Query 033826
Match_columns 111
No_of_seqs 119 out of 1071
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 06:44:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033826.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033826hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00265 MADS_MEF2_like MEF2 (m 100.0 3E-33 6.5E-38 177.5 3.7 76 2-77 1-76 (77)
2 KOG0014 MADS box transcription 100.0 2.9E-32 6.2E-37 196.5 5.5 80 1-80 1-82 (195)
3 cd00266 MADS_SRF_like SRF-like 100.0 1.5E-30 3.3E-35 167.2 5.0 78 2-79 1-79 (83)
4 smart00432 MADS MADS domain. 100.0 1.8E-29 3.9E-34 152.8 4.0 59 2-60 1-59 (59)
5 cd00120 MADS MADS: MCM1, Agamo 99.9 9.9E-29 2.1E-33 149.6 3.4 59 2-60 1-59 (59)
6 PF00319 SRF-TF: SRF-type tran 99.9 1.1E-26 2.4E-31 136.7 -1.5 51 9-59 1-51 (51)
7 KOG0015 Regulator of arginine 99.8 2.1E-21 4.6E-26 148.2 2.2 66 2-67 63-128 (338)
8 COG5068 ARG80 Regulator of arg 99.5 4.5E-15 9.8E-20 117.5 2.5 69 1-69 81-149 (412)
9 PF10584 Proteasome_A_N: Prote 58.6 1.9 4.2E-05 21.1 -0.8 13 44-56 4-16 (23)
10 PF10491 Nrf1_DNA-bind: NLS-bi 54.5 12 0.00027 27.9 2.5 48 26-73 35-89 (214)
11 COG0139 HisI Phosphoribosyl-AM 53.6 5.7 0.00012 26.8 0.6 27 27-53 69-95 (111)
12 PF11232 Med25: Mediator compl 45.4 26 0.00057 24.9 2.9 36 37-72 109-145 (152)
13 PF02009 Rifin_STEVOR: Rifin/s 42.8 29 0.00062 27.2 3.0 30 37-74 20-49 (299)
14 PF03428 RP-C: Replication pro 42.6 63 0.0014 23.3 4.6 61 41-102 96-168 (177)
15 PF09151 DUF1936: Domain of un 42.2 26 0.00056 18.5 1.9 24 34-57 2-25 (36)
16 PF14009 DUF4228: Domain of un 41.4 30 0.00065 23.6 2.7 34 39-72 12-46 (181)
17 PF09941 DUF2173: Uncharacteri 41.1 46 0.001 22.3 3.4 37 32-69 3-42 (108)
18 COG1723 Uncharacterized conser 40.4 59 0.0013 25.9 4.4 97 9-109 206-304 (331)
19 KOG4637 Adaptor for phosphoino 36.6 33 0.00072 28.1 2.6 44 33-76 367-415 (464)
20 COG4888 Uncharacterized Zn rib 34.9 26 0.00055 23.4 1.4 56 1-59 1-60 (104)
21 PTZ00046 rifin; Provisional 34.7 45 0.00097 26.9 3.0 29 36-73 39-68 (358)
22 PRK09555 feoA ferrous iron tra 32.4 61 0.0013 19.9 2.8 33 26-58 20-52 (74)
23 PF01502 PRA-CH: Phosphoribosy 32.0 17 0.00036 22.9 0.2 34 20-53 21-63 (75)
24 PF09432 THP2: Tho complex sub 31.7 76 0.0016 22.0 3.4 21 57-77 34-55 (132)
25 PRK13824 replication initiatio 31.2 97 0.0021 25.2 4.5 66 34-102 103-180 (404)
26 PF14263 DUF4354: Domain of un 30.0 17 0.00038 24.9 0.0 44 11-59 41-84 (124)
27 TIGR01477 RIFIN variant surfac 30.0 63 0.0014 26.0 3.1 30 36-74 42-72 (353)
28 PF03932 CutC: CutC family; I 29.6 50 0.0011 24.3 2.4 42 27-72 40-84 (201)
29 TIGR01916 F420_cofE F420-0:gam 29.4 40 0.00087 25.7 1.9 28 33-60 133-160 (243)
30 cd03063 TRX_Fd_FDH_beta TRX-li 28.0 90 0.002 20.1 3.1 36 38-73 44-81 (92)
31 COG4831 Roadblock/LC7 domain [ 27.7 70 0.0015 21.2 2.5 30 30-60 3-32 (109)
32 COG5179 TAF1 Transcription ini 26.9 1.1E+02 0.0024 27.0 4.2 52 21-73 441-492 (968)
33 KOG0183 20S proteasome, regula 24.4 45 0.00098 25.3 1.3 18 40-57 3-20 (249)
34 COG4917 EutP Ethanolamine util 23.9 57 0.0012 22.9 1.7 24 34-57 58-81 (148)
35 PF07676 PD40: WD40-like Beta 23.6 62 0.0013 16.5 1.5 18 42-59 10-27 (39)
36 TIGR01478 STEVOR variant surfa 23.4 86 0.0019 24.6 2.7 44 7-71 25-69 (295)
37 PRK10803 tol-pal system protei 23.0 76 0.0017 24.0 2.4 46 59-104 35-80 (263)
38 COG1918 FeoA Fe2+ transport sy 22.0 1.2E+02 0.0026 18.8 2.7 32 26-57 21-52 (75)
39 cd07429 Cby_like Chibby, a nuc 21.8 1.2E+02 0.0026 20.3 2.8 26 83-108 77-102 (108)
40 KOG2036 Predicted P-loop ATPas 21.5 94 0.002 27.9 2.8 38 34-71 608-645 (1011)
41 PF13188 PAS_8: PAS domain; PD 21.3 93 0.002 17.3 2.1 29 37-67 6-34 (64)
42 cd01365 KISc_KIF1A_KIF1B Kines 20.9 76 0.0016 24.9 2.1 24 36-59 83-109 (356)
43 PRK13293 F420-0--gamma-glutamy 20.7 78 0.0017 24.2 2.0 27 33-59 134-160 (245)
44 cd01854 YjeQ_engC YjeQ/EngC. 20.4 1.2E+02 0.0026 23.0 3.0 40 11-54 53-92 (287)
45 KOG4316 Uncharacterized conser 20.3 42 0.00092 23.9 0.5 43 33-75 43-96 (172)
46 cd00187 TOP4c DNA Topoisomeras 20.3 2.3E+02 0.0049 23.5 4.7 29 44-75 302-330 (445)
47 PF04873 EIN3: Ethylene insens 20.2 34 0.00074 27.4 0.0 43 21-63 49-92 (354)
48 KOG0184 20S proteasome, regula 20.2 61 0.0013 24.7 1.3 22 36-57 3-24 (254)
49 COG3411 Ferredoxin [Energy pro 20.1 1.4E+02 0.003 18.2 2.7 28 44-71 18-46 (64)
50 PF06667 PspB: Phage shock pro 20.0 2.4E+02 0.0051 17.6 3.9 39 65-103 22-60 (75)
No 1
>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=3e-33 Score=177.55 Aligned_cols=76 Identities=67% Similarity=0.992 Sum_probs=73.1
Q ss_pred CCcccceeEecCCCCcceeccccccchhhhhhhhhccCCcceeEEEecCCCCcccccCchHHHHHHHHHcchhhhh
Q 033826 2 VRGKIQMKKIENDTSRQVTFSKRRNGMLKKAYELSVLCDAEVAVIIFSQKGRLYEFSSSEMQKTLERYYRYTEERQ 77 (111)
Q Consensus 2 gR~ki~i~~I~~~~~R~~tf~kRk~Gl~KKa~Els~Lc~~~v~liv~~~~g~~~~~~s~~~~~vl~ry~~~~~~~~ 77 (111)
||+||+|++|+|+..|++||+||+.||||||.|||+||||+||+|||+|+|++++|+||++.+||++|...++...
T Consensus 1 gr~ki~i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s~s~~~vl~ry~~~~~~~~ 76 (77)
T cd00265 1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPSMEKIIERYQKTSGSSL 76 (77)
T ss_pred CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCCCHHHHHHHHHhcccccc
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999877643
No 2
>KOG0014 consensus MADS box transcription factor [Transcription]
Probab=99.97 E-value=2.9e-32 Score=196.53 Aligned_cols=80 Identities=60% Similarity=0.970 Sum_probs=75.6
Q ss_pred CCCcccceeEecCCCCcceeccccccchhhhhhhhhccCCcceeEEEecCCCCcccccCch--HHHHHHHHHcchhhhhc
Q 033826 1 MVRGKIQMKKIENDTSRQVTFSKRRNGMLKKAYELSVLCDAEVAVIIFSQKGRLYEFSSSE--MQKTLERYYRYTEERQI 78 (111)
Q Consensus 1 MgR~ki~i~~I~~~~~R~~tf~kRk~Gl~KKa~Els~Lc~~~v~liv~~~~g~~~~~~s~~--~~~vl~ry~~~~~~~~~ 78 (111)
|||+||+|++|+|++.|++||+||+.||||||+||||||||+||+|||||+|++|+|++|+ +.+++++|...+.....
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 9999999999999999999999999999999999999999999999999999999999976 99999999998777655
Q ss_pred ch
Q 033826 79 DR 80 (111)
Q Consensus 79 ~~ 80 (111)
+.
T Consensus 81 ~~ 82 (195)
T KOG0014|consen 81 KK 82 (195)
T ss_pred cc
Confidence 44
No 3
>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=1.5e-30 Score=167.18 Aligned_cols=78 Identities=47% Similarity=0.729 Sum_probs=73.5
Q ss_pred CCcccceeEecCCCCcceeccccccchhhhhhhhhccCCcceeEEEecCCCCcccccCch-HHHHHHHHHcchhhhhcc
Q 033826 2 VRGKIQMKKIENDTSRQVTFSKRRNGMLKKAYELSVLCDAEVAVIIFSQKGRLYEFSSSE-MQKTLERYYRYTEERQID 79 (111)
Q Consensus 2 gR~ki~i~~I~~~~~R~~tf~kRk~Gl~KKa~Els~Lc~~~v~liv~~~~g~~~~~~s~~-~~~vl~ry~~~~~~~~~~ 79 (111)
||+||+|++|+|+.+|++||+||+.||+|||+|||+||||+||+|||||+|..+.|++++ +.+++++|..++...+..
T Consensus 1 gr~Ki~i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 79 (83)
T cd00266 1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSSEVEGVISRFEVLSALERKK 79 (83)
T ss_pred CCccceeEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCcHHHHHHHHHHhhcCHhhhhc
Confidence 899999999999999999999999999999999999999999999999999999998865 999999999988866544
No 4
>smart00432 MADS MADS domain.
Probab=99.95 E-value=1.8e-29 Score=152.79 Aligned_cols=59 Identities=71% Similarity=1.064 Sum_probs=58.0
Q ss_pred CCcccceeEecCCCCcceeccccccchhhhhhhhhccCCcceeEEEecCCCCcccccCc
Q 033826 2 VRGKIQMKKIENDTSRQVTFSKRRNGMLKKAYELSVLCDAEVAVIIFSQKGRLYEFSSS 60 (111)
Q Consensus 2 gR~ki~i~~I~~~~~R~~tf~kRk~Gl~KKa~Els~Lc~~~v~liv~~~~g~~~~~~s~ 60 (111)
||+||+|++|+|++.|++||+||+.||+|||.|||+||||+||+|||+|+|.+++|++|
T Consensus 1 gR~Ki~i~~I~~~~~R~~tf~kRk~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~p 59 (59)
T smart00432 1 GRRKIEIKRIENKTNRQVTFSKRRNGLFKKAHELSVLCDAEVALIVFSPTGKLYEFASP 59 (59)
T ss_pred CCCcceeEEeeCcchhhhhhHhhhhhHHHHHHHHhhccCCeEEEEEECCCCCeeeccCC
Confidence 89999999999999999999999999999999999999999999999999999999886
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=99.95 E-value=9.9e-29 Score=149.58 Aligned_cols=59 Identities=78% Similarity=1.110 Sum_probs=57.7
Q ss_pred CCcccceeEecCCCCcceeccccccchhhhhhhhhccCCcceeEEEecCCCCcccccCc
Q 033826 2 VRGKIQMKKIENDTSRQVTFSKRRNGMLKKAYELSVLCDAEVAVIIFSQKGRLYEFSSS 60 (111)
Q Consensus 2 gR~ki~i~~I~~~~~R~~tf~kRk~Gl~KKa~Els~Lc~~~v~liv~~~~g~~~~~~s~ 60 (111)
||+||+|++|+|+..|++||+||+.||+|||+|||+||||+||+|||||+|.+++|++|
T Consensus 1 gr~Ki~i~~I~~~~~R~~tf~kR~~gl~kKa~Els~Lc~~~v~~iv~sp~g~~~~~~~~ 59 (59)
T cd00120 1 GRGKIEIKRIENKTSRQVTFSKRRNGLFKKASELSVLCDAEVAVIVFSPSGKLYEFWSS 59 (59)
T ss_pred CCccceeEEeeCcchhhhhHHHHhchHHHhhhhheeccCCcEEEEEECCCCCcccccCC
Confidence 79999999999999999999999999999999999999999999999999999999875
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=99.91 E-value=1.1e-26 Score=136.74 Aligned_cols=51 Identities=59% Similarity=1.000 Sum_probs=46.9
Q ss_pred eEecCCCCcceeccccccchhhhhhhhhccCCcceeEEEecCCCCcccccC
Q 033826 9 KKIENDTSRQVTFSKRRNGMLKKAYELSVLCDAEVAVIIFSQKGRLYEFSS 59 (111)
Q Consensus 9 ~~I~~~~~R~~tf~kRk~Gl~KKa~Els~Lc~~~v~liv~~~~g~~~~~~s 59 (111)
++|+|+..|++||+||+.||+|||+|||+||||+||+|||+|+|++++|+|
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 589999999999999999999999999999999999999999999999986
No 7
>KOG0015 consensus Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.82 E-value=2.1e-21 Score=148.25 Aligned_cols=66 Identities=42% Similarity=0.705 Sum_probs=62.3
Q ss_pred CCcccceeEecCCCCcceeccccccchhhhhhhhhccCCcceeEEEecCCCCcccccCchHHHHHH
Q 033826 2 VRGKIQMKKIENDTSRQVTFSKRRNGMLKKAYELSVLCDAEVAVIIFSQKGRLYEFSSSEMQKTLE 67 (111)
Q Consensus 2 gR~ki~i~~I~~~~~R~~tf~kRk~Gl~KKa~Els~Lc~~~v~liv~~~~g~~~~~~s~~~~~vl~ 67 (111)
||+||+|.||+|+.+|.+||+|||.||||||+||++|+|.+|.|+|.|++|.+|+|++|.++.||.
T Consensus 63 gr~kik~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaTpKLep~i~ 128 (338)
T KOG0015|consen 63 GRVKIKMEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATPKLEPMIT 128 (338)
T ss_pred ceeeccchhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEecccccccccc
Confidence 699999999999999999999999999999999999999999999999999999999986665553
No 8
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.52 E-value=4.5e-15 Score=117.53 Aligned_cols=69 Identities=38% Similarity=0.621 Sum_probs=64.7
Q ss_pred CCCcccceeEecCCCCcceeccccccchhhhhhhhhccCCcceeEEEecCCCCcccccCchHHHHHHHH
Q 033826 1 MVRGKIQMKKIENDTSRQVTFSKRRNGMLKKAYELSVLCDAEVAVIIFSQKGRLYEFSSSEMQKTLERY 69 (111)
Q Consensus 1 MgR~ki~i~~I~~~~~R~~tf~kRk~Gl~KKa~Els~Lc~~~v~liv~~~~g~~~~~~s~~~~~vl~ry 69 (111)
|||+||.|.+|+|+.+|.+||.||+.||+|||.||++|+|.+|.++|.+.+|..+.|++|..+.|+...
T Consensus 81 ~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~tp~~e~v~~~~ 149 (412)
T COG5068 81 VTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTPKLESVVKSL 149 (412)
T ss_pred cccccCCcccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecCCccccccccc
Confidence 789999999999999999999999999999999999999999999999999999999998777766443
No 9
>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=58.63 E-value=1.9 Score=21.09 Aligned_cols=13 Identities=38% Similarity=0.887 Sum_probs=9.9
Q ss_pred eEEEecCCCCccc
Q 033826 44 AVIIFSQKGRLYE 56 (111)
Q Consensus 44 ~liv~~~~g~~~~ 56 (111)
.+.+|||+|+++.
T Consensus 4 ~~t~FSp~Grl~Q 16 (23)
T PF10584_consen 4 SITTFSPDGRLFQ 16 (23)
T ss_dssp STTSBBTTSSBHH
T ss_pred CceeECCCCeEEe
Confidence 4567899999865
No 10
>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=54.53 E-value=12 Score=27.89 Aligned_cols=48 Identities=10% Similarity=0.177 Sum_probs=37.1
Q ss_pred cchhhhh----hhhhccCCcceeEEEecCC---CCcccccCchHHHHHHHHHcch
Q 033826 26 NGMLKKA----YELSVLCDAEVAVIIFSQK---GRLYEFSSSEMQKTLERYYRYT 73 (111)
Q Consensus 26 ~Gl~KKa----~Els~Lc~~~v~liv~~~~---g~~~~~~s~~~~~vl~ry~~~~ 73 (111)
.-|+.|. .|+++=+|-.+.++|++|+ +..-.|+....+.|+..|...-
T Consensus 35 ~rllrkl~~~~de~~trvGqqavvl~~~p~kp~~~f~vfGa~pL~~vv~~~~~~I 89 (214)
T PF10491_consen 35 TRLLRKLRQTIDEYTTRVGQQAVVLCCTPSKPNPVFKVFGAAPLENVVRNLKPVI 89 (214)
T ss_pred HHHHHHHHHHHHHHHHhhhceeEEEEecCCCCCCceeeecchhHHHHHHHHHHHH
Confidence 3466665 6999999999999999874 4455688878888888887643
No 11
>COG0139 HisI Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]
Probab=53.64 E-value=5.7 Score=26.79 Aligned_cols=27 Identities=26% Similarity=0.543 Sum_probs=22.3
Q ss_pred chhhhhhhhhccCCcceeEEEecCCCC
Q 033826 27 GMLKKAYELSVLCDAEVAVIIFSQKGR 53 (111)
Q Consensus 27 Gl~KKa~Els~Lc~~~v~liv~~~~g~ 53 (111)
|-+.|+.|+.+-||.|+.++++.+.|.
T Consensus 69 G~~q~v~~i~~DCD~Dall~~V~q~gg 95 (111)
T COG0139 69 GHTQKVVEIRLDCDGDALLLLVEQIGG 95 (111)
T ss_pred CceEEEEEEEcCCCCCEEEEEEEeCCC
Confidence 555667799999999999999988554
No 12
>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=45.44 E-value=26 Score=24.86 Aligned_cols=36 Identities=17% Similarity=0.422 Sum_probs=24.7
Q ss_pred ccCCcceeEEEecCCCCccc-ccCchHHHHHHHHHcc
Q 033826 37 VLCDAEVAVIIFSQKGRLYE-FSSSEMQKTLERYYRY 72 (111)
Q Consensus 37 ~Lc~~~v~liv~~~~g~~~~-~~s~~~~~vl~ry~~~ 72 (111)
.-|++.|.+++|||.-+.|. |-+-+-..+..+++..
T Consensus 109 p~c~iKvL~LlYs~kk~~flG~IP~DQ~~Fv~~lr~V 145 (152)
T PF11232_consen 109 PPCEIKVLMLLYSPKKKAFLGFIPNDQEGFVNRLRQV 145 (152)
T ss_dssp SSSS-SEEEEEEETTTTEEEEEEESTHHHHHHHHHHH
T ss_pred CCCceEEEEEEEcCCCceEEEEcCCCHHHHHHHHHHH
Confidence 56899999999999877555 5554555566665543
No 13
>PF02009 Rifin_STEVOR: Rifin/stevor family; InterPro: IPR002858 Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see []. Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens [].
Probab=42.81 E-value=29 Score=27.20 Aligned_cols=30 Identities=27% Similarity=0.531 Sum_probs=19.4
Q ss_pred ccCCcceeEEEecCCCCcccccCchHHHHHHHHHcchh
Q 033826 37 VLCDAEVAVIIFSQKGRLYEFSSSEMQKTLERYYRYTE 74 (111)
Q Consensus 37 ~Lc~~~v~liv~~~~g~~~~~~s~~~~~vl~ry~~~~~ 74 (111)
+||.+|.-...|+. -|++++|.+.|.+.+.
T Consensus 20 ~LcECely~snYDN--------DPeMK~Vme~F~rqTs 49 (299)
T PF02009_consen 20 SLCECELYTSNYDN--------DPEMKSVMENFDRQTS 49 (299)
T ss_pred chhhhcccccCCCC--------cHHHHHHHHHHHHHHH
Confidence 56776665333321 3899999999976443
No 14
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=42.64 E-value=63 Score=23.33 Aligned_cols=61 Identities=16% Similarity=0.241 Sum_probs=36.8
Q ss_pred cceeEEEe--cCCCCcccccCc----------hHHHHHHHHHcchhhhhcchhhhhhHhhhhhHHHHHHHHHHH
Q 033826 41 AEVAVIIF--SQKGRLYEFSSS----------EMQKTLERYYRYTEERQIDRNGMERYMQVRPLYLNLITFEIS 102 (111)
Q Consensus 41 ~~v~liv~--~~~g~~~~~~s~----------~~~~vl~ry~~~~~~~~~~~~~~~~~~q~LkE~~~~~~~eI~ 102 (111)
+++.||+. ||||+=|..-.+ +..+++.+|..+........ .....++.+++....+.+.|.
T Consensus 96 veaGLI~rrDS~NgkRy~~R~~~G~I~~A~GfdLsPL~~R~~El~~~a~~~~-~~~~~~r~lr~~it~~rR~i~ 168 (177)
T PF03428_consen 96 VEAGLIVRRDSPNGKRYARRDRGGRIVEAFGFDLSPLIARAEELAALAEAAR-AERRALRRLRRRITLLRRDIR 168 (177)
T ss_pred HHCCCeeeccCCCCCccCccCCCCCEEeEeCcCHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHH
Confidence 56788888 689987664321 67888888887655433211 122334455566655555554
No 15
>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=42.24 E-value=26 Score=18.46 Aligned_cols=24 Identities=29% Similarity=0.515 Sum_probs=16.8
Q ss_pred hhhccCCcceeEEEecCCCCcccc
Q 033826 34 ELSVLCDAEVAVIIFSQKGRLYEF 57 (111)
Q Consensus 34 Els~Lc~~~v~liv~~~~g~~~~~ 57 (111)
.|+--||+-|...||+..|..-.|
T Consensus 2 hlcpkcgvgvl~pvy~~kgeikvf 25 (36)
T PF09151_consen 2 HLCPKCGVGVLEPVYNQKGEIKVF 25 (36)
T ss_dssp -B-TTTSSSBEEEEE-TTS-EEEE
T ss_pred ccCCccCceEEEEeecCCCcEEEE
Confidence 467779999999999998886554
No 16
>PF14009 DUF4228: Domain of unknown function (DUF4228)
Probab=41.41 E-value=30 Score=23.58 Aligned_cols=34 Identities=12% Similarity=0.190 Sum_probs=25.5
Q ss_pred CCcceeEEEecCCCCcccccCc-hHHHHHHHHHcc
Q 033826 39 CDAEVAVIIFSQKGRLYEFSSS-EMQKTLERYYRY 72 (111)
Q Consensus 39 c~~~v~liv~~~~g~~~~~~s~-~~~~vl~ry~~~ 72 (111)
++...++-|..++|...+|..| .+.+|+..|=..
T Consensus 12 ~~~~~~vkvv~~~G~v~~~~~pv~a~evm~~~P~h 46 (181)
T PF14009_consen 12 SSSAATVKVVHPDGKVEEFKRPVTAAEVMLENPGH 46 (181)
T ss_pred cCCCceEEEEcCCCcEEEeCCCcCHHHHHHHCCCC
Confidence 4455556666689999999887 899999887544
No 17
>PF09941 DUF2173: Uncharacterized conserved protein (DUF2173); InterPro: IPR018685 This family of various hypothetical prokaryotic proteins has no known function.
Probab=41.06 E-value=46 Score=22.27 Aligned_cols=37 Identities=27% Similarity=0.337 Sum_probs=26.0
Q ss_pred hhhhhccCCcceeEEEecCCCCcccccC---chHHHHHHHH
Q 033826 32 AYELSVLCDAEVAVIIFSQKGRLYEFSS---SEMQKTLERY 69 (111)
Q Consensus 32 a~Els~Lc~~~v~liv~~~~g~~~~~~s---~~~~~vl~ry 69 (111)
..+|..|.||-+ ...||++|++.+|-. +..-+++.++
T Consensus 3 l~~Lm~lpGv~A-Ag~Fs~~G~l~e~~G~l~~~~a~m~A~m 42 (108)
T PF09941_consen 3 LDKLMKLPGVVA-AGEFSDDGKLVEYKGELDEEMAEMLAKM 42 (108)
T ss_pred HHHhhcCCCeEE-EEEECCCCeEEeeecCCCHHHHHHHHHH
Confidence 467888888854 578999999999865 3444444444
No 18
>COG1723 Uncharacterized conserved protein [Function unknown]
Probab=40.43 E-value=59 Score=25.93 Aligned_cols=97 Identities=19% Similarity=0.235 Sum_probs=55.9
Q ss_pred eEecCCCCcceeccccccchhhhhhhhhccCCcceeEEEecC--CCCcccccCchHHHHHHHHHcchhhhhcchhhhhhH
Q 033826 9 KKIENDTSRQVTFSKRRNGMLKKAYELSVLCDAEVAVIIFSQ--KGRLYEFSSSEMQKTLERYYRYTEERQIDRNGMERY 86 (111)
Q Consensus 9 ~~I~~~~~R~~tf~kRk~Gl~KKa~Els~Lc~~~v~liv~~~--~g~~~~~~s~~~~~vl~ry~~~~~~~~~~~~~~~~~ 86 (111)
+.|..+-++.-.-+.++.-++|+..+|-.+ .+-+-..|. +..-+.|..|..+++.......-+-.... ..+...
T Consensus 206 ~~~pq~la~~gkvslsr~eilk~iG~LFll---R~~iNL~s~IlDtPef~W~ePqleplY~~~~~yLdI~~Rv-nvLN~R 281 (331)
T COG1723 206 KPIPQELARTGKVSLSRKEILKQIGKLFLL---RVSINLHSDILDTPEFFWSEPQLEPLYLAVREYLDINPRV-NVLNRR 281 (331)
T ss_pred chhHHHHhhcCCccccHHHHHHHHhHHhhe---eeeeeeeeccccCchhcccCcchhHHHHHHHHHhchhHHH-HHHHHH
Confidence 344444555566678888899999988876 445555554 44457777898888865554433322221 123333
Q ss_pred hhhhhHHHHHHHHHHHhchhhcc
Q 033826 87 MQVRPLYLNLITFEISLGKRQYL 109 (111)
Q Consensus 87 ~q~LkE~~~~~~~eI~~~~~~~l 109 (111)
.+-..+.++.+...+-..+++.|
T Consensus 282 l~vi~d~l~il~e~ln~~~s~~l 304 (331)
T COG1723 282 LEVISDLLDILNEQLNHSHSTRL 304 (331)
T ss_pred HHHHHHHHHHHHHHhhhccccee
Confidence 33344555555555555555543
No 19
>KOG4637 consensus Adaptor for phosphoinositide 3-kinase [Signal transduction mechanisms]
Probab=36.63 E-value=33 Score=28.08 Aligned_cols=44 Identities=27% Similarity=0.363 Sum_probs=31.4
Q ss_pred hhhhccCCcce--eEEEecCCCCcccccC---chHHHHHHHHHcchhhh
Q 033826 33 YELSVLCDAEV--AVIIFSQKGRLYEFSS---SEMQKTLERYYRYTEER 76 (111)
Q Consensus 33 ~Els~Lc~~~v--~liv~~~~g~~~~~~s---~~~~~vl~ry~~~~~~~ 76 (111)
.-|||+||-+| |||--..+|=.|.-|. ++.++++.+|...+-+.
T Consensus 367 yalSV~~~~~V~HClIy~tatG~GFa~pyn~y~tlk~lV~hY~h~SLe~ 415 (464)
T KOG4637|consen 367 YALSVVHDGEVKHCLIYQTATGFGFAEPYNLYSTLKELVLHYQHTSLEQ 415 (464)
T ss_pred eEEEEEECCceeeeEEeeccccccccchhHHHHHHHHHHHHHhhhhHHh
Confidence 57999999888 6655556665555443 48899999998866543
No 20
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=34.86 E-value=26 Score=23.36 Aligned_cols=56 Identities=16% Similarity=0.150 Sum_probs=31.0
Q ss_pred CCCcccceeEecCCCCcceeccccccchhhhhhhhhccCCc----ceeEEEecCCCCcccccC
Q 033826 1 MVRGKIQMKKIENDTSRQVTFSKRRNGMLKKAYELSVLCDA----EVAVIIFSQKGRLYEFSS 59 (111)
Q Consensus 1 MgR~ki~i~~I~~~~~R~~tf~kRk~Gl~KKa~Els~Lc~~----~v~liv~~~~g~~~~~~s 59 (111)
|||++.+.+.|.... ...+.|+-..++ =-+|.++.|-+ .+++++++..|.-|++--
T Consensus 1 MG~rr~krr~~ik~~--~~~L~k~FtCp~-Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev 60 (104)
T COG4888 1 MGRRRRKRRKIIKRR--PQVLPKTFTCPR-CGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEV 60 (104)
T ss_pred CCcccccccccCccc--CccCCceEecCc-cCCeeeeEEEEEecCceeEEEcccCcceEEEec
Confidence 999988877664322 222333333322 11344444443 457777788888777543
No 21
>PTZ00046 rifin; Provisional
Probab=34.71 E-value=45 Score=26.90 Aligned_cols=29 Identities=31% Similarity=0.663 Sum_probs=20.0
Q ss_pred hccCCcceeEEEecCCCCcccccC-chHHHHHHHHHcch
Q 033826 36 SVLCDAEVAVIIFSQKGRLYEFSS-SEMQKTLERYYRYT 73 (111)
Q Consensus 36 s~Lc~~~v~liv~~~~g~~~~~~s-~~~~~vl~ry~~~~ 73 (111)
-+||.+|.- +| .|.+ |+|++|.+.|.+.+
T Consensus 39 R~LcECeLY----~p-----nYDNDPeMK~Vme~F~rqT 68 (358)
T PTZ00046 39 RLLCECELY----SS-----NYDNDPEMKSVMENFDRQT 68 (358)
T ss_pred hhhhhhhcC----CC-----CCCCcHHHHHHHHHHhHHH
Confidence 467887763 32 3555 89999999886643
No 22
>PRK09555 feoA ferrous iron transport protein A; Reviewed
Probab=32.43 E-value=61 Score=19.86 Aligned_cols=33 Identities=15% Similarity=0.173 Sum_probs=28.8
Q ss_pred cchhhhhhhhhccCCcceeEEEecCCCCccccc
Q 033826 26 NGMLKKAYELSVLCDAEVAVIIFSQKGRLYEFS 58 (111)
Q Consensus 26 ~Gl~KKa~Els~Lc~~~v~liv~~~~g~~~~~~ 58 (111)
..+..+-.++-++.|++|-++-.+|-|.|..+.
T Consensus 20 ~~~~~rL~~mGl~pG~~V~v~~~aP~gdPi~i~ 52 (74)
T PRK09555 20 PAYRQKLLSLGMLPGSSFNVVRVAPLGDPIHIE 52 (74)
T ss_pred hHHHHHHHHcCCCCCCEEEEEEECCCCCCEEEE
Confidence 457888999999999999999999988887764
No 23
>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=32.01 E-value=17 Score=22.86 Aligned_cols=34 Identities=26% Similarity=0.515 Sum_probs=24.3
Q ss_pred eccccccchhh---------hhhhhhccCCcceeEEEecCCCC
Q 033826 20 TFSKRRNGMLK---------KAYELSVLCDAEVAVIIFSQKGR 53 (111)
Q Consensus 20 tf~kRk~Gl~K---------Ka~Els~Lc~~~v~liv~~~~g~ 53 (111)
-|++-+.+|-. ++.|+.+-||.|+.|+.+-|.|.
T Consensus 21 y~SRSR~~lW~KGetSG~~q~v~~i~~DCD~D~ll~~V~~~G~ 63 (75)
T PF01502_consen 21 YYSRSRNRLWRKGETSGNTQKVVEIRLDCDGDALLFKVEQVGP 63 (75)
T ss_dssp EEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-
T ss_pred EEEccCCcEeeEECCCCCEEEEEEEEecCCCCeEEEEEEeCCC
Confidence 34666656544 45699999999999999988776
No 24
>PF09432 THP2: Tho complex subunit THP2; InterPro: IPR018557 The THO complex plays a role in coupling transcription elongation to mRNA export. It is composed of subunits THP2, HPR1, THO2 and MFT1 [].
Probab=31.71 E-value=76 Score=22.02 Aligned_cols=21 Identities=24% Similarity=0.523 Sum_probs=14.1
Q ss_pred ccCc-hHHHHHHHHHcchhhhh
Q 033826 57 FSSS-EMQKTLERYYRYTEERQ 77 (111)
Q Consensus 57 ~~s~-~~~~vl~ry~~~~~~~~ 77 (111)
|++| .+.++++.|...+.+..
T Consensus 34 ~~pP~el~~iLe~y~~~~~d~~ 55 (132)
T PF09432_consen 34 WNPPKELQSILEKYNTPSTDTE 55 (132)
T ss_pred CCCCHHHHHHHHHHcCCCccHH
Confidence 4454 78889999988444433
No 25
>PRK13824 replication initiation protein RepC; Provisional
Probab=31.20 E-value=97 Score=25.23 Aligned_cols=66 Identities=20% Similarity=0.236 Sum_probs=39.1
Q ss_pred hhhccCCcceeEEEe--cCCCCcccccC--c--------hHHHHHHHHHcchhhhhcchhhhhhHhhhhhHHHHHHHHHH
Q 033826 34 ELSVLCDAEVAVIIF--SQKGRLYEFSS--S--------EMQKTLERYYRYTEERQIDRNGMERYMQVRPLYLNLITFEI 101 (111)
Q Consensus 34 Els~Lc~~~v~liv~--~~~g~~~~~~s--~--------~~~~vl~ry~~~~~~~~~~~~~~~~~~q~LkE~~~~~~~eI 101 (111)
.|+.| |++.||+. ||||+=|..-. . ++..++.||..+......... ..+.++.+++..-.++++|
T Consensus 103 hla~L--veaGLI~rrDSpNGKRyarr~~~G~i~~AfGfDLsPL~~R~~El~~~A~~~~a-e~~~~r~lr~~it~~rRdi 179 (404)
T PRK13824 103 HLAAL--VEAGLIIRRDSPNGKRYARKGRGGEIEEAFGFDLAPLLARAEEFEALAEQVAA-ERKALRRLRERLTLCRRDI 179 (404)
T ss_pred HHHHH--HHCCCeEeecCCCCcccceeCCCCceeeeeccchHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH
Confidence 45555 45567777 79999775432 1 667888888776554332111 2334555666666666655
Q ss_pred H
Q 033826 102 S 102 (111)
Q Consensus 102 ~ 102 (111)
.
T Consensus 180 ~ 180 (404)
T PRK13824 180 A 180 (404)
T ss_pred H
Confidence 3
No 26
>PF14263 DUF4354: Domain of unknown function (DUF4354); PDB: 3NRF_B 3SB3_A.
Probab=29.99 E-value=17 Score=24.91 Aligned_cols=44 Identities=18% Similarity=0.388 Sum_probs=30.8
Q ss_pred ecCCCCcceeccccccchhhhhhhhhccCCcceeEEEecCCCCcccccC
Q 033826 11 IENDTSRQVTFSKRRNGMLKKAYELSVLCDAEVAVIIFSQKGRLYEFSS 59 (111)
Q Consensus 11 I~~~~~R~~tf~kRk~Gl~KKa~Els~Lc~~~v~liv~~~~g~~~~~~s 59 (111)
+.++.....||.=.-..+..+.-+|+.+| ++.|+|.|+.|...+
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 45666677788888888888988999885 999999998776544
No 27
>TIGR01477 RIFIN variant surface antigen, rifin family. This model represents the rifin branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of rifin sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 20 bits.
Probab=29.96 E-value=63 Score=26.04 Aligned_cols=30 Identities=27% Similarity=0.568 Sum_probs=19.4
Q ss_pred hccCCcceeEEEecCCCCcccccC-chHHHHHHHHHcchh
Q 033826 36 SVLCDAEVAVIIFSQKGRLYEFSS-SEMQKTLERYYRYTE 74 (111)
Q Consensus 36 s~Lc~~~v~liv~~~~g~~~~~~s-~~~~~vl~ry~~~~~ 74 (111)
-+||.+|.-.. .|.+ |++++|.+.|.+.+.
T Consensus 42 R~LcECeLy~~---------nYDNDPeMK~Vm~nF~rqTs 72 (353)
T TIGR01477 42 RSLCECELYSS---------NYDNDPEMKSVMEQFDRQTS 72 (353)
T ss_pred ehhhhhhcccc---------cCCCcHHHHHHHHHHhHHHH
Confidence 35787777421 2434 899999988866433
No 28
>PF03932 CutC: CutC family; InterPro: IPR005627 Copper transport in Escherichia coli is mediated by the products of at least six genes, cutA, cutB, cutC, cutD, cutE, and cutF. A mutation in one or more of these genes results in an increased copper sensitivity. Members of this family are between 200 and 300 amino acids in length and are found in both eukaryotes and bacteria.; GO: 0005507 copper ion binding, 0055070 copper ion homeostasis; PDB: 2BDQ_A 3IWP_I 1X8C_B 1X7I_A 1TWD_B.
Probab=29.62 E-value=50 Score=24.31 Aligned_cols=42 Identities=24% Similarity=0.419 Sum_probs=24.4
Q ss_pred chhhhhhhhhccCCcceeEEEecCCCCcccccCchHHHH---HHHHHcc
Q 033826 27 GMLKKAYELSVLCDAEVAVIIFSQKGRLYEFSSSEMQKT---LERYYRY 72 (111)
Q Consensus 27 Gl~KKa~Els~Lc~~~v~liv~~~~g~~~~~~s~~~~~v---l~ry~~~ 72 (111)
|+++.+.+ -++++|.++|. |.+.-|.|+..++..+ |..++.+
T Consensus 40 g~i~~~~~---~~~ipv~vMIR-pr~gdF~Ys~~E~~~M~~dI~~~~~~ 84 (201)
T PF03932_consen 40 GLIRQARE---AVDIPVHVMIR-PRGGDFVYSDEEIEIMKEDIRMLREL 84 (201)
T ss_dssp HHHHHHHH---HTTSEEEEE---SSSS-S---HHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHh---hcCCceEEEEC-CCCCCccCCHHHHHHHHHHHHHHHHc
Confidence 67888877 67888888887 5566788877665555 4445443
No 29
>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=29.43 E-value=40 Score=25.69 Aligned_cols=28 Identities=29% Similarity=0.362 Sum_probs=23.6
Q ss_pred hhhhccCCcceeEEEecCCCCcccccCc
Q 033826 33 YELSVLCDAEVAVIIFSQKGRLYEFSSS 60 (111)
Q Consensus 33 ~Els~Lc~~~v~liv~~~~g~~~~~~s~ 60 (111)
.+|.-.+|++|++||..+.|.++-.+.+
T Consensus 133 ~~l~~~~g~~v~VIItDt~gr~~R~G~~ 160 (243)
T TIGR01916 133 RGLRELTGVDVGVIITDTNGRPFREGQV 160 (243)
T ss_pred HHHHHHHCCCEEEEEECCCCCccccCCC
Confidence 3677789999999999999998887764
No 30
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=27.97 E-value=90 Score=20.06 Aligned_cols=36 Identities=14% Similarity=0.011 Sum_probs=25.7
Q ss_pred cCCcceeEEEecCCC-CcccccCc-hHHHHHHHHHcch
Q 033826 38 LCDAEVAVIIFSQKG-RLYEFSSS-EMQKTLERYYRYT 73 (111)
Q Consensus 38 Lc~~~v~liv~~~~g-~~~~~~s~-~~~~vl~ry~~~~ 73 (111)
+|..+-.+.|..|+| -.|...+| ++.++++.+..-+
T Consensus 44 ~C~~ePlV~V~~p~g~v~Y~~V~~edv~~Iv~~~~~~~ 81 (92)
T cd03063 44 MYWLEPLVEVETPGGRVAYGPVTPADVASLLDAGALEG 81 (92)
T ss_pred ecCCCCEEEEEeCCCcEEEEeCCHHHHHHHHHHHhhcC
Confidence 488888888887777 44544454 8889998876643
No 31
>COG4831 Roadblock/LC7 domain [Function unknown]
Probab=27.71 E-value=70 Score=21.22 Aligned_cols=30 Identities=30% Similarity=0.327 Sum_probs=24.0
Q ss_pred hhhhhhhccCCcceeEEEecCCCCcccccCc
Q 033826 30 KKAYELSVLCDAEVAVIIFSQKGRLYEFSSS 60 (111)
Q Consensus 30 KKa~Els~Lc~~~v~liv~~~~g~~~~~~s~ 60 (111)
-|..||-.+-||-++ =.|||+|++.+|-++
T Consensus 3 ekLdeLlqi~Gv~AA-Gefs~DGkLv~Ykgd 32 (109)
T COG4831 3 EKLDELLQIKGVMAA-GEFSPDGKLVEYKGD 32 (109)
T ss_pred hhHHHHhCccceeEe-ceeCCCCceEEeeCC
Confidence 467888888888654 579999999999874
No 32
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=26.94 E-value=1.1e+02 Score=26.98 Aligned_cols=52 Identities=25% Similarity=0.333 Sum_probs=41.6
Q ss_pred ccccccchhhhhhhhhccCCcceeEEEecCCCCcccccCchHHHHHHHHHcch
Q 033826 21 FSKRRNGMLKKAYELSVLCDAEVAVIIFSQKGRLYEFSSSEMQKTLERYYRYT 73 (111)
Q Consensus 21 f~kRk~Gl~KKa~Els~Lc~~~v~liv~~~~g~~~~~~s~~~~~vl~ry~~~~ 73 (111)
-.|--.+++++|.||.+=--+.+.|+=||+ ..|+..+.|.+-+.|-.|.+-+
T Consensus 441 K~K~~~e~i~t~~elTvgDtsp~~L~EySE-e~P~~Lsn~GMas~l~nYYRK~ 492 (968)
T COG5179 441 KGKDVQEIIKTAGELTVGDTSPFSLFEYSE-EEPFFLSNPGMASLLNNYYRKS 492 (968)
T ss_pred cccchhhhhccccceeccCCCceeeeeecc-cCceeecCchHHHHHHHHHHhc
Confidence 344457899999999999999999999997 5566677788888888876643
No 33
>KOG0183 consensus 20S proteasome, regulatory subunit alpha type PSMA7/PRE6 [Posttranslational modification, protein turnover, chaperones]
Probab=24.43 E-value=45 Score=25.28 Aligned_cols=18 Identities=28% Similarity=0.602 Sum_probs=14.2
Q ss_pred CcceeEEEecCCCCcccc
Q 033826 40 DAEVAVIIFSQKGRLYEF 57 (111)
Q Consensus 40 ~~~v~liv~~~~g~~~~~ 57 (111)
+-|-++-||||+|.++..
T Consensus 3 rydraltvFSPDGhL~QV 20 (249)
T KOG0183|consen 3 RYDRALTVFSPDGHLFQV 20 (249)
T ss_pred ccccceEEECCCCCEEee
Confidence 346789999999998753
No 34
>COG4917 EutP Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=23.90 E-value=57 Score=22.95 Aligned_cols=24 Identities=21% Similarity=0.342 Sum_probs=17.9
Q ss_pred hhhccCCcceeEEEecCCCCcccc
Q 033826 34 ELSVLCDAEVAVIIFSQKGRLYEF 57 (111)
Q Consensus 34 Els~Lc~~~v~liv~~~~g~~~~~ 57 (111)
=+.++||++|-+++-+-+.+...|
T Consensus 58 L~tt~~dadvi~~v~~and~~s~f 81 (148)
T COG4917 58 LITTLQDADVIIYVHAANDPESRF 81 (148)
T ss_pred HHHHhhccceeeeeecccCccccC
Confidence 467899999999988876653333
No 35
>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=23.61 E-value=62 Score=16.46 Aligned_cols=18 Identities=22% Similarity=0.346 Sum_probs=13.0
Q ss_pred ceeEEEecCCCCcccccC
Q 033826 42 EVAVIIFSQKGRLYEFSS 59 (111)
Q Consensus 42 ~v~liv~~~~g~~~~~~s 59 (111)
.-.-..+||+|+...|.+
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 445678899999888876
No 36
>TIGR01478 STEVOR variant surface antigen, stevor family. This model represents the stevor branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits.
Probab=23.38 E-value=86 Score=24.63 Aligned_cols=44 Identities=16% Similarity=0.335 Sum_probs=29.4
Q ss_pred ceeEecCCCCcceeccccccchhhhhhhhhccCCcceeEEEecCCCCcccccC-chHHHHHHHHHc
Q 033826 7 QMKKIENDTSRQVTFSKRRNGMLKKAYELSVLCDAEVAVIIFSQKGRLYEFSS-SEMQKTLERYYR 71 (111)
Q Consensus 7 ~i~~I~~~~~R~~tf~kRk~Gl~KKa~Els~Lc~~~v~liv~~~~g~~~~~~s-~~~~~vl~ry~~ 71 (111)
.+.+|.|.+.|..+=+| .||.++.+ +.| .|.. |++++|++.|..
T Consensus 25 n~~li~n~tqr~t~~sR-------------~L~Ecel~---~~p-----~Y~nDpEmK~iid~~n~ 69 (295)
T TIGR01478 25 NVSYIQNNTQMTSTKSR-------------LLAEIQRP---KNP-----HYHNDPELKEIIDKLNE 69 (295)
T ss_pred ceecccCccccccccce-------------ehhhhccc---cCC-----CCCCcHHHHHHHHHHhH
Confidence 46678888888765322 46777664 222 4544 899999998865
No 37
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=22.99 E-value=76 Score=24.05 Aligned_cols=46 Identities=7% Similarity=0.067 Sum_probs=21.3
Q ss_pred CchHHHHHHHHHcchhhhhcchhhhhhHhhhhhHHHHHHHHHHHhc
Q 033826 59 SSEMQKTLERYYRYTEERQIDRNGMERYMQVRPLYLNLITFEISLG 104 (111)
Q Consensus 59 s~~~~~vl~ry~~~~~~~~~~~~~~~~~~q~LkE~~~~~~~eI~~~ 104 (111)
+++.++=+.+..+........-..++++++.|+.++..++-+|+..
T Consensus 35 ~~~~~~r~~~le~~~~~~~~~~~~l~~ql~~lq~ev~~LrG~~E~~ 80 (263)
T PRK10803 35 SGSVEDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQEN 80 (263)
T ss_pred CCchHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence 4444544444444433332222245555666665555555544433
No 38
>COG1918 FeoA Fe2+ transport system protein A [Inorganic ion transport and metabolism]
Probab=21.96 E-value=1.2e+02 Score=18.80 Aligned_cols=32 Identities=16% Similarity=0.283 Sum_probs=28.0
Q ss_pred cchhhhhhhhhccCCcceeEEEecCCCCcccc
Q 033826 26 NGMLKKAYELSVLCDAEVAVIIFSQKGRLYEF 57 (111)
Q Consensus 26 ~Gl~KKa~Els~Lc~~~v~liv~~~~g~~~~~ 57 (111)
.++.++-.++-+.-|+++.++-.+|-|+|...
T Consensus 21 ~~~~~RL~~mG~~~G~~i~vi~~aplgdPi~v 52 (75)
T COG1918 21 NGLRRRLLSMGIVPGASITVVRKAPLGDPILV 52 (75)
T ss_pred HHHHHHHHHcCCCCCCEEEEEEecCCCCCEEE
Confidence 38899999999999999999999998876543
No 39
>cd07429 Cby_like Chibby, a nuclear inhibitor of Wnt/beta-catenin mediated transcription, and similar proteins. Chibby(Cby) is a well-conserved nuclear protein that functions as part of the Wnt/beta-catenin signaling pathway. Specifically, Cby binds directly to beta-catenin by interacting with its central region, which harbors armadillo repeats. Cby-beta-catenin interactions may also involve 14-3-3 proteins. By competing with other binding partners of beta-catenin, the Tcf/Lef transcription factors, Cby inhibits transcriptional activation. Cby has been shown to play a role in adipocyte differentiation. The C-terminal region of Cby appears to contain an alpha-helical coiled-coil motif.
Probab=21.83 E-value=1.2e+02 Score=20.33 Aligned_cols=26 Identities=15% Similarity=0.060 Sum_probs=19.6
Q ss_pred hhhHhhhhhHHHHHHHHHHHhchhhc
Q 033826 83 MERYMQVRPLYLNLITFEISLGKRQY 108 (111)
Q Consensus 83 ~~~~~q~LkE~~~~~~~eI~~~~~~~ 108 (111)
.....+.|.|++++++.+|+..-.|+
T Consensus 77 lkkk~~~LeEENNlLklKievLLDML 102 (108)
T cd07429 77 LKKKNQQLEEENNLLKLKIEVLLDML 102 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34457788899999999998766553
No 40
>KOG2036 consensus Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]
Probab=21.45 E-value=94 Score=27.89 Aligned_cols=38 Identities=13% Similarity=0.173 Sum_probs=30.1
Q ss_pred hhhccCCcceeEEEecCCCCcccccCchHHHHHHHHHc
Q 033826 34 ELSVLCDAEVAVIIFSQKGRLYEFSSSEMQKTLERYYR 71 (111)
Q Consensus 34 Els~Lc~~~v~liv~~~~g~~~~~~s~~~~~vl~ry~~ 71 (111)
++..|||+.+.-|..+|+-.-.-|++..++=+.+-|..
T Consensus 608 ~F~~l~GaRIVRIAvhP~y~~MGYGsrAvqLL~~y~eG 645 (1011)
T KOG2036|consen 608 DFPKLSGARIVRIAVHPEYQKMGYGSRAVQLLTDYFEG 645 (1011)
T ss_pred chhcccCceEEEEEeccchhccCccHHHHHHHHHHHhc
Confidence 78899999999999999877777888776644444444
No 41
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=21.31 E-value=93 Score=17.28 Aligned_cols=29 Identities=7% Similarity=0.256 Sum_probs=21.1
Q ss_pred ccCCcceeEEEecCCCCcccccCchHHHHHH
Q 033826 37 VLCDAEVAVIIFSQKGRLYEFSSSEMQKTLE 67 (111)
Q Consensus 37 ~Lc~~~v~liv~~~~g~~~~~~s~~~~~vl~ 67 (111)
++-.++.++++++ +| .+.+..+.+.+++.
T Consensus 6 l~~~~~~~i~i~d-~~-~i~~~N~~~~~l~g 34 (64)
T PF13188_consen 6 LFDNSPDGILIID-GG-RIIYVNPAFEELFG 34 (64)
T ss_dssp HHCCSSSEEEEEE-TS-BEEEE-HHHHHHHC
T ss_pred HHHcCccceEEEE-CC-ChHHhhHHHHHHhC
Confidence 4556788899999 55 78888888877664
No 42
>cd01365 KISc_KIF1A_KIF1B Kinesin motor domain, KIF1_like proteins. KIF1A (Unc104) transports synaptic vesicles to the nerve terminal, KIF1B has been implicated in transport of mitochondria. Both proteins are expressed in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. In contrast to the majority of dimeric kinesins, most KIF1A/Unc104 kinesins are monomeric motors. A lysine-rich loop in KIF1A binds to the negatively charged C-terminus of tubulin and compensates for the lack of a second motor domain, allowing KIF1A to move processively.
Probab=20.87 E-value=76 Score=24.86 Aligned_cols=24 Identities=17% Similarity=0.375 Sum_probs=18.6
Q ss_pred hccCCcceeEEEecC--CCCccc-ccC
Q 033826 36 SVLCDAEVAVIIFSQ--KGRLYE-FSS 59 (111)
Q Consensus 36 s~Lc~~~v~liv~~~--~g~~~~-~~s 59 (111)
+++.|..+++++|++ +||.|+ |++
T Consensus 83 ~~l~G~n~~i~ayGqtGSGKT~Tm~G~ 109 (356)
T cd01365 83 HAFEGYNVCLFAYGQTGSGKSYTMMGY 109 (356)
T ss_pred HHhCCCceEEEEecCCCCCCeEEecCC
Confidence 468999999999986 466776 444
No 43
>PRK13293 F420-0--gamma-glutamyl ligase; Reviewed
Probab=20.68 E-value=78 Score=24.18 Aligned_cols=27 Identities=30% Similarity=0.364 Sum_probs=22.5
Q ss_pred hhhhccCCcceeEEEecCCCCcccccC
Q 033826 33 YELSVLCDAEVAVIIFSQKGRLYEFSS 59 (111)
Q Consensus 33 ~Els~Lc~~~v~liv~~~~g~~~~~~s 59 (111)
.+|.-.+|++|++||....|.++-.+.
T Consensus 134 ~~l~~~~g~~v~VIItDt~gr~~R~G~ 160 (245)
T PRK13293 134 EGLEELTGKKVGVIITDTNGRPFRKGQ 160 (245)
T ss_pred HHHHHHHCCCEEEEEEcCCCcccccCC
Confidence 356677999999999999898887765
No 44
>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=20.41 E-value=1.2e+02 Score=23.03 Aligned_cols=40 Identities=20% Similarity=0.213 Sum_probs=28.0
Q ss_pred ecCCCCcceeccccccchhhhhhhhhccCCcceeEEEecCCCCc
Q 033826 11 IENDTSRQVTFSKRRNGMLKKAYELSVLCDAEVAVIIFSQKGRL 54 (111)
Q Consensus 11 I~~~~~R~~tf~kRk~Gl~KKa~Els~Lc~~~v~liv~~~~g~~ 54 (111)
|+.--.|+..+.++..|-- +=.++-++|++++|++.+...
T Consensus 53 i~~i~~R~~~l~R~~~~~~----~~~i~anvD~vllV~d~~~p~ 92 (287)
T cd01854 53 IVRVLPRKNLLSRPAAGGR----EQVIAANVDQLVIVVSLNEPF 92 (287)
T ss_pred EEEEECCCceEEccCCCCc----ceeEEEeCCEEEEEEEcCCCC
Confidence 4444457777777776622 566899999999999875543
No 45
>KOG4316 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.28 E-value=42 Score=23.93 Aligned_cols=43 Identities=21% Similarity=0.274 Sum_probs=26.8
Q ss_pred hhhhccCCcceeEEEec----CC-CC-cccccC-----chHHHHHHHHHcchhh
Q 033826 33 YELSVLCDAEVAVIIFS----QK-GR-LYEFSS-----SEMQKTLERYYRYTEE 75 (111)
Q Consensus 33 ~Els~Lc~~~v~liv~~----~~-g~-~~~~~s-----~~~~~vl~ry~~~~~~ 75 (111)
.++++||++...|.-.. |. -. ..-|+. -.+++||+||.++.-.
T Consensus 43 ~a~~~lcq~p~vla~r~a~~~Ps~~r~~t~Fs~~kGkrktvkaVldRFkRL~~G 96 (172)
T KOG4316|consen 43 SARNLLCQHPSVLANRMAPVLPSVVRSLTYFSARKGKRKTVKAVLDRFKRLHCG 96 (172)
T ss_pred hHHHhHhcCcHHHHhccCCCCcchhhhhhhhhhhhcccccHHHHHHHHHhcccC
Confidence 57889998877555322 22 11 122332 2799999999987543
No 46
>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=20.28 E-value=2.3e+02 Score=23.46 Aligned_cols=29 Identities=17% Similarity=0.425 Sum_probs=22.5
Q ss_pred eEEEecCCCCcccccCchHHHHHHHHHcchhh
Q 033826 44 AVIIFSQKGRLYEFSSSEMQKTLERYYRYTEE 75 (111)
Q Consensus 44 ~liv~~~~g~~~~~~s~~~~~vl~ry~~~~~~ 75 (111)
-++++.++|.+..| ++.++|+.|....-.
T Consensus 302 Nm~~~~~~g~p~~~---~l~~iL~~f~~~R~~ 330 (445)
T cd00187 302 NMVAFDPNGRPKKL---NLKEILQEFLDHRLE 330 (445)
T ss_pred eEEEEecCCeeEEe---CHHHHHHHHHHHHHH
Confidence 67788889998888 678888888775443
No 47
>PF04873 EIN3: Ethylene insensitive 3; InterPro: IPR006957 Ethylene insensitive 3 (EIN3) proteins are a family of plant DNA-binding proteins that regulate transcription in response to the gaseous plant hormone ethylene, and are essential for ethylene-mediated responses. In the presence of ethylene, dark-grown dicotyledonous seedlings undergo dramatic morphological changes collectively known as the 'triple response'. In Arabidopsis, these changes consist of a radial swelling of the hypocotyl, an exaggeration in the curvature of the apical hook, and the inhibition of cell elongation in the hypocotyl and root.; GO: 0005634 nucleus; PDB: 1WIJ_A.
Probab=20.19 E-value=34 Score=27.44 Aligned_cols=43 Identities=30% Similarity=0.437 Sum_probs=0.0
Q ss_pred ccccccchhhhhhhhhccCCcceeE-EEecCCCCcccccCchHH
Q 033826 21 FSKRRNGMLKKAYELSVLCDAEVAV-IIFSQKGRLYEFSSSEMQ 63 (111)
Q Consensus 21 f~kRk~Gl~KKa~Els~Lc~~~v~l-iv~~~~g~~~~~~s~~~~ 63 (111)
-++=..|++|=+.-..-+|+|.-++ -+++..|++.+++||++.
T Consensus 49 ~s~aqd~ilkym~~~m~~~n~~gfvy~~~~~~~k~~~~~s~slr 92 (354)
T PF04873_consen 49 MSRAQDGILKYMFPEMELCNAPGFVYTIISSSGKPVEGVSPSLR 92 (354)
T ss_dssp --------------------------------------------
T ss_pred hhhhhhHHHHhhccccccccCceeeecCCCCCCCccCCcCCccc
Confidence 3334456666667778899999998 777888999999998776
No 48
>KOG0184 consensus 20S proteasome, regulatory subunit alpha type PSMA3/PRE10 [Posttranslational modification, protein turnover, chaperones]
Probab=20.19 E-value=61 Score=24.72 Aligned_cols=22 Identities=23% Similarity=0.472 Sum_probs=17.7
Q ss_pred hccCCcceeEEEecCCCCcccc
Q 033826 36 SVLCDAEVAVIIFSQKGRLYEF 57 (111)
Q Consensus 36 s~Lc~~~v~liv~~~~g~~~~~ 57 (111)
|+=+|-|.|.-+|||+|..|..
T Consensus 3 sIGtGyDls~s~fSpdGrvfQv 24 (254)
T KOG0184|consen 3 SIGTGYDLSASTFSPDGRVFQV 24 (254)
T ss_pred cccccccccceeeCCCCceehH
Confidence 3457889999999999998763
No 49
>COG3411 Ferredoxin [Energy production and conversion]
Probab=20.11 E-value=1.4e+02 Score=18.16 Aligned_cols=28 Identities=11% Similarity=0.256 Sum_probs=20.2
Q ss_pred eEEEecCCCCcccccC-chHHHHHHHHHc
Q 033826 44 AVIIFSQKGRLYEFSS-SEMQKTLERYYR 71 (111)
Q Consensus 44 ~liv~~~~g~~~~~~s-~~~~~vl~ry~~ 71 (111)
.++++.|+|-.|...+ ++++.|++....
T Consensus 18 Pvl~vYpegvWY~~V~p~~a~rIv~~hl~ 46 (64)
T COG3411 18 PVLVVYPEGVWYTRVDPEDARRIVQSHLL 46 (64)
T ss_pred CEEEEecCCeeEeccCHHHHHHHHHHHHh
Confidence 3566677898888776 478888877644
No 50
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=20.04 E-value=2.4e+02 Score=17.57 Aligned_cols=39 Identities=13% Similarity=-0.098 Sum_probs=21.9
Q ss_pred HHHHHHcchhhhhcchhhhhhHhhhhhHHHHHHHHHHHh
Q 033826 65 TLERYYRYTEERQIDRNGMERYMQVRPLYLNLITFEISL 103 (111)
Q Consensus 65 vl~ry~~~~~~~~~~~~~~~~~~q~LkE~~~~~~~eI~~ 103 (111)
++-+|.........-+....+.++.|.+.++.++..|+-
T Consensus 22 L~lHY~sk~~~~~gLs~~d~~~L~~L~~~a~rm~eRI~t 60 (75)
T PF06667_consen 22 LILHYRSKWKSSQGLSEEDEQRLQELYEQAERMEERIET 60 (75)
T ss_pred HHHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356777654433333334445566666777776666643
Done!