Query 042438
Match_columns 89
No_of_seqs 116 out of 1125
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 06:11:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042438.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042438hhsearch_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 4.8E-34 1E-38 176.5 5.9 77 2-80 1-77 (77)
2 KOG0014 MADS box transcription 100.0 1.8E-33 3.9E-38 195.3 5.9 80 1-80 1-80 (195)
3 cd00266 MADS_SRF_like SRF-like 100.0 4E-31 8.6E-36 165.3 5.6 76 2-78 1-76 (83)
4 smart00432 MADS MADS domain. 100.0 5E-30 1.1E-34 151.7 5.1 59 2-60 1-59 (59)
5 cd00120 MADS MADS: MCM1, Agamo 100.0 4.5E-29 9.7E-34 147.6 4.2 59 2-60 1-59 (59)
6 PF00319 SRF-TF: SRF-type tran 99.9 7.7E-27 1.7E-31 134.5 2.1 51 9-59 1-51 (51)
7 KOG0015 Regulator of arginine 99.8 2.1E-20 4.6E-25 139.3 5.7 80 2-81 63-149 (338)
8 COG5068 ARG80 Regulator of arg 99.5 7.5E-15 1.6E-19 113.1 3.8 61 1-61 81-141 (412)
9 PF09151 DUF1936: Domain of un 74.7 5.3 0.00011 20.8 2.8 25 35-59 3-27 (36)
10 PF10491 Nrf1_DNA-bind: NLS-bi 67.7 18 0.00038 26.4 5.1 48 26-75 35-89 (214)
11 PF14009 DUF4228: Domain of un 57.5 16 0.00035 24.0 3.3 35 39-74 12-46 (181)
12 PF09941 DUF2173: Uncharacteri 49.0 29 0.00062 22.7 3.3 28 31-59 2-29 (108)
13 PHA01548 hypothetical protein 46.6 56 0.0012 22.6 4.5 39 44-84 106-144 (167)
14 TIGR01916 F420_cofE F420-0:gam 39.9 25 0.00053 26.1 2.1 26 34-59 134-159 (243)
15 PF11976 Rad60-SLD: Ubiquitin- 39.5 72 0.0016 18.0 4.3 36 44-79 2-38 (72)
16 COG4831 Roadblock/LC7 domain [ 39.3 63 0.0014 21.0 3.7 32 30-62 3-34 (109)
17 COG5000 NtrY Signal transducti 38.5 17 0.00037 30.7 1.2 24 36-59 374-397 (712)
18 PF13252 DUF4043: Protein of u 35.6 17 0.00036 28.1 0.7 29 31-59 270-298 (341)
19 PRK09555 feoA ferrous iron tra 35.1 90 0.002 18.6 3.8 32 26-57 20-51 (74)
20 PF10584 Proteasome_A_N: Prote 34.0 14 0.00029 17.8 0.0 12 45-56 5-16 (23)
21 COG1918 FeoA Fe2+ transport sy 30.2 1.1E+02 0.0025 18.4 3.7 33 25-57 20-52 (75)
22 PF00383 dCMP_cyt_deam_1: Cyti 29.4 82 0.0018 18.9 3.0 31 27-57 6-40 (102)
23 KOG4637 Adaptor for phosphoino 28.7 41 0.00089 26.9 1.8 41 33-75 367-412 (464)
24 PRK13293 F420-0--gamma-glutamy 27.7 50 0.0011 24.5 2.1 25 34-58 135-159 (245)
25 cd03063 TRX_Fd_FDH_beta TRX-li 26.6 68 0.0015 20.1 2.3 36 38-74 44-80 (92)
26 PF12165 DUF3594: Domain of un 26.2 93 0.002 21.2 3.0 32 21-52 10-47 (137)
27 smart00415 HSF heat shock fact 25.9 51 0.0011 20.7 1.7 45 29-75 6-51 (105)
28 PF05771 Pox_A31: Poxvirus A31 25.7 1.2E+02 0.0027 20.0 3.4 35 37-77 21-55 (114)
29 PF11232 Med25: Mediator compl 24.7 2E+02 0.0044 19.8 4.5 35 37-73 109-144 (152)
30 PF06020 Roughex: Drosophila r 23.4 40 0.00087 26.0 0.9 15 36-50 183-197 (334)
31 KOG4252 GTP-binding protein [S 22.0 63 0.0014 23.6 1.6 14 38-51 90-103 (246)
32 PF08796 DUF1797: Protein of u 21.5 1.1E+02 0.0023 18.4 2.3 19 39-57 24-42 (67)
33 COG1943 Transposase and inacti 21.2 2.4E+02 0.0052 18.6 4.3 65 16-80 22-88 (136)
34 PF15119 APOC4: Apolipoprotein 21.2 54 0.0012 21.0 1.0 20 21-40 75-96 (99)
35 PRK13294 F420-0--gamma-glutamy 21.1 75 0.0016 25.3 2.1 24 34-57 135-158 (448)
36 KOG0183 20S proteasome, regula 21.1 73 0.0016 23.6 1.8 18 40-57 3-20 (249)
37 PF08557 Lipid_DES: Sphingolip 20.6 59 0.0013 17.5 1.0 22 21-42 15-36 (39)
38 cd04922 ACT_AKi-HSDH-ThrA_2 AC 20.4 1.6E+02 0.0034 15.7 3.8 46 25-70 14-59 (66)
39 COG0529 CysC Adenylylsulfate k 20.3 1.8E+02 0.0038 21.1 3.6 24 21-44 135-160 (197)
40 PF15072 DUF4539: Domain of un 20.2 2E+02 0.0044 17.7 3.5 30 39-73 17-46 (86)
41 PF11407 RestrictionMunI: Type 20.1 1.4E+02 0.003 21.5 3.1 51 25-75 127-197 (202)
42 cd01284 Riboflavin_deaminase-r 20.1 1.5E+02 0.0032 19.1 3.0 29 29-57 1-35 (115)
43 KOG2036 Predicted P-loop ATPas 20.1 1.3E+02 0.0028 26.4 3.3 48 33-83 607-654 (1011)
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=100.00 E-value=4.8e-34 Score=176.46 Aligned_cols=77 Identities=68% Similarity=1.042 Sum_probs=74.2
Q ss_pred CcccceeEEecCCCccchhhhhhhhhHHHhhHhhhccccccEEEEEeCCCCCceeeecCCCCHHHHHHHHHhhhCCCCC
Q 042438 2 GRGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASDHHTMDKIIARYRREVGQLNS 80 (89)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~LC~~~v~~iv~~~~g~~~~~~~~~~~~~~vl~ry~~~~~~~l~ 80 (89)
||+||+|++|+|+.+|++||+||+.||||||.|||+||||+||+|||+|+|++++|++ +++++||+||++.++.++|
T Consensus 1 gr~ki~i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s--~s~~~vl~ry~~~~~~~~~ 77 (77)
T cd00265 1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSS--PSMEKIIERYQKTSGSSLW 77 (77)
T ss_pred CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecC--CCHHHHHHHHHhccccccC
Confidence 8999999999999999999999999999999999999999999999999999999988 4579999999999999887
No 2
>KOG0014 consensus MADS box transcription factor [Transcription]
Probab=100.00 E-value=1.8e-33 Score=195.32 Aligned_cols=80 Identities=56% Similarity=0.943 Sum_probs=75.3
Q ss_pred CCcccceeEEecCCCccchhhhhhhhhHHHhhHhhhccccccEEEEEeCCCCCceeeecCCCCHHHHHHHHHhhhCCCCC
Q 042438 1 MGRGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASDHHTMDKIIARYRREVGQLNS 80 (89)
Q Consensus 1 MgR~ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~LC~~~v~~iv~~~~g~~~~~~~~~~~~~~vl~ry~~~~~~~l~ 80 (89)
|||+||+|++|+|+++|++||+|||.||||||+||||||||+||+|||+|+|++|+||+|+.++++++++|.+.......
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 99999999999999999999999999999999999999999999999999999999988766699999999998766543
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=99.97 E-value=4e-31 Score=165.35 Aligned_cols=76 Identities=47% Similarity=0.803 Sum_probs=71.3
Q ss_pred CcccceeEEecCCCccchhhhhhhhhHHHhhHhhhccccccEEEEEeCCCCCceeeecCCCCHHHHHHHHHhhhCCC
Q 042438 2 GRGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASDHHTMDKIIARYRREVGQL 78 (89)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~LC~~~v~~iv~~~~g~~~~~~~~~~~~~~vl~ry~~~~~~~ 78 (89)
||+||+|++|+|+.+|++||+||+.||+|||+|||+||||+||+|||+|+|..+.|++++. +.+++++|...+...
T Consensus 1 gr~Ki~i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~~~-~~~~l~~~~~~~~~~ 76 (83)
T cd00266 1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSSE-VEGVISRFEVLSALE 76 (83)
T ss_pred CCccceeEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCcHH-HHHHHHHHhhcCHhh
Confidence 8999999999999999999999999999999999999999999999999999999977554 999999999887654
No 4
>smart00432 MADS MADS domain.
Probab=99.96 E-value=5e-30 Score=151.72 Aligned_cols=59 Identities=75% Similarity=1.174 Sum_probs=57.7
Q ss_pred CcccceeEEecCCCccchhhhhhhhhHHHhhHhhhccccccEEEEEeCCCCCceeeecC
Q 042438 2 GRGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASD 60 (89)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~LC~~~v~~iv~~~~g~~~~~~~~ 60 (89)
||+||+|++|+|+..|++||+||+.||+|||+|||+||||+||+|||+|+|.+++|++|
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 89999999999999999999999999999999999999999999999999999999875
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=4.5e-29 Score=147.62 Aligned_cols=59 Identities=73% Similarity=1.149 Sum_probs=57.2
Q ss_pred CcccceeEEecCCCccchhhhhhhhhHHHhhHhhhccccccEEEEEeCCCCCceeeecC
Q 042438 2 GRGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASD 60 (89)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~LC~~~v~~iv~~~~g~~~~~~~~ 60 (89)
||+||+|++|+|+..|++||+||+.||+|||+|||+|||++||+|||+|+|.+++|++|
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 79999999999999999999999999999999999999999999999999999999763
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=99.93 E-value=7.7e-27 Score=134.52 Aligned_cols=51 Identities=63% Similarity=1.043 Sum_probs=46.4
Q ss_pred EEecCCCccchhhhhhhhhHHHhhHhhhccccccEEEEEeCCCCCceeeec
Q 042438 9 KRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYAS 59 (89)
Q Consensus 9 k~I~~~~~R~~tf~KRk~GL~KKa~ELs~LC~~~v~~iv~~~~g~~~~~~~ 59 (89)
++|+|+..|++||+||+.||+|||+|||+||||+||+|||+|+|++++|++
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 579999999999999999999999999999999999999999999999964
No 7
>KOG0015 consensus Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.81 E-value=2.1e-20 Score=139.31 Aligned_cols=80 Identities=38% Similarity=0.556 Sum_probs=72.8
Q ss_pred CcccceeEEecCCCccchhhhhhhhhHHHhhHhhhccccccEEEEEeCCCCCceeeecCCC-------CHHHHHHHHHhh
Q 042438 2 GRGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASDHH-------TMDKIIARYRRE 74 (89)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~LC~~~v~~iv~~~~g~~~~~~~~~~-------~~~~vl~ry~~~ 74 (89)
||.||+|+||+|+..|.+||+|||.|+||||+||++|+|.+|-|+|.+++|.+|+|..|.- .=+.+|..-.+.
T Consensus 63 gr~kik~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaTpKLep~i~s~~Gk~lIq~cLn~ 142 (338)
T KOG0015|consen 63 GRVKIKMEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATPKLEPMITSDEGKALIQACLNA 142 (338)
T ss_pred ceeeccchhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEeccccccccccchhhHHHHHHHhcC
Confidence 7999999999999999999999999999999999999999999999999999999988653 237888888888
Q ss_pred hCCCCCc
Q 042438 75 VGQLNSA 81 (89)
Q Consensus 75 ~~~~l~~ 81 (89)
++.....
T Consensus 143 pd~~~~~ 149 (338)
T KOG0015|consen 143 PDTPPND 149 (338)
T ss_pred CCCCCcc
Confidence 8777665
No 8
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.52 E-value=7.5e-15 Score=113.12 Aligned_cols=61 Identities=46% Similarity=0.654 Sum_probs=59.2
Q ss_pred CCcccceeEEecCCCccchhhhhhhhhHHHhhHhhhccccccEEEEEeCCCCCceeeecCC
Q 042438 1 MGRGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASDH 61 (89)
Q Consensus 1 MgR~ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~LC~~~v~~iv~~~~g~~~~~~~~~ 61 (89)
|||+|+.|.+|+|+.+|.+||.||+.||+|||+||++|.|.+|.|+|.+++|.+++|+.|.
T Consensus 81 ~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~tp~ 141 (412)
T COG5068 81 VTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTPK 141 (412)
T ss_pred cccccCCcccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecCCc
Confidence 7899999999999999999999999999999999999999999999999999999998854
No 9
>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=74.68 E-value=5.3 Score=20.83 Aligned_cols=25 Identities=12% Similarity=0.333 Sum_probs=18.2
Q ss_pred hhccccccEEEEEeCCCCCceeeec
Q 042438 35 LSVLCDAEIALVIFSPSGKAYHYAS 59 (89)
Q Consensus 35 Ls~LC~~~v~~iv~~~~g~~~~~~~ 59 (89)
|+--||+-|.+.||+..|..-.|--
T Consensus 3 lcpkcgvgvl~pvy~~kgeikvfrc 27 (36)
T PF09151_consen 3 LCPKCGVGVLEPVYNQKGEIKVFRC 27 (36)
T ss_dssp B-TTTSSSBEEEEE-TTS-EEEEEE
T ss_pred cCCccCceEEEEeecCCCcEEEEEc
Confidence 5667999999999999998766643
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=67.67 E-value=18 Score=26.43 Aligned_cols=48 Identities=10% Similarity=0.254 Sum_probs=35.7
Q ss_pred hhHHHhh----HhhhccccccEEEEEeCCCCC---ceeeecCCCCHHHHHHHHHhhh
Q 042438 26 NGILKKA----FELSVLCDAEIALVIFSPSGK---AYHYASDHHTMDKIIARYRREV 75 (89)
Q Consensus 26 ~GL~KKa----~ELs~LC~~~v~~iv~~~~g~---~~~~~~~~~~~~~vl~ry~~~~ 75 (89)
.-|+.|. .|++|-+|-++.|++.+|+.. ...|+. ...+.|+..|+...
T Consensus 35 ~rllrkl~~~~de~~trvGqqavvl~~~p~kp~~~f~vfGa--~pL~~vv~~~~~~I 89 (214)
T PF10491_consen 35 TRLLRKLRQTIDEYTTRVGQQAVVLCCTPSKPNPVFKVFGA--APLENVVRNLKPVI 89 (214)
T ss_pred HHHHHHHHHHHHHHHHhhhceeEEEEecCCCCCCceeeecc--hhHHHHHHHHHHHH
Confidence 3455554 799999999999999997543 344544 66888888887764
No 11
>PF14009 DUF4228: Domain of unknown function (DUF4228)
Probab=57.48 E-value=16 Score=24.03 Aligned_cols=35 Identities=11% Similarity=0.256 Sum_probs=26.4
Q ss_pred ccccEEEEEeCCCCCceeeecCCCCHHHHHHHHHhh
Q 042438 39 CDAEIALVIFSPSGKAYHYASDHHTMDKIIARYRRE 74 (89)
Q Consensus 39 C~~~v~~iv~~~~g~~~~~~~~~~~~~~vl~ry~~~ 74 (89)
++...++-|..++|.+..|.+| ..+.+|+..|=..
T Consensus 12 ~~~~~~vkvv~~~G~v~~~~~p-v~a~evm~~~P~h 46 (181)
T PF14009_consen 12 SSSAATVKVVHPDGKVEEFKRP-VTAAEVMLENPGH 46 (181)
T ss_pred cCCCceEEEEcCCCcEEEeCCC-cCHHHHHHHCCCC
Confidence 4455566666689999999775 6899999887555
No 12
>PF09941 DUF2173: Uncharacterized conserved protein (DUF2173); InterPro: IPR018685 This family of various hypothetical prokaryotic proteins has no known function.
Probab=48.96 E-value=29 Score=22.68 Aligned_cols=28 Identities=32% Similarity=0.229 Sum_probs=22.8
Q ss_pred hhHhhhccccccEEEEEeCCCCCceeeec
Q 042438 31 KAFELSVLCDAEIALVIFSPSGKAYHYAS 59 (89)
Q Consensus 31 Ka~ELs~LC~~~v~~iv~~~~g~~~~~~~ 59 (89)
+..+|..|-||-+| ..|+++|++.+|-.
T Consensus 2 ~l~~Lm~lpGv~AA-g~Fs~~G~l~e~~G 29 (108)
T PF09941_consen 2 KLDKLMKLPGVVAA-GEFSDDGKLVEYKG 29 (108)
T ss_pred cHHHhhcCCCeEEE-EEECCCCeEEeeec
Confidence 45688889998665 78999999999865
No 13
>PHA01548 hypothetical protein
Probab=46.56 E-value=56 Score=22.55 Aligned_cols=39 Identities=28% Similarity=0.369 Sum_probs=32.8
Q ss_pred EEEEeCCCCCceeeecCCCCHHHHHHHHHhhhCCCCCcccc
Q 042438 44 ALVIFSPSGKAYHYASDHHTMDKIIARYRREVGQLNSADQR 84 (89)
Q Consensus 44 ~~iv~~~~g~~~~~~~~~~~~~~vl~ry~~~~~~~l~~~~~ 84 (89)
.+++.+.+|+.|.-.+ ..+-+-|++.-...++-.|-+.|
T Consensus 106 rvvlidKdGkayha~S--QgVVssIQkiisIvGpapwt~EP 144 (167)
T PHA01548 106 RVVLIDKDGKAYHAVS--QGVVSSIQKIISIVGPAPWTDEP 144 (167)
T ss_pred EEEEEccCCCEeeeeh--HHHHHHHHHHHHHhCCCCCCCCC
Confidence 4667778999988766 78889999999999999997776
No 14
>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=39.88 E-value=25 Score=26.08 Aligned_cols=26 Identities=15% Similarity=0.419 Sum_probs=20.5
Q ss_pred hhhccccccEEEEEeCCCCCceeeec
Q 042438 34 ELSVLCDAEIALVIFSPSGKAYHYAS 59 (89)
Q Consensus 34 ELs~LC~~~v~~iv~~~~g~~~~~~~ 59 (89)
+|.-.+|++|+|||++..|.++-.+.
T Consensus 134 ~l~~~~g~~v~VIItDt~gr~~R~G~ 159 (243)
T TIGR01916 134 GLRELTGVDVGVIITDTNGRPFREGQ 159 (243)
T ss_pred HHHHHHCCCEEEEEECCCCCccccCC
Confidence 45566999999999999888766544
No 15
>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins. SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....
Probab=39.48 E-value=72 Score=17.99 Aligned_cols=36 Identities=22% Similarity=0.391 Sum_probs=26.8
Q ss_pred EEEEeCCCCCceee-ecCCCCHHHHHHHHHhhhCCCC
Q 042438 44 ALVIFSPSGKAYHY-ASDHHTMDKIIARYRREVGQLN 79 (89)
Q Consensus 44 ~~iv~~~~g~~~~~-~~~~~~~~~vl~ry~~~~~~~l 79 (89)
.+.|.+.+|+...+ ..+...+..+++.|....+...
T Consensus 2 ~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~ 38 (72)
T PF11976_consen 2 TIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPP 38 (72)
T ss_dssp EEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT
T ss_pred EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCc
Confidence 46677777876555 4666789999999998876554
No 16
>COG4831 Roadblock/LC7 domain [Function unknown]
Probab=39.25 E-value=63 Score=21.01 Aligned_cols=32 Identities=34% Similarity=0.333 Sum_probs=25.8
Q ss_pred HhhHhhhccccccEEEEEeCCCCCceeeecCCC
Q 042438 30 KKAFELSVLCDAEIALVIFSPSGKAYHYASDHH 62 (89)
Q Consensus 30 KKa~ELs~LC~~~v~~iv~~~~g~~~~~~~~~~ 62 (89)
.|..||.-+-||-+| =.|+|+|++..|-.+-+
T Consensus 3 ekLdeLlqi~Gv~AA-Gefs~DGkLv~Ykgdm~ 34 (109)
T COG4831 3 EKLDELLQIKGVMAA-GEFSPDGKLVEYKGDMP 34 (109)
T ss_pred hhHHHHhCccceeEe-ceeCCCCceEEeeCCCC
Confidence 567888888888665 67999999999977544
No 17
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=38.47 E-value=17 Score=30.69 Aligned_cols=24 Identities=17% Similarity=0.192 Sum_probs=21.9
Q ss_pred hccccccEEEEEeCCCCCceeeec
Q 042438 36 SVLCDAEIALVIFSPSGKAYHYAS 59 (89)
Q Consensus 36 s~LC~~~v~~iv~~~~g~~~~~~~ 59 (89)
++|.|+-++||.++++|...++..
T Consensus 374 ~VLsgvtaGVi~~d~~g~i~t~N~ 397 (712)
T COG5000 374 AVLSGLTAGVIGFDNRGCITTVNP 397 (712)
T ss_pred HHHhcCceeEEEEcCCCeeEeecc
Confidence 699999999999999999999853
No 18
>PF13252 DUF4043: Protein of unknown function (DUF4043)
Probab=35.65 E-value=17 Score=28.05 Aligned_cols=29 Identities=21% Similarity=0.305 Sum_probs=19.9
Q ss_pred hhHhhhccccccEEEEEeCCCCCceeeec
Q 042438 31 KAFELSVLCDAEIALVIFSPSGKAYHYAS 59 (89)
Q Consensus 31 Ka~ELs~LC~~~v~~iv~~~~g~~~~~~~ 59 (89)
.+-.-++|||++++++.|+..+....|.|
T Consensus 270 ~~v~ralLlGaQA~~~A~G~~~~~~~~~w 298 (341)
T PF13252_consen 270 VAVARALLLGAQALVIAFGKSGSGMRFFW 298 (341)
T ss_pred cceeeeeeechhheeeeeeccCCCccccc
Confidence 34456789999999999996344333333
No 19
>PRK09555 feoA ferrous iron transport protein A; Reviewed
Probab=35.12 E-value=90 Score=18.57 Aligned_cols=32 Identities=22% Similarity=0.344 Sum_probs=28.2
Q ss_pred hhHHHhhHhhhccccccEEEEEeCCCCCceee
Q 042438 26 NGILKKAFELSVLCDAEIALVIFSPSGKAYHY 57 (89)
Q Consensus 26 ~GL~KKa~ELs~LC~~~v~~iv~~~~g~~~~~ 57 (89)
..+..+..++-++.|.+|-++-..|.|.+..+
T Consensus 20 ~~~~~rL~~mGl~pG~~V~v~~~aP~gdPi~i 51 (74)
T PRK09555 20 PAYRQKLLSLGMLPGSSFNVVRVAPLGDPIHI 51 (74)
T ss_pred hHHHHHHHHcCCCCCCEEEEEEECCCCCCEEE
Confidence 45888999999999999999999998877665
No 20
>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=34.01 E-value=14 Score=17.76 Aligned_cols=12 Identities=33% Similarity=0.941 Sum_probs=8.6
Q ss_pred EEEeCCCCCcee
Q 042438 45 LVIFSPSGKAYH 56 (89)
Q Consensus 45 ~iv~~~~g~~~~ 56 (89)
+.+|||+|+++.
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 346888888764
No 21
>COG1918 FeoA Fe2+ transport system protein A [Inorganic ion transport and metabolism]
Probab=30.22 E-value=1.1e+02 Score=18.37 Aligned_cols=33 Identities=21% Similarity=0.389 Sum_probs=28.2
Q ss_pred hhhHHHhhHhhhccccccEEEEEeCCCCCceee
Q 042438 25 KNGILKKAFELSVLCDAEIALVIFSPSGKAYHY 57 (89)
Q Consensus 25 k~GL~KKa~ELs~LC~~~v~~iv~~~~g~~~~~ 57 (89)
.+++.+|..++-+.-|+++.++--.|-|.+..+
T Consensus 20 ~~~~~~RL~~mG~~~G~~i~vi~~aplgdPi~v 52 (75)
T COG1918 20 GNGLRRRLLSMGIVPGASITVVRKAPLGDPILV 52 (75)
T ss_pred CHHHHHHHHHcCCCCCCEEEEEEecCCCCCEEE
Confidence 348999999999999999999999988865443
No 22
>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=29.40 E-value=82 Score=18.87 Aligned_cols=31 Identities=26% Similarity=0.382 Sum_probs=21.4
Q ss_pred hHHHhhHhhhccc----cccEEEEEeCCCCCceee
Q 042438 27 GILKKAFELSVLC----DAEIALVIFSPSGKAYHY 57 (89)
Q Consensus 27 GL~KKa~ELs~LC----~~~v~~iv~~~~g~~~~~ 57 (89)
-+++.|.+++... +..|+-+|++++|+....
T Consensus 6 ~~m~~a~~~a~~s~~~~~~~vgaviv~~~~~~i~~ 40 (102)
T PF00383_consen 6 EFMRIAIELAKRSRPCGNFPVGAVIVDPDGKIIAT 40 (102)
T ss_dssp HHHHHHHHHHHTHBTTTSSSEEEEEEETTTEEEEE
T ss_pred HHHHHHHHHHHhccccCCCCEEEEEEeccCccEEE
Confidence 3566777766665 778999999976664433
No 23
>KOG4637 consensus Adaptor for phosphoinositide 3-kinase [Signal transduction mechanisms]
Probab=28.65 E-value=41 Score=26.90 Aligned_cols=41 Identities=22% Similarity=0.515 Sum_probs=27.8
Q ss_pred HhhhccccccE--EEEEeCCCCCceeeecCC---CCHHHHHHHHHhhh
Q 042438 33 FELSVLCDAEI--ALVIFSPSGKAYHYASDH---HTMDKIIARYRREV 75 (89)
Q Consensus 33 ~ELs~LC~~~v--~~iv~~~~g~~~~~~~~~---~~~~~vl~ry~~~~ 75 (89)
+-|||+||-+| |||--.. ..|-|..|. .++++++..|+..|
T Consensus 367 yalSV~~~~~V~HClIy~ta--tG~GFa~pyn~y~tlk~lV~hY~h~S 412 (464)
T KOG4637|consen 367 YALSVVHDGEVKHCLIYQTA--TGFGFAEPYNLYSTLKELVLHYQHTS 412 (464)
T ss_pred eEEEEEECCceeeeEEeecc--ccccccchhHHHHHHHHHHHHHhhhh
Confidence 56899998776 5544434 445554443 27899999998876
No 24
>PRK13293 F420-0--gamma-glutamyl ligase; Reviewed
Probab=27.69 E-value=50 Score=24.49 Aligned_cols=25 Identities=16% Similarity=0.420 Sum_probs=19.5
Q ss_pred hhhccccccEEEEEeCCCCCceeee
Q 042438 34 ELSVLCDAEIALVIFSPSGKAYHYA 58 (89)
Q Consensus 34 ELs~LC~~~v~~iv~~~~g~~~~~~ 58 (89)
+|.-.+|++|+|||.+..|.++-.+
T Consensus 135 ~l~~~~g~~v~VIItDt~gr~~R~G 159 (245)
T PRK13293 135 GLEELTGKKVGVIITDTNGRPFRKG 159 (245)
T ss_pred HHHHHHCCCEEEEEEcCCCcccccC
Confidence 3556689999999999888765543
No 25
>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=26.58 E-value=68 Score=20.08 Aligned_cols=36 Identities=17% Similarity=0.168 Sum_probs=24.0
Q ss_pred cccccEEEEEeCCCC-CceeeecCCCCHHHHHHHHHhh
Q 042438 38 LCDAEIALVIFSPSG-KAYHYASDHHTMDKIIARYRRE 74 (89)
Q Consensus 38 LC~~~v~~iv~~~~g-~~~~~~~~~~~~~~vl~ry~~~ 74 (89)
+|..+--|.|+.|+| -.|....| +++.++++.+...
T Consensus 44 ~C~~ePlV~V~~p~g~v~Y~~V~~-edv~~Iv~~~~~~ 80 (92)
T cd03063 44 MYWLEPLVEVETPGGRVAYGPVTP-ADVASLLDAGALE 80 (92)
T ss_pred ecCCCCEEEEEeCCCcEEEEeCCH-HHHHHHHHHHhhc
Confidence 477777777887777 34444443 4688888887663
No 26
>PF12165 DUF3594: Domain of unknown function (DUF3594); InterPro: IPR021998 This presumed domain is functionally uncharacterised.This domain family is found in eukaryotes, and is approximately 140 amino acids in length. The family is found in association with PF00628 from PFAM.
Probab=26.19 E-value=93 Score=21.17 Aligned_cols=32 Identities=38% Similarity=0.730 Sum_probs=24.6
Q ss_pred hhhhhhhHHHhh----HhhhccccccE-EEEEeC-CCC
Q 042438 21 FSKRKNGILKKA----FELSVLCDAEI-ALVIFS-PSG 52 (89)
Q Consensus 21 f~KRk~GL~KKa----~ELs~LC~~~v-~~iv~~-~~g 52 (89)
|+-||.||.|-. .|+.-+||.+- .|-.|+ |+|
T Consensus 10 f~~RR~g~v~ALT~dve~Fy~~CDP~kenLCLYG~p~~ 47 (137)
T PF12165_consen 10 FSGRRAGIVRALTTDVEEFYQQCDPEKENLCLYGHPDG 47 (137)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCccccceEEecCCCC
Confidence 889999998754 67999999976 455577 555
No 27
>smart00415 HSF heat shock factor.
Probab=25.86 E-value=51 Score=20.66 Aligned_cols=45 Identities=24% Similarity=0.445 Sum_probs=29.5
Q ss_pred HHhhHhhhccccccEE-EEEeCCCCCceeeecCCCCHHHHHHHHHhhh
Q 042438 29 LKKAFELSVLCDAEIA-LVIFSPSGKAYHYASDHHTMDKIIARYRREV 75 (89)
Q Consensus 29 ~KKa~ELs~LC~~~v~-~iv~~~~g~~~~~~~~~~~~~~vl~ry~~~~ 75 (89)
..|.+++ |.+.+.. +|-.+++|..+....+..-.+.||.+|-...
T Consensus 6 ~~kL~~~--l~~~~~~~iI~W~~~G~~f~I~d~~~f~~~vLp~~Fk~~ 51 (105)
T smart00415 6 LTKLYLL--VEDPSTDKIISWSPSGKSFVIWDPEEFAKNLLPRYFKHN 51 (105)
T ss_pred HHHHHHH--HhCCCCCCEEEECCCCCEEEEcCHHHHHHHHHHHhcCCC
Confidence 4455554 3344444 7888899998887665445677888875543
No 28
>PF05771 Pox_A31: Poxvirus A31 protein; InterPro: IPR008786 This family contains the vaccinia virus A31R protein, the function of which is not known.
Probab=25.73 E-value=1.2e+02 Score=19.98 Aligned_cols=35 Identities=11% Similarity=0.358 Sum_probs=25.3
Q ss_pred ccccccEEEEEeCCCCCceeeecCCCCHHHHHHHHHhhhCC
Q 042438 37 VLCDAEIALVIFSPSGKAYHYASDHHTMDKIIARYRREVGQ 77 (89)
Q Consensus 37 ~LC~~~v~~iv~~~~g~~~~~~~~~~~~~~vl~ry~~~~~~ 77 (89)
++|...+ +++-.|-.+.|..|+ ++.++||...++.
T Consensus 21 ~ipk~K~---~~~hk~~~FiFy~Pk---~~~v~rYl~~~~l 55 (114)
T PF05771_consen 21 MIPKKKS---VYDHKNMTFIFYAPK---DSTVQRYLSRCGL 55 (114)
T ss_pred cccccee---EEeeCCcEEEEECCc---HHHHHHHHHhcCc
Confidence 4566555 344567889998886 6789999988754
No 29
>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=24.72 E-value=2e+02 Score=19.82 Aligned_cols=35 Identities=20% Similarity=0.607 Sum_probs=22.7
Q ss_pred ccccccEEEEEeCCCCCcee-eecCCCCHHHHHHHHHh
Q 042438 37 VLCDAEIALVIFSPSGKAYH-YASDHHTMDKIIARYRR 73 (89)
Q Consensus 37 ~LC~~~v~~iv~~~~g~~~~-~~~~~~~~~~vl~ry~~ 73 (89)
.-|++.|-+++|+++.+.|. |.+ -+-...+.+++.
T Consensus 109 p~c~iKvL~LlYs~kk~~flG~IP--~DQ~~Fv~~lr~ 144 (152)
T PF11232_consen 109 PPCEIKVLMLLYSPKKKAFLGFIP--NDQEGFVNRLRQ 144 (152)
T ss_dssp SSSS-SEEEEEEETTTTEEEEEEE--STHHHHHHHHHH
T ss_pred CCCceEEEEEEEcCCCceEEEEcC--CCHHHHHHHHHH
Confidence 56899999999998887544 443 344555555544
No 30
>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=23.41 E-value=40 Score=25.98 Aligned_cols=15 Identities=20% Similarity=0.414 Sum_probs=12.8
Q ss_pred hccccccEEEEEeCC
Q 042438 36 SVLCDAEIALVIFSP 50 (89)
Q Consensus 36 s~LC~~~v~~iv~~~ 50 (89)
.-+||.++||+||..
T Consensus 183 ~~~~~~EICLavYek 197 (334)
T PF06020_consen 183 GQVSGFEICLAVYEK 197 (334)
T ss_pred CccccceEEeeehhh
Confidence 457999999999984
No 31
>KOG4252 consensus GTP-binding protein [Signal transduction mechanisms]
Probab=22.02 E-value=63 Score=23.63 Aligned_cols=14 Identities=21% Similarity=0.472 Sum_probs=11.5
Q ss_pred cccccEEEEEeCCC
Q 042438 38 LCDAEIALVIFSPS 51 (89)
Q Consensus 38 LC~~~v~~iv~~~~ 51 (89)
--||++||+||+-+
T Consensus 90 yrgaqa~vLVFSTT 103 (246)
T KOG4252|consen 90 YRGAQASVLVFSTT 103 (246)
T ss_pred hccccceEEEEecc
Confidence 46899999999953
No 32
>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=21.53 E-value=1.1e+02 Score=18.39 Aligned_cols=19 Identities=11% Similarity=0.312 Sum_probs=14.8
Q ss_pred ccccEEEEEeCCCCCceee
Q 042438 39 CDAEIALVIFSPSGKAYHY 57 (89)
Q Consensus 39 C~~~v~~iv~~~~g~~~~~ 57 (89)
-|+++|.|-|++....|+.
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 6899999999976665554
No 33
>COG1943 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.23 E-value=2.4e+02 Score=18.58 Aligned_cols=65 Identities=12% Similarity=0.072 Sum_probs=43.5
Q ss_pred ccchhhhh-hhhhHHHhhHhhhccccccEEEEEeCCCCCceeee-cCCCCHHHHHHHHHhhhCCCCC
Q 042438 16 NRQVTFSK-RKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYA-SDHHTMDKIIARYRREVGQLNS 80 (89)
Q Consensus 16 ~R~~tf~K-Rk~GL~KKa~ELs~LC~~~v~~iv~~~~g~~~~~~-~~~~~~~~vl~ry~~~~~~~l~ 80 (89)
.|+..|.. =...|..-+.|.+.-.++++.-++.-||---.-+. +|..++..++.+++..+..-++
T Consensus 22 yRr~vl~~~~~~~l~~~l~~~~~~~~~eI~a~~v~pdHVHlli~~pp~~~~~~~~~~lkg~ss~~~~ 88 (136)
T COG1943 22 YRRKVLTGEVLNLLRSILREVAEQKNFEILAMEVMPDHVHLLITLPPKDSVSSIVNRLKGRSSRRLR 88 (136)
T ss_pred CchHhhhHhHHHHHHHHHHHHHHhCCCEEEEEEecCCEEEEEEecCCCCCHHHHHHHHHhHHHHHHH
Confidence 44555544 36677777888999999999999998855433333 4556788888776666554443
No 34
>PF15119 APOC4: Apolipoprotein C4
Probab=21.19 E-value=54 Score=20.96 Aligned_cols=20 Identities=30% Similarity=0.675 Sum_probs=15.4
Q ss_pred hhhhhhhHHHhhHhhh--cccc
Q 042438 21 FSKRKNGILKKAFELS--VLCD 40 (89)
Q Consensus 21 f~KRk~GL~KKa~ELs--~LC~ 40 (89)
...-|..|++|++.|+ .||+
T Consensus 75 l~sSkd~llnk~~sLCPrllC~ 96 (99)
T PF15119_consen 75 LRSSKDSLLNKTHSLCPRLLCG 96 (99)
T ss_pred HHHhHHHHHHHHHhhCchhhcc
Confidence 4566889999999886 4554
No 35
>PRK13294 F420-0--gamma-glutamyl ligase; Provisional
Probab=21.13 E-value=75 Score=25.32 Aligned_cols=24 Identities=21% Similarity=0.364 Sum_probs=19.2
Q ss_pred hhhccccccEEEEEeCCCCCceee
Q 042438 34 ELSVLCDAEIALVIFSPSGKAYHY 57 (89)
Q Consensus 34 ELs~LC~~~v~~iv~~~~g~~~~~ 57 (89)
+|.-.+|++|+|||.+..|.++-.
T Consensus 135 ~l~~~~g~~v~vii~Dt~gr~~r~ 158 (448)
T PRK13294 135 GLRERLGVDVAVVVTDTMGRAWRN 158 (448)
T ss_pred HHHHHHCCCEEEEEecCCCCcccc
Confidence 466679999999999988876544
No 36
>KOG0183 consensus 20S proteasome, regulatory subunit alpha type PSMA7/PRE6 [Posttranslational modification, protein turnover, chaperones]
Probab=21.08 E-value=73 Score=23.61 Aligned_cols=18 Identities=33% Similarity=0.663 Sum_probs=14.6
Q ss_pred cccEEEEEeCCCCCceee
Q 042438 40 DAEIALVIFSPSGKAYHY 57 (89)
Q Consensus 40 ~~~v~~iv~~~~g~~~~~ 57 (89)
+-|-|+-||||+|.++..
T Consensus 3 rydraltvFSPDGhL~QV 20 (249)
T KOG0183|consen 3 RYDRALTVFSPDGHLFQV 20 (249)
T ss_pred ccccceEEECCCCCEEee
Confidence 346789999999998765
No 37
>PF08557 Lipid_DES: Sphingolipid Delta4-desaturase (DES); InterPro: IPR013866 Sphingolipids are important membrane signalling molecules involved in many different cellular functions in eukaryotes. Sphingolipid delta 4-desaturase catalyses the formation of (E)-sphing-4-enine []. Some proteins in this entry have bifunctional delta 4-desaturase/C-4-hydroxylase activity. Delta 4-desaturated sphingolipids may play a role in early signalling required for entry into meiotic and spermatid differentiation pathways during Drosophila spermatogenesis []. This small protein associates with FA_desaturase IPR005804 from INTERPRO and appears to be specific to sphingolipid delta 4-desaturase. ; GO: 0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 0006633 fatty acid biosynthetic process, 0055114 oxidation-reduction process, 0016021 integral to membrane
Probab=20.61 E-value=59 Score=17.49 Aligned_cols=22 Identities=32% Similarity=0.445 Sum_probs=18.8
Q ss_pred hhhhhhhHHHhhHhhhcccccc
Q 042438 21 FSKRKNGILKKAFELSVLCDAE 42 (89)
Q Consensus 21 f~KRk~GL~KKa~ELs~LC~~~ 42 (89)
-..|++-+++|=-|+-.|+|.|
T Consensus 15 H~~RRk~IL~k~PeIk~L~G~d 36 (39)
T PF08557_consen 15 HASRRKEILKKHPEIKKLMGPD 36 (39)
T ss_pred cHHHHHHHHHhChHHHHHhCCC
Confidence 4678889999999999999876
No 38
>cd04922 ACT_AKi-HSDH-ThrA_2 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). This CD includes the second of two ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). The ACT domains are positioned between the N-terminal catalytic domain of AK and the C-terminal HSDH domain found in bacteria (Escherichia coli (EC) ThrA) and higher plants (Zea mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. HSDH is the first committed reaction in the branch of the pathway that leads to Thr and Met. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pathwa
Probab=20.41 E-value=1.6e+02 Score=15.74 Aligned_cols=46 Identities=13% Similarity=0.156 Sum_probs=31.8
Q ss_pred hhhHHHhhHhhhccccccEEEEEeCCCCCceeeecCCCCHHHHHHH
Q 042438 25 KNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASDHHTMDKIIAR 70 (89)
Q Consensus 25 k~GL~KKa~ELs~LC~~~v~~iv~~~~g~~~~~~~~~~~~~~vl~r 70 (89)
..|+..+..+.-.-+|+.+-++..+..+....|.=+..+.+..+..
T Consensus 14 ~~~~~~~i~~~l~~~~I~v~~i~~~~s~~~is~~v~~~~~~~~~~~ 59 (66)
T cd04922 14 TPGVAATFFSALAKANVNIRAIAQGSSERNISAVIDEDDATKALRA 59 (66)
T ss_pred CccHHHHHHHHHHHCCCCEEEEEecCcccEEEEEEeHHHHHHHHHH
Confidence 3678888888888889999999886555555555444555555554
No 39
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=20.34 E-value=1.8e+02 Score=21.06 Aligned_cols=24 Identities=21% Similarity=0.249 Sum_probs=17.8
Q ss_pred hhhhhhhHHHhh--HhhhccccccEE
Q 042438 21 FSKRKNGILKKA--FELSVLCDAEIA 44 (89)
Q Consensus 21 f~KRk~GL~KKa--~ELs~LC~~~v~ 44 (89)
=.+=-+||+||| .|+.-.+|++..
T Consensus 135 e~RDpKGLYkKAr~GeI~~fTGid~p 160 (197)
T COG0529 135 ERRDPKGLYKKARAGEIKNFTGIDSP 160 (197)
T ss_pred HhcCchHHHHHHHcCCCCCCcCCCCC
Confidence 344458999998 578888888753
No 40
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=20.19 E-value=2e+02 Score=17.73 Aligned_cols=30 Identities=17% Similarity=0.347 Sum_probs=22.3
Q ss_pred ccccEEEEEeCCCCCceeeecCCCCHHHHHHHHHh
Q 042438 39 CDAEIALVIFSPSGKAYHYASDHHTMDKIIARYRR 73 (89)
Q Consensus 39 C~~~v~~iv~~~~g~~~~~~~~~~~~~~vl~ry~~ 73 (89)
.+.|+.+++-+|+|...--.+ +++++.|..
T Consensus 17 ~~~D~~v~l~DpTG~i~~tiH-----~~v~~~y~~ 46 (86)
T PF15072_consen 17 SSEDAFVVLKDPTGEIRGTIH-----RKVLEEYGD 46 (86)
T ss_pred cCCCeEEEEECCCCcEEEEEe-----HHHHhhcCC
Confidence 344888899999998877665 677777654
No 41
>PF11407 RestrictionMunI: Type II restriction enzyme MunI; InterPro: IPR022725 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. Type II restriction enzyme MunI recognises the palindromic sequence C/AATTG. It makes contact with the DNA via the major groove []. ; PDB: 1D02_B.
Probab=20.15 E-value=1.4e+02 Score=21.51 Aligned_cols=51 Identities=20% Similarity=0.388 Sum_probs=31.7
Q ss_pred hhhHHHhhHhhhccccccEE--EEEe------------------CCCCCceeeecCCCCHHHHHHHHHhhh
Q 042438 25 KNGILKKAFELSVLCDAEIA--LVIF------------------SPSGKAYHYASDHHTMDKIIARYRREV 75 (89)
Q Consensus 25 k~GL~KKa~ELs~LC~~~v~--~iv~------------------~~~g~~~~~~~~~~~~~~vl~ry~~~~ 75 (89)
-+||++....++-|.+.++. -||| +.-++.|-+|-|..+..++|+.|++.-
T Consensus 127 tpgl~~~~r~~~~i~~~~~LPFWiV~~GdITRDpkR~REIt~Wf~~y~~nyF~Wr~~~~~~~L~~hF~~~l 197 (202)
T PF11407_consen 127 TPGLLKAYRQISNINDEEILPFWIVFEGDITRDPKRVREITFWFDEYDKNYFMWRPTKSEESLVDHFNKYL 197 (202)
T ss_dssp SHHHHHHHHHHH----TTS-SEEEEEESGGGG-HHHHHHHHHHHTT-CCCEEEE-TT--HHHHHHHHHHHT
T ss_pred CcHHHHHHHHhcCCCCCCccceEEEEecccccCcccceeeeeehhhcccceEEecCCCchHHHHHHHHHHH
Confidence 58999999999999777654 2332 224566777788789999999998763
No 42
>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=20.14 E-value=1.5e+02 Score=19.08 Aligned_cols=29 Identities=21% Similarity=0.335 Sum_probs=19.5
Q ss_pred HHhhHhhhccc------cccEEEEEeCCCCCceee
Q 042438 29 LKKAFELSVLC------DAEIALVIFSPSGKAYHY 57 (89)
Q Consensus 29 ~KKa~ELs~LC------~~~v~~iv~~~~g~~~~~ 57 (89)
|+.|-|++-.+ +..|+-+|++++|.....
T Consensus 1 m~~al~~A~~~~~~~~~~~pvGaviv~~~g~iv~~ 35 (115)
T cd01284 1 MRRALELAEKGRGLTSPNPPVGCVIVDDDGEIVGE 35 (115)
T ss_pred CHHHHHHHHhcccccCCCCCEEEEEEeCCCeEEEE
Confidence 35566666665 778888888876775443
No 43
>KOG2036 consensus Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]
Probab=20.11 E-value=1.3e+02 Score=26.37 Aligned_cols=48 Identities=19% Similarity=0.181 Sum_probs=38.6
Q ss_pred HhhhccccccEEEEEeCCCCCceeeecCCCCHHHHHHHHHhhhCCCCCccc
Q 042438 33 FELSVLCDAEIALVIFSPSGKAYHYASDHHTMDKIIARYRREVGQLNSADQ 83 (89)
Q Consensus 33 ~ELs~LC~~~v~~iv~~~~g~~~~~~~~~~~~~~vl~ry~~~~~~~l~~~~ 83 (89)
.++..|||+.+.-|-++|+-...-|++ ..-++|.+|...-.+++.+..
T Consensus 607 ~~F~~l~GaRIVRIAvhP~y~~MGYGs---rAvqLL~~y~eG~~~~i~e~~ 654 (1011)
T KOG2036|consen 607 EDFPKLSGARIVRIAVHPEYQKMGYGS---RAVQLLTDYFEGKFTSISEDV 654 (1011)
T ss_pred cchhcccCceEEEEEeccchhccCccH---HHHHHHHHHHhccCCCccccc
Confidence 468999999999999999877777765 456788999888877777443
Done!