pred HHHHHHHCCCEEEEEEcCCCcccccCC
Confidence 356667999999999999999999887
No 36
>PF03250 Tropomodulin: Tropomodulin; InterPro: IPR004934 Actin filaments have an intrinsic polarity, each with a fast-growing (barbed) end and a slow-growing (pointed) end. To regulate the dynamics at these ends, capping proteins have evolved that specifically bind to either the barbed or the pointed ends of the filament, where they block the association and dissociation of monomers. Pointed ends, for which actin monomers have significantly lower association and dissociation rate-constants than for barbed, are capped by either the Arp2/3 complex or tropomodulins []. Tropomodulin is a novel tropomyosin regulatory protein that binds to the end of erythrocyte tropomyosin and blocks head-to-tail association of tropomyosin along actin filaments []. Limited proteolysis shows this protein is composed of two domains. The unstructured tropomyosin-binding region at the N terminus has an actin pointed-end-capping activity that is dramatically up-regulated by tropomyosin coating of the actin filament[]. The second region is found near the C terminus. This tropomyosin-independent capping-domain caps pure actin. ; GO: 0005523 tropomyosin binding, 0005856 cytoskeleton
Probab=29.78 E-value=52 Score=24.00 Aligned_cols=22 Identities=36% Similarity=0.564 Sum_probs=17.7
Q ss_pred hhhhcccCHHHHHHHHHHHHHH
Q 048296 124 EQSIEDLNMEELEKYKSCLEEL 145 (167)
Q Consensus 124 ~~~l~~Ls~~eL~~L~~~Le~~ 145 (167)
++-|..||.+||.+|...|+..
T Consensus 18 DelL~~LS~EEL~~L~~el~e~ 39 (147)
T PF03250_consen 18 DELLAKLSPEELEELENELEEM 39 (147)
T ss_pred HHHHHhCCHHHHHHHHHHHHhh
Confidence 4457889999999999887653
No 37
>KOG0183 consensus 20S proteasome, regulatory subunit alpha type PSMA7/PRE6 [Posttranslational modification, protein turnover, chaperones]
Probab=29.27 E-value=38 Score=26.43 Aligned_cols=17 Identities=41% Similarity=0.790 Sum_probs=13.4
Q ss_pred cceEEEEEcCCCceeec
Q 048296 49 TEIAIIVFSPKGRLYSF 65 (167)
Q Consensus 49 v~va~ivfsp~~k~~~~ 65 (167)
-+-|+-||||+|.++.-
T Consensus 4 ydraltvFSPDGhL~QV 20 (249)
T KOG0183|consen 4 YDRALTVFSPDGHLFQV 20 (249)
T ss_pred cccceEEECCCCCEEee
Confidence 45688999999987654
No 38
>PF13186 SPASM: Iron-sulfur cluster-binding domain
Probab=28.69 E-value=51 Score=19.18 Aligned_cols=21 Identities=19% Similarity=0.520 Sum_probs=17.0
Q ss_pred cccceEEEEEcCCCceeeccc
Q 048296 47 CDTEIAIIVFSPKGRLYSFGD 67 (167)
Q Consensus 47 C~v~va~ivfsp~~k~~~~~~ 67 (167)
|++.--.+..+|+|.+++...
T Consensus 1 C~~~~~~~~I~~dG~v~pC~~ 21 (64)
T PF13186_consen 1 CGAGWNSLYIDPDGDVYPCCH 21 (64)
T ss_pred CCCcCeEEEEeeCccEEeCCC
Confidence 667777788889999999854
No 39
>cd01284 Riboflavin_deaminase-reductase Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain.
Probab=28.30 E-value=61 Score=22.39 Aligned_cols=31 Identities=16% Similarity=0.341 Sum_probs=22.8
Q ss_pred ccchhhhhccc------ccceEEEEEcCCCceeeccc
Q 048296 37 FKKASELCRLC------DTEIAIIVFSPKGRLYSFGD 67 (167)
Q Consensus 37 ~KKa~ELs~LC------~v~va~ivfsp~~k~~~~~~ 67 (167)
++.|-|++--+ +.+|+.|++.++|.+..-|.
T Consensus 1 m~~al~~A~~~~~~~~~~~pvGaviv~~~g~iv~~g~ 37 (115)
T cd01284 1 MRRALELAEKGRGLTSPNPPVGCVIVDDDGEIVGEGY 37 (115)
T ss_pred CHHHHHHHHhcccccCCCCCEEEEEEeCCCeEEEEec
Confidence 34566777766 78999999988888766554
No 40
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=28.13 E-value=75 Score=25.45 Aligned_cols=52 Identities=19% Similarity=0.289 Sum_probs=35.0
Q ss_pred eeccCCcceeeeeccccccccchhhhhcccccceEEEEEcCCCceeeccchhhhhhhh
Q 048296 18 RIENNSSRKVAFSKRRKGMFKKASELCRLCDTEIAIIVFSPKGRLYSFGDHVIDKFIE 75 (167)
Q Consensus 18 ~I~n~~~R~~tf~KRr~gL~KKa~ELs~LC~v~va~ivfsp~~k~~~~~~~Vi~ry~~ 75 (167)
.|+.--.|+-.+.++..|- + +=.++-+++++++|++.+...+++ ..+++|+.
T Consensus 52 ~i~~i~~R~~~l~R~~~~~--~--~~~i~anvD~vllV~d~~~p~~s~--~~ldr~L~ 103 (287)
T cd01854 52 VIVRVLPRKNLLSRPAAGG--R--EQVIAANVDQLVIVVSLNEPFFNP--RLLDRYLV 103 (287)
T ss_pred EEEEEECCCceEEccCCCC--c--ceeEEEeCCEEEEEEEcCCCCCCH--HHHHHHHH
Confidence 3445555666666666552 1 667889999999999987755333 46677764
No 41
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=28.05 E-value=1.4e+02 Score=24.11 Aligned_cols=41 Identities=12% Similarity=0.280 Sum_probs=30.4
Q ss_pred HHhhhhcccCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhh
Q 048296 122 WWEQSIEDLNMEELEKYKSCLEELRSNVAMKVEEMVMRRTC 162 (167)
Q Consensus 122 ~~~~~l~~Ls~~eL~~L~~~Le~~l~~v~~R~~~L~~~~~~ 162 (167)
+-.+.+++|+.+||.+|-..|......|-+-....+.+.-+
T Consensus 211 ~SrEeL~~Mt~~EL~qL~~~L~~qIq~vfeeLt~~vQEKDs 251 (285)
T PF06937_consen 211 YSREELNSMTLDELKQLNEKLLQQIQDVFEELTQQVQEKDS 251 (285)
T ss_pred cCHHHhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567999999999999988877777776666655555443
No 42
>COG4831 Roadblock/LC7 domain [Function unknown]
Probab=27.92 E-value=53 Score=22.26 Aligned_cols=29 Identities=31% Similarity=0.442 Sum_probs=22.2
Q ss_pred cchhhhhcccccceEEEEEcCCCceeeccc
Q 048296 38 KKASELCRLCDTEIAIIVFSPKGRLYSFGD 67 (167)
Q Consensus 38 KKa~ELs~LC~v~va~ivfsp~~k~~~~~~ 67 (167)
.|-.||--+-||-+| =.|||+|++..|-+
T Consensus 3 ekLdeLlqi~Gv~AA-Gefs~DGkLv~Ykg 31 (109)
T COG4831 3 EKLDELLQIKGVMAA-GEFSPDGKLVEYKG 31 (109)
T ss_pred hhHHHHhCccceeEe-ceeCCCCceEEeeC
Confidence 356677777777655 68999999988854
No 43
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=27.23 E-value=44 Score=25.06 Aligned_cols=14 Identities=21% Similarity=0.536 Sum_probs=10.1
Q ss_pred cccceEEEEEcCCC
Q 048296 47 CDTEIAIIVFSPKG 60 (167)
Q Consensus 47 C~v~va~ivfsp~~ 60 (167)
.++..|.|||-|+-
T Consensus 11 ~~~k~C~IC~Kpst 24 (182)
T PF08432_consen 11 TDAKACFICYKPST 24 (182)
T ss_pred CCCCceeEecCCCc
Confidence 56777888877763
No 44
>PF03937 Sdh5: Flavinator of succinate dehydrogenase; InterPro: IPR005631 This entry represents a group of uncharacterised small proteins found in both eukaryotes and prokaryotes, including NMA1147 from Neisseria meningitidis [] and YgfY from Escherichia coli []. YgfY may be involved in transcriptional regulation. The structure of these proteins consists of a complex bundle of five alpha-helices, which is composed of an up-down 3-helix bundle plus an orthogonal 2-helix bundle. ; PDB: 2LM4_A 1PUZ_A 2JR5_A 1X6I_A 1X6J_A.
Probab=25.07 E-value=74 Score=20.09 Aligned_cols=24 Identities=21% Similarity=0.445 Sum_probs=19.5
Q ss_pred HHHHhhhhcccCHHHHHHHHHHHH
Q 048296 120 EFWWEQSIEDLNMEELEKYKSCLE 143 (167)
Q Consensus 120 ~~~~~~~l~~Ls~~eL~~L~~~Le 143 (167)
..+....++.+|.+++..|+..|+
T Consensus 22 ~~f~~~~~~~l~~~el~~fe~lL~ 45 (74)
T PF03937_consen 22 GRFADAHLDSLSEEELDAFERLLD 45 (74)
T ss_dssp HHHHHHHHHHS-HHHHHHHHHHHT
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHc
Confidence 467788899999999999998775
No 45
>KOG4252 consensus GTP-binding protein [Signal transduction mechanisms]
Probab=25.04 E-value=45 Score=25.55 Aligned_cols=15 Identities=27% Similarity=0.534 Sum_probs=13.0
Q ss_pred cccceEEEEEcCCCc
Q 048296 47 CDTEIAIIVFSPKGR 61 (167)
Q Consensus 47 C~v~va~ivfsp~~k 61 (167)
-||.+|++|||.++.
T Consensus 91 rgaqa~vLVFSTTDr 105 (246)
T KOG4252|consen 91 RGAQASVLVFSTTDR 105 (246)
T ss_pred ccccceEEEEecccH
Confidence 489999999999874
No 46
>PF07676 PD40: WD40-like Beta Propeller Repeat; InterPro: IPR011659 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events. This region appears to be related to the IPR001680 from INTERPRO repeat. This model is likely to miss copies within a sequence.; PDB: 2HQS_D 1C5K_A 2IVZ_A 2W8B_D 3IAX_A 1CRZ_A 1N6F_D 1N6D_C 1N6E_C 1K32_A ....
Probab=25.02 E-value=90 Score=16.37 Aligned_cols=18 Identities=22% Similarity=0.410 Sum_probs=12.4
Q ss_pred ceEEEEEcCCCceeeccc
Q 048296 50 EIAIIVFSPKGRLYSFGD 67 (167)
Q Consensus 50 ~va~ivfsp~~k~~~~~~ 67 (167)
.-.-..|||+|+-..|.+
T Consensus 10 ~~~~p~~SpDGk~i~f~s 27 (39)
T PF07676_consen 10 DDGSPAWSPDGKYIYFTS 27 (39)
T ss_dssp SEEEEEE-TTSSEEEEEE
T ss_pred cccCEEEecCCCEEEEEe
Confidence 445588999998777754
No 47
>PF06020 Roughex: Drosophila roughex protein; InterPro: IPR009259 This family consists of several roughex (RUX) proteins specific to Drosophila species. Roughex can influence the intracellular distribution of cyclin A and is therefore defined as a distinct and specialised cell cycle inhibitor for cyclin A-dependent kinase activity []. Rux is though to regulate the metaphase to anaphase transition during development [].
Probab=24.97 E-value=35 Score=27.82 Aligned_cols=16 Identities=19% Similarity=0.343 Sum_probs=13.4
Q ss_pred hcccccceEEEEEcCC
Q 048296 44 CRLCDTEIAIIVFSPK 59 (167)
Q Consensus 44 s~LC~v~va~ivfsp~ 59 (167)
.-+||++||++||--.
T Consensus 183 ~~~~~~EICLavYek~ 198 (334)
T PF06020_consen 183 GQVSGFEICLAVYEKG 198 (334)
T ss_pred CccccceEEeeehhhh
Confidence 4579999999999765
No 48
>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]
Probab=24.95 E-value=51 Score=29.38 Aligned_cols=25 Identities=32% Similarity=0.759 Sum_probs=20.9
Q ss_pred EEEEcCC-----------Cceeeccc-------hhhhhhhhhh
Q 048296 53 IIVFSPK-----------GRLYSFGD-------HVIDKFIEDE 77 (167)
Q Consensus 53 ~ivfsp~-----------~k~~~~~~-------~Vi~ry~~~~ 77 (167)
+||||.+ ||||-||+ .|+..|+..+
T Consensus 546 iIVFsDnvfALk~YAikl~KpfIYG~Tsq~ERm~ILqnFq~n~ 588 (776)
T KOG1123|consen 546 IIVFSDNVFALKEYAIKLGKPFIYGPTSQNERMKILQNFQTNP 588 (776)
T ss_pred EEEEeccHHHHHHHHHHcCCceEECCCchhHHHHHHHhcccCC
Confidence 7999997 79999997 8898887543
No 49
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=23.86 E-value=55 Score=29.65 Aligned_cols=23 Identities=17% Similarity=0.312 Sum_probs=20.8
Q ss_pred hcccccceEEEEEcCCCceeecc
Q 048296 44 CRLCDTEIAIIVFSPKGRLYSFG 66 (167)
Q Consensus 44 s~LC~v~va~ivfsp~~k~~~~~ 66 (167)
|+|.|+.++||+|.++|.++.+.
T Consensus 374 ~VLsgvtaGVi~~d~~g~i~t~N 396 (712)
T COG5000 374 AVLSGLTAGVIGFDNRGCITTVN 396 (712)
T ss_pred HHHhcCceeEEEEcCCCeeEeec
Confidence 59999999999999999888864
No 50
>PF06296 DUF1044: Protein of unknown function (DUF1044); InterPro: IPR009387 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=23.70 E-value=1.4e+02 Score=21.02 Aligned_cols=35 Identities=17% Similarity=0.230 Sum_probs=29.9
Q ss_pred hhcccCHHHHHHHHHHHHHHhhhhhHHHHHHHHHH
Q 048296 126 SIEDLNMEELEKYKSCLEELRSNVAMKVEEMVMRR 160 (167)
Q Consensus 126 ~l~~Ls~~eL~~L~~~Le~~l~~v~~R~~~L~~~~ 160 (167)
.-+++|.+|+..|......++.--.+.++.++..+
T Consensus 81 ~~~nis~~El~~lk~la~~l~~~~~~~l~~~i~~g 115 (120)
T PF06296_consen 81 EKANISDKELKALKKLAKELLNLSEEQLETLIANG 115 (120)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHhCHHHHHHHHHcC
Confidence 46789999999999999999988888888887665
No 51
>PF11232 Med25: Mediator complex subunit 25 PTOV activation and synapsin 2; InterPro: IPR021394 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This family is the combined PTOV and SD2 domains. the PTOV domain being the domain through which Med25 co-operates with the histone acetyltransferase CBP, but the function of the SD2 domain is unclear []. ; PDB: 2KY6_A 2L23_A 2XNF_A 2L6U_A.
Probab=23.35 E-value=74 Score=23.37 Aligned_cols=18 Identities=22% Similarity=0.724 Sum_probs=14.5
Q ss_pred cccccceEEEEEcCCCce
Q 048296 45 RLCDTEIAIIVFSPKGRL 62 (167)
Q Consensus 45 ~LC~v~va~ivfsp~~k~ 62 (167)
.-|+++|-+++|||..+-
T Consensus 109 p~c~iKvL~LlYs~kk~~ 126 (152)
T PF11232_consen 109 PPCEIKVLMLLYSPKKKA 126 (152)
T ss_dssp SSSS-SEEEEEEETTTTE
T ss_pred CCCceEEEEEEEcCCCce
Confidence 569999999999999874
No 52
>PRK00977 exodeoxyribonuclease VII small subunit; Provisional
Probab=21.59 E-value=2e+02 Score=18.48 Aligned_cols=34 Identities=18% Similarity=0.180 Sum_probs=23.6
Q ss_pred cccCHHHH-------HHHHHHHHHHhhhhhHHHHHHHHHHh
Q 048296 128 EDLNMEEL-------EKYKSCLEELRSNVAMKVEEMVMRRT 161 (167)
Q Consensus 128 ~~Ls~~eL-------~~L~~~Le~~l~~v~~R~~~L~~~~~ 161 (167)
++++++++ ..|.......+..+..++..|+.+.-
T Consensus 29 ~~l~Lees~~lyeeg~~L~k~C~~~L~~ae~ki~~l~~~~~ 69 (80)
T PRK00977 29 GDLPLEESLAAFERGVALARQCQKKLQQAEQRVEKLLDEDG 69 (80)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 34555555 34556778888888999998876644
No 53
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=21.44 E-value=2.1e+02 Score=18.78 Aligned_cols=29 Identities=14% Similarity=0.312 Sum_probs=18.3
Q ss_pred CHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Q 048296 131 NMEELEKYKSCLEELRSNVAMKVEEMVMR 159 (167)
Q Consensus 131 s~~eL~~L~~~Le~~l~~v~~R~~~L~~~ 159 (167)
++++|......|+.....|..++.+|+..
T Consensus 34 ~LD~Lns~LD~LE~rnD~l~~~L~~LLes 62 (83)
T PF03670_consen 34 MLDQLNSCLDHLEQRNDHLHAQLQELLES 62 (83)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence 34556666666666666676666666653
No 54
>PF03785 Peptidase_C25_C: Peptidase family C25, C terminal ig-like domain; InterPro: IPR005536 This domain is found in almost all members of MEROPS peptidase family C25, (clan CD). Peptidase family C25 is a protein family found in the bacteria Porphyromonas gingivalis (Bacteroides gingivalis) a Gram-negative anaerobic bacterial species strongly associated with adult periodontitis. One of its distinguishing characteristics and putative virulence properties is the ability to agglutinate erythrocytes []. It is a highly proteolytic organism which metabolises small peptides and amino acids. Indirect evidence suggests that the proteases produced by this microorganism constitute an important virulence factor []. Protease-encoding genes have been shown to contain multiple copies of repeated nucleotide sequences. These conserved sequences have also been found in haemagglutinin genes [].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 1CVR_A.
Probab=21.27 E-value=46 Score=21.77 Aligned_cols=27 Identities=22% Similarity=0.417 Sum_probs=20.6
Q ss_pred chhhhhcccccceEEEEEcCCCceeec
Q 048296 39 KASELCRLCDTEIAIIVFSPKGRLYSF 65 (167)
Q Consensus 39 Ka~ELs~LC~v~va~ivfsp~~k~~~~ 65 (167)
=+.-+++-|+++=++|-+|.+|.+|--
T Consensus 15 ~~tS~~Vs~~~~gs~ValS~dg~l~G~ 41 (81)
T PF03785_consen 15 GQTSISVSCDVPGSYVALSQDGDLYGK 41 (81)
T ss_dssp T-SEEEEEESSTT-EEEEEETTEEEEE
T ss_pred cccEEEEEecCCCcEEEEecCCEEEEE
Confidence 345678999999999999999977543
No 55
>PF15079 DUF4546: Domain of unknown function (DUF4546)
Probab=20.66 E-value=76 Score=23.77 Aligned_cols=38 Identities=13% Similarity=0.370 Sum_probs=30.4
Q ss_pred hhcccCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhhh
Q 048296 126 SIEDLNMEELEKYKSCLEELRSNVAMKVEEMVMRRTCE 163 (167)
Q Consensus 126 ~l~~Ls~~eL~~L~~~Le~~l~~v~~R~~~L~~~~~~~ 163 (167)
+|-|=..+-|.+|...+.+..+..+++++-|+.-|-+.
T Consensus 75 diMDKDFDKL~EFVEIMKeMQkDMDEKMDvLiNiQKnn 112 (205)
T PF15079_consen 75 DIMDKDFDKLHEFVEIMKEMQKDMDEKMDVLINIQKNN 112 (205)
T ss_pred HHHhhhHHHHHHHHHHHHHHHHhHHHhhhHHhhccccc
Confidence 34455677888999999999999999999998776554
No 56
>PF06780 Erp_C: Erp protein C-terminus; InterPro: IPR009618 This entry represents the C terminus of bacterial Erp proteins that seem to be specific to Borrelia burgdorferi (a causative agent of Lyme disease). Borrelia Erp proteins are particularly heterogeneous, which might enable them to interact with a wide variety of host components [].
Probab=20.61 E-value=1.9e+02 Score=20.97 Aligned_cols=37 Identities=24% Similarity=0.373 Sum_probs=24.4
Q ss_pred hHHHHHhhhhcccCHHHHHHHHHHHHHHhhhhhHHHHH
Q 048296 118 ELEFWWEQSIEDLNMEELEKYKSCLEELRSNVAMKVEE 155 (167)
Q Consensus 118 ~~~~~~~~~l~~Ls~~eL~~L~~~Le~~l~~v~~R~~~ 155 (167)
.++..| ..+++=...+|..|...|+..+..+|.++..
T Consensus 54 SIy~~W-~~le~ee~~~L~~Ll~eL~~~R~~LR~Ki~e 90 (146)
T PF06780_consen 54 SIYSTW-EDLEEEEESGLGKLLKELSDTRSSLRTKINE 90 (146)
T ss_pred hHHHHH-hccccchhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 345667 4444334457777888888888888777654
No 57
>KOG3154 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.53 E-value=61 Score=25.46 Aligned_cols=27 Identities=19% Similarity=0.266 Sum_probs=21.9
Q ss_pred ccceEEEEEcCCCceeeccc--hhhhhhh
Q 048296 48 DTEIAIIVFSPKGRLYSFGD--HVIDKFI 74 (167)
Q Consensus 48 ~v~va~ivfsp~~k~~~~~~--~Vi~ry~ 74 (167)
|-...-||.||.|+....+. +|++++-
T Consensus 75 g~kF~GvVlSP~gk~~vsp~D~d~v~~~G 103 (263)
T KOG3154|consen 75 GQKFGGVVLSPVGKQCVSPADRDVVERSG 103 (263)
T ss_pred cCccCceEECCCCCcccCHHHHHHHHhcC
Confidence 44566799999999988887 8888874
No 58
>cd00187 TOP4c DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth.
Probab=20.44 E-value=1.6e+02 Score=25.49 Aligned_cols=60 Identities=23% Similarity=0.545 Sum_probs=37.4
Q ss_pred EEEeeccCCcc-eeeee---ccc-------cccccchhhhhcccccceEEEEEcCCCceeeccc-hhhhhhhhhh
Q 048296 15 EIKRIENNSSR-KVAFS---KRR-------KGMFKKASELCRLCDTEIAIIVFSPKGRLYSFGD-HVIDKFIEDE 77 (167)
Q Consensus 15 ~i~~I~n~~~R-~~tf~---KRr-------~gL~KKa~ELs~LC~v~va~ivfsp~~k~~~~~~-~Vi~ry~~~~ 77 (167)
.|.-|.|.+++ .+.|- ||. .+|+|+ ..|.+--.+ -+++|.|+|+|..|+- +|++.|...-
T Consensus 257 ~I~~~~D~s~~~~vrivI~lk~~~~~~~~~~~L~k~-t~L~~s~~~--Nm~~~~~~g~p~~~~l~~iL~~f~~~R 328 (445)
T cd00187 257 GISDVRDESDREGIRFVIELKRGAMAEVVLNGLYKV-TKLQTTFGI--NMVAFDPNGRPKKLNLKEILQEFLDHR 328 (445)
T ss_pred ccceeeeccCCCceEEEEEECCCccHHHHHHHHHHh-cCCceeeee--eEEEEecCCeeEEeCHHHHHHHHHHHH
Confidence 46677777776 34442 332 245533 333333322 7788999999999954 9999997643
No 59
>cd00468 HIT_like HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literacture into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Further sequence analysis reveals several new closely related, yet uncharacterized subgroups.
Probab=20.22 E-value=1.4e+02 Score=18.44 Aligned_cols=26 Identities=12% Similarity=0.233 Sum_probs=19.2
Q ss_pred hhhcccCHHHHHHHHHHHHHHhhhhh
Q 048296 125 QSIEDLNMEELEKYKSCLEELRSNVA 150 (167)
Q Consensus 125 ~~l~~Ls~~eL~~L~~~Le~~l~~v~ 150 (167)
.++.+|+.+++.++...+....+.+.
T Consensus 30 ~~~~~l~~~~~~~l~~~~~~~~~~l~ 55 (86)
T cd00468 30 ETLPDLDEALLADLVITAQRVAAELE 55 (86)
T ss_pred CChhHCCHHHHHHHHHHHHHHHHHHH
Confidence 35677888888888888777766553
No 60
>PF13082 DUF3931: Protein of unknown function (DUF3931)
Probab=20.15 E-value=61 Score=19.34 Aligned_cols=37 Identities=19% Similarity=0.304 Sum_probs=27.3
Q ss_pred eeEEEeeccCCcceeeeeccccccccchhhhh--ccccc
Q 048296 13 KIEIKRIENNSSRKVAFSKRRKGMFKKASELC--RLCDT 49 (167)
Q Consensus 13 ki~i~~I~n~~~R~~tf~KRr~gL~KKa~ELs--~LC~v 49 (167)
|-.+--|+......-||+--+--.-.|..|+| +|||-
T Consensus 7 kcnvisidgkkkksdtysypklvvenktyefssfvlcge 45 (66)
T PF13082_consen 7 KCNVISIDGKKKKSDTYSYPKLVVENKTYEFSSFVLCGE 45 (66)
T ss_pred cccEEEeccccccCCcccCceEEEeCceEEEEEEEEEcc
Confidence 34556677777777888888878888888888 56763
No 61
>PF12018 DUF3508: Domain of unknown function (DUF3508); InterPro: IPR021897 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 280 amino acids in length. This domain has two conserved sequence motifs: GFC and GLL. This family is also known as UPF0704.
Probab=20.14 E-value=1.4e+02 Score=24.03 Aligned_cols=42 Identities=21% Similarity=0.490 Sum_probs=28.4
Q ss_pred eeeeccccccccchhhhhcccccceEEEEEcCCCceeeccc-hhhhhhhhhhh
Q 048296 27 VAFSKRRKGMFKKASELCRLCDTEIAIIVFSPKGRLYSFGD-HVIDKFIEDEI 78 (167)
Q Consensus 27 ~tf~KRr~gL~KKa~ELs~LC~v~va~ivfsp~~k~~~~~~-~Vi~ry~~~~~ 78 (167)
.||.+|. ||. +--++.++++.| .|+.|.|++ +-+.+|...|.
T Consensus 210 ~tl~~~~-GLL-------lPG~p~~Gv~~~--~~k~y~F~s~~aa~~F~~~P~ 252 (281)
T PF12018_consen 210 WTLAERD-GLL-------LPGNPSIGVLKY--KDKYYAFSSREAAYRFAEDPE 252 (281)
T ss_pred EEEeccC-cee-------ecCCCccceeEE--cCEEEEeCCHHHHHHHHHCHH
Confidence 4666664 764 344567777777 679999999 55558877543
Done!