Query 037016
Match_columns 70
No_of_seqs 125 out of 1071
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 07:43:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037016.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037016hhsearch_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 2.9E-33 6.3E-38 167.8 4.0 68 2-69 1-68 (77)
2 KOG0014 MADS box transcription 100.0 8.3E-33 1.8E-37 184.0 4.5 69 1-69 1-71 (195)
3 smart00432 MADS MADS domain. 100.0 2.4E-30 5.1E-35 149.1 5.1 59 2-60 1-59 (59)
4 cd00266 MADS_SRF_like SRF-like 100.0 1.8E-30 3.9E-35 157.4 4.7 68 2-69 1-69 (83)
5 cd00120 MADS MADS: MCM1, Agamo 100.0 2.2E-29 4.8E-34 145.0 4.2 59 2-60 1-59 (59)
6 PF00319 SRF-TF: SRF-type tran 99.9 1.8E-27 4E-32 133.8 1.7 51 9-59 1-51 (51)
7 KOG0015 Regulator of arginine 99.9 1.2E-23 2.6E-28 152.4 3.5 66 2-67 63-128 (338)
8 COG5068 ARG80 Regulator of arg 99.7 5.4E-17 1.2E-21 121.1 4.4 68 1-68 81-148 (412)
9 PF14009 DUF4228: Domain of un 87.5 0.96 2.1E-05 28.8 3.5 32 39-70 12-44 (181)
10 COG4888 Uncharacterized Zn rib 71.3 2.8 6E-05 26.7 1.5 59 1-62 1-63 (104)
11 PF09151 DUF1936: Domain of un 67.3 8.4 0.00018 19.8 2.5 24 34-57 2-25 (36)
12 PF10491 Nrf1_DNA-bind: NLS-bi 55.1 17 0.00038 25.7 3.2 44 26-69 35-85 (214)
13 PRK00807 50S ribosomal protein 50.4 25 0.00055 19.3 2.8 31 34-64 2-36 (52)
14 PF13540 RCC1_2: Regulator of 49.4 24 0.00052 16.8 2.4 25 36-61 3-27 (30)
15 TIGR01916 F420_cofE F420-0:gam 48.1 17 0.00036 26.1 2.2 28 33-60 133-160 (243)
16 PF04945 YHS: YHS domain; Int 43.5 15 0.00033 19.2 1.1 29 39-67 6-37 (47)
17 PRK13293 F420-0--gamma-glutamy 38.5 28 0.0006 25.0 2.2 28 33-60 134-161 (245)
18 cd01057 AAMH_A Aromatic and Al 34.5 28 0.0006 27.0 1.8 34 35-68 382-424 (465)
19 PF04873 EIN3: Ethylene insens 34.5 13 0.00029 27.9 0.0 39 25-63 53-92 (354)
20 PF00383 dCMP_cyt_deam_1: Cyti 34.0 88 0.0019 18.0 3.6 33 27-59 6-42 (102)
21 PF00989 PAS: PAS fold; Inter 33.7 35 0.00076 18.9 1.7 29 37-66 6-34 (113)
22 PF15072 DUF4539: Domain of un 33.2 90 0.002 18.8 3.6 21 39-59 17-37 (86)
23 PF09941 DUF2173: Uncharacteri 33.0 61 0.0013 20.5 2.9 28 32-60 3-30 (108)
24 PF09158 MotCF: Bacteriophage 32.8 31 0.00067 21.9 1.5 24 5-28 19-43 (103)
25 PRK09555 feoA ferrous iron tra 31.8 1.1E+02 0.0023 17.7 3.6 33 26-58 20-52 (74)
26 PF10584 Proteasome_A_N: Prote 31.2 12 0.00025 17.7 -0.5 11 46-56 6-16 (23)
27 COG5000 NtrY Signal transducti 29.8 50 0.0011 27.2 2.5 25 36-60 374-398 (712)
28 PF07676 PD40: WD40-like Beta 29.7 74 0.0016 15.2 2.8 19 42-60 10-28 (39)
29 PF01996 F420_ligase: F420-0:G 28.9 10 0.00022 26.5 -1.3 28 33-60 141-168 (228)
30 COG4831 Roadblock/LC7 domain [ 28.6 1.2E+02 0.0025 19.4 3.6 30 30-60 3-32 (109)
31 PRK14891 50S ribosomal protein 27.6 54 0.0012 21.6 2.0 30 34-63 5-38 (131)
32 cd01253 PH_beta_spectrin Beta- 27.3 1.2E+02 0.0027 17.6 3.4 21 45-65 74-94 (104)
33 PF11232 Med25: Mediator compl 26.7 77 0.0017 21.3 2.7 19 37-55 109-127 (152)
34 COG2075 RPL24A Ribosomal prote 26.7 1E+02 0.0023 18.0 2.9 32 35-66 5-40 (66)
35 PRK13294 F420-0--gamma-glutamy 25.7 57 0.0012 25.1 2.1 28 33-60 134-161 (448)
36 cd08364 FosX FosX, a fosfomyci 25.7 1.5E+02 0.0032 17.8 3.7 26 44-69 106-131 (131)
37 COG3411 Ferredoxin [Energy pro 25.0 65 0.0014 18.7 1.8 23 45-67 19-42 (64)
38 PF13188 PAS_8: PAS domain; PD 24.9 66 0.0014 16.7 1.8 28 38-67 7-34 (64)
39 PF15119 APOC4: Apolipoprotein 24.1 40 0.00086 21.1 0.9 19 22-40 76-96 (99)
40 COG0139 HisI Phosphoribosyl-AM 23.3 28 0.0006 22.4 0.0 26 27-52 69-94 (111)
41 KOG4502 Predicted membrane pro 23.1 66 0.0014 21.1 1.8 43 28-70 43-85 (133)
42 PRK09732 hypothetical protein; 22.9 1.7E+02 0.0038 18.8 3.7 32 28-59 15-46 (134)
43 cd02980 TRX_Fd_family Thioredo 22.7 92 0.002 17.0 2.2 29 39-68 47-76 (77)
44 KOG0184 20S proteasome, regula 22.4 53 0.0012 23.8 1.3 22 36-57 3-24 (254)
45 smart00782 PhnA_Zn_Ribbon PhnA 22.4 41 0.00088 18.2 0.6 22 28-49 2-23 (47)
46 PF13174 TPR_6: Tetratricopept 22.0 47 0.001 14.7 0.7 9 62-70 23-31 (33)
47 cd03064 TRX_Fd_NuoE TRX-like [ 22.0 70 0.0015 18.0 1.6 28 39-69 52-80 (80)
48 cd01365 KISc_KIF1A_KIF1B Kines 21.9 90 0.0019 22.7 2.5 33 26-58 70-107 (356)
49 PF14263 DUF4354: Domain of un 21.6 22 0.00049 23.1 -0.6 44 11-59 41-84 (124)
50 cd03062 TRX_Fd_Sucrase TRX-lik 21.6 59 0.0013 19.5 1.3 23 45-67 55-80 (97)
51 cd00472 Ribosomal_L24e_L24 Rib 21.1 1E+02 0.0022 17.1 2.1 30 34-63 4-37 (54)
52 cd01284 Riboflavin_deaminase-r 21.1 1.7E+02 0.0037 18.2 3.3 31 29-59 1-37 (115)
53 cd01372 KISc_KIF4 Kinesin moto 20.7 84 0.0018 22.5 2.1 25 36-60 68-94 (341)
54 COG5068 ARG80 Regulator of arg 20.5 48 0.001 25.7 0.9 47 8-60 18-64 (412)
55 PF01502 PRA-CH: Phosphoribosy 20.3 30 0.00065 20.6 -0.2 33 21-53 22-63 (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=99.98 E-value=2.9e-33 Score=167.78 Aligned_cols=68 Identities=63% Similarity=0.942 Sum_probs=67.0
Q ss_pred CccceeeEEccCCCCccchhhhhhchHHHHhhhhhccccccEEEEEEcCCCceEEeeCCcHHHhhhcC
Q 037016 2 GRGKIVIQKINNSTSRQVTFSKRRKGLIKKAKELSILCDAEVGLAIFSSTAKLYEFANTRLLCSLTTV 69 (70)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KR~~gL~KKa~Els~Lc~~~v~~iv~~~~g~~~~~~s~~~~~vl~~~ 69 (70)
||+||+|++|+|+.+|++||+||+.||||||.|||+||||+|++|+++|+|++|+|++|++++||++|
T Consensus 1 gr~ki~i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s~s~~~vl~ry 68 (77)
T cd00265 1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPSMEKIIERY 68 (77)
T ss_pred CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCCCHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999987
No 2
>KOG0014 consensus MADS box transcription factor [Transcription]
Probab=99.97 E-value=8.3e-33 Score=183.96 Aligned_cols=69 Identities=57% Similarity=0.919 Sum_probs=67.6
Q ss_pred CCccceeeEEccCCCCccchhhhhhchHHHHhhhhhccccccEEEEEEcCCCceEEeeCCc--HHHhhhcC
Q 037016 1 MGRGKIVIQKINNSTSRQVTFSKRRKGLIKKAKELSILCDAEVGLAIFSSTAKLYEFANTR--LLCSLTTV 69 (70)
Q Consensus 1 mgR~ki~ik~I~~~~~R~~tf~KR~~gL~KKa~Els~Lc~~~v~~iv~~~~g~~~~~~s~~--~~~vl~~~ 69 (70)
|||+||+|++|+|+..|++||+||+.||||||+|||+||||+||+|||+|+|++|.|++++ +++++++|
T Consensus 1 M~R~ki~i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~~~~~~~~~~~~~~~~v~~~~ 71 (195)
T KOG0014|consen 1 MGRGKIEIKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPSGKLYEFGSSDESVDAVVDRF 71 (195)
T ss_pred CCCCccceeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCCCCccccCCcchhHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999997 99999887
No 3
>smart00432 MADS MADS domain.
Probab=99.96 E-value=2.4e-30 Score=149.11 Aligned_cols=59 Identities=69% Similarity=1.037 Sum_probs=58.2
Q ss_pred CccceeeEEccCCCCccchhhhhhchHHHHhhhhhccccccEEEEEEcCCCceEEeeCC
Q 037016 2 GRGKIVIQKINNSTSRQVTFSKRRKGLIKKAKELSILCDAEVGLAIFSSTAKLYEFANT 60 (70)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KR~~gL~KKa~Els~Lc~~~v~~iv~~~~g~~~~~~s~ 60 (70)
||+||+|++|+|+..|++||+||+.||+|||.|||+|||++||+|+|+|+|++++|++|
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 89999999999999999999999999999999999999999999999999999999987
No 4
>cd00266 MADS_SRF_like SRF-like/Type I subfamily of MADS (MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero- and homo-dimers. Differs from the MEF-like/Type II subgroup mainly in position of the alpha 2 helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.96 E-value=1.8e-30 Score=157.40 Aligned_cols=68 Identities=49% Similarity=0.749 Sum_probs=65.8
Q ss_pred CccceeeEEccCCCCccchhhhhhchHHHHhhhhhccccccEEEEEEcCCCceEEeeCCc-HHHhhhcC
Q 037016 2 GRGKIVIQKINNSTSRQVTFSKRRKGLIKKAKELSILCDAEVGLAIFSSTAKLYEFANTR-LLCSLTTV 69 (70)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KR~~gL~KKa~Els~Lc~~~v~~iv~~~~g~~~~~~s~~-~~~vl~~~ 69 (70)
||+||+|++|+|+.+|++||+||+.||+|||+|||+|||++||+|+|+|+|+.+.|++++ ++++|++|
T Consensus 1 gr~Ki~i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~~~~~~~l~~~ 69 (83)
T cd00266 1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSSEVEGVISRF 69 (83)
T ss_pred CCccceeEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCcHHHHHHHHHH
Confidence 799999999999999999999999999999999999999999999999999999999987 89998876
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=2.2e-29 Score=145.01 Aligned_cols=59 Identities=68% Similarity=1.041 Sum_probs=57.9
Q ss_pred CccceeeEEccCCCCccchhhhhhchHHHHhhhhhccccccEEEEEEcCCCceEEeeCC
Q 037016 2 GRGKIVIQKINNSTSRQVTFSKRRKGLIKKAKELSILCDAEVGLAIFSSTAKLYEFANT 60 (70)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KR~~gL~KKa~Els~Lc~~~v~~iv~~~~g~~~~~~s~ 60 (70)
||+||+|++|+|+..|++||+||+.||+|||.|||+|||++||+|+|+|+|+.++|++|
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 79999999999999999999999999999999999999999999999999999999986
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=1.8e-27 Score=133.79 Aligned_cols=51 Identities=55% Similarity=0.920 Sum_probs=46.9
Q ss_pred EEccCCCCccchhhhhhchHHHHhhhhhccccccEEEEEEcCCCceEEeeC
Q 037016 9 QKINNSTSRQVTFSKRRKGLIKKAKELSILCDAEVGLAIFSSTAKLYEFAN 59 (70)
Q Consensus 9 k~I~~~~~R~~tf~KR~~gL~KKa~Els~Lc~~~v~~iv~~~~g~~~~~~s 59 (70)
|+|+|+..|++||+||++||+|||+|||+|||++||+|+|+|+|++|+|+|
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=99.88 E-value=1.2e-23 Score=152.38 Aligned_cols=66 Identities=45% Similarity=0.597 Sum_probs=64.2
Q ss_pred CccceeeEEccCCCCccchhhhhhchHHHHhhhhhccccccEEEEEEcCCCceEEeeCCcHHHhhh
Q 037016 2 GRGKIVIQKINNSTSRQVTFSKRRKGLIKKAKELSILCDAEVGLAIFSSTAKLYEFANTRLLCSLT 67 (70)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KR~~gL~KKa~Els~Lc~~~v~~iv~~~~g~~~~~~s~~~~~vl~ 67 (70)
||+||+|+||+|+.+|.+||+|||.||||||+||++|+|.+|.|+|.+++|-+|+|++|.++.|+.
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 699999999999999999999999999999999999999999999999999999999999998875
No 8
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.66 E-value=5.4e-17 Score=121.08 Aligned_cols=68 Identities=40% Similarity=0.495 Sum_probs=65.3
Q ss_pred CCccceeeEEccCCCCccchhhhhhchHHHHhhhhhccccccEEEEEEcCCCceEEeeCCcHHHhhhc
Q 037016 1 MGRGKIVIQKINNSTSRQVTFSKRRKGLIKKAKELSILCDAEVGLAIFSSTAKLYEFANTRLLCSLTT 68 (70)
Q Consensus 1 mgR~ki~ik~I~~~~~R~~tf~KR~~gL~KKa~Els~Lc~~~v~~iv~~~~g~~~~~~s~~~~~vl~~ 68 (70)
||++|+.|.+|+|+.+|.+||+||+.||+|||.||++|+|.+|.+++.+++|.+++|++|..+.++..
T Consensus 81 ~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~tp~~e~v~~~ 148 (412)
T COG5068 81 VTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTPKLESVVKS 148 (412)
T ss_pred cccccCCcccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecCCcccccccc
Confidence 78999999999999999999999999999999999999999999999999999999999988887754
No 9
>PF14009 DUF4228: Domain of unknown function (DUF4228)
Probab=87.54 E-value=0.96 Score=28.78 Aligned_cols=32 Identities=13% Similarity=0.201 Sum_probs=26.0
Q ss_pred ccccEEEEEEcCCCceEEeeCC-cHHHhhhcCC
Q 037016 39 CDAEVGLAIFSSTAKLYEFANT-RLLCSLTTVP 70 (70)
Q Consensus 39 c~~~v~~iv~~~~g~~~~~~s~-~~~~vl~~~p 70 (70)
++...++-|..++|++..|..| .+.+|+..||
T Consensus 12 ~~~~~~vkvv~~~G~v~~~~~pv~a~evm~~~P 44 (181)
T PF14009_consen 12 SSSAATVKVVHPDGKVEEFKRPVTAAEVMLENP 44 (181)
T ss_pred cCCCceEEEEcCCCcEEEeCCCcCHHHHHHHCC
Confidence 3455566566689999999999 9999999998
No 10
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=71.33 E-value=2.8 Score=26.67 Aligned_cols=59 Identities=22% Similarity=0.240 Sum_probs=35.2
Q ss_pred CCccceeeEEccCCCCccchhhhhhchHHHHhhhhhcccc----ccEEEEEEcCCCceEEeeCCcH
Q 037016 1 MGRGKIVIQKINNSTSRQVTFSKRRKGLIKKAKELSILCD----AEVGLAIFSSTAKLYEFANTRL 62 (70)
Q Consensus 1 mgR~ki~ik~I~~~~~R~~tf~KR~~gL~KKa~Els~Lc~----~~v~~iv~~~~g~~~~~~s~~~ 62 (70)
|||++.+.+.|.. .|...+.|+...++=- +|.++.|- ..+++++.+.+|.-|.+--|.+
T Consensus 1 MG~rr~krr~~ik--~~~~~L~k~FtCp~Cg-he~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l 63 (104)
T COG4888 1 MGRRRRKRRKIIK--RRPQVLPKTFTCPRCG-HEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPEL 63 (104)
T ss_pred CCcccccccccCc--ccCccCCceEecCccC-CeeeeEEEEEecCceeEEEcccCcceEEEecccc
Confidence 9999888887653 2333344444444321 34444443 3567777788888888776643
No 11
>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=67.33 E-value=8.4 Score=19.78 Aligned_cols=24 Identities=17% Similarity=0.336 Sum_probs=17.0
Q ss_pred hhhccccccEEEEEEcCCCceEEe
Q 037016 34 ELSILCDAEVGLAIFSSTAKLYEF 57 (70)
Q Consensus 34 Els~Lc~~~v~~iv~~~~g~~~~~ 57 (70)
.|+--||+-|...+|+..|..-.|
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 467789999999999999865555
No 12
>PF10491 Nrf1_DNA-bind: NLS-binding and DNA-binding and dimerisation domains of Nrf1; InterPro: IPR019525 Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila []. In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human []. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, Q8C4C0 from SWISSPROT, there is also an NLS domain at 88-116, and a DNA binding and dimerisation domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity [].
Probab=55.11 E-value=17 Score=25.72 Aligned_cols=44 Identities=11% Similarity=0.144 Sum_probs=35.2
Q ss_pred chHHHHh----hhhhccccccEEEEEEcC---CCceEEeeCCcHHHhhhcC
Q 037016 26 KGLIKKA----KELSILCDAEVGLAIFSS---TAKLYEFANTRLLCSLTTV 69 (70)
Q Consensus 26 ~gL~KKa----~Els~Lc~~~v~~iv~~~---~g~~~~~~s~~~~~vl~~~ 69 (70)
.-|+.|- .|+++-+|-++.+++++| ++....|++.-++.++..|
T Consensus 35 ~rllrkl~~~~de~~trvGqqavvl~~~p~kp~~~f~vfGa~pL~~vv~~~ 85 (214)
T PF10491_consen 35 TRLLRKLRQTIDEYTTRVGQQAVVLCCTPSKPNPVFKVFGAAPLENVVRNL 85 (214)
T ss_pred HHHHHHHHHHHHHHHHhhhceeEEEEecCCCCCCceeeecchhHHHHHHHH
Confidence 3466664 799999999999999986 5688889998888877653
No 13
>PRK00807 50S ribosomal protein L24e; Validated
Probab=50.40 E-value=25 Score=19.26 Aligned_cols=31 Identities=10% Similarity=0.211 Sum_probs=21.3
Q ss_pred hhhccccccEE----EEEEcCCCceEEeeCCcHHH
Q 037016 34 ELSILCDAEVG----LAIFSSTAKLYEFANTRLLC 64 (70)
Q Consensus 34 Els~Lc~~~v~----~iv~~~~g~~~~~~s~~~~~ 64 (70)
+++.-||-+|- ...+-.+|++|.|+|+..++
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~KC~~ 36 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYFCSSKCEK 36 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEEeCHHHHH
Confidence 45667777766 33345689999999984443
No 14
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=49.42 E-value=24 Score=16.79 Aligned_cols=25 Identities=20% Similarity=0.380 Sum_probs=16.8
Q ss_pred hccccccEEEEEEcCCCceEEeeCCc
Q 037016 36 SILCDAEVGLAIFSSTAKLYEFANTR 61 (70)
Q Consensus 36 s~Lc~~~v~~iv~~~~g~~~~~~s~~ 61 (70)
++-||....+++.+ +|++|.|+..+
T Consensus 3 ~ia~G~~ht~al~~-~g~v~~wG~n~ 27 (30)
T PF13540_consen 3 QIACGGYHTCALTS-DGEVYCWGDNN 27 (30)
T ss_dssp EEEEESSEEEEEE--TTEEEEEE--T
T ss_pred EEEecCCEEEEEEc-CCCEEEEcCCc
Confidence 45678777777664 69999999753
No 15
>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=48.13 E-value=17 Score=26.14 Aligned_cols=28 Identities=18% Similarity=0.339 Sum_probs=23.6
Q ss_pred hhhhccccccEEEEEEcCCCceEEeeCC
Q 037016 33 KELSILCDAEVGLAIFSSTAKLYEFANT 60 (70)
Q Consensus 33 ~Els~Lc~~~v~~iv~~~~g~~~~~~s~ 60 (70)
.+|.-.+|++|++||.+..|.++--+++
T Consensus 133 ~~l~~~~g~~v~VIItDt~gr~~R~G~~ 160 (243)
T TIGR01916 133 RGLRELTGVDVGVIITDTNGRPFREGQV 160 (243)
T ss_pred HHHHHHHCCCEEEEEECCCCCccccCCC
Confidence 3466679999999999999999887775
No 16
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=43.48 E-value=15 Score=19.16 Aligned_cols=29 Identities=14% Similarity=0.225 Sum_probs=17.2
Q ss_pred ccccE---EEEEEcCCCceEEeeCCcHHHhhh
Q 037016 39 CDAEV---GLAIFSSTAKLYEFANTRLLCSLT 67 (70)
Q Consensus 39 c~~~v---~~iv~~~~g~~~~~~s~~~~~vl~ 67 (70)
||..| +-..+.=+|+.|-|+|+.-.+..+
T Consensus 6 cg~~v~~~~~~~~~y~G~~Y~FCS~~C~~~F~ 37 (47)
T PF04945_consen 6 CGMKVPGNAAYSVEYNGRTYYFCSEGCKEKFE 37 (47)
T ss_dssp GG-BE-----EEEEETTEEEEESSHHHHHHHH
T ss_pred CCCEEccCccEEEEECCEEEEEcCHHHHHHHH
Confidence 55555 333344479999999985555443
No 17
>PRK13293 F420-0--gamma-glutamyl ligase; Reviewed
Probab=38.55 E-value=28 Score=25.04 Aligned_cols=28 Identities=18% Similarity=0.307 Sum_probs=23.1
Q ss_pred hhhhccccccEEEEEEcCCCceEEeeCC
Q 037016 33 KELSILCDAEVGLAIFSSTAKLYEFANT 60 (70)
Q Consensus 33 ~Els~Lc~~~v~~iv~~~~g~~~~~~s~ 60 (70)
.+|.-.+|++|++||.+..|.++-.+..
T Consensus 134 ~~l~~~~g~~v~VIItDt~gr~~R~G~t 161 (245)
T PRK13293 134 EGLEELTGKKVGVIITDTNGRPFRKGQR 161 (245)
T ss_pred HHHHHHHCCCEEEEEEcCCCcccccCCc
Confidence 3466679999999999999988877764
No 18
>cd01057 AAMH_A Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain. Aromatic and Alkene Monooxygenase Hydroxylases, subunit A (AAMH_A). Subunit A of the soluble hydroxylase of multicomponent, aromatic and alkene monooxygenases are members of a superfamily of ferritin-like iron-storage proteins. AAMH exists as a hexamer (an alpha2-beta2-gamma2 homodimer) with each alpha-subunit housing one nonheme diiron center embedded in a four-helix bundle. The N-terminal domain of the alpha- and noncatalytic beta-subunits possess nearly identical folds, however, the beta-subunit lacks critical diiron ligands and a C-terminal domain found in the alpha-subunit. Methane monooxygenase is a multicomponent enzyme found in methanotrophic bacteria that catalyzes the hydroxylation of methane and higher alkenes (as large as octane). Phenol monooxygenase, found in a diverse group of bacteria, catalyses the hydroxylation of phenol, chloro- and methyl-phenol and naphtho
Probab=34.49 E-value=28 Score=26.99 Aligned_cols=34 Identities=12% Similarity=0.281 Sum_probs=22.3
Q ss_pred hhccccccEEE---------EEEcCCCceEEeeCCcHHHhhhc
Q 037016 35 LSILCDAEVGL---------AIFSSTAKLYEFANTRLLCSLTT 68 (70)
Q Consensus 35 ls~Lc~~~v~~---------iv~~~~g~~~~~~s~~~~~vl~~ 68 (70)
+|-.|++.+.. ....=+|+.|.|||+..+.+.+.
T Consensus 382 ~c~vC~~p~~~~~~~~~~~~~~~ey~G~~y~FCS~~C~~~F~~ 424 (465)
T cd01057 382 LCNVCQVPCVFTEDLTAEAPRVLEYNGRKYHFCSEGCEWIFEQ 424 (465)
T ss_pred CCCCCCCeeccccCcccccceEEEECCEEEEecCHHHHHHHHH
Confidence 56677777662 11222799999999966665543
No 19
>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=34.45 E-value=13 Score=27.93 Aligned_cols=39 Identities=28% Similarity=0.255 Sum_probs=0.0
Q ss_pred hchHHHHhhhhhccccccEEE-EEEcCCCceEEeeCCcHH
Q 037016 25 RKGLIKKAKELSILCDAEVGL-AIFSSTAKLYEFANTRLL 63 (70)
Q Consensus 25 ~~gL~KKa~Els~Lc~~~v~~-iv~~~~g~~~~~~s~~~~ 63 (70)
..||+|=+.-..-+|++.-++ -+++..|++.+|++|++.
T Consensus 53 qd~ilkym~~~m~~~n~~gfvy~~~~~~~k~~~~~s~slr 92 (354)
T PF04873_consen 53 QDGILKYMFPEMELCNAPGFVYTIISSSGKPVEGVSPSLR 92 (354)
T ss_dssp ----------------------------------------
T ss_pred hhHHHHhhccccccccCceeeecCCCCCCCccCCcCCccc
Confidence 456666667778899999998 777889999999999886
No 20
>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=33.98 E-value=88 Score=18.04 Aligned_cols=33 Identities=21% Similarity=0.255 Sum_probs=23.1
Q ss_pred hHHHHhhhhhccc----cccEEEEEEcCCCceEEeeC
Q 037016 27 GLIKKAKELSILC----DAEVGLAIFSSTAKLYEFAN 59 (70)
Q Consensus 27 gL~KKa~Els~Lc----~~~v~~iv~~~~g~~~~~~s 59 (70)
-+++.|.+++... +..|+-++++++|+....+.
T Consensus 6 ~~m~~a~~~a~~s~~~~~~~vgaviv~~~~~~i~~g~ 42 (102)
T PF00383_consen 6 EFMRIAIELAKRSRPCGNFPVGAVIVDPDGKIIATGY 42 (102)
T ss_dssp HHHHHHHHHHHTHBTTTSSSEEEEEEETTTEEEEEEE
T ss_pred HHHHHHHHHHHhccccCCCCEEEEEEeccCccEEEEe
Confidence 3567777766655 77899999987776665554
No 21
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....
Probab=33.68 E-value=35 Score=18.89 Aligned_cols=29 Identities=17% Similarity=0.301 Sum_probs=19.6
Q ss_pred ccccccEEEEEEcCCCceEEeeCCcHHHhh
Q 037016 37 ILCDAEVGLAIFSSTAKLYEFANTRLLCSL 66 (70)
Q Consensus 37 ~Lc~~~v~~iv~~~~g~~~~~~s~~~~~vl 66 (70)
++-.+..++++.+.+|+.. |.++++.+++
T Consensus 6 i~~~~~~~i~~~d~~g~I~-~~N~a~~~l~ 34 (113)
T PF00989_consen 6 ILENSPDGIFVIDEDGRIL-YVNQAAEELL 34 (113)
T ss_dssp HHHCSSSEEEEEETTSBEE-EECHHHHHHH
T ss_pred HHhcCCceEEEEeCcCeEE-EECHHHHHHH
Confidence 3456778899999888877 4555445444
No 22
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=33.23 E-value=90 Score=18.77 Aligned_cols=21 Identities=5% Similarity=0.052 Sum_probs=16.7
Q ss_pred ccccEEEEEEcCCCceEEeeC
Q 037016 39 CDAEVGLAIFSSTAKLYEFAN 59 (70)
Q Consensus 39 c~~~v~~iv~~~~g~~~~~~s 59 (70)
.+.|..+++-+|+|.+..--+
T Consensus 17 ~~~D~~v~l~DpTG~i~~tiH 37 (86)
T PF15072_consen 17 SSEDAFVVLKDPTGEIRGTIH 37 (86)
T ss_pred cCCCeEEEEECCCCcEEEEEe
Confidence 455888999999998876665
No 23
>PF09941 DUF2173: Uncharacterized conserved protein (DUF2173); InterPro: IPR018685 This family of various hypothetical prokaryotic proteins has no known function.
Probab=32.96 E-value=61 Score=20.53 Aligned_cols=28 Identities=25% Similarity=0.261 Sum_probs=21.9
Q ss_pred hhhhhccccccEEEEEEcCCCceEEeeCC
Q 037016 32 AKELSILCDAEVGLAIFSSTAKLYEFANT 60 (70)
Q Consensus 32 a~Els~Lc~~~v~~iv~~~~g~~~~~~s~ 60 (70)
-.||..|-|+-+ ...|+++|++.+|-..
T Consensus 3 l~~Lm~lpGv~A-Ag~Fs~~G~l~e~~G~ 30 (108)
T PF09941_consen 3 LDKLMKLPGVVA-AGEFSDDGKLVEYKGE 30 (108)
T ss_pred HHHhhcCCCeEE-EEEECCCCeEEeeecC
Confidence 467888888865 4678999999998764
No 24
>PF09158 MotCF: Bacteriophage T4 MotA, C-terminal; InterPro: IPR015241 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the C-terminal domain of MotA factors, which adopts a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. It contains a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end [].; PDB: 1KAF_B.
Probab=32.76 E-value=31 Score=21.88 Aligned_cols=24 Identities=33% Similarity=0.652 Sum_probs=18.0
Q ss_pred ceeeEEc-cCCCCccchhhhhhchH
Q 037016 5 KIVIQKI-NNSTSRQVTFSKRRKGL 28 (70)
Q Consensus 5 ki~ik~I-~~~~~R~~tf~KR~~gL 28 (70)
++++|-+ +|.++=.+.|.||-.|+
T Consensus 19 ~ie~K~~~~~RSN~~i~f~KRt~Gi 43 (103)
T PF09158_consen 19 KIEVKEIVIDRSNYEIRFKKRTKGI 43 (103)
T ss_dssp T--EEEEEEETTEEEEEEEEEETTE
T ss_pred ceeeeeeEeeccceEEeeecccCce
Confidence 4677766 67777889999999997
No 25
>PRK09555 feoA ferrous iron transport protein A; Reviewed
Probab=31.83 E-value=1.1e+02 Score=17.70 Aligned_cols=33 Identities=9% Similarity=0.083 Sum_probs=28.3
Q ss_pred chHHHHhhhhhccccccEEEEEEcCCCceEEee
Q 037016 26 KGLIKKAKELSILCDAEVGLAIFSSTAKLYEFA 58 (70)
Q Consensus 26 ~gL~KKa~Els~Lc~~~v~~iv~~~~g~~~~~~ 58 (70)
..+.++-.++-++.|++|-++-..|-|.+..+.
T Consensus 20 ~~~~~rL~~mGl~pG~~V~v~~~aP~gdPi~i~ 52 (74)
T PRK09555 20 PAYRQKLLSLGMLPGSSFNVVRVAPLGDPIHIE 52 (74)
T ss_pred hHHHHHHHHcCCCCCCEEEEEEECCCCCCEEEE
Confidence 457888999999999999999999977776654
No 26
>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=31.20 E-value=12 Score=17.66 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=7.8
Q ss_pred EEEcCCCceEE
Q 037016 46 AIFSSTAKLYE 56 (70)
Q Consensus 46 iv~~~~g~~~~ 56 (70)
.+|||+|+++.
T Consensus 6 t~FSp~Grl~Q 16 (23)
T PF10584_consen 6 TTFSPDGRLFQ 16 (23)
T ss_dssp TSBBTTSSBHH
T ss_pred eeECCCCeEEe
Confidence 35788888763
No 27
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=29.75 E-value=50 Score=27.23 Aligned_cols=25 Identities=12% Similarity=0.234 Sum_probs=22.5
Q ss_pred hccccccEEEEEEcCCCceEEeeCC
Q 037016 36 SILCDAEVGLAIFSSTAKLYEFANT 60 (70)
Q Consensus 36 s~Lc~~~v~~iv~~~~g~~~~~~s~ 60 (70)
++|.|+-+++|.++++|.++++...
T Consensus 374 ~VLsgvtaGVi~~d~~g~i~t~N~~ 398 (712)
T COG5000 374 AVLSGLTAGVIGFDNRGCITTVNPS 398 (712)
T ss_pred HHHhcCceeEEEEcCCCeeEeecch
Confidence 6999999999999999999998743
No 28
>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=29.75 E-value=74 Score=15.21 Aligned_cols=19 Identities=21% Similarity=0.340 Sum_probs=13.9
Q ss_pred cEEEEEEcCCCceEEeeCC
Q 037016 42 EVGLAIFSSTAKLYEFANT 60 (70)
Q Consensus 42 ~v~~iv~~~~g~~~~~~s~ 60 (70)
.-.-..++|+|+...|++.
T Consensus 10 ~~~~p~~SpDGk~i~f~s~ 28 (39)
T PF07676_consen 10 DDGSPAWSPDGKYIYFTSN 28 (39)
T ss_dssp SEEEEEE-TTSSEEEEEEE
T ss_pred cccCEEEecCCCEEEEEec
Confidence 4456778999999999874
No 29
>PF01996 F420_ligase: F420-0:Gamma-glutamyl ligase; InterPro: IPR002847 This entry contains F420-0:gamma-glutamyl ligase and related proteins. F420-0:gamma-glutamyl ligase catalyzes the GTP-dependent successive addition of multiple gamma-linked L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) to form polyglutamated F420 derivatives [, , , ].; PDB: 2G9I_A 2PHN_A.
Probab=28.85 E-value=10 Score=26.47 Aligned_cols=28 Identities=21% Similarity=0.386 Sum_probs=20.2
Q ss_pred hhhhccccccEEEEEEcCCCceEEeeCC
Q 037016 33 KELSILCDAEVGLAIFSSTAKLYEFANT 60 (70)
Q Consensus 33 ~Els~Lc~~~v~~iv~~~~g~~~~~~s~ 60 (70)
.+|.-.+|.+|+++|.+++|.++..+++
T Consensus 141 ~~l~~~~g~~v~ViI~Dt~gr~~r~G~~ 168 (228)
T PF01996_consen 141 EELKERTGKDVGVIITDTNGRPWRLGQT 168 (228)
T ss_dssp HHHHHHHS---EEEEEEEEEETTEECEE
T ss_pred HHHHHHHCCceEEEEECCCCcEEecCCc
Confidence 4577789999999999999988777764
No 30
>COG4831 Roadblock/LC7 domain [Function unknown]
Probab=28.59 E-value=1.2e+02 Score=19.35 Aligned_cols=30 Identities=27% Similarity=0.322 Sum_probs=24.1
Q ss_pred HHhhhhhccccccEEEEEEcCCCceEEeeCC
Q 037016 30 KKAKELSILCDAEVGLAIFSSTAKLYEFANT 60 (70)
Q Consensus 30 KKa~Els~Lc~~~v~~iv~~~~g~~~~~~s~ 60 (70)
.|-.||..+-|+-+| =.|||+|++..|-++
T Consensus 3 ekLdeLlqi~Gv~AA-Gefs~DGkLv~Ykgd 32 (109)
T COG4831 3 EKLDELLQIKGVMAA-GEFSPDGKLVEYKGD 32 (109)
T ss_pred hhHHHHhCccceeEe-ceeCCCCceEEeeCC
Confidence 467788888887555 458999999999986
No 31
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=27.57 E-value=54 Score=21.64 Aligned_cols=30 Identities=7% Similarity=0.134 Sum_probs=21.7
Q ss_pred hhhccccccEE----EEEEcCCCceEEeeCCcHH
Q 037016 34 ELSILCDAEVG----LAIFSSTAKLYEFANTRLL 63 (70)
Q Consensus 34 Els~Lc~~~v~----~iv~~~~g~~~~~~s~~~~ 63 (70)
++|..||..|- .+.+..+|++|.|+++...
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~ 38 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCE 38 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEEEecHHHH
Confidence 56778888764 4445678999999998433
No 32
>cd01253 PH_beta_spectrin Beta-spectrin pleckstrin homology (PH) domain. Beta-spectrin pleckstrin homology (PH) domain. Beta spectrin binds actin and functions as a major component of the cytoskeleton underlying cellular membranes. Beta spectrin consists of multiple spectrin repeats followed by a PH domain, which binds to Inositol-1,4,5-Trisphosphate. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. PH domains are often involved in targeting proteins to the plasma membrane via lipid binding. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=27.27 E-value=1.2e+02 Score=17.62 Aligned_cols=21 Identities=5% Similarity=-0.073 Sum_probs=15.0
Q ss_pred EEEEcCCCceEEeeCCcHHHh
Q 037016 45 LAIFSSTAKLYEFANTRLLCS 65 (70)
Q Consensus 45 ~iv~~~~g~~~~~~s~~~~~v 65 (70)
+-+..++|+.|.|..++.+++
T Consensus 74 F~l~~~~~~~~~f~a~s~e~~ 94 (104)
T cd01253 74 FRLRLPDGAEFLFQAPDEEEM 94 (104)
T ss_pred EEEEecCCCEEEEECCCHHHH
Confidence 334467889999998876654
No 33
>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=26.72 E-value=77 Score=21.28 Aligned_cols=19 Identities=21% Similarity=0.485 Sum_probs=14.7
Q ss_pred ccccccEEEEEEcCCCceE
Q 037016 37 ILCDAEVGLAIFSSTAKLY 55 (70)
Q Consensus 37 ~Lc~~~v~~iv~~~~g~~~ 55 (70)
.-|+..|.+++|+++-+.|
T Consensus 109 p~c~iKvL~LlYs~kk~~f 127 (152)
T PF11232_consen 109 PPCEIKVLMLLYSPKKKAF 127 (152)
T ss_dssp SSSS-SEEEEEEETTTTEE
T ss_pred CCCceEEEEEEEcCCCceE
Confidence 4688899999999987754
No 34
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=26.67 E-value=1e+02 Score=18.01 Aligned_cols=32 Identities=13% Similarity=0.394 Sum_probs=22.1
Q ss_pred hhccccccE----EEEEEcCCCceEEeeCCcHHHhh
Q 037016 35 LSILCDAEV----GLAIFSSTAKLYEFANTRLLCSL 66 (70)
Q Consensus 35 ls~Lc~~~v----~~iv~~~~g~~~~~~s~~~~~vl 66 (70)
-|..||.++ .++.+-.||+++-|+|+....++
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~k~~ 40 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCEKLF 40 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeEEEEechhHHHHH
Confidence 355677765 45566778999999998555443
No 35
>PRK13294 F420-0--gamma-glutamyl ligase; Provisional
Probab=25.68 E-value=57 Score=25.06 Aligned_cols=28 Identities=11% Similarity=0.172 Sum_probs=23.2
Q ss_pred hhhhccccccEEEEEEcCCCceEEeeCC
Q 037016 33 KELSILCDAEVGLAIFSSTAKLYEFANT 60 (70)
Q Consensus 33 ~Els~Lc~~~v~~iv~~~~g~~~~~~s~ 60 (70)
.+|.-.+|++|++||.+..|.++--++.
T Consensus 134 ~~l~~~~g~~v~vii~Dt~gr~~r~g~~ 161 (448)
T PRK13294 134 AGLRERLGVDVAVVVTDTMGRAWRNGQT 161 (448)
T ss_pred HHHHHHHCCCEEEEEecCCCCccccCcc
Confidence 3567789999999999999988877664
No 36
>cd08364 FosX FosX, a fosfomycin resistance protein, catalyzes the addition of a water molecule to the C1 position of the antibiotic with inversion of configuration at C1. This subfamily family contains FosX, a fosfomycin resistant protein. Fosfomycin inhibits the enzyme UDP-Nacetylglucosamine-3-enolpyruvyltransferase (MurA), which catalyzes the first committed step in bacterial cell wall biosynthesis. FosX catalyzes the addition of a water molecule to the C1 position of the antibiotic with inversion of the configuration at C1 in the presence of Mn(II). The hydrated fosfomycin loses the inhibition activity. FosX is evolutionarily related to glyoxalase I and type I extradiol dioxygenases.
Probab=25.68 E-value=1.5e+02 Score=17.79 Aligned_cols=26 Identities=15% Similarity=0.252 Sum_probs=21.3
Q ss_pred EEEEEcCCCceEEeeCCcHHHhhhcC
Q 037016 44 GLAIFSSTAKLYEFANTRLLCSLTTV 69 (70)
Q Consensus 44 ~~iv~~~~g~~~~~~s~~~~~vl~~~ 69 (70)
.+-+.+|+|...++.+..+..=|.+|
T Consensus 106 ~~yf~DPdG~~iEl~~~~~~~~~~~~ 131 (131)
T cd08364 106 SIYFYDFDNHLFELHTGTLEERLARY 131 (131)
T ss_pred EEEEECCCCCEEEEecCCHHHHHhcC
Confidence 56667999999999998888777765
No 37
>COG3411 Ferredoxin [Energy production and conversion]
Probab=25.04 E-value=65 Score=18.73 Aligned_cols=23 Identities=4% Similarity=0.021 Sum_probs=16.6
Q ss_pred EEEEcCCCceEEeeCC-cHHHhhh
Q 037016 45 LAIFSSTAKLYEFANT-RLLCSLT 67 (70)
Q Consensus 45 ~iv~~~~g~~~~~~s~-~~~~vl~ 67 (70)
++++.|+|-.|..-+| +++.+++
T Consensus 19 vl~vYpegvWY~~V~p~~a~rIv~ 42 (64)
T COG3411 19 VLVVYPEGVWYTRVDPEDARRIVQ 42 (64)
T ss_pred EEEEecCCeeEeccCHHHHHHHHH
Confidence 4556688999999887 5555554
No 38
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=24.90 E-value=66 Score=16.74 Aligned_cols=28 Identities=11% Similarity=0.117 Sum_probs=19.4
Q ss_pred cccccEEEEEEcCCCceEEeeCCcHHHhhh
Q 037016 38 LCDAEVGLAIFSSTAKLYEFANTRLLCSLT 67 (70)
Q Consensus 38 Lc~~~v~~iv~~~~g~~~~~~s~~~~~vl~ 67 (70)
+=.+..++++++ +| .+.+..+.+.+++.
T Consensus 7 ~~~~~~~i~i~d-~~-~i~~~N~~~~~l~g 34 (64)
T PF13188_consen 7 FDNSPDGILIID-GG-RIIYVNPAFEELFG 34 (64)
T ss_dssp HCCSSSEEEEEE-TS-BEEEE-HHHHHHHC
T ss_pred HHcCccceEEEE-CC-ChHHhhHHHHHHhC
Confidence 445677888888 55 77888887776654
No 39
>PF15119 APOC4: Apolipoprotein C4
Probab=24.15 E-value=40 Score=21.09 Aligned_cols=19 Identities=26% Similarity=0.667 Sum_probs=14.5
Q ss_pred hhhhchHHHHhhhhh--cccc
Q 037016 22 SKRRKGLIKKAKELS--ILCD 40 (70)
Q Consensus 22 ~KR~~gL~KKa~Els--~Lc~ 40 (70)
..-+.+|++||+.|| +||+
T Consensus 76 ~sSkd~llnk~~sLCPrllC~ 96 (99)
T PF15119_consen 76 RSSKDSLLNKTHSLCPRLLCG 96 (99)
T ss_pred HHhHHHHHHHHHhhCchhhcc
Confidence 455789999999987 4554
No 40
>COG0139 HisI Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]
Probab=23.34 E-value=28 Score=22.37 Aligned_cols=26 Identities=23% Similarity=0.428 Sum_probs=21.0
Q ss_pred hHHHHhhhhhccccccEEEEEEcCCC
Q 037016 27 GLIKKAKELSILCDAEVGLAIFSSTA 52 (70)
Q Consensus 27 gL~KKa~Els~Lc~~~v~~iv~~~~g 52 (70)
|=+.|..|+.+-||.|.-++++.+.|
T Consensus 69 G~~q~v~~i~~DCD~Dall~~V~q~g 94 (111)
T COG0139 69 GHTQKVVEIRLDCDGDALLLLVEQIG 94 (111)
T ss_pred CceEEEEEEEcCCCCCEEEEEEEeCC
Confidence 44555678999999999999998744
No 41
>KOG4502 consensus Predicted membrane protein [Function unknown]
Probab=23.08 E-value=66 Score=21.08 Aligned_cols=43 Identities=21% Similarity=0.088 Sum_probs=31.2
Q ss_pred HHHHhhhhhccccccEEEEEEcCCCceEEeeCCcHHHhhhcCC
Q 037016 28 LIKKAKELSILCDAEVGLAIFSSTAKLYEFANTRLLCSLTTVP 70 (70)
Q Consensus 28 L~KKa~Els~Lc~~~v~~iv~~~~g~~~~~~s~~~~~vl~~~p 70 (70)
+..-+.=|-.+|+.|+-.+.|+..|+.-.=..+-..+|+-++|
T Consensus 43 ~~~e~~~LL~~~~IE~iRi~FG~KgnL~~R~~~ls~SV~LT~P 85 (133)
T KOG4502|consen 43 RVMEFFVLLPFIPIEYLRINFGSKGNLLERTAFLALSVVLTIP 85 (133)
T ss_pred HHHHHHHHHHhcchhheeeeecCccchhhccchHHHHHHHHhh
Confidence 3344455667899999999999988887777665556665555
No 42
>PRK09732 hypothetical protein; Provisional
Probab=22.87 E-value=1.7e+02 Score=18.84 Aligned_cols=32 Identities=16% Similarity=0.222 Sum_probs=24.0
Q ss_pred HHHHhhhhhccccccEEEEEEcCCCceEEeeC
Q 037016 28 LIKKAKELSILCDAEVGLAIFSSTAKLYEFAN 59 (70)
Q Consensus 28 L~KKa~Els~Lc~~~v~~iv~~~~g~~~~~~s 59 (70)
+...|.+-+.-=|..|++.|++..|.+..|--
T Consensus 15 ~~~aA~~~A~~~g~~v~iaVvD~~G~l~a~~R 46 (134)
T PRK09732 15 IIAAGQEEAQKNNWSVSIAVADDGGHLLALSR 46 (134)
T ss_pred HHHHHHHHHHHhCCCEEEEEEcCCCCEEEEEE
Confidence 34445555555688999999999999888754
No 43
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=22.65 E-value=92 Score=17.00 Aligned_cols=29 Identities=7% Similarity=0.162 Sum_probs=17.9
Q ss_pred ccccEEEEEEcCCCceEEeeCC-cHHHhhhc
Q 037016 39 CDAEVGLAIFSSTAKLYEFANT-RLLCSLTT 68 (70)
Q Consensus 39 c~~~v~~iv~~~~g~~~~~~s~-~~~~vl~~ 68 (70)
|+.--.+++. |.+.+|...+| ++.++|+.
T Consensus 47 C~~~P~v~i~-~~~~~y~~v~~~~~~~il~~ 76 (77)
T cd02980 47 CGLAPVVVVY-PDGVWYGRVTPEDVEEIVEE 76 (77)
T ss_pred ccCCCEEEEe-CCCeEEccCCHHHHHHHHHh
Confidence 4443344444 56778877776 67777764
No 44
>KOG0184 consensus 20S proteasome, regulatory subunit alpha type PSMA3/PRE10 [Posttranslational modification, protein turnover, chaperones]
Probab=22.41 E-value=53 Score=23.78 Aligned_cols=22 Identities=18% Similarity=0.379 Sum_probs=18.4
Q ss_pred hccccccEEEEEEcCCCceEEe
Q 037016 36 SILCDAEVGLAIFSSTAKLYEF 57 (70)
Q Consensus 36 s~Lc~~~v~~iv~~~~g~~~~~ 57 (70)
|+-+|-|.+.-.|||+|+++.-
T Consensus 3 sIGtGyDls~s~fSpdGrvfQv 24 (254)
T KOG0184|consen 3 SIGTGYDLSASTFSPDGRVFQV 24 (254)
T ss_pred cccccccccceeeCCCCceehH
Confidence 4567889999999999998864
No 45
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=22.40 E-value=41 Score=18.21 Aligned_cols=22 Identities=18% Similarity=0.554 Sum_probs=17.0
Q ss_pred HHHHhhhhhccccccEEEEEEc
Q 037016 28 LIKKAKELSILCDAEVGLAIFS 49 (70)
Q Consensus 28 L~KKa~Els~Lc~~~v~~iv~~ 49 (70)
|.+.+..-+=||+++..|.+|.
T Consensus 2 L~~Rs~~kCELC~a~~~L~vy~ 23 (47)
T smart00782 2 LLARCESKCELCGSDSPLVVYA 23 (47)
T ss_pred hhHHcCCcccCcCCCCCceEEe
Confidence 4556667788999998888874
No 46
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=21.99 E-value=47 Score=14.74 Aligned_cols=9 Identities=11% Similarity=0.198 Sum_probs=4.9
Q ss_pred HHHhhhcCC
Q 037016 62 LLCSLTTVP 70 (70)
Q Consensus 62 ~~~vl~~~p 70 (70)
++.+++.||
T Consensus 23 ~~~~~~~~P 31 (33)
T PF13174_consen 23 FQRLIKRYP 31 (33)
T ss_dssp HHHHHHHST
T ss_pred HHHHHHHCc
Confidence 445555555
No 47
>cd03064 TRX_Fd_NuoE TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes. It is a multisubunit complex with at least 14 core subunits. It catalyzes the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane, providing the proton motive force required for energy-consuming processes. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE core subunit, also called the 24 kD subunit of Complex 1. This subfamily also include formate dehydrogenases, NiFe hydrogenases and NAD-reducing hydrogenases, that contain a NuoE domain. A subset of these proteins contain both NuoE and NuoF in a single chain. NuoF, also called the 51 kD subunit of Complex 1, contains one [4Fe-4S] clu
Probab=21.95 E-value=70 Score=18.03 Aligned_cols=28 Identities=18% Similarity=0.325 Sum_probs=17.6
Q ss_pred ccccEEEEEEcCCCceEEeeCC-cHHHhhhcC
Q 037016 39 CDAEVGLAIFSSTAKLYEFANT-RLLCSLTTV 69 (70)
Q Consensus 39 c~~~v~~iv~~~~g~~~~~~s~-~~~~vl~~~ 69 (70)
|+---+++| +|..|...+| .++++++.+
T Consensus 52 C~~gP~v~v---~g~~y~~vt~~~i~~i~~~~ 80 (80)
T cd03064 52 CDLAPVMMI---NDDVYGRLTPEKVDAILEAL 80 (80)
T ss_pred CCCCCEEEE---CCEEECCCCHHHHHHHHHhC
Confidence 544444444 3778877776 777777653
No 48
>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=21.94 E-value=90 Score=22.68 Aligned_cols=33 Identities=12% Similarity=0.168 Sum_probs=23.0
Q ss_pred chHHHHhhh---hhccccccEEEEEEcC--CCceEEee
Q 037016 26 KGLIKKAKE---LSILCDAEVGLAIFSS--TAKLYEFA 58 (70)
Q Consensus 26 ~gL~KKa~E---ls~Lc~~~v~~iv~~~--~g~~~~~~ 58 (70)
.-+|+.+-. -+++-|..++++.|+. +||.|+-.
T Consensus 70 ~~vf~~~~~p~v~~~l~G~n~~i~ayGqtGSGKT~Tm~ 107 (356)
T cd01365 70 EDVFEDLGRELLDHAFEGYNVCLFAYGQTGSGKSYTMM 107 (356)
T ss_pred HHHHHHHHHHHHHHHhCCCceEEEEecCCCCCCeEEec
Confidence 445555422 1478999999999986 57888754
No 49
>PF14263 DUF4354: Domain of unknown function (DUF4354); PDB: 3NRF_B 3SB3_A.
Probab=21.60 E-value=22 Score=23.09 Aligned_cols=44 Identities=18% Similarity=0.261 Sum_probs=30.8
Q ss_pred ccCCCCccchhhhhhchHHHHhhhhhccccccEEEEEEcCCCceEEeeC
Q 037016 11 INNSTSRQVTFSKRRKGLIKKAKELSILCDAEVGLAIFSSTAKLYEFAN 59 (70)
Q Consensus 11 I~~~~~R~~tf~KR~~gL~KKa~Els~Lc~~~v~~iv~~~~g~~~~~~s 59 (70)
+.++...+.||.=.-..+.++.-+|+.+ |+..|+++|+-+-.-+
T Consensus 41 v~~k~~ytktF~V~vaN~s~~~idLsk~-----Cf~a~~~~gk~f~ldT 84 (124)
T PF14263_consen 41 VGGKSFYTKTFDVTVANLSDKDIDLSKM-----CFKAYSPDGKEFKLDT 84 (124)
T ss_dssp ETTEEEEEEEEEEEEEE-SSS-EE-TT------EEEEEETTS-EEEEEE
T ss_pred ecCccceEEEEEEEEecCCCCccccccc-----hhhhccccCCEEEecc
Confidence 4566667778888888898998899888 8999999998776544
No 50
>cd03062 TRX_Fd_Sucrase TRX-like [2Fe-2S] Ferredoxin (Fd) family, Sucrase subfamily; composed of proteins with similarity to a novel plant enzyme, isolated from potato, which contains a Fd-like domain and exhibits sucrolytic activity. The putative active site of the Fd-like domain of the enzyme contains two cysteines and two histidines for possible binding to iron-sulfur clusters, compared to four cysteines present in the active site of Fd.
Probab=21.56 E-value=59 Score=19.49 Aligned_cols=23 Identities=9% Similarity=-0.000 Sum_probs=17.0
Q ss_pred EEEEcC--CCceEEeeCC-cHHHhhh
Q 037016 45 LAIFSS--TAKLYEFANT-RLLCSLT 67 (70)
Q Consensus 45 ~iv~~~--~g~~~~~~s~-~~~~vl~ 67 (70)
.+++-| +|..|...+| +++.+++
T Consensus 55 ~vvvyP~~~g~wy~~v~p~~v~~Iv~ 80 (97)
T cd03062 55 NVIIYPKGDGIWYGRVTPEHVPPIVD 80 (97)
T ss_pred EEEEEeCCCeeEEeecCHHHHHHHHH
Confidence 444557 8999999888 7777774
No 51
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=21.11 E-value=1e+02 Score=17.08 Aligned_cols=30 Identities=13% Similarity=0.314 Sum_probs=20.2
Q ss_pred hhhccccccEE----EEEEcCCCceEEeeCCcHH
Q 037016 34 ELSILCDAEVG----LAIFSSTAKLYEFANTRLL 63 (70)
Q Consensus 34 Els~Lc~~~v~----~iv~~~~g~~~~~~s~~~~ 63 (70)
|+|..||-+|- ...+..||+++.|.+...+
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~F~s~Kc~ 37 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFRFCSSKCE 37 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEEEECHHHH
Confidence 56667777653 3444568999999997433
No 52
>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=21.08 E-value=1.7e+02 Score=18.16 Aligned_cols=31 Identities=19% Similarity=0.255 Sum_probs=21.1
Q ss_pred HHHhhhhhccc------cccEEEEEEcCCCceEEeeC
Q 037016 29 IKKAKELSILC------DAEVGLAIFSSTAKLYEFAN 59 (70)
Q Consensus 29 ~KKa~Els~Lc------~~~v~~iv~~~~g~~~~~~s 59 (70)
|+.|.|++-.+ +..|+-++++++|++..-+.
T Consensus 1 m~~al~~A~~~~~~~~~~~pvGaviv~~~g~iv~~g~ 37 (115)
T cd01284 1 MRRALELAEKGRGLTSPNPPVGCVIVDDDGEIVGEGY 37 (115)
T ss_pred CHHHHHHHHhcccccCCCCCEEEEEEeCCCeEEEEec
Confidence 35566776665 66887788877787766544
No 53
>cd01372 KISc_KIF4 Kinesin motor domain, KIF4-like subfamily. Members of this group seem to perform a variety of functions, and have been implicated in neuronal organelle transport and chromosome segregation during mitosis. 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. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain,
Probab=20.71 E-value=84 Score=22.51 Aligned_cols=25 Identities=8% Similarity=0.272 Sum_probs=20.6
Q ss_pred hccccccEEEEEEcC--CCceEEeeCC
Q 037016 36 SILCDAEVGLAIFSS--TAKLYEFANT 60 (70)
Q Consensus 36 s~Lc~~~v~~iv~~~--~g~~~~~~s~ 60 (70)
+++-|.+++++.|+. +||.|+...+
T Consensus 68 ~~~~G~n~~i~ayG~tgSGKT~Tm~G~ 94 (341)
T cd01372 68 GLFEGYNATVLAYGQTGSGKTYTMGTA 94 (341)
T ss_pred HHhCCCccceeeecCCCCCCcEEecCC
Confidence 467899999999986 6799987654
No 54
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=20.55 E-value=48 Score=25.66 Aligned_cols=47 Identities=26% Similarity=0.326 Sum_probs=38.7
Q ss_pred eEEccCCCCccchhhhhhchHHHHhhhhhccccccEEEEEEcCCCceEEeeCC
Q 037016 8 IQKINNSTSRQVTFSKRRKGLIKKAKELSILCDAEVGLAIFSSTAKLYEFANT 60 (70)
Q Consensus 8 ik~I~~~~~R~~tf~KR~~gL~KKa~Els~Lc~~~v~~iv~~~~g~~~~~~s~ 60 (70)
|+.+.|...-..+|.++..| |++..|+..+-..++....-+..|+.+
T Consensus 18 i~~~~d~~~ps~~~~~~~~~------~~~~~~~g~~~~~~~~~~~~~~~~~~~ 64 (412)
T COG5068 18 IQGDSDANIPSNTINRLSPG------ELSQQNDGKFDVMIFDSKHSVRVYSNE 64 (412)
T ss_pred cccccccCCccccccccCcc------cchhhccCCcccccccccccccccCCc
Confidence 77888888889999999999 999999998888777666566666654
No 55
>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=20.26 E-value=30 Score=20.62 Aligned_cols=33 Identities=24% Similarity=0.414 Sum_probs=23.1
Q ss_pred hhhhhchH---------HHHhhhhhccccccEEEEEEcCCCc
Q 037016 21 FSKRRKGL---------IKKAKELSILCDAEVGLAIFSSTAK 53 (70)
Q Consensus 21 f~KR~~gL---------~KKa~Els~Lc~~~v~~iv~~~~g~ 53 (70)
|++-+++| +-++.|+.+-||.|.-++.+.|.|.
T Consensus 22 ~SRSR~~lW~KGetSG~~q~v~~i~~DCD~D~ll~~V~~~G~ 63 (75)
T PF01502_consen 22 YSRSRNRLWRKGETSGNTQKVVEIRLDCDGDALLFKVEQVGP 63 (75)
T ss_dssp EETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-
T ss_pred EEccCCcEeeEECCCCCEEEEEEEEecCCCCeEEEEEEeCCC
Confidence 45555555 4455789999999999999988775
Done!